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Li J, Teng W, Yu Y, Hou X, Shan Z. Linkage Analysis of the Chromosome 5q31-33 Region Identifies JAKMIP2 as a Risk Factor for Graves' Disease in the Chinese Han Population. Med Sci Monit 2019; 25:1439-1451. [PMID: 30796769 PMCID: PMC6397618 DOI: 10.12659/msm.911489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Background This study aimed to investigate susceptibility to Graves’s disease and the association with the 5q32–33.1 region on chromosome 5 in a Chinese Han population. Material/Methods Eighty Chinese Han multiplex families included first-degree and second-degree relatives with Graves’ disease. Eight microsatellite markers on chromosome 5 at the 5q32–33.1 region underwent linkage analysis and the association between the regions D5S1480–D5S2014 were studied. Results The maximal heterogeneity logarithm of the odds (HLOD) score of D5S2090 was 4.29 (α=0.42) and of D5S2014 was 4.01 (α=0.34). A nonparametric linkage (NPL) score of 3.14 (P<0.001) was found for D5S2014. The D5S1480–D5S2014 region on chromosome 5 was associated with Graves’ disease, with eight haplotype domains. There were significant differences in the sixth and eighth haplotype domains between patients with Graves’ disease compared with normal individuals. Tagging single nucleotide polymorphisms (SNPs) of the sixth and eighth haplotype domains showed that individuals with SNP62 (rs12653715 G/C) who were GG homozygous had a significantly increased risk of Graves’ disease compared GC heterozygous or CC homozygous individuals. The transmission disequilibrium test (TDT) indicated that SNP62 (rs12653715) and SNP63 (rs12653081) loci in the Janus kinase and microtubule interacting protein 2 (JAKMIP2) gene showed dominant transmission from heterozygous parents to the affected offspring, and SNPs in the secretoglobin family 3A member 2 (SCGB3A2) gene showed no transmission disequilibrium. The haplotype JAKMIP2-1 was identified as being particularly significant. Conclusions JAKMIP2 gene polymorphism require further study as potential risk factors for Graves’ disease in the Chinese Han population.
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Affiliation(s)
- Jia Li
- Department of Endocrinology and Metabolism, Instituite of Endocrinology, Liaoning Provincial Key Laboratory of Endocrine Diseases, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China (mainland).,Department of Endocrinology and Metabolism, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China (mainland)
| | - Weiping Teng
- Department of Endocrinology and Metabolism, Instituite of Endocrinology, Liaoning Provincial Key Laboratory of Endocrine Diseases, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China (mainland)
| | - Yang Yu
- Department of Endocrinology and Metabolism, Instituite of Endocrinology, Liaoning Provincial Key Laboratory of Endocrine Diseases, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China (mainland).,Department of Endocrinology and Metabolism, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China (mainland)
| | - Xin Hou
- Department of Endocrinology and Metabolism, Instituite of Endocrinology, Liaoning Provincial Key Laboratory of Endocrine Diseases, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China (mainland).,Department of Geriatric Endocrinology and Metabolism, The First Hospital of China Medical University, Shenyang, Liaoning, China (mainland)
| | - Zhongyan Shan
- Department of Endocrinology and Metabolism, Instituite of Endocrinology, Liaoning Provincial Key Laboratory of Endocrine Diseases, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China (mainland)
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Pigeyre M, Saqlain M, Turcotte M, Raja GK, Meyre D. Obesity genetics: insights from the Pakistani population. Obes Rev 2018; 19:364-380. [PMID: 29265593 DOI: 10.1111/obr.12644] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/10/2017] [Accepted: 10/15/2017] [Indexed: 01/26/2023]
Abstract
The Pakistani population is extensively diverse, indicating a genetic admixture of European and Central/West Asian migrants with indigenous South Asian gene pools. Pakistanis are organized in different ethnicities/castes based on cultural, linguistic and geographical origin. While Pakistan is facing a rapid nutritional transition, the rising prevalence of obesity is driving a growing burden of health complications and mortality. This represents a unique opportunity for the research community to study the interplay between obesogenic environmental changes and obesity predisposing genes in the time frame of one generation. This review recapitulates the ancestral origins of Pakistani population, the societal determinants of the rise in obesity and its governmental management. We describe the contribution of syndromic, monogenic non-syndromic and polygenic obesity genes identified in the Pakistani population. We then discuss the utility of gene identification approaches based on large consanguineous families and original gene × environment interaction study designs in discovering new obesity genes and causal pathways. Elucidation of the genetic basis of obesity in the Pakistani population may result in improved methods of obesity prevention and treatment globally.
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Affiliation(s)
- M Pigeyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada.,Department of Nutrition, CHRU Lille, University of Lille, Lille, France
| | - M Saqlain
- Department of Biochemistry, PMAS-Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan
| | - M Turcotte
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - G K Raja
- Department of Biochemistry, PMAS-Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan
| | - D Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
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Caldararo N. Denisovans, Melanesians, Europeans, and Neandertals: The Confusion of DNA Assumptions and the Biological Species Concept. J Mol Evol 2016; 83:78-87. [DOI: 10.1007/s00239-016-9755-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/30/2016] [Indexed: 10/21/2022]
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4
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Roseman CC. Random genetic drift, natural selection, and noise in human cranial evolution. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:582-92. [DOI: 10.1002/ajpa.22918] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/07/2015] [Accepted: 11/23/2015] [Indexed: 01/18/2023]
Affiliation(s)
- Charles C. Roseman
- Department of Cell Biology and Anatomy Cumming School of Medicine; University of Calgary; Hospital Drive NW. Calgary, AB T2N Canada
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5
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Hao Q, Wang L, Oldfield F, Guo Z. Extra-long interglacial in Northern Hemisphere during MISs 15-13 arising from limited extent of Arctic ice sheets in glacial MIS 14. Sci Rep 2015; 5:12103. [PMID: 26159304 PMCID: PMC4498323 DOI: 10.1038/srep12103] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 06/17/2015] [Indexed: 11/09/2022] Open
Abstract
Knowledge of the behavior of Northern Hemisphere (NH) ice sheets over the past million years is crucial for understanding the role of orbitally driven insolation changes on glacial/interglacial cycles. Here, based on the demonstrable link between changes in Chinese loess grain-size and NH ice-sheet extent, we use loess grain-size records to confirm that northern ice-sheets were restricted during marine oxygen isotope stage (MIS) 14. Thus, an unusually long NH interglacial climate of over 100 kyr persisted during MISs 15−13, much longer than expected from marine oxygen isotope records. Taking a global view of the paleoclimate records, MIS 14 inception seems to be a response to changes in Antarctic ice-sheets rather than to NH cooling. Orbital configuration in the two Polar regions shows that the onset of MIS 14 was forced by austral insolation changes, rather than by boreal summer insolation, as Milankovitch theory proposes. Our analysis of MIS 14 raises the possibility that southern insolation forcing may have played an important role in the inception of several other glacials. We suggest that the extra-long NH interglacial climate during MISs 15−13 provided favorable conditions for the second major dispersal episode of African hominins into Eurasia.
