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Genome-Wide Genetic Diversity and Population Structure of Local Sudanese Sheep Populations Revealed by Whole-Genome Sequencing. DIVERSITY 2022. [DOI: 10.3390/d14110895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Local Sudanese sheep populations inhabiting diverse environmental conditions and holding opposing morphologies provide opportunities for molecular-genetic research. Characterizing their genome is crucial for sustainable breeding improvement and targeting favorable genes in breeding programs. However, the genome of these sheep populations, which comprises several subtypes, remains uncharacterized using whole-genome sequence data. This study aimed to elucidate genome-wide genetic diversity and population structure of 11 local Sudanese sheep populations, namely, Hammari, Kabbashi, Meidobe, Ashgar, Dubasi, Watish, Bega, Naili, Fulani, Zagawi, and Garag. Ninety whole blood samples were collected, and we extracted DNA using a Qiagen DNeasy® extraction kit. We used the Illumina HiSeq 2000 platform to sequence all the DNA samples. We included whole-genome sequence data of three Ethiopian sheep (Doyogena, Kefis, and Gafera) and one Libyan sheep (Libyan Barbary) in the study to infer the genetic relationships of local Sudanese sheep populations from a continental perspective. A total of 44.8 million bi-allelic autosomal SNPs were detected; 28.5% and 63.3% occur in introns and intergenic regions, respectively. The mean genetic diversity ranged from 0.276 for Garag to 0.324 for Kabbashi sheep populations. The lowest FST estimates were observed between Kabbashi and Ashgar and the highest between Bega and Fulani local Sudanese sheep populations. The principal component and population structure analyses of the 11 local Sudanese sheep populations indicated three separate genetic groups categorized following their tail morphotype, geographical distribution, and population subtype. The thin-tailed local Sudanese sheep populations exhibited independent clustering from the fat-tailed Ethiopian and Libyan sheep. We also observed distinct clustering between the fat-tailed Ethiopian and Libyan sheep. The present study’s findings demonstrated the population structure and principal components related to tail morphotype, geographical distribution, and population subtype of local Sudanese sheep populations. A clear signature of admixture was observed among the studied local Sudanese sheep populations.
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Amane A, Belay G, Nasser Y, Kyalo M, Dessie T, Kebede A, Getachew T, Entfellner JBD, Edea Z, Hanotte O, Tarekegn GM. Genome-wide insights of Ethiopian indigenous sheep populations reveal the population structure related to tail morphology and phylogeography. Genes Genomics 2020; 42:1169-1178. [PMID: 32803704 PMCID: PMC7497517 DOI: 10.1007/s13258-020-00984-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 08/04/2020] [Indexed: 11/24/2022]
Abstract
BACKGROUND Ethiopian sheep living in different climatic zones and having contrasting morphologies are a most promising subject of molecular-genetic research. Elucidating their genetic diversity and genetic structure is critical for designing appropriate breeding and conservation strategies. OBJECTIVE The study was aimed to investigate genome-wide genetic diversity and population structure of eight Ethiopian sheep populations. METHODS A total of 115 blood samples were collected from four Ethiopian sheep populations that include Washera, Farta and Wollo (short fat-tailed) and Horro (long fat-tailed). DNA was extracted using Quick-DNA™ Miniprep plus kit. All DNA samples were genotyped using Ovine 50 K SNP BeadChip. To infer genetic relationships of Ethiopian sheep at national, continental and global levels, genotype data on four Ethiopian sheep (Adilo, Arsi-Bale, Menz and Black Head Somali) and sheep from east, north, and south Africa, Middle East and Asia were included in the study as reference. RESULTS Mean genetic diversity of Ethiopian sheep populations ranged from 0.352 ± 0.14 for Horro to 0.379 ± 0.14 for Arsi-Bale sheep. Population structure and principal component analyses of the eight Ethiopian indigenous sheep revealed four distinct genetic cluster groups according to their tail phenotype and geographical distribution. The short fat-tailed sheep did not represent one genetic cluster group. Ethiopian fat-rump sheep share a common genetic background with the Kenyan fat-tailed sheep. CONCLUSION The results of the present study revealed the principal component and population structure follows a clear pattern of tail morphology and phylogeography. There is clear signature of admixture among the study Ethiopian sheep populations.
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Affiliation(s)
- Agraw Amane
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia.
- Andassa Livestock Research Center, Amhara Regional Agricultural Research Institute, Bahir Dar, Ethiopia.
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya.
