DNA Metabarcoding Reveals Diet Overlap between the Endangered Walia Ibex and Domestic Goats - Implications for Conservation

Human population expansion and associated degradation of the habitat of many wildlife species cause loss of biodiversity and species extinctions. The small Simen Mountains National Park in Ethiopia is one of the last strongholds for the preservation of a number of afro-alpine mammals, plants and birds, and it is home to the rare endemic Walia ibex, Capra walie. The narrow distribution range of this species as well as potential competition for resources with livestock, especially with domestic goat, Capra hircus, may compromise its future survival. Based on a curated afro-alpine taxonomic reference library constructed for plant taxon identification, we investigated the diet of the Walia ibex and addressed the dietary overlap with domestic goat using DNA metabarcoding of faecal samples. Faeces of both species were collected from different localities in the National Park. We show that both species are browsers, with forbs, shrubs and trees comprising the largest proportion of their diet, supplemented by grasses. There was a considerable overlap in dietary preferences. Several of the preferred diet items of the Walia ibex (Alchemilla sp., Hypericum revolutum, Erica arborea and Rumex sp.) were also among the most preferred diet items of the domestic goat. These results indicate that there is potential for competition between the two species, especially during the dry season, when resources are limited. Our findings, in combination with the expected increase in domestic herbivores, suggest that management plans should consider the potential threat posed by domestic goats to ensure future survival of the endangered Walia ibex.

[1]  Katsutoshi Watanabe,et al.  IUCN Red List of Threatened Species: ビワヨシノボリ , 2018 .

[2]  P. Taberlet,et al.  obitools: a unix‐inspired software package for DNA metabarcoding , 2016, Molecular ecology resources.

[3]  David L. Erickson,et al.  DNA metabarcoding illuminates dietary niche partitioning by African large herbivores , 2015, Proceedings of the National Academy of Sciences.

[4]  P. Taberlet,et al.  Highly Overlapping Winter Diet in Two Sympatric Lemming Species Revealed by DNA Metabarcoding , 2015, PloS one.

[5]  P. Stephens,et al.  Predicting potential responses to future climate in an alpine ungulate: interspecific interactions exceed climate effects , 2014, Global change biology.

[6]  J. Poesen,et al.  Environmental conditions and human drivers for changes to north Ethiopian mountain landscapes over 145 years. , 2014, The Science of the total environment.

[7]  S. Boessenkool,et al.  Use of Ancient Sedimentary DNA as a Novel Conservation Tool for High‐Altitude Tropical Biodiversity , 2014, Conservation biology : the journal of the Society for Conservation Biology.

[8]  P. Taberlet,et al.  Fifty Thousand Years of Arctic Vegetation and Megafaunal Diet 1 Reconstruction of Arctic Vegetation from Permafrost Samples 121 , 2022 .

[9]  Christopher A. Lepczyk,et al.  Biology and Impacts of Pacific Island Invasive Species. 9. Capra hircus, the Feral Goat (Mammalia: Bovidae)1 , 2013 .

[10]  Daniel Sabatier,et al.  Unveiling the Diet of Elusive Rainforest Herbivores in Next Generation Sequencing Era? The Tapir as a Case Study , 2013, PloS one.

[11]  James Haile,et al.  Fungal palaeodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost. , 2013, Environmental microbiology.

[12]  J. Marino,et al.  Genetic structure and patterns of gene flow among populations of the endangered Ethiopian wolf , 2013 .

[13]  P. Taberlet,et al.  Assessment of the Food Habits of the Moroccan Dorcas Gazelle in M’Sabih Talaa, West Central Morocco, Using the trnL Approach , 2012, PloS one.

[14]  P. Taberlet,et al.  Who is eating what: diet assessment using next generation sequencing , 2012, Molecular ecology.

[15]  E. Willerslev,et al.  Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA , 2012, Molecular ecology.

[16]  P. Taberlet,et al.  Towards next‐generation biodiversity assessment using DNA metabarcoding , 2012, Molecular ecology.

[17]  Y. Mekasha,et al.  Population dynamics of Walia ibex (Capra walie) at Simien Mountains National Park, Ethiopia , 2011 .

[18]  P. Taberlet,et al.  New insights on diet variability revealed by DNA barcoding and high-throughput pyrosequencing: chamois diet in autumn as a case study , 2011, Ecological Research.

[19]  Y. Mekasha,et al.  The probable genetic introgression between Walia ibex (Capra walie) and domestic goats (Capra hircus) at Simien mountains national park (SMNP) in Ethiopia , 2011 .

[20]  Pierre Taberlet,et al.  Influence of management practices on large herbivore diet—Case of European bison in Białowieża Primeval Forest (Poland) , 2011 .

[21]  François Pompanon,et al.  An In silico approach for the evaluation of DNA barcodes , 2010, BMC Genomics.

[22]  Pierre Taberlet,et al.  ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases , 2010, BMC Microbiology.

[23]  Pierre Taberlet,et al.  Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures , 2009, Frontiers in Zoology.

[24]  P. Taberlet,et al.  Universal DNA-based methods for assessing the diet of grazing livestock and wildlife from feces. , 2009, Journal of agricultural and food chemistry.

[25]  I. Gordon What is the Future for Wild, Large Herbivores in Human-Modified Agricultural Landscapes? , 2009 .

