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International audience; We use multilocus molecular data and species distribution modelling to investigate the phylogenetics and the phylogeography of the White‐backed Woodpecker (Dendrocopos leucotos), a bird species widely distributed over the entire Palaearctic. Our phylogenetic results reveal three well‐supported clades within D. leucotos: the Chinese endemic subspecies (tangi, insularis), the northerly distributed subspecies (leucotos, uralensis) and the four poorly genetically differentiated Japanese subspecies (subcirris, stejnegeri, namiyei, owstoni), and the south‐western Palaearctic lilfordi subspecies. According to our results, the Amami Woodpecker, endemic to Amami Oshima Island (Ryukyu archipelago, Japan) sometimes treated as full species Dendrocopos owstoni, does not deserve a species‐level status. Based on the mitochondrial phylogeographic results, the Japanese archipelago was recently colonized only once by D. leucotos from eastern Eurasia. Our results suggest a split between the leucotos and lilfordi lineages that dates back to mid‐Pleistocene (around 0.6 Mya) with likely no gene flow between these two subspecies since then. Our results thus do not support a phylogeographic pattern in which Central Europe and Northern Europe were recolonized from one or several southern glacial refugia where lilfordi populations persisted through several Pleistocene glacial periods. Spatial variation in mitochondrial diversity across leucotos/uralensis populations and niche ecological modelling suggest a possible eastward population expansion from a unique glacial refugium likely located in Central Europe. Molecular species delimitation methods, gene flow analyses and differences in adult and juvenile plumage indicate that the lilfordi subspecies may warrant to be ranked as a valid phylogenetic species. Further studies are nevertheless needed in the Balkans, where leucotos and lilfordi came recently into contact to measure the effectiveness of reproductive barriers and gene flow.

Abstract Multiple molecular phylogenetic studies have demonstrated that two Neotropical raptors, tiny hawk Accipiter superciliosus and its sister species semicollared hawk A. collaris, are not closely related to core Accipiter, and that A. superciliosus, at least, possesses osteological characters not replicated in the remainder of the genus. Based on these data, there is a need to recognise their distinctiveness at generic level. However, as recently noted in two global bird checklists, no name is available to accommodate them, so we provide a new nomen here. Furthermore, two Asian accipitrids, crested goshawk A. trivirgatus and its presumed closest relative Sulawesi goshawk A. griseiceps, are also phylogenetically distinctive; in this case the genus-group name Lophospiza is applicable. We also designate type species for two genus-group names (Hieraspiza and Eusparvius) currently in the synonymy of Accipiter, and, as an aid to future workers, we provide a synonymy of the genus Accipiter and a list of species currently included in Accipiter for which published molecular phylogenetic data are apparently lacking.

SummaryThree subspecies of Island Thrush Turdus poliocephalus were historically found in New Caledonia. All these subspecies were considered extinct until 1978, when T. p. xanthopus was rediscovered on two small islands, Néba (∼ 3.5 km2) and Yandé (∼ 13 km2). On Néba, we estimated the population at 44–58 individuals. This Island Thrush population is dependent on the coastal forest, the richest habitat for invertebrates. However, the coastal forest habitat has been degraded in quality and extent. The Island Thrush forages in the litter by removing leaves with its bill. Fruits (diameter < 10 mm), picked from trees and swallowed whole, are also a significant component of its diet. Néba and Yandé are currently free of two nest predator species, the black rat Rattus rattus and the New Caledonian Crow Corvus moneduloides. On Néba, a low breeding success rate of 15.4% was found. To ensure conservation of these relict thrush populations, two actions at least should be implemented: setting up a biosecurity programme to keep islands free of black rats and increasing the area of coastal forest. The latter could be done by cutting down coconut trees in abandoned groves and planting tree species used by the Island Thrush to provide shade, fruits, good leaf litter, and nest support.

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., This research was funded by the French ANR (BirdIslandGenomic project, ANR-14-CE02-0002). J.C.I. was funded by the Spanish Ministry of Science, Innovation and Universities (Ref.: PGC2018-097575-B-I00) and by a GRUPIN research grant from the Regional Government of Asturias (Ref.: IDI/2018/000151). B.M. and M.R. were partly funded by the Spanish Ministry of Science and Innovation (grant PGC2018-098897-B-I00), and M.R. was supported by a doctoral fellowship from the Spanish Ministry of Education, Culture, and Sport (FPU16/05724).

