Rejoinder for discussion on “Horseshoe‐based Bayesian nonparametric estimation of effective population size trajectories”

Biometrics ◽  
2020 ◽  
Vol 76 (3) ◽  
pp. 695-699
Author(s):  
James R. Faulkner ◽  
Andrew F. Magee ◽  
Beth Shapiro ◽  
Vladimir N. Minin
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Nonparametric Estimation ◽  
Bayesian Nonparametric ◽  
Effective Population ◽  
Bayesian Nonparametric Estimation

scholarly journals Horseshoe‐based Bayesian nonparametric estimation of effective population size trajectories

Biometrics ◽  
2020 ◽  
Vol 76 (3) ◽  
pp. 677-690 ◽  
Author(s):  
James R. Faulkner ◽  
Andrew F. Magee ◽  
Beth Shapiro ◽  
Vladimir N. Minin
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Nonparametric Estimation ◽  
Bayesian Nonparametric ◽  
Effective Population ◽  
Bayesian Nonparametric Estimation

scholarly journals A phylogenetic estimator of effective population size or mutation rate.

Genetics ◽  
1994 ◽  
Vol 136 (2) ◽  
pp. 685-692 ◽  
Author(s):  
Y X Fu
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Mutation Rate ◽  
Dna Sequences ◽  
High Efficiency ◽  
Minimum Variance ◽  
Population Subdivision ◽  
Effective Population ◽  
Fisher Model ◽  
Mitochondrial Sequences

Abstract A new estimator of the essential parameter theta = 4Ne mu from DNA polymorphism data is developed under the neutral Wright-Fisher model without recombination and population subdivision, where Ne is the effective population size and mu is the mutation rate per locus per generation. The new estimator has a variance only slightly larger than the minimum variance of all possible unbiased estimators of the parameter and is substantially smaller than that of any existing estimator. The high efficiency of the new estimator is achieved by making full use of phylogenetic information in a sample of DNA sequences from a population. An example of estimating theta by the new method is presented using the mitochondrial sequences from an American Indian population.

scholarly journals Alu Evolution in Human Populations: Using the Coalescent to Estimate Effective Population Size

Genetics ◽  
1997 ◽  
Vol 147 (4) ◽  
pp. 1977-1982
Author(s):  
Stephen T Sherry ◽  
Henry C Harpending ◽  
Mark A Batzer ◽  
Mark Stoneking
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Genomic Library ◽  
Diploid Cell ◽  
Human Populations ◽  
Effective Population ◽  
Alu Repeats ◽  
Branch Lengths ◽  
Diploid Cell Line ◽  
Coalescence Theory

Abstract There are estimated to be ~1000 members of the Ya5 Alu subfamily of retroposons in humans. This Subfamily has a distribution restricted to humans, with a few copies in gorillas and chimpanzees. Fifty-seven Ya5 elements were previously cloned from a HeLaderived randomly sheared total genomic library, sequenced, and screened for polymorphism in a panel of 120 unrelated humans. Forty-four of the 57 cloned Alu repeats were monomorphic in the sample and 13 Alu repeats were dimorphic for insertion presence/absence. The observed distribution of sample frequencies of the 13 dimorphic elements is consistent with the theoretical expectation for elements ascertained in a single diploid cell line. Coalescence theory is used to compute expected total pedigree branch lengths for monomorphic and dimorphic elements, leading to an estimate of human effective population size of ~18,000 during the last one to two million years.

scholarly journals DNA Sequence Variation and the Recombinational Landscape in Drosophila pseudoobscura: A Study of the Second Chromosome

Genetics ◽  
1999 ◽  
Vol 153 (2) ◽  
pp. 859-869 ◽  
Author(s):  
Martha T Hamblin ◽  
Charles F Aquadro
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Dna Sequence ◽  
Sequence Variation ◽  
Population Expansion ◽  
Drosophila Pseudoobscura ◽  
Effective Population ◽  
Standing Variation ◽  
Dna Sequence Polymorphism ◽  
Slightly Deleterious Mutations

Abstract The relationship between rates of recombination and DNA sequence polymorphism was analyzed for the second chromosome of Drosophila pseudoobscura. We constructed integrated genetic and physical maps of this chromosome using molecular markers at 10 loci spanning most of its physical length. The total length of the map was 128.2 cM, almost twice that of the homologous chromosome arm (3R) in D. melanogaster. There appears to be very little centromeric suppression of recombination, and rates of recombination are quite uniform across most of the chromosome. Levels of sequence variation (θW, based on the number of segregating sites) at seven loci (tropomyosin 1, Rhodopsin 3, Rhodopsin 1, bicoid, Xanthine dehydrogenase, Myosin light chain 1, and ribosomal protein 49) varied from 0.0036 to 0.0167. Generally consistent with earlier studies, the average estimate of θW at total sites is 1.5-fold higher than that in D. melanogaster, while average θW at silent sites is almost 3-fold higher. These estimates of variation were analyzed in the context of a background selection model under the same parameters of mutation rate and selection as have been proposed for D. melanogaster. It is likely that a significant fraction of the higher level of sequence variation in D. pseudoobscura can be explained by differences in regional rates of recombination rather than a larger species-level effective population size. However, the distribution of variation among synonymous, nonsynonymous, and noncoding sites appears to be quite different between the species, making direct comparisons of neutral variation, and hence inferences about effective population size, difficult. Tajima’s D statistics for 6 out of the 7 loci surveyed are negative, suggesting that D. pseudoobscura may have experienced a rapid population expansion in the recent past or, alternatively, that slightly deleterious mutations constitute an important component of standing variation in this species.

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