{"help":"Return the metadata of a dataset (package) and its resources. :param id: the id or name of the dataset :type id: string","success":true,"result":[{"id":"aed6ee30-32f0-4feb-8f7d-97311cedb0cf","name":"redband-trout-whole-genome-resequencing","title":"Redband trout whole genome resequencing","author":"Kimberly Andrews","author_email":"kimberlya@uidaho.edu","maintainer":"RCDS Data Repository","maintainer_email":"rcds-web@uidaho.edu","notes":"\u003Cp\u003EWhole genome resequencing identifies local adaptation associated with environmental variation for redband trout\u003C\/p\u003E\n\u003Cp\u003E\u003Cstrong\u003EAbstract\u003C\/strong\u003E\u003Cbr \/\u003E\nAquatic ectotherms are predicted to harbour genomic signals of local adaptation resulting from selective pressures driven by the strong influence of climate conditions on body temperature. We investigated local adaptation in redband trout (Oncorhynchus mykiss gairdneri) using genome scans for 547 samples from 11 populations across a wide range of habitats and thermal gradients in the interior Columbia River. We estimated allele frequencies for millions of single nucleotide polymorphism loci (SNPs) across populations using low-coverage whole genome resequencing, and used population structure outlier analyses to identify genomic regions under divergent selection between populations. Twelve genomic regions showed signatures of local adaptation, including two regions associated with genes known to influence migration and developmental timing in salmonids (GREB1L, ROCK1, SIX6). Genotype\u2013environment association analyses indicated that diurnal temperature variation was a strong driver of local adaptation, with signatures of selection driven primarily by divergence of two populations in the northern extreme of the subspecies range. We also found evidence for adaptive differences between high-elevation desert vs. montane habitats at a smaller geographical scale. Finally, we estimated vulnerability of redband trout to future climate change using ecological niche modelling and genetic offset analyses under two climate change scenarios. These analyses predicted substantial habitat loss and strong genetic shifts necessary for adaptation to future habitats, with the greatest vulnerability predicted for high-elevation desert populations. Our results provide new insight into the complexity of local adaptation in salmonids, and important predictions regarding future responses of redband trout to climate change.\u003C\/p\u003E\n\u003Cp\u003E\u003Cstrong\u003EData Use\u003C\/strong\u003E\u003Cbr \/\u003E\n\u003Cem\u003ELicense\u003C\/em\u003E\u003Cbr \/\u003E\nCreative Commons Public Domain Dedication and Certification (\u003Ca href=\u0022https:\/\/creativecommons.org\/licenses\/publicdomain\/\u0022\u003ECC-PDDC\u003C\/a\u003E)\u003Cbr \/\u003E\n\u003Cem\u003ERecommended Citation\u003C\/em\u003E\u003Cbr \/\u003E\nAndrews K. 2022. Redband trout whole genome resequencing [Dataset]. National Center for Biotechnology Information. \u003Ca href=\u0022https:\/\/www.ncbi.nlm.nih.gov\/bioproject\/PRJNA900579\u0022\u003Ehttps:\/\/www.ncbi.nlm.nih.gov\/bioproject\/PRJNA900579\u003C\/a\u003E\u003C\/p\u003E\n\u003Cp\u003E\u003Cstrong\u003EFunding\u003C\/strong\u003E\u003Cbr \/\u003E\nUS National Science Foundation and Idaho EPSCoR: OIA-1757324\u003Cbr \/\u003E\nNational Institute of General Medical Sciences: P30 GM103324\u003C\/p\u003E\n","url":"https:\/\/dkan.nkn.uidaho.edu\/dataset\/redband-trout-whole-genome-resequencing","state":"Active","log_message":"Edited by awchild.","private":true,"revision_timestamp":"Wed, 09\/06\/2023 - 12:29","metadata_created":"Thu, 03\/23\/2023 - 12:00","metadata_modified":"Wed, 