scholarly journals Fine-scale Inference of Ancestry Segments without Prior Knowledge of Admixing Groups

2018 ◽  
Author(s):  
Michael Salter-Townshend ◽  
Simon Myers
Keyword(s):  
Natural Selection ◽  
Prior Knowledge ◽  
Markov Models ◽  
Demographic History ◽  
Eastern European ◽  
North African ◽  
Local Ancestry ◽  
History Of ◽  
Sub Saharan ◽  
The Relationship

ABSTRACTWe present an algorithm for inferring ancestry segments and characterizing admixture events, which involve an arbitrary number of genetically differentiated groups coming together. This allows inference of the demographic history of the species, properties of admixing groups, identification of signatures of natural selection, and may aid disease gene mapping. The algorithm employs nested hidden Markov models to obtain local ancestry estimation along the genome for each admixed individual. In a range of simulations, the accuracy of these estimates equals or exceeds leading existing methods that return local ancestry. Moreover, and unlike these approaches, we do not require any prior knowledge of the relationship between sub-groups of donor reference haplotypes and the unseen mixing ancestral populations. Instead, our approach infers these in terms of conditional “copying probabilities”. In application to the Human Genome Diversity Panel we corroborate many previously inferred admixture events (e.g. an ancient admixture event in the Kalash). We further identify novel events such as complex 4-way admixture in San-Khomani individuals, and show that Eastern European populations possess 1 – 5% ancestry from a group resembling modern-day central Asians. We also identify evidence of recent natural selection favouring sub-Saharan ancestry at the HLA region, across North African individuals. We make available an R and C++ software library, which we term MOSAIC (which stands for MOSAIC Organises Segments of Ancestry In Chromosomes).

scholarly journals Fine-Scale Inference of Ancestry Segments Without Prior Knowledge of Admixing Groups

Genetics ◽  
2019 ◽  
Vol 212 (3) ◽  
pp. 869-889 ◽  
Author(s):  
Michael Salter-Townshend ◽  
Simon Myers
Keyword(s):  
Natural Selection ◽  
Prior Knowledge ◽  
Markov Models ◽  
Demographic History ◽  
Human Leukocyte ◽  
Eastern European ◽  
North African ◽  
Leukocyte Antigen ◽  
History Of ◽  
Sub Saharan

We present an algorithm for inferring ancestry segments and characterizing admixture events, which involve an arbitrary number of genetically differentiated groups coming together. This allows inference of the demographic history of the species, properties of admixing groups, identification of signatures of natural selection, and may aid disease gene mapping. The algorithm employs nested hidden Markov models to obtain local ancestry estimation along the genome for each admixed individual. In a range of simulations, the accuracy of these estimates equals or exceeds leading existing methods. Moreover, and unlike these approaches, we do not require any prior knowledge of the relationship between subgroups of donor reference haplotypes and the unseen mixing ancestral populations. Our approach infers these in terms of conditional “copying probabilities.” In application to the Human Genome Diversity Project, we corroborate many previously inferred admixture events (e.g., an ancient admixture event in the Kalash). We further identify novel events such as complex four-way admixture in San-Khomani individuals, and show that Eastern European populations possess 1−3% ancestry from a group resembling modern-day central Asians. We also identify evidence of recent natural selection favoring sub-Saharan ancestry at the human leukocyte antigen (HLA) region, across North African individuals. We make available an R and C++ software library, which we term MOSAIC (which stands for MOSAIC Organizes Segments of Ancestry In Chromosomes).

scholarly journals Recurrent Collection of Drosophila melanogaster from Wild African Environments and Genomic Insights into Species History

2019 ◽  
Vol 37 (3) ◽  
pp. 627-638 ◽  
Author(s):  
Quentin D Sprengelmeyer ◽  
Suzan Mansourian ◽  
Jeremy D Lange ◽  
Daniel R Matute ◽  
Brandon S Cooper ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Demographic History ◽  
Central Africa ◽  
Model Organism ◽  
Sub Saharan Africa ◽  
Wilderness Areas ◽  
Southern Central ◽  
History Of ◽  
Sub Saharan ◽  
Improved Model

