{ "access": { "embargo": { "active": false, "reason": null }, "files": "public", "record": "public", "status": "open" }, "created": "2021-06-19T23:06:17.113856+00:00", "custom_fields": {}, "deletion_status": { "is_deleted": false, "status": "P" }, "files": { "count": 5, "enabled": true, "entries": { "ABC_inputfiles.zip": { "access": { "hidden": false }, "checksum": "md5:b63ca2e3a3f58cd3c02c5f5abe3b117d", "ext": "zip", "id": "9b3819ae-d115-461d-b15d-851e8d841f04", "key": "ABC_inputfiles.zip", "links": { "content": "https://zenodo.org/api/records/4995570/files/ABC_inputfiles.zip/content", "self": "https://zenodo.org/api/records/4995570/files/ABC_inputfiles.zip" }, "metadata": null, "mimetype": "application/zip", "size": 9378, "storage_class": "L" }, "ABC_scripts.zip": { "access": { "hidden": false }, "checksum": "md5:12b693eeaab21f8aad5f4900bec66e4b", "ext": "zip", "id": "fbdfc60b-84ac-48f7-a518-1f9e6af808b0", "key": "ABC_scripts.zip", "links": { "content": "https://zenodo.org/api/records/4995570/files/ABC_scripts.zip/content", "self": "https://zenodo.org/api/records/4995570/files/ABC_scripts.zip" }, "metadata": null, "mimetype": "application/zip", "size": 3410, "storage_class": "L" }, "ABC_summarystatistics.zip": { "access": { "hidden": false }, "checksum": "md5:624fa603a7f5a53d9b13c0d2e753a6e6", "ext": "zip", "id": "83523318-f2b8-4d99-b15a-40bdffb69029", "key": "ABC_summarystatistics.zip", "links": { "content": "https://zenodo.org/api/records/4995570/files/ABC_summarystatistics.zip/content", "self": "https://zenodo.org/api/records/4995570/files/ABC_summarystatistics.zip" }, "metadata": null, "mimetype": "application/zip", "size": 3268, "storage_class": "L" }, "Microsatellite_genotypes.zip": { "access": { "hidden": false }, "checksum": "md5:602d6b8c61cfef930db35c0aaecec7fb", "ext": "zip", "id": "ca00d406-11ac-4a0e-abf3-b1a9c83dbcaa", "key": "Microsatellite_genotypes.zip", "links": { "content": "https://zenodo.org/api/records/4995570/files/Microsatellite_genotypes.zip/content", "self": "https://zenodo.org/api/records/4995570/files/Microsatellite_genotypes.zip" }, "metadata": null, "mimetype": "application/zip", "size": 7595, "storage_class": "L" }, "Sequence_alignments.zip": { "access": { "hidden": false }, "checksum": "md5:6f7213a65f0c8744e0ad9654ba7797f7", "ext": "zip", "id": "689c56a3-a4dd-4a5f-b705-dd42dcc547dc", "key": "Sequence_alignments.zip", "links": { "content": "https://zenodo.org/api/records/4995570/files/Sequence_alignments.zip/content", "self": "https://zenodo.org/api/records/4995570/files/Sequence_alignments.zip" }, "metadata": null, "mimetype": "application/zip", "size": 22731, "storage_class": "L" } }, "order": [], "total_bytes": 46382 }, "id": "4995570", "is_draft": false, "is_published": true, "links": { "access": "https://zenodo.org/api/records/4995570/access", "access_grants": "https://zenodo.org/api/records/4995570/access/grants", "access_links": "https://zenodo.org/api/records/4995570/access/links", "access_request": "https://zenodo.org/api/records/4995570/access/request", "access_users": "https://zenodo.org/api/records/4995570/access/users", "archive": "https://zenodo.org/api/records/4995570/files-archive", "archive_media": "https://zenodo.org/api/records/4995570/media-files-archive", "communities": "https://zenodo.org/api/records/4995570/communities", "communities-suggestions": "https://zenodo.org/api/records/4995570/communities-suggestions", "doi": "https://doi.org/10.5061/dryad.1jv55", "draft": "https://zenodo.org/api/records/4995570/draft", "file_modification": "https://zenodo.org/api/records/4995570/file-modification", "files": "https://zenodo.org/api/records/4995570/files", "latest": "https://zenodo.org/api/records/4995570/versions/latest", "latest_html": "https://zenodo.org/records/4995570/latest", "media_files": "https://zenodo.org/api/records/4995570/media-files", "parent": "https://zenodo.org/api/records/4995569", "parent_html": "https://zenodo.org/records/4995569", "preview_html": "https://zenodo.org/records/4995570?preview=1", "quota_increase": "https://zenodo.org/api/records/4995570/quota-increase", "request_deletion": "https://zenodo.org/api/records/4995570/request-deletion", "requests": "https://zenodo.org/api/records/4995570/requests", "reserve_doi": "https://zenodo.org/api/records/4995570/draft/pids/doi", "self": "https://zenodo.org/api/records/4995570", "self_doi": "https://doi.org/10.5061/dryad.1jv55", "self_doi_html": "https://zenodo.org/doi/10.5061/dryad.1jv55", "self_html": "https://zenodo.org/records/4995570", "self_iiif_manifest": "https://zenodo.org/api/iiif/record:4995570/manifest", "self_iiif_sequence": "https://zenodo.org/api/iiif/record:4995570/sequence/default", "versions": "https://zenodo.org/api/records/4995570/versions" }, "media_files": { "count": 0, "enabled": false, "entries": {}, "order": [], "total_bytes": 0 }, "metadata": { "additional_descriptions": [ { "description": "
Sequence alignments
Fasta files containing alignments of all sequence loci.
