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Shyr D, Dey R, Li X, Zhou H, Boerwinkle E, Buyske S, Daly M, Gibbs RA, Hall I, Matise T, Reeves C, Stitziel NO, Zody M, Neale BM, Lin X. Semi-supervised machine learning method for predicting homogeneous ancestry groups to assess Hardy-Weinberg equilibrium in diverse whole-genome sequencing studies. Am J Hum Genet 2024:S0002-9297(24)00304-5. [PMID: 39270648 DOI: 10.1016/j.ajhg.2024.08.018] [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: 01/26/2024] [Revised: 08/22/2024] [Accepted: 08/22/2024] [Indexed: 09/15/2024] Open
Abstract
Large-scale, multi-ethnic whole-genome sequencing (WGS) studies, such as the National Human Genome Research Institute Genome Sequencing Program's Centers for Common Disease Genomics (CCDG), play an important role in increasing diversity for genetic research. Before performing association analyses, assessing Hardy-Weinberg equilibrium (HWE) is a crucial step in quality control procedures to remove low quality variants and ensure valid downstream analyses. Diverse WGS studies contain ancestrally heterogeneous samples; however, commonly used HWE methods assume that the samples are homogeneous. Therefore, directly applying these to the whole dataset can yield statistically invalid results. To account for this heterogeneity, HWE can be tested on subsets of samples that have genetically homogeneous ancestries and the results aggregated at each variant. To facilitate valid HWE subset testing, we developed a semi-supervised learning approach that predicts homogeneous ancestries based on the genotype. This method provides a convenient tool for estimating HWE in the presence of population structure and missing self-reported race and ethnicities in diverse WGS studies. In addition, assessing HWE within the homogeneous ancestries provides reliable HWE estimates that will directly benefit downstream analyses, including association analyses in WGS studies. We applied our proposed method on the CCDG dataset, predicting homogeneous genetic ancestry groups for 60,545 multi-ethnic WGS samples to assess HWE within each group.
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Affiliation(s)
- Derek Shyr
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Rounak Dey
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Xihao Li
- Department of Biostatistics, University of North Carolina at Chapel Hill Gillings School of Global Public Health, Chapel Hill, NC 27599, USA
| | - Hufeng Zhou
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health, Houston, TX 77030, USA
| | - Steve Buyske
- Department of Statistics, Rutgers University, Piscataway, NJ 08854, USA
| | - Mark Daly
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ira Hall
- Center for Genomic Health, Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Tara Matise
- Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA
| | | | - Nathan O Stitziel
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Benjamin M Neale
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Statistics, Harvard University, Cambridge, MA 02115, USA.
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Shi H, Li T, Su M, Wang H, Li Q, Lang X, Ma Y. Identification of copy number variation in Tibetan sheep using whole genome resequencing reveals evidence of genomic selection. BMC Genomics 2023; 24:555. [PMID: 37726692 PMCID: PMC10510117 DOI: 10.1186/s12864-023-09672-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 09/12/2023] [Indexed: 09/21/2023] Open
Abstract
BACKGROUND Copy number variation (CNV) is an important source of structural variation in the mammalian genome. CNV assays present a new method to explore the genomic diversity of environmental adaptations in animals and plants and genes associated with complex traits. In this study, the genome-wide CNV distribution characteristics of 20 Tibetan sheep from two breeds (10 Oula sheep and 10 Panou sheep) were analysed using whole-genome resequencing to investigate the variation in the genomic structure of Tibetan sheep during breeding. RESULTS CNVs were detected using CNVnator, and the overlapping regions of CNVs between individual sheep were combined. Among them, a total of 60,429 CNV events were detected between the indigenous sheep breed (Oula) and the synthetic sheep breed (Panou). After merging the overlapping CNVs, 4927 CNV regions (CNVRs) were finally obtained. Of these, 4559 CNVRs were shared by two breeds, and there were 368 differential CNVRs. Deletion events have a higher percentage of occurrences than duplication events. Functional enrichment analysis showed that the shared CNVRs were significantly enriched in 163 GO terms and 62 KEGG pathways, which were mainly associated with organ development, neural regulation, immune regulation, digestion and metabolism. In addition, 140 QTLs overlapped with some of the CNVRs at more than 1 kb, such as average daily gain QTL, body weight QTL, and total lambs born QTL. Many of the CNV-overlapping genes such as PPP3CA, SSTR1 and FASN, overlap with the average daily weight gain and carcass weight QTL regions. Moreover, VST analysis showed that XIRP2, ABCB1, CA1, ASPA and EEF2 differed significantly between the synthetic breed and local sheep breed. The duplication of the ABCB1 gene may be closely related to adaptation to the plateau environment in Panou sheep, which deserves further study. Additionally, cluster analysis, based on all individuals, showed that the CNV clustering could be divided into two origins, indicating that some Tibetan sheep CNVs are likely to arise independently in different populations and contribute to population differences. CONCLUSIONS Collectively, we demonstrated the genome-wide distribution characteristics of CNVs in Panou sheep by whole genome resequencing. The results provides a valuable genetic variation resource and help to understand the genetic characteristics of Tibetan sheep. This study also provides useful information for the improvement and breeding of Tibetan sheep in the future.