- LiveGene Program, International Livestock Research Institute, Addis Ababa, Ethiopia.
| | - Gurja Belay
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Yao Nasser
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Martina Kyalo
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Tadelle Dessie
- LiveGene Program, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Adebabay Kebede
- Andassa Livestock Research Center, Amhara Regional Agricultural Research Institute, Bahir Dar, Ethiopia
| | - Tesfaye Getachew
- International Center for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | | | - Zewdu Edea
- Department of Animal Science, Chungbuk National University, Cheongju, South Korea
| | - Olivier Hanotte
- LiveGene Program, International Livestock Research Institute, Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Getinet Mekuriaw Tarekegn
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Science (SLU), Uppsala, Sweden.
- Department of Animal Production and Technology, School of Animal Sciences and Veterinary Medicine, Bahir Dar University, Bahir Dar, Ethiopia.
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Arrieta-Bolaños E, Madrigal-Sánchez JJ, Stein JE, Órlich-Pérez P, Moreira-Espinoza MJ, Paredes-Carias E, Vanegas-Padilla Y, Salazar-Sánchez L, Madrigal JA, Marsh SGE, Shaw BE. High-resolution HLA allele and haplotype frequencies in majority and minority populations of Costa Rica and Nicaragua: Differential admixture proportions in neighboring countries. HLA 2019; 91:514-529. [PMID: 29687625 DOI: 10.1111/tan.13280] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 04/13/2018] [Accepted: 04/18/2018] [Indexed: 02/03/2023]
Abstract
The HLA system shows the most extensive polymorphism in the human genome. Allelic and haplotypic frequencies of HLA genes vary dramatically across human populations. Due to a complex history of migration, populations in Latin America show a broad variety of admixture proportions, usually varying not only between countries, but also within countries. Knowledge of HLA allele and haplotype frequencies is essential for medical fields such as transplantation, but also serves as a means to assess genetic diversity and ancestry in human populations. Here, we have determined high-resolution HLA-A, -B, -C, and -DRB1 allele and haplotype frequencies in a sample of 713 healthy subjects from three Mestizo populations, one population of African descent, and Amerindians of five different groups from Costa Rica and Nicaragua and compared their profiles to a large set of indigenous populations from Iberia, Sub-Saharan Africa, and the Americas. Our results show a great degree of allelic and haplotypic diversity within and across these populations, with most extended haplotypes being private. Mestizo populations show alleles and haplotypes of putative European, Amerindian, and Sub-Saharan African origin, albeit with differential proportions. Despite some degree of gene flow, Amerindians and Afro-descendants show great similarity to other Amerindian and West African populations, respectively. This is the first comprehensive study reporting high-resolution HLA diversity in Central America, and its results will shed light into the genetic history of this region while also supporting the development of medical programs for organ and stem cell transplantation.
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Affiliation(s)
- E Arrieta-Bolaños
- Institute for Experimental Cellular Therapy, University Hospital, Essen, Germany.,Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,Centro de Investigaciones en Hematología y Trastornos Afines (CIHATA), Universidad de Costa Rica, San José, Costa Rica
| | | | - J E Stein
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
| | - P Órlich-Pérez
- Centro de Investigaciones en Hematología y Trastornos Afines (CIHATA), Universidad de Costa Rica, San José, Costa Rica.,División de Banco de Células Madre, Laboratorio Clínico, Hospital San Juan de Dios, San José, Costa Rica
| | - M J Moreira-Espinoza
- Departamento de Ciencias Morfológicas, Universidad Nacional Autónoma de Nicaragua, León, Nicaragua
| | - E Paredes-Carias
- Departamento de Ciencias Morfológicas, Universidad Nacional Autónoma de Nicaragua, León, Nicaragua
| | - Y Vanegas-Padilla
- Departamento de Ciencias Morfológicas, Universidad Nacional Autónoma de Nicaragua, León, Nicaragua
| | - L Salazar-Sánchez
- Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica
| | - J A Madrigal
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,Cancer Institute, University College London, London, UK
| | - S G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,Cancer Institute, University College London, London, UK
| | - B E Shaw
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,Center for International Blood and Marrow Transplant Research, Department of Medicine, Medical College of Wisconsin, Milwaukee, USA
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4-Locus high-resolution HLA allele and haplotype frequencies in Costa Ricans from African-Caribbean descent. Hum Immunol 2019; 80:411-412. [PMID: 31122741 DOI: 10.1016/j.humimm.2019.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/06/2019] [Accepted: 05/10/2019] [Indexed: 11/22/2022]
Abstract
A total of 102 Costa Ricans of African-Caribbean descent were genotyped at high-resolution for the human leukocyte antigen loci HLA-A, -B, -C, and -DRB1 using sequence-based typing methods. The respective allele and extended haplotype frequencies, as well as Hardy-Weinberg proportions were calculated. The most frequent extended haplotype identified was A*01:01:01-B*08:01:01-C*07:01:01-DRB1*03:01:01G, with an estimated frequency of 1.96%. No deviation from Hardy-Weinberg Equilibrium was detected at any of the loci studied. The HLA genotypic data of the population sample reported here are available publicly in the Allele Frequencies Net Database under the population name "Costa Rica African-Caribbeans" and the identifier AFN3607.
