Data from: Complex Reticulation in Backbone Subfamily Relationships in Leguminosae

Contradictory lines of evidence have made it difficult to resolve the phylogenetic history of the legume diversification era; this is true for the backbone topology, and for the number and timing of whole genome duplications (WGDs). By analyzing the transcriptomic data for 473 gene families in 76 species covering all six accepted legume subfamilies, we assessed the phylogenetic relationships of the legume backbone and uncovered evidence of independent whole genome duplications in each of the six legume subfamilies. Three subfamilies — Cercidoideae, Dialioideae, and Caesalpinioideae — bear evidence of an allopolyploid duplication pattern suggestive of ancient hybridization. In Cercidoideae and Dialioideae, the hybridization appears to be within-subfamily, with the basal genera Cercis and Poeppigia appearing to be unduplicated descendants of one of the parental lineages; in Caesalpinioideae, the hybridization appears to involve a member of the Papilionoid lineage, and some other lineage, potentially extinct. Three independent lines of evidence, consisting of a concatenated superalignment, concordance factor analysis of the set of gene family alignments and topologies, and direct inference of reticulation events via maximum pseudolikelihood implemented by PhyloNet, converged on a single backbone hypothesis and the above hypotheses of reticulate evolution.

相互矛盾的多条证据链使得解析豆科植物分化时期的系统发育历史极具挑战性，这一难题既体现在豆科系统发育主干拓扑结构的解析中，也涉及全基因组复制（whole genome duplication, WGD）事件的次数与发生时间的确定。本研究针对覆盖目前公认全部6个豆科亚科的76个物种中的473个基因家族的转录组数据展开分析，对豆科植物的系统发育主干关系进行评估，并发现在6个豆科亚科中均存在独立的全基因组复制事件证据。包含紫荆亚科（Cercidoideae）、甘豆亚科（Dialioideae）和云实亚科（Caesalpinioideae）在内的3个亚科，均呈现出异源多倍体复制模式的特征，暗示其曾发生过古老的杂交事件。其中，紫荆亚科与甘豆亚科的杂交事件发生于亚科内部，其基部类群紫荆属（Cercis）与Poeppigia属被推断为其中一个亲本谱系未发生基因组复制的后裔；而云实亚科的杂交事件则似乎涉及蝶形花谱系类群与另一支可能已灭绝的谱系。本研究采用三条独立的证据链：串联超级联配分析、基因家族联配与拓扑结构集的一致性因子分析，以及借助PhyloNet工具实现的最大伪似然法直接推断网状进化事件，这些证据共同支持了单一的豆科系统发育主干假说以及前述的网状进化假说。