Publicação
Analyses of the genomic variation to study cork oak evolution and adaptation : from past to future climatic changes
| Resumo: | Current scientific literature indicates that climate change will cause an average world temperature increase between 1 and 4ºC, along with changes in precipitation patterns and extreme weather events in the next 50 years. These are likely to have a negative impact for biodiversity in general, and forest ecosystems should be particularly affected, especially those in Mediterranean areas, like the cork oak (Quercus suber L.) “montados”. In order to understand how species can respond to such alterations, it is important to know their evolutionary history and genetic architecture of adaptive traits. Advances in sequencing technologies have relatively recently brought down the cost of sequencing per base pair to a point where even small research facilities can obtain genomic information of non-model organisms. These advances made SNP markers become the most abundant type of genetic variation in eukaryotic genomes, especially with the advent of Reduced Representation libraries such as RAD-Seq and GBS. Yet, despite their widespread use, SNP data analyses still bore its own set of bioinformatics challenges. While most of these are related with the practical aspects of the process, such as being able to handle very large datasets, or discriminate between neutral and non-neutral markers, some fundamental problems, like reproducibility are also important issues affecting research in this area. In this thesis, genomic and transcriptomic data from Q. suber was used to assess the evolutionary history of the species, detect the effects of natural selection across the cork oak’s distribution range and find any associations between the obtained markers and environmental variables. The main methodological contributions of this thesis are in the form of three software suites: (1) 4Pipe4, a software for automatically mining SNP markers from NGS data when no reference genome nor strain information is present, (2) NCBI Mass Sequence Downloader, a program to automate the downloading of large datasets from the NCBI databases, and (3) Structure_threader, a software to automate and parallelize analyses using several popular clustering analyses programs. All of these programs were developed with the intent to improve the automation and reproducibility value of the analysis processes they are meant to be part of. The main findings of this thesis are that (1) the evolutionary history and population structure of Q. suber is not as neatly structured as chloroplastidial markers indicate, (2) local adaptation plays and important role in the distribution of the species’ genetic variability, and (3) the cork oak may be better equipped, from a genetic point of view, to adapt to climate change than what previous studies based solely on ecological modelling indicated. |
|---|---|
| Autores principais: | Pina-Martins |
| Assunto: | Teses de doutoramento - 2018 Sobreiro (Quercus Suber) Biologia evolutiva |
| Ano: | 2018 |
| País: | Portugal |
| Tipo de documento: | tese de doutoramento |
| Tipo de acesso: | acesso aberto |
| Instituição associada: | Universidade de Lisboa |
| Idioma: | inglês |
| Origem: | Repositório da Universidade de Lisboa |
| _version_ | 1866810299742420992 |
|---|---|
| author | Pina-Martins |
| author_facet | Pina-Martins |
| author_role | author |
| contributor_name_str_mv | Paulo, Octávio, 1963- Pappas, Georgios Joannis Repositório Científico de Acesso Aberto da ULisboa |
| country_str | PT |
| creators_json_txt | [{\"Person.name\":\"Pina-Martins\",\"Person.identifier.orcid\":\"0000-0003-1836-397X\"}] |
| datacite.contributors.contributor.contributorName.fl_str_mv | Paulo, Octávio, 1963- Pappas, Georgios Joannis Repositório Científico de Acesso Aberto da ULisboa |
| datacite.creators.creator.creatorName.fl_str_mv | Pina-Martins |
| datacite.date.Accepted.fl_str_mv | 2018-01-01T00:00:00Z |
| datacite.date.available.fl_str_mv | 2021-04-07T00:30:18Z |
| datacite.date.embargoed.fl_str_mv | 2021-04-07T00:30:18Z |
| datacite.rights.fl_str_mv | http://purl.org/coar/access_right/c_abf2 |
| datacite.subjects.subject.fl_str_mv | Teses de doutoramento - 2018 Sobreiro (Quercus Suber) Biologia evolutiva |
| datacite.titles.title.fl_str_mv | Analyses of the genomic variation to study cork oak evolution and adaptation : from past to future climatic changes |
| dc.contributor.none.fl_str_mv | Paulo, Octávio, 1963- Pappas, Georgios Joannis Repositório Científico de Acesso Aberto da ULisboa |
| dc.creator.none.fl_str_mv | Pina-Martins |
| dc.date.Accepted.fl_str_mv | 2018-01-01T00:00:00Z |
| dc.date.available.fl_str_mv | 2021-04-07T00:30:18Z |
| dc.date.embargoed.fl_str_mv | 2021-04-07T00:30:18Z |
| dc.format.none.fl_str_mv | application/pdf |
| dc.identifier.none.fl_str_mv | http://hdl.handle.net/10451/34770 |