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Ahbara A, Bahbahani H, Almathen F, Al Abri M, Agoub MO, Abeba A, Kebede A, Musa HH, Mastrangelo S, Pilla F, Ciani E, Hanotte O, Mwacharo JM. Genome-Wide Variation, Candidate Regions and Genes Associated With Fat Deposition and Tail Morphology in Ethiopian Indigenous Sheep. Front Genet 2019; 9:699. [PMID: 30687385 PMCID: PMC6334744 DOI: 10.3389/fgene.2018.00699] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 12/13/2018] [Indexed: 12/03/2022] Open
Abstract
Variations in body weight and in the distribution of body fat are associated with feed availability, thermoregulation, and energy reserve. Ethiopia is characterized by distinct agro-ecological and human ethnic farmer diversity of ancient origin, which have impacted on the variation of its indigenous livestock. Here, we investigate autosomal genome-wide profiles of 11 Ethiopian indigenous sheep populations using the Illumina Ovine 50 K SNP BeadChip assay. Sheep from the Caribbean, Europe, Middle East, China, and western, northern and southern Africa were included to address globally, the genetic variation and history of Ethiopian populations. Population relationship and structure analysis separated Ethiopian indigenous fat-tail sheep from their North African and Middle Eastern counterparts. It indicates two main genetic backgrounds and supports two distinct genetic histories for African fat-tail sheep. Within Ethiopian sheep, our results show that the short fat-tail sheep do not represent a monophyletic group. Four genetic backgrounds are present in Ethiopian indigenous sheep but at different proportions among the fat-rump and the long fat-tail sheep from western and southern Ethiopia. The Ethiopian fat-rump sheep share a genetic background with Sudanese thin-tail sheep. Genome-wide selection signature analysis identified eight putative candidate regions spanning genes influencing growth traits and fat deposition (NPR2, HINT2, SPAG8, INSR), development of limbs and skeleton, and tail formation (ALX4, HOXB13, BMP4), embryonic development of tendons, bones and cartilages (EYA2, SULF2), regulation of body temperature (TRPM8), body weight and height variation (DIS3L2), control of lipogenesis and intracellular transport of long-chain fatty acids (FABP3), the occurrence and morphology of horns (RXFP2), and response to heat stress (DNAJC18). Our findings suggest that Ethiopian fat-tail sheep represent a uniquely admixed but distinct genepool that presents an important resource for understanding the genetic control of skeletal growth, fat metabolism and associated physiological processes.
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Affiliation(s)
- Abulgasim Ahbara
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Department of Zoology, Faculty of Sciences, Misurata University, Misurata, Libya
| | - Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
| | - Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Mohammed Al Abri
- Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | | | - Ayelle Abeba
- Debre Berhan Research Centre, Debre Berhan, Ethiopia
| | - Adebabay Kebede
- Amhara Regional Agricultural Research Institute, Bahir Dar, Ethiopia
- LiveGene, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Hassan Hussein Musa
- Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie e Forestali, Viale delle Scienze, Università Palermo, Palermo, Italy
| | - Fabio Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Campobasso, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari “Aldo Moro ”, Bari, Italy
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- LiveGene, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Joram M. Mwacharo
- Small Ruminant Genomics, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
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Lujan HL, DiCarlo SE. The "African gene" theory: it is time to stop teaching and promoting the slavery hypertension hypothesis. ADVANCES IN PHYSIOLOGY EDUCATION 2018; 42:412-416. [PMID: 29972056 DOI: 10.1152/advan.00070.2018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- Heidi L Lujan
- Department of Physiology, College of Osteopathic Medicine, Michigan State University , East Lansing, Michigan
| | - Stephen E DiCarlo
- Department of Physiology, College of Osteopathic Medicine, Michigan State University , East Lansing, Michigan
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7