Few studies have quantified the extent of genetic differentiation within widely distributed polytypic African bird species with disjunct ranges. Current knowledge indicates that high levels of genetic differentiation are found for such lineages but generalization of the pattern requires further comparisons with other co-distributed taxa. We assessed the extent of phylogeographical structure across the range of the Olive Woodpecker Dendropicos griseocephalus using mitochondrial and nuclear intron data. The Olive Woodpecker occupies the forests of Central (Dendropicos griseocephalus ruwenzori) and Eastern (Dendropicos g. kilimensis) Africa, with a disjunct morphological lineage (Dendropicos g. griseocephalus) occurring in southern Africa. Each of the subspecies lineages can be diagnosed using morphology. Phylogenetic analyses of our sequence data recovered three monophyletic lineages with kilimensis sister to ruwenzori, and griseocephalus as sister to the clade uniting these two taxa. Molecular species delimitation methods and estimates of gene flow under the isolation-with-migration model suggest that the clade uniting the central and eastern subspecies may be recognized as distinct at the species level from the nominate subspecies, which is restricted to southern Africa. We conclude that D. griseocephalus (Boddaert, 1783) and D. ruwenzori (Sharpe, 1902) (including subspecies kilimensis) should be considered full species. The biogeographical pattern we uncover for the Olive Woodpecker differs from that of other co-distributed widespread species both in terms of the order of sequence divergence of lineages occupying different areas of endemism in Africa, and in the timing of divergence, being younger (0.5–0.7 mya BP) than that recovered for the co-distributed Square-tailed Drongo Dicrurus ludwigii (0.9–1.6 mya BP).

The White-vented Storm-petrel Oceanites gracilis is one of the world's least known seabirds and is listed as Data Deficient by the IUCN. To date, only one breeding colony, with less than ten pairs, is known from the Chungungo Islet in Chile. To understand the breeding habitat and the threats faced by the species, it is crucial to search for other colonies. We carried out field surveys of this species in the Atacama Desert between 2013 and 2020, searching for nests along c. 870 km of coastline, from sea level to 1700 m.a.s.l. We also revisited the breeding colony at the Chungungo Islet. To detect nests, we used endoscopic cameras and scent-trained dogs. We found two new breeding colonies in Pampa Hermosa and Pampa del Indio Muerto in the Atacama Desert, and additionally, we found two non-active breeding sites in Tocopilla and Sierra Miranda. Colonies were on different substrates, including crevices in saltpetre formations, gypsum and rocks (only Chungungo Islet). The threats identified for each breeding site include light pollution and habitat destruction by mining and energy projects. Further surveys are needed to estimate the population size and to assess the conservation status of this species.

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species., A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.

Communicating species identity is a key component of many animal signals. However, whether selection for species recognition systematically increases signal diversity during clade radiation remains debated. Here we show that in woodpecker drumming, a rhythmic signal used during mating and territorial defense, the amount of species identity information encoded remained stable during woodpeckers’ radiation. Acoustic analyses and evolutionary reconstructions show interchange among six main drumming types despite strong phylogenetic contingencies, suggesting evolutionary tinkering of drumming structure within a constrained acoustic space. Playback experiments and quantification of species discriminability demonstrate sufficient signal differentiation to support species recognition in local communities. Finally, we only find character displacement in the rare cases where sympatric species are also closely related. Overall, our results illustrate how historical contingencies and ecological interactions can promote conservatism in signals during a clade radiation without impairing the effectiveness of information transfer relevant to inter-specific discrimination., Animal signals often encode information on the emitter’s species identity. Using woodpecker drumming as a model, here the authors show that limited signal divergence during a clade radiation does not impair species discrimination, as long as the signals are adapted to local ecological requirements.

