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      Developmental Stability Covaries with Genome-Wide and Single-Locus Heterozygosity in House Sparrows

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          Abstract

          Fluctuating asymmetry (FA), a measure of developmental instability, has been hypothesized to increase with genetic stress. Despite numerous studies providing empirical evidence for associations between FA and genome-wide properties such as multi-locus heterozygosity, support for single-locus effects remains scant. Here we test if, and to what extent, FA co-varies with single- and multilocus markers of genetic diversity in house sparrow ( Passer domesticus) populations along an urban gradient. In line with theoretical expectations, FA was inversely correlated with genetic diversity estimated at genome level. However, this relationship was largely driven by variation at a single key locus. Contrary to our expectations, relationships between FA and genetic diversity were not stronger in individuals from urban populations that experience higher nutritional stress. We conclude that loss of genetic diversity adversely affects developmental stability in P. domesticus, and more generally, that the molecular basis of developmental stability may involve complex interactions between local and genome-wide effects. Further study on the relative effects of single-locus and genome-wide effects on the developmental stability of populations with different genetic properties is therefore needed.

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          Most cited references126

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          Estimation of average heterozygosity and genetic distance from a small number of individuals.

          M Nei (1978)
          The magnitudes of the systematic biases involved in sample heterozygosity and sample genetic distances are evaluated, and formulae for obtaining unbiased estimates of average heterozygosity and genetic distance are developed. It is also shown that the number of individuals to be used for estimating average heterozygosity can be very small if a large number of loci are studied and the average heterozygosity is low. The number of individuals to be used for estimating genetic distance can also be very small if the genetic distance is large and the average heterozygosity of the two species compared is low.
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            Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material.

            Procedures utilizing Chelex 100 chelating resin have been developed for extracting DNA from forensic-type samples for use with the PCR. The procedures are simple, rapid, involve no organic solvents and do not require multiple tube transfers for most types of samples. The extraction of DNA from semen and very small bloodstains using Chelex 100 is as efficient or more efficient than using proteinase K and phenol-chloroform extraction. DNA extracted from bloodstains seems less prone to contain PCR inhibitors when prepared by this method. The Chelex method has been used with amplification and typing at the HLA DQ alpha locus to obtain the DQ alpha genotypes of many different types of samples, including whole blood, bloodstains, seminal stains, buccal swabs, hair and post-coital samples. The results of a concordance study are presented in which the DQ alpha genotypes of 84 samples prepared using Chelex or using conventional phenol-chloroform extraction are compared. The genotypes obtained using the two different extraction methods were identical for all samples tested.
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              Linkage disequilibrium in the human genome.

              With the availability of a dense genome-wide map of single nucleotide polymorphisms (SNPs), a central issue in human genetics is whether it is now possible to use linkage disequilibrium (LD) to map genes that cause disease. LD refers to correlations among neighbouring alleles, reflecting 'haplotypes' descended from single, ancestral chromosomes. The size of LD blocks has been the subject of considerable debate. Computer simulations and empirical data have suggested that LD extends only a few kilobases (kb) around common SNPs, whereas other data have suggested that it can extend much further, in some cases greater than 100 kb. It has been difficult to obtain a systematic picture of LD because past studies have been based on only a few (1-3) loci and different populations. Here, we report a large-scale experiment using a uniform protocol to examine 19 randomly selected genomic regions. LD in a United States population of north-European descent typically extends 60 kb from common alleles, implying that LD mapping is likely to be practical in this population. By contrast, LD in a Nigerian population extends markedly less far. The results illuminate human history, suggesting that LD in northern Europeans is shaped by a marked demographic event about 27,000-53,000 years ago.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2011
                1 July 2011
                : 6
                : 7
                : e21569
                Affiliations
                [1 ]Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, Belgium
                [2 ]Research Group of Genetic Diversity, Research Institute for Nature and Forest, Geraardsbergen, Belgium
                [3 ]Department of Animal and Plant Sciences, University of Sheffield, Sheffield, South Yorkshire, United Kingdom
                University of Arkanas, United States of America
                Author notes

                Conceived and designed the experiments: CV JM DAD LL. Performed the experiments: CV DAD VV. Analyzed the data: CV JM LL. Contributed reagents/materials/analysis tools: CV VV. Wrote the paper: CV JM DAD VV LL. Prepared figures and tables: CV VV. Editorial review: CV LL.

                Article
                PONE-D-10-06150
                10.1371/journal.pone.0021569
                3128584
                21747940
                b1974da7-fc9b-436a-b8da-c7023e85fdd1
                Vangestel et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                History
                : 8 December 2010
                : 3 June 2011
                Page count
                Pages: 10
                Categories
                Research Article
                Biology
                Developmental Biology
                Morphogenesis
                Organism Development
                Ecology
                Ecological Environments
                Terrestrial Environments
                Bioindicators
                Urban Ecology
                Genetics
                Heredity
                Genotypes
                Phenotypes
                Trait Locus
                Zoology
                Ornithology

                Uncategorized
                Uncategorized

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