Folk Ryan A, Mandel Jennifer R, Freudenstein John V
Herbarium, Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43212, USA and.
Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA.
Syst Biol. 2017 May 1;66(3):320-337. doi: 10.1093/sysbio/syw083.
While hybridization has recently received a resurgence of attention from systematists and evolutionary biologists, there remains a dearth of case studies on ancient, diversified hybrid lineages-clades of organisms that originated through reticulation. Studies on these groups are valuable in that they would speak to the long-term phylogenetic success of lineages following gene flow between species. We present a phylogenomic view of Heuchera, long known for frequent hybridization, incorporating all three independent genomes: targeted nuclear (400,000 bp), plastid (160,000 bp), and mitochondrial (~470,000 bp) data. We analyze these data using multiple concatenation and coalescence strategies. The nuclear phylogeny is consistent with previous work and with morphology, confidently suggesting a monophyletic Heuchera. By contrast, analyses of both organellar genomes recover a grossly polyphyletic Heuchera,consisting of three primary clades with relationships extensively rearranged within these as well. A minority of nuclear loci also exhibit phylogenetic discord; yet these topologies remarkably never resemble the pattern of organellar loci and largely present low levels of discord inter alia. Two independent estimates of the coalescent branch length of the ancestor of Heuchera using nuclear data suggest rare or nonexistent incomplete lineage sorting with related clades, inconsistent with the observed gross polyphyly of organellar genomes (confirmed by simulation of gene trees under the coalescent). These observations, in combination with previous work, strongly suggest hybridization as the cause of this phylogenetic discord. [Ancient hybridization; chloroplast capture; incongruence; phylogenomics; reticulation.].
尽管杂交现象最近重新受到了分类学家和进化生物学家的关注，但对于古老的、多样化的杂交谱系（即通过网状进化起源的生物类群）的案例研究仍然匮乏。对这些类群的研究很有价值，因为它们可以说明物种间基因流动后谱系的长期系统发育成功情况。我们展示了矾根属（Heuchera）的系统基因组学观点，该属长期以来以频繁杂交而闻名，纳入了所有三个独立的基因组数据：靶向核基因组（约400,000碱基对）、质体基因组（约160,000碱基对）和线粒体基因组（约470,000碱基对）。我们使用多种串联和合并策略分析这些数据。核系统发育与先前的研究以及形态学一致，有力地表明矾根属是单系的。相比之下，对两个细胞器基因组的分析得出矾根属是高度多系的，由三个主要分支组成，这些分支内部的关系也有广泛的重排。少数核基因座也表现出系统发育不一致；然而这些拓扑结构明显从未与细胞器基因座的模式相似，并且在很大程度上表现出低水平的不一致。使用核数据对矾根属祖先的合并分支长度进行的两个独立估计表明，与相关分支的不完全谱系分选很少见或不存在，这与观察到的细胞器基因组的高度多系性不一致（通过在合并模型下模拟基因树得到证实）。这些观察结果与先前的研究相结合，强烈表明杂交是这种系统发育不一致的原因。[古代杂交；叶绿体捕获；不一致性；系统基因组学；网状进化。]
