Taxonomic and conservation implications of population genetic admixture, mito-nuclear discordance, and male-biased dispersal of a large endangered snake, Drymarchon couperi

Species clarification of fairy inkcap ("Coprinellus disseminatus") in China

Coprinellus disseminatus and other morphologically similar species are widely dispersed worldwide and are commonly referred to as "fairy inkcap". Based on the molecular phylogenetic study and morphological observation, a thorough investigation was carried out utilising 74 collections of related species that were gathered from seventeen provinces and five Chinese fungaria between 1998 and 2023 and revealed 11 lineages of "fairy inkcap", nine of which were found in China, and which belonged to the two genera Coprinellus and Tulosesus. In sect. Disseminati, genetic diversities (π), and fixation index (Fst) amongst lineages were computed, and a haplotype-based network was established to ascertain the relationships amongst each clade. A new section of Coprinellus, sect. Aureodisseminati, were discovered. In addition, four new species (C. aureodisseminatus, C. austrodisseminatus, C. parcus, and C. velutipes), a new subspecies of C. disseminatus, a new combination (Tulosesus pseudodisseminatus), the first discovery of epigamous type of C. magnoliae and a new record to China (T. subdisseminatus) were also identified and thoroughly described with accompanying illustrations. Their differences in macro- and micro-features, as well as their character sequence, were discussed.

(Not) far from home: No sex bias in dispersal, but limited genetic patch size, in an endangered species, the Spotted Turtle (Clemmys guttata)

Sex-biased dispersal is common in many animals, with male-biased dispersal often found in studies of mammals and reptiles, including interpretations of spatial genetic structure, ostensibly as a result of male-male competition and a lack of male parental care. Few studies of sex-biased dispersal have been conducted in turtles, but a handful of studies, in saltwater turtles and in terrestrial turtles, have detected male-biased dispersal as expected. We tested for sex-biased dispersal in the endangered freshwater turtle, the spotted turtle (Clemmys guttata) by investigating fine-scale genetic spatial structure of males and females. We found significant spatial genetic structure in both sexes, but the patterns mimicked each other. Both males and females typically had higher than expected relatedness at distances <25 km, and in many distance classes greater than 25 km, less than expected relatedness. Similar patterns were apparent whether we used only loci in Hardy-Weinberg equilibrium (n = 7) or also included loci with potential null alleles (n = 5). We conclude that, contrary to expectations, sex-biased dispersal is not occurring in this species, possibly related to the reverse sexual dimorphism in this species, with females having brighter colors. We did, however, detect significant spatial genetic structure in males and females, separate and combined, showing philopatry within a genetic patch size of <25 km in C. guttata, which is concerning for an endangered species whose populations are often separated by distances greater than the genetic patch size.

Assessing genomic and ecological differentiation among subspecies of the Rough-footed Mud Turtle, Kinosternon hirtipes

Combining genetic and ecological measures of differentiation can provide compelling evidence for ecological and genetic divergence among lineages. The Rough-footed Mud Turtle, Kinosternon hirtipes, is distributed from the Trans-Pecos region of Texas to the highlands of Central Mexico and contains six described subspecies, five of which are extant. We use ddRAD sequencing and species distribution models to assess levels of ecological and genetic differentiation among these subspecies. We also predict changes in climatically suitable habitat under different climate change scenarios and assess levels of genetic diversity and inbreeding within each lineage. Our results show that there is strong genetic and ecological differentiation among multiple lineages within K. hirtipes, and that this differentiation appears to be the result of vicariance associated with the Trans-Mexican Volcanic Belt. We propose changes to subspecies designations to more accurately reflect the evolutionary relationships among populations and assess threats to each subspecies.

Genetic diversity and sex‐biased dispersal in the brown spotted pitviper ( Protobothrops mucrosquamatus ): Evidence from microsatellite markers

Dispersal plays a vital role in the geographical distribution, population genetic structure, quantity dynamics, and evolution of a species. Sex‐biased dispersal is common among vertebrates and many studies have documented a tendency toward male‐biased dispersal in mammals and female‐biased dispersal in birds. However, dispersal patterns in reptiles remain poorly understood. In this study, we explored the genetic diversity and dispersal patterns of the widely distributed Asian pitviper Protobothrops mucrosquamatus. In total, 16 polymorphic microsatellite loci were screened in 150 snakes (48 males, 44 females, 58 samples without sex information) covering most of their distribution. Microsatellite analysis revealed high genetic diversity in P. mucrosquamatus. Bayesian clustering of population assignment identified two major clusters for all populations, somewhat inconsistent with the mitochondrial DNA phylogeny of P. mucrosquamatus reported in previous research. Analyses based on 92 sex‐determined and 37 samples of P. mucrosquamatus from three small sites in Sichuan, China (Mingshan, Yibin, and Zizhong) consistently suggested female‐biased dispersal in P. mucrosquamatus, which is the first example of this pattern in snakes. The female‐biased dispersal patterns in P. mucrosquamatus may be explained by local resource competition.

