Papers I have published
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(96) Mould MC, M. Huet, L. Senegas, B. Mila, C. Thébaud, Y. Bourgeois & A. Chaine. 2022. Beyond morphs: Inter-individual colour variation despite strong genetic determinism of colour morphs in a wild bird. Journal of evolutionary Biology 36, 82-94

Categorizing individuals into discrete forms in colour polymorphic species can overlook more subtle patterns in coloration that can be of functional significance. Thus, quantifying inter-individual variation in these species at both within- and between-morph levels is critical to understand the evolution of colour polymorphisms. Here we present analyses of inter-individual colour variation in the Reunion grey white-eye (Zosterops borbonicus), a colour polymorphic wild bird endemic to the island of Reunion in which all highland populations contain two sympatric colour morphs, with birds showing predominantly grey or brown plumage, respectively. We first quantified colour variation across multiple body areas by using a continuous plumage colour score to assess variation in brown-grey coloration as well as smaller scale variation in light patches. To examine the possible causes of among-individual variation, we tested if colour variation in plumage component elements could be explained by genotypes at two markers near a major-effect locus previously related to back coloration in this species, and by other factors such as age, sex and body condition. Overall, grey-brown coloration was largely determined by genetic factors and was best described by three distinct clusters that were associated to genotypic classes (homozygotes and heterozygote), with no effect of age or sex, whereas variation in smaller light patches was primarily related to age and sex. Our results highlight the importance of characterizing subtle plumage variation beyond morph categories that are readily observable since multiple patterns of colour variation may be driven by different mechanisms, have different functions and will likely respond in different ways to selection.

(95) Utami CY, A Sholihah, FL Condamine, C Thébaud, N Hubert. Cryptic diversity impacts model selection and macroevolutionary inferences in diversification analyses. Proceedings of the Royal Society B​

Species persist in landscapes through ecological dynamics but proliferate at wider spatial scales through evolutionary mechanisms. Disentangling the contribution of each dynamic is challenging, but the increasing use of dated molecular phylogenies opened new perspectives. First, the increasing use of DNA sequences in biodiversity inventory shed light on a substantial amount of cryptic diversity in species-rich ecosystems. Second, explicit diversification models accounting for various eco-evolutionary models are nowavailable. Integrating both advances, we explored diversification trajectories among 10 lineages of freshwater fishes in Sundaland, for which time-calibrated and taxonomically rich phylogenies are available. By fitting diversification models to dated phylogenies and incorporatingDNA-based species delimitation methods, the impact of cryptic diversity on diversification model selection and related inferences is explored. Eight clades display constant speciation rate model as the most likely if cryptic diversity is accounted, but nine display a signature of diversification slowdownswhen cryptic diversity is ignored. Cryptic diversification occurs during the last 5 Myr for most groups, and palaeoecologicalmodels received little support. Most cryptic lineages display restricted range distribution, supporting geographical isolation across homogeneous landscapes as the main driver of diversification. These patterns question the persistence of cryptic diversity and its role during species proliferation.

(94) Matthews Thomas J, Joseph P Wayman, Pedro Cardoso, Ferran Sayol, Julian P Hume, Werner Ulrich, Joseph A Tobias, Filipa C Soares, Christophe Thébaud, Thomas E Martin, Kostas A Triantis. Threatened and extinct island endemic birds of the world: Distribution, threats and functional diversity. Journal of Biogeography

The world's islands support disproportionate levels of endemic avian biodiversity despite suffering numerous extinctions. While intensive recent research has focused on island bird conservation or extinction, few global syntheses have considered these factors together from the perspective of morphological trait diversity. Here, we provide a global summary of the status and ecology of extant and extinct island birds, the threats they face and the implications of species loss for island functional diversity.
Here w e provide a review of the literature on threatened and extinct island birds, with a particular focus on global studies that have incorporated functional diversity. Alongside this, we analyse IUCN Red List data in relation to distribution, threats and taxonomy. Using null models and functional hypervolumes, in combination with morphological trait data, we assess the functional diversity represented by threatened and extinct island endemic birds.
We find that almost half of all island endemic birds extant in 1500 CE are currently either extinct or threatened with extinction, with the majority of threatened extant species having declining population trends. We also found evidence of 66 island endemic subspecies extinctions. The primary threats to extant island endemic birds currently are agriculture, biological resource use, and invasive species. While there is overlap between the hotspots of threatened and extinct island endemics birds, there are some notable differences, including the Philippines and Indonesia, which support a substantial number of threatened species but have no recorded post-1500 CE bird extinctions. Traits associated with threatened island endemic birds are large body mass, flightlessness, aquatic predator, omnivorous and vertivorous trophic niches, marine habitat affinity, and, paradoxically, higher dispersal ability. Critically, we find that threatened endemics (i) occupy distinct areas of beak morphospace, and (ii) represent substantial unique areas of the overall functional space of island endemics. We caution that the loss of threatened species may have severe effects on the ecological functions birds provide on islands.

(93) Emerson Brent , Paulo Borges, Pedro Cardoso, Peter Convey, Jeremy deWaard, Evan Economo, Rosemary Gillespie, Susan Kennedy, Henrik Krehenwinkel, Rudolf Meier, George Roderick, Dominique Strasberg, Christophe Thébaud, Anna Traveset, Thomas Creedy, Emmanouil Meramveliotakis, Victor Noguerales, Isaac Overcast, Hélène Morlon, Anna Papadopoulou, Alfried Vogler, Paula Arribas, Carmelo Andujar. Collective and harmonised high throughput barcoding of insular arthropod biodiversity: toward a Genomic Observatories Network for islands. Molecular Ecology

Our current understanding of ecological and evolutionary processes underlying island biodiversity is heavily shaped by empirical data from plants and birds, although arthropods comprise the overwhelming majority of known animal species. This is due to inherent problems with obtaining high-quality arthropod data. Novel high throughput sequencing approaches are now emerging as powerful tools to overcome such limitations, and thus comprehensively address existing shortfalls in arthropod biodiversity data. Here we explore how, as a community, we might most effectively exploit these tools for comprehensive and comparable inventory and monitoring of insular arthropod biodiversity. We first review the strengths, limitations and potential synergies among existing approaches of high throughput barcode sequencing. We consider how this can be complemented with deep learning approaches applied to image analysis to study arthropod biodiversity. We then explore how these approaches can be implemented within the framework of an island Genomic Observatories Network (iGON) for the advancement of fundamental and applied understanding of island biodiversity. To this end, we identify seven island biology themes at the interface of ecology, evolution and conservation biology, within which collective and harmonised efforts in HTS arthropod inventory could yield significant advances in island biodiversity research.

(92)  Triantis Kostas A., Francois Rigal, Robert J. Whittaker, Julian P. Hume, Catherine Sheard, Dimitrios Poursanidis, Jonathan Rolland, Spyros Sfenthourakis, Thomas J. Matthews, Christophe Thébaud, Joseph A. Tobias. Deterministic assembly and anthropogenic extinctions drive convergence of island bird communities. Global Ecology and Biogeography. 

Whether entire communities of organisms converge towards predictable structural properties in similar environmental conditions remains controversial. We tested for community convergence in birds by comparing the structure of oceanic archipelago assemblages with their respective regional species pools.
Here we compiled a comprehensive database of morphological trait and phylogenetic data for 6,579 bird species, including species known to have become extinct owing to human activities. We quantified morphological and phylogenetic dissimilarity among species between pairs of archipelagos, using a modified version of the mean nearest taxon distance. We tested for convergence by estimating whether overall mean turnover among archipelagos and pairwise turnover between archipelagos were lower than expected by chance.
For all land birds, we found that turnover in body plan, body mass and phylogeny among archipelagos was significantly lower than expected. Seventeen (of 18) archipelagos showed significant body plan and phylogenetic similarity with at least one other archipelago. Similar convergent patterns of community assembly were detected in different subsamples of the data (extant species, endemics, native non-endemics, and Passeriformes only). Convergence was more pronounced for extant species than for extant and extinct species combined.
Consistent convergence in phylogenetic and morphological structure among archipelagic communities arises through a combination of non-random colonization and in situ adaptation. In addition, by including data from extinct taxa, we show that community convergence both precedes and is accentuated by the anthropogenic extinction of endemic lineages. Our results highlight the potential role of non-random extinction in generating patterns of community convergence and show that convergence existed even before anthropogenic extinctions, owing to deterministic community assembly in similar environmental settings at the global scale.​

(91) Milá B., J. Bruxaux, G. Friis, K. Sam, H. Ashari, & C. Thébaud. A new, undescribed species of Melanocharis berrypecker
from western New Guinea and the evolutionary history of the family Melanocharitidae. Ibis (in press) 

Western New Guinea remains one of the last biologically underexplored regions of the world, and much remains to be learned regarding the diversity and evolutionary history of its fauna and flora. During a recent ornithological expedition to the Kumawa Mountains in West Papua, we encountered an undescribed species of Melanocharis berrypecker (Melanocharitidae) in cloud forest at an elevation of 1200 m asl. Its main characteristics are iridescent blue-black upperparts, satin-white underparts washed lemon yellow, and white outer edges to the external rectrices. Initially thought to represent a close relative of the Mid-mountain Berrypecker Melanocharis longicauda based on elevation and plumage colour traits, a complete phylogenetic analysis of the genus based on full mitogenomes and genome-wide nuclear data revealed that the new species, which we name Satin Berrypecker Melanocharis citreola sp. nov., is in fact sister to the phenotypically dissimilar Streaked Berrypecker M. striativentris. Phylogenetic relationships within the family Melanocharitidae, including all presently recognized genera (Toxorhamphus, Oedistoma, Rhamphocharis and Melanocharis), reveal that this family endemic to the island of New Guinea diversified during the main uplift of New Guinea in the Middle and Late Miocene (14-6 Mya), and represents an evolutionary radiation with high disparity in bill morphology and signalling traits across species. Rhamphocharis berrypeckers fall within the Melanocharis clade despite their larger beaks, and should be included in the latter genus. Interspecific genetic distances in Melanocharis are pronounced (average interspecific distance: 8.8% in COI, 12.4% in ND2), suggesting a long history of independent evolution of all lineages corresponding to currently recognized species, including the Satin Berrypecker, which shares a most recent common ancestor with its sister species in the early Pleistocene (~2.0 Mya). 

(90) Arida E, Ashari H, Dahruddin H, Fitriana YS, Hamidy A, Irham M, Kadarusman, Riyanto A, Wiantoro S, Zein MSA, Hadiaty RK, Apandi, Krey F, Kurnianingsih, Melmambessy EHP, Mulyadi, Ohee HL, Saidin, Salamuk A, Sauri S, Suparno, Supriatna N, Suruwaky AM, Laksono WT, Warikar EL, Wikanta H, Yohanita AM, Slembrouck J, Legendre M, Gaucher P, Cochet C, Delrieu-Trottin E, Thébaud C, Mila B, Fouquet A, Borisenko A, Steinke D, Hocdé R, Semiadi G, Pouyaud L, Hubert N. 2021. Exploring the vertebrate fauna of the Bird's Head Peninsula (Indonesia, West Papua) through DNA barcodes. Mol Ecol Resour.ces 21:2369-2387.

Biodiversity knowledge is widely heterogeneous across the Earth's biomes. Some areas, due to their remoteness and difficult access, present large taxonomic knowledge gaps. Mostly located in the tropics, these areas have frequently experienced a fast development of anthropogenic activities during the last decades and are therefore of high conservation concerns. The biodiversity hotspots of Southeast Asia exemplify the stakes faced by tropical countries. While the hotspots of Sundaland (Java, Sumatra, Borneo) and Wallacea (Sulawesi, Moluccas) have long attracted the attention of biologists and conservationists alike, extensive parts of the Sahul area, in particular the island of New Guinea, have been much less explored biologically. Here, we describe the results of a DNA-based inventory of aquatic and terrestrial vertebrate communities, which was the objective of a multidisciplinary expedition to the Bird's Head Peninsula (West Papua, Indonesia) conducted between 17 October and 20 November 2014. This expedition resulted in the assembly of 1005 vertebrate DNA barcodes. Based on the use of multiple species-delimitation methods (GMYC, PTP, RESL, ABGD), 264 molecular operational taxonomic units (MOTUs) were delineated, among which 75 were unidentified and an additional 48 were considered cryptic. This study suggests that the diversity of vertebrates of the Bird's Head is severely underestimated and considerations on the evolutionary origin and taxonomic knowledge of these biotas are discussed.

(89) Aguilée R., F. Pellerin, M. Soubeyrand, J. Choin, & C. Thébaud. 2021. Biogeographic drivers of community assembly on oceanic islands: the importance gf archipelago structure and history. J. Biogeography (in press)

Aim: Accounting for geo-environmental dynamics is crucial to understand community assembly across islands. Whittaker et al. (J Biogeogr, 35:977–994, 2008)’s General Dynamic Model (GDM) aims towards this goal. Yet, it does not explicitly consider that most islands belong to archipelagos. We examined how island biodiversity dynamics are influenced by the interaction of eco-evolutionary processes acting at the archipelago level with each island's geo-environmental dynamics.
Location: Hypothetical archipelagos.
Taxon: Any.
Methods: We used an individual-based model, ecologically neutral within the archipelago. Several islands emerge in succession with a typical volcanic ontogeny. We considered both mainland and inter-island dispersal. Geographically isolated lineages diverged over time, possibly speciating.
Results: We found diversity to be at dynamic equilibrium. In an archipelago, islands hosted more diversity and more endemic species, at both island and archipelago levels, than an equivalently-sized single isolated island. This was due to an ‘archipelago effect’: inter-island dispersal increased within-island diversity through species occurrence on multiple islands; species may undergo anagenetic changes on the colonised islands, eventually speciating, thereby increasing archipelago diversity. Biodiversity dynamics of different islands may differ even on islands with identical geo-environmental dynamics because the archipelago effect varied over time and affected each island differently (‘history effect’). By accounting for these effects, we predicted detectable deviations from the GDM predictions, which are largest for remote archipelagos, with islands located close together and with an intermediate time of island emergence. In linear stepping-stone archipelagos, we predicted higher diversity on centrally located islands.
Main conclusions: Our results demonstrate that analyses of insular biodiversity data would greatly benefit from explicitly accounting for both archipelago and history effects. We suggest incorporating variables characterising the spatio-temporalstructure of the whole archipelago. We discuss possible difficulties in distinguishing between the archipelago effect and equilibrium diversity dynamics.

(88) Leroy T., M. Rousselle, M.-K. Tilak, A.E. Caizergues, C. Scornavacca, M. Recuerda, J. Fuchs, J.C. Illera, D.H. de Swardt, G. Blanco, C. Thébaud, B. Milá, & B. Nabholz. 2021. Island songbirds as windows into evolution in small populations. Current Biology (in press)

Due to their limited ranges and inherent isolation, island species have long been recognized as crucial systems for tackling a range of evolutionary questions, including in the early study of speciation.1,2 Such species have been less studied in the understanding of the evolutionary forces driving DNA sequence evolution. Island species usually have lower census population sizes (N) than continental species and, supposedly, lower effective population sizes (Ne). Given that both the rates of change caused by genetic drift and by selection are dependent upon Ne, island species are theoretically expected to exhibit (1) lower genetic diversity, (2) less effective natural selection against slightly deleterious mutations,3,4 and (3) a lower rate of adaptive evolution.5, 6, 7, 8 Here, we have used a large set of newly sequenced and published whole-genome sequences of Passerida species (14 insular and 11 continental) to test these predictions. We confirm that island species exhibit lower census size and Ne, supporting the hypothesis that the smaller area available on islands constrains the upper bound of Ne. In the insular species, we find lower nucleotide diversity in coding regions, higher ratios of non-synonymous to synonymous polymorphisms, and lower adaptive substitution rates. Our results provide robust evidence that the lower Ne experienced by island species has affected both the ability of natural selection to efficiently remove weakly deleterious mutations and also the adaptive potential of island species, therefore providing considerable empirical support for the nearly neutral theory. We discuss the implications for both evolutionary and conservation biology.​

(87) Valente, L., Phillimore, A. B., Melo, M., Warren, B. H., Clegg, S. M., Havenstein, K., Tiedemann, R., Illera, J. C., Thébaud, C., Aschenbach, T. & Etienne, R. S. 2020. A simple dynamic model explains island bird diversity worldwide. Nature, 579: 92–96.​

Colonization, speciation and extinction are dynamic processes that influence global patterns of species richness. Island biogeography theory predicts that the contribution of these processes to the accumulation of species diversity depends on the area and isolation of the island. Notably, there has been no robust global test of this prediction for islands where speciation cannot be ignored9, because neither the appropriate data nor the analytical tools have been available. In this paper, we addressed both deficiencies to reveal, for island birds, the empirical shape of the general relationships that determine how colonization, extinction and speciation rates co-vary with the area and isolation of islands. We compiled a global molecular phylogenetic dataset of birds on islands, based on the terrestrial avifaunas of 41 oceanic archipelagos worldwide (including 596 avian taxa), and applied a new analysis method to estimate the sensitivity of island-specific rates of colonization, speciation and extinction to island features (area and isolation). Our model predicts—with high explanatory power—several global relationships. We found a decline in colonization with isolation, a decline in extinction with area and an increase in speciation with area and isolation. Combining the theoretical foundations of island biogeography with the temporal information contained in molecular phylogenies proves a powerful approach to reveal the fundamental relationships that govern variation in biodiversity across the planet.

