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Edmands S. Mother's Curse effects on lifespan and aging. FRONTIERS IN AGING 2024; 5:1361396. [PMID: 38523670 PMCID: PMC10957651 DOI: 10.3389/fragi.2024.1361396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 02/20/2024] [Indexed: 03/26/2024]
Abstract
The Mother's Curse hypothesis posits that mothers curse their sons with harmful mitochondria, because maternal mitochondrial inheritance makes selection blind to mitochondrial mutations that harm only males. As a result, mitochondrial function may be evolutionarily optimized for females. This is an attractive explanation for ubiquitous sex differences in lifespan and aging, given the prevalence of maternal mitochondrial inheritance and the established relationship between mitochondria and aging. This review outlines patterns expected under the hypothesis, and traits most likely to be affected, chiefly those that are sexually dimorphic and energy intensive. A survey of the literature shows that evidence for Mother's Curse is limited to a few taxonomic groups, with the strongest support coming from experimental crosses in Drosophila. Much of the evidence comes from studies of fertility, which is expected to be particularly vulnerable to male-harming mitochondrial mutations, but studies of lifespan and aging also show evidence of Mother's Curse effects. Despite some very compelling studies supporting the hypothesis, the evidence is quite patchy overall, with contradictory results even found for the same traits in the same taxa. Reasons for this scarcity of evidence are discussed, including nuclear compensation, factors opposing male-specific mutation load, effects of interspecific hybridization, context dependency and demographic effects. Mother's Curse effects may indeed contribute to sex differences, but the complexity of other contributing factors make Mother's Curse a poor general predictor of sex-specific lifespan and aging.
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Affiliation(s)
- Suzanne Edmands
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
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Havaš Auguštin D, Šarac J, Reidla M, Tamm E, Grahovac B, Kapović M, Novokmet N, Rudan P, Missoni S, Marjanović D, Korolija M. Refining the Global Phylogeny of Mitochondrial N1a, X, and HV2 Haplogroups Based on Rare Mitogenomes from Croatian Isolates. Genes (Basel) 2023; 14:1614. [PMID: 37628665 PMCID: PMC10454736 DOI: 10.3390/genes14081614] [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: 06/29/2023] [Revised: 07/28/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial DNA (mtDNA) has been used for decades as a predominant tool in population genetics and as a valuable addition to forensic genetic research, owing to its unique maternal inheritance pattern that enables the tracing of individuals along the maternal lineage across numerous generations. The dynamic interplay between evolutionary forces, primarily genetic drift, bottlenecks, and the founder effect, can exert significant influence on genetic profiles. Consequently, the Adriatic islands have accumulated a subset of lineages that exhibits remarkable absence or rarity within other European populations. This distinctive genetic composition underscores the islands' potential as a significant resource in phylogenetic research, with implications reaching beyond regional boundaries to contribute to a global understanding. In the initial attempt to expand the mitochondrial forensic database of the Croatian population with haplotypes from small isolated communities, we sequenced mitogenomes of rare haplogroups from different Croatian island and mainland populations using next-generation sequencing (NGS). In the next step and based on the obtained results, we refined the global phylogeny of haplogroup N1a, HV2, and X by analyzing rare haplotypes, which are absent from the current phylogenetic tree. The trees were based on 16 novel and 52 previously published samples, revealing completely novel branches in the X and HV2 haplogroups and a new European cluster in the ancestral N1a variant, previously believed to be an exclusively African-Asian haplogroup. The research emphasizes the importance of investigating geographically isolated populations and their unique characteristics within a global context.
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Affiliation(s)
- Dubravka Havaš Auguštin
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia; (D.H.A.)
- Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Jelena Šarac
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia; (D.H.A.)
- Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Maere Reidla
- Institute of Genomics, University of Tartu, 50090 Tartu, Estonia
| | - Erika Tamm
- Institute of Genomics, University of Tartu, 50090 Tartu, Estonia
| | | | | | | | - Pavao Rudan
- Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Saša Missoni
- Institute for Anthropological Research, 10000 Zagreb, Croatia
- Faculty of Dental Medicine and Health, J. J. Strossmayer University, 31000 Osijek, Croatia
| | - Damir Marjanović
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia; (D.H.A.)
- Institute for Anthropological Research, 10000 Zagreb, Croatia
- Genetics and Bioengineering Department, International Burch University, 71000 Sarajevo, Bosnia and Herzegovina
| | - Marina Korolija
- Forensic Science Centre “Ivan Vučetić”, Ministry of the Interior, 10000 Zagreb, Croatia
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Avila E, Speransa PA, Lindholz CG, Kahmann A, Alho CS. Haplotype distribution in a forensic full mtDNA genome database of admixed Southern Brazilians and its association with self-declared ancestry and pigmentation traits. Forensic Sci Int Genet 2021; 57:102650. [PMID: 34972071 DOI: 10.1016/j.fsigen.2021.102650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/01/2021] [Indexed: 11/04/2022]
Abstract
BACKGROUND The advent of massively parallel sequencing (MPS) applications focused on the generation of forensic-quality full mitochondrial genome sequences led to a popularization of the technique on a global scale. However, the lack of forensic-graded population databases has refrained a wider adoption of full genome sequences as the industry standard, despite its better discrimination capacity of individual maternal lineages. PURPOSE This work describes a forensic-oriented full mtDNA genome database comprised of 480 samples from a Southern Brazilian population. METHODS A collection of mitochondrial sequences were obtained from low-pass, full genome DNA sequencing results. The complete sample set was evaluated regarding haplotype composition and distribution. Summary statistics and forensic parameters were calculated and are presented for the database, with detailed information concerning the impact of removing genetic information in the form of specific variants or increasingly larger genomic regions. Interpopulational analysis comparing haplotypical diversity in Brazilian and 26 worldwide populations was also performed. The association between mitochondrial genetic variability and phenotypic diversity was also evaluated in populations, with self-declared ancestry and three distinct phenotypic pigmentation traits (eyes, skin and hair colors) as parameters. RESULTS The presented database can be used to evaluate mitochondrial-related genetic evidence, providing LR values of up to 20,465 for unobserved haplotypes. Haplotype distribution in Southern Brazil seems to be different than the remaining of the country, with a larger contribution of maternal lines with European origin. Despite association can be found between lighter and darker phenotypes or self-declared ancestry and haplotype distribution, prediction models cannot be reliably proposed due to the admixed nature of the Brazilian population. CONCLUSIONS The proposed database provides a basis for statistical calculation and frequency estimation of full mitochondrial genomes, and can be part of an integrated, representative, national database comprising most of the genetic diversity of maternal lineages in the country.
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Affiliation(s)
- Eduardo Avila
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Technical Scientific Section, Federal Police Department in Rio Grande do Sul State, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil.
| | - Pietro Augusto Speransa
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Catieli Gobetti Lindholz
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Alessandro Kahmann
- National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil; Institute of Mathematics, Statistics and Physics, Federal University of Rio Grande, Rio Grande, RS, Brazil.
| | - Clarice Sampaio Alho
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil.
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Al Smadi MA, Hammadeh ME, Solomayer E, Batiha O, Altalib MM, Jahmani MY, Shboul MA, Nusair B, Amor H. Impact of Mitochondrial Genetic Variants in ND1, ND2, ND5, and ND6 Genes on Sperm Motility and Intracytoplasmic Sperm Injection (ICSI) Outcomes. Reprod Sci 2021; 28:1540-1555. [PMID: 33475980 PMCID: PMC8076152 DOI: 10.1007/s43032-020-00449-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/29/2020] [Indexed: 11/30/2022]
Abstract
Sperm mitochondrial dysfunction causes the generation of an insufficient amount of energy needed for sperm motility. This will affect sperm fertilization capacity, and thus, most asthenozoospermic men usually require assisted reproductive techniques. The etiology of asthenozoospermia remains largely unknown. The current study aimed to investigate the effect of mitochondrial genetic variants on sperm motility and intracytoplasmic sperm injection (ICSI) outcomes. A total of 150 couples from the ICSI cycle were enrolled in this study. One hundred five of the male partners were asthenozoospermic patients, and they were subdivided into three groups according to their percentage of sperm motility, while forty-five of the male partners were normozoospermic. Genetic variants were screened using direct Sanger's sequencing in four mitochondrial genes (nicotinamide adenine dinucleotide hydrogen (NADH) dehydrogenase 1 (ND1), NADH dehydrogenase 2 (ND2), NADH dehydrogenase 5 (ND5), and NADH dehydrogenase 6 (ND6)). We identified three significant variants: 13708G>A (rs28359178) in ND5, 4216T>C (rs1599988) in ND1, and a novel 12506T>A in ND5 with P values 0.006, 0.036, and 0.013, respectively. The medians of sperm motility, fertilization rate, embryo cleavage score, and embryo quality score were significantly different between men showing 4216T>C, 12506T>A, 13708G>A and wild type, Mann-Whitney P values for the differences in the medians were < 0.05 in all of them. The results from this study suggest that 13708G>A, 12506T>A, and 4216 T>C variants in sperm mitochondrial DNA negatively affect sperm motility and ICSI outcomes.
