local ancestry
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2022 ◽  
Author(s):  
Siddharth Avadhanam ◽  
Amy L Williams

Population genetic analyses of local ancestry tracts routinely assume that the ancestral admixture process is identical for both parents of an individual, an assumption that may be invalid when considering recent admixture. Here we present Parental Admixture Proportion Inference (PAPI), a Bayesian tool for inferring the admixture proportions and admixture times for each parent of a single admixed individual. PAPI analyzes unphased local ancestry tracts and has two components models: a binomial model that exploits the informativeness of homozygous ancestry regions to infer parental admixture proportions, and a hidden Markov model (HMM) that infers admixture times from tract lengths. Crucially, the HMM employs an approximation to the pedigree crossover dynamics that accounts for unobserved within-ancestry recombination, enabling inference of parental admixture times. We compared the accuracy of PAPI's admixture proportion estimates with those of ANCESTOR in simulated admixed individuals and found that PAPI outperforms ANCESTOR by an average of 46% in a representative set of simulation scenarios, with PAPI's estimates deviating from the ground truth by 0.047 on average. Moreover, PAPI's admixture time estimates were strongly correlated with the ground truth in these simulations (R = 0.76), but have an average downward bias of 1.01 generations that is partly attributable to inaccuracies in local ancestry inference. As an illustration of its utility, we ran PAPI on real African Americans from the PAGE study (N = 5,786) and found strong evidence of assortative mating by ancestry proportion: couples' ancestry proportions are closer to each other than expected by chance (P<10-6), and are highly correlated (R = 0.87). We anticipate that PAPI will be useful in studying the population dynamics of admixture and will also be of interest to individuals seeking to learn about their personal genealogies.


PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12502
Author(s):  
Nikita Moshkov ◽  
Aleksandr Smetanin ◽  
Tatiana V. Tatarinova

Summary We developed PyLAE, a new tool for determining local ancestry along a genome using whole-genome sequencing data or high-density genotyping experiments. PyLAE can process an arbitrarily large number of ancestral populations (with or without an informative prior). Since PyLAE does not involve estimating many parameters, it can process thousands of genomes within a day. PyLAE can run on phased or unphased genomic data. We have shown how PyLAE can be applied to the identification of differentially enriched pathways between populations. The local ancestry approach results in higher enrichment scores compared to whole-genome approaches. We benchmarked PyLAE using the 1000 Genomes dataset, comparing the aggregated predictions with the global admixture results and the current gold standard program RFMix. Computational efficiency, minimal requirements for data pre-processing, straightforward presentation of results, and ease of installation make PyLAE a valuable tool to study admixed populations. Availability and implementation The source code and installation manual are available at https://github.com/smetam/pylae.


2021 ◽  
Vol 2 (4) ◽  
pp. 100766
Author(s):  
Jian Carrot-Zhang ◽  
Seunghun Han ◽  
Wanding Zhou ◽  
Jeffrey S. Damrauer ◽  
Anab Kemal ◽  
...  

2021 ◽  
Vol 12 ◽  
Author(s):  
Tamar E. Crum ◽  
Robert D. Schnabel ◽  
Jared E. Decker ◽  
Jeremy F. Taylor

