How to fail at species delimitation
- B. Carstens, Tara A. Pelletier, N. Reid, Jordan D. Satler
- Environmental Science, BiologyMolecular Ecology
- 1 September 2013
Researchers should apply a wide range of species delimitation analyses to their data and place their trust in delimitations that are congruent across methods, for in most contexts it is better to fail to delimit species than it is to falsely delimit entities that do not represent actual evolutionary lineages.
Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model
This paper presents a Bayesian implementation of an evolutionary model-based method, the general mixed Yule-coalescent model (GMYC), which integrates over the parameters of the model and uncertainty in phylogenetic relationships using the output of widely available phylogenetic models and Markov-Chain Monte Carlo simulation in order to produce marginal probabilities of species identities.
STEM: species tree estimation using maximum likelihood for gene trees under coalescence
UNLABELLED STEM is a software package written in the C language to obtain maximum likelihood (ML) estimates for phylogenetic species trees given a sample of gene trees under the coalescent model. It…
Applications of next-generation sequencing to phylogeography and phylogenetics.
Delimiting species without monophyletic gene trees.
The goal (and motivation of this study) is that genetic data might be used effectively as a source of complementation to other sources of data for diagnosing species, as opposed to the exclusion of other evidence for species delimitation, which will require an explicit consideration of the effects of the temporal dynamic of lineage splitting on genetic data.
SpedeSTEM: a rapid and accurate method for species delimitation
This work enables speciation investigations to identify lineages that are evolutionarily distinct and thus have the potential to form new species before these lineages acquire secondary characteristics such as reproductive isolation or morphological differentiation that are commonly used to define species.
Phylogeography's past, present, and future: 10 years after Avise, 2000.
INTEGRATING COALESCENT AND ECOLOGICAL NICHE MODELING IN COMPARATIVE PHYLOGEOGRAPHY
- B. Carstens, C. L. Richards
- Environmental Science, BiologyEvolution; international journal of organic…
- 1 June 2007
Paleodistribution models and population genetic structure are congruent across three amphibian lineages, suggesting that they have responded in a concerted manner to environmental change.
Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (mygalomorphae, antrodiaetidae, aliatypus).
- Jordan D. Satler, B. Carstens, M. Hedin
- Biology, Environmental ScienceSystematic Biology
- 1 November 2013
This study investigates species limits in a complex of morphologically conserved trapdoor spiders from California and provides a framework for identifying and defining the cryptic lineage diversity that prevails in many organismal groups.
Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers.
It is shown that incorporating a model of the stochastic loss of gene lineages by genetic drift into the phylogenetic estimation procedure can provide a robust estimate of species relationships, despite widespread incomplete sorting of ancestral polymorphism.