The Evolutionary Dynamics of Complex Polymorphisms,,

Lewontin, Richard C; Kojima, Ken-ichi

doi:10.1111/j.1558-5646.1960.tb03113.x

Cited by 250 publications

(161 citation statements)

References 14 publications

Supporting

Mentioning

159

Contrasting

Order By: Relevance

“…The main parameters used in phase software were as follows: number of interactions: 1000, thinning interval: 1, burn‐in value: 100, and Δ‐value for each locus: 1.The mean probability of the inference, which is defined as average of the probabilities of the haplotype pair with the highest probability value for each sample , was used as quality indicator for the haplotyping procedures. The classical coefficient of LD, D , which measures deviation from random association between alleles at different loci , was expressed as D = Pij − PiPj ; normalized LD, D ', was defined as coefficient D standardized by the maximum value it can take ( D max), given the allele frequencies . Fisher's exact test was performed to determine the significance of D .…”

Section: Methodsmentioning

confidence: 99%

The 5′ promoter region of MHC class I chain‐related gene B

Pan

Luo

et al. 2014

Tissue Antigens

View full text Add to dashboard Cite

In this study, the 5' promoter region of MHC class I chain-related gene B (MICB) was investigated in 104 healthy, unrelated Han individuals recruited from northern China, using polymerase chain reaction (PCR)-sequencing methodology. Fifteen variable sites were detected, which showed a mosaic pattern of significant global linkage disequilibrium (LD). Eleven different 5' promoter haplotypes were identified. MICB 5' promoter haplotype-9 carrying CT deletion at positions -139/-138, which is associated with decreased MICB promoter activity, was present in 26.9% of MICB alleles and was linked to MICB*002:01, MICB*008, and MICB*014 in this population. In addition, rs3828913 (position -176) and rs3828914 (position -152) were located adjacent to HSRE and GC box in MICB promoter, respectively. Sixteen extended haplotypes (EH) incorporating the MICB 5' promoter and MICB coding region were observed in this population, eight of which were in significant LD. Phylogenetic analysis of 5' promoter refined MICB sub-lineage structure indicated that MICB*005:02, the most common MICB allele, consists of five sub-lineages. Ewens-Watterson homozygosity statistics at MICB 5' promoter region were consistent with neutral expectations. Our study has shed new insight into MICB genetic variation at population level, suggesting that binding sites for transcription factors in MICB promoter could be interrupted by polymorphisms within this region, resulting in allele-specific regulation. The data will facilitate the understanding of regulation of MICB gene transcription, and will inform studies of evolution of the major histocompatibility complex (MHC) gene complex.

show abstract

Section: Methodsmentioning

confidence: 99%

The 5′ promoter region of MHC class I chain‐related gene B

Pan

Luo

et al. 2014

Tissue Antigens

View full text Add to dashboard Cite

show abstract

“…Here, f ij is the number of hosts of type i being infected by a parasite of type j divided by the size of the infected subsample ( n Inf ), so that . This statistic is an adaptation of the well-known linkage disequilibrium (LD) measure in population genetics (Charlesworth and Charlesworth 2010, Lewontin and Kojima 1960, p371-373) and related to the statistics performed in Bartha et al (2013) and Ansari et al (2017).…”

Section: Methodsmentioning

confidence: 99%

Cross-Species association statistics for genome-wide studies of host and parasite polymorphism data

Märkle

Tellier

John

2019

Preprint

View full text Add to dashboard Cite

1Uncovering the genes governing host-parasite coevolution is of importance for disease management 2 in agriculture and human medicine. The availability of increasing amounts of host and parasite 3 full genome-data in recent times allows to perform cross-species genome-wide association studies 4 based on sampling of genomic data of infected hosts and their associated parasites strains. We aim 5 to understand the statistical power of such approaches. We develop two indices, the cross species 6 association (CSA) and the cross species prevalence (CSP), the latter additionally incorporating 7 genomic data from uninfected hosts. For both indices, we derive genome-wide significance thresh-8 olds by computing their expected distribution over unlinked neutral loci, i.e. those not involved 9 in determining the outcome of interaction. Using a population genetics and an epidemiological 10 coevolutionary model, we demonstrate that the statistical power of these indices to pinpoint the 11 interacting loci in full genome data varies over time. This is due to the underlying GxG interactions 12 and the coevolutionary dynamics. Under trench-warfare dynamics, CSA and CSP are very accurate 13 in finding out the loci under coevolution, while under arms-race dynamics the power is limited 14 especially under a gene-for-gene interaction. Furthermore, we reveal that the combination of both 15 indices across time samples can be used to estimate the asymmetry of the underlying infection ma-16 trix. Our results provide novel insights into the power and biological interpretation of cross-species 17 association studies using samples from natural populations or controlled experiments. 18 Keywords 19 population genomics; linkage disequilibrium; single nucleotide polymorphism; host-parasite co-20 evolution 21

show abstract

“…The coefficient of gametic LD was calculated by likelihood methods, and the coefficient ( D ) was reported as the ratio of the unstandardized coefficient to its maximal value . The coefficient D′ was calculated according to Lewontin .…”

Section: Methodsmentioning

confidence: 99%

Genetic polymorphism of KIR2DL4 in the Polish population

et al. 2015

View full text Add to dashboard Cite

The KIR2DL4 gene is characterized by alleles with either 9 or 10 consecutive adenines in exon 7, which encodes the transmembrane domain. The 9A variant produces either a protein with a truncated cytoplasmic tail or one lacking the transmembrane region. This causes a lack of KIR2DL4 expression. In contrast, 10A alleles encode receptors that may be expressed at the cell surface. We tested 438 healthy individuals for polymorphism of the KIR2DL4 gene. KIR2DL4 9A/10A alleles were distinguished by the high resolution melting (HRM) method, and restriction fragment length polymorphism (RFLP) was used for genotyping of three other single nucleotide polymorphisms (SNPs) spanning the near vicinity of the poly-adenine fragment. We found a weak difference between males and females in 9769 C/A genotypes and alleles. In addition, we observed complete linkage disequilibrium (LD) between 9A insertion/deletion in the 9620 position and the 9571T/C position of the gene (r(2) = 1) both in females and males and almost complete LD with the 9797G/A position (r(2) = 0.963 for females and r(2) = 0.892 for males). Most importantly, we detected, in a group of fertile women, a high frequency (30.2%) of homozygosity for the defective 9A variant, which suggests that KIR2DL4 as a functional cell surface receptor is not absolutely necessary for reproduction. On the other hand, lower representation of 10A/10A homozygotes and high frequency of 10A/9A heterozygotes indicates a need for both cell membrane-anchored and soluble KIR2DL4 molecules. Finally, cost-reducing RFLP instead of HRM is proposed for typing 9A and 10A variants.

show abstract

The Evolutionary Dynamics of Complex Polymorphisms,,

Cited by 250 publications

References 14 publications

The 5′ promoter region of MHC class I chain‐related gene B

The 5′ promoter region of MHC class I chain‐related gene B

Cross-Species association statistics for genome-wide studies of host and parasite polymorphism data

Genetic polymorphism of KIR2DL4 in the Polish population

Contact Info

Product

Resources

About