scholarly journals Runs of Homozygosity in sub-Saharan African populations provide insights into a complex demographic and health history

2018 ◽  
Author(s):  
Francisco C. Ceballos ◽  
Scott Hazelhurst ◽  
Michele Ramsay
Keyword(s):  
Cultural Practices ◽  
Demographic History ◽  
Population History ◽  
Runs Of Homozygosity ◽  
Protein Coding ◽  
Heterogeneous Distribution ◽  
Health History ◽  
Multiple Protein ◽  
Sub Saharan ◽  
The Impact

AbstractThe study of runs of homozygosity (ROH), contiguous regions in the genome where an individual is homozygous across all sites, can shed light on the demographic history and cultural practices. We present a fine-scale ROH analysis of 1679 individuals from 28 sub-Saharan African (SSA) populations along with 1384 individuals from 17 world-wide populations. Using high-density SNP coverage, we could accurately obtain ROH as low as 300Kb using PLINK software. The analyses showed a heterogeneous distribution of autozygosity across SSA, revealing a complex demographic history. They highlight differences between African groups and can differentiate between the impact of consanguineous practices (e.g. among the Somali) and endogamy (e.g. among several Khoe-San groups1). The genomic distribution of ROH was analysed through the identification of ROH islands and regions of heterozygosity (RHZ). These homozygosity cold and hotspots harbour multiple protein coding genes. Studying ROH therefore not only sheds light on population history, but can also be used to study genetic variation related to the health of extant populations.

scholarly journals Cultural Innovations Influence Patterns of Genetic Diversity in Northwestern Amazonia

2018 ◽  
Author(s):  
Leonardo Arias ◽  
Roland Schröder ◽  
Alexander Hübner ◽  
Guillermo Barreto ◽  
Mark Stoneking ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Native American ◽  
Cultural Practices ◽  
Demographic History ◽  
Population History ◽  
Human Populations ◽  
Effective Population ◽  
Trade Networks ◽  
Males And Females ◽  
The Impact

ABSTRACTHuman populations often exhibit contrasting patterns of genetic diversity in the mtDNA and the non-recombining portion of the Y-chromosome (NRY), which reflect sex-specific cultural behaviors and population histories. Here, we sequenced 2.3 Mb of the NRY from 284 individuals representing more than 30 Native-American groups from Northwestern Amazonia (NWA) and compared these data to previously generated mtDNA genomes from the same groups, to investigate the impact of cultural practices on genetic diversity and gain new insights about NWA population history. Relevant cultural practices in NWA include postmarital residential rules and linguistic-exogamy, a marital practice in which men are required to marry women speaking a different language.We identified 2,969 SNPs in the NRY sequences; only 925 SNPs were previously described. The NRY and mtDNA data showed that males and females experienced different demographic histories: the female effective population size has been larger than that of males through time, and both markers show an increase in lineage diversification beginning ~5,000 years ago, with a male-specific expansion occurring ~3,500 years ago. These dates are too recent to be associated with agriculture, therefore we propose that they reflect technological innovations and the expansion of regional trade networks documented in the archaeological evidence. Furthermore, our study provides evidence of the impact of postmarital residence rules and linguistic exogamy on genetic diversity patterns. Finally, we highlight the importance of analyzing high-resolution mtDNA and NRY sequences to reconstruct demographic history, since this can differ considerably between males and females.

scholarly journals Re-introducing the Cambridge Group Family Reconstitutions

2020 ◽  
Vol 9 ◽  
pp. 24-48
Author(s):  
George Alter ◽  
Gill Newton ◽  
Jim Oeppen
Keyword(s):  
Demographic History ◽  
Population History ◽  
Intermediate Data ◽  
The Family ◽  
English Population ◽  
Family Reconstitution ◽  
Fertility Analysis ◽  
New Research ◽  
The Impact

