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Árnadóttir ER, Moore KHS, Guðmundsdóttir VB, Ebenesersdóttir SS, Guity K, Jónsson H, Stefánsson K, Helgason A. The rate and nature of mitochondrial DNA mutations in human pedigrees. Cell 2024; 187:3904-3918.e8. [PMID: 38851187 DOI: 10.1016/j.cell.2024.05.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 03/06/2024] [Accepted: 05/13/2024] [Indexed: 06/10/2024]
Abstract
We examined the rate and nature of mitochondrial DNA (mtDNA) mutations in humans using sequence data from 64,806 contemporary Icelanders from 2,548 matrilines. Based on 116,663 mother-child transmissions, 8,199 mutations were detected, providing robust rate estimates by nucleotide type, functional impact, position, and different alleles at the same position. We thoroughly document the true extent of hypermutability in mtDNA, mainly affecting the control region but also some coding-region variants. The results reveal the impact of negative selection on viable deleterious mutations, including rapidly mutating disease-associated 3243A>G and 1555A>G and pre-natal selection that most likely occurs during the development of oocytes. Finally, we show that the fate of new mutations is determined by a drastic germline bottleneck, amounting to an average of 3 mtDNA units effectively transmitted from mother to child.
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Affiliation(s)
| | | | - Valdís B Guðmundsdóttir
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | | | - Kamran Guity
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Kári Stefánsson
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
| | - Agnar Helgason
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Department of Anthropology, University of Iceland, Reykjavik, Iceland.
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2
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Disha B, Mathew RP, Dalal AB, Mahato AK, Satyamoorthy K, Singh KK, Thangaraj K, Govindaraj P. Mitochondria in biology and medicine - 2023. Mitochondrion 2024; 76:101853. [PMID: 38423268 DOI: 10.1016/j.mito.2024.101853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/07/2024] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
Mitochondria are an indispensable part of the cell that plays a crucial role in regulating various signaling pathways, energy metabolism, cell differentiation, proliferation, and cell death. Since mitochondria have their own genetic material, they differ from their nuclear counterparts, and dysregulation is responsible for a broad spectrum of diseases. Mitochondrial dysfunction is associated with several disorders, including neuro-muscular disorders, cancer, and premature aging, among others. The intricacy of the field is due to the cross-talk between nuclear and mitochondrial genes, which has also improved our knowledge of mitochondrial functions and their pathogenesis. Therefore, interdisciplinary research and communication are crucial for mitochondrial biology and medicine due to the challenges they pose for diagnosis and treatment. The ninth annual conference of the Society for Mitochondria Research and Medicine (SMRM)- India, titled "Mitochondria in Biology and Medicine" was organized at the Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India, on June 21-23, 2023. The latest advancements in the field of mitochondrial biology and medicine were discussed at the conference. In this article, we summarize the entire event for the benefit of researchers working in the field of mitochondrial biology and medicine.
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Affiliation(s)
- B Disha
- Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad 500039, India; Regional Centre for Biotechnology, Faridabad, Haryana 121001, India
| | - Rohan Peter Mathew
- Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad 500039, India; Manipal Academy of Higher Education, Manipal 576104, India
| | - Ashwin B Dalal
- Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad 500039, India
| | - Ajay K Mahato
- Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad 500039, India
| | - Kapaettu Satyamoorthy
- Shri Dharmasthala Manjunatheshwara (SDM) University, SDM College of Medical Sciences and Hospital, Manjushree Nagar, Sattur, Dharwad 580009, India
| | - Keshav K Singh
- Department of Genetics, School of Medicine, The University of Alabama at Birmingham, Kaul Genetics Building, Rm. 620, 720 20th St. South, Birmingham, AL, 35294, USA
| | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Periyasamy Govindaraj
- Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad 500039, India; Department of Neuropathology, National Institute of Mental Health and Neurosciences, Hosur Road, Bengaluru 560029, India.
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3
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Martins ARP, Warren NB, McMillan WO, Barrett RDH. Spatiotemporal dynamics in butterfly hybrid zones. INSECT SCIENCE 2024; 31:328-353. [PMID: 37596954 DOI: 10.1111/1744-7917.13262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/13/2023] [Accepted: 07/21/2023] [Indexed: 08/21/2023]
Abstract
Evaluating whether hybrid zones are stable or mobile can provide novel insights for evolution and conservation biology. Butterflies exhibit high sensitivity to environmental changes and represent an important model system for the study of hybrid zone origins and maintenance. Here, we review the literature exploring butterfly hybrid zones, with a special focus on their spatiotemporal dynamics and the potential mechanisms that could lead to their movement or stability. We then compare different lines of evidence used to investigate hybrid zone dynamics and discuss the strengths and weaknesses of each approach. Our goal with this review is to reveal general conditions associated with the stability or mobility of butterfly hybrid zones by synthesizing evidence obtained using different types of data sampled across multiple regions and spatial scales. Finally, we discuss spatiotemporal dynamics in the context of a speciation/divergence continuum, the relevance of hybrid zones for conservation biology, and recommend key topics for future investigation.
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Affiliation(s)
- Ananda R Pereira Martins
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
- Smithsonian Tropical Research Institute, Gamboa, Panama City, Panama
| | - Natalie B Warren
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Gamboa, Panama City, Panama
| | - Rowan D H Barrett
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
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4
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Hernández CL. Mitochondrial DNA in Human Diversity and Health: From the Golden Age to the Omics Era. Genes (Basel) 2023; 14:1534. [PMID: 37628587 PMCID: PMC10453943 DOI: 10.3390/genes14081534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is a small fraction of our hereditary material. However, this molecule has had an overwhelming presence in scientific research for decades until the arrival of high-throughput studies. Several appealing properties justify the application of mtDNA to understand how human populations are-from a genetic perspective-and how individuals exhibit phenotypes of biomedical importance. Here, I review the basics of mitochondrial studies with a focus on the dawn of the field, analysis methods and the connection between two sides of mitochondrial genetics: anthropological and biomedical. The particularities of mtDNA, with respect to inheritance pattern, evolutionary rate and dependence on the nuclear genome, explain the challenges of associating mtDNA composition and diseases. Finally, I consider the relevance of this single locus in the context of omics research. The present work may serve as a tribute to a tool that has provided important insights into the past and present of humankind.
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Affiliation(s)
- Candela L Hernández
- Department of Biodiversity, Ecology and Evolution, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
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5
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Malyarchuk BA, Derenko MV. Evaluating the role of selection in the evolution of mitochondrial genomes of aboriginal peoples of Siberia. Vavilovskii Zhurnal Genet Selektsii 2023; 27:218-223. [PMID: 37293444 PMCID: PMC10244587 DOI: 10.18699/vjgb-23-28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 07/14/2022] [Accepted: 07/14/2022] [Indexed: 06/10/2023] Open
Abstract
Studies of the nature of mitochondrial DNA (mtDNA) variability in human populations have shown that protein-coding genes are under negative (purifying) selection, since their mutation spectra are characterized by a pronounced predominance of synonymous substitutions over non-synonymous ones (Ka/Ks < 1). Meanwhile, a number of studies have shown that the adaptation of populations to various environmental conditions may be accompanied by a relaxation of negative selection in some mtDNA genes. For example, it was previously found that in Arctic populations, negative selection is relaxed in the mitochondrial ATP6 gene, which encodes one of the subunits of ATP synthase. In this work, we performed a Ka/Ks analysis of mitochondrial genes in large samples of three regional population groups in Eurasia: Siberia (N = 803), Western Asia/Transcaucasia (N = 753), and Eastern Europe (N = 707). The main goal of this work is to search for traces of adaptive evolution in the mtDNA genes of aboriginal peoples of Siberia represented by populations of the north (Koryaks, Evens) and the south of Siberia and the adjacent territory of Northeast China (Buryats, Barghuts, Khamnigans). Using standard Ka/Ks analysis, it was found that all mtDNA genes in all studied regional population groups are subject to negative selection. The highest Ka/Ks values in different regional samples were found in almost the same set of genes encoding subunits of ATP synthase (ATP6, ATP8), NADH dehydrogenase complex (ND1, ND2, ND3), and cytochrome bc1 complex (CYB). The highest Ka/Ks value, indicating a relaxation of negative selection, was found in the ATP6 gene in the Siberian group. The results of the analysis performed using the FUBAR method (HyPhy software package) and aimed at searching for mtDNA codons under the influence of selection also showed the predominance of negative selection over positive selection in all population groups. In Siberian populations, nucleotide sites that are under positive selection and associated with mtDNA haplogroups were registered not in the north (which is expected under the assumption of adaptive evolution of mtDNA), but in the south of Siberia.
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Affiliation(s)
- B A Malyarchuk
- Institute of Biological Problems of the North of the Far Eastern Branch of the Russian Academy of Sciences, Magadan, Russia
| | - M V Derenko
- Institute of Biological Problems of the North of the Far Eastern Branch of the Russian Academy of Sciences, Magadan, Russia
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6
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Monge-Ochoa B, Montoro L, Montoya J, Ruiz-Pesini E, López-Pérez MJ, de Castro F, Díez-Sánchez C. m.4216 T > C polymorphism in JT cluster determines a lower pregnancy rate in response to controlled ovarian stimulation treatment. J Assist Reprod Genet 2023; 40:671-682. [PMID: 36701026 PMCID: PMC10033795 DOI: 10.1007/s10815-023-02721-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023] Open
Abstract
PURPOSE To analyze the influence of Caucasian mitochondrial haplogroups on controlled ovarian stimulation outcome (COS), embryo (E), and pregnancy success. METHODS In a Caucasian population (n = 517) undergoing COS, mitochondrial haplogroups and physiological parameters were determined. Patients were classified, according to Bologna criteria, as good (>3)/poor ≤3) responder, on dependence of recruited oocytes (RO), and in pregnancy/non-pregnancy groups. Haplogroups were determined by sequencing mitochondrial hypervariable sequence I and confirmed by polymerase chain reaction (PCR), followed by restriction fragment length polymorphisms (RFLP). RESULTS The rank of total dose of FSH (TD FSH) was similar in all clusters/haplogroups, except in JT, which is narrower (950-3,650 IU), particularly in T (1,350-3,650 IU). The statistical analysis showed higher RO and E in JT when compared to U, although it was only Uk which accumulated significantly in pregnancy respect to JT. Pearson's correlations between TD FSH and RO showed negative statistical significance in all population (P = 0.001), H (P = 0.03), JT (P = 0.01), and T (P = 0.03). The percentage of contribution of TD FSH on RO was almost nine times in the JT cluster as compared to all population one. CONCLUSIONS JT cluster shows a different influence of TD FSH on RO. JT cluster shows higher RO and E than U, but it is Uk which exhibits a significant higher pregnancy rate than JT. The negative influence of the JT cluster on pregnancy success strongly suggests that the m.4216 T > C polymorphism could be responsible.
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Affiliation(s)
- Belén Monge-Ochoa
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
| | - Luis Montoro
- Unidad de Reproducción Asistida, Hospital Universitario Príncipe de Asturias, Universidad Complutense de Madrid, Alcalá de Henares, Madrid, Spain
| | - Julio Montoya
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Instituto de Investigación Sanitaria (IIS) de Aragón, Zaragoza, Spain
| | - Eduardo Ruiz-Pesini
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Instituto de Investigación Sanitaria (IIS) de Aragón, Zaragoza, Spain
| | - Manuel J López-Pérez
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
| | - Francisco de Castro
- Unidad de Reproducción Asistida, Hospital Universitario Príncipe de Asturias, Universidad Complutense de Madrid, Alcalá de Henares, Madrid, Spain
| | - Carmen Díez-Sánchez
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.
