scholarly journals ANALYZING GENE-FREQUENCY DATA WHEN THE EFFECTIVE POPULATION SIZE IS FINITE

Genetics ◽  
1980 ◽  
Vol 95 (2) ◽  
pp. 489-502
Author(s):  
Susan R Wilson
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Genetic Model ◽  
Size Structure ◽  
Balancing Selection ◽  
General Situation ◽  
Frequency Data ◽  
Effective Population ◽  
Data Set ◽  
Experimental Procedure

ABSTRACT The statistical methods used by SCHAFFER, YARDLEY and ANDERSON (1977) and by GIBSON et al. (1979) to analyze the variation in allele frequencies in two common types of experimental procedure, where the effective population size is finite, are extended to a more general situation involving a greater range of experiments. The analysis developed is more sensitive in detecting changes in allele frequency due to both fluctuating and balancing selection, as well as to directional selection. The error involved in many studies due to ignoring the effective population size structure would appear to be large. The range of hypotheses that can be considered may be increased as well. Finally, the method of determining bounds for the effective population size, when a particular genetic model is known to hold for a data set, is also outlined.

Population structure of the Sahiwal breed in Pakistan

1995 ◽  
Vol 60 (2) ◽  
pp. 163-168 ◽  
Author(s):  
A. Dahlin ◽  
U. N. Khan ◽  
A. H. Zafar ◽  
M. Saleem ◽  
M. A. Chaudhry ◽  
...  
Keyword(s):  
Population Structure ◽  
Population Size ◽  
Effective Population Size ◽  
Breeding Population ◽  
Effective Population ◽  
Data Set ◽  
Inbreeding Coefficients ◽  
Sahiwal Cows ◽  
The Mean ◽  
Average Population Size

AbstractThe present study was undertaken to assist conservation and improvement schemes in the Sahiwal breed of cattle in Pakistan. A data set, consisting of records of 244 pure Sahiwal breeding bulls and 5247 cows, the latter representing about 80% of all recorded Sahiwal cows in Pakistan born during a period covering about 20 years, was analysed with regard to inbreeding, additive relationships, effective population size and generation intervals. Average inbreeding coefficients of 1224 cows and 49 bulls, for which at least the grandparents and great-grandsires were known, were 0·043 and 0·046, respectively. About two-thirds of the inbreeding was due to matings between animals with parents or grandparents in common. The mean additive relationship among the cows was 0·062, with within-herd averages ranging from 0·087 to 0·358. The average population size in a subdata set of recorded Sahiwal cattle from 1980 to 1984 was 1612, whereas the most likely estimate of the effective population size was about 30 animals for the same active breeding population. The study indicated the immediate need for an active conservation programme whereby the Sahiwal subpopulations of India and Kenya also should be involved.

scholarly journals Genetic differentiation of quantitative characters between populations or species: I. Mutation and random genetic drift

1982 ◽  
Vol 39 (3) ◽  
pp. 303-314 ◽  
Author(s):  
Ranajit Chakraborty ◽  
Masatoshi Nei
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Genetic Drift ◽  
Genetic Variance ◽  
Genetic Model ◽  
Neutral Evolution ◽  
Random Genetic Drift ◽  
Effective Population ◽  
Quantitative Characters ◽  
Allelic State

SummaryIntroducing a new genetic model called the discrete allelic-state model, the evolutionary change of genetic variation of quantitative characters within and between populations is studied under the assumption of no selection. This model allows us to study the effects of mutation and random genetic drift in detail. It is shown that when the allelic effects on phenotype are additive, the rate of approach of the genetic variance within populations to the equilibrium value depends only on the effective population size. It is also shown that the distribution of genotypic value often deviates from normality particularly when the effective population size and the number of loci concerned are small. On the other hand, the interpopulational variance increases linearly with time, if the intrapopu-lational variance remains constant. Therefore, the ratio of interpopulational variance to intrapopulational variance can be used for testing the hypothesis of neutral evolution of quantitative characters.

scholarly journals Historical effective population size of North American hoary bat (Lasiurus cinereus) and challenges to estimating trends in contemporary effective breeding population size from archived samples

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11285
Author(s):  
Robert S. Cornman ◽  
Jennifer A. Fike ◽  
Sara J. Oyler-McCance ◽  
Paul M. Cryan
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
North American ◽  
Breeding Population ◽  
Data Filtering ◽  
Effective Population ◽  
Data Set ◽  
Lasiurus Cinereus ◽  
The Impact ◽  
Hoary Bats

