Unbalanced Sample Size Introduces Spurious Correlations to Genome-Wide Heterozygosity Analyses

Liu, Li; Caselli, Richard J.

doi:10.1159/000507576

Cited by 2 publications

(1 citation statement)

References 30 publications

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“…The distributions of within‐stand, per‐locus expected heterozygosity values showed a moderate excess in all species, although with quite large variation among loci (Results R6). The extent of heterozygote excess was correlated to MAF (Results R6), with more negative inbreeding coefficient values for higher MAFs, suggesting that departure from Hardy–Weinberg equilibrium may be caused by some technical bias; heterozygote excess in high‐throughput sequence data has been previously reported as partially, but not entirely, caused by paralogous alleles (Gayral et al, 2013), or as an effect of small sample sizes (Liu & Caselli, 2019). Note, however, that we applied filters to remove paralogues.…”

Section: Resultsmentioning

confidence: 89%

Common microgeographical selection patterns revealed in four European conifers

et al. 2022

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Microgeographical adaptation occurs when the effects of directional selection persist despite gene flow. Traits and genetic loci under selection can then show adaptive divergence, against the backdrop of little differentiation at other traits or loci. How common such events are and how strong the selection is that underlies them remain open questions. Here, we discovered and analysed microgeographical patterns of genomic divergence in four European and Mediterranean conifers with widely differing life-history traits and ecological requirements (Abies alba MIll., Cedrus atlantica [Endl.] Manetti, Pinus halepensis Mill. and Pinus pinaster Aiton) by screening pairs from geographically close forest stands sampled along steep ecological gradients. We inferred patterns of genomic divergence by applying a combination of divergence outlier detection methods, demographic modelling, Approximate Bayesian Computationinferences and genomic annotation to genomic data. Surprisingly for such small geographical scales, we showed that selection is strong in all species but generally affects different loci in each. A clear signature of selection was systematically detected on a fraction of the genome, of the order of 0.1%-1% of the loci depending on the species. The novel modelling method we designed for estimating selection coefficients showed that the microgeographical selection coefficient scaled by population size (Ns) was 2-30. Our results convincingly suggest that selection maintains withinpopulation diversity at microgeographical scales in spatially heterogeneous environments. Such genetic diversity is likely to be a major reservoir of adaptive potential, helping populations to adapt under fluctuating environmental conditions.

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Section: Resultsmentioning

confidence: 89%

Common microgeographical selection patterns revealed in four European conifers

et al. 2022

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SNP heterozygosity, relatedness and inbreeding of whole genomes from the isolated population of the Faroe Islands

Gislason

2023

BMC Genomics

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Background The population of the Faroe Islands is an isolated population but very little is known about it from whole genome sequencing. The population of about 50000 people has a high incidence of rare diseases e.g., 1:300 for Primary Carnitine Deficiency. A screening programme was implemented, and eleven persons were also whole genome sequenced at x37 coverage for diagnostic purposes of those cases that were not affected by the known mutations. The purpose of our study is to utilize the high coverage data to explore the genomic variation and the ancestral history of the population. We study the SNP heterozygosity, the pairwise relatedness from kinship, the inbreeding from runs of homozygosity ROH, and we find the minor allele frequency distribution. We estimate the population ancestry and the timing of the founding event by using the whole genomes from eight consenting individuals. Results We find the number of SNPs and the heterozygosity for the eight individual samples, and for merged samples, for which we also study the relatedness. We find close relatedness between the supposedly unrelated individuals. From ROH, we interpret the high relatedness as an ancient property of the isolated population. A bottleneck event is estimated starting between years $$\sim 50-300$$ ∼ 50 - 300 with a maximum consanguineous population in year $$\sim 600$$ ∼ 600 and similarly consanguineous between years $$500-700$$ 500 - 700 . The ancestry analysis shows the population descends from founders of $$>99\%$$ > 99 % European and $$<1\%$$ < 1 % Admixed American ancestry. A distinct clustering near the central European and British populations of the 1000 Genome Project is likely the result of the population isolation and genetic drift. The minor allele frequency distribution suggests many rare variants. Conclusions The ancestry is mainly European while the inbreeding is higher compared to European populations and population isolates. The Faroese population has inbreeding more like ancient Europeans. We discovered a bottlenecked and consanguineous population event and estimated it starting in the 1st-4th century as compared to the oldest archaeological findings from the 4th-6th century.

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Unbalanced Sample Size Introduces Spurious Correlations to Genome-Wide Heterozygosity Analyses

Cited by 2 publications

References 30 publications

Common microgeographical selection patterns revealed in four European conifers

Common microgeographical selection patterns revealed in four European conifers

SNP heterozygosity, relatedness and inbreeding of whole genomes from the isolated population of the Faroe Islands

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