Range-Wide Phylogeography and Ecological Niche Modeling Provide Insights into the Evolutionary History of the Mongolian Racerunner (Eremias argus) in Northeast Asia

The Mongolian racerunner, Eremias argus, is a small lizard endemic to Northeast Asia that can serve as an excellent model for investigating how geography and past climate change have jointly influenced the evolution of biodiversity in this region. To elucidate the processes underlying its diversification and demography, we reconstructed the range-wide phylogeographic pattern and evolutionary trajectory, using phylogenetic, population genetic, landscape genetic, Bayesian phylogeographic reconstruction and ecological niche modeling approaches. Phylogenetic analyses of the mtDNA cyt b gene revealed eight lineages that were unbounded by geographic region. The genetic structure of E. argus was mainly determined by geographic distance. Divergence dating indicated that E. argus and E. brenchleyi diverged during the Mid-Pliocene Warm Period. E. argus was estimated to have coalesced at~0.4351 Ma (Marine Isotope Stage 19). Bayesian phylogeographic diffusion analysis revealed out-of-Inner Mongolia and rapid colonization events from the end of the Last Interglacial to the Last Glacial Maximum, which is consistent with the expanded suitable range of the Last Glacial Maximum. Pre-Last Glacial Maximum growth of population is presented for most lineages of E. argus. The Glacial Maximum contraction model and the previous multiple glacial refugia hypotheses are rejected. This may be due to an increase in the amount of climatically favorable habitats in Northeast Asia. Furthermore, E. argus barbouri most likely represents an invalid taxon. The present study is the first to report a range-wide phylogeography of reptiles over such a large region in Northeast Asia. Our results make a significant contribution towards understanding the biogeography of the entire Northeast Asia.

Molecular phylogeny and taxonomy of the genus Vernaya (Mammalia: Rodentia: Muridae) with the description of two new species

The climbing mouse is a rare, small mammal listed as an endangered species on the China species red list. Molecular phylogenetic analyses and the evolutionary history of the genus remain unexplored because of the extreme difficulty in capturing individuals and their narrow distribution. Here, we collected 44 specimens, sequenced one mitochondrial and eight nuclear genes, and integrated morphological approaches to estimate phylogenetic relationships, delimit species boundaries, and explore evolutionary history. Molecular analyses and morphological results supported the validity of these four species. Here, we describe two new species, Vernaya meiguites sp. nov. and Vernaya nushanensis sp. nov., and recognize Vernaya foramena, previously considered a subspecies of Vernaya fulva, as a valid species. The estimated divergence time suggests that the climbing mouse began to diversify during the Pliocene (3.36 Ma).

Phylogeography and evolutionary lineage diversity in the small-eared greater galago, Otolemur garnettii (Primates: Galagidae)

Assessing the true lineage diversity in elusive nocturnal organisms is particularly challenging due to their subtle phenotypic variation in diagnostic traits. The cryptic small-eared greater galago (Otolemur garnettii) offers a great opportunity to test if currently recognized subspecies, suggested by discontinuities in coat colour pattern and geographic barriers, represent distinct evolutionary lineages. To answer this question, we conducted the first population-level phylogeographic study of the species, sampling wild specimens from across almost its entire latitudinal range, including the Zanzibar Archipelago. We applied five species-delimitation algorithms to investigate the genetic diversity and distribution pattern of mitochondrial DNA across the geographic range of three out of four subspecies. Our results suggest that far-northern populations of O. g. lasiotis potentially represent an independently evolving lineage, but populations assigned to O. g. garnettii from Zanzibar Island and of O. g panganiensis from mainland Tanzania do not constitute two independent lineages. A dated phylogeny suggests that this northern clade diverged from all remaining samples approximately 4 Mya. Such old divergence age is in line with the split between many galagid species. This northern lineage could potentially represent an incipient species; however, there is not yet enough evidence to support a new taxonomic status for this unique mitochondrial group.

