1
|
Petr M, Haller BC, Ralph PL, Racimo F. slendr: a framework for spatio-temporal population genomic simulations on geographic landscapes. PEER COMMUNITY JOURNAL 2023; 3:e121. [PMID: 38984034 PMCID: PMC11233137 DOI: 10.24072/pcjournal.354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
One of the goals of population genetics is to understand how evolutionary forces shape patterns of genetic variation over time. However, because populations evolve across both time and space, most evolutionary processes also have an important spatial component, acting through phenomena such as isolation by distance, local mate choice, or uneven distribution of resources. This spatial dimension is often neglected, partly due to the lack of tools specifically designed for building and evaluating complex spatio-temporal population genetic models. To address this methodological gap, we present a new framework for simulating spatially-explicit genomic data, implemented in a new R package called slendr (www.slendr.net), which leverages a SLiM simulation back-end script bundled with the package. With this framework, the users can programmatically and visually encode spatial population ranges and their temporal dynamics (i.e., population displacements, expansions, and contractions) either on real Earth landscapes or on abstract custom maps, and schedule splits and gene-flow events between populations using a straightforward declarative language. Additionally, slendr can simulate data from traditional, non-spatial models, either with SLiM or using an alternative built-in coalescent msprime back end. Together with its R-idiomatic interface to the tskit library for tree-sequence processing and analysis, slendr opens up the possibility of performing efficient, reproducible simulations of spatio-temporal genomic data entirely within the R environment, leveraging its wealth of libraries for geospatial data analysis, statistics, and visualization. Here, we present the design of the slendr R package and demonstrate its features on several practical example workflows.
Collapse
Affiliation(s)
- Martin Petr
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Denmark
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Denmark
| | - Benjamin C Haller
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Peter L Ralph
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Denmark
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Denmark
| |
Collapse
|
2
|
Sánchez-Barreiro F, De Cahsan B, Westbury MV, Sun X, Margaryan A, Fontsere C, Bruford MW, Russo IRM, Kalthoff DC, Sicheritz-Pontén T, Petersen B, Dalén L, Zhang G, Marquès-Bonet T, Gilbert MTP, Moodley Y. Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros. Mol Biol Evol 2023; 40:msad180. [PMID: 37561011 PMCID: PMC10500089 DOI: 10.1093/molbev/msad180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 08/01/2023] [Accepted: 08/08/2023] [Indexed: 08/11/2023] Open
Abstract
The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north-south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.
Collapse
Affiliation(s)
| | - Binia De Cahsan
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Xin Sun
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Claudia Fontsere
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
| | | | | | - Daniela C Kalthoff
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Thomas Sicheritz-Pontén
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Bent Petersen
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Love Dalén
- Department of Zoology, Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, People's Republic of China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, People's Republic of China
- BGI Research, BGI-Shenzhen, Shenzhen, People's Republic of China
| | - Tomás Marquès-Bonet
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
- National Centre for Genomic Analysis–Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Life & Medical Sciences, Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - M Thomas P Gilbert
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Natural History, NTNU University Museum, Trondheim, Norway
| | - Yoshan Moodley
- Department of Biological Sciences, University of Venda, Thohoyandou, Republic of South Africa
| |
Collapse
|
3
|
Dai X, Bian P, Hu D, Luo F, Huang Y, Jiao S, Wang X, Gong M, Li R, Cai Y, Wen J, Yang Q, Deng W, Nanaei HA, Wang Y, Wang F, Zhang Z, Rosen BD, Heller R, Jiang Y. A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species. Genome Res 2023; 33:1284-1298. [PMID: 37714713 PMCID: PMC10547261 DOI: 10.1101/gr.277481.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 06/30/2023] [Indexed: 09/17/2023]
Abstract
Chinese indicine cattle harbor a much higher genetic diversity compared with other domestic cattle, but their genome architecture remains uninvestigated. Using PacBio HiFi sequencing data from 10 Chinese indicine cattle across southern China, we assembled 20 high-quality partially phased genomes and integrated them into a multiassembly graph containing 148.5 Mb (5.6%) of novel sequence. We identified 156,009 high-confidence nonredundant structural variants (SVs) and 206 SV hotspots spanning ∼195 Mb of gene-rich sequence. We detected 34,249 archaic introgressed fragments in Chinese indicine cattle covering 1.93 Gb (73.3%) of the genome. We inferred an average of 3.8%, 3.2%, 1.4%, and 0.5% of introgressed sequence originating, respectively, from banteng-like, kouprey-like, gayal-like, and gaur-like Bos species, as well as 0.6% of unknown origin. Introgression from multiple donors might have contributed to the genetic diversity of Chinese indicine cattle. Altogether, this study highlights the contribution of interspecies introgression to the genomic architecture of an important livestock population and shows how exotic genomic elements can contribute to the genetic variation available for selection.
Collapse
Affiliation(s)
- Xuelei Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peipei Bian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dexiang Hu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Funong Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shaohua Jiao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xihong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mian Gong
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ran Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yudong Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiayue Wen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qimeng Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weidong Deng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Hojjat Asadollahpour Nanaei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran 1983969412, Iran
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland 20705, USA
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China;
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| |
Collapse
|
4
|
Carter MM, Olm MR, Merrill BD, Dahan D, Tripathi S, Spencer SP, Yu FB, Jain S, Neff N, Jha AR, Sonnenburg ED, Sonnenburg JL. Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes. Cell 2023; 186:3111-3124.e13. [PMID: 37348505 PMCID: PMC10330870 DOI: 10.1016/j.cell.2023.05.046] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 02/12/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
The gut microbiome modulates immune and metabolic health. Human microbiome data are biased toward industrialized populations, limiting our understanding of non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing on 351 fecal samples from the Hadza hunter-gatherers of Tanzania and comparative populations in Nepal and California. We recovered 91,662 genomes of bacteria, archaea, bacteriophages, and eukaryotes, 44% of which are absent from existing unified datasets. We identified 124 gut-resident species vanishing in industrialized populations and highlighted distinct aspects of the Hadza gut microbiome related to in situ replication rates, signatures of selection, and strain sharing. Industrialized gut microbes were found to be enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource, expands our understanding of microbes capable of colonizing the human gut, and clarifies the extensive perturbation induced by the industrialized lifestyle.
Collapse
Affiliation(s)
- Matthew M Carter
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Matthew R Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Bryan D Merrill
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Dylan Dahan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Surya Tripathi
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Sean P Spencer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Feiqiao B Yu
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Sunit Jain
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Aashish R Jha
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Erica D Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA.
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA 94304, USA.
| |
Collapse
|
5
|
Auerbach BM, Savell KRR, Agosto ER. Morphology, evolution, and the whole organism imperative: Why evolutionary questions need multi-trait evolutionary quantitative genetics. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023. [PMID: 37060292 DOI: 10.1002/ajpa.24733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 04/16/2023]
Abstract
Since Washburn's New Physical Anthropology, researchers have sought to understand the complexities of morphological evolution among anatomical regions in human and non-human primates. Researchers continue, however, to preferentially use comparative and functional approaches to examine complex traits, but these methods cannot address questions about evolutionary process and often conflate function with fitness. Moreover, researchers also tend to examine anatomical elements in isolation, which implicitly assumes independent evolution among different body regions. In this paper, we argue that questions asked in primate evolution are best examined using multiple anatomical regions subjected to model-bound methods built from an understanding of evolutionary quantitative genetics. A nascent but expanding number of studies over the last two decades use this approach, examining morphological integration, evolvability, and selection modeling. To help readers learn how to use these methods, we review fundamentals of evolutionary processes within a quantitative genetic framework, explore the importance of neutral evolutionary theory, and explain the basics of evolutionary quantitative genetics, namely the calculation of evolutionary potential for multiple traits in response to selection. Leveraging these methods, we demonstrate their use to understand non-independence in possible evolutionary responses across the limbs, limb girdles, and basicranium of humans. Our results show that model-bound quantitative genetic methods can reveal unexpected genetic covariances among traits that create a novel but measurable understanding of evolutionary complexity among multiple traits. We advocate for evolutionary quantitative genetic methods to be a standard whenever appropriate to keep studies of primate morphological evolution relevant for the next seventy years and beyond.
Collapse
Affiliation(s)
- Benjamin M Auerbach
- Department of Anthropology, The University of Tennessee, Knoxville, Tennessee, USA
- Department of Ecology and Evolutionary Biology, The University of Tennessee, Knoxville, Tennessee, USA
| | - Kristen R R Savell
- Department of Biology, Sacred Heart University, Fairfield, Connecticut, USA
| | - Elizabeth R Agosto
- Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| |
Collapse
|
6
|
Simulations of human migration into North America are more sensitive to demography than choice of palaeoclimate model. Ecol Modell 2022. [DOI: 10.1016/j.ecolmodel.2022.110115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Matsumura H, Tanijiri T, Kouchi M, Hanihara T, Friess M, Moiseyev V, Stringer C, Miyahara K. Global patterns of the cranial form of modern human populations described by analysis of a 3D surface homologous model. Sci Rep 2022; 12:13826. [PMID: 35970916 PMCID: PMC9378707 DOI: 10.1038/s41598-022-15883-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 06/30/2022] [Indexed: 11/09/2022] Open
Abstract
This study assessed the regional diversity of the human cranial form by using geometric homologous models based on scanned data from 148 ethnic groups worldwide. This method adopted a template-fitting technique for a nonrigid transformation via the iterative closest point algorithm to generate the homologous meshes. Through the application of principal component analysis to 342 sampled homologous models, the largest variation was detected in overall size, and small South Asian crania were clearly verified. The next greatest diversity was found in the length/breadth proportion of the neurocranium, which showed the contrast between the elongated crania of Africans and the globular crania of Northeast Asians. Notably, this component was slightly correlated with the facial profile. Well-known facial features, such as the forward projection of the cheek among Northeast Asians and compaction of the European maxilla, were reconfirmed. These facial variations were highly correlated with the calvarial outline, particularly the degree of frontal and occipital inclines. An allometric pattern was detected in facial proportions in relation to overall cranial size; in larger crania, the facial profiles tend to be longer and narrower, as demonstrated among many American natives and Northeast Asians. Although our study did not include data on environmental variables that are likely to affect cranial morphology, such as climate or dietary conditions, the large datasets of homologous cranial models will be usefully available for seeking various attributions to phenotypic skeletal characteristics.
