García Nicolás, Fuentes-Castillo Taryn, Román María José, Folk Ryan A
Herbario EIF & Laboratorio de Evolución y Sistemática, Facultad de Ciencias Forestales y de la Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile.
Science Division, Carbon Real, Santiago, Chile.
Mol Ecol. 2025 Sep;34(17):e70050. doi: 10.1111/mec.70050. Epub 2025 Jul 25.
Cryptic speciation, an endemic problem in biodiversity hotspots, arises as a result of an uncoupling among three processes: lineage splitting, morphological diversification, and ecological divergence during rapid speciation. We studied speciation processes in Phycella (Amaryllidaceae), a clade mostly restricted to the Chilean Biodiversity Hotspot, aiming to differentiate the relative roles of geographic and ecological speciation as well as the role of secondary gene flow in this radiation. We sampled a total of 137 individuals from 47 populations, including all described taxa throughout the geographic range of the group. Using 884 nuclear genes (1125 exons) and near-complete plastomes through hybrid capture, we resolved the phylogeny of Phycella with high support and demonstrated substantial phylogenetic resolution at the population level. Analyses of niche overlap among species and nuclear clades suggest that the diversification of Phycella was associated with niche divergence, supporting a predominantly geographic mode of speciation in the group, likely driven by the mountainous landscape characteristic of the central area of the Chilean Biodiversity Hotspot. Phylogenetic network and modelling approaches identified major cytonuclear discord, attributable to proximity-based secondary gene flow among species, largely restricted to cytoplasmic DNA. Finally, we present a major integrative taxonomic proposal that divides Phycella into 18 species on the basis of molecular, morphological, and ecological data. Overall, our results highlight the relevance of the mountainous landscape of central Chile to promote diversification in Phycella, and ours is among a few studies on speciation for an endemic element of the Chilean Biodiversity Hotspot.
隐秘物种形成是生物多样性热点地区特有的问题，它是在快速物种形成过程中，谱系分裂、形态多样化和生态分化这三个过程解耦的结果。我们研究了Phycella（石蒜科）的物种形成过程，该类群大多局限于智利生物多样性热点地区，旨在区分地理物种形成和生态物种形成的相对作用，以及二次基因流在这次辐射中的作用。我们总共从47个种群中采集了137个个体样本，包括该类群地理分布范围内所有已描述的分类单元。通过杂交捕获技术，利用884个核基因（1125个外显子）和近乎完整的质体基因组，我们以高支持度解析了Phycella的系统发育，并在种群水平上展示了显著的系统发育分辨率。对物种和核类群之间生态位重叠的分析表明，Phycella的多样化与生态位分化有关，支持该类群主要的地理物种形成模式，这可能是由智利生物多样性热点地区中部山区的地貌特征驱动的。系统发育网络和建模方法识别出主要的细胞核-细胞质不一致，这归因于物种间基于邻近性的二次基因流，主要局限于细胞质DNA。最后，我们提出了一项主要的综合分类学建议，根据分子、形态和生态数据将Phycella划分为18个物种。总体而言，我们的结果突出了智利中部山区地貌对促进Phycella多样化的相关性，并且我们的研究是针对智利生物多样性热点地区特有元素的少数物种形成研究之一。
