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      Range-wide genetic structure in the thorn-tailed rayadito suggests limited gene flow towards peripheral populations

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          Abstract

          Understanding the population genetic consequences of habitat heterogeneity requires assessing whether patterns of gene flow correspond to landscape configuration. Studies of the genetic structure of populations are still scarce for Neotropical forest birds. We assessed range-wide genetic structure and contemporary gene flow in the thorn-tailed rayadito ( Aphrastura spinicauda), a passerine bird inhabiting the temperate forests of South America. We used 12 microsatellite loci to genotype 582 individuals from eight localities across a large latitudinal range (30°S–56°S). Using population structure metrics, multivariate analyses, clustering algorithms, and Bayesian methods, we found evidence for moderately low regional genetic structure and reduced gene flow towards the range margins. Genetic differentiation increased with geographic distance, particularly in the southern part of the species’ distribution where forests are continuously distributed. Populations in the north seem to experience limited gene flow likely due to forest discontinuity, and may comprise a demographically independent unit. The southernmost population, on the other hand, is genetically depauperate and different from all other populations. Different analytical approaches support the presence of three to five genetic clusters. We hypothesize that the genetic structure of the species follows a hierarchical clustered pattern.

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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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            Disappearance of insectivorous birds from tropical forest fragments.

            Determining the impact of forest disturbance and fragmentation on tropical biotas is a central goal of conservation biology. Among tropical forest birds, understory insectivores are particularly sensitive to habitat disturbance and fragmentation, despite their relatively small sizes and freedom from hunting pressure. Why these birds are especially vulnerable to fragmentation is not known. Our data indicate that the best determinant of the persistence of understory insectivorous birds in small fragments is the ability to disperse through deforested countryside habitats. This finding contradicts our initial hypothesis that the decline of insectivorous birds in forest fragments is caused by impoverished invertebrate prey base in fragments. Although we observed significantly fewer insectivorous birds in smaller fragments, extensive sampling of invertebrate communities (106,082 individuals) and avian diets (of 735 birds) revealed no important differences between large and small fragments. Neither habitat specificity nor drier fragment microclimates seemed critical. Bird species that were less affected by forest fragmentation were, in general, those that used the deforested countryside more, and we suggest that the key to their conservation will be found there.
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              Evaluating the performance of a multilocus Bayesian method for the estimation of migration rates.

              Bayesian methods have become extremely popular in molecular ecology studies because they allow us to estimate demographic parameters of complex demographic scenarios using genetic data. Articles presenting new methods generally include sensitivity studies that evaluate their performance, but they tend to be limited and need to be followed by a more thorough evaluation. Here we evaluate the performance of a recent method, bayesass, which allows the estimation of recent migration rates among populations, as well as the inbreeding coefficient of each local population. We expand the simulation study of the original publication by considering multi-allelic markers and scenarios with varying number of populations. We also investigate the effect of varying migration rates and F(ST) more thoroughly in order to identify the region of parameter space where the method is and is not able to provide accurate estimates of migration rate. Results indicate that if the demographic history of the species being studied fits the assumptions of the inference model, and if genetic differentiation is not too low (F(ST) > or = 0.05), then the method can give fairly accurate estimates of migration rates even when they are fairly high (about 0.1). However, when the assumptions of the inference model are violated, accurate estimates are obtained only if migration rates are very low (m = 0.01) and genetic differentiation is high (F(ST) > or = 0.10). Our results also show that using posterior assignment probabilities as an indication of how much confidence we can place on the assignments is problematical since the posterior probability of assignment can be very high even when the individual assignments are very inaccurate.
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                Author and article information

                Contributors
                eboterod@gmail.com
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                10 June 2020
                10 June 2020
                2020
                : 10
                : 9409
                Affiliations
                [1 ]ISNI 0000 0004 0385 4466, GRID grid.443909.3, Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, , Universidad de Chile, ; Santiago, Chile
                [2 ]Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
                [3 ]SELVA: Research for conservation in the Neotropics, Bogotá, Colombia
                [4 ]ISNI 0000 0001 2156 804X, GRID grid.412848.3, Departamento de Ecología y Biodiversidad, Facultad de Ecología y Recursos Naturales, , Universidad Andrés Bello, ; Santiago, Chile
                [5 ]ISNI 0000 0001 2156 804X, GRID grid.412848.3, Centro de investigación para la sustentabilidad, , Universidad Andrés Bello, ; Santiago, Chile
                [6 ]ISNI 0000 0004 0487 6309, GRID grid.441811.9, Instituto de Ciencias Naturales, , Universidad de las Américas, ; Santiago, Chile
                [7 ]ISNI 0000 0004 0385 4466, GRID grid.443909.3, Programa de Magister en Áreas Silvestres y Conservación de la Naturaleza, Facultad de Ciencias Forestales y Conservación de la Naturaleza, , Universidad de Chile, ; Santiago, Chile
                [8 ]ISNI 0000 0001 2156 804X, GRID grid.412848.3, Doctorado en Medicina de la Conservación, Facultad de Ecología y Recursos Naturales, , Universidad Andrés Bello, ; Santiago, Chile
                [9 ]Programa de Conservación Biocultural Sub-Antártica, Parque Etnobotánico Omora, Universidad de Magallanes & Instituto de Ecología y Biodiversidad, Santiago, Chile
                [10 ]ISNI 0000 0001 1008 957X, GRID grid.266869.5, Sub-Antarctic Biocultural Conservation Program, Department of Philosophy and Religion & Department of Biological Sciences, , University of North Texas, ; Denton, TX USA
                Article
                66450
                10.1038/s41598-020-66450-7
                7287099
                32523081
                272921d5-2d27-4f84-a665-cee1364a0d30
                © The Author(s) 2020

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 15 January 2020
                : 18 May 2020
                Categories
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                © The Author(s) 2020

                Uncategorized
                population genetics,behavioural ecology,molecular ecology,population dynamics
                Uncategorized
                population genetics, behavioural ecology, molecular ecology, population dynamics

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