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Cell Lineage Analyses and Gene Function Studies Using Twin-spot MARCM
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Random roots and lineage sorting.

Jeffrey A Rosenfeld1, Ansel Payne, Rob DeSalle

  • 1IST/High Performance and Research Computing, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103, USA. rosenfj1@umdnj.edu

Molecular Phylogenetics and Evolution
|March 27, 2012
PubMed
Summary
This summary is machine-generated.

Incomplete lineage sorting causes phylogenetic incongruence, but its impact is lower than previously thought. Random rooting effects, not just lineage sorting, significantly influence phylogenetic tree accuracy.

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Area of Science:

  • Evolutionary Biology
  • Phylogenetics
  • Genomics

Background:

  • Incomplete lineage sorting is a proposed cause of phylogenetic incongruence across gene partitions.
  • Previous studies suggested lineage sorting could explain up to 50-60% of gene incongruence.
  • Accurate phylogenetic inference is crucial for understanding evolutionary history.

Purpose of the Study:

  • To investigate the role of lineage sorting and outgroup choice in phylogenetic incongruence.
  • To re-evaluate the prevalence of incomplete lineage sorting in large genomic datasets.
  • To assess the impact of outgroup selection on phylogenetic tree topology.

Main Methods:

  • Analysis of seven large, multi-partition, genome-level datasets.
  • Systematic variation of outgroup taxa to assess effects on tree topology.
  • Examination of closely related taxa triads to estimate lineage sorting.
  • Comparison of likelihood and parsimony methods in relation to random rooting.

Main Results:

  • A linear relationship was found between outgroup distance and incongruence, suggesting a strong random rooting effect.
  • Estimates of incongruence due to true lineage sorting were lower, around 10% of genes.
  • Likelihood methods showed stabilization of incongruence with increasing outgroup distance, but could increase random rooting.

Conclusions:

  • Random rooting effects significantly contribute to phylogenetic incongruence, potentially more than previously attributed to lineage sorting.
  • Outgroup selection critically impacts phylogenetic inference, necessitating careful consideration of genetic distance.
  • While lineage sorting plays a role, its contribution to genome-wide incongruence may be overestimated in some contexts.