Brandt J.R., Saidah S.H., Zhao K., Ishida Y., Apriyana I., Ryder O.A., Ramono W., Sudoyo H., Suryadi H., Van Coeverden de Groot P.J., Roca A.L.
Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States; Department of Biology, Marian University, Fond du Lac, WI 54935, United States; Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jl. Diponegoro No. 69, Jakarta, 10430, Indonesia; Institute of Conservation Research, San Diego Zoo Global, Escondido, CA 92027, United States; Rhino Foundation of Indonesia, Jl. Bima IV/10, Bogor, 16153, Indonesia; Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
Objective: The Sumatran rhinoceros is critically endangered, with fewer than 100 individuals surviving across its current range. Accurate census estimates of the remaining populations are essential for development and implementation of conservation plans. In order to enable molecular censusing, we here develop microsatellite markers with amplicon sizes of short length, appropriate for non-invasive fecal sampling. Results: Due to limited sample quantity and potential lack of genome-wide diversity, Illumina sequence reads were generated from two Sumatran rhinoceros samples. Genomic screening identified reads with short tandem repeats and loci that were polymorphic within the dataset. Twenty-nine novel polymorphic microsatellite markers were characterized (A = 2.4; HO = 0.30). These were sufficient to distinguish among individuals (PID < 0.0001), and to distinguish among siblings (PID(sib) < 0.0001). Among rhinos in Indonesia, almost all markers were established as polymorphic and effective for genotyping DNA from fecal samples. Notably, the markers amplified and displayed microsatellite polymorphisms using DNA extracted from 11 fecal samples collected non-invasively from wild Sumatran rhinoceros. These microsatellite markers provide an important resource for a census and genetic studies of wild Sumatran rhinos. © 2021, The Author(s).
Dicerorhinus sumatrensis; Non-invasive sampling; Short tandem repeats
BMC Research Notes
Publisher: BioMed Central Ltd
Volume 14, Issue 1, Art No 119, Page – , Page Count
Journal Link: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85103159046&doi=10.1186%2fs13104-021-05522-x&partnerID=40&md5=82f4bd8643a030906ecfca6cbc65c475
Type: All Open Access, Gold
Pusparini, W., Sievert, P.R., Fuller, T.K., Randhir, T.O., Andayani, N., Rhinos in the parks: an island-wide survey of the last wild population of the Sumatran rhinoceros (2015) PLoS ONE, 10; Guschanski, K., Vigilant, L., McNeilage, A., Gray, M., Kagoda, E., Robbins, M.M., Counting elusive animals: comparing field and genetic census of the entire mountain gorilla population of Bwindi Impenetrable National Park Uganda (2009) Biol Conserv, 142 (2), pp. 290-300; Goode, M.J., Beaver, J.T., Muller, L.I., Clark, J.D., van Manen, F.T., Harper, C.A., Basinger, P.S., Capture-recapture of white-tailed deer using DNA from fecal pellet groups (2014) Wildlife Biol, 20 (5), pp. 270-278; Goldstein, D.B., Schlötterer, C., (1999) Microsatellites: Evolution and Applications, , Oxford University Press, Oxford; Ishida, Y., Oleksyk, T.K., Georgiadis, N.J., David, V.A., Zhao, K., Stephens, R.M., Kolokotronis, S.O., Roca, A.L., Reconciling apparent conflicts between mitochondrial and nuclear phylogenies in African elephants (2011) PLoS ONE, 6 (6). , COI: 1:CAS:528:DC%2BC3MXns1yjur4%3D; Zhan, X., Li, M., Zhang, Z., Goossens, B., Chen, Y., Wang, H., Bruford, M.W., Wei, F., Molecular censusing doubles giant panda population estimate in a key nature reserve (2006) Curr Biol, 16 (12), pp. R451-R452. , COI: 1:CAS:528:DC%2BD28XlvF2ju78%3D; Arandjelovic, M., Vigilant, L., Non-invasive genetic censusing and monitoring of primate populations (2018) Am J Primatol, 80 (3); Ishida, Y., Demeke, Y., Van Coeverden de Groot PJ, Georgiadis NJ, Leggett KEA, Fox VE, Roca AL: Distinguishing forest and savanna African elephants using short nuclear DNA sequences (2011) J Hered, 102 (5), pp. 610-616. , COI: 1:CAS:528:DC%2BC3MXhtVyntrrL; Ishida, Y., Demeke, Y., Short amplicon microsatellite markers for low quality elephant DNA (2012) Conserv Genet Resour, 4 (2), pp. 491-494; Taberlet, P., Waits, L.P., Luikart, G., Noninvasive genetic sampling: look before you leap (1999) Trends Ecol Evol, 14 (8), pp. 323-327. , COI: 1:STN:280:DC%2BC2sbgslWgug%3D%3D; Scott, C., Foose, T., Morales, J.C., Fernando, P., Melnick, D.J., Boag, P.T., Davila, J.A., Optimization of novel polymorphic microsatellites in the endangered Sumatran rhinoceros (Dicerorhinus sumatrensis) (2004) Mol Ecol Notes, 4, pp. 194-196. , COI: 1:CAS:528:DC%2BD2cXlt1ChsLw%3D; Miller, S.A., Dykes, D.D., Polesky, H.F., A simple salting out procedure for extracting DNA from human nucleated cells (1988) Nucleic Acids Res, 16 (3), p. 1215. , COI: 1:CAS:528:DyaL1cXhsVKlsrs%3D; Archie, E.A., Moss, C.J., Alberts, S.C., Characterization of tetranucleotide microsatellite loci in the African savannah elephant (Loxodonta africana africana) (2003) Mol Ecol Notes, 3 (2), pp. 244-246. , COI: 1:CAS:528:DC%2BD3sXlt12htro%3D; Faircloth, B.C., MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locus-specific primer design (2008) Mol Ecol Resour, 8 (1), pp. 92-94. , COI: 1:CAS:528:DC%2BD1cXivVSitL8%3D; Slater, G.S., Birney, E., Automated generation of heuristics for biological sequence comparison (2005) Bmc Bioinform, 6, p. 1; Goudet, J., FSTAT (Version 1.2): A computer program to calculate F-statistics (1995) J Heredity, 86 (6), pp. 485-486; Peakall, R., Smouse, P.E., GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research (2006) Mol Ecol Notes, 6 (1), pp. 288-295; Peakall, R., Smouse, P.E., GenAlEx 6.5: genetic analysis in Excel Population genetic software for teaching and research-an update (2012) Bioinformatics, 28 (19), pp. 2537-2539. , COI: 1:CAS:528:DC%2BC38XhsVehtbjI; Kalinowski, S.T., Taper, M.L., Marshall, T.C., Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment (2007) Mol Ecol, 16 (5), pp. 1099-1106; Waits, L.P., Luikart, G., Taberlet, P., Estimating the probability of identity among genotypes in natural populations: cautions and guidelines (2001) Mol Ecol, 10 (1), pp. 249-256. , COI: 1:CAS:528:DC%2BD3MXjs1ejtbs%3D; Havmoller, R.G., Payne, J., Ramono, W., Ellis, S., Yoganand, K., Long, B., Dinerstein, E., Gawi, J., Will current conservation responses save the Critically Endangered Sumatran rhinoceros Dicerorhinus sumatrensis? (2016) Oryx, 50 (2), pp. 355-359; McKelvey, K.S., Schwartz, M.K., Providing reliable and accurate genetic capture-mark-recapture estimates in a cost-effective way (2004) J Wildl Manag, 68 (3), pp. 453-456
Indexed by Scopus