| 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 | Teses de doutoramento - 2018 Sobreiro (Quercus Suber) Biologia evolutiva |
| dc.title.fl_str_mv | Analyses of the genomic variation to study cork oak evolution and adaptation : from past to future climatic changes |
| dc.type.none.fl_str_mv | http://purl.org/coar/resource_type/c_db06 |
| description | Current scientific literature indicates that climate change will cause an average world temperature increase between 1 and 4ºC, along with changes in precipitation patterns and extreme weather events in the next 50 years. These are likely to have a negative impact for biodiversity in general, and forest ecosystems should be particularly affected, especially those in Mediterranean areas, like the cork oak (Quercus suber L.) “montados”. In order to understand how species can respond to such alterations, it is important to know their evolutionary history and genetic architecture of adaptive traits. Advances in sequencing technologies have relatively recently brought down the cost of sequencing per base pair to a point where even small research facilities can obtain genomic information of non-model organisms. These advances made SNP markers become the most abundant type of genetic variation in eukaryotic genomes, especially with the advent of Reduced Representation libraries such as RAD-Seq and GBS. Yet, despite their widespread use, SNP data analyses still bore its own set of bioinformatics challenges. While most of these are related with the practical aspects of the process, such as being able to handle very large datasets, or discriminate between neutral and non-neutral markers, some fundamental problems, like reproducibility are also important issues affecting research in this area. In this thesis, genomic and transcriptomic data from Q. suber was used to assess the evolutionary history of the species, detect the effects of natural selection across the cork oak’s distribution range and find any associations between the obtained markers and environmental variables. The main methodological contributions of this thesis are in the form of three software suites: (1) 4Pipe4, a software for automatically mining SNP markers from NGS data when no reference genome nor strain information is present, (2) NCBI Mass Sequence Downloader, a program to automate the downloading of large datasets from the NCBI databases, and (3) Structure_threader, a software to automate and parallelize analyses using several popular clustering analyses programs. All of these programs were developed with the intent to improve the automation and reproducibility value of the analysis processes they are meant to be part of. The main findings of this thesis are that (1) the evolutionary history and population structure of Q. suber is not as neatly structured as chloroplastidial markers indicate, (2) local adaptation plays and important role in the distribution of the species’ genetic variability, and (3) the cork oak may be better equipped, from a genetic point of view, to adapt to climate change than what previous studies based solely on ecological modelling indicated. |
| dirty | 0 |
| eu_rights_str_mv | openAccess |
| format | doctoralThesis |
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| funding.funder.alternateName_str_mv | FCT |
| funding.funder.identifier_str_mv | http://doi.org/10.13039/501100001871 |
| funding.funder.name_str_mv | Fundação para a Ciência e a Tecnologia |
| id | ul_7fcdd992ce2fc489ba843ef098ff8545 |
| identifier.url.fl_str_mv | http://hdl.handle.net/10451/34770 |
| instacron_str | ul |
| institution | Universidade de Lisboa |
| instname_str | Universidade de Lisboa |
| language | eng |
| network_acronym_str | ul |
| network_name_str | Repositório da Universidade de Lisboa |
| oai_identifier_str | oai:repositorio.ulisboa.pt:10451/34770 |
| organization_str_mv | urn:organizationAcronym:ul |
| person_str_mv | Pina-Martins Pina-Martins https://www.ciencia-id.pt/1E1C-2D9B-5338 1E1C-2D9B-5338 http://orcid.org/0000-0003-1836-397X 0000-0003-1836-397X |
| publishDate | 2018 |
| reponame_str | Repositório da Universidade de Lisboa |
| repository_id_str | urn:repositoryAcronym:ul |
| service_str_mv | urn:repositoryAcronym:ul |
