Demographic Models for Projecting Population and Migration: Methods for African Historical Analysis

This study presents methods for projecting population and migration over time in cases were empirical data are missing or undependable. The methods are useful for cases in which the researcher has details of population size and structure for a limited period of time (most obviously, the end point), with scattered evidence on other times. It enables estimation of population size, including its structure in age, sex, and status, either forward or backward in time. The program keeps track of all the details. The calculated data can be reported or sampled and compared to empirical findings at various times and places to expected values based on other procedures of estimation. The application of these general methods that is developed here is the projection of African populations backwards in time from 1950, since 1950 is the first date for which consistently strong demographic estimates are available for national-level populations all over the African continent. The models give particular attention to migration through enslavement, which was highly important in Africa from 1650 to 1900. Details include a sensitivity analysis showing relative significance of input variables and techniques for calibrating various dimensions of the projection with each other. These same methods may be applicable to quite different historical situations, as long as the data conform in structure to those considered here.

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Modeling human population separation history using physically phased genomes

10.1101/008367 ◽

2014 ◽

Author(s):

Shiya Song ◽

Elzbieta Sliwerska ◽

Sarah Emery ◽

Jeffrey M. Kidd

Keyword(s):

Population Size ◽

Time Estimation ◽

West African ◽

Population History ◽

Migration Rates ◽

Isolation With Migration ◽

African Populations ◽

And Migration ◽

Approximate Bayesian ◽

Population Genetic Analyses

AbstractPhased haplotype sequences are a key component in many population genetic analyses since variation in haplotypes reflects the action of recombination, selection, and changes in population size. In humans, haplotypes are typically estimated from unphased sequence or genotyping data using statistical models applied to large reference panels. To assess the importance of correct haplotype phase on population history inference, we performed fosmid pool sequencing and resolved phased haplotypes of five individuals from diverse African populations (including Yoruba, Esan, Gambia, Massai and Mende). We physically phased 98% of heterozygous SNPs into haplotype-resolved blocks, obtaining a block N50 of 1 Mbp. We combined these data with additional phased genomes from San, Mbuti, Gujarati and CEPH European populations and analyzed population size and separation history using the Pairwise Sequentially Markovian Coalescent (PSMC) and Multiple Sequentially Markovian Coalescent (MSMC) models. We find that statistically phased haplotypes yield an earlier split-time estimation compared with experimentally phased haplotypes. To better interpret patterns of cross-population coalescence, we implemented an approximate Bayesian computation (ABC) approach to estimate population split times and migration rates by fitting the distribution of coalescent times inferred between two haplotypes, one from each population, to a standard Isolation-with-Migration model. We inferred that the separation between hunter-gather populations and other populations happened around 120.0 to 140,000 years ago with gene flow continuing until 30,000 to 40,000 years ago; separation between west African and out of African populations happened around 70,000 to 80.0 years ago, while the separation between Massai and out of African populations happened around 50,000 years ago.

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Estimating Effective Population Size and Migration Rates From Genetic Samples Over Space and Time

Genetics ◽

10.1093/genetics/163.1.429 ◽

2003 ◽

Vol 163 (1) ◽

pp. 429-446 ◽

Cited By ~ 2

Author(s):

Jinliang Wang ◽

Michael C Whitlock

Keyword(s):

Population Size ◽

Effective Population Size ◽

Joint Estimation ◽

Large Sample Size ◽

Effective Population ◽

Likelihood Methods ◽

Marker Allele ◽

Migration Rates ◽

Space And Time ◽

And Migration

Abstract In the past, moment and likelihood methods have been developed to estimate the effective population size (Ne) on the basis of the observed changes of marker allele frequencies over time, and these have been applied to a large variety of species and populations. Such methods invariably make the critical assumption of a single isolated population receiving no immigrants over the study interval. For most populations in the real world, however, migration is not negligible and can substantially bias estimates of Ne if it is not accounted for. Here we extend previous moment and maximum-likelihood methods to allow the joint estimation of Ne and migration rate (m) using genetic samples over space and time. It is shown that, compared to genetic drift acting alone, migration results in changes in allele frequency that are greater in the short term and smaller in the long term, leading to under- and overestimation of Ne, respectively, if it is ignored. Extensive simulations are run to evaluate the newly developed moment and likelihood methods, which yield generally satisfactory estimates of both Ne and m for populations with widely different effective sizes and migration rates and patterns, given a reasonably large sample size and number of markers.