Collapse
Affiliation(s)
- Hirofumi Matsumura
- School of Health Sciences, Sapporo Medical University, Sapporo, 060-8556, Japan.
| | | | - Makiko Kouchi
- National Institute of Advanced Industrial Science and Technology, Tokyo, 135-0064, Japan
| | | | - Martin Friess
- Département Homme et Environnement, Musée de l'Homme, 75116, Paris, France
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, St Petersburg, 199034, Russia
| | - Chris Stringer
- Department of Earth Sciences, The Natural History Museum, London, SW7 5BD, UK
| | - Kengo Miyahara
- Kyoto City Archeological Research Institute, Kyoto, 602-8435, Japan
| |
Collapse
|
9
|
Meneganzin A, Pievani T, Manzi G. Pan-Africanism vs. single-origin of Homo sapiens: Putting the debate in the light of evolutionary biology. Evol Anthropol 2022; 31:199-212. [PMID: 35848454 PMCID: PMC9540121 DOI: 10.1002/evan.21955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 02/23/2022] [Accepted: 06/14/2022] [Indexed: 12/03/2022]
Abstract
The scenario of Homo sapiens origin/s within Africa has become increasingly complex, with a pan-African perspective currently challenging the long-established single-origin hypothesis. In this paper, we review the lines of evidence employed in support of each model, highlighting inferential limitations and possible terminological misunderstandings. We argue that the metapopulation scenario envisaged by pan-African proponents well describes a mosaic diversification among late Middle Pleistocene groups. However, this does not rule out a major contribution that emerged from a single population where crucial derived features-notably, a globular braincase-appeared as the result of a punctuated, cladogenetic event. Thus, we suggest that a synthesis is possible and propose a scenario that, in our view, better reconciles with consolidated expectations in evolutionary theory. These indicate cladogenesis in allopatry as an ordinary pattern for the origin of a new species, particularly during phases of marked climatic and environmental instability.
Collapse
Affiliation(s)
| | | | - Giorgio Manzi
- Department of Environmental BiologySapienza University of RomeRomeItaly
| |
Collapse
|
10
|
Kidd KK, Evsanaa B, Togtokh A, Brissenden JE, Roscoe JM, Dogan M, Neophytou PI, Gurkan C, Bulbul O, Cherni L, Speed WC, Murtha M, Kidd JR, Pakstis AJ. North Asian population relationships in a global context. Sci Rep 2022; 12:7214. [PMID: 35508562 PMCID: PMC9068624 DOI: 10.1038/s41598-022-10706-x] [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: 08/10/2021] [Accepted: 04/01/2022] [Indexed: 12/20/2022] Open
Abstract
Population genetic studies of North Asian ethnic groups have focused on genetic variation of sex chromosomes and mitochondria. Studies of the extensive variation available from autosomal variation have appeared infrequently. We focus on relationships among population samples using new North Asia microhaplotype data. We combined genotypes from our laboratory on 58 microhaplotypes, distributed across 18 autosomes, on 3945 individuals from 75 populations with corresponding data extracted for 26 populations from the Thousand Genomes consortium and for 22 populations from the GenomeAsia 100 K project. A total of 7107 individuals in 122 total populations are analyzed using STRUCTURE, Principal Component Analysis, and phylogenetic tree analyses. North Asia populations sampled in Mongolia include: Buryats, Mongolians, Altai Kazakhs, and Tsaatans. Available Siberians include samples of Yakut, Khanty, and Komi Zyriane. Analyses of all 122 populations confirm many known relationships and show that most populations from North Asia form a cluster distinct from all other groups. Refinement of analyses on smaller subsets of populations reinforces the distinctiveness of North Asia and shows that the North Asia cluster identifies a region that is ancestral to Native Americans.
Collapse
Affiliation(s)
- Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA.
| | - Baigalmaa Evsanaa
- Department of Nephrology, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | - Ariunaa Togtokh
- Department of Nephrology, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | | | - Janet M Roscoe
- Department of Medicine, University of Toronto, Toronto, ON, Canada.,The Scarborough Hospital, Toronto, ON, Canada
| | - Mustafa Dogan
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | | | - Cemal Gurkan
- Turkish Cypriot DNA Laboratory, Committee On Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia, North Cyprus, Turkey.,Dr. Fazıl Küçük Faculty of Medicine, Eastern Mediterranean University, Famagusta, North Cyprus, Turkey
| | - Ozlem Bulbul
- Institute of Forensic Science, Istanbul University, Cerrahpasa, 34500, Istanbul, Turkey
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia.,Higher Institute of Biotechnology of Monastir, Monastir University, 5000, Monastir, Tunisia
| | - William C Speed
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA
| | - Michael Murtha
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA
| | - Judith R Kidd
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA
| |
Collapse
|
11
|
Merrill BD, Carter MM, Olm MR, Dahan D, Tripathi S, Spencer SP, Yu B, Jain S, Neff N, Jha AR, Sonnenburg ED, Sonnenburg JL. Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Microbes.. [PMID: 36238714 PMCID: PMC9558438 DOI: 10.1101/2022.03.30.486478] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The gut microbiome is a key modulator of immune and metabolic health. Human microbiome data is biased towards industrialized populations, providing limited understanding of the distinct and diverse non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing and strain cultivation on 351 fecal samples from the Hadza, hunter-gatherers in Tanzania, and comparative populations in Nepal and California. We recover 94,971 total genomes of bacteria, archaea, bacteriophages, and eukaryotes, 43% of which are absent from existing unified datasets. Analysis of in situ growth rates, genetic pN/pS signatures, high-resolution strain tracking, and 124 gut-resident species vanishing in industrialized populations reveals differentiating dynamics of the Hadza gut microbiome. Industrialized gut microbes are enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource that expands our understanding of microbes capable of colonizing the human gut and clarifies the extensive perturbation brought on by the industrialized lifestyle.
Collapse
|
12
|
Matsumura H, Xie G, Nguyen LC, Hanihara T, Li Z, Nguyen KTK, Ho XT, Nguyen TN, Huang SC, Hung HC. Female craniometrics support the 'two-layer model' of human dispersal in Eastern Eurasia. Sci Rep 2021; 11:20830. [PMID: 34675295 PMCID: PMC8531373 DOI: 10.1038/s41598-021-00295-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/07/2021] [Indexed: 11/24/2022] Open
Abstract
This study reports a cranio-morphometric analysis of female human remains from seven archaeological sites in China, Vietnam and Taiwan that date between 16,000 and 5300 BP. The aim of the analysis is to test the “two-layer” model of human dispersal in eastern Eurasia, using previously unanalysed female remains to balance the large sample of previously-analysed males. The resulting craniometric data indicate that the examined specimens all belong to the “first layer” of dispersal, and share a common ancestor with recent Australian and Papuan populations, and the ancient Jomon people of Japan. The analysed specimens pre-date the expansion of agricultural populations of East/Northeast Asian origin—that is, the “second layer” of human dispersal proposed by the model. As a result of this study, the two-layer model, which has hitherto rested on evidence only from male skeletons, is now strongly supported by female-derived data. Further comparisons reveal that the people of the first layer were closer in terms of their facial morphology to modern Africans and Sri Lankan Veddah than to modern Asians and Europeans, suggesting that the Late Pleistocene through Middle Holocene hunter-gatherers examined in this study were direct descendants of the anatomically modern humans who first migrated out of Africa through southern Eurasia.
Collapse
Affiliation(s)
- Hirofumi Matsumura
- School of Health Science, Sapporo Medical University, Sapporo, Hokkaido, Japan.
| | - Guangmao Xie
- Guangxi Institute of Cultural Relic Protection and Archaeology, Nanning, Guangxi, China. .,College of History, Culture and Tourism, Guangxi Normal University, Guilin, Guangxi, China.
| | - Lan Cuong Nguyen
- Institute of Archaeology, Vietnam Academy of Social Science, Hanoi, Vietnam
| | - Tsunehiko Hanihara
- Department of Anatomy, School of Medicine, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Zhen Li
- Guangxi Institute of Cultural Relic Protection and Archaeology, Nanning, Guangxi, China
| | - Khanh Trung Kien Nguyen
- Southern Institute of Social Sciences, Vietnam Academy of Social Science, Ho Chi Minh City, Vietnam
| | - Xuan Tinh Ho
- Department of Culture, Sports and Tourism of Quang Nam, Tam Kỳ, Quang Nam, Vietnam
| | | | - Shih-Chiang Huang
- Department of Anthropology, National Taiwan University, Taipei, Taiwan, ROC
| | - Hsiao-Chun Hung
- Department of Archaeology and Natural History, Australian National University, Canberra, Australia.
| |
Collapse
|
13
|
Kitada S, Nakamichi R, Kishino H. Understanding population structure in an evolutionary context: population-specific FST and pairwise FST. G3-GENES GENOMES GENETICS 2021; 11:6364900. [PMID: 34549777 PMCID: PMC8527463 DOI: 10.1093/g3journal/jkab316] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 08/27/2021] [Indexed: 01/04/2023]
Abstract
Populations are shaped by their history. It is crucial to interpret population structure in an evolutionary context. Pairwise FST measures population structure, whereas population-specific FST measures deviation from the ancestral population. To understand the current population structure and a population’s history of range expansion, we propose a representation method that overlays population-specific FST estimates on a sampling location map, and on an unrooted neighbor-joining tree and a multi-dimensional scaling plot inferred from a pairwise FST distance matrix. We examined the usefulness of our procedure using simulations that mimicked population colonization from an ancestral population and by analyzing published human, Atlantic cod, and wild poplar data. Our results demonstrated that population-specific FST values identify the source population and trace the evolutionary history of its derived populations. Conversely, pairwise FST values represent the current population structure. By integrating the results of both estimators, we obtained a new picture of the population structure that incorporates evolutionary history. The generalized least squares estimate of genome-wide population-specific FST indicated that the wild poplar population expanded its distribution to the north, where daylight hours are long in summer, to coastal areas with abundant rainfall, and to the south where summers are dry. Genomic data highlight the power of the bias-corrected moment estimators of FST, whether global, pairwise, or population-specific, that provide unbiased estimates of FST. All FST moment estimators described in this paper have reasonable processing times and are useful in population genomics studies.
Collapse
Affiliation(s)
- Shuichi Kitada
- Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | | | - Hirohisa Kishino
- Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan.,The Research Institute of Evolutionary Biology, Tokyo 138-0098, Japan
| |
Collapse
|
14
|
Ancient DNA and multimethod dating confirm the late arrival of anatomically modern humans in southern China. Proc Natl Acad Sci U S A 2021; 118:2019158118. [PMID: 33558418 DOI: 10.1073/pnas.2019158118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The expansion of anatomically modern humans (AMHs) from Africa around 65,000 to 45,000 y ago (ca. 65 to 45 ka) led to the establishment of present-day non-African populations. Some paleoanthropologists have argued that fossil discoveries from Huanglong, Zhiren, Luna, and Fuyan caves in southern China indicate one or more prior dispersals, perhaps as early as ca. 120 ka. We investigated the age of the human remains from three of these localities and two additional early AMH sites (Yangjiapo and Sanyou caves, Hubei) by combining ancient DNA (aDNA) analysis with a multimethod geological dating strategy. Although U-Th dating of capping flowstones suggested they lie within the range ca. 168 to 70 ka, analyses of aDNA and direct AMS 14C dating on human teeth from Fuyan and Yangjiapo caves showed they derive from the Holocene. OSL dating of sediments and AMS 14C analysis of mammal teeth and charcoal also demonstrated major discrepancies from the flowstone ages; the difference between them being an order of magnitude or more at most of these localities. Our work highlights the surprisingly complex depositional history recorded at these subtropical caves which involved one or more episodes of erosion and redeposition or intrusion as recently as the late Holocene. In light of our findings, the first appearance datum for AMHs in southern China should probably lie within the timeframe set by molecular data of ca. 50 to 45 ka.
