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How to fail at species delimitation
Species delimitation is the act of identifying species‐level biological diversity. In recent years, the field has witnessed a dramatic increase in the number of methods available for delimitingExpand
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Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model
BackgroundSpecies are considered the fundamental unit in many ecological and evolutionary analyses, yet accurate, complete, accessible taxonomic frameworks with which to identify them are oftenExpand
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STEM: species tree estimation using maximum likelihood for gene trees under coalescence
TLDR
We describe a new software package called STEM that estimates the maximum likelihood (ML) species tree from a sample of gene trees, assuming that discord between the observed gene trees and the species tree arises solely from the coalescent process (Kingman, 1982). Expand
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Applications of next-generation sequencing to phylogeography and phylogenetics.
This is a time of unprecedented transition in DNA sequencing technologies. Next-generation sequencing (NGS) clearly holds promise for fast and cost-effective generation of multilocus sequence dataExpand
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Phylogeography's past, present, and future: 10 years after Avise, 2000.
Approximately 20 years ago, Avise and colleagues proposed the integration of phylogenetics and population genetics for investigating the connection between micro- and macroevolutionary phenomena. TheExpand
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Delimiting species without monophyletic gene trees.
Genetic data are frequently used to delimit species, where species status is determined on the basis of an exclusivity criterium, such as reciprocal monophyly. Not only are there numerous empiricalExpand
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SpedeSTEM: a rapid and accurate method for species delimitation
We describe a software package (SpedeSTEM) that allows researchers to conduct a species delimitation analysis using intraspecific genetic data. Our method operates under the assumption that a prioriExpand
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INTEGRATING COALESCENT AND ECOLOGICAL NICHE MODELING IN COMPARATIVE PHYLOGEOGRAPHY
Abstract Understanding the factors that contribute to the formation of population genetic structure is a central goal of phylogeographic research, but achieving this goal can be complicated by theExpand
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Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (mygalomorphae, antrodiaetidae, aliatypus).
Species are a fundamental unit for biological studies, yet no uniform guidelines exist for determining species limits in an objective manner. Given the large number of species concepts available,Expand
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Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandykei species group.
Mesic forests in the North American Pacific Northwest occur in two disjunct areas: along the coastal and Cascade ranges of Oregon, Washington, and British Columbia as well as the Northern RockyExpand
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