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7
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Radzvilavicius AL, Johnston IG. Organelle bottlenecks facilitate evolvability by traversing heteroplasmic fitness valleys. Front Genet 2022; 13:974472. [PMID: 36386853 PMCID: PMC9650085 DOI: 10.3389/fgene.2022.974472] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/11/2022] [Indexed: 07/09/2024] Open
Abstract
Bioenergetic organelles-mitochondria and plastids-retain their own genomes (mtDNA and ptDNA), and these organelle DNA (oDNA) molecules are vital for eukaryotic life. Like all genomes, oDNA must be able to evolve to suit new environmental challenges. However, mixed oDNA populations in cells can challenge cellular bioenergetics, providing a penalty to the appearance and adaptation of new mutations. Here we show that organelle "bottlenecks," mechanisms increasing cell-to-cell oDNA variability during development, can overcome this mixture penalty and facilitate the adaptation of beneficial mutations. We show that oDNA heteroplasmy and bottlenecks naturally emerge in evolutionary simulations subjected to fluctuating environments, demonstrating that this evolvability is itself evolvable. Usually thought of as a mechanism to clear damaging mutations, organelle bottlenecks therefore also resolve the tension between intracellular selection for pure cellular oDNA populations and the "bet-hedging" need for evolvability and adaptation to new environments. This general theory suggests a reason for the maintenance of organelle heteroplasmy in cells, and may explain some of the observed diversity in organelle maintenance and inheritance across taxa.
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Affiliation(s)
- Arunas L. Radzvilavicius
- Department of Mathematics, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Iain G. Johnston
- Department of Mathematics, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
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8
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Szeifert B, Gerber D, Csáky V, Langó P, Stashenkov DA, Khokhlov AA, Sitdikov AG, Gazimzyanov IR, Volkova EV, Matveeva NP, Zelenkov AS, Poshekhonova OE, Sleptsova AV, Karacharov KG, Ilyushina VV, Konikov BA, Sungatov FA, Kolonskikh AG, Botalov SG, Grudochko IV, Komar O, Egyed B, Mende BG, Türk A, Szécsényi-Nagy A. Tracing genetic connections of ancient Hungarians to the 6th-14th century populations of the Volga-Ural region. Hum Mol Genet 2022; 31:3266-3280. [PMID: 35531973 PMCID: PMC9523560 DOI: 10.1093/hmg/ddac106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/14/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Most of the early Hungarian tribes originated from the Volga-Kama and South-Ural regions, where they were composed of a mixed population based on historical, philological and archaeological data. We present here the uniparental genetic makeup of the mediaeval era of these regions that served as a melting pot for ethnic groups with different linguistic and historical backgrounds. Representing diverse cultural contexts, the new genetic data originate from ancient proto-Ob-Ugric people from Western Siberia (6th-13th century), the pre-Conquest period and subsisting Hungarians from the Volga-Ural region (6th-14th century) and their neighbours. By examining the eastern archaeology traits of Hungarian prehistory, we also study their genetic composition and origin in an interdisciplinary framework. We analyzed 110 deep-sequenced mitogenomes and 42 Y-chromosome haplotypes from 18 archaeological sites in Russia. The results support the studied groups' genetic relationships regardless of geographical distances, suggesting large-scale mobility. We detected long-lasting genetic connections between the sites representing the Kushnarenkovo and Chiyalik cultures and the Carpathian Basin Hungarians and confirmed the Uralic transmission of several East Eurasian uniparental lineages in their gene pool. Based on phylogenetics, we demonstrate and model the connections and splits of the studied Volga-Ural and conqueror groups. Early Hungarians and their alliances conquered the Carpathian Basin around 890 AD. Re-analysis of the Hungarian conquerors' maternal gene pool reveals numerous surviving maternal relationships in both sexes; therefore, we conclude that men and women came to the Carpathian Basin together, and although they were subsequently genetically fused into the local population, certain eastern lineages survived for centuries.
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Affiliation(s)
- Bea Szeifert
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network (ELKH), Budapest 1097, Hungary.,Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest 1117, Hungary
| | - Dániel Gerber
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network (ELKH), Budapest 1097, Hungary.,Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest 1117, Hungary
| | - Veronika Csáky
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network (ELKH), Budapest 1097, Hungary
| | - Péter Langó
- Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network (ELKH), Budapest 1097, Hungary.,Faculty of Humanities and Social Sciences, Institute of Archaeological Sciences, Pázmány Péter Catholic University, Budapest 1088, Hungary
| | - Dmitrii A Stashenkov
- Samara Regional Museum of History and Local Lore named after P. V. Alabina, Samara 443041, Russia
| | - Aleksandr A Khokhlov
- Department of Biology, Ecology and Teaching Methods, Samara State University of Social Sciences and Education, Samara 443099, Russia
| | | | | | | | | | | | - Olga E Poshekhonova
- Tyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen 625026, Russia
| | - Anastasiia V Sleptsova
- Tyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen 625026, Russia
| | | | - Viktoria V Ilyushina
- Tyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen 625026, Russia
| | - Boris A Konikov
- Omsk Popov Production Association Russia, Omsk 644009, Russia
| | - Flarit A Sungatov
- Institute of History, Language and Literature of Scientific Center in Ufa of Russian Academy of Science, Ufa 450054, Russia
| | - Alexander G Kolonskikh
- Institute of Ethnological Studies of R.G. Kuzeev, Ufa Scientific Center, Russian Academy of Sciences, Ufa 450077, Russia
| | - Sergei G Botalov
- South Ural Branch of the Institute of History and Archeology, Ural Branch of the Russian Academy of Sciences, Chelyabinsk 454080 Russia.,South Ural State University, Chelyabinsk 454080, Russia
| | - Ivan V Grudochko
- South Ural Branch of the Institute of History and Archeology, Ural Branch of the Russian Academy of Sciences, Chelyabinsk 454080 Russia.,South Ural State University, Chelyabinsk 454080, Russia
| | - Oleksii Komar
- Institute of Archaeology, National Academy of Sciences of Ukraine, Kyiv 04210, Ukraine
| | - Balázs Egyed
- Department of Genetics, ELTE Eötvös Loránd University, Budapest 1117, Hungary
| | - Balázs G Mende
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network (ELKH), Budapest 1097, Hungary
| | - Attila Türk
- Faculty of Humanities and Social Sciences, Institute of Archaeological Sciences, Pázmány Péter Catholic University, Budapest 1088, Hungary.,Early Hungarians Research Team, Research Centre for the Humanities, Eötvös Loránd Research Network (ELKH), Budapest 1097, Hungary
| | - Anna Szécsényi-Nagy
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network (ELKH), Budapest 1097, Hungary
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African mitochondrial haplogroup L7: a 100,000-year-old maternal human lineage discovered through reassessment and new sequencing. Sci Rep 2022; 12:10747. [PMID: 35750688 PMCID: PMC9232647 DOI: 10.1038/s41598-022-13856-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 05/30/2022] [Indexed: 11/17/2022] Open
Abstract
Archaeological and genomic evidence suggest that modern Homo sapiens have roamed the planet for some 300–500 thousand years. In contrast, global human mitochondrial (mtDNA) diversity coalesces to one African female ancestor (“Mitochondrial Eve”) some 145 thousand years ago, owing to the ¼ gene pool size of our matrilineally inherited haploid genome. Therefore, most of human prehistory was spent in Africa where early ancestors of Southern African Khoisan and Central African rainforest hunter-gatherers (RFHGs) segregated into smaller groups. Their subdivisions followed climatic oscillations, new modes of subsistence, local adaptations, and cultural-linguistic differences, all prior to their exodus out of Africa. Seven African mtDNA haplogroups (L0–L6) traditionally captured this ancient structure—these L haplogroups have formed the backbone of the mtDNA tree for nearly two decades. Here we describe L7, an eighth haplogroup that we estimate to be ~ 100 thousand years old and which has been previously misclassified in the literature. In addition, L7 has a phylogenetic sublineage L7a*, the oldest singleton branch in the human mtDNA tree (~ 80 thousand years). We found that L7 and its sister group L5 are both low-frequency relics centered around East Africa, but in different populations (L7: Sandawe; L5: Mbuti). Although three small subclades of African foragers hint at the population origins of L5'7, the majority of subclades are divided into Afro-Asiatic and eastern Bantu groups, indicative of more recent admixture. A regular re-estimation of the entire mtDNA haplotype tree is needed to ensure correct cladistic placement of new samples in the future.
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10
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Översti S, Palo JU. Variation in the substitution rates among the human mitochondrial haplogroup U sublineages. Genome Biol Evol 2022; 14:6613373. [PMID: 35731946 PMCID: PMC9250076 DOI: 10.1093/gbe/evac097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2022] [Indexed: 11/22/2022] Open
Abstract
Resolving the absolute timescale of phylogenetic trees stipulates reliable estimates for the rate of DNA sequence evolution. For this end, various calibration methods have been developed and studied intensively. Intraspecific rate variation among distinct genetic lineages, however, has gained less attention. Here, we have assessed lineage-specific molecular rates of human mitochondrial DNA (mtDNA) by performing tip-calibrated Bayesian phylogenetic analyses. Tip-calibration, as opposed to traditional nodal time stamps from dated fossil evidence or geological events, is based on sample ages and becoming ever more feasible as ancient DNA data from radiocarbon-dated samples accumulate. We focus on subhaplogroups U2, U4, U5a, and U5b, the data including ancient mtDNA genomes from 14C-dated samples (n = 234), contemporary genomes (n = 301), and two outgroup sequences from haplogroup R. The obtained molecular rates depended on the data sets (with or without contemporary sequences), suggesting time-dependency. More notable was the rate variation between haplogroups: U4 and U5a stand out having a substantially higher rate than U5b. This is also reflected in the divergence times obtained (U5a: 17,700 years and U5b: 29,700 years), a disparity not reported previously. After ruling out various alternative causes (e.g., selection, sampling, and sequence quality), we propose that the substitution rates have been influenced by demographic histories, widely different among populations where U4/U5a or U5b are frequent. As with the Y-chromosomal subhaplogroup R1b, the mitochondrial U4 and U5a have been associated with remarkable range extensions of the Yamnaya culture in the Bronze Age.
