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International audience; Analysis of the incisor enamel microstructure of extinct and extant West Indian caviomorph rodents emphasizes a clear microstructural distinction between the Echimyidae (Capromyinae and Heteropsomyinae) among Octodontoidea and the "Heptaxodontidae" whose phylogenetic affinities are debated. All capromyines and heteropsomyines have a pattern of enamel characterized by a rectangular crystallite arrangement, which is biomechanically strongest in limiting crack propagation most efficiently (subtype [Sbt.] 3 of multiserial Hunter-Schreger bands [HSBs]). This enamel condition is exclusive to all mainland octodontoids. In stark contrast, “heptaxodontids” sampled here exhibit much less derived enamel subtypes of multiserial HSBs with parallel to acute angular crystallite arrangement (Sbt. 1 [Clidomys], Sbt. 1–2 [Elasmodontomys], and low acute Sbt. 2 [Amblyrhiza]), less well adapted for prevention of crack propagation. The incisor enamel microstructure of Amblyrhiza and Clidomys is consistent with a chinchilloid assignment, as reflected by the anatomy of their auditory region and their unusual dental pattern. For Elasmodontomys, the primitive condition of its incisor enamel is difficult to reconcile with its highly nested phylogenetic position within the Octodontoidea clade (among the Capromyinae), as recently inferred from aDNA analyses. The different enamel patterns among extinct and extant West Indian caviomorphs indicate distinct high-level taxonomic groups, but restricted to the Octochinchilloi (Octodontoidea and Chinchilloidea) among Caviomorpha. The great diversity of caviomorphs on the Caribbean islands resulted from intra-archipelago diversification through time, but their high-level phylogenetic diversity can only be explained by distinct sources, implying de facto multiple (potentially time-staggered) natural colonizations of the West Indies. The chinchilloid-compatible enamel and dental pattern characterizing Borikenomys from lower Oligocene deposits in Puerto Rico, strongly suggest a link with some of the recently-extinct "heptaxodontids" that would substantiate their much greater antiquity in the Caribbean islands.

Linking genes to phenotypes has been a major question in evolutionary biology for the last decades. In the genomic era, few studies attempted to link olfactory-related genes to different anatomical proxies. However, they found very inconsistent results. This study is the first to investigate a potential relation between olfactory turbinals and olfactory receptor (OR) genes. We demonstrated that despite the use of similar methodology in the acquisition of data, OR genes do not correlate with the relative and the absolute surface area of olfactory turbinals. These results challenged the interpretations of several studies based on different proxies related to olfaction and their potential relation to olfactory capabilities.

A central goal of macroevolution is to understand palaeodiversity dynamics through time and space. Estimating palaeodiversity dynamics has been historically addressed with fossil data because it directly reflects the past variations of biodiversity. Unfortunately, some groups or regions lack a good fossil record, and dated phylogenies can be useful to estimate diversification dynamics. Recent methodological developments have unlocked the possibility to investigate palaeodiversity dynamics by using phylogenetic birth-death models with non-homogeneous rates through time and across clades. One of them seems particularly promising to detect clades whose diversity has declined through time. However, empirical applications of the method have been hampered by the lack of a robust, accessible implementation of the whole procedure, therefore requiring users to conduct all the steps of the analysis by hand in a time-consuming and error-prone way.Here we propose an automation of Morlon et al. (2011) clade-shift model with additional features accounting for recent developments and we implement it in the R package RPANDA. We also test the approach with simulations focusing on its ability to detect shifts of diversification and to infer palaeodiversity dynamics. Finally, we illustrate the automation by investigating the palaeodiversity dynamics of Cetacea, Vangidae, Parnassiinae, and Cycadales.Simulations showed that we accurately detected shifts of diversification although false shift detections were higher for time-dependent diversification models with extinction. The median global error of palaeodiversity dynamics estimated with the automated model is low showing that the method can capture diversity declines. We detected shifts of diversification for three of the four empirical examples considered (Cetacea, Parnassiinae and Cycadales). Our analyses unveil a waxing-and-waning pattern due to a phase of negative net diversification rate embedded in the trees after isolating recent radiations.Our work enables to easily apply non-homogeneous models of diversification in which rates can vary through time and across clades to reconstruct palaeodiversity dynamics. By doing so, we detected palaeodiversity declines among three of the four groups tested, highlighting that such periods of negative net diversification might be common. We discuss the extent to which this approach might provide reliable estimates of extinction rates and we provide guidelines for users.

International audience; The origins and evolution of the outstanding Neotropical biodiversity are a matter of intense debate. A comprehensive understanding is hindered by the lack of deep-time comparative data across wide phylogenetic and ecological contexts. Here, we quantify the prevailing diversification trajectories and drivers of Neotropical diversification in a sample of 150 phylogenies (12,512 species) of seed plants and tetrapods, and assess their variation across Neotropical regions and taxa. Analyses indicate that Neotropical diversity has mostly expanded through time (70% of the clades), while scenarios of saturated and declining diversity account for 21% and 9% of Neotropical diversity, respectively. Five biogeographic areas are identified as distinctive units of long-term Neotropical evolution, including Pan-Amazonia, the Dry Diagonal, and Bahama-Antilles. Diversification dynamics do not differ across these areas, suggesting no geographic structure in long-term Neotropical diversification. In contrast, diversification dynamics differ across taxa: plant diversity mostly expanded through time (88%), while a substantial fraction (43%) of tetrapod diversity accumulated at a slower pace or declined toward the present. These opposite evolutionary patterns may reflect different capacities for plants and tetrapods to cope with past climate changes.

With almost 2,600 species, Rodentia is the most diverse order of mammals. Here, we provide an overview of changes in our understanding of the systematics of living rodents, including species recognition and delimitation, phylogenetics, and classification, with emphasis on the last three decades. Roughly, this corresponds to the DNA sequencing era of rodent systematics, but the field is undergoing a transition into the genomic era. At least 248 species were newly described in the period 2000–2017, including novelties such as the first living member of Diatomyidae and a murid species without molars (Paucidentomys vermidax), thus highlighting the fact that our understanding of rodent diversity is going through an age of discovery. Mito-nuclear discordance (including that resulting from mitochondrial introgression) has been detected in some of the few taxonomic studies that have assessed variation of two or more unlinked loci. As studies incorporate more loci, incomplete lineage sorting and introgression are likely to gain recognition as widespread phenomena in the near future. Molecular phylogenetics has had a major impact in rodent phylogeny and allowed the identification of three major rodent clades, here recognized as suborders: 1) the Hystricomorpha (sometimes referred as the Ctenohystrica) and including two infraorders, Hystricognathi and Ctenodactylomorphi; 2) the Sciuromorpha; and 3) the Supramyomorpha, a new suborder that comprises the infraorders Castorimorphi, Anomalurimorphi, and Myomorphi. In spite of the greater understanding and ensuing stability of rodent phylogeny gained during the last three decades, several major areas of the rodent tree remain unresolved or poorly supported. We expect that the analysis of genomic-scale data will help resolve those areas of the radiation of Rodentia that still remain poorly understood.

