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Sharp PM, Plenderleith LJ, Culleton RL, Hahn BH. Origin of the human malaria parasite Plasmodium vivax. Trends Parasitol 2024; 40:562-572. [PMID: 38806300 DOI: 10.1016/j.pt.2024.05.001] [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: 03/19/2024] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/30/2024]
Abstract
The geographic origin of Plasmodium vivax, a leading cause of human malaria, has been the subject of much speculation. Here we review the evolutionary history of P. vivax and P. vivax-like parasites in humans and non-human primates on three continents, providing overwhelming evidence for an African origin. This conclusion is consistent with recent reports showing that Duffy-negative humans in Africa are, in fact, susceptible to P. vivax, with parasites invading Duffy-antigen-expressing erythroid precursors. Thus, the African origin of P. vivax not only explains the distribution of the Duffy-negative genotype but also provides new insight into the history and status of P. vivax malaria in Africa and efforts geared toward its eradication.
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Affiliation(s)
- Paul M Sharp
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK; Centre for Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK.
| | | | - Richard L Culleton
- Division of Parasitology, Proteo-Science Centre, Ehime University, 454 Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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2
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Cruz-Nicolás J, Jaramillo-Correa JP, Gernandt DS. Stochastic processes and changes in evolutionary rate are associated with diversification in a lineage of tropical hard pines (Pinus). Mol Phylogenet Evol 2024; 192:108011. [PMID: 38195010 DOI: 10.1016/j.ympev.2024.108011] [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: 06/08/2023] [Revised: 12/08/2023] [Accepted: 01/06/2024] [Indexed: 01/11/2024]
Abstract
The study of the patterns of polymorphism and molecular evolution among closely related species is key to understanding the evolutionary forces involved in the diversification of lineages. This point is a big challenge in species with slow evolutionary rates, long life cycles, and ancient, shared polymorphisms such as conifers. Under the premise of divergence in a stepwise migration process, we expect clinal geographical patterns of purifying selection efficiency, and genetic structure related to latitude or longitude. If migration is accompanied by changes in the environment, we could further expect a role of positive selection in driving species divergence. Here, we infer patterns of polymorphism, efficiency of purifying selection, and molecular evolution using a dataset of 161 nuclear genes (∼71 Kb) in a lineage of hard pines from North America, the Caribbean, Mexico, and Central America presumed to have migrated from North America toward lower latitudes with tropical conditions. Under the premise of differences in selective pressures, we also look for possible signals of positive selection. To test our hypothesis, first we estimated different indices to infer patterns of polymorphism and efficiency of purifying selection (Ka, Ks, Ka/Ks, dN, dS, dN/dS, and dxy) and compared these metrics across five clades. Also, we investigated possible clinal patterns in these indices and morphological traits (needle length and cone length). Then we inferred genetic structure and environmental differences among species to test for possible signals of positive selection using phylogenetic methods in specific clades. We found differences among clades using Ka, Ks, and Ka/Ks with a relaxation of purifying selection, especially in the Elliotti and Patula clades. We also found environmental differences related to geographic distance, and among clades suggesting differences in selective pressures. The indices Ks, dxy, and needle length had relationships with geography but not ovulate cone length. Finally, we found that most analyzed genes are under purifying selection, but there was an exception of faster evolutionary rate in some pine species, suggesting the possible action of positive selection in divergence. Our study indicated that stochastic processes have played a key role in the diversification of the group, with a possible input of positive selection in pines from Mexico and Central America.
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Affiliation(s)
- Jorge Cruz-Nicolás
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México CDMX 04510, Mexico.
| | - Juan Pablo Jaramillo-Correa
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México CDMX 04510, Mexico
| | - David S Gernandt
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México CDMX 04510, Mexico.
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3
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Cerdeña JP, Grubbs V, Non AL. Racialising genetic risk: assumptions, realities, and recommendations. Lancet 2022; 400:2147-2154. [PMID: 36502852 DOI: 10.1016/s0140-6736(22)02040-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 09/07/2022] [Accepted: 10/14/2022] [Indexed: 12/13/2022]
Affiliation(s)
- Jessica P Cerdeña
- Yale School of Medicine, Yale University, New Haven, CT, USA; Department of Anthropology, University of Connecticut, Storrs, CT, USA
| | - Vanessa Grubbs
- Department of Ambulatory and Preventive Medicine, Alameda Health System, Oakland, CA, USA
| | - Amy L Non
- Department of Anthropology, University of California, San Diego, CA, USA.
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4
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Altınışık NE, Kazancı DD, Aydoğan A, Gemici HC, Erdal ÖD, Sarıaltun S, Vural KB, Koptekin D, Gürün K, Sağlıcan E, Fernandes D, Çakan G, Koruyucu MM, Lagerholm VK, Karamurat C, Özkan M, Kılınç GM, Sevkar A, Sürer E, Götherström A, Atakuman Ç, Erdal YS, Özer F, Erim Özdoğan A, Somel M. A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition. SCIENCE ADVANCES 2022; 8:eabo3609. [PMID: 36332018 PMCID: PMC9635823 DOI: 10.1126/sciadv.abo3609] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked innovations in symbolism, technology, and diet. We present 13 ancient genomes (c. 8500 to 7500 cal BCE) from Pre-Pottery Neolithic Çayönü in the Tigris basin together with bioarchaeological and material culture data. Our findings reveal that Çayönü was a genetically diverse population, carrying mixed ancestry from western and eastern Fertile Crescent, and that the community received immigrants. Our results further suggest that the community was organized along biological family lines. We document bodily interventions such as head shaping and cauterization among the individuals examined, reflecting Çayönü's cultural ingenuity. Last, we identify Upper Mesopotamia as the likely source of eastern gene flow into Neolithic Anatolia, in line with material culture evidence. We hypothesize that Upper Mesopotamia's cultural dynamism during the Neolithic Transition was the product not only of its fertile lands but also of its interregional demographic connections.
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Affiliation(s)
- N. Ezgi Altınışık
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Duygu Deniz Kazancı
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Ayça Aydoğan
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Hasan Can Gemici
- Department of Settlement Archaeology, Middle East Technical University, 06800 Ankara, Turkey
| | - Ömür Dilek Erdal
- Husbio-L Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Savaş Sarıaltun
- Department of Museology and Cultural Heritage Management, Çanakkale Onsekiz Mart University, Çanakkale 17100, Turkey
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Dilek Koptekin
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey
| | - Kanat Gürün
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Ekin Sağlıcan
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey
| | - Daniel Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
- CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Gökhan Çakan
- Husbio-L Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Meliha Melis Koruyucu
- Husbio-L Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Vendela Kempe Lagerholm
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Cansu Karamurat
- Department of Settlement Archaeology, Middle East Technical University, 06800 Ankara, Turkey
| | - Mustafa Özkan
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Gülşah Merve Kılınç
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100 Sıhhiye, Ankara, Turkey
| | - Arda Sevkar
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Elif Sürer
- Department of Modeling and Simulation, Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Çiğdem Atakuman
- Department of Settlement Archaeology, Middle East Technical University, 06800 Ankara, Turkey
| | - Yılmaz Selim Erdal
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
- Husbio-L Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Füsun Özer
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Aslı Erim Özdoğan
- Department of Archaeology, Çanakkale Onsekiz Mart University, Çanakkale 17100, Turkey
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
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Schlichta F, Moinet A, Peischl S, Excoffier L. The Impact of Genetic Surfing on Neutral Genomic Diversity. Mol Biol Evol 2022; 39:msac249. [PMID: 36403964 PMCID: PMC9703594 DOI: 10.1093/molbev/msac249] [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] [Indexed: 11/22/2022] Open
Abstract
Range expansions have been common in the history of most species. Serial founder effects and subsequent population growth at expansion fronts typically lead to a loss of genomic diversity along the expansion axis. A frequent consequence is the phenomenon of "gene surfing," where variants located near the expanding front can reach high frequencies or even fix in newly colonized territories. Although gene surfing events have been characterized thoroughly for a specific locus, their effects on linked genomic regions and the overall patterns of genomic diversity have been little investigated. In this study, we simulated the evolution of whole genomes during several types of 1D and 2D range expansions differing by the extent of migration, founder events, and recombination rates. We focused on the characterization of local dips of diversity, or "troughs," taken as a proxy for surfing events. We find that, for a given recombination rate, once we consider the amount of diversity lost since the beginning of the expansion, it is possible to predict the initial evolution of trough density and their average width irrespective of the expansion condition. Furthermore, when recombination rates vary across the genome, we find that troughs are over-represented in regions of low recombination. Therefore, range expansions can leave local and global genomic signatures often interpreted as evidence of past selective events. Given the generality of our results, they could be used as a null model for species having gone through recent expansions, and thus be helpful to correctly interpret many evolutionary biology studies.
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Affiliation(s)
- Flávia Schlichta
- Computational and Molecular Population Genetics lab, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Antoine Moinet
- Computational and Molecular Population Genetics lab, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Interfaculty Bioinformatics Unit, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Stephan Peischl
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Interfaculty Bioinformatics Unit, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Laurent Excoffier
- Computational and Molecular Population Genetics lab, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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Thyroidal and Extrathyroidal Requirements for Iodine and Selenium: A Combined Evolutionary and (Patho)Physiological Approach. Nutrients 2022; 14:nu14193886. [PMID: 36235539 PMCID: PMC9571367 DOI: 10.3390/nu14193886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
Iodide is an antioxidant, oxidant and thyroid hormone constituent. Selenoproteins are needed for triiodothyronine synthesis, its deactivation and iodine release. They also protect thyroidal and extrathyroidal tissues from hydrogen peroxide used in the ‘peroxidase partner system’. This system produces thyroid hormone and reactive iodine in exocrine glands to kill microbes. Exocrine glands recycle iodine and with high urinary clearance require constant dietary supply, unlike the thyroid. Disbalanced iodine-selenium explains relations between thyroid autoimmune disease (TAD) and cancer of thyroid and exocrine organs, notably stomach, breast, and prostate. Seafood is iodine unconstrained, but selenium constrained. Terrestrial food contains little iodine while selenium ranges from highly deficient to highly toxic. Iodine vs. TAD is U-shaped, but only low selenium relates to TAD. Oxidative stress from low selenium, and infection from disbalanced iodine-selenium, may generate cancer of thyroid and exocrine glands. Traditional Japanese diet resembles our ancient seashore-based diet and relates to aforementioned diseases. Adequate iodine might be in the milligram range but is toxic at low selenium. Optimal selenoprotein-P at 105 µg selenium/day agrees with Japanese intakes. Selenium upper limit may remain at 300–400 µg/day. Seafood combines iodine, selenium and other critical nutrients. It brings us back to the seashore diet that made us what we currently still are.