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Affiliation(s)
- Mohammad A Al Smadi
- Department of Obstetrics & Gynecology, Reproductive Medicine Unit, Saarland University, Homburg, Germany.
| | - Mohamad Eid Hammadeh
- Department of Obstetrics & Gynecology, Reproductive Medicine Unit, Saarland University, Homburg, Germany
| | - Erich Solomayer
- Department of Obstetrics & Gynecology, Reproductive Medicine Unit, Saarland University, Homburg, Germany
| | - Osamah Batiha
- Department of Biotechnology & Genetic Engineering, Jordan University of Science and Technology, Irbid, Jordan
| | | | - Mohammad Y Jahmani
- Department of Obstetrics & Gynecology, Reproductive Medicine Unit, Saarland University, Homburg, Germany
| | - Mohammad A Shboul
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan
| | - Bassam Nusair
- Reproductive Endocrinology and IVF Unit, King Hussein Medical Centre, Amman, Jordan
| | - Houda Amor
- Department of Obstetrics & Gynecology, Reproductive Medicine Unit, Saarland University, Homburg, Germany
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Boguenet M, Bouet PE, Spiers A, Reynier P, May-Panloup P. Mitochondria: their role in spermatozoa and in male infertility. Hum Reprod Update 2021; 27:697-719. [PMID: 33555313 DOI: 10.1093/humupd/dmab001] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/22/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The best-known role of spermatozoa is to fertilize the oocyte and to transmit the paternal genome to offspring. These highly specialized cells have a unique structure consisting of all the elements absolutely necessary to each stage of fertilization and to embryonic development. Mature spermatozoa are made up of a head with the nucleus, a neck, and a flagellum that allows motility and that contains a midpiece with a mitochondrial helix. Mitochondria are central to cellular energy production but they also have various other functions. Although mitochondria are recognized as essential to spermatozoa, their exact pathophysiological role and their functioning are complex. Available literature relative to mitochondria in spermatozoa is dense and contradictory in some cases. Furthermore, mitochondria are only indirectly involved in cytoplasmic heredity as their DNA, the paternal mitochondrial DNA, is not transmitted to descendants. OBJECTIVE AND RATIONAL This review aims to summarize available literature on mitochondria in spermatozoa, and, in particular, that with respect to humans, with the perspective of better understanding the anomalies that could be implicated in male infertility. SEARCH METHODS PubMed was used to search the MEDLINE database for peer-reviewed original articles and reviews pertaining to human spermatozoa and mitochondria. Searches were performed using keywords belonging to three groups: 'mitochondria' or 'mitochondrial DNA', 'spermatozoa' or 'sperm' and 'reactive oxygen species' or 'calcium' or 'apoptosis' or signaling pathways'. These keywords were combined with other relevant search phrases. References from these articles were used to obtain additional articles. OUTCOMES Mitochondria are central to the metabolism of spermatozoa and they are implicated in energy production, redox equilibrium and calcium regulation, as well as apoptotic pathways, all of which are necessary for flagellar motility, capacitation, acrosome reaction and gametic fusion. In numerous cases, alterations in one of the aforementioned functions could be linked to a decline in sperm quality and/or infertility. The link between the mitochondrial genome and the quality of spermatozoa appears to be more complex. Although the quantity of mtDNA, and the existence of large-scale deletions therein, are inversely correlated to sperm quality, the effects of mutations seem to be heterogeneous and particularly related to their pathogenicity. WIDER IMPLICATIONS The importance of the role of mitochondria in reproduction, and particularly in gamete quality, has recently emerged following numerous publications. Better understanding of male infertility is of great interest in the current context where a significant decline in sperm quality has been observed.
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Affiliation(s)
- Magalie Boguenet
- MITOVASC Institute, CNRS 6015, INSERM U1083, Angers University, Angers 49000, France
| | - Pierre-Emmanuel Bouet
- Department of Reproductive Medicine, Angers University Hospital, Angers 49000, France
| | - Andrew Spiers
- Department of Reproductive Medicine, Angers University Hospital, Angers 49000, France
| | - Pascal Reynier
- MITOVASC Institute, CNRS 6015, INSERM U1083, Angers University, Angers 49000, France.,Department of Biochemistry and Genetics, Angers University Hospital, Angers 49000, France
| | - Pascale May-Panloup
- MITOVASC Institute, CNRS 6015, INSERM U1083, Angers University, Angers 49000, France.,Reproductive Biology Unit, Angers University Hospital, Angers 49000, France
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Zakirova EG, Muzyka VV, Mazunin IO, Orishchenko KE. Natural and Artificial Mechanisms of Mitochondrial Genome Elimination. Life (Basel) 2021; 11:life11020076. [PMID: 33498399 PMCID: PMC7909434 DOI: 10.3390/life11020076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 01/11/2023] Open
Abstract
The generally accepted theory of the genetic drift of mitochondrial alleles during mammalian ontogenesis is based on the presence of a selective bottleneck in the female germline. However, there is a variety of different theories on the pathways of genetic regulation of mitochondrial DNA (mtDNA) dynamics in oogenesis and adult somatic cells. The current review summarizes present knowledge on the natural mechanisms of mitochondrial genome elimination during mammalian development. We also discuss the variety of existing and developing methodologies for artificial manipulation of the mtDNA heteroplasmy level. Understanding of the basics of mtDNA dynamics will shed the light on the pathogenesis and potential therapies of human diseases associated with mitochondrial dysfunction.
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Affiliation(s)
- Elvira G. Zakirova
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.G.Z.); (V.V.M.)
| | - Vladimir V. Muzyka
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.G.Z.); (V.V.M.)
- Department of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Ilya O. Mazunin
- Skolkovo Institute of Science and Technology, 143026 Skolkovo, Russia;
| | - Konstantin E. Orishchenko
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.G.Z.); (V.V.M.)
- Department of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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Heidary Z, Saliminejad K, Zaki-Dizaji M, Khorram Khorshid HR. Genetic aspects of idiopathic asthenozoospermia as a cause of male infertility. HUM FERTIL 2020; 23:83-92. [PMID: 30198353 DOI: 10.1080/14647273.2018.1504325] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Infertility is a worldwide problem affecting about 15% of couples trying to conceive. Asthenozoospermia (AZS) is one of the major causes of male infertility, diagnosed by reduced sperm motility, and has no effective therapeutic treatment. To date, a few genes have been found to be associated with AZS in humans and mice, but in most of cases its molecular aetiology remains unknown. Genetic causes of AZS may include chromosomal abnormalities, specific mutations of nuclear and mitochondrial genes. However recently, epigenetic factors, altered microRNAs expression signature, and proteomics have shed light on the pathophysiological basis of AZS. This review article summarises the reported genetic causes of AZS.
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Affiliation(s)
- Zohreh Heidary
- Reproductive Biotechnology Research Centre, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Kioomars Saliminejad
- Reproductive Biotechnology Research Centre, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Majid Zaki-Dizaji
- Department of Medical Genetics School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Reza Khorram Khorshid
- Reproductive Biotechnology Research Centre, Avicenna Research Institute, ACECR, Tehran, Iran.,Genetics Research Centre University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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Zalloua P, Collins CJ, Gosling A, Biagini SA, Costa B, Kardailsky O, Nigro L, Khalil W, Calafell F, Matisoo-Smith E. Ancient DNA of Phoenician remains indicates discontinuity in the settlement history of Ibiza. Sci Rep 2018; 8:17567. [PMID: 30514893 PMCID: PMC6279797 DOI: 10.1038/s41598-018-35667-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 11/09/2018] [Indexed: 12/21/2022] Open
Abstract
Ibiza was permanently settled around the 7th century BCE by founders arriving from west Phoenicia. The founding population grew significantly and reached its height during the 4th century BCE. We obtained nine complete mitochondrial genomes from skeletal remains from two Punic necropoli in Ibiza and a Bronze Age site from Formentara. We also obtained low coverage (0.47X average depth) of the genome of one individual, directly dated to 361-178 cal BCE, from the Cas Molí site on Ibiza. We analysed and compared ancient DNA results with 18 new mitochondrial genomes from modern Ibizans to determine the ancestry of the founders of Ibiza. The mitochondrial results indicate a predominantly recent European maternal ancestry for the current Ibizan population while the whole genome data suggest a significant Eastern Mediterranean component. Our mitochondrial results suggest a genetic discontinuity between the early Phoenician settlers and the island's modern inhabitants. Our data, while limited, suggest that the Eastern or North African influence in the Punic population of Ibiza was primarily male dominated.
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Affiliation(s)
- Pierre Zalloua
- School of Medicine, Lebanese American University, Byblos, Lebanon.
| | - Catherine J Collins
- Department of Anatomy, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Anna Gosling
- Department of Anatomy, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Simone Andrea Biagini
- Department de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Benjamí Costa
- Museu Arqueològic d'Eivissa i Formentera, Universitat de Barcelona, Illes Balears, Spain
| | - Olga Kardailsky
- Department of Anatomy, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Lorenzo Nigro
- Facoltà di Lettere e Filosofia, Università di Roma, La Sapienza, Rome, Italy
| | - Wissam Khalil
- Department of Arts and Archaeology, Lebanese University, Beirut, Lebanon
| | - Francesc Calafell
- Department de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
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Ji J, Xu M, Wang R, Wang Y, Qin Y, Li L, Zheng H, Yang S, Li S, Miao D, Jin L, Zhou L, Ling X, Xia Y, Lu C, Wang X. Human mitochondrial DNA haplogroup M8a influences the penetrance of m.8684C>T in Han Chinese men with non-obstructive azoospermia. Reprod Biomed Online 2018; 37:480-488. [PMID: 30236824 DOI: 10.1016/j.rbmo.2018.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 08/02/2018] [Accepted: 08/03/2018] [Indexed: 11/29/2022]
Abstract
RESEARCH QUESTION What is the role of mitochondrial DNA (mtDNA) in the pathogenesis of non-obstructive azoospermia (NOA)? DESIGN mtDNA genome sequencing followed by an independent population validation were performed in 628 NOA cases and 584 healthy controls. Antioxidant capacity of serum was evaluated in 54 randomly selected cases out of 536 and 49 out of 489 controls. RESULTS In the screening stage, 13 mtDNA haplogroups (hg) were ascertained, and 10 susceptible variants were observed. In the validation stage, hg M8* in individuals was found to be associated with increased risk of NOA [odds ratio (OR) 2.61, 95% confidence interval (CI) 1.47-4.61] (P=0.001). Unexpectedly, the frequency of m.8684C>T, the defining marker for hg M8a, was also higher in NOA (OR 4.14, 95% CI 1.56-11.03) (P=0.002). Subsequently, the frequency distributions were compared among the sub-hg of hg M8* (including hg M8a, C and Z) and, intriguingly, no significance was found in hg C and Z. Additionally, the level of total antioxidant capacity was significantly decreased (P<0.05) compared with the control group. CONCLUSIONS hg M8a background in general played an active role in the penetrance of 8684C>T in NOA, and mtDNA genetic variants (causing low antioxidant levels) might increase mtDNA damage and impair normal spermatogenesis.
