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Protocols

NeEstimator specifications

Information


Unique identifier OMICS_19563
Name NeEstimator
Software type Application/Script
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input format GENEPOP, FSTAT
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 2.01
Registration required Yes
Maintained Yes

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Maintainer


  • person_outline Jennifer Ovenden

Publication for NeEstimator

NeEstimator citations

 (140)
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Roads to isolation: Similar genomic history patterns in two species of freshwater crabs with contrasting environmental tolerances and range sizes

2018
Ecol Evol
PMCID: 5938456
PMID: 29760905
DOI: 10.1002/ece3.4017
call_split See protocol

[…] d rank test. Contemporary effective population sizes were estimated for each sampling locality using a bias‐corrected version of the linkage disequilibrium method (LDNe; Waples & Do, ) implemented in NeEstimator v. 2.01 (Do et al., ). Lowest allele frequency was defined at 0.05 to exclude single copy alleles, as rare alleles tend to bias linkage disequilibrium estimates upward (Waples & Do, ). […]

library_books

Contrasting life histories contribute to divergent patterns of genetic diversity and population connectivity in freshwater sculpin fishes

2018
BMC Evol Biol
PMCID: 5896141
PMID: 29642844
DOI: 10.1186/s12862-018-1171-8

[…] which would be expected with founder effects or recent population bottlenecks []. Contemporary Ne was also calculated for each of the samples in both species according to the LD method implemented in NEESTIMATOR v2.01 [].Two independent Mann-Whitney U tests were conducted to test whether there were significant differences in the levels of mitochondrial (HR) and microsatellite (AR) diversities betw […]

library_books

Population genetic analysis of the recently rediscovered Hula painted frog (Latonia nigriventer) reveals high genetic diversity and low inbreeding

2018
Sci Rep
PMCID: 5882862
PMID: 29615810
DOI: 10.1038/s41598-018-23587-w

[…] rsion 1.31 under the assumption of a minimum allele frequency of 2% to minimise potential bias caused by rare alleles, (iii) the heterozygote excess method, and (iv) the molecular coanchestry method (NeEstimator v2.01).In order to infer the population structure, we used the Bayesian clustering algorithm as implemented in STRUCTURE version 2.3.4 under the assumption of an admixture model with corre […]

call_split

Volatility in the effective size of a freshwater gastropod population

2018
Ecol Evol
PMCID: 5838079
PMID: 29531691
DOI: 10.1002/ece3.3912
call_split See protocol

[…] ere calculated using GenePop version 4.5.1 (Raymond & Rousset, ; Rousset, ). Values of F IS were computed using the method of Weir and Cockerham (), and exact p‐values were by the Markov chain method.NeEstimator v2.01 is freely available software designed to estimate effective population size using three single‐sample methods and three‐two‐sample (moment‐based temporal) methods (Do et al., ). Amon […]

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Genome‐wide comparisons reveal a clinal species pattern within a holobenthic octopod—the Australian Southern blue‐ringed octopus, Hapalochlaena maculosa (Cephalopoda: Octopodidae)

2018
Ecol Evol
PMCID: 5817145
PMID: 29468041
DOI: 10.1002/ece3.3845
call_split See protocol

[…] ering SNPs for these analyses helped ensure many of the simplifying assumptions used in the calculations were met (see Do et al., ; Jones & Wang, ; Waples, ; Waples & Do, ). N eLD was calculated with NeEstimator v2.0 (Do et al., ) using the linkage disequilibrium option. The proportions of full and half‐sibling pairs were calculated using the software program COLONY v2.0.6.1 (Jones & Wang, ). […]

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Increased natural reproduction and genetic diversity one generation after cessation of a steelhead trout (Oncorhynchus mykiss) conservation hatchery program

2018
PLoS One
PMCID: 5774695
PMID: 29351326
DOI: 10.1371/journal.pone.0190799
call_split See protocol

[…] in these measures between pre- and post-supplementation samples were tested for significance with Wilcoxon signed-rank tests. Estimates of the effective number of breeders were made with the program NeEstimator [], making use of the linkage disequilibrium method []. […]


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NeEstimator institution(s)
Conservation Biology Division, Northwest Fisheries Science Center, Seattle, WA, USA; NOAA Fisheries, Northwest Fisheries Science Centre, Seattle, WA, USA; CSIRO Mathematics and Informatics and Statistics. Castray Esplanade, Hobart, Tasmania, Australia; Queensland Government, Department of Agriculture, Fisheries and Forestry Brisbane, Queensland, Australia; Australian Institute of Marine Science, UWA Oceans Institute, Crawley, Western Australia, Australia; Molecular Fisheries Laboratory, School of Biomedical Sciences, University of Queensland, St Lucia, Queensland, Australia

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