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Affiliation(s)
- Qingzhen Hao
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, P.O. Box 9825, Beijing 100029, China
| | - Luo Wang
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, P.O. Box 9825, Beijing 100029, China
| | - Frank Oldfield
- School of Environmental Sciences, University of Liverpool, Liverpool L69 7ZT, UK
| | - Zhengtang Guo
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, P.O. Box 9825, Beijing 100029, China
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Shi H, Pasaniuc B, Lange KL. A multivariate Bernoulli model to predict DNaseI hypersensitivity status from haplotype data. Bioinformatics 2015; 31:3514-21. [PMID: 26139633 DOI: 10.1093/bioinformatics/btv397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 06/24/2015] [Indexed: 01/02/2023] Open
Abstract
MOTIVATION Haplotype models enjoy a wide range of applications in population inference and disease gene discovery. The hidden Markov models traditionally used for haplotypes are hindered by the dubious assumption that dependencies occur only between consecutive pairs of variants. In this article, we apply the multivariate Bernoulli (MVB) distribution to model haplotype data. The MVB distribution relies on interactions among all sets of variants, thus allowing for the detection and exploitation of long-range and higher-order interactions. We discuss penalized estimation and present an efficient algorithm for fitting sparse versions of the MVB distribution to haplotype data. Finally, we showcase the benefits of the MVB model in predicting DNaseI hypersensitivity (DH) status--an epigenetic mark describing chromatin accessibility--from population-scale haplotype data. RESULTS We fit the MVB model to real data from 59 individuals on whom both haplotypes and DH status in lymphoblastoid cell lines are publicly available. The model allows prediction of DH status from genetic data (prediction R2=0.12 in cross-validations). Comparisons of prediction under the MVB model with prediction under linear regression (best linear unbiased prediction) and logistic regression demonstrate that the MVB model achieves about 10% higher prediction R2 than the two competing methods in empirical data. AVAILABILITY AND IMPLEMENTATION Software implementing the method described can be downloaded at http://bogdan.bioinformatics.ucla.edu/software/. CONTACT shihuwenbo@ucla.edu or pasaniuc@ucla.edu.
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Affiliation(s)
- Huwenbo Shi
- Bioinformatics Interdepartmental Program, University of California, Los Angeles
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Department of Pathology and Laboratory Medicine, Department of Human Genetics and
| | - Kenneth L Lange
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Department of Human Genetics and Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90024, USA
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Gallagher A. Absolute and relative endocranial size in Neandertals and later Pleistocene Homo. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2014; 65:349-75. [PMID: 24954798 DOI: 10.1016/j.jchb.2014.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 02/12/2014] [Indexed: 10/25/2022]
Abstract
Eurasian Neandertals encompass the entire observed range of recent and fossil Homo sapiens in absolute, but not relative endocranial volume, and Neandertals attest an average EQ significantly lower than their Upper Pleistocene successors. While the cognitive, social, and evolutionary implications of this phenomenon have been emphasised, the statistical basis of a mean inference of EQ in the Neandertal hypodigm has not been appropriately demonstrated. A demonstrable male bias in the available postcranial, not cranial, series has skewed perceptions of Neandertal brain-to-body size scaling towards a rejection of the null hypothesis. A simple resolution to this problem is a concise assessment of paired associated covariates against a suitable recent human comparator series. Permutations of Fisher's z and Student's t statistics are valid metrics in tests of significance in single datum hypotheses. Bootstrapped single observation tests determined significance in body size, absolute and relative endocranial volume in Pleistocene archaic, early modern, and late Pleistocene H. sapiens. With respect to absolute ECV, all current Middle-Upper Pleistocene crania fall within the substantial recent Homo range. Nevertheless, simple indices derived from raw and modified data in normal and logarithmic space reveal that Western European Neandertal males approach the lower extremes of our observed size range in relative ECV, yet none exceed statistical significance. Results confirm that relative ECV/brain size in Neandertals was not significantly depressed relative to recent and fossil H. sapiens and this is consistent with a substantial body of data from living humans dismissing any simple correspondence of relative brain size with intelligence and, by extension, evolutionary success.
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Affiliation(s)
- Andrew Gallagher
- Centre for Anthropological Research (CAfR), University of Johannesburg, Auckland Park 2006, Johannesburg, South Africa.
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Hodgson JA, Mulligan CJ, Al-Meeri A, Raaum RL. Early back-to-Africa migration into the Horn of Africa. PLoS Genet 2014; 10:e1004393. [PMID: 24921250 PMCID: PMC4055572 DOI: 10.1371/journal.pgen.1004393] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 04/07/2014] [Indexed: 11/19/2022] Open
Abstract
Genetic studies have identified substantial non-African admixture in the Horn of Africa (HOA). In the most recent genomic studies, this non-African ancestry has been attributed to admixture with Middle Eastern populations during the last few thousand years. However, mitochondrial and Y chromosome data are suggestive of earlier episodes of admixture. To investigate this further, we generated new genome-wide SNP data for a Yemeni population sample and merged these new data with published genome-wide genetic data from the HOA and a broad selection of surrounding populations. We used multidimensional scaling and ADMIXTURE methods in an exploratory data analysis to develop hypotheses on admixture and population structure in HOA populations. These analyses suggested that there might be distinct, differentiated African and non-African ancestries in the HOA. After partitioning the SNP data into African and non-African origin chromosome segments, we found support for a distinct African (Ethiopic) ancestry and a distinct non-African (Ethio-Somali) ancestry in HOA populations. The African Ethiopic ancestry is tightly restricted to HOA populations and likely represents an autochthonous HOA population. The non-African ancestry in the HOA, which is primarily attributed to a novel Ethio-Somali inferred ancestry component, is significantly differentiated from all neighboring non-African ancestries in North Africa, the Levant, and Arabia. The Ethio-Somali ancestry is found in all admixed HOA ethnic groups, shows little inter-individual variance within these ethnic groups, is estimated to have diverged from all other non-African ancestries by at least 23 ka, and does not carry the unique Arabian lactase persistence allele that arose about 4 ka. Taking into account published mitochondrial, Y chromosome, paleoclimate, and archaeological data, we find that the time of the Ethio-Somali back-to-Africa migration is most likely pre-agricultural.
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Affiliation(s)
- Jason A. Hodgson
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, United Kingdom
| | - Connie J. Mulligan
- Department of Anthropology and the Genetics Institute, University of Florida, Gainesville, Florida, United States of America
| | - Ali Al-Meeri
- Department of Biochemistry and Molecular Biology, Sana'a University, Sana'a, Yemen
| | - Ryan L. Raaum
- Department of Anthropology, Lehman College and The Graduate Center, The City University of New York, Bronx, New York, New York, United States of America
- The New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, United States of America
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9
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Dynamics of green Sahara periods and their role in hominin evolution. PLoS One 2013; 8:e76514. [PMID: 24146882 PMCID: PMC3797788 DOI: 10.1371/journal.pone.0076514] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 08/28/2013] [Indexed: 11/21/2022] Open
Abstract
Astronomically forced insolation changes have driven monsoon dynamics and recurrent humid episodes in North Africa, resulting in green Sahara Periods (GSPs) with savannah expansion throughout most of the desert. Despite their potential for expanding the area of prime hominin habitats and favouring out-of-Africa dispersals, GSPs have not been incorporated into the narrative of hominin evolution due to poor knowledge of their timing, dynamics and landscape composition at evolutionary timescales. We present a compilation of continental and marine paleoenvironmental records from within and around North Africa, which enables identification of over 230 GSPs within the last 8 million years. By combining the main climatological determinants of woody cover in tropical Africa with paleoenvironmental and paleoclimatic data for representative (Holocene and Eemian) GSPs, we estimate precipitation regimes and habitat distributions during GSPs. Their chronology is consistent with the ages of Saharan archeological and fossil hominin sites. Each GSP took 2–3 kyr to develop, peaked over 4–8 kyr, biogeographically connected the African tropics to African and Eurasian mid latitudes, and ended within 2–3 kyr, which resulted in rapid habitat fragmentation. We argue that the well-dated succession of GSPs presented here may have played an important role in migration and evolution of hominins.
