Landscape genomics in the Northern Patagonian fjords: neutral, adaptive, and gene expression divergence in the sub-Antarctic notothenioid fish Eleginops maclovinus
3 Assess the relative importance of the oceanographic factors (i.e. salinity and temperature) on the population structure and migration. TOTAL The genotype-environment analysis (GEA) identified several loci associated with the genetic diversity patterns observed. The environmental factors tested, ob...
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ftanid:oai:repositorio.anid.cl:10533/48436 2024-05-12T07:54:47+00:00 Landscape genomics in the Northern Patagonian fjords: neutral, adaptive, and gene expression divergence in the sub-Antarctic notothenioid fish Eleginops maclovinus Canales - Aguirre Cristian Universidad De Los Lagos Región de Valparaíso Región del Libertador General Bernardo O'Higgins Región del Maule Región del Bío-Bío Región de La Araucanía Región de Los Lagos Región Aysén del General Carlos Ibáñez del Campo Región de Magallanes y la Antártica Chilena Región de Los Ríos Región de Ñuble 2023-08-24T13:05:03Z application/pdf https://hdl.handle.net/10533/48436 unknown 11180897 Masculino https://hdl.handle.net/10533/48436 Atribución-NoComercial-SinDerivadas 3.0 Chile http://creativecommons.org/licenses/by-nc-sa/3.0/cl/ Population Genomics SNPs Aquatic environment Biologia Marina Limnologia Informe Final info:eu-repo/semantics/report 2023 ftanid 2024-04-18T17:01:17Z 3 Assess the relative importance of the oceanographic factors (i.e. salinity and temperature) on the population structure and migration. TOTAL The genotype-environment analysis (GEA) identified several loci associated with the genetic diversity patterns observed. The environmental factors tested, obtained from the BioOracle database and complemented with those obtained in the field, were able to identified 25 loci associated with dissolved oxygen, 14 loci with primary productivity, 30 loci with salinity and 9 loci with current velocity. These loci explained the genetic structure patterns observed for the adaptive loci. Relative migration rates were low from Chepu to the other localities and vice versa using all identified adaptive loci and very low to and from the Reloncavi Estuary using a small set of potentially adaptive loci. These results are in the manuscript "Neutral and adaptive loci reveal fine-scale population structure in Eleginops maclovinus from North Patagonia" published in Ecology and Evolution (Canales-Aguirre et al. 2022). 4 Generate a draft of genome reference for Eleginops maclovinus to mapping neutral and adaptive variants (SNPs) obtained from RADseq PARCIAL Currently, we are making progress in the construction of a reference genome. To date we have raw data obtained from nanopore technology. Specifically, we ran two flow cells for 19,52 hrs to obtain long read sequences. Overall, flow cells generated 644,170 reads, corresponding to 1,93 Gb. The read length estimated bases showed a N50 of 6,05kb, including sequences less than 77,8 kb, and the read length basecalled bases showed a N50 of 5,99kb, higher than 32,8 kb. Next steps will be annotated when there were possible and identify rearrangements and copy number of variants. Otro(s) aspecto(s) que Ud. considere importante(s) en la evaluación del cumplimiento de objetivos planteados en la propuesta original o en las modificaciones autorizadas por los Consejos. For the objective 3: Complementarily, to the exposed as reason of compliance with this ... Report Antarc* Antarctic Antártica Repositorio ANID (Agencia Nacional de Investigación y Desarrollo) Antarctic Patagonia Magallanes ENVELOPE(-62.933,-62.933,-64.883,-64.883) Canales ENVELOPE(-59.693,-59.693,-62.498,-62.498) Aguirre ENVELOPE(-57.933,-57.933,-63.317,-63.317) Valparaíso ENVELOPE(-62.983,-62.983,-64.833,-64.833) Bío Bío ENVELOPE(-66.450,-66.450,-66.467,-66.467) General Bernardo O'Higgins ENVELOPE(-57.900,-57.900,-63.317,-63.317) |
institution |
Open Polar |
collection |
Repositorio ANID (Agencia Nacional de Investigación y Desarrollo) |
op_collection_id |
ftanid |
language |
unknown |
topic |
Population Genomics SNPs Aquatic environment Biologia Marina Limnologia |
spellingShingle |
Population Genomics SNPs Aquatic environment Biologia Marina Limnologia Canales - Aguirre Cristian Landscape genomics in the Northern Patagonian fjords: neutral, adaptive, and gene expression divergence in the sub-Antarctic notothenioid fish Eleginops maclovinus |
topic_facet |
