Data from: Inferring species networks from gene trees in high-polyploid North American and Hawaiian violets (Viola, Violaceae)

The phylogenies of allopolyploids take the shape of networks and cannot be adequately represented as bifurcating trees. Especially for high-polyploids (i.e., organisms with more than six sets of nuclear chromosomes), the signatures of gene homoeolog loss, deep coalescence and polyploidy may become confounded, with the result that gene trees may be congruent with more than one species network. Herein, we obtained the most parsimonious species network by objective comparison of competing scenarios involving polyploidization and homoeolog loss in a high-polyploid lineage of violets (Viola, Violaceae) mostly or entirely restricted to North America, Central America, or Hawaii. We amplified homoeologs of the low-copy nuclear gene GPI by single-molecule PCR and the chloroplast trnL-F region by conventional PCR for 51 species and subspecies. Topological incongruence among GPI homoeolog subclades, owing to deep coalescence and two instances of putative loss (or lack of detection) of homoeologs, were reconciled by applying the maximum tree topology for each subclade. The most parsimonious species network and the fossil-based calibration of the homoeolog tree favored monophyly of the high-polyploids, which has resulted from allodecaploidization 9–14 Ma ago, involving sympatric ancestors from the extant Viola sections Chamaemelanium (diploid), Plagiostigma (paleotetraploid), and Viola (paleotetraploid). While two of the high-polyploid lineages (Boreali-Americanae, Pedatae) remained decaploid, recurrent polyploidization with tetraploids of section Plagiostigma within the last 5 Ma has resulted in two 14-ploid lineages (Mexicanae, Nosphinium) and one 18-ploid lineage (Langsdorffianae). This implies a more complex phylogenetic and biogeographic origin of the Hawaiian violets (Nosphinium) than that previously inferred from rDNA data and illustrates the necessity of considering polyploidy in phylogenetic and biogeographic reconstruction.

异源多倍体（allopolyploid）的系统发育呈网状结构，无法通过分叉式树形得到充分表征。针对高多倍体（high-polyploid，即核染色体组超过6套的生物）而言，部分同源基因丢失（gene homoeolog loss）、深层溯祖（deep coalescence）与多倍化（polyploidy）的信号可能会相互混淆，导致基因树（gene tree）可与不止一个物种网状系统发育（species network）相契合。本研究针对主要或完全分布于北美、中美或夏威夷的堇菜属（Viola，堇菜科Violaceae）高多倍体支系，通过客观比较涉及多倍化与部分同源基因丢失的候选演化情景，获得了最简约物种网状系统发育（most parsimonious species network）。我们针对51个物种及亚种，通过单分子PCR（single-molecule PCR）扩增低拷贝核基因GPI的部分同源基因，并通过常规PCR（conventional PCR）扩增叶绿体trnL-F区间。针对由深层溯祖以及两次疑似部分同源基因丢失（或未检测到）事件导致的GPI部分同源基因亚支拓扑结构不一致问题，我们通过采用各亚支的最大树拓扑予以解决。最简约物种网状系统发育与基于化石校准（fossil-based calibration）的部分同源基因树（homoeolog tree）均支持高多倍体为单系群（monophyly），该类群起源于9~14百万年前的异源十倍化（allodecaploidization）事件，涉及现存堇菜属组Chamaemelanium（二倍体，diploid）、Plagiostigma（古四倍体，paleotetraploid）与Viola（古四倍体，paleotetraploid）的同域祖先（sympatric ancestors）。其中两个高多倍体支系（Boreali-Americanae、Pedatae）仍保持十倍体（decaploid）状态，而在过去5百万年内，借助Plagiostigma组四倍体（tetraploid）发生的反复多倍化（recurrent polyploidization）事件，形成了两个十四倍体支系（Mexicanae、Nosphinium）与一个十八倍体支系（Langsdorffianae）。这表明夏威夷堇菜（Nosphinium）的系统发育与生物地理起源比此前基于核糖体DNA（rDNA）数据推断的更为复杂，同时也阐明了在系统发育与生物地理重建中纳入多倍化因素的必要性。