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Houldcroft CJ, Underdown S. Infectious disease in the Pleistocene: Old friends or old foes? AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:513-531. [PMID: 38006200 DOI: 10.1002/ajpa.24737] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 11/26/2023]
Abstract
The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.
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Affiliation(s)
| | - Simon Underdown
- Human Origins and Palaeoenvironmental Research Group, School of Social Sciences, Oxford Brookes University, Oxford, UK
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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2
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Lehtinen M, Pimenoff VN, Nedjai B, Louvanto K, Verhoef L, Heideman DAM, El‐Zein M, Widschwendter M, Dillner J. Assessing the risk of cervical neoplasia in the post-HPV vaccination era. Int J Cancer 2023; 152:1060-1068. [PMID: 36093582 PMCID: PMC10091767 DOI: 10.1002/ijc.34286] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/30/2022] [Accepted: 08/03/2022] [Indexed: 01/21/2023]
Abstract
This review is based on the recent EUROGIN scientific session: "Assessing risk of cervical cancer in the post-vaccination era," which addressed the demands of cervical intraepithelial neoplasia (CIN)/squamous intraepithelial lesion (SIL) triage now that the prevalence of vaccine-targeted oncogenic high-risk (hr) human papillomaviruses (HPVs) is decreasing. Change in the prevalence distribution of oncogenic HPV types that follows national HPV vaccination programs is setting the stage for loss of positive predictive value of conventional but possibly also new triage modalities. Understanding the contribution of the latter, most notably hypermethylation of cellular and viral genes in a new setting where most oncogenic HPV types are no longer present, requires studies on their performance in vaccinated women with CIN/SIL that are associated with nonvaccine HPV types. Lessons learned from this research may highlight the potential of cervical cells for risk prediction of all women's cancers.
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Affiliation(s)
- Matti Lehtinen
- Medical FacultyTampere UniversityTampereFinland
- Department of Laboratory MedicineKarolinska InstituteStockholmSweden
| | - Ville N. Pimenoff
- Department of Laboratory MedicineKarolinska InstituteStockholmSweden
| | - Belinda Nedjai
- Wolfson Institute of Population HealthQueen Mary University of LondonLondonUK
| | - Karolina Louvanto
- Medical FacultyTampere UniversityTampereFinland
- Department of Obstetrics and GynecologyTampere University HospitalTampereFinland
| | - Lisanne Verhoef
- Department of PathologyAmsterdam UMC, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
- Cancer Center Amsterdam, Imaging and BiomarkersAmsterdamThe Netherlands
| | - Daniëlle A. M. Heideman
- Department of PathologyAmsterdam UMC, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
- Cancer Center Amsterdam, Imaging and BiomarkersAmsterdamThe Netherlands
| | - Mariam El‐Zein
- Division of Cancer EpidemiologyMcGill UniversityMontrealCanada
| | - Martin Widschwendter
- European Translational Oncology Prevention and Screening (EUTOPS) InstituteUniversität InnsbruckHall in TirolAustria
- Research Institute for Biomedical Aging ResearchUniversität InnsbruckInnsbruckAustria
- Department of Women's Cancer, UCL EGA Institute for Women's HealthUniversity College LondonLondonUK
- Department of Women's and Children's Health, Division of Obstetrics and GynecologyKarolinska Institute and Karolinska University HospitalStockholmSweden
| | - Joakim Dillner
- Department of Laboratory MedicineKarolinska InstituteStockholmSweden
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Rifkin RF, Vikram S, Alcorta J, Ramond JB, Cowan DA, Jakobsson M, Schlebusch CM, Lombard M. Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago. Commun Biol 2023; 6:240. [PMID: 36869137 PMCID: PMC9984395 DOI: 10.1038/s42003-023-04582-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 02/13/2023] [Indexed: 03/05/2023] Open
Abstract
The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, e.g., the sickle cell trait which provides protection against malaria, there is inadequate direct human genomic evidence for ancient human-pathogen infection in the region. Here, we analysed shotgun metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, c. 2000 years ago. This resulted in the identification of ancient DNA sequence reads homologous to Rickettsia felis, the causative agent of typhus-like flea-borne rickettsioses, and the reconstruction of an ancient R. felis genome.
