Prioritizing livestock grazing right buyouts to safeguard Asiatic cheetahs from extinction

The article processing charge was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – 491192747 and the Open Access Publication Fund of Humboldt-Universität zu Berlin.Livestock husbandry exerts major pressures on wildlife across the world. Large carnivores are particularly at risk because they are often killed by pastoralists as a preventive or precautionary response to livestock depredation. Minimizing the overlap between pastures and carnivore habitat can thus be a conservation strategy, but it remains often unclear which pastures should be targeted to maximize conservation benefits given a limited budget. We addressed this question for the last viable population of the Asiatic cheetah (Acinonyx jubatus venaticus) in northeastern Iran. By combining species distribution modeling with a spatial prioritization framework, we aimed to identify where grazing right buyouts should take place to reduce cheetah killing by herders and their dogs. We assessed the Asiatic cheetah habitat using species distribution models, highlighting large, contiguous areas that overlap with livestock pastures (5792 km2, equaling 72% of the total predicted suitable habitat). Subsequently, we used data on the number and distribution of livestock (~47,000 animals in 80 pastures) and applied a spatial prioritization method to identify pastures for grazing right buyouts for a range of budget scenarios (US$100,000–600,000). Pastures selected had a high level of irreplaceability and were generally stable across budget scenarios. Our results provide a novel approach to minimize encounter rates between cheetah and livestock, and thus the mortality risk, for one of the world's most endangered felids and highlight the potential of spatial prioritization as a tool to devise urgent conservation actions.Peer Reviewe

The potential and shortcomings of mitochondrial DNA analysis for cheetah conservation management

There are only about 7,100 adolescent and adult cheetahs (Acinonyx jubatus) remaining in the wild. With the majority occurring outside protected areas, their numbers are rapidly declining. Evidence-based conservation measures are essential for the survival of this species. Genetic data is routinely used to inform conservation strategies, e.g., by establishing conservation units (CU). A commonly used marker in conservation genetics is mitochondrial DNA (mtDNA). Here, we investigated the cheetah’s phylogeography using a large-scale mtDNA data set to refine subspecies distributions and better assign individuals to CUs. Our dataset mostly consisted of historic samples to cover the cheetah’s whole range as the species has been extinct in most of its former distribution. While our genetic data largely agree with geography-based subspecies assignments, several geographic regions show conflicting mtDNA signals. Our analyses support previous findings that evolutionary forces such as incomplete lineage sorting or mitochondrial capture likely confound the mitochondrial phylogeography of this species, especially in East and, to some extent, in Northeast Africa. We caution that subspecies assignments solely based on mtDNA should be treated carefully and argue for an additional standardized nuclear single nucleotide polymorphism (SNP) marker set for subspecies identification and monitoring. However, the detection of the A. j. soemmeringii specific haplogroup by a newly designed Amplification-Refractory Mutation System (ARMS) can already provide support for conservation measures.info:eu-repo/semantics/publishedVersio

Effect of the habitat fragmentation on the Grévy’s zebra population genetic structure

The exponential growth of the human population is limiting the wildlife habitat all around the word. In recent years habitat loss and fragmentation is one of the main reasons that threats the wild life species. The Grévy’s zebra (Equus grevyi) is the most endangered member of Zebras. Their historical range was previously from north Ethiopia to southwest Somalia and to northern Kenya. Currently they are distributed only in fragmented habitats in central and eastern part of Ethiopia and in the north of Kenya. They are listed as endangered in the IUCN red list, as their population has declined 68% in 27 years. There are very few studies on genetic structure of this species, and investigating the genetic connection between different populations is needed. Molecular markers are one of the best tools to understand the level of fragmentation, population bottlenecks or potential inbreeding. In this study, the population structure of Ethiopian zebra population from Alledeghi Wildlife Reserve (WR) and Sarite area was studied using non-invasively obtained fecal samples collected during 2001-2011. This study analyzes genetic variation at 10 microsatellite loci and a 350-bp fragment of the mitochondrial DNA control region. The results showed that the genetic diversity is very low between the populations (π=0.00116 for Alledeghi WR and π=0 for Sarite population). The population of Alledeghi WR is probably isolated from the population of Sarite, as they don’t share any haplotypes. As the population of Alledeghi WR is separated from the ones from Sarite and Kenya, applying more conservational programs in this area is needed to protect the genetic diversity of the Grévy’s zebras in this area