[26]  P. Taberlet,et al.  Combining genetic and ecological data to assess the conservation status of the endangered Ethiopian walia ibex , 2009 .

[27]  P. Taberlet,et al.  DNA barcoding for ecologists. , 2009, Trends in ecology & evolution.

[28]  R. Shrestha,et al.  Wild sheep and livestock in Nepal Trans-Himalaya: coexistence or competition? , 2008, Environmental Conservation.

[29]  Zhigang Jiang,et al.  Dietary Overlap of Przewalski's Gazelle, Tibetan Gazelle, and Tibetan Sheep on the Qinghai-Tibet Plateau , 2008 .

[30]  Tammo S. Steenhuis,et al.  Rainfall‐discharge relationships for a monsoonal climate in the Ethiopian highlands , 2008 .

[31]  C. Chapman,et al.  Plant DNA sequences from feces: potential means for assessing diets of wild primates , 2007, American journal of primatology.

[32]  R. Mendelsohn,et al.  Climate Change Impacts on Animal Husbandry in Africa: A Ricardian Analysis , 2007 .

[33]  Thierry Vermat,et al.  Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding , 2006, Nucleic acids research.

[34]  B. Gutiérrez-Gil,et al.  Evidence of three maternal lineages in near eastern sheep supporting multiple domestication events , 2005, Proceedings of the Royal Society B: Biological Sciences.

[35]  R. Shrestha,et al.  Summer diets of wild and domestic ungulates in Nepal Himalaya , 2005 .

[36]  Y. Bhatnagar,et al.  Conflicts between traditional pastoralism and conservation of Himalayan ibex (Capra sibirica) in the Trans‐Himalayan mountains , 2004 .

[37]  Mark Blaxter,et al.  Molecular barcodes for soil nematode identification , 2002, Molecular ecology.

[38]  J. Holmberg Reconciling Conservation With Sustainable Development. A Participatory Study Inside and Around the Simen Mountains National Park, Ethiopia , 2000 .

[39]  A. Mysterud Diet overlap among ruminants in Fennoscandia , 2000, Oecologia.

[40]  Herbert H. T. Prins,et al.  Resource partitioning between sympatric wild and domestic herbivores in the Tarangire region of Tanzania , 1999, Oecologia.

[41]  R. Putman Competition and Resource Partitioning in Temperate Ungulate Assemblies , 1996, Chapman & Hall Wildlife Ecology and Behaviour Series.

[42]  W. F. Boer,et al.  Large herbivores that strive mightily but eat and drink as friends , 1990, Oecologia.

[43]  M. Hill,et al.  Data analysis in community and landscape ecology , 1987 .

[44]  C. Braak,et al.  The analysis of vegetation-environment relationships by canonical correspondence analysis , 1987, Vegetatio.

[45]  Robin I. M. Dunbar Competition and niche separation in a high altitude herbivore community in Ethiopia , 1978 .

[46]  B. Coblentz,et al.  Some range relationships of feral goats on Santa Catalina Island, California. , 1977 .

[47]  T. Schoener,et al.  Competition and the form of habitat shift. , 1974, Theoretical population biology.

[48]  H. S. Horn,et al.  Measurement of "Overlap" in Comparative Ecological Studies , 1966, The American Naturalist.

[49]  A. Melaku,et al.  Occurrence, Intensity and Parasite Composition of Gastrointestinal Helminth Parasites in Walia Ibex (Capra walie) at Semien Mountains National Park, Natural World Heritage Site, Northern Ethiopia , 2014 .

[50]  F. Hagedorn,et al.  Mountain soils under a changing climate and land-use , 2010 .

[51]  H. Hurni,,et al.  Land degradation and sustainable land management in the Highlands of Ethiopia , 2010 .

[52]  David C. Tank,et al.  An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: , 2009 .

[53]  H. Henttonen,et al.  Eliomys quercinus. The IUCN Red List of Threatened Species. Version 2014.3. , 2008 .

[54]  I. Hedberg Flora of Ethiopia and Eritrea Volume 5 , 2006 .

[55]  C. Gortázar,et al.  The Iberian ibex is under an expansion trend but displaced to suboptimal habitats by the presence of extensive goat livestock in central Spain , 2006, Biodiversity and Conservation.

[56]  M. Hill,et al.  Detrended correspondence analysis: An improved ordination technique , 2004, Vegetatio.

[57]  O Hammer-Muntz,et al.  PAST: paleontological statistics software package for education and data analysis version 2.09 , 2001 .

[58]  C.J.F. ter Braak,et al.  CANOCO Reference Manual and User's Guide to Canoco for Windows: Software for Canonical Community Ordination (Version 4) , 1998 .

[59]  I. Hedberg Flora of Ethiopia and Eritrea , 1996 .

[60]  D M Irwin,et al.  Evolution of the cytochrome b gene of mammals. , 1991, Journal of molecular evolution.

[61]  R. Langton DIET OVERLAP B,ETWEEN ATLANTIC COD, GADUS MORHUA, SILVER HAKE, MERLUCCIUS BILINEARIS, AND FIFTEEN OTHER NORTHWEST ATLANTIC FINFISH , 1982 .

[62]  B. Nievergelt Ibexes in an African environment : ecology and social system of the Walia ibex in the Simen Mountains, Ethiopia , 1981 .