International audience; The Resplendent Quetzal Pharomachrus mocinno is a rare Neotropical bird included in the IUCN red list as Near Threatened. Fragmentation of its habitat, the cloud forest, is considered as the principal threat. Two subspecies are currently recognised but genetic and morphometric studies suggested they could be considered as full species. We assessed whether male vocalisation would support a species delimitation hypothesis. We recorded in the field and downloaded from sound archives vocalisation of 57 individuals from 30 different localities distributed in 11 countries. We estimated the acoustic differences of all the Pharomachrus taxa with multivariate analyses and machine learning techniques. Our results show vocal differences between P. m. mocinno and P. m. costaricensis that could have a molecular basis, potentially due to genetic drift developed during the more than three million years of separation of P. m. mocinno (from Mexico to Nicaragua) and P. m. costaricensis (Costa Rica and Panama). We therefore suggest that P. mocinno could potentially be divided into two species. A possible separation of these taxa into two species could have important consequences for the conservation status of the Resplendent Quetzals, and redirect conservation efforts for these taxa.

Molecular phylogenetic studies of woodpeckers (Picidae) have generally focused on relationships within specific clades or have sampled sparsely across the family. We compared DNA sequences of six loci from 203 of the 217 recognized species of woodpeckers to construct a comprehensive tree of intrafamilial relationships. We recovered many known, but also numerous unknown, relationships among clades and species. We found, for example, that the three picine tribes are related as follows (Picini, (Campephilini, Melanerpini)) and that the genus Dinopium is paraphyletic. We used the tree to analyze rates of diversification and biogeographic patterns within the family. Diversification rate increased on two occasions during woodpecker history. We also tested diversification rates between temperate and tropical species but found no significant difference. Biogeographic analysis supported an Old World origin of the family and identified at least six independent cases of New World-Old World sister relationships. In light of the tree, we discuss how convergence, mimicry, and potential cases of hybridization have complicated woodpecker taxonomy.

Diversification of avifaunas associated with savannah and steppes appears to correlate with open habitats becoming available, starting in the Miocene. Few comparative analyses exist for families fo ...

International audience; The Eurasian treecreeper (Certhia familiaris) comprises two mitochondrial lineages that diverged during the mid-Pleistocene. One palaeoendemic lineage has an allopatric range currently restricted to the island of Corsica and the Caucasus region, whereas the second one has a very large Eurasian range. Here, we used microsatellites (N = 6) and mitochondrial DNA (COI) to assess the genetic structure of insular and mainland populations from Corsica, mainland France and Central Italy (N = 258) and the level of mitochondrial and nuclear gene flow among these populations. Concordant with the mitochondrial DNA signal, the results for microsatellites clearly demonstrate that the Corsican population (Certhia familiaris corsa) is strongly divergent from nearby mainland populations (Certhia familiaris macrodactyla). Microsatellite data also support significant divergence and low gene flow between the Central Italian and mainland French populations. Our results suggest low nuclear gene flow from the mainland into Corsica and no mitochondrial gene flow. Sporadic gene flow from the nearby mainland might explain the presence of continental nuclear alleles in the genome of 5% of sampled insular birds. Our study confirms the existence of an endemic Corsican treecreeper lineage with important conservation value. Our results also imply that Eurasian treecreepers from Central Italy constitute a distinct management unit.

International audience; Secondary contact zones are natural systems which can be efficiently used to measure genetic differentiation and gene flow and thus provide a good opportunity to assess the level of reproductive isolation between divergent evolutionary lineages. In this study, we used ten Z-linked and nine autosomal loci from seven chromosomes and twenty males to evaluate gene flow across a secondary contact zone between two mitochondrial lineages of the Eurasian Green Woodpecker (Picus viridis), that diverged around 1 million years ago. One lineage (Picus viridissharpei) is distributed throughout the Iberian Peninsula whereas the other one (Picus viridisviridis) is widespread across the Western Palearctic. These two lineages form a secondary contact zone in southern France. Formerly treated as two subspecies of Picus viridis, several authors have recently proposed assigning a specific rank to P. viridis sharpei and P. viridis viridis. Our results indicate no introgression of nuclear loci in allopatric populations located on both sides of the contact zone, which thus acts as an efficient barrier to gene flow. All males sampled within the contact zone and one male sampled near its eastern border were slightly admixed revealing that reproductive isolation between P. viridissharpei and P viridis viridis has not been completely achieved. In accordance with the geographical range of each lineage, the two admixed males sampled near the western border of the contact zone harboured a large proportion of P. viridissharpei alleles whereas admixed males sampled eastwardly near the Rhone Valley had a high proportion of P. viridis viridis alleles. Overall our results further support considering P. viridissharpei and P. viridisviridis as two biological species.