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Edea Z, Dessie T, Dadi H, Do KT, Kim KS. Genetic Diversity and Population Structure of Ethiopian Sheep Populations Revealed by High-Density SNP Markers. Front Genet 2017; 8:218. [PMID: 29312441 PMCID: PMC5744078 DOI: 10.3389/fgene.2017.00218] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 12/05/2017] [Indexed: 11/13/2022] Open
Abstract
Sheep in Ethiopia are adapted to a wide range of environments, including extreme habitats. Elucidating their genetic diversity is critical for improving breeding strategies and mapping quantitative trait loci associated with productivity. To this end, the present study investigated the genetic diversity and population structure of five Ethiopian sheep populations exhibiting distinct phenotypes and sampled from distinct production environments, including arid lowlands and highlands. To investigate the genetic relationships in greater detail and infer population structure of Ethiopian sheep breeds at the continental and global levels, we analyzed genotypic data of selected sheep breeds from the Ovine SNP50K HapMap dataset. All Ethiopian sheep samples were genotyped with Ovine Infinium HD SNP BeadChip (600K). Mean genetic diversity ranged from 0.29 in Arsi-Bale to 0.32 in Menz sheep, while estimates of genetic differentiation among populations ranged from 0.02 to 0.07, indicating low to moderate differentiation. An analysis of molecular variance revealed that 94.62 and 5.38% of the genetic variation was attributable to differences within and among populations, respectively. Our population structure analysis revealed clustering of five Ethiopian sheep populations according to tail phenotype and geographic origin-i.e., short fat-tailed (very cool high-altitude), long fat-tailed (mid to high-altitude), and fat-rumped (arid low-altitude), with clear evidence of admixture between long fat-tailed populations. North African sheep breeds showed higher levels of within-breed diversity, but were less differentiated than breeds from Eastern and Southern Africa. When African breeds were grouped according to geographic origin (North, South, and East), statistically significant differences were detected among groups (regions). A comparison of population structure between Ethiopian and global sheep breeds showed that fat-tailed breeds from Eastern and Southern Africa clustered together, suggesting that these breeds were introduced to the African continent via the Horn and migrated further south.
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Affiliation(s)
- Zewdu Edea
- Department of Animal Science, Chungbuk National University, Cheongju, South Korea
| | - Tadelle Dessie
- International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Hailu Dadi
- Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia
| | - Kyoung-Tag Do
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju, South Korea
| | - Kwan-Suk Kim
- Department of Animal Science, Chungbuk National University, Cheongju, South Korea
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Campos-Sánchez R, Raventós H, Barrantes R. Ancestry Informative Markers Clarify the Regional Admixture Variation in the Costa Rican Population. Hum Biol 2013; 85:721-40. [DOI: 10.3378/027.085.0505] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2013] [Indexed: 11/05/2022]
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Abstract
Admixture mapping is based on the hypothesis that differences in disease rates between populations are due in part to frequency differences in disease-causing genetic variants. In admixed populations, these genetic variants occur more often on chromosome segments inherited from the ancestral population with the higher disease variant frequency. A genome scan for disease association requires only enough markers to identify the ancestral chromosome segments; for recently admixed populations, such as African Americans, 1,500-2,500 ancestry-informative markers (AIMs) are sufficient. The method was proposed over 50 years ago, but the AIM panels and statistical methods required have only recently become available. Since the first admixture scan in 2005, the genetic bases for a range of diseases/traits have been identified by admixture mapping. Here, we provide a historical perspective, review AIM panels and software packages, and discuss recent successes and unexpected insights into human diseases that exhibit disparate rates across human populations.
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Affiliation(s)
- Cheryl A Winkler
- Basic Science Program, SAIC-Frederick, Inc., Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MD 21702, USA.