Biotic interactions between Africa and Eurasia across the Levant have invoked particular attention among scientists aiming to unravel early human dispersals. However, it remains unclear whether behavioral capacities enabled early modern humans to surpass the Saharo– Arabian deserts or if climatic changes triggered punctuated dispersals out of Africa. Here, we report an unusual subfossil assemblage discovered in a Judean Desert’s cliff cave near the Dead Sea and dated to between ∼42,000 and at least 103,000 y ago. Paleogenomic and morphological comparisons indicate that the specimens belong to an extinct subspecies of the eastern African crested rat, Lophiomys imhausi maremortum subspecies nova, which diverged from the modern eastern African populations in the lateMiddle Pleistocene ∼226,000 to 165,000 y ago. The reported paleomitogenome is the oldest so far in the Levant, opening the door for future paleo- DNA analyses in the region. Species distribution modeling points to the presence of continuous habitat corridors connecting eastern Africa with the Levant during the Last Interglacial ∼129,000 to 116,000 y ago, providing further evidence of the northern ingression of African biomes into Eurasia and reinforcing previous suggestions of the critical role of climate change in Late Pleistocene intercontinental biogeography. Furthermore, our study complements other paleoenvironmental proxies with local—instead of interregional— paleoenvironmental data, opening an unprecedented window into the Dead Sea rift paleolandscape.

Zootaxa came as a new and innovative publication medium for taxonomy, amidst a scenario of devaluation of this important biological science. After 20 years, it has ascertained itself as one of the main journals in animal taxonomy. However, the contribution of the journal to the taxonomy of Mammalia (mammals), one of the most studied groups of animals with a long-standing, dedicated spectrum of specialized journals (mammalogy), could have been expected as minor. All the current and former editors of the Mammalia section of Zootaxa analyzed the relative contribution of the journal to the description of new species of mammals since 2001. We also analyzed the contribution of Zootaxa by taxon, geographic origin of taxa, and geographic origin of first authors. The taxonomic methodology of authors in species description is described as well as the temporal trends in publications and publication subjects. We highlight the editors’ picks and eventually, the challenges for the future. We found that Zootaxa has had a significant contribution to mammalogy, being the second journal (the first being Journal of Mammalogy) in terms of number of new species described (76; 10.6% of the new mammalian species described between 2001 and 2020). The majority of the new species were described following an integrative taxonomic approach with at least two sources of data (86%). The analysis of published taxa, their geographic origin, and the country of origin of first authors shows a wide coverage and exhaustive representation, except for the species from the Nearctic. We conclude that Zootaxa has likely responded to a repressed demand for an additional taxonomic journal in mammalogy, with as possible appeals the absence of publication fees and an established publication speed. With 246 articles published in the past 20 years, the Mammalia section of Zootaxa embraces a large spectrum of systematic subjects going beyond alpha taxonomy. The challenges for the future are to encourage publications of authors from the African continent, still poorly represented, and from the palaeontology community, as the journal has been open to palaeontology since its early days.

The origins and evolution of the outstanding Neotropical biodiversity are still debated. A comprehensive understanding is hindered by the lack of deep-time comparative data across wide phylogenetic and ecological contexts. Here, we evaluate four evolutionary scenarios assuming different diversification trajectories and drivers of Neotropical diversification, and assess their variation across Neotropical regions and taxa. Our analysis of 150 phylogenies (12,512 species) of seed plants and tetrapods reveals that Neotropical diversity has mostly expanded through time (70% of the clades), while scenarios of saturated and declining diversity also account for 21% and 9% of Neotropical diversity, respectively. We identify five biogeographic areas that represent distinctive units of long-term Neotropical evolution (Pan-Amazonia, Dry Diagonal, Bahama-Antilles, Galapagos, and an ‘elsewhere’ region) and find that diversity dynamics do not differ across these areas, suggesting no geographic structure in long-term Neotropical diversification. In contrast, diversification dynamics differ substantially across taxa: plant diversity mostly expanded through time (88%), while a substantial fraction (43%) of tetrapod diversity accumulated at a slower pace or declined toward the present. These opposite evolutionary patterns may reflect different capacities for plants and tetrapods to cope with climate change, with potential implications for future adaptation and ecosystem resilience.

International audience; The West Indies are a natural laboratory for the study of biogeography and evolution, especially for mammals. The modality of their arrival in the Caribbean islands is a highly controversial issue, and palaeontological evidence remains particularly elusive. Lower Oligocene deposits of Puerto Rico (c. 29.5 Ma) have recently yielded the oldest archipelago rodents, with teeth of two chinchilloid caviomorphs of South American origin. Here we report the discovery of additional dental remains from the same level, testifying to the occurrence of another rodent group. Their morphology is singular but otherwise characteristic of North/Central American geomyin geomorphs (including extant kangaroo rats, pocket mice, and pocket gophers), and leads us to propose here a new taxon: Caribeomys merzeraudi gen. et sp. nov. The evidence of geomorphs in the West Indies challenges the view that all extinct and extant Antillean rodents derived from South American sources. The morphological singularity of this Puerto Rican geomorph also suggests an early split of this insular lineage from coeval mainland counterparts, and its dispersal towards the West Indies sometime around the Eocene–Oligocene transition. This unexpected rodent adds to the few cases of Antillean terrestrial vertebrates of North American origins, such as solenodonotan eulipotyphlans. In the absence of subaerial land connections between both landmasses, an overwater dispersal may explain mid-Palaeogene colonization of the West Indies by geomorph rodents.

New phylogenomic analyses of South American arboreal echimyids show that there are three species within the genus Toromys (T. grandis, T. rhipidurus, and T. sp. nov.) and that the genera Pattonomys and Toromys form a clade that is the sister group to the other three genera of arboreal Echimyini (Echimys, Makalata, and Phyllomys). The arboreal echimyid species Pattonomys occasius is deeply divergent from other species of Pattonomys and from members of other extant named genera, although it shares a sister relationship with Toromys. We erect a new genus, Leiuromys, for it. To clarify the relationships among the species within these three genera, we describe them with molecular and morphological characters. Because most members of these genera have never been reviewed or diagnosed at the species level, we do so now, and we describe a new species, Toromys albiventris, from the upper Ucayali basin of Peru. We illustrate taxa and morphological features not before figured in publications.

