Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48103, USA.
Department of Plant Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St Paul, MN, 55108, USA.
New Phytol. 2018 Jan;217(2):836-854. doi: 10.1111/nph.14772. Epub 2017 Sep 11.
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（WGD）在植物进化中的作用一直存在争议。WGD 与优势有关，例如优越的定植、各种适应和增加有效种群大小。然而，由于在主要植物类群中缺乏对 WGD 的全面映射，因此对于 WGD 与更高的多样化率之间的潜在关联存在不确定性。使用七个叶绿体和核核糖体基因，我们构建了 Caryophyllales 5036 种的系统发育，代表了现存物种的近一半。我们从转录组和基因组数据分析中对假定的 WGD 进行了系统发育映射，并结合气候占据和谱系多样化率的变化对其进行了分析。可以将 13 个假定的 WGD 和 27 个多样化转变映射到系统发育树上。其中，有 4 次 WGD 与多样化转变同时发生，而其他多样化转变发生在比 WGD 更近的节点上。五次 WGD 与向更寒冷的气候占据有关。虽然我们发现许多多样化转变发生在 WGD 之后，但很难认为多样化和复制是紧密相关的。我们的研究结果表明，复制通常与多样化率、气候占据或进化率的变化同时发生。
