Fossils know it best: Using a new set of fossil calibrations to improve the temporal phylogenetic framework of murid rodents (Rodentia: Muridae)

Degeneration of the Olfactory System in a Murid Rodent that Evolved Diurnalism

In mammalian research, it has been debated what can initiate an evolutionary tradeoff between different senses, and the phenomenon of sensory tradeoff in rodents, the most abundant mammalian clade, is not evident. The Nile rat (Arvicanthis niloticus), a murid rodent, recently adapted to a diurnal niche through an evolutionary acquisition of daylight vision with enhanced visual acuity. As such, this model provides an opportunity for a cross-species investigation where comparative morphological and multi-omic analyses of the Nile rat are made with its closely related nocturnal species, e.g. the mouse (Mus musculus) and the rat (Rattus norvegicus). Thus, morphological examinations were performed, and evolutionary reductions in relative sizes of turbinal bone surfaces, the cribriform plate, and the olfactory bulb were discovered in Nile rats. Subsequently, we compared multiple murid genomes, and profiled olfactory epithelium transcriptomes of mice and Nile rats at various ages with RNA sequencing. The results further demonstrate that, in comparison with mouse olfactory receptor (OR) genes, Nile rat OR genes have experienced less frequent gain, more frequent loss, and more frequent expression reduction during their evolution. Furthermore, functional degeneration of coding sequences in the Nile rat lineage was found in OR genes, yet not in other genes. Taken together, these results suggest that acquisition of improved vision in the Nile rat has been accompanied by degeneration of both olfaction-related anatomical structures and OR gene repertoires, consistent with the hypothesis of an olfaction-vision tradeoff initiated by the switch from a nocturnal to a diurnal lifestyle in mammals.

Unraveling phylogenetic relationships and species boundaries in the arid adapted Gerbillus rodents (Muridae: Gerbillinae) by RAD-seq data

Gerbillus is one of the most speciose genera among rodents, with ca. 51 recognized species. Previous attempts to reconstruct the evolutionary history of Gerbillus mainly relied on the mitochondrial cyt-b marker as a source of phylogenetic information. In this study, we utilize RAD-seq genomic data from 37 specimens representing 11 species to reconstruct the phylogenetic tree for Gerbillus, applying concatenation and coalescence methods. We identified four highly supported clades corresponding to the traditionally recognized subgenera: Dipodillus, Gerbillus, Hendecapleura and Monodia. Only two uncertain branches were detected in the resulting trees, with one leading to diversification of the main lineages in the genus, recognized by quartet sampling analysis as uncertain due to possible introgression. We also examined species boundaries for four pairs of sister taxa, including potentially new species from Morocco, using SNAPP. The results strongly supported a speciation model in which all taxa are treated as separate species. The dating analyses confirmed the Plio-Pleistocene diversification of the genus, with the uncertain branch coinciding with the beginning of aridification of the Sahara at the the Plio-Pleistocene boundary. This study aligns well with the earlier analyses based on the cyt-b marker, reaffirming its suitability as an adequate marker for estimating genetic diversity in Gerbillus.

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.

Integrative systematics and evolutionary history of Berylmys bowersi (Mammalia, Rodentia, Muridae)

The Bower's Berylmys (Berylmys bowersi) is one of the largest rodent species with a wide distribution range in southern China and the Indochinese Peninsula. The taxonomy and evolutionary history of the B. bowersi is still controversial and confusing. In this study, we used two mitochondrial (Cyt b and COI) and three nuclear (GHR, IRBP, and RAG1) genes to estimate the phylogeny, divergence times, and biogeographic history of B. bowersi. We also explored morphological variations among the specimens collected across China. Our phylogenetic analyses indicated that the traditional B. bowersi contains at least two species: B. bowersi and B. latouchei. Berylmys latouchei was considered a junior synonym of B. bowersi distributed in eastern China, which is confirmed to be distinguishable at specific level because of its larger size, relatively larger and whiter hind feet, and several cranial traits. The estimated split of B. bowersi and B. latouchei was at the early Pleistocene (ca. 2.00 Mya), which might be the outcome of the combined effects of climate change in the early Pleistocene and isolation by the Minjiang River. Our results highlight the Wuyi Mountains in northern Fujian, China, as a glacial refugia during the Pleistocene and call for more intensive surveys and systematic revisions of small mammals in eastern China.

