Data_Sheet_4_An open and continuously updated fern tree of life.PDF

Ferns, with about 12,000 species, are the second most diverse lineage of vascular plants after angiosperms. They have been the subject of numerous molecular phylogenetic studies, resulting in the publication of trees for every major clade and DNA sequences from nearly half of all species. Global fern phylogenies have been published periodically, but as molecular systematics research continues at a rapid pace, these become quickly outdated. Here, we develop a mostly automated, reproducible, open pipeline to generate a continuously updated fern tree of life (FTOL) from DNA sequence data available in GenBank. Our tailored sampling strategy combines whole plastomes (few taxa, many loci) with commonly sequenced plastid regions (many taxa, few loci) to obtain a global, species-level fern phylogeny with high resolution along the backbone and maximal sampling across the tips. We use a curated reference taxonomy to resolve synonyms in general compliance with the community-driven Pteridophyte Phylogeny Group I classification. The current FTOL includes 5,582 species, an increase of ca. 40% relative to the most recently published global fern phylogeny. Using an updated and expanded list of 51 fern fossil constraints, we find estimated ages for most families and deeper clades to be considerably older than earlier studies. FTOL and its accompanying datasets, including the fossil list and taxonomic database, will be updated on a regular basis and are available via a web portal (https://fernphy.github.io) and R packages, enabling immediate access to the most up-to-date, comprehensively sampled fern phylogeny. FTOL will be useful for anyone studying this important group of plants over a wide range of taxonomic scales, from smaller clades to the entire tree. We anticipate FTOL will be particularly relevant for macroecological studies at regional to global scales and will inform future taxonomic systems with the most recent hypothesis of fern phylogeny.

蕨类植物（Ferns）约有12000个物种，是仅次于被子植物（Angiosperms）的第二大维管植物（vascular plants）演化支系。该类群已成为众多分子系统发育研究的核心对象，相关成果已发表了所有主要演化支的系统发育树，并获取了近半数物种的DNA序列数据。全球尺度的蕨类系统发育树虽有阶段性发表，但随着分子系统学研究的快速推进，此类成果很快便会过时。本研究开发了一套半自动化、可复现的开放流程，依托GenBank中的公开DNA序列数据，构建可持续更新的蕨类生命之树（FTOL）。本研究定制的采样策略结合了全质体基因组（plastomes，类群少、基因位点多）与常规测序的质体区域（plastid regions，类群多、基因位点少）两种方案，旨在构建兼具高分辨率主干与最大程度末梢类群覆盖度的全球物种级蕨类系统发育树。本研究采用经过人工审定的参考分类系统对同物异名进行校准，整体遵循由学界主导制定的《蕨类植物系统发育小组第一版（Pteridophyte Phylogeny Group I, PPG I）》分类体系。当前版本的FTOL涵盖5582个物种，较最新发表的全球蕨类系统发育树增长约40%。依托更新并扩充后的51个蕨类化石校准点列表，本研究发现绝大多数科与深层演化支的估计分化时间远早于此前相关研究的结果。FTOL及其配套数据集（包括化石校准列表与分类学数据库）将定期更新，可通过网页门户（https://fernphy.github.io）与R软件包获取，方便使用者快速获取最新且覆盖全面的蕨类系统发育树资源。FTOL可服务于所有研究该重要植物类群的学者，其适用的分类学尺度跨度极大，从小型演化支直至整个植物生命之树均可覆盖。我们预计FTOL将尤其适用于区域至全球尺度的宏生态学研究，并可为未来基于最新蕨类系统发育假说的分类系统修订提供参考依据。