RRC ID 83034
Author Yujing Yan, Bin Shao, Charles C. Davis
Title A generative deep learning approach for global species distribution prediction
Journal bioRxiv
Abstract Anthropogenic pressures on biodiversity necessitate efficient and highly scalable methods to predict global species distributions. Current species distribution models (SDMs) face limitations with large-scale datasets, complex interspecies interactions, and data quality. Here, we introduce EcoVAE, a framework of autoencoder-based generative models trained separately on nearly 124 million georeferenced occurrences from taxa including plants, butterflies and mammals, to predict their global distributions at both genus and species levels. EcoVAE achieves high precision and speed, captures underlying distribution patterns through unsupervised learning, and reveals interspecies interactions viain silicoperturbation analyses. Additionally, it evaluates global sampling efforts and interpolates distributions without relying on environmental variables, offering new applications for biodiversity exploration and monitoring.
Published 2024-12-16
DOI 10.1101/2024.12.10.627845
Description J-OBIS data were referenced.
Resource
GBIF Herbarium Specimens of Bonin and Ryukyu Islands Fern (Pteridophyta) specimens of Toyama Science Museum Insect specimens of Natural History Museum, Kishiwada City Butterfly Specimens of Yamaguchi Prefectural Yamaguchi Museum Insect specimens of Bihoro Museum Insect specimens of Tochigi Prefectural Museum Plant specimens of Ishikawa Museum of Natural History Database of Aquatic Macrophytes in Japanese lakes Insect Specimens of Gunma Insect World The Suguru Igarashi Insect Collection (Lepidoptera: Pieridae) of The University Museum, The University of Tokyo Bryophyte specimens of Kanagawa Prefectural Museum of Natural History Bryophyte Specimens of Ishikawa Museum of Natural History (ISKW) A crowdsourcing approach to collecting photo-based insect and plant observation records Gunma Museum of Natural History, Bryophyta Specimen Insect specimens of Himeji City Science Museum Insect specimens Kubo collection of Takatsuki Nature Museum (Aquapia Akutagawa) Vertebrate fossil collection of National Museum of Nature and Science Plant Specimens of The Cattle Museum Hemiptera (Homoptera) collection of National Museum of Nature and Science Database of Japanese semi-natural grassland flora The Masayo Kato Insect Collection (Lepidoptera: Rhopalocera) of The University Museum, The University of Tokyo Plant Specimen Database of Tama Forest Science Garden, Forestry and Forest Products Research Institute, Japan Mammal specimens of Oiso Municipal Museum Long-term fauna and flora records of the experimental forests of the Forest Research Station of Hokkaido University, Japan The Insect Collection of Prof. Chûjirô Sasaki and associated researchers, The University Museum, The University of Tokyo. Vascular plant specimens of Sugadaira Research Station, Mountain Science Center, University of Tsukuba The Masao Oita Insect Collection of The University Museum, The University of Tokyo The 2nd and 3rd National Survey on the Natural Environment: Vegetation Survey (common species) The 2nd and 3rd National Survey on the Natural Environment: Vegetation Survey (rare species) Insect specimens of Obihiro Centennial City Museum Marine Biological Sample Database, JAMSTEC Spermatophyte collection of Himeji City Science Museum Plant specimens of Otaru Museum Kelp Dataset Plant specimens of Toyota City Nature Sanctuary The Shigeru Eda Insect Collection of The University Museum, The University of Tokyo Insect specimen database of Kanagawa Prefectural Museum of Natural History Crustacean collection of the National Museum of Nature and Science The south coast survey of Hatakejima Islands from 1969 Captive Primate Specimens of Japan Monkey Centre Mammal specimens of Okinawa Prefectural Museum & Art Museum Survey data of seagrass beds on the Monitoring sites 1000 project, BDCJ Plant specimens of Komatsu City Museum Ferns and Lycophytes Specimens of Kawasaki Municipal Science Museum Nagoya-Mammals Fossil specimens of Bihoro Museum The Suguru Igarashi Insect Collection (Lepidoptera: Papilionidae) of The University Museum, The University of Tokyo Tertiary vertebrate collection at Osama Museum of Natural History Bryophyte specimens of Toyama Science Museum Insect specimens of Sugadaira Montane Research Center, University of Tsukuba Insect specimens of Yonezawa Insectarium Flora of Japan Specimen Database Occurrence data of woody plants in the Ginkakuzi-san National Forest Cetacean Stranding Data in Hokkaido Mammal collection of Biodiversity Center of Japan, Ministry of the Environment (BDCJ) Insect specimens of Okinawa Prefectural Museum & Art Museum Paleobotany collection of National Museum of Nature and Science Specimen-based