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Affiliation(s)
- Huibin Shi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070, China
- College of Animal Science & Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, 450046, China
| | - Taotao Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070, China
| | - Manchun Su
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070, China
| | - Huihui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070, China
| | - Qiao Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070, China
| | - Xia Lang
- Institute of Animal & Pasture Science and Green Agriculture, Gansu Academy of Agricultural Science, Lanzhou, 730070, China
| | - Youji Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070, China.
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da Cruz PRS, Ananina G, Secolin R, Gil-da-Silva-Lopes VL, Lima CSP, de França PHC, Donatti A, Lourenço GJ, de Araujo TK, Simioni M, Lopes-Cendes I, Costa FF, de Melo MB. Demographic history differences between Hispanics and Brazilians imprint haplotype features. G3 GENES|GENOMES|GENETICS 2022; 12:6576632. [PMID: 35511163 PMCID: PMC9258545 DOI: 10.1093/g3journal/jkac111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/27/2022] [Indexed: 11/24/2022]
Abstract
Admixture is known to greatly impact the genetic landscape of a population and, while genetic variation underlying human phenotypes has been shown to differ among populations, studies on admixed subjects are still scarce. Latin American populations are the result of complex demographic history, such as 2 or 3-way admixing events, bottlenecks and/or expansions, and adaptive events unique to the American continent. To explore the impact of these events on the genetic structure of Latino populations, we evaluated the following haplotype features: linkage disequilibrium, shared identity by descent segments, runs of homozygosity, and extended haplotype homozygosity (integrated haplotype score) in Latinos represented in the 1000 Genome Project along with array data from 171 Brazilians sampled in the South and Southeast regions of Brazil. We found that linkage disequilibrium decay relates to the amount of American and African ancestry. The extent of identity by descent sharing positively correlates with historical effective population sizes, which we found to be steady or growing, except for Puerto Ricans and Colombians. Long runs of homozygosity, a particular instance of autozygosity, was only enriched in Peruvians and Native Americans. We used simulations to account for random sampling and linkage disequilibrium to filter positive selection indexes and found 244 unique markers under selection, 26 of which are common to 2 or more populations. Some markers exhibiting positive selection signals had estimated time to the most recent common ancestor consistent with human adaptation to the American continent. In conclusion, Latino populations present highly divergent haplotype characteristics that impact genetic architecture and underlie complex phenotypes.
