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NeEstimator v2: re‐implementation of software for the estimation of contemporary effective population size (Ne) from genetic data
Abstract
NeEstimator v2 is a completely revised and updated implementation of software that produces estimates of contemporary effective population size, using several different methods and a single input file. NeEstimator v2 includes three single‐sample estimators (updated versions of the linkage disequilibrium and heterozygote‐excess methods, and a new method based on molecular coancestry), as well as the two‐sample (moment‐based temporal) method. New features include the following: (i) an improved method for accounting for missing data; (ii) options for screening out rare alleles; (iii) confidence intervals for all methods; (iv) the ability to analyse data sets with large numbers of genetic markers (10 000 or more); (v) options for batch processing large numbers of different data sets, which will facilitate cross‐method comparisons using simulated data; and (vi) correction for temporal estimates when individuals sampled are not removed from the population (Plan I sampling). The user is given considerable control over input data and composition, and format of output files. The freely available software has a new JAVA interface and runs under Mac OS, Linux and Windows.
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Cited by
Kaya, C., Generalovic, T. N., Ståhls, G., Hauser, M., Samayoa, A. C., Nunes-Silva, C. G., Roxburgh, H., Wohlfahrt, J., Ewusie, E. A., Kenis, M., et al. (2021) · BMC Biology · doi:10.1186/s12915-021-01029-w · Cited by 149
Navigating the temporal continuum of effective population size
Nadachowska‐Brzyska, K., Konczal, M., & Babik, W. (2022) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.13740 · Cited by 116
Zhang, W., Gao, X., Zhang, Y., Zhao, Y., Zhang, J., Jia, Y., Zhu, B., Xu, L., Zhang, L., Gao, H., et al. (2018) · BMC Genetics · doi:10.1186/s12863-018-0705-9 · Cited by 66
Rhode, C., Badenhorst, R., Hull, K. L., Greenwood, M. P., Bester‐van der Merwe, A. E., Andere, A. A., Picard, C. J., & Richards, C. (2020) · Animal Genetics · doi:10.1111/age.12961 · Cited by 58
Patterns of Genetic Diversity and Mating Systems in a Mass-Reared Black Soldier Fly Colony
Hoffmann, L., Hull, K. L., Bierman, A., Badenhorst, R., Bester-van der Merwe, A. E., & Rhode, C. (2021) · Insects · doi:10.3390/insects12060480 · Cited by 45
Johnson, J. L., Wittgenstein, H., Mitchell, S. E., Hyma, K. E., Temnykh, S. V., Kharlamova, A. V., Gulevich, R. G., Vladimirova, A. V., Fong, H. W. F., Acland, G. M., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0127013 · Cited by 38
Unbiased estimation of linkage disequilibrium from unphased data
Ragsdale, A. P., & Gravel, S. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msz265 · Cited by 36
Gordicho, V., Vicente, J. L., Sousa, C. A., Caputo, B., Pombi, M., Dinis, J., Seixas, G., Palsson, K., Weetman, D., Rodrigues, A., et al. (2014) · Malaria Journal · doi:10.1186/1475-2875-13-423 · Cited by 29
Species-specific SNP arrays for non-invasive genetic monitoring of a vulnerable bat
Thavornkanlapachai, R., Armstrong, K. N., Knuckey, C., Huntley, B., Hanrahan, N., & Ottewell, K. (2024) · Scientific Reports · doi:10.1038/s41598-024-51461-5 · Cited by 9
Metadata
- Authors
- Do, C., Waples, R. S., Peel, D., Macbeth, G. M., Tillett, B. J., & Ovenden, J. R.
- Venue
- Molecular Ecology Resources
- Publisher
- Wiley
- Published
- 2013-08-31
- Volume
- 14
- Issue
- 1
- Pages
- 209-214
- ISSN
- 1755-098X (ISSN-L)
- 1755-0998
- OpenAlex
- W2048069305
- Cited by
- 2,101
- References
- 0
- FWCI
- 51.19
- Type
- journal article
- Language
- en
- Open access
- closed
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