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Citation for Study 20819

Citation title: "Muroid Rodent Phylogenetics: 900-species Tree Reveals Increasing Diversification Rates".

Study name: "Muroid Rodent Phylogenetics: 900-species Tree Reveals Increasing Diversification Rates".

This study is part of submission 20819 (Status: Published).

Citation

Steppan S.J., & Schenk J.J. 2017. Muroid Rodent Phylogenetics: 900-species Tree Reveals Increasing Diversification Rates. PLoS ONE, 12(8): 1031.

Authors

• Steppan S.J. (submitter) 850 644-6536
• Schenk J.J.

Abstract

We combined new sequence data for more than 300 muroid rodent species with our previously published sequences for up to five nuclear and one mitochondrial genes to generate the most widely and densely sampled hypothesis of evolutionary relationships across Muroidea. An exhaustive screening procedure for publically available sequences was implemented to avoid the propagation of taxonomic errors that are common to supermatrix studies. The combined data set of carefully screened sequences derived from all available sequences on GenBank with our new data resulted in a robust maximum likelihood phylogeny for 900 of the approximately 1,620 muroids. Several regions that were equivocally resolved in previous studies are now more decisively resolved, and we estimated a chronogram using 28 fossil calibrations for the most integrated age and topological estimates to date. The results were used to update muroid classification and highlight questions needing additional data. We also compared the results of multigene supermatrix studies like this one with the principal published supertrees and concluded that the latter are unreliable for any comparative study in muroids. In addition, we explored diversification patterns as an explanation for why muroid rodents represent one of the most species-rich groups of mammals by detecting evidence for increasing net diversification rates through time across the muroid tree. We suggest the observation of increasing rates may be due to a combination of parallel increases in rate across clades and high average extinction rates. Five increased diversification-rate-shifts were inferred, suggesting that multiple, but perhaps not independent, events have led to the remarkable species diversity in the superfamily. Our results provide a phylogenetic framework for comparative studies that is not highly dependent upon the signal from any one gene.

Keywords

systematics, biogeography, Muroidea, diversification, multi-locus, DNA sequencing

External links

• DOI: 10.1371/journal.pone.0183070

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S20819
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref27061,
  	 author = {Scott J. Steppan and John J. Schenk},
  	 title = {Muroid Rodent Phylogenetics: 900-species Tree Reveals Increasing Diversification Rates},
  	 year = {2017},
  	 keywords = {systematics, biogeography, Muroidea, diversification, multi-locus, DNA sequencing},
  	 doi = {10.1371/journal.pone.0183070},
  	 url = {http://},
  	 pmid = {},
  	 journal = {PLoS ONE},
  	 volume = {12},
  	 number = {8},
  	 pages = {1031},
  	 abstract = {We combined new sequence data for more than 300 muroid rodent species with our previously published sequences for up to five nuclear and one mitochondrial genes to generate the most widely and densely sampled hypothesis of evolutionary relationships across Muroidea. An exhaustive screening procedure for publically available sequences was implemented to avoid the propagation of taxonomic errors that are common to supermatrix studies. The combined data set of carefully screened sequences derived from all available sequences on GenBank with our new data resulted in a robust maximum likelihood phylogeny for 900 of the approximately 1,620 muroids. Several regions that were equivocally resolved in previous studies are now more decisively resolved, and we estimated a chronogram using 28 fossil calibrations for the most integrated age and topological estimates to date. The results were used to update muroid classification and highlight questions needing additional data. We also compared the results of multigene supermatrix studies like this one with the principal published supertrees and concluded that the latter are unreliable for any comparative study in muroids. In addition, we explored diversification patterns as an explanation for why muroid rodents represent one of the most species-rich groups of mammals by detecting evidence for increasing net diversification rates through time across the muroid tree. We suggest the observation of increasing rates may be due to a combination of parallel increases in rate across clades and high average extinction rates. Five increased diversification-rate-shifts were inferred, suggesting that multiple, but perhaps not independent, events have led to the remarkable species diversity in the superfamily.  Our results provide a phylogenetic framework for comparative studies that is not highly dependent upon the signal from any one gene.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 27061
  AU  - Steppan,Scott J.
  AU  - Schenk,John J.
  T1  - Muroid Rodent Phylogenetics: 900-species Tree Reveals Increasing Diversification Rates
  PY  - 2017
  KW  - systematics
  KW  - biogeography
  KW  - Muroidea
  KW  - diversification
  KW  - multi-locus
  KW  - DNA sequencing
  UR  - http://dx.doi.org/10.1371/journal.pone.0183070
  N2  - We combined new sequence data for more than 300 muroid rodent species with our previously published sequences for up to five nuclear and one mitochondrial genes to generate the most widely and densely sampled hypothesis of evolutionary relationships across Muroidea. An exhaustive screening procedure for publically available sequences was implemented to avoid the propagation of taxonomic errors that are common to supermatrix studies. The combined data set of carefully screened sequences derived from all available sequences on GenBank with our new data resulted in a robust maximum likelihood phylogeny for 900 of the approximately 1,620 muroids. Several regions that were equivocally resolved in previous studies are now more decisively resolved, and we estimated a chronogram using 28 fossil calibrations for the most integrated age and topological estimates to date. The results were used to update muroid classification and highlight questions needing additional data. We also compared the results of multigene supermatrix studies like this one with the principal published supertrees and concluded that the latter are unreliable for any comparative study in muroids. In addition, we explored diversification patterns as an explanation for why muroid rodents represent one of the most species-rich groups of mammals by detecting evidence for increasing net diversification rates through time across the muroid tree. We suggest the observation of increasing rates may be due to a combination of parallel increases in rate across clades and high average extinction rates. Five increased diversification-rate-shifts were inferred, suggesting that multiple, but perhaps not independent, events have led to the remarkable species diversity in the superfamily.  Our results provide a phylogenetic framework for comparative studies that is not highly dependent upon the signal from any one gene.
  L3  - 10.1371/journal.pone.0183070
  JF  - PLoS ONE
  VL  - 12
  IS  - 8
  ER  -