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Affiliation(s)
- Juan Ji
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Medical University, Nanjing210029, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China
| | - Miaofei Xu
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China
| | - Rong Wang
- Research Centre for Bone and Stem Cells, Department of Anatomy, Histology, and Embryology, Nanjing Medical University, Nanjing, China
| | - Ying Wang
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China
| | - Yufeng Qin
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle ParkNC27709, USA
| | - Lei Li
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai200433, China
| | - Hongxiang Zheng
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai200433, China
| | - Shuping Yang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai200433, China
| | - Shilin Li
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai200433, China
| | - Dengshun Miao
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Medical University, Nanjing210029, China; Research Centre for Bone and Stem Cells, Department of Anatomy, Histology, and Embryology, Nanjing Medical University, Nanjing, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai200433, China
| | - Lin Zhou
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Medical University, Nanjing210029, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China
| | - Xiufeng Ling
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Medical University, Nanjing210029, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Medical University, Nanjing210029, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China
| | - Chuncheng Lu
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Medical University, Nanjing210029, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China.
| | - Xinru Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Medical University, Nanjing210029, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China.
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Genomic and transcriptomic characterization of the mitochondrial-rich oncocytic phenotype on a thyroid carcinoma background. Mitochondrion 2018; 46:123-133. [PMID: 29631022 DOI: 10.1016/j.mito.2018.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 03/29/2018] [Accepted: 04/02/2018] [Indexed: 12/22/2022]
Abstract
We conducted the first systematic omics study of the oncocytic phenotype in 488 papillary thyroid carcinomas (PTC) from The Cancer Genome Atlas. Oncocytic phenotype is secondary to PTC, being unrelated to several pathologic scores. The nuclear genome had low impact on this phenotype (except in specific copy number variation), which was mostly driven by the significant accumulation of mitochondrial DNA non-synonymous and frameshift mutations at high heteroplasmy levels. Energy and mitochondrial-related pathways were significantly enriched in oncocytic tumors that also displayed increased levels of expression for genes involved in autophagy and fusion of mitochondria. Our in vitro tests confirmed that autophagy is increased and functional while mitophagy is decreased in these tumors.
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Skowronek MF, Velazquez T, Mut P, Figueiro G, Sans M, Bertoni B, Sapiro R. Associations between male infertility and ancestry in South Americans: a case control study. BMC MEDICAL GENETICS 2017; 18:78. [PMID: 28747152 PMCID: PMC5530489 DOI: 10.1186/s12881-017-0438-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 07/13/2017] [Indexed: 01/20/2023]
Affiliation(s)
| | - Tatiana Velazquez
- Departamento de Genética, Facultad de Medicina UDELAR, Montevideo, Uruguay
| | - Patricia Mut
- Departamento de Genética, Facultad de Medicina UDELAR, Montevideo, Uruguay
| | - Gonzalo Figueiro
- Departamento de Antropología, Facultad de Humanidades y Ciencias de la Educación, UDELAR, Montevideo, Uruguay
| | - Monica Sans
- Departamento de Antropología, Facultad de Humanidades y Ciencias de la Educación, UDELAR, Montevideo, Uruguay
| | - Bernardo Bertoni
- Departamento de Genética, Facultad de Medicina UDELAR, Montevideo, Uruguay
| | - Rossana Sapiro
- Departamento de Histología y Embriología, Facultad de Medicina UDELAR, Montevideo, Uruguay.
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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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Mitochondrial-Nuclear Interactions Mediate Sex-Specific Transcriptional Profiles in Drosophila. Genetics 2016; 204:613-630. [PMID: 27558138 PMCID: PMC5068850 DOI: 10.1534/genetics.116.192328] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 08/17/2016] [Indexed: 12/27/2022] Open
Abstract
The assembly and function of mitochondria require coordinated expression from two distinct genomes, the mitochondrial DNA (mtDNA) and nuclear DNA (nDNA). Mutations in either genome can be a source of phenotypic variation, yet their coexpression has been largely overlooked as a source of variation, particularly in the emerging paradigm of mitochondrial replacement therapy. Here we tested how the transcriptome responds to mtDNA and nDNA variation, along with mitonuclear interactions (mtDNA × nDNA) in Drosophila melanogaster. We used two mtDNA haplotypes that differ in a substantial number of single nucleotide polymorphisms, with >100 amino acid differences. We placed each haplotype on each of two D. melanogaster nuclear backgrounds and tested for transcription differences in both sexes. We found that large numbers of transcripts were differentially expressed between nuclear backgrounds, and that mtDNA type altered the expression of nDNA genes, suggesting a retrograde, trans effect of mitochondrial genotype. Females were generally more sensitive to genetic perturbation than males, and males demonstrated an asymmetrical effect of mtDNA in each nuclear background; mtDNA effects were nuclear-background specific. mtDNA-sensitive genes were not enriched in male- or female-limited expression space in either sex. Using a variety of differential expression analyses, we show the responses to mitonuclear covariation to be substantially different between the sexes, yet the mtDNA genes were consistently differentially expressed across nuclear backgrounds and sexes. Our results provide evidence that the main mtDNA effects can be consistent across nuclear backgrounds, but the interactions between mtDNA and nDNA can lead to sex-specific global transcript responses.
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Salas A, Martinón-Torres F, Gómez-Carballa A. 'Infertile' studies on mitochondrial DNA variation in asthenozoospermic Tunisian men. Biochem Biophys Rep 2016; 8:114-119. [PMID: 28955946 PMCID: PMC5613696 DOI: 10.1016/j.bbrep.2016.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/10/2016] [Indexed: 11/30/2022] Open
Abstract
We reviewed five studies undertaken by the same research group on the possible links between mitochondrial DNA (mtDNA) variation and asthenozoospermia, all carried out on Tunisian men. A thorough assessment of these articles reveals that all five studies were carried out on virtually the same cohort of patients, although this information was concealed by the authors. Thus, the results were ‘sliced’ in order to unjustifiably maximize the number of publications. In addition, a phylogenetic analysis of their data indicates that the reported results are notably incomplete and deficient. Overall, contrary to the original claims, the association of mtDNA variants with asthenozoospermia finds no support on this saga on Tunisian infertile men. We re-analyze the seeming association of mtDNA with infertility in Tunisians. The existing data are incomplete and deficient. The data do not support association of mtDNA and infertility.
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Affiliation(s)
- Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPop Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela, Galicia, Spain
- Corresponding author at: Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, 15872 Galicia, Spain.Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de CompostelaGalicia15872Spain
| | - Federico Martinón-Torres
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela, Galicia, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Galicia, Spain
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPop Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela, Galicia, Spain
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15
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Mossman JA, Biancani LM, Zhu CT, Rand DM. Mitonuclear Epistasis for Development Time and Its Modification by Diet in Drosophila. Genetics 2016; 203:463-84. [PMID: 26966258 PMCID: PMC4858792 DOI: 10.1534/genetics.116.187286] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 03/04/2016] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial (mtDNA) and nuclear genes have to operate in a coordinated manner to maintain organismal function, and the regulation of this homeostasis presents a substantial source of potential epistatic (G × G) interactions. How these interactions shape the fitness landscape is poorly understood. Here we developed a novel mitonuclear epistasis model, using selected strains of the Drosophila Genetic Reference Panel (DGRP) and mitochondrial genomes from within Drosophila melanogaster and D. simulans to test the hypothesis that mtDNA × nDNA interactions influence fitness. In total we built 72 genotypes (12 nuclear backgrounds × 6 mtDNA haplotypes, with 3 from each species) to dissect the relationship between genotype and phenotype. Each genotype was assayed on four food environments. We found considerable variation in several phenotypes, including development time and egg-to-adult viability, and this variation was partitioned into genetic (G), environmental (E), and higher-order (G × G, G × E, and G × G × E) components. Food type had a significant impact on development time and also modified mitonuclear epistases, evidencing a broad spectrum of G × G × E across these genotypes. Nuclear background effects were substantial, followed by mtDNA effects and their G × G interaction. The species of mtDNA haplotype had negligible effects on phenotypic variation and there was no evidence that mtDNA variation has different effects on male and female fitness traits. Our results demonstrate that mitonuclear epistases are context dependent, suggesting the selective pressure acting on mitonuclear genotypes may vary with food environment in a genotype-specific manner.
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Affiliation(s)
- Jim A Mossman
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912
| | - Leann M Biancani
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912
| | - Chen-Tseh Zhu
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912
| | - David M Rand
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912
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16
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60,000 years of interactions between Central and Eastern Africa documented by major African mitochondrial haplogroup L2. Sci Rep 2015. [PMID: 26211407 PMCID: PMC4515592 DOI: 10.1038/srep12526] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mitochondrial DNA (mtDNA) haplogroup L2 originated in Western Africa but is nowadays spread across the entire continent. L2 movements were previously postulated to be related to the Bantu expansion, but L2 expansions eastwards probably occurred much earlier. By reconstructing the phylogeny of L2 (44 new complete sequences) we provide insights on the complex net of within-African migrations in the last 60 thousand years (ka). Results show that lineages in Southern Africa cluster with Western/Central African lineages at a recent time scale, whereas, eastern lineages seem to be substantially more ancient. Three moments of expansion from a Central African source are associated to L2: (1) one migration at 70–50 ka into Eastern or Southern Africa, (2) postglacial movements (15–10 ka) into Eastern Africa; and (3) the southward Bantu Expansion in the last 5 ka. The complementary population and L0a phylogeography analyses indicate no strong evidence of mtDNA gene flow between eastern and southern populations during the later movement, suggesting low admixture between Eastern African populations and the Bantu migrants. This implies that, at least in the early stages, the Bantu expansion was mainly a demic diffusion with little incorporation of local populations.
