scholarly journals multi-dice:rpackage for comparative population genomic inference under hierarchical co-demographic models of independent single-population size changes

2017 ◽  
Vol 17 (6) ◽  
pp. e212-e224 ◽  
Author(s):  
Alexander T. Xue ◽  
Michael J. Hickerson
Keyword(s):  
Population Size ◽  
Single Population ◽  
Demographic Models ◽  
Population Genomic ◽  
Comparative Population

scholarly journals Strong neutral sweeps occurring during a population contraction

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.

Comparative population genomic analysis provides insights into breeding of modern indica rice in China

Gene ◽  
2021 ◽  
Vol 768 ◽  
pp. 145303
Author(s):  
Chao Qin ◽  
Yanru Guo ◽  
Jianzhuang Wu ◽  
Long Wang ◽  
Milton Brian Traw ◽  
...  
Keyword(s):  
Indica Rice ◽  
Genomic Analysis ◽  
Population Genomic ◽  
Comparative Population

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

2003 ◽  
Vol 35 (3) ◽  
pp. 413-431 ◽  
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.

scholarly journals Quantifying whether different demographic models produce incongruent results on population dynamics of two long-term studied rodent species

2017 ◽  
Vol 3 (1) ◽  
pp. 18-26
Author(s):  
Giovanni Amori ◽  
Valentina De Silvestro ◽  
Paolo Ciucci ◽  
Luca Luiselli
Keyword(s):  
Population Dynamics ◽  
Population Density ◽  
Population Size ◽  
Myodes Glareolus ◽  
Suitable Model ◽  
Demographic Model ◽  
Apodemus Flavicollis ◽  
Demographic Models ◽  
Long Term Studies

Abstract1. Population density (ind/ha) of long-term (>15 years) series of CMR populations, using distinct demographic models designed for both open and closed populations, were analysed for two sympatric species of rodents (Myodes glareolus and Apodemus flavicollis) from a mountain area in central Italy, in order to test the relative performance of various employed demographic models. In particular, the hypothesis that enumeration models systematically underestimate the population size of a given population was tested.2. Overall, we compared the performance of 7 distinct demographic models, including both closed and open models, for each study species. Although the two species revealed remarkable intrinsic differences in demography traits (for instance, a lower propensity for being recaptured in Apodemus flavicollis), the Robust Design appeared to be the best fitting model, showing that it is the most suitable model for long-term studies.3. Among the various analysed demographic models, Jolly-Seber returned the lower estimates of population density for both species. Thus, this demographic model could not be suggested for being applied for long-term studies of small mammal populations because it tends to remarkably underestimate the effective population size. Nonetheless, yearly estimates of population density by Jolly-Seber correlated positively with yearly estimates of population density by closed population models, thus showing that interannual trends in population dynamics were uncovered by both types of demographic models, although with different values in terms of true population size.

Comparative population genomic analyses of the reconstructed local breed “Nero di Parma” with other commercial and autochthonous Italian pig breeds

2020 ◽  
Vol 235 ◽  
pp. 104014
Author(s):  
Giuseppina Schiavo ◽  
Samuele Bovo ◽  
Silvia Tinarelli ◽  
Hamed Kazemi ◽  
Maurizio Gallo ◽  
...  
Keyword(s):  
Local Breed ◽  
Pig Breeds ◽  
Population Genomic ◽  
Genomic Analyses ◽  
Comparative Population

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

2015 ◽  
Author(s):  
Patrick Manning ◽  
Scott Nickleach ◽  
Bowen Yi ◽  
Brian McGill
Keyword(s):  
Population Size ◽  
National Level ◽  
Historical Analysis ◽  
Calculated Data ◽  
African Continent ◽  
Relative Significance ◽  
Demographic Models ◽  
African Populations ◽  
Input Variables ◽  
And Migration

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.

scholarly journals The Validity of the Coalescent Approximation for Large Samples

2017 ◽  
Author(s):  
Andrew Melfi ◽  
Divakar Viswanath
Keyword(s):  
Sample Size ◽  
Population Size ◽  
Exponential Growth ◽  
Asymptotic Theory ◽  
Triple Collision ◽  
Demographic Models ◽  
Large Samples ◽  
Population Sizes ◽  
Sample Frequency ◽  
Haploid Population

AbstractThe Kingman coalescent, widely used in genetics, is known to be a good approximation when the sample size is small relative to the population size. In this article, we investigate how large the sample size can get without violating the coalescent approximation. If the haploid population size is 2N, we prove that for samples of size N1/3−ϵ, ϵ > 0, coalescence under the Wright-Fisher (WF) model converges in probability to the Kingman coalescent in the limit of large N. For samples of size N2/5−ϵ or smaller, the WF coalescent converges to a mixture of the Kingman coalescent and what we call the mod-2 coalescent. For samples of size N1/2 or larger, triple collisions in the WF genealogy of the sample become important. The sample size for which the probability of conformance with the Kingman coalescent is 95% is found to be 1.47 × N0.31 for N ∈ [103, 105], showing the pertinence of the asymptotic theory. The probability of no triple collisions is found to be 95% for sample sizes equal to 0.92 × N0.49, which too is in accord with the asymptotic theory.Varying population sizes are handled using algorithms that calculate the probability of WF coalescence agreeing with the Kingman model or taking place without triple collisions. For a sample of size 100, the probabilities of coalescence according to the Kingman model are 2%, 0%, 1%, and 0% in four models of human population with constant N, constant N except for two bottlenecks, recent exponential growth, and increasing recent exponential growth, respectively. For the same four demographic models and the same sample size, the probabilities of coalescence with no triple collision are 92%, 73%, 88%, and 87%, respectively. Visualizations of the algorithm show that even distant bottlenecks can impede agreement between the coalescent and the WF model.Finally, we prove that the WF sample frequency spectrum for samples of size N1/3−ϵ or smaller converges to the classical answer for the coalescent.

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