Abstract The Hengduan Mountains of southwestern China constitute a classic sky-island system shaped by complex topography and climatic history. We investigated the evolutionary history of the shrew tribe Blarinellini using 272 samples representing both genera and all four recognized species. Based on mitochondrial and nuclear sequence data, we reconstructed phylogenetic relationships, estimated divergence times, and examined population genetic structure and ecological niche dynamics. Our results support an early Miocene origin of Blarinellini (~18.2 million years). Population genetic analyses recovered five and four deeply divergent geographic lineages within Blarinella quadraticauda and B. wardi , respectively. Most genetic variation was partitioned among lineages, indicating strong long-term isolation. Lineage distributions closely correspond to major river systems and montane regions, suggesting that the effects of river barriers and sky-island fragmentation may have contributed to the observed patterns of diversification. Ecological niche models identified climatically stable habitats within the Hengduan Mountains across multiple glacial–interglacial cycles, whereas demographic analyses revealed recent expansion in a subset of lineages. Together, these results suggest that river barriers, sky-island fragmentation, and climatic change may have jointly contributed to diversification in Blarinellini, and suggest that evolutionary diversity within the tribe may be substantially underestimated. These findings highlight the dual role of the Hengduan Mountains as both a refuge preserving ancient lineages and a cradle generating new diversity.
Abstract The diamond frogs of the genus Rhombophryne are a poorly understood clade of morphologically diverse frogs native to the humid forests of Madagascar. We here present a monographic revision of the taxonomy and natural history of these frogs. We first provide morphological diagnoses and contents of the established species groups in Rhombophryne. We then integrate molecular phylogenetic data from mitochondrial and nuclear genetic markers, with morphometrics, bioacoustics, and micro-CT-based osteology, to describe seven new species from across Madagascar. This brings the number of species in the genus to 27. We have obtained DNA sequences from name-bearing specimens of 23 of these species, plus topotypical specimens of two further species; we used museomics methods to sequence name-bearing types of three species collected before 1976, as well as several other specimens of interest, allowing us to clarify taxonomic assignment of those individuals. In our treatments of all existing and new species, we provide new insights into their anatomy, diet, ecology, and distribution. We provide the first published key to the genus, which we hope will make their identification more straightforward. Finally, we suggest a revised conservation assessment in light of the data that we present. We estimate 24 of the 27 species to be threatened, with two species (R. kilonjy sp. nov. and R. matavy) probably worthy of being classified as ‘Critically Endangered’. Several candidate species remain taxonomically unaddressed, due to the poor representation of specimens in museum collections. We therefore emphasise the need for increased survey efforts to fill knowledge gaps in both the taxonomy and the natural history of these frogs.
Abstract Mito-nuclear discordance is a well-recognized phenomenon; however, the limited use of nuclear data in rodent systematics has revealed few documented cases. As such, the extent to which discordant gene trees mislead taxonomic schemes remains unclear. Here, we document an example of such discordance in a taxonomic assessment of species boundaries within the subgenus Angelomys of the genus Abrothrix, based on mitochondrial, nuclear (ultraconserved elements, UCEs), and morphological data. Our analyses revealed strong discordance between the mitochondrial tree and the species tree emerging from the UCE dataset. The latter recovered three main lineages within Angelomys, each phenotypically distinct. Therefore, we propose that the taxonomic scheme that best represents the alpha taxonomy of the subgenus Angelomys recognizes three species rather than the two recently proposed. The three species we recognize are Abrothrix (Angelomys) andina, distributed from the highlands of Santiago in central Chile northward along the Pacific coast to southern Peru; Ab. (An.) dolichonyx, a highland species ranging from Mendoza in west central Argentina northward through the high Andean regions of northern Argentina, northern Chile, western Bolivia and southern Peru; and Ab. (An.) olivacea, distributed from lowland areas of central Chile and Mendoza (Argentina), extending southward through the temperate forests, Patagonia, Tierra del Fuego, nearby islands, and reaching Cape Horn. Finally, we designate a lectotype for Hesperomys dolichonyx (= Ab. dolichonyx) and restricted the type locality of Mus andinus (= Ab. andina) to a locality within the general area indicated in the species description and from which the species has been recorded.
