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Updated: Jul 12, 2026
08:02
Dissection and Flat-mounting of the Threespine Stickleback Branchial Skeleton
Published on: May 7, 2016
Genomic Distortion of Jawed Vertebrate Phylogeny
Chase D Brownstein1, Liandong Yang2, Alex Dornburg3
1Department of Ecology and Evolutionary Biology, Yale University, New Haven CT, USA.
Biorxiv : the Preprint Server for Biology
|July 10, 2026
Summary
Understanding evolutionary relationships is key, but often difficult. This study reveals how mass extinctions scramble phylogenetic signals, impacting our ability to accurately date vertebrate evolution, especially in ray-finned fishes.
Area of Science:
- Evolutionary Biology
- Phylogenetics
- Genomics
Background:
- Reconstructing species interrelationships is crucial for understanding evolution.
- Evolutionary relationships often present challenges in resolution and temporal calibration.
- Topological and temporal uncertainty are common issues in phylogenetic analyses across the Tree of Life.
Purpose of the Study:
- To investigate the dynamics of temporal and topological uncertainty in jawed vertebrate evolution.
- To assess how mass extinction events and varying genomic evolution rates impact phylogenetic inference.
- To explore the challenges in accurately inferring deep divergences, particularly in ray-finned fishes.
Main Methods:
- Generated a phylogeny of jawed vertebrates using 1105 exonic loci from 540 species.
- Analyzed phylogenetic signal across loci and DNA sites, focusing on clades originating around the Cretaceous-Paleogene mass extinction.
- Tested the impact of including ray-finned fish lineages with diverse molecular evolution rates on timescale inferences.
Main Results:
- Observed rapid reductions in statistical support for monophyly in jawed vertebrate clades originating around the Cretaceous-Paleogene mass extinction.
- Found that phylogenetic signal was differentially scrambled during rapid successive divergences in multiple unrelated lineages (birds, snakes, mammals, acanthomorph fishes).
- Demonstrated that genomic evolution rates affect the ability to infer the vertebrate evolutionary timescale, with deep ray-finned fish divergences potentially being inaccurately inferred.
Conclusions:
- Mass extinction events can significantly scramble phylogenetic signal across multiple, distantly related vertebrate clades.
- Rates of genomic evolution critically influence the accuracy of inferring evolutionary timescales.
- Accurate inference of deep divergences in some groups, like ray-finned fishes, may be limited by sequence data and fossil record constraints, highlighting macroevolutionary realities behind phylogenetic uncertainty.
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