Collapse
|
15
|
Elhaik E, Graur D. On the Unfounded Enthusiasm for Soft Selective Sweeps III: The Supervised Machine Learning Algorithm That Isn't. Genes (Basel) 2021; 12:genes12040527. [PMID: 33916341 PMCID: PMC8066263 DOI: 10.3390/genes12040527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/22/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
In the last 15 years or so, soft selective sweep mechanisms have been catapulted from a curiosity of little evolutionary importance to a ubiquitous mechanism claimed to explain most adaptive evolution and, in some cases, most evolution. This transformation was aided by a series of articles by Daniel Schrider and Andrew Kern. Within this series, a paper entitled “Soft sweeps are the dominant mode of adaptation in the human genome” (Schrider and Kern, Mol. Biol. Evolut. 2017, 34(8), 1863–1877) attracted a great deal of attention, in particular in conjunction with another paper (Kern and Hahn, Mol. Biol. Evolut. 2018, 35(6), 1366–1371), for purporting to discredit the Neutral Theory of Molecular Evolution (Kimura 1968). Here, we address an alleged novelty in Schrider and Kern’s paper, i.e., the claim that their study involved an artificial intelligence technique called supervised machine learning (SML). SML is predicated upon the existence of a training dataset in which the correspondence between the input and output is known empirically to be true. Curiously, Schrider and Kern did not possess a training dataset of genomic segments known a priori to have evolved either neutrally or through soft or hard selective sweeps. Thus, their claim of using SML is thoroughly and utterly misleading. In the absence of legitimate training datasets, Schrider and Kern used: (1) simulations that employ many manipulatable variables and (2) a system of data cherry-picking rivaling the worst excesses in the literature. These two factors, in addition to the lack of negative controls and the irreproducibility of their results due to incomplete methodological detail, lead us to conclude that all evolutionary inferences derived from so-called SML algorithms (e.g., S/HIC) should be taken with a huge shovel of salt.
Collapse
Affiliation(s)
- Eran Elhaik
- Department of Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden
- Correspondence:
| | - Dan Graur
- Department of Biology & Biochemistry, University of Houston, Science & Research Building 2, Suite #342, 3455 Cullen Bldv., Houston, TX 77204-5001, USA;
| |
Collapse
|
16
|
Vizzari MT, Benazzo A, Barbujani G, Ghirotto S. A Revised Model of Anatomically Modern Human Expansions Out of Africa through a Machine Learning Approximate Bayesian Computation Approach. Genes (Basel) 2020; 11:E1510. [PMID: 33339234 PMCID: PMC7766041 DOI: 10.3390/genes11121510] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 01/25/2023] Open
Abstract
There is a wide consensus in considering Africa as the birthplace of anatomically modern humans (AMH), but the dispersal pattern and the main routes followed by our ancestors to colonize the world are still matters of debate. It is still an open question whether AMH left Africa through a single process, dispersing almost simultaneously over Asia and Europe, or in two main waves, first through the Arab Peninsula into southern Asia and Australo-Melanesia, and later through a northern route crossing the Levant. The development of new methodologies for inferring population history and the availability of worldwide high-coverage whole-genome sequences did not resolve this debate. In this work, we test the two main out-of-Africa hypotheses through an Approximate Bayesian Computation approach, based on the Random-Forest algorithm. We evaluated the ability of the method to discriminate between the alternative models of AMH out-of-Africa, using simulated data. Once assessed that the models are distinguishable, we compared simulated data with real genomic variation, from modern and archaic populations. This analysis showed that a model of multiple dispersals is four-fold as likely as the alternative single-dispersal model. According to our estimates, the two dispersal processes may be placed, respectively, around 74,000 and around 46,000 years ago.
Collapse
Affiliation(s)
| | | | | | - Silvia Ghirotto
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (M.T.V.); (A.B.); (G.B.)
| |
Collapse
|
17
|
Loog L. Sometimes hidden but always there: the assumptions underlying genetic inference of demographic histories. Philos Trans R Soc Lond B Biol Sci 2020; 376:20190719. [PMID: 33250022 DOI: 10.1098/rstb.2019.0719] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Demographic processes directly affect patterns of genetic variation within contemporary populations as well as future generations, allowing for demographic inference from patterns of both present-day and past genetic variation. Advances in laboratory procedures, sequencing and genotyping technologies in the past decades have resulted in massive increases in high-quality genome-wide genetic data from present-day populations and allowed retrieval of genetic data from archaeological material, also known as ancient DNA. This has resulted in an explosion of work exploring past changes in population size, structure, continuity and movement. However, as genetic processes are highly stochastic, patterns of genetic variation only indirectly reflect demographic histories. As a result, past demographic processes need to be reconstructed using an inferential approach. This usually involves comparing observed patterns of variation with model expectations from theoretical population genetics. A large number of approaches have been developed based on different population genetic models that each come with assumptions about the data and underlying demography. In this article I review some of the key models and assumptions underlying the most commonly used approaches for past demographic inference and their consequences for our ability to link the inferred demographic processes to the archaeological and climate records. This article is part of the theme issue 'Cross-disciplinary approaches to prehistoric demography'.
Collapse
Affiliation(s)
- Liisa Loog
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| |
Collapse
|
18
|
Syncope in Malaysian populations. Clin Auton Res 2020; 30:101-103. [DOI: 10.1007/s10286-019-00663-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 12/25/2019] [Indexed: 10/25/2022]
|
19
|
Savell KRR. Evolvability in human postcranial traits across ecogeographic regions. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 172:110-122. [PMID: 31912894 DOI: 10.1002/ajpa.24004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/19/2019] [Accepted: 12/20/2019] [Indexed: 11/08/2022]
Abstract
OBJECTIVES Though recent quantitative genetic analyses have indicated that directional selection appears to be acting on limb lengths and measures of body size in modern humans, these studies assume equal evolvability across modern human groups. However, differences in trait covariance structure due to ancient migration patterns and/or selection may limit the evolvability of populations further from Africa. This study therefore explores patterns of human evolvability across ecogeographic regions. MATERIALS AND METHODS Mean evolvability, respondability, conditional evolvability, and autonomy were calculated from variance-covariance matrices of limb length and body size measures representing 14 human groups spanning four ecogeographic regions. Measures of evolvability were compared across groups and regions, and the minimum sample size, inaccuracy, and bias were calculated for each. RESULTS When compared between regions, humans demonstrate significant differences between indices of evolvability across regions. Despite the relatively recent evolution of modern humans, several measures of evolvability show a strong negative correlation with latitude across regions, demonstrating a reduction in genetic variance that is potentially reflective of human migration and/or response to selection. CONCLUSIONS These results demonstrate the importance of establishing patterns of evolvability prior to additional quantitative genetic analyses, and emphasize the influence of sample size on the accuracy of estimated evolvability measures. These findings also suggest that while modern human groups share similar covariance structures, there is evidence for emergent differentiation in evolvability and respondability between human groups across ecogeographic regions, further complicating our ability to apply results derived from modern human groups to ancient hominin lineages.
Collapse
|
20
|
Counting Oceanians of Non-European, Non-Asian Descent (ONENA) in the South Pacific to Make Them Count in Global Health. Trop Med Infect Dis 2019; 4:tropicalmed4030114. [PMID: 31405081 PMCID: PMC6789437 DOI: 10.3390/tropicalmed4030114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 07/30/2019] [Accepted: 08/06/2019] [Indexed: 01/07/2023] Open
Abstract
Several diseases and vulnerabilities associated with genetic or microbial factors are more frequent among populations of Oceanian, Non-European, Non-Asian descent (ONENA). ONENA are specific and have long been isolated geographically. To our knowledge, there are no published official, quantitative, aggregated data on the populations impacted by these excess vulnerabilities in Oceania. We searched official census reports for updated estimates of the total population for each of the Pacific Island Countries and Territories (including Australia) and the US State of Hawaii, privileging local official statistical or censual sources. We multiplied the most recent total population estimate by the cumulative percentage of the ONENA population as determined in official reports. Including Australia and the US State of Hawaii, Oceania counts 27 countries and territories, populated in 2016 by approximately 41 M inhabitants (17 M not counting Australia) among which approximately 12.5 M (11.6 M not counting Australia) consider themselves of entire or partial ONENA ancestry. Specific genetic and microbiome traits of ONENA may be unique and need further investigation to adjust risk estimates, risk prevention, diagnostic and therapeutic strategies, to the benefit of populations in the Pacific and beyond.
Collapse
|
21
|
Bradshaw CJA, Ulm S, Williams AN, Bird MI, Roberts RG, Jacobs Z, Laviano F, Weyrich LS, Friedrich T, Norman K, Saltré F. Minimum founding populations for the first peopling of Sahul. Nat Ecol Evol 2019; 3:1057-1063. [PMID: 31209287 DOI: 10.1038/s41559-019-0902-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 04/15/2019] [Indexed: 11/09/2022]
Abstract
The timing, context and nature of the first people to enter Sahul is still poorly understood owing to a fragmented archaeological record. However, quantifying the plausible demographic context of this founding population is essential to determine how and why the initial peopling of Sahul occurred. We developed a stochastic, age-structured model using demographic rates from hunter-gatherer societies, and relative carrying capacity hindcasted with LOVECLIM's net primary productivity for northern Sahul. We projected these populations to determine the resilience and minimum sizes required to avoid extinction. A census founding population of between 1,300 and 1,550 individuals was necessary to maintain a quasi-extinction threshold of ≲0.1. This minimum founding population could have arrived at a single point in time, or through multiple voyages of ≥130 people over ~700-900 years. This result shows that substantial population amalgamation in Sunda and Wallacea in Marine Isotope Stages 3-4 provided the conditions for the successful, large-scale and probably planned peopling of Sahul.
