LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 7 of total 7

Search options

  1. Article ; Online: Identifying signatures of natural selection in Indian populations.

    Mendes, Marla / Jonnalagadda, Manjari / Ozarkar, Shantanu / Lima Torres, Flávia Carolina / Borda Pua, Victor / Kendall, Christopher / Tarazona-Santos, Eduardo / Parra, Esteban J

    PloS one

    2022  Volume 17, Issue 8, Page(s) e0271767

    Abstract: In this study, we present the results of a genome-wide scan for signatures of positive selection using data from four tribal groups (Kokana, Warli, Bhil, and Pawara) and two caste groups (Deshastha Brahmin and Kunbi Maratha) from West of the Maharashtra ... ...

    Abstract In this study, we present the results of a genome-wide scan for signatures of positive selection using data from four tribal groups (Kokana, Warli, Bhil, and Pawara) and two caste groups (Deshastha Brahmin and Kunbi Maratha) from West of the Maharashtra State In India, as well as two samples of South Asian ancestry from the 1KG project (Gujarati Indian from Houston, Texas and Indian Telugu from UK). We used an outlier approach based on different statistics, including PBS, xpEHH, iHS, CLR, Tajima's D, as well as two recently developed methods: Graph-aware Retrieval of Selective Sweeps (GRoSS) and Ascertained Sequentially Markovian Coalescent (ASMC). In order to minimize the risk of false positives, we selected regions that are outliers in all the samples included in the study using more than one method. We identified putative selection signals in 107 regions encompassing 434 genes. Many of the regions overlap with only one gene. The signals observed using microarray-based data are very consistent with our analyses using high-coverage sequencing data, as well as those identified with a novel coalescence-based method (ASMC). Importantly, at least 24 of these genomic regions have been identified in previous selection scans in South Asian populations or in other population groups. Our study highlights genomic regions that may have played a role in the adaptation of anatomically modern humans to novel environmental conditions after the out of Africa migration.
    MeSH term(s) Asians ; Genetics, Population ; Genomics ; Haplotypes ; Humans ; India ; Polymorphism, Single Nucleotide ; Selection, Genetic ; Texas
    Language English
    Publishing date 2022-08-04
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0271767
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  2. Article ; Online: MC1R diversity and its role in skin pigmentation variation in West Maharashtra, India.

    Jonnalagadda, Manjari / Bharti, Neeraj / Kasibhatla, Sunitha Manjari / Wagh, Mayur A / Joshi, Rajendra / Ozarkar, Shantanu / Ashma, Richa

    American journal of human biology : the official journal of the Human Biology Council

    2022  Volume 34, Issue 7, Page(s) e23734

    Abstract: Objectives: MC1R polymorphisms have been reported to be under a selective constraint in populations inhabiting high UVR regions such as Africans; however, these patterns are not consistent. Here we analyze the MC1R gene in West Maharashtra, India to see ...

    Abstract Objectives: MC1R polymorphisms have been reported to be under a selective constraint in populations inhabiting high UVR regions such as Africans; however, these patterns are not consistent. Here we analyze the MC1R gene in West Maharashtra, India to see if sequence diversity corresponds to their diverse pigmentary profiles and if MC1R is constrained in dark skinned tribal as compared to lighter skinned caste populations.
    Methods: A 2648 bp region of this gene was sequenced in 102 individuals and the data was compared for π, ϴ diversity indices. Tajima's D was assessed for signatures of purifying selection and MC1R variants were associated with MI measures using the additive, dominant, and recessive models. Pairwise F
    Results: MC1R diversity was not uniquely patterned among castes and tribes. Non-synonymous variants rs2228479A, rs1805007_T, and rs885479_A showed low variability in these populations. Selection tests did not indicate any constraint on MC1R and pairwise F
    Conclusions: We do not find evidence of a selective constraint on MC1R. The presence of a large number of unique haplotypes and low F
    MeSH term(s) Haplotypes ; Humans ; India ; Polymorphism, Genetic ; Receptor, Melanocortin, Type 1/genetics ; Skin Pigmentation/genetics
    Chemical Substances MC1R protein, human ; Receptor, Melanocortin, Type 1
    Language English
    Publishing date 2022-02-21
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1025339-7
    ISSN 1520-6300 ; 1042-0533
    ISSN (online) 1520-6300
    ISSN 1042-0533
    DOI 10.1002/ajhb.23734
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 2567: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  3. Article ; Online: Skin pigmentation variation among populations of West Maharashtra, India.