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10
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Templeton AR. Biological races in humans. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2013; 44:262-71. [PMID: 23684745 PMCID: PMC3737365 DOI: 10.1016/j.shpsc.2013.04.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Races may exist in humans in a cultural sense, but biological concepts of race are needed to access their reality in a non-species-specific manner and to see if cultural categories correspond to biological categories within humans. Modern biological concepts of race can be implemented objectively with molecular genetic data through hypothesis-testing. Genetic data sets are used to see if biological races exist in humans and in our closest evolutionary relative, the chimpanzee. Using the two most commonly used biological concepts of race, chimpanzees are indeed subdivided into races but humans are not. Adaptive traits, such as skin color, have frequently been used to define races in humans, but such adaptive traits reflect the underlying environmental factor to which they are adaptive and not overall genetic differentiation, and different adaptive traits define discordant groups. There are no objective criteria for choosing one adaptive trait over another to define race. As a consequence, adaptive traits do not define races in humans. Much of the recent scientific literature on human evolution portrays human populations as separate branches on an evolutionary tree. A tree-like structure among humans has been falsified whenever tested, so this practice is scientifically indefensible. It is also socially irresponsible as these pictorial representations of human evolution have more impact on the general public than nuanced phrases in the text of a scientific paper. Humans have much genetic diversity, but the vast majority of this diversity reflects individual uniqueness and not race.
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Affiliation(s)
- Alan R Templeton
- Department of Biology, Washington University, St. Louis, MO 63130-4899, USA.
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Chiurillo MA, Griman P, Santiago L, Torres K, Moran Y, Borjas L. Distribution of GSTM1, GSTT1, GSTP1 and TP53 disease-associated gene variants in native and urban Venezuelan populations. Gene 2013; 531:106-11. [PMID: 23994684 DOI: 10.1016/j.gene.2013.08.055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 08/14/2013] [Accepted: 08/14/2013] [Indexed: 02/06/2023]
Abstract
The contemporary Venezuelan population is the product of major admixture process across various historical events, which has provided it a particular genetic background. The aim of this study concerns the analysis of glutathione S-transferase (GST) GSTM1, GSTP1 and GSTT1 genetic variants and five polymorphisms at the TP53 gene, which are related to cancer susceptibility, in an urban/admixed population and five Amerindian tribes (Bari, Panare, Pemon, Warao and Wayuu) from Venezuela. Genotyping was carried out in 120 individuals from an urban sample and 188 Amerindians. The analysis performed on TP53 haplotype and GST allele distribution showed a close correlation for Pemon and Warao populations, while Bari group appears isolated from the other populations. GSTT1 null variant frequency in our admixed (11%) and native samples (0.0-11.4%) was lower when compared with Caucasians, Africans and Asians. Frequency of the GSTP1*Val cancer-associated allele found in Bari (88.6%) and Panare (63.0%) is of the highest so far reported. Fourteen TP53 haplotypes were observed in the admixed populations, whereas only 3 to 5 in Amerindians. To our knowledge this is the first report of GST polymorphisms and TP53 haplotype distribution in Venezuelans. The distribution of most of analyzed polymorphisms in the urban sample is consistent with the admixed origin of the present-day population of Venezuela. While, the inter-ethnic variations in genetic polymorphisms found in Native American tribes seem to be the result of the influence of demographic factors. These results provide additional data for undertaking ethnographic and disease association studies in Venezuela.
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Affiliation(s)
- Miguel Angel Chiurillo
- Laboratorio de Genetica Molecular, Decanato de Ciencias de la Salud, Universidad Centroccidental Lisandro Alvarado, Barquisimeto, Venezuela.
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Lefebvre L. Brains, innovations, tools and cultural transmission in birds, non-human primates, and fossil hominins. Front Hum Neurosci 2013; 7:245. [PMID: 23761751 PMCID: PMC3674321 DOI: 10.3389/fnhum.2013.00245] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 05/18/2013] [Indexed: 11/22/2022] Open
Abstract
Recent work on birds and non-human primates has shown that taxonomic differences in field measures of innovation, tool use and social learning are associated with size of the mammalian cortex and avian mesopallium and nidopallium, as well as ecological traits like colonization success. Here, I review this literature and suggest that many of its findings are relevant to hominin intelligence. In particular, our large brains and increased intelligence may be partly independent of our ape phylogeny and the result of convergent processes similar to those that have molded avian and platyrrhine intelligence. Tool use, innovativeness and cultural transmission might be linked over our past and in our brains as operations of domain-general intelligence. Finally, colonization of new areas may have accompanied increases in both brain size and innovativeness in hominins as they have in other mammals and in birds, potentially accelerating hominin evolution via behavioral drive.
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Affiliation(s)
- Louis Lefebvre
- Department of Biology, McGill UniversityMontréal, QC, Canada
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14
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15
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A multidisciplinary reconstruction of Palaeolithic nutrition that holds promise for the prevention and treatment of diseases of civilisation. Nutr Res Rev 2012; 25:96-129. [PMID: 22894943 DOI: 10.1017/s0954422412000017] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Evolutionary medicine acknowledges that many chronic degenerative diseases result from conflicts between our rapidly changing environment, our dietary habits included, and our genome, which has remained virtually unchanged since the Palaeolithic era. Reconstruction of the diet before the Agricultural and Industrial Revolutions is therefore indicated, but hampered by the ongoing debate on our ancestors' ecological niche. Arguments and their counterarguments regarding evolutionary medicine are updated and the evidence for the long-reigning hypothesis of human evolution on the arid savanna is weighed against the hypothesis that man evolved in the proximity of water. Evidence from various disciplines is discussed, including the study of palaeo-environments, comparative anatomy, biogeochemistry, archaeology, anthropology, (patho)physiology and epidemiology. Although our ancestors had much lower life expectancies, the current evidence does neither support the misconception that during the Palaeolithic there were no elderly nor that they had poor health. Rather than rejecting the possibility of 'healthy ageing', the default assumption should be that healthy ageing posed an evolutionary advantage for human survival. There is ample evidence that our ancestors lived in a land-water ecosystem and extracted a substantial part of their diets from both terrestrial and aquatic resources. Rather than rejecting this possibility by lack of evidence, the default assumption should be that hominins, living in coastal ecosystems with catchable aquatic resources, consumed these resources. Finally, the composition and merits of so-called 'Palaeolithic diets', based on different hominin niche-reconstructions, are evaluated. The benefits of these diets illustrate that it is time to incorporate this knowledge into dietary recommendations.