Dirigent gene editing of gossypol enantiomers for toxicity-depleted cotton seeds

Axial chirality of biaryls can generate varied bioactivities. Gossypol is a binaphthyl compound made by cotton plants. Of its two axially chiral isomers, (-)-gossypol is the bioactive form in mammals and has antispermatogenic activity, and its accumulation in cotton seeds poses health concerns. Here we identified two extracellular dirigent proteins (DIRs) from Gossypium hirsutum, GhDIR5 and GhDIR6, which impart the hemigossypol oxidative coupling into (-)- and (+)-gossypol, respectively. To reduce cotton seed toxicity, we disrupted GhDIR5 by genome editing, which eliminated (-)-gossypol but had no effects on other phytoalexins, including (+)-gossypol, that provide pest resistance. Reciprocal mutagenesis identified three residues responsible for enantioselectivity. The (-)-gossypol-forming DIRs emerged later than their enantiocomplementary counterparts, from tandem gene duplications that occurred shortly after the cotton genus diverged. Our study offers insight into how plants control enantiomeric ratios and how to selectively modify the chemical spectra of cotton plants and thereby improve crop quality.

Diversification and evolutionary history of the African laminated-toothed rats (Rodentia, Otomyini)

The African continent was subjected to periodic climatic shifts during the Pliocene and Pleistocene. These habitat changes greatly affected the evolutionary processes and tempo of diversification in numerous, widely distributed mammals. The Otomyini (Family Muridae) comprises three African rodent genera, Parotomys, Otomys and Myotomys, characterized by unique laminated-shaped molars. Species within this tribe generally prefer open-habitat and show low dispersal capabilities, with previous studies suggesting that their diversification was closely associated with climatic oscillations over the last four million years. Our phylogenetic reconstructions, based on three mitochondrial (mtDNA) genes (Cytb, COI and 12S) and four nuclear introns (EF, SPTBN, MGF and THY), identified eight major genetic clades that are distributed across southern, eastern and western Africa. Our data permit the re-examination of the taxonomic status of the three genera as well as the previously proposed mesic-arid dichotomy of the 10 South African species. Moreover, multiple mtDNA species delimitation methods incorporating 168 specimens estimated the number of Otomyini species to be substantially higher than the ∼30 recognized, suggesting that the current taxonomy will necessitate an integrative approach to delimit extant species diversity within the Otomyini. The data suggests that the origin of the tribe can be dated back to ∼5.7 million years ago (Ma) in southern Africa. The distribution and phylogenetic associations among the eight major otomyine evolutionary lineages can best be explained by several waves of northward colonization from southern Africa, complemented by independent reversed dispersals from eastern back to southern Africa at different time periods. There is strong support for the hypothesis that the radiation, dispersion, and diversification of the otomyine rodents is closely linked to recent Plio-Pleistocene climatic oscillations.

Prevalence of Pathogenic Leptospira spp. in Non-Volant Small Mammals of Hutan Lipur Sekayu, Terengganu, Malaysia

Leptospirosis is an important zoonotic disease that is transmitted worldwide through infected small mammals such as rodents. In Malaysia, there is a paucity of information on the animal reservoirs that are responsible for leptospirosis transmission, with only a few studies focusing on leptospirosis risk in recreational areas. Therefore, in this study we characterized the species composition and the prevalence of pathogenic Leptospira spp. in non-volant small mammals of Hutan Lipur Sekayu, Terengganu. We performed ten trapping sessions totaling 3000 trappings between September 2019 and October 2020. Kidney samples from captured individuals were extracted for the PCR detection of pathogenic Leptospira spp. Overall, we captured 45 individuals from 8 species (1.56% successful trapping effort), with 9 individuals testing positive for pathogenic Leptospira, that is, a 20% (n = 9/45) prevalence rate. Rattus tiomanicus (n = 22) was the most dominant captured species and had the highest positive individual with pathogenic Leptospira (44.4%, n = 4/9). Despite the low successful trapping effort in this study, the results show the high diversity of non-volant small mammals in Hutan Lipur Sekayu, and that they could also maintain and transmit pathogenic Leptospira.

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.

Uncovering the diversity of endemic Ethiopian fauna: complete mitochondrial genomes of four Lophuromys species (Rodentia, Muridae)

Complete mitochondrial genomes of four species of Ethiopian speckled brush-furred rats Lophuromys (L. chrysopus, L. menageshae, L. melanonyx, and L. simensis) were assembled for the first time. We provide data concerning the sequencing, assembly, and annotation of the obtained mitogenomes; compare two widely used circular-genome annotation tools (MITOS and MitoZ), and discuss relevant points concerning relationships within both Ethiopian Lophuromys and the Muridae family.

Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola

Molecular dating methods of population splits are crucial in evolutionary biology, but they present important difficulties due to the complexity of the genealogical relationships of genes and past migrations between populations. Using the double digest restriction-site associated DNA (ddRAD) technique and an isolation-with-migration (IM) model, we studied the evolutionary history of water vole populations of the genus Arvicola, a group of complex evolution with fossorial and semi-aquatic ecotypes. To do this, we first estimated mutation rates of ddRAD loci using a phylogenetic approach. An IM model was then used to estimate split times and other relevant demographic parameters. A set of 300 ddRAD loci that included 85 calibrated loci resulted in good mixing and model convergence. The results showed that the two populations of A. scherman present in the Iberian Peninsula split 34 thousand years ago, during the last glaciation. In addition, the much greater divergence from its sister species, A. amphibius, may help to clarify the controversial taxonomy of the genus. We conclude that this approach, based on ddRAD data and an IM model, is highly useful for analyzing the origin of populations and species.

Genetic data from the extinct giant rat from Tenerife (Canary Islands) points to a recent divergence from mainland relatives

Evolution of vertebrate endemics in oceanic islands follows a predictable pattern, known as the island rule, according to which gigantism arises in originally small-sized species and dwarfism in large ones. Species of extinct insular giant rodents are known from all over the world. In the Canary Islands, two examples of giant rats, †Canariomys bravoi and †Canariomys tamarani, endemic to Tenerife and Gran Canaria, respectively, disappeared soon after human settlement. The highly derived morphological features of these insular endemic rodents hamper the reconstruction of their evolutionary histories. We have retrieved partial nuclear and mitochondrial data from †C. bravoi and used this information to explore its evolutionary affinities. The resulting dated phylogeny confidently places †C. bravoi within the African grass rat clade (Arvicanthis niloticus). The estimated divergence time, 650 000 years ago (95% higher posterior densities: 373 000–944 000), points toward an island colonization during the Günz–Mindel interglacial stage. †Canariomys bravoi ancestors would have reached the island via passive rafting and then underwent a yearly increase of mean body mass calculated between 0.0015 g and 0.0023 g; this corresponds to fast evolutionary rates (in darwins (d), ranging from 7.09 d to 2.78 d) that are well above those observed for non-insular mammals.

Demographic History and Genomic Response to Environmental Changes in a Rapid Radiation of Wild Rats

For organisms to survive and prosper in a harsh environment, particularly under rapid climate change, poses tremendous challenges. Recent studies have highlighted the continued loss of megafauna in terrestrial ecosystems and the subsequent surge of small mammals, such as rodents, bats, lagomorphs, and insectivores. However, the ecological partitioning of these animals will likely lead to large variation in their responses to environmental change. In the present study, we investigated the evolutionary history and genetic adaptations of white-bellied rats (Niviventer Marshall, 1976), which are widespread in the natural terrestrial ecosystems in Asia but also known as important zoonotic pathogen vectors and transmitters. The southeastern Qinghai-Tibet Plateau was inferred as the origin center of this genus, with parallel diversification in temperate and tropical niches. Demographic history analyses from mitochondrial and nuclear sequences of Niviventer demonstrated population size increases and range expansion for species in Southeast Asia, and habitat generalists elsewhere. Unexpectedly, population increases were seen in N. eha, which inhabits the highest elevation among Niviventer species. Genome scans of nuclear exons revealed that among the congeneric species, N. eha has the largest number of positively selected genes. Protein functions of these genes are mainly related to olfaction, taste, and tumor suppression. Extensive genetic modification presents a major strategy in response to global changes in these alpine species.

Phylogenomics of African radiation of Praomyini (Muridae: Murinae) rodents: First fully resolved phylogeny, evolutionary history and delimitation of extant genera

The tribe Praomyini is a diversified group including 64 species and eight extant rodent genera. They live in a broad spectrum of habitats across whole sub-Saharan Africa. Members of this tribe are often very abundant, they have a key ecological role in ecosystems, they are hosts of many potentially pathogenic microorganisms and comprise numerous agricultural pests. Although this tribe is well supported by both molecular and morphological data, its intergeneric relationships and the species contents of several genera are not yet fully resolved. Recent molecular data suggest that at least three genera in current sense are paraphyletic. However, in these studies the species sampling was sparse and the resolution of relationships among genera was poor, probably due to a fast radiation of the tribe dated to the Miocene and insufficient amount of genetic data. Here we used genomic scale data (395 nuclear loci = 610,965 bp long alignment and mitogenomes = 14,745 bp) and produced the first fully resolved species tree containing most major lineages of the Praomyini tribe (i.e. all but one currently delimited genera and major intrageneric clades). Results of a fossil-based divergence dating analysis suggest that the radiation started during the Messinian stage (ca. 7 Ma) and was likely linked to a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forests, while many others adapted to a broad spectrum of new open lowland and montane habitats that appeared at the beginning of Pliocene. Our analyses clearly confirmed the presence of three polyphyletic genera (Praomys, Myomyscus and Mastomys). We review current knowledge of these three genera and suggest corresponding taxonomic changes. To keep genera monophyletic, we propose taxonomic re-arrangements and delimit four new genera. Furthermore, we discovered a new highly divergent genetic lineage of Praomyini in southwestern Ethiopia, which is described as a new species and genus.

