E.C.O. Institute of Ecology
Recent publications
This book chapter explores the impacts of both early domestication and historical breeding practices on camel welfare-related traits, emphasizing the need for a holistic approach to enhance the well-being of these animals in view of the contemporaneous rise of socio-economic interest in camel breeding. Under the so-called “domestication syndrome”, several genomic regions mostly controlling neural crest development and thyroid function have been identified in Old World camels. However, these animal species remain less explored than other conventional livestock species for the genetic mechanisms underlying domestication-related traits such as behaviour, coat colour, and social communication. In this scenario, the standardization of phenotype characterization activities and the ulterior use of genomic tools for further study of genotype-phenotype associations becomes prominent to increase the knowledge on the genetic architecture of welfare-related traits, thus their potential inclusion on marker-assisted selection schemes in the camel species. Additionally, precision livestock farming technologies can significantly support herd and breeding management under the concerns of animal welfare for maintaining highly productive and healthy animals.
After the domestication of goats around 10,000 years before the present (BP), humans transported goats far beyond the range of their wild ancestor, the bezoar goat. This brought domestic goats into contact with many wild goat species such as ibex and markhor, enabling introgression between domestic and wild goats. To investigate this, while shedding light on the taxonomic status of wild and domestic goats, we analysed genome‐wide SNP data of 613 specimens from 14 taxonomic units, including Capra hircus , C. pyrenaica , C. ibex (from Switzerland, Austria, Germany and Slovenia), C. aegagrus aegagrus , C. a. cretica , C. h. dorcas , C. caucasica caucasica , C. c. severtzovi , C. c. cylindricornis , C. falconeri , C. sibirica sibirica , C. s. alaiana and C. nubiana , as well as Oreamnos americanus (mountain goat) as an outgroup. To trace gene flow between domestic and wild goats, we integrated genotype data of local goat breeds from the Alps as well as from countries such as Spain, Greece, Türkiye, Egypt, Sudan, Iran, Russia (Caucasus and Altai) and Pakistan. Our phylogenetic analyses displayed a clear separation between bezoar‐type and ibex‐type clades with wild goats from the Greek islands of Crete and Youra clustered within domestic goats, confirming their feral origin. Our analyses also revealed gene flow between the lineages of Caucasian tur and domestic goats that most likely occurred before or during early domestication. Within the clade of domestic goats, analyses inferred gene flow between African and Iberian goats. The detected events of introgression were consistent with previous reports and offered interesting insights into the historical relationships among domestic and wild goats.
Old-growth forests (OGF) provide valuable ecosystem services such as habitat provision, carbon sequestration or recreation maintaining biodiversity, carbon storage, or human well-being. Long-term human pressure caused OGFs in Europe to be rare and scattered. Their detailed extent and current status are largely unknown. This review aims to identify potential methods to map temperate old-growth forests (tOGF) by remote sensing (RS) technology, highlights the potentials and benefits, and identifies main knowledge gaps requesting further research. RS offers a wide range of data and methods to map forests and their properties, applicable from local to continental scale. We structured existing mapping approaches in three main groups. First, parameter-based approaches, which are based on forest parameters and usually applied on local to regional scale using detailed data, often from airborne laser scanning (ALS). Second, direct approaches, usually employing machine learning algorithms to generate information from RS data, with high potential for large-area mapping but so far lacking operational applications and related sound accuracy assessment. Finally, indirect approaches integrating various existing data sets to predict OGF existence. These approaches have also been used for large area mapping with a main drawback of missing physical evidence of the identified areas to really hold OGFs as compared to the likelihood of OGF existence. In conclusion, studies dealing with the mapping of OGF using remote sensing are quite limited, but there is a huge amount of knowledge from other forestry-related applications that is yet to be leveraged for OGF identification. We discuss two scenarios, where different data and approaches are suitable, recognizing that one single system cannot serve all potential needs. These may be hot spot identification, detailed area delineation, or status assessment. Further, we pledge for a combined method to overcome the identified limitations of the individual approaches.
