Divergence Dates Research Articles

Population genomics of a specialized insect, Tetraopes texanus (Coleoptera: Cerambycidae), across a fragmented grassland system

AbstractSpecialist insects are especially susceptible to loss of genetic diversity in the face of habitat destruction and fragmentation. Implementing effective conservation practices for specialist insects will benefit from knowledge of population structure and genetic diversity. Because insects are hyper-diverse, characterizing the population structure of all species within the insect community is untenable, even if focused within a particular habitat type. Thus, concentrating on a single species specialized to a particular habitat type is needed to infer general trends. Here, we investigate the range-wide population genetics of Tetraopes texanus Horn 1878 (Coleoptera: Cerambycidae), which provides a useful model of grassland insects due to its’ habitat specificity and unique biology. Tetraopes texanus occurs primarily in Texas and Oklahoma, into Northern Mexico, and possibly into eastern New Mexico but also occurs in Black Belt prairies of Mississippi and Alabama. Mitochondrial and nuclear DNA (RAD-seq) analysis identified two distinct population clusters of T. texanus corresponding to the Texas and Oklahoma population and the Mississippi and Alabama population. Demographic models indicate ongoing, though incomplete, isolation of the two populations, with estimated dates of divergence in the mid-Pleistocene, coinciding with the end of a glacial period and a shift in glacial interval. These results can inform conservation of grassland adapted insects and offers insight to the biogeography of the Gulf Coastal Plain.

Evolutionary origins, macroevolutionary dynamics, and climatic niche space of the succulent plant syndrome in the Caryophyllales.

The succulent plant syndrome is defined by the coordination of traits that enhance internal water storage within plant tissues. Although distributed globally in different habitats, succulent plants are thought to have evolved to avoid drought in arid regions, due to trait modifications that decrease tissue water deficits. We evaluated the evolution and the ecological significance of the succulent strategy at a global scale by comparing the climatic niche of species displaying succulence within the Core Caryophyllales with their non-succulent relatives. We assembled and curated a worldwide dataset of 201K georeferenced records belonging to 5447 species within 28 families, and analyzed the climatic niche of species along with their origin and evolutionary trajectories using ecological niche modeling, phylogenetic regression, divergence dates and ancestral state estimation. Results indicate the Core Caryophyllales have inhabited drylands since their origin in the Early Cretaceous. However, the succulent syndrome appeared and diversified during later geologic periods. The climatic niche space of succulents is narrower than non-succulent relatives, but no climate niche separation was detected between groups. Our results support alternative interpretations on the environmental and ecological forces that spurred the origin and diversification of the succulent plant syndrome and the radiation of rich succulent lineages.

Genomics of historical museum collections clarifies species diversity in Cuban hutias (Capromys)

Abstract Specimen-based taxonomic research is essential for understanding diversity and setting management frameworks for threatened mammal faunas, and ancient DNA techniques are increasingly used to extract information from taxonomically relevant historical specimens. The largest survivors of the depleted Caribbean mammal fauna are hutias in the genus Capromys, which is usually interpreted as containing a single species, C. pilorides. Previous studies have demonstrated genetic differentiation of Capromys populations across Cuba, but infrageneric species diversity and nomenclature remain unclear. We conducted ancient DNA analysis of historical Capromys samples using cytochrome b and complete mitogenome data sets, and including the 19th-century holotypes of 2 species now considered synonyms, C. fournieri and C. geayi. Our analyses identify distinct western and central/eastern Capromys clades that diverged 1.75 Mya based upon mitogenome data. These clades are separated by the Havana–Matanzas Channel, which represented a barrier to dispersal throughout the Neogene–Quaternary. Divergence date comparisons with other hutia species provide support for interpreting divergence between Capromys populations as species-level differentiation. Although we were unable to yield amplifiable DNA from the C. fournieri holotype, our analyses confidently assign the C. geayi holotype to the western Capromys clade. We therefore recognize 2 extant Capromys species: C. geayi (western Cuba) and C. pilorides (central/eastern Cuba and Cayman Islands).

