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Halachev M, Gountouna VE, Meynert A, Tzoneva G, Shuldiner AR, Semple CA, Wilson JF. Regionally enriched rare deleterious exonic variants in the UK and Ireland. Nat Commun 2024; 15:8454. [PMID: 39358353 PMCID: PMC11446911 DOI: 10.1038/s41467-024-51604-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 08/13/2024] [Indexed: 10/04/2024] Open
Abstract
It is unclear how patterns of regional genetic differentiation in the UK and Ireland might impact the protein-coding fraction of the genome. We exploit UK Biobank (UKB) and Viking Genes whole exome sequencing data to study regional genetic differentiation across the UK and Ireland in protein coding genes, encompassing 44,696 unrelated individuals from 20 regions of origin. We demonstrate substantial exonic differentiation among Shetlanders, Orcadians, individuals with full or partial Ashkenazi Jewish ancestry and in several mainland regions (particularly north and south Wales, southeast Scotland and Ireland). With stringent filtering criteria, we find 67 regionally enriched (≥5-fold) variants likely to have adverse biomedical consequences in homozygous individuals. Here, we show that regional genetic variation across the UK and Ireland should be considered in the design of genetic studies and may inform effective genetic screening and counselling.
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Affiliation(s)
- Mihail Halachev
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
| | - Viktoria-Eleni Gountouna
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Alison Meynert
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | | | - Colin A Semple
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
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2
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Xu Y, Baylink DJ, Xiao J, Tran L, Nguyen V, Park B, Valladares I, Lee S, Codorniz K, Tan L, Chen CS, Abdel-Azim H, Reeves ME, Mirshahidi H, Marcucci G, Cao H. Discovery of NFκB2-Coordinated Dual Regulation of Mitochondrial and Nuclear Genomes Leads to an Effective Therapy for Acute Myeloid Leukemia. Int J Mol Sci 2024; 25:8532. [PMID: 39126100 PMCID: PMC11313218 DOI: 10.3390/ijms25158532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 07/31/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
Acute myeloid leukemia (AML) has a poor survival rate for both pediatric and adult patients due to its frequent relapse. To elucidate the bioenergetic principle underlying AML relapse, we investigated the transcriptional regulation of mitochondrial-nuclear dual genomes responsible for metabolic plasticity in treatment-resistant blasts. Both the gain and loss of function results demonstrated that NFκB2, a noncanonical transcription factor (TF) of the NFκB (nuclear factor kappa-light-chain-enhancer of activated B cells) family, can control the expression of TFAM (mitochondrial transcription factor A), which is known to be essential for metabolic biogenesis. Furthermore, genetic tracking and promoter assays revealed that NFκB2 is in the mitochondria and can bind the specific "TTGGGGGGTG" region of the regulatory D-loop domain to activate the light-strand promoter (LSP) and heavy-strand promoter 1 (HSP1), promoters of the mitochondrial genome. Based on our discovery of NFκB2's novel function of regulating mitochondrial-nuclear dual genomes, we explored a novel triplet therapy including inhibitors of NFκB2, tyrosine kinase, and mitochondrial ATP synthase that effectively eliminated primary AML blasts with mutations of the FMS-related receptor tyrosine kinase 3 (FLT3) and displayed minimum toxicity to control cells ex vivo. As such, effective treatments for AML must include strong inhibitory actions on the dual genomes mediating metabolic plasticity to improve leukemia prognosis.
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Affiliation(s)
- Yi Xu
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (C.-S.C.)
- Division Regenerative Medicine, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
- Cancer Center, Loma Linda University, Loma Linda, CA 92354, USA
| | - David J. Baylink
- Division Regenerative Medicine, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Jeffrey Xiao
- Division Regenerative Medicine, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Lily Tran
- Division Regenerative Medicine, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Vinh Nguyen
- Division Regenerative Medicine, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Brandon Park
- Division Regenerative Medicine, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Ismael Valladares
- Division Regenerative Medicine, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Scott Lee
- Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Kevin Codorniz
- Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Laren Tan
- Division of Pulmonary, Critical Care, Hyperbaric and Sleep Medicine, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Chien-Shing Chen
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (C.-S.C.)
- Cancer Center, Loma Linda University, Loma Linda, CA 92354, USA
| | - Hisham Abdel-Azim
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (C.-S.C.)
- Division of Transplant and Cell Therapy, Loma Linda University Cancer Center, Loma Linda, CA 92354, USA
- Division of Hematology and Oncology, Department of Pediatrics, Loma Linda University, Loma Linda, CA 92354, USA
| | - Mark E. Reeves
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (C.-S.C.)
- Cancer Center, Loma Linda University, Loma Linda, CA 92354, USA
| | - Hamid Mirshahidi
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (C.-S.C.)
- Cancer Center, Loma Linda University, Loma Linda, CA 92354, USA
| | - Guido Marcucci
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA 91010, USA
| | - Huynh Cao
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (C.-S.C.)
- Cancer Center, Loma Linda University, Loma Linda, CA 92354, USA
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3
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Borisova TV, Cherdonova AM, Pshennikova VG, Teryutin FM, Morozov IV, Bondar AA, Baturina OA, Kabilov MR, Romanov GP, Solovyev AV, Fedorova SA, Barashkov NA. High prevalence of m.1555A > G in patients with hearing loss in the Baikal Lake region of Russia as a result of founder effect. Sci Rep 2024; 14:15342. [PMID: 38961196 PMCID: PMC11222474 DOI: 10.1038/s41598-024-66254-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 07/01/2024] [Indexed: 07/05/2024] Open
Abstract
Mitochondrial forms account approximately 1-2% of all nonsyndromic cases of hearing loss (HL). One of the most common causative variants of mtDNA is the m.1555A > G variant of the MT-RNR1 gene (OMIM 561000). Currently the detection of the m.1555A > G variant of the MT-RNR1 gene is not included in all research protocols. In this study this variant was screened among 165 patients with HL from the Republic of Buryatia, located in the Baikal Lake region of Russia. In our study, the total contribution of the m.1555A > G variant to the etiology of HL was 12.7% (21/165), while the update global prevalence of this variant is 1.8% (863/47,328). The m.1555A > G variant was notably more prevalent in Buryat (20.2%) than in Russian patients (1.3%). Mitogenome analysis in 14 unrelated Buryat families carrying the m.1555A > G variant revealed a predominant lineage: in 13 families, a cluster affiliated with sub-haplogroup A5b (92.9%) was identified, while one family had the D5a2a1 lineage (7.1%). In a Russian family with the m.1555A > G variant the lineage affiliated with sub-haplogroup F1a1d was found. Considering that more than 90% of Buryat families with the m.1555A > G variant belong to the single maternal lineage cluster we conclude that high prevalence of this variant in patients with HL in the Baikal Lake region can be attributed to a founder effect.
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Affiliation(s)
- Tuyara V Borisova
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
| | - Aleksandra M Cherdonova
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
| | - Vera G Pshennikova
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677000, Yakutsk, Russia
| | - Fedor M Teryutin
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677000, Yakutsk, Russia
| | - Igor V Morozov
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Akademika Lavrentieva 8, 630090, Novosibirsk, Russia
- Novosibirsk State University, 630090, Novosibirsk, Russia
| | - Alexander A Bondar
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Akademika Lavrentieva 8, 630090, Novosibirsk, Russia
| | - Olga A Baturina
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Akademika Lavrentieva 8, 630090, Novosibirsk, Russia
| | - Marsel R Kabilov
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Akademika Lavrentieva 8, 630090, Novosibirsk, Russia
| | - Georgii P Romanov
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
| | - Aisen V Solovyev
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
| | - Sardana A Fedorova
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677000, Yakutsk, Russia
| | - Nikolay A Barashkov
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia.
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677000, Yakutsk, Russia.
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4
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Axelsson EY, Khrennikov A. Generation of genetic codes with 2-adic codon algebra and adaptive dynamics. Biosystems 2024; 240:105230. [PMID: 38740125 DOI: 10.1016/j.biosystems.2024.105230] [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: 03/18/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
This is a brief review on modeling genetic codes with the aid of 2-adic dynamical systems. In this model amino acids are encoded by the attractors of such dynamical systems. Each genetic code is coupled to the special class of 2-adic dynamics. We consider the discrete dynamical systems, These are the iterations of a function F:Z2→Z2, where Z2 is the ring of 2-adic numbers (2-adic tree). A genetic code is characterized by the set of attractors of a function belonging to the code generating functional class. The main mathematical problem is to reduce degeneration of dynamic representation and select the optimal generating function. Here optimality can be treated in many ways. One possibility is to consider the Lipschitz functions playing the crucial role in general theory of iterations. Then we minimize the Lip-constant. The main issue is to find the proper biological interpretation of code-functions. One can speculate that the evolution of the genetic codes can be described in information space of the nucleotide-strings endowed with ultrametric (treelike) geometry. A code-function is a fitness function; the solutions of the genetic code optimization problem are attractors of the code-function. We illustrate this approach by generation of the standard nuclear and (vertebrate) mitochondrial genetics codes.
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Affiliation(s)
- Ekaterina Yurova Axelsson
- International Center for Mathematical Modeling in Physics, Engineering, Economics, and Cognitive Science Linnaeus University, Växjö-Kalmar, Sweden
| | - Andrei Khrennikov
- International Center for Mathematical Modeling in Physics, Engineering, Economics, and Cognitive Science Linnaeus University, Växjö-Kalmar, Sweden.
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5
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Diamantidis D, Fan WTL, Birkner M, Wakeley J. Bursts of coalescence within population pedigrees whenever big families occur. Genetics 2024; 227:iyae030. [PMID: 38408329 DOI: 10.1093/genetics/iyae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 01/23/2024] [Accepted: 02/18/2024] [Indexed: 02/28/2024] Open
Abstract
We consider a simple diploid population-genetic model with potentially high variability of offspring numbers among individuals. Specifically, against a backdrop of Wright-Fisher reproduction and no selection, there is an additional probability that a big family occurs, meaning that a pair of individuals has a number of offspring on the order of the population size. We study how the pedigree of the population generated under this model affects the ancestral genetic process of a sample of size two at a single autosomal locus without recombination. Our population model is of the type for which multiple-merger coalescent processes have been described. We prove that the conditional distribution of the pairwise coalescence time given the random pedigree converges to a limit law as the population size tends to infinity. This limit law may or may not be the usual exponential distribution of the Kingman coalescent, depending on the frequency of big families. But because it includes the number and times of big families, it differs from the usual multiple-merger coalescent models. The usual multiple-merger coalescent models are seen as describing the ancestral process marginal to, or averaging over, the pedigree. In the limiting ancestral process conditional on the pedigree, the intervals between big families can be modeled using the Kingman coalescent but each big family causes a discrete jump in the probability of coalescence. Analogous results should hold for larger samples and other population models. We illustrate these results with simulations and additional analysis, highlighting their implications for inference and understanding of multilocus data.
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Affiliation(s)
| | - Wai-Tong Louis Fan
- Department of Mathematics, Indiana University, Bloomington, IN 47405, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Matthias Birkner
- Institut für Mathematik, Johannes-Gutenberg-Universität, 55099 Mainz, Germany
| | - John Wakeley
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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6
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Foley RA, Mirazón Lahr M. Ghosts of extinct apes: genomic insights into African hominid evolution. Trends Ecol Evol 2024; 39:456-466. [PMID: 38302324 DOI: 10.1016/j.tree.2023.12.009] [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: 04/04/2023] [Revised: 12/13/2023] [Accepted: 12/22/2023] [Indexed: 02/03/2024]
Abstract
We are accustomed to regular announcements of new hominin fossils. There are now some 6000 hominin fossils, and up to 31 species. However, where are the announcements of African ape fossils? The answer is that there are almost none. Our knowledge of African ape evolution is based entirely on genomic analyses, which show that extant diversity is very young. This contrasts with the extensive and deep diversity of hominins known from fossils. Does this difference point to low and late diversification of ape lineages, or high rates of extinction? The comparative evolutionary dynamics of African hominids are central to interpreting living ape adaptations, as well as understanding the patterns of hominin evolution and the nature of the last common ancestor.