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17
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Fernandes V, Triska P, Pereira JB, Alshamali F, Rito T, Machado A, Fajkošová Z, Cavadas B, Černý V, Soares P, Richards MB, Pereira L. Genetic stratigraphy of key demographic events in Arabia. PLoS One 2015; 10:e0118625. [PMID: 25738654 PMCID: PMC4349752 DOI: 10.1371/journal.pone.0118625] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 01/21/2015] [Indexed: 01/01/2023] Open
Abstract
At the crossroads between Africa and Eurasia, Arabia is necessarily a melting pot, its peoples enriched by successive gene flow over the generations. Estimating the timing and impact of these multiple migrations are important steps in reconstructing the key demographic events in the human history. However, current methods based on genome-wide information identify admixture events inefficiently, tending to estimate only the more recent ages, as here in the case of admixture events across the Red Sea (∼8–37 generations for African input into Arabia, and 30–90 generations for “back-to-Africa” migrations). An mtDNA-based founder analysis, corroborated by detailed analysis of the whole-mtDNA genome, affords an alternative means by which to identify, date and quantify multiple migration events at greater time depths, across the full range of modern human history, albeit for the maternal line of descent only. In Arabia, this approach enables us to infer several major pulses of dispersal between the Near East and Arabia, most likely via the Gulf corridor. Although some relict lineages survive in Arabia from the time of the out-of-Africa dispersal, 60 ka, the major episodes in the peopling of the Peninsula took place from north to south in the Late Glacial and, to a lesser extent, the immediate post-glacial/Neolithic. Exchanges across the Red Sea were mainly due to the Arab slave trade and maritime dominance (from ∼2.5 ka to very recent times), but had already begun by the early Holocene, fuelled by the establishment of maritime networks since ∼8 ka. The main “back-to-Africa” migrations, again undetected by genome-wide dating analyses, occurred in the Late Glacial period for introductions into eastern Africa, whilst the Neolithic was more significant for migrations towards North Africa.
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Affiliation(s)
- Verónica Fernandes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Petr Triska
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Instituto de Ciências Biomédicas da Universidade do Porto (ICBAS), Porto, Portugal
| | - Joana B. Pereira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Farida Alshamali
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai, United Arab Emirates
| | - Teresa Rito
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Alison Machado
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Zuzana Fajkošová
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Bruno Cavadas
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Viktor Černý
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Pedro Soares
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Martin B. Richards
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | - Luísa Pereira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Faculdade de Medicina da Universidade do Porto, Porto, Portugal
- * E-mail:
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18
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Marques SL, Goios A, Rocha AM, Prata MJ, Amorim A, Gusmão L, Alves C, Alvarez L. Portuguese mitochondrial DNA genetic diversity-An update and a phylogenetic revision. Forensic Sci Int Genet 2014; 15:27-32. [PMID: 25457629 DOI: 10.1016/j.fsigen.2014.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 09/22/2014] [Accepted: 10/03/2014] [Indexed: 10/24/2022]
Abstract
In recent years a large amount of mitochondrial population data for forensic purposes has been produced. Current efforts are focused at increasing the number of studied populations while generating updated genetic information of forensic quality. However, complete mitochondrial control region sequences are still scarce for most populations and even more so for complete mitochondrial genomes. In the case of Portugal, previous population genetics studies have already revealed the general portrait of HVS-I and HVS-II mitochondrial diversity, becoming now important to update and expand the mitochondrial region analysed. Accordingly, a total of 292 complete control region sequences from continental Portugal were obtained, under a stringent experimental design to ensure the quality of data through double sequencing of each target region. Furthermore, H-specific coding region SNPs were examined to detail haplogroup classification and complete mitogenomes were obtained for all sequences belonging to haplogroups U4 and U5. In general, a typical Western European haplogroup composition was found in mainland Portugal, associated to high level of mitochondrial genetic diversity. Within the country, no signs of substructure were detected. The typing of extra coding region SNPs has provided the refinement or confirmation of the previous classification obtained with EMMA tool in 96% of the cases. Finally, it was also possible to enlarge haplogroup U phylogeny with 28 new U4 and U5 mitogenomes.
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Affiliation(s)
- Sofia L Marques
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Ana Goios
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Ana M Rocha
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Maria João Prata
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; Department of Biology, Faculty of Sciences of the University of Porto, Porto, Portugal
| | - António Amorim
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; Department of Biology, Faculty of Sciences of the University of Porto, Porto, Portugal
| | - Leonor Gusmão
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Cíntia Alves
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Luis Alvarez
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
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Chinnery PF, Craven L, Mitalipov S, Stewart JB, Herbert M, Turnbull DM. The challenges of mitochondrial replacement. PLoS Genet 2014; 10:e1004315. [PMID: 24762741 PMCID: PMC3998882 DOI: 10.1371/journal.pgen.1004315] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Patrick F. Chinnery
- Wellcome Trust Centre for Mitochondrial Research, Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne, United Kingdom
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - Lyndsey Craven
- Wellcome Trust Centre for Mitochondrial Research, Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Shoukhrat Mitalipov
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | | | - Mary Herbert
- Wellcome Trust Centre for Mitochondrial Research, Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne, United Kingdom
- Newcastle Fertility Centre, International Centre for Life, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Douglass M. Turnbull
- Wellcome Trust Centre for Mitochondrial Research, Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne, United Kingdom
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Rito T, Richards MB, Fernandes V, Alshamali F, Cerny V, Pereira L, Soares P. The first modern human dispersals across Africa. PLoS One 2013; 8:e80031. [PMID: 24236171 PMCID: PMC3827445 DOI: 10.1371/journal.pone.0080031] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 09/26/2013] [Indexed: 12/11/2022] Open
Abstract
The emergence of more refined chronologies for climate change and archaeology in prehistoric Africa, and for the evolution of human mitochondrial DNA (mtDNA), now make it feasible to test more sophisticated models of early modern human dispersals suggested by mtDNA distributions. Here we have generated 42 novel whole-mtDNA genomes belonging to haplogroup L0, the most divergent clade in the maternal line of descent, and analysed them alongside the growing database of African lineages belonging to L0's sister clade, L1'6. We propose that the last common ancestor of modern human mtDNAs (carried by "mitochondrial Eve") possibly arose in central Africa ~180 ka, at a time of low population size. By ~130 ka two distinct groups of anatomically modern humans co-existed in Africa: broadly, the ancestors of many modern-day Khoe and San populations in the south and a second central/eastern African group that includes the ancestors of most extant worldwide populations. Early modern human dispersals correlate with climate changes, particularly the tropical African "megadroughts" of MIS 5 (marine isotope stage 5, 135-75 ka) which paradoxically may have facilitated expansions in central and eastern Africa, ultimately triggering the dispersal out of Africa of people carrying haplogroup L3 ~60 ka. Two south to east migrations are discernible within haplogroup LO. One, between 120 and 75 ka, represents the first unambiguous long-range modern human dispersal detected by mtDNA and might have allowed the dispersal of several markers of modernity. A second one, within the last 20 ka signalled by L0d, may have been responsible for the spread of southern click-consonant languages to eastern Africa, contrary to the view that these eastern examples constitute relicts of an ancient, much wider distribution.
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Affiliation(s)
- Teresa Rito
- IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Porto, Portugal
| | - Martin B. Richards
- School of Applied Sciences, University of Huddersfield, QueensGate, Huddersfield, United Kingdom
| | - Verónica Fernandes
- IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Porto, Portugal
- Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Farida Alshamali
- Dubai Police GHQ - General Department of Forensic Sciences & Criminology, Dubai, United Arab Emirates
| | - Viktor Cerny
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
- Institute for Advanced Study, Paris, France
| | - Luísa Pereira
- IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Porto, Portugal
- Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - Pedro Soares
- IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Porto, Portugal
- * E-mail:
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21
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Luo SM, Schatten H, Sun QY. Sperm Mitochondria in Reproduction: Good or Bad and Where Do They Go? J Genet Genomics 2013; 40:549-56. [DOI: 10.1016/j.jgg.2013.08.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 08/12/2013] [Accepted: 08/27/2013] [Indexed: 11/24/2022]
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Feng GF, Zhang J, Feng LM, Shen NX, Li LJ, Zhu YM. Mitochondrial DNA haplogroup associated with sperm motility in the Han population. Asian J Androl 2013; 15:630-3. [PMID: 23912313 DOI: 10.1038/aja.2013.83] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 05/02/2013] [Accepted: 05/29/2013] [Indexed: 11/09/2022] Open
Abstract
In this study, we aimed to determine whether the main mitochondrial DNA (mtDNA) haplogroups of the Han people have an impact on spermatozoa motility. We recruited 312 men who were consecutively admitted to two affiliated hospitals of College of Medicine, Zhejiang University from May 2011 to April 2012 as part of fertility investigations. Semen and whole blood samples were collected from the men. We determined the mtDNA haplogroups by analysing the sequences of mtDNA hypervariable segment I and testing diagnostic polymorphisms in the mtDNA coding region with DNA probes. No significant differences were found in the clinical characteristics of the mtDNA haplogroup R and non-R (P>0.05). Our results suggest that mtDNA haplogroup R is a strong independent predictor of sperm motility in the Han population, conferring a 2.97-fold (95% confidence interval: 1.74-4.48, P<0.001) decreased chance of asthenozoospermia compared with those without haplogroup R.