Effect of the habitat fragmentation on the Grévy’s zebra population genetic structure

The exponential growth of the human population is limiting the wildlife habitat all around the word. In recent years habitat loss and fragmentation is one of the main reasons that threats the wild life species. The Grévy’s zebra (Equus grevyi) is the most endangered member of Zebras. Their historical range was previously from north Ethiopia to southwest Somalia and to northern Kenya. Currently they are distributed only in fragmented habitats in central and eastern part of Ethiopia and in the north of Kenya. They are listed as endangered in the IUCN red list, as their population has declined 68% in 27 years. There are very few studies on genetic structure of this species, and investigating the genetic connection between different populations is needed. Molecular markers are one of the best tools to understand the level of fragmentation, population bottlenecks or potential inbreeding. In this study, the population structure of Ethiopian zebra population from Alledeghi Wildlife Reserve (WR) and Sarite area was studied using non-invasively obtained fecal samples collected during 2001-2011. This study analyzes genetic variation at 10 microsatellite loci and a 350-bp fragment of the mitochondrial DNA control region. The results showed that the genetic diversity is very low between the populations (π=0.00116 for Alledeghi WR and π=0 for Sarite population). The population of Alledeghi WR is probably isolated from the population of Sarite, as they don’t share any haplotypes. As the population of Alledeghi WR is separated from the ones from Sarite and Kenya, applying more conservational programs in this area is needed to protect the genetic diversity of the Grévy’s zebras in this area

Phylogenetic analysis of marginal Asiatic black bears reveals a recent Iranian-Himalayan divergence and has implications for taxonomy and conservation

A small population of Asiatic black bear-known as the Baluchistan black bear-survives in the western limit of the species' range in Iran, where the species is rare, difficult to monitor and occupy an atypical habitat with extreme environmental conditions. Through the use of noninvasively collected samples, we analyzed mitochondrial DNA control region sequences to evaluate the phylogenetic relationships and divergence time between the Baluchistan Iranian black bear population and other Asian populations. Phylogenetic analyses indicate that Baluchistan and Nepalese (Himalayan) populations are monophyletic, with their divergence time estimated at circa 120 thousand years ago. The results reveal the low level of mitochondrial DNA variability in this small and marginal population, as is the case for many bear populations living in areas with similar conditions. The divergence time between the populations from Iran and Nepal dates to the Late Pleistocene, pointing to a transitional period between colder (glacial) and warmer (interglacial) conditions that allowed forests to expand and opened new habitats to population expansions. Pending further genetic and morphological corroboration, these preliminary results suggest that all Baluchistan and Himalayan (Nepalese) black bears might be considered as synonymous under the prior U. t. thibetanus trinomial (with gedrosianus just as junior synonym). Conservation efforts on this small and endangered population remain poor, and further measures are required to guarantee its long-term survival in Iran

The potential and shortcomings of mitochondrial DNA analysis for cheetah conservation management

