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      Gene flow and Andean uplift shape the diversification of Gasteracantha cancriformis (Araneae: Araneidae) in Northern South America

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          Abstract

          The Andean uplift has played a major role in shaping the current Neotropical biodiversity. However, in arthropods other than butterflies, little is known about how this geographic barrier has impacted species historical diversification. Here, we examined the phylogeography of the widespread color polymorphic spider Gasteracantha cancriformis to evaluate the effect of the northern Andean uplift on its divergence and assess whether its diversification occurred in the presence of gene flow. We inferred phylogenetic relationships and divergence times in G. cancriformis using mitochondrial and nuclear data from 105 individuals in northern South America. Genetic diversity, divergence, and population structure were quantified. We also compared multiple demographic scenarios for this species using a model‐based approach ( phrapl) to determine divergence with or without gene flow. At last, we evaluated the association between genetic variation and color polymorphism. Both nuclear and mitochondrial data supported two well‐differentiated clades, which correspond to populations occurring on opposite sides of the Eastern cordillera of the Colombian Andes. The final uplift of this cordillera was identified as the most likely force that shaped the diversification of G. cancriformis in northern South America, resulting in a cis‐ and trans‐Andean phylogeographic structure for the species. We also found shared genetic variation between the cis‐ and trans‐Andean clades, which is better explained by a scenario of historical divergence in the face of gene flow. This has been likely facilitated by the presence of low‐elevation passes across the Eastern Colombian cordillera. Our work constitutes the first example in which the Andean uplift coupled with gene flow influenced the evolutionary history of an arachnid lineage.

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          Inconsistency of phylogenetic estimates from concatenated data under coalescence.

          Although multiple gene sequences are becoming increasingly available for molecular phylogenetic inference, the analysis of such data has largely relied on inference methods designed for single genes. One of the common approaches to analyzing data from multiple genes is concatenation of the individual gene data to form a single supergene to which traditional phylogenetic inference procedures - e.g., maximum parsimony (MP) or maximum likelihood (ML) - are applied. Recent empirical studies have demonstrated that concatenation of sequences from multiple genes prior to phylogenetic analysis often results in inference of a single, well-supported phylogeny. Theoretical work, however, has shown that the coalescent can produce substantial variation in single-gene histories. Using simulation, we combine these ideas to examine the performance of the concatenation approach under conditions in which the coalescent produces a high level of discord among individual gene trees and show that it leads to statistically inconsistent estimation in this setting. Furthermore, use of the bootstrap to measure support for the inferred phylogeny can result in moderate to strong support for an incorrect tree under these conditions. These results highlight the importance of incorporating variation in gene histories into multilocus phylogenetics.
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            Bayesian inference of ancient human demography from individual genome sequences

            Besides their value for biomedicine, individual genome sequences are a rich source of information about human evolution. Here we describe an effort to estimate key evolutionary parameters from sequences for six individuals from diverse human populations. We use a Bayesian, coalescent-based approach to extract information about ancestral population sizes, divergence times, and migration rates from inferred genealogies at many neutrally evolving loci from across the genome. We introduce new methods for accommodating gene flow between populations and integrating over possible phasings of diploid genotypes. We also describe a custom pipeline for genotype inference to mitigate biases from heterogeneous sequencing technologies and coverage levels. Our analysis indicates that the San of Southern Africa diverged from other human populations 108–157 thousand years ago (kya), that Eurasians diverged from an ancestral African population 38–64 kya, and that the effective population size of the ancestors of all modern humans was ~9,000.
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              The trouble with isolation by distance.

              The genetic population structure of many species is characterised by a pattern of isolation by distance (IBD): due to limited dispersal, individuals that are geographically close tend to be genetically more similar than individuals that are far apart. Despite the ubiquity of IBD in nature, many commonly used statistical tests are based on a null model that is completely non-spatial, the Island model. Here, I argue that patterns of spatial autocorrelation deriving from IBD present a problem for such tests as it can severely bias their outcome. I use simulated data to illustrate this problem for two widely used types of tests: tests of hierarchical population structure and the detection of loci under selection. My results show that for both types of tests the presence of IBD can indeed lead to a large number of false positives. I therefore argue that all analyses in a study should take the spatial dependence in the data into account, unless it can be shown that there is no spatial autocorrelation in the allele frequency distribution that is under investigation. Thus, it is urgent to develop additional statistical approaches that are based on a spatially explicit null model instead of the non-spatial Island model. © 2012 Blackwell Publishing Ltd.
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                Author and article information

                Contributors
                camilo.salazar@urosario.edu.co
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                25 June 2018
                July 2018
                : 8
                : 14 ( doiID: 10.1002/ece3.2018.8.issue-14 )
                : 7131-7142
                Affiliations
                [ 1 ] Programa de Biología Facultad de Ciencias Naturales y Matemáticas Universidad del Rosario Bogotá Colombia
                [ 2 ] Departamento de Ciencias Biológicas Universidad de los Andes Bogotá Colombia
                [ 3 ] Smithsonian Tropical Research Institute Ancón Panamá
                [ 4 ] Department of Genetics, Evolution and Bioagents Institute of Biology University of Campinas Campinas Sao Paulo Brazil
                Author notes
                [*] [* ] Correspondence

                Camilo Salazar, Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Cra. 24 No 63C‐69, Bogotá D.C. 111221, Colombia.

                Email: camilo.salazar@ 123456urosario.edu.co

                Author information
                http://orcid.org/0000-0002-7266-4055
                http://orcid.org/0000-0002-7259-1183
                http://orcid.org/0000-0003-4586-8674
                http://orcid.org/0000-0001-6582-1449
                http://orcid.org/0000-0001-9217-6588
                Article
                ECE34237
                10.1002/ece3.4237
                6065347
                30073072
                663c8e9c-972b-4e43-a6e8-03c2d19a5356
                © 2018 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 23 January 2018
                : 27 April 2018
                : 03 May 2018
                Page count
                Figures: 4, Tables: 2, Pages: 12, Words: 9491
                Funding
                Funded by: Departamento Administrativo de Ciencia, Tecnología e Innovación
                Award ID: FP44842‐005‐2017
                Funded by: Fundação de Amparo à Pesquisa do Estado de São Paulo
                Award ID: 2012/02526‐7
                Award ID: 2013/08293‐7
                Award ID: 2013/50491‐0
                Categories
                Original Research
                Original Research
                Custom metadata
                2.0
                ece34237
                July 2018
                Converter:WILEY_ML3GV2_TO_NLMPMC version:version=5.4.4 mode:remove_FC converted:30.07.2018

                Evolutionary Biology
                andean passes,andean uplift,colombian andes,gasteracantha cancriformis,gene flow

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