International audience; Wood mice of the genus Hylomyscus, are small-sized rodents widely distributed in lowland and montane rainforests in tropical Africa, where they can be locally abundant. Recent morphological and molecular studies have increased the number of recognized species from 8 to 18 during the last 15 years. We used complete mitochondrial genomes and five nuclear genes to infer the number of candidate species within this genus and depict its evolutionary history. In terms of gene sampling and geographical and taxonomic coverage, this is the most comprehensive review of the genus Hylomyscus to date. The six species groups (aeta, alleni, anselli, baeri, denniae and parvus) defined on morphological grounds are monophyletic. Species delimitation analyses highlight undescribed diversity within this genus: perhaps up to 10 taxa need description or elevation from synonymy, pending review of type specimens. Our divergence dating and biogeographical analyses show that diversification of the genus occurred after the end of the Miocene and is closely linked to the history of the African forest. The formation of the Rift Valley combined with the declining global temperatures during the Late Miocene caused the fragmentation of the forests and explains the first split between the denniae group and remaining lineages. Subsequently, periods of increased climatic instability during Plio-Pleistocene probably resulted in elevated diversification in both lowland and montane forest taxa.

International audience; Olfaction and thermoregulation are key functions for mammals. The former is critical to feeding, mating, and predator avoidance behaviors, while the latter is essential for homeothermy. Aquatic and amphibious mammals face olfactory and thermoregulatory challenges not generally encountered by terrestrial species. In mammals, the nasal cavity houses a bony system supporting soft tissues and sensory organs implicated in either olfactory or thermoregulatory functions. It is hypothesized that to cope with aquatic environments, amphibious mammals have expanded their thermoregulatory capacity at the expense of their olfactory system. We investigated the evolutionary history of this potential trade-off using a comparative dataset of three-dimensional (3D) CT scans of 189 skulls, capturing 17 independent transitions from a strictly terrestrial to an amphibious lifestyle across small mammals (Afrosoricida, Eulipotyphla, and Rodentia). We identified rapid and repeated loss of olfactory capacities synchronously associated with gains in thermoregulatory capacity in amphibious taxa sampled from across mammalian phylogenetic diversity. Evolutionary models further reveal that these convergences result from faster rates of turbinal bone evolution and release of selective constraints on the thermoregulatory-olfaction trade-off in amphibious species. Lastly, we demonstrated that traits related to vital functions evolved faster to the optimum compared to traits that are not related to vital functions.

International audience; The present 3D Dataset contains the 3D models described in "Comparative masticatory myology in anteaters and its implications for interpreting morphological convergence in myrmecophagous placentals".

International audience; Next generation sequencing (NGS) and genomic database mining allow biologists to gather and select large molecular datasets well suited to address phylogenomics and molecular evolution questions. Here we applied this approach to a mammal family, the Echimyidae, for which generic relationships have been difficult to recover and often referred to as a star phylogeny. These South-American spiny rats represent a family of caviomorph rodents exhibiting a striking diversity of species and life history traits. Using a NGS exon capture protocol, we isolated and sequenced ca. 500 nuclear DNA exons for 35 species belonging to all major echimyid and capromyid clades. Exons were carefully selected to encompass as much diversity as possible in terms of rate of evolution, heterogeneity in the distribution of site-variation and nucleotide composition. Supermatrix inferences and coalescence-based approaches were subsequently applied to infer this family’s phylogeny. The inferred topologies were the same for both approaches, and support was maximal for each node, entirely resolving the ambiguous relationships of previous analyses. Fast-evolving nuclear exons tended to yield more reliable phylogenies, as slower-evolving sequences were not informative enough to disentangle the short branches of the Echimyidae radiation. Based on this resolved phylogeny and on molecular and morphological evidence, we confirm the rank of the Caribbean hutias – formerly placed in the Capromyidae family – as Capromyinae, a clade nested within Echimyidae. We also name and define Carterodontinae, a new subfamily of Echimyidae, comprising the extant monotypic genus Carterodon from Brazil, which is the closest living relative of West Indies Capromyinae.

International audience; Anomaluroidea, commonly known as the “scaly-tailed squirrels,” are an emblematic group of tropical African mammals that includes gliding forms. The family Anomaluridae was until recently represented by three genera: the flying scaly-tailed squirrels (Anomalurus), the flying mouse (Idiurus) and the flightless scaly-tailed squirrels (Zenkerella). Idiurus and Zenkerella have long been grouped into the Zenkerellinae subfamily, and Zenkerella was interpreted as a rare case of evolutionary reversal to non-gliding lifestyle. Recent studies have demonstrated that Zenkerella is sister to all other modern anomalurids, and represents in fact the monogeneric family Zenkerellidae. The Anomalurus genus was split into Anomalurus and Anomalurops, but no study has ever considered all Anomalurus species together in a phylogeny to test the status of Anomalurops. Here, we used mitogenomic next-generation sequencing to infer the phylogenetic relationships among all extant anomalurids and to estimate their divergence ages. We found that the arboreal Zenkerella is the sister group of all extant gliding anomalurids (Idiurus and Anomalurus). We confirmed that Anomaluroidea only evolved the gliding adaptation once. A comparison based on morphological traits indicates that Zenkerella harbours several unique morphological features. We propose new morphological characters for the novel classification of modern Anomaluroidea, which includes the families Zenkerellidae and Anomaluridae. Using different calibration schemes, we demonstrated that classical dating methods relying only on mitogenomes provide rather young Miocene estimates between Zenkerellidae and the Anomaluridae. The use of published nuclear genes, internal calibrations and tip dating converged towards an Eocene split between gliding and non-gliding scaly-tailed squirrels, which is in agreement with the African fossil record. Finally, we provide the first exhaustive species-level molecular phylogenetic inference for the genus Anomalurus. We found that Anomalurus beecrofti is the sister group of all other species of Anomalurus and branched off during the Miocene.

