Springhares, flying and flightless scaly-tailed squirrels (Anomaluromorpha, Rodentia) are the squirrely mouse: comparative anatomy of the masticatory musculature and its implications on the evolution of hystricomorphy in rodents.

Anomaluromorpha is a particularly puzzling suborder of Rodentia. Endemic to Africa, this clade includes the extant genera Idiurus, Anomalurus, Zenkerella, and Pedetes. These rodents present an hystricomorphous condition of the skull, characterized by a large infraorbital foramen, which evolved independently within the mouse-related clade over a span of approximately 57 million years. They exhibit a high disparity in craniomandibular and dental morphology that has kept their phylogenetic affinities disputed for a long time. Given the past significance of masticatory morphotypes in establishing the classification of Rodentia, we propose to explore variations in the masticatory apparatus of Anomaluromorpha in order to evaluate whether its related features can offer additional data for systematics and contribute to our understanding of the complexity of hystricomorphy. In order to do so, we used traditional dissection and diffusible iodine-based contrast-enhanced computed tomography (diceCT) to accurately describe and compare the anatomy of the specimens. We found that the muscle morphology displays clear differentiation among each anomaluromorph taxonomic unit. Specifically, the masseteric complex of Anomaluromorpha exhibits distinctive synapomorphies such as the infraorbital part of the zygomaticomandibularis muscle being separated into a rostral and orbital part and an absence of a posterior part of the zygomaticomandibularis. Additionally, the orbital portion of the infraorbital part originates from a well-marked ridge and fossa at the level of its area of origin on the anteromedial wall of the orbital cavity, a feature that is absent in other members of the mouse-related clade. This evident bony feature, among others, is strongly associated with muscular anatomy and can contribute to ascertaining the taxonomic status of extinct representatives of the clade. Finally, we showed that the hystricomorphy of Anomaluromorpha largely differs from those of Ctenohystrica and Dipodoidea and that the definition of this morphotype is complex and cannot be reduced simply to the size of the opening of the infraorbital foramen.

Rare crested rat subfossils unveil Afro-Eurasian ecological corridors synchronous with early human dispersals.

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 late Middle Pleistocene ∼226,000 to 165,000 y ago. The reported paleomitogenome is the oldest so far in the Levant, opening the door for future paleoDNA 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.

When morphology does not fit the genomes: the case of rodent olfaction.

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.

Convergent evolution of olfactory and thermoregulatory capacities in small amphibious mammals.

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.

The phylogeny of the African wood mice (Muridae, Hylomyscus) based on complete mitochondrial genomes and five nuclear genes reveals their evolutionary history and undescribed diversity.

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.

Digging for the spiny rat and hutia phylogeny using a gene capture approach, with the description of a new mammal subfamily.

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.

Mitogenomic Phylogeny, Diversification, and Biogeography of South American Spiny Rats.

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.

Endogenous Gibbon Ape Leukemia Virus Identified in a Rodent (Melomys burtoni subsp.) from Wallacea (Indonesia).

UNLABELLED: 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.

A supermatrix phylogeny of corvoid passerine birds (Aves: Corvides).

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.

Ecological and evolutionary determinants for the adaptive radiation of the Madagascan vangas.

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.

Resolving deep lineage divergences in core corvoid passerine birds supports a proto-Papuan island origin.

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.

Phylogeny and historical biogeography of gnateaters (Passeriformes, Conopophagidae) in the South America forests.

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.

Rodents of the Caribbean: origin and diversification of hutias unravelled by next-generation museomics.

The Capromyidae (hutias) are endemic rodents of the Caribbean and represent a model of dispersal for non-flying mammals in the Greater Antilles. This family has experienced severe extinctions during the Holocene and its phylogenetic affinities with respect to other caviomorph relatives are still debated as morphological and molecular data disagree. We used target enrichment and next-generation sequencing of mitochondrial and nuclear genes to infer the phylogenetic relationships of hutias, estimate their divergence ages, and understand their mode of dispersal in the Greater Antilles.We found that Capromyidae are nested within Echimyidae (spiny rats) and should be considered a subfamily thereof. We estimated that the split between hutias and Atlantic Forest spiny rats occurred 16.5 (14.8­18.2) million years ago (Ma), which is more recent than the GAARlandia land bridge hypothesis (34­35 Ma). This would suggest that during the Early Miocene, an echimyid-like ancestor colonized the Greater Antilles from an eastern South American source population via rafting. The basal divergence of the Hispaniolan Plagiodontia provides further support for a vicariant separation between Hispaniolan and western islands (Bahamas, Cuba, Jamaica) hutias. Recent divergences among these western hutias suggest Plio-Pleistocene dispersal waves associated with glacial cycles.

Major global radiation of corvoid birds originated in the proto-Papuan archipelago.

A central paradigm in island biogeography has been the unidirectional "downstream" colonization of islands from continents (source to sink) based on the idea that less-diverse island communities are easier to invade than biologically more-diverse continental communities. Recently, several cases of "upstream" colonization (from islands to continents) have been documented, challenging the traditional view. However, all these cases have involved individual island species that have colonized mainland regions. Here, using molecular phylogenetic data, divergence time estimates, lineage diversity distributions, and ancestral area analyses, we reconstruct the spread of a species-rich (>700 species) passerine bird radiation (core Corvoidea) from its late Eocene/Oligocene origin in the emerging proto-Papuan archipelago north of Australia, including multiple colonizations from the archipelago to Southeast Asia. Thus, islands apparently provided the setting for the initiation of a major songbird radiation that subsequently invaded all other continents. Morphological and behavioral adaptations of the core Corvoidea as generalist feeders in open habitats, which facilitated dispersal and colonization, apparently evolved in the descendants of sedentary forest birds that invaded the proto-Papuan archipelago. The archipelago evidently provided islands of the right size, number, and proximity to continental areas to support the adaptation and diversification of vagile colonizers that went on to increase avian diversity on a global scale.