Subspecies at crossroads: the evolutionary significance of genomic and phenotypic variation in a wide-ranging Australian lizard (Ctenotus pantherinus)

Many subspecies were described to capture phenotypic variation in wide-ranging taxa, with some later being found to correspond to divergent genetic lineages. We investigate whether currently recognized subspecies correspond to distinctive and coherent evolutionary lineages in the widespread Australian lizard Ctenotus pantherinus based on morphological, mitochondrial and genome-wide nuclear variation. We find weak and inconsistent correspondence between morphological patterns and the presumed subspecies ranges, with character polymorphism within regions and broad morphological overlap across regions. Phylogenetic analyses suggest paraphyly of populations assignable to each subspecies, mitonuclear discordance and little congruence between subspecies ranges and the distribution of inferred clades. Genotypic clustering supports admixture across regions. These results undermine the presumed phenotypic and genotypic coherence and distinctiveness of C. pantherinus subspecies. Based on our findings, we comment on the operational and conceptual shortcomings of morphologically defined subspecies and discuss practical challenges in applying the general notion of subspecies as incompletely separated population lineages. We conclude by highlighting a historical asymmetry that has implications for ecology, evolution and conservation: subspecies proposed in the past are difficult to falsify even in the face of new data that challenge their coherence and distinctiveness, whereas modern researchers appear hesitant to propose new subspecies.

Taxonomic boundaries in Lesser Treeshrews (Scandentia, Tupaiidae: Tupaia minor )

The Lesser Treeshrew, Tupaia minor  Günther, 1876, is a small mammal from Southeast Asia with four currently recognized subspecies: T. m. minor from Borneo; T. m. malaccana from the Malay Peninsula; T. m. humeralis from Sumatra; and T. m. sincepis from Singkep Island and Lingga Island. A fifth subspecies, T. m. caedis, was previously synonymized with T. m. minor; it was thought to occur in northern Borneo and on the nearby islands of Banggi and Balambangan. These subspecies were originally differentiated based on pelage color, a plastic feature that has proven to be an unreliable indicator of taxonomic boundaries in treeshrews and other mammals. To explore infraspecific variation among T. minor populations across the Malay Peninsula, Borneo, Sumatra, and smaller islands, we conducted multivariate analyses of morphometric data collected from the hands and skulls of museum specimens. Principal component and discriminant function analyses reveal limited differentiation in manus and skull proportions among populations of T. minor from different islands. We find no morphometric support for the recognition of the four allopatric subspecies and no support for the recognition of T. m. caedis as a separate subspecies on Borneo.

Misinterpretation of Genomic Data Matters for Endangered Species Listing: The Sub-specific Status of the Peñasco Least Chipmunk (Neotamias minimus atristriatus)

We provide a response to a recently published evaluation of the subspecies status of the Peñasco least chipmunk (Neotamias minimus atristriatus). The work we discuss used exon capture genomic approaches and concluded that their results did not support the distinction of this taxon as a subspecies, with recommendation that it be synonymized with N. m. operarius. We refute the interpretations, conclusions, and taxonomic recommendations of this study, and explain in clearer terms how to interpret genomic analyses for applied management. We identify four broad conceptual issues that led to errant recommendations: (1) interpretation of subspecies and diagnosability, (2) inappropriate use of reciprocal monophyly as a criterion for subspecies, (3) importance of geographic isolation, and (4) error in hypothesis testing and misinterpretation of results. We conclude that the data from this genomic appraisal add to information from prior studies providing strong support for recognition of N. m. atristriatus as a subspecies. Our conclusions have important and immediate implications for the proposed listing of N. m. atristriatus as an endangered species under the U.S. Endangered Species Act.