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Affiliation(s)
- Robert A Foley
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, The Henry Wellcome Building, Fitzwilliam Street, Cambridge, CB2 1QH, UK.
| | - Marta Mirazón Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, The Henry Wellcome Building, Fitzwilliam Street, Cambridge, CB2 1QH, UK
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7
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Kappelman J, Todd LC, Davis CA, Cerling TE, Feseha M, Getahun A, Johnsen R, Kay M, Kocurek GA, Nachman BA, Negash A, Negash T, O'Brien K, Pante M, Ren M, Smith EI, Tabor NJ, Tewabe D, Wang H, Yang D, Yirga S, Crowell JW, Fanuka MF, Habtie T, Hirniak JN, Klehm C, Loewen ND, Melaku S, Melton SM, Myers TS, Millonig S, Plummer MC, Riordan KJ, Rosenau NA, Skinner A, Thompson AK, Trombetta LM, Witzel A, Assefa E, Bodansky M, Desta AA, Campisano CJ, Dalmas D, Elliott C, Endalamaw M, Ford NJ, Foster F, Getachew T, Haney YL, Ingram BH, Jackson J, Marean CW, Mattox S, de la Cruz Medina K, Mulubrhan G, Porter K, Roberts A, Santillan P, Sollenberger A, Sponholtz J, Valdes J, Wyman L, Yadeta M, Yanny S. Adaptive foraging behaviours in the Horn of Africa during Toba supereruption. Nature 2024; 628:365-372. [PMID: 38509364 DOI: 10.1038/s41586-024-07208-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 02/19/2024] [Indexed: 03/22/2024]
Abstract
Although modern humans left Africa multiple times over 100,000 years ago, those broadly ancestral to non-Africans dispersed less than 100,000 years ago1. Most models hold that these events occurred through green corridors created during humid periods because arid intervals constrained population movements2. Here we report an archaeological site-Shinfa-Metema 1, in the lowlands of northwest Ethiopia, with Youngest Toba Tuff cryptotephra dated to around 74,000 years ago-that provides early and rare evidence of intensive riverine-based foraging aided by the likely adoption of the bow and arrow. The diet included a wide range of terrestrial and aquatic animals. Stable oxygen isotopes from fossil mammal teeth and ostrich eggshell show that the site was occupied during a period of high seasonal aridity. The unusual abundance of fish suggests that capture occurred in the ever smaller and shallower waterholes of a seasonal river during a long dry season, revealing flexible adaptations to challenging climatic conditions during the Middle Stone Age. Adaptive foraging along dry-season waterholes would have transformed seasonal rivers into 'blue highway' corridors, potentially facilitating an out-of-Africa dispersal and suggesting that the event was not restricted to times of humid climates. The behavioural flexibility required to survive seasonally arid conditions in general, and the apparent short-term effects of the Toba supereruption in particular were probably key to the most recent dispersal and subsequent worldwide expansion of modern humans.
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Affiliation(s)
- John Kappelman
- Department of Anthropology, The University of Texas, Austin, TX, USA.
- Department of Earth and Planetary Sciences, The University of Texas, Austin, TX, USA.
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA.
| | - Lawrence C Todd
- Department of Anthropology, The University of Texas, Austin, TX, USA
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
| | | | - Thure E Cerling
- Department of Geology and Geophysics, University of Utah, Salt Lake City, UT, USA
| | - Mulugeta Feseha
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
- Paleoanthropology and Paleoenvironment Program, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abebe Getahun
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
- Department of Zoological Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Racheal Johnsen
- Department of Geoscience, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Marvin Kay
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
- Department of Anthropology, University of Arkansas, Fayetteville, AR, USA
| | - Gary A Kocurek
- Department of Earth and Planetary Sciences, The University of Texas, Austin, TX, USA
| | - Brett A Nachman
- Department of Anthropology, The University of Texas, Austin, TX, USA
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
| | - Agazi Negash
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
- Paleoanthropology and Paleoenvironment Program, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tewabe Negash
- Paleoanthropology and Paleoenvironment Program, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Anthropology and Geography, Colorado State University, Fort Collins, CO, USA
| | - Kaedan O'Brien
- Department of Anthropology, University of Utah, Salt Lake City, UT, USA
- Natural History Museum of Utah, University of Utah, Salt Lake City, UT, USA
| | - Michael Pante
- Department of Anthropology and Geography, Colorado State University, Fort Collins, CO, USA
| | - Minghua Ren
- Department of Geoscience, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Eugene I Smith
- Department of Geoscience, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Neil J Tabor
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
- Huffington Department of Earth Sciences, Southern Methodist University, Dallas, TX, USA
| | - Dereje Tewabe
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
- Bahir Dar Fisheries and Other Aquatic Life Research Centre, Bahir Dar, Ethiopia
| | - Hong Wang
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
- Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Deming Yang
- Department of Geology and Geophysics, University of Utah, Salt Lake City, UT, USA
| | - Solomon Yirga
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
- Department of Zoological Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jordan W Crowell
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
| | - Matthew F Fanuka
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
| | - Teshager Habtie
- Department of History and Heritage Management, University of Gondar, Gondar, Ethiopia
| | - Jayde N Hirniak
- Institute of Human Origins, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Carla Klehm
- Department of Anthropology, The University of Texas, Austin, TX, USA
| | | | | | - Sierra M Melton
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
| | - Timothy S Myers
- Huffington Department of Earth Sciences, Southern Methodist University, Dallas, TX, USA
| | - Sarah Millonig
- Department of Anthropology and Geography, Colorado State University, Fort Collins, CO, USA
| | - Megan C Plummer
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
| | - Keenan J Riordan
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
| | - Nicholas A Rosenau
- Huffington Department of Earth Sciences, Southern Methodist University, Dallas, TX, USA
| | - Anne Skinner
- Chemistry Department, Williams College, Williamstown, MA, USA
| | - Abraham K Thompson
- Department of Anthropology and Geography, Colorado State University, Fort Collins, CO, USA
| | - Lindsey M Trombetta
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
| | - Adrienne Witzel
- Department of Anthropology, The University of Texas, Austin, TX, USA
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
| | - Ephrem Assefa
- Paleoanthropology and Paleoenvironment Program, Addis Ababa University, Addis Ababa, Ethiopia
| | - Maria Bodansky
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
| | - Ayenachew A Desta
- Department of Geology, School of Earth Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - Christopher J Campisano
- Institute of Human Origins, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Daniel Dalmas
- Department of Anthropology, University of Utah, Salt Lake City, UT, USA
- Iowa State University, Ames, IA, USA
| | - Connor Elliott
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
| | - Metasebia Endalamaw
- Paleoanthropology and Paleoenvironment Program, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Heritage Authority, Addis Ababa, Ethiopia
| | - Nicholas J Ford
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
| | - Frederick Foster
- Department of Anthropology, Rutgers University, New Brunswick, NJ, USA
| | - Tomas Getachew
- Ethiopian Heritage Authority, Addis Ababa, Ethiopia
- Laboratoire Paléontologie Évolution Paléoécosystèmes Paléoprimatologie, Université de Poitiers, Poitiers, France
| | - Yibai Li Haney
- Chemistry Department, Williams College, Williamstown, MA, USA
| | - Brittney H Ingram
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
| | - Jonayah Jackson
- Chemistry Department, Williams College, Williamstown, MA, USA
| | - Curtis W Marean
- Institute of Human Origins, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
- African Centre for Coastal Palaeoscience, Nelson Mandela University, Gqeberha, South Africa
| | - Sissi Mattox
- Department of Anthropology, The University of Texas, Austin, TX, USA
| | - Karla de la Cruz Medina
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
| | - Gebretsadkan Mulubrhan
- Paleoanthropology and Paleoenvironment Program, Addis Ababa University, Addis Ababa, Ethiopia
| | - Keri Porter
- Department of Anthropology, The University of Texas, Austin, TX, USA
| | - Alexis Roberts
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
| | - Perla Santillan
- Department of Anthropology, The University of Texas, Austin, TX, USA
| | - Alaric Sollenberger
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
| | - Julia Sponholtz
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
| | - Jessica Valdes
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
| | - Lani Wyman
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
| | - Meklit Yadeta
- Paleoanthropology and Paleoenvironment Program, Addis Ababa University, Addis Ababa, Ethiopia
- Huffington Department of Earth Sciences, Southern Methodist University, Dallas, TX, USA
| | - Sierra Yanny
- National Science Foundation Research Experience for Undergraduates Program, Department of Anthropology, The University of Texas, Austin, TX, USA
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8
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Beattie JM, Castiello T, Jaarsma T. The Importance of Cultural Awareness in the Management of Heart Failure: A Narrative Review. Vasc Health Risk Manag 2024; 20:109-123. [PMID: 38495057 PMCID: PMC10944309 DOI: 10.2147/vhrm.s392636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/27/2024] [Indexed: 03/19/2024] Open
Abstract
Heart failure is a commonly encountered clinical syndrome arising from a range of etiologic cardiovascular diseases and manifests in a phenotypic spectrum of varying degrees of systolic and diastolic ventricular dysfunction. Those affected by this life-limiting illness are subject to an array of burdensome symptoms, poor quality of life, prognostic uncertainty, and a relatively onerous and increasingly complex treatment regimen. This condition occurs in epidemic proportions worldwide, and given the demographic trend in societal ageing, the prevalence of heart failure is only likely to increase. The marked upturn in international migration has generated other demographic changes in recent years, and it is evident that we are living and working in ever more ethnically and culturally diverse communities. Professionals treating those with heart failure are now dealing with a much more culturally disparate clinical cohort. Given that the heart failure disease trajectory is unique to each individual, these clinicians need to ensure that their proposed treatment options and responses to the inevitable crises intrinsic to this condition are in keeping with the culturally determined values, preferences, and worldviews of these patients and their families. In this narrative review, we describe the importance of cultural awareness across a range of themes relevant to heart failure management and emphasize the centrality of cultural competence as the basis of appropriate care provision.
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Affiliation(s)
- James M Beattie
- School of Cardiovascular Medicine and Sciences, King’s College London, London, UK
- Department of Palliative Care and Rehabilitation, Cicely Saunders Institute, King’s College London, London, UK
| | - Teresa Castiello
- Department of Cardiology, Croydon University Hospital, London, UK
- Department of Cardiovascular Imaging, King’s College London, London, UK
| | - Tiny Jaarsma
- Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
- Department of Nursing Science, Julius Center, University Medical Center Utrecht, Utrecht, the Netherlands
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9
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Padilla-Iglesias C, Derkx I. Hunter-gatherer genetics research: Importance and avenues. EVOLUTIONARY HUMAN SCIENCES 2024; 6:e15. [PMID: 38516374 PMCID: PMC10955370 DOI: 10.1017/ehs.2024.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 01/17/2024] [Accepted: 02/02/2024] [Indexed: 03/23/2024] Open
Abstract
Major developments in the field of genetics in the past few decades have revolutionised notions of what it means to be human. Although currently only a few populations around the world practise a hunting and gathering lifestyle, this mode of subsistence has characterised members of our species since its very origins and allowed us to migrate across the planet. Therefore, the geographical distribution of hunter-gatherer populations, dependence on local ecosystems and connections to past populations and neighbouring groups have provided unique insights into our evolutionary origins. However, given the vulnerable status of hunter-gatherers worldwide, the development of the field of anthropological genetics requires that we reevaluate how we conduct research with these communities. Here, we review how the inclusion of hunter-gatherer populations in genetics studies has advanced our understanding of human origins, ancient population migrations and interactions as well as phenotypic adaptations and adaptability to different environments, and the important scientific and medical applications of these advancements. At the same time, we highlight the necessity to address yet unresolved questions and identify areas in which the field may benefit from improvements.
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Affiliation(s)
| | - Inez Derkx
- Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
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10
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Byappanahalli AM, Omoniyi V, Noren Hooten N, Smith JT, Mode NA, Ezike N, Zonderman AB, Evans MK. Extracellular vesicle mitochondrial DNA levels are associated with race and mitochondrial DNA haplogroup. iScience 2024; 27:108724. [PMID: 38226163 PMCID: PMC10788249 DOI: 10.1016/j.isci.2023.108724] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/08/2023] [Accepted: 12/11/2023] [Indexed: 01/17/2024] Open
Abstract
Circulating cell-free mitochondrial DNA (ccf-mtDNA) acts as a damage-associated molecular pattern molecule and may be cargo within extracellular vesicles (EVs). ccf-mtDNA and select mitochondrial DNA (mtDNA) haplogroups are associated with cardiovascular disease. We hypothesized that ccf-mtDNA and plasma EV mtDNA would be associated with hypertension, sex, self-identified race, and mtDNA haplogroup ancestry. Participants were normotensive (n = 107) and hypertensive (n = 108) African American and White adults from the Healthy Aging in Neighborhoods of Diversity across the Life Span study. ccf-mtDNA levels were higher in African American participants compared with White participants in both plasma and EVs, but ccf-mtDNA levels were not related to hypertension. EV mtDNA levels were highest in African American participants with African mtDNA haplogroup. Circulating inflammatory protein levels were altered with mtDNA haplogroup, race, and EV mtDNA. Our findings highlight that race is a social construct and that ancestry is crucial when examining health and biomarker differences between groups.
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Affiliation(s)
- Anjali M. Byappanahalli
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Victor Omoniyi
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Nicole Noren Hooten
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Jessica T. Smith
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Nicolle A. Mode
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Ngozi Ezike
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Alan B. Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Michele K. Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
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11
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Kitayama S, Salvador CE. Cultural Psychology: Beyond East and West. Annu Rev Psychol 2024; 75:495-526. [PMID: 37585666 DOI: 10.1146/annurev-psych-021723-063333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Research in cultural psychology over the last three decades has revealed the profound influence of culture on cognitive, emotional, and motivational processes shaping individuals into active agents. This article aims to show cultural psychology's promise in three key steps. First, we review four notable cultural dimensions believed to underlie cultural variations: independent versus interdependent self, individualism versus collectivism, tightness versus looseness of social norms, and relational mobility. Second, we examine how ecology and geography shape human activities and give rise to organized systems of cultural practices and meanings, called eco-cultural complexes. In turn, the eco-cultural complex of each zone is instrumental in shaping a wide range of psychological processes, revealing a psychological diversity that extends beyond the scope of the current East-West literature. Finally, we examine some of the non-Western cultural zones present today, including Arab, East Asian, Latin American, and South Asian zones, and discuss how they may have contributed, to varying degrees, to the formation of the contemporary Western cultural zone.