Background Hoary bats (Lasiurus cinereus) are among the bat species most commonly killed by wind turbine strikes in the midwestern United States. The impact of this mortality on species census size is not understood, due in part to the difficulty of estimating population size for this highly migratory and elusive species. Genetic effective population size (Ne) could provide an index of changing census population size if other factors affecting Ne are stable. Methods We used the NeEstimator package to derive effective breeding population size (Nb) estimates for two temporally spaced cohorts: 93 hoary bats collected in 2009–2010 and an additional 93 collected in 2017–2018. We sequenced restriction-site associated polymorphisms and generated a de novo genome assembly to guide the removal of sex-linked and multi-copy loci, as well as identify physically linked markers. Results Analysis of the reference genome with psmc suggested at least a doubling of Ne in the last 100,000 years, likely exceeding Ne = 10,000 in the Holocene. Allele and genotype frequency analyses confirmed that the two cohorts were comparable, although some samples had unusually high or low observed heterozygosities. Additionally, the older cohort had lower mean coverage and greater variability in coverage, and batch effects of sampling locality were observed that were consistent with sample degradation. We therefore excluded samples with low coverage or outlier heterozygosity, as well as loci with sequence coverage far from the mode value, from the final data set. Prior to excluding these outliers, contemporary Nb estimates were significantly higher in the more recent cohort, but this finding was driven by high values for the 2018 sample year and low values for all other years. In the reduced data set, Nb did not differ significantly between cohorts. We found base substitutions to be strongly biased toward cytosine to thymine or the complement, and further partitioning loci by substitution type had a strong effect on Nb estimates. Minor allele frequency and base quality bias thresholds also had strong effects on Nb estimates. Instability of Nb with respect to common data filtering parameters and empirically identified factors prevented robust comparison of the two cohorts. Given that confidence intervals frequently included infinity as the stringency of data filtering increased, contemporary trends in Nb of North American hoary bats may not be tractable with the linkage disequilibrium method, at least using the protocol employed here.

scholarly journals Hitchhiking and recombination in birds: evidence from Mhc-linked and unlinked loci in Red-winged Blackbirds (Agelaius phoeniceus)

2004 ◽  
Vol 84 (3) ◽  
pp. 175-192 ◽  
Author(s):  
SCOTT V. EDWARDS ◽  
MEGAN DILLON
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Effective Population Size ◽  
Recombination Rate ◽  
Nucleotide Diversity ◽  
Genetic Recombination ◽  
Balancing Selection ◽  
Agelaius Phoeniceus ◽  
Effective Population ◽  
Intron 2

Hitchhiking phenomena and genetic recombination have important consequences for a variety of fields for which birds are model species, yet we know virtually nothing about naturally occurring rates of recombination or the extent of linkage disequilibrium in birds. We took advantage of a previously sequenced cosmid clone from Red-winged Blackbirds (Agelaius phoeniceus) bearing a highly polymorphic Mhc class II gene, Agph-DAB1, to measure the extent of linkage disequilibrium across ~40 kb of genomic DNA and to determine whether non-coding nucleotide diversity was elevated as a result of physical proximity to a target of balancing selection. Application of coalescent theory predicts that the hitchhiking effect is enhanced by the larger effective population size of blackbirds compared with humans, despite the presumably higher rates of recombination in birds. We surveyed sequence polymorphism at three Mhc-linked loci occurring 1·5–40 kb away from Agph-DAB1 and found that nucleotide diversity was indistinguishable from that found at three presumably unlinked, non-coding introns (β-actin intron 2, β-fibrinogen intron 7 and rhodopsin intron 2). Linkage disequilibrium as measured by Lewontin's D' was found only across a few hundred base pairs within any given locus, and was not detectable among any Mhc-linked loci. Estimated rates of the per site recombination rate ρ derived from three different analytical methods suggest that the amounts of recombination in blackbirds are up to two orders of magnitude higher than in humans, a discrepancy that cannot be explained entirely by the higher effective population size of blackbirds relative to humans. In addition, the ratio of the number of estimated recombination events per mutation frequently exceeds 1, as in Drosophila, again much higher than estimates in humans. Although the confidence limits of the blackbird estimates themselves span an order of magnitude, these data suggest that in blackbirds the hitchhiking effect for this region is negligible and may imply that the per site per individual recombination rate is high, resembling those of Drosophila more than those of humans.

scholarly journals A pseudo-likelihood method for estimating effective population size from temporally spaced samples

2001 ◽  
Vol 78 (3) ◽  
pp. 243-257 ◽  
Author(s):  
JINLIANG WANG
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Growth Parameters ◽  
Computing Time ◽  
Likelihood Method ◽  
Effective Population ◽  
Data Set ◽  
Statistic Method ◽  
Pseudo Likelihood ◽  
Wide Range

A pseudo maximum likelihood method is proposed to estimate effective population size (Ne) using temporal changes in allele frequencies at multi-allelic loci. The computation is simplified dramatically by (1) approximating the multi-dimensional joint probabilities of all the data by the product of marginal probabilities (hence the name pseudo-likelihood), (2) exploiting the special properties of transition matrix and (3) using a hidden Markov chain algorithm. Simulations show that the pseudo-likelihood method has a similar performance but needs much less computing time and storage compared with the full likelihood method in the case of 3 alleles per locus. Due to computational developments, I was able to assess the performance of the pseudo-likelihood method against the F-statistic method over a wide range of parameters by extensive simulations. It is shown that the pseudo-likelihood method gives more accurate and precise estimates of Ne than the F-statistic method, and the performance difference is mainly due to the presence of rare alleles in the samples. The pseudo-likelihood method is also flexible and can use three or more temporal samples simultaneously to estimate satisfactorily the Nes of each period, or the growth parameters of the population. The accuracy and precision of both methods depend on the ratio of the product of sample size and the number of generations involved to Ne, and the number of independent alleles used. In an application of the pseudo-likelihood method to a large data set of an olive fly population, more precise estimates of Ne are obtained than those from the F-statistic method.