09\/06\/2023 - 12:29","creator_user_id":"6cc16f2c-77c2-4d12-ac06-56bbb86b535b","type":"Dataset","resources":[{"id":"8d7039cd-e4f6-4af5-988a-84bbc3c2c089","revision_id":"","url":"https:\/\/www.ncbi.nlm.nih.gov\/bioproject\/PRJNA900579","description":"","format":"html","state":"Active","revision_timestamp":"Wed, 09\/06\/2023 - 12:15","name":"Data Access via NCBI | Redband trout whole genome resequencing","mimetype":"html","size":"","created":"Thu, 03\/23\/2023 - 12:00","resource_group_id":"e696b239-9ecb-412e-b032-03a75b2b9fd6","last_modified":"Date changed Wed, 09\/06\/2023 - 12:15"}],"tags":[{"id":"5f859265-7d19-47f5-a15e-0e22846d565a","vocabulary_id":"2","name":"adaptation"},{"id":"08f00aa6-dd77-4923-a661-61971a7f4303","vocabulary_id":"2","name":"adaptive capacity"},{"id":"38be2134-64e3-4400-a5dc-15ebe508077e","vocabulary_id":"2","name":"adaptive potential"},{"id":"3c4b7b04-c8c8-46c4-bc38-4a5ad5c6e57a","vocabulary_id":"2","name":"climate change"},{"id":"ba8961b1-13b9-4e04-bffe-42afec4c7541","vocabulary_id":"2","name":"disturbance"},{"id":"425f965a-f839-486d-be20-95827298c8c0","vocabulary_id":"2","name":"ecology"},{"id":"4ff8f12f-597f-460d-98ea-6650f2124e30","vocabulary_id":"2","name":"environmental change"},{"id":"87ac0d6d-729d-48c5-9f37-a8a40f41001c","vocabulary_id":"2","name":"gene\/genome\/genotype-environment interaction (GxE)"},{"id":"9d10045c-9469-4162-99d1-4a4bf8a3c1f0","vocabulary_id":"2","name":"genomics"},{"id":"3e857422-f378-4e8a-9318-7e8c1f8b24e6","vocabulary_id":"2","name":"legacy data"},{"id":"3bbad4f9-7651-4bf2-aacd-d11b259f3642","vocabulary_id":"2","name":"Oncorhynchus mykiss gairdneri"},{"id":"36a2c71f-ca58-468c-8c5d-ea3b9e8510c8","vocabulary_id":"2","name":"Redband Trout"},{"id":"29b6a6e9-415d-484b-bef0-f7a115089f27","vocabulary_id":"2","name":"developmental timing"},{"id":"ae5a6efd-3cc4-4833-bc42-e02013c3573c","vocabulary_id":"2","name":"ecological niche modeling"},{"id":"d354b33d-c08f-48f0-af84-e9be40fd67f8","vocabulary_id":"2","name":"genome scan"},{"id":"3d599aa2-96d4-499b-97e9-5ada3e064631","vocabulary_id":"2","name":"genotype-enviornment association (GEA)"},{"id":"090014f0-ef39-4ddd-9fdd-ba889885b373","vocabulary_id":"2","name":"thermal gradient"}],"groups":[{"description":"\u003Cp\u003EThe primary objective of Idaho EPSCoR is to stimulate research in niche areas that can become fully competitive in the disciplinary and multidisciplinary research programs of the National Science Foundation and other relevant agencies. Idaho EPSCoR provides support for sustainable increases in Research and Development capacity and advances science and engineering capabilities within the state. \u003C\/p\u003E\n\u003Cp\u003EVisit them at \u003Ca href=\u0022https:\/\/www.idahoepscor.org\u0022\u003Ehttps:\/\/www.idahoepscor.org\u003C\/a\u003E\u003C\/p\u003E\n","id":"e696b239-9ecb-412e-b032-03a75b2b9fd6","image_display_url":"https:\/\/dkan.nkn.uidaho.edu\/sites\/default\/files\/Idaho_epscor_logo_no_white_background.png","title":"Idaho EPSCoR","name":"group\/idaho-epscor"},{"description":"\u003Cp\u003EGEM3 is an NSF EPSCoR research program seeking to understand how genetic diversity and phenotypic plasticity affect species response to environmental change, shaping both population response and adaptive capacity.\u003C\/p\u003E\n\u003Cp\u003EVisit them at: \u003Ca href=\u0022https:\/\/www.idahogem3.org\u0022\u003Ehttps:\/\/www.idahogem3.org\u003C\/a\u003E\u003C\/p\u003E\n","id":"1812a312-11a4-492d-960b-9a78b4abfe0c","image_display_url":"https:\/\/dkan.nkn.uidaho.edu\/sites\/default\/files\/GEM3_nov5_logo.png","title":"EPSCoR GEM3","name":"group\/epscor-gem3"}]}]} Error | RCDS Data Repository

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