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90 results for “Balancing selection”
Data from: Emergence of long-term balanced polymorphism under cyclic selection of spatially variable magnitude
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Data from: Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta
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Data from: Ecological factors influence balancing selection on leaf chemical profiles of a wildflower
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Data from: Multiple forms of balancing selection maintain inversion polymorphism
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Large-scale fungal strain sequencing unravels the molecular diversity in mating loci maintained by long-term balancing selection
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The evolutionary advantage of fitness-dependent recombination in diploids: a deterministic mutation–selection–balance model
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Archived data for: Balancing selection, genetic drift, and human mediated-introgression interplay to shape MHC (functional) diversity in Mediterranean brown trout
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Data from: Temporal scale of habitat selection for large carnivores: Balancing energetics, risk and finding prey
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Data from: Major histocompatibility complex class II variation in bottlenose dolphin from Adriatic Sea: inferences about the extent of balancing selection
The bottlenose dolphin (Tursiops truncatus) is the most common cetacean species worldwide and the only marine mammal species resident in the Croatian part of the Adriatic Sea. To gain insight into genetic diversity of bottlenose dolphins at adaptively important loci relevant to conservation, we analysed the polymorphism of major histocompatibility complex (MHC) genes, which play a key role in pathogen confrontation and clearance. Specifically, we examined the diversity of MHC class II DRA, DQA and DQB alleles in 50 bottlenose dolphins from the Adriatic Sea collected between 1997 and 2011 and in 12 animals from other Mediterranean locations. Notable variation in DQA, DQB and three-locus haplotypes was found, with all 10 DQA and 12 DQB alleles encoding unique protein products. Analysis of the ratio of non-synonymous to synonymous substitution rates suggests that positive selection acts at both highly variable loci. Phylogenetic analyses revealed trans-species polymorphism at the DQB locus, strongly indicating the influence of balancing selection in the long term. In fact, the balancing selection observed in bottlenose dolphins is higher than that reported for most other cetaceans and comparable to that seen in terrestrial mammals.
Data from: Beyond balancing selection: frequent mitochondrial recombination contributes to high female frequencies in gynodioecious Lobelia siphilitica L. (Campanulaceae)
(1) Gynodioecy is a sexual system where females and hermaphrodites co-occur. In most gynodioecious angiosperms, sex is determined by an interaction between mitochondrial male-sterility genes (CMS) that arise via recombination and nuclear restorer alleles that evolve to suppress them. In theory, gynodioecy occurs when multiple CMS types are maintained at equilibrium frequencies by balancing selection. However, some gynodioecious populations contain very high frequencies of females. High female frequencies are not expected under balancing selection, but could be explained by the repeated introduction of novel CMS types. (2) To test for balancing selection and/or the repeated introduction of novel CMS, we characterized cytoplasmic haplotypes from 61 populations of Lobelia siphilitica that vary widely in female frequency. (3) We confirmed that mitotype diversity and female frequency were positively correlated across populations, consistent with balancing selection. However, while low-female populations hosted mostly common mitotypes, high-female populations and female plants hosted mostly rare, recombinant mitotypes likely to carry novel CMS types. (4) Our results suggest that balancing selection maintains established CMS types across this species, but extreme female frequencies result from frequent invasion by novel CMS types. We conclude that balancing selection alone cannot account for extreme population sex-ratio variation within a gynodioecious species.
Data from: Multilocus patterns of genetic variation across Cryptosporidium species suggest balancing selection at the gp60 locus
Cryptosporidium is an apicomplexan protozoan that parasites most vertebrates, including humans. Its gp60 gene is functionally involved in its attachement to host's cells and its high level of genetic variation has made it the reference marker for sample typing in epidemiological studies. To understand the origin of such high diversity and to determine the extent to which this classification applies to the rest of the genome, we analysed the patterns of variation at gp60 and nine other nuclear loci in isolates of three Cryptosporidium species. Most loci showed low genetic polymorphism (πS < 1%) and similar levels of between-species divergence. Contrastingly, gp60 exhibited very different features: (i) it was nearly ten times more variable than the other loci, (ii) it displayed a significant excess of polymorphisms relative to between-species differences in a Maximum-likelihood Hudson-Kreitman-Aguadé test (iii) gp60 subtypes turned out to be much older than the species they were found in and (iv) showed a significant excess of polymorphic variants shared across species from random expectations. These observations suggest that this locus evolves under balancing selection, and specifically under negative frequency-dependent selection. Interestingly, genetic variation at the other loci cluster very well within the subtypes defined by gp60, which may provide new tools to understand the genome-wide patterns of genetic variation of the parasite in the wild. These results suggest that gp60 plays an active and essential role in the life cycle of the parasite and that genetic variation at this locus might be essential for the parasite's long-term success.
