Rewriting Evolution--"been There, Done That"

Overview

Journal Genome Biol Evol

Publisher Oxford University Press

Specialties Biology
Genetics
Molecular Biology

Date 2013 Apr 6

PMID 23558594

Citations 1

Authors

David Penny

Affiliations

Soon will be listed here.

Abstract

A recent paper by a science journalist in Nature shows major errors in understanding phylogenies, in this case of placental mammals. The underlying unrooted tree is probably correct, but the placement of the root just reflects a well-known error from the acceleration in the rate of evolution among some myomorph rodents.

Citing Articles

The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates.

Sarver B, Pennell M, Brown J, Keeble S, Hardwick K, Sullivan J PeerJ. 2019; 7:e6334.

PMID: 30886768 PMC: 6421065. DOI: 10.7717/peerj.6334.

References

Drake J . The distribution of rates of spontaneous mutation over viruses, prokaryotes, and eukaryotes. Ann N Y Acad Sci. 1999; 870:100-7. DOI: 10.1111/j.1749-6632.1999.tb08870.x. View

Pamilo P, Nei M . Relationships between gene trees and species trees. Mol Biol Evol. 1988; 5(5):568-83. DOI: 10.1093/oxfordjournals.molbev.a040517. View

Dolgin E . Phylogeny: Rewriting evolution. Nature. 2012; 486(7404):460-2. DOI: 10.1038/486460a. View

Song S, Liu L, Edwards S, Wu S . Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proc Natl Acad Sci U S A. 2012; 109(37):14942-7. PMC: 3443116. DOI: 10.1073/pnas.1211733109. View

Lin Y, McLenachan P, Gore A, Phillips M, Ota R, Hendy M . Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling. Mol Biol Evol. 2002; 19(12):2060-70. DOI: 10.1093/oxfordjournals.molbev.a004031. View

Hoeppner M, Gardner P, Poole A . Comparative analysis of RNA families reveals distinct repertoires for each domain of life. PLoS Comput Biol. 2012; 8(11):e1002752. PMC: 3486863. DOI: 10.1371/journal.pcbi.1002752. View

Mossel E, Steel M . A phase transition for a random cluster model on phylogenetic trees. Math Biosci. 2004; 187(2):189-203. DOI: 10.1016/j.mbs.2003.10.004. View

Stadler P, Chen J, Hackermuller J, Hoffmann S, Horn F, Khaitovich P . Evolution of vault RNAs. Mol Biol Evol. 2009; 26(9):1975-91. DOI: 10.1093/molbev/msp112. View

Meredith R, Janecka J, Gatesy J, Ryder O, Fisher C, Teeling E . Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science. 2011; 334(6055):521-4. DOI: 10.1126/science.1211028. View

10.

Lin Y, Waddell P, Penny D . Pika and vole mitochondrial genomes increase support for both rodent monophyly and glires. Gene. 2002; 294(1-2):119-29. DOI: 10.1016/s0378-1119(02)00695-9. View

11.

Penny D . Criteria for optimising phylogenetic trees and the problem of determining the root of a tree. J Mol Evol. 1976; 8(2):95-116. DOI: 10.1007/BF01739097. View

12.

Harrison G, McLenachan P, Phillips M, Slack K, Cooper A, Penny D . Four new avian mitochondrial genomes help get to basic evolutionary questions in the late cretaceous. Mol Biol Evol. 2004; 21(6):974-83. DOI: 10.1093/molbev/msh065. View

13.

Dos Reis M, Inoue J, Hasegawa M, Asher R, Donoghue P, Yang Z . Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc Biol Sci. 2012; 279(1742):3491-500. PMC: 3396900. DOI: 10.1098/rspb.2012.0683. View

14.

Lockhart P, Penny D, Hendy M, Howe C, Beanland T, Larkum A . Controversy on chloroplast origins. FEBS Lett. 1992; 301(2):127-31. DOI: 10.1016/0014-5793(92)81231-a. View

15.

Penny D, Steel M, Waddell P, Hendy M . Improved analyses of human mtDNA sequences support a recent African origin for Homo sapiens. Mol Biol Evol. 1995; 12(5):863-82. DOI: 10.1093/oxfordjournals.molbev.a040263. View

16.

Steel M, Penny D . Parsimony, likelihood, and the role of models in molecular phylogenetics. Mol Biol Evol. 2000; 17(6):839-50. DOI: 10.1093/oxfordjournals.molbev.a026364. View

17.

DErchia A, Gissi C, Pesole G, Saccone C, Arnason U . The guinea-pig is not a rodent. Nature. 1996; 381(6583):597-600. DOI: 10.1038/381597a0. View

18.

McCormack J, Faircloth B, Crawford N, Gowaty P, Brumfield R, Glenn T . Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis. Genome Res. 2011; 22(4):746-54. PMC: 3317156. DOI: 10.1101/gr.125864.111. View