Prolonged decay of molecular rate estimates for metazoan mitochondrial DNA

PeerJ
Martyna Molak, Simon Y W Ho

Abstract

Evolutionary timescales can be estimated from genetic data using the molecular clock, often calibrated by fossil or geological evidence. However, estimates of molecular rates in mitochondrial DNA appear to scale negatively with the age of the clock calibration. Although such a pattern has been observed in a limited range of data sets, it has not been studied on a large scale in metazoans. In addition, there is uncertainty over the temporal extent of the time-dependent pattern in rate estimates. Here we present a meta-analysis of 239 rate estimates from metazoans, representing a range of timescales and taxonomic groups. We found evidence of time-dependent rates in both coding and non-coding mitochondrial markers, in every group of animals that we studied. The negative relationship between the estimated rate and time persisted across a much wider range of calibration times than previously suggested. This indicates that, over long time frames, purifying selection gives way to mutational saturation as the main driver of time-dependent biases in rate estimates. The results of our study stress the importance of accounting for time-dependent biases in estimating mitochondrial rates regardless of the timescale over which they are infer...Continue Reading

References

Apr 1, 1979·Proceedings of the National Academy of Sciences of the United States of America·W M BrownA C Wilson
Jan 1, 1987·Journal of Molecular Evolution·G F Shields, A C Wilson
Sep 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·C W Birky, J B Walsh
Dec 1, 1971·Theoretical Population Biology·M Nei
Jul 5, 1994·Proceedings of the National Academy of Sciences of the United States of America·A V Brower
Jan 24, 1998·Science·A Gibbons
Mar 23, 2002·Science·D M LambertC Baroni
Jun 14, 2003·Science·Michael J Benton, Francisco J Ayala
Apr 9, 2005·Molecular Biology and Evolution·Simon Y W HoAlexei J Drummond
Sep 2, 2005·Nature Reviews. Genetics·Sudhir Kumar
Nov 1, 2005·Molecular Phylogenetics and Evolution·Jaime García-MorenoBlanca E Hernández-Baños
Dec 17, 2005·Trends in Genetics : TIG·Simon Y W Ho, Greger Larson
May 11, 2006·PLoS Biology·Alexei J DrummondAndrew Rambaut
Sep 9, 2006·Molecular Biology and Evolution·Michael Woodhams
Mar 21, 2007·Molecular Biology and Evolution·Martin J GennerGeorge F Turner
Jun 15, 2007·Systematic Biology·Simon Y W HoAlexei J Drummond
Sep 6, 2007·Biology Letters·Simon Y W HoRobin G Allaby
Nov 13, 2007·BMC Evolutionary Biology·Alexei J Drummond, Andrew Rambaut
Feb 19, 2008·Molecular Biology and Evolution·Christopher P BurridgeJonathan M Waters
Apr 22, 2008·Molecular Ecology·J T Weir, D Schluter
Oct 4, 2008·PLoS Genetics·Craig D MillarDavid M Lambert
Nov 6, 2008·Molecular Biology and Evolution·Brenna M HennJoanna L Mountain
Apr 15, 2009·Biology Letters·Lindell Bromham
Jun 9, 2009·American Journal of Human Genetics·Pedro SoaresMartin B Richards
Aug 8, 2009·Molecular Biology and Evolution·Grant I Peterson, Joanna Masel
Aug 18, 2009·Trends in Ecology & Evolution·Phillip EndicottChris Stringer
Sep 9, 2009·Molecular Ecology·Miguel Navascués, Brent C Emerson
Oct 20, 2009·Trends in Genetics : TIG·Sankar SubramanianDavid M Lambert
Feb 20, 2010·Molecular Biology and Evolution·Anna PapadopoulouAlfried P Vogler
Jun 9, 2010·Systematic Biology·Regis Debruyne, Hendrik N Poinar
Dec 21, 2010·Molecular Phylogenetics and Evolution·Federico PlazziMarco Passamonti
Dec 1, 1995·Trends in Ecology & Evolution·J W Ballard, M Kreitman
Mar 30, 2011·Proceedings of the National Academy of Sciences of the United States of America·Christopher R GignouxJoanna L Mountain
Jul 12, 2011·Molecular Ecology·Simon Y W HoAlan Cooper

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Citations

Jan 16, 2016·Molecular Ecology·Simon Y W HoBeth Shapiro
Feb 26, 2016·Scientific Reports·Ana Carolina M JunqueiraStephan C Schuster
Apr 21, 2019·Molecular Biology and Evolution·Jade Vincent MembrebePhilippe Lemey
May 18, 2018·BMC Evolutionary Biology·K Jun TongSimon Y W Ho
Mar 30, 2017·Microbial Genomics·Sebastian DuchêneEdward C Holmes
Aug 7, 2019·Molecular Ecology·Mary Morgan-RichardsSteven A Trewick
Dec 23, 2020·Proceedings. Biological Sciences·Kurt E GalbreathEric P Hoberg

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