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（allopolyploids）的系统发育（phylogenies）呈网状结构，无法通过二歧分叉树（bifurcating trees）得到充分表征。尤其是对于高多倍体（high-polyploids，即拥有6套以上核染色体的生物）而言，同祖基因缺失（gene homoeolog loss）、不完全谱系分选（deep coalescence）与多倍化的演化信号可能相互混淆，进而导致基因树（gene trees）可与多个物种网络（species network）兼容。
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）高多倍体谱系，通过客观比较涉及多倍化与同祖基因缺失的竞争演化场景，获得了最简约的物种网络。我们针对51个物种及亚种，通过单分子PCR扩增低拷贝核基因GPI的同祖基因，并通过常规PCR扩增叶绿体trnL-F区域。
因不完全谱系分选以及两次疑似同祖基因缺失（或未检测到）事件导致GPI同祖基因亚支间出现拓扑结构不一致，该问题通过为每个亚支采用最优树拓扑结构得以协调。
最简约物种网络与基于化石校准的同祖基因树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事件，涉及现存堇菜属Chamaemelanium组（二倍体）、Plagiostigma组（古四倍体）与Viola组（古四倍体）的同域祖先。
尽管其中两个高多倍体谱系（Boreali-Americanae、Pedatae）仍保持十倍体状态，但在过去5百万年内，通过与Plagiostigma组四倍体的反复多倍化，已形成两个14倍体谱系（Mexicanae、Nosphinium）与一个18倍体谱系（Langsdorffianae）。
这表明夏威夷堇菜（Nosphinium）的系统发育与生物地理起源较此前基于核糖体DNA（rDNA）数据的推断更为复杂，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。