Collapse
Affiliation(s)
- Corey J A Bradshaw
- Global Ecology, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia. .,ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia.
| | - Sean Ulm
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia.,College of Arts, Society and Education, James Cook University, Cairns, Queensland, Australia
| | - Alan N Williams
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia.,Climate Change Research Centre, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia.,Extent Heritage Pty Ltd, Sydney, New South Wales, Australia
| | - Michael I Bird
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia.,College of Science and Engineering, James Cook University, Cairns, Queensland, Australia
| | - Richard G Roberts
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia.,Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Zenobia Jacobs
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia.,Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Fiona Laviano
- Global Ecology, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Laura S Weyrich
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia.,Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia
| | - Tobias Friedrich
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Kasih Norman
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia.,Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Frédérik Saltré
- Global Ecology, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia
| |
Collapse
|
22
|
Semenza JC, Ebi KL. Climate change impact on migration, travel, travel destinations and the tourism industry. J Travel Med 2019; 26:5445924. [PMID: 30976790 PMCID: PMC7107585 DOI: 10.1093/jtm/taz026] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/02/2019] [Accepted: 04/05/2019] [Indexed: 12/19/2022]
Abstract
Background: Climate change is not only increasing ambient temperature but also accelerating the frequency, duration and intensity of extreme weather and climate events, such as heavy precipitation and droughts, and causing sea level rise, which can lead to population displacement. Climate change-related reductions in land productivity and habitability and in food and water security can also interact with demographic, economic and social factors to increase migration. In addition to migration, climate change has also implications for travel and the risk of disease. This article discusses the impact of climate change on migration and travel with implications for public health practice. Methods: Literature review. Results: Migrants may be at increased risk of communicable and non-communicable diseases, due to factors in their country of origin and their country of destination or conditions that they experience during migration. Although migration has not been a significant driver of communicable disease outbreaks to date, public health authorities need to ensure that effective screening and vaccination programmes for priority communicable diseases are in place.Population growth coupled with socio-economic development is increasing travel and tourism, and advances in technology have increased global connectivity and reduced the time required to cover long distances. At the same time, as a result of climate change, many temperate regions, including high-income countries, are now suitable for vector-borne disease transmission. This is providing opportunities for importation of vectors and pathogens from endemic areas that can lead to cases or outbreaks of communicable diseases with which health professionals may be unfamiliar. Conclusion: Health systems need to be prepared for the potential population health consequences of migration, travel and tourism and the impact of climate change on these. Integrated surveillance, early detection of cases and other public health interventions are critical to protect population health and prevent and control communicabledisease outbreaks.
Collapse
Affiliation(s)
- Jan C Semenza
- Scientific Assessment Section, European Centre for Disease Prevention and Control (ECDC), Gustav III:s boulevard 40, Solna, Sweden
| | - Kristie L Ebi
- Department of Global Health, University of Washington, PO Box 354695, Suite 2330, Seattle, WA, USA
| |
Collapse
|
23
|
Abstract
Hominin evolution is characterized by progressive regional differentiation, as well as migration waves, leading to anatomically modern humans that are assumed to have emerged in Africa and spread over the whole world. Why or whether Africa was the source region of modern humans and what caused their spread remains subject of ongoing debate. We present a spatially explicit, stochastic numerical model that includes ongoing mutations, demic diffusion, assortative mating and migration waves. Diffusion and assortative mating alone result in a structured population with relatively homogeneous regions bound by sharp clines. The addition of migration waves results in a power-law distribution of wave areas: for every large wave, many more small waves are expected to occur. This suggests that one or more out-of-Africa migrations would probably have been accompanied by numerous smaller migration waves across the world. The migration waves are considered "spontaneous", as the current model excludes environmental or other extrinsic factors. Large waves preferentially emanate from the central areas of large, compact inhabited areas. During the Pleistocene, Africa was the largest such area most of the time, making Africa the statistically most likely origin of anatomically modern humans, without a need to invoke additional environmental or ecological drivers.
Collapse
|
24
|
Smith GM, Ruebens K, Gaudzinski-Windheuser S, Steele TE. Subsistence strategies throughout the African Middle Pleistocene: Faunal evidence for behavioral change and continuity across the Earlier to Middle Stone Age transition. J Hum Evol 2019; 127:1-20. [DOI: 10.1016/j.jhevol.2018.11.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 11/20/2018] [Accepted: 11/22/2018] [Indexed: 11/25/2022]
|
25
|
Chawla K, Kumar A, Shenoy VP, Chauhan DS, Sharma P. Genetic diversity of Mycobacterium tuberculosis in south coastal Karnataka, India, using spoligotyping. Indian J Med Res 2018; 147:278-286. [PMID: 29923517 PMCID: PMC6022373 DOI: 10.4103/ijmr.ijmr_2026_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Background & objectives: Despite high occurrence of tuberculosis in India very little information is available about the genetic diversity of Mycobacterium tuberculosis isolates prevailing in coastal Karnataka, India. Thus, the present study was undertaken to explore the genetic biodiversity of M. tuberculosis isolates prevailing in south coastal region of Karnataka (Udupi District), India. Methods: A total of 111 Mycobacterial isolates were cultured in Lowenstein Jensen (LJ) medium and after obtaining growth, DNA was extracted and spoligotyping was performed. SITVIT WEB database was used to locate families of spoligotypes. Results: On analyzing the hybridization results of all 111 isolates on SITVIT WEB database 57 (51.35%) isolates were clustered into 11 Spoligotype International Types (SIT). The largest cluster of 14 (12.61%) isolates was SIT-48 (EAI1-SOM), followed by SIT-1942 (CAS1-Delhi) with 11 isolates (9.9%) and SIT-11 with seven (6.30%). Moreover, 23 isolates (20.72%) had unique spoligotypes and 31 (27.92%) were orphans. Spotclust analysis revealed that majority (67%) of orphan isolates were variants of CAS (37%) and EAI-5 (34%). Interpretation & conclusions: The present study revealed high biodiversity among the circulating isolates of M. tuberculosis in this region with the presence of mixed genotypes earlier reported from north and south India along with certain new genotypes with unique SITs. The study highlights the need for further longitudinal studies to explore the genetic diversity and to understand the transmission dynamics of prevailing isolates.
Collapse
Affiliation(s)
- Kiran Chawla
- Department of Microbiology, Kasturba Medical College, MAHE, Manipal, India
| | - Ajay Kumar
- Department of Microbiology, Kasturba Medical College, MAHE, Manipal, India
| | | | - Devendra Singh Chauhan
- Department of Microbiology & Molecular Biology, ICMR-National JALMA Institute for Leprosy & other Mycobacterial Diseases, Agra, India
| | - Pragya Sharma
- Department of Microbiology & Molecular Biology, ICMR-National JALMA Institute for Leprosy & other Mycobacterial Diseases, Agra, India
| |
Collapse
|
26
|
Markova E, Smirnov N. Phenotypic diversity arising from a limited number of founders: a study of dental variation in laboratory colonies of collared lemmings,Dicrostonyx(Rodentia: Arvicolinae). Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly172] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Evgenia Markova
- Institute of Plant & Animal Ecology, Ural Branch, Russian Academy of Sciences, Ekaterinburg, Russia
| | - Nikolai Smirnov
- Institute of Plant & Animal Ecology, Ural Branch, Russian Academy of Sciences, Ekaterinburg, Russia
| |
Collapse
|
27
|
Abstract
In humans, patterns of cranial variation mirror genetic diversity globally, implicating population history as a key driver of cranial disparity. Here, we demonstrate that the magnitude of genetic diversity within 12 extant ape taxa explains a large proportion of cranial shape variation. Taxa that are more genetically diverse tend to be more cranially diverse also. Our results suggest that neutral evolutionary processes such as mutation, genetic drift, and gene flow are reflected in both genetic and cranial diversity in apes. This work provides a perspective on intraspecific cranial variation in apes which has important implications for interpreting selective and developmental pressures on the cranium and for understanding shape variation in fossil hominin crania. Natural selection, developmental constraint, and plasticity have all been invoked as explanations for intraspecific cranial variation in humans and apes. However, global patterns of human cranial variation are congruent with patterns of genetic variation, demonstrating that population history has influenced cranial variation in humans. Here we show that this finding is not unique to Homo sapiens but is also broadly evident across extant ape species. Specifically, taxa that exhibit greater intraspecific cranial shape variation also exhibit greater genetic diversity at neutral autosomal loci. Thus, cranial shape variation within hominoid taxa reflects the population history of each species. Our results suggest that neutral evolutionary processes such as mutation, gene flow, and genetic drift have played an important role in generating cranial variation within species. These findings are consistent with previous work on human cranial morphology and improve our understanding of the evolutionary processes that generate intraspecific cranial shape diversity within hominoids. This work has implications for the analysis of selective and developmental pressures on the cranium and for interpreting shape variation in fossil hominin crania.
Collapse
|
28
|
Abstract
The first decade of ancient genomics has revolutionized the study of human prehistory and evolution. We review new insights based on prehistoric modern human genomes, including greatly increased resolution of the timing and structure of the out-of-Africa expansion, the diversification of present-day non-African populations, and the earliest expansions of those populations into Eurasia and America. Prehistoric genomes now document population transformations on every inhabited continent—in particular the effect of agricultural expansions in Africa, Europe, and Oceania—and record a history of natural selection that shapes present-day phenotypic diversity. Despite these advances, much remains unknown, in particular about the genomic histories of Asia (the most populous continent) and Africa (the continent that contains the most genetic diversity). Ancient genomes from these and other regions, integrated with a growing understanding of the genomic basis of human phenotypic diversity, will be in focus during the next decade of research in the field.
Collapse
Affiliation(s)
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19103, USA
| |
Collapse
|
29
|
Who were the Nataruk people? Mandibular morphology among late Pleistocene and early Holocene fisher-forager populations of West Turkana (Kenya). J Hum Evol 2018; 121:235-253. [PMID: 29857967 DOI: 10.1016/j.jhevol.2018.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 01/27/2023]
Abstract
Africa is the birthplace of the species Homo sapiens, and Africans today are genetically more diverse than other populations of the world. However, the processes that underpinned the evolution of African populations remain largely obscure. Only a handful of late Pleistocene African fossils (∼50-12 Ka) are known, while the more numerous sites with human fossils of early Holocene age are patchily distributed. In particular, late Pleistocene and early Holocene human diversity in Eastern Africa remains little studied, precluding any analysis of the potential factors that shaped human diversity in the region, and more broadly throughout the continent. These periods include the Last Glacial Maximum (LGM), a moment of extreme aridity in Africa that caused the fragmentation of population ranges and localised extinctions, as well as the 'African Humid Period', a moment of abrupt climate change and enhanced connectivity throughout Africa. East Africa, with its range of environments, may have acted as a refugium during the LGM, and may have played a critical biogeographic role during the heterogene`ous environmental recovery that followed. This environmental context raises a number of questions about the relationships among early Holocene African populations, and about the role played by East Africa in shaping late hunter-gatherer biological diversity. Here, we describe eight mandibles from Nataruk, an early Holocene site (∼10 Ka) in West Turkana, offering the opportunity of exploring population diversity in Africa at the height of the 'African Humid Period'. We use 3D geometric morphometric techniques to analyze the phenotypic variation of a large mandibular sample. Our results show that (i) the Nataruk mandibles are most similar to other African hunter-fisher-gatherer populations, especially to the fossils from Lothagam, another West Turkana locality, and to other early Holocene fossils from the Central Rift Valley (Kenya); and (ii) a phylogenetic connection may have existed between these Eastern African populations and some Nile Valley and Maghrebian groups, who lived at a time when a Green Sahara may have allowed substantial contact, and potential gene flow, across a vast expanse of Northern and Eastern Africa.
