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Raw data for "Linkage disequilibrium estimation of effective population size with immigrants from divergent populations: a case study on Spanish mackerel (Scomberomorus commerson)."

Ovenden, Jennifer Raw data for "Linkage disequilibrium estimation of effective population size with immigrants from divergent populations: a case study on Spanish mackerel (Scomberomorus commerson).". [Dataset]

[img] Microsoft Word (Microsatellite genotypes for Australian Spanish Mackerel collected from Northern Territory)
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Abstract

Abstract of Macbeth, G. M., Broderick, D., Buckworth, R. & Ovenden, J. R. (In press, Feb 2013). Linkage disequilibrium estimation of effective population size with immigrants from divergent populations: a case study on Spanish mackerel (Scomberomorus commerson). G3: Genes, Genomes and Genetics.

Estimates of genetic effective population size (Ne) using molecular markers are a potentially useful tool for the management of endangered through to commercial species. But, pitfalls are predicted when the effective size is large, as estimates require large numbers of samples from wild populations for statistical validity. Our simulations showed that linkage disequilibrium estimates of Ne up to 10,000 with finite confidence limits can be achieved with sample sizes around 5000. This was deduced from empirical allele frequencies of seven polymorphic microsatellite loci in a commercially harvested fisheries species, the narrow barred Spanish mackerel (Scomberomorus commerson). As expected, the smallest standard deviation of Ne estimates occurred when low frequency alleles were excluded. Additional simulations indicated that the linkage disequilibrium method was sensitive to small numbers of genotypes from cryptic species or conspecific immigrants. A correspondence analysis algorithm was developed to detect and remove outlier genotypes that could possibly be inadvertently sampled from cryptic species or non-breeding immigrants from genetically separate populations. Simulations demonstrated the value of this approach in Spanish mackerel data. When putative immigrants were removed from the empirical data, 95% of the Ne estimates from jacknife resampling were above 24,000.

Item Type:Dataset
Type of Data:Microsatellite genotypes plus metadata
Copyright Holders:State of Queensland
Projects:Buckworth, R. C., Ovenden, J. R., D., B., Macbeth, G. M., McPherson, G. R. & Phelan, M. J. (2012). Genetag: Genetic Mark-Recapture for Real-Time Harvest Rate Monitoring. Pilot Studies in Northern Australia Spanish Mackerel Fisheries. Final Report. Austral
Additional Information:By downloading this dataset you agree to the terms and conditions of the attached licence.
Subjects:Science > Statistics > Simulation modelling
Aquaculture and Fisheries > Fisheries > Fishery conservation
Deposited On:11 Mar 2013 05:51
Last Modified:18 Apr 2013 00:38

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