Phylogeny and biogeography support ancient vicariance and subsequent dispersal out of Africa in Palpimanidae spiders (Araneae)

Abstract The Palpimanidae are one of five extant Palpimanoidea families that occur mainly in South America and Africa, although there are lineages in Madagascar, islands of the Indian Ocean, and parts of Asia. Here we examine the role of plate tectonics in shaping the distribution of Palpimanidae. We perform molecular sequencing via target enrichment, which makes use of fragmented DNA, because most specimens are stored in natural history museum collections and were not properly preserved for molecular sequencing. We perform phylogenetic analysis, divergence dating, and ancestral range reconstructions to assess whether continental vicariance shaped the evolution of Palpimanidae. We also examine evolution of eye loss via ancestral character reconstruction. We report the first Palpimanidae phylogeny based on genomic data that samples the majority of Chediminae genera. Results suggest that Palpimanidae originated in the Triassic, with diversification spanning the Jurassic to the Cretaceous. Vicarance played a role in early diversification, with later range expansion out of Africa. Based on morphology and phylogenetic analysis, Sceliraptor is synonymized with Sarascelis, Sceliscelis is synonymized with Scelidocteus, and the new genus and species Sitamacho tao gen. nov., sp. nov. is described, with three species transferred from Hybosida.

Historical biogeography and the evolution of habitat preference in the North American camel spider family, Eremobatidae (Arachnida:Solifugae)

Abiotic variables can influence species distributions, often restricting taxa to an acquired climatic signature or conversely, related species are conserved in the same ecological space over millions of years. An investigation into how abiotic change has shaped geographic distributions of taxa may be key to understanding diversification of lineages, and in the absence of reliable morphological characteristics, such information may support taxonomic units at multiple scales.Here, we examine the historical biogeography and patterns of habitat preference within the North American solifuge family, Eremobatidae. A previous study demonstrated that a major taxonomic revision of Eremobatidae is warranted, however recent studies demonstrate high levels of morphological convergence within the group, thus a re-classification of generic boundaries using additional information must be prioritized before we can formally begin solid revisionary efforts. In this study, we aimed to reconstruct a well-resolved phylogenetic hypothesis of Eremobatidae by filtering UCE loci based on informativeness, by mitigating the effect of cogenic UCE on phylogenetic estimation, and by supplementing our curated UCE loci with mitochondrial information. Using our preferred topology, in conjunction with published estimated divergence dates for Eremobatidae, we inferred a time-calibrated phylogenetic hypothesis to inform the historical biogeography and patterns of habitat preference. The two major habitat types that were observed for Eremobatidae were warm deserts for early diverging taxa and a subsequent evolution to cold deserts and Mediterranean California ecoregions for later diverging taxa. Eremobatid niche space, determined by temperature and precipitation, has been conserved for at least 25 million years in North America, supporting a warm desert origin, and thus supporting high species richness in the Sonoran and Mexican Plateau. Overall, our study provides support for new generic level designations within Eremobatidae.

Species limits and hybridization in Andean leaf-eared mice (Phyllotis).

Leaf-eared mice (genus Phyllotis) are among the most widespread and abundant small mammals in the Andean Altiplano, but species boundaries and distributional limits are often poorly delineated due to sparse survey data from remote mountains and high-elevation deserts. Here we report a combined analysis of mitochondrial DNA variation and whole-genome sequence (WGS) variation in Phyllotis mice to delimit species boundaries, to assess the timescale of diversification of the group, and to examine evidence for interspecific hybridization. Estimates of divergence dates suggest that most diversification of Phyllotis occurred during the past 3 million years. Consistent with the Pleistocene Aridification hypothesis, our results suggest that diversification of Phyllotis largely coincided with climatically induced environmental changes in the mid- to late Pleistocene. Contrary to the Montane Uplift hypothesis, most diversification in the group occurred well after the major phase of uplift of the Central Andean Plateau. Species delimitation analyses revealed surprising patterns of cryptic diversity within several nominal forms, suggesting the presence of much undescribed alpha diversity in the genus. Results of genomic analyses revealed evidence of ongoing hybridization between the sister species Phyllotis limatus and P. vaccarum and suggest that the contemporary zone of range overlap between the two species represents an active hybrid zone.