Museum genomics reveals the rapid decline and extinction of Australian rodents since European settlement

Australia has the highest historically recorded rate of mammalian extinction in the world, with 34 terrestrial species declared extinct since European colonization in 1788. Among Australian mammals, rodents have been the most severely affected by these recent extinctions; however, given a sparse historical record, the scale and timing of their decline remain unresolved. Using museum specimens up to 184 y old, we generate genomic-scale data from across the entire assemblage of Australian hydromyine rodents (i.e., eight extinct species and their 42 living relatives). We reconstruct a phylogenomic tree for these species spanning ∼5.2 million years, revealing a cumulative total of 10 million years (>10%) of unique evolutionary history lost to extinction within the past ∼150 y. We find no evidence for reduced genetic diversity in extinct species just prior to or during decline, indicating that their extinction was extremely rapid. This suggests that populations of extinct Australian rodents were large prior to European colonization, and that genetic diversity does not necessarily protect species from catastrophic extinction. In addition, comparative analyses suggest that body size and biome interact to predict extinction and decline, with larger species more likely to go extinct. Finally, we taxonomically resurrect a species from extinction, Gould's mouse (Pseudomys gouldii Waterhouse, 1839), which survives as an island population in Shark Bay, Western Australia (currently classified as Pseudomys fieldi Waite, 1896). With unprecedented sampling across a radiation of extinct and living species, we unlock a previously inaccessible historical perspective on extinction in Australia. Our results highlight the capacity of collections-based research to inform conservation and management of persisting species.

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

Historical biogeography, systematics, and integrative taxonomy of the non-Ethiopian speckled pelage brush-furred rats (Lophuromys flavopunctatus group)

BACKGROUND

The speckled-pelage brush-furred rats (Lophuromys flavopunctatus group) have been difficult to define given conflicting genetic, morphological, and distributional records that combine to obscure meaningful accounts of its taxonomic diversity and evolution. In this study, we inferred the systematics, phylogeography, and evolutionary history of the L. flavopunctatus group using maximum likelihood and Bayesian phylogenetic inference, divergence times, historical biogeographic reconstruction, and morphometric discriminant tests. We compiled comprehensive datasets of three loci (two mitochondrial [mtDNA] and one nuclear) and two morphometric datasets (linear and geometric) from across the known range of the genus Lophuromys.

RESULTS

The mtDNA phylogeny supported the division of the genus Lophuromys into three primary groups with nearly equidistant pairwise differentiation: one group corresponding to the subgenus Kivumys (Kivumys group) and two groups corresponding to the subgenus Lophuromys (L. sikapusi group and L. flavopunctatus group). The L. flavopunctatus group comprised the speckled-pelage brush-furred Lophuromys endemic to Ethiopia (Ethiopian L. flavopunctatus members [ETHFLAVO]) and the non-Ethiopian ones (non-Ethiopian L. flavopunctatus members [NONETHFLAVO]) in deeply nested relationships. There were distinctly geographically structured mtDNA clades among the NONETHFLAVO, which were incongruous with the nuclear tree where several clades were unresolved. The morphometric datasets did not systematically assign samples to meaningful taxonomic units or agree with the mtDNA clades. The divergence dating and ancestral range reconstructions showed the NONETHFLAVO colonized the current ranges over two independent dispersal events out of Ethiopia in the early Pleistocene.

CONCLUSION

The phylogenetic associations and divergence times of the L. flavopunctatus group support the hypothesis that paleoclimatic impacts and ecosystem refugia during the Pleistocene impacted the evolutionary radiation of these rodents. The overlap in craniodental variation between distinct mtDNA clades among the NONETHFLAVO suggests unraveling underlying ecomorphological drivers is key to reconciling taxonomically informative morphological characters. The genus Lophuromys requires a taxonomic reassessment based on extensive genomic evidence to elucidate the patterns and impacts of genetic isolation at clade contact zones.

