The degree of association between alleles at different loci, or linkage disequilibrium, is widely used to infer details of evolutionary processes. Here I explore how associations between alleles relate to properties of the underlying genealogy of sequences. Under the neutral, infinite-sites assumption I show that there is a direct correspondence between the covariance in coalescence times at different parts of the genome and the degree of linkage disequilibrium. These covariances can be calculated exactly under the standard neutral model and by Monte Carlo simulation under different demographic models. I show that the effects of population growth, population bottlenecks, and population structure on linkage disequilibrium can be described through their effects on the covariance in coalescence times.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1462283 | PMC |
| http://dx.doi.org/10.1093/genetics/162.2.987 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Advancing allergic rhinitis research through phenome-wide association studies: Insights from known genetic loci.
World Allergy Organ J
January 2025
Institute of Life Science, Chongqing Medical University, Chongqing, China.
Background: Allergic rhinitis (AR) is a common chronic respiratory disease that can lead to the development of various other conditions. Although genetic risk loci associated with AR have been reported, the connections between these loci and AR comorbidities or other diseases remain unclear.
Methods: This study conducted a phenome-wide association study (PheWAS) using known AR risk loci to explore the impact of known AR risk variants on a broad spectrum of phenotypes.
A high-quality assembly revealing the PMEL gene for the unique plumage phenotype in Liancheng ducks.
Gigascience
January 2025
State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
Background: Plumage coloration is a distinctive trait in ducks, and the Liancheng duck, characterized by its white plumage and black beak and webbed feet, serves as an excellent subject for such studies. However, academic comprehension of the genetic mechanisms underlying duck plumage coloration remains limited. To this end, the Liancheng duck genome (GCA_039998735.
View Article and Find Full Text PDFThe evolution of preferred male traits, female preference and the G matrix: "Toto, I've a feeling we're not in Kansas anymore".
Heredity (Edinb)
January 2025
Department of Evolution, Ecology and Organismal Biology, 2710 Life Science Bldg, University of California, Riverside, CA, 92521, USA.
Female preference exerts selection on male traits. How such preferences affect male traits, how female preferences change and the genetic correlation between male traits and female preference were examined by an experiment in which females were either mated to males they preferred (S lines) or to males chosen at random from the population (R lines). Female preference was predicted to increase the time spent calling by males.
View Article and Find Full Text PDFGWAS analysis revealed genomic loci and candidate genes associated with the 100-seed weight in high-latitude-adapted soybean germplasm.
Theor Appl Genet
January 2025
Research Center for Life Sciences Computing, Zhejiang Lab, Hangzhou, 310012, China.
In the present study, we identified 22 significant SNPs, eight stable QTLs and 17 potential candidate genes associated with 100-seed weight in soybean. Soybean is an economically important crop that is rich in seed oil and protein. The 100-seed weight (HSW) is a crucial yield contributing trait.
View Article and Find Full Text PDFFunmap: integrating high-dimensional functional annotations to improve fine-mapping.
Bioinformatics
January 2025
Department of Biostatistics, City University of Hong Kong, 83 Tat Chee Avenue, Hong Kong, China.
Motivation: Fine-mapping aims to prioritize causal variants underlying complex traits by accounting for the linkage disequilibrium of GWAS risk locus. The expanding resources of functional annotations serve as auxiliary evidence to improve the power of fine-mapping. However, existing fine-mapping methods tend to generate many false positive results when integrating a large number of annotations.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!