Abstract Tadarida brasiliensis is a widespread species ranging from the United States to the southern tip of South America. Population genetics studies have been conducted mainly in the northern populations, with only a few samples from South America being included in previous studies. The study of T. brasiliensis populations is relevant due to their ecological importance as an insectivorous species that consumes agricultural pests and their role as a reservoir of diverse pathogens that may represent a potential risk to humans and other animals. Our objective was to analyze the population genetic structure of T. brasiliensis in Argentina in order to better understand the migration patterns of the species in the southern tip of its distribution, evaluate its genetic variation, and predict the impact on the spread of associated viruses, which has direct application to guide sanitary control strategies. We analyzed samples of 94 individuals from 14 provinces of Argentina and the Autonomous City of Buenos Aires using double digestion restriction site-associated DNA sequencing (ddRADseq) technology to obtain variable nuclear genomic markers (SNPs). The average statistics of 29,715 unlinked SNPs revealed high genetic diversity in the samples and an absence of population structure throughout Argentina, suggesting that the population of T. brasiliensis in Argentina behaves as a single panmictic unit. Demographic analyses indicate that the Argentine population underwent a significant growth, starting at approximately 0.27 million years ago and reaching an estimated current effective population size of 2.7 million. The results of complementary analyses using sequences of the mitochondrial gene cytochrome b are consistent with these conclusions and provide further evidence for a deep split between the populations of North America, South America, and the Caribbean. Our findings are congruent with those of previous studies focusing on North American populations, which also found evidence of population expansion and lack of genetic structure within regional populations.
Abstract We describe three new species of ground-dwelling gecko of the dry-zone clade of Cyrtodactylus (Geckoella) from peninsular India in an integrative taxonomic framework. All three new species have a spotted dorsal colour pattern; and their small body size and original tail shorter than body, besides the lack of femoral or precloacal pores in males, easily differentiate them from all other Cyrtodactylus apart from other Cyrtodactylus (Geckoella). The two new species from the Southern Western Ghats can be assigned to the C. collegalensis species complex based on homogeneous granular dorsal scalation without rows of enlarged, rounded tubercles; with 4.2–17.9 % uncorrected ND2 sequence divergence from each other and other named species of the C. collegalensis complex. The third species from central India can be assigned to the C. nebulosus species complex based on its dorsal scalation consisting of granular scales intermixed with rows of enlarged, rounded tubercles, and a 14.1–17.4 % uncorrected ND2 sequence divergence from other named species. The three new species are distinct in colour pattern from all other dry-zone Geckoella and occupy distinct positions in multivariate morphospace from phylogenetically allied taxa. Cyrtodactylus shenbagathoppuensis sp. nov. and C. kalakadensis sp. nov. are from Srivilliputhur-Megamalai Tiger Reserve and Kalakad-Mundanthurai Tiger Reserve in the Southern Western Ghats (south of the Palghat Gap) of Tamil Nadu, respectively, while C. satpuraensis sp. nov. is found in multiple Tiger Reserves across the Satpuras in central and western India. The former two species are known only from a single locality each, while the last is distributed across localities as far apart as > 700 km with very low divergence.
Abstract Two new species, Boulenophrys dongli sp. nov. and Boulenophrys raoping sp. nov., are described from the coastal mountains of Raoping County, Chaozhou City, eastern Guangdong, China, based on morphological and molecular evidence. Currently, these two new species are known only from low-altitude mountainous areas (below 500 m a.s.l.), where they inhabit fragmented patches of secondary forest interspersed with bamboo plantations. Given their extremely limited distribution, ongoing habitat loss, and isolated populations, we recommend listing these two new species as Critically Endangered (CR) in accordance with IUCN Red List criteria B1ab(i,ii,iii)c(i,ii)+B2ab(i,ii,iii)c(i,ii). Continued research is critical to fill existing knowledge gaps and to guide coordinated conservation efforts aimed at protecting these unique amphibians within the critical montane refugia of eastern Guangdong.