    Jonnalagadda, Manjari / Ozarkar, Shantanu / Ashma, Richa / Kulkarni, Shaunak

    American journal of human biology : the official journal of the Human Biology Council

    2016  Volume 28, Issue 1, Page(s) 36–43

    Abstract: Objectives: Global patterns of skin pigmentation have evolved as an adaptation to local ultraviolet radiation (UVR). Indian populations exposed to intense UVR show great variation in skin pigmentation. The UVR-based selection model cannot satisfactorily ...

    Abstract Objectives: Global patterns of skin pigmentation have evolved as an adaptation to local ultraviolet radiation (UVR). Indian populations exposed to intense UVR show great variation in skin pigmentation. The UVR-based selection model cannot satisfactorily address the high prevalence of light skin among these populations. Thus, the present study examines pigmentation variation among populations of West Maharashtra and the Indian subcontinent within the context of population structure and social hierarchy.
    Methods: Melanin index (MI) was measured from 555 individuals representing six endogamous populations of West Maharashtra. Skin pigmentation was assessed in terms of variation between populations and differences between and among castes and tribes. A linear regression analysis was run to assess the relationship among MI, UVR, and social hierarchy using published MI data from 13 Indian endogamous populations.
    Results: Skin pigmentation differed significantly among populations of West Maharashtra. Significant pigmentation variation exists between castes and tribes of West Maharashtra as well as across the Indian subcontinent. We observe a significant negative relationship between social hierarchy and skin pigmentation, whereas the relationship between UVR and MI is weak.
    Conclusions: Our results suggest that various factors may have contributed to pigmentation diversity across the Indian subcontinent. The lack of correlation between UVR and MI suggests that natural selection may not have played a significant role in shaping pigmentation variation across the subcontinent. We discuss other possible explanations, including metabolic conservation and cultural factors such as traditional social hierarchies and strict endogamy that have led to the development of population structure.
    MeSH term(s) Female ; Hierarchy, Social ; Humans ; India ; Male ; Marriage ; Skin Pigmentation ; Ultraviolet Rays
    Language English
    Publishing date 2016-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1025339-7
    ISSN 1520-6300 ; 1042-0533
    ISSN (online) 1520-6300
    ISSN 1042-0533
    DOI 10.1002/ajhb.22738
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 2567: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  4. Article ; Online: Novel insights on demographic history of tribal and caste groups from West Maharashtra (India) using genome-wide data.

    Debortoli, Guilherme / Abbatangelo, Cristina / Ceballos, Francisco / Fortes-Lima, Cesar / Norton, Heather L / Ozarkar, Shantanu / Parra, Esteban J / Jonnalagadda, Manjari

    Scientific reports

    2020  Volume 10, Issue 1, Page(s) 10075

    Abstract: The South Asian subcontinent is characterized by a complex history of human migrations and population interactions. In this study, we used genome-wide data to provide novel insights on the demographic history and population relationships of six Indo- ... ...

