Evolution of gene expression across brain regions in behaviourally divergent deer mice

The evolution of innate behaviours is ultimately due to genetic variation likely acting in the nervous system. Gene regulation may be particularly important because it can evolve in a modular brain-region specific fashion through the concerted action of cis- and trans-regulatory changes. Here, to investigate transcriptional variation and its regulatory basis across the brain, we perform RNA sequencing (RNA-Seq) on ten brain subregions in two sister species of deer mice (Peromyscus maniculatus and P. polionotus)-which differ in a range of innate behaviours, including their social system-and their F1 hybrids. We find that most of the variation in gene expression distinguishes subregions, followed by species. Interspecific differential expression (DE) is pervasive (52-59% of expressed genes), whereas the number of DE genes between sexes is modest overall (~3%). Interestingly, the identity of DE genes varies considerably across brain regions. Much of this modularity is due to cis-regulatory divergence, and while 43% of genes were consistently assigned to the same gene regulatory class across subregions (e.g. conserved, cis- or trans-regulatory divergence), a similar number were assigned to two or more different gene regulatory classes. Together, these results highlight the modularity of gene expression differences and divergence in the brain, which may be key to explain how the evolution of brain gene expression can contribute to the astonishing diversity of animal behaviours.

Quaternary rodents of South Africa: A companion guide for cranio-dental identification

Rodentia is the most species-rich order among mammals. The Republic of South Africa harbours a high rodent diversity whose taxonomy and phylogeny have been extensively studied using genetic tools. Such advances have led to the establishment of new faunal lists for the country. Because rodents are frequently recovered from archaeological cave site material and owl pellets, and constitute prime material for studying both past and present environmental conditions, it is necessary to characterize their osteological remains. The skull and teeth are the most useful diagnostic skeletal elements preserved in modern and fossil accumulations. This key provides updated craniodental criteria for identifying rodent genera found in Quaternary deposits, and modern material from the Republic of South Africa, thus facilitating research on past and present rodent diversity.

The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats

A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is often widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents (Old World mice and rats) - a large and ecologically diverse group that gave rise to the mouse and rat model systems. Combining new linked-read genome assemblies for seven murine species with eleven published rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust species tree. We then used whole genomes to examine finer-scale patterns of discordance and found that phylogenies built from proximate chromosomal regions had similar phylogenies. However, there was no relationship between tree similarity and local recombination rates in house mice, suggesting that genetic linkage influences phylogenetic patterns over deeper timescales. This signal may be independent of contemporary recombination landscapes. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to less discordance, while genes experiencing positive selection showed more discordant and variable phylogenetic signals. Finally, we show that assuming a single species tree can result in high error rates when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.

Pliocene sigmodontine rodents (Mammalia: Cricetidae) in northernmost South America: test of biogeographic hypotheses and revised evolutionary scenarios

We document the first occurrence of Sigmodontinae (Mammalia, Rodentia, Cricetidae) from the Pliocene of northern South America, from the San Gregorio Formation of northwestern Venezuela. The recovered isolated molars are identified as Oligoryzomys sp. and Zygodontomys sp., two currently widespread sigmodontines in South America. These records constitute the oldest representatives of these genera, potentially new species, and the first Pliocene occurrence for Oryzomyini and the whole subfamily outside Argentina. Hypotheses on the historical biogeography of sigmodontines have been constructed almost exclusively using genetic data and the fossils we report provide a new kind of evidence. The occurrence of Oligoryzomys sp. and Zygodontomys sp. in Venezuela provides novel information for the diversification models suggested for Oligoryzomys, by supporting a potential eastern corridor of open environments from northern to southern South America. The presence of sigmodontines from the locality home of the new reports, Norte Casa Chiguaje, is consistent with the palaeoenvironmental conditions originally proposed for it based on mammals and botanical records, being characterized as mixed open grassland/forest areas surrounding permanent freshwater systems. The new sigmodontine evidence is used to discuss the putative scenarios of the ancient evolution of the subfamily in South America, favouring a model in which open areas (savannahs) to the east of the Andes played crucial role aiding or obstructing Late Miocene-Pliocene sigmodontine dispersion southwards.

The importance of the Andes in the evolutionary radiation of Sigmodontinae (Rodentia, Cricetidae), the most diverse group of mammals in the Neotropics

The Andean mountains stand out for their striking species richness and endemicity that characterize many emblematic Neotropical clades distributed in or around these mountains. The radiation of the Sigmodontinae subfamily, the most diversified mammalian group in the Neotropics, has been historically related to Andean orogenesis. We aim to evaluate this interplay between geological processes and biological responses through the diversification dynamics, the biogeographical history, and the range evolution of the subfamily. For these, we built the most comprehensive phylogeny and gathered 14,836 occurrences for the subfamily. We identified one shift in the speciation rate in the genus Akodon, which suffered their Andean radiation after the arrival of non-Andean ancestors. Our biogeographic analyses show multiple dispersal paths throughout the evolution that allowed this subfamily to colonize all Neotropics. The Northern Andes and Central-Southern Andes were the most important sources of diversity. In addition, the Central-Southern Andes were the most relevant sink, receiving the highest number of lineages. The Andean region exhibited higher speciation and turnover rates than non-Andean regions. Thus, our results support the crucial role of the Andean Mountains in the Sigmodontinae radiation, acting as a "macroevolutionary cradle" and "species attractor" for several sigmodontine lineages at different times, and as a "species pump" becoming the biogeographic source of multiple widely distributed neotropical lineages. Then, complex macroevolutionary dynamics would explain these rodents' high extant Andean diversity and their wide distribution in the Neotropics.

TE, Solari S, Colmenares-Pinzon J, Nivelo C, Rodríguez Herrera B, Merino W, Medina CE, Murillo-García O, Pardiñas UF. Systematics and diversification of the Ichthyomyini (Cricetidae, Sigmodontinae) revisited: evidence from molecular, morphological, and combined approaches

Ichthyomyini, a morphologically distinctive group of Neotropical cricetid rodents, lacks an integrative study of its systematics and biogeography. Since this tribe is a crucial element of the Sigmodontinae, the most speciose subfamily of the Cricetidae, we conducted a study that includes most of its recognized diversity (five genera and 19 species distributed from southern Mexico to northern Bolivia). For this report we analyzed a combined matrix composed of four molecular markers (RBP3, GHR, RAG1, Cytb) and 56 morphological traits, the latter including 15 external, 14 cranial, 19 dental, five soft-anatomical and three postcranial features. A variety of results were obtained, some of which are inconsistent with the currently accepted classification and understanding of the tribe. Ichthyomyini is retrieved as monophyletic, and it is divided into two main clades that are here recognized as subtribes: one to contain the genus Anotomys and the other composed by the remaining genera. Neusticomys (as currently recognized) was found to consist of two well supported clades, one of which corresponds to the original concept of Daptomys. Accordingly, we propose the resurrection of the latter as a valid genus to include several species from low to middle elevations and restrict Neusticomys to several highland forms. Numerous other revisions are necessary to reconcile the alpha taxonomy of ichthyomyines with our phylogenetic results, including placement of the Cajas Plateau water rat (formerly Chibchanomys orcesi) in the genus Neusticomys (sensu stricto), and the recognition of at least two new species (one in Neusticomys, one in Daptomys). Additional work is necessary to confirm other unanticipated results, such as the non-monophyletic nature of Rheomys and the presence of a possible new genus and species from Peru. Our results also suggest that ichthyomyines are one of the main Andean radiations of sigmodontine cricetids, with an evolutionary history dating to the Late Miocene and subsequent cladogenesis during the Pleistocene.

