Publicação
Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera
| Resumo: | The genetic identity of the dark European honey bee, Apis mellifera mellifera is currently under pressure throughout most of its native range due to large scale commercial trade and replacement with honey bees of mainly Eastern European ancestry (C-lineage: Apis mellifera carnica and Apis mellifera ligustica). To counteract this process, numerous conservation efforts for the protection of native honey bees are sprouting across Europe. For the management of such protected areas and conservation breeding purposes, honey bee subspecies have been routinely identified through wing morphology and through DNA-hybrid tests using microsatellite markers. Currently, new methods are evolving including rapid innovations in single-nucleotide polymorphism (SNP) array technology and high-throughput sequencing. Here, we aim to quantify potential marker-specific biases of hybrid tests and give recommendations for applications in honey bee conservation management. Using an empirical dataset, we first assessed the accuracy of a recently developed reduced SNP panel to estimate C-lineage introgression in A. m. mellifera compared to whole-genome sequence (WGS) data. Using another independent data set, we estimated the differences in admixture proportions between the currently applied hybrid test based on microsatellites and the novel SNP test. We demonstrate that the SNP-based test which contains highly ancestry-informative markers is very efficient to estimate genome-wide ancestry. Furthermore, we report discrepancies between microsatellite and SNP-based admixture proportions. For conservation management, we, therefore, recommend the implementation of SNP-based hybrid tests to maintain high genetic variation within the breeding population, while minimizing influence of introduced honey bees. |
|---|---|
| Autores principais: | Parejo, Melanie |
| Outros Autores: | Henriques, Dora; Pinto, M. Alice; Soland-Reckeweg, Gabriele; Neuditschko, Markus |
| Assunto: | Apis mellifera mellifera Conservation Introgression Microsatellites SNPs |
| Ano: | 2018 |
| País: | Portugal |
| Tipo de documento: | artigo |
| Tipo de acesso: | acesso aberto |
| Instituição associada: | Instituto Politécnico de Bragança |
| Idioma: | inglês |
| Origem: | Biblioteca Digital do IPB |
| _version_ | 1863851047464730624 |
|---|---|
| author | Parejo, Melanie |
| author2 | Henriques, Dora Pinto, M. Alice Soland-Reckeweg, Gabriele Neuditschko, Markus |
| author2_role | author author author author |
| author_facet | Parejo, Melanie Henriques, Dora Pinto, M. Alice Soland-Reckeweg, Gabriele Neuditschko, Markus |
| author_role | author |
| contributor_name_str_mv | Biblioteca Digital do IPB |
| country_str | PT |
| creators_json_str | [{\"Person.name\":\"Parejo, Melanie\"},{\"Person.name\":\"Henriques, Dora\",\"Person.identifier.orcid\":\"0000-0001-7530-682X\"},{\"Person.name\":\"Pinto, M. Alice\",\"Person.identifier.orcid\":\"0000-0001-9663-8399\"},{\"Person.name\":\"Soland-Reckeweg, Gabriele\"},{\"Person.name\":\"Neuditschko, Markus\"}] |
| datacite.contributors.contributor.contributorName.fl_str_mv | Biblioteca Digital do IPB |
| datacite.creators.creator.creatorName.fl_str_mv | Parejo, Melanie Henriques, Dora Pinto, M. Alice Soland-Reckeweg, Gabriele Neuditschko, Markus |
| datacite.date.Accepted.fl_str_mv | 2018-01-01T00:00:00Z |
| datacite.date.available.fl_str_mv | 2018-01-19T10:00:00Z |
| datacite.date.embargoed.fl_str_mv | 2018-01-19T10:00:00Z |
| datacite.rights.fl_str_mv | http://purl.org/coar/access_right/c_abf2 |
| datacite.subjects.subject.fl_str_mv | Apis mellifera mellifera Conservation Introgression Microsatellites SNPs |
| datacite.titles.title.fl_str_mv | Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera |
| dc.contributor.none.fl_str_mv | Biblioteca Digital do IPB |
| dc.creator.none.fl_str_mv | Parejo, Melanie Henriques, Dora Pinto, M. Alice Soland-Reckeweg, Gabriele Neuditschko, Markus |
| dc.date.Accepted.fl_str_mv | 2018-01-01T00:00:00Z |
| dc.date.available.fl_str_mv | 2018-01-19T10:00:00Z |
| dc.date.embargoed.fl_str_mv | 2018-01-19T10:00:00Z |
| dc.format.none.fl_str_mv | application/pdf |
| dc.identifier.none.fl_str_mv | http://hdl.handle.net/10198/18739 |
| dc.language.none.fl_str_mv | eng |
| dc.rights.none.fl_str_mv | http://purl.org/coar/access_right/c_abf2 |
| dc.subject.none.fl_str_mv | Apis mellifera mellifera Conservation Introgression Microsatellites SNPs |
| dc.title.fl_str_mv | Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera |
| dc.type.none.fl_str_mv | http://purl.org/coar/resource_type/c_6501 |
| description | The genetic identity of the dark European honey bee, Apis mellifera mellifera is currently under pressure throughout most of its native range due to large scale commercial trade and replacement with honey bees of mainly Eastern European ancestry (C-lineage: Apis mellifera carnica and Apis mellifera ligustica). To counteract this process, numerous conservation efforts for the protection of native honey bees are sprouting across Europe. For the management of such protected areas and conservation breeding purposes, honey bee subspecies have been routinely identified through wing morphology and through DNA-hybrid tests using microsatellite markers. Currently, new methods are evolving including rapid innovations in single-nucleotide polymorphism (SNP) array technology and high-throughput sequencing. Here, we aim to quantify potential marker-specific biases of hybrid tests and give recommendations