Worldwide human mitochondrial haplogroup distribution from urban sewage

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Abstract

Community level genetic information can be essential to direct health measures and study demographic tendencies but is subject to considerable ethical and legal challenges. These concerns become less pronounced when analyzing urban sewage samples, which are ab ovo anonymous by their pooled nature. We were able to detect traces of the human mitochondrial DNA (mtDNA) in urban sewage samples and to estimate the distribution of human mtDNA haplogroups. An expectation maximization approach was used to determine mtDNA haplogroup mixture proportions for samples collected at each different geographic location. Our results show reasonable agreement with both previous studies of ancient evolution or migration and current US census data; and are also readily reproducible and highly robust. Our approach presents a promising alternative for sample collection in studies focusing on the ethnic and genetic composition of populations or diseases associated with different mtDNA haplogroups and genotypes.

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Most cited references 40

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Mitochondrial genome variation and the origin of modern humans.

M Ingman, H Kaessmann, S Pääbo … (2000)

The analysis of mitochondrial DNA (mtDNA) has been a potent tool in our understanding of human evolution, owing to characteristics such as high copy number, apparent lack of recombination, high substitution rate and maternal mode of inheritance. However, almost all studies of human evolution based on mtDNA sequencing have been confined to the control region, which constitutes less than 7% of the mitochondrial genome. These studies are complicated by the extreme variation in substitution rate between sites, and the consequence of parallel mutations causing difficulties in the estimation of genetic distance and making phylogenetic inferences questionable. Most comprehensive studies of the human mitochondrial molecule have been carried out through restriction-fragment length polymorphism analysis, providing data that are ill suited to estimations of mutation rate and therefore the timing of evolutionary events. Here, to improve the information obtained from the mitochondrial molecule for studies of human evolution, we describe the global mtDNA diversity in humans based on analyses of the complete mtDNA sequence of 53 humans of diverse origins. Our mtDNA data, in comparison with those of a parallel study of the Xq13.3 region in the same individuals, provide a concurrent view on human evolution with respect to the age of modern humans.

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Biparental Inheritance of Mitochondrial DNA in Humans

Shiyu Luo, C Alexander Valencia, Jinglan Zhang … (2018)

Although there has been considerable debate about whether paternal mitochondrial DNA (mtDNA) transmission may coexist with maternal transmission of mtDNA, it is generally believed that mitochondria and mtDNA are exclusively maternally inherited in humans. Here, we identified three unrelated multigeneration families with a high level of mtDNA heteroplasmy (ranging from 24 to 76%) in a total of 17 individuals. Heteroplasmy of mtDNA was independently examined by high-depth whole mtDNA sequencing analysis in our research laboratory and in two Clinical Laboratory Improvement Amendments and College of American Pathologists-accredited laboratories using multiple approaches. A comprehensive exploration of mtDNA segregation in these families shows biparental mtDNA transmission with an autosomal dominantlike inheritance mode. Our results suggest that, although the central dogma of maternal inheritance of mtDNA remains valid, there are some exceptional cases where paternal mtDNA could be passed to the offspring. Elucidating the molecular mechanism for this unusual mode of inheritance will provide new insights into how mtDNA is passed on from parent to offspring and may even lead to the development of new avenues for the therapeutic treatment for pathogenic mtDNA transmission.

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Classification of European mtDNAs from an analysis of three European populations.

Dennis D Wallace, P Francalacci, M. John Petrozzi … (1996)

Mitochondrial DNA (mtDNA) sequence variation was examined in Finns, Swedes and Tuscans by PCR amplification and restriction analysis. About 99% of the mtDNAs were subsumed within 10 mtDNA haplogroups (H, I, J, K, M, T, U, V, W, and X) suggesting that the identified haplogroups could encompass virtually all European mtDNAs. Because both hypervariable segments of the mtDNA control region were previously sequenced in the Tuscan samples, the mtDNA haplogroups and control region sequences could be compared. Using a combination of haplogroup-specific restriction site changes and control region nucleotide substitutions, the distribution of the haplogroups was surveyed through the published restriction site polymorphism and control region sequence data of Caucasoids. This supported the conclusion that most haplogroups observed in Europe are Caucasoid-specific, and that at least some of them occur at varying frequencies in different Caucasoid populations. The classification of almost all European mtDNA variation in a number of well defined haplogroups could provide additional insights about the origin and relationships of Caucasoid populations and the process of human colonization of Europe, and is valuable for the definition of the role played by mtDNA backgrounds in the expression of pathological mtDNA mutations.