(86) Gabrielli M., T. Leroy, B. Nabholz, B. Milá, & C. Thébaud. 2020. Within-island diversification in a passerine bird. Proceeding of the Royal Society B 287: 20192999. http://dx.doi.org/10.1098/rspb.2019.2999

The presence of congeneric taxa on the same island suggests the possibility of in situ divergence, but can also result from multiple colonizations of pre- viously diverged lineages. Here, using genome-wide data from a large population sample, we test the hypothesis that intra-island divergence explains the occurrence of four geographical forms meeting at hybrid zones in the Reunion grey white-eye (Zosterops borbonicus), a species complex endemic to the small volcanic island of Reunion. Using population genomic and phylogenetic analyses, we reconstructed the population history of the different forms. We confirmed the monophyly of the complex and found that one of the lowland forms is paraphyletic and basal relative to others, a pattern highly consistent with in situ divergence. Our results suggest initial colonization of the island through the lowlands, followed by expansion into the highlands, which led to the evolution of a distinct geographical form, genetically and ecologically different from the lowland ones. Lowland forms seem to have experienced periods of geographical isolation, but they diverged from one another by sexual selection rather than niche change. Overall, low dispersal capabilities in this island bird combined with both geographical and ecological opportunities seem to explain how divergence occurred at such a small spatial scale.

(85) Bourgeois Y.X.C., J.A.M Bertrand, B. Delahaie, H. Holota, C. Thébaud, and B. Milá. 2020. Differential divergence in autosomes and sex chromosomes is associated with intra-island diversification at a very small spatial scale in a songbird lineage. Molecular Ecology (in press)

Recently diverged taxa showing marked phenotypic and ecological diversity provide optimal systems to understand the genetic processes underlying speciation. We used genome-wide markers to investigate the diversification of the Reunion grey white-eye (Zosterops borbonicus) on the small volcanic island of Reunion (Mascarene archipelago), where this species complex exhibits four geographical forms that are parapatrically distributed across the island and differ strikingly in plumage colour. One form restricted to the highlands is separated by a steep ecological gradient from three distinct lowland forms which meet at narrow hybrid zones that are not associ- ated with environmental variables. Analyses of genomic variation based on single nucleotide polymorphism data from genotyping-by-sequencing and pooled RAD-seq approaches show that signatures of selection associated with elevation can be found at multiple regions across the genome, whereas most loci associated with the low- land forms are located on the Z sex chromosome. We identified TYRP1, a Z-linked colour gene, as a likely candidate locus underlying colour variation among lowland forms. Tests of demographic models revealed that highland and lowland forms di- verged in the presence of gene flow, and divergence has progressed as gene flow was restricted by selection at loci across the genome. This system holds promise for in- vestigating how adaptation and reproductive isolation shape the genomic landscape of divergence at multiple stages of the speciation process.

(84) Vacher J.P., J. Chave, F. Ficetola, G. Sommeria-Klein, S. Tao, C. Thébaud, M. Blanc, A. Camacho, J. Cassimiro, T.J. Colston, M. Dewynter, R. Ernst, P. Gaucher, J.O. Gomes, R. Jairam, P.J.R. Kok, J.D. Lima, Q. Martinez, C. Marty, B.P. Noonan, P. Nunes, P. Ouboter, R. Recoder, M.T. Rodrigues, A. Snyder, S. Maques de Souza, & A. Fouquet. 2020. Large-scale DNA-based survey of frogs in Amazonia suggests a vast underestimation of species richness and endemism. Journal of Biogeography (in press)

Mapping Amazonian biodiversity accurately is a major challenge for integrated conservation strategies and to study its origins. However, species boundaries and their respective distribution are notoriously inaccurate in this region. In this paper, we generated a georeferenced database of short mtDNA sequences from Amazonian frogs, revised the species richness and the delineation of bioregions of the Eastern Guiana Shield and estimated endemism within these bioregions.
We used an extensive DNA-based sampling of anuran amphibians of Amazonia using next-generation sequencing to delineate Operational Taxonomic Units (OTU) and their distribution. We analysed this database to infer bioregions using Latent Dirichlet Allocation modelling. We then compared endemism within these bioregions based on our results and the current IUCN database, and inferred environmental variables that contributed the most to the biogeographic pattern.
The recognized anuran species richness within the focal area increased from 440 species currently listed by the IUCN Red List to as much as 876 OTUs with our dataset. We recovered eight bioregions, among which three lie within the Eastern Guiana Shield. We estimated that up to 82% of the OTUs found in this area are en- demic, a figure three times higher than the previous estimate (28%). Environmental features related to seasonal precipitations are identified as playing an important role in shaping Amazonian amphibian bioregions.

(83) Warren B.H., R.E. Ricklefs, C. Thébaud, D. Gravel, & N. Mouquet. 2019. How consideration of islands has inspired mainstream ecology: links between the theory of island biogeography and some other key theories. Reference Module in Earth Systems and Environmental Sciences, Elsevier, 10.1016/B978-0-12-409548-9.11788-9 .

The passing of the 50th anniversary of the theory of island biogeography (IBT) has helped spur a new wave of interest in the biology of islands. Despite the longstanding acclaim of MacArthur and Wilson’s (1963, 1967) theory, the breadth of its influence in mainstream ecology today is easily overlooked. Here we summarize some of the main links between IBT and subsequent developments in ecology. These include not only modifications to the core model to incorporate greater biological complexity, but also the role of IBT in inspiring two other quantitative theories that are at least as broad in relevance—metapopulation theory and ecological neutral theory. Using habitat fragmentation and life-history evolution as examples, we also argue that a significant legacy of IBT has been in shaping and unifying ecological schools of thought.

(82) Leroy T., Y. Anselmetti, M.-K. Tilak, S. Berard, L. Csukonyi, M. Gabrielli, C. Scornavacca, B. Mila, C. Thébaud, & B. Nabholz. 2019. A bird’s white-eye view on neo-sex chromosome evolution. bioRxiv, 505610, ver. 4 peer-reviewed and recommended by PCI Evolutionary Biology. doi: 10.1101/505610

Chromosomal organization is relatively stable among avian species, especially with regards to sex chromosomes. Members of the large Sylvioidea clade however have a pair of neo-sex chromosomes which is unique to this clade and originate from a parallel translocation of a region of the ancestral 4A chromosome on both W and Z chromosomes. Here, we took advantage of this unusual event to study the early stages of sex chromosome evolution. To do so, we sequenced a female (ZW) of two Sylvioidea species, a Zosterops borbonicus and a Z. pallidus. Then, we organized the Z. borbonicus scaffolds along chromosomes and annotated genes. Molecular phylogenetic dating under various methods and calibration sets confidently confirmed the recent diversification of the genus Zosterops (1-3.5 million years ago), thus representing one of the most exceptional rates of diversification among vertebrates. We then combined genomic coverage comparisons of five males and seven females, and homology with the zebra finch genome (Taeniopygia guttata) to identify sex chromosome scaffolds, as well as the candidate chromosome breakpoints for the two translocation events. We observed reduced levels of within-species diversity in both translocated regions and, as expected, even more so on the neoW chromosome. In order to compare the rates of molecular evolution in genomic regions of the autosomal-to-sex transitions, we then estimated the ratios of non-synonymous to synonymous polymorphisms (πN/πS) and substitutions (dN/dS). Based on both ratios, no or little contrast between autosomal and Z genes was observed, thus representing a very different outcome than the higher ratios observed at the neoW genes. In addition, we report significant changes in base composition content for translocated regions on the W and Z chromosomes and a large accumulation of transposable elements (TE) on the newly W region. Our results revealed contrasted signals of molecular evolution changes associated to these autosome-to- sex chromosome transitions, with congruent signals of a W chromosome degeneration yet a surprisingly weak suport for a fast-Z effect.

(81) Dale E.J., R. L. Kitching, C. Thébaud,  S. C. Maunsell, L. A. Ashton. Moths in the Pyrénées: spatio-temporal patterns and indicators of elevational assemblages. Biodiversity and Conservation 28, 1593-1610

Understanding how assemblages of invertebrates change over continuous elevational gradients not only generates an understanding of current rules of community assembly but may also be useful for predicting the future distributions of species under global change. Temperature decreases predictably with increasing elevation and, accordingly, gradients in elevation permit the study of adjacent climates within small geographical areas. The present study examines if and how assemblages of moths change with increasing elevation in the eastern French Pyrenees. Elevation had a strong effect on the assemblage composition of moth species in both seasons. The species sets which contributed most to this strong pattern differed completely across seasons. Analysis of restrictions and fidelity to particular elevational ranges generated a set of indicator species which can be used to monitor future changes in distribution. Twelve species were identified as elevation-specific indicators (the 'predictor set’) from the spring samples and summer samples. We note the strong contrasts between species that produce overall statistical pattern and those that show strong fidelity to particular elevations and discuss this in terms of the biologies of the species concerned.
We discuss best practice for the identification and use of indicator species for monitoring future responses to climate change.

(80) Borges P.A.V., P. Cardoso, S. Fattorini, F. Rigal, T.J. Matthews, L. Di Biase, I.R. Amorim, M. Florencio, L. Borda- de-Água, C. Rego, F. Pereira, R. Nunes, R. Carvalho, M.T. Ferreira, H. López, A.J. Pérez Delgado, R. Otto, S. Fernández Lugo, L. de Nascimento, J. Caujapé-Castells, J. Casquet, S. Danflous, J. Fournel, A.-M. Sadeyen, R.B. Elias, J.M. Fernández-Palacios, P. Oromí, C. Thébaud, D. Strasberg, B.C. Emerson. Community structure of woody plants on islands along a bioclimatic gradient. Frontiers of Biogeography 10.21425/F5FBG40295

Understanding patterns of community structure and the causes for their variation can be furthered by comparative biogeographic analyses of island biotas. In this study, we used woody plant data at the local scale to investigate variations in species rarity, alpha, beta, and gamma diversity within and between three islands from the oceanic archipelagoes of Azores, Canaries and Mascarene. We used standardized protocols to sample ten 50 m × 50 m forest plots in each of the three islands with contrasting climate and regional species pools: Terceira (Azores), Tenerife (Canaries), and Reunion (Mascarene Islands). Occupancy frequency distributions and species abundance distributions were used to investigate rarity. The partitioning of beta diversity in a distance-decay framework was used to test for spatial patterns of community composition. Rarity was much more pronounced in the highly diverse islands of Tenerife and Reunion than in the regionally poorer island of Terceira. The number of species rose faster with increasing sample area in both Tenerife and Reunion. The slope of the species rank abundance curve was steeper in Terceira whereas the richer island assemblages approached a lognormal model. Compositional changes according to spatial distance were mostly due to replacement of species in Terceira and Reunion. Our results point to important differences in the community structure of Terceira, which is the less diverse and temperate region in comparison to Tenerife and Reunion which are highly diverse. High regional diversity of species in Tenerife and Reunion is a consequence of comparably long eco-evolutionary history that has promoted high levels of diversity which are not comparable to the relatively species-poor biota of the Azores, constrained by recent geological history and low environmental diversity.

(79) Warren Ben H., Oskar Hagen, Florian Gerber, Christophe Thébaud, Emmanuel Paradis, Elena Conti. Evaluating alternative explanations for an association of extinction risk and evolutionary uniqueness in multiple insular lineages. Evolution (in press)

Studies in insular environments have often documented a positive association of extinction risk and evolutionary uniqueness (i.e. how distant a species is from its closest living relative). However, the cause of this association is unclear. One explanation is that species threatened with extinction are evolutionarily unique because they are old, implying that extinction risk increases with time since speciation (age-dependent extinction). An alternative explanation is that such threatened species are last survivors of clades that have undergone an elevated extinction rate, and that their uniqueness results from the extinction of their close relatives. Distinguishing between these explanations is difficult but important, since they imply different biological processes determining extinction patterns. Here we designed a simulation approach to distinguish between these alternatives using living species, and applied it to twelve insular radiations that show a positive association between extinction risk and evolutionary uniqueness. We also tested the sensitivity of results to underlying assumptions and variable extinction rates. Despite differences among the radiations considered, age-dependent extinction was supported as best explaining the majority of the empirical cases. Biological processes driving characteristic changes in abundance with species duration (age-dependency) may merit further investigation.

(78) Kitson James J.N., Ben H. Warren, Christophe Thébaud, Dominique Strasberg, and Brent C. Emerson. Community assembly and diversification in a species-rich radiation of island weevils (Coleoptera: Cratopini). Journal of Biogeography (in press)

Aim: To test a prediction derived from island biogeographical theory that in situ speciation should make an increasingly important contribution to community assembly as islands age. This prediction is tested on estimated biogeographical histories from Mauritius (approximately 9 Myr) and Reunion (approximately 5 Myr). We additionally investigate the evolutionary dynamics of insect flight loss, as the loss of flight in island lineages can influence patterns of diversification.
Location: Mascarene Islands; Southwest Indian Ocean.
Taxon: Weevils.
Methods: Up to five individuals of each taxonomically described species sampled within each sampling site were sequenced for the mitochondrial gene Cytochrome Oxidase II to delimit operational taxonomic units (OTUs). OTUs were further sequenced for the nuclear genes Arginine Kinase, Histone 3 and ribosomal 28s, to reconstruct the phylogenetic history of the group. Timings of colonization and in situ speciation events were estimated with BEAST2.
Results: Our results support the hypothesis that present-day species richness on the older island of Mauritius is largely the result of in situ speciation, with few colonization events, of which all but the most basal are recent. In contrast, Reunion presents a more uniform temporal spectrum of colonization times. Flight loss has evolved convergently at least five times, and speciation events associated with flight loss are significantly younger than speciation events that have not resulted in flight loss.
Main conclusions: Patterns of community assembly on the islands of Mauritius and Reunion fit a model where the addition of new species and species turnover is increasingly dominated by in situ speciation as an island community matures. Repeated flight loss indicates selection for flightlessness, with the young age of flightless lineages suggesting higher extinction rates over longer evolutionary timescales and little influence on present-day species richness.

(77) Borges Paulo A. V. , Pedro Cardoso, Holger Kreft, Robert J. Whittaker, Simone Fattorini, Brent C. Emerson, Artur Gil, Rosemary G. Gillespie, Thomas J. Matthews, Ana M. C. Santos, Manuel J. Steinbauer12 · Christophe Thébaud, Claudine Ah‐Peng, Isabel R. Amorim1,2 · Silvia Calvo Aranda, Ana Moura Arroz, José Manuel N. Azevedo, Mário Boieiro, Luís Borda‐de‐Água, José Carlos Carvalho, Rui B. Elias, José María Fernández‐Palacios, Margarita Florencio,  Juana M. González‐Mancebo, Lawrence R. Heaney, Joaquín Hortal, Christoph Kueffer, Benoit Lequette, José Luis Martín‐Esquivel, Heriberto López, Lucas Lamelas‐López, José Marcelino, Rui Nunes, Pedro Oromí, Jairo Patiño, Antonio J. Pérez, Carla Rego, Sérvio P. Ribeiro, François Rigal, Pedro Rodrigues, Andrew J. Rominger, Margarida Santos‐Reis, Hanno Schaefer, Cecília Sérgio, Artur R. M. Serrano, Manuela Sim‐Sim,  P. J. Stephenson, António O. Soares, Dominique Strasberg,  Alain Vanderporten, Virgílio Vieira, Rosalina Gabriel. Global Island Monitoring Scheme (GIMS): a proposal for the long‐term coordinated survey and monitoring of native island forest biota. Biodiversity and Conservation (in press)

Islands harbour evolutionary and ecologically unique biota, which are currently disproportionately threatened by a multitude of anthropogenic factors, including habitat loss, invasive species and climate change. Native forests on oceanic islands are important refu-gia for endemic species, many of which are rare and highly threatened. Long-term monitor- ing schemes for those biota and ecosystems are urgently needed: (i) to provide quantitative baselines for detecting changes within island ecosystems, (ii) to evaluate the effectiveness of conservation and management actions, and (iii) to identify general ecological patterns andprocesses using multiple island systems as repeated ‘natural experiments’. In this contribu- tion, we call for a Global Island Monitoring Scheme (GIMS) for monitoring the remaining native island forests, using bryophytes, vascular plants, selected groups of arthropods and vertebrates as model taxa. As a basis for the GIMS, we also present new, optimized monitor- ing protocols for bryophytes and arthropods that were developed based on former standard- ized inventory protocols. Effective inventorying and monitoring of native island forests will require: (i) permanent plots covering diverse ecological gradients (e.g. elevation, age of ter- rain, anthropogenic disturbance); (ii) a multiple-taxa approach that is based on standardized and replicable protocols; (iii) a common set of indicator taxa and community properties that are indicative of native island forests’ welfare, building on, and harmonized with existing sampling and monitoring efforts; (iv) capacity building and training of local researchers, col- laboration and continuous dialogue with local stakeholders; and (v) long-term commitment by funding agencies to maintain a global network of native island forest monitoring plots.