Maintaining and improving the state of biodiversity is a primary factor guiding management activities in conservation areas, including protected areas (PAs) and other effective area-based conservation measures (OECMs). Due to the complex nature of conservation programs, a common management approach cannot be prescribed. Robust monitoring programs supporting management activities are required to evaluate the state of species and habitats. However, limited resources, poor data management practices, and competing requirements of stakeholder groups increase the challenges that must be addressed through realization of monitoring programs. We propose a framework of seven basic questions to guide conservation area managers to implement effective biodiversity monitoring techniques. The result is identification of indicators, site characteristics, and resources to promote the development of a biodiversity monitoring program. We call for adoption of a strategic guideline providing this framework to harmonize decision making processes across national and international networks. Implementation of this robust framework will support comparative monitoring data, contributing to systematic approaches for adaptive management in PAs and OECMs and improving the body of knowledge surrounding global biodiversity.
Obligatory endoparasitic mites of the genera Halarachne Allman, 1847 and Orthohalarachne Newell, 1947 (Acari: Halarachnidae) parasitize different segments of the respiratory tract of marine mammals, including pinnipeds and sea otters, and infestations can cause asymptomatic to serious respiratory diseases. However, knowledge on biology, pathogenic potential and occurence of halarachnid mites infesting pinnipeds, especially in captivity, is scarce. A two-year-old South American sea lion (Otaria flavescens Shaw, 1800) male, born and held at the Vienna Zoo, was anesthesized for routine pre-transport examinations, including computed tomography, bronchoalveolar lavage, and blood sampling. During the final phase of general anesthesia, the individual abruptly became apneic and died despite all attempts at resuscitation. At necropsy, 45 highly motile whitish millimeter-sized structures were macroscopically detected in the trachea, bifurcatio tracheae and main bronchi and were identified as adult stages of Orthohalarachne diminuata Doetschman, 1944 following morphological descriptions. After trepanation of the nasal cavity and sinus paranasalis, a total of 407 larval and 3 nymphal specimens distributed in clusters were detected. Macroscopically, sinus mucosa showed hyperemia and multiple petechial hemorrhages. Histopathological analyses of paranasal sinuses revealed mite cross-sections surrounded by sanioserous exudate and epithelial exfoliation. For the first time, O. diminuata was molecularly characterized and phylogenetically analyzed based on its 16S rDNA. Our study constitutes the first record of a severe O. diminuata infestation in captive O. flavescens and one of the few host-parasite records in general. We present clinical data and pathological results, the first scanning electron microscopic images of O. diminuata larvae and discuss the etiology of this autochthonous infestation, possible transmission pathways and detrimental effects. Further studies on biology and pathogenic effects of halarachnid mites, as well as the development of non-invasive sampling techniques is essentially required for a better understanding of (ortho-)halarachnosis in pinnipeds held in zoological gardens.
Water conservation is vital for life in the desert. The dromedary camel (Camelus dromedarius) produces low volumes of highly concentrated urine, more so when water is scarce, to conserve body water. Two hormones, arginine vasopressin and oxytocin, both produced in the supraoptic nucleus, the core hypothalamic osmoregulatory control centre, are vital for this adaptive process, but the mechanisms that enable the camel supraoptic nucleus to cope with osmotic stress are not known. To investigate the central control of water homeostasis in the camel, we first build three dimensional models of the camel supraoptic nucleus based on the expression of the vasopressin and oxytocin mRNAs in order to facilitate sampling. We then compare the transcriptomes of the supraoptic nucleus under control and water deprived conditions and identified genes that change in expression due to hyperosmotic stress. By comparing camel and rat datasets, we have identified common elements of the water deprivation transcriptomic response network, as well as elements, such as extracellular matrix remodelling and upregulation of angiotensinogen expression, that appear to be unique to the dromedary camel and that may be essential adaptations necessary for life in the desert. Comparative transcriptomic analyses between dromedary camels and rats provide insight into water homeostasis gene responses in animals under water stress conditions.
