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).

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