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7
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Gellis JJ, Foley RA. Patterns of variation in canal and root number in human post-canine teeth. J Anat 2022; 241:896-918. [PMID: 36082500 PMCID: PMC9482695 DOI: 10.1111/joa.13729] [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: 04/14/2020] [Revised: 05/31/2022] [Accepted: 07/04/2022] [Indexed: 11/28/2022] Open
Abstract
Descriptive morphology of tooth roots traditionally focuses on number of canals and roots. However, how or if canal and root number are related is poorly understood. While it is often assumed that canal number is concomitant with root number and morphology, in practice canal number and morphology do not always covary with external root features. To investigate the relationship between canal and root number, fully developed, adult post‐canine teeth were examined and quantified from computerized tomography scans from a global sample of 945 modern humans. We tested the hypotheses that root and canal number do not follow a 1:1 ratio, that canal to root ratios differ between teeth, and that canal to root ratios differ across major human geographical groups. Results indicate that not only is root number dependent on canal number, but that this relationship becomes more variable as canal number increases, varies between individual teeth and by major geographical group, and changes as these groups increase in geographical distance from Sub‐Saharan Africa. These results show that the ratio of canal number to root number is an important indicator of variation in dental phenotypes.
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Affiliation(s)
- Jason J Gellis
- University of Cambridge Leverhulme Centre for Human Evolutionary Studies, Cambridge, UK
| | - Robert A Foley
- University of Cambridge Leverhulme Centre for Human Evolutionary Studies, Cambridge, UK
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Cerdeña JP, Grubbs V, Non AL. Genomic supremacy: the harm of conflating genetic ancestry and race. Hum Genomics 2022; 16:18. [PMID: 35585650 PMCID: PMC9118726 DOI: 10.1186/s40246-022-00391-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent studies have reignited the tinderbox of debate surrounding the use of race and ancestry in medicine. These controversial studies have argued for a strong correlation between genetic ancestry and race, justifying continued use of genetic ancestry measures in studies of disease. These studies contend that increased use of continental ancestry estimates can inform clinical risk assessments and management. Further, recent studies of racial corrections used in clinical algorithms, such as those used to estimate 'normal' lung function, also advocate for use of genetic ancestry in place of race for refining risk algorithms. MAIN BODY These positions are misleading, harmful, and reflect superficial interpretations of population genetics. In this Perspective, we argue that continental genetic ancestry, often proxied by race, serves as a poor indicator of disease risk, and reinforces racialized inequities. CONCLUSION Instead, we endorse that racial disparities in disease should be investigated by rigorous measures of structural racism alongside careful measures of genetic factors in relevant disease pathways, rather than relying on genetic ancestry or race as a crude proxy for disease-causing alleles.
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Affiliation(s)
| | - Vanessa Grubbs
- Department of Ambulatory and Preventive Medicine, Alameda Health System, Oakland, CA, 94602, USA
| | - Amy L Non
- Department of Anthropology, University of California San Diego, La Jolla, CA, 92093, USA.
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Schouler-Ocak M, Bhugra D, Kastrup MC, Dom G, Heinz A, Küey L, Gorwood P. Racism and mental health and the role of mental health professionals. Eur Psychiatry 2021; 64:e42. [PMID: 34134809 PMCID: PMC8278246 DOI: 10.1192/j.eurpsy.2021.2216] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/18/2021] [Accepted: 05/31/2021] [Indexed: 11/23/2022] Open
Abstract
The concept of "race" and consequently of racism is not a recent phenomenon, although it had profound effects on the lives of populations over the last several hundred years. Using slaves and indentured labor from racial groups designated to be "the others," who was seen as inferior and thus did not deserve privileges, and who were often deprived of the right to life and basic needs as well as freedoms. Thus, creation of "the other" on the basis of physical characteristics and dehumanizing them became more prominent. Racism is significantly related to poor health, including mental health. The impact of racism in psychiatric research and clinical practice is not sufficiently investigated. Findings clearly show that the concept of "race" is genetically incorrect. Therefore, the implicit racism that underlies many established "scientific" paradigms need be changed. Furthermore, to overcome the internalized, interpersonal, and institutional racism, the impact of racism on health and on mental health must be an integral part of educational curricula, from undergraduate levels through continuing professional development, clinical work, and research. In awareness of the consequences of racism at all levels (micro, meso, and macro), recommendations for clinicians, policymakers, and researchers are worked out.
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Affiliation(s)
- M. Schouler-Ocak
- Psychiatric University Clinic of Charité at St. Hedwig Hospital, Berlin, Germany
| | - D. Bhugra
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - M. C. Kastrup
- Specialist in Psychiatryformer Treasurer World Association Social Psychiatryformer Secretary General European Psychiatric Associationformer Member Executive Committee World Psychiatric Association Copenhagen, Denmark
| | - G. Dom
- CAPRI, University of Antwerp (UAntwerp), Antwerp, Belgium
| | - A. Heinz
- Department for Psychiatry and Psychotherapy, CCM, Charité—University Medicine, Berlin, Germany
| | - L. Küey
- Istanbul Bilgi University, Istanbul, Turkey
| | - P. Gorwood
- CMME, Hopital Sainte-Anne GHU Paris Psychiatrie et Neurosciences Université de Paris, INSERM U894, Paris, France
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Gousy-Leblanc M, Yannic G, Therrien JF, Lecomte N. Mapping our knowledge on birds of prey population genetics. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01368-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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11
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Yannic G, Helfer V, Sermier R, Schmidt BR, Fumagalli L. Fine scale genetic structure in fire salamanders (Salamandra salamandra) along a rural-to-urban gradient. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01335-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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12
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Hochman A. Janus-faced race: Is race biological, social, or mythical? AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 175:453-464. [PMID: 33135802 DOI: 10.1002/ajpa.24169] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/13/2020] [Accepted: 10/10/2020] [Indexed: 01/29/2023]
Abstract
As belief in the reality of race as a biological category among U.S. anthropologists has fallen, belief in the reality of race as a social category has risen in its place. The view that race simply does not exist-that it is a myth-is treated with suspicion. While racial classification is linked to many of the worst evils of recent history, it is now widely believed to be necessary to fight back against racism. In this article, I argue that race is indeed a biological fiction, but I critique the claim that race is socially real. I defend a form of anti-realist reconstructionism about race, which says that there are no races, only racialized groups-groups mistakenly believed to be races. I argue that this is the most attractive position about race from a metaphysical perspective, and that it is also the position most conductive to public understanding and social justice.
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Affiliation(s)
- Adam Hochman
- Department of Philosophy, Faculty of Arts, Macquarie University, Macquarie Park, New South Wales, Australia
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13
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Nagar SD, Conley AB, Jordan IK. Population structure and pharmacogenomic risk stratification in the United States. BMC Biol 2020; 18:140. [PMID: 33050895 PMCID: PMC7557099 DOI: 10.1186/s12915-020-00875-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/22/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Pharmacogenomic (PGx) variants mediate how individuals respond to medication, and response differences among racial/ethnic groups have been attributed to patterns of PGx diversity. We hypothesized that genetic ancestry (GA) would provide higher resolution for stratifying PGx risk, since it serves as a more reliable surrogate for genetic diversity than self-identified race/ethnicity (SIRE), which includes a substantial social component. We analyzed a cohort of 8628 individuals from the United States (US), for whom we had both SIRE information and whole genome genotypes, with a focus on the three largest SIRE groups in the US: White, Black (African-American), and Hispanic (Latino). Our approach to the question of PGx risk stratification entailed the integration of two distinct methodologies: population genetics and evidence-based medicine. This integrated approach allowed us to consider the clinical implications for the observed patterns of PGx variation found within and between population groups. RESULTS Whole genome genotypes were used to characterize individuals' continental ancestry fractions-European, African, and Native American-and individuals were grouped according to their GA profiles. SIRE and GA groups were found to be highly concordant. Continental ancestry predicts individuals' SIRE with > 96% accuracy, and accordingly, GA provides only a marginal increase in resolution for PGx risk stratification. In light of the concordance between SIRE and GA, taken together with the fact that information on SIRE is readily available to clinicians, we evaluated PGx variation between SIRE groups to explore the potential clinical utility of race and ethnicity. PGx variants are highly diverged compared to the genomic background; 82 variants show significant frequency differences among SIRE groups, and genome-wide patterns of PGx variation are almost entirely concordant with SIRE. The vast majority of PGx variation is found within rather than between groups, a well-established fact for almost all genetic variants, which is often taken to argue against the clinical utility of population stratification. Nevertheless, analysis of highly differentiated PGx variants illustrates how SIRE partitions PGx variation based on groups' characteristic ancestry patterns. These cases underscore the extent to which SIRE carries clinically valuable information for stratifying PGx risk among populations, albeit with less utility for predicting individual-level PGx alleles (genotypes), supporting the concept of population pharmacogenomics. CONCLUSIONS Perhaps most interestingly, we show that individuals who identify as Black or Hispanic stand to gain far more from the consideration of race/ethnicity in treatment decisions than individuals from the majority White population.
