Disparity, diversity, and duplications in the Caryophyllales

• Published in: The New phytologist Vol. 217; no. 2; pp. 836 - 854
• Main Authors: 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.
• Format: Journal Article
• Language: English
• Published: England New Phytologist Trust 01-01-2018; Wiley Subscription Services, Inc
• Subjects: Adaptation; Caryophyllales; Caryophyllales - classification; Caryophyllales - genetics; Chloroplasts; Climate; climatic occupancy; Colonization; Data processing; Diversification; diversification rates; duplications; Evolution; Gene Duplication; Gene mapping; Genetic Variation; Genome, Plant; Genomes; phylogenomics; Phylogeny; Population number; Reproduction (copying); diversification rates; duplications; Caryophyllales; climatic occupancy; phylogenomics
• ISSN: 0028-646X; 1469-8137
• DOI: 10.1111/nph.14772

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.