Birds vary greatly in their life-history strategies, including their breeding systems, which range from brood parasitism to a system with multiple nonbreeding helpers at the nest. By far the most common arrangement, however, is where both parents participate in raising the young. The traits associated with parental care have been suggested to affect dispersal propensity and lineage diversification, but to date tests of this potential relationship at broad temporal and spatial scales have been limited. Here, using data from a globally distributed group of corvoid birds in concordance with state-dependent speciation and extinction models, we suggest that pair breeding is associated with elevated speciation rates. Estimates of transition between breeding systems imply that cooperative lineages frequently evolve biparental care, whereas pair breeders rarely become cooperative. We further highlight that these groups have differences in their spatial distributions, with pair breeders overrepresented on islands, and cooperative breeders mainly found on continents. Finally, we find that speciation rates appear to be significantly higher on islands compared to continents. These results imply that the transition from cooperative breeding to pair breeding was likely a significant contributing factor facilitating dispersal across tropical archipelagos, and subsequent world-wide phylogenetic expansion among the core Corvoidea.

The taxonomic position of Annandale's rat, Rattus annandalei (Bonhote, 1903), has been uncertain given its mix of Rattus-like and Sundamys-like morphological features. Annandale's rat and all described species in Sundamys (the lowland S. muelleri, and the montane S. maxi and S. infraluteus) are endemic to Sundaland, a center of diversification and endemism for their tribe, the Rattini. Using mitochondrial genomes and 3 nuclear markers (rag1, rbp3, ghr), we provide the 1st phylogenetic framework for Sundamys. We find that R. annandalei is nested within Sundamys, and that the 4 species likely diverged during the Pleistocene. We move R. annandalei to Sundamys and provide an emended diagnosis for Sundamys. Using geometric morphometric analyses of skulls and mandibles, we identify morphological differences between lowland and highland species of Sundamys that may be associated with adaptations to distinct diets., We are indebted to S. Morand, M. Pagès, J. Claude, and J. Michaux as the coordinators of the CERoPath project (French ANR Biodiversity, grant ANR 07 BDIV 012) and the BiodivHealthSEA project (www.biodivhealthsea.org) (French ANR CP&ES, grant ANR 11 CPEL 002). This research received support from the SYNTHESYS project (http://www.synthesys.info/) which is financed by the European Community Research Infrastructure Action under the FP7 Integrating Activities Program (SYNTHESYS ACCESS GB-TAF-2735, GB-TAF-5026, and GB-TAF-5737 granted to PHF to the NHM, London; NL-TAF-5588 granted to MCS to the NBC, Leiden). The Spanish Ministry of Science and Innovation grants CGL2010-21524 and CGL2014-58793-P also supported this work. MCS is supported by the Spanish Ministry of Science and Innovation Predoctoral Fellowship BES-2011-049186. PHF was funded by a Marie-Curie fellowship (PIOF-GA-2012-330582-CANARIP-RAT).

Murines are well known for their generalist diet, but several of them display specializations towards a carnivorous diet such as the amphibious Indo-Pacific water-rats. Despite the fact that carnivory evolved repeatedly in this group, few studies have investigated associated changes in jaw muscle anatomy and biomechanics. Here, we describe the jaw muscles and cranial anatomy of a carnivorous water-rat, Hydromys chrysogaster. The architecture of the jaw musculature of six specimens captured both on Obi and Papua were studied and described using dissections. We identified the origin and insertions of the jaw muscles, and quantified muscle mass, fiber length, physiological cross-sectional area, and muscle vectors for each muscle. Using a biomechanical model, we estimated maximum incisor and molar bite force at different gape angles. Finally, we conducted a 2D geometric morphometric analyses to compare jaw shape, mechanical potential, and diversity in lever-arm ratios for a set of 238 specimens, representative of Australo-Papuan carnivorous and omnivorous murids. Our study reveals major changes in the muscle proportions among Hydromys and its omnivorous close relative, Melomys. Hydromys was found to have large superficial masseter and temporalis muscles as well as a reduced deep masseter and zygomatico-mandibularis, highlighting major functional divergence among omnivorous and carnivorous murines. Changes in these muscles are also accompanied by changes in jaw shape and the lines of action of the muscles. A more vertically oriented masseter, reduced masseteric muscles, as well as an elongated jaw with proodont lower incisors are key features indicative of a reduced propalinality in carnivorous Hydromys. Differences in the fiber length of the masseteric muscles were also detected between Hydromys and Melomys, which highlight potential adaptations to a wide gape in Hydromys, allowing it to prey on larger animals. Using a biomechanical model, we inferred a greater bite force in Hydromys than in Melomys, implying a functional shift between omnivory and carnivory. However, Melomys has an unexpected greater bite force at large gape compared with Hydromys. Compared with omnivorous Melomys, Hydromys have a very distinctive low mandible with a well-developed coronoid process, and a reduced angular process that projects posteriorly to the ascending rami. This jaw shape, along with our mechanical potential and jaw lever ratio estimates, suggests that Hydromys has a faster jaw closing at the incisor, with a higher bite force at the level of the molars. The narrowing of the Hydromys jaw explains this higher lever advantage at the molars, which constitutes a good compromise between a wide gape, a reduced anterior masseteric mass, and long fiber lengths. Lever arms of the superficial and deep masseter are less favourable to force output of the mandible in Hydromys but more favourable to speed. Compared with the small input lever arm defined between the condyle and the angular process, the relatively longer mandible of Hydromys increases the speed at the expense of the output force. This unique combination of morphological features of the masticatory apparatus possibly has permitted Hydromys to become a highly successful amphibious predator in the Indo-Pacific region.

It is well established that the global expansion of songbirds (Oscines) originated in East Gondwana (present day Australo-Papua), and it has been postulated that one of the main constituent groups, the "core Corvoidea", with more than 750 species, originated in the first islands that emerged where New Guinea is now located. However, several polytomous relationships remained within the clade, obstructing detailed biogeographical interpretations. This study presents a well-resolved family-level phylogeny, based on a dataset of 22 nuclear loci and using a suite of partitioning schemes and Maximum Likelihood and Bayesian inference methods. Resolving the relationships within the core Corvoidea provides evidence for three well-supported main clades, which are in turn sister to the New Zealand genus Mohoua. Some monotypic lineages, which have previously been considered Incertae sedis, are also placed in a phylogenetic context. The well-resolved phylogeny provides a robust framework for biogeographical analyses, and provides further support for the hypothesis that core corvoids originated in the proto-Papuan island region that emerged north of Australia in the late Oligocene/early Miocene. Thus, the core Corvoidea appear to represent a true island radiation, which successfully colonized all continents except Antarctica.