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Author and article information

Contributors

István Csabai:

ORCID: http://orcid.org/0000-0001-9232-9898

csabai@complex.elte.hu

Journal

Journal ID (nlm-ta): Sci Rep

Journal ID (iso-abbrev): Sci Rep

Title: Scientific Reports

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2045-2322

Publication date (Electronic): 12 August 2019

Publication date PMC-release: 12 August 2019

Publication date Collection: 2019

Volume: 9

Electronic Location Identifier: 11624

Affiliations

[1 ]ISNI 0000 0001 2294 6276, GRID grid.5591.8, Department of Physics of Complex Systems, , ELTE Eötvös Loránd University, Pázmány P. s. 1A, ; Budapest, 1117 Hungary

[2 ]ISNI 0000 0001 2294 6276, GRID grid.5591.8, Department of Information Systems, , ELTE Eötvös Loránd University, Pázmány P. s. 1C, ; Budapest, 1117 Hungary

[3 ]ISNI 0000 0004 1759 8344, GRID grid.419766.b, Department of Computational Sciences, , Wigner Research Centre for Physics of the HAS, Konkoly-Thege Miklós út 29–33., ; Budapest, 1121 Hungary

[4 ]ISNI 0000 0001 2181 8870, GRID grid.5170.3, National Food Institute, , Technical University of Denmark, Kgs., ; Lyngby, Denmark

[5 ]ISNI 000000040459992X, GRID grid.5645.2, Viroscience department, , Erasmus Medical Center, ; Rotterdam, The Netherlands

Author information

Orsolya Anna Pipek http://orcid.org/0000-0001-8109-0340

Anna Medgyes-Horváth http://orcid.org/0000-0003-4435-5797

Rolf S. Kaas http://orcid.org/0000-0002-5050-8668

Frank M. Aarestrup http://orcid.org/0000-0002-7116-2723

István Csabai http://orcid.org/0000-0001-9232-9898

Article

Publisher ID: 48093

DOI: 10.1038/s41598-019-48093-5

PMC ID: 6690936

PubMed ID: 31406241

SO-VID: e45d9211-32cc-406a-b5bc-4c5cb85f53e1

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 19 February 2019

Date accepted : 17 July 2019

Funding

Funded by: FundRef https://doi.org/10.13039/100010661, EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020);

Award ID: 643476

Award Recipient : Marion Koopmans Frank M. Aarestrup

Funded by: FundRef https://doi.org/10.13039/100004423, World Health Organization (WHO);

Award ID: NNF16OC0021856

Award Recipient : Marion Koopmans Frank M. Aarestrup

Funded by: FundRef https://doi.org/10.13039/501100009708, Novo Nordisk Fonden (Novo Nordisk Foundation);

Award ID: NNF16OC0021856

Award Recipient : Marion Koopmans Frank M. Aarestrup

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ScienceOpen disciplines: Uncategorized

Keywords: population screening,genetic testing,data acquisition,haplotypes

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ScienceOpen disciplines: Uncategorized

Keywords: population screening, genetic testing, data acquisition, haplotypes

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Worldwide human mitochondrial haplogroup distribution from urban sewage

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Most cited references 40

Mitochondrial genome variation and the origin of modern humans.

Biparental Inheritance of Mitochondrial DNA in Humans

Classification of European mtDNAs from an analysis of three European populations.

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Cited by 6

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