Local genetic adaptation to habitat in wild chimpanzees DOI
Harrison J. Ostridge, Claudia Fontsere, Esther Lizano

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 11, 2024

Abstract How populations adapt to their environment is a fundamental question in biology. Yet we know surprisingly little about this process, especially for endangered species such as non-human great apes. Chimpanzees, our closest living relatives, are particularly interesting because they inhabit diverse habitats, from rainforest woodland-savannah. Whether genetic adaptation facilitates habitat diversity remains unknown, despite having wide implications evolutionary biology and conservation. Using 828 newly generated exomes wild chimpanzees, find evidence of fine-scale habitat. Notably, malaria forest chimpanzees mediated by the same genes underlying humans. This work demonstrates power non-invasive samples reveal adaptations highlights importance adaptive chimpanzees. One-Sentence Summary Chimpanzees show local habitat, pathogens, malaria, forests.

Language: Английский

The human and non-human primate developmental GTEx projects DOI
Tim H. H. Coorens, Amy Guillaumet-Adkins, Rothem Kovner

et al.

Nature, Journal Year: 2025, Volume and Issue: 637(8046), P. 557 - 564

Published: Jan. 15, 2025

Language: Английский

Citations

3
Long-read sequencing of 945 Han individuals identifies structural variants associated with phenotypic diversity and disease susceptibility DOI Creative Commons

Jiao Gong,

Huiru Sun,

Kaiyuan Wang

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Feb. 10, 2025

Genomic structural variants (SVs) are a major source of genetic diversity in humans. Here, through long-read sequencing 945 Han Chinese genomes, we identify 111,288 SVs, including 24.56% unreported variants, many with predicted functional importance. By integrating human population-level phenotypic and multi-omics data as well two humanized mouse models, demonstrate the causal roles SVs: one SV that emerges at common ancestor modern humans, Neanderthals, Denisovans GSDMD for bone mineral density modern-human-specific WWP2 impacting height, weight, fat, craniofacial phenotypes immunity. Our results suggest could serve rapid cost-effective biomarker assessing risk cisplatin-induced acute kidney injury. The conservation from to widespread signals positive natural selection both SVs likely influence local adaptation, diversity, disease susceptibility across diverse populations. Genetic studies individuals have been performed, but mostly short read sequencing, limiting types can be identified. authors perform long han individuals, finding under those associated traits evolutionary history.

Language: Английский

Citations

3
Structural polymorphism and diversity of human segmental duplications DOI Creative Commons
Hyeonsoo Jeong, Philip C. Dishuck, DongAhn Yoo

et al.

Nature Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 8, 2025

Abstract Segmental duplications (SDs) contribute significantly to human disease, evolution and diversity but have been difficult resolve at the sequence level. We present a population genetics survey of SDs by analyzing 170 genome assemblies (from 85 samples representing 38 Africans 47 non-Africans) in which majority autosomal are fully resolved using long-read assembly. Excluding acrocentric short arms sex chromosomes, we identify 173.2 Mb duplicated (47.4 not telomere-to-telomere reference) distinguishing fixed from structurally polymorphic events. find that intrachromosomal among most variable, with rare events mapping near their progenitor sequences. African genomes harbor more likely recently gene families higher copy numbers than non-African samples. Comparison resource 563 million full-length isoform sequencing reads identifies 201 novel, potentially protein-coding genes corresponding these number SDs.

Language: Английский

Citations

2
Local genetic adaptation to habitat in wild chimpanzees DOI
Harrison J. Ostridge, Claudia Fontsere, Esther Lizano

et al.

Science, Journal Year: 2025, Volume and Issue: 387(6730)

Published: Jan. 9, 2025

How populations adapt to their environment is a fundamental question in biology. Yet, we know surprisingly little about this process, especially for endangered species, such as nonhuman great apes. Chimpanzees, our closest living relatives, are particularly notable because they inhabit diverse habitats, from rainforest woodland-savannah. Whether genetic adaptation facilitates habitat diversity remains unknown, despite it having wide implications evolutionary biology and conservation. By using newly sequenced exomes 828 wild chimpanzees (388 postfiltering), found evidence of fine-scale habitat, with signatures positive selection forest the same genes underlying malaria humans. This work demonstrates power noninvasive samples reveal adaptations highlights importance adaptive chimpanzees.

