PMID- 34715726
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20211101
IS  - 1096-0031 (Electronic)
IS  - 0748-3007 (Linking)
VI  - 33
IP  - 3
DP  - 2017 Jun
TI  - Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence 
      support and a robust family-level tree for Mammalia.
PG  - 295-332
LID - 10.1111/cla.12170 [doi]
AB  - 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.
CI  - (c) The Willi Hennig Society 2016.
FAU - Gatesy, John
AU  - Gatesy J
AD  - Department of Biology, University of California, Riverside, CA, 92521, USA.
FAU - Meredith, Robert W
AU  - Meredith RW
AD  - Department of Biology and Molecular Biology, Montclair State University, 
      Montclair, NJ, 07043, USA.
FAU - Janecka, Jan E
AU  - Janecka JE
AD  - Department of Biological Sciences, Duquesne University, Pittsburgh, PA, 15282, 
      USA.
FAU - Simmons, Mark P
AU  - Simmons MP
AD  - Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA.
FAU - Murphy, William J
AU  - Murphy WJ
AD  - Department of Veterinary Integrative Biosciences, Texas A&M University, College 
      Station, TX, 77843, USA.
FAU - Springer, Mark S
AU  - Springer MS
AD  - Department of Biology, University of California, Riverside, CA, 92521, USA.
LA  - eng
GR  - EF0629860/NSF (USA)/
GR  - EF0629849/NSF (USA)/
GR  - DEB1457735/NSF (USA)/
PT  - Journal Article
DEP - 20160816
PL  - United States
TA  - Cladistics
JT  - Cladistics : the international journal of the Willi Hennig Society
JID - 9881057
SB  - IM
EDAT- 2017/06/01 00:00
MHDA- 2017/06/01 00:01
CRDT- 2021/10/30 01:01
PHST- 2016/06/30 00:00 [accepted]
PHST- 2021/10/30 01:01 [entrez]
PHST- 2017/06/01 00:00 [pubmed]
PHST- 2017/06/01 00:01 [medline]
AID - 10.1111/cla.12170 [doi]
PST - ppublish
SO  - Cladistics. 2017 Jun;33(3):295-332. doi: 10.1111/cla.12170. Epub 2016 Aug 16.