Ecology of Lassa Virus

Individuals living in endemic hotspots of Lassa fever have recurrent exposure to Lassa virus (LASV) via spillover from the primary host reservoir Mastomys natalensis. Despite M. natalensis being broadly distributed across sub-Saharan Africa, Lassa fever is only found in West Africa. In recent years, new LASV reservoirs have been identified. Erudition of rodent habitats, reproduction and fecundity, movement patterns, and spatial preferences are essential to institute preventative measures against Lassa fever. Evolutionary insights have also added to our knowledge of closely related mammarenavirus distribution amongst rodents throughout the continent.

Morphology and genetics of grasshopper mice revisited in a paleontological framework: reinstatement of Onychomyini (Rodentia, Cricetidae)

Grasshopper mice of the genus Onychomys, represented by three living species in North America, have a long and controversial taxonomic history. Usually allocated to either the cricetine or neotomine cricetids, they also have been considered to represent a distinct tribe. Since the discovery and description of the extinct grasshopper mouse relative Acrolophomys rhodopetros from the late Miocene of the upper Dove Spring Formation of California, dated at 9.3–8.8 Ma, it has become apparent that the grasshopper mouse clade has a long, distinct evolutionary history. Using a combination of morphological (including paleontological material) and molecular data, we reassessed the phylogenetic position of grasshopper mice. A morphological phylogenetic analysis was done on fossil and modern specimens of all recognized neotomine tribes, including craniodental, phallic, and soft tissue characters. A DNA-based matrix was constructed including 72 species representing all known living genera of Neotominae and 13 outgroup taxa belonging mostly to cricetid subfamilies. DNA sampling covered the mitochondrial protein-coding gene cytochrome-b (Cytb), and seven nuclear loci. The morphological analysis yielded a single most parsimonious tree of 42 steps, placing Ochrotomys (Ochrotomyini), Baiomys (Baiomyini), Reithrodontomys (Reithrodontomyini), and an Onychomys–Acrolophomys clade as successive sister clades to a Peromyscus clade, respectively. The molecular phylogenetic analyses recovered seven major clades: (1) a clade including Habromys, Megadontomys, Neotomodon, Osgoodomys, Podomys, and a paraphyletic Peromyscus clade, sister to (2) a second clade containing extant Onychomys species, (3) a Reithrodontomys clade, (4) an Isthmomys clade, (5) a clade including Baiomys and Scotinomys, (6) an Ochrotomys clade, and (7) a well-­supported clade containing Hodomys, Neotoma, and Xenomys. A Bayesian combined morphological and molecular analysis recovered the same major phylogenetic associations as the molecular analyses. The sum of molecular markers and morphological traits expressed by Acrolophomys and Onychomys leads to a phylogenetic position supporting their recognition as a distinct tribe.

New Guinea uplift opens ecological opportunity across a continent

Sahul unites the world's largest and highest tropical island and the oldest and most arid continent on the backdrop of dynamic environmental conditions. Massive geological uplift in New Guinea is predicted to have acted as a species pump from the late Miocene onward, but the impact of this process on biogeography and diversification remains untested across Sahul as a whole. To address this, we reconstruct the assembly of a recent and diverse radiation of rodents (Murinae: Hydromyini) spanning New Guinea, Australia, and oceanic islands. Using phylogenomic data from 270 specimens, including many recently extinct and highly elusive species, we find that the orogeny and expansion of New Guinea opened ecological opportunity and triggered diversification across a continent. After a single over-water colonization from Asia ca. 8.5 Ma, ancestral Hydromyini were restricted to the tropical rainforest of proto-New Guinea for 3.5 million years. Following a shift in diversification coincident with the orogeny of New Guinea ca. 5 Ma and subsequent colonization of Australia, transitions between geographic regions (n = 24) and biomes (n = 34) become frequent. Recurrent over-water colonization between mainland and islands demonstrate how islands can play a substantial role in the assembly of continental fauna. Our results are consistent with a model of increased ecological opportunity across Sahul following major geological uplift in New Guinea ca. 5 Ma, with sustained diversification facilitated by over-water colonization from the Pleistocene to present. We show how geological processes, biome transitions, and over-water colonization collectively drove the diversification of an expansive continental radiation.

A new genus and species of shrew-like mouse (Rodentia: Muridae) from a new center of endemism in eastern Mindanao, Philippines

The Philippine archipelago hosts an exceptional diversity of murid rodents that have diversified following several independent colonization events. Here, we report the discovery of a new species of rodent from Mt. Kampalili on eastern Mindanao Island. Molecular and craniodental analyses reveal this species as a member of a Philippine "New Endemic" clade consisting of Tarsomys, Limnomys, and Rattus everetti (tribe Rattini). This new species of "shrew-mouse" is easily distinguished from its relatives in both craniodental and external characteristics including a long, narrow snout; small eyes and ears; short, dark, dense fur dorsally and ventrally; stout body with a tapering, visibly haired tail shorter than head and body length; stout forepaws; bulbous and nearly smooth braincase; narrow, tapering rostrum; short incisive foramina; slender mandible; and narrow, slightly opisthodont incisors. This new genus and species of murid rodent illustrates that murids of the tribe Rattini have exhibited greater species and morphological diversification within the Philippines than previously known and provides evidence that Mt. Kampalili represents a previously unrecognized center of mammalian endemism on Mindanao Island that is deserving of conservation action.

