From a73a420e66ee7c5e4375a9e9407f7715e9bf85ae Mon Sep 17 00:00:00 2001 From: Joel Nitta Date: Fri, 21 Jan 2022 01:38:29 +0000 Subject: [PATCH] Update MS --- ms/SI.Rmd | 4 +- ms/manuscript.Rmd | 12 ++--- ms/references.yaml | 102 +++++++-------------------------------- ms/references_other.bib | 34 ++++++------- ms/references_other.yaml | 46 ++++++++++++++---- 5 files changed, 79 insertions(+), 119 deletions(-) diff --git a/ms/SI.Rmd b/ms/SI.Rmd index bbbbd56..001415c 100644 --- a/ms/SI.Rmd +++ b/ms/SI.Rmd @@ -702,7 +702,7 @@ ggtree(dendro_tax, size = 0.15) %<+% theme(plot.subtitle = element_markdown()) ``` -**`r s_figure("dendrogram")`**. Bioregion dendrograms. Tips are sites (names not shown). Dendrograms generated by clustering taxonomic (Sørensen) or phylogenetic (PhyloSor) distances between sites (see Materials and Methods). Color shows bioregion; bioregions not consisting of > `r english2(bioregion_cutoff)` grid-cells each are lumped into the "Other" category. (A), taxonomic bioregions. (B), phylogenetic bioregions. Dendrograms visualized with the `r pack("ggtree")` R package [@Yu2017]. +**`r s_figure("dendrogram")`**. Bioregion dendrograms. Tips are sites (names not shown). Dendrograms generated by clustering taxonomic (Sørensen) or phylogenetic (PhyloSor) distances between sites (see Materials and Methods). Color shows bioregion; bioregions not consisting of more than `r english2(bioregion_cutoff)` grid-cells each are lumped into the "Other" category. (A), taxonomic bioregions. (B), phylogenetic bioregions. Dendrograms visualized with the `r pack("ggtree")` R package [@Yu2017]. \clearpage ```{r dendrogram-b, fig.width = 7, fig.height = 9} @@ -914,7 +914,7 @@ a + b + plot_annotation(tag_levels = "A", theme(plot.tag = element_text(face = "bold")) ``` -**`r s_figure("bioregions-env")`**. Scatterplots of grid cell membership in (A) taxonomic or (B) phylogenetic bioregions arranged by mean annual temperature and annual precipitation. Points shown with partial transparency; darker areas indicate overlapping points. Bioregions not consisting of > `r english2(bioregion_cutoff)` grid-cells each are lumped into the "Other" category. +**`r s_figure("bioregions-env")`**. Scatterplots of grid cell membership in (A) taxonomic or (B) phylogenetic bioregions arranged by mean annual temperature and annual precipitation. Points shown with partial transparency; darker areas indicate overlapping points. Bioregions not consisting of more than `r english2(bioregion_cutoff)` grid-cells each are lumped into the "Other" category. \clearpage diff --git a/ms/manuscript.Rmd b/ms/manuscript.Rmd index aafff88..a3fcd27 100644 --- a/ms/manuscript.Rmd +++ b/ms/manuscript.Rmd @@ -121,7 +121,7 @@ Joel H. Nitta^1,5^, Brent D. Mishler^2^, Wataru Iwasaki^1,3^, and Atsushi Ebihar ^5^Author for correspondence: joelnitta@gmail.com -```{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 _______. @@ -262,7 +262,7 @@ We ask the following questions in our study system, the ferns of Japan: 1. How i ## MATERIALS AND METHODS -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]. ## Study Site @@ -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). We measured phylogenetic endemism (PE) as the sum of all branches at a site inversely weighted by their range size [@Rosauer2009]. @@ -468,7 +468,7 @@ $SES = \frac{obs - mean(null)}{sd(null)}$ 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]. 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. @@ -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. 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). diff --git a/ms/references.yaml b/ms/references.yaml index 7d60ff8..2ba478e 100644 --- a/ms/references.yaml +++ b/ms/references.yaml @@ -260,6 +260,7 @@ references: given: François citation-key: Courtiol2017 container-title: bioRxiv + volume: '207662' DOI: 10.1101/207662 issued: - year: 2017 @@ -271,6 +272,7 @@ references: source: www.biorxiv.org title: Modelling isoscapes using mixed models type: article-journal + URL: https://doi.org/10.1101/207662 - id: Creese2011 author: - family: Creese @@ -337,9 +339,6 @@ references: container-title: Methods in Ecology and Evolution container-title-short: Methods Ecol. Evol. DOI: 10.1111/2041-210x.13478 - editor: - - family: Silvestro - given: Daniele ISSN: 2041-210X, 2041-210X issue: '11' issued: @@ -427,37 +426,6 @@ references: publisher-place: Tokyo title: The Standard of Ferns and Lycophytes in Japan, Vol. 2 type: book -- id: Ebihara2019a - author: - - family: Ebihara - given: Atsushi - - family: Nitta - given: Joel H. - - family: Matsumoto - given: Yurika - - family: Fukazawa - given: Yuri - - family: Kurihara - given: Marie - - family: Yokote - given: Hitomi - - family: Sakuma - given: Kaoru - - family: Azakami - given: Otowa - citation-key: Ebihara2019a - container-title: Bulletin of the National Museum of Nature and Science, Series B - (Botany), Tokyo - issue: '2' - issued: - - year: 2019 - month: 5 - day: 22 - page: 77-86 - title: Growth dynamics of independent gametophytes of *Pleurosoriopsis - makinoi* (Polypodiaceae) - type: article-journal - volume: '45' - id: Ebihara2019b author: - family: Ebihara @@ -492,9 +460,6 @@ references: container-title: Journal of Biogeography container-title-short: J. Biogeogr. DOI: 10.1111/jbi.12130 - editor: - - family: Triantis - given: Kostas ISSN: '03050270' issue: '9' issued: @@ -980,9 +945,6 @@ references: container-title: Methods in Ecology and Evolution container-title-short: Methods Ecol Evol DOI: 10/f8tbrk - editor: - - family: Jones - given: Kate ISSN: 2041-210X, 2041-210X issue: '5' issued: @@ -1034,7 +996,7 @@ references: language: en page: '2959' source: joss.theoj.org - title: 'The targets R package: a dynamic Make-like function-oriented pipeline toolkit + title: 'The targets R package: A dynamic Make-like function-oriented pipeline toolkit for reproducibility and high-performance computing' title-short: The targets R package type: article-journal @@ -1077,8 +1039,7 @@ references: language: en page: 498-522 source: DOI.org (Crossref) - title: 'Fern and lycophyte diversity in the Pacific Northwest: Patterns and predictors: - Fern and lycophyte diversity in Pacific Northwest' + title: 'Fern and lycophyte diversity in the Pacific Northwest: Patterns and predictors' title-short: Fern and lycophyte diversity in the Pacific Northwest type: article-journal volume: '56' @@ -1273,7 +1234,7 @@ references: - year: 2014 page: '4473' title: Phylogenetic measures of biodiversity and neo- and paleo-endemism in Australian - Acacia + *Acacia* type: article-journal volume: '5' - id: Mishler2020 @@ -1339,30 +1300,6 @@ references: pteridophytes type: article-journal volume: '53' -- id: Murakami2021 - accessed: - - year: 2021 - month: 12 - day: 8 - author: - - family: Murakami - given: Noriaki - - family: Sakai - given: Erika - - family: Yoneoka - given: Katsuhiro - citation-key: Murakami2021 - container-title: BSJ-Review - DOI: 10.24480/bsj-review.12c3.00211 - issued: - - year: 2021 - language: Japanese - page: 159-168 - source: DOI.org (CSL JSON) - title: Inventories of fern independent gametophytes in Japan using DNA barcoding - based on nucleotide sequences of *rbcL* gene (in Japanese) - type: article-journal - volume: '12' - id: Myers2000 author: - family: Myers @@ -1434,7 +1371,7 @@ references: day: 1 page: 105-110 title: On the "*Gleichenia japonica* Line" as an indicator of the border line with - the distribution of the warm temperate species in Japan \[in Japanese] + the distribution of the warm temperate species in Japan (in Japanese) type: article-journal volume: '16' - id: Natori2012 @@ -1578,20 +1515,20 @@ references: community structure between fern sporophytes and gametophytes' type: article-journal volume: '87' -- id: Nitta2021a +- id: Nitta2022 type: webpage accessed: - - year: 2021 - month: 8 + - year: 2022 + month: 1 day: 19 author: - family: Nitta given: Joel H. issued: - - year: 2021 + - year: 2022 title: 'canaper: Categorical Analysis of Neo- and Paleo-endemism in R. R Package - Version 0.0.0.9000' - URL: https://doi.org/10.5281/zenodo.5094033 + Version 0.0.2' + URL: https://doi.org/10.5281/zenodo.5885646 - type: webpage id: Noss2016 author: @@ -1630,7 +1567,7 @@ references: year: 2021 month: 09 day: 1 - title: 'Caper: Comparative analyses of phylogenetics and evolution in r. Version + title: 'Caper: Comparative analyses of phylogenetics and evolution in R. Version 1.0.1' title-short: Caper note: R package version 1.0.1 @@ -1695,7 +1632,7 @@ references: issued: - year: 2018 language: en - page: '439' + page: 439-446 source: DOI.org (Crossref) title: 'Simple features for R: Standardized support for spatial