The present study examines the colonization history and phylogeography of the brush-warblers (Nesillas), a genus of passerines endemic to islands of the western Indian Ocean (Madagascar, Comoros, and Aldabra Atoll). 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 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 (Nesillas typica and Nesillas lantzii) are not sister taxa. The brush-warblers started to diversify approximately 1.6 Mya, commencing with the separation of the clade formed by two species endemic to the Comoros (Nesillas brevicaudata and Nesillas mariae) from the rest of the genus. The lineages leading to the two Malagasy species diverged approximately 0.9 Mya; 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.

We investigated the evolutionary history of the spotted flycatcher Muscicapa striata, a long distance migratory passerine having a widespread range, using mitochondrial markers and nuclear introns. Our mitochondrial results reveal the existence of one insular lineage restricted to the western Mediterranean islands (Balearics, Corsica, Sardinia) and possibly to the Tyrrhenian coast of Italy that diverged from the mainland lineages around 1 Mya. Mitochondrial genetic distance between insular and mainland lineages is around 3.5%. Limited levels of shared nuclear alleles among insular and mainland populations further support the genetic distinctiveness of insular spotted flycatchers with respect to their mainland counterparts. Moreover, lack of mitochondrial haplotypes sharing between Balearic birds (M. s. balearica) and Corso-Sardinian birds (M. s. tyrrhenica) suggest the absence of recent matrilineal gene flow between these two insular subspecies. Accordingly, we suggest that insular spotted flycatchers could be treated as one polytypic species (Muscicapa tyrrhenica) that differs from M. striata in morphology, migration, mitochondrial and nuclear DNA and comprises two subspecies (the nominate and M. t. balearica) that diverged recently phenotypically and in mitochondrial DNA and but still share the same nuclear alleles. This study provides an interesting case-study illustrating the crucial role of western Mediterranean islands in the evolution of a passerine showing high dispersal capabilities. Our genetic results highlight the role of glacial refugia of these islands that allowed initial allopatric divergence of insular populations. We hypothesize that differences in migratory and breeding phenology may prevent any current gene flow between insular and mainland populations of the spotted flycatcher that temporarily share the same insular habitats during the spring migration.

We describe a new species of drongo in the Square-tailed Drongo (Dicrurus ludwigii) complex using a combination of biometric and genetic data. The new species differs from previously described taxa in the Square-tailed Drongo complex by possessing a significantly heavier bill and via substantial genetic divergence (6.7%) from its sister-species D. sharpei. The new species is distributed across the gallery forests of coastal Guinea, extending to the Niger and Benue Rivers of Nigeria. We suspect that this taxon was overlooked by previous avian systematists because they either lacked comparative material from western Africa or because the key diagnostic morphological character (bill characteristics) was not measured. We provide an updated taxonomy of the Square-tailed Drongo species complex.

International audience; Background: The Cambodian Tailorbird (Orthotomus chaktomuk) was one of the most recent major ornithological discoveries in South-east Asia as it originated from lowland seasonally flooded scrub within the densely inhabited floodplain around the Tonle Sap, Mekong and Bassac rivers (Cambodia). The Cambodian Tailorbird is sister to the Dark-necked Tailorbird (O. atrogularis) with very limited genetics and biometric differentiation. Between 2004 and 2012, evidences of a new population of Ashy Tailorbird (O. ruficeps) in SE Cambodia/Vietnam accumulated but no museum specimens were ever reported. The Ashy Tailorbird currently consists of eight subspecies among which the closest geographical populations, O. r. cineraceus (SE Burma to Malay Peninsula, Sumatra, Bangka and Belitung) and O. r. borneoensis (Borneo), are allopatric. Subspecific identification of the Cambodian Ashy Tailorbirds individuals was not possible because of the limited differences in plumage among subspecies.Methods: We inspected the Orthotomus ruficeps specimens housed at the Museum National d’Histoire Naturelle (Paris) and discovered five specimens of O. ruficeps collected by Louis Rodolphe Germain in ‘Cochinchina’ (corresponding to southern Vietnam) during the nineteenth century. We sequenced one mitochondrial locus and gathered biometric data from these specimens and compared them with other Orthotomus lineages.Results: The Ashy Tailord population from SE Cambodia and Vietnam is distinct from the two geographically close subspecies O. r. borneoensis (1.7%) and O. r. cineraceus (1.3%). O. chaktomuk is nested within O. atrogularis in the mitochondrial gene tree. The SE Cambodia/Vietnam population of O. ruficeps is distinct from the two other subspecies in bill shape.Conclusion: Our study described the biometric and molecular distinctiveness of a recently re-discovered population of Ashy Tailord in SE Cambodia and Vietnam and suggests that this population constitutes an independent evolutionary lineage that we describe here as a new subspecies. The newly described Cambodian Tailorbird is nested within the Dark-necked Tailorbird and the genetic divergence is much lower than initially described (0.4‒0.7% vs 1.1‒1.4%).

