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47 results for “Hitchhiking”
Data from: Recombination and hitchhiking of deleterious alleles
When new advantageous alleles arise and spread within a population, deleterious alleles at neighbouring loci can hitchhike alongside them and spread to fixation in areas of low recombination, introducing a fixed mutation load. We use branching processes and diffusion equations to calculate the probability that a deleterious allele hitchhikes and fixes alongside an advantageous mutant. As expected, the probability of fixation of a deleterious hitchhiker rises with the selective advantage of the sweeping allele and declines with the selective disadvantage of the deleterious hitchhiker. We then use computer simulations of a genome with an infinite number of loci to investigate the increase in load after an advantageous mutant is introduced. We show that the appearance of advantageous alleles on genetic backgrounds loaded with deleterious alleles has two potential effects: it can fix deleterious alleles and also facilitate the persistence of recombinant lineages that happen to occur. The latter is expected to reduce the signals of selection in the surrounding region. We consider these results in light of human genetic data to infer how likely it is that such deleterious hitchhikers have occurred in our recent evolutionary past.
Data from: Patterns of linkage disequilibrium and long range hitchhiking in evolving experimental Drosophila melanogaster populations
Whole genome re-sequencing of experimental populations evolving under a specific selection regime has become a popular approach to determine genotype-phenotype maps and understand adaptation to new environments. Despite its conceptual appeal and success in identifying some causative genes, it has become apparent that many studies suffer from an excess of candidate loci. Several explanations have been proposed for this phenomenon, but it is clear that information about the linkage structure during such experiments is needed. Until now only Pool-Seq data were available, which do not provide sufficient information about the correlation between linked sites. We address this problem in two complementary analyses of three replicate D. melanogaster populations evolving to a new hot temperature environment for almost 70 generations. In the first analysis, we sequenced 58 haploid genomes from the founder population and evolved flies at generation 67. We show that during the experiment LD increased almost uniformly over much greater distances than typically seen in Drosophila. In the second analysis, Pool-Seq time series data of the three replicates were combined with haplotype information from the founder population to follow blocks of initial haplotypes over time. We identified 17 selected haplotype-blocks that started at low frequencies in the base population and increased in frequency during the experiment. The size of these haplotype-blocks ranged from 0.082 to 4.095 Mb. Moreover, between 42-46% of the top candidate SNPs from the comparison of founder and evolved populations fell into the genomic region covered by the haplotype-blocks. We conclude that LD in such rising haplotype-blocks results in long range hitchhiking over multiple kb sized regions. LD in such haplotype-blocks is therefore a major factor contributing to an excess of candidate loci. While modifications of the experimental design may help to reduce the hitchhiking effect and allow for more precise mapping of causative variants, we also note that such haplotype-blocks might be well suited to study the dynamics of selected genomic regions during experimental evolution studies.
Data from: Antagonistic versus non-antagonistic models of balancing selection: characterizing the relative timescales and hitchhiking effects of partial selective sweeps
Antagonistically selected alleles-–those with opposing fitness effects between sexes, environments, or fitness components-–represent an important component of additive genetic variance in fitness-related traits, with stably balanced polymorphisms often hypothesized to contribute to observed quantitative genetic variation. Balancing selection hypotheses imply that intermediate-frequency alleles disproportionately contribute to genetic variance of life-history traits and fitness. Such alleles may also associate with population genetic footprints of recent selection, including reduced genetic diversity and inflated linkage disequilibrium at linked, neutral sites. Here, we compare the evolutionary dynamics of different balancing selection models, and characterize the evolutionary timescale and hitchhiking effects of partial selective sweeps generated under antagonistic versus nonantagonistic (e.g., overdominant and frequency-dependent selection) processes. We show that the evolutionary timescales of partial sweeps tend to be much longer, and hitchhiking effects are drastically weaker, under scenarios of antagonistic selection. These results predict an interesting mismatch between molecular population genetic and quantitative genetic patterns of variation. Balanced, antagonistically selected alleles are expected to contribute more to additive genetic variance for fitness than alleles maintained by classic, nonantagonistic mechanisms. Nevertheless, classical mechanisms of balancing selection are much more likely to generate strong population genetic signatures of recent balancing selection.
Data from: The distinctive footprints of local hitchhiking in a varied environment and global hitchhiking in a subdivided population
Loci with higher levels of population differentiation than the neutral expectation are traditionally interpreted as evidence of ongoing selection that varies in space. This article emphasizes an alternative explanation which has been largely overlooked to date: in species subdivided into large subpopulations, enhanced differentiation can also be the signature left by the fixation of an unconditionally favourable mutation on its chromosomal neighbourhood. To discriminate among the two alternative scenarios one needs to investigate how genetic structure varies along the chromosomal region of the locus. Local hitchhiking is shown to generate a single sharp peak of differentiation centred on the adaptive polymorphism and the standard signature of a selective sweep only in those subpopulations where the allele is favoured. Global hitchhiking produces two domes of differentiation on either side of the fixed advantageous mutation and signatures of a selective sweep in every subpopulation, albeit of different magnitude. Investigating population differentiation around a locus that strongly differentiates two otherwise genetically similar populations of the marine mussel Mytilus edulis, plausible evidence for the global hitchhiking hypothesis has been obtained. Global hitchhiking is a neglected phenomenon that might prove to be important in species with large population sizes such as many marine invertebrates.
