Genetic diversity of Nubian ibex in comparison to other ibex and domesticated goat species
Capra nubiana is a wild ibex species that is in danger of extinction. This study aimed at assessing the genetic diversity and population structure of Nubian ibex (Capra nubiana, n = 8) in comparison to Alpine ibex (Capra ibex, n = 8), Bezoar ibex (Capra aegagrus, n = 4), and domesticated Taggar goats (Capra aegagrus hircus, n = 24). All animals were genotyped with the 50K goat SNP chip. Since commercial SNP chips are not designed for wild species, data analysis was done in two ways: (1) using all callable SNPs (33,698) and (2) with a reduced set of SNPs segregating within three out of four populations (662). Using these two sets of SNPs, the observed heterozygosity in Nubian ibex ranged from 0.02 to 0.44, in Alpine ibex from 0.01 to 0.38, and in Bezoar ibex from 0.13 to 0.38, when analyzing 33,698 or 662 SNPs, respectively. In domesticated Taggar goats, the values for the observed heterozygosity using all 33,698 callable SNPs and the reduced set of 662 SNPs were similar (0.40–0.41). Pairwise FST values for the differentiation between species ranged from 0.17–0.35 (Bezoar ibex vs. Taggar goats) to 0.47–0.91 (Bezoar vs. Alpine ibex), and was 0.33–0.90 between Bezoar and Nubian ibex, respectively, to the two sets of SNPs. The analysis of molecular variance among all animals revealed that 74–78% can be explained by differences between species, while the residual 22–26% result from differences among individuals, respectively. Cluster analysis of Nei’s genetic distance allowed to detected two distinct clusters comprising Nubian and Alpine ibex on one hand and Taggar goats and Bezoar ibex on the other hand, and clear separation of all four breeds. Principal component (PC) analysis confirmed and further refined the clusters. SNPs that contributed most to PC1 allowed us to identify genomic regions accounting for the distances between species. These regions contain known milk protein genes. The identification of milk protein genes as contributors to the differentiation between species provides insights into the domestication of wild Capra breeds.
KeywordsGenetic diversity Nubian ibex Alpine ibex Bezoar ibex Goat Conservation
We acknowledge the help with collecting animal material of Nubian ibex from Wildlife Research Center researchers and drivers especially from Dinder Wildlife Research Station. We also thank the Wildlife Conservation General Administration in Khartoum and Red Sea State as well as the managers of the local communities in the Red Sea State. The samples of Bezoar and Alpine ibex were provided by the DNA and tissue bank of the Leibniz Institute for Zoo and Wildlife Research Berlin, Germany. LMAH was partially supported by the Wildlife Research Center, Sudan, and through a scholarship of the Humboldt-Universität zu Berlin, Germany. S.A.R. is a fellow of the Alexander von Humboldt Foundation.
L.M.A.H. provided ibex samples, contributed to the study design, DNA extraction, contributed to the manuscript.
D.A. performed the data analysis and drafted the manuscript.
S.A.R. provided Taggar goat samples, contributed to the data analysis and writing the manuscript.
M.R. developed and refined the protocols for DNA extraction, contributed samples from different ibex, and contributed to the manuscript.
H.R. performed the SNP chip hybridization, genotype calling, and initial data check.
K.W. contributed to genotyping.
S.M.A.A. contributed to develop the study.
G.A.B. supervised the study through development of the study design, critical data analysis, discussing the data and results, and finalizing the manuscript.
Compliance with ethical standards
The authors declare no conflict of interest.