Abstract A long-standing enigma concerns the geographic and ecological origins of the intensively studied vinegar fly, Drosophila melanogaster. This globally distributed human commensal is thought to originate from sub-Saharan Africa, yet until recently, it had never been reported from undisturbed wilderness environments that could reflect its precommensal niche. Here, we document the collection of 288 D. melanogaster individuals from multiple African wilderness areas in Zambia, Zimbabwe, and Namibia. The presence of D. melanogaster in these remote woodland environments is consistent with an ancestral range in southern-central Africa, as opposed to equatorial regions. After sequencing the genomes of 17 wilderness-collected flies collected from Kafue National Park in Zambia, we found reduced genetic diversity relative to town populations, elevated chromosomal inversion frequencies, and strong differences at specific genes including known insecticide targets. Combining these genomes with existing data, we probed the history of this species’ geographic expansion. Demographic estimates indicated that expansion from southern-central Africa began ∼13,000 years ago, with a Saharan crossing soon after, but expansion from the Middle East into Europe did not begin until roughly 1,800 years ago. This improved model of demographic history will provide an important resource for future evolutionary and genomic studies of this key model organism. Our findings add context to the history of D. melanogaster, while opening the door for future studies on the biological basis of adaptation to human environments.

scholarly journals The demography of the Canary Islands from a genetic perspective

2020 ◽  
Author(s):  
Rosa Fregel ◽  
Alejandra C Ordóñez ◽  
Javier G Serrano
Keyword(s):  
Canary Islands ◽  
Demographic History ◽  
American Continent ◽  
North African ◽  
European Colonization ◽  
History Of ◽  
The Impact ◽  
First Time ◽  
Canarian Archipelago ◽  
North African Origin

Abstract The establishment of European colonies across the world had important demographic consequences because it brought together diverse and distant civilizations for the first time. One clear example of this phenomenon is observed in the Canary Islands. The modern Canarian population is mainly the result of the admixture of natives of North African origin and European colonizers. However, additional migratory flows reached the islands due to the importation of enslaved Africans to cultivate sugarcane and the intense commercial contact with the American continent. In this review, we evaluate how the genetic analysis of indigenous, historical, and current populations has provided a glimpse into the Canary Islands’ complex genetic composition. We show that each island subpopulation’s characterization is needed to fully disentangle the demographic history of the Canarian archipelago. Finally, we discuss what research avenues remain to be explored to improve our knowledge of the impact that the European colonization had on its native population.

scholarly journals Whole genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection

2015 ◽  
Author(s):  
PingHsun Hsieh ◽  
Krishna R Veeramah ◽  
Joseph Lachance ◽  
Sarah A Tishkoff ◽  
Jeffrey D Wall ◽  
...  
Keyword(s):  
Gene Flow ◽  
Natural Selection ◽  
Muscle Development ◽  
Demographic History ◽  
Single Pulse ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Anatomically Modern Humans ◽  
History Of ◽  
African Pygmies

African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due to their unique lifestyle in the Central African rainforest. To identify genomic targets of adaptation, we sequenced the genomes of four Biaka Pygmies from the Central African Republic and jointly analyzed these data with the genome sequences of three Baka Pygmies from Cameroon and nine Yoruba famers. To account for the complex demographic history of these populations that includes both isolation and gene flow, we fit models using the joint allele frequency spectrum and validated them using independent approaches. Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 years ago. We also find that bi-directional asymmetric gene-flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. We then applied complementary statistics to scan the genome for evidence of selective sweeps and polygenic selection. We found that conventional statistical outlier approaches were biased toward identifying candidates in regions of high mutation or low recombination rate. To avoid this bias, we assigned P-values for candidates using whole-genome simulations incorporating demography and variation in both recombination and mutation rates. We found that genes and gene sets involved in muscle development, bone synthesis, immunity, reproduction, cell signaling and development, and energy metabolism are likely to be targets of positive natural selection in Western African Pygmies or their recent ancestors.

scholarly journals Evidences of delayed size recovery in Araucaria angustifolia populations after post-glacial colonization of highlands in Southeastern Brazil

2008 ◽  
Vol 80 (3) ◽  
pp. 433-443 ◽  
Author(s):  
Valdir M. Stefenon ◽  
Hermann Behling ◽  
Oliver Gailing ◽  
Reiner Finkeldey
Keyword(s):  
Population Size ◽  
Demographic History ◽  
Southeastern Brazil ◽  
Effective Population ◽  
History Of ◽  
Natural Stands ◽  
Recovery Dynamics ◽  
The Relationship ◽  
Palynological Records ◽  
Small Effective Population Size