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Fiorini S, Tagarelli G, Boattini A, Luiselli D, Piro A, Tagarelli A, Pettener D. Ethnicity and Evolution of the Biodemographic Structure of Arbëreshe and Italian Populations of the Pollino Area, southern Italy (1820–1984). AMERICAN ANTHROPOLOGIST 2007. [DOI: 10.1525/aa.2007.109.4.735] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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11
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MADRIGAL L, WARE B, HAGEN E, BLELL M, OTÁROLA F. The East Indian Diaspora in Costa Rica: Inbreeding Avoidance, Marriage Patterns, and Cultural Survival. AMERICAN ANTHROPOLOGIST 2007. [DOI: 10.1525/aa.2007.109.2.330] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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12
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Boattini A, Calboli FCF, Blanco Villegas MJ, Gueresi P, Franceschi MG, Paoli G, Cavicchi S, Pettener D. Migration matrices and surnames in populations with different isolation patterns: Val di Lima (Italian Apennines), Val di Sole (Italian Alps), and La Cabrera (Spain). Am J Hum Biol 2006; 18:676-90. [PMID: 16917890 DOI: 10.1002/ajhb.20537] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Biodemographic methods are widely used to infer the genetic structure of human populations. In this study, we revise and standardize the procedures required by the migration matrix model of Malécot ([1950] Ann Univ Lyon Sci [A] 13:37-60), testing it in large historical-demographic databases of 85 populations from three mountain valleys with different degrees of isolation: Val di Lima (Italian Apennines, 21 parishes), Val di Sole, (Italian Alps, 27 parishes), and La Cabrera (Spain, 37 parishes). An add-on package (Biodem) for the R program is proposed to perform all calculations. Results from migration matrices are compared with those obtained from isonymic relationships. Migration and isonymy matrices are derived from 22,781 marriage records. Matrices are analyzed using a nonlinear isolation-by-distance (IBD) model and multivariate techniques (multidimensional scaling, Procrustes rotation, and cluster analysis). Microdifferentiation levels (F(ST)) from the migration data agree with the observed inbreeding values: higher values are found in La Cabrera (F(ST) = 0.0082), the most isolated population; Val di Lima (F(ST) = 0.0015) and Val di Sole (F(ST) = 0.0012) have lower values due to the larger parish population sizes and greater mobility. Temporal changes of F(ST) and IBD are analyzed using the migration matrix approach. The populations show a marked decline in F(ST) values in time, together with increased population mobility and emigration rates. In all three valleys, marital migration and isonymy yield similar results, suggesting that geographic distance is the most important factor structuring the populations. However, isonymy shows a lower correlation with geographic distance than migration matrices do. This difference can be attributed to the differing sensitivity of the methods for past migration events, and to genetic drift.
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Affiliation(s)
- Alessio Boattini
- Dipartimento di Biologia Evoluzionistica Sperimentale, Area di Antropologia, Università di Bologna, 40126 Bologna, Italy
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STOJANOWSKI CHRISTOPHERM. The Bioarchaeology of Identity in Spanish Colonial Florida: Social and Evolutionary Transformation before, during, and after Demographic Collapse. AMERICAN ANTHROPOLOGIST 2005. [DOI: 10.1525/aa.2005.107.3.417] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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14
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Pepin J. From the Old World to the New World: an ecologic study of population susceptibility to HIV infection. Trop Med Int Health 2005; 10:627-39. [PMID: 15960701 DOI: 10.1111/j.1365-3156.2005.01441.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
It remains unclear why the global distribution of human immunodeficiency virus (HIV), between and within continents, is so heterogeneous. This ecologic study of 34 populations of the Americas explored the hypothesis that populations differ in their intrinsic, biological susceptibility to HIV which, together with exposure, might determine the ultimate 'mature' prevalence. If true, national HIV prevalence in populations of the Americas should be predictable from each country's ethnic mosaic, inter-racial admixture and HIV prevalence in regions of Africa, Europe and Asia from where their ancestors migrated. For each country, the adult population (15-49 years) was multiplied by the proportion corresponding to each ethnic group by HIV prevalence in the country/region of origin of each group, yielding the predicted prevalences, which were then compared with observed prevalences documented by UNAIDS for 2001. Predicted and observed HIV prevalences were highly correlated (r = 0.70, P < 0.001). In North America, predicted prevalences were within 0.5% of the observed values, except for African-Americans and African-Canadians. In Central and South America, differences between predicted and observed prevalences were <1.0% except in Honduras and Guyana. Some Caribbean countries had a predicted prevalence identical to the observed one, but there were outliers. Overall, predicted prevalence was 0.93% and observed prevalence 0.64%; two-thirds of this difference was attributed to Brazil. Although it was not possible to adjust to the confounding effects of sexual behaviour and cofactors of transmission (such as sexually transmitted infections) because of the lack of nationally representative data for each and every country, a number of arguments reviewed in the paper suggest that confounders cannot explain all this association and that differential susceptibility might be an important determinant of steady-state HIV prevalence.
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Affiliation(s)
- Jacques Pepin
- Department of Microbiology and Infectious Diseases, University of Sherbrooke, Sherbrooke, Canada.
