Fine human genetic map based on UK10K data set

Hao, Ziqian; Du, Pengfei; Pan, Yi-Hsuan; Li, Haipeng

doi:10.1007/s00439-021-02415-8

Cited by 2 publications

(2 citation statements)

References 62 publications

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“…Moreover, the inferred population declines shown in Fig. 4A were more severe than those inferred from the real data because the simulated data were generated under the assumption of a neutrally evolved single population and a homogeneous recombination rate, whereas humans evolved with subpopulations and a heterogeneous recombination rate ( 28 , 29 ). FitCoal was not found to overestimate such severity (Fig.…”

Section: Resultsmentioning

confidence: 92%

Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition

Hu,

Hao,

et al. 2023

Science

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Population size history is essential for studying human evolution. However, ancient population size history during the Pleistocene is notoriously difficult to unravel. In this study, we developed a fast infinitesimal time coalescent process (FitCoal) to circumvent this difficulty and calculated the composite likelihood for present-day human genomic sequences of 3154 individuals. Results showed that human ancestors went through a severe population bottleneck with about 1280 breeding individuals between around 930,000 and 813,000 years ago. The bottleneck lasted for about 117,000 years and brought human ancestors close to extinction. This bottleneck is congruent with a substantial chronological gap in the available African and Eurasian fossil record. Our results provide new insights into our ancestry and suggest a coincident speciation event.

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Section: Resultsmentioning

confidence: 92%

Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition

Hu,

Hao,

et al. 2023

Science

Self Cite

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“…Pyrho uses SNPs as intervals with a step size of one SNP. Furthermore, to evaluate the recombination rate with different window sizes and methods, we also estimated historical recombination rates using a 10 kb window and a 5 kb step size for FastEPRR [33]. Following the software authors' recommended parameters, windows were excluded if they overlapped with known sequencing gaps in the pig reference genome (Sus_scrofa11.1) or if the number of non-singleton polymorphic sites was less than 10.…”

Section: Population-based Recombination Rate Estimationmentioning

confidence: 99%

Exploration of Genome-Wide Recombination Rate Variation Patterns at Different Scales in Pigs

Chen,

Zhou,

Sun

et al. 2024

Animals

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Meiotic recombination is a prevalent process in eukaryotic sexual reproduction organisms that plays key roles in genetic diversity, breed selection, and species evolution. However, the recombination events differ across breeds and even within breeds. In this study, we initially computed large-scale population recombination rates of both sexes using approximately 52 K SNP genotypes in a total of 3279 pigs from four different Chinese and Western breeds. We then constructed a high-resolution historical recombination map using approximately 16 million SNPs from a sample of unrelated individuals. Comparative analysis of porcine recombination events from different breeds and at different resolutions revealed the following observations: Firstly, the 1Mb-scale pig recombination maps of the same sex are moderately conserved among different breeds, with the similarity of recombination events between Western pigs and Chinese indigenous pigs being lower than within their respective groups. Secondly, we identified 3861 recombination hotspots in the genome and observed medium- to high-level correlation between historical recombination rates (0.542~0.683) and estimates of meiotic recombination rates. Third, we observed that recombination hotspots are significantly far from the transcription start sites of pig genes, and the silico–predicted PRDM9 zinc finger domain DNA recognition motif is significantly enriched in the regions of recombination hotspots compared to recombination coldspots, highlighting the potential role of PRDM9 in regulating recombination hotspots in pigs. Our study analyzed the variation patterns of the pig recombination map at broad and fine scales, providing a valuable reference for genomic selection breeding and laying a crucial foundation for further understanding the molecular mechanisms of pig genome recombination.

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Fine human genetic map based on UK10K data set

Cited by 2 publications

References 62 publications

Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition

Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition

Exploration of Genome-Wide Recombination Rate Variation Patterns at Different Scales in Pigs

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