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Relationships between gene trees and species trees.

P Pamilo1, M Nei

  • 1Center for Demographic and Population Genetics, University of Texas Health Science Center, Houston 77225.

Molecular Biology and Evolution
|September 1, 1988
PubMed
Summary

Phylogenetic gene trees may differ from species trees due to ancestral genetic polymorphism. Increasing gene sampling per locus won't improve accuracy; use multiple independent genetic loci for reliable evolutionary insights.

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Area of Science:

  • Evolutionary biology
  • Population genetics
  • Molecular evolution

Background:

  • Phylogenetic trees derived from DNA sequences (gene trees) often conflict with species evolutionary pathways (species trees).
  • A primary cause of this discrepancy is genetic polymorphism within ancestral species.
  • Understanding this conflict is crucial for accurate evolutionary reconstruction.

Purpose of the Study:

  • To evaluate the probability that a gene tree topology matches the species tree topology.
  • To identify factors influencing the accuracy of gene tree reconstruction.
  • To provide guidance on improving the reliability of phylogenetic analyses.

Main Methods:

  • Modeling the probability (P) of gene tree-species tree congruence under neutral mutation.
  • Analyzing the influence of evolutionary time (ti) and effective population size (N) on congruence probability.
  • Assessing the impact of sampling strategies (alleles per locus vs. multiple loci).

Main Results:

  • Congruence probability (P) is significantly reduced when internodal branch parameters (Ti = ti/(2N)) are less than 1.
  • Increasing the number of sampled alleles from a single locus does not substantially enhance the congruence probability.
  • Utilizing DNA sequences from multiple, independently evolving genetic loci is essential for increasing the probability of accurate species tree reconstruction.

Conclusions:

  • Genetic polymorphism in ancestral populations is a key driver of gene tree incongruence with species trees.
  • Single-locus, multi-allele sampling is insufficient for resolving deep evolutionary histories accurately.
  • Phylogenetic accuracy is best achieved by analyzing DNA from numerous independent genetic loci.

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