Genetic diversity of Nubian ibex in comparison to other ibex and domesticated goat species

  • Lubna M. A. Hassan
  • Danny Arends
  • Siham A. Rahmatalla
  • Monika Reissmann
  • Henry Reyer
  • Klaus Wimmers
  • Sumaia M. A. Abukashawa
  • Gudrun A. BrockmannEmail author
Original Article


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.


Genetic 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.

Authors’ contributions

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

Competing interest

The authors declare no conflict of interest.

Supplementary material

10344_2018_1212_MOESM1_ESM.txt (3.4 mb)
ESM 1 Locations of protein coding gene (TXT 3463 kb)
10344_2018_1212_MOESM2_ESM.xlsx (9 kb)
ESM 2 Estimates of pairwise genetic differentiation (FST) between species using StAMMP R package (XLSX 8 kb)
10344_2018_1212_MOESM3_ESM.xlsx (8 kb)
10344_2018_1212_MOESM4_ESM.png (22 kb)
ESM 4 Euclidean distance (PNG 22 kb)
10344_2018_1212_MOESM5_ESM.xlsx (17 kb)
ESM 5 Structure (XLSX 16 kb)
10344_2018_1212_MOESM6_ESM.png (54 kb)
ESM 6 Genomic location of SNPs with high contribution to PC1, PC2, and PC3 (PNG 54 kb)
10344_2018_1212_MOESM7_ESM.xlsx (89 kb)
ESM 7 SNPs and genes contributing to PC1, PC2, and PC3 (XLSX 89 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Lubna M. A. Hassan
    • 1
    • 2
  • Danny Arends
    • 3
  • Siham A. Rahmatalla
    • 3
    • 4
  • Monika Reissmann
    • 3
  • Henry Reyer
    • 5
  • Klaus Wimmers
    • 5
  • Sumaia M. A. Abukashawa
    • 2
  • Gudrun A. Brockmann
    • 3
    Email author
  1. 1.Wildlife Research Center, Animal Resource Research CorporationFederal Ministry of Livestock, Fisheries and RangelandsKhartoumSudan
  2. 2.Faculty of Sciences, Department of ZoologyUniversity of KhartoumKhartoumSudan
  3. 3.Albrecht Daniel Thaer-Institute for Agricultural and Horticultural SciencesHumboldt-Universität zu BerlinBerlinGermany
  4. 4.Faculty of Animal Production, Department of Dairy ProductionUniversity of KhartoumKhartoum NorthSudan
  5. 5.Institute for Genome BiologyLeibniz Institute for Farm Animal Biology (FBN)DummerstorfGermany

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