Backes Alice, Gonçalves Leonardo T, Pezzi Pedro H, Freitas Loreta B
Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
Mol Phylogenet Evol. 2025 Oct;211:108405. doi: 10.1016/j.ympev.2025.108405. Epub 2025 Jun 30.
Phylogenies are essential for understanding evolutionary relationships, testing species boundaries, and defining species status. However, hybridization and incomplete lineage sorting (ILS) can obscure these relationships in recently diversified plant lineages by creating conflicting signals across the genome and reducing phylogenetic resolution. Calibrachoa (million bells), a Neotropical genus of ornamental plants with high ecological diversity, underwent rapid diversification during the Pleistocene, leading to extensive ILS and interspecific hybridization. In this study, we sampled multiple individuals from all recognized species, a potential new species, and a commercial cultivar of Calibrachoa. We used genome-wide genotyping to investigate phylogenetic relationships, species cohesion, hybridization, and the origin of one commercial cultivar. Our results confirm the division of the genus into two subgenera: Calibrachoa sensu stricto and Stimomphis. Within Stimomphis, we observed paraphyly and polyphyly, with low support for several phylogenetic nodes. This uncertainty likely reflects challenges in species delimitation, high ILS due to recent diversification, and ongoing hybridization. We also confirm the hybrid origin of the commercial cultivar. Our findings provide new insights into the evolutionary history of Calibrachoa, improving our understanding of its taxonomy and hybridization dynamics. These results illustrate the need to account for reticulate evolution and ILS when resolving phylogenies in rapidly diversifying plant groups.
系统发育树对于理解进化关系、检验物种界限以及界定物种地位至关重要。然而，杂交和不完全谱系分选（ILS）会在新近分化的植物谱系中掩盖这些关系，因为它们会在全基因组中产生相互冲突的信号并降低系统发育分辨率。矮牵牛属（百万小铃）是一个具有高度生态多样性的新热带观赏植物属，在更新世经历了快速分化，导致广泛的ILS和种间杂交。在本研究中，我们从所有已确认的物种、一个潜在的新物种以及一个矮牵牛属商业栽培品种中采集了多个个体样本。我们使用全基因组基因分型来研究系统发育关系、物种凝聚力、杂交以及一个商业栽培品种的起源。我们的结果证实该属分为两个亚属：狭义矮牵牛属和刺萼矮牵牛亚属。在刺萼矮牵牛亚属中，我们观察到并系和多系现象，对几个系统发育节点的支持度较低。这种不确定性可能反映了物种界定的挑战、由于近期分化导致的高ILS以及正在进行的杂交。我们还证实了该商业栽培品种的杂交起源。我们的研究结果为矮牵牛属的进化历史提供了新的见解，增进了我们对其分类学和杂交动态的理解。这些结果表明，在解析快速分化的植物类群的系统发育时，需要考虑网状进化和ILS。