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Affiliation(s)
- Sanni Översti
- Transmission, Infection, Diversification and Evolution Group, Max-Planck Institute for the Science of Human History, Jena, Germany Kahlaische Straße 10, 07745, Jena, Germany.,Organismal and Evolutionary Biology Research Programme, Faculty of Biological Sciences, University of Helsinki, Helsinki, Finland P.O. Box 56, FI-00014, Helsinki, Finland
| | - Jukka U Palo
- Department of Forensic Medicine, Faculty of Medicine, University of Helsinki, Helsinki, Finland P.O. Box 40, FI-00014, Helsinki, Finland.,Forensic Chemistry Unit, Forensic Genetics Team, Finnish Institute for Health and Welfare, Helsinki, Finland P.O. Box 30, FI-00271, Helsinki, Finland
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11
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Joerin-Luque IA, Augusto DG, Calonga-Solís V, de Almeida RC, Lopes CVG, Petzl-Erler ML, Beltrame MH. Uniparental markers reveal new insights on subcontinental ancestry and sex-biased admixture in Brazil. Mol Genet Genomics 2022; 297:419-435. [DOI: 10.1007/s00438-022-01857-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
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12
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Friedrich VK, Rubel MA, Schurr TG. Mitochondrial genetic variation in human bioenergetics, adaptation, and adult disease. Am J Hum Biol 2021; 34:e23629. [PMID: 34146380 DOI: 10.1002/ajhb.23629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES Mitochondria are critical for the survival of eukaryotic organisms due to their ability to produce cellular energy, which drives virtually all aspects of host biology. However, the effects of mitochondrial DNA (mtDNA) variation in relation to disease etiology and adaptation within contemporary global human populations remains incompletely understood. METHODS To develop a more holistic understanding of the role of mtDNA diversity in human adaptation, health, and disease, we investigated mitochondrial biology and bioenergetics. More specifically, we synthesized details from studies of mitochondrial function and variation in the context of haplogroup background, climatic adaptation, and oxidative disease. RESULTS The majority of studies show that mtDNA variation arose during modern human dispersal around the world. Some of these variants appear to have been positively selected for their adaptiveness in colder climates, with these sequence changes having implications for tissue-specific function and thermogenic capacity. In addition, many variants modulating energy production are also associated with damaging metabolic byproducts and mitochondrial dysfunction, which, in turn, are implicated in the onset and severity of several different adult mitochondrial diseases. Thus, mtDNA variation that governs bioenergetics, metabolism, and thermoregulation may potentially have adverse consequences for human health, depending on the genetic background and context in which it occurs. CONCLUSIONS Our review suggests that the mitochondrial research field would benefit from independently replicating mtDNA haplogroup-phenotype associations across global populations, incorporating potentially confounding environmental, demographic, and disease covariates into studies of mtDNA variation, and extending association-based studies to include analyses of complete mitogenomes and assays of mitochondrial function.
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Affiliation(s)
- Volney K Friedrich
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Meagan A Rubel
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Center for Translational Imaging and Precision Medicine, University of California - San Diego, La Jolla, California, USA
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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13
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Kozakiewicz P, Grzybowska-Szatkowska L, Ciesielka M, Rzymowska J. The Role of Mitochondria in Carcinogenesis. Int J Mol Sci 2021; 22:ijms22105100. [PMID: 34065857 PMCID: PMC8151940 DOI: 10.3390/ijms22105100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 04/30/2021] [Accepted: 05/06/2021] [Indexed: 12/20/2022] Open
Abstract
The mitochondria are essential for normal cell functioning. Changes in mitochondrial DNA (mtDNA) may affect the occurrence of some chronic diseases and cancer. This process is complex and not entirely understood. The assignment to a particular mitochondrial haplogroup may be a factor that either contributes to cancer development or reduces its likelihood. Mutations in mtDNA occurring via an increase in reactive oxygen species may favour the occurrence of further changes both in mitochondrial and nuclear DNA. Mitochondrial DNA mutations in postmitotic cells are not inherited, but may play a role both in initiation and progression of cancer. One of the first discovered polymorphisms associated with cancer was in the gene NADH-ubiquinone oxidoreductase chain 3 (mt-ND3) and it was typical of haplogroup N. In prostate cancer, these mutations and polymorphisms involve a gene encoding subunit I of respiratory complex IV cytochrome c oxidase subunit 1 gene (COI). At present, a growing number of studies also address the impact of mtDNA polymorphisms on prognosis in cancer patients. Some of the mitochondrial DNA polymorphisms occur in both chronic disease and cancer, for instance polymorphism G5913A characteristic of prostate cancer and hypertension.
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Affiliation(s)
- Paulina Kozakiewicz
- Department of Radiotherapy, Medical University in Lublin, Chodźki 7, 20-093 Lublin, Poland; (L.G.-S.); (M.C.)
- Department of Radiotherapy, St. John’s Cancer Centre, The Regional Oncology Centre of Lublin Jaczewskiego 7, 20-090 Lublin, Poland
- Correspondence:
| | - Ludmiła Grzybowska-Szatkowska
- Department of Radiotherapy, Medical University in Lublin, Chodźki 7, 20-093 Lublin, Poland; (L.G.-S.); (M.C.)
- Department of Radiotherapy, St. John’s Cancer Centre, The Regional Oncology Centre of Lublin Jaczewskiego 7, 20-090 Lublin, Poland
| | - Marzanna Ciesielka
- Department of Radiotherapy, Medical University in Lublin, Chodźki 7, 20-093 Lublin, Poland; (L.G.-S.); (M.C.)
- Chair and Department of Forensic Medicine, Medical University in Lublin, Jaczewskiego 8b, 20-090 Lublin, Poland
| | - Jolanta Rzymowska
- Chair and Department of Biology and Genetics, Medical University of Lublin, Chodźki 4A, 20-093 Lublin, Poland;
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14
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Camacho-Sanchez M, Leonard JA. Mitogenomes Reveal Multiple Colonization of Mountains by Rattus in Sundaland. J Hered 2021; 111:392-404. [PMID: 32485737 PMCID: PMC7423070 DOI: 10.1093/jhered/esaa014] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 05/25/2020] [Indexed: 01/16/2023] Open
Abstract
Tropical mountains are cradles of biodiversity and endemism. Sundaland, tropical Southeast Asia, hosts 3 species of Rattus endemic to elevations above 2000 m with an apparent convergence in external morphology: Rattus korinchi and R. hoogerwerfi from Sumatra, and R. baluensis from Borneo. A fourth one, R. tiomanicus, is restricted to lowland elevations across the whole region. The origins of these endemics are little known due to the absence of a robust phylogenetic framework. We use complete mitochondrial genomes from the 3 high altitude Rattus, and several related species to determine their relationships, date divergences, reconstruct their history of colonization, and test for selection on the mitochondrial DNA. We show that mountain colonization happened independently in Borneo (<390 Kya) and Sumatra (~1.38 Mya), likely from lowland lineages. The origin of the Bornean endemic R. baluensis is very recent and its genetic diversity is nested within the diversity of R. tiomanicus. We found weak evidence of positive selection in the high-elevation lineages and attributed the greater nonsynonymous mutations on these branches (specially R. baluensis) to lesser purifying selection having acted on the terminal branches in the phylogeny.
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Affiliation(s)
- Miguel Camacho-Sanchez
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
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15
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Santos CGM, Rolim-Filho NG, Domingues CA, Dornelas-Ribeiro M, King JL, Budowle B, Moura-Neto RS, Silva R. Association of whole mtDNA, an NADPH G11914A variant, and haplogroups with high physical performance in an elite military troop. ACTA ACUST UNITED AC 2021; 54:e10317. [PMID: 33909855 PMCID: PMC8075130 DOI: 10.1590/1414-431x202010317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 12/29/2020] [Indexed: 11/22/2022]
Abstract
Physical performance is a multifactorial and complex trait influenced by environmental and hereditary factors. Environmental factors alone have been insufficient to characterize all outstanding phenotypes. Recent advances in genomic technologies have enabled the investigation of whole nuclear and mitochondrial genome sequences, increasing our ability to understand interindividual variability in physical performance. Our objective was to evaluate the association of mitochondrial polymorphic loci with physical performance in Brazilian elite military personnel. Eighty-eight male military personnel who participated in the Command Actions Course of the Army were selected. Total DNA was obtained from blood samples and a complete mitochondrial genome (mtDNA) was sequenced using Illumina MiSeq platform. Twenty-nine subjects completed the training program (FINISHED, 'F'), and fifty-nine failed to complete (NOT_FINISHED, 'NF'). The mtDNA from NF was slightly more similar to genomes from African countries frequently related to endurance level. Twenty-two distinct mtDNA haplogroups were identified corroborating the intense genetic admixture of the Brazilian population, but their distribution was similar between the two groups (FST=0.0009). Of 745 polymorphisms detected in the mtDNA, the position G11914A within the NADPH gene component of the electron transport chain, was statistically different between F and NF groups (P=0.011; OR: 4.286; 95%CI: 1.198-16.719), with a higher frequency of the G allele in group F individuals). The high performance of military personnel may be mediated by performance-related genomic traits. Thus, mitochondrial genetic markers such as the ND4 gene may play an important role on physical performance variability.
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Affiliation(s)
- C G M Santos
- Instituto de Biologia do Exército, Rio de Janeiro, RJ, Brasil
| | - N G Rolim-Filho
- Centro de Instrução de Operações Especiais do Exército Brasileiro, Rio de Janeiro, RJ, Brasil
| | - C A Domingues
- Centro de Instrução de Operações Especiais do Exército Brasileiro, Rio de Janeiro, RJ, Brasil
| | | | - J L King
- Center for Human Identification, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - B Budowle
- Center for Human Identification, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - R S Moura-Neto
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - R Silva
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
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16
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Thaler DS. Is Global Microbial Biodiversity Increasing, Decreasing, or Staying the Same? Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.565649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Animal and plant biodiversity is decreasing. In contrast, the global direction and the pace of change in microbial, including viral, biodiversity is unknown. Important niches for microbial diversity occur in highly specific associations with plants and animals, and these niches are lost as hosts become extinct. The taxonomic diversity of human gut bacteria is reported to be decreasing. On the other hand, SARS-CoV-2 variation is increasing. Where microbes are concerned, Darwin’s “tangled bank” of interdependent organisms may be composed mostly of other microbes. There is the likelihood that as some classes of microbes become extinct, others evolve and diversify. A better handle on all processes that affect microbial biodiversity and their net balance is needed. Lack of insight into the dynamics of evolution of microbial biodiversity is arguably the single most profound and consequential unknown with regard to human knowledge of the biosphere. If some or all parts of microbial diversity are relentlessly increasing, then survey approaches may be too slow to ever catch up. New approaches, including single-molecule or single-cell sequencing in populations, as well as focused attention on modulators and vectors of vertical and horizontal evolution may offer more direct insights into some aspects of the pace of microbial evolution.
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17
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García A, Nores R, Motti JMB, Pauro M, Luisi P, Bravi CM, Fabra M, Gosling AL, Kardailsky O, Boocock J, Solé-Morata N, Matisoo-Smith EA, Comas D, Demarchi DA. Ancient and modern mitogenomes from Central Argentina: new insights into population continuity, temporal depth and migration in South America. Hum Mol Genet 2021; 30:1200-1217. [PMID: 33856032 DOI: 10.1093/hmg/ddab105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/15/2021] [Accepted: 03/31/2021] [Indexed: 12/22/2022] Open
Abstract
The inverted triangle shape of South America places Argentina territory as a geographical crossroads between the two principal peopling streams that followed either the Pacific or the Atlantic coasts, which could have then merged in Central Argentina (CA). Although the genetic diversity from this region is therefore crucial to decipher past population movements in South America, its characterization has been overlooked so far. We report 92 modern and 22 ancient mitogenomes spanning a temporal range of 5000 years, which were compared with a large set of previously reported data. Leveraging this dataset representative of the mitochondrial diversity of the subcontinent, we investigate the maternal history of CA populations within a wider geographical context. We describe a large number of novel clades within the mitochondrial DNA tree, thus providing new phylogenetic interpretations for South America. We also identify several local clades of great temporal depth with continuity until the present time, which stem directly from the founder haplotypes, suggesting that they originated in the region and expanded from there. Moreover, the presence of lineages characteristic of other South American regions reveals the existence of gene flow to CA. Finally, we report some lineages with discontinuous distribution across the Americas, which suggest the persistence of relic lineages likely linked to the first population arrivals. The present study represents to date the most exhaustive attempt to elaborate a Native American genetic map from modern and ancient complete mitochondrial genomes in Argentina and provides relevant information about the general process of settlement in South America.