Molecular Evolution of Ecological Specialisation: Genomic Insights from the Diversification of Murine Rodents

Adaptive radiations are characterized by the diversification and ecological differentiation of species, and replicated cases of this process provide natural experiments for understanding the repeatability and pace of molecular evolution. During adaptive radiation, genes related to ecological specialization may be subject to recurrent positive directional selection. However, it is not clear to what extent patterns of lineage-specific ecological specialization (including phenotypic convergence) are correlated with shared signatures of molecular evolution. To test this, we sequenced whole exomes from a phylogenetically dispersed sample of 38 murine rodent species, a group characterized by multiple, nested adaptive radiations comprising extensive ecological and phenotypic diversity. We found that genes associated with immunity, reproduction, diet, digestion, and taste have been subject to pervasive positive selection during the diversification of murine rodents. We also found a significant correlation between genome-wide positive selection and dietary specialization, with a higher proportion of positively selected codon sites in derived dietary forms (i.e., carnivores and herbivores) than in ancestral forms (i.e., omnivores). Despite striking convergent evolution of skull morphology and dentition in two distantly related worm-eating specialists, we did not detect more genes with shared signatures of positive or relaxed selection than in a nonconvergent species comparison. Although a small number of the genes we detected can be incidentally linked to craniofacial morphology or diet, protein-coding regions are unlikely to be the primary genetic basis of this complex convergent phenotype. Our results suggest a link between positive selection and derived ecological phenotypes, and highlight specific genes and general functional categories that may have played an integral role in the extensive and rapid diversification of murine rodents.

Complex reticulate evolution of speckled brush-furred rats (Lophuromys) in the Ethiopian centre of endemism

The Ethiopian highlands represent a remarkable biodiversity 'hot spot' with a very high number of endemic species, even among vertebrates. Ethiopian representatives of a species complex of speckled brush-furred rats (Lophuromys flavopunctatus sensu lato) inhabit highland habitats ranging from low-elevation forests to Afroalpine grasslands. These may serve as a suitable model for understanding evolutionary processes leading to high genetic and ecological diversity in montane biodiversity hot spots. Here, we analyse the most comprehensive genetic data set of this group, comprising 315 specimens (all nine putative Ethiopian Lophuromys taxa sampled across most of their distribution ranges) genotyped at one mitochondrial and four nuclear markers, and thousands of SNPs from ddRAD sequencing. We performed phylogenetic analyses, delimited species and mapped their distribution and estimated divergence time between species (under the species-tree framework) and mitochondrial lineages. We found significant incongruence between mitochondrial and nuclear phylogenies, most probably caused by multiple interspecific introgression events. We discuss alternative scenarios of Ethiopian Lophuromys evolution, from retention of ancestral polymorphism to hybridization upon secondary contact of partially reproductively isolated lineages leading to reticulate evolution. Finally, we use the diversity of the speckled brush-furred rats for the description of the main biogeographic patterns in the fauna of the Ethiopian highlands.

Tempo and Mode: Evidence on a Protracted Split From a Dense Fossil Record

Fossil records generally inform paleobiologists about extinct taxa and rates of evolution measured at the scale of millions of years. Good records that are densely sampled through time can reveal species level details such as longevity in local sections. Yet fossil data normally do not address details of lineage microevolution because the density through time of lineage sampling is insufficient to perceive patterns at a precision finer than 106 years in most cases. This study concerns details of a splitting event in the evolution of murine rodents, an event for which multiple fossil samples dated to a precision of 105 years fortuitously document the tempo and mode of origin of sister species, the stems of two extant tribes of mice. Evolution of early Murinae in the northern part of the biogeographically restricted Indian subcontinent between 11.6 and 10.5 Ma involved cladogenesis of two crown taxa, the extant tribes Murini and Arvicanthini. Large samples of fossil rodent teeth document their divergence from a common morphological pool. Definitive basal Murini and Arvicanthini at 10.5 Ma are similar in size and differ by subtle features of the dentition. Those features occur sporadically in the common pool of older fossil teeth at 11.2, 11.4, and 11.6 Ma as inconsistent polymorphisms. Interpreted as a single lineage in the 11.6–11.2 Ma interval, variability of this abundant murine incorporated the roots of the two crown tribes. The pattern through time suggests morphological stasis for several hundred thousand years prior to splitting. This special case informs us on one example of evolution and shows that the tempo of splitting evolution in some cases may be measured in hundreds of thousands of years, followed by stasis once daughter species have differentiated morphologically.

Genomic insights into the host specific adaptation of the Pneumocystis genus

Pneumocystis jirovecii, the fungal agent of human Pneumocystis pneumonia, is closely related to macaque Pneumocystis. Little is known about other Pneumocystis species in distantly related mammals, none of which are capable of establishing infection in humans. The molecular basis of host specificity in Pneumocystis remains unknown as experiments are limited due to an inability to culture any species in vitro. To explore Pneumocystis evolutionary adaptations, we have sequenced the genomes of species infecting macaques, rabbits, dogs and rats and compared them to available genomes of species infecting humans, mice and rats. Complete whole genome sequence data enables analysis and robust phylogeny, identification of important genetic features of the host adaptation, and estimation of speciation timing relative to the rise of their mammalian hosts. Our data reveals insights into the evolution of P. jirovecii, the sole member of the genus able to infect humans.