Bridging macroecology and macroevolution in the radiation of sigmodontine rodents

Investigations of phenotypic disparity across geography often ignore macroevolutionary processes. As a corollary, the random null expectations to which disparity is compared and interpreted may be unrealistic. We tackle this issue by representing, in geographical space, distinct processes of phenotypic evolution underlying ecological disparity. Under divergent natural selection, assemblages in a given region should have empirical disparity higher than expected under an evolutionarily oriented null model, whereas the opposite may indicate constraints on phenotypic evolution. We gathered phylogenies, biogeographic distributions, and data on the skull morphology of sigmodontine rodents to discover which regions of the Neotropics were more influenced by divergent, neutral, or constrained phenotypic evolution. We found that regions with higher disparity than expected by the evolutionary-oriented null model, in terms of both size and shape, were concentrated in the Atlantic Forest, suggesting a larger role for divergent natural selection there. Phenotypic disparity in the rest of South America, mainly the Amazon basin, northeastern Brazil, and Southern Andes, was constrained-lower than predicted by the evolutionary model. We also demonstrated equivalence between the disparity produced by randomization-based null models and constrained-evolution null models. Therefore, including evolutionary simulations into the null modeling framework used in ecophylogenetics can strengthen inferences on the processes underlying phenotypic evolution.

Patterns of Phenotypic Evolution Associated with Marine/Freshwater Transitions in Fishes

Evolutionary transitions between marine and freshwater ecosystems have occurred repeatedly throughout the phylogenetic history of fishes. The theory of ecological opportunity predicts that lineages that colonize species-poor regions will have greater potential for phenotypic diversification than lineages invading species-rich regions. Thus, transitions between marine and freshwaters may promote phenotypic diversification in trans-marine/freshwater fish clades. We used phylogenetic comparative methods to analyze body size data in nine major fish clades that have crossed the marine/freshwater boundary. We explored how habitat transitions, ecological opportunity, and community interactions influenced patterns of phenotypic diversity. Our analyses indicated that transitions between marine and freshwater habitats did not drive body size evolution, and there are few differences in body size between marine and freshwater lineages. We found that body size disparity in freshwater lineages is not correlated with the number of independent transitions to freshwaters. We found a positive correlation between body size disparity and overall species richness of a given area, and a negative correlation between body size disparity and diversity of closely related species. Our results indicate that the diversity of incumbent freshwater species does not restrict phenotypic diversification, but the diversity of closely related taxa can limit body size diversification. Ecological opportunity arising from colonization of novel habitats does not seem to have a major effect in the trajectory of body size evolution in trans-marine/freshwater clades. Moreover, competition with closely related taxa in freshwaters has a greater effect than competition with distantly related incumbent species.

The evolution of widespread recombination suppression on the dwarf hamster (Phodopus) X chromosome

The X chromosome of therian mammals shows strong conservation among distantly related species, limiting insights into the distinct selective processes that have shaped sex chromosome evolution. We constructed a chromosome-scale de novo genome assembly for the Siberian dwarf hamster (Phodopus sungorus), a species reported to show extensive recombination suppression across an entire arm of the X chromosome. Combining a physical genome assembly based on shotgun and long-range proximity ligation sequencing with a dense genetic map, we detected widespread suppression of female recombination across ∼65% of the Phodopus X chromosome. This region of suppressed recombination likely corresponds to the Xp arm, which has previously been shown to be highly heterochromatic. Using additional sequencing data from two closely related species (P. campbelli and P. roborovskii), we show that recombination suppression on Xp appears to be independent of major structural rearrangements. The suppressed Xp arm was enriched for several transposable element families and de-enriched for genes primarily expressed in placenta, but otherwise showed similar gene densities, expression patterns, and rates of molecular evolution when compared to the recombinant Xq arm. Phodopus Xp gene content and order was also broadly conserved relative to the more distantly related rat X chromosome. These data suggest that widespread suppression of recombination has likely evolved through the transient induction of facultative heterochromatin on the Phodopus Xp arm without major changes in chromosome structure or genetic content. Thus, substantial changes in the recombination landscape have so far had relatively subtle influences on patterns of X-linked molecular evolution in these species.

Evolution of Guanylate Binding Protein (GBP) Genes in Muroid Rodents (Muridae and Cricetidae) Reveals an Outstanding Pattern of Gain and Loss

Guanylate binding proteins (GBPs) are paramount in the host immunity by providing defense against invading pathogens. Multigene families related to the immune system usually show that the duplicated genes can either undergo deletion, gain new functions, or become non-functional. Here, we show that in muroids, the Gbp genes followed an unusual pattern of gain and loss of genes. Muroids present a high diversity and plasticity regarding Gbp synteny, with most species presenting two Gbp gene clusters. The phylogenetic analyses revealed seven different Gbps groups. Three of them clustered with GBP2, GBP5 and GBP6 of primates. Four new Gbp genes that appear to be exclusive to muroids were identified as Gbpa, b, c and d. A duplication event occurred in the Gbpa group in the common ancestor of Muridae and Cricetidae (~20 Mya), but both copies were deleted from the genome of Mus musculus, M. caroli and Cricetulus griseus. The Gbpb gene emerged in the ancestor of Muridae and Cricetidae and evolved independently originating Gbpb1 in Muridae, Gbpb2 and Gbpb3 in Cricetidae. Since Gbpc appears only in three species, we hypothesize that it was present in the common ancestor and deleted from most muroid genomes. The second Gbp gene cluster, Gbp6, is widespread across all muroids, indicating that this cluster emerged before the Muridae and Cricetidae radiation. An expansion of Gbp6 occurred in M. musculus and M. caroli probably to compensate the loss of Gbpa and b. Gbpd is divided in three groups and is present in most muroids suggesting that a duplication event occurred in the common ancestor of Muridae and Cricetidae. However, in Grammomys surdaster and Mus caroli, Gbpd2 is absent, and in Arvicanthis niloticus, Gbpd1 appears to have been deleted. Our results further demonstrated that primate GBP1, GBP3 and GBP7 are absent from the genome of muroids and showed that the Gbp gene annotations in muroids were incorrect. We propose a new classification based on the phylogenetic analyses and the divergence between the groups. Extrapolations to humans based on functional studies of muroid Gbps should be re-evaluated. The evolutionary analyses of muroid Gbp genes provided new insights about the evolution and function of these genes.

Complete mitogenomes reveal limited genetic variability in the garden dormouse Eliomys quercinus of the Iberian Peninsula

The garden dormouse Eliomys quercinus is a poorly known Western Palearctic species experiencing a global decline. Even though the availability of genetic information is key to assess the driversunderlying demographic changes in wild populations and plan adequate management, data on E. quercinus are still scant. In this study, we reconstructed the complete mitogenomes of four E. quercinus individuals from southern Spain using in–solution enriched libraries, and found evidence of limited genetic variability. We then compared their cytochrome b sequences to those of conspecifics from other countries and supported the divergent but genetically depauperate position of this evolutionarily significant unit (ESU). The information produced will assist future conservation studies on this little–studied rodent.

