Sequence variability of COI in Sigmodontine rodents highlights the taxonomic bottleneck
Autor(a) principal: | |
---|---|
Data de Publicação: | 2009 |
Tipo de documento: | Trabalho de conclusão de curso |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UFRGS |
Texto Completo: | http://hdl.handle.net/10183/18979 |
Resumo: | Sigmodontinae is a high diverse rodent subfamily with difficult taxonomic identification, which plays a relevant role in environmental impact assessment and public health. We evaluated cytochrome c oxidase subunit I (COX-I) sequence variability in order to investigate the existence of ‘barcoding gap’ and to assess its phylogenetic potential in evolutionary studies. We generated 130 sequences from 21 species sampled. Also, we added 58 sequences available in Genbank. Preliminary analysis revealed some field misidentifications. Thus, we reclassified them in order to include in the further analysis. The mean distance was 14.7% overall, 15.2% among genera, and 2.4% among species. The ‘barcoding gap’ was found and an unexpected phylogenetic signal was recovered. Although it proved to be a useful tool that can enhance the discovery of biodiversity, the barcoding approach must be also supported by taxonomy and museum collections. |
id |
UFRGS-2_20bedb1d32397495cad1a54f0a55b9e8 |
---|---|
oai_identifier_str |
oai:www.lume.ufrgs.br:10183/18979 |
network_acronym_str |
UFRGS-2 |
network_name_str |
Repositório Institucional da UFRGS |
repository_id_str |
|
spelling |
Barbosa, Lívia MullerFreitas, Thales Renato Ochotorena de2010-03-27T04:15:34Z2009http://hdl.handle.net/10183/18979000731061Sigmodontinae is a high diverse rodent subfamily with difficult taxonomic identification, which plays a relevant role in environmental impact assessment and public health. We evaluated cytochrome c oxidase subunit I (COX-I) sequence variability in order to investigate the existence of ‘barcoding gap’ and to assess its phylogenetic potential in evolutionary studies. We generated 130 sequences from 21 species sampled. Also, we added 58 sequences available in Genbank. Preliminary analysis revealed some field misidentifications. Thus, we reclassified them in order to include in the further analysis. The mean distance was 14.7% overall, 15.2% among genera, and 2.4% among species. The ‘barcoding gap’ was found and an unexpected phylogenetic signal was recovered. Although it proved to be a useful tool that can enhance the discovery of biodiversity, the barcoding approach must be also supported by taxonomy and museum collections.application/pdfengSigmodontinaeBarcodingCOX-1Species identificationSequence variability of COI in Sigmodontine rodents highlights the taxonomic bottleneckinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/bachelorThesisUniversidade Federal do Rio Grande do SulInstituto de BiociênciasPorto Alegre, BR-RS2009Ciências Biológicas: Bachareladograduaçãoinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da UFRGSinstname:Universidade Federal do Rio Grande do Sul (UFRGS)instacron:UFRGSORIGINAL000731061.pdf000731061.pdfTexto completo (inglês)application/pdf6365349http://www.lume.ufrgs.br/bitstream/10183/18979/1/000731061.pdfddbe8a1460cb2656fd72d39898cbd1d2MD51TEXT000731061.pdf.txt000731061.pdf.txtExtracted Texttext/plain37428http://www.lume.ufrgs.br/bitstream/10183/18979/2/000731061.pdf.txt72a292044d4b20a401f45259ac24656fMD52THUMBNAIL000731061.pdf.jpg000731061.pdf.jpgGenerated Thumbnailimage/jpeg1814http://www.lume.ufrgs.br/bitstream/10183/18979/3/000731061.pdf.jpg5ee3f8df36b014c008358b3ed34f63e0MD5310183/189792021-05-07 05:14:49.287307oai:www.lume.ufrgs.br:10183/18979Repositório de PublicaçõesPUBhttps://lume.ufrgs.br/oai/requestopendoar:2021-05-07T08:14:49Repositório Institucional da UFRGS - Universidade Federal do Rio Grande do Sul (UFRGS)false |