Collapse
|
30
|
Royo JL, Valls J, Acemel RD, Gómez-Marin C, Pascual-Pons M, Lupiañez A, Gomez-Skarmeta JL, Fibla J. A common copy-number variant within SIRPB1 correlates with human Out-of-Africa migration after genetic drift correction. PLoS One 2018. [PMID: 29518122 PMCID: PMC5843225 DOI: 10.1371/journal.pone.0193614] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Previous reports have proposed that personality may have played a role on human Out-Of-Africa migration, pinpointing some genetic variants that were positively selected in the migrating populations. In this work, we discuss the role of a common copy-number variant within the SIRPB1 gene, recently associated with impulsive behavior, in the human Out-Of-Africa migration. With the analysis of the variant distribution across forty-two different populations, we found that the SIRPB1 haplotype containing duplicated allele significantly correlated with human migratory distance, being one of the few examples of positively selected loci found across the human world colonization. Circular Chromosome Conformation Capture (4C-seq) experiments from the SIRPB1 promoter revealed important 3D modifications in the locus depending on the presence or absence of the duplication variant. In addition, a 3’ enhancer showed neural activity in transgenic models, suggesting that the presence of the CNV may compromise the expression of SIRPB1 in the central nervous system, paving the way to construct a molecular explanation of the SIRPB1 variants role in human migration.
Collapse
Affiliation(s)
- Jose Luis Royo
- Department of Basic Medical Sciences, IRBlleida, University of Lleida, Lleida, Spain
- Department of Surgery, Biochemistry and Immunology, University of Malaga, Malaga, Spain
- * E-mail: (JLR); (JF)
| | - Joan Valls
- Biostatistics & Epidemiology Unit, IRBlleida, University of Lleida, Lleida, Spain
| | - Rafael D. Acemel
- Centro Andaluz de Biologia del Desarrollo, CSIC-Junta de Andalucia, Sevilla, Spain
| | - Carlos Gómez-Marin
- Centro Andaluz de Biologia del Desarrollo, CSIC-Junta de Andalucia, Sevilla, Spain
| | - Mariona Pascual-Pons
- Department of Basic Medical Sciences, IRBlleida, University of Lleida, Lleida, Spain
| | - Arantxa Lupiañez
- Department of Basic Medical Sciences, IRBlleida, University of Lleida, Lleida, Spain
| | | | - Joan Fibla
- Department of Basic Medical Sciences, IRBlleida, University of Lleida, Lleida, Spain
- * E-mail: (JLR); (JF)
| |
Collapse
|
31
|
Hohl DM, Bezus B, Ratowiecki J, Catanesi CI. Genetic and phenotypic variability of iris color in Buenos Aires population. Genet Mol Biol 2018; 41:50-58. [PMID: 29658972 PMCID: PMC5901501 DOI: 10.1590/1678-4685-gmb-2017-0175] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/31/2017] [Indexed: 11/21/2022] Open
Abstract
The aim of this work was to describe the phenotypic and genotypic variability related to iris color for the population of Buenos Aires province (Argentina), and to assess the usefulness of current methods of analysis for this country. We studied five Single Nucleotide Polymorphisms (SNPs) included in the IrisPlex kit, in 118 individuals, and we quantified eye color with Digital Iris Analysis Tool. The markers fit Hardy-Weinberg equilibrium for the whole sample, but not for rs12913832 within the group of brown eyes (LR=8.429; p=0.004). We found a remarkable association of HERC2 rs12913832 GG with blue color (p < 0.01) but the other markers did not show any association with iris color. The results for the Buenos Aires population differ from those of other populations of the world for these polymorphisms (p < 0,01). The differences we found might respond to the admixed ethnic composition of Argentina; therefore, methods of analysis used in European populations should be carefully applied when studying the population of Argentina. These findings reaffirm the importance of this investigation in the Argentinian population for people identification based on iris color.
Collapse
Affiliation(s)
- Diana María Hohl
- Laboratorio de Diversidad Genética, Instituto Multidisciplinario de Biología Celular IMBICE (CONICET-UNLP-CIC), La Plata, Buenos Aires, Argentina.,Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Brenda Bezus
- Laboratorio de Diversidad Genética, Instituto Multidisciplinario de Biología Celular IMBICE (CONICET-UNLP-CIC), La Plata, Buenos Aires, Argentina
| | - Julia Ratowiecki
- Centro de Estudios Médicos e Investigaciones Clínicas CEMIC CONICET, Buenos Aires, Argentina
| | - Cecilia Inés Catanesi
- Laboratorio de Diversidad Genética, Instituto Multidisciplinario de Biología Celular IMBICE (CONICET-UNLP-CIC), La Plata, Buenos Aires, Argentina.,Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| |
Collapse
|
32
|
Mekonnen E, Bekele E, Stein CM. Novel polymorphisms in TICAM2 and NOD1 associated with tuberculosis progression phenotypes in Ethiopian populations. Glob Health Epidemiol Genom 2018; 3:e1. [PMID: 29868226 PMCID: PMC5870410 DOI: 10.1017/gheg.2017.17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 12/04/2017] [Accepted: 12/08/2017] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Infection by Mycobacterium tuberculosis (Mtb) is a necessary but not sufficient cause for tuberculosis (TB). Although numerous studies suggest human genetic variation may influence TB pathogenesis, there is a conspicuous lack of replication, likely due to imprecise phenotype definition. We aimed to replicate novel findings from a Ugandan cohort in Ethiopian populations. METHOD We ascertained TB cases and household controls (n = 292) from three different ethnic groups. Latent Mtb infection was determined using Quantiferon to develop reliable TB progression phenotypes. We sequenced exonic regions of TICAM2 and NOD1. RESULT Significant novel associations were observed between two variants in NOD1 and TB: rs751770147 [unadjusted p = 7.28 × 10-5] and chr7:30477156(T), a novel variant, [unadjusted p = 1.04 × 10-4]. Two SNPs in TICAM2 were nominally associated with TB, including rs2288384 [unadjusted p = 0.003]. Haplotype-based association tests supported the SNP-based results. CONCLUSION We replicated the association of TICAM2 and NOD1 with TB and identified novel genetic associations with TB in Ethiopian populations.
Collapse
Affiliation(s)
- E. Mekonnen
- Microbial, Cellular, Molecular Biology Department, Addis Ababa University, P.O.Box:17087, Addis Ababa, Ethiopia
- Health Biotechnology Department, Institute of Biotechnology, Addis Ababa University, P.O.Box:17087, Addis Ababa, Ethiopia
| | - E. Bekele
- Microbial, Cellular, Molecular Biology Department, Addis Ababa University, Ethiopia
| | - C. M. Stein
- Department of Population & Quantitative Health Sciences, Center for Proteomics & Bioinformatics, and Tuberculosis Research Unit, Case Western Reserve University, USA
| |
Collapse
|
33
|
Reyes-Centeno H, Rathmann H, Hanihara T, Harvati K. Testing Modern Human Out-of-Africa Dispersal Models Using Dental Nonmetric Data. CURRENT ANTHROPOLOGY 2017. [DOI: 10.1086/694423] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
34
|
Tammone MN, Pardiñas UFJ, Lacey EA. Contrasting patterns of Holocene genetic variation in two parapatric species of Ctenomys from Northern Patagonia, Argentina. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Mauro N Tammone
- Instituto de Diversidad y Evolución Austral (IDEAus-CONICET), Argentina
- Programa de Estudios Aplicados a la Conservación del Parque Nacional Nahuel Huapi (CENAC-PNNH, CONICET), Argentina
| | | | - Eileen A Lacey
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, USA
| |
Collapse
|
35
|
Pimenta J, Lopes AM, Comas D, Amorim A, Arenas M. Evaluating the Neolithic Expansion at Both Shores of the Mediterranean Sea. Mol Biol Evol 2017; 34:3232-3242. [DOI: 10.1093/molbev/msx256] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
|
36
|
Walsh S, Chaitanya L, Breslin K, Muralidharan C, Bronikowska A, Pospiech E, Koller J, Kovatsi L, Wollstein A, Branicki W, Liu F, Kayser M. Global skin colour prediction from DNA. Hum Genet 2017; 136:847-863. [PMID: 28500464 PMCID: PMC5487854 DOI: 10.1007/s00439-017-1808-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/03/2017] [Indexed: 12/14/2022]
Abstract
Human skin colour is highly heritable and externally visible with relevance in medical, forensic, and anthropological genetics. Although eye and hair colour can already be predicted with high accuracies from small sets of carefully selected DNA markers, knowledge about the genetic predictability of skin colour is limited. Here, we investigate the skin colour predictive value of 77 single-nucleotide polymorphisms (SNPs) from 37 genetic loci previously associated with human pigmentation using 2025 individuals from 31 global populations. We identified a minimal set of 36 highly informative skin colour predictive SNPs and developed a statistical prediction model capable of skin colour prediction on a global scale. Average cross-validated prediction accuracies expressed as area under the receiver-operating characteristic curve (AUC) ± standard deviation were 0.97 ± 0.02 for Light, 0.83 ± 0.11 for Dark, and 0.96 ± 0.03 for Dark-Black. When using a 5-category, this resulted in 0.74 ± 0.05 for Very Pale, 0.72 ± 0.03 for Pale, 0.73 ± 0.03 for Intermediate, 0.87±0.1 for Dark, and 0.97 ± 0.03 for Dark-Black. A comparative analysis in 194 independent samples from 17 populations demonstrated that our model outperformed a previously proposed 10-SNP-classifier approach with AUCs rising from 0.79 to 0.82 for White, comparable at the intermediate level of 0.63 and 0.62, respectively, and a large increase from 0.64 to 0.92 for Black. Overall, this study demonstrates that the chosen DNA markers and prediction model, particularly the 5-category level; allow skin colour predictions within and between continental regions for the first time, which will serve as a valuable resource for future applications in forensic and anthropologic genetics.
