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      Population Genomics in Rhamdia quelen (Heptapteridae, Siluriformes) Reveals Deep Divergence and Adaptation in the Neotropical Region

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          Abstract

          Rhamdia quelen, a Neotropical fish with hybridization between highly divergent mitochondrial DNA (mtDNA) lineages, represents an interesting evolutionary model. Previous studies suggested that there might be demographic differences between coastal lagoons and riverine environments, as well as divergent populations that could be reproductively isolated. Here, we investigated the genetic diversity pattern of this taxon in the Southern Neotropical Basin system that includes the La Plata Basin, Patos-Merin lagoon basin and the coastal lagoons draining to the SW Atlantic Ocean, through a population genomics approach using 2b-RAD-sequencing-derived single nucleotide polymorphisms (SNPs). The genomic scan identified selection footprints associated with divergence and suggested local adaptation environmental drivers. Two major genomic clusters latitudinally distributed in the Northern and Southern basins were identified, along with consistent signatures of divergent selection between them. Population structure based on the whole set of loci and on the presumptive neutral vs. adaptive loci showed deep genomic divergence between the two major clusters. Annotation of the most consistent SNPs under divergent selection revealed some interesting candidate genes for further functional studies. Moreover, signals of adaptation to a coastal lagoon environment mediated by purifying selection were found. These new insights provide a better understanding of the complex evolutionary history of R. quelen in the southernmost basin of the Neotropical region.

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          Further analysts of the data by akaike' s information criterion and the finite corrections

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            The genomics of speciation-with-gene-flow.

            The emerging field of speciation genomics is advancing our understanding of the evolution of reproductive isolation from the individual gene to a whole-genome perspective. In this new view it is important to understand the conditions under which 'divergence hitchhiking' associated with the physical linkage of gene regions, versus 'genome hitchhiking' associated with reductions in genome-wide rates of gene flow caused by selection, can enhance speciation-with-gene-flow. We describe here a theory predicting four phases of speciation, defined by changes in the relative effectiveness of divergence and genome hitchhiking, and review empirical data in light of the theory. We outline future directions, emphasizing the need to couple next-generation sequencing with selection, transplant, functional genomics, and mapping studies. This will permit a natural history of speciation genomics that will help to elucidate the factors responsible for population divergence and the roles that genome structure and different forms of hitchhiking play in facilitating the genesis of new biodiversity. Copyright © 2012 Elsevier Ltd. All rights reserved.
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              2b-RAD: a simple and flexible method for genome-wide genotyping.

              We describe 2b-RAD, a streamlined restriction site-associated DNA (RAD) genotyping method based on sequencing the uniform fragments produced by type IIB restriction endonucleases. Well-studied accessions of Arabidopsis thaliana were genotyped to validate the method's accuracy and to demonstrate fine-tuning of marker density as needed. The simplicity of the 2b-RAD protocol makes it particularly suitable for high-throughput genotyping as required for linkage mapping and profiling genetic variation in natural populations.
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                Author and article information

                Journal
                Genes (Basel)
                Genes (Basel)
                genes
                Genes
                MDPI
                2073-4425
                17 January 2020
                January 2020
                : 11
                : 1
                : 109
                Affiliations
                [1 ]Sección Genética Evolutiva, Facultad de Ciencias, UdelaR, Iguá 4225, Montevideo 11400, Uruguay; ggarcia@ 123456fcien.edu.uy
                [2 ]Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus de Lugo, Universidade de Santiago de Compostela, Avenida Carballo Calero s/n, E-27002 Lugo, Spain; adrian.casanova.chiclana@ 123456gmail.com (A.C.); miguel.hermida@ 123456usc.es (M.H.); belen.gomez@ 123456usc.es (B.G.P.); paulino.martinez@ 123456usc.es (P.M.); mcarmen.bouza@ 123456usc.es (C.B.)
                [3 ]Instituto de Acuicultura, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
                Author notes
                [* ]Correspondence: nrriosp@ 123456gmail.com ; Tel.: +598-25258618 (ext. 140)
                Author information
                https://orcid.org/0000-0002-0669-7668
                https://orcid.org/0000-0002-9388-2721
                https://orcid.org/0000-0003-0327-9521
                https://orcid.org/0000-0003-3548-6306
                https://orcid.org/0000-0002-3681-3738
                Article
                genes-11-00109
                10.3390/genes11010109
                7017130
                31963477
                6716504d-0dd0-48d5-9446-14a6aa423f30
                © 2020 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 22 November 2019
                : 14 January 2020
                Categories
                Article

                genomic divergence,environmental adaptation,rhamdia quelen,rad-seq

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