Publications by authors named "R S Waples"
We introduce a new software program, MaxTemp, that increases precision of the temporal method for estimating effective population size (N) in genetic monitoring programs, which are increasingly used to systematically track changes in global biodiversity. Scientists and managers are typically most interested in N for individual generations, either to match with single-generation estimates of census size (N) or to evaluate consequences of specific management actions or environmental events. Systematically sampling every generation produces a time series of single-generation estimates of temporal F ( , which can then be used to estimate N; however, these estimates have relatively low precision because each reflects just a single episode of genetic drift.
View Article and Find Full Text PDFThe impact of rare recurrent copy number variants (rCNVs) and polygenic background attributed to common variants, on the risk of psychiatric disorders is well-established in separate studies. However, it remains unclear how polygenic background modulates the effect of rCNVs. Using the population-representative iPSYCH2015 case-cohort sample (N=96,599), we investigated the association between absolute risk of psychiatric disorders and carriage of rCNVs and polygenic scores (PGS), as well as the interaction effect between the two on disease risk.
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- Recent positive selection can lead to an accumulation of long identity-by-descent (IBD) haplotypes near specific genetic loci, which can help identify areas of adaptive evolution.
- The proposed statistical methods aim to locate these regions, identify potential sweeping alleles, and estimate the selection coefficient (s) through innovative techniques like selection scans and parametric bootstrap for uncertainty quantification.
- In extensive simulations, these methods outperform existing techniques, providing more accurate estimates of selection in data from European ancestry samples, demonstrating their effectiveness in studying recent adaptive evolution without needing known causal alleles or time series information.
Article Synopsis
- The study addresses the issue of pseudoreplication in genetic analyses due to non-independent assortment of loci on finite chromosomes, which can distort the precision of results like linkage disequilibrium (LD) measures.
- Researchers explored using entropy metrics, specifically total correlation (TC), to better assess and quantify inter-locus relationships in LD studies. Their simulations suggested a strong link between the number of loci and TC.
- While the findings support the utility of entropy-based metrics for analyzing genetic datasets, the study also notes scalability challenges, as computational limitations restrict analysis to smaller datasets.
vonHoldt et al. ((2024), Molecular Ecology, 33, e17231) (vH24) used low-coverage (average ~ 7X read depth) restriction site-associated DNA sequence data to estimate individual inbreeding and heterozygosity, and recent effective population size (N), in Great Lakes (GL) and Northern Rocky Mountain (RM) wolves. They concluded that RM heterozygosity rapidly declined between 1991 and 2020, and that N declined substantially in GL and RM over the last 50 generations.
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