Abstract
High-throughput sequencing tools promise to revolutionize many aspects of genetic research, e.g. by allowing the identification of functional adaptive genetic variation. However, the expense and expertise required to apply these tools to basic conservation questions is a challenge for applications outside academia, resulting in a so-called ‘conservation genomics gap’ (Shafer et al. 2015). The conservation genetics paradigm is that, basic information about inbreeding and gene flow are often critical to inform conservation management of small populations (Ouborg et al. 2010). This information is often needed quickly and ideally should be accessible to workers without special expertise in genomics (DeSalle and Amato 2004). While the inferential power of high-throughput sequencing to interrogate the genome is profound, the cost for population analysis is higher (though decreasing) than for traditional neutral markers. Thus, the use of neutral markers is still relevant in conservation applications. However, this assumes that neutral markers have been discovered and characterized for a given species of conservation concern, which is often untrue for nonmodel organisms. Here, we use a fast, cost-efficient, high-throughput sequencing method (Illumina MiSeq) to rapidly identify and characterize microsatellites in the mountain bongo (Tragelaphus eurycerus isaaci), which has a clear and timely conservation imperative but lacks any described neutral markers.
This is a preview of subscription content, log in via an institution to check access.
References
Blacket M. J., Robin C., Good R. T., Lee S. F. and Miller A. D. 2012 Universal primers for fluorescent labelling of PCR fragments—an efficient and cost-effective approach to genotyping by fluorescence. Mol. Ecol. Resour. 12, 456–463.
Bolger A. M., Lohse M. and Usadel B. 2014 Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120.
Bosley L. F. 2011 International studbook for eastern/mountain bongo (Tragelaphus eurycerus isaaci). WAZA, Gland, Switzerland.
Bosley L. F. 2012 International studbook for eastern/mountain bongo (Tragelaphus eurycerus isaaci). WAZA, Gland, Switzerland.
Castoe T. A., Poole A. W., Koning A. P. J., de Jones K. L., Tomback D. F., Oyler-McCance S. J. et al. 2012 Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake. PLoS One 7, e30953.
DeSalle R. and Amato G. 2004 The expansion of conservation genetics. Nat. Rev. Genet. 5, 702–712.
Estes L. D., Okin G. S., Mwangi A. G. and Shugart H. H. 2008 Habitat selection by a rare forest antelope: a multi-scale approach combining field data and imagery from three sensors. Remote Sensing Environ. 112, 2033–2050.
Estes L. D., Mwangi A. G., Reillo P. R., Shugart H. H. 2011 Predictive distribution modeling with enhanced remote sensing and multiple validation techniques to support mountain bongo antelope recovery. Anim. Conserv. 14, 521–532.
Faria P. J., Kavembe G. D., Jung’a J. O., Kimwele C. N., Estes L. D., Reillo P. R. et al. 2011 The use of non-invasive molecular techniques to confirm the presence of mountain bongo Tragelaphus eurycerus isaaci populations in Kenya and preliminary inference of their mitochondrial genetic variation. Conserv. Genet. 12, 745–751.
Griffiths S. M., Fox G., Briggs P. J., Donaldson I. J., Hood S., Richardson P. et al. 2016 A Galaxy-based bioinformatics pipeline for optimised, streamlined microsatellite development from Illumina next-generation sequencing data. Conserv. Genet. Resour. 8, 481–486.
Henkel J. R., Jones K. L., Hereford S. G., Savoie M. L., Leibo S. P. and Howard J. J. 2012 Integrating microsatellite and pedigree analyses to facilitate the captive management of the endangered Mississippi sandhill crane (Grus canadensis pulla). Zoo Biol. 31, 322–335.
IUCN SSC Antelope Specialist Group 2017 Tragelaphus eurycerus ssp. isaaci. The IUCN Red List of threatened species 2017:e.T22057A50197212. https://doi.org/10.2305/IUCN.UK.2017_2. RLTS. T22057A50197212.en. Downloaded on 9 Apr 2018.
Kingdon J., Happold D., Butynski T., Hoffmann M., Happold M. and Kalina J. 2013 Mammals of Africa. A & C Black, London.
Koressaar T. and Remm M. 2007 Enhancements and modifications of primer design program Primer3. Bioinformatics 23, 1289–1291.
Lacy R. C. 2013 Achieving true sustainability of zoo populations. Zoo Biol. 32, 19–26.
Masella A. P., Bartram A. K., Truszkowski J. M., Brown D. G. and Neufeld J. D. 2012 PANDAseq: paired-end assembler for illumina sequences. BMC Bioinformatics 13, 31.
Meirmans P. G. and Van Tienderen P. H. 2004 genotype and genodive: two programs for the analysis of genetic diversity of asexual organisms. Mol. Ecol. Notes 4, 792–794.
Ouborg N. J., Pertoldi C., Loeschcke V., Bijlsma R. and Hedrick P. W. 2010 Conservation genetics in transition to conservation genomics. Trends Genet. 26, 177–187.
Reillo P. R. 2002 Repatriation of the mountain bongo to Kenya. Gnusletter 21, 11–15.
Rousset F. 2008 Genepop’007: a complete re-implementation of the genepop software for Windows and Linux. Mol. Ecol. Resour. 8, 103–106.
Schulte-Hostedde A. I. and Mastromonaco G. F. 2015 Integrating evolution in the management of captive zoo populations. Evol. Appl. 8, 413–422.
Shafer A. B. A., Wolf J. B. W., Alves P. C., Bergström L., Bruford M. W., Brännström I. et al. 2015 Genomics and the challenging translation into conservation practice. Trends Ecol. Evol. 30, 78–87.
Spencer C. C., Neigel J. E. and Leberg P. L. 2000 Experimental evaluation of the usefulness of microsatellite DNA for detecting demographic bottlenecks. Mol. Ecol. 9, 1517–1528.
Van Oosterhout C., Hutchinson W. F., Wills D. P. M. and Shipley P. 2004 Micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Mol. Ecol. Notes 4, 535–538.
Ward J., Cole C., Febrer M. and Barton G. J. 2016 AlmostSignificant: simplifying quality control of high-throughput sequencing data. Bioinformatics 32, 3850–3851.
Acknowledgements
We kindly thank the following zoos which donated DNA samples for this study: Chester Zoo (UK), Marwell Zoo (UK), Woburn Safari Park (UK), Paignton Zoo (UK), Howletts Wild Animal Park (UK), Knowsley Safari Park (UK), Givskud Zoo (Denmark) and Antwerp Zoo (Belgium). Thanks also to the DNA Sequencing Facility and the Genomic Technologies Core Facility at the University of Manchester, for their expert advice and services. Funding for this study came from an incentivisation grant from the Manchester Metropolitan University.
Author information
Authors and Affiliations
Corresponding author
Additional information
Corresponding editor: Umesh C. Lavania
Rights and permissions
About this article
Cite this article
Combe, F.J., Taylor-Cox, E., Fox, G. et al. Rapid isolation and characterization of microsatellites in the critically endangered mountain bongo (Tragelaphus eurycerus isaaci). J Genet 97, 549–553 (2018). https://doi.org/10.1007/s12041-018-0922-z
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12041-018-0922-z