Disparity, diversity, and duplications in the Caryophyllales

Stephen A. Smith; Joseph W. Brown; Ya Yang; Riva Bruenn; Chloe P. Drummond; Samuel F. Brockington; Joseph F. Walker; Noah Last; Norman A. Douglas; Michael J. Moore

doi:10.1111/nph.14772

Disparity, diversity, and duplications in the Caryophyllales

Stephen A. Smith, Joseph W. Brown, Ya Yang, Riva Bruenn, Chloe P. Drummond, Samuel F. Brockington, Joseph F. Walker, Noah Last, Norman A. Douglas, Michael J. Moore

Plant and Microbial Biology

Research output: Contribution to journal › Article › peer-review

36 Scopus citations

Abstract

The role played by whole genome duplication (WGD) in plant evolution is actively debated. WGDs have been associated with advantages such as superior colonization, various adaptations, and increased effective population size. However, the lack of a comprehensive mapping of WGDs within a major plant clade has led to uncertainty regarding the potential association of WGDs and higher diversification rates. Using seven chloroplast and nuclear ribosomal genes, we constructed a phylogeny of 5036 species of Caryophyllales, representing nearly half of the extant species. We phylogenetically mapped putative WGDs as identified from analyses on transcriptomic and genomic data and analyzed these in conjunction with shifts in climatic occupancy and lineage diversification rate. Thirteen putative WGDs and 27 diversification shifts could be mapped onto the phylogeny. Of these, four WGDs were concurrent with diversification shifts, with other diversification shifts occurring at more recent nodes than WGDs. Five WGDs were associated with shifts to colder climatic occupancy. While we find that many diversification shifts occur after WGDs, it is difficult to consider diversification and duplication to be tightly correlated. Our findings suggest that duplications may often occur along with shifts in either diversification rate, climatic occupancy, or rate of evolution.

Original language	English (US)
Pages (from-to)	836-854
Number of pages	19
Journal	New Phytologist
Volume	217
Issue number	2
DOIs	https://doi.org/10.1111/nph.14772
State	Published - Jan 2018

Bibliographical note

Funding Information:
We thank Caroline Parins-Fukuchi for discussion of the project and comments on the manuscript. We thank Gregory Stull, Oscar Vargas, Ning Wang, Sonia Ahluwalia, Jordan Shore, Lijun Zhao, Alex Taylorm, and Drew Larson for helpful comments on the manuscript. The authors thank Hilda Flores, Helga Ochoter-ena, Tom Wendt and the staff at the Plant Resources Center at the University of Texas at Austin, the Lyon Arboretum, David Anderson, John Brittnacher, Anna Brunner, Joseph Charboneau, Arianna Goodman, Heather-Rose Kates, Patricia Herrnández Ledesma, Lucas Majure, Nidia Mendoza, Michael Powell, Rick Ree, Carl Rothfels, Flora Samis, Jeffrey Sanders, Elizabeth Saunders, Rich Spellenberg, Greg Stull, Mats Thulin, Erin Tripp, and Sophia Weinmann for help with obtaining material. We thank the Cambridge University Botanic Gardens for growing material for this study. This work was supported by NSF DEB awards 1352907 and 1354048.

Publisher Copyright:
© 2017 The Authors. New Phytologist © 2017 New Phytologist Trust

Keywords

Caryophyllales
climatic occupancy
diversification rates
duplications
phylogenomics

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10.1111/nph.14772

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title = "Disparity, diversity, and duplications in the Caryophyllales",

abstract = "The role played by whole genome duplication (WGD) in plant evolution is actively debated. WGDs have been associated with advantages such as superior colonization, various adaptations, and increased effective population size. However, the lack of a comprehensive mapping of WGDs within a major plant clade has led to uncertainty regarding the potential association of WGDs and higher diversification rates. Using seven chloroplast and nuclear ribosomal genes, we constructed a phylogeny of 5036 species of Caryophyllales, representing nearly half of the extant species. We phylogenetically mapped putative WGDs as identified from analyses on transcriptomic and genomic data and analyzed these in conjunction with shifts in climatic occupancy and lineage diversification rate. Thirteen putative WGDs and 27 diversification shifts could be mapped onto the phylogeny. Of these, four WGDs were concurrent with diversification shifts, with other diversification shifts occurring at more recent nodes than WGDs. Five WGDs were associated with shifts to colder climatic occupancy. While we find that many diversification shifts occur after WGDs, it is difficult to consider diversification and duplication to be tightly correlated. Our findings suggest that duplications may often occur along with shifts in either diversification rate, climatic occupancy, or rate of evolution.",

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author = "Smith, {Stephen A.} and Brown, {Joseph W.} and Ya Yang and Riva Bruenn and Drummond, {Chloe P.} and Brockington, {Samuel F.} and Walker, {Joseph F.} and Noah Last and Douglas, {Norman A.} and Moore, {Michael J.}",

note = "Funding Information: We thank Caroline Parins-Fukuchi for discussion of the project and comments on the manuscript. We thank Gregory Stull, Oscar Vargas, Ning Wang, Sonia Ahluwalia, Jordan Shore, Lijun Zhao, Alex Taylorm, and Drew Larson for helpful comments on the manuscript. The authors thank Hilda Flores, Helga Ochoter-ena, Tom Wendt and the staff at the Plant Resources Center at the University of Texas at Austin, the Lyon Arboretum, David Anderson, John Brittnacher, Anna Brunner, Joseph Charboneau, Arianna Goodman, Heather-Rose Kates, Patricia Herrn{\'a}ndez Ledesma, Lucas Majure, Nidia Mendoza, Michael Powell, Rick Ree, Carl Rothfels, Flora Samis, Jeffrey Sanders, Elizabeth Saunders, Rich Spellenberg, Greg Stull, Mats Thulin, Erin Tripp, and Sophia Weinmann for help with obtaining material. We thank the Cambridge University Botanic Gardens for growing material for this study. This work was supported by NSF DEB awards 1352907 and 1354048. Publisher Copyright: {\textcopyright} 2017 The Authors. New Phytologist {\textcopyright} 2017 New Phytologist Trust",

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AU - Moore, Michael J.

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Disparity, diversity, and duplications in the Caryophyllales

Abstract

Bibliographical note

Keywords

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