Data from: Ancestral gene flow and parallel organellar genome capture result in extreme phylogenomic discord in a lineage of angiosperms

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.

尽管杂交研究近期重新获得了分类学家与进化生物学家的广泛关注，但针对古老、多样化杂交谱系——即通过网状进化（reticulation）起源的生物支系——的案例研究仍较为匮乏。对这类类群开展研究，有助于阐明物种间基因流发生后谱系的长期系统发育存续能力。本研究针对因频繁杂交而广为人知的矾根属（Heuchera）开展系统基因组学分析，纳入了三类独立基因组的数据：靶向核基因组（~400,000 bp）、质体基因组（~160,000 bp）与线粒体基因组（~470,000 bp）。本研究采用多种串联法与溯祖分析策略对上述数据进行分析。核基因组系统发育结果与既往研究及形态学证据一致，有力支持矾根属为单系群。与之形成鲜明对比的是，细胞器基因组的分析结果显示矾根属整体为多系群，可划分为三个主要支系，且支系内部的演化关系也发生了大范围重排。少数核基因座也存在系统发育冲突；但值得注意的是，这些基因座的拓扑结构与细胞器基因座的模式完全不同，且整体而言系统发育冲突程度较低。本研究利用核基因组数据，通过两种独立方法估算了矾根属祖先的溯祖分支长度，结果显示其与相关支系间几乎不存在不完全谱系分选（incomplete lineage sorting），这与观测到的细胞器基因组整体多系现象相悖——该结论已通过溯祖框架下的基因树模拟得到验证。结合既往研究成果，上述观测结果有力表明，杂交正是引发该系统发育冲突的根本原因。