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      Phylogenetic Trees and Networks Can Serve as Powerful and Complementary Approaches for Analysis of Genomic Data

      1 , 2 , 3 , 4

      Systematic Biology

      Oxford University Press (OUP)

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          Abstract

          Genomic data have had a profound impact on nearly every biological discipline. In systematics and phylogenetics, the thousands of loci that are now being sequenced can be analyzed under the multispecies coalescent model (MSC) to explicitly account for gene tree discordance due to incomplete lineage sorting (ILS). However, the MSC assumes no gene flow post divergence, calling for additional methods that can accommodate this limitation. Explicit phylogenetic network methods have emerged, which can simultaneously account for ILS and gene flow by representing evolutionary history as a directed acyclic graph. In this point of view, we highlight some of the strengths and limitations of phylogenetic networks and argue that tree-based inference should not be blindly abandoned in favor of networks simply because they represent more parameter rich models. Attention should be given to model selection of reticulation complexity, and the most robust conclusions regarding evolutionary history are likely obtained when combining tree- and network-based inference.

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          Most cited references 64

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          A draft sequence of the Neandertal genome.

          Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.
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            Generating samples under a Wright-Fisher neutral model of genetic variation.

             R Hudson (2002)
            A Monte Carlo computer program is available to generate samples drawn from a population evolving according to a Wright-Fisher neutral model. The program assumes an infinite-sites model of mutation, and allows recombination, gene conversion, symmetric migration among subpopulations, and a variety of demographic histories. The samples produced can be used to investigate the sampling properties of any sample statistic under these neutral models.
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              Hybridization as an invasion of the genome.

               James Mallet (2005)
              Hybridization between species is commonplace in plants, but is often seen as unnatural and unusual in animals. Here, I survey studies of natural interspecific hybridization in plants and a variety of animals. At least 25% of plant species and 10% of animal species, mostly the youngest species, are involved in hybridization and potential introgression with other species. Species in nature are often incompletely isolated for millions of years after their formation. Therefore, much evolution of eventual reproductive isolation can occur while nascent species are in gene-flow contact, in sympatry or parapatry, long after divergence begins. Although the relative importance of geographic isolation and gene flow in the origin of species is still unknown, many key processes involved in speciation, such as 'reinforcement' of post-mating isolation by the evolution of assortative mating, will have ample opportunity to occur in the presence of continuing gene flow. Today, DNA sequence data and other molecular methods are beginning to show that limited invasions of the genome are widespread, with potentially important consequences in evolutionary biology, speciation, biodiversity, and conservation.
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                Author and article information

                Journal
                Systematic Biology
                Oxford University Press (OUP)
                1063-5157
                1076-836X
                May 2020
                May 01 2020
                September 21 2019
                May 2020
                May 01 2020
                September 21 2019
                : 69
                : 3
                : 593-601
                Affiliations
                [1 ]Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY 11201, USA
                [2 ]Biology PhD Program, CUNY Graduate Center, 365 5th Ave., New York, NY 10016, USA
                [3 ]Department of Botany, University of Wisconsin – Madison, 1300 University Ave, Madison, WI 53706, USA
                [4 ]Department of Statistics, University of Wisconsin – Madison, 1300 University Ave, Madison, WI 53706, USA
                Article
                10.1093/sysbio/syz056
                © 2019

                https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model

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