Microsatellites Can Be Misleading: An Empirical and Simulation Study

Balloux, François; Brünner, H.; Lugon-Moulin, Nicolas; Hausser, Jacques; Goudet, Jérôme

doi:10.1554/0014-3820(2000)054[1414:mcbmae]2.0.co;2

Cited by 137 publications

(179 citation statements)

References 38 publications

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“…Therefore, effects of homoplasy are expected to be common for microsatellites in marine fishes (O'Reilly et al, 2004), which has implications for the identification of genetic structuring (Carreras-Carbonell et al, 2006). Microsatellites probably suffered from higher levels of homoplasy than mtDNA because of higher mutation rates and larger effective population sizes (Balloux et al, 2000). The various microsatellite markers of P. minutus indicate homoplasy because of the high allele numbers and the limited size range of all markers (on average 1 allele per 2.053 bp).…”

Section: Discussionmentioning

confidence: 99%

Mito-nuclear discordance in the degree of population differentiation in a marine goby

et al. 2010

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An increasing number of phylogeographic studies on marine species shows discordant patterns in the degree of population differentiation between nuclear and mitochondrial markers. To understand better which factors have the potential to cause these patterns of discordance in marine organisms, a population genetic study was realized on the sand goby Pomatoschistus minutus (Pallas 1770; Gobiidae, Teleostei). Sand gobies from eight European locations were genotyped at eight microsatellite markers. Microsatellites confirmed the global phylogeographical pattern of P. minutus observed with mitochondrial DNA (mtDNA) markers and nuclear allozyme markers. Three groups consistent with the mitochondrial lineages were defined (the Mediterranean, Iberian and North Atlantic groups) and indications of a recent founder event in the northern Baltic Sea were found. Nevertheless, differences in the degree of population differentiation between the nuclear and mitochondrial markers were large (global F ST -values for microsatellites ¼ 0.0121; for allozymes ¼ 0.00831; for mtDNA ¼ 0.4293). Selection, sex-biased dispersal, homoplasy and a high effective population size are generally accepted as explanations for this mitonuclear discrepancy in the degree of population differentiation. In this study, selection on mtDNA and microsatellites, male-biased dispersal and homoplasy on microsatellite markers are unlikely to be a main cause for this discrepancy. The most likely reason for the discordant pattern is a recent demographical expansion of the sand goby, resulting in high effective population sizes slowing down the differentiation of nuclear DNA.

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Section: Discussionmentioning

confidence: 99%

Mito-nuclear discordance in the degree of population differentiation in a marine goby

et al. 2010

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“…Although it is inherently difficult to estimate proper mutation rates of both molecular markers and quantitative traits, it has been suggested that different marker types can have considerably dissimilar mutation rates (Balloux et al, 2000). Moreover, theoretical studies have shown that the F ST statistics is very sensitive to variations in the mutation rate (Fu et al, 2003) and to unequal migration rates between populations (Wilkinson-Herbots and Ettridge, 2004).…”

Section: Discussionmentioning

confidence: 99%

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

2005

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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.

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“…In all these cases, the contact zones contained few or no hybrid karyotypes. A genetic analysis is available only for the contact zone between the Cordon and Valais races: a certain level of genetic introgression of mitochondrial and nuclear markers was detected (Balloux et al, 2000). In all these reported cases, the location of the contact zone corresponded to some geographical barrier (river or stream) or to an area of unsuitable habitat.…”

Section: Discussionmentioning

confidence: 99%

Contact zones between chromosomal races of Mus musculus domesticus. 3. Molecular and chromosomal evidence of restricted gene flow between the CD race (2n = 22) and the ACR race (2n = 24)

2002

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Contact zones between chromosomal races of Mus musculus domesticus. 3. Molecular and chromosomal evidence of restricted gene flow between the CD race (2n = 22) and the ACR race (2n = 24) R Castiglia, F Annesi and E Capanna Dipartimento di Biologia Animale e dell' Uomo, Università di Roma "La Sapienza"-Via A. Borelli 50, 00161 Roma, ItalyThe contact zone between the Ancarano (ACR; 2n = 24) and Cittaducale (CD; 2n = 22) races of Mus musculus domesticus was studied. We used chromosomes and mitochondrial DNA (mtDNA) sequences of the control region as genetic markers to detect introgression between races. In total, 76 mice were trapped at 17 localities. Cytogenetic analysis was performed on 73 mice. A segment of the control region (468 bp) was sequenced in 41 specimens. The two races are distributed parapatrically and the contact zone was identified inside a village (Pizzoli). No mixed population was found in the study area. The contact zone does not correspond to any geographical or ecological barrier but is located

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Microsatellites Can Be Misleading: An Empirical and Simulation Study

Cited by 137 publications

References 38 publications

Mito-nuclear discordance in the degree of population differentiation in a marine goby

Mito-nuclear discordance in the degree of population differentiation in a marine goby

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

Contact zones between chromosomal races of Mus musculus domesticus. 3. Molecular and chromosomal evidence of restricted gene flow between the CD race (2n = 22) and the ACR race (2n = 24)

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