Abstract We investigated the taxonomic diversity of the pale-faced bat Phylloderma stenops (Chiroptera: Phyllostomidae) across South and Central America using morphological analyses and complete mitochondrial genomes. Phylogenetic reconstructions revealed two highly supported clades, with Central American populations showing consistent genetic divergence from South American lineages. Morphological comparisons corroborated this distinction, particularly in cranial and dental traits, supporting the recognition of the northern lineage as Phylloderma septentrionalis Goodwin, 1940. Our results indicate that P. septentrionalis represents a valid species restricted to northern Central America, while P. stenops sensu stricto is distributed from Panama southwards. The genome skimming approach proved effective for recovering complete mitogenomes from both recent and historical specimens, enabling robust phylogenetic inference despite limited sample sizes. These findings are consistent with the hypothesis that geographic features in Central America may have contributed to lineage divergence within Phylloderma, although the exact barrier and transition zone remain to be evaluated with samples from Costa Rica. The results also underscore the importance of integrating morphological and molecular data to reassess taxonomic limits in poorly sampled Neotropical bats. The recognition of P. septentrionalis refines the taxonomy and geographic limits of Phylloderma in Central America and provides a framework for future studies using broader geographic sampling and genomic data.
Octodontidae is a moderately speciose family (seven genera and 16 species) of South American caviomorph rodents; however, from an ecological point of view, it is a diverse clade that includes terrestrial, cursorial, scansorial, and fossorial to strictly subterranean forms. Its distribution is mostly restricted to the western portion of southern South America, on both sides of the Andes. Here we describe a new living genus and species of Octodontidae, whose distribution is restricted to the Sierra de Guasapampa (central Argentina). Phylogenetic analysis of mitochondrial molecular markers (cytochrome b) recovers this taxon as sister to Octomys; the genetic distance observed between them is similar to the range of distances found between other genera of Octodontidae (>9%). This, together with its morphological divergence from Octomys in the context of Octodontidae, supports its treatment as a separate genus. This rodent is characterized by a unique combination of morphological features, including a long and very hairy tail; grayish brown dorsal coloration, which contrasts against the whitish belly; robust skull, with a proportionally short rostrum; wide interorbital region, with slightly divergent supraorbital edges; proportionally wide incisive foramina; orbitosphenoid with its origin displaced to the basisphenoid; inflated but small auditory bullae; median lacerate foramen not covered by the bulla; and upper molariform lobes with acuminate labial tips. Specimens of the new genus and species were captured on rocky slopes with abundant bromeliad vegetation in the understory. This finding highlights the importance of continuing field research, especially in areas that have not previously been surveyed.
Abstract We examined whether phenotypic differences exist within and between two genetically delimited subspecies of the barred grass snake (Natrix helvetica helvetica and N. h. sicula) using georeferenced photographic records of approximately 3800 individuals and provide morphological diagnoses for each taxon. The nominotypical subspecies is less variable in coloration and pattern compared to the southern subspecies N. h. sicula, which typically has an extensive dark back pattern in addition to the side bars. Individuals with a dorsal pattern resembling asp vipers (Vipera aspis) and tessellated individuals are frequent in N. h. sicula, whereas most N. h. helvetica have a plain-colored back. Rare unique phenotypes occur particularly in the more southern parts of the distribution range of N. h. sicula. This variation matches its complicated mitochondrial phylogeography with multiple glacial refuges in Italy. The similarity of the dorsal pattern of barred grass snakes and asp vipers represents a case of Batesian mimicry. Barred grass snakes with such a back pattern are largely restricted to N. h. sicula, which is distributed in a region where asp vipers are broadly sympatric. In contrast, barred grass snakes with an asp-like pattern are very rare in many regions of France where the two species are sympatric as well. This suggests that the mimicry system had significantly more time to evolve in the Italian peninsula due to a longer shared distribution history of the two species.
