Rapid evolution of recombination landscapes during the divergence of cichlid ecotypes in Lake Masoko DOI Creative Commons
Marion Talbi, George F. Turner, Milan Malinsky

et al.

Evolution, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 26, 2024

Abstract Variation of recombination rate along the genome is crucial importance to rapid adaptation and organismal diversification. Many unknowns remain regarding how why landscapes evolve in nature. Here, we reconstruct maps based on linkage disequilibrium use subsampling simulations derive a new measure landscape evolution: Population Recombination Divergence Index (PRDI). Using PRDI, show that fine-scale differ substantially between two cichlid fish ecotypes Astatotilapia calliptera diverged only ~2,500 generations ago. Perhaps surprisingly, differences are not driven by divergence terms allele frequency (FST) nucleotide diversity (Δ(π)): although there some association, observe positive PRDI regions where FST Δ(π) zero. We found stronger association evolution 47 large haplotype blocks polymorphic Lake Masoko, cover 21% genome, appear include multiple inversions. Among blocks, strong clear degree heterozygosity, consistent with suppression heterozygotes. Overall, our work provides holistic view changes population during early stages speciation gene flow.

Language: Английский

PRDM9 drives the location and rapid evolution of recombination hotspots in salmonid fish DOI Creative Commons
Marie Raynaud, Paola Sanna, Julien Joseph

et al.

PLoS Biology, Journal Year: 2025, Volume and Issue: 23(1), P. e3002950 - e3002950

Published: Jan. 6, 2025

In many eukaryotes, meiotic recombination occurs preferentially at discrete sites, called hotspots. various lineages, hotspots are located in regions with promoter-like features and evolutionarily stable. Conversely, some mammals, driven by PRDM9 that targets away from promoters. Paradoxically, induces the self-destruction of its this triggers an ultra-fast evolution mammalian is ancestral to all animals, suggesting a critical importance for program, but has been lost lineages surprisingly little effect on meiosis success. However, it unclear whether function described mammals shared other species. To investigate this, we analyzed landscape several salmonids, genome which harbors one full-length truncated paralogs. We identified initiation sites Oncorhynchus mykiss mapping DNA double-strand breaks (DSBs). found DSBs clustered positioned promoters, enriched H3K4me3 H3K36me3 location depended genotype Prdm9 . observed high level polymorphism zinc finger domain , indicating diversification positive selection. Moreover, population-scaled maps O kisutch Salmo salar revealed rapid turnover caused target motif erosion. Our results imply conserved across vertebrates peculiar evolutionary runaway active hundred million years.

Language: Английский

Citations

2
Selection can favor a recombination landscape that limits polygenic adaptation DOI Creative Commons
Tom Parée, Luke M. Noble, Denis Roze

et al.

Molecular Biology and Evolution, Journal Year: 2025, Volume and Issue: 42(1)

Published: Jan. 1, 2025

Abstract Modifiers of recombination rates have been described but the selective pressures acting on them and their effect adaptation to novel environments remain unclear. We performed experimental evolution in nematode Caenorhabditis elegans using alternative rec-1 alleles modifying position meiotic crossovers along chromosomes without detectable direct fitness effects. show that a environment is impaired by allele decreases genomic regions containing variation. However, impairs indirectly favored selection, because it increases reduces associations among beneficial deleterious variation located its chromosomal vicinity. These results validate theoretical expectations about suggest genome-wide polygenic little consequence indirect selection rate modifiers.

Language: Английский

Citations

1
Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish DOI Creative Commons
Vrinda Venu,

Enni Harjunmaa,

Andreea Dréau

et al.