Ecogeographic variation and taxonomic boundaries in Large Treeshrews (Scandentia, Tupaiidae: Tupaia tana Raffles, 1821) from Southeast Asia

The Large Treeshrew, Tupaia tana Raffles, 1821, is a small mammal (~205 g) from Southeast Asia with a complicated taxonomic history. Currently, 15 subspecies are recognized from Borneo, Sumatra, and smaller islands, and many were originally differentiated based on minor pelage differences and small sample sizes. We explored intraspecific variation in T. tana using quantitative osteological data obtained from the hands and skulls of museum specimens. Multivariate analyses reveal extensive overlap among T. tana populations in morphospace, indicating that the majority of currently recognized subspecies are not morphometrically distinct. In contrast, the separation between Bornean and Sumatran populations of T. tana is sufficient to recognize them as different subspecies. Comparisons of Bornean specimens to those on small, offshore islands reveal that the latter average smaller body size. This pattern is inconsistent with Foster’s island rule, which predicts that island populations of small mammals (< 5 kg) will average larger body size relative to mainland forms. A similar lack of support for ecogeographic rules has been noted in T. glis (Diard, 1820), suggesting that these “rules” are poor predictors of geographic variation in treeshrews.

Characterizing the elusive Vancouver Island wolverine, Gulo gulo vancouverensis, using historical DNA

The wolverine (Gulo gulo) is a Holarctic species found in North America primarily across the boreal forest, the subarctic, and along the Pacific coast, including Vancouver Island (VI), British Columbia. While wolverines on VI are rare and possibly extirpated, they have been previously described as a unique subspecies, G. g. vancouverensis, distinct from G. g. luscus from the mainland of North America. However, the validity of the VI subspecies is contentious, with conflicting results from studies of skull morphology. Here, we used molecular analyses to characterize the genetic diversity of the VI population and resolve this taxonomic debate to assist with conservation priorities. Historical DNA of VI wolverines was obtained from museum specimens, amplified at 16 nuclear microsatellite loci, and sequenced at the mitochondrial D-loop control region to compare with wolverines from mainland British Columbia. The VI population had lower allelic richness and was fixed for a single common mtDNA haplotype. Bayesian and non-Bayesian assignments using microsatellites generally revealed admixture across populations, implying allele frequencies between the VI and mainland populations were not significantly different. Hence, both types of genetic markers showed little evolutionary divergence between VI and the mainland population. Combined, these results do not provide evidence of significant genetic distinction for VI wolverines, nor support the subspecific classification. Immediate conservation efforts should focus on estimating population size, while future conservation planning can assume VI wolverines likely are not a unique genetic population and there remains the potential for natural recolonization of wolverines to VI.

Geometric morphometrics of mandibular shape in the dwarf fat-tailed jerboa: relevancy for trinomial taxonomy

We explore the pattern of spatial variation in mandibular morphology in relation to subspecific taxonomy in the dwarf fat-tailed jerboa, Pygeretmus pumilio. The unguided k-means clustering on mandible shape scores, partitioned populations into two clusters, corresponding to western and eastern populations. These clusters nearly perfectly matched the two subspecies groups (pumilio and potanini groups) recognized in an independent study based on the morphology of the glans penis. The mandible, although under environmental pressure, has retained a sufficient amount of taxonomic information to retrieve grouping closely resembling the one derived from a sexually selective trait. We recommend morphometrics of the mandible as a routine step in addressing variations in mammals at species and subspecies levels. We also stress the advantage of unsupervised k-clustering in testing null expectation in subspecies taxonomies. However, the power of this approach has its limitations and in our analysis, the k-clustering failed to retrieve subspecies in the potanini group.

Are subspecies (of Eira barbara) real?