Phylogenetic systematics of Vigna sensu stricto in the context of Physostigma and allies.

Vigna includes economically vital crops and wild species. Molecular systematic studies of Vigna species resulted in generic segregates of many New World (NW) species. However, limited Old World (OW) sampling left questions regarding inter- and intraspecific relationships in Vigna s.s. African species, including the putative sister genus Physostigma, were comprehensively sampled within the context of NW relatives. Maximum likelihood and Bayesian inference analyses of the chloroplast matK-trnK and nuclear ribosomal ITS/5.8 S (ITS) DNA regions were undertaken to resolve OW Vigna taxonomic questions. Divergence dates were estimated using BEAST to date key nodes in the phylogeny. Analyses of matK and ITS data supported five clades of Vigna s.s.: subg. Lasiospron, a reduced subg. Vigna, subg. Haydonia, subg. Ceratotropis, an enlarged subg. Plectrotropis, and a clade including V. kirkii and V. stenophylla. Genome size estimates of 601 Mb for V. kirkii are near the overall mean of the genus, whereas V. stenophylla had a larger genome (810 Mb), similar to some Vigna subg. Ceratotropis or Plectrotropis species. Former subg. Vigna is reduced to yellow- and blue-flowered species and subg. Plectrotropis is enlarged to mostly all white-, pink-, and purple-flowered species. The age of the split between NW and OW Vigna lineages is ~6-7 Myr. Genome size estimates cannot rule out a polyploid or hybrid origin for V. stenophylla, potentially involving extinct lineage ancestors of Vigna subg. Ceratotropis or Plectrotropis, as indicated by network and phylogenetic analyses. Taxonomic revisions are suggested based on these results.

Investigating the emergence of a zoonotic virus: phylogenetic analysis of European bat lyssavirus 1 in the UK.

European bat lyssavirus 1 (EBLV-1, Lyssavirus hamburg) is predominantly detected in serotine bats (Eptesicus serotinus) and is responsible for the majority of bat rabies cases in mainland Europe. A passive bat rabies surveillance scheme detected the virus in a serotine bat in the UK for the first time in October 2018. As of May 2024, 34 cases have been reported, 20 of which involved contact with an animal and 5 reported human contact. We investigated the emergence of EBLV-1 by undertaking comprehensive sequence analysis and Bayesian phylogenetics, based on complete virus genomes of 33 UK sequences and 108 sequences covering six countries in mainland Europe (1968-2023), including 21 French EBLV-1-positive RNA samples sequenced for this study. Sequence analysis revealed extreme similarity among UK EBLV-1 sequences (99.9%-100%), implying a single source of introduction rather than multiple independent introductions. Bayesian analysis revealed that the UK EBLV-1 sequences shared their most recent common ancestor with an EBLV-1 sequence from a serotine bat detected in Brittany, France, in 2001, with an estimated date of divergence of 1997. Within the UK sequences, the earliest divergence was estimated to occur in 2007. This study provides valuable insights into the molecular epidemiology of an emerging zoonotic pathogen and improved understanding of the risks posed to public and animal health.

Identification and Characterization of an Alphacoronavirus in Rhinolophus sinicus and a Betacoronavirus in Apodemus ilex in Yunnan, China.

