title: Gene duplication, population genomics, and species-level differentiation within a tropical mountain shrub.
abstract: Gene duplication leads to paralogy, which complicates the de novo assembly of genotyping-by-sequencing (GBS) data. The issue of paralogous genes is exacerbated in plants, because they are particularly prone to gene duplication events. Paralogs are normally filtered from GBS data before undertaking population genomics or phylogenetic analyses. However, gene duplication plays an important role in the functional diversification of genes and it can also lead to the formation of postzygotic barriers. Using populations and closely related species of a tropical mountain shrub, we examine 1) the genomic differentiation produced by putative orthologs, and 2) the distribution of recent gene duplication among lineages and geography. We find high differentiation among populations from isolated mountain peaks and species-level differentiation within what is morphologically described as a single species. The inferred distribution of paralogs among populations is congruent with taxonomy and shows that GBS could be used to examine recent gene duplication as a source of genomic differentiation of nonmodel species.
authors.affiliation: Centre for Ecology, Evolution and Conservation, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom a.yanes@uea.ac.uk.
authors.forename: Alicia
authors.initials: A
authors.lastname: Mastretta-Yanes
authors.affiliation: Centro Regional del Bajío, Instituto de Ecología A. C., Pátzcuaro, Michoacán, México.
authors.forename: Sergio
authors.initials: S
authors.lastname: Zamudio
authors.affiliation: Department of Bioscience, Aarhus University, Denmark.
authors.forename: Tove H
authors.initials: TH
authors.lastname: Jorgensen
authors.affiliation: Department of Ecology and Evolution, Biophore Building, University of Lausanne, Switzerland.
authors.forename: Nils
authors.initials: N
authors.lastname: Arrigo
authors.affiliation: Department of Ecology and Evolution, Biophore Building, University of Lausanne, Switzerland.
authors.forename: Nadir
authors.initials: N
authors.lastname: Alvarez
authors.affiliation: Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico.
authors.forename: Daniel
authors.initials: D
authors.lastname: Piñero
authors.affiliation: Centre for Ecology, Evolution and Conservation, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain.
authors.forename: Brent C
authors.initials: BC
authors.lastname: Emerson
mesh_terms: D020440:Gene Duplication / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D010802:Phylogeny; D010944:Plants / Q000235:genetics*
keywords: Berberis; GBS; RAD-seq; Transmexican Volcanic Belt; de novo assembly; paralogy