Genotype and individual data for genetic structure in Louisiana Iris species reveals patterns of recent and historical admixture

Premise: When divergent lineages come into secondary contact reproductive isolation may be incomplete, thus providing an opportunity to investigate how speciation is manifested in the genome. The Louisiana Irises (Iris, series Hexagonae) comprise a group of three or more ecologically and reproductively divergent lineages that can produce hybrids where they come into contact. In this study we sought to estimate standing genetic variation to understand the current distribution of population structure in the Louisiana Irises.

Methods: We used genotyping-by-sequencing techniques to sample the genomes of Louisiana Iris species across their ranges. Twenty populations were sampled (total n=632) across 11,249 loci. Population genetic data were assessed using ENTROPY and PCA models. 

Results: We discovered evidence for interspecific gene flow in parts of the range and revealed patterns of population structure at odds with widely accepted nominal taxonomy. Undescribed hybrid populations were discovered that were designated as belonging to the I. brevicaulis lineage. Iris nelsonii shared significant ancestry with only one of the purported parent species, I. fulva, evidence inconsistent with a hybrid origin.

Conclusions: This study provides several key findings important to the investigation of standing genetic variation in the Louisiana Iris species complex. Iris brevicaulis has a large amount of genetic diversity within it relative to the other nominal species. In addition, this study has discovered a previously unknown hybrid zone between I. brevicaulis and I. hexagona along the Texas coast. Finally, I. nelsonii does not appear to have mixed ancestry from three parental taxa as has been the longstanding hypothesis.

前提：当分化的谱系发生二次接触时，生殖隔离可能并不完全，这为探究物种形成如何在基因组中得以体现提供了契机。路易斯安那鸢尾（Iris，Hexagonae系列）包含3个及以上生态与生殖分化的谱系，当它们相遇时可产生杂交后代。本研究旨在评估现存遗传变异，以解析路易斯安那鸢尾种群结构的当前分布格局。
方法：我们采用测序分型（genotyping-by-sequencing, GBS）技术，对分布范围内的路易斯安那鸢尾物种的基因组进行采样。本研究共采集20个种群的样本（总样本量n=632），覆盖11249个基因座。利用ENTROPY软件与主成分分析（PCA）模型对种群遗传数据开展分析。
结果：我们在该属部分分布区域发现了种间基因交流的证据，并揭示了与广泛认可的命名分类学相悖的种群结构模式。研究发现了未被记载的杂交种群，其被归为短茎鸢尾（I. brevicaulis）谱系。纳尔逊鸢尾（I. nelsonii）仅与一个假定的亲本物种——红棕鸢尾（I. fulva）共享大量祖先遗传成分，该证据与其杂交起源的假说不符。
结论：本研究为路易斯安那鸢尾复合群的现存遗传变异研究提供了多项关键发现。相较于其他命名物种，短茎鸢尾（I. brevicaulis）具有更高的种群内遗传多样性。此外，本研究在得克萨斯州沿岸发现了一处此前未被报道的短茎鸢尾与六棱鸢尾（I. hexagona）之间的杂交带。最后，纳尔逊鸢尾（I. nelsonii）似乎并不像长期以来的假说所认为的那样，源自三个亲本类群的混合祖先。