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. 2022 May;109(5):727-745.
doi: 10.1002/ajb2.1848. Epub 2022 May 19.

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

Joel H Nitta  1 , Brent D Mishler  2 , Wataru Iwasaki  1   3 , Atsushi Ebihara  4
Affiliations

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

Joel H Nitta et al. Am J Bot. 2022 May.

Abstract

Premise: Biodiversity is often only measured with species richness; however, this metric ignores evolutionary history and is not sufficient for making conservation decisions. Here, we characterize multiple facets and drivers of biodiversity to understand how these relate to bioregions and conservation status in the ferns of Japan.

Methods: We compiled a community data set of 1239 grid cells (20 × 20 km each) including 672 taxa based on >300,000 specimen records. We combined the community data with a phylogeny and functional traits to analyze taxonomic, phylogenetic, and functional diversity and modeled biodiversity metrics in response to environmental factors and reproductive mode. Hierarchical clustering was used to delimit bioregions. Conservation status and threats were assessed by comparing the overlap of significantly diverse grid cells with conservation zones and range maps of native Japanese deer.

Results: Taxonomic richness was highest at mid-latitudes. Phylogenetic and functional diversity and phylogenetic endemism were highest in small southern islands. Relative phylogenetic and functional diversity were high at high and low latitudes, and low at mid-latitudes. Grid cells were grouped into three (phylogenetic) or four (taxonomic) major bioregions. Temperature and apomixis were identified as drivers of biodiversity patterns. Conservation status was generally high for grid cells with significantly high biodiversity, but the threat due to herbivory by deer was greater for taxonomic richness than other metrics.

Conclusions: Our integrative approach reveals previously undetected patterns and drivers of biodiversity in the ferns of Japan. Future conservation efforts should recognize that threats can vary by biodiversity metric and consider multiple metrics when establishing conservation priorities.

Keywords: CANAPE; Japan; apomixis; biodiversity; biogeography; conservation; ferns; phylogenetic diversity.

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Figures

Figure 1
Figure 1
Map of Japan showing names of places mentioned in the text. Names of the four main islands in bold. The Ryukyu Islands include Yakushima, Amami, Okinawa, Miyako, and Iriomote. Solid line shows location of Tsugaru Strait; dashed line shows Tokara Strait.
Figure 2
Figure 2
Raw (observed) biodiversity metrics of the ferns of Japan. (A) Raw taxonomic diversity. (B) Raw phylogenetic diversity. (C) Raw functional diversity. For (B) and (C), raw branch lengths were transformed to relative values by dividing each branch length by the sum of all branch lengths.
Figure 3
Figure 3
Results of randomization tests for phylogenetic and functional diversity of ferns of Japan. (A) Phylogenetic diversity (PD). (B) Relative phylogenetic diversity (RPD). (C) Functional diversity (FD). (D) Relative functional diversity (RFD). For each metric, raw values were compared to a null distribution of 999 random values, and the p‐value was calculated using a two‐tailed test. For details, see Materials and Methods.
Figure 4
Figure 4
Regression coefficient t‐values (coefficient divided by standard error) of general mixed models for the effect of environment and reproductive mode on biodiversity metrics in the ferns of Japan. (A–E) Environmental (env.) models (models including temperature). (F, G) Reproductive (repro.) models (models including % apomictic taxa). Precip., precipitation; Temp., temperature; SES, standard effect size; PD, phylogenetic diversity; RPD, relative PD; FD, functional diversity; RFD, relative FD. Statistical significance was assessed with a likelihood ratio test (LRT) between the full model and a model with the focal independent variable removed (null model); p‐values indicate probability of no difference between the full and null model. Response variable and model type are indicated above each subplot. Independent variable with greatest absolute t‐value is in bold for each model.
Figure 5
Figure 5
Relationship between biodiversity metrics and selected predictor variables in the ferns of Japan. (A–E) Environmental models (models including temperature). (F, G) Reproductive models (models including % apomictic taxa). Ribbon shows 95% confidence interval of model. Line fit with the focal predictor variable while averaging over other predictors. For phylogenetic diversity (PD), relative PD (RPD), functional diversity (FD), and relative FD (RFD), the standard effect size (SES) was calculated by comparing raw values to a null distribution of 999 random values, and significance (p‐value) determined using a two‐tailed test (see Materials and Methods).
Figure 6
Figure 6
Phylogenetic endemism of the ferns of Japan measured using categorical analysis of neo‐ and paleoendemism (CANAPE). neo, grid cells with an overabundance of rare short branches; paleo, grid cells with an overabundance of rare long branches; mixed, significantly endemic grid cells that have neither an overabundance of short nor long branches; super, highly significantly endemic grid cells that have neither an overabundance of short nor long branches. Grid cells without significant endemism in light grey. For details, see Materials and Methods.
Figure 7
Figure 7
Bioregions of the ferns of Japan. (A) Taxonomic bioregions. (B) Phylogenetic bioregions. Bioregions determined by clustering taxonomic (Sørensen) or phylogenetic (PhyloSor) distances between grid cells. Bioregions not consisting of more than two grid cells each were lumped into category “Other”.
Figure 8
Figure 8
Phylogenetic and morphological diversity of the ferns of Japan by taxonomic bioregion. (A) Standard effect size (SES) of phylogenetic diversity (PD). (B) SES of relative PD (RPD). (C) SES of functional diversity (FD). (D) SES of relative FD (RFD). (E) The p‐score for observed phylogenetic endemism (PE) relative to 999 random communities.
Figure 9
Figure 9
Conservation status and threat due to herbivory by deer in areas with high levels of biodiversity for ferns of Japan. (A) Percentage of land area with medium or high protected status for grid cells with significantly high biodiversity by protection status. (B) Percentage of land area occupied by deer for grid cells with significantly high biodiversity by deer range data source (1978 survey, 2003 survey, or range estimated from model based on 2003 survey data). Biodiversity metrics include taxon richness, phylogenetic diversity (PD), functional diversity (FD), and phylogenetic endemism (PE). Significance of PD, FD, and PE assessed by a one‐tailed test comparing observed values to a null distribution of 999 random values; for richness, grid cells in the top 5% considered highly diverse (see Materials and Methods). For (A), vertical lines indicate total percentage area protected across Japan (baseline protection rate). For (B), vertical lines indicate total percentage of land area occupied by deer across Japan (baseline threat rate).
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