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

Research output: Contribution to journalArticle

11 Citations (Scopus)

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 languageEnglish (US)
Pages (from-to)836-854
Number of pages19
JournalNew Phytologist
Volume217
Issue number2
DOIs
StatePublished - Jan 1 2018

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Caryophyllales
Phylogeny
phylogeny
Chloroplasts
Population Density
transcriptomics
Uncertainty
population size
uncertainty
chloroplasts
Genome
genomics
genome
Genes
genes

Keywords

  • Caryophyllales
  • climatic occupancy
  • diversification rates
  • duplications
  • phylogenomics

Cite this

Smith, S. A., Brown, J. W., Yang, Y., Bruenn, R., Drummond, C. P., Brockington, S. F., ... Moore, M. J. (2018). Disparity, diversity, and duplications in the Caryophyllales. New Phytologist, 217(2), 836-854. https://doi.org/10.1111/nph.14772

Disparity, diversity, and duplications in the Caryophyllales. / Smith, Stephen A.; Brown, Joseph W.; Yang, Ya; Bruenn, Riva; Drummond, Chloe P.; Brockington, Samuel F.; Walker, Joseph F.; Last, Noah; Douglas, Norman A.; Moore, Michael J.

In: New Phytologist, Vol. 217, No. 2, 01.01.2018, p. 836-854.

Research output: Contribution to journalArticle

Smith, SA, Brown, JW, Yang, Y, Bruenn, R, Drummond, CP, Brockington, SF, Walker, JF, Last, N, Douglas, NA & Moore, MJ 2018, 'Disparity, diversity, and duplications in the Caryophyllales', New Phytologist, vol. 217, no. 2, pp. 836-854. https://doi.org/10.1111/nph.14772
Smith SA, Brown JW, Yang Y, Bruenn R, Drummond CP, Brockington SF et al. Disparity, diversity, and duplications in the Caryophyllales. New Phytologist. 2018 Jan 1;217(2):836-854. https://doi.org/10.1111/nph.14772
Smith, Stephen A. ; Brown, Joseph W. ; Yang, Ya ; Bruenn, Riva ; Drummond, Chloe P. ; Brockington, Samuel F. ; Walker, Joseph F. ; Last, Noah ; Douglas, Norman A. ; Moore, Michael J. / Disparity, diversity, and duplications in the Caryophyllales. In: New Phytologist. 2018 ; Vol. 217, No. 2. pp. 836-854.
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