Table_3_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.

在进化生物学领域，理解物种多样性在空间和时间框架中的演化至关重要。评估高度多样化的快速辐射谱系的地理起源和扩散历史，可能受到适当采样、解析并得到强烈支持的系统发育背景的缺乏而受到阻碍。目前可用的成本效益测序策略，使得能够为密集的分类采样生成大量的序列数据，这些数据与精心整理的地理信息和生物地理模型相结合，使我们能够正式测试快速连续发生的扩散事件的模式和节奏。在此，我们评估了扩张谱系K的起源和扩散历史的空间和时间框架，扩张谱系K是一个高度多样化的Tillandsia亚属Tillandsia（凤梨科，兰目）谱系，据推测在新生代地区经历了快速的辐射。我们利用Hyb-Seq数据组装了全叶绿体基因组，为扩张谱系K的密集分类采样以及精心挑选的外群物种，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进行基于广泛地理信息汇编的生物地理模型测试和祖先区域重建。扩张谱系K通过从南美洲的长距离扩散，至少在4.86百万年前，即墨西哥大部分高原已经形成的时期，殖民了北美和中美洲，特别是墨西哥过渡区和中美洲领土。在随后的2.8百万年前，发生了几次向北方至近北地区的南部、向东至加勒比海和向南方至太平洋领土的扩散事件，这一时期以明显的气候波动为特征，这些波动源于冰河时期与间冰期的气候振荡以及显著的火山活动，主要在墨西哥火山带。我们的分类采样设计使我们能够首次校准几个节点，不仅限于扩张谱系K的焦点群内，还包括其他Tillandsioideae谱系。我们期望这一时间校准的系统发育框架将促进未来的宏观进化学研究，并为其他Tillandsioideae谱系进行二级校准提供参考年龄估计。