Competition and geography underlie speciation and morphological evolution in Indo-Australasian monitor lizards

How biotic and abiotic factors act together to shape biological diversity is a major question in evolutionary biology. The recent availability of large datasets and development of new methodological approaches provide new tools to evaluate the predicted effects of ecological interactions and geography on lineage diversification and phenotypic evolution. Here, we use a near complete phylogenomic-scale phylogeny and a comprehensive morphological dataset comprising more than a thousand specimens to assess the role of biotic and abiotic processes in the diversification of monitor lizards (Varanidae). This charismatic group of lizards shows striking variation in species richness among its clades and multiple instances of endemic radiation in Indo-Australasia (i.e., the Indo-Australian Archipelago and Australia), one of Earth's most biogeographically complex regions. We found heterogeneity in diversification dynamics across the family. Idiosyncratic biotic and geographic conditions appear to have driven diversification and morphological evolution in three endemic Indo-Australasian radiations. Furthermore, incumbency effects partially explain patterns in the biotic exchange between Australia and New Guinea. Our results offer insight into the dynamic history of Indo-Australasia, the evolutionary significance of competition, and the long-term consequences of incumbency effects.

Skull morphological evolution in Malagasy endemic Nesomyinae rodents

Madagascar is a large island to the south-east of Africa and in many ways continental in size and ecological complexity. Here we aim to define how skull morphology of an endemic and monophyletic clade of rodents (sub-family Nesomyinae), that show considerable morphological variation, have evolved and how their disparity is characterized in context of the geographical and ecological complexity of the island. We performed a two-dimensional geometric morphometric analysis on 370 dorsal and 399 ventral skull images of 19 species (comprising all nine extant endemic genera) and tested the influence of three ecological parameters (climate, locomotor habitat and nychthemeral cycle) in a phylogenetic context on size and shape. The results indicate that skull shape appears to importantly reflect phylogeny, whereas skull size does not carry a significant phylogenetic signal. Skull shape is significantly influenced by climate while, skull size is not impacted by any of the ecological factors tested, which is controversial to expectations in an insular context. In conclusion, Nesomyinae must have evolved under unusual types of local constraints, preventing this radiation from demonstrating strong ecological release.

Molecular systematics of the Reithrodontomys tenuirostris group (Rodentia: Cricetidae) highlighting the Reithrodontomys microdon species complex

The Reithrodontomys tenuirostris species group is considered "the most specialized" within the genus Reithrodontomys from morphological and ecological perspectives. Previous studies based on molecular data recommended changes in the taxonomy of the group. In particular, R. microdon has been the most taxonomically questioned, with the suggestion that it constitutes a complex of cryptic species. We analyzed the phylogenetic relationships of the R. tenuirostris species group using DNA sequences from the mitochondrial Cytochrome b gene and Intron 7 of the nuclear beta fibrinogen gene. In addition, divergence times were estimated, and possible new taxa delimited with three widely used species delimitation methods. Finally, possible connectivity routes based on shared haplotypes were tested among the R. microdon populations. All species were recovered as monophyletic with the exception of R. microdon, whose individuals were grouped into four different haplogroups, one of which included specimens of R. bakeri. Diversification within the R. tenuirostris species group began about 3 Ma, in the Pleistocene. The bGMYC and STACEY delimitation methods were congruent with each other, delimiting at the species-level each haplogroup within R. microdon, while the mPTP suggested a greater number of species. Moreover, none of the haplogroups showed potential connectivity routes between them, evidencing lack of gene flow. Our results suggest the existence of a higher number of species in the R. tenuirostris group, because we show that there are four species within what is currently recognized as R. microdon.

A rodent anchored hybrid enrichment probe set for a range of phylogenetic utility: From order to species

Rodents are the largest order of mammals and contain several model organisms important to scientific research in a variety of fields, yet no large set of genomic markers have been designed for this group to date, hindering evolutionary studies into relationships of the group as a whole. Here we present a genomic probe set designed and optimized for rodents with a protocol that is easy to replicate with little laboratory investment. This design utilizes an anchored hybrid enrichment approach specifically targeting rodents to generate longer loci with a higher substitution rate than existing vertebrate probes to provide utility at various taxonomic levels. Using a test set of rodents from all five suborders, we successfully obtained alignments for 416 of the 418 target loci with an average of 1379 bp per locus and a total alignment of more than half a million base pairs. This genomic data set performed well in all phylogenetic analyses, especially in recent phylogenetic splits, with ample parsimony-informative sites within genera and even within species, showing more than four times as many single nucleotide polymorphisms per locus than a recent vertebrate ultraconserved elements study. Additional support is provided in resolving deeper clades in Rodentia. By providing this probe design, we hope that more laboratories can easily generate data for answering questions in rodents from species delimitation to understanding relationships among families in rapid radiations.

A mitochondrial genome phylogeny of voles and lemmings (Rodentia: Arvicolinae): Evolutionary and taxonomic implications

Arvicolinae is one of the most impressive placental radiations with over 150 extant and numerous extinct species that emerged since the Miocene in the Northern Hemisphere. The phylogeny of Arvicolinae has been studied intensively for several decades using morphological and genetic methods. Here, we sequenced 30 new mitochondrial genomes to better understand the evolutionary relationships among the major tribes and genera within the subfamily. The phylogenetic and molecular dating analyses based on 11,391 bp concatenated alignment of protein-coding mitochondrial genes confirmed the monophyly of the subfamily. While Bayesian analysis provided a high resolution across the entire tree, Maximum Likelihood tree reconstruction showed weak support for the ordering of divergence and interrelationships of tribal level taxa within the most ancient radiation. Both the interrelationships among tribes Lagurini, Ellobiusini and Arvicolini, comprising the largest radiation and the position of the genus Dinaromys within it also remained unresolved. For the first time complex relationships between genus level taxa within the species-rich tribe Arvicolini received full resolution. Particularly Lemmiscus was robustly placed as sister to the snow voles Chionomys in the tribe Arvicolini in contrast with a long-held belief of its affinity with Lagurini. Molecular dating of the origin of Arvicolinae and early divergences obtained from the mitogenome data were consistent with fossil records. The mtDNA estimates for putative ancestors of the most genera within Arvicolini appeared to be much older than it was previously proposed in paleontological studies.

Parallel power posterior analyses for fast computation of marginal likelihoods in phylogenetics

In Bayesian phylogenetic inference, marginal likelihoods can be estimated using several different methods, including the path-sampling or stepping-stone-sampling algorithms. Both algorithms are computationally demanding because they require a series of power posterior Markov chain Monte Carlo (MCMC) simulations. Here we introduce a general parallelization strategy that distributes the power posterior MCMC simulations and the likelihood computations over available CPUs. Our parallelization strategy can easily be applied to any statistical model despite our primary focus on molecular substitution models in this study. Using two phylogenetic example datasets, we demonstrate that the runtime of the marginal likelihood estimation can be reduced significantly even if only two CPUs are available (an average performance increase of 1.96x). The performance increase is nearly linear with the number of available CPUs. We record a performance increase of 13.3x for cluster nodes with 16 CPUs, representing a substantial reduction to the runtime of marginal likelihood estimations. Hence, our parallelization strategy enables the estimation of marginal likelihoods to complete in a feasible amount of time which previously needed days, weeks or even months. The methods described here are implemented in our open-source software RevBayes which is available from http://www.RevBayes.com.

