scholarly journals Variance and limiting distribution of coalescence times in a diploid model of a consanguineous population

2020 ◽  
Author(s):  
Alissa L. Severson ◽  
Shai Carmi ◽  
Noah A. Rosenberg
Keyword(s):  
Population Size ◽  
Kinship Coefficient ◽  
Demographic Parameters ◽  
Mating Pair ◽  
Runs Of Homozygosity ◽  
Identity By Descent ◽  
Coalescence Time ◽  
Diploid Populations ◽  
Diploid Model ◽  
Coalescence Times

AbstractRecent modeling studies interested in runs of homozygosity (ROH) and identity by descent (IBD) have sought to connect these properties of genomic sharing to pairwise coalescence times. Here, we examine a variety of features of pairwise coalescence times in models that consider consanguinity. In particular, we extend a recent diploid analysis of mean coalescence times for lineage pairs within and between individuals in a consanguineous population to derive the variance of coalescence times, studying its dependence on the frequency of consanguinity and the kinship coefficient of consanguineous relationships. We also introduce a separation-of-time-scales approach that treats consanguinity models analogously to mathematically similar phenomena such as partial selfing, using this approach to obtain coalescence-time distributions. This approach shows that the consanguinity model behaves similarly to a standard coalescent, scaling population size by a factor 1 − 3c, where c represents the kinship coefficient of a randomly chosen mating pair. It provides the explanation for an earlier result describing mean coalescence time in the consanguinity model in terms of c. The results extend the potential to make predictions about ROH and IBD in relation to demographic parameters of diploid populations.

scholarly journals Equilibrium Values of Measures of Population Subdivision for Stepwise Mutation Processes

Genetics ◽  
1996 ◽  
Vol 142 (4) ◽  
pp. 1357-1362
Author(s):  
François Rousset
Keyword(s):  
Population Structure ◽  
Population Subdivision ◽  
Identity By Descent ◽  
Infinite Allele Model ◽  
Coalescence Time ◽  
Stepwise Mutation ◽  
Expected Values ◽  
The Relationship ◽  
Allele Model ◽  
Coalescence Times

Abstract Expected values of Wright'sF-statistics are functions of probabilities of identity in state. These values may be quite different under an infinite allele model and under stepwise mutation processes such as those occurring at microsatellite loci. However, a relationship between the probability of identity in state in stepwise mutation models and the distribution of coalescence times can be deduced from the relationship between probabilities of identity by descent and the distribution of coalescence times. The values of FIS and FST can be computed using this property. Examination of the conditional probability of identity in state given some coalescence time and of the distribution of coalescence times are also useful for explaining the properties of FIS and FST at high mutation rate loci, as shown here in an island model of population structure.

scholarly journals Sensitivity analysis of effective population size to demographic parameters in house sparrow populations

2017 ◽  
Vol 26 (9) ◽  
pp. 2449-2465 ◽  
Author(s):  
Marlene Waege Stubberud ◽  
Ane Marlene Myhre ◽  
Håkon Holand ◽  
Thomas Kvalnes ◽  
Thor Harald Ringsby ◽  
...  
Keyword(s):  
Sensitivity Analysis ◽  
Population Size ◽  
Effective Population Size ◽  
House Sparrow ◽  
Demographic Parameters ◽  
Effective Population

scholarly journals High-throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability

2018 ◽  
Author(s):  
Pier Francesco Palamara ◽  
Jonathan Terhorst ◽  
Yun S. Song ◽  
Alkes L. Price
Keyword(s):  
Positive Selection ◽  
Snp Array ◽  
Complex Trait ◽  
Joint Analysis ◽  
Background Selection ◽  
Sequencing Data ◽  
Data Set ◽  
Coalescence Time ◽  
Recent Positive Selection ◽  
Coalescence Times

AbstractInterest in reconstructing demographic histories has motivated the development of methods to estimate locus-specific pairwise coalescence times from whole-genome sequence data. We developed a new method, ASMC, that can estimate coalescence times using only SNP array data, and is 2-4 orders of magnitude faster than previous methods when sequencing data are available. We were thus able to apply ASMC to 113,851 phased British samples from the UK Biobank, aiming to detect recent positive selection by identifying loci with unusually high density of very recent coalescence times. We detected 12 genome-wide significant signals, including 6 loci with previous evidence of positive selection and 6 novel loci, consistent with coalescent simulations showing that our approach is well-powered to detect recent positive selection. We also applied ASMC to sequencing data from 498 Dutch individuals (Genome of the Netherlands data set) to detect background selection at deeper time scales. We observed highly significant correlations between average coalescence time inferred by ASMC and other measures of background selection. We investigated whether this signal translated into an enrichment in disease and complex trait heritability by analyzing summary association statistics from 20 independent diseases and complex traits (average N=86k) using stratified LD score regression. Our background selection annotation based on average coalescence time was strongly enriched for heritability (p = 7×10−153) in a joint analysis conditioned on a broad set of functional annotations (including other background selection annotations), meta-analyzed across traits; SNPs in the top 20% of our annotation were 3.8x enriched for heritability compared to the bottom 20%. These results underscore the widespread effects of background selection on disease and complex trait heritability.