Development of the American Breeds of beef cattle began in the 1920s as breeders and U. S. Experiment Station researchers began to create Bos taurus taurus × Bos taurus indicus hybrids using Brahman as the B. t. indicus source. By 1954, U.S. Breed Associations had been formed for Brangus (5/8 Angus × 3/8 Brahman), Beefmaster (½ Brahman × ¼ Shorthorn × ¼ Hereford), and Santa Gertrudis (5/8 Shorthorn × 3/8 Brahman). While these breeds were developed using mating designs expected to create base generation animals with the required genome contributions from progenitor breeds, each association has now registered advanced generation animals in which selection or drift may have caused the realized genome compositions to differ from initial expected proportions. The availability of high-density SNP genotypes for 9,161 Brangus, 3,762 Beefmaster, and 1,942 Santa Gertrudis animals allowed us to compare the realized genomic architectures of breed members to the base generation expectations. We used RFMix to estimate local ancestry and identify genomic regions in which the proportion of Brahman ancestry differed significantly from a priori expectations. For all three breeds, lower than expected levels of Brahman composition were found genome-wide, particularly in early-generation animals where we demonstrate that selection on beef production traits was likely responsible for the taurine enrichment. Using a proxy for generation number, we also contrasted the genomes of early- and advanced-generation animals and found that the indicine composition of the genome has increased with generation number likely due to selection on adaptive traits. Many of the most-highly differentiated genomic regions were breed specific, suggesting that differences in breeding objectives and selection intensities exist between the breeds. Global ancestry estimation is commonly performed in admixed animals to control for stratification in association studies. However, local ancestry estimation provides the opportunity to investigate the evolution of specific chromosomal segments and estimate haplotype effects on trait variation in admixed individuals. Investigating the genomic architecture of the American Breeds not only allows the estimation of indicine and taurine genome proportions genome-wide, but also the locations within the genome where either taurine or indicine alleles confer a selective advantage.


2021 ◽  
Vol 12 ◽  
Author(s):  
Yolandi Swart ◽  
Caitlin Uren ◽  
Paul D. van Helden ◽  
Eileen G. Hoal ◽  
Marlo Möller

Pulmonary tuberculosis (TB), caused by Mycobacterium tuberculosis, is a complex disease. The risk of developing active TB is in part determined by host genetic factors. Most genetic studies investigating TB susceptibility fail to replicate association signals particularly across diverse populations. South African populations arose because of multi-wave genetic admixture from the indigenous KhoeSan, Bantu-speaking Africans, Europeans, Southeast Asian-and East Asian populations. This has led to complex genetic admixture with heterogenous patterns of linkage disequilibrium and associated traits. As a result, precise estimation of both global and local ancestry is required to prevent both false positive and false-negative associations. Here, 820 individuals from South Africa were genotyped on the SNP-dense Illumina Multi-Ethnic Genotyping Array (∼1.7M SNPs) followed by local and global ancestry inference using RFMix. Local ancestry adjusted allelic association (LAAA) models were utilized owing to the extensive genetic heterogeneity present in this population. Hence, an interaction term, comprising the identification of the minor allele that corresponds to the ancestry present at the specific locus under investigation, was included as a covariate. One SNP (rs28647531) located on chromosome 4q22 was significantly associated with TB susceptibility and displayed a SNP minor allelic effect (G allele, frequency = 0.204) whilst correcting for local ancestry for Bantu-speaking African ancestry (p-value = 5.518 × 10−7; OR = 3.065; SE = 0.224). Although no other variants passed the significant threshold, clear differences were observed between the lead variants identified for each ancestry. Furthermore, the LAAA model robustly captured the source of association signals in multi-way admixed individuals from South Africa and allowed the identification of ancestry-specific disease risk alleles associated with TB susceptibility that have previously been missed.


2021 ◽  
Vol 51 ◽  
pp. e68-e69
Author(s):  
Mireille Kamariza ◽  
Kristin Tsuo ◽  
Zan Koenig ◽  
Benjamin Neale ◽  
Mark Daly ◽  
...  

2021 ◽  
Vol 51 ◽  
pp. e17-e18
Author(s):  
Marcos Santoro ◽  
Jessica Mauer ◽  
Caroline Nievergelt ◽  
Sintia Belangero ◽  
Elizabeth Atkinson

2021 ◽  
Vol 12 ◽  
Author(s):  
Bernadette Yougbaré ◽  
Dominique Ouédraogo ◽  
Arnaud S. R. Tapsoba ◽  
Albert Soudré ◽  
Bienvenue L. Zoma ◽  
...  

