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Mol Phylogenet Evol. 2020 Feb 3;146:106751. doi: 10.1016/j.ympev.2020.106751. [Epub ahead of print]

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

Author information

1
Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA; Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington, DC 20560, USA. Electronic address: rpyron@colubroid.org.
2
Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA; Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington, DC 20560, USA; Global Genome Initiative, National Museum of Natural History Smithsonian Institution, Washington, DC 20560, USA.
3
Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA.
4
Department of Scientific Computing, Florida State University, Tallahassee, FL 32306-4120, USA.
5
Department of Natural Sciences, Nash Community College, Rocky Mount, NC, 27804, USA.

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" and multiple paraphyletic taxa 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 do not estimate fully resolved 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.

KEYWORDS:

Candidate species; Desmognathus; Hybridization; Networks

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