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Affiliation(s)
- Pedro Rodrigues Sousa da Cruz
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas—UNICAMP , Campinas, SP 13083-875, Brazil
| | - Galina Ananina
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas—UNICAMP , Campinas, SP 13083-875, Brazil
| | - Rodrigo Secolin
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
- The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN) , Campinas, SP 13083-887, Brazil
| | - Vera Lúcia Gil-da-Silva-Lopes
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
| | - Carmen Silvia Passos Lima
- Clinical Oncology Service, Department of Internal Medicine, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
| | | | - Amanda Donatti
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
- The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN) , Campinas, SP 13083-887, Brazil
| | - Gustavo Jacob Lourenço
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
| | - Tânia Kawasaki de Araujo
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
| | - Milena Simioni
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
| | - Iscia Lopes-Cendes
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
- The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN) , Campinas, SP 13083-887, Brazil
| | - Fernando Ferreira Costa
- Hematology and Hemotherapy Center, University of Campinas—UNICAMP, Campinas, SP, 13083-878 , Brazil
| | - Mônica Barbosa de Melo
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas—UNICAMP , Campinas, SP 13083-875, Brazil
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Hayakawa T, Terahara M, Fujito NT, Matsunaga T, Teshima KM, Hane M, Kitajima K, Sato C, Takahata N, Satta Y. Lower promoter activity of the ST8SIA2 gene has been favored in evolving human collective brains. PLoS One 2021; 16:e0259897. [PMID: 34914745 PMCID: PMC8675693 DOI: 10.1371/journal.pone.0259897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 10/28/2021] [Indexed: 11/18/2022] Open
Abstract
ST8SIA2 is an important molecule regulating expression of the phenotype involved in schizophrenia. Lowered promoter activity of the ST8SIA2 gene is considered to be protective against schizophrenia by conferring tolerance to psychosocial stress. Here, we examined the promoter-type composition of anatomically modern humans (AMHs) and archaic humans (AHs; Neanderthals and Denisovans), and compared the promoter activity at the population level (population promoter activity; PPA) between them. In AMHs, the TCT-type, showing the second lowest promoter activity, was most prevalent in the ancestral population of non-Africans. However, the detection of only the CGT-type from AH samples and recombination tracts in AH sequences showed that the CGT- and TGT-types, exhibiting the two highest promoter activities, were common in AH populations. Furthermore, interspecies gene flow occurred into AMHs from AHs and into Denisovans from Neanderthals, influencing promoter-type compositions independently in both AMHs and AHs. The difference of promoter-type composition makes PPA unique in each population. East and Southeast Asian populations show the lowest PPA. This results from the selective increase of the CGC-type, showing the lowest promoter activity, in these populations. Every non-African population shows significantly lower PPA than African populations, resulting from the TCT-type having the highest prevalence in the ancestral population of non-Africans. In addition, PPA reduction is also found among subpopulations within Africa via a slight increase of the TCT-type. These findings indicate a trend toward lower PPA in the spread of AMHs, interpreted as a continuous adaptation to psychosocial stress arising in migration. This trend is considered as genetic tuning for the evolution of collective brains. The inferred promoter-type composition of AHs differed markedly from that of AMHs, resulting in higher PPA in AHs than in AMHs. This suggests that the trend toward lower PPA is a unique feature in AMH spread.
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Affiliation(s)
- Toshiyuki Hayakawa
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
- Faculty of Arts and Science, Kyushu University, Fukuoka, Japan
- * E-mail:
| | - Masahiro Terahara
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Naoko T. Fujito
- School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
| | - Takumi Matsunaga
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | | | - Masaya Hane
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, Japan
| | - Ken Kitajima
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Aichi, Japan
| | - Chihiro Sato
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Aichi, Japan
| | - Naoyuki Takahata
- School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
| | - Yoko Satta
- School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
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Differences in MTHFR and LRRK2 variant's association with sporadic Parkinson's disease in Mexican Mestizos correlated to Native American ancestry. NPJ Parkinsons Dis 2021; 7:13. [PMID: 33574311 PMCID: PMC7878860 DOI: 10.1038/s41531-021-00157-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 01/08/2021] [Indexed: 01/30/2023] Open
Abstract
Parkinson's disease (PD), a common neurodegenerative disorder, has a complex etiology where environmental and genetic factors intervene. While a number of genes and variants have been identified in recent decades as causative or protective agents of this condition, a limited number of studies have been conducted in mixed populations, such as Mexican Mestizos. The historical convergence of two founding groups and three ethnicities, and the increasing north-to-south gradient of Native American ancestry in Mexico resulted in a subpopulation structure with considerable genetic diversity. In this work, we investigate the influence of 21 known susceptibility variants for PD. Our case-control study, with a cohort of 311 Mexican Mestizo subjects, found a significant risk association for the variant rs1491942 in LRRK2. However, when stratification by ancestry was performed, a risk effect for MTHFR rs1801133 was observed only in the group with the highest percentage of European ancestry, and the PD risk effect for LRRK2 rs1491942 was significant in subjects with a higher ratio of Native American ancestry. Meta-analyses of these SNP revealed the effect of LRRK2 rs1491942 to be even more significant than previously described in populations of European descent. Although corroboration is necessary, our findings suggest that polymorphism rs1491942 may be useful as a risk marker of PD in Mexican Mestizos with greater Native American ancestry. The absence of associations with the remaining known risk factors is, in itself, a relevant finding and invites further research into the shared risk factors' role in the pathophysiological mechanisms of this neurodegenerative disorder.
