Publicação
Searching for signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) using allele-environment association approaches
| Resumo: | In the current context of a global human-mediated environmental crisis, understanding which genes and mechanisms are responsible for adaptation to different climates will enable predictions on how organisms will respond to a rapidly changing world. This is particularly important for the honey bee, a key-stone species for ecosystem functioning and economy, which is facing increasing pressures from the effects of intensified land use, climate change, and the spread of pests and pathogens. In this study we used Illumina technology to sequence the whole genomes of 86 Iberian honey bees, collected across three longitudinal transects in the Iberian Peninsula. Then, we searched for signatures of selection using two different methods (LFMM and Samβada), which combine genetic and non-genetic (environmental) data. The LFMM approach identified 2193, 449 and 275 SNPs for FDR values of 0.05, 0.02, and 0.01, respectively. The environmental variables associated with the highest number of SNP outliers were precipitation, latitude and longitude. The LFMM findings were concordant with those obtained with Samβada. Gene ontology analyses show that clusters with higher score are related with immune system development and sensory organ development for the outlier genes associated with longitude. Precipitation is associated with genes related with biological regulation and sequence-specific DNA binding. This represents the most comprehensive study of positive selection that integrates genetic information, and environmental variables performed so far in Iberian honeybees. |
|---|---|
| Autores principais: | Henriques, Dora |
| Outros Autores: | Wallberg, Andreas; Chávez-Galarza, Julio; Neves, Cátia J.; Rufino, José; Costa, Filipe Oliveira; Webster, Matthew T.; Pinto, M. Alice |
| Ano: | 2016 |
| País: | Portugal |
| Tipo de documento: | documento de conferência |
| Tipo de acesso: | acesso aberto |
| Instituição associada: | Instituto Politécnico de Bragança |
| Idioma: | inglês |
| Origem: | Biblioteca Digital do IPB |
| _version_ | 1867173393144479744 |
|---|---|
| author | Henriques, Dora |
| author2 | Wallberg, Andreas Chávez-Galarza, Julio Neves, Cátia J. Rufino, José Costa, Filipe Oliveira Webster, Matthew T. Pinto, M. Alice |
| author2_role | author author author author author author author |
| author_facet | Henriques, Dora Wallberg, Andreas Chávez-Galarza, Julio Neves, Cátia J. Rufino, José Costa, Filipe Oliveira Webster, Matthew T. Pinto, M. Alice |
| author_role | author |
| contributor_name_str_mv | Biblioteca Digital do IPB |
| country_str | PT |
| creators_json_txt | [{\"Person.name\":\"Henriques, Dora\",\"Person.identifier.orcid\":\"0000-0001-7530-682X\"},{\"Person.name\":\"Wallberg, Andreas\"},{\"Person.name\":\"Chávez-Galarza, Julio\"},{\"Person.name\":\"Neves, Cátia J.\"},{\"Person.name\":\"Rufino, José\",\"Person.identifier.orcid\":\"0000-0002-1344-8264\"},{\"Person.name\":\"Costa, Filipe Oliveira\"},{\"Person.name\":\"Webster, Matthew T.\"},{\"Person.name\":\"Pinto, M. Alice\",\"Person.identifier.orcid\":\"0000-0001-9663-8399\"}] |
| datacite.contributors.contributor.contributorName.fl_str_mv | Biblioteca Digital do IPB |
| datacite.creators.creator.creatorName.fl_str_mv | Henriques, Dora Wallberg, Andreas Chávez-Galarza, Julio Neves, Cátia J. Rufino, José Costa, Filipe Oliveira Webster, Matthew T. Pinto, M. Alice |
| datacite.date.Accepted.fl_str_mv | 2016-01-01T00:00:00Z |
| datacite.date.available.fl_str_mv | 2018-03-28T09:16:01Z |
| datacite.date.embargoed.fl_str_mv | 2018-03-28T09:16:01Z |
| datacite.rights.fl_str_mv | http://purl.org/coar/access_right/c_abf2 |
| datacite.titles.title.fl_str_mv | Searching for signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) using allele-environment association approaches |
| dc.contributor.none.fl_str_mv | Biblioteca Digital do IPB |
