Guide to population genomics applied to Neotropical mammals
From experimental design to basic analysis with single nucleotide polymorphisms (SNPs)
DOI:
https://doi.org/10.32673/bjm.vie92.120Keywords:
ddRAD-Sequencing, ipyrad, Proechimys, R Scripts, StacksAbstract
Single nucleotide polymorphisms (SNPs) are genetic markers can be used in population genomic studies of Neotropical mammals. This essay is a guide with suggestions and tips for the main stages of a project involving SNPs and population genomics from a Reduced Representation Sequencing technique or RRS. This essay discusses how to think about an efficient experimental design, from the choice of samples and how to prepare the genomic libraries to tips for verifying the sequencing and the data quality. The key points of studies on population genomics are discussed in the text, with indications of references to support research projects. Notably, the guide contains suggestions rather than rules for this type of research. In the end, a database of the rodent species Proechimys steerei of the family Echimyidae is provided, and a pipeline to carry out in practice the steps of filtering SNPs and some fundamental statistical analysis using R packages. I hope this essay improve the understanding of students and researchers who are starting in the field of genomics. Even if it is a guide using examples from Neotropical mammals and RRS, much of what is discussed in this guide can be applied to any database of SNPs from any study group or generated from any genomic sequencing technique.
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