Data from: Spatially explicit models of divergence and genome hitchhiking
Strong barriers to genetic exchange can exist at divergently selected loci, whereas alleles at neutral loci flow more readily between populations, thus impeding divergence and speciation in the face of gene flow. However, 'divergence hitchhiking' theory posits that divergent selection can generate large regions of differentiation around selected loci. 'Genome hitchhiking' theory suggests that selection can also cause reductions in average genome-wide rates of gene flow, resulting in widespread genomic divergence (rather than divergence only around specific selected loci). Spatial heterogeneity is ubiquitous in nature, yet previous models of genetic barriers to gene flow have explored limited combinations of spatial and selective scenarios. Using simulations of secondary contact of populations, we explore barriers to gene flow in various selective and spatial contexts in continuous, two-dimensional, spatially explicit environments. In general, effects of hitchhiking are strongest in environments with regular spatial patterning of starkly divergent habitat types. When divergent selection is very strong, the absence of intermediate habitat types increases the effects of hitchhiking. However, when selection is moderate or weak, regular (versus random) spatial arrangement of habitat types becomes more important than the presence of intermediate habitats per se. We also document counterintuitive processes arising from the stochastic interplay of selection, gene flow, and drift. Our results indicate that generalization of results from two-deme models requires caution and increase understanding of the genomic and geographic basis of population divergence.
Supplementary material 4 from: Hintikka S, Carlsson JE, Carlsson J (2022) The bacterial hitchhiker's guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind. Metabarcoding and Metagenomics 6: e80416. https://doi.org/10.3897/mbmg.6.80416
COI library ASV tax
Supplementary material 1 from: Hintikka S, Carlsson JE, Carlsson J (2022) The bacterial hitchhiker's guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind. Metabarcoding and Metagenomics 6: e80416. https://doi.org/10.3897/mbmg.6.80416
File S1
Supplementary material 3 from: Hintikka S, Carlsson JE, Carlsson J (2022) The bacterial hitchhiker's guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind. Metabarcoding and Metagenomics 6: e80416. https://doi.org/10.3897/mbmg.6.80416
16S library ASV tax
Supplementary material 5 from: Hintikka S, Carlsson JE, Carlsson J (2022) The bacterial hitchhiker's guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind. Metabarcoding and Metagenomics 6: e80416. https://doi.org/10.3897/mbmg.6.80416
Unassigned COIASVs krona
Supplementary material 2 from: Hintikka S, Carlsson JE, Carlsson J (2022) The bacterial hitchhiker's guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind. Metabarcoding and Metagenomics 6: e80416. https://doi.org/10.3897/mbmg.6.80416
Metadata all
Supplementary material 1 from: Petrović A, Čkrkić J, Jamhour A, Petrović-Obradović O, Mitrović M, Starý P, Nedstam B, Tomanović Ž (2017) First record of Aphidius ericaphidis (Hymenoptera, Braconidae) in Europe: North American hitchhiker or overlooked Holarctic citizen? Journal of Hymenoptera Research 57: 143-153. https://doi.org/10.3897/jhr.57.12517
Table S1. Parasitoids of Ericaphis aphids from North America and Europe :
Figure 2 from: Petrović A, Čkrkić J, Jamhour A, Petrović-Obradović O, Mitrović M, Starý P, Nedstam B, Tomanović Ž (2017) First record of Aphidius ericaphidis (Hymenoptera, Braconidae) in Europe: North American hitchhiker or overlooked Holarctic citizen? Journal of Hymenoptera Research 57: 143-153. https://doi.org/10.3897/jhr.57.12517
Figure 2 - Phylogenetic tree based on COI sequences inferred by Maximum Likelihood (ML) method. Bootstrap values over 80% are shown.
Figure 1 from: Petrović A, Čkrkić J, Jamhour A, Petrović-Obradović O, Mitrović M, Starý P, Nedstam B, Tomanović Ž (2017) First record of Aphidius ericaphidis (Hymenoptera, Braconidae) in Europe: North American hitchhiker or overlooked Holarctic citizen? Journal of Hymenoptera Research 57: 143-153. https://doi.org/10.3897/jhr.57.12517
Figure 1 - Aphidius ericaphidis female: A antenna B head C mesonotum – dorsal aspect D propodeum – dorsal aspect E petiole – dorsal aspect F ovipositor – lateral aspect.
Data from: On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity
A central focus of population genetics has been examining the contribution of selective and neutral processes in shaping patterns of intraspecies diversity. In terms of selection specifically, surveys of higher organisms have shown considerable variation in the relative contributions of background selection and genetic hitchhiking in shaping the distribution of polymorphisms, though these analyses have rarely been extended to bacteria and viruses. Here, we study the evolution of a ubiquitous, viral pathogen, human cytomegalovirus (HCMV), by analyzing the relationship among intraspecies diversity, interspecies divergence, and rates of recombination. We show that there is a strong correlation between diversity and divergence, consistent with expectations of neutral evolution. However, after correcting for divergence, there remains a significant correlation between intraspecies diversity and recombination rates, with additional analyses suggesting that this correlation is largely due to the effects of background selection. In addition, a small number of loci, centered on long non-coding RNAs, also show evidence of selective sweeps. These data suggest that HCMV evolution is dominated by neutral mechanisms as well as background selection, expanding our understanding of linked selection to a novel class of organisms.
Figure 1 in Hitchhiking with the Vikings? The anthropogenic bumblebee fauna of Iceland - past and present
Figure 1. Distribution records of bumblebee species in Iceland.
Data from: The distinctive footprints of local hitchhiking in a varied environment and global hitchhiking in a subdivided population
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Data from: Patterns of linkage disequilibrium and long range hitchhiking in evolving experimental Drosophila melanogaster populations
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Data from: Non-adaptive female pursuit of extra-pair copulations can evolve through hitchhiking
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Data from: Recombination and hitchhiking of deleterious alleles
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Data from: On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity
Open the record for dataset details and reuse information.
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