Abstract
Here we document the addition of thousands of potentially amplifiable microsatellite loci (PALs) and associated primer sequences for public use. We conducted whole-genome shotgun sequencing to obtain ultra-low coverage, random genomic sampling from ten African and Asian squamate reptile species (representing ten genera). We used unique genomic processing methods and generated PALs for the following species: Acrochordus granulatus, Ahaetulla prasina, Cerberus rhynchops, Gonocephalus kuhlii, Ophiophagus hannah, Python bivittatus, Tribolonotus gracilis, Trimeresurus sabahi (Popeia sabahi), Uromastyx geryi and Varanus exanthematicus. All taxa included, as well as other related taxa not included in our study, are exploited heavily by the international skin and pet trades, yet researchers and conservation agencies currently lack substantial genetic resources for guiding conservation and management. Using stringent filtering methods, we generated between 467 and 8641 PALs for each of the ten species (52,164 PALs total), yielding a rich database of microsatellite loci and amplification primers for these taxa. In addition to the ten species targeted in our study, microsatellite markers provided in this database can likely be applied to a variety of closely related taxa that are also of conservation and commercial interest.
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Acknowledgments
We are grateful to representatives of LIPI at the Museum Zoologicum Bogoriense for facilitating the study of specimens from Indonesia and providing field research permits, namely Boadi, M. Amir, R. Ubaidillah, I Sidik, and Ir. R. M. Marwoto. We are grateful to the Ministry of Research and Technology of the Republic of Indonesia (RISTEK), for coordinating and granting research permissions. Pak S. Wahyono (RISTEK) provided assistance throughout the permitting process. RISTEK and LIPI reviewed and approved our fieldwork in Indonesia and provided export permits for specimens to the United States for study and deposition at UTA. W. Trilaksono, I. Sidik, and A. Ryanto provided laboratory assistance at MZB. Mr. Widodo and Marwoto from the Faculty of Mathematicas and Natural Sciences of Universitas Brawijaya (MIPA-UB) kindly provided logistical support. The Forestry Department of Indonesia provided research permits for areas under their jurisdiction. We thank the local communities for their support, advice and kindness during our travels. We thank the members of the field expeditions throughout Java and Sumatra: G. Barraza (Broward College); U. Arifin (Institut Teknologi Bandung), W. Trilaksono (MZB); C. Franklin, K. O’Connell, U. Smart, E. Wostl (UTA), and A. M. Kadafi, D. R. Wulandari, R. Darmawan, K. I. Nawie, A. Dharasa, and S. Pratassi (MIPA- UB). Funding was provided by a National Science Foundation Grant (DEB-1146324) to E. N. Smith and M. B. Harvey, and startup funds to T. A. Castoe.
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Shaney, K.J., Adams, R., Kurniawan, N. et al. A suite of potentially amplifiable microsatellite loci for ten reptiles of conservation concern from Africa and Asia. Conservation Genet Resour 8, 307–311 (2016). https://doi.org/10.1007/s12686-016-0534-y
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DOI: https://doi.org/10.1007/s12686-016-0534-y