98%
921
2 minutes
20
The combination of experimental evolution with high-throughput sequencing of pooled individuals-, evolve and resequence (E&R)-is a powerful approach to study adaptation from standing genetic variation under controlled, replicated conditions. Nevertheless, E&R studies in have frequently resulted in inordinate numbers of candidate SNPs, particularly for complex traits. Here, we contrast the genomic signature of adaptation following ∼60 generations in a novel hot environment for and For , the regions carrying putatively selected loci were far more distinct, and thus harbored fewer false positives, than those in We propose that species without segregating inversions and higher recombination rates, such as , are better suited for E&R studies that aim to characterize the genetic variants underlying the adaptive response.
Download full-text PDF |
Source |
---|---|
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499140 | PMC |
http://dx.doi.org/10.1534/g3.117.043349 | DOI Listing |
Nat Commun
July 2025
Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba, Spain.
Genomes of clonally reproducing fungal pathogens are often compartmentalized into conserved core and lineage-specific accessory regions (ARs), enriched in transposable elements (TEs). ARs and TEs are thought to promote pathogen adaptation, but direct experimental evidence is sparse. Using an evolve and re-sequence approach, we found that serial passaging of the cross-kingdom fungal pathogen Fusarium oxysporum through tomato plants or axenic media rapidly increased fitness under the selection condition.
View Article and Find Full Text PDFNat Commun
July 2025
School of Life Sciences, Chongqing University, No.55 Daxuecheng South Road, Shapingba, Chongqing, China.
How SARS-CoV-2 Omicron evolved remains obscure. T492I, an Omicron-specific mutation encountered in SARS-CoV-2 nonstructural protein 4 (NSP4), enhances viral replication and alters nonstructural protein cleavage, inferring potentials to drive evolution. Through evolve-and-resequence experiments of SARS-CoV-2 wild-type (hCoV-19/USA/WA-CDC-02982585-001/2020, A) and Delta strains (B.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
June 2025
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.
Evolutionary adaptation to new environments likely results from a combination of selective sweeps and polygenic shifts, depending on the genetic architecture of traits under selection. While selective sweeps have been widely studied, polygenic responses are thought to be more prevalent but remain challenging to quantify. The infinitesimal model makes explicit the hypothesis about the dynamics of changes in allele frequencies under selection, where only allelic effect sizes, frequencies, linkage, and gametic disequilibrium matter.
View Article and Find Full Text PDFG3 (Bethesda)
August 2025
Department of Ecology and Evolution, University of Chicago, 1101 E. 57th St., Chicago, IL 60637, USA.
Whole-genome time-series allele frequency data are becoming more prevalent as ancient DNA sequences and data from evolve-and-resequence experiments are generated at a rapid pace. Such data present unprecedented opportunities to elucidate the dynamics of genetic variation under selection. However, despite many methods to infer parameters of selection models from allele frequency trajectories available in the literature, few provide user-friendly implementations for large-scale empirical applications.
View Article and Find Full Text PDFNat Ecol Evol
June 2025
Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
Climate warming is threatening biodiversity by increasing temperatures beyond the optima of many ectotherms. Owing to the inherent non-linear relationship between temperature and the rate of cellular processes, such shifts towards hot temperature are predicted to impose stronger selection compared with corresponding shifts towards cold temperature. This suggests that when adaptation to warming occurs, it should be relatively rapid and predictable.
View Article and Find Full Text PDF