| spelling | engpt_PTCurrent scientific literature indicates that climate change will cause an average world temperature increase between 1 and 4ºC, along with changes in precipitation patterns and extreme weather events in the next 50 years. These are likely to have a negative impact for biodiversity in general, and forest ecosystems should be particularly affected, especially those in Mediterranean areas, like the cork oak (Quercus suber L.) “montados”. In order to understand how species can respond to such alterations, it is important to know their evolutionary history and genetic architecture of adaptive traits. Advances in sequencing technologies have relatively recently brought down the cost of sequencing per base pair to a point where even small research facilities can obtain genomic information of non-model organisms. These advances made SNP markers become the most abundant type of genetic variation in eukaryotic genomes, especially with the advent of Reduced Representation libraries such as RAD-Seq and GBS. Yet, despite their widespread use, SNP data analyses still bore its own set of bioinformatics challenges. While most of these are related with the practical aspects of the process, such as being able to handle very large datasets, or discriminate between neutral and non-neutral markers, some fundamental problems, like reproducibility are also important issues affecting research in this area. In this thesis, genomic and transcriptomic data from Q. suber was used to assess the evolutionary history of the species, detect the effects of natural selection across the cork oak’s distribution range and find any associations between the obtained markers and environmental variables. The main methodological contributions of this thesis are in the form of three software suites: (1) 4Pipe4, a software for automatically mining SNP markers from NGS data when no reference genome nor strain information is present, (2) NCBI Mass Sequence Downloader, a program to automate the downloading of large datasets from the NCBI databases, and (3) Structure_threader, a software to automate and parallelize analyses using several popular clustering analyses programs. All of these programs were developed with the intent to improve the automation and reproducibility value of the analysis processes they are meant to be part of. The main findings of this thesis are that (1) the evolutionary history and population structure of Q. suber is not as neatly structured as chloroplastidial markers indicate, (2) local adaptation plays and important role in the distribution of the species’ genetic variability, and (3) the cork oak may be better equipped, from a genetic point of view, to adapt to climate change than what previous studies based solely on ecological modelling indicated.application/pdfpt_PTAnalyses of the genomic variation to study cork oak evolution and adaptation : from past to future climatic changesPersonalPina-MartinsDSpacehttp://dspace.org/items/78fd172f-1d2d-471d-a35b-8abb75e9fb7eDSpacehttp://dspace.org/items/78fd172f-1d2d-471d-a35b-8abb75e9fb7ePina MartinsFranciscoCiência IDhttps://www.ciencia-id.pt1E1C-2D9B-5338ORCIDhttp://orcid.org0000-0003-1836-397XScopus Author IDhttps://www.scopus.com25630967600Paulo, Octávio, 1963-Pappas, Georgios JoannisHostingInstitutionOrganizationalRepositório Científico de Acesso Aberto da ULisboae-mailmailto:repositorio@reitoria.ulisboa.ptrepositorio@reitoria.ulisboa.ptURNurn:tid:1014741132021-04-07T00:30:18Z201820172018-01-01T00:00:00ZHandlehttp://hdl.handle.net/10451/34770http://purl.org/coar/access_right/c_abf2open accessTeses de doutoramento - 2018Sobreiro (Quercus Suber)Biologia evolutiva10972492 bytesFundação para a Ciência e a TecnologiaPROGRAMA DOUTORAL EM BIOLOGIA E ECOLOGIA DAS ALTERAÇÕES GLOBAIS DA UNIV. DE AVEIROCrossref Funder IDhttp://doi.org/10.13039/501100001871literaturehttp://purl.org/coar/resource_type/c_db06doctoral thesishttp://purl.org/coar/access_right/c_abf2application/pdffulltexthttps://repositorio.ulisboa.pt/bitstreams/d9bd86ca-5713-45ff-8c26-8d30a4122508/download |
| spellingShingle | Analyses of the genomic variation to study cork oak evolution and adaptation : from past to future climatic changes Pina-Martins Teses de doutoramento - 2018 Sobreiro (Quercus Suber) Biologia evolutiva |
| status | SINGLETON |
| subject.fl_str_mv | Teses de doutoramento - 2018 Sobreiro (Quercus Suber) Biologia evolutiva |
| title | Analyses of the genomic variation to study cork oak evolution and adaptation : from past to future climatic changes |
| title_full | Analyses of the genomic variation to study cork oak evolution and adaptation : from past to future climatic changes |
| title_fullStr | Analyses of the genomic variation to study cork oak evolution and adaptation : from past to future climatic changes |
| title_full_unstemmed | Analyses of the genomic variation to study cork oak evolution and adaptation : from past to future climatic changes |
| title_short | Analyses of the genomic variation to study cork oak evolution and adaptation : from past to future climatic changes |
| title_sort | Analyses of the genomic variation to study cork oak evolution and adaptation : from past to future climatic changes |
| topic | Teses de doutoramento - 2018 Sobreiro (Quercus Suber) Biologia evolutiva |
| topic_facet | Teses de doutoramento - 2018 Sobreiro (Quercus Suber) Biologia evolutiva |
| url | http://hdl.handle.net/10451/34770 |
| visible | 1 |