Lessons from a Beetle and an Ant: Coping with Taxon-Dependent Differences in Microsatellite Development Success Wolfgang Arthofer Æ Birgit C. Schlick-Steiner Æ Florian M. Steiner Æ Dimitrios N. Avtzis Æ Ross H. Crozier Æ Christian Stauffer Received: 15 January 2007 / Accepted: 6 July 2007 / Published online: 29 August 2007 Ó Springer Science+Business Media, LLC 2007 Abstract Microsatellites are powerful markers often isolated de novo for species yet to be investigated. Enri- ched genomic libraries are usually used for isolation purposes. We critically evaluate the outcome of an enrichment-based protocol applied to two insect species (the ant Lasius austriacus and the beetle Pityogenes chal- cographus) which yielded contrasting numbers of suitable loci. Our findings of differences in microsatellite isolation are consistent with the available data on differences in genomic characteristics across these taxa. In the beetle repeated isolation of identical motifs, difficulties in primer development, and multibanded products caused loss of most candidate clones. We identified critical steps during marker development. Keywords Microsatellites Á Microsatellite isolation Á Enriched genomic library Á Molecular marker Á Informative locus Á Coleoptera Á Hymenoptera Introduction Microsatellites are short DNA stretches in which a one- to six-nucleotide motif is tandemly repeated. Found in all pro- and eukaryotic genomes, microsatellites show high muta- tion rates and intraspecific length polymorphisms, making them a powerful marker for population genetics. Devel- opment of universal, cross-species-amplifying primers for microsatellites is often not possible and the necessity of de novo isolation for taxa yet to be analyzed is a drawback in the applicability of microsatellites (Zane et al. 2002). Most new microsatellites are isolated using enriched genomic libraries. Marker development consists of (i) enrichment of microsatellite-containing fragments of genomic DNA, (ii) construction of a partial genomic library, (iii) screening of the library by colony hybridization, (iv) sequencing of candidate clones, (v) development of flanking primers, and (vi) exclusion of nonamplifying and monomorphic loci. Poor yields of suitable loci may occur due to technical problems in any of the steps but also due to peculiarities of the analyzed organism. Low abundance of microsatellites in the genome (Fagerberg et al. 2001) and occurrence of multicopy microsatellite families with similar flanking regions (Megle ´cz et al. 2004) have been considered reasons for such difficulties. We suspect, however, that in most cases isolation failure is not reported. We evaluated the impact of taxon-specific traits on microsatellite development following the FIASCO protocol (Zane et al. 2002). Applying identical laboratory proce- dures to a beetle, Pityogenes chalcographus (Scolytinae), and an ant, Lasius austriacus (Formicinae), we address whether (i) numbers of micrsosatellite harboring clones in the enriched libraries, (ii) loss of candidate clones due to subsequent difficulties in amplification, and (iii) rate of polymorphism are comparable between the two species. Reviewing Editor: Dr. John Oakeshott W. Arthofer (&) Á B. C. Schlick-Steiner Á F. M. Steiner Á D. N. Avtzis Á C. Stauffer Institute of Forest Entomology, Forest Pathology and Forest Protection, Department of Forest and Soil Sciences, Boku, University of Natural Resources & Applied Life Sciences, Vienna, Austria e-mail: wolfgang.arthofer@boku.ac.at B. C. Schlick-Steiner Á F. M. Steiner Institute of Zoology, Department of Integrative Biology and Biodiversity Research, Boku, University of Natural Resources & Applied Life Sciences, Vienna, Austria B. C. Schlick-Steiner Á F. M. Steiner Á R. H. Crozier School of Marine and Tropical Biology, James Cook University, Townsville, Australia 123 J Mol Evol (2007) 65:304–307 DOI 10.1007/s00239-007-9012-1