| dc.creator.none.fl_str_mv | Henriques, Dora Wallberg, Andreas Chávez-Galarza, Julio Neves, Cátia J. Rufino, José Costa, Filipe Oliveira Webster, Matthew T. Pinto, M. Alice |
| dc.date.Accepted.fl_str_mv | 2016-01-01T00:00:00Z |
| dc.date.available.fl_str_mv | 2018-03-28T09:16:01Z |
| dc.date.embargoed.fl_str_mv | 2018-03-28T09:16:01Z |
| dc.format.none.fl_str_mv | application/pdf |
| dc.identifier.none.fl_str_mv | http://hdl.handle.net/10198/16602 |
| dc.language.none.fl_str_mv | eng |
| dc.publisher.none.fl_str_mv | Universidade do Porto |
| dc.rights.cclincense.fl_str_mv | http://creativecommons.org/licenses/by/4.0/ |
| dc.rights.none.fl_str_mv | http://purl.org/coar/access_right/c_abf2 |
| dc.title.fl_str_mv | Searching for signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) using allele-environment association approaches |
| dc.type.none.fl_str_mv | http://purl.org/coar/resource_type/c_c94f |
| description | In the current context of a global human-mediated environmental crisis, understanding which genes and mechanisms are responsible for adaptation to different climates will enable predictions on how organisms will respond to a rapidly changing world. This is particularly important for the honey bee, a key-stone species for ecosystem functioning and economy, which is facing increasing pressures from the effects of intensified land use, climate change, and the spread of pests and pathogens. In this study we used Illumina technology to sequence the whole genomes of 86 Iberian honey bees, collected across three longitudinal transects in the Iberian Peninsula. Then, we searched for signatures of selection using two different methods (LFMM and Samβada), which combine genetic and non-genetic (environmental) data. The LFMM approach identified 2193, 449 and 275 SNPs for FDR values of 0.05, 0.02, and 0.01, respectively. The environmental variables associated with the highest number of SNP outliers were precipitation, latitude and longitude. The LFMM findings were concordant with those obtained with Samβada. Gene ontology analyses show that clusters with higher score are related with immune system development and sensory organ development for the outlier genes associated with longitude. Precipitation is associated with genes related with biological regulation and sequence-specific DNA binding. This represents the most comprehensive study of positive selection that integrates genetic information, and environmental variables performed so far in Iberian honeybees. |
| dirty | 0 |
| eu_rights_str_mv | openAccess |
| format | conferenceObject |
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| identifier.url.fl_str_mv | http://hdl.handle.net/10198/16602 |
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| institution | Instituto Politécnico de Bragança |
| instname_str | Instituto Politécnico de Bragança |
| language | eng |
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| person_str_mv | Henriques, Dora Henriques, Dora https://www.ciencia-id.pt/291F-986F-07DA 291F-986F-07DA http://orcid.org/0000-0001-7530-682X 0000-0001-7530-682X Wallberg, Andreas Chávez-Galarza, Julio Neves, Cátia J. Rufino, José Rufino, José https://www.ciencia-id.pt/C414-F47F-6323 C414-F47F-6323 http://orcid.org/0000-0002-1344-8264 0000-0002-1344-8264 Costa, Filipe Oliveira Webster, Matthew T. Pinto, M. Alice Pinto, M. Alice https://www.ciencia-id.pt/F814-A1D0-8318 F814-A1D0-8318 http://orcid.org/0000-0001-9663-8399 0000-0001-9663-8399 |
| publishDate | 2016 |
| publisher.none.fl_str_mv | Universidade do Porto |
| reponame_str | Biblioteca Digital do IPB |