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Affiliation(s)
- Shashwat Deepali Nagar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA USA
- PanAmerican Bioinformatics Institute, Cali, Colombia
| | - Andrew B. Conley
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA USA
- PanAmerican Bioinformatics Institute, Cali, Colombia
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, 950 Atlantic Drive, Atlanta, GA 30332 USA
| | - I. King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA USA
- PanAmerican Bioinformatics Institute, Cali, Colombia
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, 950 Atlantic Drive, Atlanta, GA 30332 USA
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14
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Ji L, Wu D, Xie H, Yao B, Chen Y, Irwin DM, Huang D, Xu J, Tang NLS, Zhang Y. Ambient Temperature is A Strong Selective Factor Influencing Human Development and Immunity. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:489-500. [PMID: 32822870 PMCID: PMC8377383 DOI: 10.1016/j.gpb.2019.11.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 08/22/2019] [Accepted: 11/29/2019] [Indexed: 01/22/2023]
Abstract
Solar energy, which is essential for the origin and evolution of all life forms on Earth, can be objectively recorded through attributes such as climatic ambient temperature (CAT), ultraviolet radiation (UVR), and sunlight duration (SD). These attributes have specific geographical variations and may cause different adaptation traits. However, the adaptation profile of each attribute and the selective role of solar energy as a whole during human evolution remain elusive. Here, we performed a genome-wide adaptation study with respect to CAT, UVR, and SD using the Human Genome Diversity Project-Centre Etude Polymorphism Humain (HGDP-CEPH) panel data. We singled out CAT as the most important driving force with the highest number of adaptive loci (6 SNPs at the genome-wide 1 × 10−7 level; 401 at the suggestive 1 × 10−5 level). Five of the six genome-wide significant adaptation SNPs were successfully replicated in an independent Chinese population (N = 1395). The corresponding 316 CAT adaptation genes were mostly involved in development and immunity. In addition, 265 (84%) genes were related to at least one genome-wide association study (GWAS)-mapped human trait, being significantly enriched in anthropometric loci such as those associated with body mass index (χ2; P < 0.005), immunity, metabolic syndrome, and cancer (χ2; P < 0.05). For these adaptive SNPs, balancing selection was evident in Euro-Asians, whereas obvious positive and/or purifying selection was observed in Africans. Taken together, our study indicates that CAT is the most important attribute of solar energy that has driven genetic adaptation in development and immunity among global human populations. It also supports the non-neutral hypothesis for the origin of disease-predisposition alleles in common diseases.
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Affiliation(s)
- Lindan Ji
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Department of Biochemistry, Medical School of Ningbo University, Ningbo 315211, China
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Haibing Xie
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Binbin Yao
- Department of Preventive Medicine, Medical School of Ningbo University, Ningbo 315211, China
| | - Yanming Chen
- Department of Preventive Medicine, Medical School of Ningbo University, Ningbo 315211, China
| | - David M Irwin
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; Banting and Best Diabetes Centre, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Dan Huang
- Department of Chemical Pathology, and Laboratory for Genetics of Disease Susceptibility, Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China
| | - Jin Xu
- Department of Preventive Medicine, Medical School of Ningbo University, Ningbo 315211, China.
| | - Nelson L S Tang
- Department of Chemical Pathology, and Laboratory for Genetics of Disease Susceptibility, Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China.
| | - Yaping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, China.
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15
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Botero-Delgadillo E, Quirici V, Poblete Y, Acevedo M, Cuevas É, Bravo C, Cragnolini M, Rozzi R, Poulin E, Mueller JC, Kempenaers B, Vásquez RA. Range-wide genetic structure in the thorn-tailed rayadito suggests limited gene flow towards peripheral populations. Sci Rep 2020; 10:9409. [PMID: 32523081 PMCID: PMC7287099 DOI: 10.1038/s41598-020-66450-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/18/2020] [Indexed: 12/17/2022] Open
Abstract
Understanding the population genetic consequences of habitat heterogeneity requires assessing whether patterns of gene flow correspond to landscape configuration. Studies of the genetic structure of populations are still scarce for Neotropical forest birds. We assessed range-wide genetic structure and contemporary gene flow in the thorn-tailed rayadito (Aphrastura spinicauda), a passerine bird inhabiting the temperate forests of South America. We used 12 microsatellite loci to genotype 582 individuals from eight localities across a large latitudinal range (30°S–56°S). Using population structure metrics, multivariate analyses, clustering algorithms, and Bayesian methods, we found evidence for moderately low regional genetic structure and reduced gene flow towards the range margins. Genetic differentiation increased with geographic distance, particularly in the southern part of the species’ distribution where forests are continuously distributed. Populations in the north seem to experience limited gene flow likely due to forest discontinuity, and may comprise a demographically independent unit. The southernmost population, on the other hand, is genetically depauperate and different from all other populations. Different analytical approaches support the presence of three to five genetic clusters. We hypothesize that the genetic structure of the species follows a hierarchical clustered pattern.
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Affiliation(s)
- Esteban Botero-Delgadillo
- Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile. .,Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany. .,SELVA: Research for conservation in the Neotropics, Bogotá, Colombia.
| | - Veronica Quirici
- Departamento de Ecología y Biodiversidad, Facultad de Ecología y Recursos Naturales, Universidad Andrés Bello, Santiago, Chile.,Centro de investigación para la sustentabilidad, Universidad Andrés Bello, Santiago, Chile
| | - Yanina Poblete
- Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.,Instituto de Ciencias Naturales, Universidad de las Américas, Santiago, Chile
| | - Matías Acevedo
- Programa de Magister en Áreas Silvestres y Conservación de la Naturaleza, Facultad de Ciencias Forestales y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile
| | - Élfego Cuevas
- Doctorado en Medicina de la Conservación, Facultad de Ecología y Recursos Naturales, Universidad Andrés Bello, Santiago, Chile
| | - Camila Bravo
- Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Margherita Cragnolini
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
| | - Ricardo Rozzi
- Programa de Conservación Biocultural Sub-Antártica, Parque Etnobotánico Omora, Universidad de Magallanes & Instituto de Ecología y Biodiversidad, Santiago, Chile.,Sub-Antarctic Biocultural Conservation Program, Department of Philosophy and Religion & Department of Biological Sciences, University of North Texas, Denton, TX, USA
| | - Elie Poulin
- Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Jakob C Mueller
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
| | - Rodrigo A Vásquez
- Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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Next generation sequencing of a set of ancestry-informative SNPs: ancestry assignment of three continental populations and estimating ancestry composition for Mongolians. Mol Genet Genomics 2020; 295:1027-1038. [PMID: 32206883 DOI: 10.1007/s00438-020-01660-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 02/27/2020] [Indexed: 12/31/2022]
Abstract
When traditional short tandem repeat profiling fails to provide valuable information to arrest the criminal, forensic ancestry inference of the biological samples left at the crime scene will probably offer investigative leads and facilitate the investigation process of the case. That is why there are consistent efforts in developing panels for ancestry inference in forensic science. Presently, a 30-plex next generation sequencing-based assay was exploited in this study by assembling well-differentiated single nucleotide polymorphisms for ancestry assignment of unknown individuals from three continental populations (African, European and East Asian). And meanwhile, relatively balanced population-specific differentiation values were maintained to avoid the over-estimation or under-estimation of co-ancestry proportions in individuals with admixed ancestry. The principal component analysis and STRUCTURE analysis of reference populations, test populations and the studied Mongolian group indicated that the novel assay was efficient enough to determine the ancestry origin of an unknown individual from the three continental populations. Besides, ancestry membership proportion estimations for the Mongolian group revealed that a large fraction of the ancestry was contributed by East Asian genetic component (approximately 83.9%), followed by European (approximately 12.6%) and African genetic components (approximately 3.5%), respectively. And next generation sequencing technology applied in this study offers possibility to incorporate more single nucleotide polymorphisms for individual identification and phenotype prediction into the same assay to provide as many as possible investigative clues in the future.
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17
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Benn Torres J. Anthropological perspectives on genomic data, genetic ancestry, and race. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 171 Suppl 70:74-86. [DOI: 10.1002/ajpa.23979] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 11/04/2019] [Accepted: 11/11/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Jada Benn Torres
- Vanderbilt UniversityDepartment of Anthropology Nashville Tennessee
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18
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Subramanian S. Population size influences the type of nucleotide variations in humans. BMC Genet 2019; 20:93. [PMID: 31805852 PMCID: PMC6894472 DOI: 10.1186/s12863-019-0798-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 12/01/2019] [Indexed: 11/24/2022] Open
Abstract
Background It is well known that the effective size of a population (Ne) is one of the major determinants of the amount of genetic variation within the population. However, it is unclear whether the types of genetic variations are also dictated by the effective population size. To examine this, we obtained whole genome data from over 100 populations of the world and investigated the patterns of mutational changes. Results Our results revealed that for low frequency variants, the ratio of AT→GC to GC→AT variants (β) was similar across populations, suggesting the similarity of the pattern of mutation in various populations. However, for high frequency variants, β showed a positive correlation with the effective population size of the populations. This suggests a much higher proportion of high frequency AT→GC variants in large populations (e.g. Africans) compared to those with small population sizes (e.g. Asians). These results imply that the substitution patterns vary significantly between populations. These findings could be explained by the effect of GC-biased gene conversion (gBGC), which favors the fixation of G/C over A/T variants in populations. In large population, gBGC causes high β. However, in small populations, genetic drift reduces the effect of gBGC resulting in reduced β. This was further confirmed by a positive relationship between Ne and β for homozygous variants. Conclusions Our results highlight the huge variation in the types of homozygous and high frequency polymorphisms between world populations. We observed the same pattern for deleterious variants, implying that the homozygous polymorphisms associated with recessive genetic diseases will be more enriched with G or C in populations with large Ne (e.g. Africans) than in populations with small Ne (e.g. Europeans).
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Affiliation(s)
- Sankar Subramanian
- GeneCology Research Centre, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD 4556, Australia.