In South Africa, cheetahs (Acinonyx jubatus) occur as a relictual, unmanaged population of ‘free‐roamers’, a managed metapopulation across fenced reserves, and in various captive facilities. To ensure that the Cheetah Metapopulation Project (CMP) is not at risk of losing overall genetic variation to drift or inbreeding, we propose various interventions, including exchanges between free‐roamers and the metapopulation or supplementation with unrelated individuals from captivity. Simulated trajectories of genetic diversity under such intervention strategies over time could directly inform conservation action and policy towards securing the long‐term genetic integrity of the CMP. Single Nucleotide Polymorphisms (SNPs) were genotyped for 172 adult cheetahs across the free‐roamer population, the metapopulation, and three major captive facilities. Management intervention trajectory models were tested including, (1) no intervention, (2) genetic exchange between free‐roamers and the metapopulation, (3) translocation from a single captive facility and (4) translocation from several captive facilities into the metapopulation. Discriminant Analysis of Principal Components (DAPC) showed that two captive populations are highly differentiated from the metapopulation and each other, whilst the third captive and free‐roamer populations are genetically more similar to the metapopulation. Simulated genetic variation over 25 generations indicated that models 1 and 2 show significant losses of heterozygosity due to genetic drift and present a proportional increase in the frequencies of 1st‐ and 2nd‐degree relatives, whilst this variation and pairwise relatedness remain relatively constant under models 3 and 4. We emphasise the potential importance of captive facilities as reservoirs of genetic diversity in metapopulation management and threatened species recovery.
The coat color of dromedary is usually uniform and varies from black to white, although dark- to light-brown colors are the most common phenotypes. This project was designed to gain knowledge on novel color-related variants using genotyping-by-sequencing (GBS). The association between the SNPs and coat color was tested using MLM (mixed linear models) with kinship matrix. Three GWAS models including white color vs. non-white color, black vs. non-black color, and light�brown vs. dark-brown color were performed. There were no distinct genetic clusters detected based on the color phenotypes. However, admixture occurred among all individuals of the four different coat color groups. We identified nine significant SNPs associated with white color after Bonferroni correction, located close to ANKRD26, GNB1, TSPYL4, TEKT5, DEXI, CIITA, TVP23B, CLEC16A, TMPRSS13, FXYD6, MPZL3, ANKRD26, HFM1, CDC7, TGFBR3, and HACE1 genes in neighboring flanking regions. The 13 significant SNPs associated with black color and the candidate genes were: CAPN7, CHRM4, CIITA, CLEC16A, COL4A4, COL6A6, CREB3L1, DEXI, DGKZ, DGKZ, EAF1, HDLBP, INPP5F, MCMBP, MDK, SEC23IP, SNAI1, TBX15, TEKT5, TMEM189, trpS, TSPYL4, TVP23B, and UBE2V1. The SNAI1 gene interacted with MCIR, ASIP and KIT genes. These genes play a key role in the melanin biosynthetic and pigmentation biological process and melanogenesis biological pathway.Further research using a larger sample size and pedigree data will allow confirmation of associated SNPs and the identified candidate genes.
Recent technological advances in the field of genomics offer conservation managers and practitioners new tools to explore for conservation applications. Many of these tools are well developed and used by other life science fields, while others are still in development. Considering these technological possibilities, choosing the right tool(s) from the toolbox is crucial and can pose a challenging task. With this in mind, we strive to inspire, inform and illuminate managers and practitioners on how conservation efforts can benefit from the current genomic and biotechnological revolution. With inspirational case studies we show how new technologies can help resolve some of the main conservation challenges, while also informing how implementable the different technologies are. We here focus specifically on small population management, highlight the potential for genetic rescue, and discuss the opportunities in the field of gene editing to help with adaptation to changing environments. In addition, we delineate potential applications of gene drives for controlling invasive species. We illuminate that the genomic toolbox offers added benefit to conservation efforts, but also comes with limitations for the use of these novel emerging techniques.
