Avian diversity changes in traditional agricultural landscapes of Japan over ten years
Data files
Apr 03, 2025 version files 575.44 KB
-
Dataset_Birds_Satoyama.xlsx
566.37 KB
-
README.md
9.07 KB
Abstract
Agricultural intensification is a leading cause of biodiversity loss worldwide. However, the traditional agroecosystems are often associated with high avian diversity because of their landscape heterogeneity offering available niches to different bird species. Here, we focused on the temporal changes in taxonomic, functional, and phylogenetic diversity of avian communities from Satoyama traditional agricultural landscapes of Japan. We found significant temporal trends (e.g., increasing) in overall species richness, forest specialist species richness, phylogenetic diversity and phylogenetic relatedness within avian assemblages, regardless of the land use composition surrounding the sites. The simultaneous increase in species richness and phylogenetic relatedness could highlight a process of biotic homogenization, typical of anthropized environments. Avian diversity was also significantly affected by the proportion of water bodies (e.g., increasing functional richness and dispersion, but decreasing functional evenness or redundancy) and other land use types (e.g., a negative association between species richness and the proportion of fields). The proportion of paddy fields affected each type of bird richness differently: inverse u-shape for forest generalists, negative for forest specialists species, and positive for open land specialists. When assessing the temporal stability of bird community composition, we found that such stability was significantly correlated to the proportion of grasslands, waterbodies and urban landscapes. Specifically, avian communities surrounded by grasslands were characterized by higher species replacement over time. Additionally, very low or very high proportions of urban landscapes were associated with a relative instability of bird community composition. Our findings support the hypothesis that traditional farming systems represent valuable landscapes supporting avian diversity. However, the relative composition of land use types plays a crucial role in shaping different components of taxonomic, functional and phylogenetic diversity in bird assemblages, as well as their temporal stability.
Sheet 1 (e.g., “dataset”)
Metadata
Variable Detail
site.year Code identification of the site concatenated with year of survey
site Code identification of the site
year Year of survey
Falco_amurensis No. individuals
Synthliboramphus_antiquus No. individuals
Pericrocotus_divaricatus No. individuals
Muscicapa_dauurica No. individuals
Delichon_dasypus No. individuals
Leucosticte_arctoa No. individuals
Urosphena_squameiceps No. individuals
Cyanopica_cyanus No. individuals
Hirundo_rustica No. individuals
Milvus_migrans No. individuals
Dryocopus_martius No. individuals
Acrocephalus_bistrigiceps No. individuals
Nycticorax_nycticorax No. individuals
Emberiza_spodocephala No. individuals
Larus_crassirostris No. individuals
Monticola_solitarius No. individuals
Cyanoptila_cyanomelana No. individuals
Fringilla_montifringilla No. individuals
Cinclus_pallasii No. individuals
Lanius_cristatus No. individuals
Rallus_indicus No. individuals
Hypsipetes_amaurotis No. individuals
Turdus_chrysolaus No. individuals
Lanius_bucephalus No. individuals
Corvus_corone No. individuals
Agropsar_philippensis No. individuals
Emberiza_fucata No. individuals
Periparus_ater No. individuals
Cuculus_canorus No. individuals
Tringa_nebularia No. individuals
Falco_tinnunculus No. individuals
Alcedo_atthis No. individuals
Gallinula_chloropus No. individuals
Tringa_totanus No. individuals
Emberiza_schoeniclus No. individuals
Actitis_hypoleucos No. individuals
Gallinago_gallinago No. individuals
Syrmaticus_soemmerringii No. individuals
Pernis_ptilorhynchus No. individuals
Megaceryle_lugubris No. individuals
Muscicapa_sibirica No. individuals
Phoenicurus_auroreus No. individuals
Turdus_eunomus No. individuals
Buteo_japonicus No. individuals
Bubulcus_coromandus No. individuals
Phylloscopus_coronatus No. individuals
Circus_spilonotus No. individuals
Anas_zonorhyncha No. individuals
Pyrrhula_pyrrhula No. individuals
Fulica_atra No. individuals
Garrulus_glandarius No. individuals
Sitta_europaea No. individuals
Spinus_spinus No. individuals
Alauda_arvensis No. individuals
Accipiter_nisus No. individuals
Anas_crecca No. individuals
Passer_montanus No. individuals
Certhia_familiaris No. individuals
Mareca_penelope No. individuals
Scolopax_rusticola No. individuals
Troglodytes_troglodytes No. individuals
Jynx_torquilla No. individuals
Turdus_obscurus No. individuals
Pitta_nympha No. individuals
Mareca_falcata No. individuals
Regulus_regulus No. individuals
Phalacrocorax_carbo No. individuals
Ardea_alba No. individuals
Dendrocopos_major No. individuals
Aythya_marila No. individuals
Phasianus_versicolor No. individuals
Tringa_ochropus No. individuals
Emberiza_variabilis No. individuals
Ardea_cinerea No. individuals
Caprimulgus_jotaka No. individuals
Pluvialis_squatarola No. individuals
Motacilla_cinerea No. individuals
Chloris_sinica No. individuals
Butastur_indicus No. individuals
Vanellus_cinereus No. individuals
Picus_canus No. individuals
Muscicapa_griseisticta No. individuals
Tringa_brevipes No. individuals
Coccothraustes_coccothraustes No. individuals
Cuculus_saturatus No. individuals
Apus_nipalensis No. individuals
Ardea_intermedia No. individuals
Prunella_rubida No. individuals
Horornis_diphone No. individuals
Phalacrocorax_capillatus No. individuals