Revisiting the Pneumocystis host specificity paradigm and transmission ecology in wild Southeast Asian rodents

Pneumocystis fungi are opportunistic parasites of mammalian lungs whose evolution, ecology and host specificity in natural host populations remain poorly understood and controversial. Using an extensive collection of 731 lung samples from 27 rodent species sampled in five Southeast Asian countries, and nested PCR amplification of mitochondrial and nuclear genes, we investigated the host specificity and genetic structure of Pneumocystis lineages infecting wild rodents. We also identified the rodent species playing a central role in the transmission of these parasites using network analysis and centrality measurement and we characterized the environmental conditions allowing Pneumocystis infection in Southeast Asia using generalized linear mixed models. Building upon an unprecedented Pneumocystis sampling from numerous rodent species belonging to closely related genera, our findings provide compelling evidence that the host specificity of Pneumocystis lineages infecting rodents is not restricted to a single host species or genus as often presented in the literature but it encompasses much higher taxonomic levels and more distantly related rodent host species. The phylogenetic species status at both mitochondrial and nuclear genetic markers of at least three new Pneumocystis lineages, highly divergent from Pneumocystis species currently described, is also suggested by our data. Our models show that the probability of Pneumocystis infection in rodent hosts is positively correlated to environmental variables reflecting habitat fragmentation and landscape patchiness. Synanthropic and habitat-generalist rodents belonging to the Rattus, Sundamys and Bandicota genera played a role of bridge host species for Pneumocystis spreading in these heterogeneous habitats, where they can reach high population densities. These are critical findings improving our understanding of the ecology of these enigmatic parasites and the role played by cospeciation and host switches in their evolution. Our results also confirmed the role of land-use change and habitat fragmentation in parasite amplification and spillover in rodents.

Leishmaniosis in Rodents Caused by Leishmania infantum: A Review of Studies in the Mediterranean Area

Leishmaniosis infection begins when a phlebotomine sand fly vector inoculates pathogenic protozoan parasites of the genus Leishmania into a mammalian host. In the case of Leishmania infantum, the domestic dog is considered to be the main parasite reservoir, and canine leishmaniosis (CanL) has a high mortality rate in untreated dogs. Hundreds of cases of human leishmaniosis (HL) are reported in the world each year, the incidence in Europe being relatively low. Leishmaniosis control is primarily focused on the dog, combining methods that prevent sand fly bites and boost host resistance to infection. However, these measures are only partially effective and new solutions need to be found. One of the main factors limiting CanL and HL control is the existence of a sylvatic Leishmania transmission cycle that interacts with the domestic cycle maintained by dogs. It is suspected that the main reservoir of infection in wildlife are rodents, whose expansion and rapid population growth worldwide is increasing the risk of human and zoonotic pathogen transfer. The aim of this review is therefore to analyze reports in the literature that may shed light on the potential role of rodents in the leishmaniosis transmission cycle in the Mediterranean area. Following the general methodology recommended for reviews, six databases (Google Scholar, Ovid, PubMed, Science Direct, Scopus and Web of Science) were explored for the period January 1995 to December 2020. The results extracted from 39 publications that met the established inclusion criteria were analyzed. It was found that 23 species of rodents have been studied in nine countries of the Mediterranean basin. Of the 3,643 specimens studied, 302 tested positive for L. infantum infection by serology, microscopy and/or molecular techniques.

A subterranean adaptive radiation of amphipods in Europe

Adaptive radiations are bursts of evolutionary species diversification that have contributed to much of the species diversity on Earth. An exception is modern Europe, where descendants of ancient adaptive radiations went extinct, and extant adaptive radiations are small, recent and narrowly confined. However, not all legacy of old radiations has been lost. Subterranean environments, which are dark and food-deprived, yet buffered from climate change, have preserved ancient lineages. Here we provide evidence of an entirely subterranean adaptive radiation of the amphipod genus Niphargus, counting hundreds of species. Our modelling of lineage diversification and evolution of morphological and ecological traits using a time-calibrated multilocus phylogeny suggests a major adaptive radiation, comprised of multiple subordinate adaptive radiations. Their spatio-temporal origin coincides with the uplift of carbonate massifs in South-Eastern Europe 15 million years ago. Emerging subterranean environments likely provided unoccupied, predator-free space, constituting ecological opportunity, a key trigger of adaptive radiation. This discovery sheds new light on the biodiversity of Europe.

Mitogenomics and Evolutionary History of Rodent Whipworms (Trichuris spp.) Originating from Three Biogeographic Regions

Trichuris spp. is a widespread nematode which parasitizes a wide range of mammalian hosts including rodents, the most diverse mammalian order. However, genetic data on rodent whipworms are still scarce, with only one published whole genome (Trichuris muris) despite an increasing demand for whole genome data. We sequenced the whipworm mitogenomes from seven rodent hosts belonging to three biogeographic regions (Palearctic, Afrotropical, and Indomalayan), including three previously described species: Trichuris cossoni, Trichurisarvicolae, and Trichurismastomysi. We assembled and annotated two complete and five almost complete mitogenomes (lacking only the long non-coding region) and performed comparative genomic and phylogenetic analyses. All the mitogenomes are circular, have the same organisation, and consist of 13 protein-coding, 2 rRNA, and 22 tRNA genes. The phylogenetic analysis supports geographical clustering of whipworm species and indicates that T. mastomysi found in Eastern Africa is able to infect multiple closely related rodent hosts. Our results are informative for species delimitation based on mitochondrial markers and could be further used in studies on phylogeny, phylogeography, and population genetics of rodent whipworms

Linking population-level and microevolutionary processes to understand speciation dynamics at the macroevolutionary scale

Although speciation dynamics have been described for several taxonomic groups in distinct geographic regions, most macroevolutionary studies still lack a detailed mechanistic view on how or why speciation rates change. To help partially fill this gap, we suggest that the interaction between the time taken by a species to geographically expand and the time populations take to evolve reproductive isolation should be considered when we are trying to understand macroevolutionary patterns. We introduce a simple conceptual index to guide our discussion on how demographic and microevolutionary processes might produce speciation dynamics at macroevolutionary scales. Our framework is developed under different scenarios: when speciation is mediated by geographical or resource-partitioning opportunities, and when diversity is limited or not. We also discuss how organismal intrinsic properties and different overall geographical settings can influence the tempo and mode of speciation. We argue that specific conditions observed at the microscale might produce a pulse in speciation rates even without a pulse in either climate or physical barriers. We also propose a hypothesis to reconcile the apparent inconsistency between speciation measured at the microscale and macroscale, and emphasize that diversification rates are better seen as an emergent property. We hope to bring the reader's attention to interesting mechanisms to be further studied, to motivate the development of new theoretical models that connect microevolution and macroevolution, and to inspire new empirical and methodological approaches to more adequately investigate speciation dynamics either using neontological or paleontological data.