High-mountain plant communities are strongly determined by abiotic conditions, especially low temperature, and are therefore susceptible to effects of climate warming. Rising temperatures, however, also lead to increased evapotranspiration, which, together with projected shifts in seasonal precipitation patterns, could lead to prolonged, detrimental water deficiencies. The current study aims at comparing alpine plant communities along elevation and water availability gradients from humid conditions (north-eastern Alps) to a moderate (Central Apennines) and a pronounced dry period during summer (Lefka Ori, Crete) in the Mediterranean area. We do this in order to (1) detect relationships between community-based indices (plant functional leaf and growth traits, thermic vegetation indicator, plant life forms, vegetation cover and diversity) and soil temperature and snow duration and (2) assess if climatic changes have already affected the vegetation, by determining directional changes over time (14-year period; 2001–2015) in these indices in the three regions. Plant community indices responded to decreasing temperatures along the elevation gradient in the NE-Alps and the Apennines, but this elevation effect almost disappeared in the summer-dry mountains of Crete. This suggests a shift from low-temperature to drought-dominated ecological filters. Leaf trait (Leaf Dry Matter Content and Specific Leaf Area) responses changed in direction from the Alps to the Apennines, indicating that drought effects already become discernible at the northern margin of the Mediterranean. Over time, a slight increase in vegetation cover was found in all regions, but thermophilisation occurred only in the NE-Alps and Apennines, accompanied by a decline of cold-adapted cushion plants in the Alps. On Crete, xeromorphic shrubs were increasing in abundance. Although critical biodiversity losses have not yet been observed, an intensified monitoring of combined warming-drought impacts will be required in view of threatened alpine plants that are either locally restricted in the south or weakly adapted to drought in the north.
In the case of camels, there is little data in the literature on the relationship between body building features and the evaluation of milk yield. In the last decade, a rising interest in camel milk has been observed due to its nutritional and health-promoting properties, resulting in a growing market demand. Despite the remarkable importance of camels, very little improvement in camel breeding and selection for dairy purposes has been achieved. The current study aimed to provide a practical approach to the evaluation of dairy dromedaries based on test day milk and morphometric records. A total of 62 Sindi dairy camels were evaluated and 4176 daily milk records were registered in February, March, April, and May 2021. She-camels were milked twice per day (at morning and evening) by hand before calf sucking. The farming system was intensive with two times feeding. Three measurements had the highest scores in assessing: udder, teats distance and placement, and teats size, which included 45 out of 100 scores. Test day milk records were analysed using a simple repeatability model with two random effects. The range of daily milk yields was estimated between 0.1 to 8.70 kg. The mean of body scores was 77.19 (CI = 74.19–80.19). Daily milk yields moderately correlated with body score (r = +0.27). Additionally, udder circumference and abdomen girth were correlated to milk production. Using test day milk records in breeding programs can be appropriate for the selection and replacement of she-camels, but due to difficulties in accessing these data, using morphometric data is a good criterion for the evaluation of dromedaries in extensive systems.
The genomes of crossbred (admixed) individuals are a mosaic of ancestral haplotypes formed by recombination in each generation. The proportion of these ancestral haplotypes in certain genomic regions can be responsible for either susceptibility or tolerance against pathogens, and for performances in production traits. Using a medium-density genomic marker panel from the Illumina Bovine SNP50 BeadChip, we estimated individual admixture proportions for Baoulé x Zebu crossbred cattle in Burkina Faso, which were tested for trypanosome infection by direct ELISA from blood samples. Furthermore, we calculated local ancestry deviation from average for each SNP across 29 autosomes to identify potential regions under selection in the trypanotolerant Baoulé cattle and their crossbreds. We identified significant deviation from the local average ancestry (above 5 and 10% genome-wide thresholds) on chromosomes 8 and 19 in the positive animals, while the negative ones showed higher deviation on chromosomes 6, 19, 21, and 22. Some candidate genes on chromosome 6 (PDGFRA) and chromosome 19 (CDC6) have been found associated to trypanotolerance in West African taurines. Screening for FST outliers in trypanosome positive/negative animals we detected seven variants putatively under selection. Finally, we identified a minimum set of highly ancestry informative markers for routine admixture testing. The results of this study contribute to a better understanding of the genetic basis of trypanotolerance in Baoulé cattle and their crossbreeds. Furthermore, we provide a small informative marker set to monitor admixture in this valuable indigenous breed. As such, our results are important for conserving the genetic uniqueness and trypanotolerance of Baoulé cattle, as well as for the improvement of Baoulé and Zebu crossbreds in specific community-based breeding programs.
