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Inferring phylogeny despite incomplete lineage sorting.

Wayne P Maddison1, L Lacey Knowles

  • 1Department of Zoology Research Centre, University of British Columbia, V6T 1Z4 Vancouver, B.C., Canada. wmaddisn@interchange.ubc.ca

Systematic Biology
|March 2, 2006
PubMed
Summary
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Accurate species phylogenies can be reconstructed despite incomplete lineage sorting. Sampling more individuals per species improves accuracy, especially for shallow divergences, while more loci benefit deeper trees.

Area of Science:

  • Phylogenetics
  • Population Genetics
  • Evolutionary Biology

Background:

  • Incomplete lineage sorting (ILS) poses significant challenges for accurate phylogenetic inference.
  • Existing phylogenetic methods often overlook the population processes driving ILS.

Purpose of the Study:

  • To explore phylogenetic inference methods that explicitly account for ancestral polymorphism retention and sorting.
  • To investigate the impact of locus number and individuals sampled per species on phylogenetic reconstructability.

Main Methods:

  • Simulated phylogenetic datasets with varying degrees of incomplete lineage sorting.
  • Analysis of the trade-offs between sampling more loci versus more individuals per species.
  • Evaluation of species tree accuracy under different divergence times (1 Ne and 10 Ne generations).

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Main Results:

  • Species tree reconstruction accuracy was maintained even with substantial ILS (divergence < 1 Ne generations) when sufficient individuals were sampled.
  • Sampling more individuals per species yielded better results than sampling more loci for shallow species trees (depth = 1 Ne).
  • Increasing the number of loci improved tree accuracy for deeper species trees (depth = 10 Ne generations).

Conclusions:

  • Gene sequences retain sufficient phylogenetic signal to overcome widespread ILS.
  • Accurate species-level phylogeny reconstruction necessitates a compound model incorporating population genetics processes like lineage sorting alongside substitution models.