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15
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Smith MW, O'Brien SJ. Mapping by admixture linkage disequilibrium: advances, limitations and guidelines. Nat Rev Genet 2005; 6:623-32. [PMID: 16012528 DOI: 10.1038/nrg1657] [Citation(s) in RCA: 172] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mapping by admixture linkage disequilibrium (MALD) is a theoretically powerful, although unproven, approach to mapping genetic variants that are involved in human disease. MALD takes advantage of long-range haplotypes that are generated by gene flow among recently admixed ethnic groups, such as African-Americans and Latinos. Under ideal circumstances, MALD will have more power to detect some genetic variants than other types of genome-wide association study that are carried out among more ethnically homogeneous populations. It will also require 200-500 times fewer markers, providing a significant economic advantage. The MALD approach is now being applied, with results expected in the near future.
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Affiliation(s)
- Michael W Smith
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702, USA.
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Madrigal L, Ware B, Melendez M. Widow and widower remarriage: an analysis in a rural 19th century Costa Rican population and a cross-cultural discussion. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2004; 122:355-60. [PMID: 14614756 DOI: 10.1002/ajpa.10282] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Although the topic of remarriage features saliently in the cultural anthropological literature, it is virtually absent in the biological anthropology journals. This is perplexing, given that remarriage affects the differential reproductive success of males and females in a community, and could well impact a community's population structure. In this paper, we research remarriage practices in a rural 19th century community in Costa Rica. Although we find support for the proposition that males are more likely to remarry than females, we find that widows who remarry are not all young and able to reproduce. Our findings support the cross-culturally-generated suggestion that a female's ability not to remarry is tied to her to ability to own property. Remarriage is a topic of interest to biological anthropologists from a cross-cultural and biocultural perspective.
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Affiliation(s)
- L Madrigal
- Department of Anthropology, University of South Florida, Tampa, Florida 33620, USA.
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Vilà C, Walker C, Sundqvist AK, Flagstad Ø, Andersone Z, Casulli A, Kojola I, Valdmann H, Halverson J, Ellegren H. Combined use of maternal, paternal and bi-parental genetic markers for the identification of wolf-dog hybrids. Heredity (Edinb) 2003; 90:17-24. [PMID: 12522421 DOI: 10.1038/sj.hdy.6800175] [Citation(s) in RCA: 143] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The identification of hybrids is often a subject of primary concern for the development of conservation and management strategies, but can be difficult when the hybridizing species are closely related and do not possess diagnostic genetic markers. However, the combined use of mitochondrial DNA (mtDNA), autosomal and Y chromosome genetic markers may allow the identification of hybrids and of the direction of hybridization. We used these three types of markers to genetically characterize one possible wolf-dog hybrid in the endangered Scandinavian wolf population. We first characterized the variability of mtDNA and Y chromosome markers in Scandinavian wolves as well as in neighboring wolf populations and in dogs. While the mtDNA data suggested that the target sample could correspond to a wolf, its Y chromosome type had not been observed before in Scandinavian wolves. We compared the genotype of the target sample at 18 autosomal microsatellite markers with those expected in pure specimens and in hybrids using assignment tests. The combined results led to the conclusion that the animal was a hybrid between a Scandinavian female wolf and a male dog. This finding confirms that inter-specific hybridization between wolves and dogs can occur in natural wolf populations. A possible correlation between hybridization and wolf population density and disturbance deserves further research.
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Affiliation(s)
- C Vilà
- Department of Evolutionary Biology, Uppsala University, Sweden.
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Abstract
The general population of Costa Rica has sometimes been considered to be the product of an amalgamation of groups of diverse origin. To determine the magnitude of accumulated admixture since Spanish colonization, 11 classic genetic markers were analyzed in a total of 2196 individuals originating from five distinct regions of the country. A maximum likelihood approach was used. The proportions of genes of European, Amerindian and African ancestry were found to be 61%, 30% and 9% of the total population, respectively. Variation was observed at a regional level, with an increased European influence in the North (66%) and Central (65%) regions. Meanwhile an increase in Amerindian ancestry was found in the South (38%), and a higher incidence in the contribution of African genes was detected in the coastal regions (13% in the Atlantic and 14% in the North Pacific). A principal component (PC) analysis showed that 76% of the existing variability can be explained by the first two PCs, which is in agreement with the variations observed in the admixture process by geographic area. It has been concluded that the Costa Rican population is truly trihybrid, similar to populations in other Latin American countries; however, it differs from them fundamentally by the proportion of gene flow from ancestral populations.
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Affiliation(s)
- B Morera
- Unitat de Biologia Evolutiva, Facultad de Ciencias de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain.
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