| General Information: |
| Title: | Database of Aquatic Macrophytes in Japanese lakes |
| Identifier: | ERDP-2024-02.1.2 |
| Abstract: |
Macrophytes, comprising aquatic vascular plants, bryophytes and macroalgae, including charophytes, are crucial components of lake ecosystems. Their diversity affects ecosystem functions and services, and they are sensitive to environmental changes, making them effective indicators of lake health. Historical records of macrophyte species composition are essential for evaluating environmental changes and conservation goals. In this study, we compiled a comprehensive database of macrophytes, along with lake and survey information from the literature, providing a historical record of macrophyte biodiversity for lakes in Japan. This database enables the analysis of changes in the flora of Japanese lakes and fluctuations in species distribution, facilitating future monitoring. The complete data set for this abstract published in the Data Article section of the journal is available in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2024-02.1/jalter-en.
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Involved Parties
| Data Set Owners: |
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Individual: | Syou Kato |
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Organization: | Faculty of Education, Niigata University |
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Address: |
| 8050 Ikarashi 2-no-cho, Nishi-ku, |
| Niigata, Niigata 950-2181 Japan |
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Email Address:
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Individual: | Takashi Shiga |
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Organization: | Faculty of Education, Niigata University |
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Address: |
| 8050 Ikarashi 2-no-cho, Nishi-ku, |
| Niigata, Niigata Japan |
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Email Address:
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Individual: | Takashi Yamanouchi |
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Organization: | Faculty of Symbiotic Systems Science, Fukushima University |
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Address: |
| 1 Kanayagawa, |
| Fukushima City, Fukushima 960-1296 Japan |
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Individual: | Jun Nishihiro |
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Organization: | Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies |
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Address: |
| 16‑2 Onogawa, |
| Tsukuba, Ibaraki 305‑8506 Japan |
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| Data Set Contacts: |
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Individual: | Jun Nishihiro |
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Organization: | Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies |
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Address: |
| 16‑2 Onogawa, |
| Tsukuba, Ibaraki 305‑8506 Japan |
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Data Set Characteristics
| Geographic Region: |
| Geographic Description: | the target lakes |
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Bounding Coordinates:
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| West: | 129.449 degrees
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| East: | 145.75 degrees
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| North: | 45.4317 degrees
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| South: | 25.855 degrees
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Sampling, Processing and Quality Control Methods
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Step by Step Procedures
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| Step 1: |
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Description:
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Literature
Data collection was based on the literature database compiled by Nishihiro et al. (2014) and published as the “LiteratureDB.txt” file (https://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2014-01.1/default), which contains 395 literature sources with occurrence records of plant species surveyed in Japanese lakes. During data collection in the present study, the bibliographical data in the LiteratureDB.txt was revalidated, and errors found in the title, journal name, and author name were corrected. Seven reports were removed owing to duplicate contents or misreading, and 10 reports were added that needed to be cited. As a result, 398 literature sources were compiled in the JL_LITERATURE.csv file.
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| Step 2: |
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Description:
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Data processing - Data collection
The framework for selecting lakes for data collection was primarily based on the lakes listed by Tanaka (2004), which is the limnological monograph of lakes in Japan, “The lakes in Japan II.” Tanaka’s list comprises 929 lakes in Japan, offering diverse information on the limnological characteristics of each lake. This list is derived from studies by Horie (1956, 1962), and Ministry of Environment (1983), incorporating additional literature and Tanaka’s own research. It stands out as one of the most extensive and informative compilations of Japanese lakes, primarily featuring natural lakes with an area of 1 ha or more, while also including some artificial and smaller lakes. Lakes not listed in Tanaka (2014) were included for data collection when species occurrence data were obtained during the data collection process. For instance, data for such lakes were described in literature associated with the lakes listed by Tanaka (2014). The coordinates (latitude and longitude) of each lake’s location were identified based on the descriptions in the referenced literature and/or Tanaka (2004). Information on whether a lake is of natural or artificial origin is provided in a data field in the JL_LAKE.csv file.
Occurrence records of plant species, including their Japanese and scientific names, locality data (lake information), and historical data (survey year), were extracted from the literature. Unidentified records at the species level were also treated as occurrence data. If species from surrounding areas, such as grasslands and forests, were described as part of a lake’s flora, they were also included in the extraction. In total, 45,500 occurrence records from 493 lakes (469 natural, 12 artificial, and 12 unidentified origin) were compiled and included in the JL_FLORA.csv file.