An ideal taxonomy for organisms incorporates comprehensive knowledge of existing species diversity and their phylogenetic relationships. This knowledge is used in developing consistent criteria for recognizing and naming species as well as monophyletic groups (clades) above the species level, including genera, families, and orders. This provides well-justified, consensus names for taxa that can be used globally in studying and managing the health of species and their populations. Having the taxonomic hierarchy of names reflects evolutionary history and advances our understanding of the origins and causes of change over time in biological diversity.

We report here the successful assembly of the complete mitochondrial genomes of the northern spotted owl (Strix occidentalis caurina) and the barred owl (S. varia). We utilized sequence data from two sequencing methodologies, Illumina paired-end sequence data with insert lengths ranging from approximately 250 nucleotides (nt) to 9,600 nt and read lengths from 100–375 nt and Sanger-derived sequences. We employed multiple assemblers and alignment methods to generate the final assemblies. The circular genomes ofS. o. caurinaandS. variaare comprised of 19,948 nt and 18,975 nt, respectively. Both code for two rRNAs, twenty-two tRNAs, and thirteen polypeptides. They both have duplicated control region sequences with complex repeat structures. We were not able to assemble the control regions solely using Illumina paired-end sequence data. By fully spanning the control regions, Sanger-derived sequences enabled accurate and complete assembly of these mitochondrial genomes. These are the first complete mitochondrial genome sequences of owls (Aves: Strigiformes) possessing duplicated control regions. We searched the nuclear genome ofS. o. caurinafor copies of mitochondrial genes and found at least nine separate stretches of nuclear copies of gene sequences originating in the mitochondrial genome (Numts). TheNumtsranged from 226–19,522 nt in length and included copies of all mitochondrial genes excepttRNAPro,ND6, andtRNAGlu.Strix occidentalis caurinaandS. variaexhibited an average of 10.74% (8.68% uncorrectedp-distance) divergence across the non-tRNA mitochondrial genes.

In this study we investigated the phylogenetics of the Eurasian treecreeper (Certhia familiaris), a forest passerine with a wide Palaearctic range including Corsica, using three mitochondrial genes and three nuclear introns, and its phylogeographic history using the COI gene. Our phylogenetic results, including eight of the ten sub-species currently recognized, support the monophyly of C. familiaris with respect to its Indo-Asian sister species C. hodgsoni. C. familiaris comprises two lineages that diverged during the mid-Pleistocene (c. 1 Myr): one palaeoendemic lineage has an allopatric range nowadays restricted to the Corsica island and the Caucasus region whereas the second one, more recent and widespread, is distributed over most of Eurasia and in northern China. The most likely scenario that may explain such a pattern is a double colonization of the western Palaearctic from the eastern range of the species. During the middle Pleistocene period, a first lineage expanded its range up into Europe but did not persist through glacial cycles except in Corsica and the Caucasus region. Later, during the upper Pleistocene, a second lineage began to diversify around 0.09 Myr, spreading towards the western Palaearctic from a unique refuge likely located in the eastern Palaearctic [correction added on 6 March 2015 after first online publication: 0.9 Myr amended to 0.09 Myr]. Apart from C. f. corsa, our results do not suggest any distinct evolutionary history for other sub-species previously described on morphological grounds in Europe. Our study highlights the important conservation value of the Corsican treecreeper and emphasizes the major role of mature pine forests in the evolution of endemic bird taxa in Corsica. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115, 134–153.

