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Inferring phylogeny despite incomplete lineage sorting.
TLDR
Improved methods to reconstruct phylogeny near the species level will require a shift to a compound model that considers not only nucleotide or character state substitutions, but also the population genetics processes of lineage sorting. Expand
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. ItExpand
Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshopprers
  • L. Knowles
  • Biology, Medicine
  • Molecular ecology
  • 1 March 2001
TLDR
Rather than inhibiting differentiation, the glaciations appear to have promoted population divergence in M. oregonensis, suggesting that they may have contributed to the radiation of Melanoplus species during the Pleistocene. Expand
DOES NICHE DIVERGENCE ACCOMPANY ALLOPATRIC DIVERGENCE IN APHELOCOMA JAYS AS PREDICTED UNDER ECOLOGICAL SPECIATION?: INSIGHTS FROM TESTS WITH NICHE MODELS
TLDR
The results do not support an ecological speciation model for Mexican Jay lineages because, in most cases, the allopatric environments they occupy are not significantly more divergent than expected under a null model. Expand
Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences.
TLDR
It is demonstrated that the intuitive appeals about being conservative by removing loci may be misguided, and as the tolerance for missing data becomes more stringent, the mutational spectrum represented in the sampled loci becomes truncated such that loci with the highest mutation rates are disproportionately excluded. Expand
Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers.
TLDR
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. Expand
Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design.
TLDR
A new maximum-likelihood method that incorporates stochastic models of both nucleotide substitution and lineage sorting for species-tree estimation results in more accurate species trees than a summary-statistic based approach, and demonstrates that information contained in discordant gene trees can be effectively extracted using a full probabilistic model. Expand
Coupling Genetic and Ecological-Niche Models to Examine How Past Population Distributions Contribute to Divergence
TLDR
The coupling of genetic and ecological-niche modeling provides a new and flexible tool for integrating paleoenvironmental details into species-specific predictions of population structure that can increase the understanding of why the glacial cycles promoted speciation in some taxa and yet inhibited diversification in others. Expand
Distribution modelling and statistical phylogeography: an integrative framework for generating and testing alternative biogeographical hypotheses
TLDR
It is illustrated how two such techniques – species distribution modelling and its historical extension, palaeodistribution modelling – in conjunction with coalescent simulations can be used to generate and test alternative hypotheses. Expand
Sources of error inherent in species-tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing among different methods.
TLDR
Differences in accuracy scores between methods for different sampling regimes highlight the strengths and limits of different methods for species-tree estimation, and explain why using more information contained in gene trees does not necessarily translate into pronounced gains in accuracy. Expand
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