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Evolution of cranial capacity revisited: A view from the late Middle Pleistocene cranium from Xujiayao, China. J Hum Evol 2022; 163:103119. [PMID: 35026677 DOI: 10.1016/j.jhevol.2021.103119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 12/11/2022]
Abstract
The Late Middle Pleistocene hominin fossils from the Xujiayao site in northern China have been closely studied in light of their morphological variability. However, all previous studies have focused on separated cranial fragments. Here, we report the first reconstruction of a fairly complete posterior cranium, Xujiayao 6 (XJY 6), confidently dated to ∼200-160 ka, which facilitated an assessment of its overall cranial size. XJY 6 was reconstructed from three of the original fragments-the PA1486 (No.7/XJY 6a) occipital bone, PA1490 (No.10/XJY 6b) right parietal bone, and PA1498 (No.17/XJY 15) left temporal bone-which originated from the same young adult individual. The XJY 6 endocranial capacity, estimated by measuring endocranial volume, was estimated using multiple regression formulae derived from ectocranial and endocranial measurements on select samples of Pleistocene hominins and recent modern humans. The results indicate that the larger pooled sample of both Pleistocene and recent modern humans was more robust for the endocranial capacity estimate. Based on the pooled sample using the ectocranial and endocranial measurements, we conservatively estimate the XJY 6 endocranial volume to be ∼1700 cm3 with a 95% confidence interval of 1555-1781 cm3. This is close to Xuchang 1, which dates to 125-105 ka and whose endocranial volume is ∼1800 cm3. Thus, XJY 6 provides the earliest evidence of a brain size that falls in the upper range of Neanderthals and modern Homo sapiens. XJY 6, together with Xuchang 1, Homo floresiensis, Homo luzonensis, and Homo naledi, challenge the general pattern that brain size gradually increases over geological time. This study also finds that hominin brain size expansion occurred at different rates across time and space.
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2
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Athreya S, Hopkins A. Conceptual issues in hominin taxonomy: Homo heidelbergensis and an ethnobiological reframing of species. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 175 Suppl 72:4-26. [PMID: 34117636 DOI: 10.1002/ajpa.24330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 12/29/2022]
Abstract
Efforts to name and classify Middle Pleistocene Homo, often referred to as "Homo heidelbergensis" are hampered by confusing patterns of morphology but also by conflicting paleoanthropological ideologies that are embedded in approaches to hominin taxonomy, nomenclature, and the species concept. We deconstruct these issues to show how the field's search for a "real" species relies on strict adherence to pre-Darwinian essentialist naming rules in a post-typological world. We then examine Middle Pleistocene Homo through the framework of ethnobiology, which examines on how Indigenous societies perceive, classify, and name biological organisms. This research reminds us that across human societies, taxonomies function to (1) identify and classify organisms based on consensus pattern recognition and (2) construct a stable nomenclature for effective storage, retrieval and communication of information. Naming Middle Pleistocene Homo as a "real" species cannot be verified with the current data; and separating regional groups into distinct evolutionary lineages creates taxa that are not defined by readily perceptible or universally salient differences. Based on ethnobiological studies of this kind of patterning, referring to these hominins above the level of the species according to their generic category with modifiers (e.g., "European Middle Pleistocene Homo") is consistent with observed human capabilities for cognitive differentiation, is both necessary and sufficient given the current data, and will allow for the most clear communication across ideologies going forward.