vector data' title-short: Simple Features for R @@ -1865,9 +1802,6 @@ references: container-title: Global Ecology and Biogeography container-title-short: Global Ecol Biogeogr DOI: 10.1111/geb.13349 - editor: - - family: Baselga - given: Andres ISSN: 1466-822X, 1466-8238 issue: '9' issued: @@ -1894,7 +1828,7 @@ references: title-short: Raster note: R package version 3.1-5 URL: https://CRAN.R-project.org/package=raster -- id: RCoreTeam2020 +- id: RCoreTeam2021 type: webpage author: - literal: R Core Team @@ -1904,7 +1838,7 @@ references: year: 2021 month: 09 day: 1 - title: 'R: A language and environment for statistical computing. Version 4.0.0. + title: 'R: A language and environment for statistical computing. Version 4.1.2. R Foundation for Statistical Computing, Vienna, Austria' URL: https://www.R-project.org/ - id: Revell2012 @@ -1983,7 +1917,7 @@ references: - year: 2009 month: 10 page: 4061-4072 - title: 'Phylogenetic endemism: a new approach for identifying geographical concentrations + title: 'Phylogenetic endemism: A new approach for identifying geographical concentrations of evolutionary history' type: article-journal volume: '18' @@ -2032,7 +1966,7 @@ references: given: Yoshikazu container-title: Chiikigaku-kenkyu ISSN: 0915-4094 - issue: '27' + volume: '27' issued: - year: 2014 month: 3 diff --git a/ms/references_other.bib b/ms/references_other.bib index 57f68ad..fc8b275 100644 --- a/ms/references_other.bib +++ b/ms/references_other.bib @@ -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} } @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", -} \ No newline at end of file + 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", +} diff --git a/ms/references_other.yaml b/ms/references_other.yaml index f1b6107..b3b095a 100644 --- a/ms/references_other.yaml +++ b/ms/references_other.yaml @@ -1,19 +1,19 @@ --- references: -- id: Nitta2021a +- id: Nitta2022 type: webpage accessed: - - year: 2021 - month: 8 + - year: 2022 + month: 1 day: 19 author: - family: Nitta given: Joel H. issued: - - year: 2021 - title: 'canaper: Categorical Analysis of Neo- and Paleo-endemism in R. R Package Version 0.0.0.9000' - URL: https://doi.org/10.5281/zenodo.5094033 + - year: 2022 + title: 'canaper: Categorical Analysis of Neo- and Paleo-endemism in R. R Package Version 0.0.2' + URL: https://doi.org/10.5281/zenodo.5885646 - id: kankyosho2022 type: webpage @@ -64,7 +64,7 @@ references: title: 'Yaseichoju ni yoru seitaikei heno eikyo ga kennen sareru chiiki (Areas where effects of wild animals on the environment is a concern; in Japanese)' URL: https://www.biodic.go.jp/biodiversity/activity/policy/map/map14/index.html -- id: RCoreTeam2020 +- id: RCoreTeam2021 type: webpage author: - literal: R Core Team @@ -74,7 +74,7 @@ references: year: 2021 month: 09 day: 01 - title: 'R: A language and environment for statistical computing. Version 4.0.0. R Foundation for Statistical Computing, Vienna, Austria' + title: 'R: A language and environment for statistical computing. Version 4.1.2. R Foundation for Statistical Computing, Vienna, Austria' URL: https://www.R-project.org/ - id: Orme2018 @@ -100,7 +100,7 @@ references: year: 2021 month: 09 day: 01 - title: 'Caper: Comparative analyses of phylogenetics and evolution in r. Version 1.0.1' + title: 'Caper: Comparative analyses of phylogenetics and evolution in R. Version 1.0.1' title-short: Caper note: R package version 1.0.1 URL: https://CRAN.R-project.org/package=caper @@ -228,7 +228,7 @@ references: given: Yoshikazu container-title: Chiikigaku-kenkyu ISSN: 0915-4094 - issue: '27' + volume: '27' issued: - year: 2014 month: 3 @@ -236,3 +236,29 @@ references: source: CiNii title: 'Process of the formation of Japanese forest and typification of vegetation zone: From an East Asian viewpoint (In Japanese)' type: article-journal + +- id: Courtiol2017 + accessed: + - year: 2021 + month: 5 + day: 28 + author: + - family: Courtiol + given: Alexandre + - family: Rousset + given: François + citation-key: Courtiol2017 + container-title: bioRxiv + volume: '207662' + DOI: 10.1101/207662 + issued: + - year: 2017 + month: 10 + day: 23 + language: en + publisher: Cold Spring Harbor Laboratory + section: New Results + source: www.biorxiv.org + title: Modelling isoscapes using mixed models + type: article-journal + URL: https://doi.org/10.1101/207662