scholarly journals Long-term balancing selection on chromosomal variants associated with crypsis in a stick insect

2017 ◽  
Vol 26 (22) ◽  
pp. 6189-6205 ◽  
Author(s):  
Dorothea Lindtke ◽  
Kay Lucek ◽  
Víctor Soria-Carrasco ◽  
Romain Villoutreix ◽  
Timothy E. Farkas ◽  
...  
Keyword(s):  
Balancing Selection ◽  
Stick Insect ◽  
Chromosomal Variants

scholarly journals Recent Selection Changes in Human Genes under Long-Term Balancing Selection

2016 ◽  
Vol 33 (6) ◽  
pp. 1435-1447 ◽  
Author(s):  
Cesare de Filippo ◽  
Felix M. Key ◽  
Silvia Ghirotto ◽  
Andrea Benazzo ◽  
Juan R. Meneu ◽  
...  
Keyword(s):  
Balancing Selection ◽  
Human Genes ◽  
Recent Selection

Supergene degeneration opposes polymorphism: The curious case of balanced lethals

2021 ◽  
Author(s):  
Emma Berdan ◽  
Alexandre Blanckaert ◽  
Roger K Butlin ◽  
Thomas Flatt ◽  
Tanja Slotte ◽  
...  
Keyword(s):  
Equilibrium State ◽  
Balancing Selection ◽  
Mutation Accumulation ◽  
Small Population ◽  
Quasi Equilibrium ◽  
Deleterious Mutations ◽  
Critical Factors ◽  
Critical Aspect ◽  
Allopatric Divergence

Supergenes offer some of the most spectacular examples of long-term balancing selection in nature but their origin and maintenance remain a mystery. A critical aspect of supergenes is reduced recombination between arrangements. Reduced recombination protects adaptive multi-trait phenotypes, but can also lead to degeneration through mutation accumulation. Mutation accumulation can stabilize the system through the emergence of associative overdominance (AOD), destabilize the system, or lead to new evolutionary outcomes. One such outcome is the formation of balanced lethal systems, a maladaptive system where both supergene arrangements have accumulated deleterious mutations to the extent that both homozygotes are inviable, leaving only heterozygotes to reproduce. Here, we perform a simulation study to understand the conditions under which these different outcomes occur, assuming a scenario of introgression after allopatric divergence. We found that AOD aids the invasion of a new supergene arrangement and the establishment of a polymorphism. However, this polymorphism is easily destabilized by further mutation accumulation. While degradation may strengthen AOD, thereby stabilizing the supergene polymorphism, it is often asymmetric, which is the key disrupter of the quasi-equilibrium state of the polymorphism. Furthermore, mechanisms that accelerate degeneration also tend to amplify asymmetric mutation accumulation between the supergene arrangements and vice versa. As the evolution of a balanced lethal system requires symmetric degradation of both arrangements, this leaves highly restricted conditions under which such a system could evolve. We show that small population size and low dominance coefficients are critical factors, as these reduce the efficacy of selection. The dichotomy between the persistence of a polymorphism and degradation of supergene arrangements likely underlies the rarity of balanced lethal systems in nature.

scholarly journals Population genetics of the coral Acropora millepora: Towards a genomic predictor of bleaching

2019 ◽  
Author(s):  
Zachary L. Fuller ◽  
Veronique J.L. Mocellin ◽  
Luke Morris ◽  
Neal Cantin ◽  
Jihanne Shepherd ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Balancing Selection ◽  
Genome Wide Association ◽  
Conservation Strategies ◽  
Genome Sequences ◽  
Acropora Millepora ◽  
Genome Wide ◽  
A Genome ◽  
In The Wild

AbstractAlthough reef-building corals are rapidly declining worldwide, responses to bleaching vary both within and among species. Because these inter-individual differences are partly heritable, they should in principle be predictable from genomic data. Towards that goal, we generated a chromosome-scale genome assembly for the coral Acropora millepora. We then obtained whole genome sequences for 237 phenotyped samples collected at 12 reefs distributed along the Great Barrier Reef, among which we inferred very little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin. We further used 213 of the samples to conduct a genome-wide association study of visual bleaching score, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for the use of genomics-based approaches in conservation strategies.

