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      Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake.

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          Abstract

          The genomic causes and effects of divergent ecological selection during speciation are still poorly understood. Here we report the discovery and detailed characterization of early-stage adaptive divergence of two cichlid fish ecomorphs in a small (700 meters in diameter) isolated crater lake in Tanzania. The ecomorphs differ in depth preference, male breeding color, body shape, diet, and trophic morphology. With whole-genome sequences of 146 fish, we identified 98 clearly demarcated genomic "islands" of high differentiation and demonstrated the association of genotypes across these islands with divergent mate preferences. The islands contain candidate adaptive genes enriched for functions in sensory perception (including rhodopsin and other twilight-vision-associated genes), hormone signaling, and morphogenesis. Our study suggests mechanisms and genomic regions that may play a role in the closely related mega-radiation of Lake Malawi.

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          Most cited references31

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          Gene Ontology: tool for the unification of biology

          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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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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              Inferring human population size and separation history from multiple genome sequences

              The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model their ancestral relationship under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20-30 thousand years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The Multiple Sequentially Markovian Coalescent (MSMC) analyses the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals. Results from applying MSMC to genome sequences from nine populations across the world suggest that the genetic separation of non-African ancestors from African Yoruban ancestors started long before 50,000 years ago, and give information about human population history as recently as 2,000 years ago, including the bottleneck in the peopling of the Americas, and separations within Africa, East Asia and Europe.
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                Author and article information

                Journal
                Science
                Science (New York, N.Y.)
                1095-9203
                0036-8075
                Dec 18 2015
                : 350
                : 6267
                Affiliations
                [1 ] Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK. Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1QN, UK.
                [2 ] School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK.
                [3 ] Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK.
                [4 ] Department of Evolutionary Studies of Biosystems, SOKENDAI, Kanagawa 240-0193, Japan.
                [5 ] Tanzania Fisheries Research Institute, Box 9750, Dar es Salaam, Tanzania.
                [6 ] School of Biological Sciences, Life Sciences Building, 24 Tyndall Avenue, University of Bristol, Bristol BS8 1TQ, UK. george.turner@bangor.ac.uk m.genner@bristol.ac.uk.
                [7 ] School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK. george.turner@bangor.ac.uk m.genner@bristol.ac.uk.
                Article
                350/6267/1493 EMS66047
                10.1126/science.aac9927
                26680190
                074155c5-b832-4a41-9dd0-031cb5d1de29
                Copyright © 2015, American Association for the Advancement of Science.
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