Table_1_Plastome phylogenomics reveals an early Pliocene North- and Central America colonization by long-distance dispersal from South America of a highly diverse bromeliad lineage.xlsx

Understanding the spatial and temporal frameworks of species diversification is fundamental in evolutionary biology. Assessing the geographic origin and dispersal history of highly diverse lineages of rapid diversification can be hindered by the lack of appropriately sampled, resolved, and strongly supported phylogenetic contexts. The use of currently available cost-efficient sequencing strategies allows for the generation of a substantial amount of sequence data for dense taxonomic samplings, which together with well-curated geographic information and biogeographic models allow us to formally test the mode and tempo of dispersal events occurring in quick succession. Here, we assess the spatial and temporal frameworks for the origin and dispersal history of the expanded clade K, a highly diverse Tillandsia subgenus Tillandsia (Bromeliaceae, Poales) lineage hypothesized to have undergone a rapid radiation across the Neotropics. We assembled full plastomes from Hyb-Seq data for a dense taxon sampling of the expanded clade K plus a careful selection of outgroup species and used them to estimate a time- calibrated phylogenetic framework. This dated phylogenetic hypothesis was then used to perform biogeographic model tests and ancestral area reconstructions based on a comprehensive compilation of geographic information. The expanded clade K colonized North and Central America, specifically the Mexican transition zone and the Mesoamerican dominion, by long-distance dispersal from South America at least 4.86 Mya, when most of the Mexican highlands were already formed. Several dispersal events occurred subsequently northward to the southern Nearctic region, eastward to the Caribbean, and southward to the Pacific dominion during the last 2.8 Mya, a period characterized by pronounced climate fluctuations, derived from glacial–interglacial climate oscillations, and substantial volcanic activity, mainly in the Trans-Mexican Volcanic Belt. Our taxon sampling design allowed us to calibrate for the first time several nodes, not only within the expanded clade K focal group but also in other Tillandsioideae lineages. We expect that this dated phylogenetic framework will facilitate future macroevolutionary studies and provide reference age estimates to perform secondary calibrations for other Tillandsioideae lineages.

深入理解物种多样性的空间与时间框架对于进化生物学至关重要。评估高度多样化且快速演化的谱系的地理起源与扩散历史，往往受到缺乏恰当采样、解析且具有强有力支持的系统发育背景的限制。利用目前可用的成本效益测序策略，可以为密集的物种采样生成大量序列数据，这些数据与精心整理的地理信息和生物地理模型相结合，使我们能够正式检验一系列快速连续发生的扩散事件的模式与节奏。在本研究中，我们评估了扩展谱系K的起源与扩散历史的空间与时间框架，扩展谱系K是一个高度多样化的Tillandsia亚属Tillandsia（凤梨科，禾本科）谱系，据推测在泛新热带地区经历了快速辐射。我们通过对扩展谱系K进行密集的分类群采样以及对外群物种的精心选择，从Hyb-Seq数据中组装了完整的叶绿体基因组，并利用这些数据估计了一个时间校准的系统发育框架。此时间校准的系统发育假说随后被用于在综合地理信息的基础上执行生物地理模型测试和祖先区域重建。扩展谱系K通过从南美洲的长距离扩散，至少在4.86百万年前（当时墨西哥的大部分高原已经形成）殖民了北美洲和中美洲，特别是墨西哥过渡区和中美洲统治区。在过去的2.8百万年中，发生了多次扩散事件，向北至近北区的南部，向东至加勒比海，向南至太平洋统治区，这一时期以显著的气候变化为特征，这些变化源自冰川-间冰期气候振荡和大量的火山活动，主要发生在墨西哥火山带。我们的分类群采样设计使我们能够首次校准几个节点，不仅限于扩展谱系K的焦点群体内，还包括其他Tillandsioideae谱系。我们预期，这个时间校准的系统发育框架将促进未来的宏观进化研究，并为进行其他Tillandsioideae谱系的二级校准提供参考年龄估计。