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Affiliation(s)
- Sheela Athreya
- Liberal Arts Program, Texas A&M University-Qatar, Doha, Qatar.,Department of Anthropology, Texas A&M University, College Station, Texas, USA
| | - Allison Hopkins
- Department of Anthropology, Texas A&M University, College Station, Texas, USA
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3
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Late Middle Pleistocene hominin teeth from Tongzi, southern China. J Hum Evol 2019; 130:96-108. [DOI: 10.1016/j.jhevol.2019.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/28/2019] [Accepted: 03/04/2019] [Indexed: 12/29/2022]
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4
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Chen Z, DeSalle R, Schiffman M, Herrero R, Wood CE, Ruiz JC, Clifford GM, Chan PKS, Burk RD. Niche adaptation and viral transmission of human papillomaviruses from archaic hominins to modern humans. PLoS Pathog 2018; 14:e1007352. [PMID: 30383862 PMCID: PMC6211759 DOI: 10.1371/journal.ppat.1007352] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/22/2018] [Indexed: 02/07/2023] Open
Abstract
Recent discoveries on the origins of modern humans from multiple archaic hominin populations and the diversity of human papillomaviruses (HPVs) suggest a complex scenario of virus-host evolution. To evaluate the origin of HPV pathogenesis, we estimated the phylogeny, timing, and dispersal of HPV16 variants using a Bayesian Markov Chain Monte Carlo framework. To increase precision, we identified and characterized non-human primate papillomaviruses from New and Old World monkeys to set molecular clock models. We demonstrate specific host niche adaptation of primate papillomaviruses with subsequent coevolution with their primate hosts for at least 40 million years. Analyses of 212 HPV16 complete genomes and 3582 partial sequences estimated ancient divergence of HPV16 variants (between A and BCD lineages) from their most recent common ancestors around half a million years ago, roughly coinciding with the timing of the split between archaic Neanderthals and modern Homo sapiens, and nearly three times longer than divergence times of modern Homo sapiens. HPV16 A lineage variants were significantly underrepresented in present African populations, whereas the A sublineages were highly prevalent in European (A1-3) and Asian (A4) populations, indicative of viral sexual transmission from Neanderthals to modern non-African humans through multiple interbreeding events in the past 80 thousand years. Remarkably, the human leukocyte antigen B*07:02 and C*07:02 alleles associated with increased risk in cervix cancer represent introgressed regions from Neanderthals in present-day Eurasians. The archaic hominin-host-switch model was also supported by other HPV variants. Niche adaptation and virus-host codivergence appear to influence the pathogenesis of papillomaviruses.
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Affiliation(s)
- Zigui Chen
- Departments of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Rob DeSalle
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY, United States of America
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, United States of America
| | - Rolando Herrero
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- Proyecto Epidemiológico Guanacaste, Fundación INCIENSA, San José, Costa Rica
| | - Charles E. Wood
- Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC, United States of America
| | - Julio C. Ruiz
- Department of Veterinary Sciences, The University of Texas MD Anderson Cancer Center, Bastrop, Texas, United States of America
| | - Gary M. Clifford
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Paul K. S. Chan
- Departments of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Robert D. Burk
- Departments of Pediatrics, Microbiology and Immunology; Epidemiology and Population Health; Obstetrics, Gynecology and Woman’s Health, Albert Einstein College of Medicine, Bronx, NY, United States of America
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5
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The Role of aDNA in Understanding the Coevolutionary Patterns of Human Sexually Transmitted Infections. Genes (Basel) 2018; 9:genes9070317. [PMID: 29941858 PMCID: PMC6070984 DOI: 10.3390/genes9070317] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 12/18/2022] Open
Abstract
Analysis of pathogen genome data sequenced from clinical and historical samples has made it possible to perform phylogenetic analyses of sexually transmitted infections on a global scale, and to estimate the diversity, distribution, and coevolutionary host relationships of these pathogens, providing insights into pathogen emergence and disease prevention. Deep-sequenced pathogen genomes from clinical studies and ancient samples yield estimates of within-host and between-host evolutionary rates and provide data on changes in pathogen genomic stability and evolutionary responses. Here we examine three groups of pathogens transmitted mainly through sexual contact between modern humans to provide insight into ancient human behavior and history with their pathogens. Exploring ancient pathogen genomic divergence and the ancient viral-host parallel evolutionary histories will help us to reconstruct the origin of present-day geographical distribution and diversity of clinical pathogen infections, and will hopefully allow us to foresee possible environmentally induced pathogen evolutionary responses. Lastly, we emphasize that ancient pathogen DNA research should be combined with modern clinical pathogen data, and be equitable and provide advantages for all researchers worldwide, e.g., through shared data.
