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Gene Tree Discordance Does Not Explain Away the Temporal Decline of Convergence in Mammalian Protein Sequence Evolution

26/26 checkable references clean · checked 2026-07-22

Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.

2 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.

The 26 checked references that resolve

resolves10.1111/j.0014-3820.2006.tb01107.x

EXTENSIVE INTROGRESSION OF MITOCHONDRIAL DNA RELATIVE TO NUCLEAR GENES IN THE DROSOPHILA YAKUBA SPECIES GROUP

resolves10.1093/oxfordjournals.molbev.a026394

When One Is Not Enough: Introgression of Mitochondrial DNA in Drosophila

resolves10.1186/1745-6150-2-20

Extensive parallelism in protein evolution

resolves10.1073/pnas.0900233106

Evidence for an ancient adaptive episode of convergent molecular evolution

resolves10.1038/nrg2526

Effective population size and patterns of molecular evolution and variation

resolves10.1016/j.tig.2010.06.005

Causes and evolutionary significance of genetic convergence

resolves10.1016/0968-0004(94)90167-8

Convergent evolution: the need to be explicit

resolves10.1093/molbev/msu132

OrthoMaM v8: A Database of Orthologous Exons and Coding Sequences for Comparative Genomics in Mammals

resolves10.1038/ng.3198

Convergent evolution of the genomes of marine mammals

resolves10.1093/molbev/msv041

Nonadaptive Amino Acid Convergence Rates Decrease over Time

resolves10.1111/j.1558-5646.1983.tb05528.x

TESTING THE CONSTANT-RATE NEUTRAL ALLELE MODEL WITH PROTEIN SEQUENCE DATA

resolves10.1080/00949650008812035

Comparison of permutation methods for the partial correlation and partial mantel tests

resolves10.1002/bies.201500149

How reticulated are species?

resolves10.1093/molbev/msw197

Gene Tree Discordance Can Generate Patterns of Diminishing Convergence over Time

resolves10.1098/rsbl.2012.0356

Fitness conferred by replaced amino acids declines with time

resolves10.1038/nature12511

Genome-wide signatures of convergent evolution in echolocating mammals

resolves10.1038/nature09105

Sequence space and the ongoing expansion of the protein universe

resolves10.1186/1745-6150-3-7

Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series

resolves10.1093/molbev/msn143

Frequent and Widespread Parallel Evolution of Protein Sequences

resolves10.1093/bioinformatics/btu033

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

resolves10.1038/330401a0

Adaptive evolution in the stomach lysozymes of foregut fermenters

resolves10.1038/nrg.2016.11

Causes of molecular convergence and parallelism in protein evolution

resolves10.1093/molbev/msv013

Determining the Null Model for Detecting Adaptive Convergence from Genomic Data: A Case Study using Echolocating Mammals

resolves10.1093/oxfordjournals.molbev.a025789

Detection of convergent and parallel evolution at the amino acid sequence level

resolves10.1093/molbev/msv091

Are Convergent and Parallel Amino Acid Substitutions in Protein Evolution More Prevalent Than Neutral Expectations?

resolves10.1093/molbev/msv014

No Genome-Wide Protein Sequence Convergence for Echolocation

The 2 references without a DOI — listed, not checked

no DOI — not checkedThe rapid generation of mutation data matrices from protein sequences

no DOI — not checkedRelationships between gene trees and species trees

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