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Affiliation(s)
- Shinobu Kitayama
- Department of Psychology, University of Michigan, Ann Arbor, Michigan, USA;
| | - Cristina E Salvador
- Department of Psychology and Neuroscience, Duke University, Durham, North Carolina, USA;
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12
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Houldcroft CJ, Underdown S. Infectious disease in the Pleistocene: Old friends or old foes? AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:513-531. [PMID: 38006200 DOI: 10.1002/ajpa.24737] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 11/26/2023]
Abstract
The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.
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Affiliation(s)
| | - Simon Underdown
- Human Origins and Palaeoenvironmental Research Group, School of Social Sciences, Oxford Brookes University, Oxford, UK
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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13
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Fähnrich A, Stephan I, Hirose M, Haarich F, Awadelkareem MA, Ibrahim S, Busch H, Wohlers I. North and East African mitochondrial genetic variation needs further characterization towards precision medicine. J Adv Res 2023; 54:59-76. [PMID: 36736695 PMCID: PMC10703728 DOI: 10.1016/j.jare.2023.01.021] [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: 10/04/2022] [Revised: 01/16/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
INTRODUCTION Mitochondria are maternally inherited cell organelles with their own genome, and perform various functions in eukaryotic cells such as energy production and cellular homeostasis. Due to their inheritance and manifold biological roles in health and disease, mitochondrial genetics serves a dual purpose of tracing the history as well as disease susceptibility of human populations across the globe. This work requires a comprehensive catalogue of commonly observed genetic variations in the mitochondrial DNAs for all regions throughout the world. So far, however, certain regions, such as North and East Africa have been understudied. OBJECTIVES To address this shortcoming, we have created the most comprehensive quality-controlled North and East African mitochondrial data set to date and use it for characterizing mitochondrial genetic variation in this region. METHODS We compiled 11 published cohorts with novel data for mitochondrial genomes from 159 Sudanese individuals. We combined these 641 mitochondrial sequences with sequences from the 1000 Genomes (n = 2504) and the Human Genome Diversity Project (n = 828) and used the tool haplocheck for extensive quality control and detection of in-sample contamination, as well as Nanopore long read sequencing for haplogroup validation of 18 samples. RESULTS Using a subset of high-coverage mitochondrial sequences, we predict 15 potentially novel haplogroups in North and East African subjects and observe likely phylogenetic deviations from the established PhyloTree reference for haplogroups L0a1 and L2a1. CONCLUSION Our findings demonstrate common hitherto unexplored variants in mitochondrial genomes of North and East Africa that lead to novel phylogenetic relationships between haplogroups present in these regions. These observations call for further in-depth population genetic studies in that region to enable the prospective use of mitochondrial genetic variation for precision medicine.
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Affiliation(s)
- Anke Fähnrich
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Isabel Stephan
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Misa Hirose
- Genetics Division, Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Franziska Haarich
- Institute for Cardiogenetics, University of Lübeck, DZHK (German Research Centre for Cardiovascular Research), Partner Site Hamburg/Lübeck/Kiel, and University Heart Center, Lübeck, Lübeck, Germany
| | - Mosab Ali Awadelkareem
- Faculty of Medical Laboratory Sciences, Al-Neelain University, Khartoum, Sudan; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Saleh Ibrahim
- Genetics Division, Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; Khalifa University, Abu Dhabi, United Arab Emirates
| | - Hauke Busch
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538 Lübeck, Germany
| | - Inken Wohlers
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; Biomedical Data Science, Research Center Borstel, 23845 Borstel, Germany.
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14
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Guevara E, Gopalan S, Massey DJ, Adegboyega M, Zhou W, Solis A, Anaya AD, Churchill SE, Feldblum J, Lawler RR. Getting it right: Teaching undergraduate biology to undermine racial essentialism. Biol Methods Protoc 2023; 8:bpad032. [PMID: 38023347 PMCID: PMC10674104 DOI: 10.1093/biomethods/bpad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/03/2023] [Accepted: 11/10/2023] [Indexed: 12/01/2023] Open
Abstract
How we teach human genetics matters for social equity. The biology curriculum appears to be a crucial locus of intervention for either reinforcing or undermining students' racial essentialist views. The Mendelian genetic models dominating textbooks, particularly in combination with racially inflected language sometimes used when teaching about monogenic disorders, can increase middle and high school students' racial essentialism and opposition to policies to increase equity. These findings are of particular concern given the increasing spread of racist misinformation online and the misappropriation of human genomics research by white supremacists, who take advantage of low levels of genetics literacy in the general public. Encouragingly, however, teaching updated information about the geographical distribution of human genetic variation and the complex, multifactorial basis of most human traits, reduces students' endorsement of racial essentialism. The genetics curriculum is therefore a key tool in combating misinformation and scientific racism. Here, we describe a framework and example teaching materials for teaching students key concepts in genetics, human evolutionary history, and human phenotypic variation at the undergraduate level. This framework can be flexibly applied in biology and anthropology classes and adjusted based on time availability. Our goal is to provide undergraduate-level instructors with varying levels of expertise with a set of evidence-informed tools for teaching human genetics to combat scientific racism, including an evolving set of instructional resources, as well as learning goals and pedagogical approaches. Resources can be found at https://noto.li/YIlhZ5. Additionally, we hope to generate conversation about integrating modern genetics into the undergraduate curriculum, in light of recent findings about the risks and opportunities associated with teaching genetics.
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Affiliation(s)
- Elaine Guevara
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Shyamalika Gopalan
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Dashiell J Massey
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Mayowa Adegboyega
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Wen Zhou
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
- Department of Evolutionary Anthropology, Duke Kunshan University, Kunshan, Jiangsu 215316, China
| | - Alma Solis
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Alisha D Anaya
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Steven E Churchill
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Joseph Feldblum
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Richard R Lawler
- Department of Sociology and Anthropology, James Madison University, Harrisonburg, Virginia 22807, United States
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15
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Flore L, Francalacci P, Massidda M, Robledo R, Calò CM. Influence of Different Evolutive Forces on GDF5 Gene Variability. Genes (Basel) 2023; 14:1895. [PMID: 37895244 PMCID: PMC10606091 DOI: 10.3390/genes14101895] [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: 09/11/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
The GDF5 gene is involved in the development of skeletal elements, synovial joint formation, tendons, ligaments, and cartilage. Several polymorphisms are present within the gene, and two of them, rs143384 and 143383, were reported to be correlated with osteoarticular disease or muscle flexibility. The aim of this research is to verify if the worldwide distribution of the rs143384 polymorphism among human populations was shaped by selective pressure, or if it was the result of random genetic drift events. Ninety-four individuals of both the male and female sexes, 18-28 years old, from Sardinia were analyzed. We observed the following genotype frequencies: 28.72% of AA homozygotes, 13.83% of GG homozygotes, and 57.45% of AG heterozygotes. The allele frequencies were 0.574 for allele A and 0.426 for allele G. The relationships between the populations were verified via Multidimensional Scaling (MDS). Our data show (i) a clear heterogeneity within the African populations; (ii) a strong differentiation between the African populations and the other populations; and that (iii) the Sardinian population is placed within the European cluster. To reveal possible traces of selective pressure, the Population Branch Statistic (PBS) was calculated; both the rs143384 and 143383 SNPs have low PBS values, suggesting that there are no signals of selective pressure in those areas of the gene.
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Affiliation(s)
- Laura Flore
- Department of Life and Environment Sciences, University of Cagliari, 09042 Cagliari, Italy; (L.F.); (P.F.); (C.M.C.)
| | - Paolo Francalacci
- Department of Life and Environment Sciences, University of Cagliari, 09042 Cagliari, Italy; (L.F.); (P.F.); (C.M.C.)
| | - Myosotis Massidda
- Department of Medical Sciences and Public Health, University of Cagliari, 09042 Cagliari, Italy;
| | - Renato Robledo
- Department of Biomedical Sciences, University of Cagliari, 09042 Cagliari, Italy
| | - Carla Maria Calò
- Department of Life and Environment Sciences, University of Cagliari, 09042 Cagliari, Italy; (L.F.); (P.F.); (C.M.C.)
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16
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Mahar NS, Satyam R, Sundar D, Gupta I. A systematic comparison of human mitochondrial genome assembly tools. BMC Bioinformatics 2023; 24:341. [PMID: 37704952 PMCID: PMC10498642 DOI: 10.1186/s12859-023-05445-3] [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: 01/25/2023] [Accepted: 08/14/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Mitochondria are the cell organelles that produce most of the chemical energy required to power the cell's biochemical reactions. Despite being a part of a eukaryotic host cell, the mitochondria contain a separate genome whose origin is linked with the endosymbiosis of a prokaryotic cell by the host cell and encode independent genomic information throughout their genomes. Mitochondrial genomes accommodate essential genes and are regularly utilized in biotechnology and phylogenetics. Various assemblers capable of generating complete mitochondrial genomes are being continuously developed. These tools often use whole-genome sequencing data as an input containing reads from the mitochondrial genome. Till now, no published work has explored the systematic comparison of all the available tools for assembling human mitochondrial genomes using short-read sequencing data. This evaluation is required to identify the best tool that can be well-optimized for small-scale projects or even national-level research. RESULTS In this study, we have tested the mitochondrial genome assemblers for both simulated datasets and whole genome sequencing (WGS) datasets of humans. For the highest computational setting of 16 computational threads with the simulated dataset having 1000X read depth, MitoFlex took the least execution time of 69 s, and IOGA took the longest execution time of 1278 s. NOVOPlasty utilized the least computational memory of approximately 0.098 GB for the same setting, whereas IOGA utilized the highest computational memory of 11.858 GB. In the case of WGS datasets for humans, GetOrganelle and MitoFlex performed the best in capturing the SNPs information with a mean F1-score of 0.919 at the sequencing depth of 10X. MToolBox and NOVOPlasty performed consistently across all sequencing depths with a mean F1 score of 0.897 and 0.890, respectively. CONCLUSIONS Based on the overall performance metrics and consistency in assembly quality for all sequencing data, MToolBox performed the best. However, NOVOPlasty was the second fastest tool in execution time despite being single-threaded, and it utilized the least computational resources among all the assemblers when tested on simulated datasets. Therefore, NOVOPlasty may be more practical when there is a significant sample size and a lack of computational resources. Besides, as long-read sequencing gains popularity, mitochondrial genome assemblers must be developed to use long-read sequencing data.
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Affiliation(s)
- Nirmal Singh Mahar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, 110016, India
| | - Rohit Satyam
- Jamia Millia Islamia, Jamia Nagar, Okhla, New Delhi, 110025, India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, 110016, India
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, 110016, India.
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17
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Shen-Gunther J, Gunther RS, Cai H, Wang Y. A Customized Human Mitochondrial DNA Database (hMITO DB v1.0) for Rapid Sequence Analysis, Haplotyping and Geo-Mapping. Int J Mol Sci 2023; 24:13505. [PMID: 37686313 PMCID: PMC10488239 DOI: 10.3390/ijms241713505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/22/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
The field of mitochondrial genomics has advanced rapidly and has revolutionized disciplines such as molecular anthropology, population genetics, and medical genetics/oncogenetics. However, mtDNA next-generation sequencing (NGS) analysis for matrilineal haplotyping and phylogeographic inference remains hindered by the lack of a consolidated mitogenome database and an efficient bioinformatics pipeline. To address this, we developed a customized human mitogenome database (hMITO DB) embedded in a CLC Genomics workflow for read mapping, variant analysis, haplotyping, and geo-mapping. The database was constructed from 4286 mitogenomes. The macro-haplogroup (A to Z) distribution and representative phylogenetic tree were found to be consistent with published literature. The hMITO DB automated workflow was tested using mtDNA-NGS sequences derived from Pap smears and cervical cancer cell lines. The auto-generated read mapping, variants track, and table of haplotypes and geo-origins were completed in 15 min for 47 samples. The mtDNA workflow proved to be a rapid, efficient, and accurate means of sequence analysis for translational mitogenomics.