English Population History from Family Reconstitution 1580–1837 was important both for its scope and its methodology. The volume was based on data from family reconstitutions of 26 parishes carefully selected to represent 250 years of English demographic history. These data remain relevant for new research questions, such as studying the intergenerational inheritance of fertility and mortality. To expand their availability the family reconstitutions have been translated into new formats: a relational database, the Intermediate Data Structure (IDS) and an episode file for fertility analysis. This paper describes that process and examines the impact of methodological decisions on analysis of the data. Wrigley, Davies, Oeppen, and Schofield were sensitive to changes in the quality of the parish registers and cautiously applied the principles of family reconstitution developed by Louis Henry. We examine how these choices affect the measurement of fertility and biases that are introduced when important principles are ignored.

scholarly journals The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives

2016 ◽  
Author(s):  
Yuval B. Simons ◽  
Guy Sella
Keyword(s):  
Demographic History ◽  
Population History ◽  
Human Populations ◽  
Data Sets ◽  
Loss Of Function ◽  
Mutation Load ◽  
Synonymous Mutations ◽  
Show Evidence ◽  
Out Of Africa ◽  
The Impact

AbstractOver the past decade, there has been both great interest and confusion about whether recent demographic events—notably the Out-of-Africa-bottleneck and recent population growth—have led to differences in mutation load among human populations. The confusion can be traced to the use of different summary statistics to measure load, which lead to apparently conflicting results. We argue, however, that when statistics more directly related to load are used, the results of different studies and data sets consistently reveal little or no difference in the load of non-synonymous mutations among human populations. Theory helps to understand why no such differences are seen, as well as to predict in what settings they are to be expected. In particular, as predicted by modeling, there is evidence for changes in the load of recessive loss of function mutations in founder and inbred human populations. Also as predicted, eastern subspecies of gorilla, Neanderthals and Denisovans, who are thought to have undergone reductions in population sizes that exceed the human Out-of-Africa bottleneck in duration and severity, show evidence for increased load of non-synonymous mutations (relative to western subspecies of gorillas and modern humans, respectively). A coherent picture is thus starting to emerge about the effects of demographic history on the mutation load in populations of humans and close evolutionary relatives.

scholarly journals Fine-scale population structure and demographic history of British Pakistanis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Elena Arciero ◽  
Sufyan A. Dogra ◽  
Daniel S. Malawsky ◽  
Massimo Mezzavilla ◽  
Theofanis Tsismentzoglou ◽  
...  
Keyword(s):  
Population Structure ◽  
Disease Risk ◽  
Demographic History ◽  
Population History ◽  
Genomic Diversity ◽  
Fine Scale ◽  
Effective Population ◽  
Scale Population ◽  
The Impact ◽  
British Pakistanis

AbstractPrevious genetic and public health research in the Pakistani population has focused on the role of consanguinity in increasing recessive disease risk, but little is known about its recent population history or the effects of endogamy. Here, we investigate fine-scale population structure, history and consanguinity patterns using genotype chip data from 2,200 British Pakistanis. We reveal strong recent population structure driven by the biraderi social stratification system. We find that all subgroups have had low recent effective population sizes (Ne), with some showing a decrease 15‒20 generations ago that has resulted in extensive identity-by-descent sharing and homozygosity, increasing the risk of recessive disorders. Our results from two orthogonal methods (one using machine learning and the other coalescent-based) suggest that the detailed reporting of parental relatedness for mothers in the cohort under-represents the true levels of consanguinity. These results demonstrate the impact of cultural practices on population structure and genomic diversity in Pakistanis, and have important implications for medical genetic studies.

scholarly journals Runs of homozygosity in killer whale genomes provide a global record of demographic histories

2021 ◽  
Author(s):  
Andy Foote ◽  
Rebecca Hooper ◽  
Alana Alexander ◽  
Robin Baird ◽  
Charles Baker ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Killer Whale ◽  
Demographic History ◽  
Population History ◽  
Runs Of Homozygosity ◽  
Effective Population ◽  
High Background ◽  
Genome Wide ◽  
Conservation Concern

Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically the probability of inbreeding mediated by mating system and/or population demography. Here, we investigate whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global dataset of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage. We first reconstruct demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We find a subset of populations declined in effective population size during the Late Pleistocene, while others had more stable demography. Genomes inferred to have undergone ancestral declines in effective population size, were autozygous at hundreds of short ROH (<1Mb), reflecting high background relatedness due to coalescence of haplotypes deep within the pedigree. In contrast, longer and therefore younger ROH (>1.5 Mb) were found in low latitude populations and populations of known conservation concern, including a Scottish population, for which 37.8% of the autosomes comprised of ROH >1.5 Mb in length.