The subspecies concept is one of the most controversial in Linnean taxonomy. In the past, subspecies were described without a clear conceptual framework, triggering confusion and motivating criticism of the very concept of a subspecies. At present, subspecies are conceived as aggregates of populations that are geographically isolated, are composed of interfertile individuals, and are morphologically diagnosable. The tayra, Eira barbara, was described in 1758 and has had a stable taxonomic history at the species level. However, below the species level, 16 subspecies have been named, with from two to seven subspecies recognized as valid by different authors. None of the subspecies were, however, described within a clear conceptual framework. Using the modern concept of a subspecies, I analyzed subspecies of E. barbara recognized by recent authors. I gathered morphometric data from 155 specimens in mammal collections, georeferenced each specimen, and recorded membership to subspecies assigned by different references and by its location. I gathered climate and geographic data for each location. I analyzed data using Principal Components Analysis (PCA) and analysis of variance (ANOVA). Specimens exhibited sexual dimorphism in size but not in skull shape. I used regression analysis to test for associations between skull shape and size and climate data. Geographic analyses documented that subspecies are not allopatric, violating one of the main properties of the subspecies concept. ANOVA showed significant differences in skull morphology between some pairs of recognized subspecies but not others. However, none of the subspecies segregated in the PCA. Thus, the recognized subspecies could not be diagnosed from morphological data, violating another property of the subspecies concept. Size varied greatly between the sexes using different schemes for recognized subspecies. Climate variables explained between 4% and 6% of size variation for males and females. Skull shape proved not to be geographically variable.

A precarious future for distinctive peripheral populations of meadow voles (Microtus pennsylvanicus)

Conservation efforts rely on robust taxonomic assessments that should be based on critical assessment of interspecific boundaries, infraspecific variation, and potentially distinctive peripheral populations. The meadow vole (Microtus pennsylvanicus) is widely distributed across North America, including 28 morphologically defined subspecies and numerous isolated populations. Because some subspecies are of high conservation concern, we examined geographic variation across the range of the species to test existing infraspecific taxonomy in terms of local and regional diversification. We sequenced mitochondrial DNA (mtDNA) from 20 subspecies of M. pennsylvanicus and contextualized infraspecific variation through comparison of pairwise genetic distances derived from an extended data set of 63 species of Microtus. We found strong support for at least three divergent clades within M. pennsylvanicus, with observed intraspecific clade divergence exceeding that between several pairwise comparisons of sister species within Microtus. Six nuclear genes were then sequenced to test the validity of mtDNA structure and to further evaluate the possibility of cryptic, species-level diversity using Bayes factor species delimitation (BFD) analyses. BFD consistently and decisively supported multiple species based on the multilocus approach. We propose that taxonomic revision of the meadow vole is required, with the eastern clade now identified as M. pennsylvanicus (Ord 1815), the western clade as M. drummondii (Audubon and Bachman 1853), and the coastal Florida clade as M. dukecampbelli (Woods, Post, and Kilpatrick 1982). We suggest that such an arrangement would more closely reflect evolutionary history and provide critical context for further examination of distinctive southern peripheral populations that harbor novel evolutionary legacies and adaptive potential.

Phylogeography of moose in western North America

Subspecies designations within temperate species’ ranges often reflect populations that were isolated by past continental glaciation, and glacial vicariance is believed to be a primary mechanism behind the diversification of several subspecies of North American cervids. We used genetics and the fossil record to study the phylogeography of three moose subspecies (Alces alces andersoni, A. a. gigas, and A. a. shirasi) in western North America. We sequenced the complete mitochondrial genome (16,341 base pairs; n = 60 moose) and genotyped 13 nuclear microsatellites (n = 253) to evaluate genetic variation among moose samples. We also reviewed the fossil record for detections of all North American cervids to comparatively assess the evidence for the existence of a southern refugial population of moose corresponding to A. a. shirasi during the last glacial maximum of the Pleistocene. Analysis of mtDNA molecular variance did not support distinct clades of moose corresponding to currently recognized subspecies, and mitogenomic haplotype phylogenies did not consistently distinguish individuals according to subspecies groupings. Analysis of population structure using microsatellite loci showed support for two to five clusters of moose, including the consistent distinction of a southern group of moose within the range of A. a. shirasi. We hypothesize that these microsatellite results reflect recent, not deep, divergence and may be confounded by a significant effect of geographic distance on gene flow across the region. Review of the fossil record showed no evidence of moose south of the Wisconsin ice age glaciers ≥ 15,000 years ago. We encourage the integration of our results with complementary analyses of phenotype data, such as morphometrics, originally used to delineate moose subspecies, for further evaluation of subspecies designations for North American moose.