Abstract Species delimitation in recently evolving taxa presents unique challenges. Such taxa may not have accumulated enough genetic or morphological differences to be easily distinguished using traditional methods, while processes such as incomplete lineage sorting or gene flow may obscure these distinctions. One paradigmatic recently evolved taxon is the Corrientes group of the subterranean genus Ctenomys (Rodentia, Ctenomyidae), a set of populations with different chromosomal forms occurring in the homonymous province of Argentina. Previously, three nominal species and several independently evolving lineages had been proposed; however, a comprehensive integrative approach—including qualitative and quantitative morphological analyses, as well as additional molecular proxies for lineage delimitation—was still lacking, and these results had not been evaluated in a taxonomic context. In this study, we added new lines of evidence, including Bayesian phylogenetics and divergence time estimation, haplotype networks, and genetic distances. We integrated this information with karyotypic and microsatellite data to discuss previously proposed lineages, as well as to analyze the evolutionary processes that shaped the history of this group. Finally, we analyzed the qualitative and quantitative morphology of individuals from the nominal species and a chromosomally derived lineage, and we propose a revised species-level and infraspecific classification for this complex group of rodents. This resulted in the delimitation of two species, C. roigi and C. perrensi, the latter being subdivided into three subspecies: Ctenomys perrensi perrensi, C. perrensi dorbignyi, and C. perrensi iberaensis subsp. nov. In addition, other identified lineages, such as Sarandicito, Manantiales, and Santa Rosa, deserve future taxonomic investigation.
Abstract We describe three new species of lungless salamanders (Plethodontidae) in the genus Pseudoeurycea from Cerro Rabon, located on the eastern slopes of the Sierra Mazateca, Oaxaca, Mexico. This mid-elevation mountain, largely surrounded by warmer lowlands, remains relatively understudied. We present molecular and morphological evidence distinguishing the three new species from their congeners. According to our phylogenetic analysis, one of the new species belongs to the P. leprosa group, while the other two are members of the P. juarezi group. Notably, one of the new species represents the fourth worm salamander known from west of the Isthmus of Tehuantepec, and another exhibits morphological features resembling those of cave- or saxicolous salamanders. In addition, we obtain genetic information from Pseudoeurycea werleri and find high divergence between populations of Los Tuxtlas region, Veracruz and Sierra Mazateca, Oaxaca. With the species described herein, the number of recognized species in the genus Pseudoeurycea rises to 44, of which 43 are distributed in Mexico. Due to their occurrence at high elevations and in rainforest (low elevation) on Cerro Rabon, the new species are likely at risk of extinction. However, the protection of communal lands by Mazatec communities could support the conservation of these species and the rest of the biodiversity on a regional scale.
Abstract The systematics of blind mole rats (Spalacinae), a group of highly specialized subterranean rodents, remain a subject of debate. Within the genus Spalax, the greater blind mole rat (Spalax microphthalmus) is distinguished by its unique diploid chromosome number (2n = 60 versus 2n = 62 in others) and the most extensive geographic range. However, its intraspecific variation has been insufficiently studied. Previous finding of specimens with 2n = 62 in the North Caucasus were attributed to chromosomal polymorphism within S. microphthalmus. In this study, we conducted a comprehensive analysis of morphometric, morphological, molecular, and chromosomal variation across the entire range of S. microphthalmus, integrated with a comparative analysis of the genus Spalax. Our results demonstrate that the North Caucasian populations (2n = 62) exhibit consistent species-level differences in molecular genetics (from 8% to 12% divergence in cyt b), karyotype, and cranial morphology, distinguishing them from S. microphthalmus and all other congeners. This lineage also possesses a unique combination of morphological traits, including features that bring it closer to the hypothetical common ancestor of all modern Spalax species. Based on this integrative evidence, we describe this lineage as a new species: Spalax lyapunovae sp. nov., increasing the number of extant Spalax species to nine. This newly recognized species, endemic to the central North Caucasus, requires further ecological and distributional studies. Given its presumably limited range, an urgent assessment of its conservation status is warranted.
Abstract The taxonomy of genus Myotis (Chiroptera: Vespertilionidae) has long posed considerable challenges, with numerous species in China remaining poorly defined. To address long-standing taxonomic ambiguities in Chinese Myotis, this study integrates over 15 years of fieldwork and conducts a comprehensive assessment of 197 specimens collected primarily in eastern China, which represent approximately 70% of the country’s known species. Molecular species delimitation, phylogenetic reconstruction, and multivariate analyses of morphological data were jointly employed to reassess species diagnostic traits. Phylogenetic and molecular delimitation supported the validity of 30 Myotis species in China, and resolved several long-debated complexes, including M. davidii, M. siligorensis, and M. frater. Principal component and hierarchical clustering analyses revealed mixed and overlapping patterns among species, particularly within small to medium size taxa. These results highlighted the limitations of traditional morphometric traits for distinguishing closely related Myotis. Initial classification accuracy using morphological traits alone was modest. However, when categorical phenotypic data was added into the dataset, model performance improved markedly: Random forest accuracy increased from 77.9% to 90.5%, and the decision tree model successfully discriminated 16 taxonomic units. These suggested that categorical phenotypic data can substantially enhance identification within morphologically conservative groups. Based on integrative evidence, we established an updated identification key. In addition, high-resolution 3D digital models of craniodental structures were generated to facilitate open access for future research. This study provided a foundation for subsequent phylogeny, ecology, and conservation biology studies on this taxonomically difficult genus.