(76) Bruxaux J, Gabrielli M, Ashari H, Prŷs-Jones R, Joseph L, Milá B, Besnard G, Thébaud C. Recovering the evolutionary history of crowned pigeons (Columbidae: Goura): Implications for the biogeography and conservation of New Guinean lowland birds. Molecular Phylogenetics and Evolution (in press)

Assessing the relative contributions of immigration and diversification into the buildup of species diversity is key to understanding the role of historical processes in driving biogeographical and diversification patterns in species-rich regions. Here, we investigated how colonization, in situ speciation, and extinction history may have generated the present-day distribution and diversity of Goura crowned pigeons (Columbidae), a group of large forest-dwelling pigeons comprising four recognized species that are all endemic to New Guinea. We used a comprehensive geographical and taxonomic sampling based mostly on historical museum samples, and shallow shotgun sequencing, to generate complete mitogenomes, nuclear ribosomal clusters and independent nuclear conserved DNA elements. We used these datasets independently to reconstruct molecular phylogenies. Divergence time estimates were obtained using mitochondrial data only. All analyses revealed similar genetic divisions within the genus Goura and recovered as monophyletic groups the four species currently recognized, providing support for recent taxonomic changes based on differences in plumage characters. These four species are grouped into two pairs of strongly supported sister species, which were previously not recognized as close relatives: Goura sclaterii with Goura cristata, and Goura victoria with Goura scheepmakeri. While the geographical origin of the Goura lineage remains elusive, the crown age of 5.73 Ma is consistent with present-day species diversity being the result of a recent diversification within New Guinea. Although the orogeny of New Guinea's central cordillera must have played a role in driving diversification in Goura, cross-barrier dispersal seems more likely than vicariance to explain the speciation events having led to the four current species. Our results also have important conservation implications. Future assessments of the conservation status of Goura species should consider threat levels following the taxonomic revision proposed by del Hoyo and Collar (HBW and BirdLife International illustrated checklist of the birds of the world 1: non-passerines, 2014), which we show to be fully supported by genomic data. In particular, distinguishing G. sclaterii from G. scheepmakeri seems to be particularly relevant.

(75) Delahaie Boris, Josselin Cornuault, Charline Masson, Joris Bertrand, Yann Bourgeois, Borja Milá and Christophe Thébaud. Narrow hybrid zones in spite of very low population differentiation in neutral markers in an island bird species complex. Journal of evolutionary Biology 30:2132-2145

Patterns of phenotypic and genic frequencies across hybrid zones provide insight into the origin and evolution of reproductive isolation. The Reunion grey white-eye, Zosterops borbonicus, exhibits parapatrically distributed plumage colour forms across the lowlands of the small volcanic island of Reunion (Mascarene archipelago). These forms meet and hybridize in regions that are natural barriers to dispersal (rivers, lava fields). Here, we investigated the relationship among patterns of differentiation at neutral genetic (microsatellite) markers, phenotypic traits (morphology and plumage colour) and niche characteristics across three independent hybrid zones. Patterns of phenotypic divergence revealed that these hybrid zones are among the narrowest ever documented in birds. However, the levels of phenotypic divergence stand in stark contrast to the lack of clear population neutral genetic structure between forms. The position of the hybrid zones coincides with different natural physical barriers, yet is not associated with steep changes in vegetation and related climatic variables, and major habitat transitions are shifted from these locations by at least 18 km. This suggests that the hybrid zones are stabilized over natural dispersal barriers, independently of environmental boundaries, and are not associated with niche divergence. A striking feature of these hybrid zones is the very low levels of genetic differentiation in neutral markers between forms, suggesting that phenotypic divergence has a narrow genetic basis and may reflect recent divergence at a few linked genes under strong selection, with a possible role for assortative mating in keeping these forms apart.

(74) Ducatez Simon, Mathieu Giraudeau, Christophe Thébaud and Lisa Jacquin. Colour polymorphism is associated with lower extinction risk in birds. Global Change Biology 23, 3030-3039

Colour polymorphisms have played a major role in enhancing current understanding of how selection and demography can impact phenotypes. Because different morphs often display alternative strategies and exploit alternative ecological niches, colour polymorphism can be expected to promote adaptability to environmental changes. However, whether and how it could influence populations' and species' response to global changes remains debated. To address this question, we built an up-to-date and complete database on avian colour polymorphism based on the examination of available data from all 10,394 extant bird species. We distinguished between true polymorphism (where different genetically determined morphs co-occur in sympatry within the same population) and geographic variation (parapatric or allopatric colour variation), because these two patterns of variation are expected to have different consequences on populations' persistence. Using the IUCN red list, we then showed that polymorphic bird species are at lesser risk of extinction than nonpolymorphic ones, after controlling for a range of factors such as geographic range size, habitat breadth, life history, and phylogeny. This appears consistent with the idea that high genetic diversity and/or the existence of alternative strategies in polymorphic species promotes the ability to adaptively respond to changing environmental conditions. In contrast, polymorphic species were not less vulnerable than nonpolymorphic ones to specific drivers of extinction such as habitat alteration, direct exploitation, climate change, and invasive species. Thus, our results suggest that colour polymorphism acts as a buffer against environmental changes, although further studies are now needed to understand the underlying mechanisms. Developing accurate quantitative indices of sensitivity to specific threats is likely a key step towards a better understanding of species response to environmental changes.

(73) Vacher Jean-Pierre, Philippe Kok, Miguel Rodrigues, Jucivaldo Lima, Andy Lorenzini, Quentin Martinez, Manon Fallet, Elodie Courtois, Michel Blanc, Philippe Gaucher, Mael Dewynter, Rawien Jairam, Paul Ouboter, Christophe Thebaud, Antoine Fouquet. Cryptic diversity in Amazonian frogs: integrative taxonomy of the genus Anomaloglossus (Amphibia: Anura: Aromobatidae) reveals a unique case of diversification within the Guiana Shield. Molecular Phylogenetics and Evolution 112, 158-173
 
Lack of resolution on species boundaries and distribution can hamper inferences in many fields of biology, notably biogeography and conservation biology. This is particularly true in megadiverse and under-surveyed regions such as Amazonia, where species richness remains vastly underestimated. Integrative approaches using a combination of phenotypic and molecular evidence have proved extremely successful in reducing knowledge gaps in species boundaries, especially in animal groups displaying high levels of cryptic diversity like amphibians. Here we combine molecular data (mitochondrial 16S rRNA and nuclear TYR, POMC, and RAG1) from 522 specimens of Anomaloglossus, a frog genus endemic to the Guiana Shield, including 16 of the 26 nominal species, with morphometrics, bioacoustics, tadpole development mode, and habitat use to evaluate species delineation in two lowlands species groups. Molecular data reveal the existence of 18 major mtDNA lineages among which only six correspond to described species. Combined with other lines of evidence, we confirm the existence of at least 12 Anomaloglossus species in the Guiana Shield lowlands. Anomaloglossus appears to be the only amphibian genus to have largely diversified within the eastern part of the Guiana Shield. Our results also reveal strikingly different phenotypic evolution among lineages. Within the A. degranvillei group, one subclade displays acoustic and morphological conservatism, while the second subclade displays less molecular divergence but clear phenotypic divergence. In the A. stepheni species group, a complex evolutionary diversification in tadpole development is observed, notably with two closely related lineages each displaying exotrophic and endotrophic tadpoles.

(72) Bourgeois Yann X. C., Boris Delahaie, Mathieu Gautier, Emeline Lhuillier, Pierre-Jean G. Malé, Joris A. M. Bertrand, Josselin Cornuault, Kazumasa Wakamatsu, Olivier Bouchez, Claire Mould, Jade Bruxaux, Hélène Holota, Borja Milá and
Christophe Thébaud. A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird. Royal Society Open Science 4:160805

Understanding the mechanisms responsible for phenotypic diversification within and among species ultimately rests with linking naturally occurring mutations to functionally and ecologically significant traits. Colour polymorphisms are of great interest in this context because discrete colour patterns within a population are often controlled by just a few genes in a common environment. We investigated how and why phenotypic diversity arose and persists in the Zosterops borbonicus white-eye of Reunion (Mascarene archipelago), a colour polymorphic songbird in which all highland populations contain individuals belonging to either a brown or a grey plumage morph. Using extensive phenotypic and genomic data, we demonstrate that this melanin-based colour polymorphism is controlled by a single locus on chromosome 1 with two large-effect alleles, which was not previously described as affecting hair or feather colour. Differences between colour morphs appear to rely upon complex cis-regulatory variation that either prevents the synthesis of pheomelanin in grey feathers, or increases its production in brown ones. We used coalescent analyses to show that, from a ‘brown’ ancestral population, the dominant ‘grey’ allele spread quickly once it arose froma new mutation. Since colour morphs are always found inmixture, this implies that the selected allele does not go to fixation, but instead reaches an intermediate frequency, as would be expected under balancing selection.

(71) Cicconardi Francesco, Paulo A. V. Borges, Dominique Strasberg, Pedro Oromí, Heriberto López, Antonio J. Pérez-Delgado, Juliane Casquet, Juli Caujapé-Castells, José María Fernández-Palacios, Christophe Thébaud, Brent C. Emerson. MtDNA metagenomics reveals large-scale invasion of belowground arthropod communities by introduced species. Molecular Ecology 26, 3104-3115

Using a series of standardised sampling plots within forest ecosystems in remote oceanic islands, we reveal fundamental differences between the structuring of aboveground and belowground arthropod biodiversity that are likely due to large-scale species introductions by humans. Species of beetle and spider were sampled almost exclusively from single islands, while soil dwelling Collembola exhibited more than tenfold higher species sharing among islands. Comparison of Collembola mitochondrial metagenomic data to a database of more than 80,000 Collembola barcode sequences revealed almost 30% of sampled island species are genetically identical, or near identical, to individuals sampled from often very distant geographic regions of the world. Patterns of mtDNA relatedness among Collembola implicate human-mediated species introductions, with minimum estimates for the proportion of introduced species on the sampled islands ranging from 45-88%. Our results call for more attention to soil mesofauna to understand the global extent and ecological consequences of species introductions.

​(70) Emerson B.C., J. Casquet, H. Lopez, P. Cardoso, P.A.V. Borges, N. Mollaret, P. Oromi, D. Strasberg, & C. Thébaud. A combined field survey and molecular identification protocol for comparing forest arthropod biodiversity across spatial scales. Molecular Ecology Resources 17, 694-707

Obtaining fundamental biodiversity metrics such as alpha, beta and gamma diversity for arthropods is often complicated by a lack of prior taxonomic information and/or taxonomic expertise, which can result in unreliable morphologically based estimates. We provide a set of standardized ecological and molecular sampling protocols that can be employed by researchers whose taxonomic skills may be limited, and where there may be a lack of robust a priori information regarding the regional pool of species. These protocols combine mass sampling of arthropods, classification of samples into parataxonomic units (PUs) and selective sampling of individuals for mtDNA sequencing to infer biological species. We sampled ten lowland rainforest plots located on the volcanic oceanic island of Réunion (Mascarene archipelago) for spiders, a group with limited taxonomic and distributional data for this region. We classified adults and juveniles into PUs and then demonstrated the reconciliation of these units with presumed biological species using mtDNA sequence data, ecological data and distributional data. Because our species assignment protocol is not reliant upon prior taxonomic information, or taxonomic expertise, it minimizes the problem of the Linnean shortfall to yield diversity estimates that can be directly compared across independent studies. Field sampling can be extended to other arthropod groups and habitats by adapting our field sampling protocol accordingly.

(69) Hansen D.M, J.J. Austin, R.H. Baxter, E.J. de Boer, W. Falcón, S.J. Norder, K.F. Rijsdijk, C. Thébaud, N.J. Bunbury, & B.H. Warren. Origins of endemic island tortoises in the western Indian Ocean: A critique of the human-translocation hypothesis. Journal of Biogeography 44, 1430-1435

This paper is a reply to a paper that recently argued that giant tortoises could have been introduced to the Indian Ocean islands by early Austronesian sailors, possibly to establish provisioning stations for their journeys, just as European sailors did in more recent historical times. We present evidence from DNA phylogeny, Plio-Pleistocene ocean currents, giant tortoise dispersal, evolution of plant defences, radiocarbon dates and archaeology that indicates that the endemic giant tortoises on the Mascarenes and Seychelles colonized naturally and were not translocated there by humans.

(68) Fuchs J., D. Lemoine, J. L. Parra, J.-M. Pons, M. J. Raherilalao, R. Prys-Jones, C. Thébaud, B. H. Warren, and S. M. Goodman. Long-distance dispersal and inter-island colonization across the western Malagasy Region explain diversification in brush-warblers (Passeriformes: Nesillas). Biological Journal of the Linnean Society 119, 873-889

This study examines the colonization history and phylogeography of the brush-warblers (genus Nesillas), a genus of passerines endemic to islands of the western Indian Ocean (Madagascar, Comoros and Aldabra). The phylogeny of all recognized Nesillas taxa was reconstructed employing Bayesian phylogenetic methods and divergence times were estimated using a range of substitution rates and clock assumptions. Spatiotemporal patterns of population expansion were inferred using Spread, and niches of different lineages were compared using ecological niche modelling. Our results indicate that taxa endemic to the Comoros are paraphyletic and that the two endemic species on Madagascar (N. typica and N. lantzii) are not sister taxa. The brush-warblers started to diversify about 1.6 Myr, commencing with the separation of the clade formed by two species endemic to the Comoros (N. brevicaudata and N. mariae) from the rest of the genus. The lineages leading to the two Malagasy species diverged about 0.9 Myr; each with significantly different modern ecological niches and the subject of separate demographic processes. Patterns of diversification and endemism in Nesillas were shaped by multiple long distance dispersal events and inter-island colonization, a recurring pattern for different lineages on western Indian Ocean islands. The diversification dynamics observed for Nesillas are also consistent with the taxon cycle hypothesis. 

(67) Bertrand J., B. Delahaie, Y. Bourgeois, T. Duval, R. Garcia-Jimenez, J. Cornuault, B. Pujol, C. Thébaud, B. Mila. The role of selection and historical factors in driving population differentiation along an elevational gradient in an island bird. Journal of evolutionary Biology 29, 824-836

Adaptation to local environmental conditions and the range dynamics of populations can influence evolutionary divergence along environmental gradients. Thus, it is important to investigate patterns of both phenotypic and genetic variations among populations to reveal the respective roles of these two types of factors in driving population differentiation. Here, we test for evidence of phenotypic and genetic structure across populations of a passerine bird (Zosterops borbonicus) distributed along a steep elevational gradient on the island of R
eunion. Using 11 microsatellite loci screened in 401 individuals from 18 localities distributed along the gradient, we found that genetic differentiation occurred at two spatial levels: (i) between two main population groups corresponding to highland and lowland areas, respectively, and (ii) within each of these two groups. In contrast, several morphological traits varied gradually along the gradient. Comparison of neutral genetic differentiation (FST) and phenotypic differentiation (PST) showed that PST largely exceeds FST at several morphological traits, which is consistent with a role for local adaptation in driving morphological divergence along the gradient. Overall, our results revealed an area of secondary contact midway up the gradient between two major, cryptic, population groups likely diverged in allopatry. Remarkably, local adaptation has shaped phenotypic differentiation irrespective of population history, resulting in different patterns of variation along the elevational gradient. Our findings underscore the importance of understanding both historical and selective factors when
trying to explain variation along environmental gradients.

