Abstract The speciose genus Aegla Leach, 1820 is the only valid extant genus of the anomuran family Aeglidae, bearing 83 known species. This diversity may be even greater since there is some evidence for cryptic speciation. The genus is endemic to southern South America, occurring in freshwater habitats. We assessed the conservation status of 82 species of Aegla and found almost 70% of them under some level of threat, which represents a concerning proportion. Major threats to the group include freshwater pollution with urban, agricultural and industrial effluents, habitat modification and fragmentation, riparian forest removal, among others. Conservation measures are required to mitigate the major threats to freshwater ecosystems along rivers where the group occurs.

Protocols for microsatellite-enrichment libraries have been widely applied to several species in order to supply the most informative molecular markers for population and inbreeding studies. One drawback of these protocols is the ratio of designed primer pairs that fail to amplify the expected fragment, even after exhaustive optimization attempts. A possible cause of unsuccessful microsatellite primers may be that such loci are artifacts resulting from chimeric PCR products, instead of real genomic sequences. The microsatellite-enriched library constructed for Aegla longirostri (Crustacea, Decapoda, Anomura) showed that 29% of sequenced clones were chimeric products because these sequences shared one of the flanking regions around the same repeat motif but not the other. PCR-mediated recombination is a well-known event described for several procedures in which related sequences are used as a template. We have associated this phenomenon with microsatellite marker development. This study explained the high ratio of recombinant sequences generated in the A. longirostri microsatellite-enriched library. We discuss the mechanism and implications of PCR chimeric-product formation during microsatellite isolation.