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6
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Trinkaus E. One hundred years of paleoanthropology: An American perspective. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 165:638-651. [PMID: 29574840 DOI: 10.1002/ajpa.23330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/18/2017] [Accepted: 09/18/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Erik Trinkaus
- Department of Anthropology, Washington University, Saint Louis, Missouri, 63130
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7
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Chen Z, Schiffman M, Herrero R, DeSalle R, Anastos K, Segondy M, Sahasrabuddhe VV, Gravitt PE, Hsing AW, Chan PKS, Burk RD. Classification and evolution of human papillomavirus genome variants: Alpha-5 (HPV26, 51, 69, 82), Alpha-6 (HPV30, 53, 56, 66), Alpha-11 (HPV34, 73), Alpha-13 (HPV54) and Alpha-3 (HPV61). Virology 2018; 516:86-101. [PMID: 29331867 PMCID: PMC6093212 DOI: 10.1016/j.virol.2018.01.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 12/25/2017] [Accepted: 01/02/2018] [Indexed: 11/17/2022]
Abstract
HPV variants from the same type can be classified into lineages and sublineages based on the complete genome differences and the phylogenetic topologies. We examined nucleotide variations of twelve HPV types within the species Alpha-5 (HPV26, 51, 69, 82), Alpha-6 (HPV30, 53, 56, 66), Alpha-11 (HPV34, 73), Alpha-13 (HPV54) and Alpha-3 (HPV61) by analyzing 1432 partial sequences and 181 complete genomes from multiple geographic populations. The inter-lineage and inter-sublineage mean differences of HPV variants ranged between 0.9-7.3% and 0.3-0.9%, respectively. The heterogeneity and phylogenies of HPV isolates indicate an independent evolutionary history for each type. The noncoding regions were the most variable regions whereas the capsid proteins were relatively conserved. Certain variant lineages and/or sublineages were geographically-associated. These data provide the basis to further classify HPV variants and should foster future studies on the evolution of HPV genomes and the associations of HPV variants with cancer risk.
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Affiliation(s)
- Zigui Chen
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States
| | - Rolando Herrero
- Proyecto Epidemiológico Guanacaste, Fundación INCIENSA, San José, Costa Rica; Prevention and Implementation Group, International Agency for Research on Cancer, World Health Organization, France
| | - Rob DeSalle
- Sackler Institute of Comparative Genomics, American Museum of Natural History, NY, United States
| | - Kathryn Anastos
- Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, United States; Departments of Epidemiology & Population Health and Obstetrics, Gynecology & Woman's Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Michel Segondy
- Department of Biology and Pathology, Montpellier University Hospital, Montpellier, France
| | | | - Patti E Gravitt
- Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Ann W Hsing
- Stanford Cancer Institute and Stanford Prevention Research Center, Stanford School of Medicine, Stanford University, CA, United States
| | - Paul K S Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Robert D Burk
- Departments of Epidemiology & Population Health and Obstetrics, Gynecology & Woman's Health, Albert Einstein College of Medicine, Bronx, NY, United States; Departments of Pediatrics, and Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY, United States.
