Webster Carmen P, Paris Margot, Olivares Ingrid, Wojciechowski Martin F, Kessler Michael, Sanín María José
School of Life Sciences, Arizona State University, Tempe, AZ, USA.
School of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ, USA.
Genome Biol Evol. 2025 Jul 3;17(7). doi: 10.1093/gbe/evaf130.
Palms (family Arecaceae) are integral to understanding the evolution of tropical rainforests due to their long evolutionary history, high species richness, and hyper dominance in these ecosystems. Some palm genera, like Geonoma, are regionally and locally species-rich and abundant in Neotropical rainforests, but factors contributing to their divergence and ultimately their diversification remain poorly explored. A recent phylogenomic study identified the Geonoma undata complex, with high levels of genetic distinctiveness of different geographically proximal groups, describing it as a hyper-cryptic radiation. Here, we seek to disentangle the factors that contribute to genetic divergence in the G. undata cryptic species complex in the Northern Colombian Andes, where various forms ascribable to different taxonomic, morphological, and genetic groups exist. To address this, we pursued three main aims using nuclear single nucleotide polymorphisms distributed along over 4,000 genomic regions from 156 individuals. (i) We identified populations and used diversity metrics to understand evolutionary scenarios across pairwise comparisons of those populations. Geographically sympatric populations display evidence for allopatric selection that is likely explained by elevational segregation. (ii) Tajima's D was used to infer broad genomic trends in selection and drift. In general, divergence between populations is enhanced by drift through population expansions. (iii) Lastly, we used outlier divergence and selection statistics to identify genes with outstanding divergence under significant positive selection. Two genes were identified that fit this description and are found to play functional roles in phenology, such as light response and flowering time.
棕榈科（槟榔科）对于理解热带雨林的进化至关重要，这是由于它们漫长的进化历史、丰富的物种多样性以及在这些生态系统中的高度优势地位。一些棕榈属，如Geonoma，在新热带雨林中具有区域和局部的物种丰富度且数量众多，但导致它们分化并最终实现多样化的因素仍未得到充分探索。最近一项系统发育基因组学研究鉴定出了Geonoma undata复合体，不同地理上相邻的群体具有高度的遗传独特性，将其描述为一种高度隐秘的辐射。在这里，我们试图厘清在哥伦比亚安第斯山脉北部导致Geonoma undata隐秘物种复合体遗传分化的因素，在那里存在着可归因于不同分类学、形态学和遗传群体的各种形态。为了解决这个问题，我们使用来自156个个体的分布在4000多个基因组区域的核单核苷酸多态性，追求三个主要目标。（i）我们识别了种群，并使用多样性指标来理解这些种群两两比较之间的进化情景。地理上同域分布的种群显示出异域选择的证据，这可能由海拔隔离来解释。（ii）使用 Tajima's D来推断选择和漂变的广泛基因组趋势。一般来说，种群之间的分化通过种群扩张导致的漂变而增强。（iii）最后，我们使用离群值分化和选择统计来识别在显著正选择下具有突出分化的基因。鉴定出了两个符合此描述的基因，发现它们在物候学中发挥功能作用，如光反应和开花时间。