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Macholán M, Vyskočilová MM, Bejček V, Šťastný K. Mitochondrial DNA sequence variation and evolution of Old World house mice (Mus musculus). FOLIA ZOOLOGICA 2012. [DOI: 10.25225/fozo.v61.i3.a12.2012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Miloš Macholán
- Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, v.v.i., Veveří 97, 602 00 Brno, Czech Republic
| | - Martina Mrkvicová Vyskočilová
- Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, v.v.i., Veveří 97, 602 00 Brno, Czech Republic
| | - Vladimír Bejček
- Department of Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences, Kamýcká 129, 165 21 Prague, Czech Republic
| | - Karel Šťastný
- Department of Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences, Kamýcká 129, 165 21 Prague, Czech Republic
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Neves AGM, Serva M. Extremely rare interbreeding events can explain neanderthal DNA in living humans. PLoS One 2012; 7:e47076. [PMID: 23112810 PMCID: PMC3480414 DOI: 10.1371/journal.pone.0047076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 09/11/2012] [Indexed: 11/18/2022] Open
Abstract
Considering the recent experimental discovery of Green et al that present-day non-Africans have 1 to of their nuclear DNA of Neanderthal origin, we propose here a model which is able to quantify the genetic interbreeding between two subpopulations with equal fitness, living in the same geographic region. The model consists of a solvable system of deterministic ordinary differential equations containing as a stochastic ingredient a realization of the neutral Wright-Fisher process. By simulating the stochastic part of the model we are able to apply it to the interbreeding ofthe African ancestors of Eurasians and Middle Eastern Neanderthal subpopulations and estimate the only parameter of the model, which is the number of individuals per generation exchanged between subpopulations. Our results indicate that the amount of Neanderthal DNA in living non-Africans can be explained with maximum probability by the exchange of a single pair of individuals between the subpopulations at each 77 generations, but larger exchange frequencies are also allowed with sizeable probability. The results are compatible with a long coexistence time of 130,000 years, a total interbreeding population of order individuals, and with all living humans being descendants of Africans both for mitochondrial DNA and Y chromosome.
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Affiliation(s)
- Armando G M Neves
- Departamento de Matemática, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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Bednarik RG. An aetiology of hominin behaviour. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2012; 63:319-35. [DOI: 10.1016/j.jchb.2012.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Accepted: 07/20/2012] [Indexed: 11/25/2022]
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Population genetic structure of Simulium degrangei (Diptera: Simuliidae) from Western Carpathians. Biologia (Bratisl) 2012. [DOI: 10.2478/s11756-012-0057-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Guerreiro JF, Meyer D, Diniz IG, Santos ARD, Santos EJMD, Clegg JB. β-Globin polymorphisms in Amerindian populations from the Brazilian Amazon. Am J Hum Biol 2012; 24:432-5. [PMID: 22323332 DOI: 10.1002/ajhb.22235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 12/16/2011] [Accepted: 12/17/2011] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES This investigation was performed to examine genetic variation at the β-globin locus in a sample of 30 healthy individuals from native populations in South America. The patterns of haplotypic variation were compared with those of previous studies including samples for various worldwide populations in an attempt to make inferences about the occupation of the Americas from a deeper temporal perspective than is typically available with haploid markers. METHODS A 2.67-kb segment containing the β-globin gene and its flanking regions was examined for genetic variation in a sample of 60 chromosomes from native populations in South America. The fragment was PCR-amplified and directly sequenced. To determine linkage relationships in compound heterozygotes, we used the amplification refractory mutation system. In addition, we assessed genetic variability and differentiation among populations, and we performed tests of selective neutrality. These analyses were performed for Brazilian Amerindian group and other worldwide populations previously studied. RESULTS Eleven polymorphic sites were found in the studied fragment, which distinguished eight different haplotypes, three recombinants haplotypes (present as single copies) and five previously described haplotypes, including some of those most highly differentiated. Genetic variation found in the pooled sample is substantial. CONCLUSIONS Although only five known haplotypes are observed in Amazonia, some of these are highly divergent, resulting in patterns of molecular polymorphism equal to or higher than those from other world regions.
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Affiliation(s)
- João Farias Guerreiro
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, 66075-970 Belém, PA, Brasil.
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Ghirotto S, Tassi F, Benazzo A, Barbujani G. No evidence of Neandertal admixture in the mitochondrial genomes of early European modern humans and contemporary Europeans. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 146:242-52. [DOI: 10.1002/ajpa.21569] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 05/10/2011] [Indexed: 11/06/2022]
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Litvintseva AP, Carbone I, Rossouw J, Thakur R, Govender NP, Mitchell TG. Evidence that the human pathogenic fungus Cryptococcus neoformans var. grubii may have evolved in Africa. PLoS One 2011; 6:e19688. [PMID: 21589919 PMCID: PMC3092753 DOI: 10.1371/journal.pone.0019688] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 04/04/2011] [Indexed: 12/15/2022] Open
Abstract
Most of the species of fungi that cause disease in mammals, including Cryptococcus neoformans var. grubii (serotype A), are exogenous and non-contagious. Cryptococcus neoformans var. grubii is associated worldwide with avian and arboreal habitats. This airborne, opportunistic pathogen is profoundly neurotropic and the leading cause of fungal meningitis. Patients with HIV/AIDS have been ravaged by cryptococcosis – an estimated one million new cases occur each year, and mortality approaches 50%. Using phylogenetic and population genetic analyses, we present evidence that C. neoformans var. grubii may have evolved from a diverse population in southern Africa. Our ecological studies support the hypothesis that a few of these strains acquired a new environmental reservoir, the excreta of feral pigeons (Columba livia), and were globally dispersed by the migration of birds and humans. This investigation also discovered a novel arboreal reservoir for highly diverse strains of C. neoformans var. grubii that are restricted to southern Africa, the mopane tree (Colophospermum mopane). This finding may have significant public health implications because these primal strains have optimal potential for evolution and because mopane trees contribute to the local economy as a source of timber, folkloric remedies and the edible mopane worm.
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Affiliation(s)
- Anastasia P Litvintseva
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America.
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Rosset S, Tzur S, Behar DM, Wasser WG, Skorecki K. The population genetics of chronic kidney disease: insights from the MYH9-APOL1 locus. Nat Rev Nephrol 2011; 7:313-26. [PMID: 21537348 DOI: 10.1038/nrneph.2011.52] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Many rare kidney disorders exhibit a monogenic, Mendelian pattern of inheritance. Population-based genetic studies have identified many genetic variants associated with an increased risk of developing common kidney diseases. Strongly associated variants have potential clinical uses as predictive markers and may advance our understanding of disease pathogenesis. These principles are elegantly illustrated by a region within chromosome 22q12 that has a strong association with common forms of kidney disease. Researchers had identified DNA sequence variants in this locus that were highly associated with an increased prevalence of common chronic kidney diseases in people of African ancestry. Initial research concentrated on MYH9 as the most likely candidate gene; however, population-based whole-genome analysis enabled two independent research teams to discover more strongly associated mutations in the neighboring APOL1 gene. The powerful evolutionary selection pressure of an infectious pathogen in West Africa favored the spread of APOL1 variants that protect against a lethal form of African sleeping sickness but are highly associated with an increased risk of kidney disease. We describe the data sources, process of discovery, and reasons for initial misidentification of the candidate gene, as well as the lessons that can be learned for future population genetics research.