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Affiliation(s)
- Jane Shen-Gunther
- Gynecologic Oncology & Clinical Investigation, Department of Clinical Investigation, Brooke Army Medical Center, Fort Sam Houston, San Antonio, TX 78234, USA
| | - Rutger S. Gunther
- Nuclear Medicine & Molecular Imaging, Department of Radiology, Brooke Army Medical Center, Fort Sam Houston, San Antonio, TX 78234, USA;
| | - Hong Cai
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA;
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Yufeng Wang
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA;
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA
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18
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French CM, Bertola LD, Carnaval AC, Economo EP, Kass JM, Lohman DJ, Marske KA, Meier R, Overcast I, Rominger AJ, Staniczenko PPA, Hickerson MJ. Global determinants of insect mitochondrial genetic diversity. Nat Commun 2023; 14:5276. [PMID: 37644003 PMCID: PMC10465557 DOI: 10.1038/s41467-023-40936-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 08/15/2023] [Indexed: 08/31/2023] Open
Abstract
Understanding global patterns of genetic diversity is essential for describing, monitoring, and preserving life on Earth. To date, efforts to map macrogenetic patterns have been restricted to vertebrates, which comprise only a small fraction of Earth's biodiversity. Here, we construct a global map of predicted insect mitochondrial genetic diversity from cytochrome c oxidase subunit 1 sequences, derived from open data. We calculate the mitochondrial genetic diversity mean and genetic diversity evenness of insect assemblages across the globe, identify their environmental correlates, and make predictions of mitochondrial genetic diversity levels in unsampled areas based on environmental data. Using a large single-locus genetic dataset of over 2 million globally distributed and georeferenced mtDNA sequences, we find that mitochondrial genetic diversity evenness follows a quadratic latitudinal gradient peaking in the subtropics. Both mitochondrial genetic diversity mean and evenness positively correlate with seasonally hot temperatures, as well as climate stability since the last glacial maximum. Our models explain 27.9% and 24.0% of the observed variation in mitochondrial genetic diversity mean and evenness in insects, respectively, making an important step towards understanding global biodiversity patterns in the most diverse animal taxon.
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Affiliation(s)
- Connor M French
- Biology Department, City College of New York, New York, NY, USA.
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, USA.
| | - Laura D Bertola
- Biology Department, City College of New York, New York, NY, USA
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, N 2200, Denmark
| | - Ana C Carnaval
- Biology Department, City College of New York, New York, NY, USA
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, USA
| | - Evan P Economo
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Jamie M Kass
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
- Macroecology Laboratory, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - David J Lohman
- Biology Department, City College of New York, New York, NY, USA
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, USA
- Entomology Section, National Museum of Natural History, Manila, Philippines
| | | | - Rudolf Meier
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde Berlin, Berlin, Germany
| | - Isaac Overcast
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, USA
- Institut de Biologie de l'Ecole Normale Superieure, Paris, France
- Department of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Andrew J Rominger
- School of Biology and Ecology, University of Maine, Orono, ME, USA
- Maine Center for Genetics in the Environment, University of Maine, Orono, ME, USA
| | | | - Michael J Hickerson
- Biology Department, City College of New York, New York, NY, USA
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
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19
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Gupta R, Kanai M, Durham TJ, Tsuo K, McCoy JG, Kotrys AV, Zhou W, Chinnery PF, Karczewski KJ, Calvo SE, Neale BM, Mootha VK. Nuclear genetic control of mtDNA copy number and heteroplasmy in humans. Nature 2023; 620:839-848. [PMID: 37587338 PMCID: PMC10447254 DOI: 10.1038/s41586-023-06426-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 07/11/2023] [Indexed: 08/18/2023]
Abstract
Mitochondrial DNA (mtDNA) is a maternally inherited, high-copy-number genome required for oxidative phosphorylation1. Heteroplasmy refers to the presence of a mixture of mtDNA alleles in an individual and has been associated with disease and ageing. Mechanisms underlying common variation in human heteroplasmy, and the influence of the nuclear genome on this variation, remain insufficiently explored. Here we quantify mtDNA copy number (mtCN) and heteroplasmy using blood-derived whole-genome sequences from 274,832 individuals and perform genome-wide association studies to identify associated nuclear loci. Following blood cell composition correction, we find that mtCN declines linearly with age and is associated with variants at 92 nuclear loci. We observe that nearly everyone harbours heteroplasmic mtDNA variants obeying two principles: (1) heteroplasmic single nucleotide variants tend to arise somatically and accumulate sharply after the age of 70 years, whereas (2) heteroplasmic indels are maternally inherited as mixtures with relative levels associated with 42 nuclear loci involved in mtDNA replication, maintenance and novel pathways. These loci may act by conferring a replicative advantage to certain mtDNA alleles. As an illustrative example, we identify a length variant carried by more than 50% of humans at position chrM:302 within a G-quadruplex previously proposed to mediate mtDNA transcription/replication switching2,3. We find that this variant exerts cis-acting genetic control over mtDNA abundance and is itself associated in-trans with nuclear loci encoding machinery for this regulatory switch. Our study suggests that common variation in the nuclear genome can shape variation in mtCN and heteroplasmy dynamics across the human population.
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Affiliation(s)
- Rahul Gupta
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Masahiro Kanai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Timothy J Durham
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kristin Tsuo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jason G McCoy
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anna V Kotrys
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wei Zhou
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Konrad J Karczewski
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Sarah E Calvo
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin M Neale
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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20
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Graves JL. Favored Races in the Struggle for Life: Racism and the Speciation Concept. Cold Spring Harb Perspect Biol 2023; 15:a041454. [PMID: 37463717 PMCID: PMC10411861 DOI: 10.1101/cshperspect.a041454] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Evolutionary speciation, whether it be cladistic or phyletic, has always been associated with race concepts. Biological races are conceived as definable stages of divergence from a common ancestor. However, the species concept in Western science began within a special creationist framework. The sixteenth century European voyages of discovery resulted in special creationist schemes explaining the origin of the new peoples encountered. These were designed to provide the moral justification for their colonization and enslavement. By the seventeenth century, European naturalists were beginning to seriously question the meaning of the variation within the animals and plants they observed within the context of God's role in creation. By the middle of the nineteenth century, "the species question" was the most important intellectual enterprise within biology. Here I discuss how notions of speciation influenced and were influenced by conceptions of race within Homo sapiens.
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Affiliation(s)
- Joseph L Graves
- Department of Biological Sciences, North Carolina A&T State University, Greensboro, North Carolina 27410, USA
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21
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Jacobs HT. A century of mitochondrial research, 1922-2022. Enzymes 2023; 54:37-70. [PMID: 37945177 DOI: 10.1016/bs.enz.2023.07.002] [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] [Indexed: 11/12/2023]
Abstract
Although recognized earlier as subcellular entities by microscopists, mitochondria have been the subject of functional studies since 1922, when their biochemical similarities with bacteria were first noted. In this overview I trace the history of research on mitochondria from that time up to the present day, focussing on the major milestones of the overlapping eras of mitochondrial biochemistry, genetics, pathology and cell biology, and its explosion into new areas in the past 25 years. Nowadays, mitochondria are considered to be fully integrated into cell physiology, rather than serving specific functions in isolation.
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Affiliation(s)
- Howard T Jacobs
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Department of Environment and Genetics, La Trobe University, Melbourne, VIC, Australia.
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22
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Hernández CL. Mitochondrial DNA in Human Diversity and Health: From the Golden Age to the Omics Era. Genes (Basel) 2023; 14:1534. [PMID: 37628587 PMCID: PMC10453943 DOI: 10.3390/genes14081534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is a small fraction of our hereditary material. However, this molecule has had an overwhelming presence in scientific research for decades until the arrival of high-throughput studies. Several appealing properties justify the application of mtDNA to understand how human populations are-from a genetic perspective-and how individuals exhibit phenotypes of biomedical importance. Here, I review the basics of mitochondrial studies with a focus on the dawn of the field, analysis methods and the connection between two sides of mitochondrial genetics: anthropological and biomedical. The particularities of mtDNA, with respect to inheritance pattern, evolutionary rate and dependence on the nuclear genome, explain the challenges of associating mtDNA composition and diseases. Finally, I consider the relevance of this single locus in the context of omics research. The present work may serve as a tribute to a tool that has provided important insights into the past and present of humankind.
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Affiliation(s)
- Candela L Hernández
- Department of Biodiversity, Ecology and Evolution, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
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23
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Tuncay IO, DeVries D, Gogate A, Kaur K, Kumar A, Xing C, Goodspeed K, Seyoum-Tesfa L, Chahrour MH. The genetics of autism spectrum disorder in an East African familial cohort. CELL GENOMICS 2023; 3:100322. [PMID: 37492102 PMCID: PMC10363748 DOI: 10.1016/j.xgen.2023.100322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/09/2023] [Accepted: 04/16/2023] [Indexed: 07/27/2023]
Abstract
Autism spectrum disorder (ASD) is a group of complex neurodevelopmental conditions affecting communication and social interaction in 2.3% of children. Studies that demonstrated its complex genetic architecture have been mainly performed in populations of European ancestry. We investigate the genetics of ASD in an East African cohort (129 individuals) from a population with higher prevalence (5%). Whole-genome sequencing identified 2.13 million private variants in the cohort and potentially pathogenic variants in known ASD genes (including CACNA1C, CHD7, FMR1, and TCF7L2). Admixture analysis demonstrated that the cohort comprises two ancestral populations, African and Eurasian. Admixture mapping discovered 10 regions that confer ASD risk on the African haplotypes, containing several known ASD genes. The increased ASD prevalence in this population suggests decreased heterogeneity in the underlying genetic etiology, enabling risk allele identification. Our approach emphasizes the power of African genetic variation and admixture analysis to inform the architecture of complex disorders.
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Affiliation(s)
- Islam Oguz Tuncay
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Darlene DeVries
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ashlesha Gogate
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kiran Kaur
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ashwani Kumar
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kimberly Goodspeed
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Maria H Chahrour
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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24
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Wu S, Li X, Huang G, Guo J, Zhang X, Liao L, Zhi W, Li K, Wang Y, Chu Z, Shang L, Yu X, Yu K, Xu W. Dissecting Sperm Mitochondrial G-Quadruplex Structures Using a Fluorescent Probe Biomarker to Monitor and Regulate Fertilization Capability. ACS Sens 2023; 8:2186-2196. [PMID: 37224082 PMCID: PMC10295354 DOI: 10.1021/acssensors.3c00068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023]
Abstract
To monitor the levels of mitochondrial DNA G-quadruplexes (mtDNA G4s) in spermatozoa and to explore the possibility using mtDNA G4s as a reliable marker in patients with multiple clinical insemination failures, a novel chemical TPE-mTO probe engineered in our previous work was used on both samples from the mice sperm and from patients with fertilization failure. Expression of valosin-containing protein and the zona-free hamster egg assay were used to evaluate mitophagy and human sperm penetration. RNA-sequencing was used to explore expression changes of key genes affected by mtDNA G4s. Results showed that the probe can track mtDNA G4s in spermatozoa easily and quickly with fewer backgrounds. Significantly increased mtDNA G4s were also found in patients with fertilization failure, using the flow-cytometry-based TPE-mTO probe detection method. A sperm-hamster egg penetration experiment showed that abnormal fertilization caused by increased mtDNA G4s can be effectively restored by a mitophagy inducer. This study provides a novel method for monitoring etiological biomarkers in patients with clinical infertility and treatment for patients with abnormal fertilization caused by mtDNA G4 dysfunction.
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Affiliation(s)
- Sixian Wu
- Joint
Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Obstetric,
Gynaecologic and Paediatric Diseases and Birth Defects of Ministry
of Education, West China Second University
Hospital, Med-X Centre for Manufacturing, Sichuan University, Chengdu 610041, People’s Republic of China
| | - Xiaoliang Li
- Joint
Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Obstetric,
Gynaecologic and Paediatric Diseases and Birth Defects of Ministry
of Education, West China Second University
Hospital, Med-X Centre for Manufacturing, Sichuan University, Chengdu 610041, People’s Republic of China
- Reproduction
Medical Centre, West China Second University
Hospital, Sichuan University, Chengdu 610041, China
| | - Gelin Huang
- Joint
Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Obstetric,
Gynaecologic and Paediatric Diseases and Birth Defects of Ministry
of Education, West China Second University
Hospital, Med-X Centre for Manufacturing, Sichuan University, Chengdu 610041, People’s Republic of China
| | - Juncen Guo
- Joint
Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Obstetric,
Gynaecologic and Paediatric Diseases and Birth Defects of Ministry
of Education, West China Second University
Hospital, Med-X Centre for Manufacturing, Sichuan University, Chengdu 610041, People’s Republic of China
| | - Xueguang Zhang
- Joint
Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Obstetric,
Gynaecologic and Paediatric Diseases and Birth Defects of Ministry
of Education, West China Second University
Hospital, Med-X Centre for Manufacturing, Sichuan University, Chengdu 610041, People’s Republic of China
| | - Lu Liao
- Puhua
Technology Co., Ltd., Chengdu 610200, China
| | - Weiwei Zhi
- Sichuan
Provincial Maternity and Child Health Care Hospital, Chengdu 610045, China
| | - Kun Li
- Key
Laboratory of Green Chemistry and Technology (Ministry of Education),
College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Yan Wang
- Reproduction
Medical Centre, West China Second University
Hospital, Sichuan University, Chengdu 610041, China
| | - Zhiwen Chu
- West
China School of Pharmacy, Sichuan University, Chengdu 610064, China
| | - Lijun Shang
- School of
Human Sciences, London Metropolitan University, London N7 8DB, U.K.
