Failed species, innominate forms, and the vain search for species limits: cryptic diversity in dusky salamanders (<i><scp>D</scp>esmognathus</i>) of eastern <scp>T</scp>ennessee

Tilley, Stephen G.; Bernardo, Joseph; Katz, Laura A.; López, Lizmarie; Roll, J. Devon; Eriksen, Renée L.; Kratovil, Justin D.; Bittner, Noëlle K. J.; Crandall, Keith A.

doi:10.1002/ece3.780

Cited by 7 publications

(18 citation statements)

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“…These climate differences do not follow any known geographic barriers that would prevent migration between the two areas, suggesting that climate may have played a role in divergence. Furthermore, the pattern we found may be an important component underlying the radiation of salamanders in the southern Appalachians, as it corresponds to a break point common to multiple species, including D. carolinensis (see Tilley and Mahoney 1996;Kozak and Wiens 2006;Rissler and Smith 2010;Tilley et al 2013).…”

Section: Divergencementioning

confidence: 85%

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

Jones

Weisrock

2018

Evolution

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Closely related taxa with dissimilar morphologies are often considered to have diverged via natural selection favoring different phenotypes. However, some studies have found these scenarios to be paired with limited or no genetic differentiation. Desmognathus quadramaculatus and D. marmoratus are sympatric salamander species thought to represent a case of ecological speciation based on distinct morphologies, but the results of previous studies have not resolved corresponding patterns of lineage divergence. Here, we use genome‐wide data to test this hypothesis of ecological speciation. Population structure analyses partitioned individuals geographically, but not morphologically, into two adjacent regions of western North Carolina: Pisgah and Nantahala. Phylogenetic analyses confirmed the nominal species are nonmonophyletic and resolved deep divergence between the two geographic clusters. Model‐testing overwhelmingly supported the hypothesis that lineage divergence followed geography. Finally, ecological niche modeling showed that Pisgah and Nantahala individuals occupy different climatic niches, and geographic boundaries for the two lineages correspond to differences in precipitation regimes across southern Appalachia. Overall, we reject the previous hypothesis of ecological speciation based on microhabitat partitioning. Instead, our results suggest that there are two cryptic lineages, each containing the same pair of morphotypes.

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Section: Divergencementioning

confidence: 85%

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

Jones

Weisrock

2018

Evolution

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“…Similarly, STRUCTURE assumes no isolation by distance or population structure (Meirmans, ). The problem of high levels of genetic structure is particularly acute in terrestrial plethodontid salamanders, which are territorial and exhibit very limited vagility (Kuchta, Parks, Mueller, et al ; Martínez‐Solano et al., ; Tilley et al., ). At the same time, a high degree of phenotypic and ecological conservatism is also common (Kozak & Wiens, ; Wake et al., ).…”

Section: Discussionmentioning

confidence: 99%

“…Species are a fundamental category of biological organization, as important for biodiversity studies as the cell is to lower levels of biological integration (Mayr, ; de Queiroz, ). Nonetheless, species formation is a lengthy and multifaceted process, including the formation of incompletely separated lineages, and a common challenge faced by systematists working on species complexes is how to identify species boundaries given high levels of population structure and discordance among data sets (Kuchta & Wake, ; Lumbsch & Leavitt, ; Niemiller, Near, & Fitzpatrick, ; Tilley et al., ). Recent advances in genomics and analytical theory have led to the development of computational methods of identifying putative genetic lineages, which have the key advantage of providing an objective means of species delimitation (Fujita, Leaché, Burbrink, McGuire, & Moritz, ; Pritchard, Stephens, & Donnelly, ; Rannala & Yang, ; Reid & Carstens, ; Yang & Rannala, ).…”

Section: Introductionmentioning

confidence: 99%

“…Salamanders in the family Plethodontidae provide challenging conditions for species delimitation (Tilley et al., ). In particular, many terrestrial species are characterized by non‐adaptive radiation, or species formation by fragmentation, whereby a species expands its range, then slowly disintegrates into a complex of divergent allopatric or parapatric units (Rundell & Price, ).…”

Section: Introductionmentioning

confidence: 99%

“…Moreover, home ranges are small, on the order of a few square metres (Hall & Stafford, ; Kleeberger & Werner, ). Small home ranges, territoriality and limited vagility promote the accumulation of genetic differences among populations, including high levels of phylogeographic structure (Kuchta, Parks, Mueller, & Wake, ; Martínez‐Solano et al., ; Tilley et al., ).…”

Section: Introductionmentioning

confidence: 99%

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Disintegrating over space and time: Paraphyly and species delimitation in the Wehrle's Salamander complex

2018

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Accurate species delimitation is critical for biodiversity studies. However, species complexes characterized by introgression, high levels of population structure and subtle phenotypic differentiation can be challenging to delimit. Here, we report on a molecular systematic investigation of the woodland salamanders Plethodon wehrlei and Plethodon punctatus, which traditionally have been placed in the Plethodon wehrlei species group. To quantify patterns of genetic variation, we collected genetic samples from throughout the range of both species, including 22 individuals from nine populations of P. punctatus, and 60 individuals from 26 populations of P. wehrlei. From these samples, we sequenced three mtDNA loci (5596 base pairs) and five nuclear loci (3377 base pairs). We inferred time-calibrated gene trees and species trees using BEAST 2.4.6, and we delimited putative species using a Bayesian implementation of the general mixed Yule-coalescent model (bGMYC) and STRUCTURE.Finally, we validated putative species using the multispecies coalescent as implemented in Bayesian Phylogenetics and Phylogeography (BPP). We found substantial phylogeographic diversity in P. wehrlei, including multiple geographically cohesive clades and an inferred mitochondrial common ancestor at 11.5 myr (95% HPD: 9.6-13.6 myr) that separated populations formerly assigned to P. dixi from all other populations. We also found that P. punctatus is deeply nested within P. wehrlei, rendering the latter paraphyletic. After discussing the challenges faced by modern species delimitation methods, we recommend retaining P. punctatus because it is ecologically and phenotypically distinct. We further recommend that P. dixi be recognized as a valid species. |KUCHTA eT Al.

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

Pyron

O’Connell

Lemmon

et al. 2022

Ecology and Evolution

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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.

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Failed species, innominate forms, and the vain search for species limits: cryptic diversity in dusky salamanders (Desmognathus) of eastern Tennessee

Cited by 7 publications

References 0 publications

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

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

Disintegrating over space and time: Paraphyly and species delimitation in the Wehrle's Salamander complex

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

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