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Affiliation(s)
- Guo-Fang Feng
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Pennarun E, Kivisild T, Metspalu E, Metspalu M, Reisberg T, Moisan JP, Behar DM, Jones SC, Villems R. Divorcing the Late Upper Palaeolithic demographic histories of mtDNA haplogroups M1 and U6 in Africa. BMC Evol Biol 2012. [PMID: 23206491 PMCID: PMC3582464 DOI: 10.1186/1471-2148-12-234] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Background A Southwest Asian origin and dispersal to North Africa in the Early Upper Palaeolithic era has been inferred in previous studies for mtDNA haplogroups M1 and U6. Both haplogroups have been proposed to show similar geographic patterns and shared demographic histories. Results We report here 24 M1 and 33 U6 new complete mtDNA sequences that allow us to refine the existing phylogeny of these haplogroups. The resulting phylogenetic information was used to genotype a further 131 M1 and 91 U6 samples to determine the geographic spread of their sub-clades. No southwest Asian specific clades for M1 or U6 were discovered. U6 and M1 frequencies in North Africa, the Middle East and Europe do not follow similar patterns, and their sub-clade divisions do not appear to be compatible with their shared history reaching back to the Early Upper Palaeolithic. The Bayesian Skyline Plots testify to non-overlapping phases of expansion, and the haplogroups’ phylogenies suggest that there are U6 sub-clades that expanded earlier than those in M1. Some M1 and U6 sub-clades could be linked with certain events. For example, U6a1 and M1b, with their coalescent ages of ~20,000–22,000 years ago and earliest inferred expansion in northwest Africa, could coincide with the flourishing of the Iberomaurusian industry, whilst U6b and M1b1 appeared at the time of the Capsian culture. Conclusions Our high-resolution phylogenetic dissection of both haplogroups and coalescent time assessments suggest that the extant main branching pattern of both haplogroups arose and diversified in the mid-later Upper Palaeolithic, with some sub-clades concomitantly with the expansion of the Iberomaurusian industry. Carriers of these maternal lineages have been later absorbed into and diversified further during the spread of Afro-Asiatic languages in North and East Africa.
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Affiliation(s)
- Erwan Pennarun
- Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu, Estonia.
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Bellizzi D, D'Aquila P, Giordano M, Montesanto A, Passarino G. Global DNA methylation levels are modulated by mitochondrial DNA variants. Epigenomics 2012; 4:17-27. [PMID: 22332655 DOI: 10.2217/epi.11.109] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
AIM In the present study, we investigated whether global DNA methylation levels are affected by mitochondrial DNA (mtDNA) variants, which are known to modulate mitochondrial functions. MATERIALS & METHODS Global DNA methylation levels were evaluated in peripheral blood DNA collected from adult subjects and in vitro using the DNA of cybrid cells harboring mtDNAs of different haplogroups. In these cells, mRNA expression of genes involved in DNA methylation processes, and ATP and reactive oxygen species levels were also analyzed. RESULTS The analysis revealed that methylation levels were higher in the subjects carrying the J haplogroup than in non-J carriers. Consistently, cybrids with J haplogroup mtDNA showed higher methylation levels than other cybrids. Interestingly, we observed overexpression of the MAT1A gene and low ATP and ROS levels in J cybrids. CONCLUSION Our findings indicate that mtDNA-specific interactions between mitochondria and the nucleus regulate epigenetic changes, possibly by affecting oxidative phosphorylation efficiency.
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Affiliation(s)
- Dina Bellizzi
- Department of Cell Biology, University of Calabria, 87036 Rende, Italy
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25
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Fu Q, Rudan P, Pääbo S, Krause J. Complete mitochondrial genomes reveal neolithic expansion into Europe. PLoS One 2012; 7:e32473. [PMID: 22427842 PMCID: PMC3302788 DOI: 10.1371/journal.pone.0032473] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 01/31/2012] [Indexed: 11/18/2022] Open
Abstract
The Neolithic transition from hunting and gathering to farming and cattle breeding marks one of the most drastic cultural changes in European prehistory. Short stretches of ancient mitochondrial DNA (mtDNA) from skeletons of pre-Neolithic hunter-gatherers as well as early Neolithic farmers support the demic diffusion model where a migration of early farmers from the Near East and a replacement of pre-Neolithic hunter-gatherers are largely responsible for cultural innovation and changes in subsistence strategies during the Neolithic revolution in Europe. In order to test if a signal of population expansion is still present in modern European mitochondrial DNA, we analyzed a comprehensive dataset of 1,151 complete mtDNAs from present-day Europeans. Relying upon ancient DNA data from previous investigations, we identified mtDNA haplogroups that are typical for early farmers and hunter-gatherers, namely H and U respectively. Bayesian skyline coalescence estimates were then used on subsets of complete mtDNAs from modern populations to look for signals of past population expansions. Our analyses revealed a population expansion between 15,000 and 10,000 years before present (YBP) in mtDNAs typical for hunters and gatherers, with a decline between 10,000 and 5,000 YBP. These corresponded to an analogous population increase approximately 9,000 YBP for mtDNAs typical of early farmers. The observed changes over time suggest that the spread of agriculture in Europe involved the expansion of farming populations into Europe followed by the eventual assimilation of resident hunter-gatherers. Our data show that contemporary mtDNA datasets can be used to study ancient population history if only limited ancient genetic data is available.
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Affiliation(s)
- Qiaomei Fu
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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26
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Fernandes V, Alshamali F, Alves M, Costa MD, Pereira JB, Silva NM, Cherni L, Harich N, Cerny V, Soares P, Richards MB, Pereira L. The Arabian cradle: mitochondrial relicts of the first steps along the southern route out of Africa. Am J Hum Genet 2012; 90:347-55. [PMID: 22284828 DOI: 10.1016/j.ajhg.2011.12.010] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 12/11/2011] [Accepted: 12/14/2011] [Indexed: 11/20/2022] Open
Abstract
A major unanswered question regarding the dispersal of modern humans around the world concerns the geographical site of the first human steps outside of Africa. The "southern coastal route" model predicts that the early stages of the dispersal took place when people crossed the Red Sea to southern Arabia, but genetic evidence has hitherto been tenuous. We have addressed this question by analyzing the three minor west-Eurasian haplogroups, N1, N2, and X. These lineages branch directly from the first non-African founder node, the root of haplogroup N, and coalesce to the time of the first successful movement of modern humans out of Africa, ∼60 thousand years (ka) ago. We sequenced complete mtDNA genomes from 85 Southwest Asian samples carrying these haplogroups and compared them with a database of 300 European examples. The results show that these minor haplogroups have a relict distribution that suggests an ancient ancestry within the Arabian Peninsula, and they most likely spread from the Gulf Oasis region toward the Near East and Europe during the pluvial period 55-24 ka ago. This pattern suggests that Arabia was indeed the first staging post in the spread of modern humans around the world.
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Affiliation(s)
- Verónica Fernandes
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal
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Mossman JA, Slate J, Birkhead TR, Moore HD, Pacey AA. Mitochondrial haplotype does not influence sperm motility in a UK population of men. Hum Reprod 2012; 27:641-51. [PMID: 22215629 DOI: 10.1093/humrep/der438] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Sperm motility is regulated by mitochondrial enzymes that are partially encoded by mitochondrial DNA (mtDNA). MtDNA has therefore been suggested as a putative genetic marker of male fertility. However, recent studies in different populations have identified both significant and non-significant associations between mtDNA variation and sperm motility. Here, we tested whether mtDNA variation was associated with sperm motility in a large cohort of men from the UK, to test the robustness of previous studies and the reliability of mtDNA as a marker of poor sperm motility. METHODS A total of 463 men attending for semen analysis as part of infertility investigations were recruited from a UK laboratory. Sperm motility was measured using both computer-assisted sperm analysis and traditional manual measurements. MtDNA haplogroup and haplotype were determined in 357 and 298 men, respectively, using single nucleotide polymorphism (SNP) markers throughout the mtDNA genome, and compared with sperm motility data. The linkage between the SNP markers, and possible associations between individual SNPs and motility, were also investigated. RESULTS We found no statistical association between haplogroup or haplotype and sperm motility, regardless of how it was measured (P > 0.05 in all cases). Moreover, individual SNPs which were in linkage disequilibrium and dispersed across the mitochondrial genome, and therefore sensitive to mtDNA variation, were not predictive of sperm motility. CONCLUSIONS Mitochondrial haplotype is unlikely to be a reliable genetic marker of male factor infertility.
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Affiliation(s)
- Jim A Mossman
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK.
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28
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Soares P, Alshamali F, Pereira JB, Fernandes V, Silva NM, Afonso C, Costa MD, Musilova E, Macaulay V, Richards MB, Cerny V, Pereira L. The Expansion of mtDNA Haplogroup L3 within and out of Africa. Mol Biol Evol 2011; 29:915-27. [DOI: 10.1093/molbev/msr245] [Citation(s) in RCA: 193] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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29
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Mitochondrial DNA variants in Drosophila melanogaster are expressed at the level of the organismal phenotype. Mitochondrion 2011; 11:756-63. [DOI: 10.1016/j.mito.2011.06.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 05/30/2011] [Accepted: 06/28/2011] [Indexed: 11/24/2022]
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30
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Musilová E, Fernandes V, Silva NM, Soares P, Alshamali F, Harich N, Cherni L, Gaaied ABAE, Al-Meeri A, Pereira L, Cerný V. Population history of the Red Sea--genetic exchanges between the Arabian Peninsula and East Africa signaled in the mitochondrial DNA HV1 haplogroup. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 145:592-8. [PMID: 21660931 DOI: 10.1002/ajpa.21522] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 02/07/2011] [Indexed: 11/11/2022]
Abstract
Archaeological studies have revealed cultural connections between the two sides of the Red Sea dating to prehistory. The issue has still not been properly addressed, however, by archaeogenetics. We focus our attention here on the mitochondrial haplogroup HV1 that is present in both the Arabian Peninsula and East Africa. The internal variation of 38 complete mitochondrial DNA sequences (20 of them presented here for the first time) affiliated into this haplogroup testify to its emergence during the late glacial maximum, most probably in the Near East, with subsequent dispersion via population expansions when climatic conditions improved. Detailed phylogeography of HV1 sequences shows that more recent demographic upheavals likely contributed to their spread from West Arabia to East Africa, a finding concordant with archaeological records suggesting intensive maritime trade in the Red Sea from the sixth millennium BC onwards. Closer genetic exchanges are apparent between the Horn of Africa and Yemen, while Egyptian HV1 haplotypes seem to be more similar to the Near Eastern ones.