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8
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Xing S, Martinón-Torres M, Bermúdez de Castro JM. The fossil teeth of the Peking Man. Sci Rep 2018; 8:2066. [PMID: 29391445 PMCID: PMC5794973 DOI: 10.1038/s41598-018-20432-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 01/18/2018] [Indexed: 01/06/2023] Open
Abstract
This study provides new original data, including the endostructure of most Zhoukoudian H. erectus teeth preserved to date, since the publication of Black in 1927 and Weidenreich in 1937. The new evidence ratifies the similarities of Zhoukoudian with other East Asian mid-Middle Pleistocene hominins such as Hexian and Yiyuan, and allows defining a dental pattern potentially characteristic of this population commonly referred to as classic H. erectus. Given the possible chronological overlaps of classic H. erectus with other archaic Homo, the characterization of this group becomes a key issue when deciphering the taxonomy and evolutionary scenario of the Middle Pleistocene hominins in East Asia. Internally, the most remarkable feature of Zhoukoudian teeth is the highly crenulated enamel-dentine junction (EDJ) and its imprint on the roof of the pulp cavity. So far, this "dendrite-like" EDJ has been found only in East Asia Middle Pleistocene hominins although a large group of samples were assessed, and it could be useful to dentally define classic H. erectus in China. The crenulated EDJ surface, together with the stout roots and the taurodontism could be a mechanism to withstand high biomechanical demand despite a general dentognathic reduction, particularly of the crowns, in these populations.
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Affiliation(s)
- Song Xing
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China.
| | - María Martinón-Torres
- National Research Center on Human Evolution (CENIEH), Paseo de la Sierra de Atapuerca 3, 09002, Burgos, Spain.,University College London (UCL) Anthropology, 14 Taviton Street, London, WC1H 0BW, UK
| | - José María Bermúdez de Castro
- National Research Center on Human Evolution (CENIEH), Paseo de la Sierra de Atapuerca 3, 09002, Burgos, Spain.,University College London (UCL) Anthropology, 14 Taviton Street, London, WC1H 0BW, UK
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9
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Martinón-Torres M, Wu X, Bermúdez de Castro JM, Xing S, Liu W. Homo sapiens in the Eastern Asian Late Pleistocene. CURRENT ANTHROPOLOGY 2017. [DOI: 10.1086/694449] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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10
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Kaifu Y. Archaic Hominin Populations in Asia before the Arrival of Modern Humans. CURRENT ANTHROPOLOGY 2017. [DOI: 10.1086/694318] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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11
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Ancient Evolution and Dispersion of Human Papillomavirus 58 Variants. J Virol 2017; 91:JVI.01285-17. [PMID: 28794033 PMCID: PMC5640864 DOI: 10.1128/jvi.01285-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 08/01/2017] [Indexed: 01/03/2023] Open
Abstract
Human papillomavirus 58 (HPV58) is found in 10 to 18% of cervical cancers in East Asia but is rather uncommon elsewhere. The distribution and oncogenic potential of HPV58 variants appear to be heterogeneous, since the E7 T20I/G63S variant is more prevalent in East Asia and confers a 7- to 9-fold-higher risk of cervical precancer and cancer. However, the underlying genomic mechanisms that explain the geographic and carcinogenic diversity of HPV58 variants are still poorly understood. In this study, we used a combination of phylogenetic analyses and bioinformatics to investigate the deep evolutionary history of HPV58 complete genome variants. The initial splitting of HPV58 variants was estimated to occur 478,600 years ago (95% highest posterior density [HPD], 391,000 to 569,600 years ago). This divergence time is well within the era of speciation between Homo sapiens and Neanderthals/Denisovans and around three times longer than the modern Homo sapiens divergence times. The expansion of present-day variants in Eurasia could be the consequence of viral transmission from Neanderthals/Denisovans to non-African modern human populations through gene flow. A whole-genome sequence signature analysis identified 3 amino acid changes, 16 synonymous nucleotide changes, and a 12-bp insertion strongly associated with the E7 T20I/G63S variant that represents the A3 sublineage and carries higher carcinogenetic potential. Compared with the capsid proteins, the oncogenes E7 and E6 had increased substitution rates indicative of higher selection pressure. These data provide a comprehensive evolutionary history and genomic basis of HPV58 variants to assist further investigation of carcinogenic association and the development of diagnostic and therapeutic strategies.IMPORTANCE Papillomaviruses (PVs) are an ancient and heterogeneous group of double-stranded DNA viruses that preferentially infect the cutaneous and mucocutaneous epithelia of vertebrates. Persistent infection by specific oncogenic human papillomaviruses (HPVs), including HPV58, has been established as the primary cause of cervical cancer. In this work, we reveal the complex evolutionary history of HPV58 variants that explains the heterogeneity of oncogenic potential and geographic distribution. Our data suggest that HPV58 variants may have coevolved with archaic hominins and dispersed across the planet through host interbreeding and gene flow. Certain genes and codons of HPV58 variants representing higher carcinogenic potential and/or that are under positive selection may have important implications for viral host specificity, pathogenesis, and disease prevention.