We re-examine evidence from the voyage of the corvette La Coquille in respect of the Pomarea monarch flycatchers from Tahiti and Maupiti, and conclude that Pomarea maupitiensisGarnot, 1829, should be recognised as a distinct but extinct species for which we designate a lectotype, necessarily represented by the image in a colour plate.

The dynamics of species accumulation of African terrestrial vertebrates over time remains underexplored in comparison with those in the New World, despite Africa hosting about 25% of the world’s avian diversity. This lack of knowledge hampers our understanding of the fundamental processes that drive biodiversity and the dynamics of speciation. To begin to address this gap, we reconstructed species-level phylogenies of two unrelated clades of African woodpeckers (12 species of Geocolaptes/Campethera and 13 species of Chloropicus/Mesopicos/Dendropicos/Ipophilus) that diverged from their closest Indo-Malayan relatives at similar times. Our results demonstrate that the current taxonomy is misleading: three (Campethera, Dendropicos and Mesopicos) out of four polytpic genera/subgenera are not monophyletic. Our results also show that current estimates of diversity at the species level are significantly understated, as up to 18 species for the ‘Campethera clade’ and 19 for the ‘Dendropicos clade’ could be recognized. The first splits within both clades involve species that are largely restricted to the Guineo-Congolian biogeographic regions, followed by later adaptations to particular habitats (forest versus savannah) and colonization of other regions (e.g. Southern Africa), each of which occurred multiple times in both clades. Assuming a conservative species delimitation scheme, our results indicate that diversification rates are decreasing through time for both clades. Applying a more extreme species recognition scheme (18 and 19 species for the Campethera and Dendropicos clades, respectively), our results support a decrease in diversification rates only for the Dendropicos clade and thus underline the importance of the number of species included in our diversification analyses. Greater ecological diversity of the Campethera clade where multiple species exhibit either an arboreal or terrestrial foraging strategy might explain the constant diversification rates through time we found under the eighteen species scheme.

International audience; Mitochondrial DNA remains one of the most widely used molecular markers to reconstruct the phylogeny and phylogeography of closely-related birds. It has been proposed that bird mitochondrial genomes evolve at a constant rate of ~0.01 substitution per site per Million years, i.e. that they evolve according to a strict molecular clock. This molecular clock is often used in studies of bird mitochondrial phylogeny and molecular dating. However, rates of mitochondrial genome evolution vary among bird species, and correlate with life-history traits such as body mass and generation time. These correlations could cause systematic biases in molecular dating studies that assume a strict molecular clock. In this study, we overcome this issue by estimating corrected molecular rates for birds. Using complete or nearly complete mitochondrial genomes of 475 species, we show that there are strong relationships between body mass and substitution rates across birds. We use this information to build models that use bird species' body mass to estimate their substitution rates across a wide range of common mitochondrial markers. We demonstrate the use of these corrected molecular rates on two recently-published datasets. In one case, we obtained molecular dates that are twice as old as the estimates obtained using the strict molecular clock. We hope that this method to estimate molecular rates will increase the accuracy of future molecular dating studies in birds.

International audience; The Indo-Malayan bioregion has provided some of the most spectacular discoveries of new vertebrate species (e.g. saola, khanyou, bare-faced bulbul) over the last 25 years. Yet, very little is known about the processes that led to the current biodiversity in this region. We reconstructed the phylogeographic history of a group of closely related passerines, the Alophoixus bulbuls. These birds are continuously distributed in Indo-Malaya around the Thailand lowlands such that their distribution resembles a ring. Our analyses revealed a single colonization event of the mainland from Sundaland with sequential divergence of taxa from southwest to northeast characterized by significant gene flow between parapatric taxa, and reduced or ancient gene flow involving the two taxa at the extremities of the ring. We detected evidence of population expansion in two subspecies, including one that was involved in the closing of the ring. Hence, our analyses indicate that the diversification pattern of Alophoixus bulbuls fits a ring species model driven by geographic isolation. To our knowledge, the Alophoixus bulbuls represent the first case of a putative broken ring species complex in Indo-Malaya. We also discuss the implications of our results on our understanding of the biogeography in Indo-Malaya.