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| Step 3: |
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Description:
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Data processing - Taxonomic validation
To ensure taxonomic accuracy, the taxonomically appropriate scientific name and standard Japanese name for each species were included in the JL_FLORA.csv file based on various taxonomic sources, such as plant monographs and databases (listed in Table 2). The work of Kadono (2014) was primarily used a taxonomic guidebook on Japanese aquatic plants, although additional taxonomic sources were consulted to cover a wide range of species across different lineages (see Table 2). In cases of disagreement among sources, species names were adopted following the priority order of “A Field Guide to Aquatic Plants of Japan” (APJ), “Wild Flowers of Japan” (WFJ), “Ylist” (YL), “GreenList” (GL), and “Naturalized Plants of Japan” (NPJ) for seed plants and APJ and “The Standard of Ferns and Lycophytes in Japan” (FLJ) for pteridophytes (see Table 2 for the details of each source). Errors, such as typographical errors, were corrected during the taxonomic validation process. The original Japanese name and scientific names used in the literature were included in the JL_FLORA.csv file, along with the taxonomic source used to assign appropriate names for each species. For all species in the JL_FLORA.csv file, the taxonomically appropriate scientific and standard Japanese name, as well as typical synonyms for vascular plants, were compiled in the JL_SPECIES.csv file. To enhance usability, the category of each species, such as angiosperms, gymnosperms, pteridophytes, bryophytes, freshwater algae (charophytes, other green algae, and red algae), and marine algae (green algae, red algae, and brown algae), was also provided in the JL_SPECIES.csv file.
Macrophytes includes many taxa that are difficult to identify and often prone to misidentification (Kadono, 1994). Species misidentification has had adverse effects on analyses utilizing species occurrence data (Aubry et al., 2017; Banner et al., 2018; Costa et al., 2015). Issues related to misidentification have been noted in aquatic plant inventorying and in conservation assessments (Yamanouchi and Ikeda, 2019; Yamanouchi et al., 2016, 2023). Nishihiro et al. (2014)’s database necessitated users to independently assess the reliability of the data. In this study, annotations regarding species identification were provided in the JL_FLORA.csv file as needed and feasible. Correct names were provided when misidentifications could be rectified based on arguments, such as apparent misidentification or revisions in later published literature based on specimen examination. For data where misidentification was suspected, a taxonomic note was added in the JL_FLORA.csv file if corresponding literature was available. It is essential to note that these corrections and annotations pertaining to individual taxonomic issues could not be exhaustive. In future updates, species data will undergo revisions to enhance the database’s reliability and value, incorporating the latest information from literature. Users are advised to carefully select data that ensures sufficient accuracy and reliability for their specific analytical objectives.
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| Step 4: |
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Description:
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Data processing - Inclusion of aquatic species information
The JL_SPECIES.csv file contains species that are not limited to aquatic plants, as all plant occurrences were extracted from the literature. Therefore, ecological categories were included in the JL_SPECIES.csv file to identify aquatic species, according to the checklist of wetland plants in Japan (Shutoh et al., 2019b). Shutoh et al. (2019b) defined the four categories based on growth forms and habitats of species and assessed these categories to each of the 4,351 species of vascular plants in Japan: “Aquatic-1,” “Aquatic-2,” “Hygrophytic,” and “NonWet” (Table 3). The first two categories contain aquatic plants, including submerged, floating, floating-leaved, and emergent plants (Table 3; e.g., Kadono, 2014; Sculthope, 1967). The categorization of species listed by Kadono (2014) but notcovered by Shutoh et al. (2019b) was also assessed in the present study. Algal species in the JL_SPECIES.csv file were classified as “Aquatic-1” because they solely inhabit aquatic environments. For unidentified taxa, if a higher taxon included only species categorized as “Aquatic-1,” “Aquatic-2,” or “Hygrophytic,” the corresponding category was assigned. For example, Nymphaea sp., Potamogeton sp., and Ranunculus subgen. Batrachium sp. were assigned to “Aquatic-1,” Typha sp. was assigned to “Aquatic-2,” and Utricularia sp. was assigned to “Aquatic-1” and “Hygrophytic.” The summary of the number of taxa and occurrence records by ecological category is shown in Table 3.
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| Step 5: |
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Description:
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Data processing - Inclusion of native/alien species information
The JL_SPECIES.csv file includes information on whether a species is native or alien to Japan, based on the resources of Shimizu (2003), Yonekura and Kajita (2003–) (YList), and Kadono (2014). In cases of disagreement among these sources, information on native/alien species was determined based on the most recently published source. Regarding unidentified taxa and algae, this information was not provided owing to insufficient data. The summary of the number of taxa and occurrence records by native/alien is shown in Table 4.
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Data Set Usage Rights
| This dataset is provided under the Creative Commons Attribution 4.0 International License(CC BY-NC 4.0). |
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