Christian Schlötterer

Evolutionary dynamics of microsatellite DNA.

Abstract. Within the past decade microsatellites have developed into one of the most popular genetic markers. Despite the widespread use of microsatellite analysis, an integral picture of the mutational dynamics of microsatellite DNA is just beginning to emerge. Here, I review both generally agreed and controversial results about the mutational dynamics of microsatellite DNA.

The evolution of molecular markers--just a matter of fashion?

In less than half a century, molecular markers have totally changed our view of nature, and in the process they have evolved themselves. However, all of the molecular methods developed over the years to detect variation do so in one of only three conceptually different classes of marker: protein variants (allozymes), DNA sequence polymorphism and DNA repeat variation. The latest techniques promise to provide cheap, high-throughput methods for genotyping existing markers, but might other traditional approaches offer better value for some applications?

SciRoKo: a new tool for whole genome microsatellite search and investigation

UNLABELLEDnSciRoKo is a user-friendly software tool for the identification of microsatellites in genomic sequences. The combination of an extremely fast search algorithm with a built-in summary statistic tool makes SciRoKo an excellent tool for full genome analysis. Compared to other already existing tools, SciRoKo also allows the analysis of compound microsatellites.nnnAVAILABILITYnfree for use: www.kofler.or.at/Bioinformatics.nnnSUPPLEMENTARY INFORMATIONnSupplementary data are available at Bioinformatics online.

Hitchhiking mapping – functional genomics from the population genetics perspective

Several statistical tests based on population genetic theory are used to identify genes that have recently acquired a beneficial mutation. Here, I describe the extension of these tests to a multilocus approach for a genome-wide survey for genes that have been under recent positive selection. As this strategy could potentially identify genes with weak phenotypic effects, it will be very useful in population genetic approaches aimed at understanding adaptation processes in natural populations. Furthermore, this hitchhiking mapping could also help in the functional characterization of genomes.

Amplification of hypervariable simple sequence repeats (microsatellites) from excremental DNA of wild living bonobos (Pan paniscus)

We show that nuclear DNA extracted from faeces of free living bonobos (Pan paniscus) can be used to amplify hypervariable simple sequence repeats, which can be used for paternity analysis and kinship studies. Of 130 DNA extractions of samples from 33 different animals, about two‐thirds yielded PCR products at the first attempt. For several samples only a second extraction resulted in positive amplifications. Consistency tests revealed that in some cases only one of the two alleles was amplified. Presumably this is due to a very limited amount of bonobo DNA in the sample and we suggest therefore that a sample found to be homozygous at a given locus should be typed repeatedly for verification.

Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms.

With the delivery of millions of sequence reads in a single experiment, next‐generation sequencing (NGS) is currently revolutionizing surveys of microorganism diversity. In particular, when applied to Eukaryotes, we are still lacking a rigorous comparison of morphological and NGS‐based diversity estimates. In this report, we studied the diversity and the seasonal community turnover of alveolates (Ciliophora and Dinophyceae) in an oligotrophic freshwater lake by SSU amplicon sequencing with NGS as well as by classical morphological analysis. We complemented the morphological analysis by single‐cell PCR followed by Sanger sequencing to provide an unambiguous link to the NGS data. We show that NGS and morphological analyses generally capture frequency shifts of abundant taxa over our seasonal samples. The observed incongruencies are probably largely due to rDNA copy number variation among taxa and heterogeneity in the efficiency of cell lysis. Overall, NGS‐based amplicon sequencing was superior in detecting rare species. We propose that in the absence of other nuclear markers less susceptible to copy number variation, rDNA‐based diversity studies need to be adjusted for confounding effects of copy number variation.

Chromosomal homogeneity of Drosophila ribosomal DNA arrays suggests intrachromosomal exchanges drive concerted evolution

BACKGROUNDnThe individual copies of tandemly repeated genes, such as ribosomal DNA (rDNA), evolve coordinately within a species. This phenomenon has been called concerted evolution, and is thought to be caused by sequence-homogenizing mechanisms, such as gene conversion or unequal crossing-over between individual copies of the gene family. As these processes would act between the arrays on homologous and non-homologous chromosomes, the whole family of repeats would be expected to undergo homogenization in a given interbreeding population.nnnRESULTSnIn order to study the homogenization process, we have examined polymorphisms within the internal transcribed spacer (ITS) of the rDNA in populations of Drosophila melanogaster at the sequence level, by DNA sequencing and temperature-gradient gel electrophoresis. Among 84 ITS clones sequenced from five different wild-type strains, we found three polymorphic sites that are apparently in the process of homogenization. However, these three sites, as well as combinations of them, occurred at different frequencies in the different strains. Moreover, temperature-gradient gel electrophoresis analysis of an ITS fragment including these three sites shows that single chromosomes from locally interbreeding populations can harbor rDNA arrays that are largely homogenized for different sequence variants.nnnCONCLUSIONSnThe presence of chromosomal arrays that are homogeneous for different variants in interbreeding populations of Drosophila melanogaster indicates that there is little recombination between the chromosomes while new mutations are being homogenized along the individual arrays. The most likely explanation for this finding is that intrachromosomal recombination events occur at much higher rates than recombination between homologous chromosomes. Thus, the first step of the homogenization process would occur mainly within chromosomal lines. Such behavior of tandem repeat arrays suggests a simple explanation of how selection can act on a multigene family, namely by acting on whole chromosomally confined repeat arrays rather than on individual repeat units.

Hitchhiking mapping: A population-based fine-mapping strategy for adaptive mutations in Drosophila melanogaster

The identification of genes contributing to the adaptation of local populations is of great biological interest. In an attempt to characterize functionally important differences among African and non-African Drosophila melanogaster populations, we surveyed neutral microsatellite variation in an 850-kb genomic sequence. Three genomic regions were identified that putatively bear an adaptive mutation associated with the habitat expansion of D. melanogaster. A further inspection of two regions by sequence analysis of multiple fragments confirmed the presence of a recent beneficial mutation in the non-African populations. Our study suggests that hitchhiking mapping is a universal approach for the identification of ecologically important mutations.

Evidence for shared ancestral polymorphism rather than recurrent gene flow at microsatellite loci differentiating two hybridizing oaks (Quercus spp.)

Quercus petraea and Quercus robur are two closely related oak species, considered to hybridize. Genetic markers, however, indicate that despite sharing most alleles, the two species remain separate genetic units. Analysis of 20 microsatellite loci in multiple populations from both species suggested a genome‐wide differentiation. Thus, the allele sharing between both species could be explained either by low rates of gene flow or shared ancestral variation. We performed further analyses of population differentiation in a biogeographical setting and an admixture analysis in mixed oak stands to distinguish between both hypotheses. Based on our results we propose that the low genetic differentiation among these species results from shared ancestry rather than high rates of gene flow.

Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity

With the advent of molecular methods, it became clear that microbial biodiversity had been vastly underestimated. Since then, species abundance patterns were determined for several environments, but temporal changes in species composition were not studied to the same level of resolution. Using massively parallel sequencing on the 454 GS FLX platform we identified a highly dynamic turnover of the seasonal abundance of protists in the Austrian lake Fuschlsee. We show that seasonal abundance patterns of protists closely match their biogeographic distribution. The stable predominance of few highly abundant taxa, which previously led to the suggestion of a low global protist species richness, is contrasted by a highly dynamic turnover of rare species. We suggest that differential seasonality of rare and abundant protist taxa explains the—so far—conflicting evidence in the ‘everything is everywhere’ dispute. Consequently temporal sampling is basic for adequate diversity and species richness estimates.