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

Citation

Pyron, Robert Alexander et al. (2020), Data from: Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus), Dryad, Dataset, https://doi.org/10.5061/dryad.34tmpg4g1

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.

Methods

Sanger sequencing - Mitochondria

Anchored Hybrid Enrichment - Phylogenomics

See MS & SI for details.

Usage Notes

desmo161_381loci_trim_names_astrid_mlbs.tre - ASTRID tree estimated from AHE loci with multi-locus bootstrapping

desmo161_381loci_trim_names_astrid.tre - ASTRID tree estimated from AHE loci with quartet support

desmo161_381loci_trim_names_concatenated.tre - ML tree estimated from concatenated AHE loci

desmo161_381loci_trim_names.charSets - partitions for concatenated AHE loci

desmo161_381loci_trim_names.phy - concatenated AHE loci

desmo161_381loci_trim_names.trees - individual gene trees for AHE loci

desmo161_mt.charSets - partitions for mitochondrial data

desmo161_mt.phy - mitochondrial alignment

desmo161_mt.tre - ML phylogeny of mitochondrial data

JW_161_58_concat.part - partitions for ddRAD + AHE loci 

JW_161_58_concat.phy - concatenated dataset for ddRAD + AHE loci

JW_161_58_concat.tre - ML phylogeny for concatenated ddRAD + AHE loci

Funding

National Science Foundation, Award: DEB-1655737

National Science Foundation, Award: DEB-1441719

National Science Foundation, Award: DBI-0905765

National Science Foundation, Award: DEB-1656111