Turbinal bones are still one of the last frontiers of the tetrapod skull: hypotheses, challenges and perspectives.

Turbinals are bony or cartilaginous structures that are present in the nasal cavity of most tetrapods. They are involved in key functions such as olfaction, heat, and moisture conservation, as well as protection of the respiratory tract. Despite recent studies that challenged long-standing hypotheses about their physiological and genomic correlation, turbinals remain largely unexplored, particularly for non-mammalian species. Herein, we review and synthesise the current knowledge of turbinals using an integrative approach that includes comparative anatomy, physiology, histology and genomics. In addition, we provide synonyms and correspondences of tetrapod turbinals from about 80 publications. This work represents a first step towards drawing hypotheses of homology for the whole clade, and provides a strong basis to develop new research avenues.

Disparity of turbinal bones in placental mammals.

Turbinals are key bony elements of the mammalian nasal cavity, involved in heat and moisture conservation as well as olfaction. While turbinals are well known in some groups, their diversity is poorly understood at the scale of placental mammals, which span 21 orders. Here, we investigated the turbinal bones and associated lamellae for one representative of each extant order of placental mammals. We segmented and isolated each independent turbinal and lamella and found an important diversity of variation in the number of turbinals, as well as their size, and shape. We found that the turbinal count varies widely, from zero in the La Plata dolphin, (Pontoporia blainvillei) to about 110 in the African bush elephant (Loxodonta africana). Multiple turbinal losses and additional gains took place along the phylogeny of placental mammals. Some changes are clearly attributed to ecological adaptation, while others are probably related to phylogenetic inertia. In addition, this work highlights the problem of turbinal nomenclature in some placental orders with numerous and highly complex turbinals, for which homologies are extremely difficult to resolve. Therefore, this work underscores the importance of developmental studies to better clarify turbinal homology and nomenclature and provides a standardized comparative framework for further research.

The spatio-temporal colonization and diversification across the Indo-Pacific by a 'great speciator' (Aves, Erythropitta erythrogaster).

The Indo-Pacific region has arguably been the most important area for the formulation of theories about biogeography and speciation, but modern studies of the tempo, mode and magnitude of diversification across this region are scarce. We study the biogeographic history and characterize levels of diversification in the wide-ranging passerine bird Erythropitta erythrogaster using molecular, phylogeographic and population genetics methods, as well as morphometric and plumage analyses. Our results suggest that E. erythrogaster colonized the Indo-Pacific during the Pleistocene in an eastward direction following a stepping stone pathway, and that sea-level fluctuations during the Pleistocene may have promoted gene flow only locally. A molecular species delimitation test suggests that several allopatric island populations of E. erythrogaster may be regarded as species. Most of these putative new species are further characterized by diagnostic differences in plumage. Our study reconfirms the E. erythrogaster complex as a 'great speciator': it represents a complex of up to 17 allopatrically distributed, reciprocally monophyletic and/or morphologically diagnosable species that originated during the Pleistocene. Our results support the view that observed latitudinal gradients of genetic divergence among avian sister species may have been affected by incomplete knowledge of taxonomic limits in tropical bird species.

Molecular phylogeny of the Indian Ocean Terpsiphone paradise flycatchers: undetected evolutionary diversity revealed amongst island populations.

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.

A new species of masked-owl (Aves: Strigiformes: Tytonidae) from Seram, Indonesia.

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.

Phylogeny, Ecology, and Gene Families Covariation Shaped the Olfactory Subgenome of Rodents.

Olfactory receptor (OR) genes represent the largest multigenic family in mammalian genomes and encode proteins that bind environmental odorant molecules. The OR repertoire is extremely variable among species and is subject to many gene duplications and losses, which have been linked to ecological adaptations in mammals. Although they have been studied on a broad taxonomic scale (i.e., placental), finer sampling has rarely been explored in order to better capture the mechanisms that drove the evolution of the OR repertoire. Among placental mammals, rodents are well-suited for this task, as they exhibit diverse life history traits, and genomic data are available for most major families and a diverse array of lifestyles. In this study, 53 rodent published genomes were mined for their OR subgenomes. We retrieved more than 85,000 functional and pseudogene OR sequences that were subsequently classified into phylogenetic clusters. Copy number variation among rodents is similar to that of other mammals. Using our OR counts along with comparative phylogenetic approaches, we demonstrated that ecological niches such as diet, period of activity, and a fossorial lifestyle strongly impacted the proportion of OR pseudogenes. Within the OR subgenome, phylogenetic inertia was the main factor explaining the relative variations of the 13 OR gene families. However, a striking exception was a convergent 10-fold expansion of the OR family 14 among the phylogenetically divergent subterranean mole-rat lineages belonging to Bathyergidae and Spalacidae families. This study illustrates how the diversity of the OR repertoire has evolved among rodents, both shaped by selective forces stemming from species life history traits and neutral evolution along the rodent phylogeny.