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Affiliation(s)
- Angelina García
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Rodrigo Nores
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Josefina M B Motti
- FACSO (NEIPHPA), Universidad Nacional del Centro de la Provincia de Buenos Aires, CONICET, Quequén 7631, Argentina
| | - Maia Pauro
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Pierre Luisi
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Claudio M Bravi
- Instituto Multidisciplinario de Biología Celular (IMBICE), CCT La Plata CONICET, CICPBA, Universidad Nacional de La Plata, La Plata 1906, Argentina
| | - Mariana Fabra
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Anna L Gosling
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
| | - Olga Kardailsky
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
| | - James Boocock
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand.,Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Neus Solé-Morata
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona 08003, Spain
| | | | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Darío A Demarchi
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
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18
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Shinde P, Whitwell HJ, Verma RK, Ivanchenko M, Zaikin A, Jalan S. Impact of modular mitochondrial epistatic interactions on the evolution of human subpopulations. Mitochondrion 2021; 58:111-122. [PMID: 33618020 DOI: 10.1016/j.mito.2021.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/22/2020] [Accepted: 02/03/2021] [Indexed: 12/23/2022]
Abstract
Investigation of human mitochondrial (mt) genome variation has been shown to provide insights to the human history and natural selection. By analyzing 24,167 human mt-genome samples, collected for five continents, we have developed a co-mutation network model to investigate characteristic human evolutionary patterns. The analysis highlighted richer co-mutating regions of the mt-genome, suggesting the presence of epistasis. Specifically, a large portion of COX genes was found to co-mutate in Asian and American populations, whereas, in African, European, and Oceanic populations, there was greater co-mutation bias in hypervariable regions. Interestingly, this study demonstrated hierarchical modularity as a crucial agent for these co-mutation networks. More profoundly, our ancestry-based co-mutation module analyses showed that mutations cluster preferentially in known mitochondrial haplogroups. Contemporary human mt-genome nucleotides most closely resembled the ancestral state, and very few of them were found to be ancestral-variants. Overall, these results demonstrated that subpopulation-based biases may favor mitochondrial gene specific epistasis.
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Affiliation(s)
- Pramod Shinde
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore 453552, India.
| | - Harry J Whitwell
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK; Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK; Centre for Analysis of Complex Systems, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Rahul Kumar Verma
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore 453552, India
| | - Mikhail Ivanchenko
- Department of Applied Mathematics and Centre of Bioinformatics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Alexey Zaikin
- Centre for Analysis of Complex Systems, Sechenov First Moscow State Medical University, Moscow, Russia; Department of Applied Mathematics and Centre of Bioinformatics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia; Department of Mathematics and Institute for Women's Health, University College London, London WC1E 6BT, UK
| | - Sarika Jalan
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore 453552, India; Complex Systems Lab, Department of Physics, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore 453552, India; Center for Theoretical Physics of Complex Systems, Institute for Basic Science(IBS), Daejeon 34126, Korea.
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19
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Stewart JB, Chinnery PF. Extreme heterogeneity of human mitochondrial DNA from organelles to populations. Nat Rev Genet 2020; 22:106-118. [PMID: 32989265 DOI: 10.1038/s41576-020-00284-x] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2020] [Indexed: 02/06/2023]
Abstract
Contrary to the long-held view that most humans harbour only identical mitochondrial genomes, deep resequencing has uncovered unanticipated extreme genetic variation within mitochondrial DNA (mtDNA). Most, if not all, humans contain multiple mtDNA genotypes (heteroplasmy); specific patterns of variants accumulate in different tissues, including cancers, over time; and some variants are preferentially passed down or suppressed in the maternal germ line. These findings cast light on the origin and spread of mtDNA mutations at multiple scales, from the organelle to the human population, and challenge the conventional view that high percentages of a mutation are required before a new variant has functional consequences.
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Affiliation(s)
- James B Stewart
- Max Planck Institute for Biology of Ageing, Cologne, Germany.,Wellcome Centre for Mitochondrial Research, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK. .,Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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20
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Hill GE. Genetic hitchhiking, mitonuclear coadaptation, and the origins of mt DNA barcode gaps. Ecol Evol 2020; 10:9048-9059. [PMID: 32953045 PMCID: PMC7487244 DOI: 10.1002/ece3.6640] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 01/02/2023] Open
Abstract
DNA barcoding based on mitochondrial (mt) nucleotide sequences is an enigma. Neutral models of mt evolution predict DNA barcoding cannot work for recently diverged taxa, and yet, mt DNA barcoding accurately delimits species for many bilaterian animals. Meanwhile, mt DNA barcoding often fails for plants and fungi. I propose that because mt gene products must cofunction with nuclear gene products, the evolution of mt genomes is best understood with full consideration of the two environments that impose selective pressure on mt genes: the external environment and the internal genomic environment. Moreover, it is critical to fully consider the potential for adaptive evolution of not just protein products of mt genes but also of mt transfer RNAs and mt ribosomal RNAs. The tight linkage of genes on mt genomes that do not engage in recombination could facilitate selective sweeps whenever there is positive selection on any element in the mt genome, leading to the purging of mt genetic diversity within a population and to the rapid fixation of novel mt DNA sequences. Accordingly, the most important factor determining whether or not mt DNA sequences diagnose species boundaries may be the extent to which the mt chromosomes engage in recombination.
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21
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Fendt L, Fazzini F, Weissensteiner H, Bruckmoser E, Schönherr S, Schäfer G, Losso JL, Streiter GA, Lamina C, Rasse M, Klocker H, Kofler B, Kloss-Brandstätter A, Huck CW, Kronenberg F, Laimer J. Profiling of Mitochondrial DNA Heteroplasmy in a Prospective Oral Squamous Cell Carcinoma Study. Cancers (Basel) 2020; 12:E1933. [PMID: 32708892 PMCID: PMC7409097 DOI: 10.3390/cancers12071933] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 01/25/2023] Open
Abstract
While a shift in energy metabolism is essential to cancers, the knowledge about the involvement of the mitochondrial genome in tumorigenesis and progression in oral squamous cell carcinoma (OSCC) is still very limited. In this study, we evaluated 37 OSCC tumors and the corresponding benign mucosa tissue pairs by deep sequencing of the complete mitochondrial DNA (mtDNA). After extensive quality control, we identified 287 variants, 137 in tumor and 150 in benign samples exceeding the 1% threshold. Variant heteroplasmy levels were significantly increased in cancer compared to benign tissues (p = 0.0002). Furthermore, pairwise high heteroplasmy frequency difference variants (∆HF% > 20) with potential functional impact were increased in the cancer tissues (p = 0.024). Fourteen mutations were identified in the protein-coding region, out of which thirteen were detected in cancer and only one in benign tissue. After eight years of follow-up, the risk of mortality was higher for patients who harbored at least one ∆HF% > 20 variant in mtDNA protein-coding regions relative to those with no mutations (HR = 4.6, (95%CI = 1.3-17); p = 0.019 in primary tumor carriers). Haplogroup affiliation showed an impact on survival time, which however needs confirmation in a larger study. In conclusion, we observed a significantly higher accumulation of somatic mutations in the cancer tissues associated with a worse prognosis.
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Affiliation(s)
- Liane Fendt
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Federica Fazzini
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Hansi Weissensteiner
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Emanuel Bruckmoser
- Oral and Maxillofacial Surgeon, Private Practice, A-5020 Salzburg, Austria;
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Georg Schäfer
- Institute for Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, A-6020 Innsbruck, Austria;
| | - Jamie Lee Losso
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Gertraud A. Streiter
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Claudia Lamina
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Michael Rasse
- University Hospital for Craniomaxillofacial and Oral Surgery, Medical University of Innsbruck, A-6020 Innsbruck, Austria;
- Clinic for Maxillofacial Surgery, Sechenov University, Trubetskaya Str. 8 b.2, 119992 Moscow, Russia
| | - Helmut Klocker
- Division of Experimental Urology, Department of Urology, Medical University of Innsbruck, A-6020 Innsbruck, Austria;
| | - Barbara Kofler
- Department of Otorhinolaryngology, Medical University of Innsbruck, Anichstrasse 35, A-6020 Innsbruck, Austria;
| | - Anita Kloss-Brandstätter
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
- Carinthia University of Applied Sciences, A-9524 Villach, Austria
| | - Christian W. Huck
- Institute of Analytical Chemistry and Radiochemistry, CCB-Center for Chemistry and Biomedicine, Leopold Franzens University Innsbruck, A-6020 Innsbruck, Austria;
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Johannes Laimer
- University Hospital for Craniomaxillofacial and Oral Surgery, Medical University of Innsbruck, A-6020 Innsbruck, Austria;
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22
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Chan EKF, Timmermann A, Baldi BF, Moore AE, Lyons RJ, Lee SS, Kalsbeek AMF, Petersen DC, Rautenbach H, Förtsch HEA, Bornman MSR, Hayes VM. Human origins in a southern African palaeo-wetland and first migrations. Nature 2019; 575:185-189. [PMID: 31659339 DOI: 10.1038/s41586-019-1714-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 09/24/2019] [Indexed: 01/17/2023]
Abstract
Anatomically modern humans originated in Africa around 200 thousand years ago (ka)1-4. Although some of the oldest skeletal remains suggest an eastern African origin2, southern Africa is home to contemporary populations that represent the earliest branch of human genetic phylogeny5,6. Here we generate, to our knowledge, the largest resource for the poorly represented and deepest-rooting maternal L0 mitochondrial DNA branch (198 new mitogenomes for a total of 1,217 mitogenomes) from contemporary southern Africans and show the geographical isolation of L0d1'2, L0k and L0g KhoeSan descendants south of the Zambezi river in Africa. By establishing mitogenomic timelines, frequencies and dispersals, we show that the L0 lineage emerged within the residual Makgadikgadi-Okavango palaeo-wetland of southern Africa7, approximately 200 ka (95% confidence interval, 240-165 ka). Genetic divergence points to a sustained 70,000-year-long existence of the L0 lineage before an out-of-homeland northeast-southwest dispersal between 130 and 110 ka. Palaeo-climate proxy and model data suggest that increased humidity opened green corridors, first to the northeast then to the southwest. Subsequent drying of the homeland corresponds to a sustained effective population size (L0k), whereas wet-dry cycles and probable adaptation to marine foraging allowed the southwestern migrants to achieve population growth (L0d1'2), as supported by extensive south-coastal archaeological evidence8-10. Taken together, we propose a southern African origin of anatomically modern humans with sustained homeland occupation before the first migrations of people that appear to have been driven by regional climate changes.
