Skip to main content
Dryad

Data from: Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus)

Pyron, Robert Alexander1; O'Connell, Kyle A.2; Lemmon, Emily Moriarty3; Lemmon, Alan R.3; Beamer, David A.4

Published May 01, 2020 on Dryad. https://doi.org/10.5061/dryad.34tmpg4g1

Data files

Abstract

Gene flow between evolutionarily distinct lineages is increasingly recognized as a common occurrence. Such processes distort our ability to diagnose and delimit species, as well as confound attempts to estimate phylogenetic relationships. A conspicuous example is Dusky Salamanders (Desmognathus), a common model-system for ecology, evolution, and behavior. Only 22 species are described; 7 in the last 40 years. However, mitochondrial datasets indicate the presence of up to 45 “candidate species” presenting a complex history of reticulation. Some authors have even suggested that the search for species boundaries in the group may be in vain. Here, we analyze nuclear and mitochondrial data containing 161 individuals from at least 49 distinct evolutionary lineages that we treat as candidate species. Concatenated and species-tree methods fail to provide satisfactory resolution for relationships among these taxa. Comparing topologies and applying methods for estimating phylogenetic networks, we find strong support for numerous instances of hybridization throughout the history of the group. We suggest that these processes may be more common than previously thought across the phylogeography-phylogenetics continuum, and that while the search for species boundaries in Desmognathus may not be in vain, it will be complicated by factors such as crypsis, parallelism, and gene-flow.