Development of multilocus putatively neutral DNA markers in the X-chromosome for population genetic studies in humans

Khan, Naazneen; Chittoria, Anita; Pande, Veena; Jaiswal, Yogesh K.; Das, Ashim

doi:10.3109/03014460.2012.689326

Cited by 3 publications

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“…Population data from multiple individuals further enables in determination of the frequency of three different alleles ( FY*A , FY*B and FY*O ) which could be utilized in evolutionary inference of the FY gene [5], [6]. Since eco-climatic factors are highly variable in India (large longitudinal and latitudinal transects) with complex malaria epidemiology due to both P. vivax and P. falciparum infections [11] and Indians are genetically heterogeneous with complex population history [12], [13], [14]; we were interested to determine (i) the variable distribution of FY gene polymorphisms and genetic differentiations among populations living in different eco-climatic conditions, and (ii) possible correlation between FY gene polymorphisms and vivax malaria epidemiology by population genetic analyses in India. Although previous studies have indicated the distribution of different serological phenotypes of the Fy antigen in different local populations in India [15], [16], [17], [18], neither any survey on the distribution of different FY alleles representing the whole of India has been conducted, nor any correlation of FY polymorphisms to eco-climatic and/or vivax malaria epidemiology has been established.…”

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confidence: 99%

Natural Selection Mediated Association of the Duffy (FY) Gene Polymorphisms with Plasmodium vivax Malaria in India

et al. 2012

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The Duffy (Fy) antigens act as receptors for chemokines as well as for Plasmodium vivax to invade human RBCs. A recent study has correlated the occurrence of the FY*A allele of Duffy gene with decreased susceptibility to vivax malaria, but no epidemiological correlation between the distribution of FY*A allele and incidences of vivax malaria has been established so far. Furthermore, if such correlations exist, whether natural selection has mediated the association, is an important question. Since India is highly endemic to P. vivax malaria with variable eco-climatic and varying vivax malaria epidemiology across different regions, such a question could well be answered in Indians. For this, we have genotyped the FY gene at the −33rd and the 125th nucleotide positions in 250 Indians sampled from six different zonal plus one tribal population covering the whole of India and studied possible correlations with eco-climatic and vivax malaria incidences. No FY*O allele was found, however, both the FY*A and FY*B alleles forming FY*A/FY*A, FY*A/FY*B and FY*B/FY*B genotypes were widely distributed among Indians. Five out of seven population samples significantly deviated from the Hardy-Weinberg equilibrium expectation, and two alleles (FY*A and FY*B) and the homozygote genotype, FY*B/FY*B were clinally distributed over the population coordinates. Furthermore, vivax malaria incidences over the past five years were significantly negatively and positively associated with the frequencies of the FY*A and FY*B alleles, respectively. The Northern Indians were highly differentiated from the other zonal population samples at the FY gene, as evidenced from the reconstructed Neighbor-Joining phylogenetic tree. The results specify the role of natural selection in the distribution of FY gene polymorphism in India. Furthermore, the hypotheses on the part of the FY*A allele in conferring protection to vivax malaria could be validated following population genetic studies in a vivax malaria epidemiological setting, such as India.

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Section: Introductionmentioning

confidence: 99%

Natural Selection Mediated Association of the Duffy (FY) Gene Polymorphisms with Plasmodium vivax Malaria in India

et al. 2012

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“…; Bachtrog & Andolfatto ; Khan et al . ). This is because loci present in the X chromosome form accessible haplotypes in males and have small effective population size leading to lower recombination rate, lower mutation rate and faster genetic drift, resulting in greater Linkage Disequilibrium (LD) and population structure, as compared with autosomal DNA (Schaffner ; Tomas et al .…”

Section: Introductionmentioning

confidence: 97%

“…) and more recently in humans (Khan et al . ) and the malaria parasite (Gupta et al . ) in successfully inferring population genetic structure and demography of the respective species populations.…”

Section: Introductionmentioning

confidence: 99%

“…This method has been followed in a wide array of organisms, viz. Drosophila (Das et al 2004;Bachtrog & Andolfatto 2006), plants (Arunyawat et al 2007) and more recently in humans (Khan et al 2012) and the malaria parasite (Gupta et al 2012) in successfully inferring population genetic structure and demography of the respective species populations. The majority of the above studies have considered SNPs present in multiple DNA fragments located in X chromosome of diploid organisms (Glinka et al 2003;Das et al 2004;Bachtrog & Andolfatto 2006;Khan et al 2012).…”