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Affiliation(s)
- Eva K F Chan
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Axel Timmermann
- Center for Climate Physics, Institute for Basic Science, Busan, South Korea. .,Pusan National University, Busan, South Korea.
| | - Benedetta F Baldi
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Andy E Moore
- Department of Geology, Rhodes University, Grahamstown, South Africa
| | - Ruth J Lyons
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Sun-Seon Lee
- Center for Climate Physics, Institute for Basic Science, Busan, South Korea.,Pusan National University, Busan, South Korea
| | - Anton M F Kalsbeek
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Desiree C Petersen
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,The Centre for Proteomic and Genomic Research, Cape Town, South Africa
| | - Hannes Rautenbach
- Climate Change and Variability, South African Weather Service, Pretoria, South Africa.,School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa.,Akademia, Johannesburg, South Africa
| | | | - M S Riana Bornman
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Vanessa M Hayes
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia. .,St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia. .,School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa. .,Faculty of Health Sciences, University of Limpopo, Sovenga, South Africa. .,Central Clinical School, University of Sydney, Sydney, New South Wales, Australia.
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23
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Surowiec A, Snyder KT, Creanza N. A worldwide view of matriliny: using cross-cultural analyses to shed light on human kinship systems. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180077. [PMID: 31303161 DOI: 10.1098/rstb.2018.0077] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although matriliny and matrilocality are relatively rare in contemporary human populations, these female-based descent and residence systems are present in different cultural contexts and across the globe. Previous research has generated numerous hypotheses about which cultural traits are associated with the stability or loss of matrilineal descent. In addition, several studies have examined matrilineal descent with phylogenetic analyses; however, the use of language phylogenies has restricted these analyses to comparisons within a single language family, often confined to a single continent. Cross-cultural comparisons are particularly informative when they account for the relationships between widely distributed populations, as opposed to treating each population as an independent sample or focusing on a single region. Here, we study the evolution of descent systems on a worldwide scale. First, we test for significant associations between matriliny and numerous cultural traits that have been theoretically associated with its stability or loss, such as subsistence strategy, animal domestication, mating system, residence pattern, wealth transfer and property succession. In addition, by combining genetic and linguistic information to build a global supertree that includes 16 matrilineal populations, we also perform phylogenetically controlled analyses to assess the patterns of correlated evolution between descent and other traits: for example, does a change in subsistence strategy generally predict a shift in the rules of descent, or do these transitions happen independently? These analyses enable a worldwide perspective on the pattern and process of the evolution of matriliny and matrilocality. This article is part of the theme issue 'The evolution of female-biased kinship in humans and other mammals'.
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Affiliation(s)
- Alexandra Surowiec
- Department of Biological Sciences, Vanderbilt University , Nashville, TN 37240 , USA
| | - Kate T Snyder
- Department of Biological Sciences, Vanderbilt University , Nashville, TN 37240 , USA
| | - Nicole Creanza
- Department of Biological Sciences, Vanderbilt University , Nashville, TN 37240 , USA
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24
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Laaksonen J, Seppälä I, Raitoharju E, Mononen N, Lyytikäinen LP, Waldenberger M, Illig T, Lepistö M, Almusa H, Ellonen P, Hutri-Kähönen N, Juonala M, Kähönen M, Raitakari O, Salonen JT, Lehtimäki T. Discovery of mitochondrial DNA variants associated with genome-wide blood cell gene expression: a population-based mtDNA sequencing study. Hum Mol Genet 2019; 28:1381-1391. [PMID: 30629177 DOI: 10.1093/hmg/ddz011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/14/2018] [Accepted: 01/07/2019] [Indexed: 01/01/2023] Open
Abstract
The effect of mitochondrial DNA (mtDNA) variation on peripheral blood transcriptomics in health and disease is not fully known. Sex-specific mitochondrially controlled gene expression patterns have been shown in Drosophila melanogaster but in humans, evidence is lacking. Functional variation in mtDNA may also have a role in the development of type 2 diabetes and its precursor state, i.e. prediabetes. We examined the associations between mitochondrial single-nucleotide polymorphisms (mtSNPs) and peripheral blood transcriptomics with a focus on sex- and prediabetes-specific effects. The genome-wide blood cell expression data of 19 637 probes, 199 deep-sequenced mtSNPs and nine haplogroups of 955 individuals from a population-based Young Finns Study cohort were used. Significant associations were identified with linear regression and analysis of covariance. The effects of sex and prediabetes on the associations between gene expression and mtSNPs were studied using random-effect meta-analysis. Our analysis identified 53 significant expression probe-mtSNP associations after Bonferroni correction, involving 7 genes and 31 mtSNPs. Eight probe-mtSNP signals remained independent after conditional analysis. In addition, five genes showed differential expression between haplogroups. The meta-analysis did not show any significant differences in linear model effect sizes between males and females but identified the association between the OASL gene and mtSNP C16294T to show prediabetes-specific effects. This study pinpoints new independent mtSNPs associated with peripheral blood transcriptomics and replicates six previously reported associations, providing further evidence of the mitochondrial genetic control of blood cell gene expression. In addition, we present evidence that prediabetes might lead to perturbations in mitochondrial control.
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Affiliation(s)
- Jaakko Laaksonen
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Ilkka Seppälä
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Emma Raitoharju
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Nina Mononen
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Illig
- Hannover Unified Biobank, Hannover Medical School, Hannover Germany.,Institute for Human Genetics, Hannover Medical School, Hannover, Germany
| | - Maija Lepistö
- Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland
| | - Henrikki Almusa
- Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland
| | - Pekka Ellonen
- Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland
| | - Nina Hutri-Kähönen
- Department of Pediatrics, Tampere University Hospital and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Markus Juonala
- Department of Medicine, University of Turku, Turku, Finland.,Division of Medicine, Turku University Hospital, Turku, Finland.,Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Olli Raitakari
- Department of Clinical Physiology and Nuclear Medicine, University of Turku and Turku University Hospital, Turku, Finland.,Research Centre for Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Jukka T Salonen
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,MAS-Metabolic Analytical Services Oy, Helsinki, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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25
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Gu X, Kang X, Liu J. Mutation signatures in germline mitochondrial genome provide insights into human mitochondrial evolution and disease. Hum Genet 2019; 138:613-624. [PMID: 30968252 DOI: 10.1007/s00439-019-02009-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 04/02/2019] [Indexed: 01/06/2023]
Abstract
Variations in mitochondrial DNA (mtDNA) have been fundamental for understanding human evolution and are causative for a plethora of inherited mitochondrial diseases, but the mutation signatures of germline mtDNA and their value in understanding mitochondrial pathogenicity remain unknown. Here, we carried out a systematic analysis of mutation patterns in germline mtDNA based on 97,566 mtDNA variants from 45,494 full-length sequences and revealed a highly non-stochastic and replication-coupled mutation signature characterized by nucleotide-specific mutation pressure (G > T>A > C) and position-specific selection pressure, suggesting the existence of an intensive mutation-selection interplay in germline mtDNA. We provide evidence that this mutation-selection interplay has strongly shaped the mtDNA sequence during evolution, which not only manifests as an oriented alteration of amino acid compositions of mitochondrial encoded proteins, but also explains the long-lasting mystery of CpG depletion in mitochondrial genome. Finally, we demonstrated that these insights may be integrated to better understand the pathogenicity of disease-implicated mitochondrial variants.
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Affiliation(s)
- Xiwen Gu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, China.
| | - Xinyun Kang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, China
| | - Jiankang Liu
- Center for Mitochondrial Biology and Medicine & Douglas C. Wallace Institute for Mitochondrial and Epigenetic Information Sciences, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China.
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26
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Chen M, Yin H, Gu H, Zhang L, Xu ZX, Ma T, Li D. Genetic Diversity of atp6 and cox3 Gene in Wild Drosophila melanogaster. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419030037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Macaulay V, Soares P, Richards MB. Rectifying long-standing misconceptions about the ρ statistic for molecular dating. PLoS One 2019; 14:e0212311. [PMID: 30779770 PMCID: PMC6380571 DOI: 10.1371/journal.pone.0212311] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 01/19/2019] [Indexed: 01/01/2023] Open
Abstract
When divided by a given mutation rate, the ρ (rho) statistic provides a simple estimator of the age of a clade within a phylogenetic tree by averaging the number of mutations from each sample in the clade to its root. However, a long-standing critique of the use of ρ in genetic dating has been quite often cited. Here we show that the critique is unfounded. We demonstrate by a formal mathematical argument and illustrate with a simulation study that ρ estimates are unbiased and also that ρ and maximum likelihood estimates do not differ in any systematic fashion. We also demonstrate that the claim that the associated confidence intervals commonly estimate the uncertainty inappropriately is flawed since it relies on a means of calculating standard errors that is not used by any other researchers, whereas an established expression for the standard error is largely unproblematic. We conclude that ρ dating, alongside approaches such as maximum likelihood (ML) and Bayesian inference, remains a useful tool for genetic dating.
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Affiliation(s)
- Vincent Macaulay
- School of Mathematics and Statistics, University of Glasgow, Glasgow, United Kingdom
| | - Pedro Soares
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- * E-mail:
| | - Martin B. Richards
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, United Kingdom
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28
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Exogenous Factors May Differentially Influence the Selective Costs of mtDNA Mutations. CELLULAR AND MOLECULAR BASIS OF MITOCHONDRIAL INHERITANCE 2019; 231:51-74. [DOI: 10.1007/102_2018_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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29
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Molinaro L, Pagani L. Human evolutionary history of Eastern Africa. Curr Opin Genet Dev 2018; 53:134-139. [DOI: 10.1016/j.gde.2018.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/31/2018] [Accepted: 10/08/2018] [Indexed: 01/16/2023]
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30
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Beadnell TC, Scheid AD, Vivian CJ, Welch DR. Roles of the mitochondrial genetics in cancer metastasis: not to be ignored any longer. Cancer Metastasis Rev 2018; 37:615-632. [PMID: 30542781 PMCID: PMC6358502 DOI: 10.1007/s10555-018-9772-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mitochondrial DNA (mtDNA) encodes for only a fraction of the proteins that are encoded within the nucleus, and therefore has typically been regarded as a lesser player in cancer biology and metastasis. Accumulating evidence, however, supports an increased role for mtDNA impacting tumor progression and metastatic susceptibility. Unfortunately, due to this delay, there is a dearth of data defining the relative contributions of specific mtDNA polymorphisms (SNP), which leads to an inability to effectively use these polymorphisms to guide and enhance therapeutic strategies and diagnosis. In addition, evidence also suggests that differences in mtDNA impact not only the cancer cells but also the cells within the surrounding tumor microenvironment, suggesting a broad encompassing role for mtDNA polymorphisms in regulating the disease progression. mtDNA may have profound implications in the regulation of cancer biology and metastasis. However, there are still great lengths to go to understand fully its contributions. Thus, herein, we discuss the recent advances in our understanding of mtDNA in cancer and metastasis, providing a framework for future functional validation and discovery.
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Affiliation(s)
- Thomas C Beadnell
- Department of Cancer Biology, The Kansas University Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA
| | - Adam D Scheid
- Department of Cancer Biology, The Kansas University Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA
| | - Carolyn J Vivian
- Department of Cancer Biology, The Kansas University Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA
| | - Danny R Welch
- Department of Cancer Biology, The Kansas University Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA.