We describe Halmaheramys bokimekot Fabre, Pages, Musser, Fitriana, Semiadi & Helgen gen. et sp. nov., a new genus and species of murine rodent from the North Moluccas, and study its phylogenetic placement using both molecular and morphological data. We generated a densely sampled mitochondrial and nuclear DNA data set that included most genera of Indo-Pacific Murinae, and used probabilistic methodologies to infer their phylogenetic relationships. To reconstruct their biogeographical history, we first dated the topology and then used a Lagrange analysis to infer ancestral geographic areas. Finally, we combined the ancestral area reconstructions with temporal information to compare patterns of murine colonization among Indo-Pacific archipelagos. We provide a new and comprehensive molecular phylogenetic reconstruction for Indo-Pacific Murinae, with a focus on the Rattus division. Using previous results and those presented in this study, we define a new Indo-Pacific group within the Rattus division, composed of Bullimus, Bunomys, Paruromys, Halmaheramys, Sundamys, and Taeromys. Our phylogenetic reconstructions revealed a relatively recent diversification from the Middle Miocene to Plio-Pleistocene associated with several major dispersal events. We identified two independent Indo-Pacific dispersal events from both western and eastern Indo-Pacific archipelagos to the isolated island of Halmahera, which led to the speciations of H. bokimekot gen. et sp. nov. and Rattus morotaiensis Kellogg, 1945. We propose that a Middle Miocene collision between the Halmahera and Sangihe arcs may have been responsible for the arrival of the ancestor of Halmaheramys to eastern Wallacea. Halmaheramys bokimekot gen. et sp. nov. is described in detail, and its systematics and biogeography are documented and illustrated. © 2013 The Linnean Society of London

Aim Islands and archipelagos have played an important role in the development of ecological and evolutionary theories. Using a newly compiled molecular phylogeny we infer the biogeographical history of a monarch flycatcher genus, Myiagra, which is distributed across the Indo-Pacific. We subsequently integrate biogeographical and ecomorphological data to examine the role of dispersal and trait evolution in the build-up of avian assemblages. Location Australia, the Moluccas, New Guinea and Pacific islands. Methods We generated a taxonomically densely sampled mitochondrial DNA dataset that included almost all species and subspecies of the reciprocally monophyletic genera Myiagra and Arses. We then used maximum likelihoood and Bayesian inference to infer their phylogenetic relationships. To reconstruct their biogeographical history, we first dated the tree topology and then used Lagrange to infer ancestral geographical areas. Finally, we combined ancestral area reconstructions with information on ecomorphological traits to infer mechanisms underlying community assembly. Results We provide the first comprehensive molecular phylogenetic reconstruction for Myiagra and Arses monarch flycatchers. Our phylogenetic reconstruction reveals a relatively recent diversification from the Miocene associated with several major dispersal events. Ancestral area reconstruction reveals several independent colonizations of the Moluccas, Melanesia, Fiji and the Micronesian islands. Ancestral state reconstruction of ecological traits suggests that the diversity of traits in co-occurring species of monarch flycatchers results from independent colonization events and ecological niche conservatism rather than in situ diversification. Main conclusions Three waves of colonization, non-overlapping in time, led to independent speciation events in the Bismarcks, Fiji and the Moluccas, in addition to in situ speciation events on remote islands of Micronesia, the Solomons, Vanuatu and Samoa. Few of these colonizations have led to the co-occurrence of congenerics or species with similar ecomorphological profiles on the same island. Thus, we suggest that priority effects might prevent new colonizers from establishing themselves if they share high levels of ecological similarity with resident species. We conclude that historical dispersal to and colonization of new islands, combined with ecologically deterministic priority effects, drove the assembly of insular monarch flycatcher communities across the Indo-Pacific.

We construct a molecular phylogeny of Terpsiphone flycatchers of the Indian Ocean and use this to investigate their evolutionary relationships. A total of 4.4 kb of mitochondrial (cyt-b, ND3, ND2, control region) and nuclear (G3PDH, MC1R) sequence data were obtained from all species, sub-species and island populations of the region. Colonisation of the western Indian Ocean has been within the last two million years and greatly postdates the formation of the older islands of the region. A minimum of two independent continent-island colonisation events must have taken place in order to explain the current distribution and phylogenetic placement of Terpsiphone in this region. While five well-diverged Indian Ocean clades are detected, the relationship between them is unclear. Short intermodal branches are indicative of rapid range expansion across the region, masking exact routes and chronology of colonisation. The Indian Ocean Terpsiphone taxa fall into five well supported clades, two of which (the Seychelles paradise flycatcher and the Mascarene paradise flycatcher) correspond with currently recognised species, whilst a further three (within the Madagascar paradise flycatcher) are not entirely predicted by taxonomy, and are neither consistent with distance-based nor island age-based models of colonisation. We identify the four non-Mascarene clades as Evolutionarily Significant Units (ESUs), while the Mascarene paradise flycatcher contains two ESUs corresponding to the Mauritius and Réunion subspecies. All six ESUs are sufficiently diverged to be worthy of management as if they were separate species. This phylogenetic reconstruction highlights the importance of sub-specific molecular phylogenetic reconstructions in complex island archipelago settings in clarifying phylogenetic history and ESUs that may otherwise be overlooked and inadvertently lost. Our phylogenetic reconstruction has identified hidden pockets of evolutionary distinctiveness, which provide a valuable platform upon which to re-evaluate investment of conservation resources within the Terpsiphone flycatchers of the Indian Ocean.

We describe a new species of masked-owl from the lower montane forestof Seram, one of the largest islands in the Moluccasof eastern Indonesia, for which we propose the name Tyto almae (Seram Masked-Owl), sp. nov. Molecular (mitochondrial cyt-b) differences show that Tyto sororcula of Buru and Tanimbar is closely related to T. novaehollandiae of Australia and New Guinea (~1% uncorrected pairwise distance), and that Tyto almae of Seram differs by ~3% (uncorrected pairwise distance) from both of them. These differences are further corroborated by morphology and colouration. Although a photograph from Seram published in 1987 had already established the presence of a Tyto owl on the island, ours represents the first specimen of this species. The bird was mist-netted in wet, mossy lower montane forest at an elevation of 1,350 m. No further observations of the owl were made during four weeks of fieldwork in Seram.

International audience; Echimyidae is one of the most speciose and ecologically diverse rodent families in the world, occupying a wide range of habitats in the Neotropics. However, a resolved phylogeny at the genus-level is still lacking for these 22 genera of South American spiny rats, including the coypu (Myocastorinae), and 5 genera of West Indian hutias (Capromyidae) relatives. Here, we used Illumina shotgun sequencing to assemble 38 new complete mitogenomes, establishing Echimyidae, and Capromyidae as the first major rodent families to be completely sequenced at the genus-level for their mitochondrial DNA. Combining mitogenomes and nuclear exons, we inferred a robust phylogenetic framework that reveals several newly supported nodes as well as the tempo of the higher level diversification of these rodents. Incorporating the full generic diversity of extant echimyids leads us to propose a new higher level classification of two subfamilies: Euryzygomatomyinae and Echimyinae. Of note, the enigmatic Carterodon displays fast-evolving mitochondrial and nuclear sequences, with a long branch that destabilizes the deepest divergences of the echimyid tree, thereby challenging the sister-group relationship between Capromyidae and Euryzygomatomyinae. Biogeographical analyses involving higher level taxa show that several vicariant and dispersal events impacted the evolutionary history of echimyids. The diversification history of Echimyidae seems to have been influenced by two major historical factors, namely (1) recurrent connections between Atlantic and Amazonian Forests and (2) the Northern uplift of the Andes.

