Does urbanization level predict C-kit-ligand allele frequency in domestic goat suggesting a role in Human-animal relationship?

Linkage disequilibrium in two‐stage marker‐assisted selection

Panels of informative biallelic single nucleotide polymorphisms (SNPs) have been proposed to be an economical method to fast-track the population genetic analysis of Plasmodium falciparum in malaria-endemic areas. Whilst used successfully in low-transmission areas where infections are monoclonal and highly related, we present the first study to evaluate the performance of these 24- and 96-SNP molecular barcodes in African countries, characterised by moderate-to-high transmission, where multiclonal infections are prevalent. For SNP barcodes it is generally recommended that the SNPs chosen i) are biallelic, ii) have a minor allele frequency greater than 0.10, and iii) are independently segregating, to minimise bias in the analysis of genetic diversity and population structure. Further, to be standardised and used in many population genetic studies, these barcodes should maintain characteristics i) to iii) across various iv) geographies and v) time points. Using haplotypes generated from the MalariaGEN P. falciparum Community Project version six database, we investigated the ability of these two barcodes to fulfil these criteria in moderate-to-high transmission African populations in 25 sites across 10 countries. Predominantly clinical infections were analysed, with 52.3% found to be multiclonal, generating high proportions of mixed-allele calls (MACs) per isolate thereby impeding haplotype construction. Of the 24- and 96-SNPs, loci were removed if they were not biallelic and had low minor allele frequencies in all study populations, resulting in 20- and 75-SNP barcodes respectively for downstream population genetics analysis. Both SNP barcodes had low expected heterozygosity estimates in these African settings and consequently biased analyses of similarity. Both minor and major allele frequencies were temporally unstable. These SNP barcodes were also shown to identify weak genetic differentiation across large geographic distances based on Mantel Test and DAPC. These results demonstrate that these SNP barcodes are vulnerable to ascertainment bias and as such cannot be used as a standardised approach for malaria surveillance in moderate-to-high transmission areas in Africa, where the greatest genomic diversity of P. falciparum exists at local, regional and country levels.

Background. VNTR-polymorphism at 5 HTTLPR regulatory region of human serotonin transporter gene SLC6A4, which is associated with some psychiatric diseases and personality traits, is presented by two alleles, S and L, affecting the gene transcription level. A correlation between the S allele frequency in populations of European and Asian origin and a Hofstede’s individualism-collectivism index was revealed and a hypothesis of culture-gene coevolution was suggested (Chiao, Blizinsky, 2010). Methods. As another reason for the correlation we examined underlying population genetic substructure, which may affect genetic association level. Results. We have experimentally established the 5 HTTLPR genotypes for 2144 individuals to calculate S and L allele frequencies in 21 populations of Eurasia and Africa. In contrast to Eurasia populations, we have found low S allele frequencies in all four African populations studied, although the collectivism index in the populations was high. The total set of Eurasian and African populations analysis does not confirm the correlation (R= 0.263, p=0.146). We have applied principal component (PC) analysis to check a correlation between S allele frequency distribution and a frequency distribution for alleles which are supposed to be neutral. PC analysis for 68 alleles of five CODIS STR loci revealed correlation between PC2 and S allele frequency (R= 0.820, p0.0001). The correlation means that S allele frequency distribution corresponds to general genetic variability distribution in the human populations studied. The correlation between the Hofestede’s index and frequency of four out of 68 STR alleles is even higher than the correlation with S allele frequency in the same populations. Conclusion. Our findings do not support the hypothesis on culture-gene coevolution of “individualism-collectivism” and the S allele frequency of serotonin transporter gene.

Importance of allele frequency estimates in epidemiological studies.

In order to estimate migration and gene flow, allele frequencies in populations at two sites separated by 120 m were differentially perturbed by the continuous release over 413 days of flies homozygous at particular allozyme loci. The effects of perturbation were determined by genotype assay at two collections prior to, thirteen during and nine after the perturbation period. Maximum likelihood methods were developed to estimate migration into the two populations from the homozygous releases, and migration between the two populations. The successful perturbation of allele frequencies in a natural population is demonstrated. A plateau in allele frequencies during perturbation and a return to original frequencies following cessation of perturbation was most likely due to selection during development against recessive alleles concurrently introduced into the populations by the released flies. There is unequivocal evidence for short distance gene flow between the two populations. The migration rates estimated at ten times over a nine month period were extremely variable, but with higher population density at one site positively related with migration from that site to the other.

The effects of four cycles of recurrent selection on the allele frequencies of simple sequence repeat (SSR) markers and population structure were examined in the Maksimir 3 Synthetic (M3S) maize population (Zea mays L.). Genotyping of 32 plants from each selection cycle at 38 SSR loci revealed that the mean number of alleles per locus and the mean expected heterozygosity were preserved across selection cycles, indicating the maintenance of sufficient genetic variability in the population required for future genetic gain. The Waples test of selective neutrality revealed that genetic drift was the main force in changing allele frequencies in the population. The proportion of selectively non-neutral loci in single cycles of selection varied between 16% and 37%. Some non-neutral loci shared the same genomic locations with previously published QTLs controlling important agronomic traits. An analysis of molecular variance revealed that 5.6% of the genetic variation occurred among and 94.4% within cycle populations. Between 5% and 29% of loci were found to be in a significant Hardy–Weinberg (HW) disequilibrium, with the majority showing an excess of homozygosity. The excess of homozygosity at several loci was highly consistent across cycle populations, suggesting positive assortative mating as a possible cause of the observed HW disequilibrium. Linkage disequilibrium (LD) tests revealed that the M3S population was essentially in linkage equilibrium. The proportion of pairs of loci in significant LD varied from 0.1% to 1.8% across selection cycles, probably due to the effects of genetic drift and epistatic selection.

