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

Abstract

Aim: To characterize multiple facets and drivers of biodiversity and understand how these relate to bioregions and conservation status. Location: Japan. Taxon: Ferns. Methods: We used data from >300,000 fern specimens in Japan to compile a community dataset of 1,240 0.2 degree grid-cells including 674 native, non-hybrid taxa. We combined this with a phylogenetic tree and functional trait data to analyze taxonomic, phylogenetic, and functional diversity, and modeled the distribution of biodiversity in response to environmental factors and reproductive mode. We conducted categorical analysis of neo- and paleo-endemism to identify areas of significant phylogenetic endemism. We used hierarchical clustering of taxonomic and phylogenetic distances to analyze bioregions. We compared the overlap of significantly diverse grid-cells with existing conservation zones to assess conservation status. Results: We observe three major patterns in the spatial distribution of biodiversity: that of taxonomic richness, which is highest at mid-latitudes, that of phylogenetic and functional diversity and phylogenetic endemism, which are highest in small southern islands, and that of relative phylogenetic and functional diversity, which are high at both high and low latitudes, and low at mid-latitudes. Grid-cells were grouped in to three (phylogenetic) or four (taxonomic) major bioregions. Temperature and apomixis were identified as likely drivers of patterns of taxonomic and phylogenetic diversity. Conservation status (% protected area) is generally higher than the overall rate for grid-cells with significantly high biodiversity. Main conclusions: The integrative approach used here reveals previously undetected patterns and drivers of biodiversity in the ferns of Japan. The different distributions of each diversity type reflect the major bioregions. Although peak areas of different diversity types are largely non-overlapping, each one has a relatively high protection status. Despite this, future conservation efforts must be cognizant of dangers not addressed here such as climate change and herbivory by deer.

canaper: Categorical analysis of neo- and paleo-endemism in R

“…This will simplify workflows and facilitate reproducibility for researchers studying spatial biodiversity with R. Furthermore, features efficient computing routines and simple yet flexible implementation of parallel computing, thereby decreasing computation time. has already been used at least three studies while in development (Ellepola et al, 2022; Lu et al, 2022; Nitta et al, 2022). We expect will become a major tool in the toolkit of the emerging field of spatial phylogenetics alongside Biodiverse.…”

“…This became possible with the development of phylogenetic measures of biodiversity, such as phylogenetic diversity (PD; Faith, 1992) and phylogenetic endemism (PE; Rosauer et al, 2009) (Box 1). Such analyses are becoming much more common due to the widespread availability of robust molecular phylogenies and large spatial datasets (e.g., Mishler et al, 2020; Nitta et al, 2022; Thornhill et al, 2017).…”

An Open and Continuously Updated Fern Tree of Life

“…, DNA alignments, fossil calibrations) available so that other researchers can use these to conduct analyses such as further investigations of divergence times or phylogenetic analysis including custom sets of DNA sequences ( e.g. , Nitta et al, 2022a).…”

“…FTOL is available via the "ftolr" R package (FTOL working group, 2022b), as well as a web portal (https://fernphy.github.io). Furthermore, we have made all the underlying data (e.g., DNA alignments, fossil calibrations) available so that other researchers can use these to conduct analyses such as further investigations of divergence times or phylogenetic analysis including custom sets of DNA sequences (e.g., Nitta et al, 2022a).…”