Coronaviruses (CoVs), the largest positive-sense RNA viruses, have caused infections in both humans and animals. The cross-species transmission of CoVs poses a serious threat to public health. Rodents and bats, the two largest orders of mammals, serve as significant natural reservoirs for CoVs. It is important to monitor the CoVs carried by bats and rodents. In this study, we collected 410 fecal samples from bats and 74 intestinal samples from rats in Yunnan Province, China. Using RT-PCR, we identified one positive sample for alphacoronavirus (TC-14) from Rhinolophus sinicus (Chinese rufous horseshoe bat) and two positive samples for betacoronavirus (GS-53, GS-56) from Apodemus ilex (Rodentia: Muridae). We successfully characterized the complete genomes of TC-14 and GS-56. Phylogenetic analysis revealed that TC-14 clustered with bat CoV HKU2 and SADS-CoV, while GS-56 was closely related to rat CoV HKU24. The identification of positive selection sites and estimation of divergence dates further helped characterize the genetic evolution of TC-14 and GS-56. In summary, this research reveals the genetic evolution characteristics of TC-14 and GS-56, providing valuable references for the study of CoVs carried by bats and rodents in Yunnan Province.

Population genetics and phylogeography of Trachylepis sulcata (Peters, 1867) and T. ansorgii (Boulenger, 1907) in south-western Africa

ABSTRACT Ansorge’s Rock Skink Trachylepis ansorgii (Boulenger, 1907) is an Angolan taxon, the taxonomic distinctiveness and geographic distribution of which are poorly understood. It is closely related to the widespread Western Rock Skink T. sulcata (Peters, 1867) from Namibia and South Africa, but heretofore a lack of samples has prevented a comprehensive assessment of T. ansorgii in a molecular phylogenetic context. We combine new genetic sampling from south-western Angola, including topotypical material of T. ansorgii, with published sequences from South Africa and Namibia to identify population structure, phylogenetic relationships, and divergence dates within this species complex. A multi-locus dataset of three nuclear and two mitochondrial loci recovered significant population structuring with a centre of diversity in south-western Angola and northern Namibia. Mitochondrial data recovered seven clades representing distinct geographic populations, while the nuclear data supported either two or three deeper groupings. Mito-nuclear discordance was observed with respect to the geographic boundary between T. ansorgii and T. sulcata. The nuclear data support a break along the western Kunene River (the political boundary between Angola and Namibia), while the mitochondrial data support this break ∼250 km to the north in south-western Angola. A time-calibrated BEAST phylogeny found the deepest species-level divergence to have occurred in the late Miocene/early Pliocene (∼6 mya), potentially related to the formation of the Kunene River. Our results support the recognition of both taxa at the species level, and add further evidence that south-western Angola is a centre of reptile diversity.

First fossil species of family Hyidae (Arachnida: Pseudoscorpiones) confirms 99 million years of ecological stasis in a Gondwanan lineage.

Burmese amber preserves a diverse assemblage of Cretaceous arachnids, and among pseudoscorpions (Arachnida: Pseudoscorpiones), ten species in five families have already been named. Here, we describe a new fossil species from Burmese amber in the pseudoscorpion family Hyidae, providing detailed measurements, photographs and 3D-models from synchrotron scanning. Based on morphology, the new fossil, Hya fynni sp. nov. is placed in the genus Hya, and is nearly identical to extant species in the genus, except for the position of trichobothrium est on the pedipalpal chela, thereby indicating extreme morphological stasis in this invertebrate lineage over the last 99 million years. Hya fynni represents the first described fossil species in Hyidae, and the third described Burmese fossil in the superfamily Neobisioidea. It also joins the garypinid, Amblyolpium burmiticum, in representing the oldest fossil records for extant pseudoscorpion genera. Considering proposed divergence dates, the newly described fossil species bolsters a Gondwanan origin for Hyidae, and provides evidence for the "Late Jurassic Rifting" hypothesis for the Burma Terrane, in which this landmass rifted from Gondwana in the Late Jurassic and collided with Eurasia by the Cretaceous/Eocene. Like Hya species today, H. fynni likely inhabited humicolous microhabitats in tropical forests on the Burma Terrane, supporting ecological niche stasis for this family since the Mesozoic.

