DOI: 10.5061/dryad.02v6wwqf4
title: Avian diversity changes in traditional agricultural landscapes of Japan over ten years

description: 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.
description: # Avian diversity changes in traditional agricultural landscapes of Japan
 over ten years ### 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](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