scholarly journals Long-Term Balancing Selection at the Blood Group-Related Gene B4galnt2 in the Genus Mus (Rodentia; Muridae)

2011 ◽  
Vol 28 (11) ◽  
pp. 2999-3003 ◽  
Author(s):  
Miriam Linnenbrink ◽  
Jill M. Johnsen ◽  
Inka Montero ◽  
Christine R. Brzezinski ◽  
Bettina Harr ◽  
...  
Keyword(s):  
Blood Group ◽  
Balancing Selection ◽  
Related Gene

scholarly journals Long-term balancing selection in LAD1 maintains a missense trans-species polymorphism in humans, chimpanzees and bonobos

2014 ◽  
Author(s):  
João C. Teixeira ◽  
Cesare de Filippo ◽  
Antje Weihmann ◽  
Juan R. Meneu ◽  
Fernando Racimo ◽  
...  
Keyword(s):  
Balancing Selection ◽  
Phenotypic Diversity ◽  
Intermediate Frequency ◽  
High Genetic Diversity ◽  
Protein Coding ◽  
Missense Change ◽  
Linear Iga Disease ◽  
Filament Protein

Balancing selection maintains advantageous genetic and phenotypic diversity in populations. When selection acts for long evolutionary periods selected polymorphisms may survive species splits and segregate in present-day populations of different species. Here, we investigate the role of long-term balancing selection in the evolution of protein-coding sequences in the Homo-Pan clade. We sequenced the exome of 20 humans, 20 chimpanzees and 20 bonobos and detected eight coding trans-species polymorphisms (trSNPs) that are shared among the three species and have segregated for approximately 14 million years of independent evolution. While the majority of these trSNPs were found in three genes of the MHC cluster, we also uncovered one coding trSNP (rs12088790) in the gene LAD1. All these trSNPs show clustering of sequences by allele rather than by species and also exhibit other signatures of long-term balancing selection, such as segregating at intermediate frequency and lying in a locus with high genetic diversity. Here we focus on the trSNP in LAD1, a gene that encodes for Ladinin-1, a collagenous anchoring filament protein of basement membrane that is responsible for maintaining cohesion at the dermal-epidermal junction; the gene is also an autoantigen responsible for linear IgA disease. This trSNP results in a missense change (Leucine257Proline) and, besides altering the protein sequence, is associated with changes in gene expression of LAD1.

scholarly journals Long-term balancing selection drives evolution of immunity genes in Capsella

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Daniel Koenig ◽  
Jörg Hagmann ◽  
Rachel Li ◽  
Felix Bemm ◽  
Tanja Slotte ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Balancing Selection ◽  
Protein Sequences ◽  
Population Bottleneck ◽  
Genomic Variability ◽  
Immune Systems ◽  
Immunity Genes ◽  
Evolution Of Immunity

Genetic drift is expected to remove polymorphism from populations over long periods of time, with the rate of polymorphism loss being accelerated when species experience strong reductions in population size. Adaptive forces that maintain genetic variation in populations, or balancing selection, might counteract this process. To understand the extent to which natural selection can drive the retention of genetic diversity, we document genomic variability after two parallel species-wide bottlenecks in the genus Capsella. We find that ancestral variation preferentially persists at immunity related loci, and that the same collection of alleles has been maintained in different lineages that have been separated for several million years. By reconstructing the evolution of the disease-related locus MLO2b, we find that divergence between ancient haplotypes can be obscured by referenced based re-sequencing methods, and that trans-specific alleles can encode substantially diverged protein sequences. Our data point to long-term balancing selection as an important factor shaping the genetics of immune systems in plants and as the predominant driver of genomic variability after a population bottleneck.

scholarly journals Multiple targets of balancing selection in Leishmania donovani complex parasites

2021 ◽  
Author(s):  
Cooper Alastair Grace ◽  
Sarah Forrester ◽  
Vladimir Costa Silva ◽  
Aleksander Aare ◽  
Hannah Kilford ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Species Complex ◽  
Leishmania Donovani ◽  
Balancing Selection ◽  
Genomic Data ◽  
Causative Agents ◽  
Signatures Of Selection ◽  
Attachment Proteins ◽  
Multiple Metrics