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19
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Nebel C, Gamauf A, Haring E, Segelbacher G, Väli Ü, Villers A, Zachos FE. New insights into population structure of the European golden eagle (Aquila chrysaetos) revealed by microsatellite analysis. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz130] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractConnectivity between golden eagle (Aquila chrysaetos) populations is poorly understood. Field studies exploring natal dispersal suggest that this raptor is a philopatric species, but with the ability to roam far. However, little is known about the population structure of the species in Europe. Our study is based on 14 microsatellite loci and is complemented by new and previously published mitochondrial control region DNA data. The present dataset includes 121 eagles from Scotland, Norway, Finland, Estonia, the Mediterranean and Alpine regions. Our sampling focused on the Alpine and Mediterranean populations because both mitochondrial DNA (mtDNA) lineages found in golden eagles, the Holarctic and the Mediterranean, are known to co-occur there. Cluster analyses of nuclear DNA support a shallow split into northern and southern populations in Europe, similar to the distribution of the two mtDNA lineages, with the Holarctic lineage occurring in the north and the Mediterranean lineage predominating in the south. Additionally, Scotland shows significant differentiation and low relative migration levels that indicate isolation from the mainland populations. Alpine and Mediterranean golden eagles do not show nuclear structure corresponding to divergent mtDNA lineages. This indicates that the presence of northern Holarctic mitochondrial haplotypes in the Alps and the Mediterranean is attributable to past admixture rather than recent long-distance dispersal.
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Affiliation(s)
- Carina Nebel
- FitzPatrick Institute of African Ornithology, University of Cape Town, Cape Town, South Africa
- Natural History Museum Vienna, Vienna, Austria
| | - Anita Gamauf
- Natural History Museum Vienna, Vienna, Austria
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | - Elisabeth Haring
- Natural History Museum Vienna, Vienna, Austria
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | | | - Ülo Väli
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Alexandre Villers
- Centre d’Etudes Biologiques de Chizé, UMR7372, CNRS – Université de la Rochelle, Beauvoir sur Niort, France
- Section of Ecology, Department of Biology, University of Turku, Turku, Finland
- Unité Avifaune Migratrice, Office National de la Chasse et de la Faune Sauvage, Station de Chizé, Villiers-en-Bois, France
| | - Frank E Zachos
- Natural History Museum Vienna, Vienna, Austria
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
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20
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Andersen LW, Dirksen R, Nikulina EA, Baagøe HJ, Petersons G, Estók P, Orlov OL, Orlova MV, Gloza‐Rausch F, Göttsche M, Fjederholt ET, Krüger F, Elmeros M. Conservation genetics of the pond bat ( Myotis dasycneme) with special focus on the populations in northwestern Germany and in Jutland, Denmark. Ecol Evol 2019; 9:5292-5308. [PMID: 31110680 PMCID: PMC6509384 DOI: 10.1002/ece3.5119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/26/2019] [Accepted: 03/04/2019] [Indexed: 11/07/2022] Open
Abstract
Conservation genetics is important in the management of endangered species, helping to understand their connectivity and long-term viability, thus identifying populations of importance for conservation. The pond bat (Myotis dasycneme) is a rare species classified as "Near Threatened" with a wide but patchy Palearctic distribution. A total of 277 samples representing populations in Denmark, Germany, Latvia, Hungary, and Russia were used in the genetic analyses; 224 samples representing Denmark, Germany, and Russia were analyzed at 10 microsatellite loci; 241 samples representing all areas were analyzed using mitochondrial D-loop and cytochrome B sequences. A Bayesian clustering approach revealed two poorly resolved clusters, one representing the Danish and German groups and the other the Russian group. However, significantly different pairwise F ST and D EST estimates were observed between the Danish and German groups and between the Danish and Russian groups suggesting a recent population structure. These conflicting results might be attributed to the effect of migration or low resolution due to the number of microsatellite markers used. After concatenating the two mitochondrial sequences, analysis detected significant genetic differentiation between all populations, probably due to genetic drift combined with a founder event. The phylogenetic tree suggested a closer relationship between the Russian and Northern European populations compared to the Hungarian population, implying that the latter belongs to an older ancestral population. This was supported by the observed haplotype network and higher nucleotide diversity in this population. The genetic structuring observed in the Danish/German pond bat stresses the need for a cross-border management between the two countries. Further, the pronounced mtDNA structuring, together with the indicated migration between nearby populations suggest philopatric female behavior but male migration, emphasizes the importance of protecting suitable habitat mosaics to maintain a continuum of patches with dense pond bat populations across the species' distribution range.
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Affiliation(s)
| | - Ronja Dirksen
- Population Genetics Group, Department of Biology, Zoological InstituteChristian‐Albrechts University of KielKielGermany
| | - Elena A. Nikulina
- Centre for Baltic and Scandinavian Archaeology (ZBSA)Schleswig‐Holstein State Museums FoundationSchleswigGermany
| | | | - Gunars Petersons
- Faculty of Veterinary MedicineLatvia University of Life Sciences and TechnologiesJelgavaLatvia
| | | | - Oleg L. Orlov
- International Complex Research Laboratory for Study of Climate Change, Land Use and BiodiversityUniversity of TyumenTyumenRussia
- Department of BiochemistryUral State Medical UniversityEkaterinburgRussia
| | - Maria V. Orlova
- International Complex Research Laboratory for Study of Climate Change, Land Use and BiodiversityUniversity of TyumenTyumenRussia
- Laboratory of Biodiversity MonitoringNational Research Tomsk State UniversityTomskRussia
| | | | - Matthias Göttsche
- Faunistisch‐ Ökologische Arbeitsgemeinschaft, AG WirbeltiereChristian‐Albrechts‐Universität KielKielGermany
| | | | | | - Morten Elmeros
- Department of BioscienceKalø, Aarhus UniversityGrenåDenmark
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Abstract
Factors that limit the geographic distribution of species are broadly important in ecology and evolutionary biology, and understanding distribution limits is imperative for predicting how species will respond to environmental change. Good data indicate that factors such as dispersal limitation, small effective population size, and isolation are sometimes important. But empirical research highlights no single factor that explains the ubiquity of distribution limits. In this article, we outline a guide to tackling distribution limits that integrates established causes, such as dispersal limitation and spatial environmental heterogeneity, with understudied causes, such as mutational load and genetic or developmental integration of traits limiting niche expansion. We highlight how modeling and quantitative genetic and genomic analyses can provide insight into sources of distribution limits. Our practical guide provides a framework for considering the many factors likely to determine species distributions and how the different approaches can be integrated to predict distribution limits using eco-evolutionary modeling. The framework should also help predict distribution limits of invasive species and of species under climate change.
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22
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Evidence for Recent Polygenic Selection on Educational Attainment and Intelligence Inferred from Gwas Hits: A Replication of Previous Findings Using Recent Data. PSYCH 2019. [DOI: 10.3390/psych1010005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Genetic variants identified by three large genome-wide association studies (GWAS) of educational attainment (EA) were used to test a polygenic selection model. Weighted and unweighted polygenic scores (PGS) were calculated and compared across populations using data from the 1000 Genomes (n = 26), HGDP-CEPH (n = 52) and gnomAD (n = 8) datasets. The PGS from the largest EA GWAS was highly correlated to two previously published PGSs (r = 0.96–0.97, N = 26). These factors are both highly predictive of average population IQ (r = 0.9, N = 23) and Learning index (r = 0.8, N = 22) and are robust to tests of spatial autocorrelation. Monte Carlo simulations yielded highly significant p values. In the gnomAD samples, the correlation between PGS and IQ was almost perfect (r = 0.98, N = 8), and ANOVA showed significant population differences in allele frequencies with positive effect. Socioeconomic variables slightly improved the prediction accuracy of the model (from 78–80% to 85–89%), but the PGS explained twice as much of the variance in IQ compared to socioeconomic variables. In both 1000 Genomes and gnomAD, there was a weak trend for lower GWAS significance SNPs to be less predictive of population IQ. Additionally, a subset of SNPs were found in the HGDP-CEPH sample (N = 127). The analysis of this sample yielded a positive correlation with latitude and a low negative correlation with distance from East Africa. This study provides robust results after accounting for spatial autocorrelation with Fst distances and random noise via an empirical Monte Carlo simulation using null SNPs.
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23
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A serial founder effect model of phonemic diversity based on phonemic loss in low-density populations. PLoS One 2018; 13:e0198346. [PMID: 29856877 PMCID: PMC5983421 DOI: 10.1371/journal.pone.0198346] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 05/17/2018] [Indexed: 11/19/2022] Open
Abstract
It has been observed that the number of phonemes in languages in use today tends to decrease with increasing distance from Africa. A previous formal model has recently reproduced the observed cline, but under two strong assumptions. Here we tackle the question of whether an alternative explanation for the worldwide phonemic cline is possible, by using alternative assumptions. The answer is affirmative. We show this by formalizing a proposal, following Atkinson, that this pattern may be due to a repeated bottleneck effect and phonemic loss. In our simulations, low-density populations lose phonemes during the Out-of-Africa dispersal of modern humans. Our results reproduce the observed global cline for the number of phonemes. In addition, we also detect a cline of phonemic diversity and reproduce it using our simulation model. We suggest how future work could determine whether the previous model or the new one (or even a combination of them) is valid. Simulations also show that the clines can still be present even 300 kyr after the Out-of-Africa dispersal, which is contrary to some previous claims which were not supported by numerical simulations.
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Abstract
The cavity system of the inner ear—the so-called bony labyrinth—houses the senses of balance and hearing. This structure is embedded in dense petrous bone, fully formed by birth and generally well preserved in human skeletal remains, thus providing a rich source of morphological information about past populations. Here we show that labyrinthine morphology tracks genetic distances and geography in an isolation-by-distance model with dispersal from Africa. Because petrous bones have become prime targets of ancient DNA recovery, we propose that all destructive studies first acquire high-resolution 3D computed-tomography data prior to any invasive sampling. Such data will constitute an important archive of morphological variation in past and present populations, and will permit individual-based genotype–phenotype comparisons. The dispersal of modern humans from Africa is now well documented with genetic data that track population history, as well as gene flow between populations. Phenetic skeletal data, such as cranial and pelvic morphologies, also exhibit a dispersal-from-Africa signal, which, however, tends to be blurred by the effects of local adaptation and in vivo phenotypic plasticity, and that is often deteriorated by postmortem damage to skeletal remains. These complexities raise the question of which skeletal structures most effectively track neutral population history. The cavity system of the inner ear (the so-called bony labyrinth) is a good candidate structure for such analyses. It is already fully formed by birth, which minimizes postnatal phenotypic plasticity, and it is generally well preserved in archaeological samples. Here we use morphometric data of the bony labyrinth to show that it is a surprisingly good marker of the global dispersal of modern humans from Africa. Labyrinthine morphology tracks genetic distances and geography in accordance with an isolation-by-distance model with dispersal from Africa. Our data further indicate that the neutral-like pattern of variation is compatible with stabilizing selection on labyrinth morphology. Given the increasingly important role of the petrous bone for ancient DNA recovery from archaeological specimens, we encourage researchers to acquire 3D morphological data of the inner ear structures before any invasive sampling. Such data will constitute an important archive of phenotypic variation in present and past populations, and will permit individual-based genotype–phenotype comparisons.
