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Phylogenomics and population genomics applied to species from genus Cereus (Cactaceae)

Grant number: 19/10341-6
Support Opportunities:Scholarships abroad - Research
Effective date (Start): February 04, 2020
Effective date (End): April 04, 2020
Field of knowledge:Biological Sciences - Genetics - Plant Genetics
Principal Investigator:Fernando de Faria Franco
Grantee:Fernando de Faria Franco
Host Investigator: Deren Eaton
Host Institution: Centro de Ciências Humanas e Biológicas (CCHB). Universidade Federal de São Carlos (UFSCAR). Sorocaba , SP, Brazil
Research place: Columbia University in the City of New York, United States  


In this study, genetic data generated by the double-digest Restriction-site Associated DNA sequencing (ddRAD-seq) will be used to investigate biogeographic and evolutionary aspects in species from genus Cereus (Cactaceae). The proposal is subdivided in two subprojects. In subproject 1, ddRAD data already obtained in a previous project for 64 samples subdivided into 36 species (24 ingroups and 11 outgroups) will be used to perform different coalescing analyzes for phylogenetic inference, calibrate the phylogeny and perform biogeographic reconstruction for Cereus. In addition, further analyzes will be carry out to identify SNPs under selection and with phylogenetic signal which could be associated to candidate functional phenotypes and/or climatic variables, in order to identify candidate sequences that are relevant to explain the diversification of the group. For subproject 2, the ddRAD data are partially collected and, after complementation, will be used to investigate the population structure, genealogical relationships, demographic fluctuations and gene flow estimates for two species of Cereus, which compose a monophyletic group occurring in the coastal region of Brazil: C. fernambucensis and C. insularis. In this subproject, alternative models will be established to test a previous hypothesis for peripatric origin of C. insularis, a species endemic to Fernando de Noronha islands. Finally, with the expertise acquired during the execution of this project, a theoretical-practical course, postgraduate level, about SNP filtering and data analysis will be organized. (AU)

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