Spatial phylogenetics of Japanese ferns: Patterns, processes, and implications for conservation

A list of native, non-hybrid fern specimens mostly housed at the herbarium of the Museum of Science and Nature, Japan was converted to a community data matrix at four grain sizes (square grid-cells spanning Japan, each 10, 20, 30, or 40 km per side). The 20 km grain size was selected for further analysis based on redundancy (ratio of number of specimens to number of taxa per cell).All taxon names are based on the Green List (http://www.rdplants.org/gl/; English version available at https://datadryad.org/stash/dataset/doi:10.5061/dryad.4362p32).Traits were measured on each species as described in Ebihara and Nitta (2019).Phylogenetic analysis was conducted with maximum likelihood in IQ-TREE v1.6.12 (Nguyen et al. 2015) by combining plastid rbcL sequences of each taxon with a globally sampled data matrix (Nitta et al, in prep). Next, dating analysis was carried out using treePL v1.0 (Smith and O’Meara 2012) with 26 fossil calibration points after Testo and Sundue (2016). The dated phylogeny was then trimmed to include Japanese taxa only.The community matrix, traits, and phylogeny were used to analyze spatial patterns of phylogenetic diversity and endemism.Data files were generated from raw data (not included here) using scripts available at https://github.com/joelnitta/japan_ferns_spatial_phy, in particular https://github.com/joelnitta/japan_ferns_spatial_phy/blob/main/R/process_raw_data.R.For full methods, see Nitta JH, Mishler BD, Iwasaki W, Ebihara A (2021) Spatial phylogenetics of Japanese ferns: Patterns, processes, and implications for conservation https://doi.org/10.1101/2021.08.26.457744

一组源自本土的非杂交蕨类植物标本，主要存放在日本自然科学博物馆的标本馆，已转换为四种粒度（覆盖日本的正方形网格单元，每边长度分别为10、20、30或40公里）的社区数据矩阵。基于冗余度（每个单元中标本数量与分类群数量的比率）选择了20公里粒度进行进一步分析。所有分类群名称均依据绿色名录（http://www.rdplants.org/gl/；英文版本可在https://datadryad.org/stash/dataset/doi:10.5061/dryad.4362p32获取）。每个物种的性状均按照Ebihara和Nitta（2019）的描述进行测量。利用IQ-TREE v1.6.12（Nguyen等人，2015年）通过结合每个分类群的叶绿体rbcL序列与全球样本数据矩阵（Nitta等人，待发表）进行最大似然性系统发育分析。随后，采用treePL v1.0（Smith和O’Meara，2012年）在Testo和Sundue（2016年）的基础上，利用26个化石校准点进行年代分析。然后，对所得到的年代系统发育树进行修剪，仅保留日本分类群。社区矩阵、性状和系统发育树被用于分析系统发育多样性和特有性在空间上的分布模式。数据文件是通过在https://github.com/joelnitta/japan_ferns_spatial_phy处可获得的脚本（特别是https://github.com/joelnitta/japan_ferns_spatial_phy/blob/main/R/process_raw_data.R）从原始数据（此处未包含）生成的。关于完整方法，请参阅Nitta JH，Mishler BD，Iwasaki W，Ebihara A（2021年）发表的《日本蕨类植物的时空系统发育学：模式、过程及对保护的启示》https://doi.org/10.1101/2021.08.26.457744。