Up to date, little is known about the relationship between historical demography and the current genetic structure of A. Angus As a first effort towards overcoming this lack, microsatellite data scored in six populations and isozyme allele frequencies published for 11 natural stands of this species were analysed in order to assess molecular signatures of populations' demographic history. Signatures of genetic bottlenecks were captured in all analysed populations of southeastern Brazil. Among southern populations, signatures of small effective population size were observed in only three out of 13 populations. Southern populations likely experienced faster recovery of population size after migration onto highlands. Accordingly, current genetic diversity of the southern populations gives evidence of fast population size recovery. In general, demographic history of A. Angusmatches climatic dynamics of southern and southeastern Brazil during the Pleistocene and Holocene. Palynological records and reconstruction of the past climatic dynamics of southeastern and southern Brazil support the hypothesis of different population size recovery dynamics for populations from these regions.

scholarly journals La peste nord-africaine et la théorie de Charles Nicolle sur les maladies infectieuses

Gesnerus ◽  
2010 ◽  
Vol 67 (1) ◽  
pp. 30-56
Author(s):  
Kmar Ben Néfissa ◽  
Anne Marie Moulin
Keyword(s):  
Local History ◽  
High Morbidity ◽  
North African ◽  
Migrant Populations ◽  
Middle East Countries ◽  
Immune Deficiencies ◽  
History Of ◽  
Sub Saharan ◽  
Typhus Fever

Many infectious diseases were described in North Africa in 18th–19th centuries by European travellers. Most of them were allegedly imported by new migrant populations coming from sub-Saharan, European or Middle East countries. Plague outbreaks have been described since the Black Death as diseases of the Mediterranean harbours. Charles Nicolle and his collaborators at the Pasteur Institute were witnesses to the extinction of plague and typhus fever in Tunisia. Both could be considered as endemo-epidemic diseases propagated by ancient nomad communities for centuries. Typhus was exported to other countries; plague was imported by Mediterranean travellers but also hid in unknown wild-animal reservoirs. The role of the bite of a rat’s flea was not confirmed and the pneumonic form might have prevailed in the medieval North African cities. Association between plague, typhus, flu and other causes of immune deficiencies could explain the high morbidity and mortality caused by plague in the past. The authors comment the local history of plague at the light of the evolutionary laws of infectious disease proposed by Charles Nicolle in 1930.

scholarly journals Estimation of coalescence probabilities and population divergence times from SNP data

Heredity ◽  
2021 ◽  
Author(s):  
Kristy Mualim ◽  
Christoph Theunert ◽  
Montgomery Slatkin
Keyword(s):  
Demographic History ◽  
Population History ◽  
Divergence Times ◽  
Population Divergence ◽  
High Coverage ◽  
Snp Data ◽  
Population Sizes ◽  
History Of ◽  
Relationship Of ◽  
The Relationship

AbstractWe present a method called the G(A|B) method for estimating coalescence probabilities within population lineages from genome sequences when one individual is sampled from each population. Population divergence times can be estimated from these coalescence probabilities if additional assumptions about the history of population sizes are made. Our method is based on a method presented by Rasmussen et al. (2014) to test whether an archaic genome is from a population directly ancestral to a present-day population. The G(A|B) method does not require distinguishing ancestral from derived alleles or assumptions about demographic history before population divergence. We discuss the relationship of our method to two similar methods, one introduced by Green et al. (2010) and called the F(A|B) method and the other introduced by Schlebusch et al. (2017) and called the TT method. When our method is applied to individuals from three or more populations, it provides a test of whether the population history is treelike because coalescence probabilities are additive on a tree. We illustrate the use of our method by applying it to three high-coverage archaic genomes, two Neanderthals (Vindija and Altai) and a Denisovan.

Admixture mapping of asthma in southwestern Europeans with North African ancestry influences

2020 ◽  
Vol 318 (5) ◽  
pp. L965-L975
Author(s):  
Beatriz Guillen-Guio ◽  
Tamara Hernández-Beeftink ◽  
Itahisa Marcelino-Rodríguez ◽  
Héctor Rodríguez-Pérez ◽  
Jose M. Lorenzo-Salazar ◽  
...  
Keyword(s):  
Fine Mapping ◽  
African Ancestry ◽  
European Population ◽  
Sub Saharan Africa ◽  
Admixture Mapping ◽  
Sequencing Data ◽  
North African ◽  
Mapping Study ◽  
Local Ancestry ◽  
Sub Saharan