| | - Xiaoqi Yu
- Key
Laboratory of Green Chemistry and Technology (Ministry of Education),
College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Kangkang Yu
- Key
Laboratory of Bio-resources and Eco-environment (Ministry of Education),
College of Life Sciences, Sichuan University, Chengdu 610064, China
- Key
Laboratory of Green Chemistry and Technology (Ministry of Education),
College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Wenming Xu
- Joint
Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Obstetric,
Gynaecologic and Paediatric Diseases and Birth Defects of Ministry
of Education, West China Second University
Hospital, Med-X Centre for Manufacturing, Sichuan University, Chengdu 610041, People’s Republic of China
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25
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Jackson F, Clinton C, Caldwell J. Core issues, case studies, and the need for expanded Legacy African American genomics. Front Genet 2023; 14:843209. [PMID: 37359364 PMCID: PMC10287052 DOI: 10.3389/fgene.2023.843209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 04/18/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction: Genomic studies of Legacy African Americans have a tangled and convoluted history in western science. In this review paper, core issues affecting African American genomic studies are addressed and two case studies, the New York African Burial Ground and the Gullah Geechee peoples, are presented to highlight the current status of genomic research among Africa Americans. Methods: To investigate our target population's core issues, a metadatabase derived from 22 publicly accessible databases were reviewed, evaluated, and synthesized to identify the core bioethical issues prevalent during the centuries of the African American presence in North America. The sequence of metadatabase development included 5 steps: identification of information, record screening and retention of topic relevant information, identification of eligibility via synthesis for concept identifications, and inclusion of studies used for conceptual summaries and studies used for genetic and genomic summaries. To these data we added our emic perspectives and specific insights from our case studies. Results: Overall, there is a paucity of existing research on underrepresent African American genomic diversity. In every category of genomic testing (i.e., diagnostic, clinical predictive, pharmacogenomic, direct-to-consumer, and tumor testing), African Americans are disproportionately underrepresented compared to European Americans. The first of our case studies is from the New York African Burial Ground Project where genomic studies of grave soil derived aDNA yields insights into the causes of death of 17th and 18th Century African Americans. In the second of our case studies, research among the Gullah Geechee people of the Carolina Lowcountry reveals a connection between genomic studies and health disparities. Discussion: African Americans have historically borne the brunt of the earliest biomedical studies used to generate and refine primitive concepts in genetics. As exploited victims these investigations, African American men, women, and children were subjected to an ethics-free western science. Now that bioethical safeguards have been added, underrepresented and marginalized people who were once the convenient targets of western science, are now excluded from its health-related benefits. Recommendations to enhance the inclusion of African Americans in global genomic databases and clinical trials should include the following: emphasis on the connection of inclusion to advances in precision medicine, emphasis on the relevance of inclusion to fundamental questions in human evolutionary biology, emphasis on the historical relevance of inclusion for Legacy African Americans, emphasis on the ability of inclusion to foster expanded scientific expertise in the target population, ethical engagement with their descendants, and increase the number of science researchers from these communities.
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Affiliation(s)
- Fatimah Jackson
- Department of Biology, Howard University, Washington, DC, United States
| | - Carter Clinton
- Department of Biology, North Carolina State University, Raleigh, NC, United States
| | - Jennifer Caldwell
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA, United States
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26
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Pereson MJ, Sanabria DJ, Torres C, Liotta DJ, Campos RH, Schurr TG, Di Lello FA, Badano I. Evolutionary analysis of JC polyomavirus in Misiones' population yields insight into the population dynamics of the early human dispersal in the Americas. Virology 2023; 585:100-108. [PMID: 37327595 DOI: 10.1016/j.virol.2023.05.009] [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: 03/14/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND JC polyomavirus (JCV) has an ethno-geographical distribution across human populations. OBJECTIVE Study the origins of the population of Misiones (Argentina) by using JCV as genetic marker. METHODS Viral detection and characterization was conducted by PCR amplification and evolutionary analysis of the intergenic region sequences. RESULTS 22 out of 121 samples were positive for JCV, including 5 viral lineages: MY (n = 8), Eu-a (n = 7), B1-c (n = 4), B1-b (n = 2) and Af2 (n = 1). MY sequences clustered within a branch of Native American origin that diverged from its Asian counterpart about 21,914 years ago (HPD 95% interval 15,383-30,177), followed by a sustained demographic expansion around 5000 years ago. CONCLUSIONS JCV in Misiones reflects the multiethnic origin of the current population, with an important Amerindian contribution. Analysis of the MY viral lineage shows a pattern consistent with the arrival of early human migrations to the Americas and a population expansion by the pre-Columbian native societies.
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Affiliation(s)
- Matias J Pereson
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Daiana J Sanabria
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina; Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Laboratorio de Biología Molecular Aplicada (LaBiMAp). Posadas, Misiones, Argentina
| | - Carolina Torres
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Domingo J Liotta
- Instituto Nacional de Medicina Tropical-ANLIS ''Dr. Malbrán'', Neuquén y Jujuy S/n, N3370, Puerto Iguazú, Misiones, Argentina
| | - Rodolfo H Campos
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina
| | - Theodore G Schurr
- Laboratory of Molecular Anthropology, Department of Anthropology, University of Pennsylvania. Philadelphia, PA 19104-6398, USA
| | - Federico A Di Lello
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Inés Badano
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina; Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Laboratorio de Biología Molecular Aplicada (LaBiMAp). Posadas, Misiones, Argentina; Universidad Nacional de Misiones. Red de Laboratorios. Laboratorio de Antropología Biológica y Bioinformática Aplicada (LABBA). Misiones, Argentina.
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27
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Scerri EML, Will M. The revolution that still isn't: The origins of behavioral complexity in Homo sapiens. J Hum Evol 2023; 179:103358. [PMID: 37058868 DOI: 10.1016/j.jhevol.2023.103358] [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: 07/27/2022] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 04/16/2023]
Abstract
The behavioral origins of Homo sapiens can be traced back to the first material culture produced by our species in Africa, the Middle Stone Age (MSA). Beyond this broad consensus, the origins, patterns, and causes of behavioral complexity in modern humans remain debated. Here, we consider whether recent findings continue to support popular scenarios of: (1) a modern human 'package,' (2) a gradual and 'pan-African' emergence of behavioral complexity, and (3) a direct connection to changes in the human brain. Our geographically structured review shows that decades of scientific research have continuously failed to find a discrete threshold for a complete 'modernity package' and that the concept is theoretically obsolete. Instead of a continent-wide, gradual accumulation of complex material culture, the record exhibits a predominantly asynchronous presence and duration of many innovations across different regions of Africa. The emerging pattern of behavioral complexity from the MSA conforms to an intricate mosaic characterized by spatially discrete, temporally variable, and historically contingent trajectories. This archaeological record bears no direct relation to a simplistic shift in the human brain but rather reflects similar cognitive capacities that are variably manifested. The interaction of multiple causal factors constitutes the most parsimonious explanation driving the variable expression of complex behaviors, with demographic processes such as population structure, size, and connectivity playing a key role. While much emphasis has been given to innovation and variability in the MSA record, long periods of stasis and a lack of cumulative developments argue further against a strictly gradualistic nature in the record. Instead, we are confronted with humanity's deep, variegated roots in Africa, and a dynamic metapopulation that took many millennia to reach the critical mass capable of producing the ratchet effect commonly used to define contemporary human culture. Finally, we note a weakening link between 'modern' human biology and behavior from around 300 ka ago.
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Affiliation(s)
- Eleanor M L Scerri
- Pan-African Evolution Research Group, Max Planck Institute for Geoanthropology, Kahlaische Str. 10, 07749, Jena, Germany; Department of Classics and Archaeology, University of Malta, Msida, MSD 2080, Malta; Department of Prehistory, University of Cologne, 50931, Cologne, Germany.
| | - Manuel Will
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Schloss Hohentübingen, Burgsteige 11, 72070, Tübingen, Germany
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28
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Winther RG, Willerslev E. Wilson and Sarich (1969): The birth of a molecular evolution research paradigm. Proc Natl Acad Sci U S A 2023; 120:e2220473120. [PMID: 36893264 PMCID: PMC10243126 DOI: 10.1073/pnas.2220473120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Affiliation(s)
- Rasmus Grønfeldt Winther
- Humanities Division, University of California, Santa Cruz, CA95064
- GeoGenetics Section, Globe Institute, University of Copenhagen, 1350Copenhagen K, Denmark
| | - Eske Willerslev
- GeoGenetics Section, Globe Institute, University of Copenhagen, 1350Copenhagen K, Denmark
- Department of Zoology, University of Cambridge, CambridgeCB2 3EJ, United Kingdom
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29
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Kaplan JRH. The "Greenberg Controversy" and the Interdisciplinary Study of Global Linguistic Relationships. BERICHTE ZUR WISSENSCHAFTSGESCHICHTE 2023; 46:114-132. [PMID: 36646516 DOI: 10.1002/bewi.202200038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
This paper examines the controversy that followed the 1987 publication of Joseph Greenberg's book, Language in the Americas, attending to the role of language and linguistic research within overlapping disciplinary traditions. With this text, Greenberg presented a macro-level tripartite classification that opposed then dominant fine-grained analyses recognizing anywhere from 150 to 200 distinct language families. His proposal was the subject of a landmark conference, examining strengths and weaknesses, the unpublished proceedings of which are presented here for the first time. For specialists in the anthropological and comparative-historical study of Indigenous American languages, Greenberg's intervention highlighted the tension between language, conceived as an abstract object of study, and languages, understood to be carriers of specific cultural knowledge. For physical anthropologists and archaeologists, his theory was initially fortuitous on programmatic, substantive, and methodological grounds. The essay will show how interdisciplinary appeals were figured by supporters as a virtue, and by critics as a vice. The essay further highlights ethical reasons for integrating historical narratives of science and the humanities.
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Affiliation(s)
- Judith R H Kaplan
- Consortium for History of Science, Technology and Medicine, Philadelphia, USA
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30
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Gupta R, Kanai M, Durham TJ, Tsuo K, McCoy JG, Chinnery PF, Karczewski KJ, Calvo SE, Neale BM, Mootha VK. Nuclear genetic control of mtDNA copy number and heteroplasmy in humans. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.19.23284696. [PMID: 36711677 PMCID: PMC9882621 DOI: 10.1101/2023.01.19.23284696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Human mitochondria contain a high copy number, maternally transmitted genome (mtDNA) that encodes 13 proteins required for oxidative phosphorylation. Heteroplasmy arises when multiple mtDNA variants co-exist in an individual and can exhibit complex dynamics in disease and in aging. As all proteins involved in mtDNA replication and maintenance are nuclear-encoded, heteroplasmy levels can, in principle, be under nuclear genetic control, however this has never been shown in humans. Here, we develop algorithms to quantify mtDNA copy number (mtCN) and heteroplasmy levels using blood-derived whole genome sequences from 274,832 individuals of diverse ancestry and perform GWAS to identify nuclear loci controlling these traits. After careful correction for blood cell composition, we observe that mtCN declines linearly with age and is associated with 92 independent nuclear genetic loci. We find that nearly every individual carries heteroplasmic variants that obey two key patterns: (1) heteroplasmic single nucleotide variants are somatic mutations that accumulate sharply after age 70, while (2) heteroplasmic indels are maternally transmitted as mtDNA mixtures with resulting levels influenced by 42 independent nuclear loci involved in mtDNA replication, maintenance, and novel pathways. These nuclear loci do not appear to act by mtDNA mutagenesis, but rather, likely act by conferring a replicative advantage to specific mtDNA molecules. As an illustrative example, the most common heteroplasmy we identify is a length variant carried by >50% of humans at position m.302 within a G-quadruplex known to serve as a replication switch. We find that this heteroplasmic variant exerts cis -acting genetic control over mtDNA abundance and is itself under trans -acting genetic control of nuclear loci encoding protein components of this regulatory switch. Our study showcases how nuclear haplotype can privilege the replication of specific mtDNA molecules to shape mtCN and heteroplasmy dynamics in the human population.
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Affiliation(s)
- Rahul Gupta
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, United States
- Broad Institute of MIT and Harvard, United States
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, United States
| | - Masahiro Kanai
- Broad Institute of MIT and Harvard, United States
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, United States
| | - Timothy J Durham
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, United States
- Broad Institute of MIT and Harvard, United States
| | - Kristin Tsuo
- Broad Institute of MIT and Harvard, United States
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, United States
| | - Jason G McCoy
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, United States
- Broad Institute of MIT and Harvard, United States
| | - Patrick F Chinnery
- Department of Clinical Neurosciences & MRC Mitochondrial Biology Unit, University of Cambridge, United Kingdom
| | - Konrad J Karczewski
- Broad Institute of MIT and Harvard, United States
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, United States
| | - Sarah E Calvo
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, United States
- Broad Institute of MIT and Harvard, United States
| | - Benjamin M Neale
- Broad Institute of MIT and Harvard, United States
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, United States
| | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, United States
- Broad Institute of MIT and Harvard, United States
- Department of Systems Biology, Harvard Medical School, United States
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Cho EO, Cowgill LW, Middleton KM, Blomquist GE, Savoldi F, Tsoi J, Bornstein MM. The influence of climate and population structure on East Asian skeletal morphology. J Hum Evol 2022; 173:103268. [PMID: 36288639 DOI: 10.1016/j.jhevol.2022.103268] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/06/2022]
Abstract
Recent studies have shown that global variation in body proportions is more complex than previously thought as some traits formerly associated with climate adaptation are better explained by geographic proximity and neutral evolutionary forces. While the recent incorporation of quantitative genetic methodologies has improved understanding of patterns related to climate in Africa, Europe, and the Americas, Asia remains underrepresented in recent and historic studies of body form. As ecogeographic studies tend to focus on male morphology, potential sex differences in features influenced by climate remain largely unexplored. Skeletal measurements encompassing the dimensions of the skull, pelvis, limbs, hands, and feet were collected from male (n = 459) and female (n = 442) remains curated in 13 collections across seven countries in East Asia (n = 901). Osteological data were analyzed with sex and minimum temperature as covariates adjusted by autosomal single-nucleotide polymorphism population genetic distance using univariate Bayesian linear mixed models, and credible intervals were calculated for each trait. Analysis supports a relationship between specific traits and climate as well as providing the magnitude of response in both sexes. After accounting for genetic distance between populations, greater association between climate and morphology was found in postcranial traits, with the relationship between climate and the skull limited primarily to breadth measurements. Larger body size is associated with colder climates with most measurements increasing with decreased temperature. The same traits were not always associated with climate for males and females nor correlated with the same intensity for both sexes. The varied directional association with climate for different regions of the skeleton and between the sexes underscores the necessity of future ecogeographic research to holistically evaluate body form and to look for sex-specific patterns to better understand population responses to environmental stresses.
