SYSTEMATIC ANALYSES OF AUTOSOMAL RECOMBINATION RATES FROM THE 1000 GENOMES PROJECT UNCOVERS THE GLOBAL RECOMBINATION LANDSCAPE IN HUMANS

Manu, S.; Acharya, K. K.; Thiyagarajan, S.

doi:10.1101/246702

Home/Archive/bioRxiv

bioRxiv · 10.1101/246702

SYSTEMATIC ANALYSES OF AUTOSOMAL RECOMBINATION RATES FROM THE 1000 GENOMES PROJECT UNCOVERS THE GLOBAL RECOMBINATION LANDSCAPE IN HUMANS

Manu, S.·Acharya, K. K.·Thiyagarajan, S.

View original source ↗Export metadata ↓

Abstract

BackgroundMeiotic recombination plays an important role in evolution by shuffling different alleles along the chromosomes, thus generating the genetic diversity across generations that is vital for adaptation. The plasticity of recombination rates and presence of hotspots of recombination along the genome has attracted much attention over two decades due to their contribution to the evolution of the genome. Yet, the variation in genome-wide recombination landscape and the differences in the location and strength of hotspots across worldwide human populations remains little explored.\n\nResultsWe make use of the untapped linkage disequilibrium (LD) based genetic maps from the 1000 Genomes Project (1KGP) to perform in-depth analyses of finescale variation in the autosomal recombination rates across 20 human populations to uncover the global recombination landscape. We have generated a detailed map of human recombination landscape comprising of a comprehensive set of 88,841 putative hotspots and 80,129 coldspots with their respective strengths across populations, about 2/3rd of which were previously unknown. We have validated and assessed the number of historical putative hotspots derived from the patterns of LD that are currently active in the contemporary populations using a recently published high-resolution pedigree-based genetic map, constructed and refined using 3.38 million crossovers from various populations. For the first time, we provide statistics regarding the conserved, shared, and unique hotspots across all the populations studied.\n\nConclusionsOur analysis yields clusters of continental groups, reflecting their shared ancestry and genetic similarities in the recombination rates that are linked to the migratory and evolutionary histories of the populations. We provide the genomic locations and strengths of hotspots and coldspots across all the populations studied which are a valuable set of resources arising out our analyses of 1KGP data. The findings are of great importance for further research on human hotspots as we approach the dusk of retiring HapMap-based resources.

Explore related subjects

evolutionary biology Preprint

Keep this discovery

BibTeX RIS

Manu, S., Acharya, K. K., Thiyagarajan, S.. 2018-01-12. SYSTEMATIC ANALYSES OF AUTOSOMAL RECOMBINATION RATES FROM THE 1000 GENOMES PROJECT UNCOVERS THE GLOBAL RECOMBINATION LANDSCAPE IN HUMANS. https://doi.org/10.1101/246702

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Geometry of antigenic evolution improves influenza vaccine selection

Anticipating antigenic evolution is essential for selecting effective seasonal influenza A/H3N2 vaccine strains. To this end, we integrated hemagglutination-inhibition and neutralization titers spanning 2002 to 2025 into a unified Bayesian antigenic map. The map resolves twelve antigenic clusters advancing in discrete steps, with several clusters co-circulating in most seasons. In 15 of 21 seasons, the WHO-recommended vaccine belonged to an earlier cluster than the dominant circulating cluster. The direction of each vaccine update relative to recent viral drift predicted vaccine effectiveness one season ahead in out-of-sample forecasts. Antigenic distance, the conventional measure of vaccine-virus match, was weakly associated with effectiveness until update direction was accounted for. Retrospectively ranking candidate strains by predicted effectiveness would have selected a strain predicted to outperform the WHO recommendation in every season, raising mean predicted effectiveness by 10 percentage points.

evolutionary biology↗

bioRxiv2026

Evolutionary replay of duplicate-gene retention across independent whole-genome duplications

Whole-genome duplications repeatedly expose ancestral gene lineages to the same broad evolutionary outcome-retention or loss of duplicated copies-but it remains unclear whether this history replays similarly across evolutionary scales. We placed duplicate retention in shared hierarchical orthologous-group coordinates and compared percentile ranks defined within each event-wide mapped universe. Three independent angiosperm whole-genome duplications showed reproducible replay (global rank effect T-replay = 0.210, bootstrap 95% confidence interval 0.172-0.248; permutation P = 1/100,001). A plant reference-panel score specified before target outcomes were examined predicted retention after the Apple/Pear duplication ({rho} = 0.169, n = 373). Deep transfer was heterogeneous: the teleost-genome-duplication estimate was positive but unresolved ({rho} = 0.107, n = 151, 95% confidence interval -0.050 to 0.260), whereas transfer to the ancient budding-yeast whole-genome duplication (yeast WGD) was supported ({rho} = 0.280, n = 186). Independently reconstructed animal outcomes also replayed between teleost and Stylommatophora duplications (r = 0.226, n = 146, P = 0.00326), although the effect remained below a prespecified strong-effect threshold. A strict plant-animal comparison was limited to 25 deeply one-to-one lineages and was unresolved (r = 0.033, 95% confidence interval -0.303 to 0.340). Thus, ancestral gene-lineage identity contributes reproducibly to duplicate retention after independent whole-genome duplications, but replay is structured by evolutionary lineage and modified by event-specific history rather than governed by one universal gene-fate ranking.

evolutionary biology↗

bioRxiv2026

A Hymenoptera-restricted gene mediating ant castes co-opts deeply conserved machinery to control organ size

Lineage-specific genes are widespread and have been implicated as phenotypic innovation inducers, but how they acquire complex developmental functions remains poorly understood. Ant queens and workers develop dramatically different organ sizes from identical genomes under juvenile hormone (JH) control, yet the molecular effectors translating JH signalling into caste-specific organ growth remain unknown. Here we identify torch, a Hymenoptera-restricted gene, as the most consistently gyne-biased and JH-responsive gene across 68 ant species. Knockdown of torch in virgin queens of Monomorium pharaonis produces a worker-like, multi-organ growth-restricted phenotype. Mechanistically, torch harbours an E-box-like motif activated by the JH receptor Gce-Tai and acts as a GA-repeat-binding transcription factor that regulates Hippo signalling, the deeply conserved organ-size control pathway in animals. Expressing torch heterologously in mice and a growth-restricted Drosophila background shows that the gene retained its general growth-promoting activity across more than 700 million years of animal evolution in lineages that lack the gene, establishing that its function is mediated through conserved rather than ant-specific machinery. A lineage-specific gene can therefore acquire complex morphogenetic function by co-opting ancient organ-size circuitry, providing a general route by which novel genes can drive phenotypic innovation.

evolutionary biology↗