Ultraconserved Elements Improve the Resolution of Difficult Nodes within the Rapid Radiation of Neotropical Sigmodontine Rodents (Cricetidae: Sigmodontinae)

Sigmodontine rodents (Cricetidae, Sigmodontinae) represent the second largest muroid subfamily and the most species-rich group of New World mammals, encompassing above 410 living species and ca. 87 genera. Even with advances on the clarification of sigmodontine phylogenetic relationships that have been made recently, the phylogenetic relationships among the 12 main group of genera (i.e., tribes) remain poorly resolved, in particular among those forming the large clade Oryzomyalia. This pattern has been interpreted as consequence of a rapid radiation upon the group entrance into South America. Here, we attempted to resolve phylogenetic relationships within Sigmodontinae using target capture and high-throughput sequencing of ultraconserved elements (UCEs). We enriched and sequenced UCEs for 56 individuals and collected data from four already available genomes. Analyses of distinct data sets, based on the capture of 4,634 loci, resulted in a highly resolved phylogeny consistent across different methods. Coalescent species-tree based approaches, concatenated matrices, and Bayesian analyses recovered similar topologies that were congruent at the resolution of difficult nodes. We recovered good support for the intertribal relationships within Oryzomyalia; for instance, the tribe Oryzomyini appears as the sister taxa of the remaining oryzomyalid tribes. The estimates of divergence times agree with results of previous studies. We inferred the crown age of the sigmodontine rodents at the end of Middle Miocene, while the main lineages of Oryzomyalia appear to have radiated in a short interval during the Late Miocene. Thus, the collection of a genomic scale data set with a wide taxonomic sampling, provided resolution for the first time of the relationships among the main lineages of Sigmodontinae. We expect the phylogeny presented here will become the backbone for future systematic and evolutionary studies of the group.

Tempo and mode of evolution of oryzomyine rodents (Rodentia, Cricetidae, Sigmodontinae): A phylogenomic approach

The tribe Oryzomyini is an impressive group of rodents, comprising 30 extant genera and an estimated 147 species. Recent remarkable advances in the understanding of the diversity, taxonomy and systematics of the tribe have mostly derived from analyses of single or few genetic markers. However, the evolutionary history and biogeography of Oryzomyini, its origin and diversification across the Neotropics, remain unrevealed. Here we use a multi-locus dataset (over 400 loci) obtained through anchored phylogenomics to provide a genome-wide phylogenetic hypothesis for Oryzomyini and to investigate the tempo and mode of its evolution. Species tree and supermatrix analyses produced topologies with strong support for most branches, with all genera confirmed as monophyletic, a result that previous studies failed to obtain. Our analyses also corroborated the monophyly and phylogenetic relationship of three main clades of Oryzomyini (B, C and D). The origin of the tribe is estimated to be in the Miocene (8.93-5.38 million years ago). The cladogenetic events leading to the four main clades occurred during the late Miocene and early Pliocene and most speciation events in the Pleistocene. Geographic range estimates suggested an east of Andes origin for the ancestor of oryzomyines, most likely in the Boreal Brazilian region, which includes the north bank of Rio Amazonas and the Guiana Shield. Oryzomyini rodents are an autochthonous South America radiation, that colonized areas and dominions of this continent mainly by dispersal events. The evolutionary history of the tribe is deeply associated with the Andean cordillera and the landscape history of Amazon basin.

Morphological similarity and dental homologies in two sigmodontine rodents (Mammalia, Cricetidae) from different tribes: A topological analysis to explore convergence

We present a topological analysis of the third upper molars (M3) using the recently developed ICAMER nomenclatural system as a way to understand the dental morphological similarity in sigmodontine rodents, the most speciose subfamily of cricetids. The method is explored in Scapteromys aquaticus and Abrothrix olivacea, taxa belonging to two diverse tribes, Akodontini and Abrotrichini, respectively, which exhibit high similarity regarding several craniodental traits as well as external anatomy. Both species show morphologically similar M3 in adults characterized by cylindrification and the isolation of a large central fossette arising from the marginal fusion of the anterior and posterior lobes. The results indicate that, before the wear, these rodents have a strongly different topological pattern at the cuspal level, mostly involving production of the connection between the main cusps. The central fossette derives from the isolation of part of the metaflexus in Scapteromys, while in Abrothrix it originates from the hypoflexus. The topological analysis provides a new approach to sigmodontine systematics, including the ability to detect diagnostic characters of both tribes. More important, it constitutes a new step toward an integrative phylogeny of fossil and living cricetids.

Nuclear phylogenomics, but not mitogenomics, resolves the most successful Late Miocene radiation of African mammals (Rodentia: Muridae: Arvicanthini)

The tribe Arvicanthini (Muridae: Murinae) is a highly diversified group of rodents (ca. 100 species) and with 18 African genera (plus one Asiatic) represents probably the most successful adaptive radiation of extant mammals in Africa. They colonized a broad spectrum of habitats (from rainforests to semi-deserts) in whole sub-Saharan Africa and their members often belong to most abundant parts of mammal communities. Despite intensive efforts, the phylogenetic relationships among major lineages (i.e. genera) remained obscured, which was likely caused by the intensive radiation of the group, dated to the Late Miocene. Here we used genomic scale data (377 nuclear loci; 581,030 bp) and produced the first fully resolved species tree containing all currently delimited genera of the tribe. Mitogenomes were also extracted, and while the results were largely congruent, there was less resolution at basal nodes of the mitochondrial phylogeny. Results of a fossil-based divergence dating analysis suggest that the African radiation started early after the colonization of Africa by a single arvicanthine ancestor from Asia during the Messinian stage (ca. 7 Ma), and was likely linked with a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forest, while many others successfully colonized broad spectrum of new open habitats (e.g. savannas, wetlands or montane moorlands) that appeared at the beginning of Pliocene. One lineage even evolved partially arboricolous life style in savanna woodlands, which allowed them to re-colonize equatorial forests. We also discuss delimitation of genera in Arvicanthini and propose corresponding taxonomic changes.

