Ancestral Gene Flow and Parallel Organellar Genome Capture Result in Extreme Phylogenomic Discord in a Lineage of Angiosperms
Ancestral Gene Flow and Parallel Organellar Genome Capture Result in Extreme Phylogenomic Discord in a Lineage of Angiosperms
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DOI：
10.1093/sysbio/syw083
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发表时间：
2017-05-01
影响因子：
6.5
通讯作者：
Freudenstein, John V.
中科院分区：
文献类型：
--
作者：
Folk, Ryan A.;Mandel, Jennifer R.;Freudenstein, John V.
虽然杂交最近重新引起了系统学家和进化生物学家的关注，但关于古老的、多样化的杂交谱系--起源于网状结构的有机体分支--的案例研究仍然很少。对这些类群的研究是有价值的，因为它们将讲述物种之间基因流动后谱系的长期系统发育成功。我们提出了Heuchera的系统基因组学观点，长期以来，Heuchera以频繁杂交而闻名，它包含了所有三个独立的基因组：靶向核(类似于400,000 bp)、叶绿体(类似于160,000 bp)和线粒体(类似于47,000 bp)数据。我们使用多种连接和合并策略来分析这些数据。核系统发育与以前的工作和形态一致，自信地表明是一个单系的轮叶属。相比之下，对这两个细胞器基因组的分析恢复了一个大体多系的Heuchera，它由三个初级支系组成，其中的关系也进行了广泛的重新安排。少数核基因座也表现出系统发育不一致；然而，这些拓扑结构显著地从未类似于细胞器基因座的模式，尤其是在很大程度上呈现出低水平的不一致。使用核数据对Heuchera祖先的合生分支长度的两个独立估计表明，与相关支系的不完全谱系分类很少或根本不存在，这与观察到的细胞器基因组的总多态不一致(通过合生下的基因树模拟证实了这一点)。这些观察结合以前的工作，强烈地表明杂交是导致这种系统发育不一致的原因。
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 (similar to 400,000 bp), plastid (similar to 160,000 bp), and mitochondrial (similar to 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.