Next-Generation Biogeography In 1876, Alfred Russel Wallace mapped the zoogeographical regions of the world, based on the distributions and taxonomic relationships of broadly defined mammalian families. Wallace's classification of zoogeographical regions became a cornerstone of modern biogeography and a reference for a wide variety of biological disciplines, including global biodiversity and conservation sciences. Holt et al. (p. 74 , published online 20 December) present a next-generation map of wallacean zoogeographic regions, incorporating phylogenetic data on >20,000 vertebrate species to discern and characterize their natural biogeographic patterns.

Gibbon ape leukemia virus (GALV) and koala retrovirus (KoRV) most likely originated from a cross-species transmission of an ancestral retrovirus into koalas and gibbons via one or more intermediate as-yet-unknown hosts. A virus highly similar to GALV has been identified in an Australian native rodent ( Melomys burtoni ) after extensive screening of Australian wildlife. GALV-like viruses have also been discovered in several Southeast Asian species, although screening has not been extensive and viruses discovered to date are only distantly related to GALV. We therefore screened 26 Southeast Asian rodent species for KoRV- and GALV-like sequences, using hybridization capture and high-throughput sequencing, in the attempt to identify potential GALV and KoRV hosts. Only the individuals belonging to a newly discovered subspecies of Melomys burtoni from Indonesia were positive, yielding an endogenous provirus very closely related to a strain of GALV. The sequence of the critical receptor domain for GALV infection in the Indonesian M. burtoni subsp. was consistent with the susceptibility of the species to GALV infection. The second record of a GALV in M. burtoni provides further evidence that M. burtoni , and potentially other lineages within the widespread subfamily Murinae , may play a role in the spread of GALV-like viruses. The discovery of a GALV in the most western part of the Australo-Papuan distribution of M. burtoni , specifically in a transitional zone between Asia and Australia (Wallacea), may be relevant to the cross-species transmission to gibbons in Southeast Asia and broadens the known distribution of GALVs in wild rodents. IMPORTANCE Gibbon ape leukemia virus (GALV) and the koala retrovirus (KoRV) are very closely related, yet their hosts neither are closely related nor overlap geographically. Direct cross-species infection between koalas and gibbons is unlikely. Therefore, GALV and KoRV may have arisen via a cross-species transfer from an intermediate host whose range overlaps those of both gibbons and koalas. Using hybridization capture and high-throughput sequencing, we have screened a wide range of rodent candidate hosts from Southeast Asia for KoRV- and GALV-like sequences. Only a Melomys burtoni subspecies from Wallacea (Indonesia) was positive for GALV. We report the genome sequence of this newly identified GALV, the critical domain for infection of its potential cellular receptor, and its phylogenetic relationships with the other previously characterized GALVs. We hypothesize that Melomys burtoni , and potentially related lineages with an Australo-Papuan distribution, may have played a key role in cross-species transmission to other taxa.

Fabre, P.-H., Galewski, T., Tilak, M.-k. & Douzery, E.J.P. (2012) Diversification of South American spiny rats (Echimyidae): a multigene phylogenetic approach. —Zoologica Scripta, 00, 000‐000. We investigated the phylogenetic relationships of 14 Echimyidae (spiny rats), one Myocastoridae (nutrias) and one Capromyidae (hutias) genera based on three newly sequenced nuclear genes (APOB, GHR and RBP3) and five previously published markers (the nuclear RAG1 and vWF, and the mitochondrial cytochrome b, 12S rRNA and 16S rRNA). We recovered a well-supported phylogeny within the Echimyidae, although the evolutionary relationships among arboreal echimyid taxa remain unresolved. Molecular divergence times estimated using a Bayesian relaxed molecular clock suggest a Middle Miocene origin for most of the extant echimyid genera. Echimyidae seems to constitute an example of evolutionary radiation with high species diversity, yet they exhibit only narrow skull morphological changes, and the arboreal and terrestrial taxa are shown to retain numerous plesiomorphic features. The most recent common ancestor of spiny rats is inferred to be a ground-dwelling taxon that has subsequently diverged into fossorial, semiaquatic and arboreal habitats. The arboreal clade polytomy and ancestral character estimations suggest that the colonization of the arboreal niche constituted the keystone event of the echimyid radiation. However, biogeographical patterns suggest a strong influence of allopatric speciation in addition to ecology-driven diversification among South American spiny rats.

Aim We use parametric biogeographical reconstruction based on an extensive DNA sequence dataset to characterize the spatio‐temporal pattern of colonization of the Old World monarch flycatchers (Monarchidae). We then use this framework to examine the role of dispersal and colonization in their evolutionary diversification and to compare plumages between island and continental Terpsiphone species. Location Africa, Asia and the Indian Ocean. Methods We generate a DNA sequence dataset of 2300 bp comprising one nuclear and three mitochondrial markers for 89% (17/19) of the Old World Monarchidae species and 70% of the Terpsiphone subspecies. By applying maximum likelihood and Bayesian phylogenetic methods and implementing a Bayesian molecular clock to provide a temporal framework, we reveal the evolutionary history of the group. Furthermore, we employ both Lagrange and Bayes‐Lagrange analyses to assess ancestral areas at each node of the phylogeny. By combining the ancestral area reconstruction with information on plumage traits we are able to compare patterns of plumage evolution on islands and continents. Results We provide the first comprehensive molecular phylogenetic reconstruction for the Old World Monarchidae. Our phylogenetic results reveal a relatively recent diversification associated with several dispersal events within this group. Moreover, ancestral area analyses reveal an Asian origin of the Indian Ocean and African clades. Ancestral state reconstruction analyses of plumage characters provide an interpretation of the plumage differentiation on islands and continents. Ancestral plumage traits are inferred to be close to those of the Asian paradise‐flycatcher (Terpsiphone paradisi), and island species display a high degree of plumage autapomorphy compared with continental species. Main conclusions Terpsiphone paradisi is polyphyletic and comprises populations that have retained the ancestral plumage of the widespread Terpsiphone genus. The genus appears to have colonized south‐west Asia, the Indian Ocean and Africa from eastern Asia. The phylogeny and divergence time estimates indicate multiple simultaneous colonizations of the western Old World by Terpsiphone. These results reinforce a hypothesis of range expansions of a Terpsiphone paradisi‐like ancestor into eastern Asia and the western Old World.

