ArticleGenome biology and evolution2019
Fine-Scale Characterization of Genomic Structural Variation in the Human Genome Reveals Adaptive and Biomedically Relevant Hotspots.
Article in Genome biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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42 citing papers in PubMed, 80 citations in OpenAlex.
- Large-scale human genomic resources drive innovations toward forensic intelligent source attribution and precision identification.International journal of legal medicine · 2026Review
- Genomes From 117 Vertebrate Species Reveal Rapidly Evolving Segmental-Duplication Landscapes.Genome biology and evolution · 2026Article
- Convergent evolution through independent rearrangements in the primate amylase locus.Cell reports · 2026Article
- Mapping structural variants in Populus tomentosa reveals adaptive signatures and improves prediction of wood properties.Nature communications · 2026Article
- Structural variation in context: mechanisms, functions and selection regimes across the tree of life.Heredity · 2026Article
- Evolutionary hotspots of structural variation drive inter-individual differences in the expression of fusion transcripts in the human brain.Nucleic acids research · 2025Article
- CompletebioRxiv : the preprint server for biology · 2025Article
- Genomes from 117 vertebrate species reveal rapidly evolving segmental duplication landscapes.bioRxiv : the preprint server for biology · 2025Article
- The Landscape of Structural Variation in Aye-Ayes (Daubentonia madagascariensis).Genome biology and evolution · 2025Article
- Multi-ancestry GWAS reveals loci linked to human variation in LINE-1- and Alu-insertion numbers.bioRxiv : the preprint server for biology · 2025Article
- Multi-ancestry GWAS reveals loci linked to human variation in LINE-1- and Alu-insertion numbers.Translational medicine of aging · 2025Article
- A Catalogue of Structural Variation across Ancestrally Diverse Asian Genomes.Nature communications · 2024Article
- Deciphering the role of structural variation in human evolution: a functional perspective.Current opinion in genetics & development · 2024Review
- Plant genome evolution in the genusGenome research · 2024Article
- Exploration of Genome-Wide Recombination Rate Variation Patterns at Different Scales in Pigs.Animals : an open access journal from MDPI · 2024Article
- Human pangenome analysis of sequences missing from the reference genome reveals their widespread evolutionary, phenotypic, and functional roles.Nucleic acids research · 2024Article
- The impact of FASTQ and alignment read order on structural variant calling from long-read sequencing data.PeerJ · 2024Article
- Structural variants involved in high-altitude adaptation detected using single-molecule long-read sequencing.Nature communications · 2023Article
- Article
- Genomic structural variation: A complex but important driver of human evolution.American journal of biological anthropology · 2023Review
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2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomic structural variants (SVs) are distributed nonrandomly across the human genome. The "hotspots" of SVs have been implicated in evolutionary innovations, as well as medical conditions. However, the evolutionary and biomedical features of these hotspots remain incompletely understood. Here, we analyzed data from 2,504 genomes to construct a refined map of 1,148 SV hotspots in human genomes. We confirmed that segmental duplication-related nonallelic homologous recombination is an important mechanistic driver of SV hotspot formation. However, to our surprise, we also found that a majority of SVs in hotspots do not form through such recombination-based mechanisms, suggesting diverse mechanistic and selective forces shaping hotspots. Indeed, our evolutionary analyses showed that the majority of SV hotspots are within gene-poor regions and evolve under relaxed negative selection or neutrality. However, we still found a small subset of SV hotspots harboring genes that are enriched for anthropologically crucial functions and evolve under geography-specific and balancing adaptive forces. These include two independent hotspots on different chromosomes affecting alpha and beta hemoglobin gene clusters. Biomedically, we found that the SV hotspots coincide with breakpoints of clinically relevant, large de novo SVs, significantly more often than genome-wide expectations. For example, we showed that the breakpoints of multiple large SVs, which lead to idiopathic short stature, coincide with SV hotspots. Therefore, the mutational instability in SV hotpots likely enables chromosomal breaks that lead to pathogenic structural variation formations. Overall, our study contributes to a better understanding of the mutational and adaptive landscape of the genome.
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