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Affiliation(s)
- Elizabeth O Cho
- Department of Anthropology, University of Missouri, Columbia, MO 65211, USA; Center for Anatomical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA.
| | - Libby W Cowgill
- Department of Anthropology, University of Missouri, Columbia, MO 65211, USA
| | - Kevin M Middleton
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | | | - Fabio Savoldi
- Orthodontics, Division of Paediatric Dentistry & Orthodontics, Faculty of Dentistry, The University of Hong Kong, Sai Ying Pun, Hong Kong S.A.R., P.R. China
| | - James Tsoi
- Dental Materials Science, Division of Applied Oral Sciences & Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Sai Ying Pun, Hong Kong S.A.R., P.R. China
| | - Michael M Bornstein
- Oral and Maxillofacial Radiology, Division of Applied Oral Sciences & Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Sai Ying Pun, Hong Kong S.A.R., P.R. China; Department of Oral Health and Medicine, University Center for Dental Medicine Basel UZB, University of Basel, Basel 4058, Switzerland
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Askapuli A, Vilar M, Garcia-Ortiz H, Zhabagin M, Sabitov Z, Akilzhanova A, Ramanculov E, Schamiloglu U, Martinez-Hernandez A, Contreras-Cubas C, Barajas-Olmos F, Schurr TG, Zhumadilov Z, Flores-Huacuja M, Orozco L, Hawks J, Saitou N. Kazak mitochondrial genomes provide insights into the human population history of Central Eurasia. PLoS One 2022; 17:e0277771. [PMID: 36445929 PMCID: PMC9707748 DOI: 10.1371/journal.pone.0277771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 11/03/2022] [Indexed: 11/30/2022] Open
Abstract
As a historical nomadic group in Central Asia, Kazaks have mainly inhabited the steppe zone from the Altay Mountains in the East to the Caspian Sea in the West. Fine scale characterization of the genetic profile and population structure of Kazaks would be invaluable for understanding their population history and modeling prehistoric human expansions across the Eurasian steppes. With this mind, we characterized the maternal lineages of 200 Kazaks from Jetisuu at mitochondrial genome level. Our results reveal that Jetisuu Kazaks have unique mtDNA haplotypes including those belonging to the basal branches of both West Eurasian (R0, H, HV) and East Eurasian (A, B, C, D) lineages. The great diversity observed in their maternal lineages may reflect pivotal geographic location of Kazaks in Eurasia and implies a complex history for this population. Comparative analyses of mitochondrial genomes of human populations in Central Eurasia reveal a common maternal genetic ancestry for Turko-Mongolian speakers and their expansion being responsible for the presence of East Eurasian maternal lineages in Central Eurasia. Our analyses further indicate maternal genetic affinity between the Sherpas from the Tibetan Plateau with the Turko-Mongolian speakers.
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Affiliation(s)
- Ayken Askapuli
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Miguel Vilar
- The Genographic Project, National Geographic Society, Washington, DC, United States of America
- Department of Anthropology, University of Maryland, College Park, Maryland, United States of America
| | - Humberto Garcia-Ortiz
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Maxat Zhabagin
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | | | - Ainur Akilzhanova
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Erlan Ramanculov
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
| | - Uli Schamiloglu
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
| | - Angelica Martinez-Hernandez
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Theodore G. Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Zhaxybay Zhumadilov
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Marlen Flores-Huacuja
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - John Hawks
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Anthropology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Naruya Saitou
- Population Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
- Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Okinawa Ken, Japan
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Meneganzin A, Pievani T, Manzi G. Pan-Africanism vs. single-origin of Homo sapiens: Putting the debate in the light of evolutionary biology. Evol Anthropol 2022; 31:199-212. [PMID: 35848454 PMCID: PMC9540121 DOI: 10.1002/evan.21955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 02/23/2022] [Accepted: 06/14/2022] [Indexed: 12/03/2022]
Abstract
The scenario of Homo sapiens origin/s within Africa has become increasingly complex, with a pan-African perspective currently challenging the long-established single-origin hypothesis. In this paper, we review the lines of evidence employed in support of each model, highlighting inferential limitations and possible terminological misunderstandings. We argue that the metapopulation scenario envisaged by pan-African proponents well describes a mosaic diversification among late Middle Pleistocene groups. However, this does not rule out a major contribution that emerged from a single population where crucial derived features-notably, a globular braincase-appeared as the result of a punctuated, cladogenetic event. Thus, we suggest that a synthesis is possible and propose a scenario that, in our view, better reconciles with consolidated expectations in evolutionary theory. These indicate cladogenesis in allopatry as an ordinary pattern for the origin of a new species, particularly during phases of marked climatic and environmental instability.
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Affiliation(s)
| | | | - Giorgio Manzi
- Department of Environmental BiologySapienza University of RomeRomeItaly
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African mitochondrial haplogroup L7: a 100,000-year-old maternal human lineage discovered through reassessment and new sequencing. Sci Rep 2022; 12:10747. [PMID: 35750688 PMCID: PMC9232647 DOI: 10.1038/s41598-022-13856-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 05/30/2022] [Indexed: 11/17/2022] Open
Abstract
Archaeological and genomic evidence suggest that modern Homo sapiens have roamed the planet for some 300–500 thousand years. In contrast, global human mitochondrial (mtDNA) diversity coalesces to one African female ancestor (“Mitochondrial Eve”) some 145 thousand years ago, owing to the ¼ gene pool size of our matrilineally inherited haploid genome. Therefore, most of human prehistory was spent in Africa where early ancestors of Southern African Khoisan and Central African rainforest hunter-gatherers (RFHGs) segregated into smaller groups. Their subdivisions followed climatic oscillations, new modes of subsistence, local adaptations, and cultural-linguistic differences, all prior to their exodus out of Africa. Seven African mtDNA haplogroups (L0–L6) traditionally captured this ancient structure—these L haplogroups have formed the backbone of the mtDNA tree for nearly two decades. Here we describe L7, an eighth haplogroup that we estimate to be ~ 100 thousand years old and which has been previously misclassified in the literature. In addition, L7 has a phylogenetic sublineage L7a*, the oldest singleton branch in the human mtDNA tree (~ 80 thousand years). We found that L7 and its sister group L5 are both low-frequency relics centered around East Africa, but in different populations (L7: Sandawe; L5: Mbuti). Although three small subclades of African foragers hint at the population origins of L5'7, the majority of subclades are divided into Afro-Asiatic and eastern Bantu groups, indicative of more recent admixture. A regular re-estimation of the entire mtDNA haplotype tree is needed to ensure correct cladistic placement of new samples in the future.
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Pedigree derived mutation rate across the entire mitochondrial genome of the Norfolk Island population. Sci Rep 2022; 12:6827. [PMID: 35473946 PMCID: PMC9042960 DOI: 10.1038/s41598-022-10530-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/17/2022] [Indexed: 11/09/2022] Open
Abstract
Estimates of mutation rates for various regions of the human mitochondrial genome (mtGenome) vary widely, depending on whether they are inferred using a phylogenetic approach or obtained directly from pedigrees. Traditionally, only the control region, or small portions of the coding region have been targeted for analysis due to the cost and effort required to produce whole mtGenome Sanger profiles. Here, we report one of the first pedigree derived mutation rates for the entire human mtGenome. The entire mtGenome from 225 individuals originating from Norfolk Island was analysed to estimate the pedigree derived mutation rate and compared against published mutation rates. These individuals were from 45 maternal lineages spanning 345 generational events. Mutation rates for various portions of the mtGenome were calculated. Nine mutations (including two transitions and seven cases of heteroplasmy) were observed, resulting in a rate of 0.058 mutations/site/million years (95% CI 0.031-0.108). These mutation rates are approximately 16 times higher than estimates derived from phylogenetic analysis with heteroplasmy detected in 13 samples (n = 225, 5.8% individuals). Providing one of the first pedigree derived estimates for the entire mtGenome, this study provides a better understanding of human mtGenome evolution and has relevance to many research fields, including medicine, anthropology and forensics.
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Griesemer J, Barragán CA. Re-situations of scientific knowledge: a case study of a skirmish over clusters vs clines in human population genomics. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2022; 44:16. [PMID: 35445860 PMCID: PMC9023434 DOI: 10.1007/s40656-022-00497-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
We track and analyze the re-situation of scientific knowledge in the field of human population genomics ancestry studies. We understand re-situation as a process of accommodating the direct or indirect transfer of objects of knowledge from one site/situation to (one or many) other sites/situations. Our take on the concept borrows from Mary S. Morgan's work on facts traveling while expanding it to include other objects of knowledge such as models, data, software, findings, and visualizations. We structure a specific case study by tracking the re-situation of these objects between three research projects studying human population diversity reported in three articles in Science, Genome Research and PLoS Genetics between 2002 and 2005. We characterize these three engagements as a unit of analysis, a "skirmish," in order to compare: (a) the divergence of interests in how life-scientists answer similar research questions and (b) to track the challenging transformation of workflows in research laboratories as these scientific objects are re-situated individually or in bundles. Our analysis of the case study shows that an accurate understanding of re-situation requires tracking the whole bundle of objects in a project because they interact in particular key ways. The absence or dismissal of these interactions opens the door to unforeseen trade-offs, misunderstandings and misrepresentations about research design(s) and workflow(s) and what these say about the questions asked and the findings produced.
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Affiliation(s)
- James Griesemer
- Department of Philosophy, University of California, Davis, One Shields Avenue, Davis, CA 95616 USA
- Department of Science and Technology Studies, University of California, Davis, One Shields Avenue, Davis, CA 95616 USA
| | - Carlos Andrés Barragán
- Department of Philosophy, University of California, Davis, One Shields Avenue, Davis, CA 95616 USA
- Department of Science and Technology Studies, University of California, Davis, One Shields Avenue, Davis, CA 95616 USA
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37
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Peter BM. A geometric relationship of
F
2
,
F
3
and
F
4
-statistics with principal component analysis. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200413. [PMID: 35430884 PMCID: PMC9014194 DOI: 10.1098/rstb.2020.0413] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Principal component analysis (PCA) and
F
-statistics
sensu
Patterson are two of the most widely used population genetic tools to study human genetic variation. Here, I derive explicit connections between the two approaches and show that these two methods are closely related.
F
-statistics have a simple geometrical interpretation in the context of PCA, and orthogonal projections are a key concept to establish this link. I show that for any pair of populations, any population that is admixed as determined by an
F
3
-statistic will lie inside a circle on a PCA plot. Furthermore, the
F
4
-statistic is closely related to an angle measurement, and will be zero if the differences between pairs of populations intersect at a right angle in PCA space. I illustrate my results on two examples, one of Western Eurasian, and one of global human diversity. In both examples, I find that the first few PCs are sufficient to approximate most
F
-statistics, and that PCA plots are effective at predicting
F
-statistics. Thus, while
F
-statistics are commonly understood in terms of discrete populations, the geometric perspective illustrates that they can be viewed in a framework of populations that vary in a more continuous manner.
This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
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Affiliation(s)
- Benjamin M. Peter
- Max-Planck-Institute for Evolutionary Anthropology, Leipzig 04103, Germany
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Laricchia KM, Lake NJ, Watts NA, Shand M, Haessly A, Gauthier L, Benjamin D, Banks E, Soto J, Garimella K, Emery J, Rehm HL, MacArthur DG, Tiao G, Lek M, Mootha VK, Calvo SE. Mitochondrial DNA variation across 56,434 individuals in gnomAD. Genome Res 2022; 32:569-582. [PMID: 35074858 PMCID: PMC8896463 DOI: 10.1101/gr.276013.121] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/19/2022] [Indexed: 11/25/2022]
Abstract
Genomic databases of allele frequency are extremely helpful for evaluating clinical variants of unknown significance; however, until now, databases such as the Genome Aggregation Database (gnomAD) have focused on nuclear DNA and have ignored the mitochondrial genome (mtDNA). Here, we present a pipeline to call mtDNA variants that addresses three technical challenges: (1) detecting homoplasmic and heteroplasmic variants, present, respectively, in all or a fraction of mtDNA molecules; (2) circular mtDNA genome; and (3) misalignment of nuclear sequences of mitochondrial origin (NUMTs). We observed that mtDNA copy number per cell varied across gnomAD cohorts and influenced the fraction of NUMT-derived false-positive variant calls, which can account for the majority of putative heteroplasmies. To avoid false positives, we excluded contaminated samples, cell lines, and samples prone to NUMT misalignment due to few mtDNA copies. Furthermore, we report variants with heteroplasmy ≥10%. We applied this pipeline to 56,434 whole-genome sequences in the gnomAD v3.1 database that includes individuals of European (58%), African (25%), Latino (10%), and Asian (5%) ancestry. Our gnomAD v3.1 release contains population frequencies for 10,850 unique mtDNA variants at more than half of all mtDNA bases. Importantly, we report frequencies within each nuclear ancestral population and mitochondrial haplogroup. Homoplasmic variants account for most variant calls (98%) and unique variants (85%). We observed that 1/250 individuals carry a pathogenic mtDNA variant with heteroplasmy above 10%. These mtDNA population allele frequencies are freely accessible and will aid in diagnostic interpretation and research studies.
