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      Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants ( Pedicularis: Orobanchaceae)

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      1 , 2 , * , 1 , 2
      Systematic Biology
      Oxford University Press

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          Abstract

          Phylogenetic relationships among recently diverged species are often difficult to resolve due to insufficient phylogenetic signal in available markers and/or conflict among gene trees. Here we explore the use of reduced-representation genome sequencing, specifically in the form of restriction-site associated DNA (RAD), for phylogenetic inference and the detection of ancestral hybridization in non-model organisms. As a case study, we investigate Pedicularis section Cyathophora, a systematically recalcitrant clade of flowering plants in the broomrape family (Orobanchaceae). Two methods of phylogenetic inference, maximum likelihood and Bayesian concordance, were applied to data sets that included as many as 40,000 RAD loci. Both methods yielded similar topologies that included two major clades: a “rex-thamnophila” clade, composed of two species and several subspecies with relatively low floral diversity, and geographically widespread distributions at lower elevations, and a “superba” clade, composed of three species characterized by relatively high floral diversity and isolated geographic distributions at higher elevations. Levels of molecular divergence between subspecies in the rex-thamnophila clade are similar to those between species in the superba clade. Using Patterson’s D-statistic test, including a novel extension of the method that enables finer-grained resolution of introgression among multiple candidate taxa by removing the effect of their shared ancestry, we detect significant introgression among nearly all taxa in the rex-thamnophila clade, but not between clades or among taxa within the superba clade. These results suggest an important role for geographic isolation in the emergence of species barriers, by facilitating local adaptation and differentiation in the absence of homogenizing gene flow. [Concordance factors; genotyping-by-sequencing; hybridization; partitioned D-statistic test; Pedicularis; restriction-site associated DNA.]

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          A high-coverage genome sequence from an archaic Denisovan individual.

          We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of "missing evolution" in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.
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            Gene Trees in Species Trees

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              Testing for ancient admixture between closely related populations.

              One enduring question in evolutionary biology is the extent of archaic admixture in the genomes of present-day populations. In this paper, we present a test for ancient admixture that exploits the asymmetry in the frequencies of the two nonconcordant gene trees in a three-population tree. This test was first applied to detect interbreeding between Neandertals and modern humans. We derive the analytic expectation of a test statistic, called the D statistic, which is sensitive to asymmetry under alternative demographic scenarios. We show that the D statistic is insensitive to some demographic assumptions such as ancestral population sizes and requires only the assumption that the ancestral populations were randomly mating. An important aspect of D statistics is that they can be used to detect archaic admixture even when no archaic sample is available. We explore the effect of sequencing error on the false-positive rate of the test for admixture, and we show how to estimate the proportion of archaic ancestry in the genomes of present-day populations. We also investigate a model of subdivision in ancestral populations that can result in D statistics that indicate recent admixture.
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                Author and article information

                Journal
                Syst Biol
                Syst. Biol
                sysbio
                sysbio
                Systematic Biology
                Oxford University Press
                1063-5157
                1076-836X
                September 2013
                14 June 2013
                14 June 2013
                : 62
                : 5
                : 689-706
                Affiliations
                1Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637, USA; and 2Botany Department, Field Museum of Natural History, Chicago, IL 60605, USA
                Author notes

                Associate Editor: Cécile Ané

                *Correspondence to be sent to: Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th Street, Chicago, IL 60637, USA; E-mail: daeaton@ 123456uchicago.edu .
                Article
                syt032
                10.1093/sysbio/syt032
                3739883
                23652346
                6214699f-91ee-469b-99d4-f28de6af0733
                © The Author(s) 2013. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 23 January 2013
                : 19 March 2013
                : 1 May 2013
                Page count
                Pages: 18
                Categories
                Regular Articles

                Animal science & Zoology
                Animal science & Zoology

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