The prevalence of asthma symptoms in Canary Islanders, a southwestern European population from Spain, is almost three times higher than the country average. Because the genetic risks identified so far explain <5% of asthma heritability, here we aimed to discover new asthma loci by completing the first admixture mapping study in Canary Islanders leveraging their distinctive genetic makeup, where significant northwest African influences coexist in the European genetic diversity landscape. A 2-stage study was conducted in 1,491 unrelated individuals self-declaring having a Canary Islands origin for the 4 grandparents. Local ancestry estimates were obtained for the shared positions with reference data from putative ancestral populations from Europe, North Africa, and sub-Saharan Africa. Case-control deviations in local ancestry were tested for each ancestry separately using logistic regressions adjusted for principal components, followed by fine-mapping analyses based on imputed genotypes and analyses of the likely deleterious exonic variants. The admixture mapping analysis of asthma detected that local North African ancestry in a locus spanning 365 kb of chromosome 16q23.3 was associated with asthma risk at study-wide significance [lowest P = 1.12 × 10−4; odds ratio (OR) = 2.05; 95% confidence interval (CI) = 1.41–3.00]. Fine-mapping studies identified a variant associated with asthma, and results were replicated in independent samples (rs3852738, OR = 1.34; 95% CI = 1.13–1.59, P = 7.58 × 10−4). Whole exome sequencing data from a subset of individuals revealed an enrichment of likely deleterious variants among asthma cases in 16q23.3, particularly in the phospholipase Cγ2 ( PLCG2) gene ( P = 3.67 × 10−4). By completing the first mapping study of asthma in admixed populations from Europe, our results revealed a new plausible asthma locus.

scholarly journals Demographic history and admixture dynamics in African Sahelian populations

2020 ◽  
Author(s):  
Viktor Černý ◽  
Cesar Fortes-Lima ◽  
Petr Tříska
Keyword(s):  
Demographic History ◽  
Distribution Patterns ◽  
Human Populations ◽  
African Region ◽  
Genetic Studies ◽  
Genomic Studies ◽  
History Of ◽  
Sub Saharan ◽  
High Degree ◽  
The Impact

Abstract The Sahel/Savannah belt of Africa is a contact zone between two subsistence systems (nomadic pastoralism and sedentary farming) and of two groups of populations, namely Eurasians penetrating from northern Africa southwards and sub-Saharan Africans migrating northwards. Because pastoralism is characterised by a high degree of mobility, it leaves few significant archaeological traces. Demographic history seen through the lens of population genetic studies complements our historical and archaeological knowledge in this African region. In this review, we highlight recent advances in our understanding of demographic history in the Sahel/Savannah belt as revealed by genetic studies. We show the impact of food-producing subsistence strategies on population structure as well as the somewhat different migration patterns in the western and eastern part of the region. Genomic studies show that the gene pool of various groups of Sahelians consists in a complex mosaic of several ancestries. We also touch upon various signals of genetic adaptations such as lactase persistence, taste sensitivity, and malaria resistance, all of which have different distribution patterns among Sahelian populations. Overall, genetic studies contribute to gain a deeper understanding about the demographic and adaptive history of human populations in this specific African region and beyond.

scholarly journals Using human demographic history to infer natural selection reveals contrasting patterns on different families of immune genes

2010 ◽  
Vol 278 (1711) ◽  
pp. 1587-1594 ◽  
Author(s):  
William Amos ◽  
Clare Bryant
Keyword(s):  
Natural Selection ◽  
Human Genome ◽  
Demographic History ◽  
Time Interval ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Immune Genes ◽  
Geographical Patterns ◽  
Human Genes ◽  
The Relationship

Detecting regions of the human genome that are, or have been, influenced by natural selection remains an important goal for geneticists. Many methods are used to infer selection, but there is a general reliance on an accurate understanding of how mutation and recombination events are distributed, and the well-known link between these processes and their evolutionary transience introduces uncertainty into inferences. Here, we present and apply two new, independent approaches; one based on single nucleotide polymorphisms (SNPs) that exploits geographical patterns in how humans lost variability as we colonized the world, the other based on the relationship between microsatellite repeat number and heterozygosity. We show that the two methods give concordant results. Of these, the SNP-based method is both widely applicable and detects selection over a well-defined time interval, the last 50 000 years. Analysis of all human genes by their Gene Ontology codes reveals how accelerated and decelerated loss of variability are both preferentially associated with immune genes. Applied to 168 immune genes used as the focus of a previous study, we show that members of the same gene family tend to yield similar indices of selection, even when located on different chromosomes. We hope our approach will provide a useful tool with which to infer where selection has acted to shape the human genome.

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