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@@ -121,7 +121,7 @@ Joel H. Nitta^1,5^, Brent D. Mishler^2^, Wataru Iwasaki^1,3^, and Atsushi Ebihar | |
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| ^5^Author for correspondence: [email protected] | ||
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| ```{r author-page-doc, results = "asis", echo = FALSE, eval = params$doc_type == "docx"} | ||
| ```{r author-page-doc, results = "asis", echo = FALSE, eval = params$doc_type == "doc"} | ||
| # Author page, version for submission to journal | ||
| cat(' | ||
| Manuscript received _______; revision accepted _______. | ||
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@@ -262,7 +262,7 @@ We ask the following questions in our study system, the ferns of Japan: 1. How i | |
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| ## MATERIALS AND METHODS | ||
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| All computational analyses were carried out in R v`r getRversion()` [@RCoreTeam2020] unless otherwise stated. The R package `r pack("targets")` was used to control analysis workflow [@Landau2021]. | ||
| All computational analyses were carried out in R v`r getRversion()` [@RCoreTeam2021] unless otherwise stated. The R package `r pack("targets")` was used to control analysis workflow [@Landau2021]. | ||
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| ## Study Site | ||
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@@ -452,7 +452,7 @@ We measured functional diversity (FD) following the method of @Petchey2002. | |
| We first calculated functional distances using Gower's method [@Gower1971] on the trait data with the `r func("gowdis")` function in the R package `r pack("FD")` [@Laliberte2010]. | ||
| We weighted continuous and qualitative traits equally, weighted each binary component trait of each qualitative trait equally, and log-transformed and scaled continuous traits prior to calculating distances. | ||
| We also tested alternative weighting schemes, but these produced very similar results (data not shown). | ||
| We then used the distances to build a trait dendrogram using the `r func("hclust")` function in the R package `r pack("stats")` [@RCoreTeam2020], and used the dendogram in place of a phylogenetic tree to calculate PD and RPD as described above. | ||
| We then used the distances to build a trait dendrogram using the `r func("hclust")` function in the R package `r pack("stats")` [@RCoreTeam2021], and used the dendogram in place of a phylogenetic tree to calculate PD and RPD as described above. | ||
| These functional analogs of PD and RPD are hereafter referred to as FD (functional diversity) and RFD (relative functional diversity). | ||
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| We measured phylogenetic endemism (PE) as the sum of all branches at a site inversely weighted by their range size [@Rosauer2009]. | ||
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@@ -468,7 +468,7 @@ $SES = \frac{obs - mean(null)}{sd(null)}$ | |
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| We tested whether centers of endemism have an over-representation of old (paleoendemic) or new (neoendemic) lineages using categorical analysis of neo- and paleo-endemism (CANAPE), which involves measuring PE with an alternate tree where all branch lengths are equal, then comparing the ratio between raw PE and alternative PE (RPE) [@Mishler2014]. | ||
| Low RPE indicates short range-restricted branches (neoendemism) and high RPE indicates long range-restricted branches (paleoendemism). | ||
| Since all of these measures are affected by species richness, categorization of endemism is done using the rank of each observed variable relative to those calculated for the null distribution. All measures of biodiversity and CANAPE were carried out using the R package `r pack("canaper")` [@Nitta2021a]. | ||
| Since all of these measures are affected by species richness, categorization of endemism is done using the rank of each observed variable relative to those calculated for the null distribution. All measures of biodiversity and CANAPE were carried out using the R package `r pack("canaper")` [@Nitta2022]. | ||
