Data from: Phylogeny and evolution of the neotropical radiation of Lachemilla (Rosaceae): uncovering a history of reticulate evolution and implications for infrageneric classification

Reticulate evolution often leads to incongruence between nuclear and plastid phylogenies and comparisons between them have been used as a first approximation to disentangle patterns of hybridization. Because other processes like incomplete lineage sorting and phylogenetic error also produce similar incongruence patterns, additional sources of evidence must be incorporated. Here we focus on reconstructing the phylogeny of genus Lachemilla using nuclear ribosomal ITS and plastid trnL-F DNA sequences, and explore widespread patterns of cytonuclear discordance in this group. Lachemilla is a highly morphologically variable group of perennial herbs and shrubs, and a nearly ubiquitous member of the diverse Neotropical high-altitude grasslands. Our analyses identified four major clades within Lachemilla that are in part congruent with previous morphological classifications of the group. Furthermore, using multiple sources of evidence, including a procrustean approach to cophylogeny estimation, coalescent-based simulations, phylogenetic networks, chromosome counts, and genome size estimations, we also revealed a large-scale pattern of incongruence between the plastid and nuclear phylogenies in Lachemilla, which is mainly the result of widespread hybridization and polyploidy. We also estimated that the origin of Lachemilla in South America (~14.5 mya) predates the "rapid-uplift" diversification model that has been suggested for other high species-richness Andean plant clades, but following the formation of the high-elevation Andean grasslands during the last 5 mya, a rapid accumulation of particular nested lineages occurred has contributed to the ubiquitous presence of Lachemilla in these biomes.网状进化（Reticulate evolution）常导致核系统发育与质体系统发育之间的不一致性，二者的比较已被用作初步手段以厘清杂交模式。由于不完全谱系分选（incomplete lineage sorting）和系统发育误差等其他过程也会产生相似的不一致模式，因此须纳入额外的证据来源。本研究聚焦于利用核糖体核内转录间隔区（nuclear ribosomal ITS）与质体trnL-F DNA序列，重建拉契木属（Lachemilla）的系统发育，并探究该类群中广泛存在的核质体冲突（cytonuclear discordance）模式。拉契木属是一类形态高度多样的多年生草本与灌木类群，亦是多样的新热带区高海拔草原中几乎无处不在的成员。我们的分析在拉契木属中鉴定出四个主要演化支，其与该类群此前的形态学分类部分吻合。此外，通过整合多项证据来源，包括用于共系统发育推断的普洛克鲁斯忒斯方法（procrustean approach to cophylogeny estimation）、基于溯祖的模拟（coalescent-based simulations）、系统发育网络（phylogenetic networks）、染色体计数（chromosome counts）以及基因组大小估算（genome size estimations），我们还揭示了拉契木属中质体与核系统发育间存在大规模不一致模式，这一现象主要由广泛的杂交和多倍体化所致。我们还估算出，拉契木属在南美洲的起源时间（约1450万年前）早于针对其他物种丰富度较高的安第斯植物演化支提出的"快速隆升"多样化模型，但在过去500万年间高海拔安第斯草原形成之后，特定嵌套演化支的快速积累推动了拉契木属在这些生物群系中的广泛分布。