Systematics and biogeography of a Sunda-Papuan snake lineage (Natricidae: Tropidonophis Jan 1863)

Abstract Sunda-Papuan keelback snakes (Serpentes: Natricidae: Tropidonophis Jan 1863) include 20 species distributed from the Philippines south-east through the Moluccas to New Guinea and Australia. Diversity of this insular snake lineage peaks on the island of New Guinea. Previous phylogenetic studies incorporating Tropidonophis have been limited to multi-locus Sanger-sequenced datasets with broad squamate or family-level focus. We used a targeted-sequence capture approach to sequence thousands of nuclear ultraconserved elements (UCEs) to construct the most comprehensive sequence-based phylogenetic hypothesis for this genus and estimate ancestral biogeography. Phylogenies indicate the genus is monophyletic given recent taxonomic reassignment of Rhabdophis spilogaster to Tropidonophis. All UCE phylogenies recovered a monophyletic Tropidonophis with reciprocally monophyletic Philippine and New Guinean clades. Divergence dating and ancestral range estimation suggest dispersal to New Guinea from the Philippines to have occurred during the Mid-Miocene via the Oceanic Arc Terranes. From Late Miocene into the Pliocene the genus experienced rapid diversification from orogeny of the New Guinean Central Cordillera from Oceanic Arc Terrane accretion on the northern boundary of the Sahul Shelf. Future collecting of missing taxa from the Moluccas and Indonesian Papua will better the understanding of non-volant faunal biogeography and diversification in this tectonically complex Pacific arena.

Genomic analysis reveals deep population divergence in the water snake Trimerodytes percarinatus (Serpentes, Natricidae).

Although several phylogeographic studies of Asian snakes have been conducted, most have focused on pitvipers, with non-venomous snakes, such as colubrids or natricids, remaining poorly studied. The Chinese keelback water snake (Trimerodytes percarinatus Boulenger) is a widespread, semiaquatic, non-venomous species occurring in China and southeastern Asia. Based on mitochondrial DNA (mtDNA) and single nucleotide polymorphism (SNP) data, we explored the population genetic structure, genetic diversity, and evolutionary history of this species. MtDNA-based phylogenetic analysis showed that T. percarinatus was composed of five highly supported and geographically structured lineages. SNP-based phylogenetic analysis, principal component analysis, and population structure analysis consistently revealed four distinct, geographically non-overlapping lineages, which was different from the mtDNA-based analysis in topology. Estimation of divergence dates and ancestral area of origin suggest that T. percarinatus originated ~12.68 million years ago (95% highest posterior density: 10.36-15.96 Mya) in a region covering southwestern China and Vietnam. Intraspecific divergence may have been triggered by the Qinghai-Xizang Plateau uplift. Population demographics and ecological niche modeling indicated that the effective population size fluctuated during 0.5 Mya and 0.002 Mya. Based on the data collected here, we also comment on the intraspecific taxonomy of T. percarinatus and question the validity of the subspecies T. p. suriki.

A winged relative of ice-crawlers in amber bridges the cryptic extant Xenonomia and a rich fossil record.

Until the advent of phylogenomics, the atypical morphology of extant representatives of the insect orders Grylloblattodea (ice-crawlers) and Mantophasmatodea (gladiators) had confounding effects on efforts to resolve their placement within Polyneoptera. This recent research has unequivocally shown that these species-poor groups are closely related and form the clade Xenonomia. Nonetheless, divergence dates of these groups remain poorly constrained, and their evolutionary history debated, as the few well-identified fossils, characterized by a suite of morphological features similar to that of extant forms, are comparatively young. Notably, the extant forms of both groups are wingless, whereas most of the pre-Cretaceous insect fossil record is composed of winged insects, which represents a major shortcoming of the taxonomy. Here, we present new specimens embedded in mid-Cretaceous amber from Myanmar and belonging to the recently described species Aristovia daniili. The abundant material and pristine preservation allowed a detailed documentation of the morphology of the species, including critical head features. Combined with a morphological data set encompassing all Polyneoptera, these new data unequivocally demonstrate that A.daniili is a winged stem Grylloblattodea. This discovery demonstrates that winglessness was acquired independently in Grylloblattodea and Mantophasmatodea. Concurrently, wing apomorphic traits shared by the new fossil and earlier fossils demonstrate that a large subset of the former "Protorthoptera" assemblage, representing a third of all known insect species in some Permian localities, are genuine representatives of Xenonomia. Data from the fossil record depict a distinctive evolutionary trajectory, with the group being both highly diverse and abundant during the Permian but experiencing a severe decline from the Triassic onwards.

