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- Publisher Website: 10.1093/sysbio/syy077
- Scopus: eid_2-s2.0-85061857539
- PMID: 30445627
- WOS: WOS:000493313500008
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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
Title | Morphological Data Sets Fit a Common Mechanism Much More Poorly than DNA Sequences and Call Into Question the Mkv Model |
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Authors | |
Keywords | biological model classification computer simulation molecular evolution nucleotide sequence |
Issue Date | 2019 |
Publisher | Oxford 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? |
Abstract | The 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 Identifier | http://hdl.handle.net/10722/272895 |
ISSN | 2023 Impact Factor: 6.1 2023 SCImago Journal Rankings: 3.098 |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Goloboff, PA | - |
dc.contributor.author | Pittman, M | - |
dc.contributor.author | Pol, D | - |
dc.contributor.author | Xu, X | - |
dc.date.accessioned | 2019-08-06T09:18:36Z | - |
dc.date.available | 2019-08-06T09:18:36Z | - |
dc.date.issued | 2019 | - |
dc.identifier.citation | Systematic Biology, 2019, v. 68 n. 3, p. 494-504 | - |
dc.identifier.issn | 1063-5157 | - |
dc.identifier.uri | http://hdl.handle.net/10722/272895 | - |
dc.description.abstract | The 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.language | eng | - |
dc.publisher | Oxford University Press. The Journal's web site is located at https://academic.oup.com/sysbio/ | - |
dc.relation.ispartof | Systematic Biology | - |
dc.rights | This 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.subject | biological model | - |
dc.subject | classification | - |
dc.subject | computer simulation | - |
dc.subject | molecular evolution | - |
dc.subject | nucleotide sequence | - |
dc.title | Morphological Data Sets Fit a Common Mechanism Much More Poorly than DNA Sequences and Call Into Question the Mkv Model | - |
dc.type | Article | - |
dc.identifier.email | Pittman, M: mpittman@hku.hk | - |
dc.identifier.authority | Pittman, M=rp01622 | - |
dc.description.nature | postprint | - |
dc.identifier.doi | 10.1093/sysbio/syy077 | - |
dc.identifier.pmid | 30445627 | - |
dc.identifier.scopus | eid_2-s2.0-85061857539 | - |
dc.identifier.hkuros | 300842 | - |
dc.identifier.volume | 68 | - |
dc.identifier.issue | 3 | - |
dc.identifier.spage | 494 | - |
dc.identifier.epage | 504 | - |
dc.identifier.isi | WOS:000493313500008 | - |
dc.publisher.place | United Kingdom | - |
dc.identifier.issnl | 1063-5157 | - |