- The University of Kansas Cancer Center, 3901 Rainbow Blvd., Kansas City, KS, 66160, USA.
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31
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Wright JL, Wasef S, Heupink TH, Westaway MC, Rasmussen S, Pardoe C, Fourmile GG, Young M, Johnson T, Slade J, Kennedy R, Winch P, Pappin M, Wales T, Bates W“B, Hamilton S, Whyman N, van Holst Pellekaan S, McAllister PJ, Taçon PS, Curnoe D, Li R, Millar C, Subramanian S, Willerslev E, Malaspinas AS, Sikora M, Lambert DM. Ancient nuclear genomes enable repatriation of Indigenous human remains. SCIENCE ADVANCES 2018; 4:eaau5064. [PMID: 30585290 PMCID: PMC6300400 DOI: 10.1126/sciadv.aau5064] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 11/20/2018] [Indexed: 05/21/2023]
Abstract
After European colonization, the ancestral remains of Indigenous people were often collected for scientific research or display in museum collections. For many decades, Indigenous people, including Native Americans and Aboriginal Australians, have fought for their return. However, many of these remains have no recorded provenance, making their repatriation very difficult or impossible. To determine whether DNA-based methods could resolve this important problem, we sequenced 10 nuclear genomes and 27 mitogenomes from ancient pre-European Aboriginal Australians (up to 1540 years before the present) of known provenance and compared them to 100 high-coverage contemporary Aboriginal Australian genomes, also of known provenance. We report substantial ancient population structure showing strong genetic affinities between ancient and contemporary Aboriginal Australian individuals from the same geographic location. Our findings demonstrate the feasibility of successfully identifying the origins of unprovenanced ancestral remains using genomic methods.
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Affiliation(s)
- Joanne L. Wright
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
| | - Sally Wasef
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
| | - Tim H. Heupink
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
- Global Health Institute, Epidemiology and Social Medicine, University of Antwerp, Belgium
| | - Michael C. Westaway
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
| | - Simon Rasmussen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Colin Pardoe
- Department of Archaeology and Natural History, Australian National University, Canberra, ACT, Australia
| | | | - Michael Young
- Barkandji/Paakantyi Elder, Red Cliffs, VIC, Australia
| | - Trish Johnson
- Barkandji/Paakantyi Elder, Pooncarie, NSW, Australia
| | - Joan Slade
- Ngiyampaa Elder, Ivanhoe, NSW, Australia
| | | | - Patsy Winch
- Mutthi Mutthi Elder, Balranald, NSW, Australia
| | - Mary Pappin
- Mutthi Mutthi Elder, Broken Hill, NSW, Australia
| | - Tapij Wales
- Thanynakwith Elder, Napranum, QLD, Australia
| | | | | | | | - Sheila van Holst Pellekaan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
- School of Biological Sciences, University of Sydney, Sydney, NSW, Australia
| | | | - Paul S.C. Taçon
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
| | - Darren Curnoe
- ARC Centre of Excellence for Australian Biodiversity and Heritage and Paleontology, Geobiology and Earth Archives Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Craig Millar
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Sankar Subramanian
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, UK
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Corresponding author. (M.S.); (D.M.L.)
| | - David M. Lambert
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
- Corresponding author. (M.S.); (D.M.L.)
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32
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Experimental evidence that thermal selection shapes mitochondrial genome evolution. Sci Rep 2018; 8:9500. [PMID: 29934612 PMCID: PMC6015072 DOI: 10.1038/s41598-018-27805-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/04/2018] [Indexed: 12/11/2022] Open
Abstract
Mitochondria are essential organelles, found within eukaryotic cells, which contain their own DNA. Mitochondrial DNA (mtDNA) has traditionally been used in population genetic and biogeographic studies as a maternally-inherited and evolutionary-neutral genetic marker. However, it is now clear that polymorphisms within the mtDNA sequence are routinely non-neutral, and furthermore several studies have suggested that such mtDNA polymorphisms are also sensitive to thermal selection. These observations led to the formulation of the “mitochondrial climatic adaptation” hypothesis, for which all published evidence to date is correlational. Here, we use laboratory-based experimental evolution in the fruit fly, Drosophila melanogaster, to test whether thermal selection can shift population frequencies of two mtDNA haplogroups whose natural frequencies exhibit clinal associations with latitude along the Australian east-coast. We present experimental evidence that the thermal regime in which the laboratory populations were maintained drove changes in haplogroup frequencies across generations. Our results strengthen the emerging view that intra-specific mtDNA variants are sensitive to selection, and suggest spatial distributions of mtDNA variants in natural populations of metazoans might reflect adaptation to climatic environments rather than within-population coalescence and diffusion of selectively-neutral haplotypes across populations.
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33
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Jin Y, Wo Y, Tong H, Song S, Zhang L, Brown RP. Evolutionary analysis of mitochondrially encoded proteins of toad-headed lizards, Phrynocephalus, along an altitudinal gradient. BMC Genomics 2018; 19:185. [PMID: 29510674 PMCID: PMC5840783 DOI: 10.1186/s12864-018-4569-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 02/28/2018] [Indexed: 11/17/2022] Open
Abstract
Background Animals living at high altitude must adapt to environments with hypoxia and low temperatures, but relatively little is known about underlying genetic changes. Toad-headed lizards of the genus Phrynocephalus cover a broad altitudinal gradient of over 4000 m and are useful models for studies of such adaptive responses. In one of the first studies to have considered selection on mitochondrial protein-coding regions in an ectothermic group distributed over such a wide range of environments, we analysed nineteen complete mitochondrial genomes from all Chinese Phrynocephalus (including eight genomes sequenced for the first time). Initial analyses used site and branch-site model (program: PAML) approaches to examine nonsynonymous: synonymous substitution rates across the mtDNA tree. Results Ten positively selected sites were discovered, nine of which corresponded to subunits ND2, ND3, ND4, ND5, and ND6 within the respiratory chain enzyme mitochondrial Complex I (NADH Coenzyme Q oxidoreductase). Four of these sites showed evidence of general long-term selection across the group while the remainder showed evidence of episodic selection across different branches of the tree. Some of these branches corresponded to increases in altitude and/or latitude. Analyses of physicochemical changes in protein structures revealed that residue changes at sites that were under selection corresponded to major functional differences. Analyses of coevolution point to coevolution of selected sites within the ND4 subunit, with key sites associated with proton translocation across the mitochondrial membrane. Conclusions Our results identify mitochondrial Complex I as a target for environment-mediated selection in this group of lizards, a complex that frequently appears to be under selection in other organisms. This makes these lizards good candidates for more detailed future studies of molecular evolution. Electronic supplementary material The online version of this article (10.1186/s12864-018-4569-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuanting Jin
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, 310018, People's Republic of China.
| | - Yubin Wo
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, 310018, People's Republic of China
| | - Haojie Tong
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, 310018, People's Republic of China
| | - Sen Song
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Lixun Zhang
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Richard P Brown
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, L3 3AF, UK
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34
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Skonieczna K, Malyarchuk B, Jawień A, Marszałek A, Banaszkiewicz Z, Jarmocik P, Grzybowski T. Mitogenomic differences between the normal and tumor cells of colorectal cancer patients. Hum Mutat 2018; 39:691-701. [PMID: 29330893 DOI: 10.1002/humu.23402] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 12/18/2017] [Accepted: 01/05/2018] [Indexed: 12/13/2022]
Abstract
So far, a reliable spectrum of mitochondrial DNA mutations in colorectal cancer cells is still unknown, and neither is their significance in carcinogenesis. Indeed, it remains debatable whether mtDNA mutations are "drivers" or "passengers" of colorectal carcinogenesis. Thus, we analyzed 200 mitogenomes from normal and cancer tissues of 100 colorectal cancer patients. Minority variant mutations were detected at the 1% level. We showed that somatic mutations frequently occur in colorectal cancer cells (75%) and are randomly distributed across the mitochondrial genome. Mutational signatures of somatic mitogenome mutations suggest that they might arise through nucleotide deamination due to oxidative stress. The majority of somatic mutations localized within the coding region (in positions not known from the human phylogeny) and was potentially pathogenic to cell metabolism. Further analysis suggested that the relaxation of negative selection in the mitogenomes of colorectal cancer cells may allow accumulation of somatic mutations. Thus, a shift in glucose metabolism from oxidative phosphorylation to glycolysis may create advantageous conditions for accumulation of mtDNA mutations. Considering the fact that the presence of somatic mtDNA mutations was not associated with any clinicopathological features, we suggested that mtDNA somatic mutations are "passengers" rather than the cause of colorectal carcinogenesis.
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Affiliation(s)
- Katarzyna Skonieczna
- Division of Molecular and Forensic Genetics, Department of Forensic Medicine, Faculty of Medicine, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | - Boris Malyarchuk
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Magadan, Russia
| | - Arkadiusz Jawień
- Department of Vascular Surgery and Angiology, Faculty of Medicine, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | - Andrzej Marszałek
- Department of Pathology, Faculty of Medicine, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland.,Department of Tumor Pathology and Prophylaxis, Poznan University of Medical Sciences and Greater Poland Cancer Center, Poznan, Poland
| | - Zbigniew Banaszkiewicz
- Department of Vascular Surgery and Angiology, Faculty of Medicine, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | - Paweł Jarmocik
- Department of Vascular Surgery and Angiology, Faculty of Medicine, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | - Tomasz Grzybowski
- Division of Molecular and Forensic Genetics, Department of Forensic Medicine, Faculty of Medicine, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
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35
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Burr SP, Pezet M, Chinnery PF. Mitochondrial DNA Heteroplasmy and Purifying Selection in the Mammalian Female Germ Line. Dev Growth Differ 2018; 60:21-32. [PMID: 29363102 DOI: 10.1111/dgd.12420] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 12/08/2017] [Indexed: 01/19/2023]
Abstract
Inherited mutations in the mitochondrial (mt)DNA are a major cause of human disease, with approximately 1 in 5000 people affected by one of the hundreds of identified pathogenic mtDNA point mutations or deletions. Due to the severe, and often untreatable, symptoms of many mitochondrial diseases, identifying how these mutations are inherited from one generation to the next has been an area of intense research in recent years. Despite large advances in our understanding of this complex process, many questions remain unanswered, with one of the most hotly debated being whether or not purifying selection acts against pathogenic mutations during germline development.
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Affiliation(s)
- Stephen P Burr
- MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Mikael Pezet
- MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Patrick F Chinnery
- MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
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36
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Sharma I, Sharma V, Khan A, Kumar P, Rai E, Bamezai RNK, Vilar M, Sharma S. Ancient Human Migrations to and through Jammu Kashmir- India were not of Males Exclusively. Sci Rep 2018; 8:851. [PMID: 29339819 PMCID: PMC5770440 DOI: 10.1038/s41598-017-18893-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 12/19/2017] [Indexed: 11/09/2022] Open
Abstract
Jammu and Kashmir (J&K), the Northern most State of India, has been under-represented or altogether absent in most of the phylogenetic studies carried out in literature, despite its strategic location in the Himalayan region. Nonetheless, this region may have acted as a corridor to various migrations to and from mainland India, Eurasia or northeast Asia. The belief goes that most of the migrations post-late-Pleistocene were mainly male dominated, primarily associated with population invasions, where female migration may thus have been limited. To evaluate female-centered migration patterns in the region, we sequenced 83 complete mitochondrial genomes of unrelated individuals belonging to different ethnic groups from the state. We observed a high diversity in the studied maternal lineages, identifying 19 new maternal sub-haplogroups (HGs). High maternal diversity and our phylogenetic analyses suggest that the migrations post-Pleistocene were not strictly paternal, as described in the literature. These preliminary observations highlight the need to carry out an extensive study of the endogamous populations of the region to unravel many facts and find links in the peopling of India.