Cissé, Ma et al. utilize genomic data from Pneumocystis species infecting macaques, rabbit, dogs and rats to investigate the molecular basis of host specificity in Pneumocystis. Their analyses provide insight to the specific adaptations enabling the infection of humans by P. jirovecii.

ZP4 Is Present in Murine Zona Pellucida and Is Not Responsible for the Specific Gamete Interaction

Mammalian eggs are surrounded by an extracellular matrix called the zona pellucida (ZP). This envelope participates in processes such as acrosome reaction induction, sperm binding, protection of the oviductal embryo, and may be involved in speciation. In eutherian mammals, this coat is formed of three or four glycoproteins (ZP1–ZP4). While Mus musculus has been used as a model to study the ZP for more than 35 years, surprisingly, it is the only eutherian species in which the ZP is formed of three glycoproteins Zp1, Zp2, and Zp3, Zp4 being a pseudogene. Zp4 was lost in the Mus lineage after it diverged from Rattus, although it is not known when precisely this loss occurred. In this work, the status of Zp4 in several murine rodents was tested by phylogenetic, molecular, and proteomic analyses. Additionally, assays of cross in vitro fertilization between three and four ZP rodents were performed to test the effect of the presence of Zp4 in murine ZP and its possible involvement in reproductive isolation. Our results showed that Zp4 pseudogenization is restricted to the subgenus Mus, which diverged around 6 MYA. Heterologous in vitro fertilization assays demonstrate that a ZP formed of four glycoproteins is not a barrier for the spermatozoa of species with a ZP formed of three glycoproteins. This study identifies the existence of several mouse species with four ZPs that can be considered suitable for use as an experimental animal model to understand the structural and functional roles of the four ZP proteins in other species, including human.

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.

Locomotory mode transitions alter phenotypic evolution and lineage diversification in an ecologically rich clade of mammals

The relationship between organismal function and form is a cornerstone of biology because functional diversity is key to generating and maintaining ecological diversity. Morphological changes often occur in unison with behavioral or ecological transitions, and this process may foster diversification, but alternately could trap a species on an adaptive peak. We estimated the most comprehensive phylogenetic hypothesis of Murinae, a young (∼15 million years) and diverse (∼700 species) clade of mammals. We then tested for correlated evolution among four morphological traits with potential links to locomotor modes (Arboreal, General, Terrestrial, and Amphibious), then investigated the effects of locomotion on morphological and lineage diversification. We found unique combinations of trait values for each locomotor mode, including strong covariance between the tail and hindfoot lengths of specialized Arboreal and ecologically flexible General species. Low diversification rates and long branch lengths suggest that specialized lineages represent stable evolutionary "cul-de-sacs." General species, characterized by the classic "rat-like" body plan and broad locomotor abilities, have narrow optimal trait values and slow phenotypic evolution, but high lineage diversification rates. Our findings suggest that versatile, generalist forms act as seeds of species diversity and morphological specialization, which together build ecologically diverse radiations.

Multilocus phylogeny of African striped grass mice (Lemniscomys): Stripe pattern only partly reflects evolutionary relationships

Murine rodents are one of the most evolutionary successful groups of extant mammals. They are also important for human as vectors and reservoirs of zoonoses and agricultural pests. Unfortunately, their fast and relatively recent diversification impedes our understanding of phylogenetic relationships and species limits of many murine taxa, including those with very conspicuous phenotype that has been frequently used for taxonomic purposes. One of such groups are the striped grass mice (genus Lemniscomys), distributed across sub-Saharan Africa in 11 currently recognized species. These are traditionally classified into three morphological groups according to different pelage colouration on the back: (a) L. barbarus group (three species) with several continuous pale longitudinal stripes; (b) L. striatus group (four species) with pale stripes diffused into short lines or dots; and (c) L. griselda group (four species) with a single mid-dorsal black stripe. Here we reconstructed the most comprehensive molecular phylogeny of the genus Lemniscomys to date, using the largest currently available multi-locus genetic dataset of all but two species. The results show four main lineages (=species complexes) with the distribution corresponding to the major biogeographical regions of Africa. Surprisingly, the four phylogenetic lineages are only in partial agreement with the morphological classification, suggesting that the single-stripe and/or multi-striped phenotypes evolved independently in multiple lineages. Divergence dating showed the split of Lemniscomys and Arvicanthis genera at the beginning of Pleistocene; most of subsequent speciation processes within Lemniscomys were affected by Pleistocene climate oscillations, with predominantly allopatric diversification in fragmented savanna biome. We propose taxonomic suggestions and directions for future research of this striking group of African rodents.