​(66) Bourgeois Y., J. Bertrand, B. Delahaie, J. Cornuault, T. Duval, B. Mila, & C. Thébaud. Candidate gene analysis suggests untapped genetic complexity in melanin-based pigmentation in birds. Journal of Heredity 107, 327-335

Studies on melanin-based color variation in a context of natural selection have provided a wealth of information on the link between phenotypic and genetic variation. Here, we evaluated associations between melanic plumage patterns and genetic polymorphism in the Réunion grey white-eye (Zosterops borbonicus), a species in which mutations on MC1R do not seem to play any role in explaining melanic variation. This species exhibits five plumage color variants that can be grouped into three color forms which occupy discrete geographic regions in the lowlands of Réunion, and a fourth high-elevation form which comprises two color morphs (grey and brown) and represents a true color polymorphism. We conducted a comprehensive survey of sequence variation in 96 individuals at a series of seven candidate genes other than MC1R that have been previously shown to influence melanin-based color patterns in vertebrates, including genes that have rarely been studied in a wild bird species before: POMC, Agouti, TYR, TYRP1, DCT, Corin and SLC24A5. Of these seven genes, two (Corin and TYRP1) displayed an interesting shift in allele frequencies between lowland and highland forms and a departure from mutation-drift equilibrium consistent with balancing selection in the polymorphic highland form only. Sequence variation at Agouti, a gene frequently involved in melanin-based pigmentation patterning, was not associated with color forms or morphs. Thus, we suggest that functionally important changes in loci other than those classically studied are involved in the color polymorphism exhibited by the Réunion grey white-eye and possibly many other non-model species.​

(65) Jaworski C., C. Thébaud, and J. Chave. Dynamics and persistence in a metacommunity centred on the plant Antirrhinum majus: theoretical predictions and an empirical test. Journal of Ecology 104, 456-468

Spatial processes have a major influence on the stability of species interaction networks and their resilience to environmental fluctuations.  Here we combine field observations and a dynamic model to understand how spatial processes may affect a network composed of the flowering plant Antirrhinum majus, its cohort of pollinators, and a specialist seed-predator and its parasitoid.
The interactions taking place within this system were investigated by determining the fate of flowers and fruits on flowering and fruiting stems at sixteen study sites.  We then used this information to estimate spatial and temporal variation in the pollination rate, parasitism rate, and hyperparasitism rate.
We found that the plants were pollinator-limited, with relatively variable fruit-to-flower ratios across sites.  On almost all sites, plants were both parasitised and hyperparasitised, at a low to moderate rate.
Comparing our field observations with a tritrophic Nicholson-Bailey model, we found that empirical data are not always consistent with the conditions for local tritrophic persistence.  This suggests that other mechanisms such as random disturbances and recolonisations (patch dynamics) or inter-site migration through metacommunity dynamics (source-sink dynamics) play a role in this system.  Model simulations showed that dispersal could contribute to increasing tritrophic persistence in this system, and that source-sink structure, not just environmental stochasticity, may cause the observed pattern of spatial variation.

(64) Mills J., C. Teplitsky, and 59 other authors. Archiving primary data: solutions for long-term-studies. Trends in Ecology and Evolution 30, 581-589

The recent trend for journals to require open access to primary data included in publications has been embraced by many biologists, but has caused apprehen- sion amongst researchers engaged in long-term ecological and evolutionary studies. A worldwide survey of 73 principal investigators (Pls) with long-term studies revealed positive attitudes towards sharing data with the agreement or involvement of the PI, and 93% of PIs have historically shared data. Only 8% were in favor of uncontrolled, open access to primary data while 63% expressed serious concern. We present here their viewpoint on an issue that can have non-trivial scientific consequences. We discuss potential costs of public data archiving and provide possible solutions to meet the needs of journals and researchers.

(63) Vacher J.P., A. Fouquet, H. Holota & C. Thébaud. The complete mitochondrial genome of Anomaloglossus baeobatrachus (Amphibia: Anura: Aromobatidae). Mitochondrial DNA Part B, 1:1, 338-340

(62) Jaworski CC, Andalo C, Raynaud C, Simon V, Thébaud C, Chave J. 2015. The Influence of prior learning experience on pollinator choice: an experiment using bumblebees on two wild floral types of Antirrhinum majus. PLoS ONE 10(8):e0130225. doi:10.1371/journal.pone.0130225.

Understanding how pollinator behavior may influence pollen transmission across floral types is a major challenge, as pollinator decision depends on a complex range of environmental cues and prior experience. Here we report an experiment using the plant Antirrhinum majus and the bumblebee Bombus terrestris to investigate how prior learning experience may affect pollinator preferences between floral types when these are presented together. We trained naive bumblebees to forage freely on flowering individuals of either A. majus pseudomajus (magenta flowers) or A. majus striatum (yellow flowers) in a flight cage. We then used a Y-maze device to expose trained bumblebees to a dual choice between the floral types. We tested the influence of training on their choice, depending on the type of plant signals available (visual signals, olfactory signals, or both). Bumblebees had no innate preference for either subspecies. Bumblebees trained on the yellow-flowered subspecies later preferred the yellow type, even when only visual or only olfactory signals were available, and their preference was not reinforced when both signal types were available. In contrast, bumblebees trained on the magenta-flowered subspecies showed no further preference between floral types and took slightly more time to make their choice. Since pollinator constancy has been observed in wild populations of A. majus with mixed floral types, we suggest that such constancy likely relies on short-term memory rather than acquired preference through long-term memory induced by prior learning.

(61) Courchamp F., J. Dunne, Y. Le Maho, R. May, C. Thébaud & M. Hochberg. Back to fundamentals: a reply to Barot et al. Trends in Ecology and Evolution 30: 370-371

In this reply to Barot et al.'s comment on our paper "Fundamental Ecology is Fundamental", we argue that, of course, researchers can easily reconcile a search for basic understanding with a quest to solve societally relevant problems. However, we do not see why all ecologists should do so, nor why any given ecologist cannot conduct research projects that are basic science, others with additional applied objectives, and yet other projects which are purely applied. Systematically intermingling applied and fundamental ecology may be tempting but, we argue, will result in the gradual demise of fundamental ecology, and will negatively impact on ecology as a science. While not foregoing support for applied ecology, we think that a plea for renewed support for fundamental ecology is incompatible with the merger proposed by Barot et al. who insist that science should be co-designed with stakeholders at multiple levels. We argue that the basis of fundamental ecology is understanding. It must remain, be protected, and be promoted as an end unto itself.

(60) Besnard G., J. Bertand, B. Delahaie, Y. Bourgeois, E. Lhuillier, and C. Thébaud. Valuing museum specimens: high-throughput DNA sequencing using historical collections of New Guinea crowned pigeons (Goura). Biological Journal of the Linnean Society 117, 71-82

Museum specimens are of particular importance for investigating systematics and the biogeography as well as other aspects of the evolution of biodiversity. They are also a depository of specimens accumulated over recent historical times and often the only way to study recently extinct or rare species. Unfortunately, most museum specimens yield low-quality DNA limiting their generalized use in phylogenetic and population genetic studies. Advances in sequencing technologies now offer opportunities to analyse such material even from very small tissue. Here, we applied the Illumina technology (HiSeq) on three specimens of crowned pigeon (Goura spp.) collected in New Guinea between 1879 and 1934. A shotgun strategy allowed us to quickly and reliably assemble complete mitochondrial genomes and fragments of three single-copy gene phylogenetic markers even with low double- stranded DNA quantity (9 to 69 ng). Phylogenetic assignments of these new sequences confirmed them as Goura sequences. Therefore, our study confirms the power of using next-generation sequencing methods to investigate the evolutionary history of species for which access to fresh samples is limited but museum collections are available. These approaches are considerably increasing the value of many natural history collections for genetic investigations, particularly from biodiversity hotspots that are presently difficult to prospect.

(59) Bertrand J., Y. Bourgeois, & C. Thébaud. Population density of the Réunion Grey White-eye (Zosterops borbonicus) within the summit ecosystems of Réunion (Mascarene Islands). Ostrich 87, 85-88

Assessing population density is crucial for studying ecology and evolutionary biology of species as well as for conservation purposes. Here we used point count methods to infer population density in a single-island endemic passerine bird, the Réunion Grey White-eye (Zosterops borbonicus), that displays striking evidence of differentiation at a small spatial scale.. Population density was estimated at 5.17 birds per hectare (CL: 4.85-5.50), a value somewhat higher than previously believed. This estimation provides the first detailed estimation of bird population density in the vulnerable summit ecosystems of Réunion and will possibly allow a better understanding of the evolutionary causes of this plumage colour variation. 

(58) Warren B.H., 22 other authors, & C. Thébaud. Islands as model systems in ecology and evolution: progress and prospects fifty years after MacArthur-Wilson. Ecology Letters 18: 200-217

The study of islands as model systems has played an important role in the development of evolutionary and ecological theory. The 50th anniversary of MacArthur and Wilson’s (December 1963) article, “An equilibrium theory of insular zoogeography”, was a recent milestone for this theme. Since 1963, island systems have provided new insights into the formation of ecological communities. Here, building on such developments, we highlight prospects for research on islands to improve our understanding of the ecology and evolution of communities in general. Throughout, we emphasise how attributes of islands combine to provide unusual research opportunities, the implications of which stretch far beyond islands. Molecular tools and increasing data acquisition now permit re-assessment of some fundamental issues that interested MacArthur and Wilson. These include the formation of ecological networks, species abundance distributions, and the contribution of evolution to community assembly. We also extend our prospects to other fields of ecology and evolution – understanding ecosystem functioning, speciation, and diversification – frequently employing assets of oceanic islands in inferring the geographic area within which evolution has occurred, and potential barriers to gene flow. Although island-based theory is continually being enriched, incorporating non-equilibrium dynamics is identified as a major challenge for the future. 

(57) Courchamp F., J. Dunne, Y. Le Maho, R. May, C. Thébaud, &  M. Hochberg. Fundamental ecology is fundamental. Trends in Ecology and Evolution 30: 9-16 

The primary reasons for conducting fundamental research are satisfying curiosity, acquiring knowledge, and achieving understanding. Here we develop why we believe it is essential to promote basic ecological research, despite increased impetus for ecologists to conduct and present their research in the light of poten- tial applications. This includes the understanding of our environment, for intellectual, economical, social, and political reasons, and as a major source of innovation. We contend that we should focus less on short-term, objective-driven research and more on creativity and exploratory analyses, quantitatively estimate the bene- fits of fundamental research for society, and better ex- plain the nature and importance of fundamental ecology to students, politicians, decision makers, and the general public. Our perspective and underlying arguments should also apply to evolutionary biology and to many of the other biological and physical sciences.

(56) Guidot A., W. Jiang, J.B. Ferdy, C. Thébaud, P. Barberis, J. Gouzy & S. Genin. 2014. Multihost experimental evolution of the pathogen Ralstonia solanacearum unveils genes involved in adaptation to plants. Molecular Biology and Evolution 31: 2913-2928

Ralstonia solanacearum, the causal agent of a lethal bacterial wilt plant disease, infects an unusually wide range of hosts. These hosts can further be split into plants where R. solanacearum is known to cause disease (original hosts) and those where this bacterium can grow asymptomatically (distant hosts). Moreover, this pathogen is able to adapt to many plants as supported by field observations reporting emergence of strains with enlarged pathogenic properties. To investigate the genetic bases of host adaptation, we conducted evolution experiments by serial passages of a single clone of the pathogen on three original and two distant hosts over 300 bacterial generations and then analyzed the whole-genome of nine evolved clones. Phenotypic analysis of the evolved clones showed that the pathogen can increase its fitness on both original and distant hosts although the magnitude of fitness increase was greater on distant hosts. Only few genomic modifications were detected in evolved clones compared with the ancestor but parallel evolutionary changes in two genes were observed in independent evolved populations. Independent mutations in the regulatory gene efpR were selected for in three populations evolved on beans, a distant host. Reverse genetic approaches confirmed that these mutations were associated with fitness gain on bean plants. This work provides a first step toward understanding the within-host evolutionary dynamics of R. solanacearum during infection and identifying bacterial genes subjected to in planta selection. The discovery of EfpR as a determinant conditioning host adaptation of the pathogen illustrates how experimental evolution coupled with whole-genome sequencing is a potent tool to identify novel molecular players involved in central life-history traits.

(55) Cornuault J., B. Delahaie, J. Bertrand, Y. Bourgeois, B. Mila, P. Heeb, & C. Thébaud. 2015. Morphological and plumage colour variation in the Réunion grey white-eye (Aves: Zosterops borbonicus): assessing the role of selection. Biological Journal of the Linnean Society 114: 459-473

The Réunion grey white-eye (Zosterops borbonicus), a small passerine endemic to the island of Réunion (Mascarene archipelago), constitutes an extraordinary case of phenotypic variation within a bird species, with conspicuous plumage colour differentiation at a microgeographical scale. To understand whether natural selection could explain such variability, we compared patterns of variation in morphological and plumage colour traits within and among populations. To quantify morphological variation, we used measurements obtained by Frank Gill in the 1960s from 239 individuals collected in 60 localities distributed over the entire island of Réunion. To quantify colour variation, we measured the reflectance spectra of plumage patches of 50 males from a subset of Gill's specimens belonging to the five recognized plumage colour variants and used a visual model to project these colours in an avian-appropriate, tetrachromatic, colour space. We found that variants occupy different regions of the avian colour space and that between-variant differences for most plumage patches could be discriminated by the birds. Differences in morphology were also detected, but these were, in general, smaller than colour differences. Overall, we found that variation in both plumage colour and morphology among variants is greater than would be expected if genetic drift alone was responsible for phenotypic divergence. As the plumage colour variants correspond to four geographical forms, our results suggest that phenotypic evolution in the Réunion grey white-eye is at least partly explained by divergent selection in different habitats or regions.

(54) Casquet J., R. Gillespie & C. Thébaud. 2015. Community assembly on remote islands: a comparison of Hawaiian and Mascarene spiders. Journal of Biogeography 42: 39-50

Aim : Spider communities on oceanic islands are assembled through multiple immigration and/or diversification events. In this study, we use a phylogenetic approach to investigate the role of such processes in shaping current patterns of diversity in Tetragnatha spiders from the Mascarene archipelago and to compare these patterns with those found in the Hawaiian archipelago.
Location : Mascarene archipelago, south-western Indian Ocean; Hawaiian archipelago, Pacific Ocean.
Methods : Primary techniques included phylogeny reconstruction (mitochondrial cytochrome c oxidase subunit I; histone H3) with and without time calibration, delimitation of species using the general mixed Yule coalescent (GMYC) model, and testing for the presence of gene flow between geographically separated populations using the model of isolation with migration (IMa).
Results : The current diversity of Tetragnatha on the Mascarenes has arisen through three independent colonization events with no evidence for in situ diversification. This finding is in stark contrast to the pattern observed in Hawaiʻi where two to four independent colonization events have been followed by two massive in situ diversification episodes leading to at least 38 species in total.
Main conclusions : While net rates of immigration by Tetragnatha lineages appear relatively similar in the two archipelagos, in situ diversification in Tetragnatha only occurred in Hawaiʻi, possibly associated with the extreme geographical isolation of this archipelago relative to the Mascarene archipelago. Owing to the greater geographical proximity of the Mascarene archipelago to source pools such as Madagascar, it seems likely that the persistence of gene flow between the source and the islands and/or niche pre-emption by other spider lineages may have reduced opportunities for diversification despite an apparently favourable ecological context.

(53) Fernandez-Palacios J.M., R. Otto, C. Thébaud, & J. Price. 2014. Overview of habitat history in subtropical oceanic island summit ecosystems. Arctic, Antarctic, and Alpine Research 46: 801-809

Summit ecosystems of tropical and subtropical oceanic islands constitute one of the most ephemeral and isolated ecosystems existing, harbouring thus specific characteristics that confer their biota an outstanding singularity.
Summits are ephemeral in the sense that they are the last ecosystems to be constructed during the growth of the new oceanic island, as well as the first to vanished due either to island subsidence, island erosion, or both of them. Whereas their geological emergence/disappearance is controlled by the volcanic/erosion activity, the Pleistocene glaciations, forcing in the last million years the altitudinal shift of the timberline, have also created or destroyed summit ecosystems, enabling in glaciation maxima the appearance of alpine ecosystems where they were not present in interglacial periods and vice versa. On the other hand, summit ecosystems constitute islands within islands, in the sense that they are more isolated from similar ecosystems than the coastal lines of the islands containing them. Thus summit biota, frequently displaying a very high endemicity, may originate either through dispersal from other close summit ecosystems during peak periods (multiple summit endemics), when a dispersal window remains open for pre-adapted summit biota, or more usually from the colonization of the summits and later evolution to the new conditions from low or mid-altitude generalistic species of the same island (single summit endemics). Conversely, if peak periods are absent, the disappearance of summit ecosystems implies the extinction or extirpation of their constitutive species.

(52) Liberal I.M., M. Burrus, C. Suchet, C. Thébaud, & P. Vargas. 2014. The evolutionary history of Antirrhinum in the Pyrenees inferred from phylogeographic analyses. BMC Evolutionary Biology 14: 146 doi:10.1186/1471-2148-14-146

The origin and colonisation history after the Quaternary ice ages remain largely unresolved for many plant lineages, mainly owing to a lack of fine-scale studies. In this paper, we present a molecular phylogeny and a phylogeographic analysis of Antirrhinum, an important model system in plant biology, in the Pyrenees range. Our goal was to reconstruct the evolutionary and colonisation history of four taxa endemic to this region (A. majus subsp. majus, A. majus. subsp. striatum, A. molle, and A. sempervirens) by using a dense sampling strategy, with a total of 452 individuals from 99 populations whose collective distribution spans nearly the entirety of the Pyrenees and adjacent mountains.
Phylogenetic and phylogeographic analyses of the sequences of two plastid (trnS-trnG and trnK-matK) regions revealed the following: (i) historical relationship between the Pyrenees and Iberia (but not with the Alps); (ii) the long persistence of populations in the Pyrenees, at least since the Late Pleistocene; (iii) three different colonisation histories for populations from the Western, Central, and Eastern Pyrenees; (iv) the deep phylogeographic separation of the eastern and western populations; and (v) the colonisation of southern France from the Eastern Pyrenees.
 This study underlines the enormous influence of the glacial history of the mountain ranges on the current configuration of intra- and inter-specific genetic diversity in Antirrhinum, as well as the importance of periglacial areas for the survival of species during glacial periods of the Quaternary.