The Campephagidae (minivets, cuckoo-shrikes and trillers, seven genera and 81 species) represents an Old World corvid clade of tropical birds with a mixed diet that forage in different manners, i.e., flycatching, foliage-gleaning or shriking. This family has never been the focus of any phylogenetic survey, so their phylogenetic relationships and biogeographic history remain largely unknown. To address these questions, we sequenced four loci (ND2, myoglobin intron-2, GAPDH intron-11 and c-mos) for 27 species of Campephagidae. Our analyses suggest that Coracina consists of five unrelated lineages and that Lalage is paraphyletic. Our dating analyses, using a Bayesian relaxed-clock method, indicate that the split between the Indo-Malayan genus Pericrocotus and the remaining Campephagidae occurred synchronously with other splits involving Indo-Malayan corvid lineages, suggesting that several lineages of Indo-Malayan birds were isolated at the same time from their closest relatives. The African stock of cuckoo-shrikes is likely the result of three independent trans-oceanic dispersals from Australasia.

Synchronous intercontinental splits between assemblages of woodpeckers suggested by molecular data

The subfamily Picumninae (piculets) includes 3 genera and 30 species of tiny and short-tailed woodpeckers with a pantropical distribution. Within the Picumninae, two cases of intercontinentally disrupted distributions at the genus level occur. The first one concerns the genus Sasia (one species in Africa and two in southeast Asia) while the second concerns Picumnus (one species in southeast Asia and 25 in South America). These disrupted distributions, as well as several morphological differences, have lead some authors to place the African representative of Sasia and the southeast Asian representative of Picumnus in their own monotypic genera (Verreauxia and Vivia, respectively). To address the taxonomic status and biogeographic history of the piculets, we sequenced 2676 bp of DNA from one mitochondrial (ND2) and two nuclear markers (myoglobin intron 2 and β-fibrinogen intron 7). Monophyly of Picumninae could not be recovered with confidence, while monophyly of Sasia and Picumnus were always strongly supported. Molecular dating analyses revealed that the splits both between the African and Indo-Malayan Sasia and between the New World and Old World Picumnus occurred at ca 7.9 Myr BP. This time corresponds to the beginning of the formation of the northern Hemisphere ice sheets and the accompanying expansion of grasslands throughout the world. The spread of open areas in the northern parts of Eurasia and America prevented gene flow between tropical forest birds, such as the piculets, in Africa, southeast Asia and South America, respectively.

Background The island of Madagascar and surrounding volcanic and coralline islands are considered to form a biodiversity hotspot with large numbers of unique taxa. The origin of this endemic fauna can be explained by two different factors: vicariance or over-water-dispersal. Deciphering which factor explains the current distributional pattern of a given taxonomic group requires robust phylogenies as well as estimates of divergence times. The lineage of Indian Ocean scops-owls (Otus: Strigidae) includes six or seven species that are endemic to Madagascar and portions of the Comoros and Seychelles archipelagos; little is known about the species limits, biogeographic affinities and relationships to each other. In the present study, using DNA sequence data gathered from six loci, we examine the biogeographic history of the Indian Ocean scops-owls. We also compare the pattern and timing of colonization of the Indian Ocean islands by scops-owls with divergence times already proposed for other bird taxa. Results Our analyses revealed that Indian Ocean islands scops-owls do not form a monophyletic assemblage: the Seychelles Otus insularis is genetically closer to the South-East Asian endemic O. sunia than to species from the Comoros and Madagascar. The Pemba Scops-owls O. pembaensis, often considered closely related to, if not conspecific with O. rutilus of Madagascar, is instead closely related to the African mainland O. senegalensis. Relationships among the Indian Ocean taxa from the Comoros and Madagascar are unresolved, despite the analysis of over 4000 bp, suggesting a diversification burst after the initial colonization event. We also highlight one case of putative back-colonization to the Asian mainland from an island ancestor (O. sunia). Our divergence date estimates, using a Bayesian relaxed clock method, suggest that all these events occurred during the last 3.6 myr; albeit colonization of the Indian Ocean islands were not synchronous, O. pembaensis diverged from O. senegalensis about 1.7 mya while species from Madagascar and the Comoro diverged from their continental sister-group about 3.6 mya. We highlight that our estimates coincide with estimates of diversification from other bird lineages. Conclusion Our analyses revealed the occurrence of multiple synchronous colonization events of the Indian Ocean islands by scops-owls, at a time when faunistic exchanges involving Madagascar was common as a result of lowered sea-level that would have allowed the formation of stepping-stone islands. Patterns of diversification that emerged from the scops-owls data are: 1) a star-like pattern concerning the order of colonization of the Indian Ocean islands and 2) the high genetic distinctiveness among all Indian Ocean taxa, reinforcing their recognition as distinct species.