The Arabian camel (Camelus dromedarius) is the most important livestock animal in arid and semi-arid regions and provides basic necessities to millions of people. In the current context of climate change, there is renewed interest in the mechanisms that enable camelids to survive in arid conditions. Recent investigations described genomic signatures revealing evolutionary adaptations to desert environments. We now present a comprehensive catalogue of the transcriptomes and proteomes of the dromedary kidney and describe how gene expression is modulated as a consequence of chronic dehydration and acute rehydration. Our analyses suggested an enrichment of the cholesterol biosynthetic process and an overrepresentation of categories related to ion transport. Thus, we further validated differentially expressed genes with known roles in water conservation which are affected by changes in cholesterol levels. Our datasets suggest that suppression of cholesterol biosynthesis may facilitate water retention in the kidney by indirectly facilitating the AQP2-mediated water reabsorption. Fernando Alvira-Iraizoz and Benjamin T. Gillard et al. comprehensively catalogue the kidney transcriptome and proteome of dromedary camels in response to chronic dehydration stress and subsequent acute rehydration. Their results suggest that the suppression of the cholesterol biosynthesis may facilitate water retention in the dromedary camel kidney, providing further insight into how these animals survive in arid conditions.
For thousands of years, camels have produced meat, milk, and fiber in harsh desert conditions. For a sustainable development to provide protein resources from desert areas, it is necessary to pay attention to genetic improvement in camel breeding. By using genotyping-by-sequencing (GBS) method we produced over 14,500 genome wide markers to conduct a genome- wide association study (GWAS) for investigating the birth weight, daily gain, and body weight of 96 dromedaries in the Iranian central desert. A total of 99 SNPs were associated with birth weight, daily gain, and body weight (p-value < 0.002). Genomic breeding values (GEBVs) were estimated with the BGLR package using (i) all 14,522 SNPs and (ii) the 99 SNPs by GWAS. Twenty-eight SNPs were associated with birth weight, daily gain, and body weight (p-value < 0.001). Annotation of the genomic region (s) within ± 100 kb of the associated SNPs facilitated prediction of 36 candidate genes. The accuracy of GEBVs was more than 0.65 based on all 14,522 SNPs, but the regression coefficients for birth weight, daily gain, and body weight were 0.39, 0.20, and 0.23, respectively. Because of low sample size, the GEBVs were predicted using the associated SNPs from GWAS. The accuracy of GEBVs based on the 99 associated SNPs was 0.62, 0.82, and 0.57 for birth weight, daily gain, and body weight. This report is the first GWAS using GBS on dromedary camels and identifies markers associated with growth traits that could help to plan breeding program to genetic improvement. Further researches using larger sample size and collaboration of the camel farmers and more profound understanding will permit verification of the associated SNPs identified in this project. The preliminary results of study show that genomic selection could be the appropriate way to genetic improvement of body weight in dromedary camels, which is challenging due to a long generation interval, seasonal reproduction, and lack of records and pedigrees.
Sustainability is not a single concept, but a bundle of concepts that has broadened significantly in recent decades. Education for Sustainable Development (ESD) must therefore not only impart new knowledge but should also focus on supporting its students in acquiring new competences, both on a personal and an institutional level. Games and gamification can be important instruments for developing these competencies and experimenting in very different situations, simulating different scenarios and experiencing unexpected situations and outcomes.
Cheetahs (Acinonyx jubatus) are listed as vulnerable on the International Union for Conservation of Nature Red List of Threatened Species. Threats include loss of habitat, human-wildlife conflict and illegal wildlife trade. In South Africa, the export of wild cheetah is a restricted activity under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), however, limited legal trade is permitted of animals born to captive parents. To effectively monitor the legal and illegal trade in South Africa, it was thus essential to develop a validated molecular test. Here, we designed a single nucleotide polymorphism (SNP) array for cheetah from Double Digest Restriction Associated DNA sequencing data for individual identification and parentage testing. In order to validate the array, unrelated individuals and 16 family groups consisting of both parents and one to three offspring were genotyped using the Applied Biosystems™ QuantStudio™ 12K Flex Real-Time PCR System. In addition, parentage assignments were compared to microsatellite data. Cross-species amplification was tested in various felids and cheetah sub-species in order to determine the utility of the SNP array in other species. We obtained successful genotyping results for 218 SNPs in cheetah (A. j. jubatus) with an optimal DNA input concentration ranging from 10 to 30 ng/µl. The combination of SNPs had a higher resolving power for individual identification compared to microsatellites and provided high assignment accuracy in known pedigrees. Cross-species amplification in other felids was determined to be limited. However, the SNP array demonstrated a clear genetic discrimination of two cheetah subspecies tested here. We conclude that the described SNP array is suitable for accurate parentage assignment and provides an important traceability tool for forensic investigations of cheetah trade.