Adaptive radiation is the rapid diversification of a single lineage into many species that inhabit a variety of environments or use a variety of resources and differ in traits required to exploit these. Why some lineages undergo adaptive radiation is not well-understood, but filling unoccupied ecological space appears to be a common feature. We construct a complete, dated, species-level phylogeny of the endemic Vangidae of Madagascar. This passerine bird radiation represents a classic, but poorly known, avian adaptive radiation. Our results reveal an initial rapid increase in evolutionary lineages and diversification in morphospace after colonizing Madagascar in the late Oligocene some 25 Mya. A subsequent key innovation involving unique bill morphology was associated with a second increase in diversification rates about 10 Mya. The volume of morphospace occupied by contemporary Madagascan vangas is in many aspects as large (shape variation)—or even larger (size variation)—as that of other better-known avian adaptive radiations, including the much younger Galapagos Darwin's finches and Hawaiian honeycreepers. Morphological space bears a close relationship to diet, substrate use, and foraging movements, and thus our results demonstrate the great extent of the evolutionary diversification of the Madagascan vangas.

International audience; Recent phylogenetic studies and taxonomic reviews have led to nearly complete resolution of the phylogenetic divisions within the old world rats and mice (Muridae, Murinae). The Micromys division and Pithecheir division are two notable exceptions where groupings of species into these divisions based on morphology and arboreal lifestyle have not been supported by phylogenetic evidence. Several enigmatic species from these divisions have been missing from molecular studies, preventing a rigorous revision of phylogenetic relationships. In this study, we sequenced for the first time one mitochondrial and three nuclear genes from South-East Asian keystone species of these two arboreal divisions: Hapalomys delacouri (Micromys division), Lenothrix canus and Pithecheir parvus (Pithecheir division). We also complemented the molecular data already available for the two divisions with new data from Sundaic Chiropodomys, Indian Vandeleuria oleracea and the recently described Sulawesian Margaretamys christinae. Using this new phylogenetic framework and molecular dating methodologies, our study allows some more detailed classification of the former Micromys and Pithecheir divisions, while confirming their polyphyletic status. Specifically, the former Micromys division should now be split into four monotypic divisions: Chiropodomys, Hapalomys, Micromys and Vandeleuria divisions. The former Pithecheir division is likely to be refined and restricted to Pithecheir and probably Pithecheirops, whereas Lenothrix and Margaretamys should now be recognized as representatives of the Dacnomys division. Our findings have profound implications with regard to the systematics of Murinae, as well as to the early evolution of murine morphology and dental characters.

We describe a new species of masked-owl from the lower montane forest of Seram, one of the largest islands in the Moluccas of eastern Indonesia, for which we propose the name Tyto almae (Seram Masked-Owl), sp. nov. Molecular (mitochondrial cyt-b) differences show that Tyto sororcula of Buru and Tanimbar is closely related to T novaehollandiae of Australia and New Guinea (-1% uncorrected pairwise distance), and that Tyto almae of Seram differs by -3% (uncorrected pairwise distance) from both of them. These differences are further corroborated by morphology and colouration. Although a photograph from Seram published in 1987 had already established the presence of a Tyto owl on the island, ours represents the first specimen of this species. The bird was mist-netted in wet, mossy lower montane forest at an elevation of 1,350 m. No further observations of the owl were made during four weeks of fieldwork in Seram.

The Corvides (previously referred to as the core Corvoidea) are a morphologically diverse clade of passerine birds comprising nearly 800 species. The group originated some 30 million years ago in the proto-Papuan archipelago, to the north of Australia, from where lineages have dispersed and colonized all of the world's major continental and insular landmasses (except Antarctica). During the last decade multiple species-level phylogenies have been generated for individual corvoid families and more recently the inter-familial relationships have been resolved, based on phylogenetic analyses using multiple nuclear loci. In the current study we analyse eight nuclear and four mitochondrial loci to generate a dated phylogeny for the majority of corvoid species. This phylogeny includes 667 out of 780 species (85.5%), 141 out of 143 genera (98.6%) and all 31 currently recognized families, thus providing a baseline for comprehensive macroecological, macroevolutionary and biogeographical analyses. Using this phylogeny we assess the temporal consistency of the current taxonomic classification of families and genera. By adopting an approach that enforces temporal consistency by causing the fewest possible taxonomic changes to currently recognized families and genera, we find the current familial classification to be largely temporally consistent, whereas that of genera is not.

Birds vary greatly in their life-history strategies, including their breeding systems, which range from brood parasitism to a system with multiple nonbreeding helpers at the nest. By far the most common arrangement, however, is where both parents participate in raising the young. The traits associated with parental care have been suggested to affect dispersal propensity and lineage diversification, but to date tests of this potential relationship at broad temporal and spatial scales have been limited. Here, using data from a globally distributed group of corvoid birds in concordance with state-dependent speciation and extinction models, we suggest that pair breeding is associated with elevated speciation rates. Estimates of transition between breeding systems imply that cooperative lineages frequently evolve biparental care, whereas pair breeders rarely become cooperative. We further highlight that these groups have differences in their spatial distributions, with pair breeders overrepresented on islands, and cooperative breeders mainly found on continents. Finally, we find that speciation rates appear to be significantly higher on islands compared to continents. These results imply that the transition from cooperative breeding to pair breeding was likely a significant contributing factor facilitating dispersal across tropical archipelagos, and subsequent world-wide phylogenetic expansion among the core Corvoidea.

We inferred the phylogenetic relationships, divergence time and biogeography of Conopophagidae (gnateaters) based on sequence data of mitochondrial genes (ND2, ND3 and cytb) and nuclear introns (TGFB2 and G3PDH) from 45 tissue samples (43 Conopophaga and 2 Pittasoma) representing all currently recognized species of the family and the majority of subspecies. Phylogenetic relationships were estimated by maximum likelihood and Bayesian inference. Divergence time estimates were obtained based on a Bayesian relaxed clock model. These chronograms were used to calculate diversification rates and reconstruct ancestral areas of the genus Conopophaga. The phylogenetic analyses support the reciprocal monophyly of the two genera, Conopophaga and Pittasoma. All species were monophyletic with the exception of C. lineata, as C. lineata cearae did not cluster with the other two C. lineata subspecies. Divergence time estimates for Conopophagidae suggested that diversification took place during the Neogene, and that the diversification rate within Conopophaga clade was highest in the late Miocene, followed by a slower diversification rate, suggesting a diversity-dependent pattern. Our analyses of the diversification of family Conopophagidae provided a scenario for evolution in Terra Firme forest across tropical South America. The spatio-temporal pattern suggests that Conopophaga originated in the Brazilian Shield and that a complex sequence of events possibly related to the Andean uplift and infilling of former sedimentation basins and erosion cycles shaped the current distribution and diversity of this genus.

