De novo Development and Characterization of Tetranucleotide Microsatellite Loci Markers from a Southeastern Population of the House Finch (Haemorhous mexicanus)

Abstract

Microsatellites are short tandem repeats (e.g. TAGATAGA) of base pairs in a species’ genome. High mutation rates in these regions produce variation in the number of repeats across individuals that can be utilized to study patterns of population-and landscape-level genetics and to determine parentage genetically. In this project our objective was to develop microsatellite markers for the House Finch, Haemorhous mexicanus . This species has become one of the most well-studied species of songbirds due to its unique geographical, evolutionary, and epidemiological history. Using mist-nets we captured birds on the Arkansas Tech University campus and collected blood samples to obtain genomic DNA. Samples were processed in The Field Museum’s Pritzker Laboratory for Molecular Systematics and Evolution, where we fragmented genomic DNA and isolated fragments that contained potential microsatellites using specially designed biotin labelled probes. These DNA fragments were transformed into competent E. coli cells which were then PCR-amplified and Sanger sequenced. After sequencing DNA fragments from approximately 500 E. coli colonies, we designed and characterized a set of 13 tetranucleotide microsatellite loci. The average number of alleles and heterozygosity found in 12 individuals from Arkansas was 8.69 and 0.80, respectively. This finalized set of microsatellites can be utilized by researchers to determine parentage and characterize genetic differences across