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Affiliation(s)
- Eliška Musilová
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
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31
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Gómez-Carballa A, Cerezo M, Balboa E, Heredia C, Castro-Feijóo L, Rica I, Barreiro J, Eirís J, Cabanas P, Martínez-Soto I, Fernández-Toral J, Castro-Gago M, Pombo M, Carracedo Á, Barros F, Salas A. Evolutionary analyses of entire genomes do not support the association of mtDNA mutations with Ras/MAPK pathway syndromes. PLoS One 2011; 6:e18348. [PMID: 21526175 PMCID: PMC3079712 DOI: 10.1371/journal.pone.0018348] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2011] [Accepted: 02/25/2011] [Indexed: 01/23/2023] Open
Abstract
Background There are several known autosomal genes responsible for
Ras/MAPK pathway syndromes, including
Noonan syndrome (NS) and related disorders (such as LEOPARD,
neurofibromatosis type 1), although mutations of these genes do not explain
all cases. Due to the important role played by the mitochondrion in the
energetic metabolism of cardiac muscle, it was recently proposed that
variation in the mitochondrial DNA (mtDNA) genome could be a risk factor in
the Noonan phenotype and in hypertrophic cardiomyopathy (HCM), which is a
common clinical feature in Ras/MAPK pathway syndromes. In order to test
these hypotheses, we sequenced entire mtDNA genomes in the largest series of
patients suffering from Ras/MAPK pathway
syndromes analyzed to date (n = 45),
most of them classified as NS patients
(n = 42). Methods/Principal Findings The results indicate that the observed mtDNA lineages were mostly of European
ancestry, reproducing in a nutshell the expected haplogroup (hg) patterns of
a typical Iberian dataset (including hgs H, T, J, and U). Three new branches
of the mtDNA phylogeny (H1j1, U5b1e, and L2a5) are described for the first
time, but none of these are likely to be related to NS or
Ras/MAPK pathway syndromes when
observed under an evolutionary perspective. Patterns of variation in tRNA
and protein genes, as well as redundant, private and heteroplasmic variants,
in the mtDNA genomes of patients were as expected when compared with the
patterns inferred from a worldwide mtDNA phylogeny based on more than 8700
entire genomes. Moreover, most of the mtDNA variants found in patients had
already been reported in healthy individuals and constitute common
polymorphisms in human population groups. Conclusions/Significance As a whole, the observed mtDNA genome variation in the NS patients was
difficult to reconcile with previous findings that indicated a pathogenic
role of mtDNA variants in NS.
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Affiliation(s)
- Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía
Patolóxica e Ciencias Forenses, and Instituto de Medicina Legal,
Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de
Compostela, Galicia, Spain
| | - María Cerezo
- Unidade de Xenética, Departamento de Anatomía
Patolóxica e Ciencias Forenses, and Instituto de Medicina Legal,
Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de
Compostela, Galicia, Spain
| | - Emilia Balboa
- Unidad de Medicina Molecular, Fundación Pública Galega de
Medicina Xenómica, CIBERER, Santiago de Compostela, Galicia,
Spain
| | - Claudia Heredia
- Unidad de Endocrinología Pediátrica, Crecimiento y
Adolescencia, Departamento de Pediatría, Hospital Clínico
Universitario y Universidad de Santiago de Compostela, Santiago de Compostela,
Galicia, Spain
| | - Lidia Castro-Feijóo
- Unidad de Endocrinología Pediátrica, Crecimiento y
Adolescencia, Departamento de Pediatría, Hospital Clínico
Universitario y Universidad de Santiago de Compostela, Santiago de Compostela,
Galicia, Spain
| | - Itxaso Rica
- Servicio de Endocrinología Infantil, Hospital de Cruces,
Barakaldo, Basque Country, Spain
| | - Jesús Barreiro
- Unidad de Endocrinología Pediátrica, Crecimiento y
Adolescencia, Departamento de Pediatría, Hospital Clínico
Universitario y Universidad de Santiago de Compostela, Santiago de Compostela,
Galicia, Spain
| | - Jesús Eirís
- Unidad de Neurología Pediátrica, Departamento de
Pediatría, Hospital Clínico Universitario y Universidad de
Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - Paloma Cabanas
- Unidad de Endocrinología Pediátrica, Crecimiento y
Adolescencia, Departamento de Pediatría, Hospital Clínico
Universitario y Universidad de Santiago de Compostela, Santiago de Compostela,
Galicia, Spain
| | - Isabel Martínez-Soto
- Unidad de Cardiología Infantil, Departamento de Pediatría,
Hospital Clínico Universitario de Santiago de Compostela, Santiago de
Compostela, Galicia, Spain
| | | | - Manuel Castro-Gago
- Unidad de Neurología Pediátrica, Departamento de
Pediatría, Hospital Clínico Universitario y Universidad de
Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - Manuel Pombo
- Unidad de Endocrinología Pediátrica, Crecimiento y
Adolescencia, Departamento de Pediatría, Hospital Clínico
Universitario y Universidad de Santiago de Compostela, Santiago de Compostela,
Galicia, Spain
| | - Ángel Carracedo
- Unidade de Xenética, Departamento de Anatomía
Patolóxica e Ciencias Forenses, and Instituto de Medicina Legal,
Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de
Compostela, Galicia, Spain
- Unidad de Medicina Molecular, Fundación Pública Galega de
Medicina Xenómica, CIBERER, Santiago de Compostela, Galicia,
Spain
| | - Francisco Barros
- Unidad de Medicina Molecular, Fundación Pública Galega de
Medicina Xenómica, CIBERER, Santiago de Compostela, Galicia,
Spain
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía
Patolóxica e Ciencias Forenses, and Instituto de Medicina Legal,
Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de
Compostela, Galicia, Spain
- * E-mail:
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Ienco EC, Simoncini C, Orsucci D, Petrucci L, Filosto M, Mancuso M, Siciliano G. May "mitochondrial eve" and mitochondrial haplogroups play a role in neurodegeneration and Alzheimer's disease? Int J Alzheimers Dis 2011; 2011:709061. [PMID: 21423558 PMCID: PMC3056451 DOI: 10.4061/2011/709061] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 12/29/2010] [Indexed: 12/26/2022] Open
Abstract
Mitochondria, the powerhouse of the cell, play a critical role in several metabolic processes and apoptotic pathways. Multiple evidences suggest that mitochondria may be crucial in ageing-related neurodegenerative diseases. Moreover, mitochondrial haplogroups have been linked to multiple area of medicine, from normal ageing to diseases, including neurodegeneration. Polymorphisms within the mitochondrial genome might lead to impaired energy generation and to increased amount of reactive oxygen species, having either susceptibility or protective role in several diseases. Here, we highlight the role of the mitochondrial haplogroups in the pathogenetic cascade leading to diseases, with special attention to Alzheimer's disease.
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Affiliation(s)
- Elena Caldarazzo Ienco
- Department of Neuroscience, Neurological Clinic, University of Pisa, Via Roma 67, 56126 Pisa, Italy
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Cerny V, Mulligan CJ, Fernandes V, Silva NM, Alshamali F, Non A, Harich N, Cherni L, El Gaaied ABA, Al-Meeri A, Pereira L. Internal Diversification of Mitochondrial Haplogroup R0a Reveals Post-Last Glacial Maximum Demographic Expansions in South Arabia. Mol Biol Evol 2010; 28:71-8. [DOI: 10.1093/molbev/msq178] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Wai T, Ao A, Zhang X, Cyr D, Dufort D, Shoubridge EA. The role of mitochondrial DNA copy number in mammalian fertility. Biol Reprod 2010; 83:52-62. [PMID: 20130269 PMCID: PMC2888963 DOI: 10.1095/biolreprod.109.080887] [Citation(s) in RCA: 293] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Revised: 09/15/2009] [Accepted: 01/13/2010] [Indexed: 12/31/2022] Open
Abstract
Mammalian mitochondrial DNA (mtDNA) is a small, maternally inherited genome that codes for 13 essential proteins in the respiratory chain. Mature oocytes contain more than 150 000 copies of mtDNA, at least an order of magnitude greater than the number in most somatic cells, but sperm contain only approximately 100 copies. Mitochondrial oxidative phosphorylation has been suggested to be an important determinant of oocyte quality and sperm motility; however, the functional significance of the high mtDNA copy number in oocytes, and of the low copy number in sperm, remains unclear. To investigate the effects of mtDNA copy number on fertility, we genetically manipulated mtDNA copy number in the mouse by deleting one copy of Tfam, an essential component of the mitochondrial nucleoid, at different stages of germline development. We show that males can tolerate at least a threefold reduction in mtDNA copy number in their sperm without impaired fertility, and in fact, they preferentially transmit a deleted Tfam allele. Surprisingly, oocytes with as few as 4000 copies of mtDNA can be fertilized and progress normally through preimplantation development to the blastocyst stage. The mature oocyte, however, has a critical postimplantation developmental threshold of 40 000-50 000 copies of mtDNA in the mature oocyte. These observations suggest that the high mtDNA copy number in the mature oocyte is a genetic device designed to distribute mitochondria and mtDNAs to the cells of the early postimplantation embryo before mitochondrial biogenesis and mtDNA replication resumes, whereas down-regulation of mtDNA copy number is important for normal sperm function.