Population structure and gene flow of Geoffroy’s cat (Leopardus geoffroyi) in the Uruguayan Savanna ecoregion

Felids are among the species most threatened by habitat fragmentation resulting from land-use change. In the Uruguayan Savanna ecoregion, about 30% of natural habitats have been lost, large felids have been eradicated from most of the region, and the impact of anthropogenic threats over the smaller species that remain is unknown. To develop management strategies, it is important to enhance knowledge about species population structure and landscape connectivity, particularly when land-use change will continue and intensify in the next years. In this study, we evaluate the population structure and gene flow of Geoffroy’s cat in the Uruguayan Savanna ecoregion. We generated a matrix of 11 microsatellite loci for 70 individuals. Based on Bayesian approaches we found that within the Uruguayan Savanna, Geoffroy’s cat shows high levels of genetic variability and no population structure. However, we observed genetic differences between individuals from the Uruguayan Savanna and those from the contiguous ecoregion, the Argentinian Humid Pampa. Four first-generation migrants from Humid Pampa were identified in the Uruguayan Savanna, suggesting a stronger gene flow in the west-east direction. We detected a past bottleneck followed by a subsequent recovery in Geoffroy’s cat populations in both ecoregions. These results lay the groundwork to understand the population dynamics and conservation status of Geoffroy’s cat in the Uruguayan Savanna ecoregion, and provide baseline data to establish population monitoring.

The legacy of Eastern Mediterranean mountain uplifts: rapid disparity of phylogenetic niche conservatism and divergence in mountain vipers

BACKGROUND

The orogeny of the eastern Mediterranean region has substantially affected ecological speciation patterns, particularly of mountain-dwelling species. Mountain vipers of the genus Montivipera are among the paramount examples of Mediterranean neo-endemism, with restricted ranges in the mountains of Anatolia, the Levant, Caucasus, Alborz, and Zagros. Here we explore the phylogenetic and ecological diversification of Montivipera to reconstruct its ecological niche evolution and biogeographic history. Using 177 sequences of three mitochondrial genes, a dated molecular phylogeny of mountain vipers was reconstructed. Based on 320 occurrence points within the entire range of the genus and six climatic variables, ecological niches were modelled and used to infer ancestral niche occupancy. In addition, the biogeographic history and ancestral states of the species were reconstructed across climate gradients.

RESULTS

Dated phylogenetic reconstruction revealed that the ancestor of mountain vipers split into two major clades at around 12.18 Mya followed by multiple vicariance events due to rapid orogeny. Montivipera colonised coastal regions from a mountain-dwelling ancestor. We detected a highly complex ecological niche evolution of mountain vipers to temperature seasonality, a variable that also showed a strong phylogenetic signal and high contribution in niche occupation.

CONCLUSION

Raising mountain belts in the Eastern Mediterranean region and subsequent remarkable changes in temperature seasonality have led to the formation of important centres of diversification and endemism in this biodiversity hotspot. High rates of niche conservatism, low genetic diversity, and segregation of ranges into the endemic distribution negatively influenced the adaptive capacity of mountain vipers. We suggest that these species should be considered as evolutionary significant units and priority species for conservation in Mediterranean mountain ecosystems.

Multiscale assessment of functional connectivity: Landscape genetics of eastern indigo snakes in an anthropogenically fragmented landscape in central Florida

Landscape features can strongly influence gene flow and the strength and direction of these effects may vary across spatial scales. However, few studies have evaluated methodological approaches for selecting spatial scales in landscape genetics analyses, in part because of computational challenges associated with optimizing landscape resistance surfaces (LRS). We used the federally threatened eastern indigo snake (Drymarchon couperi) in central Florida as a case study with which to compare the importance of landscape features and their scales of effect in influencing gene flow. We used genetic algorithms (ResistanceGA) to empirically optimize LRS using categorical land cover surfaces, multiscale resource selection surfaces (RSS), and four combinations of landscape covariates measured at multiple spatial scales (multisurface multiscale LRS). We compared LRS where scale was selected using pseudo- and full optimization. Multisurface multiscale LRS received more empirical support than LRS optimized from categorical land cover surfaces or RSS. Multiscale LRS with scale selected using full optimization generally outperformed those with scale selected using pseudo-optimization. Multiscale LRS with large spatial scales (1200-1800 m) received the most empirical support. Our results highlight the importance of considering landscape features across multiple spatial scales in landscape genetic analyses, particularly broad scales relative to species movement potential. Different effects of scale on home range-level movements and dispersal could explain weak associations between habitat suitability and gene flow in other studies. Our results also demonstrate the importance of large tracts of undeveloped upland habitat with heterogenous vegetation communities and low urbanization for promoting indigo snake connectivity.

Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis)

In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for gene flow, spatial, and environmental processes that can obfuscate phylogenetic inference and bias species delimitation. As a case study, we sequenced genome-wide exons and introns to evince the processes that underlie the diversification of Philippine Puddle Frogs-a group that is widespread, phenotypically conserved, and exhibits high levels of geographically-based genetic structure. We showed that widely adopted tree- and distance-based approaches inferred up to 20 species, compared to genomic analyses that inferred an optimal number of five distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the five groups and elucidate two specific ways in which gene flow can cause overestimations of species diversity: (1) admixed populations can be inferred as distinct lineages characterized by long branches in phylograms; and (2) admixed lineages can appear to be genetically divergent, even from their parental populations when simple measures of genetic distance are used. We demonstrate that the relationship between mitochondrial and genome-wide nuclear p-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and, consequently, species diversity. Additionally, genetic distance was also biased by spatial and environmental processes. Overall, we showed that high levels of genetic diversity in Philippine Puddle Frogs predominantly comprise metapopulation lineages that arose through complex patterns of admixture, isolation-by-distance, and isolation-by-environment as opposed to species divergence. Our findings suggest that speciation may not be the major process underlying the high levels of hidden diversity observed in many taxonomic groups and that widely-adopted tree- and distance-based methods overestimate species diversity in the presence of gene flow.

Only males care about their environment: sex-biased dispersal in the asp viper (Vipera aspis)

Sex-biased dispersal is common among vertebrates and numerous studies have documented a tendency towards male-biased dispersal in mammals and female-biased dispersal in birds. A few studies have demonstrated that male-biased dispersal seems to be prevalent in reptiles. However, most of these studies considered only a single study site without taking into account possible local variability. We investigated sex-biased dispersal in Vipera aspis in four study sites in Switzerland using microsatellite markers and we predicted a higher dispersal in males than females. In two study sites, females were more spatially autocorrelated and showed a stronger isolation by distance compared with males, which suggests male-biased dispersal. In the other two study sites, the absence of sex-biased dispersal could have been the result of habitat fragmentation. Surprisingly, the dispersal ability of females was similar in the four sites, regardless of habitat fragmentation. This finding suggests a limited impact of habitat on female dispersal and the opposite for male dispersal. Our study demonstrates the importance of inferring sex-biased dispersal in different habitats, because local barriers can affect the outcome of such studies. Hence, general conclusions about patterns of sex-biased dispersal should be drawn with caution when studies are conducted at a single study site.

Biogeographic barriers, Pleistocene refugia, and climatic gradients in the southeastern Nearctic drive diversification in cornsnakes (Pantherophis guttatus complex)

The southeastern Nearctic is a biodiversity hotspot that is also rich in cryptic species. Numerous hypotheses (e.g., vicariance, local adaptation, and Pleistocene speciation in glacial refugia) have been tested in an attempt to explain diversification and the observed pattern of extant biodiversity. However, previous phylogeographic studies have both supported and refuted these hypotheses. Therefore, while data support one or more of these diversification hypotheses, it is likely that taxa are forming within this region in species-specific ways. Here, we generate a genomic data set for the cornsnakes (Pantherophis guttatus complex), which are widespread across this region, spanning both biogeographic barriers and climatic gradients. We use phylogeographic model selection combined with hindcast ecological niche models to determine regions of habitat stability through time. This combined approach suggests that numerous drivers of population differentiation explain the current diversity of this group of snakes. The Mississippi River caused initial speciation in this species complex, with more recent divergence events linked to adaptations to ecological heterogeneity and allopatric Pleistocene refugia. Lastly, we discuss the taxonomy of this group and suggest there may be additional cryptic species in need of formal recognition.

The Multispecies Coalescent Over-Splits Species in the Case of Geographically Widespread Taxa

Many recent species delimitation studies rely exclusively on limited analyses of genetic data analyzed under the multispecies coalescent (MSC) model, and results from these studies often are regarded as conclusive support for taxonomic changes. However, most MSC-based species delimitation methods have well-known and often unmet assumptions. Uncritical application of these genetic-based approaches (without due consideration of sampling design, the effects of a priori group designations, isolation by distance, cytoplasmic-nuclear mismatch, and population structure) can lead to over-splitting of species. Here, we argue that in many common biological scenarios, researchers must be particularly cautious regarding these limitations, especially in cases of well-studied, geographically variable, and parapatrically distributed species complexes. We consider these points with respect to a historically controversial species group, the American milksnakes (Lampropeltis triangulum complex), using genetic data from a recent analysis (Ruane et al. 2014). We show that over-reliance on the program Bayesian Phylogenetics and Phylogeography, without adequate consideration of its assumptions and of sampling limitations, resulted in over-splitting of species in this study. Several of the hypothesized species of milksnakes instead appear to represent arbitrary slices of continuous geographic clines. We conclude that the best available evidence supports three, rather than seven, species within this complex. More generally, we recommend that coalescent-based species delimitation studies incorporate thorough analyses of geographic variation and carefully examine putative contact zones among delimited species before making taxonomic changes.