GBE Gene Duplication, Population Genomics, and Species-Level Differentiation within a Tropical Mountain Shrub Downloaded from https://academic.oup.com/gbe/article-abstract/6/10/2611/609646 by CSIC - Instituto De Ganaderia Montana user on 12 April 2019 Alicia Mastretta-Yanes1,*, Sergio Zamudio2, Tove H. Jorgensen3, Nils Arrigo4,NadirAlvarez4, Daniel Pin˜ ero5, and Brent C. Emerson1,6 1Centre for Ecology, Evolution and Conservation, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom 2Centro Regional del Bajı´o, Instituto de Ecologı´aA.C.,Pa´tzcuaro, Michoaca´n, Me´xico 3Department of Bioscience, Aarhus University, Denmark 4Department of Ecology and Evolution, Biophore Building, University of Lausanne, Switzerland 5Departamento de Ecologı´a Evolutiva, Instituto de Ecologı´a, Universidad Nacional Auto´ nomadeMe´xico, Mexico 6Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiologı´a (IPNA-CSIC), San Cristo´ bal de La Laguna, Santa Cruz de Tenerife, Spain *Corresponding author: E-mail:
[email protected]. Accepted: September 8, 2014 Data deposition: This project has been deposited at Dryad Repository under the accession doi:10.5061/dryad.n3jk5. 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.