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Affiliation(s)
- Timothy Wai
- Montreal Neurological Institute and Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Asangla Ao
- Departments of Obstetrics and Gynecology and Human Genetics and Division of Experimental Medicine, McGill University Health Center, Royal Victoria Hospital, Montreal, Quebec, Canada
| | - Xiaoyun Zhang
- Departments of Obstetrics and Gynecology and Human Genetics and Division of Experimental Medicine, McGill University Health Center, Royal Victoria Hospital, Montreal, Quebec, Canada
| | - Daniel Cyr
- INRS-Instiut Armand Frappier, Université du Québec, Laval, Québec, Canada
| | - Daniel Dufort
- Departments of Obstetrics and Gynecology and Human Genetics and Division of Experimental Medicine, McGill University Health Center, Royal Victoria Hospital, Montreal, Quebec, Canada
| | - Eric A. Shoubridge
- Montreal Neurological Institute and Department of Human Genetics, McGill University, Montreal, Quebec, Canada
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Harich N, Costa MD, Fernandes V, Kandil M, Pereira JB, Silva NM, Pereira L. The trans-Saharan slave trade - clues from interpolation analyses and high-resolution characterization of mitochondrial DNA lineages. BMC Evol Biol 2010; 10:138. [PMID: 20459715 PMCID: PMC2875235 DOI: 10.1186/1471-2148-10-138] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 05/10/2010] [Indexed: 12/02/2022] Open
Abstract
Background A proportion of 1/4 to 1/2 of North African female pool is made of typical sub-Saharan lineages, in higher frequencies as geographic proximity to sub-Saharan Africa increases. The Sahara was a strong geographical barrier against gene flow, at least since 5,000 years ago, when desertification affected a larger region, but the Arab trans-Saharan slave trade could have facilitate enormously this migration of lineages. Till now, the genetic consequences of these forced trans-Saharan movements of people have not been ascertained. Results The distribution of the main L haplogroups in North Africa clearly reflects the known trans-Saharan slave routes: West is dominated by L1b, L2b, L2c, L2d, L3b and L3d; the Center by L3e and some L3f and L3w; the East by L0a, L3h, L3i, L3x and, in common with the Center, L3f and L3w; while, L2a is almost everywhere. Ages for the haplogroups observed in both sides of the Saharan desert testify the recent origin (holocenic) of these haplogroups in sub-Saharan Africa, claiming a recent introduction in North Africa, further strengthened by the no detection of local expansions. Conclusions The interpolation analyses and complete sequencing of present mtDNA sub-Saharan lineages observed in North Africa support the genetic impact of recent trans-Saharan migrations, namely the slave trade initiated by the Arab conquest of North Africa in the seventh century. Sub-Saharan people did not leave traces in the North African maternal gene pool for the time of its settlement, some 40,000 years ago.
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Affiliation(s)
- Nourdin Harich
- Laboratoire d'Anthropogénétique, Départment de Biologie, Faculté des Sciences, Université Chouaïb Doukkali, El Jadida, Morocco
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Using mitochondrial DNA to test the hypothesis of a European post-glacial human recolonization from the Franco-Cantabrian refuge. Heredity (Edinb) 2010; 106:37-45. [PMID: 20407470 DOI: 10.1038/hdy.2010.47] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
It has been proposed that the distribution patterns and coalescence ages found in Europeans for mitochondrial DNA (mtDNA) haplogroups V, H1 and H3 are the result of a post-glacial expansion from a Franco-Cantabrian refuge that recolonized central and northern areas. In contrast, in this refined mtDNA study of the Cantabrian Cornice that contributes 413 partial and 9 complete new mtDNA sequences, including a large Basque sample and a sample of Asturians, no experimental evidence was found to support the human refuge-expansion theory. In fact, all measures of gene diversity point to the Cantabrian Cornice in general and the Basques in particular, as less polymorphic for V, H1 and H3 than other southern regions in Iberia or in Central Europe. Genetic distances show the Cantabrian Cornice is a very heterogeneous region with significant local differences. The analysis of several minor subhaplogroups, based on complete sequences, also suggests different focal expansions over a local and peninsular range that did not affect continental Europe. Furthermore, all detected clinal trends show stronger longitudinal than latitudinal profiles. In Northern Iberia, it seems that the highest diversity values for some haplogroups with Mesolithic coalescence ages are centred on the Mediterranean side, including Catalonia and South-eastern France.
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37
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SMITH STEVE, TURBILL CHRISTOPHER, SUCHENTRUNK FRANZ. Introducing mother’s curse: low male fertility associated with an imported mtDNA haplotype in a captive colony of brown hares. Mol Ecol 2010; 19:36-43. [DOI: 10.1111/j.1365-294x.2009.04444.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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38
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Mossman JA, Slate J, Birkhead TR. Mitochondrial haplotype does not affect sperm velocity in the zebra finch Taeniopygia guttata. J Evol Biol 2009; 23:422-32. [PMID: 20040001 DOI: 10.1111/j.1420-9101.2009.01913.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mitochondrial DNA (mtDNA) variation has been suggested as a possible cause of variation in male fertility because sperm activity is tightly coupled to mitochondrial oxidative phosphorylation and ATP production, both of which are sensitive to mtDNA mutations. Since male-specific phenotypes such as sperm have no fitness consequences for mitochondria due to maternal mitochondrial (and mtDNA) inheritance, mtDNA mutations that are deleterious in males but which have negligible or no fitness effect in females can persist in populations. How often such mutations arise and persist is virtually unknown. To test whether there were associations between mtDNA variation and sperm performance, we haplotyped 250 zebra finches Taeniopygia guttata from a large pedigreed-population and measured sperm velocity using computer-assisted sperm analysis. Using quantitative genetic 'animal' models, we found no effect of mtDNA haplotype on sperm velocity. Therefore, there is no evidence that in this system mitochondrial mutations have asymmetric fitness effects on males and females, leading to genetic variation in male fertility that is blind to natural selection.
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Affiliation(s)
- J A Mossman
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
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Cerezo M, Bandelt HJ, Martín-Guerrero I, Ardanaz M, Vega A, Carracedo Á, García-Orad Á, Salas A. High mitochondrial DNA stability in B-cell chronic lymphocytic leukemia. PLoS One 2009; 4:e7902. [PMID: 19924307 PMCID: PMC2775629 DOI: 10.1371/journal.pone.0007902] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 10/20/2009] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Chronic Lymphocytic Leukemia (CLL) leads to progressive accumulation of lymphocytes in the blood, bone marrow, and lymphatic tissues. Previous findings have suggested that the mtDNA could play an important role in CLL. METHODOLOGY/PRINCIPAL FINDINGS The mitochondrial DNA (mtDNA) control-region was analyzed in lymphocyte cell DNA extracts and compared with their granulocyte counterpart extract of 146 patients suffering from B-Cell CLL; B-CLL (all recruited from the Basque country). Major efforts were undertaken to rule out methodological artefacts that would render a high false positive rate for mtDNA instabilities and thus lead to erroneous interpretation of sequence instabilities. Only twenty instabilities were finally confirmed, most of them affecting the homopolymeric stretch located in the second hypervariable segment (HVS-II) around position 310, which is well known to constitute an extreme mutational hotspot of length polymorphism, as these mutations are frequently observed in the general human population. A critical revision of the findings in previous studies indicates a lack of proper methodological standards, which eventually led to an overinterpretation of the role of the mtDNA in CLL tumorigenesis. CONCLUSIONS/SIGNIFICANCE Our results suggest that mtDNA instability is not the primary causal factor in B-CLL. A secondary role of mtDNA mutations cannot be fully ruled out under the hypothesis that the progressive accumulation of mtDNA instabilities could finally contribute to the tumoral process. Recommendations are given that would help to minimize erroneous interpretation of sequencing results in mtDNA studies in tumorigenesis.
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MESH Headings
- Base Sequence
- DNA Primers/genetics
- DNA, Mitochondrial/genetics
- Databases, Genetic
- Granulocytes/cytology
- Haplotypes
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Lymphocytes/cytology
- Models, Statistical
- Molecular Sequence Data
- Mutation
- Phylogeny
- Sequence Analysis, DNA
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Affiliation(s)
- María Cerezo
- Unidade de Xenética, Instituto de Medicina Legal, and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | | | - Idoia Martín-Guerrero
- Laboratorio Interdepartamental de Medicina Molecular, Departamento de Genética Antropología Física y Fisiología Animal, Facultad de Medicina, Universidad del País Vasco- Euskal Herriko Unibertsitatea, Leioa, Spain
| | - Maite Ardanaz
- Servicio de Hematología, Hospital Txagorritxu, Vitoria, Spain
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Hospital Clínico Universitario, Universidad de Santiago de Compostela, Galicia, Spain
| | - Ángel Carracedo
- Unidade de Xenética, Instituto de Medicina Legal, and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - África García-Orad
- Laboratorio Interdepartamental de Medicina Molecular, Departamento de Genética Antropología Física y Fisiología Animal, Facultad de Medicina, Universidad del País Vasco- Euskal Herriko Unibertsitatea, Leioa, Spain
| | - Antonio Salas
- Unidade de Xenética, Instituto de Medicina Legal, and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia, Spain
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40
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Kujanová M, Pereira L, Fernandes V, Pereira JB, Cerný V. Near eastern neolithic genetic input in a small oasis of the Egyptian Western Desert. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2009; 140:336-46. [PMID: 19425100 DOI: 10.1002/ajpa.21078] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Egyptian Western Desert lies on an important geographic intersection between Africa and Asia. Genetic diversity of this region has been shaped, in part, by climatic changes in the Late Pleistocene and Holocene epochs marked by oscillating humid and arid periods. We present here a whole genome analysis of mitochondrial DNA (mtDNA) and high-resolution molecular analysis of nonrecombining Y-chromosomal (NRY) gene pools of a demographically small but autochthonous population from the Egyptian Western Desert oasis el-Hayez. Notwithstanding signs of expected genetic drift, we still found clear genetic evidence of a strong Near Eastern input that can be dated into the Neolithic. This is revealed by high frequencies and high internal variability of several mtDNA lineages from haplogroup T. The whole genome sequencing strategy and molecular dating allowed us to detect the accumulation of local mtDNA diversity to 5,138 +/- 3,633 YBP. Similarly, theY-chromosome gene pool reveals high frequencies of the Near Eastern J1 and the North African E1b1b1b lineages, both generally known to have expanded within North Africa during the Neolithic. These results provide another piece of evidence of the relatively young population history of North Africa.