International audience; We address the phylogenetic relationships of the drongos (Dicruridae) at the species-level using sequences from two nuclear (myoglobin intron-2 and c-mos) and two mitochondrial (ND2 and cytochrome b) loci. The resulting phylogenetic tree shows that the most basal species is D. aeneus, followed in the tree by a trichotomy including (1) the Asian D. remifer, (2) a clade of all African and Indian Ocean islands species as well as two Asian species (D. macrocercus and D. leucophaeus) and (3) a clade that includes all other Asian species as well as two Australasian species (D. megarhynchus and D. bracteatus). Our phylogenetic hypotheses are compared to [Mayr, E., Vaurie, C., 1948. Evolution of the family Dicruridae (Birds). Evolution 2, 238–265.] hypothetical family ‘‘tree'' based on traditional phenotypic analysis and biogeography. We point out a general discrepancy between the so-called ‘‘primitive'' or ‘‘unspecialized'' species and their position in the phylogenetic tree, although our results for other species are congruent with previous hypotheses. We conduct dating analyses using a relaxed-clock method, and propose a chronology of clades formation. A particular attention is given to the drongo radiation in Indian Ocean islands and to the extinction– invasion processes involved. The first large diversification of the family took place both in Asia and Africa at 11.9 and 13.3 Myr, respectively, followed by a dispersal event from Africa to Asia at ca 10.6 Myr; dispersal over Wallace line occurred later at ca 6 Myr. At 5 Myr, Principe and Indian Ocean Islands have been colonized from an African ancestor; the most recent colonization event concerned Anjouan by an immigrating population from Madagascar.

The Malaconotidae, Platysteiridae and Vangidae represent an African and Malagasy assemblage of closely related corvoid taxa with distinctive morphology. Their relationships with their putative Asian closest relatives, and thus their biogeographic history, have not hitherto been thoroughly evaluated. We present evidence that the African and Malagasy groups originated through a single African colonization event c. 37.7 ± 4.6 Myr BP. Three main groups that differ in their foraging behaviour diverged c. 35.8 ± 4.5 Myr BP, suggesting that an African radiation occurred around that time. Several disperal events out of Africa to Madagascar (Vangidae) and Indo-Malaya (Philentoma, Hemipus and Tephrodornis) took place about 28.9 ± 4.0 Myr BP (Oligocene), a period when faunistic exchanges between Eurasia and Africa seem to have been common. Our estimation of the colonization of Madagascar by the Vangidae is 28.9 ± 4.0 Myr BP, in congruence with the estimated colonization of Madagascar by several African vertebrate groups (carnivorous mammals, snakes, sylvioid passerines, treefrogs, turtles).

The African genus Hyliota includes three or four species of warbler-like birds of uncertain phylogenetic affinities, as it has historically been placed in different avian families that are now known to represent unrelated lineages: Malaconotidae (bush-shrikes), Platysteiridae (batises and wattle-eyes), Muscicapidae (Old World flycatchers) and Sylviidae (Old-World Warblers). To assess the affinities of Hyliota we sequenced a mitochondrial protein-coding gene (ND2, 1018 bp) and a nuclear intron (myoglobin intron-2, 685 bp). Our analyses suggest that all previous hypotheses concerning the affinities of Hyliota are erroneous. Instead, Hyliota represents a basal branch in the Passerida radiation with no close relatives. Our results, which also include analyses of relationships among other of other atypical songbird genera, lend support to an African origin of the Passerida songbird radiation.