Mating patterns do not alter allelic frequencies in natural populations. Therefore, if evolution is defined as changes in allelic frequencies in a population through time, then mating system is not an evolutionary force. There is no direct causal link between mating patterns and the familiar measures of genetic variability applied to allele frequency data from haploid gametophyte populations. In this paper we focus on how mating patterns may affect intralocus variability when acting together with evolutionary forces, like selection and drift. Moreover, we address how levels of inbreeding can have a profound influence on haplotypic variation. Measures for estimating the extent of recombination from haplotypic variation are presented. It seems that high levels of selfing are not necessarily associated with bisexuality in bryophytes.

Population genetics often serves as a bridge between units on Mendelian genetics and neo-Darwinian evolution in the teaching of introductory college biology and advanced high school biology. The value of teaching the Hardy-Weinberg principle to determine allelic frequencies in populations at equilibrium was presented several years ago to readers of The American Biology Teacher. Because there continues to be great interest in population biology and evolution, the principle is presently included in most introductory college textbooks (Schefler 1968). When students have mastered the Hardy-Weinberg concept and gained competence in calculating alternate allele frequencies, they begin asking for methods to determine allelic frequencies when series of multiple alleles for a gene locus exist. This paper presents a novel shortcut algorithm for solving problems related to multiple allelic frequencies in populations at equilibrium. Ceppellini et al. (1955) seem to be among the first to have presented an algebraic approach to the solution of multiple allelic frequency problems. Falconer (1960) simplified the method for applications dealing with the major alleles of the human ABO blood groups. Some standard introductory genetics textbooks (Burns 1983; Gardner et al. 1985) include Falconer's method for solving problems where three alleles of a gene locus exist. This paper, however, demonstrates how Falconer's method may be applied to determine multiple allelic frequencies in populations at equilibrium when more than three alleles of a gene locus exist. Coat Color in Rabbits

Recommendations for Clinical CYP2D6 Genotyping Allele Selection: A Joint Consensus Recommendation of the Association for Molecular Pathology, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, and the European Society for Pharmacogenomics and Personalized Therapy

Human neutrophil antigen-1, -3, -4, and -5 allele and genotype frequencies in the Croatian blood donor population and their clinical significance.

We conducted surveys of mutant allele frequencies of four cat populations in Arkansas and Tennessee during 2002. Our calculations and analyses support that Southwestern cat populations were relatively more genetically similar to each other than compared to cat populations in other areas of North America. However, the cat population of Fort Smith is slightly different from the other cat populations studied in the Southwestern United States. Although there is a clear significant spatial geographic pattern for many mutant coat allele frequencies in the United States and Canada cat populations (d, l, S, and W), our results revealed that there is not a significant isolation-by-distance model affecting these cat populations. Our data also support the historical migration hypothesis because our calculated allele frequencies were genetically similar to cat populations located in ancestral areas of Europe. Different phenograms, including new European cat genetic profiles, showed that the Southwestern cat populations studied are of a clear British origin. Therefore, migration routes of early Arkansas and Tennessee settlers help explain the similarities of allele frequencies among domestic cat populations.

Decision letter: The lingering effects of Neanderthal introgression on human complex traits

Author response: The lingering effects of Neanderthal introgression on human complex traits

Editor's evaluation: The lingering effects of Neanderthal introgression on human complex traits

The frequencies of human platelet antigens (HPAs) vary between different populations and are a major determinant for the prevalence of HPA alloimmunization and its clinically associated entities. No report on HPA prevalence has previously been published for the Algerian populations which are ethnically diverse. The aim of this study was to determine the HPA allele frequencies in Algerian populations and to identify situations of incompatibility possibly leading to alloimmunization. A total of 485 healthy volunteer Algerian blood donors from different regions and representing different ethnic groups were included. HPA genotyping was determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and/or polymerase chain reaction-sequence specific primer (PCR-SSP). The HPA-1 allele frequencies were close to the frequencies found in Caucasian populations. The presence of the molecule human leukocyte antigen (HLA)-DRB3*0101 (17.9%) increases the risk of alloimmunization. We observed an increase in the frequency of homozygous HPA-5b, particularly in the population of Annaba (7.61%) and the Mzab population (5.13%). The allele frequency HPA-2b (0.193-0.147) was similar to that seen in Sub-Saharan African populations. The high frequency of homozygotic HPA-2b (Kabyle 5%; Mzab 2.44% and Annaba 2.19%) could increase the risk of alloimmunization. GPIIb A(k) mutation (2614C>A) was found in these populations. This study is the first to report on HPA allele frequencies in Algerian populations. High allele frequencies were observed for HPA-1b (0.209-0.112), HPA-3b (0.411-0.312) and HPA-5b (0.217-0.087), leading to a high risk of alloimmunization in this population, especially the Mzab and the population of Annaba. Our results could have some impact in the diagnosis, prevention and treatment of alloimmune thrombocytopenia.