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Affiliation(s)
- Martina Kujanová
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
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41
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Unckless RL, Herren JK. Population genetics of sexually antagonistic mitochondrial mutants under inbreeding. J Theor Biol 2009; 260:132-6. [DOI: 10.1016/j.jtbi.2009.06.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Revised: 06/01/2009] [Accepted: 06/02/2009] [Indexed: 10/20/2022]
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Soares P, Ermini L, Thomson N, Mormina M, Rito T, Röhl A, Salas A, Oppenheimer S, Macaulay V, Richards MB. Correcting for purifying selection: an improved human mitochondrial molecular clock. Am J Hum Genet 2009; 84:740-59. [PMID: 19500773 DOI: 10.1016/j.ajhg.2009.05.001] [Citation(s) in RCA: 487] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Revised: 04/20/2009] [Accepted: 05/01/2009] [Indexed: 11/15/2022] Open
Abstract
There is currently no calibration available for the whole human mtDNA genome, incorporating both coding and control regions. Furthermore, as several authors have pointed out recently, linear molecular clocks that incorporate selectable characters are in any case problematic. We here confirm a modest effect of purifying selection on the mtDNA coding region and propose an improved molecular clock for dating human mtDNA, based on a worldwide phylogeny of > 2000 complete mtDNA genomes and calibrating against recent evidence for the divergence time of humans and chimpanzees. We focus on a time-dependent mutation rate based on the entire mtDNA genome and supported by a neutral clock based on synonymous mutations alone. We show that the corrected rate is further corroborated by archaeological dating for the settlement of the Canary Islands and Remote Oceania and also, given certain phylogeographic assumptions, by the timing of the first modern human settlement of Europe and resettlement after the Last Glacial Maximum. The corrected rate yields an age of modern human expansion in the Americas at approximately 15 kya that-unlike the uncorrected clock-matches the archaeological evidence, but continues to indicate an out-of-Africa dispersal at around 55-70 kya, 5-20 ky before any clear archaeological record, suggesting the need for archaeological research efforts focusing on this time window. We also present improved rates for the mtDNA control region, and the first comprehensive estimates of positional mutation rates for human mtDNA, which are essential for defining mutation models in phylogenetic analyses.
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Affiliation(s)
- Pedro Soares
- Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
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43
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Pereira L, Freitas F, Fernandes V, Pereira JB, Costa MD, Costa S, Máximo V, Macaulay V, Rocha R, Samuels DC. The diversity present in 5140 human mitochondrial genomes. Am J Hum Genet 2009; 84:628-40. [PMID: 19426953 DOI: 10.1016/j.ajhg.2009.04.013] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Revised: 04/10/2009] [Accepted: 04/20/2009] [Indexed: 11/26/2022] Open
Abstract
We analyzed the current status (as of the end of August 2008) of human mitochondrial genomes deposited in GenBank, amounting to 5140 complete or coding-region sequences, in order to present an overall picture of the diversity present in the mitochondrial DNA of the global human population. To perform this task, we developed mtDNA-GeneSyn, a computer tool that identifies and exhaustedly classifies the diversity present in large genetic data sets. The diversity observed in the 5140 human mitochondrial genomes was compared with all possible transitions and transversions from the standard human mitochondrial reference genome. This comparison showed that tRNA and rRNA secondary structures have a large effect in limiting the diversity of the human mitochondrial sequences, whereas for the protein-coding genes there is a bias toward less variation at the second codon positions. The analysis of the observed amino acid variations showed a tolerance of variations that convert between the amino acids V, I, A, M, and T. This defines a group of amino acids with similar chemical properties that can interconvert by a single transition.
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Breton S, Stewart DT, Blier PU. Role-reversal of gender-associated mitochondrial DNA affects mitochondrial function in Mytilus edulis (Bivalvia: Mytilidae). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2009; 312:108-17. [PMID: 19097171 DOI: 10.1002/jez.b.20251] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Mussel species of the genus Mytilus possess an unusual system of mitochondrial DNA (mtDNA) transmission termed doubly uniparental inheritance. They are characterized by the presence of two highly divergent gender-associated mtDNA genomes (often with>20 and>10% divergences in DNA and amino acid sequences, respectively) that are inherited either maternally (F mtDNA) or paternally (M mtDNA). Females are typically homoplasmic for the F mtDNA and males are heteroplasmic with the F mtDNA being most common in all tissues except the gonad that is dominated by the M mtDNA. Collectively, males are polymorphic for two classes of M mtDNAs known as the "standard male" and "recently masculinized" M types (SM and RM, respectively). The coding portions of the RM mtDNA genome differ from the SM mtDNA by as much as the maternally inherited F mtDNA genome differs from the SM type. Because the SM and RM types exhibit considerable amino acid sequence divergence, we hypothesized that these differences could affect mitochondrial respiratory chain complex enzyme activities. To test this hypothesis, the activity of the major mitochondrial respiratory chain complexes (complexes II, I+III and IV) as well as the activity of citrate synthase were measured on gonad samples from males containing either the SM or RM mtDNA. Our data demonstrate that the mitochondrial subunits encoded by the RM mtDNA are associated with higher enzymatic activities than the gene products of the SM mtDNA.
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Affiliation(s)
- Sophie Breton
- Département de Biologie, Université du Québec à Rimouski, Rimouski, Qué., Canada.
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Costa MD, Cherni L, Fernandes V, Freitas F, Ammar El Gaaied AB, Pereira L. Data from complete mtDNA sequencing of Tunisian centenarians: testing haplogroup association and the "golden mean" to longevity. Mech Ageing Dev 2008; 130:222-6. [PMID: 19133286 DOI: 10.1016/j.mad.2008.12.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2008] [Revised: 11/18/2008] [Accepted: 12/06/2008] [Indexed: 10/21/2022]
Abstract
Since the mitochondrial theory of ageing was proposed, mitochondrial DNA (mtDNA) diversity has been largely studied in old people, however complete genomes are still rare, being limited to Japanese and UK/US samples. In this work, we evaluated possible longevity associated polymorphisms/haplogroups in an African population, from Tunisia, by performing complete mtDNA sequencing. This population has a mixed Eurasian/sub-Saharan mtDNA gene pool, which could potentially facilitate the evaluation of association for sub-Saharan lineages. Sub-Saharan haplogroups were shown to be significantly less represented in centenarians (9.5%) than in controls (54.5%), but it is not possible to rule out an influence of population structure, which is high in these populations. No recurrent polymorphism were more frequent in centenarians than in controls, and although the Tunisian centenarians presented less synonymous and replacement polymorphisms than controls, this difference was not statistically significant. So far, it does not seem that centenarians have significantly less mildly deleterious substitutions, not only in Tunisia but also in Japanese and UK/US samples, as tested here, not favouring a "golden mean" to longevity.
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Affiliation(s)
- Marta D Costa
- IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Porto, Portugal
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46
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Les souris génétiquement modifiées au service de la reproduction. ACTA ACUST UNITED AC 2008; 36:1224-9. [DOI: 10.1016/j.gyobfe.2008.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2008] [Accepted: 10/03/2008] [Indexed: 11/22/2022]
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47
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Ermini L, Olivieri C, Rizzi E, Corti G, Bonnal R, Soares P, Luciani S, Marota I, De Bellis G, Richards MB, Rollo F. Complete mitochondrial genome sequence of the Tyrolean Iceman. Curr Biol 2008; 18:1687-93. [PMID: 18976917 DOI: 10.1016/j.cub.2008.09.028] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Revised: 08/22/2008] [Accepted: 09/03/2008] [Indexed: 11/29/2022]
Abstract
The Tyrolean Iceman was a witness to the Neolithic-Copper Age transition in Central Europe 5350-5100 years ago, and his mummified corpse was recovered from an Alpine glacier on the Austro-Italian border in 1991 [1]. Using a mixed sequencing procedure based on PCR amplification and 454 sequencing of pooled amplification products, we have retrieved the first complete mitochondrial-genome sequence of a prehistoric European. We have then compared it with 115 related extant lineages from mitochondrial haplogroup K. We found that the Iceman belonged to a branch of mitochondrial haplogroup K1 that has not yet been identified in modern European populations. This is the oldest complete Homo sapiens mtDNA genome generated to date. The results point to the potential significance of complete-ancient-mtDNA studies in addressing questions concerning the genetic history of human populations that the phylogeography of modern lineages is unable to tackle.
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Affiliation(s)
- Luca Ermini
- Laboratorio di Archeo-Antropologia Molecolare/DNA Antico, Dipartimento di Biologia Molecolare, Cellulare e Animale, University of Camerino, 62032 Camerino, Italy
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49
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Dahmani Y, Marcuello A, Díez-Sanchez C, Ruiz-Pesini E, Montoya J, López-Pérez MJ. Association of human mitochondrial DNA variants with plasma LDL levels. Mitochondrion 2008; 8:247-53. [DOI: 10.1016/j.mito.2008.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Revised: 03/05/2008] [Accepted: 04/15/2008] [Indexed: 10/22/2022]
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50
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Pereira L, Gonçalves J, Bandelt HJ. Mutation C11994T in the mitochondrial ND4 gene is not a cause of low sperm motility in Portugal. Fertil Steril 2008; 89:738-41. [PMID: 17517394 DOI: 10.1016/j.fertnstert.2007.03.048] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Revised: 03/13/2007] [Accepted: 03/13/2007] [Indexed: 11/26/2022]
Abstract
It has recently been suggested that a hitherto unobserved mutation, C11994T, causes oligoasthenozoospermia in men from India but at the same time does not affect systems other than the motility of the sperm. There are good reasons to question this proposition, in view of the worldwide mtDNA database and the Indian record in particular. We have further analyzed the oligoasthenozoospermic samples from a previous systematic study of infertile Portuguese men and found no instance of C11994T.
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Affiliation(s)
- Luísa Pereira
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
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