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Affiliation(s)
- Indu Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, 182320, India
| | - Varun Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, 182320, India
| | - Akbar Khan
- Department of Zoology, University of Jammu, Jammu and Kashmir, 180006, India
| | - Parvinder Kumar
- Department of Zoology, University of Jammu, Jammu and Kashmir, 180006, India
- Institute of Human Genetics, University of Jammu, Jammu and Kashmir, 180006, India
| | - Ekta Rai
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, 182320, India
| | | | - Miguel Vilar
- The Genographic Project, National Geographic Society, Washington, DC, 20036, USA
| | - Swarkar Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, 182320, India.
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37
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Burden CJ, Wei Y. Mutation in populations governed by a Galton-Watson branching process. Theor Popul Biol 2017; 120:52-61. [PMID: 29233675 DOI: 10.1016/j.tpb.2017.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 12/01/2017] [Accepted: 12/04/2017] [Indexed: 11/25/2022]
Abstract
A population genetics model based on a multitype branching process, or equivalently a Galton-Watson branching process for multiple alleles, is presented. The diffusion limit forward Kolmogorov equation is derived for the case of neutral mutations. The asymptotic stationary solution is obtained and has the property that the extant population partitions into subpopulations whose relative sizes are determined by mutation rates. An approximate time-dependent solution is obtained in the limit of low mutation rates. This solution has the property that the system undergoes a rapid transition from a drift-dominated phase to a mutation-dominated phase in which the distribution collapses onto the asymptotic stationary distribution. The changeover point of the transition is determined by the per-generation growth factor and mutation rate. The approximate solution is confirmed using numerical simulations.
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Affiliation(s)
- Conrad J Burden
- Mathematical Sciences Institute, Australian National University, Canberra, Australia; Research School of Biology, Australian National University, Canberra, Australia.
| | - Yi Wei
- Mathematical Sciences Institute, Australian National University, Canberra, Australia.
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38
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Melvin RG, Ballard JWO. Cellular and population level processes influence the rate, accumulation and observed frequency of inherited and somatic mtDNA mutations. Mutagenesis 2017; 32:323-334. [PMID: 28521046 DOI: 10.1093/mutage/gex004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mitochondria are found in all animals and have the unique feature of containing multiple copies of their own small, circular DNA genome (mtDNA). The rate and pattern of mutation accumulation in the mtDNA are influenced by molecular, cellular and population level processes. We distinguish between inherited and somatic mtDNA mutations and review evidence for the often-made assumption that mutations accumulate at a higher rate in mtDNA than in nuclear DNA (nDNA). We conclude that the whole genome mutation accumulation rate is higher for mtDNA than for nDNA but include the caveat that rates overlap considerably between the individual mtDNA- and nDNA-encoded genes. Next, we discuss the postulated causal mechanisms for the high rate of mtDNA mutation accumulation in both inheritance and in somatic cells. Perhaps unexpectedly, mtDNA is resilient to many mutagens of nDNA but is prone to errors of replication. We then consider the influence of maternal inheritance, recombination and selection on the observed accumulation pattern of inherited mtDNA mutations. Finally, we discuss environmental influences of temperature and diet on the observed frequency of inherited and somatic mtDNA mutations. We conclude that it is necessary to understand the cellular processes to fully interpret the pattern of mutations and how they influence our interpretations of evolution and disease.
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Affiliation(s)
- Richard G Melvin
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - John William O Ballard
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
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39
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Venter M, van der Westhuizen FH, Elson JL. The aetiology of cardiovascular disease: a role for mitochondrial DNA? Cardiovasc J Afr 2017; 29:122-132. [PMID: 28906532 PMCID: PMC6009096 DOI: 10.5830/cvja-2017-037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 07/17/2017] [Indexed: 01/03/2023] Open
Abstract
Cardiovascular disease (CVD) is a world-wide cause of mortality in humans and its incidence is on the rise in Africa. In this review, we discuss the putative role of mitochondrial dysfunction in the aetiology of CVD and consequently identify mitochondrial DNA (mtDNA) variation as a viable genetic risk factor to be considered. We then describe the contribution and pitfalls of several current approaches used when investigating mtDNA in relation to complex disease. We also propose an alternative approach, the adjusted mutational load hypothesis, which would have greater statistical power with cohorts of moderate size, and is less likely to be affected by population stratification. We therefore address some of the shortcomings of the current haplogroup association approach. Finally, we discuss the unique challenges faced by studies done on African populations, and recommend the most viable methods to use when investigating mtDNA variation in CVD and other common complex disease.
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Affiliation(s)
- Marianne Venter
- Human Metabolomics, North-West University, Potchefstroom, South Africa.
| | | | - Joanna L Elson
- Human Metabolomics, North-West University, Potchefstroom, South Africa; Institute of Genetic Medicine, Newcastle University, United Kingdom
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40
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MtDNA genomes reveal a relaxation of selective constraints in low-BMI individuals in a Uyghur population. Hum Genet 2017; 136:1353-1362. [DOI: 10.1007/s00439-017-1829-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/15/2017] [Indexed: 10/19/2022]
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41
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Mizuno F, Wang L, Sugiyama S, Kurosaki K, Granados J, Gomez-Trejo C, Acuña-Alonzo V, Ueda S. Characterization of complete mitochondrial genomes of indigenous Mayans in Mexico. Ann Hum Biol 2017; 44:652-658. [PMID: 28724311 DOI: 10.1080/03014460.2017.1358393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
BACKGROUND The authors have previously published the complete mitochondrial genome (mitogenome) sequences of two indigenous Mesoamerican populations, Mazahua (n = 25) and Zapotec (n = 88). METHODS This study determined the complete mitogenome sequences of nine unrelated individuals from the indigenous Maya population living in Mexico. RESULTS Their mitogenome sequences could be classified into either of the haplogroups A2 and C1. Surprisingly, there were no mitogenome sequences (haplotypes) that the Maya, Mazahua, and Zapotec people share in common. CONCLUSIONS This indicates that no genetic exchange, at least matrilineally, has occurred among them.
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Affiliation(s)
- Fuzuki Mizuno
- a Department of Legal Medicine , Toho University School of Medicine , Ota-ku , Tokyo , Japan.,b Department of Biological Sciences, Graduate School of Science , The University of Tokyo , Bunkyo-ku , Tokyo , Japan
| | - Li Wang
- c School of Medicine, Hangzhou Normal University School of Medicine , Hangzhou , Zhejiang , China
| | - Saburo Sugiyama
- d Graduate School of International Cultural Studies, Cultural Symbiosis Research Institute , Aichi Prefectural University , Nagakute , Aichi , Japan
| | - Kunihiko Kurosaki
- a Department of Legal Medicine , Toho University School of Medicine , Ota-ku , Tokyo , Japan
| | - Julio Granados
- e Department of Transplants , Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán , Mexico City , Mexico
| | - Celta Gomez-Trejo
- f Molecular Genetics Laboratory , National Institute of Anthropology and History , Mexico City , Mexico
| | - Víctor Acuña-Alonzo
- f Molecular Genetics Laboratory , National Institute of Anthropology and History , Mexico City , Mexico
| | - Shintaroh Ueda
- b Department of Biological Sciences, Graduate School of Science , The University of Tokyo , Bunkyo-ku , Tokyo , Japan.,c School of Medicine, Hangzhou Normal University School of Medicine , Hangzhou , Zhejiang , China
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42
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Experimental Support That Natural Selection Has Shaped the Latitudinal Distribution of Mitochondrial Haplotypes in Australian Drosophila melanogaster. Mol Biol Evol 2017. [DOI: 10.1093/molbev/msx184] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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43
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Nagle N, van Oven M, Wilcox S, van Holst Pellekaan S, Tyler-Smith C, Xue Y, Ballantyne KN, Wilcox L, Papac L, Cooke K, van Oorschot RAH, McAllister P, Williams L, Kayser M, Mitchell RJ. Aboriginal Australian mitochondrial genome variation - an increased understanding of population antiquity and diversity. Sci Rep 2017; 7:43041. [PMID: 28287095 PMCID: PMC5347126 DOI: 10.1038/srep43041] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/17/2017] [Indexed: 01/06/2023] Open
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.
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Affiliation(s)
- Nano Nagle
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Mannis van Oven
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, The Netherlands
| | - Stephen Wilcox
- Australian Genome Research Facility, Melbourne, Victoria, Australia
| | - Sheila van Holst Pellekaan
- Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, Australia.,School of Biological Sciences, University of Sydney, Sydney, Australia
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Kaye N Ballantyne
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, The Netherlands.,Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Melbourne, Victoria, Australia
| | - Leah Wilcox
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Luka Papac
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Karen Cooke
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Roland A H van Oorschot
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Melbourne, Victoria, Australia
| | | | - Lesley Williams
- Community Elder and Cultural Advisor, Brisbane, Queensland, Australia
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, The Netherlands
| | - R John Mitchell
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
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44
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Massey SE. Strong Amerindian Mitonuclear Discordance in Puerto Rican Genomes Suggests Amerindian Mitochondrial Benefit. Ann Hum Genet 2017; 81:59-77. [DOI: 10.1111/ahg.12185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 01/06/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Steven E. Massey
- Biology Department; University of Puerto Rico - Rio Piedras; PO Box 23360 San Juan Puerto Rico 00931
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45
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Ben Slimen H, Schaschl H, Knauer F, Suchentrunk F. Selection on the mitochondrial ATP synthase 6 and the NADH dehydrogenase 2 genes in hares (Lepus capensis L., 1758) from a steep ecological gradient in North Africa. BMC Evol Biol 2017; 17:46. [PMID: 28173765 PMCID: PMC5297179 DOI: 10.1186/s12862-017-0896-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 01/26/2017] [Indexed: 11/30/2022] Open
Abstract
Background Recent studies of selection on mitochondrial (mt) OXPHOS genes suggest adaptation due mainly to environmental variation. In this context, Tunisian hares that display several external phenotypes with phylogenetically rather homogenous gene pool and shallow population structure provide a good precondition to detect positive selection on mt genes related to environmental/climatic variation, specifically ambient temperature and precipitation. Results We used codon-based methods along with population genetic data to test for positive selection on ATPase synthase 6 (ATP6) and NADH dehydrogenase 2 (ND2) of cape hares (Lepus capensis) collected along a steep ecological gradient in Tunisia. We found significantly higher differentiation at the ATP6 locus across Tunisia, with sub-humid Mediterranean, semi-arid, and arid Sahara climate than for fourteen unlinked supposedly neutrally evolving nuclear microsatellites and mt control region sequences. This suggested positive selection on ATP6 sequences, which was confirmed by several codon-based tests for one sequence site that together with a second site translated into four different amino acids. Positive selection on ND2 sequences was also confirmed by several codon-based tests. The corresponding frequencies of the two most prevalent variants at each locus varied significantly across climate regions, and our logistic general linear models of occurrence of those proteins indicated significant effects of mean annual temperature for ATP6 and mean minimum temperature of the coldest month of the year for ND2, independent of geographical location, annual precipitation, and the respective co-occurring protein at the second locus. Moreover, presence of the ancestral ATP6 protein, as inferred from phylogenetic networks, was positively affected by the simultaneous presence of the derived ND2 protein and vice versa, independent of temperature, precipitation, or geographic location. Finally, we obtained a significant coevolution signal for the ancestral ATP6 and derived ND2 sequences and vice versa. Conclusions positive selection was strongly suggested by the population genetic approach and the codon-based tests in both mtDNA genes. Moreover, the two most prevalent proteins at the ATP6 locus were distributed at significantly varying frequencies across the study area with a significant effect of mean annual temperature on the occurrence of the ATP6 proteins independent of geographical coordinates and the co-occuring ND2 protein variant. For ND2, occurrence of the two most frequent protein variants was significantly influenced by the mean minimum temperature of the coldest month, independent of the co-occurring ATP6 protein variant and geographical coordinates. This strongly suggests direct involvement of ambient temperature in the adaptation of the studied mtOXPHOS genes. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0896-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hichem Ben Slimen
- UR Génomique des Insectes Ravageurs des Cultures d'Intérêt Agronomique (GIRC), Université de Tunis El-Manar, 2092, El Manar, Tunisia. .,Institut Supérieur de Biotechnologie de Béja, Beja, 9000, Tunisia.