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25
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Kanitz R, Guillot EG, Antoniazza S, Neuenschwander S, Goudet J. Complex genetic patterns in human arise from a simple range-expansion model over continental landmasses. PLoS One 2018; 13:e0192460. [PMID: 29466398 PMCID: PMC5821356 DOI: 10.1371/journal.pone.0192460] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/23/2018] [Indexed: 12/21/2022] Open
Abstract
Although it is generally accepted that geography is a major factor shaping human genetic differentiation, it is still disputed how much of this differentiation is a result of a simple process of isolation-by-distance, and if there are factors generating distinct clusters of genetic similarity. We address this question using a geographically explicit simulation framework coupled with an Approximate Bayesian Computation approach. Based on six simple summary statistics only, we estimated the most probable demographic parameters that shaped modern human evolution under an isolation by distance scenario, and found these were the following: an initial population in East Africa spread and grew from 4000 individuals to 5.7 million in about 132 000 years. Subsequent simulations with these estimates followed by cluster analyses produced results nearly identical to those obtained in real data. Thus, a simple diffusion model from East Africa explains a large portion of the genetic diversity patterns observed in modern humans. We argue that a model of isolation by distance along the continental landmasses might be the relevant null model to use when investigating selective effects in humans and probably many other species.
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Affiliation(s)
- Ricardo Kanitz
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Elsa G. Guillot
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | | | - Samuel Neuenschwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Vital-IT, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
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26
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‘Reparational’ Genetics: Genomic Data and the Case for Reparations in the Caribbean. GENEALOGY 2018. [DOI: 10.3390/genealogy2010007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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27
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Ehler E, Vanek D. Forensic genetic analyses in isolated populations with examples of central European Valachs and Roma. J Forensic Leg Med 2017; 48:46-52. [PMID: 28454050 DOI: 10.1016/j.jflm.2017.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 03/22/2017] [Accepted: 04/09/2017] [Indexed: 01/27/2023]
Abstract
Isolated populations present a constant threat to the correctness of forensic genetic casework. In this review article we present several examples of how analyzing samples from isolated populations can bias the results of the forensic statistics and analyses. We select our examples from isolated populations from central and southeastern Europe, namely the Valachs and the European Roma. We also provide the reader with general strategies and principles to improve the laboratory practice (best practice) and reporting of samples from supposedly isolated populations. These include reporting the precise population data used for computing the forensic statistics, using the appropriate θ correction factor for calculating allele frequencies, typing ancestry informative markers in samples of unknown or uncertain ethnicity and establishing ethnic-specific forensic databases.
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Affiliation(s)
- Edvard Ehler
- Department of Biology and Environmental Studies, Charles University in Prague, Faculty of Education, Magdaleny Rettigove 4, Prague, 116 39, Czech Republic; Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland.
| | - Daniel Vanek
- Forensic DNA Service, Janovskeho 18, Prague 7, 170 00, Czech Republic; Charles University in Prague, 2nd Faculty of Medicine, V Uvalu 84, Prague, 150 06, Czech Republic; Nemocnice Na Bulovce, Institute of Legal Medicine, Budinova 2, Prague, 180 81, Czech Republic.
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Herrera B, Peart D, Hernandez N, Spradley K, Hubbe M. Morphological variation among late holocene Mexicans: Implications for discussions about the human occupation of the Americas. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 163:75-84. [DOI: 10.1002/ajpa.23186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 01/18/2017] [Accepted: 01/24/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Brianne Herrera
- Department of Anthropology; The Ohio State University; Columbus Ohio
| | - Daniel Peart
- Department of Anthropology; The Ohio State University; Columbus Ohio
| | - Nicole Hernandez
- Department of Anthropology; The Ohio State University; Columbus Ohio
| | - Kate Spradley
- Department of Anthropology; Texas State University; San Marcos Texas
| | - Mark Hubbe
- Department of Anthropology; The Ohio State University; Columbus Ohio
- Instituto de Arqueología y Antropología; Universidad Católica del Norte; Chile
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Population genetics of the Manila clam (Ruditapes philippinarum) introduced in North America and Europe. Sci Rep 2017; 7:39745. [PMID: 28045054 PMCID: PMC5206634 DOI: 10.1038/srep39745] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 11/28/2016] [Indexed: 11/09/2022] Open
Abstract
Globally, the Manila clam (Ruditapes philippinarum) stands as the second most important bivalve species in fisheries and aquaculture. Native to the Pacific coast of Asia, it is now well-established in North America and Europe, where its on-going management reflects local economic interests. The historic record of transfers spans the 20th century and suggests sequential movement from Japan to North America, as a hitch-hiker on oysters, and then intentional introduction in Europe, but global genetic data are missing. We have studied mitochondrial DNA and microsatellite markers in nine populations from Asia, North America and Europe. The results from the two types of markers indicated a good concordance of present-day genetic structure with the reported history of clam transfers across continents, and no evidence of relevant concealed introductions from continental Asia in Europe and North America. However, European populations showed a loss of genetic variability and significant genetic differentiation as compared to their American counterparts. Our study shows that in spite of the increasing ease for species to spread out of their native range, in the case of the Manila clam this has not resulted in new invasion waves in the two studied continents.
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The indeterminacy of race: The dilemma of difference in medicine and health care. SOCIAL THEORY & HEALTH 2016. [DOI: 10.1057/s41285-016-0001-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Cultural differentiation does not entail group-level structure: The case for geographically explicit analysis. Behav Brain Sci 2016; 39:e49. [PMID: 27562351 DOI: 10.1017/s0140525x15000217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Richerson et al. argue that relatively large cultural F ST values provide evidence for group structure and therefore scope for group selection. However, recent research on spatial patterns of cultural variation demonstrates that, as in the genetic case, apparent group structure can be a consequence of geographic clines, not group barriers. Such a pattern limits the scope for cultural group selection.
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Streicher JW, McEntee JP, Drzich LC, Card DC, Schield DR, Smart U, Parkinson CL, Jezkova T, Smith EN, Castoe TA. Genetic surfing, not allopatric divergence, explains spatial sorting of mitochondrial haplotypes in venomous coralsnakes. Evolution 2016; 70:1435-49. [DOI: 10.1111/evo.12967] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 04/30/2016] [Accepted: 05/16/2016] [Indexed: 01/16/2023]
Affiliation(s)
- Jeffrey W. Streicher
- Department of Life Sciences The Natural History Museum London United Kingdom
- Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona
- Department of Biology University of Texas at Arlington Arlington Texas
| | - Jay P. McEntee
- Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona
- Department of Biology University of Florida Gainesville Florida
| | - Laura C. Drzich
- Department of Biology University of Texas at Arlington Arlington Texas
| | - Daren C. Card
- Department of Biology University of Texas at Arlington Arlington Texas
| | - Drew R. Schield
- Department of Biology University of Texas at Arlington Arlington Texas
| | - Utpal Smart
- Department of Biology University of Texas at Arlington Arlington Texas
| | | | - Tereza Jezkova
- Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona
| | - Eric N. Smith
- Department of Biology University of Texas at Arlington Arlington Texas
| | - Todd A. Castoe
- Department of Biology University of Texas at Arlington Arlington Texas
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33
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Hochman A. Race: Deflate or pop? STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2016; 57:60-68. [PMID: 27060241 DOI: 10.1016/j.shpsc.2016.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/22/2016] [Accepted: 03/03/2016] [Indexed: 06/05/2023]
Abstract
Neven Sesardic has recently defended his arguments in favour of racial naturalism-the view that race is a valid biological category-in response to my criticism of his work. While Sesardic claims that a strong version of racial naturalism can survive critique, he has in fact weakened his position considerably. He concedes that conventional racial taxonomy is arbitrary and he no longer identifies 'races' as human subspecies. Sesardic now relies almost entirely on Theodosius Dobzhansky's notion of race-as-population. This weak approach to 'race'-according to which all genetic difference between populations is 'racial' and 'the races' are simply the populations we choose to call races-survived its early critiques. As it is being mobilised to support racial naturalism once more, we need to continue the debate about whether we should weaken the concept of race to mean 'population', or abandon it as a failed biological category. I argue that Sesardic's case for racial naturalism is only supported by his continued mischaracterisation of anti-realism about biological race and his appeal to Dobzhansky's authority. Rather than deflating the meaning of 'race', it should be eliminated from our biological ontology.
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Affiliation(s)
- Adam Hochman
- Department of Philosophy, Macquarie University, Building W6A, Room 733, Sydney, NSW 2109, Australia.
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34
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Messina F, Scano G, Contini I, Martínez-Labarga C, De Stefano GF, Rickards O. Linking between genetic structure and geographical distance: Study of the maternal gene pool in the Ethiopian population. Ann Hum Biol 2016; 44:53-69. [PMID: 26883569 DOI: 10.3109/03014460.2016.1155646] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Background The correlation between genetics and geographical distance has already been examined through the study of the dispersion of human populations, especially in terms of uniparental genetic markers. Aim The present work characterises, at the level of the mitochondrial DNA (mtDNA), two new samples of Amhara and Oromo populations from Ethiopia to evaluate the possible pattern of distribution for mtDNA variation and to test the hypothesis of the Isolation-by-Distance (IBD) model among African, European and Middle-Eastern populations. Subjects and methods This study analysed 173 individuals belonging to two ethnic groups of Ethiopia, Amhara and Oromo, by assaying HVS-I and HVS-II of mtDNA D-loop and informative coding region SNPs of mtDNA. Results The analysis suggests a relationship between genetic and geographic distances, affirming that the mtDNA pool of Africa, Europe and the Middle East might be coherent with the IBD model. Moreover, the mtDNA gene pools of the Sub-Saharan African and Mediterranean populations were very different. Conclusion In this study the pattern of mtDNA distribution, beginning with the Ethiopian plateau, was tested in the IBD model. It could be affirmed that, on a continent scale, the mtDNA pool of Africa, Europe and the Middle East might fall under the IBD model.