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12
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Stringer C. The origin and evolution of Homo sapiens. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0237. [PMID: 27298468 DOI: 10.1098/rstb.2015.0237] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2016] [Indexed: 02/07/2023] Open
Abstract
If we restrict the use of Homo sapiens in the fossil record to specimens which share a significant number of derived features in the skeleton with extant H. sapiens, the origin of our species would be placed in the African late middle Pleistocene, based on fossils such as Omo Kibish 1, Herto 1 and 2, and the Levantine material from Skhul and Qafzeh. However, genetic data suggest that we and our sister species Homo neanderthalensis shared a last common ancestor in the middle Pleistocene approximately 400-700 ka, which is at least 200 000 years earlier than the species origin indicated from the fossils already mentioned. Thus, it is likely that the African fossil record will document early members of the sapiens lineage showing only some of the derived features of late members of the lineage. On that basis, I argue that human fossils such as those from Jebel Irhoud, Florisbad, Eliye Springs and Omo Kibish 2 do represent early members of the species, but variation across the African later middle Pleistocene/early Middle Stone Age fossils shows that there was not a simple linear progression towards later sapiens morphology, and there was chronological overlap between different 'archaic' and 'modern' morphs. Even in the late Pleistocene within and outside Africa, we find H. sapiens specimens which are clearly outside the range of Holocene members of the species, showing the complexity of recent human evolution. The impact on species recognition of late Pleistocene gene flow between the lineages of modern humans, Neanderthals and Denisovans is also discussed, and finally, I reconsider the nature of the middle Pleistocene ancestor of these lineages, based on recent morphological and genetic data.This article is part of the themed issue 'Major transitions in human evolution'.
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Affiliation(s)
- Chris Stringer
- Department of Earth Sciences, The Natural History Museum, London SW7 5BD, UK
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13
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Tracing the peopling of the world through genomics. Nature 2017; 541:302-310. [PMID: 28102248 DOI: 10.1038/nature21347] [Citation(s) in RCA: 288] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 12/13/2016] [Indexed: 12/13/2022]
Abstract
Advances in the sequencing and the analysis of the genomes of both modern and ancient peoples have facilitated a number of breakthroughs in our understanding of human evolutionary history. These include the discovery of interbreeding between anatomically modern humans and extinct hominins; the development of an increasingly detailed description of the complex dispersal of modern humans out of Africa and their population expansion worldwide; and the characterization of many of the genetic adaptions of humans to local environmental conditions. Our interpretation of the evolutionary history and adaptation of humans is being transformed by analyses of these new genomic data.
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14
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Li ZY, Wu XJ, Zhou LP, Liu W, Gao X, Nian XM, Trinkaus E. Late Pleistocene archaic human crania from Xuchang, China. Science 2017; 355:969-972. [DOI: 10.1126/science.aal2482] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/09/2017] [Indexed: 11/02/2022]
Affiliation(s)
- Zhan-Yang Li
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
- Henan Provincial Institute of Cultural Relics and Archaeology, Zhengzhou 450000, China
| | - Xiu-Jie Wu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Li-Ping Zhou
- Laboratory for Earth Surface Processes, Department of Geography, Peking University, Beijing 100871, China
| | - Wu Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Xing Gao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Mei Nian
- Laboratory for Earth Surface Processes, Department of Geography, Peking University, Beijing 100871, China
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Erik Trinkaus
- Department of Anthropology, Washington University, St. Louis, MO 63130, USA
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15
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Nielsen R, Akey JM, Jakobsson M, Pritchard JK, Tishkoff S, Willerslev E. Tracing the peopling of the world through genomics. Nature 2017; 541. [PMID: 28102248 PMCID: PMC5772775 DOI: 10.1038/nature21347;pmid:28102248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Advances in the sequencing and the analysis of the genomes of both modern and ancient peoples have facilitated a number of breakthroughs in our understanding of human evolutionary history. These include the discovery of interbreeding between anatomically modern humans and extinct hominins; the development of an increasingly detailed description of the complex dispersal of modern humans out of Africa and their population expansion worldwide; and the characterization of many of the genetic adaptions of humans to local environmental conditions. Our interpretation of the evolutionary history and adaptation of humans is being transformed by analyses of these new genomic data.