Sequence_alignments.zip
Microsatellite genotypes
Text files containing tab-delimited tables of microsatellite genotypes (one individual per row).
Microsatellite_genotypes.zip
Summary statistics for ABC analysis
Text files containing summary statistics used in the ABC analysis.
ABC_summarystatistics.zip
Input files for ABC analysis
Input files used for ABC analysis with ABCtoolbox/fastsimcoal.
ABC_inputfiles.zip
Scripts for ABC analysis
Custom-made scripts used in the ABC analysis with ABCtoolbox/fastsimcoal.
ABC_scripts.zip
", "type": { "id": "notes", "title": { "de": "Anmerkungen", "en": "Notes" } } } ], "creators": [ { "affiliations": [ { "name": "University of Zurich" } ], "person_or_org": { "family_name": "Nater", "given_name": "Alexander", "name": "Nater, Alexander", "type": "personal" } }, { "affiliations": [ { "name": "University of Zurich" } ], "person_or_org": { "family_name": "Greminger", "given_name": "Maja P.", "name": "Greminger, Maja P.", "type": "personal" } }, { "affiliations": [ { "name": "University of Zurich" } ], "person_or_org": { "family_name": "Arora", "given_name": "Natasha", "name": "Arora, Natasha", "type": "personal" } }, { "affiliations": [ { "name": "University of Zurich" } ], "person_or_org": { "family_name": "van Schaik", "given_name": "Carel P.", "name": "van Schaik, Carel P.", "type": "personal" } }, { "affiliations": [ { "name": "Cardiff University" } ], "person_or_org": { "family_name": "Goossens", "given_name": "Benoit", "name": "Goossens, Benoit", "type": "personal" } }, { "affiliations": [ { "name": "Foundation for a Sustainable Ecosystem (YEL); Jl. Wahid Hasyim No. 51/74 Medan 20154 Indonesia*" } ], "person_or_org": { "family_name": "Singleton", "given_name": "Ian", "name": "Singleton, Ian", "type": "personal" } }, { "affiliations": [ { "name": "Biomedical Primate Research Centre" } ], "person_or_org": { "family_name": "Verschoor", "given_name": "Ernst J.", "name": "Verschoor, Ernst J.", "type": "personal" } }, { "affiliations": [ { "name": "University of Zurich" } ], "person_or_org": { "family_name": "Warren", "given_name": "Kristen S.", "name": "Warren, Kristen S.", "type": "personal" } }, { "affiliations": [ { "name": "University of Zurich" } ], "person_or_org": { "family_name": "Kr\u00fctzen", "given_name": "Michael", "name": "Kr\u00fctzen, Michael", "type": "personal" } }, { "affiliations": [ { "name": "Murdoch University" } ], "person_or_org": { "family_name": "Warren", "given_name": "Kristin S.", "name": "Warren, Kristin S.", "type": "personal" } } ], "description": "Investigating how different evolutionary forces have shaped patterns of DNA variation within and among species requires detailed knowledge of their demographic history. Orang-utans, whose distribution is currently restricted to the Southeast Asian islands of Borneo (Pongo pygmaeus) and Sumatra (Pongo abelii), have likely experienced a complex demographic history, influenced by recurrent changes in climate and sea levels, volcanic activities and anthropogenic pressures. Using the most extensive sample set of wild orang-utans to date, we employed an approximate Bayesian computation (ABC) approach to test the fit of 12 different demographic scenarios to the observed patterns of variation in autosomal, X-chromosomal, mitochondrial and Y-chromosomal markers. In the best-fitting model, Sumatran orang-utans exhibit a deep split of populations north and south of Lake Toba, probably caused by multiple eruptions of the Toba volcano. In addition, we found signals for a strong decline in all Sumatran populations ~24 ka, probably associated with hunting by human colonizers. In contrast, Bornean orang-utans experienced a severe bottleneck ~135 ka, followed by a population expansion and substructuring starting ~82 ka, which we link to an expansion from