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Affiliation(s)
- Francesco Messina
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Giuseppina Scano
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Irene Contini
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Cristina Martínez-Labarga
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Gian Franco De Stefano
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Olga Rickards
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
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35
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Maglo KN, Mersha TB, Martin LJ. Population Genomics and the Statistical Values of Race: An Interdisciplinary Perspective on the Biological Classification of Human Populations and Implications for Clinical Genetic Epidemiological Research. Front Genet 2016; 7:22. [PMID: 26925096 PMCID: PMC4756148 DOI: 10.3389/fgene.2016.00022] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 02/02/2016] [Indexed: 01/14/2023] Open
Abstract
The biological status and biomedical significance of the concept of race as applied to humans continue to be contentious issues despite the use of advanced statistical and clustering methods to determine continental ancestry. It is thus imperative for researchers to understand the limitations as well as potential uses of the concept of race in biology and biomedicine. This paper deals with the theoretical assumptions behind cluster analysis in human population genomics. Adopting an interdisciplinary approach, it demonstrates that the hypothesis that attributes the clustering of human populations to "frictional" effects of landform barriers at continental boundaries is empirically incoherent. It then contrasts the scientific status of the "cluster" and "cline" constructs in human population genomics, and shows how cluster may be instrumentally produced. It also shows how statistical values of race vindicate Darwin's argument that race is evolutionarily meaningless. Finally, the paper explains why, due to spatiotemporal parameters, evolutionary forces, and socio-cultural factors influencing population structure, continental ancestry may be pragmatically relevant to global and public health genomics. Overall, this work demonstrates that, from a biological systematic and evolutionary taxonomical perspective, human races/continental groups or clusters have no natural meaning or objective biological reality. In fact, the utility of racial categorizations in research and in clinics can be explained by spatiotemporal parameters, socio-cultural factors, and evolutionary forces affecting disease causation and treatment response.
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Affiliation(s)
- Koffi N Maglo
- Department of Philosophy, Center for Clinical and Translational Science and Training, University of Cincinnati Cincinnati, OH, USA
| | - Tesfaye B Mersha
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati Cincinnati, OH, USA
| | - Lisa J Martin
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati Cincinnati, OH, USA
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36
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Forni D, Pozzoli U, Cagliani R, Tresoldi C, Menozzi G, Riva S, Guerini FR, Comi GP, Bolognesi E, Bresolin N, Clerici M, Sironi M. Genetic adaptation of the human circadian clock to day-length latitudinal variations and relevance for affective disorders. Genome Biol 2015; 15:499. [PMID: 25358694 PMCID: PMC4237747 DOI: 10.1186/s13059-014-0499-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Indexed: 01/18/2023] Open
Abstract
Background The temporal coordination of biological processes into daily cycles is a common feature of most living organisms. In humans, disruption of circadian rhythms is commonly observed in psychiatric diseases, including schizophrenia, bipolar disorder, depression and autism. Light therapy is the most effective treatment for seasonal affective disorder and circadian-related treatments sustain antidepressant response in bipolar disorder patients. Day/night cycles represent a major circadian synchronizing signal and vary widely with latitude. Results We apply a geographically explicit model to show that out-of-Africa migration, which led humans to occupy a wide latitudinal area, affected the evolutionary history of circadian regulatory genes. The SNPs we identify using this model display consistent signals of natural selection using tests based on population genetic differentiation and haplotype homozygosity. Signals of natural selection driven by annual photoperiod variation are detected for schizophrenia, bipolar disorder, and restless leg syndrome risk variants, in line with the circadian component of these conditions. Conclusions Our results suggest that human populations adapted to life at different latitudes by tuning their circadian clock systems. This process also involves risk variants for neuropsychiatric conditions, suggesting possible genetic modulators for chronotherapies and candidates for interaction analysis with photoperiod-related environmental variables, such as season of birth, country of residence, shift-work or lifestyle habits. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0499-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. Medea, 23842 Bosisio Parini, LC, Italy
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37
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Oliveira J, Debnath M, Etain B, Bennabi M, Hamdani N, Lajnef M, Bengoufa D, Fortier C, Boukouaci W, Bellivier F, Kahn JP, Henry C, Charron D, Krishnamoorthy R, Leboyer M, Tamouza R. Violent suicidal behaviour in bipolar disorder is associated with nitric oxide synthase 3 gene polymorphism. Acta Psychiatr Scand 2015; 132:218-25. [PMID: 25939888 DOI: 10.1111/acps.12433] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/15/2015] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Given the importance of nitric oxide system in oxidative stress, inflammation, neurotransmission and cerebrovascular tone regulation, we postulated its potential dysfunction in bipolar disorder (BD) and suicide. By simultaneously analysing variants of three isoforms of nitric oxide synthase (NOS) genes, we explored interindividual genetic liability to suicidal behaviour in BD. METHOD A total of 536 patients with BD (DSM-IV) and 160 healthy controls were genotyped for functionally relevant NOS1, NOS2 and NOS3 polymorphisms. History of suicidal behaviour and violent suicide attempt was documented for 511 patients with BD. Chi-squared test was used to perform genetic association analyses and logistic regression to test for gene-gene interactions. RESULTS NOS3 rs1799983 T homozygous state was associated with violent suicide attempts (26.4% vs. 10.8%, in patients and controls, P = 0.002, corrected P (Pc) = 0.004, OR: 2.96, 95% CI = 1.33-6.34), and this association was restricted to the early-onset BD subgroup (37.9% vs. 10.8%, in early-onset BD and controls, P = 0.0003, Pc = 0.0006 OR: 5.05, 95% CI: 1.95-12.45), while we found no association with BD per se and no gene-gene interactions. CONCLUSION Our results bring further evidence for the potential involvement of endothelial NOS gene variants in susceptibility to suicidal behaviour. Future exploration of this pathway on larger cohort of suicidal behaviour is warranted.
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Affiliation(s)
- J Oliveira
- INSERM, U1160, Hôpital Saint Louis, Paris, France.,Fondation FondaMental, Créteil, France
| | - M Debnath
- INSERM, U1160, Hôpital Saint Louis, Paris, France.,Fondation FondaMental, Créteil, France
| | - B Etain
- Fondation FondaMental, Créteil, France.,INSERM, U955, Psychopathologie et Génétique des maladies psychiatriques, Créteil, France.,Faculté de Médecine, Université Paris-Est, Créteil, France.,AP-HP, Pôle de Psychiatrie et d'Addictologie des Hôpitaux Universitaires Henri Mondor, Créteil, France
| | - M Bennabi
- INSERM, U1160, Hôpital Saint Louis, Paris, France.,Fondation FondaMental, Créteil, France
| | - N Hamdani
- Fondation FondaMental, Créteil, France.,INSERM, U955, Psychopathologie et Génétique des maladies psychiatriques, Créteil, France.,Faculté de Médecine, Université Paris-Est, Créteil, France.,AP-HP, Pôle de Psychiatrie et d'Addictologie des Hôpitaux Universitaires Henri Mondor, Créteil, France
| | - M Lajnef
- Fondation FondaMental, Créteil, France.,INSERM, U955, Psychopathologie et Génétique des maladies psychiatriques, Créteil, France.,Faculté de Médecine, Université Paris-Est, Créteil, France
| | - D Bengoufa
- Laboratoire Jean Dausset and LabEx Transplantex, Hôpital Saint Louis, Paris, France
| | - C Fortier
- Laboratoire Jean Dausset and LabEx Transplantex, Hôpital Saint Louis, Paris, France
| | - W Boukouaci
- INSERM, U1160, Hôpital Saint Louis, Paris, France
| | - F Bellivier
- Fondation FondaMental, Créteil, France.,INSERM, U955, Psychopathologie et Génétique des maladies psychiatriques, Créteil, France.,Faculté de Médecine, Université Paris-Est, Créteil, France.,AP-HP, Pôle de Psychiatrie et d'Addictologie des Hôpitaux Universitaires Henri Mondor, Créteil, France
| | - J-P Kahn
- Fondation FondaMental, Créteil, France.,Service de Psychiatrie et Psychologie Clinique, CHU de Nancy, Hôpitaux de Brabois, Vandoeuvre Les Nancy, France
| | - C Henry
- Fondation FondaMental, Créteil, France.,INSERM, U955, Psychopathologie et Génétique des maladies psychiatriques, Créteil, France.,Faculté de Médecine, Université Paris-Est, Créteil, France.,AP-HP, Pôle de Psychiatrie et d'Addictologie des Hôpitaux Universitaires Henri Mondor, Créteil, France
| | - D Charron
- INSERM, U1160, Hôpital Saint Louis, Paris, France.,Fondation FondaMental, Créteil, France.,Laboratoire Jean Dausset and LabEx Transplantex, Hôpital Saint Louis, Paris, France.,Sorbonne Paris-Cité, Université Paris Diderot, Paris, France
| | | | - M Leboyer
- Fondation FondaMental, Créteil, France.,INSERM, U955, Psychopathologie et Génétique des maladies psychiatriques, Créteil, France.,Faculté de Médecine, Université Paris-Est, Créteil, France.,AP-HP, Pôle de Psychiatrie et d'Addictologie des Hôpitaux Universitaires Henri Mondor, Créteil, France
| | - R Tamouza
- INSERM, U1160, Hôpital Saint Louis, Paris, France.,Fondation FondaMental, Créteil, France.,Laboratoire Jean Dausset and LabEx Transplantex, Hôpital Saint Louis, Paris, France.,Sorbonne Paris-Cité, Université Paris Diderot, Paris, France
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Human Leukocyte Antigen Diversity: A Southern African Perspective. J Immunol Res 2015; 2015:746151. [PMID: 26347896 PMCID: PMC4549606 DOI: 10.1155/2015/746151] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/26/2015] [Indexed: 12/30/2022] Open
Abstract
Despite the increasingly well-documented evidence of high genetic, ethnic, and linguistic diversity amongst African populations, there is limited data on human leukocyte antigen (HLA) diversity in these populations. HLA is part of the host defense mechanism mediated through antigen presentation to effector cells of the immune system. With the high disease burden in southern Africa, HLA diversity data is increasingly important in the design of population-specific vaccines and the improvement of transplantation therapeutic interventions. This review highlights the paucity of HLA diversity data amongst southern African populations and defines a need for information of this kind. This information will support disease association studies, provide guidance in vaccine design, and improve transplantation outcomes.
