Data from: Forget-me-not phylogenomics: Improving the resolution and taxonomy of a rapid island and mountain radiation in Aotearoa New Zealand (Myosotis; Boraginaceae)

Island and mountain systems represent natural laboratories for studies of
species radiations, but they often present several challenges for
phylogenetic inference and species delimitation. The southern hemisphere
forget-me-nots (Myosotis, Boraginaceae) comprise a geologically recent
radiation centred in Aotearoa New Zealand, a mountainous archipelago, with
about 50 species that are morphologically and ecologically divergent but
lack genetic variation sufficient to resolve phylogenetic relationships
and species boundaries using standard DNA Sanger sequencing markers,
AFLPs, or microsatellites. Many of these Myosotis species are
geographically restricted in alpine areas, uncommon or threatened, have
polyploid and dysploid genomes, and are of high taxonomic and conservation
priority. Here we present phylogenomic analyses using target-capture of
Angiosperms353 baits, and genome skimming of whole plastomes and nrDNA, to
improve resolution of the radiation, explore biogeographic and
morphological patterns within it, and address specific taxonomic questions
for each species. Our comprehensive sampling includes over 300 individuals
representing nearly all species from New Zealand and Australia, which is
~2–3x more taxon sampling and ~80–120× more molecular data than previously
published for Myosotis. Exploration of different data filtering,
curation and analyses (coalescent vs. concatenation) improved the
resolution of the Angiosmperms353 tree, which despite short backbone
branches with low support values, showed taxonomic and geographic
patterns, including multiple switches between ebracteate and bracteate
inflorescences and multiple expansions within New Zealand from Te
Waipounamu South Island to Te Ika-a-Māui North Island, Rakiura Stewart
Island, subantarctic islands, and Australia. Some of these patterns were
also seen in the genome skimming datasets, and comparison of the three
datasets was useful for improving our understanding of the taxonomy and
resolution of this radiation. Although this phylogenomic study does not
fully overcome all of the challenges regarding species delimitation of
this rapid island and mountain species radiation, it nevertheless makes an
important contribution to an integrative taxonomic revision of the
southern hemisphere species of Myosotis.

岛屿与山地系统是物种辐射演化研究的天然实验室，但这类系统往往为系统发育推断与物种界定带来诸多挑战。南半球勿忘草属（Myosotis，紫草科Boraginaceae）是一个地质年代较新的辐射演化类群，其演化中心位于多山群岛国家新西兰（奥特亚罗瓦Aotearoa），包含约50个物种。该类群物种间形态与生态分化显著，但现有遗传变异不足以通过标准DNA桑格测序（Sanger sequencing）标记、扩增片段长度多态性（AFLPs）或微卫星（microsatellites）解析其系统发育关系与物种边界。该属诸多物种仅局限分布于高山区域，种群稀少或处于受威胁状态，且具有多倍体及非整倍体基因组，兼具极高的分类学与保护学研究优先级。本研究采用被子植物353基因（Angiosperms353）捕获探针开展目标捕获测序，并对完整质体基因组与核糖体DNA（nrDNA）进行基因组浅层测序，以此实施系统发育基因组学分析，旨在提升该辐射演化类群的系统发育分辨率，探究其内部的生物地理与形态演化模式，并解答各物种对应的分类学疑问。本研究的综合采样覆盖新西兰与澳大利亚的几乎所有勿忘草属物种，共包含300余份个体样本；相较于此前已发表的勿忘草属研究，本研究的类群采样量提升了约2-3倍，分子数据量提升了约80-120倍。通过对不同数据过滤、整理与分析策略（溯祖分析与串联分析）的探索，我们优化了被子植物353基因树的分辨率。尽管该树的主干分支较短且支持度较低，但仍呈现出显著的分类学与地理分布模式，包括无苞片花序（ebracteate inflorescences）与有苞片花序（bracteate inflorescences）的多次演化转换，以及勿忘草属在新西兰境内的多次扩散事件：从南岛（特瓦波纳穆Te Waipounamu）扩散至北岛（特伊卡阿毛伊Te Ika-a-Māui）、斯图尔特岛（拉基乌拉Rakiura Stewart Island）、亚南极岛屿，乃至澳大利亚。部分上述模式在基因组浅层测序数据集中也得到了验证，通过对三类数据集的比较分析，我们得以进一步加深对该辐射演化类群分类学与系统发育分辨率的理解。尽管本项系统发育基因组学研究尚未完全解决该快速岛屿山地物种辐射演化类群的物种界定难题，但仍为南半球勿忘草属物种的整合分类学修订提供了重要支撑。