Nature Ecology & Evolution, Journal Year: 2024, Volume and Issue: 8(7), P. 1337 - 1352

Published: June 5, 2024

Despite deep evolutionary conservation, recombination rates vary greatly across the genome and among individuals, sexes populations. Yet impact of this variation on adaptively diverging populations is not well understood. Here we characterized fine-scale landscapes in an divergent pair marine freshwater threespine stickleback from River Tyne, Scotland. Through whole-genome sequencing large nuclear families, identified genomic locations almost 50,000 crossovers built maps for marine, hybrid individuals at a resolution 3.8 kb. We used these to quantify factors driving rates. found strong heterochiasmy between but also differences ecotypes. Hybrids showed evidence significant suppression overall map length individual loci. Recombination were lower only within marine-freshwater-adaptive loci, loci same chromosome, suggesting selection linked gene 'cassettes'. temporal sampling along natural zone, that recombinants traits associated with reduced fitness. Our results support predictions divergence cis-acting modifiers, whose functions are disrupted hybrids, may play important role maintaining

Language: Английский

Citations

6
Ancient stickleback genomes reveal the chronology of parallel adaptation DOI Creative Commons
Jan Laine, Jana Nickel, Anders Romundset

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 18, 2025

Abstract Parallel evolution of traits and their underlying genetic basis is well-studied, however, studies parallel chronology adaptive changes remain scarce. Threespine stickleback are a model system for studying evolution. We present genomic data from nine subfossil bones dated to 14.8-0.7 KYR BP in age. Comparing the four highest coverage genomes, which represent different stages along marine-freshwater continuum, we find that freshwater ancestry often clustered rather than randomly distributed throughout divergent regions genome. consistently on chromosome IV at early adaptation. Regions contain greatest differentiation between marine ecotypes among density quantitative trait loci. These include EDA , large-effect pleiotropic locus associated with defensive armour variation neurosensory behavioural traits. Freshwater also found inversions subfossils process. Our findings add growing body evidence adaptation threespine has staggered but predictable temporal dynamic. The probability change should be increased by clustering alleles suppressed recombination, particularly genes have large phenotypic effect.

Language: Английский

Citations

0
Abundant genetic variation is retained in many laboratory schistosome populations DOI Creative Commons
JUTZELER Kathrin, Roy N. Platt,

Robbie Diaz

et al.

Published: Oct. 24, 2024

ABSTRACT Schistosomes are obligately sexual blood flukes that can be maintained in the laboratory using freshwater snails as intermediate and rodents definitive hosts. The genetic composition of schistosome populations is poorly understood: whether variation has been purged due to serial inbreeding or retained unclear. We sequenced 19 – 24 parasites from each five Schistosoma mansoni compared their genomes with published exome data four S. field populations. found abundant genomic (0.897 1.22 million variants) within populations: these on average 49% (π = 3.27e-04 8.94e-04) nucleotide diversity observed parasite 1.08e-03 2.2e-03). However, pattern was very different Tajima’s D positive all except SmBRE, indicative recent population bottlenecks, but negative Current effective size estimates were lower (2 258) (3,174 infinity). distance between markers at which linkage disequilibrium (LD) decayed 0.5 longer (59 bp 180 kb) (9 9.5 kb). SmBRE least variable; this also shows low fitness across lifecycle, consistent depression. present most several important implications: (i) measurement phenotypes, such drug resistance, will determine values underestimate trait variation; (ii) genome-wide association studies (GWAS) conducted by measuring phenotypes genotypes individual worms; (iii) drift may lead divergence laboratories. conclude many provide valuable, untapped opportunities for research.

Language: Английский

Citations

2
Rapid evolution of recombination landscapes during the divergence of cichlid ecotypes in Lake Masoko DOI Creative Commons
Marion Talbi, George F. Turner, Milan Malinsky

et al.

Evolution, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 26, 2024

Abstract Variation of recombination rate along the genome is crucial importance to rapid adaptation and organismal diversification. Many unknowns remain regarding how why landscapes evolve in nature. Here, we reconstruct maps based on linkage disequilibrium use subsampling simulations derive a new measure landscape evolution: Population Recombination Divergence Index (PRDI). Using PRDI, show that fine-scale differ substantially between two cichlid fish ecotypes Astatotilapia calliptera diverged only ~2,500 generations ago. Perhaps surprisingly, differences are not driven by divergence terms allele frequency (FST) nucleotide diversity (Δ(π)): although there some association, observe positive PRDI regions where FST Δ(π) zero. We found stronger association evolution 47 large haplotype blocks polymorphic Lake Masoko, cover 21% genome, appear include multiple inversions. Among blocks, strong clear degree heterozygosity, consistent with suppression heterozygotes. Overall, our work provides holistic view changes population during early stages speciation gene flow.

Language: Английский

Citations

0