    Abstract The South Asian subcontinent is characterized by a complex history of human migrations and population interactions. In this study, we used genome-wide data to provide novel insights on the demographic history and population relationships of six Indo-European populations from the Indian State of West Maharashtra. The samples correspond to two castes (Deshastha Brahmins and Kunbi Marathas) and four tribal groups (Kokana, Warli, Bhil and Pawara). We show that tribal groups have had much smaller effective population sizes than castes, and that genetic drift has had a higher impact in tribal populations. We also show clear affinities between the Bhil and Pawara tribes, and to a lesser extent, between the Warli and Kokana tribes. Our comparisons with available modern and ancient DNA datasets from South Asia indicate that the Brahmin caste has higher Ancient Iranian and Steppe pastoralist contributions than the Kunbi Marathas caste. Additionally, in contrast to the two castes, tribal groups have very high Ancient Ancestral South Indian (AASI) contributions. Indo-European tribal groups tend to have higher Steppe contributions than Dravidian tribal groups, providing further support for the hypothesis that Steppe pastoralists were the source of Indo-European languages in South Asia, as well as Europe.
    MeSH term(s) Ethnic Groups/genetics ; Genetic Drift ; Genotyping Techniques ; Humans ; India/ethnology ; Population Density ; Social Class ; Whole Genome Sequencing/methods
    Language English
    Publishing date 2020-06-22
    Publishing country England
    Document type Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-020-66953-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  5. Article ; Online: Association of genetic variants with skin pigmentation phenotype among populations of west Maharashtra, India.

    Jonnalagadda, Manjari / Norton, Heather / Ozarkar, Shantanu / Kulkarni, Shaunak / Ashma, Richa

    American journal of human biology : the official journal of the Human Biology Council

    2016  Volume 28, Issue 5, Page(s) 610–618

    Abstract: Objectives: South Asians exhibit extensive variation in skin melanin index (MI) which is observed across the broader region of South Asia as well as within restricted geographic regions. However, the genetic variants associated with variation in the ... ...

    Abstract Objectives: South Asians exhibit extensive variation in skin melanin index (MI) which is observed across the broader region of South Asia as well as within restricted geographic regions. However, the genetic variants associated with variation in the skin pigmentation phenotype are poorly understood in these populations. The present study examines the association between MI measures and genetic variants from 5 candidate pigmentation genes among 533 individuals representing 6 populations of West Maharashtra.
    Methods: Associations between five single nucleotide polymorphisms (SNPs) known to play a role in pigmentation (rs1426654-SLC24A5, rs1042602-TYR, rs16891982-SLC45A2, rs6058017-ASIP, and rs642742-KITLG) and MI measures were tested using standard one-way analysis of variance (ANOVA) within each population. Multiple linear regression was used to test the effects of these SNPs in the full West Maharashtra sample using sex, age, and population or social group as covariates.
    Results: rs1426654 showed significant association with MI in all six study populations (P < 0.01). Association tests using sex, age, and population as covariates showed rs1426654 and rs1042602 to be significantly (P < 0.01) associated with lighter skin pigmentation in West Maharashtra as a whole. By contrast, when social group was added as a covariate instead of population, rs1426654, rs1042602, and rs16891982 were significantly (P < 0.01) associated with lighter skin pigmentation.
    Conclusions: Only rs1426654 is significantly associated with MI in each individual population; however, rs1426654, rs1042602, and rs16891982 are significantly associated with pigmentation in the broader West Maharashtra region after controlling for population and social group, with rs1426654 (SLC24A5) explaining the majority of the observed variation. Am. J. Hum. Biol. 28:610-618, 2016. © 2016 Wiley Periodicals, Inc.
    MeSH term(s) Female ; Gene Frequency ; Humans ; India ; Male ; Phenotype ; Polymorphism, Single Nucleotide ; Skin Pigmentation/genetics
    Language English
    Publishing date 2016-02-26
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1025339-7
    ISSN 1520-6300 ; 1042-0533
    ISSN (online) 1520-6300
    ISSN 1042-0533
    DOI 10.1002/ajhb.22836
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 2567: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  6. Article ; Online: A Genome-Wide Association Study of Skin and Iris Pigmentation among Individuals of South Asian Ancestry.

    Jonnalagadda, Manjari / Faizan, Muhammad Ashhad / Ozarkar, Shantanu / Ashma, Richa / Kulkarni, Shaunak / Norton, Heather L / Parra, Esteban

    Genome biology and evolution

    2017  Volume 11, Issue 4, Page(s) 1066–1076

    Abstract: South Asia has a complex history of migrations and is characterized by substantial pigmentary and genetic diversity. For this reason, it is an ideal region to study the genetic architecture of normal pigmentation variation. Here, we present a meta- ... ...