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Wragg D, Techer MA, Canale-Tabet K, Basso B, Bidanel JP, Labarthe E, Bouchez O, Le Conte Y, Clémencet J, Delatte H, Vignal A. Autosomal and Mitochondrial Adaptation Following Admixture: A Case Study on the Honeybees of Reunion Island. Genome Biol Evol 2018; 10:220-238. [PMID: 29202174 PMCID: PMC5814903 DOI: 10.1093/gbe/evx247] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2017] [Indexed: 12/28/2022] Open
Abstract
The honeybee population of the tropical Reunion Island is a genetic admixture of the Apis mellifera unicolor subspecies, originally described in Madagascar, and of European subspecies, mainly A. m. carnica and A. m. ligustica, regularly imported to the island since the late 19th century. We took advantage of this population to study genetic admixing of the tropical-adapted indigenous and temperate-adapted European genetic backgrounds. Whole genome sequencing of 30 workers and 6 males from Reunion, compared with samples from Europe, Madagascar, Mauritius, Rodrigues, and the Seychelles, revealed the Reunion honeybee population to be composed on an average of 53.2 ± 5.9% A. m. unicolor nuclear genomic background, the rest being mainly composed of A. m. carnica and to a lesser extent A. m. ligustica. In striking contrast to this, only 1 out of the 36 honeybees from Reunion had a mitochondrial genome of European origin, suggesting selection has favored the A. m. unicolor mitotype, which is possibly better adapted to the island’s bioclimate. Local ancestry was determined along the chromosomes for all Reunion samples, and a test for preferential selection for the A. m. unicolor or European background revealed 15 regions significantly associated with the A. m. unicolor lineage and 9 regions with the European lineage. Our results provide insights into the long-term consequences of introducing exotic specimen on the nuclear and mitochondrial genomes of locally adapted populations.
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Affiliation(s)
- David Wragg
- GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet Tolosan, France.,The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Maéva Angélique Techer
- CIRAD, UMR PVBMT, Saint Pierre, La Réunion, France.,UMR PVBMT, Université de La Réunion, Saint Pierre, La Réunion, France.,Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa, Japan
| | - Kamila Canale-Tabet
- GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet Tolosan, France
| | - Benjamin Basso
- Institut de l'abeille (ITSAP), UMT PrADE, Avignon, France
| | | | - Emmanuelle Labarthe
- GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet Tolosan, France
| | - Olivier Bouchez
- INRA, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Yves Le Conte
- INRA, UR 406 Abeilles et Environnement, UMT PrADE, Avignon, France
| | - Johanna Clémencet
- UMR PVBMT, Université de La Réunion, Saint Pierre, La Réunion, France
| | | | - Alain Vignal
- GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet Tolosan, France
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Pilot M, Greco C, vonHoldt BM, Randi E, Jędrzejewski W, Sidorovich VE, Konopiński MK, Ostrander EA, Wayne RK. Widespread, long-term admixture between grey wolves and domestic dogs across Eurasia and its implications for the conservation status of hybrids. Evol Appl 2018; 11:662-680. [PMID: 29875809 PMCID: PMC5978975 DOI: 10.1111/eva.12595] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 01/03/2018] [Indexed: 01/05/2023] Open
Abstract
Hybridisation between a domesticated species and its wild ancestor is an important conservation problem, especially if it results in the introgression of domestic gene variants into wild species. Nevertheless, the legal status of hybrids remains unregulated, partially because of the limited understanding of the hybridisation process and its consequences. The occurrence of hybridisation between grey wolves and domestic dogs is well documented from different parts of the wolf geographic range, but little is known about the frequency of hybridisation events, their causes and the genetic impact on wolf populations. We analysed 61K SNPs spanning the canid genome in wolves from across Eurasia and North America and compared that data to similar data from dogs to identify signatures of admixture. The haplotype block analysis, which included 38 autosomes and the X chromosome, indicated the presence of individuals of mixed wolf-dog ancestry in most Eurasian wolf populations, but less admixture was present in North American populations. We found evidence for male-biased introgression of dog alleles into wolf populations, but also identified a first-generation hybrid resulting from mating between a female dog and a male wolf. We found small blocks of dog ancestry in the genomes of 62% Eurasian wolves studied and melanistic individuals with no signs of recent admixed ancestry, but with a dog-derived allele at a locus linked to melanism. Consequently, these results suggest that hybridisation has been occurring in different parts of Eurasia on multiple timescales and is not solely a recent phenomenon. Nevertheless, wolf populations have maintained genetic differentiation from dogs, suggesting that hybridisation at a low frequency does not diminish distinctiveness of the wolf gene pool. However, increased hybridisation frequency may be detrimental for wolf populations, stressing the need for genetic monitoring to assess the frequency and distribution of individuals resulting from recent admixture.
