Resolution of a concatenation/coalescence kerfuffle

partitioned coalescence support and a robust family-level tree for Mammalia

John Gatesy, Robert Meredith, Jan E. Janecka, Mark P. Simmons, William J. Murphy, Mark S. Springer

Research output: Contribution to journalArticleResearchpeer-review

16 Citations (Scopus)

Abstract

Recent phylogenetic analyses of a large dataset for mammalian families (169 taxa, 26 loci) portray contrasting results. Supermatrix (concatenation) methods support a generally robust tree with only a few inconsistently resolved polytomies, whereas MP-EST coalescence analysis of the same dataset yields a weakly supported tree that conflicts with many traditionally recognized clades. Here, we evaluate this discrepancy via improved coalescence analyses with reference to the rich history of phylogenetic studies on mammals. This integration clearly demonstrates that both supermatrix and coalescence analyses of just 26 loci yield a congruent, well-supported phylogenetic hypothesis for Mammalia. Discrepancies between published studies are explained by implementation of overly simple DNA substitution models, inadequate tree-search routines and limitations of the MP-EST method. We develop a simple measure, partitioned coalescence support (PCS), which summarizes the distribution of support and conflict among gene trees for a given clade. Extremely high PCS scores for outlier gene trees at two nodes in the mammalian tree indicate a troubling bias in the MP-EST method. We conclude that in this age of phylogenomics, a solid understanding of systematics fundamentals, choice of valid methodology and a broad knowledge of a clade's taxonomic history are still required to yield coherent phylogenetic inferences.

Original languageEnglish
Pages (from-to)295-332
Number of pages38
JournalCladistics
Volume33
Issue number3
DOIs
StatePublished - 1 Jun 2017

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Mammalia
coalescence
phylogenetics
phylogeny
history
loci
gene
outlier
methodology
family
substitution
mammal
genes
mammals
taxonomy
DNA
method

Cite this

Gatesy, John ; Meredith, Robert ; Janecka, Jan E. ; Simmons, Mark P. ; Murphy, William J. ; Springer, Mark S. / Resolution of a concatenation/coalescence kerfuffle : partitioned coalescence support and a robust family-level tree for Mammalia. In: Cladistics. 2017 ; Vol. 33, No. 3. pp. 295-332.
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Resolution of a concatenation/coalescence kerfuffle : partitioned coalescence support and a robust family-level tree for Mammalia. / Gatesy, John; Meredith, Robert; Janecka, Jan E.; Simmons, Mark P.; Murphy, William J.; Springer, Mark S.

In: Cladistics, Vol. 33, No. 3, 01.06.2017, p. 295-332.

Research output: Contribution to journalArticleResearchpeer-review

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