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Trends in Ecology & Evolution Mar 2019Empirical data suggest that inversions in many species contain genes important for intraspecific divergence and speciation, yet mechanisms of evolution remain unclear....
Empirical data suggest that inversions in many species contain genes important for intraspecific divergence and speciation, yet mechanisms of evolution remain unclear. While genes inside an inversion are tightly linked, inversions are not static but evolve separately from the rest of the genome by new mutations, recombination within arrangements, and gene flux between arrangements. Inversion polymorphisms are maintained by different processes, for example, divergent or balancing selection, or a mix of multiple processes. Moreover, the relative roles of selection, drift, mutation, and recombination will change over the lifetime of an inversion and within its area of distribution. We believe inversions are central to the evolution of many species, but we need many more data and new models to understand the complex mechanisms involved.
Topics: Chromosome Inversion; Evolution, Molecular; Genetic Speciation; Models, Genetic; Polymorphism, Genetic
PubMed: 30691998
DOI: 10.1016/j.tree.2018.12.005 -
Cell May 2022Unlike copy number variants (CNVs), inversions remain an underexplored genetic variation class. By integrating multiple genomic technologies, we discover 729 inversions...
Unlike copy number variants (CNVs), inversions remain an underexplored genetic variation class. By integrating multiple genomic technologies, we discover 729 inversions in 41 human genomes. Approximately 85% of inversions <2 kbp form by twin-priming during L1 retrotransposition; 80% of the larger inversions are balanced and affect twice as many nucleotides as CNVs. Balanced inversions show an excess of common variants, and 72% are flanked by segmental duplications (SDs) or retrotransposons. Since flanking repeats promote non-allelic homologous recombination, we developed complementary approaches to identify recurrent inversion formation. We describe 40 recurrent inversions encompassing 0.6% of the genome, showing inversion rates up to 2.7 × 10 per locus per generation. Recurrent inversions exhibit a sex-chromosomal bias and co-localize with genomic disorder critical regions. We propose that inversion recurrence results in an elevated number of heterozygous carriers and structural SD diversity, which increases mutability in the population and predisposes specific haplotypes to disease-causing CNVs.
Topics: Chromosome Inversion; DNA Copy Number Variations; Genome, Human; Genomics; Humans; Segmental Duplications, Genomic
PubMed: 35525246
DOI: 10.1016/j.cell.2022.04.017 -
Philosophical Transactions of the Royal... Jul 2022At the birth of supergenes, the genomic landscape is dramatically re-organized leading to pronounced differences in phenotypes and increased intrasexual diversity. Two... (Review)
Review
At the birth of supergenes, the genomic landscape is dramatically re-organized leading to pronounced differences in phenotypes and increased intrasexual diversity. Two of the best-studied supergenes in vertebrates are arguably the inversion polymorphisms on chromosomes 2 and 11 in the white-throated sparrow () and the ruff (), respectively. In both species, regions of suppressed recombination determine plumage coloration and social behavioural phenotypes. Despite the apparent lack of gene overlap between these two supergenes, in both cases the alternative phenotypes seem to be driven largely by alterations in steroid hormone pathways. Here, we explore the interplay between genomic architecture and steroid-related genes. Due to the highly pleiotropic effects of steroid-related genes and their universal involvement in social behaviour and transcriptomic regulation, processes favouring their linkage are likely to have substantial effects on the evolution of behavioural phenotypes, individual fitness, and life-history strategies. We propose that inversion-related differentiation and regulatory changes in steroid-related genes lie at the core of phenotypic differentiation in both of these interesting species. This article is part of the theme issue 'Genetic basis of adaptation and speciation: from loci to causative mutations'.
Topics: Animals; Chromosome Inversion; Genome; Social Behavior; Sparrows; Steroids
PubMed: 35634926
DOI: 10.1098/rstb.2020.0507 -
PloS One 2022Although muscle strength training is a prevalent treatment for patients with functional ankle instability (FAI), previous investigations on the efficacy have yielded... (Randomized Controlled Trial)
Randomized Controlled Trial
BACKGROUND
Although muscle strength training is a prevalent treatment for patients with functional ankle instability (FAI), previous investigations on the efficacy have yielded conflicting results.
OBJECTIVE
This study aims to compare the efficacy of 6-week isokinetic strength training and Thera-Band strength training on improving ankle strength, dynamic balance ability, and function in individuals with FAI.
METHODS
Fifty-two FAI patients were randomized into two treatment groups: an isokinetic strength training (IST, n = 26) group and a Thera-Band resistance training (TBT, n = 26) group. The IST group engaged in isokinetic concentric strength training with inversion, eversion, dorsiflexion, and plantar flexion, whereas the TBT group engaged in progressive resistance training with Thera-Band three times per week for six weeks. Before and after the training, an isokinetic concentric strength test of the involved ankle joint, Star Excursion Balance Test (SEBT), and Cumberland Ankle Instability Tool (CAIT) function assessment were performed.
