DNA Damage, Genome Stability and Adaptation: a Question of Chance or Necessity? DOI Open Access
John H. Herrick

Published: March 18, 2024

DNA damage causes the mutations that are principal source of genetic variation. detection and repair mechanisms therefore play a determining role in generating diversity on which natural selection acts. Speciation, it is commonly assumed, occurs at rate set by level standing allelic population. The process speciation driven combination two evolutionary forces: drift ecological selection. Genetic takes place under conditions relaxed selection, results balance between rates mutation substitution. These processes, necessarily mediated variety guaranteeing genome stability any given species. One outstanding questions biology concerns origin widely varying phylogenetic distribution biodiversity across tree life, how forces contribute to shaping distribution. following examines some molecular underlying adaptive radiations associated with species richness evenness different eukaryotic lineages.

Language: Английский

Next-generation data filtering in the genomics era DOI
William Hemstrom, Jared A. Grummer, Gordon Luikart

et al.

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: June 14, 2024

Language: Английский

Citations

15
A whole-genome scan for evidence of recent positive and balancing selection in aye-ayes (Daubentonia madagascariensis) utilizing a well-fit evolutionary baseline model DOI Creative Commons
Vivak Soni, John W. Terbot, Cyril J. Versoza

et al.

Published: Nov. 11, 2024

The aye-aye (

Language: Английский

Citations

8
Temporal challenges in detecting balancing selection from population genomic data DOI Creative Commons
Vivak Soni, Jeffrey D. Jensen

G3 Genes Genomes Genetics, Journal Year: 2024, Volume and Issue: 14(6)

Published: March 29, 2024

Abstract The role of balancing selection in maintaining genetic variation remains an open question population genetics. Recent years have seen numerous studies identifying candidate loci potentially experiencing selection, most predominantly human populations. There are however alternative evolutionary processes that may leave similar patterns variation, thereby confounding inference, and the expected signatures additionally change a temporal fashion. Here we use forward-in-time simulations to quantify statistical power detect using both site frequency spectrum- linkage disequilibrium-based methods under variety evolutionarily realistic null models. We find whilst spectrum-based little immediately after balanced mutation begins segregating, increases with time since introduction allele. Conversely, considerable allele is young, dissipates rapidly as increases. Taken together, this suggests effective at detecting long-term (>25N generations allele) over much shorter timescales (<1N generations), leaving large frame which current action selection. Finally, investigate extent mimic these patterns, demonstrate need for caution attempting distinguish from those neutral (e.g. structure admixture) well selective partial sweeps).

Language: Английский

Citations

6
Tradeoffs and constraints on the evolution of tailocins DOI Creative Commons

Talia Backman,

Hernán A. Burbano, Talia L. Karasov

et al.

Trends in Microbiology, Journal Year: 2024, Volume and Issue: 32(11), P. 1084 - 1095

Published: June 18, 2024

Phage tail-like bacteriocins (tailocins) are protein complexes produced by bacteria with the potential to kill their neighbors. Widespread throughout Gram-negative bacteria, tailocins exhibit extreme specificity in targets, largely killing closely related strains. Despite presence diverse impact of these competitive weapons on surrounding microbiota is unknown. Recent studies revealed rapid evolution and genetic diversity microbial communities suggest that there constraints resistance. Given precision targeted ease engineering new specificities, understanding ecological may enable design promising candidates for novel antibiotics.

Language: Английский

Citations

4
Structural variation in humans and our primate kin in the era of telomere-to-telomere genomes and pangenomics DOI Creative Commons

Joana L. Rocha,

Runyang Nicolas Lou, Peter H. Sudmant

et al.

Current Opinion in Genetics & Development, Journal Year: 2024, Volume and Issue: 87, P. 102233 - 102233

Published: July 23, 2024

Structural variants (SVs) account for the majority of base pair differences both within and between primate species. However, our understanding inter- intra-species SV has been historically hampered by quality draft genomes absence genome resources key taxa. Recently, advances in long-read sequencing assembly have begun to radically reshape SVs. Two landmark achievements include publication a human telomere-to-telomere (T2T) as well development first pangenome reference. In this review, we look back major works laying foundation these projects. We then examine ways which T2T assemblies pangenomes are transforming approach SV. Finally, discuss what future research may like era pangenomics.

Language: Английский

Citations

4
Natural selection and adaptive traits in the Maniq, a nomadic hunter-gatherer society from Mainland Southeast Asia DOI Creative Commons

T.J. Herzog,

Maximilian Larena, Wibhu Kutanan

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Feb. 9, 2025

Abstract Asia is home to diverse hunter-gatherer populations characterized by significant morphological, anthropological, cultural, and linguistic diversity. Despite their importance in understanding ancestral human subsistence, little known about the essential genetic adaptations of these groups. This study investigates evolutionary pressures shaping genome Maniq population, a nomadic group inhabiting rainforests southern Thailand. Using genome-wide approaches, including iHS, xp-EHH, PBE, beta statistics, we identified signatures positive balancing selection. Genes under selection were enriched pathways related immunity, metabolic regulation, structural adaptation, cardiovascular performance, neuromodulatory traits. Several genes associated with Southeast Asian ‘negrito-like’ phenotype also Balancing was primarily detected immune-related genes, particularly within HLA region, underscoring critical role diversity surviving pathogen-rich environments. Additionally, olfactory receptor highlights environmental sensing adaptation. These results reveal intricate interplay landscape population highlight ecological lifestyle challenges life rainforest. contributes our processes tropical environments societies.