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Affiliation(s)
- Riaan F Rifkin
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa.
- Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK.
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Jaime Alcorta
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
- Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Mattias Jakobsson
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen, Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa
- SciLifeLab, Uppsala, Sweden
| | - Carina M Schlebusch
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen, Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa
- SciLifeLab, Uppsala, Sweden
| | - Marlize Lombard
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa.
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Dalal V, Pasupuleti N, Chaubey G, Rai N, Shinde V. Advancements and Challenges in Ancient DNA Research: Bridging the Global North-South Divide. Genes (Basel) 2023; 14:479. [PMID: 36833406 PMCID: PMC9956214 DOI: 10.3390/genes14020479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Ancient DNA (aDNA) research first began in 1984 and ever since has greatly expanded our understanding of evolution and migration. Today, aDNA analysis is used to solve various puzzles about the origin of mankind, migration patterns, and the spread of infectious diseases. The incredible findings ranging from identifying the new branches within the human family to studying the genomes of extinct flora and fauna have caught the world by surprise in recent times. However, a closer look at these published results points out a clear Global North and Global South divide. Therefore, through this research, we aim to emphasize encouraging better collaborative opportunities and technology transfer to support researchers in the Global South. Further, the present research also focuses on expanding the scope of the ongoing conversation in the field of aDNA by reporting relevant literature published around the world and discussing the advancements and challenges in the field.
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Affiliation(s)
- Vasundhra Dalal
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | | | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Niraj Rai
- Ancient DNA Lab, Birbal Sahni Institute of Palaeosciences, Lucknow 226007, Uttar Pradesh, India
| | - Vasant Shinde
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
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Clinical Significance of the Interaction between Human Papillomavirus (HPV) Type 16 and Other High-Risk Human Papillomaviruses in Women with Cervical Intraepithelial Neoplasia (CIN) and Invasive Cervical Cancer. JOURNAL OF ONCOLOGY 2020; 2020:6508180. [PMID: 33178274 PMCID: PMC7648694 DOI: 10.1155/2020/6508180] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/23/2020] [Accepted: 10/09/2020] [Indexed: 12/29/2022]
Abstract
The aim is to evaluate the clinical consequences of coinfection between HPV 16 and other high-risk HPVs among women with a histological diagnosis of CIN or invasive cervical cancer. A total of 2985 women, with a diagnosis of either CIN or cancer (<IB) on cervical or cone biopsy, were included. HPV genotypes were identified using the INNO-LiPA HPV genotyping assay, version EXTRA, on cervical scraping, before the colposcopic evaluation and the colposcopic biopsies or conization. In the overall population, HPV16 interacted positively with HPV18 (RR = 2, 95% CI 1.5–2.6) and negatively with HPV33, 51, 52, and 66, in log-linear analysis. There was an excess of CIN3 diagnoses among subjects coinfected with HPV16 and HPV18 or HPV52, although the absolute number of cases was relatively small. In a logistic model, the odds ratio of CIN3+ associated with coinfection of HPV16 and HPV18 (OR = 3.8, 95% CI 2.5–5.7, p=0.004 compared to single HPV16) or HPV52 (OR = 3.6, 95% CI 2.6–5.1, p=0.009 compared to single HPV) was higher than that associated with single HPV 16 infections. Finally, multiple infections had no effect on residual disease and did not influence the recurrence of high-grade CIN during a median follow-up of 25 months (IR 17–41). HPV16 interacted positively with HPV18 and negatively with HPV33, 51, 52, and 66 supporting the notion that HPV16 interacts mostly negatively with other HR-HPVs in CIN lesions. Among specimens coinfected with HPV16 and 18 or 52, there was an excess of CIN3+ although the impact on the prevalence of severe cervical lesions was limited.