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Strong neutral sweeps occurring during a population contraction

10.1101/2021.08.25.457712 ◽

2021 ◽

Author(s):

Antoine Moinet ◽

Laurent Excoffier ◽

Stephan Peischl

Keyword(s):

Population Size ◽

Selective Sweep ◽

Fixation Time ◽

Size Change ◽

Similar Reduction ◽

Demographic Models ◽

Local Diversity ◽

Rapid Fixation ◽

Demographic Processes ◽

Specific Locus

A strong reduction in diversity around a specific locus is often interpreted as a recent rapid fixation of a positively selected allele, a phenomenon called a selective sweep. Rapid fixation of neutral variants can however lead to similar reduction in local diversity, especially when the population experiences changes in population size, e.g., bottlenecks or range expansions. The fact that demographic processes can lead to signals of nucleotide diversity very similar to signals of selective sweeps is at the core of an ongoing discussion about the roles of demography and natural selection in shaping patterns of neutral variation. Here we quantitatively investigate the shape of such neutral valleys of diversity under a simple model of a single population size change, and we compare it to signals of a selective sweep. We analytically describe the expected shape of such neutral sweeps and show that selective sweep valleys of diversity are, for the same fixation time, wider than neutral valleys. On the other hand, it is always possible to parametrize our model to find a neutral valley that has the same width as a given selected valley. We apply our framework to the case of a putative selective sweep signal around the gene Quetzalcoatl in D. melanogaster and show that the valley of diversity in the vicinity of this gene is compatible with a short bottleneck scenario without selection. Our findings provide further insight in how simple demographic models can create valleys of genetic diversity that may falsely be attributed to positive selection.

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Historical and current distribution, population size and possible migration routes of the Blue Swallow Hirundo atrocaerulea in Africa

Bird Conservation International ◽

10.1017/s0959270910000158 ◽

2010 ◽

Vol 20 (3) ◽

pp. 240-254 ◽

Cited By ~ 5

Author(s):

STEVEN W. EVANS ◽

H. BOUWMAN

Keyword(s):

Population Size ◽

Democratic Republic ◽

Sub Saharan Africa ◽

Total Current ◽

Migration Routes ◽

Breeding Grounds ◽

Republic Of The Congo ◽

Migratory Routes ◽

Sub Saharan ◽

And Migration

SummaryThe Blue Swallow Hirundo atrocaerulea is restricted to sub-Saharan Africa, its population size previously estimated at fewer than 1,500 pairs, and is classified as Vulnerable. A better understanding of its current distributional range, population size, protection status and migration routes would improve our ability to conserve the species and the grassland and wetland habitat on which it depends. We now estimate that the Blue Swallow population in the 1850s may have numbered between 1,560 and 2,300 pairs. Based on an assessment of available data, we now estimate the total current Blue Swallow population at 1,006 pairs or 2,012 individuals, an estimated 36–56% decline over the last 150 years. There may be three separate Blue Swallow sub-populations and seven separate migratory routes between their breeding and non-breeding grounds. The Blue Swallow’s range in South Africa and Swaziland has contracted by 74%. The majority of Blue Swallows occupy unprotected areas on their non-breeding grounds in the Democratic Republic of the Congo, Uganda and Kenya. The Blue Swallow population in Africa will continue to decline unless the causes of reduction in Blue Swallow habitat quantity and quality can be stopped and sufficient and additional habitat set aside to sustain viable Blue Swallow populations throughout their range.