| | - Helmut Schaschl
- Department of Anthropology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Felix Knauer
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160, Vienna, Austria
| | - Franz Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160, Vienna, Austria
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46
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Mitochondrial DNA diversity of present-day Aboriginal Australians and implications for human evolution in Oceania. J Hum Genet 2016; 62:343-353. [PMID: 27904152 DOI: 10.1038/jhg.2016.147] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/21/2016] [Accepted: 10/27/2016] [Indexed: 12/30/2022]
Abstract
Aboriginal Australians are one of the more poorly studied populations from the standpoint of human evolution and genetic diversity. Thus, to investigate their genetic diversity, the possible date of their ancestors' arrival and their relationships with neighboring populations, we analyzed mitochondrial DNA (mtDNA) diversity in a large sample of Aboriginal Australians. Selected mtDNA single-nucleotide polymorphisms and the hypervariable segment haplotypes were analyzed in 594 Aboriginal Australians drawn from locations across the continent, chiefly from regions not previously sampled. Most (~78%) samples could be assigned to mtDNA haplogroups indigenous to Australia. The indigenous haplogroups were all ancient (with estimated ages >40 000 years) and geographically widespread across the continent. The most common haplogroup was P (44%) followed by S (23%) and M42a (9%). There was some geographic structure at the haplotype level. The estimated ages of the indigenous haplogroups range from 39 000 to 55 000 years, dates that fit well with the estimated date of colonization of Australia based on archeological evidence (~47 000 years ago). The distribution of mtDNA haplogroups in Australia and New Guinea supports the hypothesis that the ancestors of Aboriginal Australians entered Sahul through at least two entry points. The mtDNA data give no support to the hypothesis of secondary gene flow into Australia during the Holocene, but instead suggest long-term isolation of the continent.
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47
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Phylogenetic and population-based approaches to mitogenome variation do not support association with male infertility. J Hum Genet 2016; 62:361-371. [PMID: 27904151 DOI: 10.1038/jhg.2016.130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/26/2016] [Accepted: 09/29/2016] [Indexed: 11/08/2022]
Abstract
Infertility has a complex multifactorial etiology and a high prevalence worldwide. Several studies have pointed to variation in the mitochondrial DNA (mtDNA) molecule as a factor responsible for the different disease phenotypes related to infertility. We analyzed 53 mitogenomes of infertile males from Galicia (northwest Spain), and these haplotypes were meta-analyzed phylogenetically with 43 previously reported from Portugal. Taking advantage of the large amount of information available, we additionally carried out association tests between patient mtDNA single-nucleotide polymorphisms (mtSNPs) and haplogroups against Iberian matched controls retrieved from The 1000 Genomes Project and the literature. Phylogenetic and association analyses did not reveal evidence of association between mtSNPs/haplogroups and infertility. Ratios and patterns in patients of nonsynonymous/synonymous changes, and variation at homoplasmic, heteroplasmic and private variants, fall within expected values for healthy individuals. Moreover, the haplogroup background of patients was variable and fits well with patterns typically observed in healthy western Europeans. We did not find evidence of association of mtSNPs or haplogroups pointing to a role for mtDNA in male infertility. A thorough review of the literature on mtDNA variation and infertility revealed contradictory findings and methodological and theoretical problems that overall undermine previous positive findings.
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48
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Gnaiger E, Boushel R, Søndergaard H, Munch-Andersen T, Damsgaard R, Hagen C, Díez-Sánchez C, Ara I, Wright-Paradis C, Schrauwen P, Hesselink M, Calbet JAL, Christiansen M, Helge JW, Saltin B. Mitochondrial coupling and capacity of oxidative phosphorylation in skeletal muscle of Inuit and Caucasians in the arctic winter. Scand J Med Sci Sports 2016; 25 Suppl 4:126-34. [PMID: 26589126 DOI: 10.1111/sms.12612] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2015] [Indexed: 01/02/2023]
Abstract
During evolution, mitochondrial DNA haplogroups of arctic populations may have been selected for lower coupling of mitochondrial respiration to ATP production in favor of higher heat production. We show that mitochondrial coupling in skeletal muscle of traditional and westernized Inuit habituating northern Greenland is identical to Danes of western Europe haplogroups. Biochemical coupling efficiency was preserved across variations in diet, muscle fiber type, and uncoupling protein-3 content. Mitochondrial phenotype displayed plasticity in relation to lifestyle and environment. Untrained Inuit and Danes had identical capacities to oxidize fat substrate in arm muscle, which increased in Danes during the 42 days of acclimation to exercise, approaching the higher level of the Inuit hunters. A common pattern emerges of mitochondrial acclimatization and evolutionary adaptation in humans at high latitude and high altitude where economy of locomotion may be optimized by preservation of biochemical coupling efficiency at modest mitochondrial density, when submaximum performance is uncoupled from VO2max and maximum capacities of oxidative phosphorylation.
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Affiliation(s)
- E Gnaiger
- Department of Visceral, Transplant and Thoracic Surgery, D. Swarovski Research Laboratory, Medical University of Innsbruck, Innsbruck, Austria
| | - R Boushel
- The Copenhagen Muscle Research Centre, Copenhagen, Denmark.,School of Kinesiology, University of British Columbia, Vancouver, BC, Canada
| | - H Søndergaard
- The Copenhagen Muscle Research Centre, Copenhagen, Denmark
| | | | - R Damsgaard
- The Copenhagen Muscle Research Centre, Copenhagen, Denmark
| | - C Hagen
- National Serum Institute, Copenhagen, Denmark
| | - C Díez-Sánchez
- Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, Spain
| | - I Ara
- GENUD Toledo Research Group, University of Castilla-La Mancha, Toledo, Spain
| | - C Wright-Paradis
- Department of Exercise Science, Concordia University, Montreal, QC, Canada
| | - P Schrauwen
- NUTRIM - School for Nutrition, Toxicology and Metabolism, Department of Human Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - M Hesselink
- NUTRIM - School for Nutrition, Toxicology and Metabolism, Department of Human Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - J A L Calbet
- Department of Physical Education, Research Institute of Biomedical and Health Sciences (IUIBS), University of Las Palmas de Gran Canaria, Las Palmas, Spain
| | | | - J W Helge
- The Copenhagen Muscle Research Centre, Copenhagen, Denmark.,X-Lab, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - B Saltin
- The Copenhagen Muscle Research Centre, Copenhagen, Denmark
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49
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MtDNA analysis reveals enriched pathogenic mutations in Tibetan highlanders. Sci Rep 2016; 6:31083. [PMID: 27498855 PMCID: PMC4976311 DOI: 10.1038/srep31083] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 07/13/2016] [Indexed: 12/21/2022] Open
Abstract
Tibetan highlanders, including Tibetans, Monpas, Lhobas, Dengs and Sherpas, are considered highly adaptive to severe hypoxic environments. Mitochondrial DNA (mtDNA) might be important in hypoxia adaptation given its role in coding core subunits of oxidative phosphorylation. In this study, we employed 549 complete highlander mtDNA sequences (including 432 random samples) to obtain a comprehensive view of highlander mtDNA profile. In the phylogeny of a total of 36,914 sequences, we identified 21 major haplogroups representing founding events of highlanders, most of which were coalesced in 10 kya. Through founder analysis, we proposed a three-phase model of colonizing the plateau, i.e., pre-LGM Time (30 kya, 4.68%), post-LGM Paleolithic Time (16.8 kya, 29.31%) and Neolithic Time (after 8 kya, 66.01% in total). We observed that pathogenic mutations occurred far more frequently in 22 highlander-specific lineages (five lineages carrying two pathogenic mutations and six carrying one) than in the 6,857 haplogroups of all the 36,914 sequences (P = 4.87 × 10−8). Furthermore, the number of possible pathogenic mutations carried by highlanders (in average 3.18 ± 1.27) were significantly higher than that in controls (2.82 ± 1.40) (P = 1.89 × 10−4). Considering that function-altering and pathogenic mutations are enriched in highlanders, we therefore hypothesize that they may have played a role in hypoxia adaptation.
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Niedzwiecka K, Kabala AM, Lasserre JP, Tribouillard-Tanvier D, Golik P, Dautant A, di Rago JP, Kucharczyk R. Yeast models of mutations in the mitochondrial ATP6 gene found in human cancer cells. Mitochondrion 2016; 29:7-17. [PMID: 27083309 DOI: 10.1016/j.mito.2016.04.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 04/08/2016] [Accepted: 04/08/2016] [Indexed: 01/09/2023]
Abstract
Since the discovery of somatic mtDNA mutations in tumor cells, multiple studies have focused on establishing a causal relationship between those changes and alterations in energy metabolism, a hallmark of cancer cells. Yet the consequences of these mutations on mitochondrial function remain largely unknown. In this study, Saccharomyces cerevisiae has been used as a model to investigate the functional consequences of four cancer-associated missense mutations (8914C>A, 8932C>T, 8953A>G, 9131T>C) found in the mitochondrial MT-ATP6 gene. This gene encodes the a-subunit of F1FO-ATP synthase, which catalyzes the last steps of ATP production in mitochondria. Although the four studied mutations affected well-conserved residues of the a-subunit, only one of them (8932C>T) had a significant impact on mitochondrial function, due to a less efficient incorporation of the a-subunit into ATP synthase. Our findings indicate that these ATP6 genetic variants found in human tumors are neutral mitochondrial genome substitutions with a limited, if any, impact on the energetic function of mitochondria.
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Affiliation(s)
- Katarzyna Niedzwiecka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Magdalena Kabala
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux Cedex, France
| | - Jean-Paul Lasserre
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux Cedex, France
| | - Déborah Tribouillard-Tanvier
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux Cedex, France
| | - Pawel Golik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Poland
| | - Alain Dautant
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux Cedex, France
| | - Jean-Paul di Rago
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux Cedex, France
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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