Population Genomics SNPs Aquatic environment Biologia Marina Limnologia |
description |
3 Assess the relative importance of the oceanographic factors (i.e. salinity and temperature) on the population structure and migration. TOTAL The genotype-environment analysis (GEA) identified several loci associated with the genetic diversity patterns observed. The environmental factors tested, obtained from the BioOracle database and complemented with those obtained in the field, were able to identified 25 loci associated with dissolved oxygen, 14 loci with primary productivity, 30 loci with salinity and 9 loci with current velocity. These loci explained the genetic structure patterns observed for the adaptive loci. Relative migration rates were low from Chepu to the other localities and vice versa using all identified adaptive loci and very low to and from the Reloncavi Estuary using a small set of potentially adaptive loci. These results are in the manuscript "Neutral and adaptive loci reveal fine-scale population structure in Eleginops maclovinus from North Patagonia" published in Ecology and Evolution (Canales-Aguirre et al. 2022). 4 Generate a draft of genome reference for Eleginops maclovinus to mapping neutral and adaptive variants (SNPs) obtained from RADseq PARCIAL Currently, we are making progress in the construction of a reference genome. To date we have raw data obtained from nanopore technology. Specifically, we ran two flow cells for 19,52 hrs to obtain long read sequences. Overall, flow cells generated 644,170 reads, corresponding to 1,93 Gb. The read length estimated bases showed a N50 of 6,05kb, including sequences less than 77,8 kb, and the read length basecalled bases showed a N50 of 5,99kb, higher than 32,8 kb. Next steps will be annotated when there were possible and identify rearrangements and copy number of variants. Otro(s) aspecto(s) que Ud. considere importante(s) en la evaluación del cumplimiento de objetivos planteados en la propuesta original o en las modificaciones autorizadas por los Consejos. For the objective 3: Complementarily, to the exposed as reason of compliance with this ... |
author2 |
Universidad De Los Lagos |
format |
Report |
author |
Canales - Aguirre Cristian |
author_facet |
Canales - Aguirre Cristian |
author_sort |
Canales - Aguirre |
title |
Landscape genomics in the Northern Patagonian fjords: neutral, adaptive, and gene expression divergence in the sub-Antarctic notothenioid fish Eleginops maclovinus |
title_short |
Landscape genomics in the Northern Patagonian fjords: neutral, adaptive, and gene expression divergence in the sub-Antarctic notothenioid fish Eleginops maclovinus |
title_full |
Landscape genomics in the Northern Patagonian fjords: neutral, adaptive, and gene expression divergence in the sub-Antarctic notothenioid fish Eleginops maclovinus |
title_fullStr |
Landscape genomics in the Northern Patagonian fjords: neutral, adaptive, and gene expression divergence in the sub-Antarctic notothenioid fish Eleginops maclovinus |
title_full_unstemmed |
Landscape genomics in the Northern Patagonian fjords: neutral, adaptive, and gene expression divergence in the sub-Antarctic notothenioid fish Eleginops maclovinus |
title_sort |
landscape genomics in the northern patagonian fjords: neutral, adaptive, and gene expression divergence in the sub-antarctic notothenioid fish eleginops maclovinus |
publishDate |
2023 |
url |
https://hdl.handle.net/10533/48436 |
op_coverage |
Región de Valparaíso Región del Libertador General Bernardo O'Higgins Región del Maule Región del Bío-Bío Región de La Araucanía Región de Los Lagos Región Aysén del General Carlos Ibáñez del Campo Región de Magallanes y la Antártica Chilena Región de Los Ríos Región de Ñuble |
long_lat |
ENVELOPE(-62.933,-62.933,-64.883,-64.883) ENVELOPE(-59.693,-59.693,-62.498,-62.498) ENVELOPE(-57.933,-57.933,-63.317,-63.317) ENVELOPE(-62.983,-62.983,-64.833,-64.833) ENVELOPE(-66.450,-66.450,-66.467,-66.467) ENVELOPE(-57.900,-57.900,-63.317,-63.317) |
geographic |
Antarctic Patagonia Magallanes Canales Aguirre Valparaíso Bío Bío General Bernardo O'Higgins |
geographic_facet |
Antarctic Patagonia Magallanes Canales Aguirre Valparaíso Bío Bío General Bernardo O'Higgins |
genre |
Antarc* Antarctic Antártica |
genre_facet |
Antarc* Antarctic Antártica |
op_relation |
11180897 Masculino https://hdl.handle.net/10533/48436 |
op_rights |
Atribución-NoComercial-SinDerivadas 3.0 Chile http://creativecommons.org/licenses/by-nc-sa/3.0/cl/ |
_version_ |
1798852208984326144 |