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Affiliation(s)
- Saharon Rosset
- Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
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Kersulyte D, Kalia A, Gilman RH, Mendez M, Herrera P, Cabrera L, Velapatiño B, Balqui J, Paredes Puente de la Vega F, Rodriguez Ulloa CA, Cok J, Hooper CC, Dailide G, Tamma S, Berg DE. Helicobacter pylori from Peruvian amerindians: traces of human migrations in strains from remote Amazon, and genome sequence of an Amerind strain. PLoS One 2010; 5:e15076. [PMID: 21124785 PMCID: PMC2993954 DOI: 10.1371/journal.pone.0015076] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Accepted: 10/15/2010] [Indexed: 02/06/2023] Open
Abstract
Background The gastric pathogen Helicobacter pylori is extraordinary in its genetic diversity, the differences between strains from well-separated human populations, and the range of diseases that infection promotes. Principal Findings Housekeeping gene sequences from H. pylori from residents of an Amerindian village in the Peruvian Amazon, Shimaa, were related to, but not intermingled with, those from Asia. This suggests descent of Shimaa strains from H. pylori that had infected the people who migrated from Asia into The Americas some 15,000+ years ago. In contrast, European type sequences predominated in strains from Amerindian Lima shantytown residents, but with some 12% Amerindian or East Asian-like admixture, which indicates displacement of ancestral purely Amerindian strains by those of hybrid or European ancestry. The genome of one Shimaa village strain, Shi470, was sequenced completely. Its SNP pattern was more Asian- than European-like genome-wide, indicating a purely Amerind ancestry. Among its unusual features were two cagA virulence genes, each distinct from those known from elsewhere; and a novel allele of gene hp0519, whose encoded protein is postulated to interact with host tissue. More generally, however, the Shi470 genome is similar in gene content and organization to those of strains from industrialized countries. Conclusions Our data indicate that Shimaa village H. pylori descend from Asian strains brought to The Americas many millennia ago; and that Amerind strains are less fit than, and were substantially displaced by, hybrid or European strains in less isolated communities. Genome comparisons of H. pylori from Amerindian and other communities should help elucidate evolutionary forces that have shaped pathogen populations in The Americas and worldwide.
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Affiliation(s)
- Dangeruta Kersulyte
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Awdhesh Kalia
- Department of Biology, University of Louisville, Louisville, Kentucky, United States of America
| | - Robert H. Gilman
- Departemento de Microbiologia, Universidad Peruana Cayetano Heredia, Lima, Peru
- Asociacion Benefica PRISMA, Lima, Peru
- Department of International Health, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Melissa Mendez
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Departemento de Microbiologia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Phabiola Herrera
- Departemento de Microbiologia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Billie Velapatiño
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Departemento de Microbiologia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jacqueline Balqui
- Departemento de Microbiologia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | | | - Jaime Cok
- Policlinico Peruano Japones, Lima, Peru
| | - Catherine C. Hooper
- Departemento de Microbiologia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Giedrius Dailide
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sravya Tamma
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Douglas E. Berg
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Departments of Genetics and Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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Bae CJ. The late Middle Pleistocene hominin fossil record of eastern Asia: Synthesis and review. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2010; 143 Suppl 51:75-93. [PMID: 21086528 DOI: 10.1002/ajpa.21442] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Christopher J Bae
- Department of Anthropology, University of Hawaii, Honolulu, HI 96822, USA.
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Human remains from Zhirendong, South China, and modern human emergence in East Asia. Proc Natl Acad Sci U S A 2010; 107:19201-6. [PMID: 20974952 DOI: 10.1073/pnas.1014386107] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The 2007 discovery of fragmentary human remains (two molars and an anterior mandible) at Zhirendong (Zhiren Cave) in South China provides insight in the processes involved in the establishment of modern humans in eastern Eurasia. The human remains are securely dated by U-series on overlying flowstones and a rich associated faunal sample to the initial Late Pleistocene, >100 kya. As such, they are the oldest modern human fossils in East Asia and predate by >60,000 y the oldest previously known modern human remains in the region. The Zhiren 3 mandible in particular presents derived modern human anterior symphyseal morphology, with a projecting tuber symphyseos, distinct mental fossae, modest lateral tubercles, and a vertical symphysis; it is separate from any known late archaic human mandible. However, it also exhibits a lingual symphyseal morphology and corpus robustness that place it close to later Pleistocene archaic humans. The age and morphology of the Zhiren Cave human remains support a modern human emergence scenario for East Asia involving dispersal with assimilation or populational continuity with gene flow. It also places the Late Pleistocene Asian emergence of modern humans in a pre-Upper Paleolithic context and raises issues concerning the long-term Late Pleistocene coexistence of late archaic and early modern humans across Eurasia.
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Saraswathy KN, Meitei SY, Gupta V, Murry B, Sachdeva MP, Ghosh PK. Brief communication: Allelic and haplotypic structure at the DRD2 locus among five North Indian caste populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2010; 141:651-7. [PMID: 20091846 DOI: 10.1002/ajpa.21246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The dopamine D2 receptor (DRD2) gene, with its known human-specific derived alleles that can facilitate haplotype reconstruction, presents an important locus for anthropological studies. The three sites (TaqIA, TaqIB, and TaqID) of the DRD2 gene are widely studied in various world populations. However, no work has been previously published on DRD2 gene polymorphisms among North Indian populations. Thus, the present study attempts to understand the genetic structure of North Indian upper caste populations using the allele and haplotype frequencies and distribution patterns of the three TaqI sites of the DRD2 gene. Two hundred forty-six blood samples were collected from five upper caste populations of Himachal Pradesh (Brahmin, Rajput and Jat) and Delhi (Aggarwal and Sindhi), and analysis was performed using standard protocols. All three sites were found to be polymorphic in all five of the studied populations. Uniform allele frequency distribution patterns, low heterozygosity values, the sharing of five common haplotypes, and the absence of two of the eight possible haplotypes observed in this study suggest a genetic proximity among the selected populations. The results also indicate a major genetic contribution from Eurasia to North Indian upper castes, apart from the common genetic unity of Indian populations. The study also demonstrates a greater genetic inflow among North Indian caste populations than is observed among South Indian caste and tribal populations.
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Affiliation(s)
- Kallur N Saraswathy
- Biochemical and Molecular Anthropology Laboratory, Department of Anthropology, University of Delhi (North Campus), Delhi 110007, India.
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Panchal M, Beaumont MA. Evaluating nested clade phylogeographic analysis under models of restricted gene flow. Syst Biol 2010; 59:415-32. [PMID: 20547778 DOI: 10.1093/sysbio/syq022] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nested clade phylogeographic analysis (NCPA) is a widely used method that aims to identify past demographic events that have shaped the history of a population. In an earlier study, NCPA has been fully automated, allowing it to be tested with simulated data sets generated under a null model in which samples simulated from a panmictic population are geographically distributed. It was noted that NCPA was prone to inferring false positives, corroborating earlier findings. The present study aims to evaluate both single-locus and multilocus NCPA under the scenario of restricted gene flow among spatially distributed populations. We have developed a new program, ANeCA-ML, which implements multilocus NCPA. Data were simulated under 3 models of gene flow: a stepping stone model, an island model, and a stepping stone model with some long-distance dispersal. Results indicate that single-locus NCPA tends to give a high frequency of false positives, but, unlike the random-mating scenario presented previously, inferences are not limited to restricted gene flow with isolation by distance or contiguous range expansion. The proportion of single-locus data sets that contained false inferences was 76% for the panmictic case, 87% for the stepping stone model, 79% for the stepping stone model with long-distance dispersal, and more than 99% for the island model. The frequency of inferences is inversely related to the amount of gene flow between demes. We performed multilocus NCPA by grouping the simulated loci into data sets of 5 loci. The false-positive rate was reduced in multilocus NCPA for some inferences but remained high for others. The proportion of multilocus data sets that contained false inferences was 17% for the panmictic case, 30% for the stepping stone model, 4% for the stepping stone model with long-distance dispersal, and 54% for the island model. Multilocus NCPA reduces the false-positive rate by restricting the sensitivity of the method but does not appear to increase the accuracy of the approach. Three classical tests-the analysis of molecular variance method, Fu's Fs, and the Mantel test-show that there is information in the data that gives rise to explicable results using these standard approaches. In conclusion, for the scenarios that we have examined, our simulation study suggests that the NCPA method is unreliable and its inferences may be misleading. We suggest that the NCPA method should not be used without objective simulation-based testing by independent researchers.