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 Fine-scale population structure and demographic history of British Pakistanis

2020 ◽  
Author(s):  
Elena Arciero ◽  
Sufyan A. Dogra ◽  
Massimo Mezzavilla ◽  
Theofanis Tsismentzoglou ◽  
Qin Qin Huang ◽  
...  
Keyword(s):  
Population Structure ◽  
Disease Risk ◽  
Demographic History ◽  
Population History ◽  
Genomic Diversity ◽  
Fine Scale ◽  
Effective Population ◽  
Scale Population ◽  
The Impact ◽  
British Pakistanis

AbstractPrevious genetic and public health research in the Pakistani population has focused on the role of consanguinity in increasing recessive disease risk, but little is known about its recent population history or the effects of endogamy. Here, we investigate fine-scale population structure, history and consanguinity patterns using genetic and questionnaire data from >4,000 British Pakistani individuals, mostly with roots in Azad Kashmir and Punjab. We reveal strong recent population structure driven by the biraderi social stratification system. We find that all subgroups have had low effective population sizes (Ne) over the last 50 generations, with some showing a decrease in Ne 15-20 generations ago that has resulted in extensive identity-by-descent sharing and increased homozygosity. Using new theory, we show that the footprint of regions of homozygosity in the two largest subgroups is about twice that expected naively based on the self-reported consanguinity rates and the inferred historical Ne trajectory. These results demonstrate the impact of the cultural practices of endogamy and consanguinity on population structure and genomic diversity in British Pakistanis, and have important implications for medical genetic studies.

Comparing the Impact of Religious Discourse on HIV/AIDS in Islam and Christianity in Africa

2012 ◽  
Vol 8 ◽  
Author(s):  
Sloane Speakman
Keyword(s):  
Social Factors ◽  
Negative Relationship ◽  
Hiv Prevalence ◽  
Religious Discourse ◽  
Prevalence Rates ◽  
The Social ◽  
High Prevalence ◽  
Islam And Christianity ◽  
Sub Saharan ◽  
The Impact

In examining the strikingly high prevalence rates of HIV in many parts of Africa, reaching as high as 5% in some areas, how does the discourse promoted by the predominant religions across the continent, Islam and Christianity, affect the outlook of their followers on the epidemic? This question becomes even more intriguing after discovering the dramatic difference in rate of HIV prevalence between Muslims and Christians in Africa, confirmed by studies that have found a negative relationship to exist between HIV prevalence and being Muslim in Africa, even in Sub-Saharan African nations. Why does this gap in prevalence rates exist? Does Islam advocate participating in less risky behavior more so than Christianity? By comparing the social construction, epidemiological understanding and public responses among Muslim populations in Africa with Christian ones, it becomes apparent that many similarities exist between the two regarding discourse and that, rather than religious discourse itself, other social factors, such as circumcision practices, contribute more to the disparity in HIV prevalence than originally thought.

Systematic review methodology for development: An example from microfinance

2018 ◽  
Vol 43 (1) ◽  
pp. 65-77 ◽  
Author(s):  
Carina Van Rooyen ◽  
Ruth Stewart ◽  
Thea De Wet
Keyword(s):  
Systematic Review ◽  
International Development ◽  
Health Sector ◽  
Evidence Based ◽  
Systematic Review Methodology ◽  
Development Interventions ◽  
The Us ◽  
Sub Saharan ◽  
The Impact ◽  
Evidence Based Decision Making

Big international development donors such as the UK’s Department for International Development and USAID have recently started using systematic review as a methodology to assess the effectiveness of various development interventions to help them decide what is the ‘best’ intervention to spend money on. Such an approach to evidence-based decision-making has long been practiced in the health sector in the US, UK, and elsewhere but it is relatively new in the development field. In this article we use the case of a systematic review of the impact of microfinance on the poor in sub-Saharan African to indicate how systematic review as a methodology can be used to assess the impact of specific development interventions.

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