Collapse
Affiliation(s)
- Susan Walsh
- Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, IN, USA.
| | - Lakshmi Chaitanya
- Department of Genetic Identification, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Krystal Breslin
- Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, IN, USA
| | - Charanya Muralidharan
- Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, IN, USA
| | - Agnieszka Bronikowska
- Department of Dermatology, Collegium Medicum of the Jagiellonian University, Kraków, Poland
| | - Ewelina Pospiech
- Faculty of Biology and Earth Sciences, Institute of Zoology, Jagiellonian University, Kraków, Poland
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Julia Koller
- Department of Genetic Identification, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Leda Kovatsi
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Andreas Wollstein
- Section of Evolutionary Biology, Department of Biology II, University of Munich LMU, Planegg-Martinsried, Germany
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Fan Liu
- Department of Genetic Identification, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands.
| |
Collapse
|
37
|
β-Thalassemia Distribution in the Old World: an Ancient Disease Seen from a Historical Standpoint. Mediterr J Hematol Infect Dis 2017; 9:e2017018. [PMID: 28293406 PMCID: PMC5333734 DOI: 10.4084/mjhid.2017.018] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 02/05/2017] [Indexed: 11/12/2022] Open
Abstract
Background Haemoglobinopathies constitute the commonest recessive monogenic disorders worldwide, and the treatment of affected individuals presents a substantial global disease burden. β-thalassaemia is characterised by the reduced synthesis (β+) or absence (βo) of the β-globin chains in the HbA molecule, resulting in accumulation of excess unbound α-globin chains that precipitate in erythroid precursors in the bone marrow and in the mature erythrocytes, leading to ineffective erythropoiesis and peripheral haemolysis. Approximately 1.5% of the global population are heterozygotes (carriers) of the β-thalassemias; there is a high incidence in populations from the Mediterranean basin, throughout the Middle East, the Indian subcontinent, Southeast Asia, and Melanesia to the Pacific Islands. Aim The principal aim of this paper is to review, from a historical standpoint, our knowledge about an ancient disease, the β-thalassemias, and in particular, when, how and in what way β-thalassemia spread worldwide to reach such high incidences in certain populations. Results Mutations involving the β-globin gene are the most common cause of genetic disorders in humans. To date, more than 350 β-thalassaemia mutations have been reported. Considering the current distribution of β- thalassemia, the wide diversity of mutations and the small number of specific mutations in individual populations, it seems unlikely that β-thalassemia originated in a single place and time. Conclusions Various processes are known to determine the frequency of genetic disease in human populations. However, it is almost impossible to decide to what extent each process is responsible for the presence of a particular genetic disease. The wide spectrum of β-thalassemia mutations could well be explained by looking at their geographical distribution, the history of malaria, wars, invasions, mass migrations, consanguinity, and settlements. An analysis of the distribution of the molecular spectrum of haemoglobinopathies allows for the development and improvement of diagnostic tests and management of these disorders.
Collapse
|
38
|
Genetic polymorphism and evolutionary differentiation of Eastern Chinese Han: a comprehensive and comparative analysis on KIRs. Sci Rep 2017; 7:42486. [PMID: 28205529 PMCID: PMC5311978 DOI: 10.1038/srep42486] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 01/10/2017] [Indexed: 11/23/2022] Open
Abstract
Killer cell immunoglobulin-like receptor genes, namely KIRs, cluster together within the 160 kb genomic DNA region. In this study, we used PCR-SSP approach and successfully identified the genotype of 17 KIR genes in 123 independent healthy donors residing in the Jiangsu province, China. All individuals were positive at the 7 genes. The observed carrier gene frequencies (OFs) of remaining 10 KIRs ranged from 14.63% (KIR2DS3) to 95.93% (KIR3DL1). We found 27 distinct genotypes excluding KIR1D. The most frequent occurred in 63 individuals (51.22%). The linkage disequilibrium analysis signified 29 positive and 6 negative relations in 45 pairwise comparisons. To study population differentiation, we drew a Heatmap based on the data of KIRs from 59 populations and conducted Hierarchical Clustering by Euclidean distances. We next validated our results by estimating pairwise DA distances and illustrating a Neighbor-Joining tree, as well as a MDS plot covering 3 additional Chinese Han groups. The phylogenetic reconstruction and cluster analysis strongly indicated a genetically close relationship between Eastern and Jilin Hans. In conclusion, the present study provided a meritorious resource of KIR genotyping for population genetics, and could be helpful to uncover the genetic mechanism of KIRs in immune disease in the future.
Collapse
|
39
|
Sugden LA, Ramachandran S. Integrating the signatures of demic expansion and archaic introgression in studies of human population genomics. Curr Opin Genet Dev 2016; 41:140-149. [PMID: 27743539 DOI: 10.1016/j.gde.2016.09.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/19/2016] [Accepted: 09/23/2016] [Indexed: 12/12/2022]
Abstract
Human population genomic studies have repeatedly observed a decrease in heterozygosity and an increase in linkage disequilibrium with geographic distance from Africa. While multiple demographic models can generate these patterns, many studies invoke the serial founder effect model, in which populations expand from a single origin and each new population's founders represent a subset of genetic variation in the previous population. The model assumes no admixture with archaic hominins, however, recent studies have identified loci in Homo sapiens bearing signatures of archaic introgression. These results appear to contradict the validity of analyses invoking the serial founder effect model, but we show these two perspectives are compatible. We also propose using the serial founder effect model as a null model for determining the signature of archaic admixture in modern human genomes at different geographic and genomic scales.
Collapse
Affiliation(s)
- Lauren Alpert Sugden
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA; Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
| | - Sohini Ramachandran
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA; Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA.
| |
Collapse
|
40
|
Reconstructing Demography and Social Behavior During the Neolithic Expansion from Genomic Diversity Across Island Southeast Asia. Genetics 2016; 204:1495-1506. [PMID: 27683274 PMCID: PMC5161281 DOI: 10.1534/genetics.116.191379] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 09/16/2016] [Indexed: 11/18/2022] Open
Abstract
Archaeology, linguistics, and increasingly genetics are clarifying how populations moved from mainland Asia, through Island Southeast Asia, and out into the Pacific during the farming revolution. Yet key features of this process remain poorly understood, particularly how social behaviors intersected with demographic drivers to create the patterns of genomic diversity observed across Island Southeast Asia today. Such questions are ripe for computer modeling. Here, we construct an agent-based model to simulate human mobility across Island Southeast Asia from the Neolithic period to the present, with a special focus on interactions between individuals with Asian, Papuan, and mixed Asian-Papuan ancestry. Incorporating key features of the region, including its complex geography (islands and sea), demographic drivers (fecundity and migration), and social behaviors (marriage preferences), the model simultaneously tracks a full suite of genomic markers (autosomes, X chromosome, mitochondrial DNA, and Y chromosome). Using Bayesian inference, model parameters were determined that produce simulations that closely resemble the admixture profiles of 2299 individuals from 84 populations across Island Southeast Asia. The results highlight that greater propensity to migrate and elevated birth rates are related drivers behind the expansion of individuals with Asian ancestry relative to individuals with Papuan ancestry, that offspring preferentially resulted from marriages between Asian women and Papuan men, and that in contrast to current thinking, individuals with Asian ancestry were likely distributed across large parts of western Island Southeast Asia before the Neolithic expansion.
Collapse
|
41
|
Abstract
The magnitude of genetic diversity within human populations varies in a way that reflects the sequence of migrations by which people spread throughout the world. Beyond its use in human evolutionary genetics, worldwide variation in genetic diversity sometimes can interact with social processes to produce differences among populations in their relationship to modern societal problems. We review the consequences of genetic diversity differences in the settings of familial identification in forensic genetic testing, match probabilities in bone marrow transplantation, and representation in genome-wide association studies of disease. In each of these three cases, the contribution of genetic diversity to social differences follows from population-genetic principles. For a fourth setting that is not similarly grounded, we reanalyze with expanded genetic data a report that genetic diversity differences influence global patterns of human economic development, finding no support for the claim. The four examples describe a limit to the importance of genetic diversity for explaining societal differences while illustrating a distinction that certain biologically based scenarios do require consideration of genetic diversity for solving problems to which populations have been differentially predisposed by the unique history of human migrations.
Collapse
|
42
|
López S, van Dorp L, Hellenthal G. Human Dispersal Out of Africa: A Lasting Debate. Evol Bioinform Online 2016; 11:57-68. [PMID: 27127403 PMCID: PMC4844272 DOI: 10.4137/ebo.s33489] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 02/21/2016] [Accepted: 02/21/2016] [Indexed: 01/01/2023] Open
Abstract
Unraveling the first migrations of anatomically modern humans out of Africa has invoked great interest among researchers from a wide range of disciplines. Available fossil, archeological, and climatic data offer many hypotheses, and as such genetics, with the advent of genome-wide genotyping and sequencing techniques and an increase in the availability of ancient samples, offers another important tool for testing theories relating to our own history. In this review, we report the ongoing debates regarding how and when our ancestors left Africa, how many waves of dispersal there were and what geographical routes were taken. We explore the validity of each, using current genetic literature coupled with some of the key archeological findings.
Collapse
Affiliation(s)
- Saioa López
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Lucy van Dorp
- Department of Genetics, Evolution and Environment, University College London, London, UK
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, UK
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment, University College London, London, UK
| |
Collapse
|
43
|
Galland M, Friess M. A three-dimensional geometric morphometrics view of the cranial shape variation and population history in the New World. Am J Hum Biol 2016; 28:646-61. [PMID: 26924543 DOI: 10.1002/ajhb.22845] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 11/25/2015] [Accepted: 01/30/2016] [Indexed: 01/10/2023] Open
Abstract
OBJECTIVES Craniofacial variation in past and present Amerindians has been attributed to the effect of multiple founder events, or to one major migration followed by in situ differentiation and possibly recurrent contacts among Circum-Arctic groups. Our study aims to: (i) detect morphological differences that may indicate several migrations; (ii) test for the presence of genetic isolation; and (iii) test the correlation between shape data and competing settlement hypotheses by taking into account geography, chronology, climate effects, the presence of genetic isolation and recurrent gene flow. METHODS We analyzed a large sample of three-dimensional (3D) cranial surface scans (803 specimens) including past and modern groups from America and Australasia. Shape variation was investigated using geometric morphometrics. Differential external gene flow was evaluated by applying genetic concepts to morphometric data (Relethford-Blangero approach). Settlement hypotheses were tested using a matrix correlation approach (Mantel tests). RESULTS Our results highlight the strong dichotomy between Circum-Arctic and continental Amerindians as well as the impact of climate adaptation, and possibly recurrent gene flow in the Circum-Arctic area. There is also evidence for the impact of genetic isolation on phenetic variation in Baja California. Several settlement hypotheses are correlated with our data. CONCLUSIONS The three approaches used in this study highlight the importance of local processes especially in Baja California, and caution against the use of overly simplistic models when searching for the number of migration events. The results stress the complexity of the settlement of the Americas as well as the mosaic nature of the processes involved in this process. Am. J. Hum. Biol. 28:646-661, 2016. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Manon Galland
- School of Archaeology and Earth Institute, University College Dublin, Dublin, Ireland. .,Département Hommes, Natures, Sociétés & UMR 7206, Muséum national d'Histoire naturelle, Paris, France.
