Genomic data reject the hypothesis of sympatric ecological speciation in a clade of Desmognathus salamanders

Complex Hybridization in a Clade of Polytypic Salamanders (Plethodontidae: Desmognathus) Uncovered by Estimating Higher-Level Phylogenetic Networks

Reticulation between radiating lineages is a common feature of diversification. We examine these phenomena in the Pisgah clade of Desmognathus salamanders from the southern Appalachian Mountains of the eastern United States. The group contains 4-7 species exhibiting 2 discrete phenotypes, aquatic "shovel-nosed" and semi-aquatic "black-bellied" forms. These ecomorphologies are ancient and have apparently been transmitted repeatedly between lineages through introgression. Geographically proximate populations of both phenotypes exhibit admixture, and at least 2 black-bellied lineages have been produced via reticulations between shovel-nosed parentals, suggesting potential hybrid speciation dynamics. However, computational constraints currently limit our ability to reconstruct network radiations from gene-tree data. Available methods are limited to level-1 networks wherein reticulations do not share edges, and higher-level networks may be non-identifiable in many cases. We present a heuristic approach to recover information from higher-level networks across a range of potentially identifiable empirical scenarios, supported by theory and simulation. When extrinsic information indicates the location and direction of reticulations, our method can successfully estimate a reduced possible set of nonlevel-1 networks. Phylogenomic data support a single backbone topology with up to 5 overlapping hybrid edges in the Pisgah clade. These results suggest an unusual mechanism of ecomorphological hybrid speciation, wherein a binary threshold trait causes some hybrid populations to shift between microhabitat niches, promoting ecological divergence between sympatric hybrids and parentals. This contrasts with other well-known systems in which hybrids exhibit intermediate, novel, or transgressive phenotypes. The genetic basis of these phenotypes is unclear and further data are needed to clarify the evolutionary basis of morphological changes with ecological consequences.

Predicting genetic biodiversity in salamanders using geographic, climatic, and life history traits

The geographic distribution of genetic variation within a species reveals information about its evolutionary history, including responses to historical climate change and dispersal ability across various habitat types. We combine genetic data from salamander species with geographic, climatic, and life history data collected from open-source online repositories to develop a machine learning model designed to identify the traits that are most predictive of unrecognized genetic lineages. We find evidence of hidden diversity distributed throughout the clade Caudata that is largely the result of variation in climatic variables. We highlight some of the difficulties in using machine-learning models on open-source data that are often messy and potentially taxonomically and geographically biased.

Determinants of genetic diversity in Neotropical salamanders (Plethodontidae: Bolitoglossini)

Genetic diversity is the raw material of evolution, yet the reasons why it varies among species remain poorly understood. While studies at deeper phylogenetic scales point to the influence of life history traits on genetic diversity, it appears to be more affected by population size but less predictable at shallower scales. We used proxies for population size, mutation rate, direct selection, and linked selection to test factors affecting genetic diversity within a diverse assemblage of Neotropical salamanders, which vary widely for these traits. We estimated genetic diversity of noncoding loci using ddRADseq and coding loci using RNAseq for an assemblage of Neotropical salamanders distributed from northern Mexico to Costa Rica. Using ddRADseq loci, we found no significant association with genetic diversity, while for RNAseq data we found that environmental heterogeneity and proxies of population size predict a substantial portion of the variance in genetic diversity across species. Our results indicate that diversity of coding loci may be more predictable than that of noncoding loci, which appears to be mostly unpredictable at shallower phylogenetic scales. Our results suggest that coding loci may be more appropriate for genetic diversity estimates used in conservation planning because of the lack of any association between the variables we used and genetic diversity of noncoding loci.