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Affiliation(s)
- Mahesh Panchal
- School of Biological Sciences, University of Reading, Whiteknights, PO Box 228, Reading RG6 6AJ, UK.
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Dubertret C, Bardel C, Ramoz N, Martin PM, Deybach JC, Adès J, Gorwood P, Gouya L. A genetic schizophrenia-susceptibility region located between the ANKK1 and DRD2 genes. Prog Neuropsychopharmacol Biol Psychiatry 2010; 34:492-9. [PMID: 20138949 DOI: 10.1016/j.pnpbp.2010.02.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Revised: 01/27/2010] [Accepted: 02/01/2010] [Indexed: 10/19/2022]
Abstract
BACKGROUND The gene coding for the D2 dopamine receptor (DRD2) is considered to be one of the most pertinent candidate genes in schizophrenia. However, genetic studies have yielded conflicting results whereas the promising TaqIA variant/rs1800497 has been mapped in a novel gene, ANKK1. METHODS We investigated eleven single nucleotide polymorphisms (SNPs) spanning the DRD2 and ANKK1 genes, using both a case-control association study comparing 144 independent patients to 142 matched healthy subjects, and a transmission disequilibrium test in 108 trios. This classical genetic study was coupled with a cladistic phylogeny-based association test of human variants, and with an interspecies evolution study of ANKK1. RESULTS Case-control study, followed by a 108 trios family-based association analysis for replication, revealed an association between schizophrenia and the ANKK1 rs1800497 (p=0.01, Odds Ratio=1.5, 95% Confidence Interval=1.1-2.2), and the intergenic rs2242592 (p=2.10(-4), OR=1.8, 95%CI=1.3-2.5). A significant SNP-SNP interaction was also found (p<10(-5), OR=2.0, 95%CI=1.6-2.5). The phylogeny-based association test also identified an association between both these polymorphisms and schizophrenia. Finally, interspecies comparison of the sequences from chimpanzee, orangutan, rhesus macaque and human species suggested specific involvement of ANKK1 in the human lineage. CONCLUSIONS Intergenic rs2242592 appears to be involved in the genetic vulnerability to schizophrenia, whereas the ANKK1 rs1800497 appears to have a modifying rather than causative effect. Finally, ANKK1 may be a specific human lineage-trait involved in a specific human disease, schizophrenia.
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Affiliation(s)
- Caroline Dubertret
- INSERM U894 (exU675), Center of Psychiatry and Neurosciences, Paris, France.
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Coherent and incoherent inference in phylogeography and human evolution. Proc Natl Acad Sci U S A 2010; 107:6376-81. [PMID: 20308555 DOI: 10.1073/pnas.0910647107] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A hypothesis is nested within a more general hypothesis when it is a special case of the more general hypothesis. Composite hypotheses consist of more than one component, and in many cases different composite hypotheses can share some but not all of these components and hence are overlapping. In statistics, coherent measures of fit of nested and overlapping composite hypotheses are technically those measures that are consistent with the constraints of formal logic. For example, the probability of the nested special case must be less than or equal to the probability of the general model within which the special case is nested. Any statistic that assigns greater probability to the special case is said to be incoherent. An example of incoherence is shown in human evolution, for which the approximate Bayesian computation (ABC) method assigned a probability to a model of human evolution that was a thousand-fold larger than a more general model within which the first model was fully nested. Possible causes of this incoherence are identified, and corrections and restrictions are suggested to make ABC and similar methods coherent. Another coalescent-based method, nested clade phylogeographic analysis, is coherent and also allows the testing of individual components of composite hypotheses, another attribute lacking in ABC and other coalescent-simulation approaches. Incoherence is a highly undesirable property because it means that the inference is mathematically incorrect and formally illogical, and the published incoherent inferences on human evolution that favor the out-of-Africa replacement hypothesis have no statistical or logical validity.
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Affiliation(s)
- Alan R Templeton
- Department of Biology, Washington University, St. Louis, MO 63130-4899, USA.
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The diverse applications of cladistic analysis of molecular evolution, with special reference to nested clade analysis. Int J Mol Sci 2010; 11:124-39. [PMID: 20162005 PMCID: PMC2820993 DOI: 10.3390/ijms11010124] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Revised: 01/06/2010] [Accepted: 01/06/2010] [Indexed: 11/17/2022] Open
Abstract
The genetic variation found in small regions of the genomes of many species can be arranged into haplotype trees that reflect the evolutionary genealogy of the DNA lineages found in that region and the accumulation of mutations on those lineages. This review demonstrates some of the many ways in which clades (branches) of haplotype trees have been applied in recent years, including the study of genotype/phenotype associations at candidate loci and in genome-wide association studies, the phylogeographic history of species, human evolution, the conservation of endangered species, and the identification of species.
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Abstract
It has been claimed that hundreds of researchers use nested clade phylogeographic analysis (NCPA) based on what the method promises rather than requiring objective validation of the method. The supposed failure of NCPA is based upon the argument that validating it by using positive controls ignored type I error, and that computer simulations have shown a high type I error. The first argument is factually incorrect: the previously published validation analysis fully accounted for both type I and type II errors. The simulations that indicate a 75% type I error rate have serious flaws and only evaluate outdated versions of NCPA. These outdated type I error rates fall precipitously when the 2003 version of single-locus NCPA is used or when the 2002 multilocus version of NCPA is used. It is shown that the tree-wise type I errors in single-locus NCPA can be corrected to the desired nominal level by a simple statistical procedure, and that multilocus NCPA reconstructs a simulated scenario used to discredit NCPA with 100% accuracy. Hence, NCPA is a not a failed method at all, but rather has been validated both by actual data and by simulated data in a manner that satisfies the published criteria given by its critics. The critics have come to different conclusions because they have focused on the pre-2002 versions of NCPA and have failed to take into account the extensive developments in NCPA since 2002. Hence, researchers can choose to use NCPA based upon objective critical validation that shows that NCPA delivers what it promises.
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Affiliation(s)
- Alan R Templeton
- Department of Biology, Campus Box 1137, Washington University, St. Louis, Missouri 63130, USA.
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Krebes L, Blank M, Jürss K, Zettler ML, Bastrop R. Glacial-driven vicariance in the amphipod Gammarus duebeni. Mol Phylogenet Evol 2009; 54:372-85. [PMID: 19654046 DOI: 10.1016/j.ympev.2009.07.034] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Revised: 07/28/2009] [Accepted: 07/29/2009] [Indexed: 10/20/2022]
Abstract
We have examined the genetic diversity using mitochondrial COI and ND2 sequence data from 306 specimens of the amphi-Atlantic-distributed amphipod Gammarus duebeni. Marine populations from the Atlantic Ocean, the Baltic and North Sea, as well as freshwater populations from Ireland, Cornwall and Brittany were analysed. G. duebeni is a complex of five allopatric lineages. Freshwater populations result from multiple invasions of marine ancestors, represented by distinct lineages. We interpret the recent distribution of lineages as the outcome of a series of spatio-temporal vicariant events caused by Pleistocene glaciations and sea level changes. The freshwater lineages are therefore regarded as 'glacial relicts'. Furthermore, inter-specific competition with, for example, Gammarus pulex (which is absent in Ireland and western Brittany) may be another important determinant in the distribution of freshwater G. duebeni. In Ireland and Brittany, three freshwater refugia are suggested. The significantly limited gene flow detected among marine populations is more likely due to inter-specific competition than to salinity. The G. duebeni-complex represents a model system for the study of allopatric speciation accompanied by major habitat shifts. The pattern of spatio-temporal origins of the freshwater entities we describe here provides an excellent system for investigating evolutionary adaptations to the freshwater environment. Our data did not confirm the presently used subspecies classification but are only preliminary in the absence of nuclear genetic analyses.