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| spelling | engUniversidade do Portopt_PTIn the current context of a global human-mediated environmental crisis, understanding which genes and mechanisms are responsible for adaptation to different climates will enable predictions on how organisms will respond to a rapidly changing world. This is particularly important for the honey bee, a key-stone species for ecosystem functioning and economy, which is facing increasing pressures from the effects of intensified land use, climate change, and the spread of pests and pathogens. In this study we used Illumina technology to sequence the whole genomes of 86 Iberian honey bees, collected across three longitudinal transects in the Iberian Peninsula. Then, we searched for signatures of selection using two different methods (LFMM and Samβada), which combine genetic and non-genetic (environmental) data. The LFMM approach identified 2193, 449 and 275 SNPs for FDR values of 0.05, 0.02, and 0.01, respectively. The environmental variables associated with the highest number of SNP outliers were precipitation, latitude and longitude. The LFMM findings were concordant with those obtained with Samβada. Gene ontology analyses show that clusters with higher score are related with immune system development and sensory organ development for the outlier genes associated with longitude. Precipitation is associated with genes related with biological regulation and sequence-specific DNA binding. This represents the most comprehensive study of positive selection that integrates genetic information, and environmental variables performed so far in Iberian honeybees.application/pdfpt_PTSearching for signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) using allele-environment association approachesPersonalHenriques, DoraDSpacehttp://dspace.org/items/d2abd09f-a90c-4cfb-9a60-7fc32f56184dDSpacehttp://dspace.org/items/d2abd09f-a90c-4cfb-9a60-7fc32f56184dHenriquesDoraCiência IDhttps://www.ciencia-id.pt291F-986F-07DAORCIDhttp://orcid.org0000-0001-7530-682XScopus Author IDhttps://www.scopus.com55761737300Wallberg, AndreasChávez-Galarza, JulioNeves, Cátia J.PersonalRufino, JoséDSpacehttp://dspace.org/items/1e24d2ce-a354-442a-bef8-eebadd94b385DSpacehttp://dspace.org/items/1e24d2ce-a354-442a-bef8-eebadd94b385RufinoJoséCiência IDhttps://www.ciencia-id.ptC414-F47F-6323ORCIDhttp://orcid.org0000-0002-1344-8264Scopus Author IDhttps://www.scopus.com55947199100Scopus Author IDhttps://www.scopus.com57188967176Costa, Filipe OliveiraWebster, Matthew T.PersonalPinto, M. AliceDSpacehttp://dspace.org/items/0667fe04-7078-483d-9198-56d167b19bc5DSpacehttp://dspace.org/items/0667fe04-7078-483d-9198-56d167b19bc5PintoM. AliceCiência IDhttps://www.ciencia-id.ptF814-A1D0-8318ORCIDhttp://orcid.org0000-0001-9663-8399Scopus Author IDhttps://www.scopus.com8085507800HostingInstitutionOrganizationalBiblioteca Digital do IPBe-mailmailto:dspace@ipb.ptdspace@ipb.pt2018-03-28T09:16:01Z20162016-01-01T00:00:00ZHandlehttp://hdl.handle.net/10198/16602http://purl.org/coar/access_right/c_abf2open access749209 bytesother research producthttp://purl.org/coar/resource_type/c_c94fconference object2016http://creativecommons.org/licenses/by/4.0/http://purl.org/coar/access_right/c_abf2application/pdffulltexthttps://bibliotecadigital.ipb.pt/bitstreams/ab36f1fb-18af-41ae-a07f-22af4f7ac3c8/downloadAbstract Book of the Conference on Conservation Genomics (Congenomics 2016)8181Vairão |
| spellingShingle | Searching for signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) using allele-environment association approaches Henriques, Dora |
| status | SINGLETON |
| title | Searching for signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) using allele-environment association approaches |
| title_full | Searching for signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) using allele-environment association approaches |
| title_fullStr | Searching for signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) using allele-environment association approaches |
| title_full_unstemmed | Searching for signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) using allele-environment association approaches |
| title_short | Searching for signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) using allele-environment association approaches |
| title_sort | Searching for signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) using allele-environment association approaches |
| url | http://hdl.handle.net/10198/16602 |
| visible | 1 |