title: Linkage Disequilibrium Estimation of Effective Population Size with Immigrants from Divergent Populations: A Case Study on Spanish Mackerel (Scomberomorus commerson).
abstract: Estimates of genetic effective population size (Ne) using molecular markers are a potentially useful tool for the management of endangered through to commercial species. However, pitfalls are predicted when the effective size is large because 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 of approximately 5000. This number 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 SD 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 nonbreeding 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 greater than 24,000.
authors.affiliation: Molecular Fisheries Laboratory, Queensland Government, St Lucia, Queensland, 4072, Australia gilbert.macbeth1@uq.net.au.
authors.forename: Gilbert Michael
authors.initials: GM
authors.lastname: Macbeth
authors.affiliation: Molecular Fisheries Laboratory, Queensland Government, St Lucia, Queensland, 4072, Australia.
authors.forename: Damien
authors.initials: D
authors.lastname: Broderick
authors.affiliation: CSIRO Marine & Atmospheric Research, Wealth from Oceans National Research Flagship, Brisbane, Queensland, 4001, Australia.
authors.forename: Rik C
authors.initials: RC
authors.lastname: Buckworth
authors.affiliation: Molecular Fisheries Laboratory, Queensland Government, St Lucia, Queensland, 4072, Australia.
authors.forename: Jennifer R
authors.initials: JR
authors.lastname: Ovenden
keywords: bias; correspondence analysis; effective population size; nontarget populations; outliers
references.citation: Genetics. 2011 Oct;189(2):633-44
references.pmid: 21840864
references.citation: Proc Biol Sci. 2010 Mar 7;277(1682):679-88
references.pmid: 19889703
references.citation: Mol Ecol. 2008 Aug;17(15):3428-47
references.pmid: 19160474
references.citation: J Fish Biol. 2012 May;80(6):2140-58
references.pmid: 22551174
references.citation: Heredity (Edinb). 2011 Oct;107(5):444-55
references.pmid: 21522167
references.citation: J Hered. 2008 Nov-Dec;99(6):694-5
references.pmid: 18703539
references.citation: Genetics. 2000 Jun;155(2):945-59
references.pmid: 10835412
references.citation: Evol Appl. 2010 May;3(3):244-62
references.pmid: 25567922
references.citation: Genetics. 1996 Sep;144(1):383-7
references.pmid: 8878701
references.citation: Theor Popul Biol. 1971 Jun;2(2):125-41
references.pmid: 5170716
references.citation: Theor Popul Biol. 2011 Sep;80(2):80-99
references.pmid: 21718713
references.citation: Mol Ecol Resour. 2008 Jul;8(4):753-6
references.pmid: 21585883
references.citation: Theor Popul Biol. 2011 Nov;80(3):185-96
references.pmid: 21763337
references.citation: Mol Ecol. 2011 Nov;20(21):4452-71
references.pmid: 21951766
references.citation: Genetics. 1931 Mar;16(2):97-159
references.pmid: 17246615
references.citation: Conserv Biol. 2011 Jun;25(3):438-49
references.pmid: 21284731
references.citation: Genetics. 1989 Feb;121(2):379-91
references.pmid: 2731727
references.citation: Mol Ecol. 2007 Jan;16(1):127-38
references.pmid: 17181726
references.citation: Genetics. 2004 Jan;166(1):505-12
references.pmid: 15020439