Dataset Information

Genetic variation in the acorn barnacle from allozymes to population genomics.

ABSTRACT: Understanding the patterns of genetic variation within and among populations is a central problem in population and evolutionary genetics. We examine this question in the acorn barnacle, Semibalanus balanoides, in which the allozyme loci Mpi and Gpi have been implicated in balancing selection due to varying selective pressures at different spatial scales. We review the patterns of genetic variation at the Mpi locus, compare this to levels of population differentiation at mtDNA and microsatellites, and place these data in the context of genome-wide variation from high-throughput sequencing of population samples spanning the North Atlantic. Despite considerable geographic variation in the patterns of selection at the Mpi allozyme, this locus shows rather low levels of population differentiation at ecological and trans-oceanic scales (F(ST) ~ 5%). Pooled population sequencing was performed on samples from Rhode Island (RI), Maine (ME), and Southwold, England (UK). Analysis of more than 650 million reads identified approximately 335,000 high-quality SNPs in 19 million base pairs of the S. balanoides genome. Much variation is shared across the Atlantic, but there are significant examples of strong population differentiation among samples from RI, ME, and UK. An F(ST) outlier screen of more than 22,000 contigs provided a genome-wide context for interpretation of earlier studies on allozymes, mtDNA, and microsatellites. F(ST) values for allozymes, mtDNA and microsatellites are close to the genome-wide average for random SNPs, with the exception of the trans-Atlantic F(ST) for mtDNA. The majority of F(ST) outliers were unique between individual pairs of populations, but some genes show shared patterns of excess differentiation. These data indicate that gene flow is high, that selection is strong on a subset of genes, and that a variety of genes are experiencing diversifying selection at large spatial scales. This survey of polymorphism in S. balanoides provides a number of genomic tools that promise to make this a powerful model for ecological genomics of the rocky intertidal.

SUBMITTER: Flight PA

PROVIDER: S-EPMC3417161 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature

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Genetic variation in the acorn barnacle from allozymes to population genomics.

Flight Patrick A PA Rand David M DM

Integrative and comparative biology 20120704 3

Understanding the patterns of genetic variation within and among populations is a central problem in population and evolutionary genetics. We examine this question in the acorn barnacle, Semibalanus balanoides, in which the allozyme loci Mpi and Gpi have been implicated in balancing selection due to varying selective pressures at different spatial scales. We review the patterns of genetic variation at the Mpi locus, compare this to levels of population differentiation at mtDNA and microsatellite ...[more]

PMID: 22767487

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Project description:BackgroundVitiligo is an auto-immune progressive depigmentation disorder of the skin due to loss of melanocytes. Genetic risk is one of the important factors for development of vitiligo. Preponderance of vitiligo in certain ethnicities is known which can be analysed by understanding the distribution of allele frequencies across normal populations. Earlier GWAS identified 108 risk alleles for vitiligo in Europeans and East Asians. In this study, 64 of these risk alleles were used for analysing their enrichment and depletion across populations (1000 Genomes Project and IndiGen) with reference to 1000 Genomes dataset. Genetic risk scores were calculated and Fisher's exact test was performed to understand statistical significance of their variation in each population with respect to 1000 Genomes dataset as reference. In addition to SNPs reported in GWAS, significant variation in allele frequencies of 1079 vitiligo-related genes were also analysed. Two-tailed Chi-square test and Bonferroni's multiple adjustment values along with fixation index (≥ 0.5) and minimum allele frequency (≥ 0.05) were calculated and used to prioritise the variants based on pairwise comparison across populations.ResultsRisk alleles rs1043101 and rs10768122 belong to 3 prime UTR of glutamate receptor gene SLC1A2 are found to be highly enriched in the South Asian population when compared with the 'global normal' population. Intron variant rs4766578 (ATXN2) was found to be deleted in SAS, EAS and AFR and enriched in EUR and AMR1. This risk allele is found to be under positive selection in SAS, AMR1 and EUR. From the ancillary vitiligo gene list, nonsynonymous variant rs16891982 was found to be enriched in the European and the Admixed American populations and depleted in all others. rs2279238 and rs11039155 belonging to the LXR-α gene involved in regulation of metalloproteinase 2 and 9 (melanocyte precursors) were found to be associated with vitiligo in the North Indian population (in earlier study).ConclusionThe differential enrichment/depletion profile of the risk alleles provides insight into the underlying inter-population variations. This would provide clues towards prioritisation of SNPs associated with vitiligo thereby elucidating its preponderance in different ethnic groups.

Project description:Aims -Annually variable, but synchronous production of large seed crops ('masting') is a widespread phenomenon in temperate trees. Mounting concerns about the impacts of anthropogenic climate change (ACC) on plant reproduction, gives urgency to our need to understand better the role of climate on tree reproduction, and in particular, mast events. Unlike our understanding of reproductive phenology however, there is little consensus regarding how climate affects plant reproductive effort, or indeed the actual environmental triggers that underpin masting behaviour.Methods -We used a 27-year record of acorn yield from a population of 12 Quercus robur trees located in southern England to compare masting frequency and post-dispersal acorn yield each year for each tree, with long-term weather data over the same period. We focussed on discrete or sequential climate cues (temperature, precipitation, and frost days) as likely predictors of oak reproduction.Important findings -Annual post-dispersal acorn crop varied greatly; i.e. no acorns in 14 of the 27 years, but there was no sequential pattern of crop versus non-crop years indicating that weather, rather than resource limitation alone, dictated the timing of reproduction. Crop years were instead most closely associated with relatively cool late summer conditions in the preceding year, followed by anomalous summer warmth within crop year. Acorn yield increased following dry April and above average May and June temperatures within crop year. Although our results support a general association between warm late spring and summer conditions, and crop frequency and yield respectively, the influence of cooler later summer conditions in the year prior to masting highlights how a combination of weather cues may dictate the occurrence of mast years. Consequently, our results corroborate not only the hypothesis that temperature differentials between consecutive years, not absolute temperatures, may be the better predictor of mast seeding events, but lend support also to the suggestion that reproductive failure and resource accumulation resulting from a climate-linked environmental veto, drives future reproductive synchronization in temperate tree species.

Dataset Information

Genetic variation in the acorn barnacle from allozymes to population genomics.

Publications

Genetic variation in the acorn barnacle from allozymes to population genomics.

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