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Inferring phylogeny despite incomplete lineage sorting.
It is now well known that incomplete lineage sorting can cause serious difficulties for phylogenetic inference, but little attention has been paid to methods that attempt to overcome theseExpand
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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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Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshopprers
  • L. Knowles
  • Medicine, Biology
  • Molecular ecology
  • 1 March 2001
There is a long‐standing debate over whether or not the Pleistocene glaciations promoted speciation. While some models predict that extensive mixing of populations during interglacial expansion wouldExpand
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Statistical phylogeography.
While studies of phylogeography and speciation in the past have largely focused on the documentation or detection of significant patterns of population genetic structure, the emerging field ofExpand
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DOES NICHE DIVERGENCE ACCOMPANY ALLOPATRIC DIVERGENCE IN APHELOCOMA JAYS AS PREDICTED UNDER ECOLOGICAL SPECIATION?: INSIGHTS FROM TESTS WITH NICHE MODELS
The role of ecology in the origin of species has been the subject of long‐standing interest to evolutionary biologists. New sources of spatially explicit ecological data allow for large‐scale testsExpand
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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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Multispecies coalescent delimits structure, not species
Significance Despite its widespread application to the species delimitation problem, our study demonstrates that what the multispecies coalescent actually delimits is structure. The currentExpand
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The burgeoning field of statistical phylogeography
  • L. Knowles
  • Medicine, Biology
  • Journal of evolutionary biology
  • 10 November 2003
In the newly emerging field of statistical phylogeography, consideration of the stochastic nature of genetic processes and explicit reference to theoretical expectations under various models hasExpand
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TESTS OF PLEISTOCENE SPECIATION IN MONTANE GRASSHOPPERS (GENUS MELANOPLUS) FROM THE SKY ISLANDS OF WESTERN NORTH AMERICA
  • L. Knowles
  • Biology, Medicine
  • Evolution; international journal of organic…
  • 1 August 2000
Abstract. There has a been a resurgence of debate on whether the Pleistocene glaciations inhibited speciation. This study tests a model of Pleistocene speciation, estimating the phylogeneticExpand
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Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers.
Estimating phylogenetic relationships among closely related species can be extremely difficult when there is incongruence among gene trees and between the gene trees and the species tree. Here weExpand
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