Total-evidence phylogeny of the subfamily Cylapinae and the divergence dates for its subgroupings (Insecta: Heteroptera: Miridae)

Abstract Representatives of the subfamily Cylapinae (Insecta: Heteroptera: Miridae) mostly inhabit the subtropics and tropics. The group currently comprises five tribes: Bothriomirini, Cylapini, Fulviini, Rhinomirini, and Vanniini. Additionally, the Psallopinae are sometimes included in this subfamily as a tribe. The interrelationships within Cylapinae are unknown, the monophyly is doubtful, and a phylogenetic study focusing on the entire subfamily has never been published. The molecular and fossil data analyses show that Miridae occurred at least in the Jurassic. The divergence dates for Cyalpinae tribes are unknown. We performed the phylogenetic analysis of Cylapinae based on molecular and morphological data, in addition to a combined dataset. We calibrated the molecular trees with fossil data. The results suggested non-monophyly of Cylapinae. The monophyly of Bothriomirini was confirmed. Cylapini were rendered as non-monophyletic. The Cylapus complex formed a clade with Vanniini, and the monophyly of Vanniini was doubtful. Fulviini were recovered as non-monophyletic, and the representatives fell into two separate well-supported clades. Dating analyses showed that the groups of the suprageneric level distributed across different continents diverged near the boarder between Mesosoic and Cenosoic, that was also true for the Asian suprageneric groups and the South American Cylapus complex. Australian groups of genera diverged in the Cenozoic.

Assembling an illustrated family‐level tree of life for exploration in mobile devices

AbstractSince the concept of the tree of life was introduced about 150 years ago, a considerable fraction of the scientific community has focused its efforts on its reconstruction, with remarkable progress during the last two decades with the advent of DNA sequences. However, the assemblage of a comprehensive and explorable tree of life has been a difficult task to achieve due to two main obstacles: (i) information is scattered into several individual sources and (ii) practical visualization tools for exploring large trees are needed. To overcome both challenges, we aimed to synthesize a family‐level tree of life by compiling over 1400 published phylogenetic studies, choosing the source trees that represent the best phylogenetic hypotheses to date based on a set of objective criteria. Moreover, we dated the tree by employing over 550 secondary calibrations using publicly available sequences for more than 5000 taxa and by incorporating age ranges from the fossil record for over 2800 taxa. Additionally, we developed a mobile app for smartphones to facilitate the visualization and exploration of the resulting tree. Interactive features include exploration by the zooming and panning gestures of touch screens, collapsing branches, visualizing specific clades as subtrees, a search engine, and a timescale to determine extinction and divergence dates, among others. Small illustrations of organisms are displayed at the terminals to better visualize the morphological diversity of life. Our assembled tree currently includes over 7000 families, and its content will be expanded through regular updates to cover all life on earth at the family level.

First record of Ramari's beaked whale Mesoplodon eueu (Cetacea: Ziphiidae) for Uruguay

Abstract We report the first record of Ramari's beaked whale (Mesoplodon eueu) from the temperate Southwestern Atlantic. Our analysis is based on an adult female and a plausibly associated calf/juvenile that stranded on the coast of Canelones Department, Uruguay. The species of the two individuals was identified via a combination of morphometric and molecular mitochondrial data and provide new insights into the Ramari's beaked whale, including previously unknown polymorphisms in the mitochondrial genome and a re-estimated date of divergence from Mesoplodon mirus at 2.5902 Mya.