a glacial refugium. Therefore, we showed that orang-utans went through drastic changes in population size and connectedness, caused by the recurrent contraction and expansion of rainforest habitat during Pleistocene glaciations, and probably also by the impact of hunting by early humans. Our findings also emphasize the fact that important aspects of the evolutionary past of species with complex demographic histories might remain obscured when applying overly simplified models.", "locations": { "features": [ { "place": "Sundaland" }, { "place": "Southeast Asia" }, { "place": "Malaysia" }, { "place": "Indonesia" } ] }, "publication_date": "2014-12-03", "publisher": "Zenodo", "related_identifiers": [ { "identifier": "10.1111/mec.13027", "relation_type": { "id": "iscitedby", "title": { "de": "Wird zitiert von", "en": "Is cited by" } }, "scheme": "doi" } ], "resource_type": { "id": "dataset", "title": { "de": "Datensatz", "en": "Dataset" } }, "rights": [ { "description": { "en": "CC0 waives copyright interest in a work you've created and dedicates it to the world-wide public domain. Use CC0 to opt out of copyright entirely and ensure your work has the widest reach." }, "icon": "cc-cc0-icon", "id": "cc0-1.0", "props": { "scheme": "spdx", "url": "https://creativecommons.org/publicdomain/zero/1.0/legalcode" }, "title": { "en": "Creative Commons Zero v1.0 Universal" } } ], "subjects": [ { "subject": "Pongo abelii" }, { "subject": "Holocene" }, { "subject": "Pongo pygmaeus" } ], "title": "Data from: Reconstructing the demographic history of orang-utans using approximate Bayesian computation" }, "parent": { "access": { "owned_by": { "user": "90070" } }, "communities": { "default": "734b6452-1f40-4db0-b218-08ab1d568b7f", "entries": [ { "access": { "member_policy": "open", "members_visibility": "public", "record_submission_policy": "open", "review_policy": "open", "visibility": "public" }, "children": { "allow": false }, "created": "2020-02-04T14:03:17.992421+00:00", "custom_fields": {}, "deletion_status": { "is_deleted": false, "status": "P" }, "id": "734b6452-1f40-4db0-b218-08ab1d568b7f", "links": {}, "metadata": { "curation_policy": "

The Dryad collection in Zenodo contains datasets mirrored from the Dryad Digital Repository. If you want your dataset to appear here, submit it through https://datadryad.org. No other datasets will be accepted.

", "description": "Dryad is an international open-access repository of research data, especially data underlying scientific and medical publications. Dryad is a curated general-purpose repository that makes data discoverable, freely reusable, and citable.", "organizations": [ { "id": "00x6h5n95" } ], "page": "

Dryad is a community-governed open data publishing and curation repository. Through Dryad and Zenodo's partnership, Zenodo hosts a preservation copy of Dryad datasets, available through this Zenodo Community. For more information or to access the original published datasets, visit https://datadryad.org.

", "title": "Dryad", "type": { "id": "organization" }, "website": "https://datadryad.org" }, "revision_id": 3, "slug": "dryad", "updated": "2024-02-01T21:26:57.292847+00:00" } ], "ids": [ "734b6452-1f40-4db0-b218-08ab1d568b7f" ] }, "id": "4995569", "pids": {} }, "pids": { "doi": { "identifier": "10.5061/dryad.1jv55", "provider": "external" }, "oai": { "identifier": "oai:zenodo.org:4995570", "provider": "oai" } }, "revision_id": 3, "stats": { "all_versions": { "data_volume": 814842.0, "downloads": 84, "unique_downloads": 84, "unique_views": 115, "views": 116 }, "this_version": { "data_volume": 814842.0, "downloads": 84, "unique_downloads": 84, "unique_views": 115, "views": 116 } }, "status": "published", "swh": {}, "updated": "2022-05-31T02:53:48.071292+00:00", "versions": { "index": 1, "is_latest": true } }