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Power ML, Snead C, Reed EG, Schulkin J. Integrating evolution into medical education for women's health care practitioners. Evol Med Public Health 2020; 2020:60-67. [PMID: 32382419 PMCID: PMC7196338 DOI: 10.1093/emph/eoaa009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/27/2020] [Accepted: 03/31/2020] [Indexed: 12/24/2022] Open
Abstract
Evolution is a fundamental principle in biology; however, it has been neglected in medical education. We argue that an evolutionary perspective is especially important for women's health care providers, as selection will act strongly on reproductive parameters, and the biological costs of female reproduction are generally more resource expensive than for men (e.g. due to gestation and lactation) with greater effects on health and wellbeing. An evolutionary perspective is needed to understand antibiotic resistance, disease and health risks associated with mismatches between our evolved adaptations and current conditions, the importance of the microbiome and the maternal role in how infants acquire and develop their early-life microbiome (vaginal birth, lactation), and the importance of breastmilk as a biochemical signal from mothers to their babies. We present data that obstetrician-gynecologists' views regarding the inclusion of evolution within their training is generally positive, but many barriers are perceived. Requiring coursework in evolutionary biology with an emphasis on evolutionary medicine prior to enrollment in medical school may be a solution.
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Affiliation(s)
- Michael L Power
- Smithsonian National Zoological Park and Conservation Biology Institute, Washington, DC 20013-7012, USA
- American College of Obstetricians and Gynecologists, Washington, DC 20024-2188, USA
| | - Carrie Snead
- American College of Obstetricians and Gynecologists, Washington, DC 20024-2188, USA
| | - Eda G Reed
- Smithsonian National Zoological Park and Conservation Biology Institute, Washington, DC 20013-7012, USA
- Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jay Schulkin
- Obstetrics & Gynecology, University of Washington School of Medicine, Seattle, WA 98195, USA
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Disease transmission and introgression can explain the long-lasting contact zone of modern humans and Neanderthals. Nat Commun 2019; 10:5003. [PMID: 31676766 PMCID: PMC6825168 DOI: 10.1038/s41467-019-12862-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 09/26/2019] [Indexed: 12/11/2022] Open
Abstract
Neanderthals and modern humans both occupied the Levant for tens of thousands of years prior to the spread of modern humans into the rest of Eurasia and their replacement of the Neanderthals. That the inter-species boundary remained geographically localized for so long is a puzzle, particularly in light of the rapidity of its subsequent movement. Here, we propose that infectious-disease dynamics can explain the localization and persistence of the inter-species boundary. We further propose, and support with dynamical-systems models, that introgression-based transmission of alleles related to the immune system would have gradually diminished this barrier to pervasive inter-species interaction, leading to the eventual release of the inter-species boundary from its geographic localization. Asymmetries between the species in the characteristics of their associated ‘pathogen packages’ could have generated feedback that allowed modern humans to overcome disease burden earlier than Neanderthals, giving them an advantage in their subsequent spread into Eurasia. Modern humans and Neanderthals coexisted in the Levant for tens of thousands of years before modern humans spread and replaced Neanderthals. Here, Greenbaum et al. develop a model showing that transmission of disease and genes can explain the maintenance and then collapse of this contact zone.
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8
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Houldcroft CJ, Rifkin RF, Underdown SJ. Human biology and ancient DNA: exploring disease, domestication and movement. Ann Hum Biol 2019; 46:95-98. [DOI: 10.1080/03014460.2019.1629536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Charlotte J. Houldcroft
- Department of Medicine, Addenbrooke’s Hospital, University of Cambridge, Cambridge, UK
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
- Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Riaan F. Rifkin
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
- Human Origins and Palaeo-Environments Research Group, Department of Anthropology and Geography, Oxford Brookes University, Oxford, UK
| | - Simon J. Underdown
- Human Origins and Palaeo-Environments Research Group, Department of Anthropology and Geography, Oxford Brookes University, Oxford, UK
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Childs LM, El Moustaid F, Gajewski Z, Kadelka S, Nikin-Beers R, Smith JW, Walker M, Johnson LR. Linked within-host and between-host models and data for infectious diseases: a systematic review. PeerJ 2019; 7:e7057. [PMID: 31249734 PMCID: PMC6589080 DOI: 10.7717/peerj.7057] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/28/2019] [Indexed: 12/17/2022] Open
Abstract
The observed dynamics of infectious diseases are driven by processes across multiple scales. Here we focus on two: within-host, that is, how an infection progresses inside a single individual (for instance viral and immune dynamics), and between-host, that is, how the infection is transmitted between multiple individuals of a host population. The dynamics of each of these may be influenced by the other, particularly across evolutionary time. Thus understanding each of these scales, and the links between them, is necessary for a holistic understanding of the spread of infectious diseases. One approach to combining these scales is through mathematical modeling. We conducted a systematic review of the published literature on multi-scale mathematical models of disease transmission (as defined by combining within-host and between-host scales) to determine the extent to which mathematical models are being used to understand across-scale transmission, and the extent to which these models are being confronted with data. Following the PRISMA guidelines for systematic reviews, we identified 24 of 197 qualifying papers across 30 years that include both linked models at the within and between host scales and that used data to parameterize/calibrate models. We find that the approach that incorporates both modeling with data is under-utilized, if increasing. This highlights the need for better communication and collaboration between modelers and empiricists to build well-calibrated models that both improve understanding and may be used for prediction.
