COMPUTER PROGRAMS: onesamp: a program to estimate effective population size using approximate Bayesian computation

@article{Tallmon2008COMPUTERPO,
  title={COMPUTER PROGRAMS: onesamp: a program to estimate effective population size using approximate Bayesian computation},
  author={David A. Tallmon and Ally Koyuk and Gordon Luikart and Mark A. Beaumont},
  journal={Molecular Ecology Resources},
  year={2008},
  volume={8}
}
The estimation of effective population size from one sample of genotypes has been problematic because most estimators have been proven imprecise or biased. We developed a web‐based program, onesamp that uses approximate Bayesian computation to estimate effective population size from a sample of microsatellite genotypes. onesamp requires an input file of sampled individuals’ microsatellite genotypes along with information about several sampling and biological parameters. onesamp provides an… 

Estimating Effective Population Size from Temporally Spaced Samples with a Novel, Efficient Maximum-Likelihood Algorithm

A new likelihood-based estimator NB^ for contemporary effective population size using temporal data is developed, and the results show that it is more accurate and has lower variance than previous methods.

When are genetic methods useful for estimating contemporary abundance and detecting population trends?

Monitoring Ne proved a more robust means of identifying stable and declining populations than monitoring N over most of the parameter space explored, and performance of the Ne estimator is further enhanced if the Ne/N ratio is low.

A comparison of single‐sample estimators of effective population sizes from genetic marker data

Extensive simulations show that SF estimator is more accurate, has a much wider application scope (e.g. suitable to nonrandom mating such as selfing, haplodiploid species, dominant markers) and is more robust than the other estimators.

Evaluating methods for estimating local effective population size with and without migration

Seven of the most cited methods for estimating Ne from genetic data are employed across simulated datasets with populations experiencing migration or no migration, finding considerable variance in performance of these methods, both within and across demographic scenarios.

Accounting for missing data in the estimation of contemporary genetic effective population size (Ne)

To evaluate bias and precision of several statistical approaches for dealing with missing data, simulated populations with known Ne and various degrees of missing data showed one method of correcting for missing data consistently performed the best for both single‐sample and two‐sample methods of estimating Ne and outperformed some methods currently in widespread use.

Testing single-sample estimators of effective population size in genetically structured populations

It was found that disregarding the population substructure resulted in TotalNe estimates with a low coefficient of variation but these estimates were systematically lower than the expected values, whereas hierarchical estimates accounting for population structure were closer to the expectedvalues but had a higher coefficient of variations.

Making sense of genetic estimates of effective population size

Wang showed that the sibship frequency (SF) and linkage disequilibrium (LD) methods perform dramatically better than the heterozygote excess and molecular coancestry methods under most scenarios, and he concluded that SF is generally more versatile than LD.

Inferring past demographic changes from contemporary genetic data: A simulation‐based evaluation of the ABC methods implemented in diyabc

It is concluded that diyabc‐based assessments are not suited to capture a detailed demographic history, but might be efficient at capturing simple, major demographic changes.

A comparison of single‐sample effective size estimators using empirical toad (Bufo calamita) population data: genetic compensation and population size‐genetic diversity correlations

Although the Bayesian method was the most precise, on most criteria the sibship method performed best, and provided evidence of genetic compensation in natterjack toads, and highlighted how the relationship between effective size and genetic diversity can vary as a function of geographical scale.

The use of approximate Bayesian computation in conservation genetics and its application in a case study on yellow-eyed penguins

The ABC approach is described and specific parts of its algorithm are identified that are being the subject of intensive studies in order to further expand its usability and discuss applications of this Bayesian algorithm in conservation studies, providing insights on the potentialities of these tools.
...

References

SHOWING 1-10 OF 17 REFERENCES

Comparative Evaluation of a New Effective Population Size Estimator Based on Approximate Bayesian Computation

Simulations of a Wright-Fisher population with known Ne show that theSummStat estimator is useful across a realistic range of individuals and loci sampled, generations between samples, and Ne values, and under the conditions simulated, SummStat confidence intervals were more conservative than the likelihood-based estimators and more likely to include true Ne.

Approximate Bayesian computation in population genetics.

A key advantage of the method is that the nuisance parameters are automatically integrated out in the simulation step, so that the large numbers of nuisance parameters that arise in population genetics problems can be handled without difficulty.

Estimating effective population size from linkage disequilibrium: severe bias in small samples

A computer program is developed and a way to determine whether a given sample size exceeds the population Ne and can therefore be used for the computation of an unbiased estimate is proposed to improve the method’s reliability and usefulness.

Estimating the effective number of breeders from heterozygote excess in progeny.

The method gave nearly unbiased estimates of Neb under all three mating systems, but the confidence intervals on the point estimates were sufficiently small to be useful only in polygamous and polygynous populations that were produced by <10 effective breeders, unless samples included > approximately 60 individuals and 20 multiallelic loci.

A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci*

It is shown that for realistic numbers of loci and alleles, the linkage disequilibrium method can provide precision comparable to that of the temporal method, but computer simulations show that estimates of Ne based on r^2 for unlinked, diallelic gene loci are sharply biased downwards.

Detection of reduction in population size using data from microsatellite loci

It is demonstrated that the mean ratio of the number of alleles to the range in allele size, which is calculated from a population sample of microsatellite loci, can be used to detect reductions in population size and that the value of M consistently predicts the reported demographic history for these populations.

Estimation of effective population size from data on linkage disequilibrium

A method is proposed for estimating effective population size from data on linkage disequilibrium among neutral genes at several polymorphic loci or restriction sites, but for very tightly linked genes estimates of N are more dependent on long-term than on recent population history.

A power analysis of microsatellite-based statistics for inferring past population growth.

The analysis indicates that the statistic based on the imbalance between allele size variance and heterozygosity at a locus has the highest power for detection of population growth, particularly when mutation rates vary across loci.

Inferring coalescence times from DNA sequence data.

Extensions are presented that allow for the effects of uncertainty in knowledge of population size and mutation rates, for variability in population sizes, for regions of different mutation rate, and for inference concerning the coalescence time of the entire population.

Molecular Evolutionary Genetics

Recent developments of statistical methods in molecular phylogenetics are reviewed and it is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used.