- Alkon PU et al (2008) Capra nubiana (Nubian Ibex). International Union for Conservation of Nature. http://www.iucnredlist.org/details/3796/0. Accessed 2018–02-06
- Bushara I, Abu Nikhaila MMAA (2012) Productivity performance of Taggar female kids under grazing condition. J Anim Prod Adv 2:74–79Google Scholar
- Butynski T, Happold D, Happold M, Hoffmann M (2013) Mammals of Africa, vol IV. Bloomsbury Publishing, LondonGoogle Scholar
- El-Naim Y (1979) Some reproductive and productive traits of Sudan nubian goats. MVSc dissertation, University of Khartoum, SudanGoogle Scholar
- Grubb P (2005) Order artiodactyla. In: Wilson DE, Reeder DM (eds) Mammal species of the world: a taxonomic and geographic reference, vol 1/2, 3rd edn. The Johns Hopkins University Press, Baltimore, pp 637–722Google Scholar
- Grzimek B, Zingg R (1990) Alpine ibex (Capra ibex ibex). In: Parker SP (ed) Grzimek's encyclopedia of mammals, vol 5, 3rd edn. McGraw-Hill, New York, pp 516–523Google Scholar
- HCENR (2014) Fifth National Report to the convention on biological diversity (CBD). Ministry of Environment, Forestry and Physical Development, SudanGoogle Scholar
- IUCN (2018) The IUCN Red List of Threatened Species, 2017—3rd edn. International Union for Conservation of Nature, http://www.iucnredlist.org
- Kijas JW, Ortiz JS, McCulloch R, James A, Brice B, Swain B, Tosser-Klopp G, the International Goat Genome Consortium (2013) Genetic diversity and investigation of polledness in divergent goat populations using 52 088 SNPs. Anim Genet 44:325–335. https://doi.org/10.1111/age.12011 CrossRefPubMedGoogle Scholar
- Mendelssohn H (1990) Nubian ibex (Capra ibex nubiana). In: Parker SP (ed) In Grzimek's encyclopedia of mammals, vol 5. McGraw-Hill, New York, pp 525–527Google Scholar
- Muffarah MB (1995) Goat breeds and varieties in Sudan. Proceeding of Training Course, Sheep and Goat Production, Arab Centre for Studies of Arid and Dryland (ACSAD), Khartoum 17–27 January, SudanGoogle Scholar
- Nimir MB (1997) Sudan—chapter 4–11. IUCN/SSC Caprinae Specialist Group, IUCN, Gland, Switzerland and Cambridge, UKGoogle Scholar
- Nowak RM (1999) Walker’s mammals of the world, vol 1. The John Hopkins University Press, BaltimoreGoogle Scholar
- Rahmatalla SA, Arends D, Reissmann M, Said Ahmed A, Wimmers K, Reyer H, Brockmann GA (2017) Whole genome population genetics analysis of Sudanese goats identifies regions harboring genes associated with major traits. BMC Genet 18:92. https://doi.org/10.1186/s12863-017-0553-z CrossRefPubMedPubMedCentralGoogle Scholar
- Scherf BD (2000) World watch list for domestic animal diversity vol, 3rd edn. Food and Agriculture Organization of the United Nations, RomeGoogle Scholar
- Shackleton DM (1997) Wild sheep and goats and their relatives: status survey and conservation action plan for Caprinae IUCN/SSC Caprinae specialist group. IUCN, GlandGoogle Scholar
- Stuart C, Stuart T (2016) Mammals of North Africa and the Middle East. Bloomsbury Publishing, LondonGoogle Scholar
- Talenti A, Nicolazzi EL, Chessa S, Frattini S, Moretti R, Coizet B, Nicoloso L, Colli L, Pagnacco G, Stella A, Ajmone-Marsan P, Ptak G, Crepaldi P (2016) A method for single nucleotide polymorphism selection for parentage assessment in goats. J Dairy Sci 99:3646–3653. https://doi.org/10.3168/jds.2015-10077 CrossRefPubMedGoogle Scholar
- TheRCoreTeam (2014) R: a language and environment for statistical computing. R Foundation for Statistical Computing, ViennaGoogle Scholar
- Tosser-Klopp G, Bardou P, Bouchez O, Cabau C, Crooijmans R, Dong Y, Donnadieu-Tonon C, Eggen A, Heuven HCM, Jamli S, Jiken AJ, Klopp C, Lawley CT, McEwan J, Martin P, Moreno CR, Mulsant P, Nabihoudine I, Pailhoux E, Palhière I, Rupp R, Sarry J, Sayre BL, Tircazes A, Wang J, Wang W, Zhang W, International Goat Genome Consortium (2016) Correction: design and characterization of a 52K SNP Chip for goats. PLoS One 11:e0152632. https://doi.org/10.1371/journal.pone.0152632 CrossRefPubMedPubMedCentralGoogle Scholar
- Wilson T (1991) Small ruminant production and the small ruminant genetic resource in tropical Africa FAO animal production and health paper 88Google Scholar
- Wright S (1969) Evolution and the genetics of populations, vol 2: the theory of gene frequencies. The University of Chicago Press, Chicago and LondonGoogle Scholar