Language: Английский

Citations

0
Genomic investigations of successful invasions: the picture emerging from recent studies DOI Creative Commons
Joanna Kołodziejczyk, Anna Fijarczyk, Ilga Porth

et al.

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 16, 2025

ABSTRACT Invasion biology aims to identify traits and mechanisms that contribute successful invasions, while also providing general insights into the underlying population expansion adaptation rapid climate habitat changes. Certain phenotypic attributes have been linked role of genetics has critical in understanding invasive species. Nevertheless, a comprehensive summary evaluating most common evolutionary associated with invasions across species environments is still lacking. Here we present systematic review studies since 2015 applied genomic tools investigate different organisms. We examine demographic patterns such as changes diversity at level, presence genetic bottlenecks gene flow range. selection from standing variation de novo mutations, hybridisation introgression, all which can an impact on invasion success. This recent articles led creation searchable database provide researchers accessible resource. Analysis this allowed quantitative assessment adaptive acting A predominant admixture increasing levels enabling molecular novel habitats important finding our study. The “genetic paradox” was not validated data ecosystems. Even though drift commonly reported upon invasion, large reduction rarely observed. Any decrease often relatively mild almost always restored via between populations. fact loci under are frequently detected suggests level hindered. above findings confirmed herein for first time semi‐quantitative manner by data. point gaps potential improvements design driving These include scarcity sampling multiple native populations, identification sources, longitudinal sampling, integration fitness measures analyses. note whole genome exploited fully predicting potential. Comparative identifying features promoting underrepresented despite their use tool control.

Language: Английский

Citations

0
Rapid Evolution in Action: Environmental Filtering Supports Coral Adaptation to a Hot, Acidic, and Deoxygenated Extreme Habitat DOI Creative Commons
Carlos Leiva, Gergely Torda, Chengran Zhou

et al.

Global Change Biology, Journal Year: 2025, Volume and Issue: 31(3)

Published: March 1, 2025

The semienclosed Bouraké lagoon in New Caledonia is a natural system that enables observation of evolution action with respect to stress tolerance marine organisms, topic directly relevant understanding the consequences global climate change. Corals inhabiting endure extreme conditions elevated temperature (> 33°C), acidification (7.2 pH units), and deoxygenation (2.28 mg O2 L-1), which fluctuate tide due lagoon's geomorphology. To investigate underlying bases apparent these corals, we combined whole genome resequencing coral host ITS2 metabarcoding photosymbionts from 90 Acropora tenuis colonies three localities along steep environmental gradient two nearby control reefs. Our results highlight importance flexibility associate different facilitating holobiont; but, perhaps more significantly, strong selective effects were detected at specific loci genome. Fifty-seven genes contained SNPs highly associated environment enriched functions related sphingolipid metabolism. Within genes, conserved sensor noxious stimuli TRPA1 ABCC4 transporter stood out high number environmentally selected they contained. Protein 3D structure predictions suggest single-point mutation causes rotation main regulatory domain TRPA1, may be behind this case selection through filtering. While corals provide striking example rapid adaptation conditions, overall, our need preserve current standing genetic variation populations safeguard their adaptive potential ongoing

Language: Английский

Citations

0
Museomics of an extinct European flat oyster population DOI Creative Commons
Christine Ewers, Dirk Brandis, Nicolas Antonio da Silva

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: April 22, 2025

Abstract Understanding the factors that predispose species and populations to decline extinction is a major challenge of biodiversity research. In present study, we investigated historical population genomics an extinct European oyster ( Ostrea edulis L.) from Wadden Sea collected between 1868 1888, compared it French English sampled at same time. Our museomic results indicate now-extinct was genetically isolated showed signs local adaptation in form Fst outlier loci other two populations. Thus oysters may have been predisposed for because they were not naturally replenished A comparison population-wide genomic diversity hint towards sudden contraction population, possibly being result stronger - or earlier this than others. summary, our exploration hints some potential causes flat Sea, which might led their extinction.

Language: Английский

Citations

0
Evolutionary Forces Shaping Trans-Species Polymorphisms in Genus Cucumis DOI Creative Commons
Xiaofeng Su, Yi Liu, Yueting Li

et al.

Horticulturae, Journal Year: 2025, Volume and Issue: 11(5), P. 452 - 452

Published: April 23, 2025

Trans-species polymorphisms (TSPs) are fundamental to preserving ancient genetic diversity, yet the evolutionary forces driving their long-term maintenance remain largely unexplored. Here, we investigate genome-wide TSPs in two Cucumis species, cucumber and melon, using whole-genome sequencing data from over 1200 accessions. A total of 5149 were identified, which predominantly located genic promoter regions. Coalescent analysis indicated that both gene flow balancing selection have contributed persistence these ancestral alleles. Moreover, among 99 genes with shared coding-region polymorphisms, cluster by alleles rather than species provide evidence selection. These involved immune stress response processes pleiotropic effects. Our findings elucidate complex Cucumis, providing mechanistic insights into intraspecific diversity plants across deep timescales.

Language: Английский

Citations

0