{"id":15722,"date":"2024-11-25T14:50:14","date_gmt":"2024-11-25T17:50:14","guid":{"rendered":"https:\/\/www.ufrgs.br\/ppgbm\/?p=15722"},"modified":"2024-11-25T14:50:14","modified_gmt":"2024-11-25T17:50:14","slug":"27-11-seminario-de-dados-mestrado-karen-estefania-valencia-aguilar","status":"publish","type":"post","link":"https:\/\/www.ufrgs.br\/ppgbm\/27-11-seminario-de-dados-mestrado-karen-estefania-valencia-aguilar\/","title":{"rendered":"27\/11 &#8211; SEMIN\u00c1RIO DE DADOS (Mestrado) &#8211; Karen Estefania Valencia Aguilar"},"content":{"rendered":"<p><strong>27 de novembro de 2024 &#8211; 12h SEMIN\u00c1RIO DE DADOS (Mestrado)<\/strong><\/p>\n<p>&nbsp;<\/p>\n<p><strong>KAREN ESTEFANIA VALENCIA\u00a0AGUILAR<\/strong><\/p>\n<p><strong>Phylogenomics of <em>Homonota uruguayensis<\/em>: An approach to the evolutionary history of population lineages using ddRAD-seq<\/strong><\/p>\n<p>Orientador: Dr. Nelson J. Rosa Fagundes<\/p>\n<p>Avaliadora: Dra. Caroline Turchetto<\/p>\n<p>27 de novembro de\u00a02024 (quarta-feira)<\/p>\n<p><strong>12h<\/strong><\/p>\n<p><strong>Presencial:\u00a0<\/strong>Anfiteatro do\u00a0Departamento\u00a0de\u00a0Gen\u00e9tica da UFRGS (Campus do Vale, pr\u00e9dio 43312)<\/p>\n<p>&nbsp;<\/p>\n<p><strong>Abstract<\/strong><\/p>\n<p>The gecko <em>Homonota uruguayensis<\/em> (Vaz-Ferreira &amp; Sierra De Soriano 1961), is a Pampean lizard distributed in the northwest of Uruguay and the southwest of Brazil. It is characterized by its specialized ecological preferences, inhabiting basalt and sandstone rocky outcrops, relying on these structures for shelter and nesting. Earlier research, employing mitochondrial DNA and autosomal genes, revealed distinct genealogical lineages, one of which was later diagnosed as a new species, <em>H. xiru<\/em>. Considering this, the aim of the present study is to elucidate the evolutionary history of <em>H. uruguayensis<\/em> using genomic data covering the species known distribution. For this purpose, we extracted DNA from <em>H. uruguayensis<\/em> following standardized protocols and employed the ddRAD-seq technique to characterize the genomic diversity of 60 individuals sampled across their entire distribution range. The samples were sequenced in 95 bp fragments using single-end reads on the Illumina NovaSeq platform (X100). For sequence processing and the generation of the final variant set, we used the STACKS software and explored various parameters for locus assembly and missing data. The degree of genetic structure is being assessed using principal component analysis (PCA), multivariate methods such as DAPC, and genetic clustering algorithms like ADMIXTURE to characterize the populations. A comparison of mitochondrial DNA data with genomic SNP will also be performed. Phylogenetic inferences will be made through concatenated maximum likelihood trees using RAxML, as well as species trees based on coalescent models with SVDquartets to analyze the population lineages of the species. The potential existence of new species will be evaluated in Beast2 (SNAPPER) using the Bayesian factor between alternative taxonomic delimitations as the criterion, and the most plausible evolutionary scenario will be selected based on fastsimcoal2, using the allele frequency spectrum (SFS). Preliminary results revealed a total of 11,796 SNPs ascertained in 46 individuals sampled from 40 locations in Uruguay and Brazil. Principal Component Analysis (PCA) indicated clear genetic differentiation, with the presence of three distinct clusters. Additionally, ADMIXTURE analysis showed varying proportions of admixture across the individuals, suggesting K=3 as the best number of genetic populations, even though these were different from the groups in the PCA. Overall, a value of K as large as five was able to identify geographically meaningful groups. The phylogenetic tree based on SNP data revealed several well-supported clades, in some agreement to the patterns observed in mitochondrial DNA data. The preliminary results suggest that the genetic structure in <em>H. uruguayensis<\/em> is distributed along a north-south gradient, with a relatively lower level of genetic structure compared to those observed in mtDNA.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>27 de novembro de 2024 &#8211; 12h SEMIN\u00c1RIO DE DADOS (Mestrado) &nbsp; KAREN ESTEFANIA VALENCIA\u00a0AGUILAR Phylogenomics of Homonota uruguayensis: An approach to the evolutionary history of population lineages using ddRAD-seq [&hellip;]<\/p>\n","protected":false},"author":3,"featured_media":15723,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[108],"tags":[],"class_list":["post-15722","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-seminarios-e-defesas"],"_links":{"self":[{"href":"https:\/\/www.ufrgs.br\/ppgbm\/wp-json\/wp\/v2\/posts\/15722","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ufrgs.br\/ppgbm\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.ufrgs.br\/ppgbm\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.ufrgs.br\/ppgbm\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ufrgs.br\/ppgbm\/wp-json\/wp\/v2\/comments?post=15722"}],"version-history":[{"count":1,"href":"https:\/\/www.ufrgs.br\/ppgbm\/wp-json\/wp\/v2\/posts\/15722\/revisions"}],"predecessor-version":[{"id":15724,"href":"https:\/\/www.ufrgs.br\/ppgbm\/wp-json\/wp\/v2\/posts\/15722\/revisions\/15724"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.ufrgs.br\/ppgbm\/wp-json\/wp\/v2\/media\/15723"}],"wp:attachment":[{"href":"https:\/\/www.ufrgs.br\/ppgbm\/wp-json\/wp\/v2\/media?parent=15722"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ufrgs.br\/ppgbm\/wp-json\/wp\/v2\/categories?post=15722"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ufrgs.br\/ppgbm\/wp-json\/wp\/v2\/tags?post=15722"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}