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Affiliation(s)
- Kristen M Laricchia
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Nicole J Lake
- Yale School of Medicine, New Haven, Connecticut 06510, USA
- Murdoch Children's Research Institute, Melbourne, Victoria 3052, Australia
| | - Nicholas A Watts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Megan Shand
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Andrea Haessly
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Laura Gauthier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - David Benjamin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Eric Banks
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Jose Soto
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kiran Garimella
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - James Emery
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Daniel G MacArthur
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Murdoch Children's Research Institute, Melbourne, Victoria 3052, Australia
- Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales 2010, Australia
| | - Grace Tiao
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Monkol Lek
- Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Vamsi K Mootha
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute and Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Sarah E Calvo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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Human mitochondrial DNA diversity is compatible with the multiregional continuity theory of the origin of Homo sapiens. ANTHROPOLOGICAL REVIEW 2022. [DOI: 10.2478/anre-2021-0032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Confidence intervals for estimates of human mtDNA sequence diversity, chimpanzee-human mtDNA sequence divergence, and the time of splitting of the pongid-hominid lineages are presented. Consistent with all the data used in estimating the coalescence time for human mitochondrial lineages to a common ancestral mitochondrion is a range of dates from less than 79,000 years ago to more than 1,139,000 years ago. Consequently, the hypothesis that a migration of modern humans (Homo sapiens) out of Africa in the range of 140,000 to 280,000 years ago resulted in the complete replacement, without genetic interchange, of earlier Eurasian hominid populations (Homo erectus) is but one of several possible interpretations of the mtDNA data. The data are also compatible with the hypothesis, suggested earlier and supported by fossil evidence, of a single, more ancient expansion of the range of Homo erectus from Africa, followed by a gradual transition to Homo sapiens in Europe, Asia, and Africa.
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Un modelo biocultural para entender a la persona y su ejemplificación. REVISTA DIGITAL INTERNACIONAL DE PSICOLOGÍA Y CIENCIA SOCIAL 2022. [DOI: 10.22402/j.rdipycs.unam.e.8.01.2022.396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
El objetivo del trabajo es presentar un sencillo modelo biocultural para entender al ser humano a partir de la categoría de persona. Se propone comprender a la persona a partir de los siguientes componentes: la apariencia, su fundamento, la conciencia, su identidad, el desarrollo, la vida social y la sacralidad. El modelo se compone de tres semiosis: herencia, desarrollo y momentos clave en la vida. La semiosis de herencia presenta todo lo que al heredar le hace persona, desde lo evolutivo de la especie hasta lo histórico. La semiosis de desarrollo ejemplifica el contenido ontogénico de hacerse persona y cómo hace posible la unidad biocultural de lo humano. La semiosis de momentos clave presenta los momentos más importantes en la vida para cada persona. Como conclusiones se propone que la persona sirve como índice de lo humano y puede estudiarse para responder a qué es el ser humano.
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Roksandic M, Radović P, Wu X, Bae CJ. Resolving the "muddle in the middle": The case for Homo bodoensis sp. nov. Evol Anthropol 2022; 31:20-29. [PMID: 34710249 PMCID: PMC9297855 DOI: 10.1002/evan.21929] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 09/15/2021] [Accepted: 10/08/2021] [Indexed: 01/01/2023]
Abstract
Recent developments in the field of palaeoanthropology necessitate the suppression of two hominin taxa and the introduction of a new species of hominins to help resolve the current nebulous state of Middle Pleistocene (Chibanian) hominin taxonomy. In particular, the poorly defined and variably understood hominin taxa Homo heidelbergensis (both sensu stricto and sensu lato) and Homo rhodesiensis need to be abandoned as they fail to reflect the full range of hominin variability in the Middle Pleistocene. Instead, we propose: (1) introduction of a new taxon, Homo bodoensis sp. nov., as an early Middle Pleistocene ancestor of the Homo sapiens lineage, with a pan-African distribution that extends into the eastern Mediterranean (Southeast Europe and the Levant); (2) that many of the fossils from Western Europe (e.g. Sima de los Huesos) currently assigned to H. heidelbergensis s.s. be reassigned to Homo neanderthalensis to reflect the early appearance of Neanderthal derived traits in the Middle Pleistocene in the region; and (3) that the Middle Pleistocene Asian fossils, particularly from China, likely represent a different lineage altogether.
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Affiliation(s)
- Mirjana Roksandic
- Department of AnthropologyUniversity of WinnipegWinnipegManitobaCanada
- DFG, Words Bones Genes ToolsUniversity of TübingenTübingenGermany
| | - Predrag Radović
- Department of Archaeology, Faculty of PhilosophyUniversity of BelgradeBelgradeSerbia
- National Museum KraljevoKraljevoSerbia
| | - Xiu‐Jie Wu
- Key Laboratory of Vertebrate Evolution and Human Origin of Chinese Academy of SciencesInstitute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of SciencesBeijingChina
| | - Christopher J. Bae
- Department of AnthropologyUniversity of Hawai'i at ManoaHonoluluHawaiiUSA
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Liu A, Wei Q, Lin H, Ding Y, Sun YV, Zhao D, He J, Ma Z, Li F, Zhou S, Chen X, Shen W, Gao M, He N. Baseline Characteristics of Mitochondrial DNA and Mutations Associated With Short-Term Posttreatment CD4+T-Cell Recovery in Chinese People With HIV. Front Immunol 2022; 12:793375. [PMID: 34970271 PMCID: PMC8712318 DOI: 10.3389/fimmu.2021.793375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 11/16/2021] [Indexed: 11/25/2022] Open
Abstract
Background Mitochondrial DNA (mtDNA) profiles and contributions of mtDNA variants to CD4+T-cell recovery in Euramerican people living with HIV (PLWH) may not be transferred to East-Asian PLWH, highlighting the need to consider more regional studies. We aimed to identify mtDNA characteristics and mutations that explain the variability of short-term CD4+T-cell recovery in East-Asian PLWH. Method Eight hundred fifty-six newly reported antiretroviral therapy (ART)-naïve Chinese PLWH from the Comparative HIV and Aging Research in Taizhou (CHART) cohort (Zhejiang Province, Eastern China) were enrolled. MtDNA was extracted from peripheral whole blood of those PLWH at HIV diagnosis, amplified, and sequenced using polymerase chain reaction and gene array. Characterization metrics such as mutational diversity and momentum were developed to delineate baseline mtDNA mutational patterns in ART-naïve PLWH. The associations between mtDNA genome-wide single nucleotide variants and CD4+T-cell recovery after short-term (within ~48 weeks) ART in 724 PLWH were examined using bootstrapping median regressions. Results Of 856 participants, 74.18% and 25.82% were male and female, respectively. The median age was 37 years; 94.51% were of the major Han ethnicity, and 69.04% and 28.62% were of the heterosexual and homosexual transmission, respectively. We identified 2,352 types of mtDNA mutations and mtDNA regions D-loop, ND5, CYB, or RNR1 with highest mutational diversity or volume. Female PLWH rather than male PLWH at the baseline showed remarkable age-related uptrends of momentum and mutational diversity as well as correlations between CD4+T <200 (cells/μl) and age-related uptrends of mutational diversity in many mtDNA regions. After adjustments of important sociodemographic and clinical variables, m.1005T>C, m.1824T>C, m.3394T>C, m.4491G>A, m.7828A>G, m.9814T>C, m.10586G>A, m.12338T>C, m.13708G>A, and m.14308T>C (at the Bonferroni-corrected significance) were negatively associated with short-term CD4+T-cell recovery whereas m.93A>G, m.15218A>G, and m.16399A>G were positively associated with short-term CD4+T-cell recovery. Conclusion Our baseline mtDNA characterization stresses the attention to East-Asian female PLWH at risk of CD4+T-cell loss-related aging and noncommunicable chronic diseases. Furthermore, mtDNA variants identified in regression analyses account for heterogeneity in short-term CD4+T-cell recovery of East-Asian PLWH. These results may help individualize the East-Asian immune recovery strategies under complicated HIV management caused by CD4+T-cell loss.
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Affiliation(s)
- Anni Liu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China.,Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, United States
| | - Qian Wei
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Haijiang Lin
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China.,Department of AIDS/STD Control and Prevention, Taizhou City Center for Disease Control and Prevention, Taizhou, China
| | - Yingying Ding
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Yan V Sun
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States.,Department of Biomedical Informatics, School of Medicine, Emory University, Atlanta, GA, United States
| | - Dan Zhao
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Jiayu He
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Zhonghui Ma
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Feihu Li
- School of Mathematical Sciences, Fudan University, Shanghai, China
| | - Sujuan Zhou
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Xiaoxiao Chen
- Department of AIDS/STD Control and Prevention, Taizhou City Center for Disease Control and Prevention, Taizhou, China
| | - Weiwei Shen
- Department of AIDS/STD Control and Prevention, Taizhou City Center for Disease Control and Prevention, Taizhou, China
| | - Meiyang Gao
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Na He
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China.,Key Laboratory of Health Technology Assessment, National Commission of Health, Fudan University, Shanghai, China
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Association of m.5178C>A variant with serum lipid levels: a systematic review and meta-analysis. Biosci Rep 2021; 41:230366. [PMID: 34859818 PMCID: PMC8685646 DOI: 10.1042/bsr20212246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 01/01/2023] Open
Abstract
Background: Emerging evidence shows that m.5178C>A variant is associated with a lower risk of coronary artery disease (CAD). However, the specific mechanisms remain elusive. Since dyslipidemia is one of the most critical risk factors for CAD and accounts for at least 50% of the population-attributable risk, it is tempting to speculate that the reduced CAD risk caused by the m.5178C>A variant may stem from an improved lipid profile. In order to verify this hypothesis, we conducted the present study to clarify the association of m.5178C>A variant with lipid levels. Methods: By searching ten databases for studies published before 30 June 2021. Thirteen East Asian populations (7587 individuals) were included for the analysis. Results: The present study showed that m.5178C>A variant was associated with higher high-density lipoprotein cholesterol (HDL-C) [standardized mean difference (SMD) = 0.12, 95% confidence interval (CI) = 0.06–0.17, P<0.001] and total cholesterol (TC) (SMD = 0.08, 95% CI = 0.02–0.14, P=0.01) levels. In subgroup analysis, the association of m.5178C>A variant with higher HDL-C levels were observed in Japanese (SMD = 0.09, 95% CI = 0.01–0.17, P=0.03) and Chinese populations (SMD = 0.13, 95% CI = 0.07–0.20, P<0.001). However, the association of m.5178C>A variant with lower low-density lipoprotein cholesterol (LDL-C) levels were only observed in Japanese populations (SMD = −0.11, 95% CI = −0.22 to 0.00, P=0.04). Conclusions: The m.5178C>A variant was associated with higher HDL-C and lower LDL-C levels in Japanese populations, which may contribute to decreased CAD risk and longevity of Japanese.
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Lankheet I, Vicente M, Barbieri C, Schlebusch C. The performance of common SNP arrays in assigning African mitochondrial haplogroups. BMC Genom Data 2021; 22:43. [PMID: 34674637 PMCID: PMC8532338 DOI: 10.1186/s12863-021-01000-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 10/12/2021] [Indexed: 11/20/2022] Open
Abstract
Background Mitochondrial haplogroup assignment is an important tool for forensics and evolutionary genetics. African populations are known to display a high diversity of mitochondrial haplogroups. In this research we explored mitochondrial haplogroup assignment in African populations using commonly used genome-wide SNP arrays. Results We show that, from eight commonly used SNP arrays, two SNP arrays outperform the other arrays when it comes to the correct assignment of African mitochondrial haplogroups. One array enables the recognition of 81% of the African mitochondrial haplogroups from our compiled dataset of full mitochondrial sequences. Other SNP arrays were able to assign 4–62% of the African mitochondrial haplogroups present in our dataset. We also assessed the performance of available software for assigning mitochondrial haplogroups from SNP array data. Conclusions These results provide the first cross-checked quantification of mitochondrial haplogroup assignment performance from SNP array data. Mitochondrial haplogroup frequencies inferred from most common SNP arrays used for human population analysis should be considered with caution. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-01000-2.
