Many traits in populations are well understood as being Mendelian effects at single loci or additive polygenic effects across numerous loci. However, there are important phenomena and traits that are intermediate between these two extremes and are known as oligogenic traits. Here we investigate digenic, or two-locus, traits and how their frequencies in populations are affected by non-random mating, specifically inbreeding, linkage disequilibrium, and selection. These effects are examined both separately and in combination to demonstrate how many digenic traits, especially double homozygous ones, can show significant, sometimes unexpected, changes in population frequency with inbreeding, linkage, and linkage disequilibrium. The effects of selection on deleterious digenic traits are also detailed. These results are applied to both digenic traits of medical significance as well as measuring inbreeding in natural populations.
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http://dx.doi.org/10.1016/j.tpb.2023.03.003 | DOI Listing |
Evol Appl
December 2024
Univ. Lille, CNRS, UMR 8198-Evo-Eco-Paleo Lille France.
The effective population size ( ) is a key parameter in conservation and evolutionary biology, reflecting the strength of genetic drift and inbreeding. Although demographic estimations of are logistically and time-consuming, genetic methods have become more widely used due to increasing data availability. Nonetheless, accurately estimating remains challenging, with few studies comparing estimates across molecular markers types and estimators such as single-sample methods based on linkage disequilibrium or sibship analyses versus methods based on temporal variance in allele frequencies.
View Article and Find Full Text PDFSci Rep
December 2024
Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
Lancet Microbe
December 2024
MRC Centre for Genomics and Global Health, Big Data Institute, Oxford University, Oxford, UK.
Background: The population structure of the malaria parasite Plasmodium falciparum can reveal underlying adaptive evolutionary processes. Selective pressures to maintain complex genetic backgrounds can encourage inbreeding, producing distinct parasite clusters identifiable by population structure analyses.
Methods: We analysed population structure in 3783 P falciparum genomes from 21 countries across Africa, provided by the MalariaGEN Pf7 dataset.
bioRxiv
October 2024
Disease Intervention and Prevention program, Texas Biomedical Research Institute, P.O. Box 760549, 78245 San Antonio, Texas, USA.
Schistosomes are obligately sexual blood flukes that can be maintained in the laboratory using freshwater snails as intermediate and rodents as definitive hosts. The genetic composition of laboratory schistosome populations is poorly understood: whether genetic variation has been purged due to serial inbreeding or retained is unclear. We sequenced 19 - 24 parasites from each of five laboratory populations and compared their genomes with published exome data from four field populations.
View Article and Find Full Text PDFInt J Mol Sci
October 2024
Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China.
The oil content of maize kernels is essential to determine its nutritional and economic value. A multiparent population (MPP) consisting of five recombinant inbred line (RIL) subpopulations was developed to elucidate the genetic basis of the total oil content (TOC) in maize. The MPP used the subtropical maize inbred lines CML312 and CML384, along with the tropical maize inbred lines CML395, YML46, and YML32 as the female parents, and Ye107 as the male parent.
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