Roman History

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.

scholarly journals Comparative biology of two congeneric stinkbugs, Chinavia impicticornis and C. ubica (Hemiptera: Pentatomidae)

2015 ◽  
Vol 50 (5) ◽  
pp. 355-362 ◽  
Author(s):  
Cleonor Cavalcante Alves Silva ◽  
Raul Alberto Laumann ◽  
Maria Carolina Blassioli Moraes ◽  
Michely Ferreira Santos de Aquino ◽  
Miguel Borges
Keyword(s):  
Population Size ◽  
Life Table ◽  
Egg Production ◽  
Oviposition Period ◽  
Demographic Parameters ◽  
Comparative Biology ◽  
Immature Stages ◽  
Survival Curves ◽  
High Fecundity ◽  
Time Required

The objective of this work was to compare the biology of Chinavia impicticornis and C. ubica (Hemiptera: Pentatomidae), two species of stinkbugs that occur as secondary pests in soybean. Life table procedures were used for evaluating nymphs, and fecundity tables for evaluating adults, in order to establish the demographics of the two species. The two species have similar demographic parameters, and the development of immature stages, from egg to adult, had similar duration periods of approximately 30 days. In both species, eggs and second-instar nymphs were the stages with higher mortality. Total egg production did not differ between females of both species. Fecundity and survival curves for adults showed similar trends in both species. However, C. ubica had greater potential to increase its populations, since its fecundity parameters were significantly higher than those of C. impicticornis. Moreover, the generational time and the time required to double the population size were shorter in C. ubica. Prolonged longevity, long oviposition period, high fecundity, and the ability to rapidly increase their populations indicate that both species can become potential pests in favorable environments.

Dynamic modes of exploited limited population: results of modeling and numerical study

2016 ◽  
Vol 11 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Г.П. Неверова ◽  
G.P. Neverova
Keyword(s):  
Population Dynamics ◽  
Density Dependence ◽  
Population Size ◽  
Age Structure ◽  
Birth Rate ◽  
Numerical Study ◽  
Dynamic Regime ◽  
Demographic Parameters ◽  
Current Population

The paper investigates the model of population dynamics with age structure and density dependence of birth rate. We consider two situations: 1) the population develops freely and 2) the population is exploited. It was shown that harvesting leads to the stabilization of the dynamics. There is multiregimism, i.e. different dynamic regimes are possible with the same values of demographic parameters. It is shown that even a single harvesting in the current population size could lead to a change of the observed dynamic regime.

scholarly journals Genome-Wide Patterns of Homozygosity and Relevant Characterizations on the Population Structure in Piétrain Pigs

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 577
Author(s):  
Huiwen Zhan ◽  
Saixian Zhang ◽  
Kaili Zhang ◽  
Xia Peng ◽  
Shengsong Xie ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Effective Population Size ◽  
Average Length ◽  
The Other ◽  
Runs Of Homozygosity ◽  
Effective Population ◽  
Inbreeding Coefficients ◽  
Genome Wide ◽  
Genomic Regions

Investigating the patterns of homozygosity, linkage disequilibrium, effective population size and inbreeding coefficients in livestock contributes to our understanding of the genetic diversity and evolutionary history. Here we used Illumina PorcineSNP50 Bead Chip to identify the runs of homozygosity (ROH) and estimate the linkage disequilibrium (LD) across the whole genome, and then predict the effective population size. In addition, we calculated the inbreeding coefficients based on ROH in 305 Piétrain pigs and compared its effect with the other two types of inbreeding coefficients obtained by different calculation methods. A total of 23,434 ROHs were detected, and the average length of ROH per individual was about 507.27 Mb. There was no regularity on how those runs of homozygosity distributed in genome. The comparisons of different categories suggested that the formation of long ROH was probably related with recent inbreeding events. Although the density of genes located in ROH core regions is lower than that in the other genomic regions, most of them are related with Piétrain commercial traits like meat qualities. Overall, the results provide insight into the way in which ROH is produced and the identified ROH core regions can be used to map the genes associated with commercial traits in domestic animals.

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