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Affiliation(s)
- L Krebes
- University of Rostock, Institute of Biology, Albert-Einstein-Strasse 3, D-18051 Rostock, Germany.
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Wolpoff MH. How Neandertals inform human variation. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2009; 139:91-102. [PMID: 19226640 DOI: 10.1002/ajpa.20930] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Since their first discovery, Neandertals have served as an out-group for interpreting human variation. Their out-group role has changed over the years because in spite of the fact that Neandertals are the most abundant of all fossil remains (or perhaps because of this) their interpretation is the most controversial of all human fossils. Many believe them to be a different, albeit human-like species, but recent genetic evidence supports anatomical interpretations indicating that interbreeding with other humans was an important aspect of human evolution. The combination of anatomical difference and restricted gene flow between populations suggests the possibility that Neandertals may have been a true human race.
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Affiliation(s)
- Milford H Wolpoff
- Department of Anthropology, University of Michigan, Ann Arbor, 48109-1092, USA.
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Early modern human diversity suggests subdivided population structure and a complex out-of-Africa scenario. Proc Natl Acad Sci U S A 2009; 106:6094-8. [PMID: 19307568 DOI: 10.1073/pnas.0808160106] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The interpretation of genetic evidence regarding modern human origins depends, among other things, on assessments of the structure and the variation of ancient populations. Because we lack genetic data from the time when the first anatomically modern humans appeared, between 200,000 and 60,000 years ago, instead we exploit the phenotype of neurocranial geometry to compare the variation in early modern human fossils with that in other groups of fossil Homo and recent modern humans. Variation is assessed as the mean-squared Procrustes distance from the group average shape in a representation based on several hundred neurocranial landmarks and semilandmarks. We find that the early modern group has more shape variation than any other group in our sample, which covers 1.8 million years, and that they are morphologically similar to recent modern humans of diverse geographically dispersed populations but not to archaic groups. Of the currently competing models of modern human origins, some are inconsistent with these findings. Rather than a single out-of-Africa dispersal scenario, we suggest that early modern humans were already divided into different populations in Pleistocene Africa, after which there followed a complex migration pattern. Our conclusions bear implications for the inference of ancient human demography from genetic models and emphasize the importance of focusing research on those early modern humans, in particular, in Africa.
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Kaszycka KA, Štrkalj G, Strzałko J. Current Views of European Anthropologists on Race: Influence of Educational and Ideological Background. AMERICAN ANTHROPOLOGIST 2009. [DOI: 10.1111/j.1548-1433.2009.01076.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Templeton AR. Statistical hypothesis testing in intraspecific phylogeography: nested clade phylogeographical analysis vs. approximate Bayesian computation. Mol Ecol 2009; 18:319-31. [PMID: 19192182 DOI: 10.1111/j.1365-294x.2008.04026.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nested clade phylogeographical analysis (NCPA) and approximate Bayesian computation (ABC) have been used to test phylogeographical hypotheses. Multilocus NCPA tests null hypotheses, whereas ABC discriminates among a finite set of alternatives. The interpretive criteria of NCPA are explicit and allow complex models to be built from simple components. The interpretive criteria of ABC are ad hoc and require the specification of a complete phylogeographical model. The conclusions from ABC are often influenced by implicit assumptions arising from the many parameters needed to specify a complex model. These complex models confound many assumptions so that biological interpretations are difficult. Sampling error is accounted for in NCPA, but ABC ignores important sources of sampling error that creates pseudo-statistical power. NCPA generates the full sampling distribution of its statistics, but ABC only yields local probabilities, which in turn make it impossible to distinguish between a good fitting model, a non-informative model, and an over-determined model. Both NCPA and ABC use approximations, but convergences of the approximations used in NCPA are well defined whereas those in ABC are not. NCPA can analyse a large number of locations, but ABC cannot. Finally, the dimensionality of tested hypothesis is known in NCPA, but not for ABC. As a consequence, the 'probabilities' generated by ABC are not true probabilities and are statistically non-interpretable. Accordingly, ABC should not be used for hypothesis testing, but simulation approaches are valuable when used in conjunction with NCPA or other methods that do not rely on highly parameterized models.
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Affiliation(s)
- Alan R Templeton
- Department of Biology, Washington University, St. Louis, MO 63130-4899, USA.
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Divergence between human populations estimated from linkage disequilibrium. Am J Hum Genet 2008; 83:737-43. [PMID: 19012875 DOI: 10.1016/j.ajhg.2008.10.019] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Revised: 10/07/2008] [Accepted: 10/22/2008] [Indexed: 11/21/2022] Open
Abstract
Observed linkage disequilibrium (LD) between genetic markers in different populations descended independently from a common ancestral population can be used to estimate their absolute time of divergence, because the correlation of LD between populations will be reduced each generation by an amount that, approximately, depends only on the recombination rate between markers. Although drift leads to divergence in allele frequencies, it has less effect on divergence in LD values. We derived the relationship between LD and time of divergence and verified it with coalescent simulations. We then used HapMap Phase II data to estimate time of divergence between human populations. Summed over large numbers of pairs of loci, we find a positive correlation of LD between African and non-African populations at levels of up to approximately 0.3 cM. We estimate that the observed correlation of LD is consistent with an effective separation time of approximately 1,000 generations or approximately 25,000 years before present. The most likely explanation for such relatively low separation times is the existence of substantial levels of migration between populations after the initial separation. Theory and results from coalescent simulations confirm that low levels of migration can lead to a downward bias in the estimate of separation time.
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Timescales and cultural process at 40,000BP in the light of the Campanian Ignimbrite eruption, Western Eurasia. J Hum Evol 2008; 55:834-57. [DOI: 10.1016/j.jhevol.2008.08.012] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Revised: 04/26/2008] [Accepted: 06/27/2008] [Indexed: 11/19/2022]
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Beheregaray LB. Twenty years of phylogeography: the state of the field and the challenges for the Southern Hemisphere. Mol Ecol 2008; 17:3754-74. [PMID: 18627447 DOI: 10.1111/j.1365-294x.2008.03857.x] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phylogeography is a young, vigorous and integrative field of study that uses genetic data to understand the history of populations. This field has recently expanded into many areas of biology and also into several historical disciplines of Earth sciences. In this review, I present a numerical synthesis of the phylogeography literature based on an examination of over 3000 articles published during the first 20 years of the field (i.e. from 1987 to 2006). Information from several topics needed to evaluate the progress, tendencies and deficiencies of the field is summarized for 10 major groups of organisms and at a global scale. The topics include the geography of phylogeographic surveys, comparative nature of studies, temporal scales and major environments investigated, and genetic markers used. I also identify disparities in research productivity between the developing and the developed world, and propose ways to reduce some of the challenges faced by phylogeographers from less affluent countries. Phylogeography has experienced explosive growth in recent years fuelled by developments in DNA technology, theory and statistical analysis. I argue that the intellectual maturation of the field will eventually depend not only on these recent developments, but also on syntheses of comparative information across different regions of the globe. For this to become a reality, many empirical phylogeographic surveys in regions of the Southern Hemisphere (and in developing countries of the Northern Hemisphere) are needed. I expect the information and views presented here will assist in promoting international collaborative work in phylogeography and in guiding research efforts at both regional and global levels.
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Affiliation(s)
- Luciano B Beheregaray
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia.