Subspecies definitions and legislation: from eastern wallaroo (Osphranter robustus robustus) to euro (Osphranter robustus erubescens)

As a consequence of genetic studies of population structuring, the usefulness of subspecies has been questioned, with opinions divided. The situation is further confused by the use of varying species and subspecies concepts. Most alternatives require each taxon to be following an independent evolutionary trajectory. These include traditional approaches and the more recent phylogenetic species concept. The latter has led to large increases in the apparent number of taxa in some groups, though strong objections have been raised to this approach. An alternative, the ecological species concept, has been opposed by phylogeneticists. These two approaches are compared using morphological and genetic data from common wallaroo (Osphranter robustus) populations. The different taxonomies that might result (many species, one species with two subspecies, one species with no subspecies) can have significant consequences for legislative and management decisions. The ecological approach is considered preferable for subspecies and the present taxonomy is maintained. A potential location of the boundary between the wallaroo subspecies is proposed. How the use of the different subspecies definitions would affect legislative decisions is explored.

Evolutionary relationships and climatic niche evolution in the genus Handleyomys (Sigmodontinae: Oryzomyini)

Mesoamerica is considered a biodiversity hot spot with levels of endemism and species diversity likely underestimated. Unfortunately, the region continues to experience some of the highest deforestation rates in the world. For mammals, the evolutionary relationships of many endemic taxa are controversial, as it is the case for members of the genus Handleyomys. Estimation of a time-calibrated hypothesis for the evolution of these six genera (Euryoryzomys, Handleyomys, Hylaeamys, Nephelomys, Oecomys and Transandinomys) supported a monophyletic Handleyomys sensu lato. Based on their distinctive morphology and the amount of inter-generic genetic divergence, Handleyomys sensu stricto, H. alfaroi, the H. chapmani, and the H. melanotis species groups warrant recognition as separate genera. In addition, species delimitation documents the existence of cryptic species-level lineages within H. alfaroi and H. rostratus. Cryptic lineages within H. rostratus exhibited significant niche differentiation, but this was not the pattern among species-level clades within H. alfaroi. Similarly, age-range correlations revealed that niche evolution within Handleyomys is not correlated with evolutionary time, instead, ancestral climate tolerance reconstructions show niche disparities at specific diversification events within the chapmani and melanotis species groups, while the climatic niche of the rest of species of Handleyomys tended to be conservative.

Delineating modern variation from extinct morphology in the fossil record using shells of the Eastern Box Turtle (Terrapene carolina)

Characterization of morphological variation in the shells of extant Eastern Box Turtles, Terrapene carolina, provides a baseline for comparison to fossil populations. It also provides an example of the difficulties inherent to recognizing intraspecific diversity in the fossil record. The degree to which variation in fossils of T. carolina can be accommodated by extant variation in the species has been disagreed upon for over eighty years. Using morphometric analyses of the carapace, I address the relationship between modern and fossil T. carolina in terms of sexual dimorphism, geographic and subspecific variation, and allometric variation. Modern T. carolina display weak male-biased sexual size dimorphism. Sexual shape dimorphism cannot be reliably detected in the fossil record. Rather than a four-part subspecific division, patterns of geographic variation are more consistent with clinal variation between various regions in the species distribution. Allometric patterns are qualitatively similar to those documented in other emydid turtles and explain a significant amount of shape variation. When allometric patterns are accounted for, Holocene specimens are not significantly different from modern specimens. In contrast, several geologically older specimens have significantly different carapace shape with no modern analogue. Those large, fossilized specimens represent extinct variation occupying novel portions of morphospace. This study highlights the need for additional documentation of modern osteological variation that can be used to test hypotheses of intraspecific evolution in the fossil record.