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Wollstein A, Lao O. Detecting individual ancestry in the human genome. INVESTIGATIVE GENETICS 2015; 6:7. [PMID: 25937887 PMCID: PMC4416275 DOI: 10.1186/s13323-015-0019-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 01/12/2015] [Indexed: 01/26/2023]
Abstract
Detecting and quantifying the population substructure present in a sample of individuals are of main interest in the fields of genetic epidemiology, population genetics, and forensics among others. To date, several algorithms have been proposed for estimating the amount of genetic ancestry within an individual. In the present review, we introduce the most widely used methods in population genetics for detecting individual genetic ancestry. We further show, by means of simulations, the performance of popular algorithms for detecting individual ancestry in various controlled demographic scenarios. Finally, we provide some hints on how to interpret the results from these algorithms.
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Affiliation(s)
- Andreas Wollstein
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands ; Section of Evolutionary Biology, Department of Biology II, University of Munich, 82152 Planegg-Martinsried, Germany
| | - Oscar Lao
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands ; Current address: Centro Nacional de Análisis Genómico, Baldiri Reixac, 4, Barcleona Science Park - Tower I, 08028 Barcelona, Spain
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40
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Genetic structure characterization of Chileans reflects historical immigration patterns. Nat Commun 2015; 6:6472. [PMID: 25778948 PMCID: PMC4382693 DOI: 10.1038/ncomms7472] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 01/30/2015] [Indexed: 12/25/2022] Open
Abstract
Identifying the ancestral components of genomes of admixed individuals helps uncovering the genetic basis of diseases and understanding the demographic history of populations. We estimate local ancestry on 313 Chileans and assess the contribution from three continental populations. The distribution of ancestry block-length suggests an average admixing time around 10 generations ago. Sex-chromosome analyses confirm imbalanced contribution of European men and Native-American women. Previously known genes under selection contain SNPs showing large difference in allele frequencies. Furthermore, we show that assessing ancestry is harder at SNPs with higher recombination rates and easier at SNPs with large difference in allele frequencies at the ancestral populations. Two observations, that African ancestry proportions systematically decrease from North to South, and that European ancestry proportions are highest in central regions, show that the genetic structure of Chileans is under the influence of a diffusion process leading to an ancestry gradient related to geography. Chileans are genetically admixed. Here, the authors find that the average admixing time is around 10 generations ago and show the contribution of European men and Native-American women to the Chilean population.
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41
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Noback ML, Harvati K. The contribution of subsistence to global human cranial variation. J Hum Evol 2015; 80:34-50. [PMID: 25661439 DOI: 10.1016/j.jhevol.2014.11.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 11/20/2014] [Accepted: 11/28/2014] [Indexed: 11/29/2022]
Abstract
Diet-related cranial variation in modern humans is well documented on a regional scale, with ample examples of cranial changes related to the agricultural transition. However, the influence of subsistence strategy on global cranial variation is less clear, having been confirmed only for the mandible, and dietary effects beyond agriculture are often neglected. Here we identify global patterns of subsistence-related human cranial shape variation. We analysed a worldwide sample of 15 populations (n = 255) with known subsistence strategies using 3-D landmark datasets designed to capture the shape of different units of the cranium. Results show significant correlations between global cranial shape and diet, especially for temporalis muscle shape and general cranial shape. Importantly, the differences between populations with either a plant- or an animal-based diet are more pronounced than those between agriculturalists and hunter-gatherers, suggesting that the influence of diet as driver of cranial variation is not limited to Holocene transitions to agricultural subsistence. Dental arch shape did not correlate with subsistence pattern, possibly indicating the high plasticity of this region of the face in relation to age, disease and individual use of the dentition. Our results highlight the importance of subsistence strategy as one of the factors underlying the evolution of human geographic cranial variation.
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Affiliation(s)
- Marlijn L Noback
- Paleoanthropology Section, Senckenberg Center for Human Evolution and Paleoenvironment, Eberhard Karls Universität Tübingen, Rümelinstrasse 23, 72070, Tübingen, Germany.
| | - Katerina Harvati
- Paleoanthropology Section, Senckenberg Center for Human Evolution and Paleoenvironment, Eberhard Karls Universität Tübingen, Rümelinstrasse 23, 72070, Tübingen, Germany.
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42
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Hatin WI, Nur-Shafawati AR, Etemad A, Jin W, Qin P, Xu S, Jin L, Tan SG, Limprasert P, Feisal MA, Rizman-Idid M, Zilfalil BA. A genome wide pattern of population structure and admixture in peninsular Malaysia Malays. THE HUGO JOURNAL 2014; 8:5. [PMID: 27090253 PMCID: PMC7735395 DOI: 10.1186/s11568-014-0005-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 05/19/2014] [Indexed: 12/23/2022]
Abstract
Background The Malays consist of various sub-ethnic groups which are believed to have different ancestral origins based on their migrations centuries ago. The sub-ethnic groups can be divided based on the region they inhabit; the northern (Melayu Kedah and Melayu Kelantan), western (Melayu Minang) and southern parts (Melayu Bugis and Melayu Jawa) of Peninsular Malaysia. We analyzed 54,794 autosomal single nucleotide polymorphisms (SNPs) which were shared by 472 unrelated individuals from 17 populations to determine the genetic structure and distributions of the ancestral genetic components in five Malay sub-ethnic groups namely Melayu Bugis, Melayu Jawa, Melayu Minang, Melayu Kedah, and Melayu Kelantan. We also have included in the analysis 12 other study populations from Thailand, Indonesia, China, India, Africa and Orang Asli sub-groups in Malay Peninsula, obtained from the Pan Asian SNP Initiative (PASNPI) Consortium and International HapMap project database. Results We found evidence of genetic influx from Indians to Malays, more in Melayu Kedah and Melayu Kelantan which are genetically different from the other Malay sub-ethnic groups, but similar to Thai Pattani. More than 98% of these northern Malays haplotypes could be found in either Indians or Chinese populations, indicating a highly admixture pattern among populations. Nevertheless, the ancestry lines of Malays, Indonesians and Thais were traced back to have shared a common ancestor with the Proto-Malays and Chinese. Conclusions These results support genetic admixtures in the Peninsular Malaysia Malay populations and provided valuable information on the enigmatic demographical history as well as shed some insights into the origins of the Malays in the Malay Peninsula.
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Affiliation(s)
- Wan Isa Hatin
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kelantan, Malaysia
| | - Ab Rajab Nur-Shafawati
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kelantan, Malaysia
| | - Ali Etemad
- Department of Pediatrics, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kelantan, Malaysia
| | - Wenfei Jin
- Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Pengfei Qin
- Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Shuhua Xu
- Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Li Jin
- Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Soon-Guan Tan
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Selangor, Malaysia
| | - Pornprot Limprasert
- Human Genetics Unit, Department of Pathology, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Merican Amir Feisal
- Institute of Biological Sciences, 50603, Kuala Lumpur, Malaysia.,Centre of Research for Computational Sciences and Informatics in Biology, Bioindustry, Environment, Agriculture and Healthcare (CRYSTAL),Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | | | - Bin Alwi Zilfalil
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kelantan, Malaysia. .,Department of Pediatrics, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kelantan, Malaysia.
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Patterns and dynamics of genetic diversity in Plasmodium falciparum: what past human migrations tell us about malaria. Parasitol Int 2014; 64:238-43. [PMID: 25305418 DOI: 10.1016/j.parint.2014.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 08/14/2014] [Accepted: 09/12/2014] [Indexed: 01/23/2023]
Abstract
Plasmodium falciparum is the main agent of malaria, one of the major human infectious diseases affecting millions of people worldwide. The genetic diversity of P. falciparum populations is an essential factor in the parasite's ability to adapt to changes in its environment, enabling the development of drug resistance and the evasion from the host immune system through antigenic variation. Therefore, characterizing these patterns and understanding the main drivers of the pathogen's genetic diversity can provide useful inputs for informing control strategies. In this paper, we review the pioneering work led by Professor Kazuyuki Tanabe on the genetic diversity of P. falciparum populations. In a first part, we recall basic results from population genetics for quantifying within-population genetic diversity, and discuss the main mechanisms driving this diversity. Then, we show how these approaches have been used for reconstructing the historical spread of malaria worldwide, and how current patterns of genetic diversity suggest that the pathogen followed our ancestors in their journey out of Africa. Because these results are robust to different types of genetic markers, they provide a baseline for predicting the pathogen's diversity in unsampled populations, and some useful elements for predicting vaccine efficacy and informing malaria control strategies.