Abstract Several populations of forest-living chameleons in the genus Nadzikambia have been recorded from the montane sky island forests in northern Mozambique. These populations have not been evaluated for their species status, despite the potential for these allopatric populations having diverged at the species level due to vicariance of forest since the mid-Miocene. With only two described species of Nadzikambia, we hypothesised that candidate (new) species occur on each of four additional montane sky islands surveyed. We applied an integrative taxonomic approach to evaluate this, using morphological and genetic data collected from each population. Their distributions were mapped, the morphological dataset was quantitatively analysed using a multivariate analysis, and one nuclear and three mitochondrial genes were sequenced to generate a phylogeny and allele networks. Independent species delimitation analyses were applied to the genetic dataset (mPTP, SpeciesIdentifier, p distances) as supporting evidence for candidate species. By applying integrative taxonomy under the General Lineage Species Concept, we find support for four new species of Nadzikambia. The montane forests where they occur have declined in extent due to slash and burn agriculture and these forest endemics are presumed to be in a proportional decline as their habitat contracts. By examining historical and present-day satellite imagery, we show that all Nadzikambia species have lost significant proportions of their range. Given they do not occur outside these forests, these species are in imminent danger of extinction.
The European Pleistocene populations of the narrow-headed vole (Stenocranius gregalis), an index species of the Palearctic glacial communities, were recently found to differ from the extant Asian species by a deep genetic divergence and are to be considered a separate species, Stenocranius anglicus, which had to persist through the interglacial stages in local European refugia. Here, we analyze over 2000 first lower molars from 14 stratified localities in the Czech Republic and Slovakia, spanning the Middle Pleistocene to Holocene, employing geometric morphometrics, biometric measurements, and morphotype classifications to assess molar shape variation. Our results demonstrate persistent morphological variability, with particularly high morphotype diversity during MIS 5–3, followed by simplification and reduced variance in post–LGM populations. Morphological divergence was greater among geographic localities than stratigraphic stages, suggesting strong regional and ecological influences. Stratified sequences reveal diverse evolutionary trajectories from long-term morphological stability in refugia to gradual simplification preceding extinction in the early Holocene. These patterns align with broader Eurasian trends but also highlight regionally specific responses to climatic and ecological change accompanying the species’ extinction dynamics during the early to middle Holocene. The paper underscores the importance of integrating detailed morphometrics with stratigraphic and ecological evidence to shed light on these topics.
Abstract Madascincus is a genus of quadrupedal skinks endemic to Madagascar, with 12 recognized species described between the 19th and 21st centuries, occupying diverse habitats from humid forests to arid southern regions and even high-altitude areas. Recent field expeditions uncovered two morphologically distinct forms that did not match any known species, prompting integrative taxonomic analyses that combine multilocus phylogenetics and morphology. Results revealed that each of these forms represents a highly divergent and likely ancient lineage, as evidenced by the substantial branch lengths in both mitochondrial and nuclear phylogenetic trees. These investigations led to the formal description of two new species with restricted distribution ranges: Madascincus irery sp. nov., likely endemic to the island of Nosy Be, and Madascincus minotaurus sp. nov., apparently restricted to the Tsingy de Namoroka karst system.