for applications in honey bee conservation management. Using an empirical dataset, we first assessed the accuracy of a recently developed reduced SNP panel to estimate C-lineage introgression in A. m. mellifera compared to whole-genome sequence (WGS) data. Using another independent data set, we estimated the differences in admixture proportions between the currently applied hybrid test based on microsatellites and the novel SNP test. We demonstrate that the SNP-based test which contains highly ancestry-informative markers is very efficient to estimate genome-wide ancestry. Furthermore, we report discrepancies between microsatellite and SNP-based admixture proportions. For conservation management, we, therefore, recommend the implementation of SNP-based hybrid tests to maintain high genetic variation within the breeding population, while minimizing influence of introduced honey bees. |
| dirty | 0 |
| eu_rights_str_mv | openAccess |
| format | article |
| fulltext.url.fl_str_mv | https://bibliotecadigital.ipb.pt/bitstreams/3be78e59-507b-43ba-b70d-b2012889e67c/download |
| id | ipb_28bb9f577a5eedcb4abd1b9fb78ed46c |
| identifier.url.fl_str_mv | http://hdl.handle.net/10198/18739 |
| instacron_str | ipb |
| institution | Instituto Politécnico de Bragança |
| instname_str | Instituto Politécnico de Bragança |
| language | eng |
| network_acronym_str | ipb |
| network_name_str | Biblioteca Digital do IPB |
| oai_identifier_str | oai:bibliotecadigital.ipb.pt:10198/18739 |
| organization_str_mv | urn:organizationAcronym:ipb |
| person_str_mv | Parejo, Melanie 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 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 Soland-Reckeweg, Gabriele Neuditschko, Markus |
| publishDate | 2018 |
| reponame_str | Biblioteca Digital do IPB |
| repository_id_str | urn:repositoryAcronym:ipb |
| service_str_mv | urn:repositoryAcronym:ipb |
| spelling | engen_ENThe genetic identity of the dark European honey bee, Apis mellifera mellifera is currently under pressure throughout most of its native range due to large scale commercial trade and replacement with honey bees of mainly Eastern European ancestry (C-lineage: Apis mellifera carnica and Apis mellifera ligustica). To counteract this process, numerous conservation efforts for the protection of native honey bees are sprouting across Europe. For the management of such protected areas and conservation breeding purposes, honey bee subspecies have been routinely identified through wing morphology and through DNA-hybrid tests using microsatellite markers. Currently, new methods are evolving including rapid innovations in single-nucleotide polymorphism (SNP) array technology and high-throughput sequencing. Here, we aim to quantify potential marker-specific biases of hybrid tests and give recommendations for applications in honey bee conservation management. Using an empirical dataset, we first assessed the accuracy of a recently developed reduced SNP panel to estimate C-lineage introgression in A. m. mellifera compared to whole-genome sequence (WGS) data. Using another independent data set, we estimated the differences in admixture proportions between the currently applied hybrid test based on microsatellites and the novel SNP test. We demonstrate that the SNP-based test which contains highly ancestry-informative markers is very efficient to estimate genome-wide ancestry. Furthermore, we report discrepancies between microsatellite and SNP-based admixture proportions. For conservation management, we, therefore, recommend the implementation of SNP-based hybrid tests to maintain high genetic variation within the breeding population, while minimizing influence of introduced honey bees.application/pdfen_ENEmpirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera melliferaParejo, MelaniePersonalHenriques, 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.com55761737300PersonalPinto, 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.com8085507800Soland-Reckeweg, GabrieleNeuditschko, MarkusHostingInstitutionOrganizationalBiblioteca Digital do IPBe-mailmailto:dspace@ipb.ptdspace@ipb.ptISSNIsPartOf0021-8839DOIIsPartOf10.1080/00218839.2018.14948942018-01-19T10:00:00Z20182018-01-01T00:00:00ZHandlehttp://hdl.handle.net/10198/18739http://purl.org/coar/access_right/c_abf2open accessApis mellifera melliferaConservationIntrogressionMicrosatellitesSNPs685368 bytesliteraturehttp://purl.org/coar/resource_type/c_6501journal articlehttp://purl.org/coar/access_right/c_abf2application/pdffulltexthttps://bibliotecadigital.ipb.pt/bitstreams/3be78e59-507b-43ba-b70d-b2012889e67c/download |
| spellingShingle | Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera Parejo, Melanie Apis mellifera mellifera Conservation Introgression Microsatellites SNPs |
| subject.fl_str_mv | Apis mellifera mellifera Conservation Introgression Microsatellites SNPs |
| title | Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera |
| title_full | Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera |
| title_fullStr | Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera |
| title_full_unstemmed | Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera |
| title_short | Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera |
| title_sort | Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera |
| topic | Apis mellifera mellifera Conservation Introgression Microsatellites SNPs |
| topic_facet | Apis mellifera mellifera Conservation Introgression Microsatellites SNPs |
| url | http://hdl.handle.net/10198/18739 |
| visible | 1 |