Comparing Bayesian estimates of genetic differentiation of molecular markers and quantitative traits: an application to Pinus sylvestris

Abstract

Comparison of the level of differentiation at neutral molecular markers (estimated as F ST or G ST ) with the level of differentiation at quantitative traits (estimated as Q ST ) has become a standard tool for inferring that there is differential selection between populations. We estimated Q ST of timing of bud set from a latitudinal cline of Pinus sylvestris with a Bayesian hierarchical variance component method utilizing the information on the pre-estimated population structure from neutral molecular markers. Unfortunately, the betweenfamily variances differed substantially between populations that resulted in a bimodal posterior of Q ST that could not be compared in any sensible way with the unimodal posterior of the microsatellite F ST . In order to avoid publishing studies with flawed Q ST estimates, we recommend that future studies should present heritability estimates for each trait and population. Moreover, to detect variance heterogeneity in frequentist methods (ANOVA and REML), it is of essential importance to check also that the residuals are normally distributed and do not follow any systematically deviating trends. Heredity (2005) 94, 623-629.

Development and transferability of two multiplexes nSSR in Scots pine (Pinus sylvestris L.)

“…The transferability of SSR between Scots pine and P. taeda was previously demonstrated successfully (e.g., RobledoArnuncio et al 2005;Waldmann et al 2005;García-Gil et al 2009;Robledo-Arnuncio et al 2009). However, the transferability of our two multiplexes to other Pinus species required the initial testing of the expected sizes of the involved loci to avoid overlapping.…”

“…In conifers, nSSRs are applied in multiple research areas such as population studies (e.g., Marshall et al 2002;A 0 Hara and Cottrell 2004;Waldmann et al 2005;García-Gil et al 2009;Gugerli et al 2009;Tollefsrud et al 2009), genetic map construction (Pelgas et al 2006;Echt et al 2011) and paternity analysis (Lian et al 2001;Torimaru et al 2009). Despite the wide application of nSSRs, examples on the application of SSR multiplexing in conifers remain scarce (Devey et al 2002;Bell et al 2004;Karhu et al 2006;Gugerli et al 2009;Salzer et al 2009;Kawase et al 2010;Wagner et al 2012).…”

Bias and Precision in QST Estimates: Problems and Some Solutions

“…Clearly, if the parametric assumptions are reasonable, then this is not a problem. However, the assumptions underlying the parametric methods do need to be checked (Waldmann et al 2005), as was done here. If the assumptions are not correct then remedial action may be needed.…”

Low efficiency of pseudotestcross mapping design was consistent with limited genetic diversity and low heterozygosity in hoop pine (Araucaria cunninghamii, Araucariaceae)

“…This is apparently at odds with the observations of low levels of heterozygosity and limited genetic divergence identified in this study. It must be noted, however, that this study focused on neutral genetic markers, and there is growing evidence that neutral markers are poor indicators of adaptive or quantitative variation in conifers [30,70]. Within the Araucariaceae, a study of Araucaria araucana [5] found that neutral DNA markers (RAPDs) and quantitative variation were essentially uncorrelated.…”