Abstract A diverse array of early Eocene zygodactyl birds has been assigned to the Psittacopasseres, the clade including parrots and passerines, but the exact affinities of the fossils are controversially resolved. Here, new analyses are performed based on a revised character matrix. Concerning critical taxa, the results of the primary analysis and that of the analyses constrained to a molecular backbone phylogeny show disparate tree topologies, and probably none correctly reflects the true interrelationships of the fossil taxa. The new taxon Psittacomimidae fam. nov. is introduced for a clade formed by the taxa Psittacomimus and Parapsittacopes, which were before assigned to the Psittacopedidae. The Psittacomimidae fam. nov. are likely to be the sister taxon of the Parapasseres, that is, the clade formed by the Zygodactylidae and Passeriformes, with the Morsoravidae branching next. A clade formed by all or most Halcyornithidae and the Messelasturidae is termed Messelasturiformes. A derived morphology of the proximal tarsometatarsus is reported, which may support a clade including the Vastanavidae and Messelasturiformes. However, although psittacopasserine affinities of the Vastanavidae conform to the overall osteology of these birds, the higher-level affinities of the Messelasturiformes are more elusive.
We analysed the genetic and morphological variation in Philodryas patagoniensis, a widely distributed South American racer snake. Two well-differentiated haplogroups were identified using mitochondrial gene sequences (12S and 16S) and the nuclear gene c-mos. Genetic divergence between these haplogroups correlates strongly with morphological differences, allowing the recognition of two morphotypes within P. patagoniensis. We integrated genetic and morphological data into a total evidence analysis using parsimony. Our results support the distinction between the two haplogroups/morphotypes, consistent with recognising two species within P. patagoniensis. Accordingly, we re-describe P. patagoniensis, refining its morphological variation and geographical distribution to reflect the observed genetic differentiation, and describe a new species. Morphological characteristics can distinguish the two species, including body measurements, scale patterns, and cranial osteology. The new species differs from P. patagoniensis sensu stricto in traits associated with arboreal habits, which are strongly correlated with the distribution of the two taxa across forested and open habitats in South America. Furthermore, P. patagoniensis sensu stricto has a significant Lycosa spider component in its diet, which is absent in the newly described species.
The genus Cercomacra includes six species, among them C. cinerascens, which is widespread throughout the Amazon Basin. Historically, six names have been proposed for this species complex, but only four are currently recognized. Past studies have explored relationships among Cercomacra species using either morphological or molecular data, with taxonomic assessments mainly conducted in the early 20th century. To reevaluate the validity of the currently accepted C. cinerascens taxa, we performed a comprehensive taxonomic revision that combined traditional morphological and vocal analyses. Additionally, we used BirdNET, a pre-trained deep learning algorithm developed for bird sound classification. We examined 682 specimens and 347 recordings and identified two distinct morphotypes distributed north and south of the Amazon Basin, along with four recognizable loudsong types. Using both morphological and vocal features, we identified five distinct lineages, two of which are newly described and named. Cercomacra cinerascens occurs north of the Pastaza and Amazon Rivers in northern Amazonia; C. sclateri is found in eastern Ecuador and Peru, south of the Pastaza River and east of the Andes, east to the Ucayali River; and C. iterata stat. nov. is located east of the Tapajos River. The two newly described species are found south of the Amazon and Marañon Rivers. Cercomacra mura sp. nov. occupies the Ucayali-Madeira interfluve, and Cercomacra raucisona sp. nov. inhabits the Madeira-Tapajos interfluve.
The role of regional diversification versus the effect of migration in generating local species assemblages remains poorly known. Here, we contribute to the understanding of the role of colonisation and in situ diversification by studying an assemblage of miniaturised microhylid frogs of the genus Stumpffia Boettger, 1881, of which six species have been known to occur on Montagne d’Ambre, a volcanic mountain in the north of Madagascar. These six species are distributed over different, partly overlapping elevational levels. We examined this assemblage based on molecular data (16S mtDNA and Rag1 nDNA), new data on the elevational distribution among local Stumpffia species, and differences in advertisement calls. Our results revealed several genetic lineages constituting distinct species, including another species record for the mountain, S. mamitika Rakotoarison et al., 2017, as well as the new candidate species Stumpffia sp. aff. angeluci. This brings the total number of described species known to occur on the mountain to seven, four of which are micro-endemic. Our data indicate that one clade, consisting of four species, has arisen in situ as a microendemic radiation. We discuss alternative evolutionary scenarios for the biogeographic origin of the observed Stumpffia species.