(51) Tastard E., C. Andalo, M. Burrus, L. Gigord, & C. Thébaud. 2014. Effects of floral diversity and pollinator behavior on the persistence of hybrid zones between plants sharing pollinators. Plant Ecology and Diversity 7, 391-400

Plant hybrid zones often display a large diversity in floral traits due to segregation and recombination occurring in the second and later hybrid generations. Such diversity can have important effects on pollinator behaviour. In this study, we hypothesised that the number of floral types and their relative densities may influence pollinator preferences and level of flower constancy.
To test the influence of floral diversity on the number of visits to inflorescences of the most common type and on the level of flower constancy, we monitored bumblebees’ behaviour in experimental arrays of artificial inflorescences with a common (‘parental’) floral type mixed with either one or three uncommon (‘hybrid’) floral types. We found that pollinators preferentially visited the most common flower colour and showed slightly greater constancy when the number of uncommon floral types was increased.
This led us to conclude that diversity in flower colour could promote moderate pollinator constancy in some types of hybrid zones. Segregation of floral phenotypes due to hybridisation may result in small levels of pollinator-mediated assortative mating and contribute, to a small extent, and most probably in combination with other factors, to the persistence of some hybrid zones.

(50) Bertrand J., Y.X.C. Bourgeois, B. Delahaie, T. Duval, R. Garcia-Jimenez, J. Cornuault, P. Heeb, B. Mila, B. Pujol, & C. Thébaud. 2014. Extremely reduced dispersal and gene flow in an island bird. Heredity 112, 190-196

The Réunion grey white-eye, Zosterops borbonicus, a passerine bird endemic to Re ́union Island in the Mascarene archipelago, represents an extreme case of microgeographical plumage colour variation in birds, with four distinct colour forms occupying different parts of this small island (2512 km2). To understand whether such population differentiation may reflect low levels of dispersal and gene flow at a very small spatial scale, we examined population structure and gene flow by analysing variation at 11 microsatellite loci among four geographically close localities (o26 km apart) sampled within the distribution range of one of the colour forms, the brown-headed brown form. Our results revealed levels of genetic differentiation that are exceptionally high for birds at such a small spatial scale. This strong population structure appears to reflect low levels of historical and contemporary gene flow among populations, unless very close geographically (o10km). Thus, we suggest that the Reunion grey white-eye may shows an extremely reduced propensity to disperse, which is likely to be related to behavioural processes

(49) Cornuault J., B.H. Warren, B. Mila, C. Thébaud, & P. Heeb. 2013. Timing and number of colonizations but not diversification rates affect diversity patterns in haemosporidian lineages on a remote oceanic archipelago. American Naturalist 182, 820-833

Parasite diversity on remote oceanic archipelagos is determined by the number and timing of colonizations and by in situ diversification rate. In this study, we compare intra-archipelago diversity of two hemosporidian parasite genera, Plasmodium and Leucocytozoon, infecting birds of the Mascarene archipelago. Despite the generally higher vagility of Plasmodium parasites, we report a diversity of Plasmodium cytochrome b haplotypes in the archipelago much lower than that of Leucocytozoon. Using phylogenetic data, we find that this difference in diversity is consistent with differences in the timing and number of colonizations, while rates of diversification do not vary significantly between the two genera. The prominence of immigration history in explaining current diversity patterns highlights the importance of historical contingencies in driving disparate biogeographic patterns in potentially harmful blood parasites infecting island birds.

(48) Bourgeois Y.X.C., E. Lhuillier, T. Cézard, J. Bertrand, B. Delahaie, J. Cornuault, T. Duval, O. Bouchez, B. Mila, & C. Thébaud. 2013. Mass production of SNP markers in a non-model passerine bird through RAD-sequencing and contig mapping to the zebra finch genome. Molecular Ecology Resources 13, 899-907

Here, we present an adaptation of restriction-site-associated DNA sequencing (RAD-seq) to the Illumina HiSeq2000 technology that we used to produce SNP markers in very large quantities at low cost per unit in the Reunion grey white-eye (Zosterops borbonicus), a nonmodel passerine bird species with no reference genome. We sequenced a set of six pools of 18–25 individuals using a single sequencing lane. This allowed us to build around 600 000 contigs, among which at least 386 000 could be mapped to the zebra finch (Taeniopygia guttata) genome. This yielded more than 80 000 SNPs that could be mapped unambiguously and are evenly distributed across the genome. Thus, our approach provides a good illustration of the high potential of paired-end RAD sequencing of pooled DNA samples combined with comparative assembly to the zebra finch genome to build large contigs and characterize vast numbers of informative SNPs in nonmodel passerine bird species in a very efficient and cost-effective way.

(47) Cornuault J, A Khimoun, RJ Harrigan, YXC Bourgeois, B Mila, C Thébaud, & P Heeb. 2013. The role of ecology in the geographical separation of blood parasites infecting an insular bird. Journal of Biogeography 40, 1313-1323

Niche modelling is increasingly used to predict species’ geographical distributions or to infer the evolutionary or ecological processes that constrain them, but relatively few studies have examined the ecological processes governing the distributions of parasites. Among such processes, niche divergence is frequently invoked to explain species range variation. Here, we test whether the geographical distributions of two lineages of Leucocytozoon (Haemosporida) avian parasites on the island of Réunion (Mascarene Archipelago) are linked to climatic conditions and whether niche divergence can explain their geographical separation.
Leucocytozoon prevalence data were obtained by PCR screening of avian blood samples. Prevalence data and 20 environmental layers were used to build species distribution models (SDMs). SDMs were built by averaging the predictions of five different models: random forests (RF), generalized linear models (GLM), generalized additive models (GAM), multivariate adaptive regression splines (MARS) and support vector machines (SVM). Niche identity and background tests were used to test for a role of niche divergence in explaining parasite distributions. 
The geographical ranges of the two lineages of Leucocytozoon under study showed little overlap. Species distribution modelling suggested that niche divergence may explain the spatial variation observed in Leucocytozoon distribution, implying that the geographical separation of parasites is linked to environmental conditions. The variables that best explained parasite distribution were all related to precipitation patterns.
As precipitation cannot directly affect endosymbiotic Leucocytozoon parasites, we suggest that the geographical separation of Leucocytozoon lineages is the result of an underlying geographical structure in the dipteran vectors that transmit these parasites. This illustrates the need to consider the ecology of vectors when predicting the distribution of vector-borne parasites. Our study also shows that different parasite lineages, contained within broadly defined parasitic taxa, may have very different ecologies, and that these differences should be taken into account when attempting to understand the ecolog- ical determinants of parasite distribution and disease emergence.

(46) Khimoun A., J. Cornuault, M. Burrus, B. Pujol, C. Thébaud, & C. Andalo. 2013. Ecology predicts parapatric distribution in two closely related Antirrhinum subspecies. Evolutionary Ecology 27, 51-64

Using a species distribution model, we reconstructed the environmental niches of Antirrhinum majus pseudomajus and Antirrhinum majus striatum, two closely related species with parapatric distributions. We tested whether retention of ancestral environmental niche (i.e. niche conservatism) or adaptation to different ecological conditions (i.e. niche divergence) could explain the maintenance of their non-overlapping geographic ranges. We found that the environmental niche of A. m. pseudomajus is almost twice as large as that of A. m. striatum, with substantial overlap indicating that A. m. pseudomajus and A. m. striatum should co-occur frequently within the geographic range of A. m. striatum. By analysing contact zones where both subspecies are geographically close, we found that the presence of one subspecies instead of the other was significantly influenced by particular combinations of climatic factors. Since independent genetic evidence indicates that the two subspecies have experienced phases of range overlap at or near contact zones over the course of their evolutionary history, we propose that ecological niche displacement might be an important factor in explaining the absence of current range overlap between A. majus subspecies.

(45) Bourgeois YXC, Bertrand JAM, Thébaud C, Milá B (2012) Investigating the Role of the Melanocortin-1 Receptor Gene in an Extreme Case of Microgeographical Variation in the Pattern of Melanin-Based Plumage Pigmentation. PLoS ONE 7(12): e50906.

The Réunion grey white-eye (Zosterops borbonicus) is a single-island endemic passerine bird that exhibits striking geographically structured melanic polymorphism at a very small spatial scale. We investigated the genetic basis of this color polymorphism by testing whether the melanocortin-1 receptor (MC1R), a gene often involved in natural melanic polymorphism in birds, was associated with the observed plumage variation. Although we found three non-synonymous mutations, we detected no association between MC1R variants and color morphs, and the main amino-acid variant found in the Réunion grey white-eye was also present at high frequency in the Mauritius grey white-eye (Zosterops mauritianus), its sister species which shows no melanic polymorphism. In addition, neutrality tests and analysis of population structure did not reveal any obvious pattern of positive or balancing selection acting on MC1R. Altogether these results indicate that MC1R does not play a role in explaining the melanic variation observed in the Réunion grey white-eye. We propose that other genes such asPOMC, Agouti or any other genes involved in pigment synthesis will need to be investigated in future studies if we are to understand how selection shapes complex patterns of melanin-based plumage pigmentation.

(44) Warren B.H., E. Bermingham, Y. Bourgeois, L. Estep, R. Prys-Jones, D. Strasberg, & C. Thébaud. 2012. Hybridization and barriers to gene flow in an island bird radiation. Evolution 66, 1490-1505

While reinforcement may play a role in all major modes of speciation, relatively little is known about the timescale over which species hybridize without evolving complete reproductive isolation. Birds have high potential for hybridization, and islands provide simple settings for uncovering speciation and hybridization patterns. Here we develop a phylogenetic hypothesis for a phenotypically diverse radiation of finch-like weaver-birds (Foudia) endemic to the western Indian Ocean islands. We find that unlike Darwin’s finches, each island-endemic Foudia population is a monophyletic entity for which speciation can be considered complete. In explaining the only exceptions—mismatches between taxonomy, mitochondrial, and nuclear data—phylogenetic and coalescent methods support introgressive hybridization rather than incomplete lineage sorting. Human introductions of known timing of one island-endemic species, to all surrounding archipelagos provide two fortuitous experiments; (1) population sampling at known times in recent evolutionary history, (2) bringing allopatric lineages of an island radiation into secondary contact. Our results put a minimum time bound on introgression (235 years), and support hybridization between species in natural close contact (parapatry), but not between those in natural allopatry brought into contact by human introduction. Time in allopatry, rather than in sympatry, appears key in the reproductive isolation of Foudia species.

(43) Salmona J., M. Salamolard, D. Fouillot, T. Ghestemme, J. Larose, J.-F. Centon, V. Sousa, D.A. Dawson, C. Thébaud, & L. Chikhi. 2012. Signature of a pre-human population decline in the critically endangered Réunion Island endemic forest bird Coracina newtoni. PLoS ONE 7(8): e43524. doi:10.1371/journal.pone.0043524

The exceptional biodiversity of Reunion Island is threatened by anthropogenic landscape changes that took place during the 350 years of human colonization. During this period the human population size increased dramatically from 250 to 800,000. The arrival of humans together with the development of agriculture, invasive species such as rats and cats, and deforestation has led to the extinction of more than half of the original vertebrate species of the island. For the remaining species, significant work is being carried out to identify threats and conservation status, but little genetic work has been done even on some of the most endangered species. In the last decade theoretical studies have shown the ability of neutral genetic markers to infer the demographic history of endangered species and identify and date past population size changes (expansions or bottlenecks). In this study we provide the first genetic data on the critically endangered Reunion cuckoo-shrike Coracina newtoni. The Reunion cuckoo-shrike is a rare endemic forest bird surviving in a restricted 12-km2 area of forested uplands and mountains. The total known population consists of less than one hundred individuals out of which 45 were genotyped using seventeen polymorphic microsatellite loci. We found a limited level of genetic variability and weak population structure, probably due to the limited geographic distribution. Using Bayesian methods, we identified a strong decline in population size during the Holocene, most likely caused by an ancient climatic or volcanic event around 5000 years ago. This result was surprising as it appeared in apparent contradiction with the accepted theory of recent population collapse due to deforestation and predator introduction. These results suggest that new methods allowing for more complex demographic models are necessary to reconstruct the demographic history of populations.

(42) Strijk J.S., R.D. Noyes, D. Strasberg, C. Cruaud, F. Gavory, M.W. Chase, R.J. Abbott, & C. Thébaud. 2012. In and out of Madagascar : dispersal to peripheral islands, insular speciation and diversification of Indian Ocean daisy trees (Psiadia, Asteraceae). PLoS ONE 7(8): e42932. doi:10.1371/journal.pone.0042932

Madagascar is surrounded by archipelagos varying widely in origin, age and structure. Although small and geologically young, these archipelagos have accumulated disproportionate numbers of unique lineages in comparison to Madagascar, highlighting the role of waif-dispersal and rapid in situ diversification processes in generating endemic biodiversity. We reconstruct the evolutionary and biogeographical history of the genus Psiadia (Asteraceae), a plant genus with near equal numbers of species in Madagascar and surrounding islands. Analyzing patterns and processes of diversification, we explain species accumulation on peripheral islands and aim to offer new insights on the origin and potential causes for diversification in the Madagascar and Indian Ocean Islands biodiversity hotspot. Our results provide support for an African origin of the group, with strong support for non-monophyly. Colonization of the Mascarenes took place by two evolutionary distinct lineages from Madagascar, via two independent dispersal events, each unique for their spatial and temporal properties. Significant shifts in diversification rate followed regional expansion, resulting in co-occurring and phenotypically convergent species on high-elevation volcanic slopes. Like other endemic island lineages, Psiadia have been highly successful in dispersing to and radiating on isolated oceanic islands, typified by high habitat diversity and dynamic ecosystems fuelled by continued geological activity. Results stress the important biogeographical role for Rodrigues in serving as an outlying stepping stone from which regional colonization took place. We discuss how isolated volcanic islands contribute to regional diversity by generating substantial numbers of endemic species on short temporal scales. Factors pertaining to the mode and tempo of archipelago formation and its geographical isolation strongly govern evolutionary pathways available for species diversification, and the potential for successful diversification of dispersed lineages, therefore, appears highly dependent on the timing of arrival, as habitat and resource properties change dramatically over the course of oceanic island evolution.

(41) Cornuault J., A. Bataillard, B.H. Warren, A. Lootvoet, P. Mirleau, T. Duval, B. Mila, C. Thébaud, & P. Heeb. 2012. The role of immigration and in-situ radiation in explaining blood parasite assemblages in an island bird clade. Molecular Ecology 21, 1438-1452

Parasite communities on islands are assembled through multiple immigrations and⁄or in-situ diversification. In this study, we used a phylogenetic approach to investigate the role of such processes in shaping current patterns of diversity in Leucocytozoon, a group of haemosporidian blood parasites infecting whites eyes (Zosterops) endemic to the Mascarene archipelago (south-western Indian Ocean). We found that this parasite community arose through a combination of multiple immigrations and in-situ diversi- fication, highlighting the importance of both processes in explaining island diversity. Specifically, two highly diverse parasite clades appear to have been present in the Mascarenes for most of their evolutionary history and have diversified within the archipelago, while another lineage apparently immigrated more recently, probably with human-introduced birds. Interestingly, the evolutionary histories of one clade of parasites and Indian Ocean Zosterops seem tightly associated with a significant signal for phylogenetic congruence, suggesting that host–parasite co-divergence may have occurred in this system.

(40) Bertrand J.A.M., R. Garcia-Jiménez, Y. Bourgeois, T. Duval, P. Heeb, C. Thébaud, & B. Mila. 2012. Isolation and characterization of twelve polymorphic micro satellite loci for investigating an extreme case of micro geographical variation in an island bird (Zosterops borbonicus). Conservation Genetics Resources 4, 323-326.

Twelve polymorphic microsatellite loci were characterized in order to investigate an extreme case of microgeographical variation in an island-dwelling passer- ine (Zosterops borbonicus). Variation was examined in two distinct natural populations of 27 individuals each. The loci displayed 5–20 alleles, with observed heterozygosities ranging between 0.33 and 0.93. All but one loci (Z16) conformed to Hardy–Weinberg equilibrium. None of the pairwise comparisons among loci showed significant link- age disequilibrium after sequential Bonferonni correction. Successful cross-species amplification in additional Zosterops species and other passerines suggests their broad applicability.