    Abstract South Asia has a complex history of migrations and is characterized by substantial pigmentary and genetic diversity. For this reason, it is an ideal region to study the genetic architecture of normal pigmentation variation. Here, we present a meta-analysis of two genome-wide association studies (GWASs) of skin pigmentation using skin reflectance (M-index) as a quantitative phenotype. The meta-analysis includes a sample of individuals of South Asian descent living in Canada (N = 348), and a sample of individuals from two caste and four tribal groups from West Maharashtra, India (N = 480). We also present the first GWAS of iris color in South Asian populations. This GWAS was based on quantitative measures of iris color obtained from high-resolution iris pictures. We identified genome-wide significant associations of variants within the well-known gene SLC24A5, including the nonsynonymous rs1426654 polymorphism, with both skin pigmentation and iris color, highlighting the pleiotropic effects of this gene on pigmentation. Variants in the HERC2 gene (e.g., rs12913832) were also associated with iris color and iris heterochromia. Our study emphasizes the usefulness of quantitative methods to study iris color variation. We also identified novel genome-wide significant associations with skin pigmentation and iris color, but we could not replicate these associations due to the lack of independent samples. It will be critical to expand the number of studies in South Asian populations in order to better understand the genetic variation driving the diversity of skin pigmentation and iris color observed in this region.
    MeSH term(s) Eye Color/genetics ; Genome, Human ; Genome-Wide Association Study ; Humans ; India/ethnology ; Skin Pigmentation/genetics
    Language English
    Publishing date 2017-07-12
    Publishing country England
    Document type Journal Article ; Meta-Analysis ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1759-6653
    ISSN (online) 1759-6653
    DOI 10.1093/gbe/evz057
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  7. Article ; Online: Identifying signatures of positive selection in pigmentation genes in two South Asian populations.

    Jonnalagadda, Manjari / Bharti, Neeraj / Patil, Yatish / Ozarkar, Shantanu / K, Sunitha Manjari / Joshi, Rajendra / Norton, Heather

    American journal of human biology : the official journal of the Human Biology Council

    2017  Volume 29, Issue 5

    Abstract: Objectives: Skin pigmentation is a polygenic trait showing wide phenotypic variations among global populations. While numerous pigmentation genes have been identified to be under positive selection among European and East populations, genes contributing ...

    Abstract Objectives: Skin pigmentation is a polygenic trait showing wide phenotypic variations among global populations. While numerous pigmentation genes have been identified to be under positive selection among European and East populations, genes contributing to phenotypic variation in skin pigmentation within and among South Asian populations are still poorly understood. The present study uses data from the Phase 3 of the 1000 genomes project focusing on two South Asian populations-GIH (Gujarati Indian from Houston, Texas) and ITU (Indian Telugu from UK), so as to decode the genetic architecture involved in adaptation to ultraviolet radiation in South Asian populations.
    Methods: Statistical tests included were (1) tests to identify deviations of the Site Frequency Spectrum (SFS) from neutral expectations (Tajima's D, Fay and Wu's H and Fu and Li's D* and F*), (2) tests focused on the identification of high-frequency haplotypes with extended linkage disequilibrium (iHS and Rsb), and (3) tests based on genetic differentiation between populations (LSBL).
    Results: Twenty-two pigmentation genes fall in the top 1% for at least one statistic in the GIH population, 5 of which (LYST, OCA2, SLC24A5, SLC45A2, and TYR) have been previously associated with normal variation in skin, hair, or eye color. In comparison, 17 genes fall in the top 1% for at least one statistic in the ITU population. Twelve loci which are identified as outliers in the ITU scan were also identified in the GIH population.
    Conclusions: These results suggest that selection may have affected these loci broadly across the region.
    Language English
    Publishing date 2017-09-10
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1025339-7
    ISSN 1520-6300 ; 1042-0533
    ISSN (online) 1520-6300
    ISSN 1042-0533
    DOI 10.1002/ajhb.23012
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 2567: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

To top