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.

Population structure of Apodemus flavicollis and comparison to Apodemus sylvaticus in northern Poland based on RAD-seq

Background

Mice of the genus Apodemus are one the most common mammals in the Palaearctic region. Despite their broad range and long history of ecological observations, there are no whole-genome data available for Apodemus, hindering our ability to further exploit the genus in evolutionary and ecological genomics context.

Results

Here we present results from the double-digest restriction site-associated DNA sequencing (ddRAD-seq) on 72 individuals of A. flavicollis and 10 A. sylvaticus from four populations, sampled across 500 km distance in northern Poland. Our data present clear genetic divergence of the two species, with average p-distance, based on 21377 common loci, of 1.51% and a mutation rate of 0.0011 - 0.0019 substitutions per site per million years. We provide a catalogue of 117 highly divergent loci that enable genetic differentiation of the two species in Poland and to a large degree of 20 unrelated samples from several European countries and Tunisia. We also show evidence of admixture between the three A. flavicollis populations but demonstrate that they have negligible average population structure, with largest pairwise F_ST<0.086.

Conclusion

Our study demonstrates the feasibility of ddRAD-seq in Apodemus and provides the first insights into the population genomics of the species.

The fossil record of spiders revisited: implications for calibrating trees and evidence for a major faunal turnover since the Mesozoic

Studies in evolutionary biology and biogeography increasingly rely on the estimation of dated phylogenetic trees using molecular clocks. In turn, the calibration of such clocks is critically dependent on external evidence (i.e. fossils) anchoring the ages of particular nodes to known absolute ages. In recent years, a plethora of new fossil spiders, especially from the Mesozoic, have been described, while the number of studies presenting dated spider phylogenies based on fossil calibrations increased sharply. We critically evaluate 44 of these studies, which collectively employed 67 unique fossils in 180 calibrations. Approximately 54% of these calibrations are problematic, particularly regarding unsupported assignment of fossils to extant clades (44%) and crown (rather than stem) dating (9%). Most of these cases result from an assumed equivalence between taxonomic placement of fossils and their phylogenetic position. To overcome this limitation, we extensively review the literature on fossil spiders, with a special focus on putative synapomorphies and the phylogenetic placement of fossil species with regard to their importance for calibrating higher taxa (families and above) in the spider tree of life. We provide a curated list including 41 key fossils intended to be a basis for future estimations of dated spider phylogenies. In a second step, we use a revised set of 23 calibrations to estimate a new dated spider tree of life based on transcriptomic data. The revised placement of key fossils and the new calibrated tree are used to resolve a long-standing debate in spider evolution - we tested whether there has been a major turnover in the spider fauna between the Mesozoic and Cenozoic. At least 17 (out of 117) extant families have been recorded from the Cretaceous, implying that at least 41 spider lineages in the family level or above crossed the Cretaeous-Paleogene (K-Pg) boundary. The putative phylogenetic affinities of families known only from the Mesozoic suggest that at least seven Cretaceous families appear to have no close living relatives and might represent extinct lineages. There is no unambiguous fossil evidence of the retrolateral tibial apophysis clade (RTA-clade) in the Mesozoic, although molecular clock analyses estimated the major lineages within this clade to be at least ∼100 million years old. Our review of the fossil record supports a major turnover showing that the spider faunas in the Mesozoic and the Cenozoic are very distinct at high taxonomic levels, with the Mesozoic dominated by Palpimanoidea and Synspermiata, while the Cenozoic is dominated by Araneoidea and RTA-clade spiders.

Commensalism outweighs phylogeographical structure in its effect on phenotype of a Sudanian savanna rodent

The murid rodent Praomys daltoni is widespread in Sudanian savanna and woodlands of West Africa, and previous study of mitochondrial DNA variability suggested that it encompasses the phenotypically (small, grey-bellied) and ecologically (commensal) distinct form, Praomys derooi. Here, we comprehensively examined the genetic and morphological diversity within the complex. Six mitochondrial lineages showed a fine-scale phylogeographical pattern, whereas delimitation based on nuclear loci pooled four of them into a single widespread unit. A newly discovered lineage from southern Mauritania stands apart from the rest of the complex and might represent an unrecognized species. At the same time, the internal position of P. derooi (C2 mitochondrial lineage) was confirmed by the multilocus analysis. The magnitude of genetic distances between major phylogeographical lineages was typical for interspecific divergence in other clades of Praomys, despite the little differences among them in morphology (skull and upper molar row shapes). The most pronounced morphological shift was associated with a transition to commensalism, especially in P. derooi, but also in other lineages. This makes the whole complex a suitable model for the study of phenotypic novelty, the evolution of commensalism and conditions for ecological speciation.