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Zhang W, Dolan ME. Exploring the evolutionary history of the differentially expressed genes between human populations: action of recent positive selection. Evol Bioinform Online 2008; 4:171-9. [PMID: 19030115 PMCID: PMC2585739 DOI: 10.4137/ebo.s744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Though debates exist on the early human evolutionary models such as the “Out of Africa” theory, which hypothesizes that modern humans migrated from Africa to Europe about 50,000 to 100,000 years ago, Africans and Europeans were geographically separated with minimal gene flow for tens of thousands of years. The variations between the current European and African populations, therefore, should have evolved during this timeframe. To gain more insights into the evolutionary history of human phenotypes including gene expression, it is critical to tell how recent positive selection has played a role in the variations observed in the current populations. Using the list of differentially expressed genes we previously identified between the HapMap samples derived from individuals of African (from Ibadan, Nigeria) and European (from Utah, USA) ancestry, we searched for evidence of selection among these differential genes. We found that 27 differentially expressed genes (out of 356 tested) between these two European and African populations have been under recent positive selection. Our findings suggest that the variation between these two populations appears to be affected primarily by neutral genetic drift and/or stabilizing selection and to a lesser degree by positive selection. Further annotation enrichment analyses showed that these 27 genes under selection were overrepresented in certain Gene Ontology biological processes, molecular functions and cellular components such as transcription, lipid binding and lysosome. Our results can provide unique insights into the evolutionary history of the variation in the gene expression phenotype between these two human populations.
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Affiliation(s)
- Wei Zhang
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, IL 60637, U.S.A
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Affiliation(s)
- Mark A Beaumont
- School of Biological Sciences, University of Reading, Reading RG6 6BX, UK.
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Curnoe D. Affinities of the Swartkrans early Homo mandibles. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2008; 59:123-47. [DOI: 10.1016/j.jchb.2006.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2006] [Accepted: 09/19/2006] [Indexed: 11/30/2022]
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Templeton AR. Nested clade analysis: an extensively validated method for strong phylogeographic inference. Mol Ecol 2008; 17:1877-80. [PMID: 18346121 DOI: 10.1111/j.1365-294x.2008.03731.x] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alan R Templeton
- Department of Biology, Washington University, St Louis, Missouri 63130-4899, USA.
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Abstract
A continued debate in anthropology concerns the evolutionary origin of 'anatomically modern humans' (Homo sapiens sapiens). Different models have been proposed to examine the related questions of (1) where and when anatomically modern humans first appeared and (2) the genetic and evolutionary relationship between modern humans and earlier human populations. Genetic data have been increasingly used to address these questions. Genetic data on living human populations have been used to reconstruct the evolutionary history of the human species by considering how global patterns of human variation could be produced given different evolutionary scenarios. Of particular interest are gene trees that reconstruct the time and place of the most recent common ancestor of humanity for a given haplotype and the analysis of regional differences in genetic diversity. Ancient DNA has also allowed a direct assessment of genetic variation in European Neandertals. Together with the fossil record, genetic data provide insight into the origin of modern humans. The evidence points to an African origin of modern humans dating back to 200,000 years followed by later expansions of moderns out of Africa across the Old World. What is less clear is what happened when these early modern humans met preexisting 'archaic human' populations outside of Africa. At present, it is difficult to distinguish between a model of total genetic replacement and a model that includes some degree of genetic mixture.
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Weaver TD, Roseman CC. New developments in the genetic evidence for modern human origins. Evol Anthropol 2008. [DOI: 10.1002/evan.20161] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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48
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Abstract
Recent studies of genomic DNA from Neanderthal fossils support earlier studies showing no contribution of Neanderthals to the gene pool of modern humans. The relationship between Neanderthals and modern humans is contentious, but recent advances in Neanderthal genomics have shed new light on their evolutionary history. Here we review the available evidence and find no indication of any Neanderthal contribution to modern genetic diversity.
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Affiliation(s)
- Jason A Hodgson
- Center for the Study of Human Origins, Department of Anthropology, New York University, Waverly Place, New York, NY 10003, USA
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Abstract
Germline mutations in the BRCA1 or BRCA2 tumour-suppressor genes are strong predictors of breast and/or ovarian cancer development. The contribution of these mutations to breast cancer risk within any specific population is a function of both their prevalence and their penetrance. Mutation prevalence varies among ethnic groups and may be influenced by founder mutations. Penetrance can be influenced by mutation-specific phenotypes and the potential modifying effects of the patient's own genetic and environmental background. Although estimates of both mutation prevalence and mutation penetrance rates are inconsistent and occasionally controversial, understanding them is crucial for providing accurate risk information to each patient.
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Affiliation(s)
- James D Fackenthal
- Department of Medicine and Center for Clinical Cancer Genetics, University of Chicago, Box MC2115, 5841 S. Maryland Avenue, Chicago, Illinois 60615, USA
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Fagundes NJR, Ray N, Beaumont M, Neuenschwander S, Salzano FM, Bonatto SL, Excoffier L. Statistical evaluation of alternative models of human evolution. Proc Natl Acad Sci U S A 2007; 104:17614-9. [PMID: 17978179 PMCID: PMC2077041 DOI: 10.1073/pnas.0708280104] [Citation(s) in RCA: 335] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Indexed: 11/18/2022] Open
Abstract
An appropriate model of recent human evolution is not only important to understand our own history, but it is necessary to disentangle the effects of demography and selection on genome diversity. Although most genetic data support the view that our species originated recently in Africa, it is still unclear if it completely replaced former members of the Homo genus, or if some interbreeding occurred during its range expansion. Several scenarios of modern human evolution have been proposed on the basis of molecular and paleontological data, but their likelihood has never been statistically assessed. Using DNA data from 50 nuclear loci sequenced in African, Asian and Native American samples, we show here by extensive simulations that a simple African replacement model with exponential growth has a higher probability (78%) as compared with alternative multiregional evolution or assimilation scenarios. A Bayesian analysis of the data under this best supported model points to an origin of our species approximately 141 thousand years ago (Kya), an exit out-of-Africa approximately 51 Kya, and a recent colonization of the Americas approximately 10.5 Kya. We also find that the African replacement model explains not only the shallow ancestry of mtDNA or Y-chromosomes but also the occurrence of deep lineages at some autosomal loci, which has been formerly interpreted as a sign of interbreeding with Homo erectus.
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Affiliation(s)
- Nelson J. R. Fagundes
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), 90619-900 Porto Alegre, RS, Brazil
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre, RS, Brazil
- Computational and Molecular Population Genetics (CMPG), Zoological Institute, University of Bern, CH-3012 Bern, Switzerland
| | - Nicolas Ray
- Computational and Molecular Population Genetics (CMPG), Zoological Institute, University of Bern, CH-3012 Bern, Switzerland
| | - Mark Beaumont
- School of Animal and Microbial Sciences, University of Reading, Reading RG6 6AJ, United Kingdom; and
| | - Samuel Neuenschwander
- Computational and Molecular Population Genetics (CMPG), Zoological Institute, University of Bern, CH-3012 Bern, Switzerland
- Department of Ecology and Evolution, University of Lausanne, Biophore, CH-1015 Lausanne, Switzerland
| | - Francisco M. Salzano
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre, RS, Brazil
| | - Sandro L. Bonatto
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), 90619-900 Porto Alegre, RS, Brazil
| | - Laurent Excoffier
- Computational and Molecular Population Genetics (CMPG), Zoological Institute, University of Bern, CH-3012 Bern, Switzerland
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