Language: Английский

Citations

2
Complete sequencing of ape genomes DOI Creative Commons
DongAhn Yoo, Arang Rhie,

Prajna Hebbar

et al.

Nature, Journal Year: 2025, Volume and Issue: unknown

Published: April 9, 2025

Abstract The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies 1–3 . Consequently, our understanding the evolution species is incomplete. Here we present haplotype-resolved reference analyses six species: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan siamang. We achieve chromosome-level contiguity with substantial sequence accuracy (<1 error in 2.7 megabases) completely 215 gapless chromosomes telomere-to-telomere. resolve challenging regions, such as major histocompatibility complex immunoglobulin loci, to provide in-depth evolutionary insights. Comparative enabled investigations diversity previously uncharacterized or incompletely studied without bias mapping human genome. Such include newly minted gene families lineage-specific segmental duplications, centromeric DNA, acrocentric subterminal heterochromatin. This resource serves a comprehensive baseline for future humans closest living relatives.

Language: Английский

Citations

2
Complete sequencing of ape genomes DOI Creative Commons
DongAhn Yoo, Arang Rhie,

Prajna Hebbar

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 31, 2024

We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran siamang. achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. resolve challenging regions, such as the major histocompatibility complex immunoglobulin loci, providing more in-depth evolutionary insights. Comparative analyses, including human, allow us to investigate evolution diversity regions previously uncharacterized or incompletely studied without bias from mapping human reference. This includes newly minted gene families within lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes, subterminal heterochromatin. resource should serve a definitive baseline for all future studies humans our closest living relatives.

Language: Английский

Citations

14
Integrated analysis of the complete sequence of a macaque genome DOI
Shilong Zhang, Ning Xu,

Lianting Fu

et al.

Nature, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 26, 2025

Language: Английский

Citations

1
Ribosomal DNA arrays are the most H-DNA rich element in the human genome DOI Creative Commons
Nikol Chantzi, Candace S. Y. Chan,

Michail Patsakis

et al.

NAR Genomics and Bioinformatics, Journal Year: 2025, Volume and Issue: 7(1)

Published: Jan. 7, 2025

Repetitive DNA sequences can form noncanonical structures such as H-DNA. The new telomere-to-telomere genome assembly for the human has eliminated gaps, enabling examination of highly repetitive regions including centromeric and pericentromeric repeats ribosomal arrays. We find that H-DNA appears once every 25 000 base pairs in genome. Its distribution is inhomogeneous with motif hotspots being detectable acrocentric chromosomes. Ribosomal arrays are genomic element a 40.94-fold enrichment. Across chromosomes, we report 54.82% motifs found these chromosomes rDNA array loci. discover binding sites PRDM9-B allele, variant PRDM9 protein, enriched motifs. further investigate findings through an analysis PRDM-9 ChIP-seq data across various alleles, observing enrichment A-like alleles (including A, B, N alleles), but not C-like C L4 alleles). at consistent nonhuman great ape genomes. conclude most loci other

Language: Английский

Citations

1
Independent expansion, selection and hypervariability of theTBC1D3gene family in humans DOI Creative Commons
Xavi Guitart, David Porubský, DongAhn Yoo

et al.

Genome Research, Journal Year: 2024, Volume and Issue: 34(11), P. 1798 - 1810

Published: Aug. 6, 2024

is a primate-specific gene family that has expanded in the human lineage and been implicated neuronal progenitor proliferation expansion of frontal cortex. The its expression have challenging to investigate because it embedded high-identity highly variable segmental duplications. We sequenced assembled using long-read sequencing data from 34 humans 11 nonhuman primate species. Our analysis shows this particular independently duplicated at least five lineages, loci are enriched sites large-scale chromosomal rearrangements on Chromosome 17. find all copy-number variation maps two distinct clusters located 17q12 structurally locus, differing by as many 20 copies ∼1 Mbp length depending haplotypes. also show evidence positive selection, well significant change predicted TBC1D3 protein sequence. Last, we that, despite multiple duplications,

Language: Английский

Citations

8
The landscape of structural variation in aye-ayes (Daubentonia madagascariensis) DOI Creative Commons
Cyril J. Versoza, Jeffrey D. Jensen, Susanne P. Pfeifer

et al.

Published: Nov. 11, 2024

Aye-ayes (

Language: Английский

Citations

7