Tropical Niche Conservatism Explains the Eocene Migration from India to Southeast Asia in Ochyroceratid Spiders

Biological migrations between India and Southeast (SE) Asia provide an ideal system for exploring the effects of geology and climate on species ranges. Geologists have confirmed that the direct collision between India and Eurasia occurred in the Early Eocene, but most migrations occurred between the Indian subcontinent and SE Asia rather than the former and the southern margin of Eurasia. To explain this seemingly paradoxical disconnect between the routes of plate movement and biological migration, we studied the evolutionary history of the tropical spider family Ochyroceratidae based on 101 globally distributed species. We infer a robust dated phylogeny using both transcriptomic data and a data set of classical markers and relate these to biogeographic and climatic analyses. Our results indicate that the monophyly of Ochyroceratidae is strongly supported, and the divergence times suggest a Cretaceous Gondwanan origin of the family. Reconstructed biogeographic histories support a dispersal event from the Indian subcontinent to islands of SE Asia 55-38 Ma. Climatic analyses and the fossil record reveal that ochyroceratids are characterized by a high degree of tropical niche conservatism, and that the ancestor of the Indian and SE Asian clades originated in very warm, wet environments. Early Eocene tropical, perhumid climates in India, and SE Asia may have facilitated ochyroceratid migration, whereas the dry or seasonal climate extending from the eastern coast of China to Central Asia may have acted as a barrier, preventing dispersal. Our analyses suggest that climate plays a more important role than geology in biological migration from the Indian subcontinent to SE Asia, providing new insights into the Indian-Asian biogeographic link. [Biogeography; ecology; geological connections; macroevolution; paleoclimate.].

Australian Rodents Reveal Conserved Cranial Evolutionary Allometry across 10 Million Years of Murid Evolution

AbstractAmong vertebrates, placental mammals are particularly variable in the covariance between cranial shape and body size (allometry), with rodents being a major exception. Australian murid rodents allow an assessment of the cause of this anomaly because they radiated on an ecologically diverse continent notably lacking other terrestrial placentals. Here, we use 3D geometric morphometrics to quantify species-level and evolutionary allometries in 38 species (317 crania) from all Australian murid genera. We ask whether ecological opportunity resulted in greater allometric diversity compared with other rodents or whether conserved allometry suggests intrinsic constraints and/or stabilizing selection. We also assess whether cranial shape variation follows the proposed rule of craniofacial evolutionary allometry (CREA), whereby larger species have relatively longer snouts and smaller braincases. To ensure we could differentiate parallel versus nonparallel species-level allometric slopes, we compared the slopes of rarefied samples across all clades. We found exceedingly conserved allometry and CREA-like patterns across the 10-million-year split between Mus and Australian murids. This could support both intrinsic-constraint and stabilizing-selection hypotheses for conserved allometry. Large-bodied frugivores evolved faster than other species along the allometric trajectory, which could suggest stabilizing selection on the shape of the masticatory apparatus as body size changes.

Impact of different Leishmania reservoirs on sand fly transmission: Perspectives from xenodiagnosis and other one health observations

Leishmania has biologically adapted to specific phlebotomine sand flies through long co-evolution. The ability of Leishmania spp. to bind to sand fly midgut allows each Leishmania species to propagate and differentiate into infectious promastigotes and be transmitted. Sand fly feeding upon a mammalian host is the first step towards being infected and a host of Leishmania. Once deposited into the skin, host susceptibility to infection vs. ability to mount a sterilizing immune response predicts which hosts could be reservoirs of different Leishmania spp. Materials, in addition to parasites, are expelled during sand fly during feeding, including salivary antigens and other factors that promote local inflammatory responses. These factors aid visceralization of infection increasing the likelihood that systemic infection is established. Any environmental factor that increases sand fly biting of a particular host increases that host's role in Leishmania transmission. First descriptions of reservoir species were based on association with local human disease and ability to observe infected leukocytes on cytology. This approach was one pathogen for one reservoir host. Advances in sensitive molecular tools greatly increased the breadth of mammals found to host Leishmania infection. Visceralizing species of Leishmania, particularly L. infantum, are now known to have multiple mammalian hosts. L. donovani, long been described as an anthroponotic parasite, was recently identified through molecular and serologic surveys to have additional mammalian hosts. The epidemiological role of these animals as a source of parasites to additional hosts via vector transmission is not known. Current evidence suggests that dogs and other domestic animals either control infection or do not have sufficient skin parasitemia to be a source of L. donovani to P. argentipes. Further xenodiagnosis and characterization of skin parasitemia in these different hosts is required to more broadly understand which Leishmania spp. hosts can be a source of parasites to sand flies and which ones are dead-end hosts.

Whole mitochondrial genome of long-clawed mole vole (Prometheomys schaposchnikowi) from Turkey, with its phylogenetic relationships

The mitogenome of Prometheomys schaposchnikowi was characterized for the first time as a circular DNA molecule (16.284 bp), containing 37 coding and 2 non-coding regions. In the mitogenome, ND6 and 8 tRNA genes were encoded on the light chain, while 12 PCGs, 14 tRNAs, 2 rRNAs, D-loop and O_L were encoded on the heavy chain. The most common initiation codon in PCGs was ATG. As in many mammals, incomplete stop codons in P. schaposchnikowi were in the COX3, ND1 and ND4. Phylogenetic relationships were revealed using Bayesian method and the 13 PCGs. Seven genera (Arvicola, Dicrostonyx, Lasiopodomys, Myodes, Ondatra, Proedromys and Prometheomys) formed a monophyletic group, while Eothenomys, Microtus and Neodon were paraphyletic. P. schaposchnikowi constituted the most basal group within Arvicolinae. Divergence time estimation suggested that P. schaposchnikowi diversified during the Miocene (16.28 Mya). Further molecular studies are needed to test the distinctiveness and diversity of the genus Prometheomys.

Phylogenomics, Biogeography, and Morphometrics Reveal Rapid Phenotypic Evolution in Pythons After Crossing Wallace’s Line

Ecological opportunities can be provided to organisms that cross stringent biogeographic barriers towards environments with new ecological niches. Wallace’s and Lyddeker’s lines are arguably the most famous biogeographic barriers, separating the Asian and Australo-Papuan biotas. One of the most ecomorphologically diverse groups of reptiles, the pythons, is distributed across these lines, and are remarkably more diverse in phenotype and ecology east of Lydekker’s line in Australo-Papua. We used an anchored hybrid enrichment approach, with near complete taxon sampling, to extract mitochondrial genomes and 376 nuclear loci to resolve and date their phylogenetic history. Biogeographic reconstruction demonstrates that they originated in Asia around 38-45 Ma and then invaded Australo-Papua around 23 Ma. Australo-Papuan pythons display a sizeable expansion in morphological space, with shifts towards numerous new adaptive optima in head and body shape, coupled with the evolution of new micro-habitat preferences. We provide an updated taxonomy of pythons and our study also demonstrates how ecological opportunity following colonization of novel environments can promote morphological diversification in a formerly ecomorphologically conservative group. [Adaptive radiation; anchored hybrid enrichment; biogeography; morphometrics; snakes.]