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Roman History

Greece and Rome ◽

10.1017/s0017383513000302 ◽

2014 ◽

Vol 61 (1) ◽

pp. 129-133

Author(s):

B. M. Levick

Keyword(s):

Population Size ◽

Roman History ◽

Demographic Parameters ◽

Roman Economy ◽

Turn On ◽

The Past ◽

The Subject ◽

Ecological Parameters ◽

Roman Italy ◽

And Migration

A quality not much considered here in the past, how often a work is likely be taken from the shelf, prompts me to put Saskia's Hin'sThe Demography of Roman Italyin first position. For that depends in turn on how reliable, clear, and broad of outlook the chapters are, and where they lead the reader. Though dry and plain it might seem (for all the developing technologies), the subject moves directly towards a hot, polarized topic – ‘the Roman economy’ and its development – with oscillation between extreme positions. It is a particular merit, then, to put forward a fresh view (though previously adumbrated elsewhere) that is not extreme and must be taken seriously. That is where Hin will take historians. But the book is structured in three sections: economic and ecological parameters, demographic parameters (morality, fertility, and migration), and population size. The separate chapters are well supported from a variety of evidence, judiciously treated and well written up. That on climate, with a mildly positive conclusion, needed no apology. If I have a complaint is it about the index: dive into a passage involving ‘Brass modelling’ and you will have to rummage back in the text (111) for hope of identifying it.

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Structure and Governance in American Higher Education: Historical and Comparative Analysis in State Policy

Journal of Policy History ◽

10.1017/s0898030600004607 ◽

1989 ◽

Vol 1 (1) ◽

pp. 80-107 ◽

Cited By ~ 9

Author(s):

Hugh Davis Graham

Keyword(s):

Higher Education ◽

Liberal Arts ◽

Baby Boom ◽

National Level ◽

Historical Analysis ◽

State Level ◽

Manhattan Project ◽

The United States ◽

Cultural Tradition ◽

American Higher Education

Historians of public policy, who typically share a conviction that historical analysis can clarify the options available to policymakers, have witnessed this decade's quickening debate over the role and control of American higher education with, in one of Yogi Berra's immortal phrases, a sense of “déjà vu all over again.” Political leaders have continued, in a near vacuum of historical knowledge, to manipulate present variables and project them into the future with little awareness, beyond current political memory, of their past consequences, or of a legacy of political and cultural tradition that would constrain their manipulation. At the national level of debate, which is not where educational policy in the United States historically has been made, the level of historical awareness generally has been greater than at the state level. In the flurry of national commissions and foundation reports that probed the deficiencies of American higher education in 1984–85, the historical evolution of the college curriculum was addressed in reasonably informed historical terms.1 Even though the urgency of debate in the 1980s was fueled by the common pain of recession and post-baby-boom retrenchment, and also by fears of increasing vulnerability to oil boycotts and Japanese economic competition, the national elites who wrote the reports were mindful of the roots of Big Science in the Manhattan Project. Their ties to the academic establishment were intimate, and their historical memories embraced the wisdom of the liberal arts as well as the efficacy of land-grant agriculture and Silicon Valley.

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Masai and Kikuyu: An Historical Analysis of Culture Transmission

The Journal of African History ◽

10.1017/s002185370000904x ◽

1968 ◽

Vol 9 (4) ◽

pp. 571-583 ◽

Cited By ~ 10

Author(s):

William L. Lawren

Keyword(s):

Population Size ◽

East Africa ◽

Historical Analysis ◽

Significant Degree ◽

East African ◽

Relative Population ◽

Actual Nature ◽

History Of ◽

Great Damage ◽

Cultural Features

The tendency of East African Bantu tribes to borrow cultural features from pastoral or semi-pastoral ‘Nilo-Hamitic’ peoples has often been observed, but thus far only two serious attempts have been made to explain this phenomenon. Herskovits first put forward the idea that the tribes of East Africa formed a ‘cattle complex’ epitomized and shaped by the ‘Nilo-Hamitic’ pastoralists. In a more limited study, LeVine and Sangree concluded that the proclivity of a Bantu tribe to borrow from a ‘Nilo-Hamitic’ group was dependent upon the relative population size of the peoples in question, the success or failure of the Bantu group in defending itself against attack, and the need of the Bantu to ally themselves with a ‘Nilo-Hamitic’ tribe.The tentative history of relations between the Bantu Kikuyu and the ‘Nilo-Hamitic’ Masai established in this paper suggests that both these theories err. Beginning with the first meeting of the two tribes about 1750, the Masai inflicted great damage on the Kikuyu while both were resident on the plains near Mount Kenya. When the Kikuyu secluded themselves in the forests after about 1800, they began to experience a significant degree of success in warding off the Masai, without any need for allies. Yet borrowing went on almost without interruption throughout both periods.The actual nature of that borrowing was very different from the process which Herskovits imagined. Rather than being influenced by the way in which cattle functioned in Masai society, the Kikuyu were much impressed with the Masai as militarists, and this is reflected by the fact that the Kikuyu borrowed far more from the Masai military system than from anything relating to cattle.

