A comparison of methods for estimating substitution rates from ancient DNA sequence data

BMC Evolutionary Biology
K Jun TongSimon Y Ho

Abstract

Phylogenetic analysis of DNA from modern and ancient samples allows the reconstruction of important demographic and evolutionary processes. A critical component of these analyses is the estimation of evolutionary rates, which can be calibrated using information about the ages of the samples. However, the reliability of these rate estimates can be negatively affected by among-lineage rate variation and non-random sampling. Using a simulation study, we compared the performance of three phylogenetic methods for inferring evolutionary rates from time-structured data sets: regression of root-to-tip distances, least-squares dating, and Bayesian inference. We also applied these three methods to time-structured mitogenomic data sets from six vertebrate species. Our results from 12 simulation scenarios show that the three methods produce reliable estimates when the substitution rate is high, rate variation is low, and samples of similar ages are not all grouped together in the tree (i.e., low phylo-temporal clustering). The interaction of these factors is particularly important for least-squares dating and Bayesian estimation of evolutionary rates. The three estimation methods produced consistent estimates of rates across most of the si...Continue Reading

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Citations

Sep 13, 2019·PLoS Pathogens·Fabrizio MenardoSebastien Gagneux
Sep 11, 2019·Nature Communications·Joan Garcia-PortaKatharina C Wollenberg Valero
Sep 9, 2020·Molecular Biology and Evolution·Sebastian DucheneGuy Baele
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May 22, 2021·BMC Genomics·Vinícius Bonetti FranceschiClaudia Elizabeth Thompson
Jul 15, 2021·Ecology and Evolution·Paul J Wilson, Linda Y Rutledge
Aug 8, 2021·Virus Research·Vinícius Bonetti FranceschiClaudia Elizabeth Thompson

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Software Mentioned

R package phangorn
TempEst
LSD
LogAnalyser
NELSI
BEAST
RAxML

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