Abstract
In population genetic studies, a proper sampling design is crucial for reliable population differentiation estimates. For genetic studies on amphibians, fish or insects, larvae are often sampled instead of adults due to their higher accessibility and abundance. However, population genetic parameters derived from larval (sibling) sampling can be biased if adults are represented unevenly in the larval population. The removal of full-siblings from data may improve the quality of the results but entails in a low number of individuals per site, especially in small populations. Using simulated data of ten microsatellite loci for ten populations, we estimated pairwise FST and RST values as well as FIS and RIS values for the F0 generation (parental) and the F1 generation (descendant). We applied a repeated randomized selection of genotypes (RRSG) to investigate the impact of removing full-siblings from the data. We also investigated the impact of reduced sample size on the results generated by RRSG as well as the advantages of RRSG over a single estimate of genetic parameters after removal of full-siblings. The RRSG approach produced pairwise FST values that deviated on average only by 0.0050 (N = 45) from their respective estimates for F0. Estimates for HE deviated less the 5% over all data sets. We henceforth suggest applying the described method to interpretations of genetic differentiations in studies with (i) small effective population sizes and (ii) data containing siblings where (iii) offspring can be assigned to at least one parent due to reproduction practice.
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References
Balloux F (2001) EASYPOP (version 1.7): a computer program for population genetics simulations. J Hered 92:301–302
Cavers S, Degen B, Caron H et al (2005) Optimal sampling strategy for estimation of spatial genetic structure in tree populations. Heredity (Edinb) 95:281–289. doi:10.1038/sj.hdy.6800709
Eichler A, Vogel M (2011) Leitfaden Stochastik, 1st ed. doi: 10.1007/978-3-8348-9909-5
Ficetola GF, Bonin A, Miaud C (2008) Population genetics reveals origin and number of founders in a biological invasion. Mol Ecol 17:773–782. doi:10.1111/j.1365-294X.2007.03622.x
Goldberg CS, Waits LP (2010) Quantification and reduction of bias from sampling larvae to infer population and landscape genetic structure. Mol Ecol Resour 10:304–313. doi:10.1111/j.1755-0998.2009.02755.x
Hansen MM, Nielsen EE, Mensberg K-LD (1997) The problem of sampling families rather than populations: relatedness among individuals in samples of juvenile brown trout Salmo trutta L. Mol Ecol 6:469–474. doi:10.1046/j.1365-294X.1997.t01-1-00202.x
Kalinowski ST (2005) Do polymorphic loci require large sample sizes to estimate genetic distances? Heredity (Edinb) 94:33–36. doi:10.1038/sj.hdy.6800548
Morgan MJ, Hunter D, Pietsch R et al (2008) Assessment of genetic diversity in the critically endangered Australian corroboree frogs, Pseudophryne corroboree and Pseudophryne pengilleyi, identifies four evolutionarily significant units for conservation. Mol Ecol 17:3448–3463. doi:10.1111/j.1365-294X.2008.03841.x
Morin PA, Martien KK, Taylor BL (2009) Assessing statistical power of SNPs for population structure and conservation studies. Mol Ecol Resour 9:66–73. doi:10.1111/j.1755-0998.2008.02392.x
Niemelä E, Orell P, Erkinaro J et al (2006) Previously spawned Atlantic salmon ascend a large subarctic river earlier than their maiden counterparts. J Fish Biol 69:1151–1163. doi:10.1111/j.1095-8649.2006.01190.x
Olafsson K, Pampoulie C, Hjorleifsdottir S et al (2014) Present-day genetic structure of Atlantic salmon (Salmo salar) in Icelandic rivers and ice-cap retreat models. PLoS One 9:e86809. doi:10.1371/journal.pone.0086809
Peterman W, Anderson T, Ousterhout BH et al (2015) Differential dispersal shapes population structure and patterns of genetic differentiation in two sympatric pond breeding salamanders. Conserv Genet 16:59–69
Raymond M, Rousset F (2004) GENEPOP version 3.4—population genetics software for exact tests and ecumenicism. Laboratoire de Genetique et Environment, Montpellier
Rousset F (2008) genepop’007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resour 8:103–106. doi:10.1111/j.1471-8286.2007.01931.x
Selkoe KA, Toonen RJ (2006) Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecol Lett 9:615–629. doi:10.1111/j.1461-0248.2006.00889.x
Slatkin M (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457–462
Storfer A, Murphy MA, Spear SF et al (2010) Landscape genetics: where are we now? Mol Ecol 19:3496–3514. doi:10.1111/j.1365-294X.2010.04691.x
Taberlet P, Luikart G (1999) Non-invasive genetic sampling and individual identification. Biol J Linn Soc 68:41–55
Taubmann J, Theissinger K, Feldheim KA et al (2011) Modelling range shifts and assessing genetic diversity distribution of the montane aquatic mayfly Ameletus inopinatus in Europe under climate change scenarios. Conserv Genet 12:503–516
Trumbo DR, Spear SF, Baumsteiger J, Storfer A (2013) Rangewide landscape genetics of an endemic Pacific northwestern salamander. Mol Ecol 22:1250–1266. doi:10.1111/mec.12168
Wang IJ (2012) Environmental and topographic variables shape genetic structure and effective population sizes in the endangered Yosemite toad. Divers Distrib 18:1033–1041. doi:10.1111/j.1472-4642.2012.00897.x
Whiteley AR, McGarigal K, Schwartz MK (2014) Pronounced differences in genetic structure despite overall ecological similarity for two Ambystoma salamanders in the same landscape. Conserv Genet 15:573–591. doi:10.1007/s10592-014-0562-7
Willing E-M, Dreyer C, van Oosterhout C (2012) Estimates of genetic differentiation measured by F(ST) do not necessarily require large sample sizes when using many SNP markers. PLoS One 7:e42649. doi:10.1371/journal.pone.0042649
Wright S (1951) The genetical structure of populations. Ann Eugenics 15:323–354
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Lenhardt, P.P., Theissinger, K. Repeated randomized selection of genotypes for reliable estimates of population differentiation in data containing siblings. Eur J Wildl Res 63, 8 (2017). https://doi.org/10.1007/s10344-016-1061-6
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DOI: https://doi.org/10.1007/s10344-016-1061-6