Population History of Europe: Genetics

Barbujani, Guido

doi:10.1002/9780470015902.a0005962

“…By contrast, Europe is now very well represented by HLA population data, and a clear genetic variation (yet with still unexplained discrepancies between loci, probably due to selection) is observed, mainly along a north to south‐east geographic axis (Buhler et al ., , ). Although neighbouring populations such as North Africans and West Asians overlap to some extent to Europeans, possibly as a signature of past immune adaptations to pathogen‐rich environments (Currat et al ., ; Sanchez‐Mazas et al ., ,b), the observed pattern may easily be related to the demic diffusion of Neolithic farmers from Anatolia advocated by many scholars based on other genetic results (Ammerman & Cavalli‐Sforza, ; Chikhi et al ., , ; Barbujani & Bertorelle, ; Barbujani, ; Balaresque et al ., ). Finally, as several samples from the Pacific area (‘Polynesians’ taken in a broad sense) have been submitted to the present project (Cook Islanders, Maori, Maori‐Polynesians, Niueans, Samoans and Tongas), our new results can also be interpreted in relation to population genetic relationships in Oceania.…”

Section: Discussionmentioning

confidence: 98%

16^th IHIW: Analysis of HLA Population Data, with updated results for 1996 to 2012 workshop data (AHPD project report)

Riccio

¹

,

Bühler

²

,

Nunes

³

et al. 2012

Int J Immunogenetics

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We present here the results of the Analysis of HLA Population Data (AHPD) project of the 16th International HLA and Immunogenetics Workshop (16IHIW) held in Liverpool in May-June 2012. Thanks to the collaboration of 25 laboratories from 18 different countries, HLA genotypic data for 59 new population samples (either well-defined populations or donor registry samples) were gathered and 55 were analysed statistically following HLA-NET recommendations. The new data included, among others, large sets of well-defined populations from north-east Europe and West Asia, as well as many donor registry data from European countries. The Gene[rate] computer tools were combined to create a Gene[rate] computer pipeline to automatically (i) estimate allele frequencies by an expectation-maximization algorithm accommodating ambiguities, (ii) estimate heterozygosity, (iii) test for Hardy-Weinberg equilibrium (HWE), (iv) test for selective neutrality, (v) generate frequency graphs and summary statistics for each sample at each locus and (vi) plot multidimensional scaling (MDS) analyses comparing the new samples with previous IHIW data. Intrapopulation analyses show that HWE is rarely rejected, while neutrality tests often indicate a significant excess of heterozygotes compared with neutral expectations. The comparison of the 16IHIW AHPD data with data collected during previous workshops (12th-15th) shows that geography is an excellent predictor of HLA genetic differentiations for HLA-A, -B and -DRB1 loci but not for HLA-DQ, whose patterns are probably more influenced by natural selection. In Europe, HLA genetic variation clearly follows a north to south-east axis despite a low level of differentiation between European, North African and West Asian populations. Pacific populations are genetically close to Austronesian-speaking South-East Asian and Taiwanese populations, in agreement with current theories on the peopling of Oceania. Thanks to this project, HLA genetic variation is more clearly defined worldwide and better interpreted in relation to human peopling history and HLA molecular evolution.

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“…West Asians overlap to some extent to Europeans, possibly as a signature of past immune adaptations to pathogen-rich environments (Currat et al, 2010;Sanchez-Mazas et al, 2012a,b), the observed pattern may easily be related to the demic diffusion of Neolithic farmers from Anatolia advocated by many scholars based on other genetic results (Ammerman & Cavalli-Sforza, 1984;Chikhi et al, 1998Chikhi et al, , 2002Barbujani & Bertorelle, 2001;Barbujani, 2006;Balaresque et al, 2010). Taiwanese is congruent with the widely supported "out of-Taiwan" hypothesis of the peopling history of Oceania (Diamond & Bellwood, 2003;Bellwood & Dizon, 2008).…”

Section: Acknowledgementsupporting

confidence: 55%

Molecular approaches to tissue transplantation and transfusion medicine in Maori and Polynesians in New Zealand

Atan¹

0

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<p>My thesis is focused on using new and existing molecular technologies to survey immune system (i.e. HLA, KIR and MICA), blood group and HPA genes in Polynesian and Maori subjects. I have compiled large datasets for these individuals including first ever molecular typing blood group, HPA and MICA. I have also compared my data with those from previous genetic studies of KIR and HLA for the four Polynesian sub-populations and HLA for Maori. Combined with previous information in a small scale meta-analysis, the results presented here were interpreted for the first time in the light of new theories about the hybrid origin of Proto-Polynesians via gender-biased gene flow between Austronesian-speaking Mongoloids and Papuan-speaking Australoids. Phylogenetic and principal component/coordinate analyses show that Polynesian sub-populations are closer to each other and are end populations of the great Austronesian Diaspora. Estimation based on HLA class I and II allele frequencies show a wide range (55:45 to 90:10) of ASM:P-SA ancestral fractions in Maori and other Polynesians. The same phenomenon was observed for blood group, HPA and KIR data. Thus, findings from the present study generally support the account deduced from Y-chromosome, mtDNA and genome wide SNP data, and are in accord with the emergent picture from linguistics and archaeology studies. The data collected bear more or less directly on questions of health including tissue matching for transfusion and transplant surgery, disease resistance and the relative incidence of autoimmune disease in these ethnic groups. Tissue matching of HLA, MICA, KIR, blood group and HPA is a fundamental element in transfusion and transplant surgery and it is vital that these technologies take accurate account of the ethnic origins of both donors and recipients. This is important due to significant differences between Polynesians and people of European origin, who form the majority segment of the modern day multi-ethnic country of New Zealand. The prevalence of HLA, MICA, KIR, blood group and HPA and their potential influence on the health of modern day Maori and Polynesians were also discussed. This study was intentionally designed to validate new molecular blood group and HPA typing methods in Polynesian and Maori populations. Scores for the other loci are based on the application of pre-existing technologies. Validation using three different blood group and HPA genotyping methods (i.e. PCR-SSP, SBT and SNP assay) gave 100% concordance and thus reflects the accuracy of the new DNA-based methods. Overall, molecular genotyping does seem to offer the opportunity to improve the efficiency of high quality transfusion services, but should include all known variants that are associated with serological expression. In conclusion, the present molecular genetics study has successfully compiled new HLA, MICA, blood groups, HPA and KIR datasets for Polynesians and Maori, used the datasets for dual analyses of ancestry and health, and demonstrated the reliability of current genotyping platforms that would suit well the needs of transfusion and transplantation centres. In general, this thesis has strongly endorsed the indigenous biomedicine approach, and particularly will be valuable to Asia-Pacific populations of Austronesian peoples.</p>