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| It is possible that endemism may be affected by species that are actually wide-ranging, but only have a small range in Japan (a "border effect"). | ||
| This is especially expected for southern, sub-tropical islands, which harbor many tropical species with small ranges in Japan but wider ranges outside of the country. | ||
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@@ -517,8 +517,8 @@ To prevent double-counting, all protected areas within a protection status were | |
| Besides habitat loss due to human activity, one major threat to ferns in Japan is herbivory by Japanese deer (*Cervus nippon*). | ||
| Although native, Japanese deer have caused extensive damage to native plant communities due to rapid population growth and range expansion since the 1970s [@Takatsuki2009]. | ||
| Decrease or extirpation of fern populations due to deer herbivory has been observed in multiple sites and species across the country [@Minamitani2005; @Yahara2006; @Hattori2010]. | ||
| Furthermore, 33 of 212 (15.5%) fern taxa listed as endangered (Red List status CR, EN or VU) in Japan include herbivory by deer as one of the reasons for their endangered status, and one taxon (*Arachniodes yasu-inouei* Sa. Kurata var. *angustipinnula* Seriz.) is thought to have gone extinct due to deer herbivory, among other causes [@MOJ2015; @kankyosho2022]. | ||
| Although not all species of ferns are equally susceptible to deer herbivory [a small number are apparently unpalatable to deer\; @Minamitani2005], these studies show it is a clear danger to many species. | ||
| Furthermore, 33 of 212 (15.5%) fern taxa listed as endangered (Red List status CR, EN or VU) in Japan include herbivory by deer as one of the reasons for their endangered status [@MOJ2015; @kankyosho2022]. | ||
| Although not all species of ferns are equally susceptible to deer herbivory [some are unpalatable to deer\; @Minamitani2005], these studies show it is an existential threat to many species. | ||
| Therefore, analysis of the threat posed to fern biodiversity by deer herbivory is needed to inform future conservation policies. | ||
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| We downloaded distribution maps (SHP and TIF) of *Cervus nippon* from the Japan Ministry of the Environment (https://www.biodic.go.jp/biodiversity/activity/policy/map/map14/index.html). | ||
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| @@ -1,21 +1,21 @@ | ||
| @book{Woodward1987, | ||
| title={Climate and Plant Distribution}, | ||
| author={Woodward, Frank Ian}, | ||
| year={1987}, | ||
| publisher={Cambridge University Press} | ||
| title = {{Climate and Plant Distribution}}, | ||
| author = {Woodward, Frank Ian}, | ||
| year = {1987}, | ||
| publisher = {Cambridge University Press} | ||
| } | ||
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| @article{Hattori2010, | ||
| author="Hattori, Tamotsu and Tochimoto, Daisuke and Minamiyama, Noriko and Hashimoto, Yoshinobu and Fujiki, Daisuke and Ishida, Hiroaki", | ||
| title="Influence of feeding pressure by Sika deer (Cervus nippon) on the primeval lucidophyllous forest in Kawanaka, Aya, Miyazaki Prefecture (in Japanese)", | ||
| journal="Vegetation Science", | ||
| ISSN="1342-2448", | ||
| publisher="The Society of Vegetation Science", | ||
| year="2010", | ||
| month="", | ||
| volume="27", | ||
| number="1", | ||
| pages="35-42", | ||
| URL="https://ci.nii.ac.jp/naid/110007641919/en/", | ||
| DOI="10.15031/vegsci.27.35", | ||
| } | ||
| author = "Hattori, Tamotsu and Tochimoto, Daisuke and Minamiyama, Noriko and Hashimoto, Yoshinobu and Fujiki, Daisuke and Ishida, Hiroaki", | ||
| title = {{Influence of feeding pressure by Sika deer (\textit{Cervus} \textit{nippon}) on the primeval lucidophyllous forest in Kawanaka, Aya, Miyazaki Prefecture (in Japanese)}}, | ||
| journal = "Vegetation Science", | ||
| ISSN = "1342-2448", | ||
| publisher = "The Society of Vegetation Science", | ||
| year = "2010", | ||
| month = "", | ||
| volume = "27", | ||
| number = "1", | ||
| pages = "35-42", | ||
| URL = "https://ci.nii.ac.jp/naid/110007641919/en/", | ||
| DOI = "10.15031/vegsci.27.35", | ||
| } |
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