dc.title.pt_BR.fl_str_mv |
Sequence variability of COI in Sigmodontine rodents highlights the taxonomic bottleneck |
title |
Sequence variability of COI in Sigmodontine rodents highlights the taxonomic bottleneck |
spellingShingle |
Sequence variability of COI in Sigmodontine rodents highlights the taxonomic bottleneck Barbosa, Lívia Muller Sigmodontinae Barcoding COX-1 Species identification |
title_short |
Sequence variability of COI in Sigmodontine rodents highlights the taxonomic bottleneck |
title_full |
Sequence variability of COI in Sigmodontine rodents highlights the taxonomic bottleneck |
title_fullStr |
Sequence variability of COI in Sigmodontine rodents highlights the taxonomic bottleneck |
title_full_unstemmed |
Sequence variability of COI in Sigmodontine rodents highlights the taxonomic bottleneck |
title_sort |
Sequence variability of COI in Sigmodontine rodents highlights the taxonomic bottleneck |
author |
Barbosa, Lívia Muller |
author_facet |
Barbosa, Lívia Muller |
author_role |
author |
dc.contributor.author.fl_str_mv |
Barbosa, Lívia Muller |
dc.contributor.advisor1.fl_str_mv |
Freitas, Thales Renato Ochotorena de |
contributor_str_mv |
Freitas, Thales Renato Ochotorena de |
dc.subject.por.fl_str_mv |
Sigmodontinae |
topic |
Sigmodontinae Barcoding COX-1 Species identification |
dc.subject.eng.fl_str_mv |
Barcoding COX-1 Species identification |
description |
Sigmodontinae is a high diverse rodent subfamily with difficult taxonomic identification, which plays a relevant role in environmental impact assessment and public health. We evaluated cytochrome c oxidase subunit I (COX-I) sequence variability in order to investigate the existence of ‘barcoding gap’ and to assess its phylogenetic potential in evolutionary studies. We generated 130 sequences from 21 species sampled. Also, we added 58 sequences available in Genbank. Preliminary analysis revealed some field misidentifications. Thus, we reclassified them in order to include in the further analysis. The mean distance was 14.7% overall, 15.2% among genera, and 2.4% among species. The ‘barcoding gap’ was found and an unexpected phylogenetic signal was recovered. Although it proved to be a useful tool that can enhance the discovery of biodiversity, the barcoding approach must be also supported by taxonomy and museum collections. |
publishDate |
2009 |
dc.date.issued.fl_str_mv |
2009 |
dc.date.accessioned.fl_str_mv |
2010-03-27T04:15:34Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/bachelorThesis |
format |
bachelorThesis |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10183/18979 |
dc.identifier.nrb.pt_BR.fl_str_mv |
000731061 |
url |
http://hdl.handle.net/10183/18979 |
identifier_str_mv |
000731061 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.source.none.fl_str_mv |
reponame:Repositório Institucional da UFRGS instname:Universidade Federal do Rio Grande do Sul (UFRGS) instacron:UFRGS |
instname_str |
Universidade Federal do Rio Grande do Sul (UFRGS) |
instacron_str |
UFRGS |
institution |
UFRGS |
reponame_str |
Repositório Institucional da UFRGS |
collection |
Repositório Institucional da UFRGS |
bitstream.url.fl_str_mv |
http://www.lume.ufrgs.br/bitstream/10183/18979/1/000731061.pdf http://www.lume.ufrgs.br/bitstream/10183/18979/2/000731061.pdf.txt http://www.lume.ufrgs.br/bitstream/10183/18979/3/000731061.pdf.jpg |
bitstream.checksum.fl_str_mv |
ddbe8a1460cb2656fd72d39898cbd1d2 72a292044d4b20a401f45259ac24656f 5ee3f8df36b014c008358b3ed34f63e0 |
bitstream.checksumAlgorithm.fl_str_mv |
MD5 MD5 MD5 |
repository.name.fl_str_mv |
Repositório Institucional da UFRGS - Universidade Federal do Rio Grande do Sul (UFRGS) |
repository.mail.fl_str_mv |
|
_version_ |
1801224391461175296 |