(39) Tastard E., J.B. Ferdy, M. Burrus, C. Thébaud & C. Andalo. 2012. Patterns of flower colour neighbourhood and their effects on female reproductive success in an Antirrhinum hybrid zone. Journal of evolutionary Biology 25, 388-399

The maintenance of genetic integrity of parental populations is often explained by selection against hybrids. However, the selection agents are usually unknown. The role of environmental biotic interactions is often suspected but has rarely been demonstrated. In plants for instance, mutualism with pollinators may be involved. In this paper, we used an individual-based study and a representation of pollinator colour perception to test the effects of local plant density and floral colour neighbourhood on female reproductive success in a hybrid zone between two Antirrhinum species that are pollination-limited in the wild . In addition to flower colour and density effects, the of the floral neighbourhood was found to influence fruit set. This reveals that most plants were usually better fertilized when similar to their neighbours. However, the plants of one particular type were sometimes favoured when very different from their neighbours. Thus, while the local phenotypic composition of the neighbourhood clearly influences individual female fitness natural, natural  selection in this  hybrid zone may be quite variable in time. Over 10 years of observation, the Antirrhinum hybrid zone always appeared very sharp and one may wonder if the pollinator-mediated selection through female fitness demonstrated in this study  is strong enough to account for the apparent stability of the cline. Other selective agents, such as several specialist insect herbivores that feed on Antirrhinum including one abundant seed predator (Rhinusa hispida, Coleoptera : Curculionidae), could also contribute to flower colour selection and to the entire hybrid zone dynamics. 

(38) Casquet J., C. Thébaud, & R. Gillespie. 2012. Chelex without boiling, a rapid and easy technique to obtain stable amplifiable DNA from small amounts of ethanol-stored spiders. Molecular Ecology Resources 12, 136-141.

DNA barcoding projects require high-throughput generation of sequence data to assemble the comprehensive reference databases that are required to perform large-scale biodiversity inventories and molecular ecology studies. With the advent of new sequencing technologies, the extraction step, which often requires a considerable amount of time and money, repre- sents a significant bottleneck in many studies. Here, we present a one-step Chelex double-stranded DNA extraction proto- col that is quick, cheap, easy and works with a small quantity of ethanol-stored tissue. We developed this protocol by removing the denaturation step appearing in classic methods. This modification reduces the number of handling steps to one, thus simplifying the extraction procedure and reducing the risk of sample contamination, and yields double-stranded DNA instead of the single-stranded form that classical Chelex extraction protocols usually release. DNA obtained through our method is then suitable for long-term conservation (over 1.5 years). We tested our protocol on a highly diverse genus of spiders comprised of mainly very small species. We also apply the method to two other genera of spiders, one with average size species, the other one with giant species, to test the efficacy of the method with varying amounts of input tissue. We also discuss the advantages and limitations of this DNA extraction technique when working with arthropods.
 
(37) Debout G, Lhuillier E, Malé P-JG, Pujol B, & C. Thébaud. 2012. Development and characterization of 24 polymorphic microsatellite loci in two Antirrhinum majus subspecies (Plantaginaceae) using pyrosequencing technology. Conservation Genetics Resources 4, 75-79

The recently described procedure of microsat- ellite-enriched libraries pyrosequencing was used to isolate 557 microsatellite loci in two subspecies of the snapdragon Antirrhinum majus (Plantaginaceae). Four multiplex PCR sets were optimized to genotype 24 polymorphic markers. The number of alleles per locus ranged from one to 19 and observed heterozygosity varied from zero to 0.95 in four Pyrenean populations. Cross-species amplification of these loci was successfully demonstrated in additional Antirrhi- num species. This set of microsatellite markers will be useful for studying population genetics, plant-pollinators  interactions and inheritance of developmental genes in A. majus.
 
(36) Khimoun A., M. Burrus, C. Andalo, Z.L. Liu, C. Vicédo-Cazettes, C. Thébaud, & B. Pujol. 2011. Locally asymmetric introgressions between subspecies suggest circular range expansion at the Antirrhinum majus global scale. Journal of evolutionary Biology 24, 1433-1441 [PDF]

Assessing processes of geographic expansion in contact zones is a crucial step towards an accurate prediction of the evolution of species genetic diversity. The geographic distribution of cytonuclear discordance often reflects genetic introgression patterns across a species geographic range. Antirrhinum majus pseudomajus and A. m. striatum are two interfertile subspecies that occupy nonoverlapping areas but enter in contact in many locations at the margin of their geographic distribution. In this paper, we showed that genetic introgression between both subspecies was asymmetric at the local scale and geographically oriented in opposite directions at both ends of their contact zone perimeter in the Pyrenees.Thus, geographic expansion of A. majus subspecies may have been  circular around the perimeter of subspecies contact zone. This work pinpoints the need to integrate different spatial scales to unravel complex patterns of species geographic expansion.

(35) Mila B., B.W. Warren, P. Heeb, & C. Thébaud. 2010. The geographic scale of diversification on islands: genetic and morphological divergence at a very small spatial scale in the Mascarene grey white-eye (Aves: Zosterops borbonicus). BMC Evolutionary Biology 10: 158. [PDF]

Oceanic islands provide unique scenarios for studying the roles of geography and ecology in driving population divergence and speciation. Assessing the relative importance of selective and neutral factors in driving population divergence is central to understanding how such divergence may lead to speciation in small oceanic islands, where opportunities for gene flow and population mixing are potentially high. Here we report a case of genetic and morphological structure in the Mascarene grey white-eye (Zosterops borbonicus) a species that shows a striking, geographically structured plumage polymorphism (first described by the famous american ornithlogist Frank Gill 40 yr ago) on the topographically and ecologically complex island of Réunion, yet is monotypic on the relatively uniform neighbouring island of Mauritius.
We conducted an analysis of 276 AFLP loci in 197 individuals which revealed prolonged independent evolution of Réunion and Mauritius populations, a result which is congruent with previous mtDNA assessments. Furthermore, populations on Réunion showed significant differentiation into three main genetic groups separating lowland from highland areas despite the small geographic distances involved. Genetic differentiation along the altitudinal gradient is consistent with morphometric analysis of fitness-related traits. Birds in the highlands were larger, yet had relatively smaller beaks than in the lowlands, suggesting the role of selection in shaping morphology and restricting gene flow along the gradient. No genetic differentiation between plumage morphs was detected in neutral markers, suggesting that plumage differences are of recent origin.
In conclusion, our results suggest a dual role of vicariance and natural selection in differentiating populations of a passerine bird in an oceanic island at very small spatial scales. We propose a combination of past microallopatry driven by volcanic activity and selection-constrained dispersal along steep ecological gradients to explain the striking levels of population structure found within the island, although the possibility that genetic differences evolved in situ along the gradient cannot be ruled out at present. The lack of congruence between genetic groups and plumage morphs suggests that the latter are of recent origin and likely due to social or sexual selection acting on few loci. The presence of sharp and stable contact zones between plumage morphs suggests that they could be on independent evolutionary trajectories. To test whether or not they represent incipient species, we are currently trying to directly assess the degree of reproductive isolation among them.

(34) Andalo C., M.B. Cruzan, C. Cazettes, B. Pujol, M. Burrus, & C. Thébaud. 2010. Post-pollination barriers do not explain the persistence of two distinct Antirrhinum subspecies with parapatric distribution. Plant Systematics and Evolution 286, 223-234 [PDF]

Empirical studies of post-pollination barriers to gene flow between recently diverged plant species are important to understand ecological processes underlying speciation. Using greenhouse and common garden experiments, we investigated the strength of post-pollination barriers that restrict or prevent gene flow between two subspecies of Antirrhinum: Antirrhinum majus pseudomajus and A. m. striatum. The two are distributed parapatrically but share the same major pollinators (bumblebees), and form narrow hybrid zone in many areas of southern France and northern Spain where they come into close contact. We assessed the strength and symmetry of mating barriers and their homogeneity among populations by comparing fruit set, seed set and offspring performances between intra- and inter-subspecific crosses performed in parental and hybrid populations. Although all populations showed high levels of self-incompatibility, we found very little evidence for barriers to gene flow once pollen had been transferred to the stigma. Reproductive isolation in this system mostly involves barriers related to processes occurring before pollination, with little or no role of post-pollination barriers.

(33) Renner S.S., J.S. Strijk, D. Strasberg, & C. Thébaud. 2010. Biogeography of the Monimiaceae (Laurales): a role for East Gondwana and long-distance dispersal, but not Western Gondwana. Journal of Biogeography 37: 1227-1238. [PDF]

The biogeography of the tropical plant family Monimiaceae has long been thought to reflect the break-up of West and East Gondwana, followed by limited transoceanic dispersal. In this paper, we use phylogenetic analysis of DNA sequences from 67 of the c. 200 species, representing 26 of the 28 genera of Monimiaceae, and a Bayesian relaxedclock model with fossil prior constraints to estimate species relationships anddivergence times. Likelihood optimization is used to infer switches between biogeographical regions on the highest likelihood tree. We found that tree topology, fossils, inferred divergence times and ancestral area reconstruction fit with the break-up of East Gondwana having left a still discernible signature consisting of sister clades in Chile and Australia. There is no support for previous hypotheses that the break-up of West Gondwana (Africa/South America) explains disjunctions in the Monimiaceae. The South American Mollinedia clade is only 28–16 Myr old, and appears to have arrived via trans-Pacific dispersal from Australasia. The clade apparently spread in southern South America prior to the Andean orogeny, fitting with its first-diverging lineage (Hennecartia) having a southern-temperate range. The crown ages of the other major clades (II–V) range from 20 to 29 Ma, implying over-water dispersal between Australia, New Caledonia, New Zealand, and across the Indian Ocean to Madagascar and the Mascarenes. The endemic genus Monimia on the Mascarenes provides an interesting example of an island lineage being much older than the islands on which it presently occurs.

(32) Warren B.H., D. Strasberg, J.H. Bruggemann, R. Prys-Jones, & C. Thébaud. 2010. Why does the Madagascar biota have such a strong Asiatic flavour? Cladistics 26, 526-538. [PDF]

A corollary of island biogeographic theory is that islands are largely colonized from their nearest mainland source. Despite Madagascar’s extreme isolation from India and proximity to Africa, a high proportion of the biota of the region has Asian affinities. This pattern has rarely been viewed as surprising, since it is consistent with Gondwanan vicariance. Molecular phylogenetic data provide strong support for such Asian affinities, but often not for their vicariant origin; most divergences between lineages in Asia and the Madagascar region postdate the separation of India and Madagascar considerably (up to 87 Myr ago), implying a high frequency of dispersal that mirrors colonization of the Hawaiian archipelago in distance. Indian Ocean bathymetry and the magnitude of recent sea level lowstands support the repeated existence of sizeable islands across the western Indian Ocean, greatly reducing the isolation of Madagascar from Asia. We put forward a list of testable predictions to demonstrate the role of this historical factor in the assembly of the regional biota.

(31) Gonzalez M.A., A. Roger, E. Courtois, F. Jabot, N. Norden, C.E.T Paine, C. Baraloto, C. Thébaud, & J. Chave. 2010. Shifts in species and phylogenetic diversity between sapling and tree communities indicate negative density-dependence in a lowland rainforest. Journal of Ecology 98, 137-146 [PDF]

As trees in a given cohort progress through ontogeny, many individuals die. This risk of mortality is unevenly distributed across species because of many processes such as habitat filtering, interspecific competition and negative density dependence. Here, we predict and test the patterns that such ecological processes should inscribe on both species and phylogenetic diversity as plants recruit from saplings to the canopy.
We compared species and phylogenetic diversity of sapling and tree communities at two sites in French Guiana. We surveyed 2084 adult trees in four 1-ha tree plots and 943 saplings in sixteen 16-m2 subplots nested within the tree plots. Species diversity was measured using Fisher’s alpha (species richness) and Simpson’s index (species evenness). Phylogenetic diversity was measured using Faith’s phylogenetic diversity (phylogenetic richness) and Rao’s quadratic entropy index (phylogenetic evenness). The phylogenetic diversity indices were inferred using four phylogenetic hypotheses: two based on rbcLa plastid DNA sequences obtained from the inventoried individuals with different branch lengths, a global phylogeny available from the Angiosperm Phylogeny Group, and a combination of both. Taxonomic identification of the saplings was performed by combining morphological and DNA barcoding techniques using three plant DNA barcodes (psbA-trnH, rpoC1 and rbcLa). DNA barcoding enabled us to increase species assignment and to assign unidentified saplings to molecular operational taxonomic units.
Species richness was similar between saplings and trees, but in about half of our comparisons, species evenness was higher in trees than in saplings. This suggests that negative density dependence plays an important role during the sapling-to-tree transition. Phylogenetic richness increased between saplings and trees in about half of the comparisons. Phylogenetic evenness increased significantly between saplings and trees in a few cases (4 out of 16) and only with the most resolved phylogeny. These results suggest that negative density dependence operates largely independently of the phylogenetic structure of communities.
By contrasting species richness and evenness across size classes, we suggest that negative density dependence drives shifts in composition during the sapling-to-tree transition. In addition, we found little evidence for a change in phylogenetic diversity across age classes, suggesting that the observed patterns are not phylogenetically constrained.

(30) Salmona J., Dawson D.A., Fouillot D., Ghestemme T., Thébaud C., Chikhi L., & Salamolard M. 2010. The utility of existing passerine microsatellite markers for genetic studies in endangered species as demonstrated for a critically endangered forest bird endemic to Reunion Island, the Reunion cuckooshrike (Coracina newtoni). Conservation Genetic Resources (DOI 10.1007/s12686-010-9254-x)

The Reunion Cuckoo shrike, Coracina newtoni, a forest bird endemic to Reunion Island, is among the rarest and most threatened bird species in the world and was recently classified as critically endangered by  IUCN. The single remaining population is currently confined to a small area of 12 km2 at altitudes ranging from 1,300 to 1,800 m and the total population size estimate is of 70–100 individuals. The causes of such a narrow distribution range are still debated and include introduced predators (rats and cats).
Genetic approaches using neutral genetic markers have the potential to quickly improve our knowledge for endangered species by describing diversity, inferring demographic history. C. newtoni belongs to the Campephagidae subfamily, which contains eighty species currently listed by the IUCN, out of which 48 belong to the Coracina genus. Since no specific markers were available for Campephagidae we selected and screened a large set of microsatellite loci. We show in this paper that this strategy can be very useful, having identified 18 polymorphic loci after testing 110 passerine microsatellite primer sets. We believe that the microsatellite markers we have successfully identified will be crucial to study genetic diversity in the numerous endangered Campephagidae species of the Indian Ocean and elsewhere.

(29) Gonzalez M.A., C. Baraloto, J. Engel, S.A. Mori, P. Pétronelli, B. Riéra, A. Roger, C. Thébaud, & J. Chave. 2009. Identification of Amazonian trees with DNA barcodes. PLoS ONE 4(10): e7483. doi:10.1371/journal.pone.000748. [PDF]

Large-scale plant diversity inventories are critical to develop informed conservation strategies. However, the workload required for classic taxonomic surveys remains high and is particularly problematic for megadiverse tropical forests.
Based on a comprehensive census of all trees in two hectares of a tropical forest in French Guiana, we examined whether plant DNA barcoding could contribute to increasing the quality and the pace of tropical plant biodiversity surveys. Of the eight plant DNA markers we tested (rbcLa, rpoC1, rpoB, matK, ycf5, trnL, psbA-trnH, ITS), matK and ITS had a low rate of sequencing success. More critically, none of the plastid markers achieved a rate of correct plant identification greater than 70%, either alone or combined. The performance of all barcoding markers was noticeably low in few species-rich clades, such as the Laureae, and the Sapotaceae. A field test of the approach enabled us to detect 130 molecular operational taxonomic units in a sample of 252 juvenile trees. Including molecular markers increased the identification rate of juveniles from 72% (morphology alone) to 96% (morphology and molecular) of the individuals assigned to a known tree taxon.
We conclude that while DNA barcoding is an invaluable tool for detecting errors in identifications and for identifying plants at juvenile stages, its limited ability to identify collections will constrain the practical implementation of DNA-based tropical plant biodiversity programs.

(28) Thébaud C, B.H. Warren, A.C. Cheke, D. Strasberg. 2009. Mascarene Islands, Biology. In : R.G. Gillespie & D. Clague, eds. Encyclopedia of Islands. Univ. of California Press, Berkeley, USA. [PDF]

The Mascarenes are an island group lying near the Tropic of Capricorn in the southwestern Indian Ocean ca. 700 km east of Madagascar. This archipelago comprises three high volcanic islands (Réunion, Mauritius, Rodrigues), scattered along a ca. 600 km west-east axis, and a group of small coralline islands (Cargados Carajos Shoals) ca. 400 km to the north of Mauritius that sit upon a submarine bank of volcanic origin that extends a further 700 km or more to the northeast. The Mascarene Islands have an extraordinary status among islands : Mauritius was the former home of the Dodo, the universal symbol of human-caused species extinction on islands. While their recent history, since the first permanent human settlements in the 17th century, has been an endless series of ecological disasters and species extinctions, these islands still harbour up to 25% of their original forest cover and are extremely rich in species and habitats, with high degrees of endemism. Consequently, they are listed among the world’s top Biodiversity Hotspots. This chapter provides an overview of the Mascarene Islands for ecologists and evolutionary biologists.