show abstract

Molecular approaches to tissue transplantation and transfusion medicine in Maori and Polynesians in New Zealand

Atan¹

0

View full text Add to dashboard Cite

<p>My thesis is focused on using new and existing molecular technologies to survey immune system (i.e. HLA, KIR and MICA), blood group and HPA genes in Polynesian and Maori subjects. I have compiled large datasets for these individuals including first ever molecular typing blood group, HPA and MICA. I have also compared my data with those from previous genetic studies of KIR and HLA for the four Polynesian sub-populations and HLA for Maori. Combined with previous information in a small scale meta-analysis, the results presented here were interpreted for the first time in the light of new theories about the hybrid origin of Proto-Polynesians via gender-biased gene flow between Austronesian-speaking Mongoloids and Papuan-speaking Australoids. Phylogenetic and principal component/coordinate analyses show that Polynesian sub-populations are closer to each other and are end populations of the great Austronesian Diaspora. Estimation based on HLA class I and II allele frequencies show a wide range (55:45 to 90:10) of ASM:P-SA ancestral fractions in Maori and other Polynesians. The same phenomenon was observed for blood group, HPA and KIR data. Thus, findings from the present study generally support the account deduced from Y-chromosome, mtDNA and genome wide SNP data, and are in accord with the emergent picture from linguistics and archaeology studies. The data collected bear more or less directly on questions of health including tissue matching for transfusion and transplant surgery, disease resistance and the relative incidence of autoimmune disease in these ethnic groups. Tissue matching of HLA, MICA, KIR, blood group and HPA is a fundamental element in transfusion and transplant surgery and it is vital that these technologies take accurate account of the ethnic origins of both donors and recipients. This is important due to significant differences between Polynesians and people of European origin, who form the majority segment of the modern day multi-ethnic country of New Zealand. The prevalence of HLA, MICA, KIR, blood group and HPA and their potential influence on the health of modern day Maori and Polynesians were also discussed. This study was intentionally designed to validate new molecular blood group and HPA typing methods in Polynesian and Maori populations. Scores for the other loci are based on the application of pre-existing technologies. Validation using three different blood group and HPA genotyping methods (i.e. PCR-SSP, SBT and SNP assay) gave 100% concordance and thus reflects the accuracy of the new DNA-based methods. Overall, molecular genotyping does seem to offer the opportunity to improve the efficiency of high quality transfusion services, but should include all known variants that are associated with serological expression. In conclusion, the present molecular genetics study has successfully compiled new HLA, MICA, blood groups, HPA and KIR datasets for Polynesians and Maori, used the datasets for dual analyses of ancestry and health, and demonstrated the reliability of current genotyping platforms that would suit well the needs of transfusion and transplantation centres. In general, this thesis has strongly endorsed the indigenous biomedicine approach, and particularly will be valuable to Asia-Pacific populations of Austronesian peoples.</p>

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Population History of Europe: Genetics

Cited by 3 publications

References 24 publications

16^th IHIW: Analysis of HLA Population Data, with updated results for 1996 to 2012 workshop data (AHPD project report)

16^th IHIW: Analysis of HLA Population Data, with updated results for 1996 to 2012 workshop data (AHPD project report)

Molecular approaches to tissue transplantation and transfusion medicine in Maori and Polynesians in New Zealand

Molecular approaches to tissue transplantation and transfusion medicine in Maori and Polynesians in New Zealand

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About

Population History of Europe: Genetics

Cited by 3 publications

References 24 publications

16th IHIW: Analysis of HLA Population Data, with updated results for 1996 to 2012 workshop data (AHPD project report)

16th IHIW: Analysis of HLA Population Data, with updated results for 1996 to 2012 workshop data (AHPD project report)

Molecular approaches to tissue transplantation and transfusion medicine in Maori and Polynesians in New Zealand

Molecular approaches to tissue transplantation and transfusion medicine in Maori and Polynesians in New Zealand

Contact Info

Product

Resources

About

16^th IHIW: Analysis of HLA Population Data, with updated results for 1996 to 2012 workshop data (AHPD project report)

16^th IHIW: Analysis of HLA Population Data, with updated results for 1996 to 2012 workshop data (AHPD project report)