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      Spatial patterns of extra-pair paternity in a waterbird colony: separating the effects of nesting density and nest site location

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          Abstract

          Centres of avian colonies are usually associated with reduced predation risk and, thus, attract individuals of high quality, while poor-quality individuals are relegated to peripheral zones. Assuming that the incidence of extra-pair paternity (EPP) is dependent on individual quality, we could expect lower incidence of extra-pair offspring in the central parts of colonies. On the other hand, central pairs often nest in higher densities, which might increase EPP rate. To test these hypotheses, we sampled 124 great cormorant Phalacarocorax carbo sinensis chicks from 30 broods from different zones of a colony and genotyped them at seven highly polymorphic microsatellite loci. Sibship reconstruction confirmed the presence of at least one extra-pair chick in 30.0 % of broods. We found that EPP varied significantly between the zones of the colony, with higher incidence of extra-pair broods in the peripheral zone (53.3 vs. 6.7 % of broods). Centre-edge difference in EPP was consistent with the expected distribution of pair quality and suggested that poor-quality peripheral females were more likely to solicit extra-pair interactions, possibly to gain ‘good genes’ for their offspring. By contrast, we found no evidence for density dependence in EPP rate, indicating that likelihood of raising extra-pair offspring was not constrained by limited availability of local males. The results indicate that spatial randomization of sampling within avian colonies is critical to obtain robust estimations of EPP for non-solitary species. To our knowledge, this study provides the first evidence for the centre-edge difference in EPP within a breeding colony of birds.

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          Estimating Relatedness Using Genetic Markers

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            Sibship reconstruction from genetic data with typing errors.

            Likelihood methods have been developed to partition individuals in a sample into full-sib and half-sib families using genetic marker data without parental information. They invariably make the critical assumption that marker data are free of genotyping errors and mutations and are thus completely reliable in inferring sibships. Unfortunately, however, this assumption is rarely tenable for virtually all kinds of genetic markers in practical use and, if violated, can severely bias sibship estimates as shown by simulations in this article. I propose a new likelihood method with simple and robust models of typing error incorporated into it. Simulations show that the new method can be used to infer full- and half-sibships accurately from marker data with a high error rate and to identify typing errors at each locus in each reconstructed sib family. The new method also improves previous ones by adopting a fresh iterative procedure for updating allele frequencies with reconstructed sibships taken into account, by allowing for the use of parental information, and by using efficient algorithms for calculating the likelihood function and searching for the maximum-likelihood configuration. It is tested extensively on simulated data with a varying number of marker loci, different rates of typing errors, and various sample sizes and family structures and applied to two empirical data sets to demonstrate its usefulness.
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              Parentage and sibship inference from multilocus genotype data under polygamy.

              Likelihood methods have been developed to partition individuals in a sample into sibling clusters using genetic marker data without parental information. Most of these methods assume either both sexes are monogamous to infer full sibships only or only one sex is polygamous to infer full sibships and paternal or maternal (but not both) half sibships. We extend our previous method to the more general case of both sexes being polygamous to infer full sibships, paternal half sibships, and maternal half sibships and to the case of a two-generation sample of individuals to infer parentage jointly with sibships. The extension not only expands enormously the scope of application of the method, but also increases its statistical power. The method is implemented for both diploid and haplodiploid species and for codominant and dominant markers, with mutations and genotyping errors accommodated. The performance and robustness of the method are evaluated by analyzing both simulated and empirical data sets. Our method is shown to be much more powerful than pairwise methods in both parentage and sibship assignments because of the more efficient use of marker information. It is little affected by inbreeding in parents and is moderately robust to nonrandom mating and linkage of markers. We also show that individually much less informative markers, such as SNPs or AFLPs, can reach the same power for parentage and sibship inferences as the highly informative marker simple sequence repeats (SSRs), as long as a sufficient number of loci are employed in the analysis.
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                Author and article information

                Contributors
                pminias@biol.uni.lodz.pl
                Journal
                Behav Ecol Sociobiol
                Behav. Ecol. Sociobiol. (Print)
                Behavioral Ecology and Sociobiology
                Springer Berlin Heidelberg (Berlin/Heidelberg )
                0340-5443
                14 January 2016
                14 January 2016
                2016
                : 70
                : 369-376
                Affiliations
                [ ]Department of Teacher Training and Biodiversity Studies, University of Łódź, Banacha 1/3, 90-237 Łódź, Poland
                [ ]Department of Vertebrate Ecology and Zoology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
                [ ]Department of Molecular and Biometrical Techniques, Museum and Institute of Zoology PAS, 00-679 Warsaw, Poland
                [ ]Medical University of Łódź, Sterlinga 1/3, 91-425 Łódź, Poland
                Author notes

                Communicated by C. R. Brown

                Article
                2056
                10.1007/s00265-015-2056-0
                4748001
                26900213
                572d2909-38c0-4d71-9b5e-b3df03db51cd
                © The Author(s) 2016

                Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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.

                History
                : 24 September 2015
                : 27 December 2015
                : 29 December 2015
                Funding
                Funded by: University of Gdańsk
                Award ID: BW/L120-5-0422-0
                Award Recipient :
                Funded by: Ministry of Science and Higher Education in Poland
                Award ID: N N303 319940
                Award Recipient :
                Categories
                Original Article
                Custom metadata
                © Springer-Verlag Berlin Heidelberg 2016

                Ecology
                coloniality,great cormorant,microsatellites,phalacrocorax carbo sinensis,sibship reconstruction

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