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Article: Morphological Data Sets Fit a Common Mechanism Much More Poorly than DNA Sequences and Call Into Question the Mkv Model

TitleMorphological Data Sets Fit a Common Mechanism Much More Poorly than DNA Sequences and Call Into Question the Mkv Model
Authors
Keywordsbiological model
classification
computer simulation
molecular evolution
nucleotide sequence
Issue Date2019
PublisherOxford University Press. The Journal's web site is located at https://academic.oup.com/sysbio/
Citation
Systematic Biology, 2019, v. 68 n. 3, p. 494-504 How to Cite?
AbstractThe Mkv evolutionary model, based on minor modifications to models of molecular evolution, is being increasingly used to infer phylogenies from discrete morphological data, often producing different results from parsimony. The critical difference between Mkv and parsimony is the assumption of a “common mechanism” in the Mkv model, with branch lengths determining that probability of change for all characters increases or decreases at the same tree branches by the same exponential factor. We evaluate whether the assumption of a common mechanism applies to morphology, by testing the implicit prediction that branch lengths calculated from different subsets of characters will be significantly correlated. Our analysis shows that DNA (38 data sets tested) is often compatible with a common mechanism, but morphology (86 data sets tested) generally is not, showing very disparate branch lengths for different character partitions. The low levels of branch length correlation demonstrated for morphology (fitting models without a common mechanism) suggest that the Mkv model is too unrealistic and inadequate for the analysis of most morphological data sets. [Bayesian analysis; Mkv model; morphological data; phylogenetics.]
Persistent Identifierhttp://hdl.handle.net/10722/272895
ISSN
2019 Impact Factor: 10.408
2015 SCImago Journal Rankings: 10.507

 

DC FieldValueLanguage
dc.contributor.authorGoloboff, PA-
dc.contributor.authorPittman, M-
dc.contributor.authorPol, D-
dc.contributor.authorXu, X-
dc.date.accessioned2019-08-06T09:18:36Z-
dc.date.available2019-08-06T09:18:36Z-
dc.date.issued2019-
dc.identifier.citationSystematic Biology, 2019, v. 68 n. 3, p. 494-504-
dc.identifier.issn1063-5157-
dc.identifier.urihttp://hdl.handle.net/10722/272895-
dc.description.abstractThe Mkv evolutionary model, based on minor modifications to models of molecular evolution, is being increasingly used to infer phylogenies from discrete morphological data, often producing different results from parsimony. The critical difference between Mkv and parsimony is the assumption of a “common mechanism” in the Mkv model, with branch lengths determining that probability of change for all characters increases or decreases at the same tree branches by the same exponential factor. We evaluate whether the assumption of a common mechanism applies to morphology, by testing the implicit prediction that branch lengths calculated from different subsets of characters will be significantly correlated. Our analysis shows that DNA (38 data sets tested) is often compatible with a common mechanism, but morphology (86 data sets tested) generally is not, showing very disparate branch lengths for different character partitions. The low levels of branch length correlation demonstrated for morphology (fitting models without a common mechanism) suggest that the Mkv model is too unrealistic and inadequate for the analysis of most morphological data sets. [Bayesian analysis; Mkv model; morphological data; phylogenetics.]-
dc.languageeng-
dc.publisherOxford University Press. The Journal's web site is located at https://academic.oup.com/sysbio/-
dc.relation.ispartofSystematic Biology-
dc.rightsThis is a pre-copy-editing, author-produced PDF of an article accepted for publication in Systematic Biology following peer review. The definitive publisher-authenticated version Systematic Biology, 2019, v. 68 n. 3, p. 494-504 is available online at: https://doi.org/10.1093/sysbio/syy077-
dc.subjectbiological model-
dc.subjectclassification-
dc.subjectcomputer simulation-
dc.subjectmolecular evolution-
dc.subjectnucleotide sequence-
dc.titleMorphological Data Sets Fit a Common Mechanism Much More Poorly than DNA Sequences and Call Into Question the Mkv Model-
dc.typeArticle-
dc.identifier.emailPittman, M: mpittman@hku.hk-
dc.identifier.authorityPittman, M=rp01622-
dc.description.naturepostprint-
dc.identifier.doi10.1093/sysbio/syy077-
dc.identifier.pmid30445627-
dc.identifier.scopuseid_2-s2.0-85061857539-
dc.identifier.hkuros300842-
dc.identifier.volume68-
dc.identifier.issue3-
dc.identifier.spage494-
dc.identifier.epage504-
dc.publisher.placeUnited Kingdom-

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