scholarly journals Joint estimation of selection intensity and mutation rate under balancing selection withapplications to HLA

2021 ◽  
Author(s):  
Montgomery Slatkin
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Balancing Selection ◽  
Composite Likelihood ◽  
Joint Estimation ◽  
Likelihood Method ◽  
Mutation Rates ◽  
Symmetric Model ◽  
Effective Population ◽  
Selection Intensities

A composite likelihood method is introduced for jointly estimating the intensity of selection and the rate of mutation, both scaled by the effective population size, when there is balancing selection at a single multi-allelic locus in an isolated population at demographic equilibrium. The performance of the method is tested using simulated data. Average estimated mutation rates and selection intensities are close to the true values but there is considerable variation about the averages. Allowing for both population growth and population subdivision do not result in qualitative differences but the estimated mutation rates and selection intensities do not in general reflect the current effective population size. The method is applied to three class I (HLA-A, HLA-B and HLA-C) and two class II loci (HLA-DRB1 and HLA-DQA1) in the 1000 Genomes populations. Allowing for asymmetric balancing selection has only a slight effect on the results from the symmetric model. Mutations that restore symmetry of the selection model are preferentially retained because of the tendency of natural selection to maximize average fitness. However, slight differences in selective effects result in much longer persistence time of some alleles. Trans-species polymorphism (TSP), which is characteristic of MHC in vertebrates, is more likely when there are small differences in allelic fitness than when complete symmetry is assumed. Therefore, variation in allelic fitness expands the range of parameter values consistent with observations of TSP.

scholarly journals Somatic drift and rapid loss of heterozygosity suggest small effective population size of stem cells and high somatic mutation rate in asexual planaria

2019 ◽  
Author(s):  
Hosseinali Asgharian ◽  
Joseph Dunham ◽  
Paul Marjoram ◽  
Sergey V. Nuzhdin
Keyword(s):  
Stem Cells ◽  
Population Size ◽  
Effective Population Size ◽  
Somatic Mutation ◽  
Mutation Rate ◽  
Nucleotide Diversity ◽  
Genetic Model ◽  
Neutral Evolution ◽  
Multiple Time ◽  
Effective Population

AbstractPlanarian flatworms have emerged as highly promising models of body regeneration due to the many stem cells scattered through their bodies. Currently, there is no consensus as to the number of stem cells active in each cycle of regeneration or the equality of their relative contributions. We approached this problem with a population genetic model of somatic genetic drift. We modeled the fissiparous life cycle of asexual planarians as an asexual population of cells that goes through repeated events of splitting into two subpopulations followed by population growth to restore the original size. We sampled a pedigree of obligate asexual clones of Girardia cf. tigrina at multiple time points encompassing 14 generations. Effective population size of stem cells was inferred from the magnitude of temporal fluctuations in the frequency of somatic variants and under most of the examined scenarios was estimated to be in the range of a few hundreds. Average genomic nucleotide diversity was 0.00398. Assuming neutral evolution and mutation-drift equilibrium, the somatic mutation rate was estimated in the 10−5 − 10−7 range. Alternatively, we estimated Ne and somatic μ from temporal changes in nucleotide diversity π without the assumption of equilibrium. This second method suggested even smaller Ne and larger μ. A key unknown parameter in our model on which estimates of Ne and μ depend is g, the ratio of cellular to organismal generations determined by tissue turnover rate. Small effective number of propagating stem cells might contribute to reducing reproductive conflicts in clonal organisms.

Estimation of Population Growth or Decline in Genetically Monitored Populations

Genetics ◽  
2003 ◽  
Vol 164 (3) ◽  
pp. 1139-1160 ◽  
Author(s):  
Mark A Beaumont
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Importance Sampling ◽  
Data Sets ◽  
Frequency Data ◽  
Effective Population ◽  
Equivalent Effect ◽  
Recent Sample ◽  
Fully Bayesian ◽  
General Method

AbstractThis article introduces a new general method for genealogical inference that samples independent genealogical histories using importance sampling (IS) and then samples other parameters with Markov chain Monte Carlo (MCMC). It is then possible to more easily utilize the advantages of importance sampling in a fully Bayesian framework. The method is applied to the problem of estimating recent changes in effective population size from temporally spaced gene frequency data. The method gives the posterior distribution of effective population size at the time of the oldest sample and at the time of the most recent sample, assuming a model of exponential growth or decline during the interval. The effect of changes in number of alleles, number of loci, and sample size on the accuracy of the method is described using test simulations, and it is concluded that these have an approximately equivalent effect. The method is used on three example data sets and problems in interpreting the posterior densities are highlighted and discussed.

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