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Affiliation(s)
- Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California 94720, USA
- Department of Statistics, University of California, Berkeley, Berkeley, California 942720, USA
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Joshua M Akey
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195-5065, USA
| | - Mattias Jakobsson
- Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- Department of Biology, Stanford University, Stanford, California 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
| | - Sarah Tishkoff
- Department of Genetics, University of Pennsylvania, Pennsylvania 19104, USA
- Department of Biology, University of Pennsylvania, Pennsylvania 19104, USA
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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16
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Pimenoff VN, de Oliveira CM, Bravo IG. Transmission between Archaic and Modern Human Ancestors during the Evolution of the Oncogenic Human Papillomavirus 16. Mol Biol Evol 2017; 34:4-19. [PMID: 28025273 PMCID: PMC5854117 DOI: 10.1093/molbev/msw214] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Every human suffers through life a number of papillomaviruses (PVs) infections, most of them asymptomatic. A notable exception are persistent infections by Human papillomavirus 16 (HPV16), the most oncogenic infectious agent for humans and responsible for most infection-driven anogenital cancers. Oncogenic potential is not homogeneous among HPV16 lineages, and genetic variation within HPV16 exhibits some geographic structure. However, an in-depth analysis of the HPV16 evolutionary history was still wanting. We have analyzed extant HPV16 diversity and compared the evolutionary and phylogeographical patterns of humans and of HPV16. We show that codivergence with modern humans explains at most 30% of the present viral geographical distribution. The most explanatory scenario suggests that ancestral HPV16 already infected ancestral human populations and that viral lineages co-diverged with the hosts in parallel with the split between archaic Neanderthal-Denisovans and ancestral modern human populations, generating the ancestral HPV16A and HPV16BCD viral lineages, respectively. We propose that after out-of-Africa migration of modern human ancestors, sexual transmission between human populations introduced HPV16A into modern human ancestor populations. We hypothesize that differential coevolution of HPV16 lineages with different but closely related ancestral human populations and subsequent host-switch events in parallel with introgression of archaic alleles into the genomes of modern human ancestors may be largely responsible for the present-day differential prevalence and association with cancers for HPV16 variants.
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Affiliation(s)
- Ville N Pimenoff
- Infections and Cancer Laboratory, Cancer Epidemiology Research Programme, Catalan Institute of Oncology, Barcelona, Spain
- Unit of Biomarkers and Susceptibility, Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain
| | - Cristina Mendes de Oliveira
- Infections and Cancer Laboratory, Cancer Epidemiology Research Programme, Catalan Institute of Oncology, Barcelona, Spain
- Virology Laboratory, Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil
| | - Ignacio G Bravo
- Infections and Cancer Laboratory, Cancer Epidemiology Research Programme, Catalan Institute of Oncology, Barcelona, Spain
- MIVEGEC (UMR CNRS 5290, IRD 224, UM), National Center for Scientific Research (CNRS), Montpellier, France
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Why are there no persisting hybrids of humans with Denisovans, Neanderthals, or anyone else? Proc Natl Acad Sci U S A 2016; 113:E2354. [PMID: 27044111 DOI: 10.1073/pnas.1602270113] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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