Picus_awokera No. individuals
Eophona_personata No. individuals
Phylloscopus_xanthodryas No. individuals
Terpsiphone_atrocaudata No. individuals
Yungipicus_kizuki No. individuals
Larvivora_akahige No. individuals
Accipiter_gularis No. individuals
Turdus_cardis No. individuals
Parus_minor No. individuals
Motacilla_grandis No. individuals
Bombycilla_japonica No. individuals
Zosterops_japonicus No. individuals
Columba_janthina No. individuals
Charadrius_alexandrinus No. individuals
Locustella_lanceolata No. individuals
Corvus_macrorhynchos No. individuals
Gallinago_hardwickii No. individuals
Cuculus_poliocephalus No. individuals
Dryobates_minor No. individuals
Egretta_garzetta No. individuals
Tachybaptus_ruficollis No. individuals
Charadrius_dubius No. individuals
Sternula_albifrons No. individuals
Charadrius_placidus No. individuals
Carpodacus_sibiricus No. individuals
Aegithalos_caudatus No. individuals
Hierococcyx_fugax No. individuals
Anas_platyrhynchos No. individuals
Aix_galericulata No. individuals
Poecile_palustris No. individuals
Emberiza_cioides No. individuals
Larus_canus No. individuals
Helopsaltes_ochotensis No. individuals
Ficedula_mugimaki No. individuals
Ficedula_narcissina No. individuals
Ninox_japonica No. individuals
Accipiter_gentilis No. individuals
Anas_acuta No. individuals
Spatula_clypeata No. individuals
Anthus_hodgsoni No. individuals
Eurystomus_orientalis No. individuals
Acrocephalus_orientalis No. individuals
Otus_sunia No. individuals
Streptopelia_orientalis No. individuals
Egretta_sacra No. individuals
Apus_pacificus No. individuals
Turdus_pallidus No. individuals
Falco_peregrinus No. individuals
Loxia_curvirostra No. individuals
Tarsiger_cyanurus No. individuals
Calidris_ruficollis No. individuals
Cecropis_daurica No. individuals
Halcyon_coromanda No. individuals
Arenaria_interpres No. individuals
Porzana_fusca No. individuals
Passer_cinnamomeus No. individuals
Emberiza_rustica No. individuals
Helopsaltes_amnicola No. individuals
Phylloscopus_borealoides No. individuals
Riparia_riparia No. individuals
Larvivora_cyane No. individuals
Calliope_calliope No. individuals
Geokichla_sibirica No. individuals
Larus_schistisagus No. individuals
Tringa_erythropus No. individuals
Saxicola_stejnegeri No. individuals
Haliaeetus_pelagicus No. individuals
Butorides_striata No. individuals
Uria_lomvia No. individuals
Lanius_tigrinus No. individuals
Aythya_fuligula No. individuals
Strix_uralensis No. individuals
Sittiparus_varius No. individuals
Larus_vegae No. individuals
Anthus_spinoletta No. individuals
Pandion_haliaetus No. individuals
Numenius_phaeopus No. individuals
Treron_formosae No. individuals
Motacilla_alba No. individuals
Dendrocopos_leucotos No. individuals
Treron_sieboldii No. individuals
Spodiopsar_cineraceus No. individuals
Zoothera_aurea No. individuals
Haliaeetus_albicilla No. individuals
Hirundapus_caudacutus No. individuals
Poecile_montanus No. individuals
Tringa_glareola No. individuals
Emberiza_sulphurata No. individuals
Cisticola_juncidis No. individuals
TotalAbundance Sum all individuals
SR Species richness (e.g., sum of number of species)
Natural.grassland Percentage of such type of land use in 1-km buffer
Secondary.grassland Percentage of such type of land use in 1-km buffer
Artificial.grassland Percentage of such type of land use in 1-km buffer
Other.natural.grassland Percentage of such type of land use in 1-km buffer
Natural.forest Percentage of such type of land use in 1-km buffer
Secondary.forest Percentage of such type of land use in 1-km buffer
Planted.forest Percentage of such type of land use in 1-km buffer
Other.forests Percentage of such type of land use in 1-km buffer
Wetland Percentage of such type of land use in 1-km buffer
Shore Percentage of such type of land use in 1-km buffer
Unique.substrate Percentage of such type of land use in 1-km buffer
Paddy.field Percentage of such type of land use in 1-km buffer
Field Percentage of such type of land use in 1-km buffer
Other.fields Percentage of such type of land use in 1-km buffer
Urban.and.residential.district Percentage of such type of land use in 1-km buffer
Open.water Percentage of such type of land use in 1-km buffer
FRic Functional richness (Villéger et al. 2008)
FEve Functional evenness (Villéger et al. 2008)
FDiv Functional divergence (Villéger et al. 2008)
FDis Functional dispersion (Villéger et al. 2008)
RaoQ Rao’s Q diversity index (e.g., https://doi.org/10.1016/j.ecolind.2016.07.039)
PD Phylogenetic diversity (Faith 1992, Faith and Baker 2007, Tucker et al. 2016)
PSVs Phylogenetic species variability or relatedness (PSV) (Helmus et al., 2007)
SR_forest_generalist Number of species classified by using this type of habitat (Katayama et al. 2024)
SR_forest_specialists Number of species classified by using this type of habitat (Katayama et al. 2024)
SR_open_land_specialist Number of species classified by using this type of habitat (Katayama et al. 2024)
SR_other Number of species classified by using this type of habitat (Katayama et al. 2024)
Sheet 2 (e.g., “species x habitat type”)
Metadata
Variable Detail
N Number of species (as ordered in the dataset)
Species Scientific name
English name English name
Observations Number of sampled sites where the species was observed during all surveys
Frequency Frequency of the species concerning all sampled sites during all surveys (e.g., Observations * 100 / Total sampled sites)
Habitat type in Japan (species classified by habitat guild and specialization as forest specialists, forest generalists, open land specialists and species richness of other species) (from Katayama et al. 2024) Class