Data from: A tight balance between natural selection and gene flow in a southern African arid-zone endemic bird
Gene flow is traditionally thought to be antagonistic to population differentiation and local adaptation. However, recent studies have demonstrated that local adaptation can proceed provided that selection is greater than the homogenising effects of gene flow. We extend these initial studies by combining ecology (climate), phenotype (body size), physiological genetics (oxidative phosphorylation genes) and neutral loci (nuclear microsatellites and introns) to test whether selection can counter-balance gene flow and hence promote local adaptation in a bird whose distribution spans an aridity gradient. Our results show that the Karoo scrub-robin's climatic niche is spatially structured, providing the potential for local adaptation to develop. We found remarkably discordant patterns of divergence among mtDNA, morphology and neutral loci. For the mitochondrial genes, two amino acid replacements, strong population structure and reduced gene flow were associated with the environmental gradient separating western coastal sites from the interior of southern Africa. In contrast, morphology and the neutral loci exhibited variation independent of environmental variables, and revealed extensive levels of gene flow across the aridity gradient, 50 times larger than the estimates for mitochondrial genes. Together, our results suggest that selective pressures on physiology, mediated by the mitochondrial genome, may well be a common mechanism for facilitating local adaptation to new climatic conditions.
Data from: A treefrog with reproductive mode plasticity reveals a changing balance of selection for non-aquatic egg-laying
Non-aquatic reproduction has evolved repeatedly, but the factors that select for laying eggs on land are not well understood. The treefrog Dendropsophus ebraccatus has plasticity in reproductive mode, laying eggs that successfully develop in or out of water. This permits the first experimental comparison of the selective agents that shape adult oviposition behavior and embryo developmental capacity. I quantified the sources and strength of arboreal and aquatic egg mortality, how mortality varies with weather patterns, and assessed 39 years of daily rainfall patterns to infer historic levels of egg mortality and effects of climate change on the selective balance between aquatic and non-aquatic egg deposition. Aquatic predators and desiccation were the strongest selective agents in water and air, respectively. Egg mortality varied with weather such that aquatic oviposition was advantageous when rainfall was low, but laying eggs out of water increased survival when rainfall was high. Additionally, I found that since 1972 there have been significant changes in the patterns of rainfall in central Panama, which has altered the selective landscape acting on egg-laying behavior. This work provides insight into both the evolution and maintenance of adaptive phenotypic plasticity as well as historic and current selection on reproduction.
Data from: Genetics and evidence for balancing selection of a sex-linked colour polymorphism in a songbird
Colour polymorphisms play a key role in sexual selection and speciation, yet the mechanisms that generate and maintain them are not fully understood. Here, we use genomic and transcriptomic tools to identify the precise genetic architecture and evolutionary history of a sex-linked colour polymorphism in the Gouldian finch Erythrura gouldiae that is also accompanied by remarkable differences in behaviour and physiology. We find that differences in colour are associated with an ~72-kbp region of the Z chromosome in a putative regulatory region for follistatin, an antagonist of the TGF-β superfamily genes. The region is highly differentiated between morphs, unlike the rest of the genome, yet we find no evidence that an inversion is involved in maintaining the distinct haplotypes. Coalescent simulations confirm that there is elevated nucleotide diversity and an excess of intermediate frequency alleles at this locus. We conclude that this pleiotropic colour polymorphism is most probably maintained by balancing selection.
Data from: Extensive variation at MHC DRB in the New Zealand sea lion (Phocarctos hookeri) provides evidence for balancing selection
Marine mammals are often reported to possess reduced variation of major histocompatibility complex (MHC) genes compared with their terrestrial counterparts. We evaluated diversity at two MHC class II B genes, DQB and DRB, in the New Zealand sea lion (Phocarctos hookeri, NZSL) a species that has suffered high mortality owing to bacterial epizootics, using Sanger sequencing and haplotype reconstruction, together with next-generation sequencing. Despite this species' prolonged history of small population size and highly restricted distribution, we demonstrate extensive diversity at MHC DRB with 26 alleles, whereas MHC DQB is dimorphic. We identify four DRB codons, predicted to be involved in antigen binding, that are evolving under adaptive evolution. Our data suggest diversity at DRB may be maintained by balancing selection, consistent with the role of this locus as an antigen-binding region and the species' recent history of mass mortality during a series of bacterial epizootics. Phylogenetic analyses of DQB and DRB sequences from pinnipeds and other carnivores revealed significant allelic diversity, but little phylogenetic depth or structure among pinniped alleles; thus, we could neither confirm nor refute the possibility of trans-species polymorphism in this group. The phylogenetic pattern observed however, suggests some significant evolutionary constraint on these loci in the recent past, with the pattern consistent with that expected following an epizootic event. These data may help further elucidate some of the genetic factors underlying the unusually high susceptibility to bacterial infection of the threatened NZSL, and help us to better understand the extent and pattern of MHC diversity in pinnipeds.
Data from: Natural selection on MHC IIβ in parapatric lake and stream stickleback: balancing, divergent, both or neither?