Purpose Alveolar echinococcosis is a severe helminthic disease in humans caused by larvae of the fox tapeworm Echinococcus multilocularis. Austria is considered an endemic area with hotspots having up to 45% prevalence (Bagó et al. in Proceedings of the Zoo and Wildlife Health Conference 2019, Berlin, p. 91, 2019). At our facility, we have registered a notifiable increase of animals submitted for the diagnosis of E. multilocularis since 2016. Therefore, we investigated high throughput diagnostic methods to provide rapid and reliable results in comparison with our current method. Methods We have developed and compared a novel method of detection using droplet digital PCR (ddPCR) combined with previous target specific extraction according to Maas et al. (Vet Parasitol 230:20–24, 2016), with our current macroscopic method “Shaking in a Vessel Technique” (SVT) by Duscher et al. (Parasitol Res 95(1):40–42, 2005). We investigated 77 wild canids (72 red foxes, 5 golden jackals) using both methods. The data were analyzed using a non-Bayesian approach, applying bootstrapping to create confidentiality intervals. Results Sensitivity for droplet digital PCR was 90.51% with the 95% credibility interval ranging from 82.50 to 96.92%, whereas mean sensitivity for SVT was 92.04% with a 95% credibility interval ranging from 84.75% to 98.36%. Additionally, a non-linear regression similar to R ² could be pointed out between the counted worms and the results gathered from ddPCR. Conclusion Magnetic capture extraction followed by ddPCR shows strong potential as a high throughput method for diagnosing E. multilocularis prevalence in diverse canid populations as well as infection intensities of individual animals, giving valuable epidemiological insights of the distribution amongst wild canids as an alternative to conventional qPCR or macroscopic methods.
For thousands of years, camels have produced meat, milk, and fiber in harsh desert conditions. For a sustainable development to provide protein resources from desert areas, it is necessary to pay attention to genetic improvement in camel breeding. By using genotyping-by-sequencing (GBS) method we produced over 14,500 genome wide markers to conduct a genome- wide association study (GWAS) for investigating the birth weight, daily gain, and body weight of 96 dromedaries in the Iranian central desert. A total of 99 SNPs were associated with birth weight, daily gain, and body weight (p-value < 0.002). Genomic breeding values (GEBVs) were estimated with the BGLR package using (i) all 14,522 SNPs and (ii) the 99 SNPs by GWAS. Twenty-eight SNPs located in 36 candidate genes were associated with birth weight, daily gain, and body weight (p-value < 0.001). The accuracy of GEBVs was more than 0.65 based on all 14,522 SNPs, but the regression coefficients for birth weight, daily gain, and body weight were 0.39, 0.20, and 0.23, respectively. Because of low sample size, the GEBVs were predicted using the associated SNPs from GWAS. The accuracy of GEBVs based on the 99 associated SNPs was 0.62, 0.82, and 0.57 for birth weight, daily gain, and body weight. This report is the first GWAS using GBS on dromedary camels and identifies markers associated with growth traits that could help to plan breeding program to genetic improvement. Further researches using larger sample size and collaboration of the camel farmers and more profound understanding will permit verification of the associated SNPs identified in this project. The preliminary results of study show that genomic selection could be the appropriate way to genetic improvement of body weight in dromedary camels, which is challenging due to a long generation interval, seasonal reproduction, and lack of records and pedigrees.
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Dr. Hanns Kirchmeir