RESULTS
After six weeks of intervention, the strength of inversion and eversion was significantly improved in both the IST and TBT groups (p < 0.05), with the IST group exhibiting a significant (p < 0.05) improvement when compared to the TBT group. The SEBT and CAIT results were significantly (p < 0.05) improved in the IST group compared to the TBT group.
CONCLUSIONS
The six-week of isokinetic strength training is more effective than the Thera-Band progressive resistance training in improving the physical function of FAI patients.
CLINICAL TRIAL REGISTRATION NUMBER
This randomized controlled clinical trial has been registered in the China Clinical Trial Registry (ChiCTR2100044444) https://www.google.com/search?client=firefox-b-d&q=ChiCTR2100044444.
Topics: Humans; Resistance Training; Ankle; Exercise Therapy; Medicine; Joint Instability; Chromosome Inversion
PubMed: 36454876
DOI: 10.1371/journal.pone.0278284 -
Molecular Ecology Jun 2021The coexistence of discrete morphs that differ in multiple traits is common within natural populations of many taxa. Such morphs are often associated with chromosomal... (Review)
Review
The coexistence of discrete morphs that differ in multiple traits is common within natural populations of many taxa. Such morphs are often associated with chromosomal inversions, presumably because the recombination suppressing effects of inversions help maintain alternate adaptive combinations of alleles across the multiple loci affecting these traits. However, inversions can also harbour selected mutations at their breakpoints, leading to their rise in frequency in addition to (or independent from) their role in recombination suppression. In this review, we first describe the different ways that breakpoints can create mutations. We then critically examine the evidence for the breakpoint-mutation and recombination suppression hypotheses for explaining the existence of discrete morphs associated with chromosomal inversions. We find that the evidence that inversions are favoured due to recombination suppression is often indirect. The evidence that breakpoints harbour mutations that are adaptive is also largely indirect, with the characterization of inversion breakpoints at the sequence level being incomplete in most systems. Direct tests of the role of suppressed recombination and breakpoint mutations in inversion evolution are thus needed. Finally, we emphasize how the two hypotheses of recombination suppression and breakpoint mutation can act in conjunction, with implications for understanding the emergence of supergenes and their evolutionary dynamics. We conclude by discussing how breakpoint characterization could improve our understanding of complex, discrete phenotypic forms in nature.
Topics: Alleles; Chromosome Inversion; Evolution, Molecular; Phenotype
PubMed: 33786937
DOI: 10.1111/mec.15907 -
Philosophical Transactions of the Royal... Aug 2022Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel... (Review)
Review
Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.
Topics: Acclimatization; Adaptation, Physiological; Alleles; Chromosome Inversion; Evolution, Molecular; Genomics; Humans
PubMed: 35694747
DOI: 10.1098/rstb.2021.0203 -
BMC Genomics Sep 2021Inversion Symmetry is a generalization of the second Chargaff rule, stating that the count of a string of k nucleotides on a single chromosomal strand equals the count...
BACKGROUND
Inversion Symmetry is a generalization of the second Chargaff rule, stating that the count of a string of k nucleotides on a single chromosomal strand equals the count of its inverse (reverse-complement) k-mer. It holds for many species, both eukaryotes and prokaryotes, for ranges of k which may vary from 7 to 10 as chromosomal lengths vary from 2Mbp to 200 Mbp. Building on this formalism we introduce the concept of k-mer distances between chromosomes. We formulate two k-mer distance measures, D and D, which depend on k. D takes into account all k-mers (for a single k) appearing on single strands of the two compared chromosomes, whereas D takes into account both strands of each chromosome. Both measures reflect dissimilarities in global chromosomal structures.
RESULTS
After defining the various distance measures and summarizing their properties, we also define proximities that rely on the existence of synteny blocks between chromosomes of different bacterial strains. Comparing pairs of strains of bacteria, we find negative correlations between synteny proximities and k-mer distances, thus establishing the meaning of the latter as measures of evolutionary distances among bacterial strains. The synteny measures we use are appropriate for closely related bacterial strains, where considerable sections of chromosomes demonstrate high direct or reversed equality. These measures are not appropriate for comparing different bacteria or eukaryotes. K-mer structural distances can be defined for all species. Because of the arbitrariness of strand choices, we employ only the D measure when comparing chromosomes of different species. The results for comparisons of various eukaryotes display interesting behavior which is partially consistent with conventional understanding of evolutionary genomics. In particular, we define ratios of minimal k-mer distances (KDR) between unmasked and masked chromosomes of two species, which correlate with both short and long evolutionary scales.
