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A Genomic Perspective on the Evolutionary Diversification of Turtles
Simone M Gable1, Michael I Byars1, Robert Literman2
1School of Informatics, Computing, and Cyber Systems, Northern Arizona University, PO Box 5693, Flagstaff, AZ 8601, USA.
Systematic Biology
|March 7, 2022
Summary
Phylogenetic heterogeneity is common in turtle evolution, even in well-resolved groups. Analyzing genomes reveals that incomplete lineage sorting, not other factors, drives discordance in gene trees versus species trees.
Area of Science:
- Evolutionary Biology
- Genomics
- Phylogenetics
Background:
- Understanding evolutionary relationships is crucial for biodiversity and conservation.
- Turtle phylogeny has been challenging due to complex evolutionary histories.
Purpose of the Study:
- To investigate phylogenetic heterogeneity in turtle evolution using genomic data.
- To identify drivers of discordance between gene trees and species trees in turtles.
Main Methods:
- Collected thousands of single-copy orthologs from 19 turtle genome assemblies.
- Reconstructed phylogenies using multispecies coalescent and concatenated partitioned methods.
- Analyzed millions of biallelic markers from 26 species, examining annotated genomic regions.
Main Results:
- Strong support for major turtle clades, but significant gene tree-species tree discordance observed.
- Incomplete lineage sorting identified as the primary driver of discordance.
- Little evidence for substitutional saturation, codon usage bias, or compositional heterogeneity influencing topologies.
Conclusions:
- Phylogenetic heterogeneity is expected even in well-resolved clades like turtles.
- Maximizing genomic data is essential for accurate phylogenies and conservation assessments in turtles.
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