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）的系统发育呈网络状，无法通过二歧分支树（bifurcating trees）得到充分表征。尤其是核染色体组超过六套的高倍体（high-polyploids），其同源基因丢失（gene homoeolog loss）、深度溯祖（deep coalescence）以及多倍化的信号可能相互混淆，导致基因树可能与多个物种网络（species network）同时契合。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，Violaceae）高倍体谱系，通过客观比较涉及多倍化与同源基因丢失的竞争场景，获得了最简约的物种网络（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的同源基因，并通过常规PCR扩增叶绿体trnL-F区域（chloroplast trnL-F region）。由于深度溯祖以及两次疑似同源基因丢失（或未检测到）事件，GPI同源基因亚分支（subclades）间存在拓扑冲突，我们通过为每个亚分支采用最大树拓扑结构（maximum tree topology）的方式解决了这一冲突。最简约的物种网络与基于化石校准（fossil-based calibration）的同源基因树均支持高倍体为单系群（monophyly），该类群起源于9~14百万年前的异源十倍化事件（allodecaploidization），涉及现存堇菜属三个组的同域祖先（sympatric ancestors）：Chamaemelanium组（二倍体）、Plagiostigma组（古四倍体）以及Viola组（古四倍体）。尽管其中两个高倍体谱系（Boreali-Americanae、Pedatae）仍保持十倍体状态，但在过去5百万年间，与Plagiostigma组四倍体的反复多倍化事件，催生了两个14倍体谱系（Mexicanae、Nosphinium）以及一个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比此前基于核糖体DNA数据推断的更为复杂，同时也说明在系统发育与生物地理重建中考虑多倍化因素的必要性。