A Likelihood-Ratio Test for Lumpability of Phylogenetic Data: Is the Markovian Property of an Evolutionary Process Retained in Recoded DNA?

dc.contributor.authorVera-Ruiz, Victor A.
dc.contributor.authorRobinson, John
dc.contributor.authorJermiin, Lars
dc.date.accessioned2024-04-03T01:02:29Z
dc.date.issued2022
dc.date.updated2022-11-13T07:19:46Z
dc.description.abstractIn molecular phylogenetics, it is typically assumed that the evolutionary process for DNA can be approximated by independent and identically distributed Markovian processes at the variable sites and that these processes diverge over the edges of a rooted bifurcating tree. Sometimes the nucleotides are transformed from a 4-state alphabet to a 3- or 2-state alphabet by a procedure that is called recoding, lumping, or grouping of states. Here, we introduce a likelihood-ratio test for lumpability for DNA that has diverged under different Markovian conditions, which assesses the assumption that the Markovian property of the evolutionary process over each edge is retained after recoding of the nucleotides. The test is derived and validated numerically on simulated data. To demonstrate the insights that can be gained by using the test, we assessed two published data sets, one of mitochondrial DNA from a phylogenetic study of the ratites and the other of nuclear DNA from a phylogenetic study of yeast. Our analysis of these data sets revealed that recoding of the DNA eliminated some of the compositional heterogeneity detected over the sequences. However, the Markovian property of the original evolutionary process was not retained by the recoding, leading to some significant distortions of edge lengths in reconstructed trees.[Evolutionary processes; likelihood-ratio test; lumpability; Markovian processes; Markov models; phylogeny; recoding of nucleotides.]en_AU
dc.format.mimetypeapplication/pdfen_AU
dc.identifier.issn1063-5157en_AU
dc.identifier.urihttp://hdl.handle.net/1885/316479
dc.language.isoen_AUen_AU
dc.publisherTaylor & Francis Groupen_AU
dc.rights© 2021 The authorsen_AU
dc.sourceSystematic Biologyen_AU
dc.source.urihttps://doi-org.virtual.anu.edu.au/10.1093/sysbio/syab074en_AU
dc.titleA Likelihood-Ratio Test for Lumpability of Phylogenetic Data: Is the Markovian Property of an Evolutionary Process Retained in Recoded DNA?en_AU
dc.typeJournal articleen_AU
local.bibliographicCitation.issue3en_AU
local.bibliographicCitation.lastpage675en_AU
local.bibliographicCitation.startpage660en_AU
local.contributor.affiliationVera-Ruiz, Victor A., University of Sydneyen_AU
local.contributor.affiliationRobinson, John, University of Sydneyen_AU
local.contributor.affiliationJermiin, Lars, College of Science, ANUen_AU
local.contributor.authoremailu5268558@anu.edu.auen_AU
local.contributor.authoruidJermiin, Lars, u5268558en_AU
local.description.embargo2099-12-31
local.description.notesImported from ARIESen_AU
local.identifier.absfor310510 - Molecular evolutionen_AU
local.identifier.absseo280102 - Expanding knowledge in the biological sciencesen_AU
local.identifier.ariespublicationu9511635xPUB2251en_AU
local.identifier.citationvolume71en_AU
local.identifier.uidSubmittedByu9511635en_AU
local.publisher.urlhttps://academic.oup.com/en_AU
local.type.statusPublished Versionen_AU

Downloads

Original bundle

Now showing 1 - 1 of 1
No Thumbnail Available
Name:
TMP478945113202443115752.pdf
Size:
647.47 KB
Format:
Adobe Portable Document Format
Description:
Back to topicon-arrow-up-solid
 
APRU
IARU
 
edX
Group of Eight Member

Acknowledgement of Country

The Australian National University acknowledges, celebrates and pays our respects to the Ngunnawal and Ngambri people of the Canberra region and to all First Nations Australians on whose traditional lands we meet and work, and whose cultures are among the oldest continuing cultures in human history.


Contact ANUCopyrightDisclaimerPrivacyFreedom of Information

+61 2 6125 5111 The Australian National University, Canberra

TEQSA Provider ID: PRV12002 (Australian University) CRICOS Provider Code: 00120C ABN: 52 234 063 906