| | - Martin Friess
- Département Hommes, Natures, Sociétés & UMR 7206, Muséum national d'Histoire naturelle, Paris, France
| |
Collapse
|
44
|
Dahdouh A, Taleb M, Blecha L, Benyamina A. Genetics and psychotic disorders: A fresh look at consanguinity. Eur J Med Genet 2015; 59:104-10. [PMID: 26721321 DOI: 10.1016/j.ejmg.2015.12.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 12/20/2015] [Indexed: 10/22/2022]
Abstract
Consanguineous unions refer to marriages between related individuals who share a common ancestor. These unions are still commonplace in certain regions of the world such as the southern coast of the Mediterranean, throughout the Middle East and South-East Asia. According to available data, couples of second cousins or closer and their offspring currently represent 10.4% of the world's population, thus resulting in increased frequencies of autosomal recessive disorders. Furthermore, consanguinity may be implicated in the increased frequency of multifactorial pathologies such as mental disorders. The few existing epidemiological studies in consanguineous and/or geographically isolated populations confirm that there is a significant association between consanguinity and mental disorders and a higher risk of schizophrenia or bipolar disorders among offspring from consanguineous couples. There exists a strong and complex genetic component in the predisposition to psychotic disorders that has been confirmed in numerous studies. However, the genetic basis of these disorders remains poorly understood. GWAS studies (Genome Wide Association Studies) over the past 10 years have identified a few weak associations, thus refuting the "common diseases-common variants" hypothesis. A model implicating numerous rare variants has been supported by the recent discovery of CNVs (Copy Number Variants) and their statistically significant association with psychiatric disorders such as schizophrenia, bipolar disorders and autism. The study of consanguineous families may contribute to identifying rare variants in homogenous populations who have conserved certain alleles. Major developments in molecular biology techniques would facilitate these studies as well as contributing to identifying major genes. These results emphasize the need for genetic counseling in high-risk communities and the importance of implementing preventive actions and raising awareness concerning the risk of consanguineous unions.
Collapse
Affiliation(s)
| | - Mohammed Taleb
- Pavillon Calmette, 5 rue du DR Burnet, 27200, Vernon, France.
| | - Lisa Blecha
- Department of Psychiatry and Addictology, Paris-Sud University Hospital (AP-HP), U1178 Inserm, 94804, Villejuif Cedex, France
| | - Amine Benyamina
- Department of Psychiatry and Addictology, Paris-Sud University Hospital (AP-HP), U1178 Inserm, 94804, Villejuif Cedex, France.
| |
Collapse
|
45
|
Alves I, Arenas M, Currat M, Sramkova Hanulova A, Sousa VC, Ray N, Excoffier L. Long-Distance Dispersal Shaped Patterns of Human Genetic Diversity in Eurasia. Mol Biol Evol 2015; 33:946-58. [PMID: 26637555 PMCID: PMC4776706 DOI: 10.1093/molbev/msv332] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Most previous attempts at reconstructing the past history of human populations did not explicitly take geography into account or considered very simple scenarios of migration and ignored environmental information. However, it is likely that the last glacial maximum (LGM) affected the demography and the range of many species, including our own. Moreover, long-distance dispersal (LDD) may have been an important component of human migrations, allowing fast colonization of new territories and preserving high levels of genetic diversity. Here, we use a high-quality microsatellite data set genotyped in 22 populations to estimate the posterior probabilities of several scenarios for the settlement of the Old World by modern humans. We considered models ranging from a simple spatial expansion to others including LDD and a LGM-induced range contraction, as well as Neolithic demographic expansions. We find that scenarios with LDD are much better supported by data than models without LDD. Nevertheless, we show evidence that LDD events to empty habitats were strongly prevented during the settlement of Eurasia. This unexpected absence of LDD ahead of the colonization wave front could have been caused by an Allee effect, either due to intrinsic causes such as an inbreeding depression built during the expansion or due to extrinsic causes such as direct competition with archaic humans. Overall, our results suggest only a relatively limited effect of the LGM contraction on current patterns of human diversity. This is in clear contrast with the major role of LDD migrations, which have potentially contributed to the intermingled genetic structure of Eurasian populations.
Collapse
Affiliation(s)
- Isabel Alves
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland Population and Conservation Genetics Group, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Miguel Arenas
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Mathias Currat
- Anthropology, Genetics and Peopling History Lab, Department of Genetics & Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - Anna Sramkova Hanulova
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Vitor C Sousa
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicolas Ray
- EnviroSPACE Lab, Institute for Environmental Sciences, University of Geneva, Geneva, Switzerland
| | - Laurent Excoffier
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland
| |
Collapse
|
46
|
Reyes-Centeno H, Hubbe M, Hanihara T, Stringer C, Harvati K. Testing modern human out-of-Africa dispersal models and implications for modern human origins. J Hum Evol 2015; 87:95-106. [DOI: 10.1016/j.jhevol.2015.06.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 03/02/2015] [Accepted: 06/14/2015] [Indexed: 11/26/2022]
|
47
|
Frydman GH, Davis N, Beck PL, Fox JG. Helicobacter pylori Eradication in Patients with Immune Thrombocytopenic Purpura: A Review and the Role of Biogeography. Helicobacter 2015; 20:239-51. [PMID: 25728540 PMCID: PMC4506733 DOI: 10.1111/hel.12200] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Idiopathic thrombocytopenic purpura (ITP) is typically a diagnosis of exclusion, assigned by clinicians after ruling out other identifiable etiologies. Since a report by Gasbarrini et al. in 1998, an accumulating body of evidence has proposed a pathophysiological link between ITP and chronic Helicobacter pylori (H. pylori) infection. Clinical reports have described a spontaneous resolution of ITP symptoms in about 50% of chronic ITP patients following empirical treatment of H. pylori infection, but response appears to be geography dependent. Studies have also documented that ITP patients in East Asian countries are more likely to express positive antibody titers against H. pylori-specific cytotoxic-associated gene A (CagA), a virulence factor that is associated with an increased risk for gastric diseases including carcinoma. While a definitive mechanism by which H. pylori may induce thrombocytopenia remains elusive, proposed pathways include molecular mimicry of CagA by host autoantibodies against platelet surface glycoproteins, as well as perturbations in the phagocytic activity of monocytes. Traditional treatments of ITP have been largely empirical, involving the use of immunosuppressive agents and immunoglobulin therapy. However, based on the findings of clinical reports emerging over the past 20 years, health organizations around the world increasingly suggest the detection and eradication of H. pylori as a treatment for ITP. Elucidating the exact molecular mechanisms of platelet activation in H. pylori-positive ITP patients, while considering biogeographical differences in response rates, could offer insight into how best to use clinical H. pylori eradication to treat ITP, but will require well-designed studies to confirm the suggested causative relationship between bacterial infection and an autoimmune disease state.
Collapse
Affiliation(s)
- Galit H. Frydman
- Department of Biological Engineering, Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nick Davis
- Department of Biological Engineering, Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Paul L. Beck
- The Gastrointestinal Research Group, Division of Gastroenterology, University of Calgary, Calgary, AB, Canada
| | - James G. Fox
- Department of Biological Engineering, Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| |
Collapse
|
48
|
Singh J, Sankar MM, Kumar P, Couvin D, Rastogi N, Singh S. Genetic diversity and drug susceptibility profile of Mycobacterium tuberculosis isolated from different regions of India. J Infect 2015; 71:207-19. [PMID: 25934327 DOI: 10.1016/j.jinf.2015.04.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/04/2015] [Accepted: 04/21/2015] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Molecular genotyping profiles of Mycobacterium tuberculosis (MTB) provide a valuable insight into the evolution and transmission of the bacilli. Due to the lack of comprehensive national level data from India on this subject, we performed this study to determine the recent trends and distribution of various MTB lineages circulating in India. METHODS A total of 628 MTB isolates were obtained from North, West, South, Central and Eastern India. Spoligotyping and drug susceptibility testing was performed by using manufacturer's instructions. RESULTS Spoligotyping detected 102 distinct spoligo-patterns. A total of 536 (85.3%) isolates were distributed into 85 SITs which matched the pre-existing database, whereas 17 SITs were newly created for 34 (5.4%) isolates. Overall, CAS family genotype was predominant, comprising 222 (35.4%) isolates, followed by EAI in 152 (24.2%), Beijing in 108 (17.2%), Manu in 41 (6.5%), T in 30 (4.8%), H in 6 (0.9%), X in 3 (0.5%) and one (0.2%) each in Ural and AFRI. Drug susceptibility testing identified 134 (21.3%) isolates as multi drug resistant (MDR). CONCLUSIONS The CAS lineage had a pan India presence but EAI lineage was confined to southern parts of India. Beijing genotype of MTB was significantly associated (p-value <0.0001) with MDR.
Collapse
Affiliation(s)
- Jitendra Singh
- Division of Clinical Microbiology and Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Manimuthu Mani Sankar
- Division of Clinical Microbiology and Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Parveen Kumar
- Division of Clinical Microbiology and Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - David Couvin
- WHO Supranational TB Reference Laboratory, Institute Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Institute Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
| | - Sarman Singh
- Division of Clinical Microbiology and Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi, India.
| | | |
Collapse
|
49
|
Raghavan M, Steinrücken M, Harris K, Schiffels S, Rasmussen S, DeGiorgio M, Albrechtsen A, Valdiosera C, Ávila-Arcos MC, Malaspinas AS, Eriksson A, Moltke I, Metspalu M, Homburger JR, Wall J, Cornejo OE, Moreno-Mayar JV, Korneliussen TS, Pierre T, Rasmussen M, Campos PF, de Barros Damgaard P, Allentoft ME, Lindo J, Metspalu E, Rodríguez-Varela R, Mansilla J, Henrickson C, Seguin-Orlando A, Malmström H, Stafford T, Shringarpure SS, Moreno-Estrada A, Karmin M, Tambets K, Bergström A, Xue Y, Warmuth V, Friend AD, Singarayer J, Valdes P, Balloux F, Leboreiro I, Vera JL, Rangel-Villalobos H, Pettener D, Luiselli D, Davis LG, Heyer E, Zollikofer CPE, Ponce de León MS, Smith CI, Grimes V, Pike KA, Deal M, Fuller BT, Arriaza B, Standen V, Luz MF, Ricaut F, Guidon N, Osipova L, Voevoda MI, Posukh OL, Balanovsky O, Lavryashina M, Bogunov Y, Khusnutdinova E, Gubina M, Balanovska E, Fedorova S, Litvinov S, Malyarchuk B, Derenko M, Mosher MJ, Archer D, Cybulski J, Petzelt B, Mitchell J, Worl R, Norman PJ, Parham P, Kemp BM, Kivisild T, Tyler-Smith C, Sandhu MS, Crawford M, Villems R, Smith DG, Waters MR, Goebel T, Johnson JR, Malhi RS, Jakobsson M, Meltzer DJ, Manica A, Durbin R, Bustamante CD, Song YS, Nielsen R, Willerslev E. POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans. Science 2015. [PMID: 26198033 DOI: 10.1126/science.aab3884] [Citation(s) in RCA: 255] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative "Paleoamerican" relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.
