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）常会导致核系统发育与质体系统发育之间的拓扑不一致，二者的比较曾被用作解析杂交模式的初步近似手段。由于不完全谱系分选（incomplete lineage sorting）、系统发育误差等其他过程也会产生类似的不一致模式，因此必须纳入更多证据来源。本研究以拉氏莓属（Lachemilla）为对象，利用核糖体核基因ITS（Internal Transcribed Spacer）序列与质体trnL-F DNA序列重建其系统发育关系，并探究该类群中广泛存在的核质体冲突（cytonuclear discordance）模式。拉氏莓属（Lachemilla）是一类形态变异度极高的多年生草本与灌木类群，同时也是新热带区多样高海拔草原中几乎无处不在的类群。我们的分析在拉氏莓属中识别出4个主要演化支（clades），其与该类群既往的形态分类系统部分吻合。此外，通过多种证据手段——包括用于协同系统发育估计的普氏旋转法（procrustean approach to cophylogeny estimation）、基于溯祖理论的模拟（coalescent-based simulations）、系统发育网络（phylogenetic networks）、染色体计数以及基因组大小估算——我们还揭示了拉氏莓属中质体与核系统发育间的大规模拓扑不一致模式，该模式主要由频繁的杂交与多倍体化（polyploidy）导致。我们还估算得出，拉氏莓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极高的安第斯植物演化支所提出的"快速隆升"多样化模型，但在过去500万年间安第斯高海拔草原形成后，特定嵌套支系的快速积累推动了拉氏莓属在这类生物群系中的广泛分布。