CONCLUSIONS
k-mer distances reflect dissimilarities among global chromosomal structures. They carry information which aggregates all mutations. As such they can complement traditional evolution studies , which mainly concentrate on coding regions.
Topics: Chromosome Inversion; Chromosomes; Eukaryota; Evolution, Molecular; Genomics; Humans; Synteny
PubMed: 34488632
DOI: 10.1186/s12864-021-07952-0 -
Nature Communications Mar 2022Chromosomal inversions frequently underlie major phenotypic variation maintained by divergent selection within and between sexes. Here we examine whether and how...
Chromosomal inversions frequently underlie major phenotypic variation maintained by divergent selection within and between sexes. Here we examine whether and how intralocus conflicts contribute to balancing selection stabilizing an autosomal inversion polymorphism in the ruff Calidris pugnax. In this lekking shorebird, three male mating morphs (Independents, Satellites and Faeders) are controlled by an inversion-based supergene. We show that in a captive population, Faeder females, who are smaller and whose inversion haplotype has not undergone recombination, have lower average reproductive success in terms of laying rate, egg size, and offspring survival than Independent females, who lack the inversion. Satellite females, who carry a recombined inversion haplotype and have intermediate body size, more closely resemble Independent than Faeder females in reproductive performance. We inferred that the lower reproductive output of Faeder females is most likely balanced by higher than average reproductive success of individual Faeder males. These findings suggest that intralocus conflicts may play a major role in the evolution and maintenance of supergene variants.
Topics: Animals; Charadriiformes; Chromosome Inversion; Female; Haplotypes; Male; Polymorphism, Genetic; Reproduction
PubMed: 35296671
DOI: 10.1038/s41467-022-29033-w -
The Journal of Heredity Jan 2017Progress on understanding how genome structure evolves is accelerating with the arrival of new genomic, comparative, and theoretical approaches. This article reviews... (Review)
Review
Progress on understanding how genome structure evolves is accelerating with the arrival of new genomic, comparative, and theoretical approaches. This article reviews progress in understanding how chromosome inversions and sex chromosomes evolve, and how their evolution affects species' ecology. Analyses of clines in inversion frequencies in flies and mosquitoes imply strong local adaptation, and roles for both over- and under dominant selection. Those results are consistent with the hypothesis that inversions become established when they capture locally adapted alleles. Inversions can carry alleles that are beneficial to closely related species, causing them to introgress following hybridization. Models show that this "adaptive cassette" scenario can trigger large range expansions, as recently happened in malaria mosquitoes. Sex chromosomes are the most rapidly evolving genome regions of some taxa. Sexually antagonistic selection may be the key force driving transitions of sex determination between different pairs of chromosomes and between XY and ZW systems. Fusions between sex-chromosomes and autosomes most often involve the Y chromosome, a pattern that can be explained if fusions are mildly deleterious and fix by drift. Sexually antagonistic selection is one of several hypotheses to explain the recent discovery that the sex determination system has strong effects on the adult sex ratios of tetrapods. The emerging view of how genome structure evolves invokes a much richer constellation of forces than was envisioned during the Golden Age of research on Drosophila karyotypes.
Topics: Adaptation, Biological; Animals; Chromosome Aberrations; Chromosome Inversion; Evolution, Molecular; Genome; Models, Genetic; Selection, Genetic; Sex Chromosomes; Sex Determination Processes; Sex Ratio
PubMed: 27388336
DOI: 10.1093/jhered/esw041 -
Trends in Ecology & Evolution Jun 2018Chromosomal inversions have long fascinated evolutionary biologists due to their suppression of recombination, which can protect co-adapted alleles. Emerging research... (Review)
Review
Chromosomal inversions have long fascinated evolutionary biologists due to their suppression of recombination, which can protect co-adapted alleles. Emerging research documents that inversions are commonly linked to spectacular phenotypes and have a pervasive role in eco-evolutionary processes, from mating systems, social organisation, environmental adaptation, and reproductive isolation to speciation. Studies also reveal that inversions are taxonomically widespread, with many being old and large, and that balancing selection is commonly facilitating their maintenance. This challenges the traditional view that the role of balancing selection in maintaining variation is relatively minor. The ubiquitous importance of inversions in ecological and evolutionary processes suggests that structural variation should be better acknowledged and integrated in studies pertaining to the molecular basis of adaptation and speciation.
Topics: Chromosome Inversion; Evolution, Molecular; Genomics; Models, Genetic; Polymorphism, Genetic
PubMed: 29731154
DOI: 10.1016/j.tree.2018.04.002