Major histocompatibility (MHC) genes encode proteins that play a central role in vertebrates' adaptive immunity to parasites. MHC loci are among the most polymorphic in vertebrates' genomes, inspiring many studies to identify evolutionary processes driving MHC polymorphism within populations, and divergence between populations. Leading hypotheses include balancing selection favoring rare alleles within populations, and spatially divergent selection. These hypotheses do not always produce diagnosably distinct predictions, causing many studies of MHC to yield inconsistent or ambiguous results. We suggest a novel strategy to distinguish balancing versus divergent selection on MHC, taking advantage of natural admixture between parapatric populations. With divergent selection, individuals with immigrant alleles will be more infected and less fit because they are susceptible to novel parasites in their new habitat. With balancing selection, individuals with locally-rare immigrant alleles will be more fit (less infected). We tested these contrasting predictions using threespine stickleback from three replicate pairs of parapatric lake and stream habitats. We found numerous positive and negative associations between particular MHC IIβ alleles and particular parasite taxa. A few allele-parasite comparisons supported balancing selection, others supported divergent selection between habitats. But, there was no overall tendency for fish with immigrant MHC alleles to be more or less heavily infected. Instead, locally rare MHC alleles (not necessarily immigrants) were associated with heavier infections. Our results illustrate the complex relationship between MHC IIβ allelic variation and spatially varying multi-species parasite communities: different hypotheses may be concurrently true for different allele-parasite combinations.
Data from: Low major histocompatibility complex class II variation in the endangered Indo-Pacific humpback dolphin (Sousa chinensis): inferences about the role of balancing selection
It has been widely reported that the major histocompatibility complex (MHC) is under balancing selection due to its immune function across terrestrial and aquatic mammals. The comprehensive studies at MHC and other neutral loci could give us a synthetic evaluation about the major force determining genetic diversity of species. Previously, a low level of genetic diversity has been reported among the Indo-Pacific humpback dolphin (Sousa chinensis) in the Pearl River Estuary (PRE) using both mitochondrial marker and microsatellite loci. Here, the expression and sequence polymorphism of 2 MHC class II genes (DQB and DRB) in 32 S. chinensis from PRE collected between 2003 and 2011 were investigated. High ratios of non-synonymous to synonymous substitution rates, codon-based selection analysis, and trans-species polymorphism (TSP) support the hypothesis that balancing selection acted on S. chinensis MHC sequences. However, only 2 haplotypes were detected at either DQB or DRB loci. Moreover, the lack of deviation from the Hardy–Weinberg expectation at DRB locus combined with the relatively low heterozygosity at both DQB locus and microsatellite loci suggested that balancing selection might not be sufficient, which further suggested that genetic drift associated with historical bottlenecks was not mitigated by balancing selection in terms of the loss of MHC and neutral variation in S. chinensis. The combined results highlighted the importance of maintaining the genetic diversity of the endangered S. chinensis.
Data from: Cast adrift on an island: introduced populations experience an altered balance between selection and drift
A long-standing question in evolutionary biology is what becomes of adaptive traits when a species expands its range into novel environments. Here we report the results of a study on an adaptive colour pattern polymorphism (stripes) of the coqui frog following its introduction to Hawaii from Puerto Rico. We compared population differentiation (φ'ST and FST) for the stripes locus —which underlies this colour pattern polymorphism— with neutral microsatellite loci to test for a signature of selection among native and introduced populations. Among native populations, φ'ST and FST for stripes were lower than expected under the neutral model, suggesting uniform balancing selection. Alternatively, among introduced populations, φ'ST and FST for stripes did not differ from the neutral model. These results suggest that the evolutionary dynamics of this previously adaptive trait have become dominated by random genetic drift following the range expansion.
Data from: Balancing selection and introgression of newt immune-response genes
The importance of interspecific introgression as a source of adaptive variation is increasingly recognized. Theory predicts that beneficial genetic variants cross species boundaries easily even when interspecific hybridization is rare and gene flow is strongly constrained throughout the genome. However, it remains unclear whether certain classes of genes are particularly prone to adaptive introgression. Genes affected by balancing selection (BS) may constitute such a class, because forms of BS that favor novel, initially rare alleles, should facilitate introgression. We tested this hypothesis in hybridizing newts by comparing 13 genes with signatures of BS, in particular an excess of common nonsynonymous polymorphisms, to the genomic background (154 genes). Parapatric hybridizing taxa were less differentiated in BS candidate genes than more closely related allopatric lineages, while the opposite was observed in the control genes. Coalescent and forward simulations that explored neutral and BS scenarios under isolation and migration, showed that processes other than differential gene flow are unlikely to account for this pattern. We conclude that BS, probably involving a form of novel allele advantage, promotes introgression. This mechanism may be a source of adaptively relevant variation in hybridizing species over prolonged periods.
Movement-integrated habitat selection reveals wolves balance ease of travel with human avoidance in a risk-reward trade-off
<p>We captured and collared 46 wolves across 12 packs in eastern Manitoba between 2014-2019. Each wolf was fit with a GPS telemetry collar programmed to collect a GPS relocation every two hours across all seasons.</p> <p>To produce the dataset, GPS locations were used to generate steps (linear connection between consecutive locations) using the integrated Step Selection Function (iSSA) framework. For a given used step, we randomly generated ten steps based on observed distributions of individual-level movement behaviour. We then extracted habitat covariates for each start and end point of a step, including proportion of forest, distance to linear features, and time of day. </p>
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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