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44
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Ruiz-Linares A. How genes have illuminated the history of early Americans and Latino Americans. Cold Spring Harb Perspect Biol 2014; 7:cshperspect.a008557. [PMID: 25256008 DOI: 10.1101/cshperspect.a008557] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The American continent currently accounts for ∼15% of the world population. Although first settled thousands of years ago and fitting its label as "the New World," the European colonial expansion initiated in the late 15th century resulted in people from virtually every corner of the globe subsequently settling in the Americas. The arrival of large numbers of immigrants led to a dramatic decline of the Native American population and extensive population mixing. A salient feature of the current human population of the Americas is, thus, its great diversity. The genetic variation of the Native peoples that recent immigrants encountered had been shaped by demographic events acting since the initial peopling of the continent. Similarly, but on a compressed timescale, the colonial history of the Americas has had a major impact on the genetic makeup of the current population of the continent. A range of genetic analyses has been used to study both the ancient settlement of the continent and more recent history of population mixing. Here, I show how these two strands of research overlap and make use of results from other scientific disciplines to produce a fuller picture of the settlement of the continent at different time periods. The biological diversity of the Americas also provides prominent examples of the complex interaction between biological and social factors in constructing human identities and of the difficulties in defining human populations.
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Affiliation(s)
- Andrés Ruiz-Linares
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
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45
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Maglo KN, Rubinstein J, Huang B, Ittenbach RF. BiDil in the Clinic: An Interdisciplinary Investigation of Physicians' Prescription Patterns of a Race-Based Therapy. AJOB Empir Bioeth 2014; 5:37-52. [PMID: 25177710 DOI: 10.1080/23294515.2014.907371] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND The African American Heart Failure Trial (A-HeFT) and the FDA approval of BiDil for race-specific prescription have stirred the debate about the scientific and medical status of race. Yet there is no assessment of the potential fallouts of this dispute on physicians' willingness to prescribe the drug. We present here an analysis of the factors influencing physicians' prescription of BiDil and investigate whether exposure to the controversy has an impact on their therapeutic judgments about the drug. METHODS We conducted an electronic survey with physicians in the department of internal medicine at the University of Cincinnati. Participants were randomly assigned to two groups, with one group receiving information about the controversy over BiDil. We used various statistical tests, including a linear mixed effects model, to analyze the results. RESULTS 27% of the participants reported using patients' race as a major factor in making treatment decisions. 33% reported the inefficacy of standard therapies, 25% the severity of the disease, and 15% other unspecified factors as primary determining criteria in prescribing BiDil. With respect to the controversy, 68% of physicians reported that they were not aware of any controversy surrounding BiDil. Physicians' willingness to prescribe BiDil as a therapy was associated with their awareness of the controversy surrounding A-HeFT (p < 0.003). But their willingness to prescribe the therapy along racial lines did not vary significantly with exposure to the controversy. CONCLUSIONS Overall, physicians prescribe and are willing to prescribe BiDil more to black patients than to white patients. However, physicians' lack of awareness about the controversial scientific status of A-HeFT suggests the need for more efficient ways to convey scientific information about BiDil to clinicians. Furthermore, the uncertainties about the determination of clinical utility of BiDil for the individual patient raise questions about whether this specific race-based therapy is in patients' best interest.
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Affiliation(s)
- Koffi N Maglo
- Department of Philosophy, 206 McMicken Hall, PO Box 210374, University of Cincinnati, Cincinnati, OH 45221-0374, Tel (513) 556-6337,
| | | | - Bin Huang
- University of Cincinnati and Cincinnati Children's Hospital Medical Center
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Tsuchida K, Kudô K, Ishiguro N. Genetic structure of an introduced paper wasp,Polistes chinensis antennalis(Hymenoptera, Vespidae) in New Zealand. Mol Ecol 2014; 23:4018-34. [DOI: 10.1111/mec.12852] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 06/21/2014] [Accepted: 06/25/2014] [Indexed: 12/29/2022]
Affiliation(s)
- Koji Tsuchida
- Laboratory of Insect Ecology; Faculty of Applied Biological Sciences; Gifu University; Yanagido1-1 Gifu 501-1193 Japan
- School of Biological Sciences; Faculty of Science; University of Auckland; Auckland 1072 New Zealand
| | - Kazuyuki Kudô
- Laboratory of Entomology; Faculty of Education and Human Sciences; Niigata University; Niigata 950-2181 Japan
| | - Norio Ishiguro
- Laboratory of Insect Ecology; Faculty of Applied Biological Sciences; Gifu University; Yanagido1-1 Gifu 501-1193 Japan
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47
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The interaction of neutral evolutionary processes with climatically-driven adaptive changes in the 3D shape of the human os coxae. J Hum Evol 2014; 73:64-74. [PMID: 24935167 DOI: 10.1016/j.jhevol.2014.02.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 02/03/2014] [Accepted: 02/04/2014] [Indexed: 11/21/2022]
Abstract
Differences in the breadth of the pelvis among modern human populations and among extinct hominin species have often been interpreted in the light of thermoregulatory adaptation, whereby a larger pelvic girdle would help preserve body temperature in cold environments while a narrower pelvis would help dissipate heat in tropical climates. There is, however, a theoretical problem in interpreting a pattern of variation as evidence of selection without first accounting for the effects of neutral evolutionary processes (i.e., mutation, genetic drift and migration). Here, we analyse 3D configurations of 27 landmarks on the os coxae of 1494 modern human individuals representing 30 male and 23 female populations from five continents and a range of climatic conditions. We test for the effects of climate on the size and shape of the pelvic bone, while explicitly accounting for population history (i.e., geographically-mediated gene flow and genetic drift). We find that neutral processes account for a substantial proportion of shape variance in the human os coxae in both sexes. Beyond the neutral pattern due to population history, temperature is a significant predictor of shape and size variation in the os coxae, at least in males. The effect of climate on the shape of the pelvic bone, however, is comparatively limited, explaining only a small percentage of shape variation in males and females. In accordance with previous hypotheses, the size of the os coxae tends to increase with decreasing temperature, although the significance of the association is reduced when population history is taken into account. In conclusion, the shape and size of the human os coxae reflect both neutral evolutionary processes and climatically-driven adaptive changes. Neutral processes have a substantial effect on pelvic variation, suggesting such factors will need to be taken into account in future studies of human and fossil hominin coxal variation.
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Lao O, Liu F, Wollstein A, Kayser M. GAGA: a new algorithm for genomic inference of geographic ancestry reveals fine level population substructure in Europeans. PLoS Comput Biol 2014; 10:e1003480. [PMID: 24586132 PMCID: PMC3930519 DOI: 10.1371/journal.pcbi.1003480] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 01/03/2014] [Indexed: 02/04/2023] Open
Abstract
Attempts to detect genetic population substructure in humans are troubled by the fact that the vast majority of the total amount of observed genetic variation is present within populations rather than between populations. Here we introduce a new algorithm for transforming a genetic distance matrix that reduces the within-population variation considerably. Extensive computer simulations revealed that the transformed matrix captured the genetic population differentiation better than the original one which was based on the T1 statistic. In an empirical genomic data set comprising 2,457 individuals from 23 different European subpopulations, the proportion of individuals that were determined as a genetic neighbour to another individual from the same sampling location increased from 25% with the original matrix to 52% with the transformed matrix. Similarly, the percentage of genetic variation explained between populations by means of Analysis of Molecular Variance (AMOVA) increased from 1.62% to 7.98%. Furthermore, the first two dimensions of a classical multidimensional scaling (MDS) using the transformed matrix explained 15% of the variance, compared to 0.7% obtained with the original matrix. Application of MDS with Mclust, SPA with Mclust, and GemTools algorithms to the same dataset also showed that the transformed matrix gave a better association of the genetic clusters with the sampling locations, and particularly so when it was used in the AMOVA framework with a genetic algorithm. Overall, the new matrix transformation introduced here substantially reduces the within population genetic differentiation, and can be broadly applied to methods such as AMOVA to enhance their sensitivity to reveal population substructure. We herewith provide a publically available (http://www.erasmusmc.nl/fmb/resources/GAGA) model-free method for improved genetic population substructure detection that can be applied to human as well as any other species data in future studies relevant to evolutionary biology, behavioural ecology, medicine, and forensics.
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Affiliation(s)
- Oscar Lao
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
- * E-mail:
| | - Fan Liu
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Andreas Wollstein
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | - Manfred Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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Charles C. Roseman. Troublesome Reflection: Racism as the Blind Spot in the Scientific Critique of Race. Hum Biol 2014. [DOI: 10.13110/humanbiology.86.3.0233] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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May A, Hazelhurst S, Li Y, Norris SA, Govind N, Tikly M, Hon C, Johnson KJ, Hartmann N, Staedtler F, Ramsay M. Genetic diversity in black South Africans from Soweto. BMC Genomics 2013; 14:644. [PMID: 24059264 PMCID: PMC3850641 DOI: 10.1186/1471-2164-14-644] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 08/17/2013] [Indexed: 11/17/2022] Open
Abstract
Background Due to the unparalleled genetic diversity of its peoples, Africa is attracting growing research attention. Several African populations have been assessed in global initiatives such as the International HapMap and 1000 Genomes Projects. Notably excluded, however, is the southern Africa region, which is inhabited predominantly by southeastern Bantu-speakers, currently suffering under the dual burden of infectious and non-communicable diseases. Limited reference data for these individuals hampers medical research and prevents thorough understanding of the underlying population substructure. Here, we present the most detailed exploration, to date, of genetic diversity in 94 unrelated southeastern Bantu-speaking South Africans, resident in urban Soweto (Johannesburg). Results Participants were typed for ~4.3 million SNPs using the Illumina Omni5 beadchip. PCA and ADMIXTURE plots were used to compare the observed variation with that seen in selected populations worldwide. Results indicated that Sowetans, and other southeastern Bantu-speakers, are a clearly distinct group from other African populations previously investigated, reflecting a unique genetic history with small, but significant contributions from diverse sources. To assess the suitability of our sample as representative of Sowetans, we compared our results to participants in a larger rheumatoid arthritis case–control study. The control group showed good clustering with our sample, but among the cases were individuals who demonstrated notable admixture. Conclusions Sowetan population structure appears unique compared to other black Africans, and may have clinical implications. Our data represent a suitable reference set for southeastern Bantu-speakers, on par with a HapMap type reference population, and constitute a prelude to the Southern African Human Genome Programme.
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Affiliation(s)
- Andrew May
- Division of Human Genetics, School of Pathology, University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa.
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