High throughput sequencing enables discovery of microsatellites from the puff-throated bulbul (Alophoixus pallidus) and assessment of genetic diversity in Khao Yai National Park, Thailand

Bulbuls (family Pycnonotidae) are a diverse family of songbirds that carry out a number of ecologically important functions associated with seed dispersal. Since, 2003, a puff-throated bulbul (Alophoixus pallidus) population in the Mo-Singto Long-term Biodiversity Research Plot in Khao Yai National Park, Thailand has served as a model system for examining how bulbul behavior, movement, and demographics affect Southeast Asian forests. In this study, we used 454 pyrosequencing to discover microsatellites from A. pallidus that will enable the long-term mark-recapture work conducted at Mo-Singto to be complemented by molecular ecology and population genetic studies. In addition, we conducted fragment analysis to examine the level of genetic diversity exhibited by the Mo-Singto population. In total, we identified 103 DNA fragments containing microsatellite repeats and 66 fragments with sufficient flanking sequences to allow for primer design. Upon screening 26 loci via PCR-based genotyping assays, we identified nine polymorphic loci and used eight of these to examine genetic diversity in the Mo-Singto population. The results of these analyses suggest that the Mo-Singto population is moderately diverse (mean number of effective alleles across eight loci = 3.36, standard deviation = 1.78), is more-or-less in Hardy-Weinberg equilibrium, and has not recently been subject to severe population reduction.