Comparative and population genomics approaches reveal the basis of adaptation to deserts in a small rodent

Organisms that live in deserts offer the opportunity to investigate how species adapt to environmental conditions that are lethal to most plants and animals. In the hot deserts of North America, high temperatures and lack of water are conspicuous challenges for organisms living there. The cactus mouse (Peromyscus eremicus) displays several adaptations to these conditions, including low metabolic rate, heat tolerance, and the ability to maintain homeostasis under extreme dehydration. To investigate the genomic basis of desert adaptation in cactus mice, we built a chromosome‐level genome assembly and resequenced 26 additional cactus mouse genomes from two locations in southern California (USA). Using these data, we integrated comparative, population, and functional genomic approaches. We identified 16 gene families exhibiting significant contractions or expansions in the cactus mouse compared to 17 other Myodontine rodent genomes, and found 232 sites across the genome associated with selective sweeps. Functional annotations of candidate gene families and selective sweeps revealed a pervasive signature of selection at genes involved in the synthesis and degradation of proteins, consistent with the evolution of cellular mechanisms to cope with protein denaturation caused by thermal and hyperosmotic stress. Other strong candidate genes included receptors for bitter taste, suggesting a dietary shift towards chemically defended desert plants and insects, and a growth factor involved in lipid metabolism, potentially involved in prevention of dehydration. Understanding how species adapted to deserts will provide an important foundation for predicting future evolutionary responses to increasing temperatures, droughts and desertification in the cactus mouse and other species.

Dietary morphology of two island-endemic murid rodent clades is consistent with persistent, incumbent-imposed competitive interactions

A lineage colonizing a geographic region with no competitors may exhibit rapid diversification due to greater ecological opportunity. The resultant species diversity of this primary-colonizing (incumbent) clade may limit subsequent lineages' ability to persist unless these non-incumbent lineages are ecologically distinct. We compare the diversity in diet-related mandibular morphology of two sympatric murid rodent clades endemic to Luzon Island, Philippines-incumbent Phloeomyini and secondary-colonizing Chrotomyini-to the mandibular morphological diversity of Sahul Hydromyini, the sister clade of Chrotomyini and the incumbent murid lineage on the supercontinent of Sahul. This three-clade comparison allows us to test the hypothesis that incumbent lineages can force persistent ecological distinction of subsequent colonists at the time of colonization and throughout the subsequent history of the two sympatric clades. We find that Chrotomyini forms a subset of the diversity of their clade plus Sahul Hydromyini that minimizes overlap with Phloeomyini. We also infer that this differentiation extends to the stem ancestor of Chrotomyini and Sahul Hydromyini, consistent with a biotic filter imposed by Phloeomyini. Our work illustrates that incumbency has the potential to have a profound influence on the ecomorphological diversity of colonizing lineages at the island scale even when the traits in question are evolving at similar rates among independently colonizing clades.

The uplift of the Qinghai-Tibet Plateau and glacial oscillations triggered the diversification of Tetraogallus (Galliformes, Phasianidae)

The Qinghai-Tibet Plateau (QTP) plays an important role in avian diversification. To reveal the relationship between the QTP uplift and avian diversification since the Late Cenozoic, here, we analyzed the phylogenetic relationship and biogeographical pattern of the genus Tetraogallus (Galliformes, Phasianidae) and the probable factors of speciation in the period of the QTP uplift inferred from concatenated data of four nuclear and five mitochondrial genes using the method of the Bayesian inference. Phylogenetic analysis indicated that T. himalayensis had a close relationship with T. altaicus and conflicted with the previous taxonomy of dark-bellied and white-bellied groups. The molecular clock showed that the speciation of Tetraogallus was profoundly affected by the uplift of the QTP and glacial oscillations. Biogeographic analysis suggested that the extant snowcocks originated from the QTP, and the QTP uplift and glacial oscillations triggered the diversification of Tetraogallus ancestor. Specifically, the uplift of the mountain provided a prerequisite for the colonization of snowcocks Tetraogallus as a result of the collision between the Indian and the Arab plates and the Eurasian plate, in which ecological isolation (the glacial and interglacial periods alternate) and geographical barrier had accelerated the Tetraogallus diversification process. Interestingly, we discovered hybrids between T. tibetanus and T. himalayensis for the first time and suggested that T. tibetanus and T. himalayensis hybridized after a second contact during the glacial period. Here, we proposed that the hybrid offspring was the ancestor of the T. altaicus. In conclusion, the uplift of QTP and glacial oscillations triggered the snowcocks colonization, and then, isolation and introgression hybridization promoted diversification.

The evolutionary diversity of locomotor innovation in rodents is not linked to proximal limb morphology

Rodents are the most species-rich order within Mammalia and have evolved disparate morphologies to accommodate numerous locomotor niches, providing an excellent opportunity to understand how locomotor innovation can drive speciation. To evaluate the connection between the evolutionary success of rodents and the diversity of rodent locomotor ecologies, we used a large dataset of proximal limb CT scans from across Myomorpha and Geomyoidea to examine internal and external limb shape. Only fossorial rodents displayed a major reworking of their proximal limbs in either internal or external morphology, with other locomotor modes plotting within a generalist morphospace. Fossorial rodents were also the only locomotor mode to consistently show increased rates of humerus/femur morphological evolution. We propose that these rodent clades were successful at spreading into ecological niches due to high behavioral plasticity and small body sizes, allowing them to modify their locomotor mode without requiring major changes to their proximal limb morphology.

A new species of crab-eating rat of the genus Ichthyomys, from Ecuador (Rodentia, Cricetidae, Sigmodontinae)

Based on two adult specimens collected in the Río León (Azuay, Ecuador), we describe a new highland species of a small crab-eating rat of the genus Ichthyomys Thomas (Rodentia, Cricetidae, Ichthyomyini). It is distinguishable from Ichthyomys hydrobates (Winge, 1891), the species phenetically closest to it, by its smaller size, bicolored tail (unicolored in I. hydrobates), broad and heavily fringed hindfoot (narrower and moderately fringed in I. hydrobates), and several craniodental traits (e.g. rostrum short broad; nasals anteriorly truncated; interorbital region narrow; supraorbital margins smoothly rounded; supraorbital foramina small, zygomatic plate very narrow; incisors opisthodont; length of M3 half that of M2). The new species occurs in the western Andes in southern Ecuador and is allopatric with Ichthyomys stolzmanni Thomas, 1893, which also has a bicolored tail but is larger. The new species brings the number of Ecuadorean Ichthyomys to four, Ecuador thus becoming the country with the greatest diversity of Ichthyomyini (four genera and eight species).

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.