Kreft and Jetz’s critique of our recent update of Wallace’s zoogeographical regions disregards the extensive sensitivity analyses we undertook, which demonstrate the robustness of our results to the choice of phylogenetic data and clustering algorithm. Their suggested distinction between “transition zones” and biogeographic regions is worthy of further investigation but is thus far unsubstantiated.

An RNA-Seq strategy was used to obtain the complete set of protein-coding mitochondrial genes from two rodent taxa. Thanks to the next generation sequencing (NGS) 454 approach, we determined the complete mitochondrial DNA genome from Graphiurus kelleni (Mammalia: Rodentia: Gliridae) and partial mitogenome from Pedetes capensis (Pedetidae), and compared them with published rodent and outgroup mitogenomes. We finished the mitogenome sequencing by a series of amplicons using conserved PCR primers to fill the gaps corresponding to tRNA, rRNA and control regions. Phylogenetic analyses of the mitogenomes suggest a well-supported rodent phylogeny in agreement with nuclear gene trees. Pedetes groups with Anomalurus into the clade Anomaluromorpha, while Graphiurus branches within the squirrel-related clade. Moreover, Pedetes+Anomalurus branch with Castor into the mouse-related clade. Our study demonstrates the utility of NGS for obtaining new mitochondrial genomes as well as the importance of choosing adequate models of sequence evolution to infer the phylogeny of rodents.

There is much evidence to support past contact between the Atlantic and the Amazon forests through the South American dry vegetation diagonal, but the spatiotemporal dynamics of this contact still need to be investigated to allow a better understanding of its biogeographic implications for birds. Here, we combined phylogenetic data with distributional data using a supermatrix approach in order to depict the historical connection dynamics between these biomes for New World suboscines. We examined the variation in divergence time and then compared the spatial distributions of taxon pairs representing old and recent divergences. Our results pointed to two distinct spatiotemporal pathways connecting the Atlantic and the Amazonian forests in the past: (1) old connections (middle to late Miocene) through the current southern Cerrado and Mato Grosso and the transition towards the Chaco and palm savannas of Bolivia and Paraguay; (2) young connections (Pliocene to Pleistocene) that possibly occurred through the Cerrado and Caatinga in northeastern Brazil. We suggest that the main events that played important roles in these connections were geotectonic events during the late Tertiary associated with the uplift of the Andes (old connections) and Quaternary climate changes that promoted the expansion of gallery forest through the Cerrado and Caatinga in northeastern Brazil (young connections). Our results provide the first general temporal and spatial model of how the Atlantic and Amazonian forests were connected in the past, which was derived using bird data.

Background Development of phylogenetic methods that do not rely on fossils for the study of evolutionary processes through time have revolutionized the field of evolutionary biology and resulted in an unprecedented expansion of our knowledge about the tree of life. These methods have helped to shed light on the macroevolution of many taxonomic groups such as the placentals (Mammalia). However, despite the increase of studies addressing the diversification patterns of organisms, no synthesis has addressed the case of the most diversified mammalian clade: the Rodentia. Results Here we present a rodent maximum likelihood phylogeny inferred from a molecular supermatrix. It is based on 11 mitochondrial and nuclear genes that covers 1,265 species, i.e., respectively 56% and 81% of the known specific and generic rodent diversity. The inferred topology recovered all Rodentia clades proposed by recent molecular works. A relaxed molecular clock dating approach provided a time framework for speciation events. We found that the Myomorpha clade shows a greater degree of variation in diversification rates than Sciuroidea, Caviomorpha, Castorimorpha and Anomaluromorpha. We identified a number of shifts in diversification rates within the major clades: two in Castorimorpha, three in Ctenohystrica, 6 within the squirrel-related clade and 24 in the Myomorpha clade. The majority of these shifts occurred within the most recent familial rodent radiations: the Cricetidae and Muridae clades. Using the topological imbalances and the time line we discuss the potential role of different diversification factors that might have shaped the rodents radiation. Conclusions The present glimpse on the diversification pattern of rodents can be used for further comparative meta-analyses. Muroid lineages have a greater degree of variation in their diversification rates than any other rodent group. Different topological signatures suggest distinct diversification processes among rodent lineages. In particular, Muroidea and Sciuroidea display widespread distribution and have undergone evolutionary and adaptive radiation on most of the continents. Our results show that rodents experienced shifts in diversification rate regularly through the Tertiary, but at different periods for each clade. A comparison between the rodent fossil record and our results suggest that extinction led to the loss of diversification signal for most of the Paleogene nodes.

Background Crows and ravens (Passeriformes: Corvus) are large-brained birds with enhanced cognitive abilities relative to other birds. They are among the few non-hominid organisms on Earth to be considered intelligent and well-known examples exist of several crow species having evolved innovative strategies and even use of tools in their search for food. The 40 Corvus species have also been successful dispersers and are distributed on most continents and in remote archipelagos. Results This study presents the first molecular phylogeny including all species and a number of subspecies within the genus Corvus. We date the phylogeny and determine ancestral areas to investigate historical biogeographical patterns of the crows. Additionally, we use data on brain size and a large database on innovative behaviour and tool use to test whether brain size (i) explains innovative behaviour and success in applying tools when foraging and (ii) has some correlative role in the success of colonization of islands. Our results demonstrate that crows originated in the Palaearctic in the Miocene from where they dispersed to North America and the Caribbean, Africa and Australasia. We find that relative brain size alone does not explain tool use, innovative feeding strategies and dispersal success within crows. Conclusions Our study supports monophyly of the genus Corvus and further demonstrates the direction and timing of colonization from the area of origin in the Palaearctic to other continents and archipelagos. The Caribbean was probably colonized from North America, although some North American ancestor may have gone extinct, and the Pacific was colonized multiple times from Asia and Australia. We did not find a correlation between relative brain size, tool use, innovative feeding strategies and dispersal success. Hence, we propose that all crows and ravens have relatively large brains compared to other birds and thus the potential to be innovative if conditions and circumstances are right.