AbstractThe Leishmania donovani species complex are the causative agents of visceral leishmaniasis, which cause 20-40,000 fatalities a year. Here, we conduct a screen for balancing selection in this specie complex. We sequence 93 isolates of L. infantum from Brazil and used 387 publicly-available L. donovani and L. infantum genomes, to describe the global diversity of this species complex. We identify five genetically-distinct populations that are sufficiently represented by genomic data to search for signatures of selection. We show that multiple metrics identify genes with robust signatures of balancing selection. We produce a curated set of 19 genes with robust signatures, including zeta toxin, nodulin-like and flagellum attachment proteins. Candidate genes were generally not shared between populations, consistent with divergent rather than long-term balancing selection in these species. This study highlights the extent of genetic divergence between L. donovani complex parasites and provides candidate genes for further study.

scholarly journals Evidence for widespread selection in shaping the genomic landscape during speciation of Populus

2019 ◽  
Author(s):  
Jing Wang ◽  
Nathaniel R. Street ◽  
Eung-Jun Park ◽  
Jianquan Liu ◽  
Pär K. Ingvarsson
Keyword(s):  
Recurrent Selection ◽  
Balancing Selection ◽  
Forest Tree ◽  
Species Variation ◽  
Recombination Rates ◽  
Genome Wide ◽  
Genomic Landscape ◽  
Speciation Continuum ◽  
Whole Genome Resequencing

AbstractIncreasing our understanding of how various evolutionary processes drive the genomic landscape of variation is fundamental to a better understanding of the genomic consequences of speciation. However, the genome-wide patterns of within- and between-species variation have not been fully investigated in most forest tree species despite their global ecological and economic importance. Here, we use whole-genome resequencing data from four Populus species spanning the speciation continuum to reconstruct their demographic histories, investigate patterns of diversity and divergence, infer their genealogical relationships and estimate the extent of ancient introgression across the genome. Our results show substantial variation in these patterns along the genomes although this variation is not randomly distributed but is strongly predicted by the local recombination rates and the density of functional elements. This implies that the interaction between recurrent selection and intrinsic genomic features has dramatically sculpted the genomic landscape over long periods of time. In addition, our findings provide evidence that, apart from background selection, recent positive selection and long-term balancing selection are also crucial components in shaping patterns of genome-wide variation during the speciation process.

scholarly journals Flexible Mixture Model Approaches That Accommodate Footprint Size Variability for Robust Detection of Balancing Selection

2020 ◽  
Vol 37 (11) ◽  
pp. 3267-3291 ◽  
Author(s):  
Xiaoheng Cheng ◽  
Michael DeGiorgio
Keyword(s):  
Pain Perception ◽  
Balancing Selection ◽  
Genomic Data ◽  
Composite Likelihood ◽  
Ratio Test ◽  
Data Set ◽  
Robust Detection ◽  
Population Genomic ◽  
Genomic Regions

Abstract Long-term balancing selection typically leaves narrow footprints of increased genetic diversity, and therefore most detection approaches only achieve optimal performances when sufficiently small genomic regions (i.e., windows) are examined. Such methods are sensitive to window sizes and suffer substantial losses in power when windows are large. Here, we employ mixture models to construct a set of five composite likelihood ratio test statistics, which we collectively term B statistics. These statistics are agnostic to window sizes and can operate on diverse forms of input data. Through simulations, we show that they exhibit comparable power to the best-performing current methods, and retain substantially high power regardless of window sizes. They also display considerable robustness to high mutation rates and uneven recombination landscapes, as well as an array of other common confounding scenarios. Moreover, we applied a specific version of the B statistics, termed B2, to a human population-genomic data set and recovered many top candidates from prior studies, including the then-uncharacterized STPG2 and CCDC169–SOHLH2, both of which are related to gamete functions. We further applied B2 on a bonobo population-genomic data set. In addition to the MHC-DQ genes, we uncovered several novel candidate genes, such as KLRD1, involved in viral defense, and SCN9A, associated with pain perception. Finally, we show that our methods can be extended to account for multiallelic balancing selection and integrated the set of statistics into open-source software named BalLeRMix for future applications by the scientific community.

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