Data from: Disparity, diversity, and duplications in the Caryophyllales

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.

全基因组复制（whole genome duplication, WGD）在植物演化中所扮演的角色，至今仍在学界引发热烈讨论。全基因组复制事件常被认为与诸多演化优势相关，包括更强的定殖能力、多样的适应性以及有效种群规模的提升。然而，由于缺乏对主要植物演化支内全基因组复制事件的全面定位，学界对于全基因组复制与更高类群分化速率之间的潜在关联仍存在诸多不确定性。本研究基于7个叶绿体基因与核核糖体基因序列，构建了涵盖5036种石竹目（Caryophyllales）物种的系统发育树，覆盖该类群现存物种的近半数。我们对通过转录组与基因组数据分析得到的推定全基因组复制事件进行系统发育定位，并结合气候生态位转变与类群分化速率偏移开展联合分析。本研究共在该系统发育树上定位到13处推定的全基因组复制事件与27次类群分化速率偏移。其中4处全基因组复制事件与分化速率偏移同时发生，其余分化速率偏移则出现在晚于对应全基因组复制事件的系统发育节点处。另有5处全基因组复制事件与气候生态位向更寒冷环境的转变相关联。尽管本研究发现多数类群分化速率偏移发生在全基因组复制事件之后，但我们仍难以将类群分化与基因复制二者视作紧密相关的过程。本研究结果表明，基因复制事件往往伴随类群分化速率、气候生态位或演化速率的转变而发生。