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Affiliation(s)
- Imke Lankheet
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden
| | - Mário Vicente
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden.,Centre for Palaeogenetics, Svante Arrhenius vägen 20C, SE-106 91, Stockholm, Sweden
| | - Chiara Barbieri
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Department of Linguistic and Cultural Evolution (DLCE), Max-Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Str. 10, 07745, Jena, Germany
| | - Carina Schlebusch
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden. .,Palaeo-Research Institute, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa. .,SciLifeLab, Uppsala, Sweden.
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45
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An etiology of human modernity. ANTHROPOLOGICAL REVIEW 2021. [DOI: 10.2478/anre-2021-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Following the refutation of the replacement hypothesis, which had proposed that a ‘superior’ hominin species arose in Africa and replaced all other humans existing at the time, the auto-domestication hypothesis remains the only viable explanation for the relatively abrupt change from robust to gracile humans in the Late Pleistocene. It invokes the incidental institution of the domestication syndrome in humans, most probably by newly introduced cultural practices. It also postulates that the induction of exograms compensated for the atrophy of the brain caused by domestication. This new explanation of the origins of modernity in humans elucidates practically all its many aspects, in stark contrast to the superseded replacement hypothesis, which explained virtually nothing. The first results of the domestication syndrome’s genetic exploration have become available in recent years, and they endorse the human self-domestication hypothesis.
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46
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The unidirectional phylogeny of Homo sapiens anchors the origin of modern humans in Eurasia. Hereditas 2021; 158:36. [PMID: 34521476 PMCID: PMC8442309 DOI: 10.1186/s41065-021-00197-7] [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: 06/10/2021] [Accepted: 08/10/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Out of Africa hypothesis, OOAH, was challenged recently in an extended mtDNA analysis, PPA (Progressive Phylogenetic Analysis), that identified the African human populations as paraphyletic, a finding that contradicted the common OOAH understanding that Hss had originated in Africa and invaded Eurasia from there. The results were consistent with the molecular Out of Eurasia hypothesis, OOEH, and Eurasian palaeontology, a subject that has been largely disregarded in the discussion of OOAH. RESULTS In the present study the mtDNA tree, a phylogeny based on maternal inheritance, was compared to the nuclear DNA tree of the paternally transmitted Y-chromosome haplotypes, Y-DNAs. The comparison showed full phylogenetic coherence between these two separate sets of data. The results were consistent with potentially four translocations of modern humans from Eurasia into Africa, the earliest taking place ≈ 250,000 years before present, YBP. The results were in accordance with the postulates behind OOEH at the same time as they lent no support to the OOAH. CONCLUSIONS The conformity between the mtDNA and Y-DNA phylogenies of Hss is consistent with the understanding that Eurasia was the donor and not the receiver in human evolution. The evolutionary problems related to OOAH became similarly exposed by the mtDNA introgression that took place from Hss into Neanderthals ≈ 500,000 YBP, a circumstance that demonstrated the early coexistence of the two lineages in Eurasia.
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47
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Liu C, Fetterman JL, Qian Y, Sun X, Blackwell TW, Pitsillides A, Cade BE, Wang H, Raffield LM, Lange LA, Anugu P, Abecasis G, Adrienne Cupples L, Redline S, Correa A, Vasan RS, Wilson JG, Ding J, Levy D. Presence and transmission of mitochondrial heteroplasmic mutations in human populations of European and African ancestry. Mitochondrion 2021; 60:33-42. [PMID: 34303007 PMCID: PMC8464516 DOI: 10.1016/j.mito.2021.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 06/13/2021] [Accepted: 07/19/2021] [Indexed: 11/20/2022]
Abstract
We investigated the concordance of mitochondrial DNA heteroplasmic mutations (heteroplasmies) in 6745 maternal pairs of European (EA, n = 4718 pairs) and African (AA, n = 2027 pairs) Americans in whole blood. Mother-offspring pairs displayed the highest concordance rate, followed by sibling-sibling and more distantly-related maternal pairs. The allele fractions of concordant heteroplasmies exhibited high correlation (R2 = 0.8) between paired individuals. Discordant heteroplasmies were more likely to be in coding regions, be nonsynonymous or nonsynonymous-deleterious (p < 0.001). The number of deleterious heteroplasmies was significantly correlated with advancing age (20-44, 45-64, and ≥65 years, p-trend = 0.01). One standard deviation increase in heteroplasmic burden (i.e., the number of heteroplasmies carried by an individual) was associated with 0.17 to 0.26 (p < 1e - 23) standard deviation decrease in mtDNA copy number, independent of age. White blood cell count and differential count jointly explained 0.5% to 1.3% (p ≤ 0.001) variance in heteroplasmic burden. A genome-wide association and meta-analysis identified a region at 11p11.12 (top signal rs779031139, p = 2.0e - 18, minor allele frequency = 0.38) associated with the heteroplasmic burden. However, the 11p11.12 region is adjacent to a nuclear mitochondrial DNA (NUMT) corresponding to a 542 bp area of the D-loop. This region was no longer significant after excluding heteroplasmies within the 542 bp from the heteroplasmic burden. The discovery that blood mtDNA heteroplasmies were both inherited and somatic origins and that an increase in heteroplasmic burden was strongly associated with a decrease in average number of mtDNA copy number in blood are important findings to be considered in association studies of mtDNA with disease traits.
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Affiliation(s)
- Chunyu Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA.
| | - Jessica L Fetterman
- Evans Department of Medicine and Whitaker Cardiovascular Institute, School of Medicine, Boston University, Boston, MA 20118, USA
| | - Yong Qian
- Longitudinal Studies Section, Translational Gerontology Branch, NIA/NIH, Baltimore, MD 21224, USA
| | - Xianbang Sun
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Thomas W Blackwell
- TOPMed Informatics Research Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Achilleas Pitsillides
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Heming Wang
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Leslie A Lange
- School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Pramod Anugu
- Coordinating Center, University of Mississippi of Medical Center, Jackson, MS 39216, USA
| | - Goncalo Abecasis
- TOPMed Informatics Research Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - L Adrienne Cupples
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Ramachandran S Vasan
- Framingham Heart Study, Framingham, MA 01702, USA; Sections of Preventive Medicine and Epidemiology, and Cardiovascular Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Jun Ding
- Longitudinal Studies Section, Translational Gerontology Branch, NIA/NIH, Baltimore, MD 21224, USA
| | - Daniel Levy
- Framingham Heart Study, Framingham, MA 01702, USA; Population Sciences Branch, NHLBI/NIH, Bethesda, MD 20892, USA
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Edwards SV, Robin V, Ferrand N, Moritz C. The evolution of comparative phylogeography: putting the geography (and more) into comparative population genomics. Genome Biol Evol 2021; 14:6339579. [PMID: 34347070 PMCID: PMC8743039 DOI: 10.1093/gbe/evab176] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
Comparative population genomics is an ascendant field using genomic comparisons between species to draw inferences about forces regulating genetic variation. Comparative phylogeography, by contrast, focuses on the shared lineage histories of species codistributed geographically and is decidedly organismal in perspective. Comparative phylogeography is approximately 35 years old, and, by some metrics, is showing signs of reduced growth. Here, we contrast the goals and methods of comparative population genomics and comparative phylogeography and argue that comparative phylogeography offers an important perspective on evolutionary history that succeeds in integrating genomics with landscape evolution in ways that complement the suprageographic perspective of comparative population genomics. Focusing primarily on terrestrial vertebrates, we review the history of comparative phylogeography, its milestones and ongoing conceptual innovations, its increasingly global focus, and its status as a bridge between landscape genomics and the process of speciation. We also argue that, as a science with a strong “sense of place,” comparative phylogeography offers abundant “place-based” educational opportunities with its focus on geography and natural history, as well as opportunities for collaboration with local communities and indigenous peoples. Although comparative phylogeography does not yet require whole-genome sequencing for many of its goals, we conclude that it nonetheless plays an important role in grounding our interpretation of genetic variation in the fundamentals of geography and Earth history.
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Affiliation(s)
- Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Vv Robin
- Indian Institute of Science Education and Research (IISER) Tirupati, Karakambadi Road, Tirupati, Andhra Pradesh, 517507, India
| | - Nuno Ferrand
- CIBIO/InBIO, Laboratório Associado, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Portugal
| | - Craig Moritz
- Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
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49
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Rohrlach AB, Papac L, Childebayeva A, Rivollat M, Villalba-Mouco V, Neumann GU, Penske S, Skourtanioti E, van de Loosdrecht M, Akar M, Boyadzhiev K, Boyadzhiev Y, Deguilloux MF, Dobeš M, Erdal YS, Ernée M, Frangipane M, Furmanek M, Friederich S, Ghesquière E, Hałuszko A, Hansen S, Küßner M, Mannino M, Özbal R, Reinhold S, Rottier S, Salazar-García DC, Diaz JS, Stockhammer PW, de Togores Muñoz CR, Yener KA, Posth C, Krause J, Herbig A, Haak W. Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe. Sci Rep 2021; 11:15005. [PMID: 34294811 PMCID: PMC8298398 DOI: 10.1038/s41598-021-94491-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 07/09/2021] [Indexed: 01/08/2023] Open
Abstract
Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240 k capture, YMCA significantly improves the mean coverage and number of sites covered on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe.
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Affiliation(s)
- Adam B Rohrlach
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. .,ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
| | - Luka Papac
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Maïté Rivollat
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,Université de Bordeaux, CNRS, PACEA-UMR 5199, 33615, Pessac, France
| | - Vanessa Villalba-Mouco
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Sandra Penske
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Eirini Skourtanioti
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Marieke van de Loosdrecht
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Murat Akar
- Department of Archaeology, Mustafa Kemal University, 31060, Alahan-Antakya, Hatay, Turkey
| | - Kamen Boyadzhiev
- National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, 1000, Sofia, Bulgaria
| | - Yavor Boyadzhiev
- National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, 1000, Sofia, Bulgaria
| | | | - Miroslav Dobeš
- Department of Prehistory, Institute of Archaeology CAS, Prague, Czech Republic
| | - Yilmaz S Erdal
- Department of Anthropology, Hacettepe University, 06800, Ankara, Turkey
| | - Michal Ernée
- Department of Prehistory, Institute of Archaeology CAS, Prague, Czech Republic
| | | | | | - Susanne Friederich
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Halle, Germany
| | - Emmanuel Ghesquière
- Inrap Grand Ouest, Bourguébus, France.,Université de Rennes 1, CNRS, CReAAH-UMR, 6566, Rennes, France
| | - Agata Hałuszko
- Institute of Archaeology, University of Wrocław, Wrocław, Poland.,Archeolodzy.org Foundation, Wrocław, Poland
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Mario Küßner
- Thuringian State Office for Heritage Management and Archeology, Weimar, Germany
| | - Marcello Mannino
- Department of Archaeology, School of Culture and Society, Aarhus University, 8270, Højbjerg, Denmark
| | - Rana Özbal
- Department of Archaeology and History of Art, Koç University, 34450, Istanbul, Turkey
| | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Stéphane Rottier
- Université de Bordeaux, CNRS, PACEA-UMR 5199, 33615, Pessac, France
| | - Domingo Carlos Salazar-García
- Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain.,Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, Valencia, Spain.,Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | | | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,Ludwig Maximilian University Munich, 80799, Munich, Germany
| | | | - K Aslihan Yener
- Institute for the Study of the Ancient World (ISAW), New York University, New York, NY, 10028, USA
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,Archaeo- and Palaeogenetics Group, Institute for Archaeological Sciences Eberhard Karls University Tübingen, 72070, Tübingen, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. .,School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
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The absolute chronology of Boker Tachtit (Israel) and implications for the Middle to Upper Paleolithic transition in the Levant. Proc Natl Acad Sci U S A 2021; 118:2014657118. [PMID: 34161257 DOI: 10.1073/pnas.2014657118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The Initial Upper Paleolithic (IUP) is a crucial lithic assemblage type in the archaeology of southwest Asia because it marks a dramatic shift in hominin populations accompanied by technological changes in material culture. This phase is conventionally divided into two chronocultural phases based on the Boker Tachtit site, central Negev, Israel. While lithic technologies at Boker Tachtit are well defined, showing continuity from one phase to another, the absolute chronology is poorly resolved because the radiocarbon method used had a large uncertainty. Nevertheless, Boker Tachtit is considered to be the origin of the succeeding Early Upper Paleolithic Ahmarian tradition that dates in the Negev to ∼42,000 y ago (42 ka). Here, we provide 14C and optically stimulated luminescence dates obtained from a recent excavation of Boker Tachtit. The new dates show that the early phase at Boker Tachtit, the Emirian, dates to 50 through 49 ka, while the late phase dates to 47.3 ka and ends by 44.3 ka. These results show that the IUP started in the Levant during the final stages of the Late Middle Paleolithic some 50,000 y ago. The later IUP phase in the Negev chronologically overlaps with the Early Upper Paleolithic Ahmarian of the Mediterranean woodland region between 47 and 44 ka. We conclude that Boker Tachtit is the earliest manifestation of the IUP in Eurasia. The study shows that distinguishing the chronology of the IUP from the Late Middle Paleolithic, as well as from the Early Upper Paleolithic, is much more complex than previously thought.
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