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Affiliation(s)
- Lauren M Childs
- Department of Mathematics, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Fadoua El Moustaid
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA.,Global Change Center, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Zachary Gajewski
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA.,Global Change Center, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA.,Department of Statistics, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Sarah Kadelka
- Department of Mathematics, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Ryan Nikin-Beers
- Department of Mathematics, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA.,Department of Mathematics, University of Florida, Gainesville, FL, USA
| | - John W Smith
- Department of Statistics, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Melody Walker
- Department of Mathematics, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Leah R Johnson
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA.,Global Change Center, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA.,Department of Statistics, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA.,Computational Modeling and Data Analytics, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
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Dolgova O, Lao O. Medicine in the Light of Evolution. Genes (Basel) 2018; 10:genes10010003. [PMID: 30583455 PMCID: PMC6356894 DOI: 10.3390/genes10010003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 12/18/2018] [Indexed: 11/26/2022] Open
Affiliation(s)
- Olga Dolgova
- Population Genomics Group, Centre Nacional d'Anàlisi Genòmica, Centre de Regulació Genòmica (CRG-CNAG), Parc Científic de Barcelona, Baldiri Reixac 4, 08028 Barcelona, Catalonia, Spain.
| | - Oscar Lao
- Population Genomics Group, Centre Nacional d'Anàlisi Genòmica, Centre de Regulació Genòmica (CRG-CNAG), Parc Científic de Barcelona, Baldiri Reixac 4, 08028 Barcelona, Catalonia, Spain.
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11
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Dolgova O, Lao O. Evolutionary and Medical Consequences of Archaic Introgression into Modern Human Genomes. Genes (Basel) 2018; 9:E358. [PMID: 30022013 PMCID: PMC6070777 DOI: 10.3390/genes9070358] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/07/2018] [Accepted: 07/11/2018] [Indexed: 01/13/2023] Open
Abstract
The demographic history of anatomically modern humans (AMH) involves multiple migration events, population extinctions and genetic adaptations. As genome-wide data from complete genome sequencing becomes increasingly abundant and available even from extinct hominins, new insights of the evolutionary history of our species are discovered. It is currently known that AMH interbred with archaic hominins once they left the African continent. Current non-African human genomes carry fragments of archaic origin. This review focuses on the fitness consequences of archaic interbreeding in current human populations. We discuss new insights and challenges that researchers face when interpreting the potential impact of introgression on fitness and testing hypotheses about the role of selection within the context of health and disease.
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Affiliation(s)
- Olga Dolgova
- Population Genomics Group, Centre Nacional d'Anàlisi Genòmica, Centre de Regulació Genòmica (CRG-CNAG), Parc Científic de Barcelona, Baldiri Reixac 4, 08028 Barcelona, Catalonia, Spain.
| | - Oscar Lao
- Population Genomics Group, Centre Nacional d'Anàlisi Genòmica, Centre de Regulació Genòmica (CRG-CNAG), Parc Científic de Barcelona, Baldiri Reixac 4, 08028 Barcelona, Catalonia, Spain.
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