The genomes of crossbred (admixed) individuals are a mosaic of ancestral haplotypes formed by recombination in each generation. The proportion of these ancestral haplotypes in certain genomic regions can be responsible for either susceptibility or tolerance against pathogens, and for performances in production traits. Using a medium-density genomic marker panel from the Illumina Bovine SNP50 BeadChip, we estimated individual admixture proportions for Baoulé x Zebu crossbred cattle in Burkina Faso, which were tested for trypanosome infection by direct ELISA from blood samples. Furthermore, we calculated local ancestry deviation from average for each SNP across 29 autosomes to identify potential regions under selection in the trypanotolerant Baoulé cattle and their crossbreds. We identified significant deviation from the local average ancestry (above 5 and 10% genome-wide thresholds) on chromosomes 8 and 19 in the positive animals, while the negative ones showed higher deviation on chromosomes 6, 19, 21, and 22. Some candidate genes on chromosome 6 (PDGFRA) and chromosome 19 (CDC6) have been found associated to trypanotolerance in West African taurines. Screening for FST outliers in trypanosome positive/negative animals we detected seven variants putatively under selection. Finally, we identified a minimum set of highly ancestry informative markers for routine admixture testing. The results of this study contribute to a better understanding of the genetic basis of trypanotolerance in Baoulé cattle and their crossbreeds. Furthermore, we provide a small informative marker set to monitor admixture in this valuable indigenous breed. As such, our results are important for conserving the genetic uniqueness and trypanotolerance of Baoulé cattle, as well as for the improvement of Baoulé and Zebu crossbreds in specific community-based breeding programs.


2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yong Wang ◽  
Shiya Song ◽  
Joshua G. Schraiber ◽  
Alisa Sedghifar ◽  
Jake K. Byrnes ◽  
...  

Abstract Background We present ARCHes, a fast and accurate haplotype-based approach for inferring an individual’s ancestry composition. Our approach works by modeling haplotype diversity from a large, admixed cohort of hundreds of thousands, then annotating those models with population information from reference panels of known ancestry. Results The running time of ARCHes does not depend on the size of a reference panel because training and testing are separate processes, and the inferred population-annotated haplotype models can be written to disk and reused to label large test sets in parallel (in our experiments, it averages less than one minute to assign ancestry from 32 populations using 10 CPU). We test ARCHes on public data from the 1000 Genomes Project and the Human Genome Diversity Project (HGDP) as well as simulated examples of known admixture. Conclusions Our results demonstrate that ARCHes outperforms RFMix at correctly assigning both global and local ancestry at finer population scales regardless of the amount of population admixture.


2021 ◽  
Author(s):  
James A. Ward ◽  
Gillian P. McHugo ◽  
Michael J. Dover ◽  
Thomas J. Hall ◽  
Said Ismael Ng’ang’a ◽  
...  

AbstractDomestic cattle have a key economic role in African societies, providing an important source of mobile wealth through supply of meat, milk, cowhide, fuel, transport, and traction. The phenotypic diversity of African cattle reflects adaptation to a wide range of agroecological conditions and complex patterns of admixture between the humpless Bos taurus (taurine) and humped Bos indicus (zebu) subspecies, which share a common ancestor 150-500 thousand years ago. Human migration and trade from Asia have left a peak of zebu nuclear ancestry in East Africa and most cattle populations across the continent have a hybrid genetic composition. Notwithstanding this, all African cattle possess taurine mitochondrial haplotypes, even populations with significant zebu nuclear ancestry. In this regard, the efficient functioning of the mitochondrion relies on a network of biochemical interactions between the products of 37 mitochondrial genes and more than one thousand nuclear genes; therefore, admixed African cattle represent ideal populations for evaluating mitonuclear interactions and mismatch between the nuclear and mitochondrial genomes. Using high-density SNP array data from 18 different cattle populations, including ten African admixed breeds, we find strong evidence for mitonuclear coevolution in hybrid African cattle with significant retention of Bos taurus alleles at mitochondrially-targeted nuclear genes, particularly those genes with products that directly interact with mtDNA-encoded protein subunits in OXPHOS and ribosomal complexes, or that have functions in mtDNA replication. We also show that subspecific local ancestry varies substantially across the genomes of admixed populations, with a marked signal of taurine ancestry at the major histocompatibility (MHC) gene cluster, which likely reflects adaptation to infectious disease challenges facing African livestock. Our results demonstrate that African admixed cattle represent an excellent comparative model for studying the phenotypic consequences of mitonuclear mismatch and genomic introgression in humans and other large mammals.


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