Collapse
Affiliation(s)
- Maanasa Raghavan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Matthias Steinrücken
- Computer Science Division, University of California, Berkeley, CA 94720, USA.,Department of Statistics, University of California, Berkeley, CA 94720, USA.,Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Kelley Harris
- Department of Mathematics, University of California, Berkeley, CA 94720, USA
| | - Stephan Schiffels
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Simon Rasmussen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark
| | - Michael DeGiorgio
- Departments of Biology and Statistics, Pennsylvania State University, 502 Wartik Laboratory, University Park, PA 16802, USA
| | - Anders Albrechtsen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Cristina Valdiosera
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Department of Archaeology and History, La Trobe University, Melbourne, Victoria 3086, Australia
| | - María C Ávila-Arcos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA
| | - Anna-Sapfo Malaspinas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Anders Eriksson
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.,Integrative Systems Biology Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ida Moltke
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Mait Metspalu
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Julian R Homburger
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA
| | - Jeff Wall
- Institute for Human Genetics, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Omar E Cornejo
- School of Biological Sciences, Washington State University, PO Box 644236, Heald 429, Pullman, Washington 99164, USA
| | - J Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Thorfinn S Korneliussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Tracey Pierre
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal
| | - Peter de Barros Damgaard
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - John Lindo
- Department of Anthropology, University of Illinois at Urbana-Champaign, 607 S. Mathews Ave, Urbana, IL 61801, USA
| | - Ene Metspalu
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Ricardo Rodríguez-Varela
- Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humano, Madrid, Spain
| | - Josefina Mansilla
- Instituto Nacional de Antropología e Historia, Moneda 13, Centro, Cuauhtémoc, 06060 Mexico Mexico City, Mexico
| | - Celeste Henrickson
- University of Utah, Department of Anthropology, 270 S 1400 E, Salt Lake City, Utah 84112, USA
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Helena Malmström
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Thomas Stafford
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,AMS 14C Dating Centre, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus, Denmark
| | - Suyash S Shringarpure
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA
| | - Andrés Moreno-Estrada
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA.,Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, Mexico
| | - Monika Karmin
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Kristiina Tambets
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia
| | - Anders Bergström
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Vera Warmuth
- UCL Genetics Institute, Gower Street, London WC1E 6BT, UK.,Evolutionsbiologiskt Centrum, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Andrew D Friend
- Department of Geography, University of Cambridge, Downing Place, Cambridge CB2 3EN, UK
| | - Joy Singarayer
- Centre for Past Climate Change and Department of Meteorology, University of Reading, Earley Gate, PO Box 243, Reading, UK
| | - Paul Valdes
- School of Geographical Sciences, University Road, Clifton, Bristol BS8 1SS, UK
| | | | - Ilán Leboreiro
- Instituto Nacional de Antropología e Historia, Moneda 13, Centro, Cuauhtémoc, 06060 Mexico Mexico City, Mexico
| | - Jose Luis Vera
- Escuela Nacional de AntropologÍa e Historia, Periférico Sur y Zapote s/n. Colonia Isidro Fabela, Tlalpan, Isidro Fabela, 14030 Mexico City, Mexico
| | | | - Davide Pettener
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Donata Luiselli
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Loren G Davis
- Department of Anthropology, Oregon State University, 238 Waldo Hall, Corvallis, OR, 97331 USA
| | - Evelyne Heyer
- Museum National d'Histoire Naturelle, CNRS, Université Paris 7 Diderot, Sorbonne Paris Cité, Sorbonne Universités, Unité Eco-Anthropologie et Ethnobiologie (UMR7206), Paris, France
| | - Christoph P E Zollikofer
- Anthropological Institute and Museum, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Marcia S Ponce de León
- Anthropological Institute and Museum, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Colin I Smith
- Department of Archaeology and History, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Vaughan Grimes
- Department of Archaeology, Memorial University, Queen's College, 210 Prince Philip Drive, St. John's, Newfoundland, A1C 5S7, Canada.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany
| | - Kelly-Anne Pike
- Department of Archaeology, Memorial University, Queen's College, 210 Prince Philip Drive, St. John's, Newfoundland, A1C 5S7, Canada
| | - Michael Deal
- Department of Archaeology, Memorial University, Queen's College, 210 Prince Philip Drive, St. John's, Newfoundland, A1C 5S7, Canada
| | - Benjamin T Fuller
- Department of Earth System Science, University of California, Irvine, Keck CCAMS Group, B321 Croul Hall, Irvine, California, 92697, USA
| | - Bernardo Arriaza
- Instituto de Alta Investigación, Universidad de Tarapacá, 18 de Septiembre 2222, Carsilla 6-D Arica, Chile
| | - Vivien Standen
- Departamento de Antropologia, Universidad de Tarapacá, 18 de Septiembre 2222. Casilla 6-D Arica, Chile
| | - Maria F Luz
- Fundação Museu do Homem Americano, Centro Cultural Sérgio Motta, Campestre, 64770-000 Sao Raimundo Nonato, Brazil
| | - Francois Ricaut
- Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, CNRS, Université de Toulouse, 31073 Toulouse, France
| | - Niede Guidon
- Fundação Museu do Homem Americano, Centro Cultural Sérgio Motta, Campestre, 64770-000 Sao Raimundo Nonato, Brazil
| | - Ludmila Osipova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia.,Novosibirsk State University, 2 Pirogova Str., 630090 Novosibirsk, Russia
| | - Mikhail I Voevoda
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia.,Institute of Internal Medicine, Siberian Branch of RAS, 175/1 ul. B. Bogatkova, Novosibirsk 630089, Russia.,Novosibirsk State University, Laboratory of Molecular Epidemiology and Bioinformatics, 630090 Novosibirsk, Russia
| | - Olga L Posukh
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia.,Novosibirsk State University, 2 Pirogova Str., 630090 Novosibirsk, Russia
| | - Oleg Balanovsky
- Vavilov Institute of General Genetics, Gubkina 3, 119333 Moscow, Russia.,Research Centre for Medical Genetics, Moskvorechie 1, 115478 Moscow, Russia
| | | | - Yuri Bogunov
- Vavilov Institute of General Genetics, Gubkina 3, 119333 Moscow, Russia
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Prospekt Oktyabrya 71, 450054 Ufa, Russia.,Department of Genetics and Fundamental Medicine, Bashkir State University, Zaki Validi 32, 450076 Ufa, Russia
| | - Marina Gubina
- Fundação Museu do Homem Americano, Centro Cultural Sérgio Motta, Campestre, 64770-000 Sao Raimundo Nonato, Brazil
| | - Elena Balanovska
- Research Centre for Medical Genetics, Moskvorechie 1, 115478 Moscow, Russia
| | - Sardana Fedorova
- Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Sergelyahskoe Shosse 4, 677010 Yakutsk, Russia.,Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, 677000 Yakutsk, Russia
| | - Sergey Litvinov
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Prospekt Oktyabrya 71, 450054 Ufa, Russia
| | - Boris Malyarchuk
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street 18, Magadan 685000, Russia
| | - Miroslava Derenko
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street 18, Magadan 685000, Russia
| | - M J Mosher
- Department of Anthropology, Western Washington University, Bellingham Washington 98225, USA
| | - David Archer
- Department of Anthropology, Northwest Community College, 353 Fifth Street, Prince Rupert, British Columbia V8J 3L6, Canada
| | - Jerome Cybulski
- Canadian Museum of History, 100 Rue Laurier, Gatineau, Quebec K1A 0M8, Canada.,University of Western Ontario, London, Ontario N6A 3K7, Canada.,Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Barbara Petzelt
- Metlakatla Treaty Office, PO Box 224, Prince Rupert, BC, Canada V8J 3P6
| | | | - Rosita Worl
- Sealaska Heritage Institute, 105 S. Seward Street, Juneau, Alaska 99801, USA
| | - Paul J Norman
- Department of Structural Biology, Stanford University School of Medicine, D100 Fairchild Science Building, Stanford, California 94305-5126, USA
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, D100 Fairchild Science Building, Stanford, California 94305-5126, USA
| | - Brian M Kemp
- School of Biological Sciences, Washington State University, PO Box 644236, Heald 429, Pullman, Washington 99164, USA.,Department of Anthropology, Washington State University, Pullman Washington 99163, USA
| | - Toomas Kivisild
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Division of Biological Anthropology, University of Cambridge, Henry Wellcome Building, Fitzwilliam Street, CB2 1QH, Cambridge, UK
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Manjinder S Sandhu
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.,Dept of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Michael Crawford
- Laboratory of Biological Anthropology, University of Kansas, 1415 Jayhawk Blvd., 622 Fraser Hall, Lawrence, Kansas 66045, USA
| | - Richard Villems
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - David Glenn Smith
- Molecular Anthropology Laboratory, 209 Young Hall, Department of Anthropology, University of California, One Shields Avenue, Davis, California 95616, USA
| | - Michael R Waters
- Center for the Study of the First Americans, Texas A&M University, College Station, Texas 77843-4352, USA.,Department of Anthropology, Texas A&M University, College Station, Texas 77843-4352, USA.,Department of Geography, Texas A&M University, College Station, Texas 77843-4352, USA
| | - Ted Goebel
- Center for the Study of the First Americans, Texas A&M University, College Station, Texas 77843-4352, USA
| | - John R Johnson
- Santa Barbara Museum of Natural History, 2559 Puesta del Sol, Santa Barbara, CA 93105, USA
| | - Ripan S Malhi
- Department of Anthropology, University of Illinois at Urbana-Champaign, 607 S. Mathews Ave, Urbana, IL 61801, USA.,Carle R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, USA
| | - Mattias Jakobsson
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - David J Meltzer
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Department of Anthropology, Southern Methodist University, Dallas, Texas 75275, USA
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Carlos D Bustamante
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, CA 94720, USA.,Department of Statistics, University of California, Berkeley, CA 94720, USA.,Department of Integrative Biology, University of California, 3060 Valley Life Sciences Bldg #3140, Berkeley, CA 94720, USA
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, 3060 Valley Life Sciences Bldg #3140, Berkeley, CA 94720, USA
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| |
Collapse
|
50
|
Betti L, Lycett SJ, von Cramon-Taubadel N, Pearson OM. Are human hands and feet affected by climate? A test of Allen's rule. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 158:132-40. [DOI: 10.1002/ajpa.22774] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 05/12/2015] [Accepted: 05/14/2015] [Indexed: 01/02/2023]
Affiliation(s)
- Lia Betti
- Centre for Research in Evolutionary and Environmental Anthropology, Department of Life Sciences, University of Roehampton; London SW15 4JD UK
| | - Stephen J. Lycett
- Department of Anthropology; University at Buffalo, SUNY; Buffalo NY 14261
| | | | - Osbjorn M. Pearson
- Department of Anthropology; University of New Mexico; Albuquerque NM 87131
| |
Collapse
|