Dataset Information

Aboriginal Australian mitochondrial genome variation - an increased understanding of population antiquity and diversity.

ABSTRACT: Aboriginal Australians represent one of the oldest continuous cultures outside Africa, with evidence indicating that their ancestors arrived in the ancient landmass of Sahul (present-day New Guinea and Australia) ~55 thousand years ago. Genetic studies, though limited, have demonstrated both the uniqueness and antiquity of Aboriginal Australian genomes. We have further resolved known Aboriginal Australian mitochondrial haplogroups and discovered novel indigenous lineages by sequencing the mitogenomes of 127 contemporary Aboriginal Australians. In particular, the more common haplogroups observed in our dataset included M42a, M42c, S, P5 and P12, followed by rarer haplogroups M15, M16, N13, O, P3, P6 and P8. We propose some major phylogenetic rearrangements, such as in haplogroup P where we delinked P4a and P4b and redefined them as P4 (New Guinean) and P11 (Australian), respectively. Haplogroup P2b was identified as a novel clade potentially restricted to Torres Strait Islanders. Nearly all Aboriginal Australian mitochondrial haplogroups detected appear to be ancient, with no evidence of later introgression during the Holocene. Our findings greatly increase knowledge about the geographic distribution and phylogenetic structure of mitochondrial lineages that have survived in contemporary descendants of Australia's first settlers.

SUBMITTER: Nagle N

PROVIDER: S-EPMC5347126 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature

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Aboriginal Australian mitochondrial genome variation - an increased understanding of population antiquity and diversity.

Nagle Nano N van Oven Mannis M Wilcox Stephen S van Holst Pellekaan Sheila S Tyler-Smith Chris C Xue Yali Y Ballantyne Kaye N KN Wilcox Leah L Papac Luka L Cooke Karen K van Oorschot Roland A H RA McAllister Peter P Williams Lesley L Kayser Manfred M Mitchell R John RJ

Scientific reports 20170313

Aboriginal Australians represent one of the oldest continuous cultures outside Africa, with evidence indicating that their ancestors arrived in the ancient landmass of Sahul (present-day New Guinea and Australia) ~55 thousand years ago. Genetic studies, though limited, have demonstrated both the uniqueness and antiquity of Aboriginal Australian genomes. We have further resolved known Aboriginal Australian mitochondrial haplogroups and discovered novel indigenous lineages by sequencing the mitoge ...[more]

PMID: 28287095

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Project description:A body mass index (BMI) >22kg/m2 is a risk factor for type 2 diabetes (T2D) in Aboriginal Australians. To identify loci associated with BMI and T2D we undertook a genome-wide association study using 1,075,436 quality-controlled single nucleotide polymorphisms (SNPs) genotyped (Illumina 2.5M Duo Beadchip) in 402 individuals in extended pedigrees from a Western Australian Aboriginal community. Imputation using the thousand genomes (1000G) reference panel extended the analysis to 6,724,284 post quality-control autosomal SNPs. No associations achieved genome-wide significance, commonly accepted as P<5x10-8. Nevertheless, genes/pathways in common with other ethnicities were identified despite the arrival of Aboriginal people in Australia >45,000 years ago. The top hit (rs10868204 Pgenotyped = 1.50x10-6; rs11140653 Pimputed_1000G = 2.90x10-7) for BMI lies 5' of NTRK2, the type 2 neurotrophic tyrosine kinase receptor for brain-derived neurotrophic factor (BDNF) that regulates energy balance downstream of melanocortin-4 receptor (MC4R). PIK3C2G (rs12816270 Pgenotyped = 8.06x10-6; rs10841048 Pimputed_1000G = 6.28x10-7) was associated with BMI, but not with T2D as reported elsewhere. BMI also associated with CNTNAP2 (rs6960319 Pgenotyped = 4.65x10-5; rs13225016 Pimputed_1000G = 6.57x10-5), previously identified as the strongest gene-by-environment interaction for BMI in African-Americans. The top hit (rs11240074 Pgenotyped = 5.59x10-6, Pimputed_1000G = 5.73x10-6) for T2D lies 5' of BCL9 that, along with TCF7L2, promotes beta-catenin's transcriptional activity in the WNT signaling pathway. Additional hits occurred in genes affecting pancreatic (KCNJ6, KCNA1) and/or GABA (GABRR1, KCNA1) functions. Notable associations observed for genes previously identified at genome-wide significance in other populations included MC4R (Pgenotyped = 4.49x10-4) for BMI and IGF2BP2 Pimputed_1000G = 2.55x10-6) for T2D. Our results may provide novel functional leads in understanding disease pathogenesis in this Australian Aboriginal population.

Project description:IntroductionOtitis media (OM) is one of the most common infectious diseases affecting children globally and the most common reason for antibiotic prescription and paediatric surgery. Australian Aboriginal children have higher rates of OM than non-Aboriginal children; however, there are no data comparing OM hospitalization rates between them at the population level. We report temporal trends for OM hospitalizations and in-hospital tympanostomy tube insertion (TTI) in a cohort of 469,589 Western Australian children born between 1996 and 2012.Materials and methodsWe used the International Classification of Diseases codes version 10 to identify hospitalizations for OM or TTI recorded as a surgical procedure. Using age-specific population denominators, we calculated hospitalization rates per 1,000 child-years by age, year and level of socio-economic deprivation.ResultsThere were 534,674 hospitalizations among 221,588 children hospitalized at least once before age 15 years. Aboriginal children had higher hospitalization rates for OM than non-Aboriginal children (23.3/1,000 [95% Confidence Interval (CI) 22.8,24.0] vs 2.4/1,000 [95% CI 2.3,2.4] child-years) with no change in disparity over time. Conversely non-Aboriginal children had higher rates of TTI than Aboriginal children (13.5 [95% CI 13.2,13.8] vs 10.1 [95% CI 8.9,11.4]). Children from lower socio-economic backgrounds had higher OM hospitalization rates than those from higher socio-economic backgrounds, although for Aboriginal children hospitalization rates were not statistically different across all levels of socio-economic disadvantage. Hospitalizations for TTI among non-Aboriginal children were more common among those from higher socio-economic backgrounds. This was also true for Aboriginal children; however, the difference was not statistically significant. There was a decline in OM hospitalization rates between 1998 and 2005 and remained stable thereafter.ConclusionAboriginal children and children from lower socio-economic backgrounds were over-represented with OM-related hospitalizations but had fewer TTIs. Despite a decrease in OM and TTI hospitalization rates during the first half of the study for all groups, the disparity between Aboriginal and non-Aboriginal children and between those of differing socioeconomic deprivation remained.

Dataset Information

Aboriginal Australian mitochondrial genome variation - an increased understanding of population antiquity and diversity.

Publications

Aboriginal Australian mitochondrial genome variation - an increased understanding of population antiquity and diversity.

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