records of geometrid, pyralid, and crambid moths (Lepidoptera) with location information from the collection of Dr. Hiroshi Inoue Mammalian Specimens of the Yamagata Prefectural Museum The 6-7th National Survey on the Natural Environment: Vegetation Survey Mammal assemblages recorded by camera traps inside and outside the evacuation zone of the Fukushima Daiichi Nuclear Power Plant accident Herbaceous and arboreous plants list on the Komaba Campus of University of Tokyo, Japan Vascular Plant Specimens of Yamagata Prefectural Museum Nagoya-Plants Mammal specimens of Ryukyu University Museum (Fujukan) Entomological Specimens of Museum of Nature and Human Activities, Hyogo Pref., Japan Insect specimens of Sagamihara City Museum Morihiro Tozu Specimens of Saga Prefectural Space and Science Museum Gunma Museum of Natural History, Vertebrate Fossil Specimen Vascular plant specimens of Omachi Alpine Museum Monitoring Sites 1000 Satoyama Mammals Herbarium of Shinshu University Lepidoptera collection of National Museum of Nature and Science Insects Specimens of Kagoshima Prefectural Museum Plant specimens of Parthenon Tama Museum (PTHM) Mammal specimens of Obihiro Centennial City Museum Plant specimens of Obihiro Centennial City Museum Vascular plant specimens of Nagano Environmental Conservation Research Institute, Nagano Prefecture Plant Observation Records of Japan Mammal specimens of Saitama Museum of Natural History Insect collection of Biodiversity Center of Japan, Ministry of the Environment Moss specimens of Kushiro City Museum Survey data of rocky shores on the Monitoring sites 1000 project, BDCJ Vascular plant specimens of The Shirakami Research Center for Environmental Sciences, Hirosaki University The Suguru Igarashi Insect Collection (Lepidoptera: Hesperiidae) of The University Museum, The University of Tokyo The Keiichi Omoto Butterfly Collection(Papilionidae), The University Museum, The University of Tokyo JODC Dataset Insect specimens of Natural Museum of Geihoku Mammal specimens of Toyota City Nature Sanctuary Vertebrate specimens of Kumamoto City Museum Insect specimens of Kushiro City Museum RIKEN BioResource Center, Experimental Animal Division Tree survey in the tropical forest of Pasoh Forest Reserve, Malaysia from 2016 to 2018 Vascular Plants Collection of National Museum of Nature and Science Sakurai Insect Specimens Collection of Tamarokuto Science Center Insect specimens of Mie Prefectural Museum Fossil specimens in the Museum of Nature and Human Activities, Hyogo Prefecture, Japan Lepidoptera specimen database of Japan Bryophyte specimens of Iwate Prefectural Museum Vascular plant specimens of Akita Prefectural Museum Akita Prefectural Museum, Insect Collection Insect Specimens Deposited in Saga Prefectural Space and Science Museum, JAPAN Herbarium, University Archives and Collections, Fukushima University, Japan (FKSE) Plant specimens of Toyota City Nature Sanctuary (from non-museum circle) Bryophytes specimens of Okinawa Prefectural Museum & Art Museum Angiospermatatophytina Collection of Saitama Museum of Natural History Brown algae specimens of Komatsu City Museum Insect Collection of Yokosuka City Museum Herbarium Specimens of The Kagoshima University Museum (KAG) Vascular plant specimens of Toyama Science Museum Echigo-Matsunoyama Museum of Natural Science, Usuke Shiga butterfly collection Yasuhiro Fudouji Specimens of Saga Prefectural Space and Science Museum Insect specimens of Otaru Museum AIS Wildtype Populations of Arabidopsis Plankton&BenthosResearch Insect specimens of Kaizuka City Museum of Natural History Insect specimens of Oiso Municipal Museum Plant specimens of Oiso Municipal Museum Insect specimens of Rikuzen-Takata City Museum Herbarium of Hokkaido University Museum (SAPS) Bryophyte Collection of Natural History Museum and Institute, Chiba Insect specimens of Iwate Prefectural Museum Vascular Plant Collection of Natural History Museum and Institute, Chiba Bryophytes specimens of Akita Prefectural Museum Herbarium Specimens of Museum of Nature and Human Activities, Hyogo Pref., Japan Insect Collection of Saitama Museum of Natural History Mammalians Specimens of Akita Prefectural Museum Japanese Woody Plants Pteridophyta specimens of Iwate Prefectural Museum Insect specimens of Toyota City Nature Sanctuary Ibaraki Nature Museum, Arthropoda collection Ibaraki Nature Museum, Mammals collection Ibaraki Nature Museum, Bryophyta collection Survey data of algal beds on the Monitoring sites 1000 project, BDCJ Ibaraki Nature Museum, Fungi collection Ibaraki Nature Museum, Algae collection Asia-Pacific Dataset Ibaraki Nature Museum, Vascular Plants collection Vascular plant collection of The University Museum, The University of Tokyo The Suguru Igarashi Insect Collection (Lepidoptera: Lycaenidae) of The University Museum, The University