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Affiliation(s)
| | - Claudia Greco
- Department of Environmental Monitoring and Biodiversity ConservationItalian National Institute for Environmental Protection and ResearchBolognaItaly
| | - Bridgett M. vonHoldt
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNJUSA
| | - Ettore Randi
- Department of Environmental Monitoring and Biodiversity ConservationItalian National Institute for Environmental Protection and ResearchBolognaItaly
- Department 18/Section of Environmental EngineeringAalborg UniversityAalborgDenmark
| | - Włodzimierz Jędrzejewski
- Mammal Research InstitutePolish Academy of SciencesBiałowieżaPoland
- Present address:
Instituto Venezolano de Investigaciones Cientificas (IVIC)Centro de EcologiaCaracasVenezuela
| | | | | | - Elaine A. Ostrander
- Cancer Genetics and Comparative Genomics BranchNational Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Robert K. Wayne
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaLos AngelesCAUSA
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Duan Q, Xu Z, Raffield L, Chang S, Wu D, Lange EM, Reiner AP, Li Y. A robust and powerful two-step testing procedure for local ancestry adjusted allelic association analysis in admixed populations. Genet Epidemiol 2018; 42:288-302. [PMID: 29226381 PMCID: PMC5851818 DOI: 10.1002/gepi.22104] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 09/07/2017] [Accepted: 10/20/2017] [Indexed: 12/23/2022]
Abstract
Genetic association studies in admixed populations allow us to gain deeper understanding of the genetic architecture of human diseases and traits. However, population stratification, complicated linkage disequilibrium (LD) patterns, and the complex interplay of allelic and ancestry effects on phenotypic traits pose challenges in such analyses. These issues may lead to detecting spurious associations and/or result in reduced statistical power. Fortunately, if handled appropriately, these same challenges provide unique opportunities for gene mapping. To address these challenges and to take these opportunities, we propose a robust and powerful two-step testing procedure Local Ancestry Adjusted Allelic (LAAA) association. In the first step, LAAA robustly captures associations due to allelic effect, ancestry effect, and interaction effect, allowing detection of effect heterogeneity across ancestral populations. In the second step, LAAA identifies the source of association, namely allelic, ancestry, or the combination. By jointly modeling allele, local ancestry, and ancestry-specific allelic effects, LAAA is highly powerful in capturing the presence of interaction between ancestry and allele effect. We evaluated the validity and statistical power of LAAA through simulations over a broad spectrum of scenarios. We further illustrated its usefulness by application to the Candidate Gene Association Resource (CARe) African American participants for association with hemoglobin levels. We were able to replicate independent groups' previously identified loci that would have been missed in CARe without joint testing. Moreover, the loci, for which LAAA detected potential effect heterogeneity, were replicated among African Americans from the Women's Health Initiative study. LAAA is freely available at https://yunliweb.its.unc.edu/LAAA.
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Affiliation(s)
- Qing Duan
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, USA
- Department of Statistics, University of North Carolina, Chapel Hill, NC, USA
| | - Zheng Xu
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
- Department of Statistics, University of Nebraska-Lincoln, Lincoln, NE
- Initiative of Quantitative Life Sciences, University of Nebraska-Lincoln, Lincoln, NE
| | - Laura Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Suhua Chang
- Institute of Psychology, Chinese Academy of Science, Beijing, China
| | - Di Wu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
- Department of Periodontology, University of North Carolina, Chapel Hill, NC, USA
| | - Ethan M. Lange
- Department of Medicine, University of Colorado at Denver, Anschutz Medical Campus, Aurora, CO, USA
- Department of Biostatistics and Informatics, University of Colorado at Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Alex P. Reiner
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
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