Section: Introductionmentioning

confidence: 99%

“…Drosophila (Das et al 2004;Bachtrog & Andolfatto 2006), plants (Arunyawat et al 2007) and more recently in humans (Khan et al 2012) and the malaria parasite (Gupta et al 2012) in successfully inferring population genetic structure and demography of the respective species populations. The majority of the above studies have considered SNPs present in multiple DNA fragments located in X chromosome of diploid organisms (Glinka et al 2003;Das et al 2004;Bachtrog & Andolfatto 2006;Khan et al 2012). This is because loci present in the X chromosome form accessible haplotypes in males and have small effective population size leading to lower recombination rate, lower mutation rate and faster genetic drift, resulting in greater Linkage Disequilibrium (LD) and population structure, as compared with autosomal DNA (Schaffner 2004;Tomas et al 2008).…”

Section: Introductionmentioning

confidence: 99%

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Multilocus nuclear DNA markers reveal population structure and demography of Anopheles minimus

et al. 2014

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Utilization of multiple putatively neutral DNA markers for inferring evolutionary history of species population is considered to be the most robust approach. Molecular population genetic studies have been conducted in many species of Anopheles genus, but studies based on single nucleotide polymorphism (SNP) data are still very scarce. Anopheles minimus is one of the principal malaria vectors of Southeast (SE) Asia including the Northeastern (NE) India. Although population genetic studies with mitochondrial genetic variation data have been utilized to infer phylogeography of the SE Asian populations of this species, limited information on the population structure and demography of Indian An. minimus is available. We herewith have developed multilocus nuclear genetic approach with SNP markers located in X chromosome of An. minimus in eight Indian and two SE Asian population samples (121 individual mosquitoes in total) to infer population history and test several hypotheses on the phylogeography of this species. While the Thai population sample of An. minimus presented the highest nucleotide diversity, majority of the Indian samples were also fairly diverse. In general, An. minimus populations were moderately substructured in the distribution range covering SE Asia and NE India, largely falling under three distinct genetic clusters. Moreover, demographic expansion events could be detected in the majority of the presently studied populations of An. minimus. Additional DNA sequencing of the mitochondrial COII region in a subset of the samples (40 individual mosquitoes) corroborated the existing hypothesis of Indian An. minimus falling under the earlier reported mitochondrial lineage B.

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Short Tandem Repeats as a High-Resolution Marker for Capturing Recent Orangutan Population Evolution

2021

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The genus Pongo is ideal to study population genetics adaptation, given its remarkable phenotypic divergence and the highly contrasting environmental conditions it’s been exposed to. Studying its genetic variation bears the promise to reveal a motion picture of these great apes’ evolutionary and adaptive history, and also helps us expand our knowledge of the patterns of adaptation and evolution. In this work, we advance the understanding of the genetic variation among wild orangutans through a genome-wide study of short tandem repeats (STRs). Their elevated mutation rate makes STRs ideal markers for the study of recent evolution within a given population. Current technological and algorithmic advances have rendered their sequencing and discovery more accurate, therefore their potential can be finally leveraged in population genetics studies. To study patterns of population variation within the wild orangutan population, we genotyped the short tandem repeats in a population of 21 individuals spanning four Sumatran and Bornean (sub-) species and eight Southeast Asian regions. We studied the impact of sequencing depth on our ability to genotype STRs and found that the STR copy number changes function as a powerful marker, correctly capturing the demographic history of these populations, even the divergences as recent as 10 Kya. Moreover, gene ontology enrichments for genes close to STR variants are aligned with local adaptations in the two islands. Coupled with more advanced STR-compatible population models, and selection tests, genomic studies based on STRs will be able to reduce the gap caused by the missing heritability for species with recent adaptations.

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Development of multilocus putatively neutral DNA markers in the X-chromosome for population genetic studies in humans

Abstract: All eight DNA fragments seem to bear the characteristics to be considered as 'putatively neutral genetic markers' and thus, could be utilized for inference of human population and demographic histories.

Cited by 3 publications

References 60 publications

Natural Selection Mediated Association of the Duffy (FY) Gene Polymorphisms with Plasmodium vivax Malaria in India

Natural Selection Mediated Association of the Duffy (FY) Gene Polymorphisms with Plasmodium vivax Malaria in India

Multilocus nuclear DNA markers reveal population structure and demography of Anopheles minimus

Short Tandem Repeats as a High-Resolution Marker for Capturing Recent Orangutan Population Evolution

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