Statistical analysis of microsatellite DNA data.
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Journal Article↗
Biomedical subjects
G Luikart
Publications and source records attributed to G Luikart.
Noninvasive genetic sampling: look before you leap.
Noninvasive sampling allows genetic studies of free-ranging animals without the need to capture or even observe them, and thus allows questions to be addressed that cannot be answered using conventional methods. Initially, this sampling strategy promised to exploit fully the existing DNA-based technology for studies in ethology, conservation biology and population genetics. However, recent work now indicates the need for a more cautious approach, which includes quantifying the genotyping error rate. Despite this, many of the difficulties of noninvasive sampling will probably be overcome with improved methodology.
Journal Article↗
Power of 22 microsatellite markers in fluorescent multiplexes for parentage testing in goats (Capra hircus).
Two multiplex systems, each containing 11 microsatellite loci, were developed for semiautomated parentage testing in goats. Eight of the loci originate from goats, nine from cattle and five from sheep. Eighteen of the loci have been mapped to 16 different autosomes (in goats and cattle). Parentage exclusion probabilities were computed from allele frequencies in approximately 30 unrelated individuals from each of four economically important breeds: Mongolian Native Cashmere, Turkish Angora, Swiss Saanen, and Spanish Murciana-Grenadina. In cases where genotypes are known for one parent and an offspring, the 22 markers will exclude an (erroneously) alleged parent with a probability of > 0.999999 in the cashmere breed, > 0.99999 in Angora and Murciana-Grenadina, and > 0.9999 in Saanen. The multiplexes provide very high power for individual identification as the probability of finding two identical genotypes for the 22 loci is < 1 in 1.10(15) in each of the four breeds. The multiplexes will also be useful for studies of population structure, history, and diversity in goats and also in wild Capra species that represent important resources for genetic improvement of domestic breeds.
Animals↗
Estimating the effective number of breeders from heterozygote excess in progeny.
The heterozygote-excess method is a recently published method for estimating the effective population size (Ne). It is based on the following principle: When the effective number of breeders (Neb) in a population is small, the allele frequencies will (by chance) be different in males and females, which causes an excess of heterozygotes in the progeny with respect to Hardy-Weinberg equilibrium expectations. We evaluate the accuracy and precision of the heterozygote-excess method using empirical and simulated data sets from polygamous, polygynous, and monogamous mating systems and by using realistic sample sizes of individuals (15-120) and loci (5-30) with varying levels of polymorphism. The method gave nearly unbiased estimates of Neb under all three mating systems. However, the confidence intervals on the point estimates of Neb were sufficiently small (and hence the heterozygote-excess method useful) only in polygamous and polygynous populations that were produced by <10 effective breeders, unless samples included > approximately 60 individuals and 20 multiallelic loci.
Animals↗
New methods employing multilocus genotypes to select or exclude populations as origins of individuals.
A new method for assigning individuals of unknown origin to populations, based on the genetic distance between individuals and populations, was compared to two existing methods based on the likelihood of multilocus genotypes. The distribution of the assignment criterion (genetic distance or genotype likelihood) for individuals of a given population was used to define the probability that an individual belongs to the population. Using this definition, it becomes possible to exclude a population as the origin of an individual, a useful extension of the currently available assignment methods. Using simulated data based on the coalescent process, the different methods were evaluated, varying the time of divergence of populations, the mutation model, the sample size, and the number of loci. Likelihood-based methods (especially the Bayesian method) always performed better than distance methods. Other things being equal, genetic markers were always more efficient when evolving under the infinite allele model than under the stepwise mutation model, even for equal values of the differentiation parameter F(st). Using the Bayesian method, a 100% correct assignment rate can be achieved by scoring ca. 10 microsatellite loci (H approximately 0.6) on 30-50 individuals from each of 10 populations when the F(st) is near 0.1.
Bayes Theorem↗
Usefulness of molecular markers for detecting population bottlenecks via monitoring genetic change.
It is important to detect population bottlenecks in threatened and managed species because bottlenecks can increase the risk of population extinction. Early detection is critical and can be facilitated by statistically powerful monitoring programs for detecting bottleneck-induced genetic change. We used Monte Carlo computer simulations to evaluate the power of the following tests for detecting genetic changes caused by a severe reduction in a population's effective size (Ne): a test for loss of heterozygosity, two tests for loss of alleles, two tests for change in the distribution of allele frequencies, and a test for small Ne based on variance in allele frequencies (the 'variance test'). The variance test was most powerful; it provided an 85% probability of detecting a bottleneck of size Ne = 10 when monitoring five microsatellite loci and sampling 30 individuals both before and one generation after the bottleneck. The variance test was almost 10-times more powerful than a commonly used test for loss of heterozygosity, and it allowed for detection of bottlenecks before 5% of a population's heterozygosity had been lost. The second most powerful tests were generally the tests for loss of alleles. However, these tests had reduced power for detecting genetic bottlenecks caused by skewed sex ratios. We provide guidelines for the number of loci and individuals needed to achieve high-power tests when monitoring via the variance test. We also illustrate how the variance test performs when monitoring loci that have widely different allele frequency distributions as observed in five wild populations of mountain sheep (Ovis canadensis).
Alleles↗
Characterization of microsatellite loci in the endangered long-footed potoroo Potorous longipes.
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Alleles↗
Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data.
When a population experiences a reduction of its effective size, it generally develops a heterozygosity excess at selectively neutral loci, i.e., the heterozygosity computed from a sample of genes is larger than the heterozygosity expected from the number of alleles found in the sample if the population were at mutation drift equilibrium. The heterozygosity excess persists only a certain number of generations until a new equilibrium is established. Two statistical tests for detecting a heterozygosity excess are described. They require measurements of the number of alleles and heterozygosity at each of several loci from a population sample. The first test determines if the proportion of loci with heterozygosity excess is significantly larger than expected at equilibrium. The second test establishes if the average of standardized differences between observed and expected heterozygosities is significantly different from zero. Type I and II errors have been evaluated by computer simulations, varying sample size, number of loci, bottleneck size, time elapsed since the beginning of the bottleneck and level of variability of loci. These analyses show that the most useful markers for bottleneck detection are those evolving under the infinite allele model (IAM) and they provide guidelines for selecting sample sizes of individuals and loci. The usefulness of these tests for conservation biology is discussed.
Alleles↗
Distortion of allele frequency distributions provides a test for recent population bottlenecks.
We use population genetics theory and computer simulations to demonstrate that population bottlenecks cause a characteristic mode-shift distortion in the distribution of allele frequencies at selectively neutral loci. Bottlenecks cause alleles at low frequency (< 0.1) to become less abundant than alleles in one or more intermediate allele frequency class (e.g., 0.1-0.2). This distortion is transient and likely to be detectable for only a few dozen generations. Consequently only recent bottlenecks are likely to be detected by tests for distortions in distributions of allele frequencies. We illustrate and evaluate a qualitative graphical method for detecting a bottleneck-induced distortion of allele frequency distributions. The simple novel method requires no information on historical population sizes or levels of genetic variation; it requires only samples of 5 to 20 polymorphic loci and approximately 30 individuals. The graphical method often differentiates between empirical datasets from bottlenecked and nonbottlenecked natural populations. Computer simulations show that the graphical method is likely (P > .80) to detect an allele frequency distortion after a bottleneck of < or = 20 breeding individuals when 8 to 10 polymorphic microsatellite loci are analyzed.
Alleles↗