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A RE-EXAMINATION OF LEVELS AND DIFFERENTIAL IN FERTILITY IN SOUTH AFRICA FROM RECENT EVIDENCE

Journal of Biosocial Science ◽

10.1017/s0021932003004139 ◽

2003 ◽

Vol 35 (3) ◽

pp. 413-431 ◽

Cited By ~ 8

Author(s):

ERIC O. UDJO

Keyword(s):

South Africa ◽

Population Size ◽

Total Population ◽

Demographic Models ◽

Final Estimate

The final estimate of South Africa's population as of October 1996 from the first post-apartheid census by Statistics South Africa was lower (40·6 million) than expected (42 million). The expectation of a total population of 42 million was largely based on results of apartheid projections of South Africa's population. The results of the last apartheid census in South Africa in 1991 had been adjusted such that it was consistent with results modelling the population size of South Africa. The discrepancy between the final estimate of the 1996 census and that expected from the modelling described above, and the departure by Statistics South Africa from previous practice of adjusting the census results to be consistent with demographic models, has generated controversies regarding the accuracy of the final results from the 1996 census. This study re-examines levels and differential in fertility in South Africa from recent evidence in order to assess whether or not the fertility inputs in projections of South Africa's population during the apartheid era overestimated fertility.

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U.S. National Higher Education Internationalization Policy

Journal of Comparative & International Higher Education ◽

10.32674/jcihe.v12i6s1.1884 ◽

2021 ◽

Vol 12 (6S1) ◽

Author(s):

Yovana Soobrayen Veerasamy

Keyword(s):

Higher Education ◽

Policy Making ◽

National Level ◽

Historical Analysis ◽

Multiple Sources ◽

The Public ◽

Policy Making Process ◽

Higher Education Internationalization ◽

The U.S ◽

Multiple Actors

Situated within the context of globalization, the purpose of this historical policy analysis study is to identify and describe the ways in which multiple actors shape national higher education internationalization policy within the U.S., and to capture the emerging direction in higher education internationalization policy at the national level between 2000 and 2019. Data will be collected from multiple sources at the national level essentially from organizations within the public, private and voluntary policy-making sectors. The guiding theoretical framework for this study will rely on horizontal and vertical historical analysis. The study aims to describe (1) how policy is shaped in a pluralistic policy-making process, (2) identify factors that influenced policy trajectory, and (3) outline policy rationales between 2000 and 2019.

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Genetic structure correlates with ethnolinguistic diversity in eastern and southern Africa

10.1101/2021.05.19.444732 ◽

2021 ◽

Author(s):

Elizabeth G. Atkinson ◽

Shareefa Dalvie ◽

Yakov Pichkar ◽

Allan Kalungi ◽

Lerato Majara ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Variant Interpretation ◽

African Continent ◽

Transmission Rates ◽

Genetics Research ◽

African Populations ◽

The World ◽

Eastern And Southern Africa ◽

Language Transmission

African populations are the most diverse in the world yet are sorely underrepresented in medical genetics research. Here, we examine the structure of African populations using genetic and comprehensive multigenerational ethnolinguistic data from the Neuropsychiatric Genetics of African Populations-Psychosis study (NeuroGAP-Psychosis) consisting of 900 individuals from Ethiopia, Kenya, South Africa, and Uganda. We find that self-reported language classifications meaningfully tag underlying genetic variation that would be missed with consideration of geography alone, highlighting the importance of culture in shaping genetic diversity. Leveraging our uniquely rich multi-generational ethnolinguistic metadata, we track language transmission through the pedigree, observing the disappearance of several languages in our cohort as well as notable shifts in frequency over three generations. We further find significantly higher language transmission rates for matrilineal groups as compared to patrilineal. We highlight both the diversity of variation within the African continent, as well as how within-Africa variation can be informative for broader variant interpretation; many variants appearing rare elsewhere are common in parts of Africa. The work presented here improves the understanding of the spectrum of genetic variation in African populations and highlights the enormous and complex genetic and ethnolinguistic diversity within Africa.

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