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Incomplete Lineage Sorting in Mammalian Phylogenomics.

Celine Scornavacca1, Nicolas Galtier1

  • 1UMR 5554-Institute of Evolutionary Sciences, University Montpellier, CNRS, IRD, EPHE, Place E. Bataillon-CC64, Montpellier, France.

Systematic Biology
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Summary

Incomplete lineage sorting (ILS) is debated in phylogenomics. This study finds ILS is a minor factor in placental mammal gene conflicts, questioning ILS-aware methods for protein-coding sequences.

Keywords:
CoalescenceexonSupertreephylogenyplacental

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Phylogenetic conflicts among genes are common, with incomplete lineage sorting (ILS) proposed as a major cause.
  • The utility of species tree reconstruction methods that account for ILS remains controversial, particularly for protein-coding sequences.
  • Assumptions underlying ILS-aware methods require empirical validation using large-scale genomic data.

Purpose of the Study:

  • To empirically test key assumptions of methods accounting for incomplete lineage sorting (ILS) in phylogenomic analyses.
  • To investigate the relative contribution of ILS to phylogenetic conflict using full-genome data from placental mammals.
  • To clarify the conditions under which ILS-aware methods are applicable to protein-coding gene data.

Main Methods:

  • Analysis of full-genome data from placental mammals.
  • Evaluation of gene genealogies for distinct exons within the same gene.
  • Assessment of incomplete lineage sorting (ILS) as a determinant of phylogenetic conflict.

Main Results:

  • Distinct exons from a single gene do not consistently share a common genealogy in placental mammals.
  • Incomplete lineage sorting (ILS) explains only a small fraction of the observed phylogenetic conflict among genes.
  • Phylogenomic analyses of protein-coding sequences may not require explicit accounting for ILS.

Conclusions:

  • The assumption of shared genealogy among exons from the same gene is violated in this dataset.
  • Incomplete lineage sorting (ILS) is not the primary driver of phylogenetic conflict in placental mammal protein-coding genes.
  • The applicability and relevance of ILS-aware methods in phylogenomics of protein-coding sequences need re-evaluation.