A comparison of several measures of genetic distance and population structure with microsatellite data: bias and sampling variance

Ruzzante, Daniel E.

doi:10.1139/cjfas-55-1-1

Cited by 117 publications

(98 citation statements)

References 47 publications

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“…One reason for the low level of allele variation is probably the small sample size (Galbusera et al 1996). Ruzzante (1998) suggested a population size of at least 50 individuals for the study of microsatellite loci. As H. nigricollaris is very rare, we could collect only 21 specimens for the population analysis.…”

Section: Discussionmentioning

confidence: 99%

Development and Characterization of RAPD and Microsatellite Markers for Genetic Variation Analysis in the Critically Endangered Yellow Catfish Horabagrus nigricollaris (Teleostei: Horabagridae)

et al. 2010

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Random-amplified polymorphic DNA (RAPD) and microsatellite markers were developed and used for the analysis of genetic variability in the critically endangered yellow catfish Horabagrus nigricollaris, sampled from the Chalakkudy River, Kerala, India. Eight RAPD and five microsatellite markers were detected to genotype the species. In RAPD, the 73 fragments were 20.55% polymorphic, whereas 4 polymorphic loci (80%) were obtained in microsatellites. In microsatellites, the number of alleles across the 5 loci was 1-5, and the range of heterozygosity was 0.25-0.5. The mean observed number of alleles was 2.4, and the effective number was 1.775 per locus. The average heterozygosity across all investigated samples was 0.29, indicating a significant deficiency of heterozygotes in this species. RAPD and microsatellite methods report a low degree of gene diversity and lack of genetic heterogeneity in the population of H. nigricollaris, emphasizing the need for fishery management, conservation, and rehabilitation of this species.

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Section: Discussionmentioning

confidence: 99%

Development and Characterization of RAPD and Microsatellite Markers for Genetic Variation Analysis in the Critically Endangered Yellow Catfish Horabagrus nigricollaris (Teleostei: Horabagridae)

et al. 2010

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“…Similarly, Waples and Gaggiotti (2006) found STRUCTURE to perform poorly when F ST~0 .01. While the number of loci and number of individuals from each population (except Paris) genotyped in this study should provide sufficient power for genetic distance and population structure measures (Ruzzante 1997;Ryman et al 2006), when gene flow is moderate or high, it maybe insufficient for Bayesian assignment methods such as STRUCTURE (Waples and Gaggiotti 2006). This explanation, however, cannot be used to interpret the results of Lippe et al (2006), who genotyped 22 microsatellite loci.…”

Section: Population Genetic Structurementioning

confidence: 94%

Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed

et al. 2007

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Dams have the potential to affect population size and connectivity, reduce genetic diversity, and increase genetic differences among isolated riverine fish populations. Previous research has reported adverse effects on the distribution and demographics of black redhorse (Moxostoma duquesnei), a threatened fish species in Canada. However, effects on genetic diversity and population structure are unknown. We used microsatellite DNA markers to assess the number of genetic populations in the Grand River (Ontario) and to test whether dams have resulted in a loss of genetic diversity and increased genetic differentiation among populations. Three hundred and seventy-seven individuals from eight Grand River sites were genotyped at eight microsatellite loci. Measures of genetic diversity were moderately high and not significantly different among populations; strong evidence of recent population bottlenecks was not detected. Pairwise F ST and exact tests identified weak (global F ST = 0.011) but statistically significant population structure, although little population structuring was detected using either genetic distances or an individual-based clustering method. Neither geographic distance nor the number of intervening dams were correlated with pairwise differences among populations. Tests for regional equilibrium indicate that Grand River populations were either in equilibrium between gene flow and genetic drift or that gene flow is more influential than drift. While studies on other species have identified strong dam-related effects on genetic diversity and population structure, this study suggests that barrier permeability, river fragment length and the ecological characteristics of affected species can counterbalance dam-related effects.

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“…Overall, increased sampling intensity led to increased precision (i.e., decreased variance) of the estimate. Special attention should be drawn to the datasets of 50 randomly sampled individuals, as this size is most characteristic of sampling effort in the literature (Ruzzante 1998;van Oppen and Gates 2006). Notice that when estimating H O with 50 randomly sampled individuals, while the median value (0.405) of twenty replicate subsets is close to the true value (0.397), there is a large range associated with this sampling intensity (0.35-0.46).…”

Section: Spatial Autocorrelation Analysismentioning

confidence: 99%

The importance of sampling design: spatial patterns and clonality in estimating the genetic diversity of coral reefs

2015

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demonstrate by rarefaction analysis that the bias in estimating clonal richness (i.e., the proportion of unique genotypes in a given sampling area relative to the total number of samples surveyed) for small sample numbers is due to the predominance of clones (i.e., high level of clonality) and not skew in genet frequency distribution. Overall, we argue that: (1) consideration of sampling design is important in population genetic studies, particularly since non-random sampling in the presence of SGS can give biased estimates of genetic diversity and (2) intense to near-exhaustive sampling schemes may be important for characterizing genetic diversity in highly clonal populations.

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A comparison of several measures of genetic distance and population structure with microsatellite data: bias and sampling variance

Cited by 117 publications

References 47 publications

Development and Characterization of RAPD and Microsatellite Markers for Genetic Variation Analysis in the Critically Endangered Yellow Catfish Horabagrus nigricollaris (Teleostei: Horabagridae)

Development and Characterization of RAPD and Microsatellite Markers for Genetic Variation Analysis in the Critically Endangered Yellow Catfish Horabagrus nigricollaris (Teleostei: Horabagridae)

Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed

The importance of sampling design: spatial patterns and clonality in estimating the genetic diversity of coral reefs

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