Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany.
Ann Bot. 2020 Jan 8;125(1):29-47. doi: 10.1093/aob/mcz123.
Whole-genome duplication (WGD) events are considered important driving forces of diversification. At least 11 out of 52 Brassicaceae tribes had independent mesopolyploid WGDs followed by diploidization processes. However, the association between mesopolyploidy and subsequent diversification is equivocal. Herein we show the results from a family-wide diversification analysis on Brassicaceae, and elaborate on the hypothesis that polyploidization per se is a fundamental driver in Brassicaceae evolution.
We established a time-calibrated chronogram based on whole plastid genomes comprising representative Brassicaceae taxa and published data spanning the entire Rosidae clade. This allowed us to set multiple calibration points and anchored various Brassicaceae taxa for subsequent downstream analyses. All major splits among Brassicaceae lineages were used in BEAST analyses of 48 individually analysed tribes comprising 2101 taxa in total using the internal transcribed spacers of nuclear ribosomal DNA. Diversification patterns were investigated on these tribe-wide chronograms using BAMM and were compared with family-wide data on genome size variation and species richness.
Brassicaceae diverged 29.9 million years ago (Mya) during the Oligocene, and the majority of tribes started diversification in the Miocene with an average crown group age of about 12.5 Mya. This matches the cooling phase right after the Mid Miocene climatic optimum. Significant rate shifts were detected in 12 out of 52 tribes during the Mio- and Pliocene, decoupled from preceding mesopolyploid WGDs. Among the various factors analysed, the combined effect of tribal crown group age and net diversification rate (speciation minus extinction) is likely to explain sufficiently species richness across Brassicaceae tribes.
The onset of the evolutionary splits among tribes took place under cooler and drier conditions. Pleistocene glacial cycles may have contributed to the maintenance of high diversification rates. Rate shifts are not consistently associated with mesopolyploid WGD. We propose, therefore, that WGDs in general serve as a constant 'pump' for continuous and high species diversification.
全基因组加倍（WGD）事件被认为是多样化的重要驱动力。在 52 个芸薹科族中，至少有 11 个经历了独立的中间多倍体 WGD 事件，随后经历了二倍化过程。然而，中间多倍体与随后的多样化之间的联系尚无定论。本文通过对芸薹科的全家族多样化分析，展示了结果，并详细阐述了多倍体化本身是芸薹科进化的基本驱动力的假说。
我们基于包含芸薹科代表类群和已发表数据的整个蔷薇科的全质体基因组，建立了一个时间校准的时标。这使我们能够设置多个校准点，并为随后的下游分析锚定各种芸薹科类群。在 BEAST 分析中，使用核核糖体 DNA 的内部转录间隔区，对总共包含 2101 个分类单元的 48 个单独分析的族进行了分析，这些族的主要分支都被用于分析。在这些族级时标上，使用 BAMM 分析了多样化模式，并将其与关于基因组大小变化和物种丰富度的全家族数据进行了比较。
芸薹科在渐新世（29.9 百万年前）分化，大多数族在中新世开始多样化，平均冠群年龄约为 12.5 百万年前。这与中中新世气候最优期之后的冷却阶段相吻合。在中新世和上新世，在 52 个族中有 12 个族检测到显著的速率变化，与之前的中间多倍体 WGD 无关。在分析的各种因素中，族冠群年龄和净多样化率（物种形成速度减去灭绝速度）的综合效应可能足以解释芸薹科族的物种丰富度。
族间进化分裂的开始发生在较凉爽和干燥的条件下。更新世的冰期循环可能有助于维持高多样化率。速率变化与中间多倍体 WGD 不一致。因此，我们提出，一般来说，WGD 是持续和高物种多样化的恒定“泵”。