(27) Norden, J Chave, P Belbenoit, A Caubere, P Chatelet, P-M Forget, B Riera, J Viers, C Thébaud. 2009. Interspecific variation in seedling responses to seed limitation and habitat conditions for 14 Neotropical woody species. Journal of Ecology 97, 186-197.[PDF]

1. We assessed the relative importance of dispersal and niche processes in structuring plant populations at the seedling stage for 14 woody plant species (12 trees and 2 lianas) in an old-growth tropical forest of French Guiana. 
2. We combined long-term data from a network of 160 stations, each comprising a seed trap and two to three neighbouring seedling plots, with fine-scale quantification of environmental variables. 
3. For each species, we quantified seed limitation as the proportion of seed traps that were not reached by seeds, and establishment limitation as the proportion of stations where seeds arrived but where seedlings did not occur. All species showed strong seed limitation, whereas only one species showed significant establishment limitation. 
4. We determined the proportion of variance in local seedling density explained by either seed density or environmental factors, and we assessed the effect of environment on seedling survival. 
5. Although seeds showed considerable spatial clumping in all species, seed density explained a significant fraction of the variance in seedling density for only five species. Habitat preferences explained a significant fraction of the variance in seedling density for six species. Of the remaining species, four showed no significant relationship with either seed arrival or habitat conditions. 
6. Environmental effects on local seedling abundance were weakly related to those on seedling survival. When seedling density was significantly correlated with a given environmental factor, survival was usually not correlated with that factor. Habitat association patterns might change over time, as environmental filtering operates. 
7. Synthesis: Our results show that both seed arrival and habitat preferences contribute to explaining the abundance of tropical woody species at the seedling stage, but their relative importance showed important interspecific differences. Although our study was limited to a subset of woody species, they accounted for 27% of the individuals composing the seedling layer. Thus, our findings are likely to have important consequences in the structuring of the seedling community.

(26) Tastard E, C Andalo, M Giurfa, M Burrus, C. Thébaud. 2008. Flower colour variation across a hybrid zone in Antirrhinum as perceived by bumblebee pollinators. Arthropod-Plant Interactions 2: 237-246. [PDF]

To assess if pollinators’ behaviour could explain the maintenance of hybrid zones between different flower colour morphs, we analyzed flower colour variation in an Antirrhinum hybrid zone using spectrometry and a model of bee perception. Some colours generated by hybridization were not observed in any Antirrhinum species and even appeared to be rare among angiosperms. Variation in flower colours within the hybrid zone was continuous; the most similar colours were predicted not to be discriminated from one another in natural foraging situations.However, when compared at a scale corresponding to bees’ foraging range, some flower colours could be discriminated from all colours displayed by neighbouring plants. This could affect pollinator behaviour and explain lower visitation rates within the centre of the hybrid zone. Behavioural studies involving bumblebees and plant mixtures of parental and hybrid flower colours carefully characterized with appropriate visual models will be necessary to test this hypothesis.

(25) S Baret, L Cournac, C Thébaud, P Edwards and Dominique Strasberg. 2008. Effects of canopy gap size on recruitment and invasion of the non-indigenous Rubus alceifolius in lowland tropical rainforest on Réunion. Journal of Tropical Ecology  24: 337-343. [PDF]

An important challenge of invasion biology is to understand how interactions between species traits and ecosystem properties enable alien species to become invasive at particular locations. We investigated how gap dynamics in a tropical rain forest on the island of Reunion affected the invasiveness of alien plants. In the 12 000-m2 study area, alien plants occupied 24.9% of the area of gaps, which represented 5.62% of the forest area, but only 0.8% of the understorey area. The most abundant invasive species was Rubus alceifolius, which formed dense, monospecific stands in the largest gaps (> 25 m2 ). Although plants could persist in the shade, a germination experiment revealed that canopy openings were essential for seedling establishment. A cyclone that struck the study area in 2002 caused a temporary thinning of the canopy, increasing light levels to above the threshold needed for germination of R. alceifolius and also stimulating the growth of established plants. We conclude that the ability of this and other alien species to colonize intact lowland tropical rain forest is strongly influenced by the prevailing gap dynamics. Because gaps are also essential for the regeneration of many native trees in our study area, there is a real danger of the forest being progressively degraded by alien plants. There are no simple solutions to controlling species such as Rubus alceifolius, but efforts should be focused mainly upon the larger gaps where the species are most invasive.

(24) N Norden, Chave J, Belbenoit P, Caubère A, Châtelet P, Forget PM, and C Thébaud (2007) Mast Fruiting Is a Frequent Strategy in Woody Species of Eastern South America. PLoS ONE 2(10): e1079 doi:10.1371/journal.pone.0001079 [PDF]

It is thought that mast seeding is a rare reproductive strategy in the tropics, since tropical climates are less variable, and fruit consumers tend to be more generalist in these regions. However, previous tests of this hypothesis were based on only few tropical datasets, and none from tropical South America. Moreover, reproductive strategies have been quantified based on the coefficient of variation of interannual seed production, an index that potentially confounds masting and high interannual variability in seed production. We developed a new approach to model the monthly variability in seed production for 28 tree species, and 20 liana species monitored during 5 years in a tropical forest of Central French Guiana. We found that 23% of the species showed a masting pattern, 54% an annual fruiting pattern, and 23% an irregular fruiting pattern. The majority of masting species were trees (8 out of 11), most of them animal-dispersed. The classification into reproductive strategies based on the coefficient of variation was inconsistent with our results in nearly half of the cases. Our study is the first to clearly evidence the frequency of the masting strategy in a tropical forest community of Eastern South America. The commonness of the masting strategy in tropical plants may promote species coexistence through storage dynamics.

(23) T Ukizintambara, L white, K Abernethy, and C Thébaud. 2007. Gallery forests versus bosquets: conservation of natural fragments at Lopé National Park in central Gabon. African Journal of Ecology 45: 476-482. [PDF]

Human-induced forest fragmentation has been relatively well-studied, however, we know very little about the role of natural fragmentation in sustaining rare or marginal species that could have been lost if the advancement of continuous forest had not been controlled. Between February 2001 and January 2003, we conducted a study on characteristics of natural forest fragments in the mosaic of forests and savannas in the north of Lopé National Park in Central Gabon. We surveyed 61 vegetation plots (0.08 ha each) and compared vegetation characteristics of isolated forest fragments (bosquets) with those of gallery forests. Both shared 39% of all 251 species inventoried. Gallery forests contained 45% plant species on their own, while 16% were encountered only in bosquets. Therefore, bosquets were found to be valuable component of the Lopé landscape worth protecting. In addition, the Shannon–Wienner diversity index (H') was higher for bosquets neighbouring gallery forests or continuous forests regardless of their sizes because seeds of new plant species were easily dispersed in these bosquets. To protect these gallery forests and bosquets, one of the traditional conservation tools – a controlled savanna burning – should still be used to prevent forest fragments from being engulfed by the expanding continuous forest.

(22) J. Chave, G. Chust, C. Thébaud. 2007. The importance of phylogenetic structure in biodiversity studies. In pp 151-167, Eds D Storch, P Marquet, and JH Brown. Scaling Biodiversity. Santa Fe Institute Editions. [PDF]

This paper discusses the issue that the diversity represented by species richness and overlap  is only part of the overall evolutionary diversity in communities and illustrates the differences between phylogenetic  and conventional beta diversity measures. We also defined a simple and consistent measure of phylogenetic diversity based on existing population genetic theory and used AH Gentry’s data on south American plant communities to show how  the interplay between ecological and evolutionary processes determine biodiversity patterns.

(21) N Norden, J Chave, A Caubère, P Châtelet, N Ferroni, P-M Forget, C Thébaud. 2007. Is seedling dynamics determined by environment or by seed arrival? A test in a neotropical forest. J Ecol 95, 507-516. [PDF]

Both spatial and temporal processes are assumed to play an important role in driving seedling dynamics. We assessed the magnitude of these two processes in a neotropical forest in French Guiana. We first quantified temporal changes in seedling community structure, then evaluated the relative importance of environmental heterogeneity and temporal fluctuations in seed arrival in determining seedling dynamics. We monitored the seedling dynamics of 6244 seedlings by censusing 370 1-m2 seedling plots in 160 stations over 20 months. At each station, we quantified environmental variability (light availability, soil resources, litter depth, topography), and measured temporal fluctuations in seed input by sampling seed arrival into seed traps located in each station. Temporal changes in seedling density and diversity between four consecutive censuses were compared with those predicted by a neutral model assuming random recruitment and mortality. Seedling density fluctuations were considerably more variable over time than expected under the neutral assumption. Diversity changes showed less consistent results. For the two first census intervals, seedling diversity was more constant than under the neutral expectations. For the last census interval, seedling diversity was more variable than expected under neutrality. Seedling recruitment, mortality and diversity of recruits were modelled against environmental variables and seed arrival. Sites with higher light availability and soil fertility had more diverse recruits (P < 0.01) but lower seedling survival (P < 0.05). Both density and diversity of local seed arrival had a positive effect, respectively, on density and diversity of recruited seedlings (P < 0.05). Our results show that temporal pulses in seedling community are mainly driven by large temporal fluctuations in seedling recruitment. Annual variation in seedfall and environmental filtering both contribute to explaining spatio-temporal variation in seedling dynamics to a large degree. Irrespective of species identity, tropical seedling communities are both seed- and establishment-limited. The temporal component of seed-limitation appears to be of critical relevance in the structuring of tropical seedling communities.

(20) Whibley A.C., N.B. Langlade, C. Andalo, A.I. Hanna, A. Bangham, C. Thébaud, E. Coen. 2007. Reply to comment on « Evolutionary paths underlying flower color variation in Antirrhinum ». Science, 461

In this reply to a comment on our previous paper, we argue that the assertion that divergent selection across a hybrid zone is incompatible with adaptive ridges, although intuitively reasonable, is incorrect on several fronts. We point out that the alternative hypothesis of a single moveable peak predicts a sharp environmental transition across hybrid zones that is not supported by observations. Thus, a high fitness path still provides the most straightforward explanation of data from Antirrhinum hybrid zones. 

(19) Whibley A.C., N.B. Langlade, C. Andalo, A.I. Hanna, A. Bangham, C. Thébaud, E. Coen. 2006. Evolutionary paths underlying flower color variation in Antirrhinum. Science 313, 963-966. [PDF]

To understand evolutionary paths connecting diverse biological forms, we defined a threedimensional genotypic space separating two flower color morphs of Antirrhinum. A hybrid zone between morphs showed a steep cline specifically at genes controlling flower color differences, indicating that these loci are under selection. Antirrhinum species with diverse floral phenotypes formed a U-shaped cloud within the genotypic space. We propose that this cloud defines an evolutionary path that allows flower color to evolve while circumventing less-adaptive regions. Hybridization between morphs located in different arms of the U-shaped path yields low-fitness genotypes, accounting for the observed steep clines at hybrid zones.

(18) Warren, B.H. Bermingham, E., Prys-Jones, R.P. and Thébaud, C. (2006) Immigration, species radiation and extinction in a highly diverse songbird lineage: white-eyes on Indian Ocean islands. Molecular Ecology 15 (12), 3769–3786. [PDF]

Molecular phylogenetic hypotheses of species-rich lineages in regions where geological history can be reliably inferred may provide insights into the scale of processes driving diversification. Here we sample all extant or recently extinct white-eye (Zosterops) taxa of the southwest Indian Ocean, combined with samples from all principal continental lineages. Results support a high dispersal capability, with at least two independent continental sources for white-eyes of the region. An early (within 1.8 million years ago) expansion into the Indian Ocean may have originated either from Asia or Africa; the three resulting lineages show a disparate distribution consistent with considerable extinction following their arrival. Africa is supported as the origin of a later expansion into the region (within 1.2 million years ago). On two islands, a pair of Zosterops species derived from independent immigrations into the Indian Ocean co-occur or may have formerly co-occurred, providing strong support for their origin by double-island colonization rather than within-island (sympatric or microallopatric) speciation. On Mauritius and La Réunion, phylogenetic placement of sympatric white-eyes allow us to rule out a scenario in which independent within-island speciation occurred on both islands; one of the species pairs must have arisen by double colonization, while the other pair is likely to have arisen by the same mechanism. Long-distance immigration therefore appears to be responsible for much of the region’s white-eye diversity. Independent immigrations into the region have resulted in lineages with mutually exclusive distributions and it seems likely that competition with congeneric species, rather than arrival frequency, may limit present-day diversity.

(17) N.B. Langlade, Xianzhong Feng, Tracy Dransfield, Lucy Copsey, Andrew I. Hanna, Christophe Thébaud, Andrew Bangham, Andrew Hudson, and Enrico Coen. 2005. Evolution through genetically controlled allometry space. PNAS 102: 10221-10226.[PDF]

Understanding evolutionary change requires phenotypic differences between organisms to be placed in a genetic context. However, there are few cases where it has been possible to define an appropriate genotypic space for a range of species. Here we address this problem by defining a genetically controlled space that captures variation in shape and size between closely related species of Antirrhinum. The axes of the space are based on an allometric model of leaves from an F2 of an interspecific cross between Antirrhinum majus and Antirrhinum charidemi. Three principal components were found to capture most of the genetic variation in shape and size, allowing a three-dimensional allometric space to be defined. The contribution of individual genetic loci was determined from QTL analysis, allowing each locus to be represented as a vector in the allometric space. Leaf shapes and sizes of 18 different Antirrhinum taxa, encompassing a broad range of leaf morphologies, could be accurately represented as clouds within the space. Most taxa overlapped with, or were near to, at least one other species in the space, so that together they defined a largely interconnected domain of viable forms. It is likely that the pattern of evolution within this domain reflects a combination of directional selection and evolutionary tradeoffs within a high dimensional space.

(16) B.H. Warren, E. Bermingham, R. P. Prys-Jones and C. Thébaud. 2005. Tracking island colonization history and phenotypic shifts in Indian Ocean bulbuls (Hypsipetes: Pycnonotidae). Biological Journal of the Linnean Society 85 : 271-287. [PDF]

Molecular phylogenies of island organisms provide useful systems for testing hypotheses of convergent or parallel evolution, since selectively neutral molecular characters are likely to be independent of phenotype, and the existence of similar environments on multiple isolated islands provides numerous opportunities for populations to evolve independentlyunder the same constraints. Here we construct a phylogenetic hypothesis for Hypsipetes bulbuls of the western Indian Ocean, and use this to test hypotheses of colonization pattern and phenotypic change among islands of the region. Mitochondrial sequence data were collected from all extant taxa of the region, combined with sequence data from relevant lineages in Asia. Data are consistent with a single Hypsipetes colonization of the western Indian Ocean from Asia within the last 2.6 Myr. The expansion of Hypsipetes appears to have occurred rapidly, with descendants found across the breadth of its western Indian Ocean range. The data suggest that a more recent expansion of Hypsipetes madagascariensis from Madagascar led to the colonization of Aldabra and a secondary colonization of the Comoros. Groupings of western Indian Ocean Hypsipetes according to phenotypic similarities do not correspond to mtDNA lineages, suggesting that these similarities have evolved by convergence or parallelism. The direction of phenotypic change cannot be inferred with confidence, since the primary expansion occurred rapidly relative to the rate of mtDNA substitution, and the colonization sequence remains uncertain. However, evidence from biogeography and comparison of independent colonization events are consistent with the persistence of a small grey continental bulbul in India and Madagascar, and multiple independent origins of large size and green plumage in insular island populations of the Comoros, Mascarenes and Seychelles.

(15) Warren B.H., E. Bermingham, R. C. K. Bowie, R. P. Prys-Jones and C. Thébaud 2003. Molecular phylogeography reveals island colonization history and diversification of western Indian Ocean sunbirds (Nectarinia : Nectariniidae). Molecular Phylogenetics and Evolution 29, 67-85. [PDF]

We constructed a phylogenetic hypothesis for western Indian Ocean sunbirds (Nectarinia) and used this to investigate the geographic pattern of their diversification among the islands of the Indian Ocean. A total of 1309 bp of mitochondrial sequence data was collected from the island sunbird taxa of the western Indian Ocean region, combined with sequence data from a selection of continental (African and Asian) sunbirds. Topological and branch length information combined with estimated divergence times are used to present hypotheses for the direction and sequence of colonization events in relation to the geological history of the Indian Ocean region. Indian Ocean sunbirds fall into two well-supported clades, consistent with two independent colonizations from Africa within the last 3.9 million years. The first clade contains island populations representing the species Nectarinia notata, while the second includes Nectarinia souimanga, Nectarinia humbloti, Nectarinia dussumieri, and Nectarinia coquereli. With respect to the latter clade, application of Bremer s [Syst. Biol. 41 (1992) 436] ancestral areas method permits us to posit the Comoros archipelago as the point of initial colonization in the Indian Ocean. The subsequent expansion of the souimanga clade across its Indian Ocean range occurred rapidly, with descendants of this early expansion remaining on the Comoros and granitic Seychelles. The data suggest that a more recent expansion from Anjouan in the Comoros group led to the colonization of Madagascar by sunbirds representing the souimanga clade. In concordance with the very young geological age of the Aldabra group, the sunbirds of this archipelago have diverged little from the Madagascar population; this is attributed to colonization of the Aldabra archipelago in recent times, in one or possibly two or more waves originating from Madagascar. The overall pattern of sunbird radiation across Indian Ocean islands indicates that these birds disperse across ocean barriers with relative ease, but that their subsequent evolutionary success probably depends on a variety of factors including prior island occupation by competing species.