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.

A simple skeletal measurement effectively predicts climbing behaviour in a diverse clade of small mammals

Arboreal locomotion allows access to above-ground resources and might have fostered the diversification of mammals. Nevertheless, simple morphological measurements that consistently correlate with arboreality remain indefinable. As such, the climbing habits of many species of mammals, living and extinct, remain speculative. We collected quantitative data on the climbing tendencies of 20 species of murine rodents, an ecologically and morphologically diverse clade. We leveraged Bayesian phylogenetic mixed models (BPMMs), incorporating intraspecific variation and phylogenetic uncertainty, to determine which, if any, traits (17 skeletal indices) predict climbing frequency. We used ordinal BPMMs to test the ability of the indices to place 48 murine species that lack quantitative climbing data into three qualitative locomotor categories (terrestrial, general and arboreal). Only two indices (both measures of relative digit length) accurately predict locomotor styles, with manus digit length showing the best fit. Manus digit length has low phylogenetic signal, is largely explained by locomotor ecology and might effectively predict locomotion across a multitude of small mammals, including extinct species. Surprisingly, relative tail length, a common proxy for locomotion, was a poor predictor of climbing. In general, detailed, quantitative natural history data, such as those presented here, are needed to enhance our understanding of the evolutionary and ecological success of clades.

The complete mitochondrial genome of marmoset rats Hapalomys delacouri (Rodentia: Muridae)

The marmoset rats (Hapalomys delacouri) is a rarely investigated rodent. It occupies important ecological niche and phylogenetic position. The complete mitochondrial genome of H. delacouri was determined for the first time by long PCR and second-generation sequencing. The results showed that the entire mitogenome of H. delacouri was 16,316 bp long (deposited in GenBank with accession number MK850463). The gene order and orientation were the same as the most rodent. Only tRNA^Lys (TTT) and tRNA^Ser (AGN) of 22 transfer RNAs showed atypical cloverleaf structures, lacking a dihydrouridine (DHU) arm. The newly added H. delacouri mitogenome will benefit population genetic and phylogenetic studies in the rodent.

Multiple radiations of spiny mice (Rodentia: Acomys) in dry open habitats of Afro-Arabia: evidence from a multi-locus phylogeny

Background

Spiny mice of the genus Acomys are distributed mainly in dry open habitats in Africa and the Middle East, and they are widely used as model taxa for various biological disciplines (e.g. ecology, physiology and evolutionary biology). Despite their importance, large distribution and abundance in local communities, the phylogeny and the species limits in the genus are poorly resolved, and this is especially true for sub-Saharan taxa. The main aims of this study are (1) to reconstruct phylogenetic relationships of Acomys based on the largest available multilocus dataset (700 genotyped individuals from 282 localities), (2) to identify the main biogeographical divides in the distribution of Acomys diversity in dry open habitats in Afro-Arabia, (3) to reconstruct the historical biogeography of the genus, and finally (4) to estimate the species richness of the genus by application of the phylogenetic species concept.

Results

The multilocus phylogeny based on four genetic markers shows presence of five major groups of Acomys called here subspinosus, spinosissimus, russatus, wilsoni and cahirinus groups. Three of these major groups (spinosissimus, wilsoni and cahirinus) are further sub-structured to phylogenetic lineages with predominantly parapatric distributions. Combination of alternative species delimitation methods suggests the existence of 26 molecular operational taxonomic units (MOTUs), potentially corresponding to separate species. The highest genetic diversity was found in Eastern Africa. The origin of the genus Acomys is dated to late Miocene (ca. 8.7 Ma), when the first split occurred between spiny mice of eastern (Somali-Masai) and south-eastern (Zambezian) savannas. Further diversification, mostly in Plio-Pleistocene, and the current distribution of Acomys were influenced by the interplay of global climatic factors (e.g., Messinian salinity crisis, intensification of Northern Hemisphere glaciation) with local geomorphology (mountain chains, aridity belts, water bodies). Combination of divergence dating, species distribution modelling and historical biogeography analysis suggests repeated “out-of-East-Africa” dispersal events into western Africa, the Mediterranean region and Arabia.

Conclusions

The genus Acomys is very suitable model for historical phylogeographic and biogeographic reconstructions of dry non-forested environments in Afro-Arabia. We provide the most thorough phylogenetic reconstruction of the genus and identify major factors that influenced its evolutionary history since the late Miocene. We also highlight the urgent need of integrative taxonomic revision of east African taxa.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1380-9) contains supplementary material, which is available to authorized users.