What kind of “lion” was the Natodomeri lion? – a comparative analysis of the Natodomeri lion with other Pleistocene lions

ABSTRACT The history of the lion in Africa is obscure. A giant lion was reported from Natodomeri, a MIS 8–7 site located in East Africa. Initial analysis showed intriguing features of the specimen. However, further analysis on what kind of lion (e.g. modern Panthera leo, Pleistocene Panthera spelaea) has not yet been performed. The purpose of this study is to elucidate the phylogenetic position of the Natodomeri lion through statistical morphometric analysis. To this end, the Natodomeri lion is compared with lions from Pleistocene Eurasia and Holocene Africa. Results show a surprising affinity between the Mauer lion (Panthera spelaea fossilis) and the Natodomeri lion. Such may be indicative of a more recent divergence date between P. leo and P. spelaea. However, if a divergence date between extant P. leo and Eurasian P. spelaea of 1.85 mya is used (based on recent phylogenetic studies), the close affinity between the Mauer and Natodomeri lions suggests that the Natodomeri lion is an African form of early P. spelaea. Under this theory, the Natodomeri lion may have originated through a ‘reverse’ migration of Panthera spelaea fossilis into Africa.

The status of Tomopterna pulchra Boulenger, 1896 (Anura: Pyxicephalidae).

Tomopterna pulchra (Boulenger, 1896) was described from Lake Tanganyika based on a single specimen. It was synonymised with Tomopterna tuberculosa (Boulenger, 1882) by Loveridge (1957) who noted that it did not fully agree with the description of T. tuberculosa, especially in the difference in dorsal colouration. Genetic differences show that two species are confused, although their advertisement calls and morphology are similar, except for the presence of a pale vertebral stripe mostly in eastern populations. We consider the advertisement calls, morphology, and genetic differences, and remove Tomopterna pulchra (Boulenger, 1896) from the synonymy of Tomopterna tuberculosa. Divergence dating shows that these two species separated in the mid-Miocene. Tomopterna pulchra breeds in rocky habitats, whereas T. tuberculosa breeds in sandy areas, typical of the genus. Based on genetically confirmed specimens, presently T. tuberculosa is known in the west (Angola and Namibia) while T. pulchra is only known from the east (Zambia and Tanzania). The examination of specimens for the presence or absence of a vertebral stripe infers that these species are widespread. Further work is required to determine if the two species are sympatric, and the extent of their ranges.

Phylogenomics of Fresh and Formalin Specimens Resolves the Systematics of Old World Mud Snakes (Serpentes: Homalopsidae) and Expands Biogeographic Inference

Our knowledge of the biodiversity of Asia and Australasia continues to expand with more focused studies on systematics of various groups and their biogeography. Historically, fluctuating sea levels and cyclic connection and separation of now-disjunct landmasses have been invoked to explain the accumulation of biodiversity via species pump mechanisms. However, recent research has shown that geological shifts of the mainland and species dispersal events may be better explanations of the biodiversity in these regions. We investigate these processes using the poorly studied and geographically widespread Mud Snakes (Serpentes: Homalopsidae) using a target capture approach of ~4,800 nuclear loci from fresh tissues and supplemental mitochondrial data from formalin tissues from museum specimens. We use these datasets to reconstruct the first resolved phylogeny of the group, identify their biogeographic origins, and test hypotheses regarding the roles of sea-level change and habitat selection on their diversification. Divergence dating and ancestral range estimation yielded support for an Oligocene origin and diversification from mainland Southeast Asia and Sundaland in the rear-fanged group ~20 million years ago, followed by eastward and westward dispersal. GeoHiSSE models indicate that niche expansion of ancestral, rear-fanged lineages into aquatic environments did not impact their diversification rates. Our results highlight that Pleistocene sea-level changes and habitat specificity did not primarily lead to the extant species richness of Homalopsidae and that, alternatively, geological shifts in mainland Southeast Asia may have been a major driver of diversity in this group. We also emphasize the importance of using fresh and degraded tissues, and both nuclear and mitochondrial DNA, for filling knowledge gaps in poorly known but highly diverse and conceptually important groups. Here, Homalopsidae represents a non-traditional but effective model study system for understanding transitions between terrestrial, marine, and freshwater environments.