(14) Ukizintambara T. and C. Thébaud. 2002. Assessing extinction risk in Cercopithecus monkeys. Pp. 393-409 In M.E. Glenn and M. Cords. The Guenons: Diversity and Adaptation in African Monkeys. Kluwer Academic/Plenum Publishers, NY.

We conducted a comprehensive literature survey of distribution and abundance data in 19 Cercopithecus species.  This enabled us to investigate the socio-economic and political situation in countries where these occur and to model deforestation trends in specific area of occupancy.  We determined the intrinsic and extrinsic causes of Cercopithecus monkeys’ vulnerability by analyzing specific characteristics and the effects of habitat loss on specific distribution and survival, and by evaluating the impact of socio-economic and political factors on species conservation in Africa.  We found that specific area of occupancy is declining in most countries but substantial variation in habitat decline trends and specific long-term survival exists. Cercopithecus monkeys conform to the general triangular relationship found elsewhere between closely related species, with relationships between specific area of occupancy, body mass and threat categories. Small-bodied species with restricted distribution, specific habitat requirements and specific dietary preferences are the most threatened.  Socio-economic constraints and lack of representative protected areas exacerbate the risk of extinction, as well as the additional occurrence of civil unrest.  Cercopithecus monkeys are particularly at risk in the Upper Guinea refugium of West Africa, especially in Sierra Leone where species may be extinct in about 30 years, if the present trends continue, due mainly to deforestation and other human disturbances.  In addition, bushmeat trade is widespread in specific hotspots, especially in areas controlled by rebels e.g. the great lakes region.

(13) Blondel, J., Perret, P., Anstett, M.-C. & Thébaud, C. 2002. Evolution of sexual size dimorphism in birds: test of hypotheses using blue tits in contrasted Mediterranean habitats. Journal of Evolutionary Biology 15, 440-450. [PDF]

Many hypotheses, either sex-related or environment-related, have been proposed to explain sexual size dimorphism in birds. Two populations of blue tits provide an interesting case study for testing these hypotheses because they live in contrasting environments in continental France and in Corsica and exhibit different degree of sexual size dimorphism. Contrary to several predictions, the insular population is less dimorphic than the continental one but neither the sexual selection hypothesis nor the niche variation hypothesis explain the observed patterns. In the mainland population both sexes have an advantage to be large whereas in Corsica, the opposite is true with the most important for a pair being to include a small male, which reduces sexual size dimorphism. The most likely explanation is that interpopulation differences in sexual size dimorphism are determined not by sex-related factors, but by differences in sex-specific reproductive roles and responses to environmental factors. Because of environmental stress on the island as a result of food shortage and high parasite infestations, the share of parents in caring for young favours small size in males so that a reduced sexual size dimorphism is not the target of selection but a by-product of mechanisms that operate at the level of individual sexes.

(12) Thébaud C. and D. Simberloff. 2001. Are plants really larger in their introduced range?  American Naturalist 157, 231-236. [PDF]

The “rule” that individuals of nonindigenous plant species are larger where they are introduced than where they are native is not borne out in detailed comparisons of European species introduced to California or the Carolinas and species from California and the Carolinas introduced to Europe. On average, individuals of California species are taller in California than in Europe, while individuals of species native to Europe do not differ between Europe and California. Similarly, individuals of species from the Carolinas are, on average, taller in the Carolinas than in Europe, while individuals of European species are the same height in Europe and the Carolinas or, depending on the nature of the statistical analysis, taller in Europe. Results for herbaceous species only are substantially the same. Although there is no general tendency for species to be taller in their introduced ranges, many species are, in fact, taller in some regions where they are introduced than in their native ranges. Absence of natural enemies in the introduced range is one hypothesis for such observations, but other hypotheses are possible, and the specific reasons for height differences must be sought case by case. The absence of a general tendency casts doubt on the biological control strategy of introducing sequences of phytophages, none of which delivers a knockout blow to a weed, with the expectation that each successive phytophage will force the plant to devote more resources to defense and fewer to traits such as increased size that make it more competitive.

(11) Emerson B.C., E. Paradis & C. Thébaud. 2001. DNA sequences reveal the demographic history of species. Trends in Ecology and Evolution 16, 707-716. [PDF]

Various methodological approaches using molecular sequence data have been developed and applied across several fields, including phylogeography, conservation biology, virology and human evolution. The aim of these approaches is to obtain predictive estimates of population history from DNA sequence data that can then be used for hypothesis testing with empirical data. For example, they provide opportunities to evaluate hypotheses of constant population size through time, of population growth or decline, of the rate of growth or decline, and of migration and growth in subdivided populations. At the core of many of these approaches is the extraction of information from the structure of phylogenetic trees to infer the demographic history of a population, and underlying nearly all methods is coalescent theory. Because of  the increasing availability of DNA sequence data, we reviewed in this article the different ways in which information can be extracted from DNA sequence data to estimate demographic parameters.

(10) Probst J. M., M. Lecorre, and C. Thébaud. 2000. Breeding habitat and conservation priorities in Pterodroma baraui, an endangered gadfly petrel of the Mascarene Archipelago. Biological Conservation 93, 135-138. [PDF]

The endemic Barau's petrel (Pterodroma baraui) is restricted to the island of La Réunion in the Mascarene archipelago where it breeds on the upper slopes of the highest mountains in areas that are virtually inaccessible to humans. Although the species is considered to be critically endangered, little is known about its biology and the actual threats for Barau's petrel on its breeding grounds have never been investigated. In this paper we report data that were collected during the first ever visit of a Barau's petrel colony. The species breeds underground in upland elfin forests between 2400 and 2700 m above sea level. A thick, undisturbed, humus layer appears to be a prerequisite to burrow establishment, which implies that the species may be especially susceptible to trampling by humans or other large vertebrates. We found evidence of past exploitation of Barau's petrel by humans. In addition, the colony is inhabited by three, possibly four, species of introduced commensals, including Rattus sp., which imposes predation on eggs and chicks and may affect the breeding success. We stress the need to establish control campaigns to eradicate potential predators from the nesting colonies and long-term monitoring projects for the Barau's petrel before it undergoes irreversible population decline.

(9) Abbott R.J., F.C. Bretagnolle and C. Thébaud. 1998. Evolution of a polymorphism for outcrossing rate in Senecio vulgaris: influence of germination behavior. Evolution , 52, 1593-1601. [PDF]

A difference in germination behavior between the highly selfing, nonradiate variant of Senecio vulgaris and the more outcrossing, radiate form, had a large effect on the relative female fitness of these two morphs raised in mixed stands under conditions similar to those experienced in the wild. Of particular significance was the finding that female fitness differences between morphs were reversed in early- and late-sown plots. This was because a greater proportion of nonradiate than radiate seed germinated directly after sowing, and in early-sown plots a relatively large proportion of early-germinated nonradiate seedlings survived winter to produce large, highly fecund plants the following summer, that contributed greatly to the total female fitness of the nonradiate morph. In contrast, in late-sown plots (i.e., sown two weeks later), survivorship of early germinated seedlings was much reduced, and the radiate morph had an advantage because most radiate seed delayed germination until spring, therefore avoiding seedling mortality during winter. The effect of the association between morph type and germination behavior on morph female fitness in S. vulgaris is clearly important in regard to the evolution of the polymorphism for outcrossing rate in the species. This, in turn, emphasizes the point that an understanding of factors responsible for the evolution and maintenance of polymorphisms for outcrossing rate in the wild should be based on a detailed examination of the ecological genetics of such polymorphisms that extend beyond traditional studies of pollen discounting and inbreeding depression.

See also the paper by our collaborators who recently nailed down the gene underlying this floral polymorphism!

Minsung Kim, Min-Long Cui, Pilar Cubas, Amanda Gillies, Karen Lee, Mark A. Chapman, Richard J. Abbott, and Enrico Coen. 2008.  Regulatory Genes Control a Key Morphological and Ecological Trait Transferred Between Species. Science 322 (5904), 1116. [DOI: 10.1126/science.1164371]

(8) Thébaud C., and D. Strasberg. 1997. Plant dispersal in fragmented landscapes: a field study of woody colonization in rainforest remnants of the Mascarene Archipelago. Pp. 321-335 In W. Laurance, R. Bierregaard, and C. Moritz, editors. Tropical forest remnants: ecology, conservation, and management. Chicago University Press.

Theoretical metapopulation models have emphasized the importance of dispersal as a process that may promote persistence of species at a regional scale. Unfortunately, quantifying dispersal in fragmented landscapes is no easy task. Here we report on woody plant colonization in a naturally fragmented landscape in lowland tropical rainforest on Réunion Island (Mascarene archipelago). The purpose of the study was to assess how quickly plant species inhabiting forest fragments colonize intervening areas and to explore the mechanisms that may underlie the observed patterns. Our results indicate that knowledge of how species recolonize fragmented landscapes, and why they differ in their colonization ability, can be essential if we are to understand how habitat fragmentation contributes to declines of species. Most woody species from the lowland rainforest remnants of Réunion Is. colonize the landscape very slowly and only over short distances. The degree to which colonization rates are similar in upland remnants remains an open question, although we suspect that the patterns are not dramatically different. Different plant species may respond very differently to fragmentation. We found that fleshy-fruited woody species dispersed by vertebrates had remarkably low rates of colonization. This finding probably relates to the extinction of most seed dispersers in the Mascarene Archipelago, and may well reflect the inability of many plants to adjust to disperser loss. Given the high incidence of fleshy-fruitedness in the woody flora of the Mascarenes, these findings cast some doubt on the long-term survival prospects of many species, including thosethat are still locally abundant in forest remnants.

(7) Thébaud C., and A. Johnston, 1997. Plant responses to global changes in CO2: unfinished business? Trends in Ecology and Evolution 12: 425-426.

(6) Kitching R. L., H. Mitchell, G. Morse, and C. Thébaud. 1997. Determinants of species richness in canopy arthropods in rainforests. Pp. 131-150 In N. E. Stork, J. Adis, and R. K. Didham, editors. Canopy Arthropods . Chapman and Hall, London.

(5) Thébaud C., A. C. Finzi, L. Affre, M. Debussche, and J. Escarre, 1996. Assessing why two introduced Conyza differ in their ability to invade Mediterranean old fields. Ecology 77: 791-804. [PDF]

Researchers have suggested that species-community interactions determine invasion success. Therefore, it is likely that small biological differences between species interact with habitat characteristics to produce distinct patterns of distribution and abundance throughout a new range. In this study we test the hypothesis that differences in the distribution and abundance of species sharing an identical set of "ideal weed characteristics" are explicable in terms of species-specific responses to environmental variation within their new range. Using multifactor experiments, we investigated some of the ecological interactions influencing reproductive success in two very closely related species of annuals having invaded the French Mediterranean region for 150 yr and showing marked differences in their local distribution and abundance patterns. We transplanted seedlings of Conyza canadensis (a species restricted to recently disturbed areas) and C. sumatrensis (a species colonizing early- to mid-successional old fields) at equal densities in three contrasting old fields (6 mo, 4 yr, 17-yr abandonment, respectively) during 1991-1992, a growing season with average rainfall. Individual performances (measured as survivorship, reproductive timing, and reproductive output) were evaluated with respect to: (1) competition with plant neighbors (tested with a weeding treatment), (2) resource availability (tested with nutrient and water addition), and (3) herbivory (tested with chemical limitation). Manipulated factors interacted in a rather complex fashion to influence survivorship and reproduction in both species. However, patterns of relative performance were consistent with relative distribution patterns across Mediterranean landscapes: C. sumatrensis performed better than C. canadensis in all fields, including the youngest one (6 mo old). Herbivory only slightly affected transplant performances. In contrast, competition with plant neighbors had substantial effects on either Conyza species and may be the most important determinant of performance in Mediterranean old fields. The experiment showed unambiguously that the two species differ markedly in their competitive ability, with C. sumatrensis performing better than C. canadensis in the presence of neighboring vegetation. In addition, C. sumatrensis displayed a superior ability to take up and/or to use water and nutrient resources when they become available in competitive environments. We argue that potential physiological or anatomical species differences responsible for this differential susceptibility to local resource reduction by neighbors could involve differences in constructional organization, leaf morphology, and reproductive phenologies.

(4) Thébaud C. and R.J. Abbott, 1995. Characterization of Conyza spp. (Asteraceae) introduced into Europe: quantitative trait and isozyme analyses. American Journal of Botany 82: 360-368. [PDF]

The genus Conyza (Asteraceae) represents one of the foremost examples of intercontinental plant invasions from the New World to the Old World that has resulted in a number of taxonomic problems owing to the dearth of knowledge concerning the biosystematics of the genus. In this study, quantitative trait and enzyme electrophoresis analysis was used to assess the pattern of variation within and among five short_lived taxa of Conyza (C. blakei, C. bonariensis, C. canadensis, C. floribunda, C. sumatrensis), introduced into Europe, and to test the hypothesis of a recent hybrid origin of C. floribunda. The five taxa exhibit marked differences in morphological and life-history characteristics that are concordant with divergence in genes encoding isozymes. In addition, a recent hybrid origin of C. floribunda is clearly not supported by either quantitative or electrophoretic data. These findings suggest that the five taxa differentiated genetically in their native range prior to their introduction in Europe. As formerly suggested by Arthur Cronquist (Bulletin of the Torrey Botanical Club 70: 629-632, 1943), C. canadensis appears to be more closely related to the genus Erigeron than the other taxa. The electrophoretic results also confirm that this particular species is diploid, while the presence of multiple bands and fixed heterozygosity demonstrates that the other Conyza taxa are all genetic allopolyploids. Both quantitative and electrophoretic data suggest the presence of two groups among the polyploid taxa: one comprising C. bonariensis and C. sumatrensis, the other C. blakei and C. floribunda. The latter grouping is supported by the observation that C. blakei and C. floribunda, both native to Argentina, exhibit a striking ability to shift from semelparous to iteroparous reproduction, while the other taxa are strictly semelparous.

(3) Thébaud C. and M. Debussche, 1992. A field test of the infructescence size on fruit removal by birds in Viburnum tinus. Oikos 65, 391-394. [PDF]

A field experiment was designed to examine the effect of infructescence size on fruit removal rates by bird dispersers, using the Mediterranean shrub Viburnum tinus. The proportion of fruit removed during a single season was consistently high, but did not differ over a range of manipulated infructescence sizes (2, 5, 10 and 20 fruit infructescence-1). Logistic regression models revealed significant effects of both individual plants and groups of infructescences within plants on fruit removal rates. It is suggested that the pattern of fruit removal in V. tinus is determined more by the structure and composition of the surrounding vegetation than by individual plant characteristics such as infructescence size. Selective pressures on infructescences are thus not likely to be related to bird dispersers' activity.

(2) Thébaud C. and M. Debussche, 1991. Rapid invasion of Fraxinus ornus L. along the Hérault River in southern France: the importance of seed dispersal by water. Journal of Biogeography 18, 7-1. [PDF]

To document the range extension of a plant species in a region in which it was previously absent, we have examined the distribution pattern of Fraxinus ornus L. 65 years after its introduction to the Herault River in southern France. Censuses of flowering individuals showed that Fraxinus ornus successfully colonized, but remained mainly restricted to, flood-disturbed riparian habitats in the Herault River system. The present distribution of this species showed that it spread along the river system at an average rate of 970 m/yr. We suggest that this very rapid spread, of a usually wind-dispersed, has resulted from water transport of seeds during periodic flooding in autumn.

(1) Macdonald I.A.W., C. Thébaud, W.A. Strahm, and D. Strasberg. 1991. Effects of alien plant invasions on the native vegetation remnants on La Réunion (Mascarene Islands, Indian Ocean). Environmental Conservation 18, 51-61. [PDF]

Although most of the lowland endemic forests of the mountainous Indian Ocean island of La Reunion have been converted by Man to other land-uses, relatively intact ecosystems still survive at higher elevations. Most invaders colonize human-disturbed sites most successfully. However, such alien plants are also frequent in the Reunion primary forest remnants, with at least 62 species penetrating into areas which have experienced no or little human disturbance. Nevertheless, the forest remnants were still mainly dominated by indigenous or endemic plant species and maintain what is, presumably, their original vegetational structure. We found the early stages of primary succession on young volcanic sites to be dominated by aggressively expanding populations of alien species. It appears very unlikely that native species will replace the invaders as the succession proceeds, and furthermore the survival of many indigenous species probably hinges on the active control of alien species.