# 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…

## 351 Citations

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

- MathematicsGenetics
- 2015

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?

- Environmental ScienceMolecular ecology resources
- 2010

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

- BiologyMolecular ecology
- 2016

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

- BiologyEvolution; international journal of organic evolution
- 2015

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)

- MathematicsMolecular ecology resources
- 2013

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

- BiologyConservation Genetics
- 2013

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

- BiologyMolecular ecology
- 2016

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

- BiologyMolecular ecology resources
- 2017

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

- BiologyMolecular ecology
- 2009

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

- Computer ScienceConservation Genetics
- 2009

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.

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