Nucleotide Sequence Analyses of Human Complement 6 (C6) Gene Suggest Balancing Selection

Soejima, Mikiko; Tachida, Hidenori; Tsuneoka, Makoto; Takenaka, Osamu; Kimurâ, Hiroshi; Koda, Yoshiro

doi:10.1046/j.1469-1809.2005.00165.x

Cited by 9 publications

(3 citation statements)

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“…For example, Tajima's D can become strongly negative when the population has gone through a prolonged bottleneck and expanded thereafter (Sano and Tachida 2005). However, our previous studies suggest that such a severe population bottleneck is unlikely to be the cause (Koda et al 2004;Soejima et al 2005). In addition, the GOF test proposed by Jensen et al (2005) suggested that the original rejection of neutrality in Europeans by the CLR test is more likely to be due to a selective sweep than demography alone.…”

Section: Aim1 Polymorphism 185mentioning

confidence: 87%

Evidence for Recent Positive Selection at the Human AIM1 Locus in a European Population

Soejima¹,

Tachida²,

Ishida³

et al. 2005

Molecular Biology and Evolution

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Two missense polymorphisms (E272K and L374F) of the AIM1 locus, encoding a melanocyte differentiation antigen, were shown to have a clear association with human ethnicities. These two nonpathogenic single nucleotide polymorphisms (SNPs) may be associated with human pigmentation variation. In this study, we investigated sequence variation in the coding region and exon-flanking sequence and found low genetic variation only in subjects of European descent. All four statistical tests applied to the 7.55-kb region surrounding the L374F polymorphism detected statistically significant deviations from selective neutrality in Europeans. In addition, haplotype analysis revealed that one haplotype carrying 374F was overrepresented in this population, and the low rate of variation, with some features of selective sweeps, was shown to be statistically significant. These results suggest that positive selection recently has been acting or has acted on at least this region of the melanogenic gene and that an advantageous haplotype spread rapidly in Europe.

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Section: Aim1 Polymorphism 185mentioning

confidence: 87%

Evidence for Recent Positive Selection at the Human AIM1 Locus in a European Population

Soejima¹,

Tachida²,

Ishida³

et al. 2005

Molecular Biology and Evolution

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“…We also identified a region, characterized by high F ST and low π diff , that contained the complement genes C6 and C7. The complement system plays an important role in innate immunity (58), and our results could indicate that balancing selection is acting in this region of the genome to favor a diverse set of alleles, as is known for C6 in humans (59). Based on the analysis of individual outlier variants, the RIN3 gene showed a consistent pattern of allele frequency differences across all nine of the frog populations sampled in this study, indicating consistent selection in populations distributed across a wide geographic area.…”

Section: Discussionmentioning

confidence: 68%

Reintroduction of resistant frogs facilitates landscape-scale recovery in the presence of a lethal fungal disease

Knapp¹,

Wilber

Byrne

et al. 2023

Preprint

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Vast alteration of the biosphere by humans is causing a sixth mass extinction. Adaptation to modified environments often is the only means for species to persist, but the extent to which such "evolutionary rescue" can prevent or reverse biodiversity loss is largely unknown. Using results from genomic analyses, a 15-year reintroduction effort, and population modeling, we provide a compelling example of evolution reversing the declines of an imperiled amphibian and allowing the reestablishment of extirpated populations. The once-common mountain yellow-legged (MYL) frog is threatened with extinction by the human-facilitated emergence of a lethal fungal pathogen (Batrachochytrium dendrobatidis; "Bd"). Although most MYL frog populations are extirpated following disease outbreaks, some persist and eventually begin to recover. Using an exome capture approach, we show that MYL frogs have undergone substantial evolutionary change following disease outbreaks. Moreover, in naturally recovering populations observed changes in immune function loci are associated with increased resistance/tolerance to Bd infection. Large-scale reintroduction of frogs from rescued populations resulted in the establishment of reproducing populations despite ongoing disease. In addition, results from viability modeling suggest that established populations have a low probability of extinction over 50 years. Collectively, these results provide a rare example of how evolutionary rescue and the reintroduction of resistant/tolerant individuals can allow the landscape-scale recovery of disease-impacted species. This example has potentially broad implications for the many taxa worldwide that are threatened with extinction by anthropogenic stressors.

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“…Dobzhansky proposed the ‘balanced hypothesis’, which suggests that many genes are polymorphic and that these polymorphisms are maintained by heterozygote advantage [1]. However, systematic studies that have been carried out on various organisms have so far reported little evidence of balancing selection [2–8]. …”

Section: Introductionmentioning

confidence: 99%

A genome-wide scan for genes under balancing selection in Drosophila melanogaster

et al. 2017

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BackgroundIn the history of population genetics balancing selection has been considered as an important evolutionary force, yet until today little is known about its abundance and its effect on patterns of genetic diversity. Several well-known examples of balancing selection have been reported from humans, mice, plants, and parasites. However, only very few systematic studies have been carried out to detect genes under balancing selection. We performed a genome scan in Drosophila melanogaster to find signatures of balancing selection in a derived (European) and an ancestral (African) population. We screened a total of 34 genomes searching for regions of high genetic diversity and an excess of SNPs with intermediate frequency.ResultsIn total, we found 183 candidate genes: 141 in the European population and 45 in the African one, with only three genes shared between both populations. Most differences between both populations were observed on the X chromosome, though this might be partly due to false positives. Functionally, we find an overrepresentation of genes involved in neuronal development and circadian rhythm. Furthermore, some of the top genes we identified are involved in innate immunity.ConclusionOur results revealed evidence of genes under balancing selection in European and African populations. More candidate genes have been found in the European population. They are involved in several different functions.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0857-z) contains supplementary material, which is available to authorized users.

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Nucleotide Sequence Analyses of Human Complement 6 (C6) Gene Suggest Balancing Selection

Cited by 9 publications

References 50 publications

Evidence for Recent Positive Selection at the Human AIM1 Locus in a European Population

Evidence for Recent Positive Selection at the Human AIM1 Locus in a European Population

Reintroduction of resistant frogs facilitates landscape-scale recovery in the presence of a lethal fungal disease

A genome-wide scan for genes under balancing selection in Drosophila melanogaster

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