A systematic revision of the Shovel-nosed Salamander (Plethodontidae: Desmognathus marmoratus), with re-description of the related D. aureatus and D. intermedius

Shovel-nosed Salamanders, Desmognathus marmoratus (Moore, 1899), were long thought to represent a single species from the southern Appalachian Mountains of the eastern United States, ranging from northeastern Georgia to extreme southwestern Virginia. These populations have a highly derived ecomorphology, being fully aquatic with a specialized flattened and elongated phenotype adapted to rocky riffle zones in fast-flowing, high-gradient mountain streams. Because of this, they were originally described in a separate genus, Leurognathus Moore, 1899. Four additional species or subspecies were described from 1928-1956 based on regional geographic variation in phenotype before being synonymized with L. marmoratus in 1962, which was reassigned to Desmognathus in 1996. Molecular analyses subsequently revealed four distinct candidate lineages in two distantly related clades, which were recently re-delimited into three species. These are D. aureatus (Martof, 1956) from northeastern Georgia, D. intermedius (Pope, 1928) from western North Carolina, and D. marmoratus from northwestern North Carolina. We provide a systematic revision of these taxa, which do not represent a natural group but instead exhibit convergent phenotypes across multiple species, potentially driven by ancient episodes of adaptive introgression between ancestral lineages. Our recent fieldwork revealed an astonishingly disjunct and morphologically distinct population of D. marmoratus in the New River Gorge of West Virginia, which were previously confused with D. kanawha Pyron and Beamer, 2022. This locality is ~120 airline km away from the nearest populations of D. marmoratus in Virginia. No Shovel-nosed Salamanders have ever been found in the New River drainage during our extensive previous explorations or credibly reported in museum specimens or the literature. Additional cryptic populations of these taxa may remain.

Ecology and the origin of non-ephemeral species

AbstractResearch over the past three decades has shown that ecology-based extrinsic reproductive barriers can rapidly arise to generate incipient species-but such barriers can also rapidly dissolve when environments change, resulting in incipient species collapse. Understanding the evolution of unconditional, "intrinsic" reproductive barriers is therefore important for understanding the longer-term buildup of biodiversity. In this article, we consider ecology's role in the evolution of intrinsic reproductive isolation. We suggest that this topic has fallen into a gap between disciplines: while evolutionary ecologists have traditionally focused on the rapid evolution of extrinsic isolation between co-occurring ecotypes, speciation geneticists studying intrinsic isolation in other taxa have devoted little attention to the ecological context in which it evolves. We argue that for evolutionary ecology to close this gap, the field will have to expand its focus beyond rapid adaptation and its traditional model systems. Synthesizing data from several subfields, we present circumstantial evidence for and against different forms of ecological adaptation as promoters of intrinsic isolation and discuss alternative forces that may be significant. We conclude by outlining complementary approaches that can better address the role of ecology in the evolution of nonephemeral reproductive barriers and, by extension, less ephemeral species.

Evidence of morphological homoplasy among large, semi-aquatic species of Desmognathus

The salamander family Plethodontidae is replete with instances of repeated homoplasy. We tested for morphological homoplasy in distantly related species of the plethodontid genus Desmognathus that share similar ecologies. Specifically, we compared species that are large and nearly aquatic. Using morphometric analyses, we compared the respective morphologies of four large, nearly aquatic forms, specifically the Black Mountain Salamander (Desmognathus welteri), the Dwarf Black-bellied Salamander (D. folkertsi), and two phylogenetically divergent lineages of the Black-bellied Salamander (D. quadramaculatus). Morphometric analysis uncovered distinct differences among them. However, all of the large-bodied lineages exhibited the same extent of tail-fin development in spite of D. welteri’s closer phylogenetic relationship to smaller, more-terrestrial species than to the other large, nearly aquatic forms we tested. We hypothesize that large body size is also a consequence of aquatic adaptation. These morphological consequences of a nearly aquatic ecology represent another case of homoplasy within this salamander family.

Candidate-species delimitation in Desmognathus salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones

Dusky Salamanders (genus Desmognathus) currently comprise only 22 described, extant species. However, recent mitochondrial and nuclear estimates indicate the presence of up to 49 candidate species based on ecogeographic sampling. Previous studies also suggest a complex history of hybridization between these lineages. Studies in other groups suggest that disregarding admixture may affect both phylogenetic inference and clustering-based species delimitation. With a dataset comprising 233 Anchored Hybrid Enrichment (AHE) loci sequenced for 896 Desmognathus specimens from all 49 candidate species, we test three hypotheses regarding (i) species-level diversity, (ii) hybridization and admixture, and (iii) misleading phylogenetic inference. Using phylogenetic and population-clustering analyses considering gene flow, we find support for at least 47 candidate species in the phylogenomic dataset, some of which are newly characterized here while others represent combinations of previously named lineages that are collapsed in the current dataset. Within these, we observe significant phylogeographic structure, with up to 64 total geographic genetic lineages, many of which hybridize either narrowly at contact zones or extensively across ecological gradients. We find strong support for both recent admixture between terminal lineages and ancient hybridization across internal branches. This signal appears to distort concatenated phylogenetic inference, wherein more heavily admixed terminal specimens occupy apparently artifactual early-diverging topological positions, occasionally to the extent of forming false clades of intermediate hybrids. Additional geographic and genetic sampling and more robust computational approaches will be needed to clarify taxonomy, and to reconstruct a network topology to display evolutionary relationships in a manner that is consistent with their complex history of reticulation.

The role of glacial-interglacial climate change in shaping the genetic structure of eastern subterranean termites in the southern Appalachian Mountains, USA

The eastern subterranean termite, Reticulitermes flavipes, currently inhabits previously glaciated regions of the northeastern U.S., as well as the unglaciated southern Appalachian Mountains and surrounding areas. We hypothesized that Pleistocene climatic fluctuations have influenced the distribution of R. flavipes, and thus the evolutionary history of the species. We estimated contemporary and historical geographic distributions of R. flavipes by constructing Species Distribution Models (SDM). We also inferred the evolutionary and demographic history of the species using mitochondrial (cytochrome oxidase I and II) and nuclear (endo-beta-1,4-glucanase) DNA sequence data. To do this, genetic populations were delineated using Bayesian spatial-genetic clustering, competing hypotheses about population divergence were assessed using approximate Bayesian computation (ABC), and changes in population size were estimated using Bayesian skyline plots. SDMs identified areas in the north with suitable habitat during the transition from the Last Interglacial to the Last Glacial Maximum, as well as an expanding distribution from the mid-Holocene to the present. Genetic analyses identified three geographically cohesive populations, corresponding with northern, central, and southern portions of the study region. Based on ABC analyses, divergence between the Northern and Southern populations was the oldest, estimated to have occurred 64.80 thousand years ago (kya), which corresponds with the timing of available habitat in the north. The Central and Northern populations diverged in the mid-Holocene, 8.63 kya, after which the Central population continued to expand. Accordingly, phylogeographic patterns of R. flavipes in the southern Appalachians appear to have been strongly influenced by glacial-interglacial climate change.

OPEN RESEARCH BADGES

This article has been awarded Open Materials, Open Data Badges. All materials and data are publicly accessible via the Open Science Framework at https://doi.org/10.5061/dryad.5hr7f31.

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

Accurate species delimitation and description are necessary to guide effective conservation of imperiled species, and this synergy is maximized when multiple data sources are used to delimit species. We illustrate this point by examining Drymarchon couperi (Eastern Indigo Snake), a large, federally-protected species in North America that was recently divided into two species based on gene sequence data from three loci and heuristic morphological assessment. Here, we re-evaluate the two-species hypothesis for D. couperi by evaluating both population genetic and gene sequence data. Our analyses of 14 microsatellite markers revealed 6–8 genetic population clusters with significant admixture, particularly across the contact zone between the two hypothesized species. Phylogenetic analyses of gene sequence data with maximum-likelihood methods suggested discordance between mitochondrial and nuclear markers and provided phylogenetic support for one species rather than two. For these reasons, we place Drymarchon kolpobasileus into synonymy with D. couperi. We suggest inconsistent patterns between mitochondrial and nuclear DNA are driven by high dispersal of males relative to females. We advocate for species delimitation exercises that evaluate admixture and gene flow in addition to phylogenetic analyses, particularly when the latter reveal monophyletic lineages. This is particularly important for taxa, such as squamates, that exhibit strong sex-biased dispersal. Problems associated with over-delimitation of species richness can become particularly acute for threatened and endangered species, because of high costs to conservation when taxonomy demands protection of more individual species than are supported by accumulating data.