of Tokyo Vertebrate specimens of Iwate Prefectural Museum Kitami Region Museum of Science History and Art(KIRM) Vascular plant specimens of the herbarium of the Tohoku University (TUS) Fish Collection of Yokosuka City Museum Fish Collection of Hokkaido University Spermatophyta Specimens of Kawasaki Municipal Science Museum Bryophyte specimens of National Museum of Nature and Science (TNS) Macroalgal collection of National Museum of Nature and Science (TNS) Botanical collection of Gifu Prefecture Museum Vascular plant specimens of National Museum of Nature and Science (TNS) Insect specimens of Kashihara City Museum of Insect Plankton image dataset from a cabled observatory system (JEDI System/OCEANS) deployed at coastal area of Oshima island, Tokyo, Japan Plant Specimens of Kurashiki Museum of Natural History Herbarium Specimens of Tokushima Prefectural Museum, Japan Insect Specimen Database of Fukui City Museum of Natural History Occurrence data of seagrasses in Southeast Asia extracted from literature Insect specimens of Omogo Mountain Museum Osaka Prefectural Minoh Park Insects Museum Simultaneous surveys of littoral organisms in Osaka Bay Insect specimens of Komatsu City Museum Insect species recorded in sugarcane fields of Khon Kaen Province, Thailand, over three seasons in 2012 A Specimen List of Hymenophyllaceae of Seram and Ambon collected on Indonesian-Japanese botanical expeditions 1983–1986 Bryophyte specimens database of Mr. Tsutomu Kodama collection Mammal collection of National Museum of Nature and Science Insect specimens of Toyama Science Museum Plantae collection of Hokkaido Museum Spermatophyta specimens of Iwate Prefectural Museum Plant distribution data with photograph Vascular Plants Collection of Sagamihara City Museum Insect Collection in Shiojiri City Museum of Natural History Plant specimens in the Museum of Nature and Human Activities, Hyogo Prefecture, Japan Insect specimens in the Museum of Nature and Human Activities, Hyogo Prefecture, Japan Insect Specimens of Kitami Region Museum of Science History and Art Mammals specimens of Taga Town Museum, Shiga Pref., Japan Insect specimens of Taga Town Museum, Shiga Pref., Japan Lepidoptera specimen database of Osaka Museum of Natural History Plant specimens deposited in Osaka Museum of Natural History, Japan Insect collection of Itami City Museum of Insects Vascular Plant Specimens of Kochi Prefectural Makino Botanical Garden Zoological specimens of Gifu Prefectural Museum Plant specimens of Kiritappu Wetland Center Insecta specimens of Okutama Visitor Center, Tokyo Invertebrate fossil collection of National Museum of Nature and Science Insecta Specimens of Kawasaki Municipal Science Museum Mammal specimens of Komatsu City Museum Mammal specimens of Kawasaki Municipal Science Museum Mammal specimens of Natural History Museum, Kishiwada City Coastal Ecosystem Monitoring in the Tsugaru strait side of Shimokita Insect specimens of Ryukyu University Museum (Fujukan) Vascular Plant Specimen database of Kanagawa Prefectural Museum of Natural History Mammal specimen database of Kanagawa Prefectural Museum of Natural History Insect specimen database of Atsugi City Museum Gunma Museum of Natural History, Vascular Plant Specimen Gunma Museum of Natural History, Insect Specimen Gunma Museum of Natural History, Mammal Specimen Insect Collection of Natural History Museum and Institute, Chiba Fungi specimen database of Kanagawa Prefectural Museum of Natural History Vascular plants collection of Hiratsuka City Museum Insecta collection of Museum of Natural and Environmental History, Shizuoka Vascular Plant Specimens of the URO Herbarium (Faculty of Education, University of the Ryukyus) Plant specimens of Kushiro City Museum Insect specimens of Nasunogahara Museum Mammal Specimens of The Cattle Museum Mammal specimens of Takatsuki Nature Museum (Aquapia Akutagawa) A dataset for vascular plant diversity monitoring for the natural World Heritage site on Amami-Oshima Island, Tokunoshima Island, and the northern Okinawa Island Bryophytes specimens of Mitake Visitor Center Fossil Specimens of Ibaraki Nature Museum Lepidopterous specimens of Yamagata Prefectural Museum Mollusca specimens of Manazuru Shell Museum Fossil Specimens of Komatsu City Museum Vascular Plant Specimens of the RYU Herbarium (Faculty of Science, University of the Ryukyus) Coleoptera collection of National Museum of Nature and Science Insect specimens of Tokushima Prefectural Museum Mammal specimens of Tochigi Prefectural Museum Insect specimens of Hokkaido University Forest monitoring data of 45 plots over the Japanese archipelago during the period of 1980-2021 Bryophyte specimens of Toyota City Nature Sanctuary (TCNS). Microbial Culture Collection, National Institute for Environmental Studies Plant specimens of Mie Prefectural Museum