There are only about 7,100 adolescent and adult cheetahs (Acinonyx jubatus) remaining in the wild. With the majority occurring outside protected areas, their numbers are rapidly declining. Evidence-based conservation measures are essential for the survival of this species. Genetic data is routinely used to inform conservation strategies, e.g., by establishing conservation units (CU). A commonly used marker in conservation genetics is mitochondrial DNA (mtDNA). Here, we investigated the cheetah's phylogeography using a large-scale mtDNA data set to refine subspecies distributions and better assign individuals to CUs. Our dataset mostly consisted of historic samples to cover the cheetah's whole range as the species has been extinct in most of its former distribution. While our genetic data largely agree with geography-based subspecies assignments, several geographic regions show conflicting mtDNA signals. Our analyses support previous findings that evolutionary forces such as incomplete lineage sorting or mitochondrial capture likely confound the mitochondrial phylogeography of this species, especially in East and, to some extent, in Northeast Africa. We caution that subspecies assignments solely based on mtDNA should be treated carefully and argue for an additional standardized nuclear single nucleotide polymorphism (SNP) marker set for subspecies identification and monitoring. However, the detection of the A. j. soemmeringii specific haplogroup by a newly designed Amplification-Refractory Mutation System (ARMS) can already provide support for conservation measures.Funding provided by: Austrian Science FundCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100002428Award Number: I5081- B/ GACRFunding provided by: OeAD-GmbHCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100005203Award Number: ZA02/201

Deliverable 4.5 (D4.5): Protocol for the processing of DNA sequence data generated by next-gen platforms, EnMetaGen project (Grant Agreement No 668981)

The overall goal of the EnvMetaGen project No 668981 is to expand the research and innovation potential of InBIO – Research network in Biodiversity and Evolutionary Biology - through the creation of an ERA Chair in Environmental Metagenomics. This field was selected as the focus of the ERA Chair, because Environmental DNA (eDNA) analysis is increasingly being used for biodiversity assessment, diet analysis, detection of rare or invasive species, population genetics and ecosystem functional analysis. In this context, the work plan of EnvMetaGen includes one work package dedicated to the Deployment of an eDNA Lab (WP4), which involves the training of InBIO researchers and technicians for implementing best practice protocols for the analysis of eDNA (Task 4.2). These protocols are essential to the development of research projects in association with business partners and other stakeholders in key application areas identified in the project, and thus to the strengthening of InBIO triple-helix initiatives (InBIO-Industry-Government; WP5). This report (Deliverable D4.5) builds upon previous ones (Deliverables D4.2-D4.4, respectively Ferreira et al. (2018), Egeter et al. (2018), Paupério et al. (2018)) and provides an overview of the processing protocols for DNA sequence data generated by next-gen platforms within EnvMetaGen-affiliated projects. Deliverables D4.2-D4.5 form a detailed account of the successful deployment of a fully functional eDNA lab under the EnvMetaGen project and provide a valuable resource for eDNA practitioners in all spheres of the triple-helix model. This development was made possible through the recruitment of the ERA Chair team (WP2), secondments and Junior Researcher exchanges through the collaboration with international networks (WP3), an enhancement of computational infrastructure at InBIO (WP4) and participation of team members in workshops and conferences (WP6)

Deliverable 4.3 (D4.3): Protocol for field collection and preservation of eDNA samples, EnvMetaGen project (Grant Agreement No 668981)

The overall goal of ERA Chair/EnvMetaGen project No 668981 is to expand the research and innovation potential of InBIO – Research network in Biodiversity and Evolutionary Biology, through the creation of an ERA Chair in Environmental Metagenomics. This field was selected as the focus of the ERA Chair, because Environmental DNA (eDNA) analysis is increasingly being used for biodiversity assessment, diet analysis, detection of rare or invasive species, population genetics and ecosystem functional analysis. In this context, the work plan of EnvMetaGen includes one work package dedicated to the Deployment of an eDNA Lab (WP4), which involves the training of InBIO researchers and technicians for implementing best practice protocols for the analysis of eDNA (Task 4.2). These protocols are essential for key application areas and to the development of research projects in association with business partners and other stakeholders, and thus to the strengthening of InBIO triple-helix initiatives (InBIO-Industry-Government; WP5). This report provides an overview of the current state of the art for collecting and preserving eDNA samples, with particular focus on vertebrate faecal samples, water samples and bulk invertebrate samples, which have been selected as key targets for the development of triple helix strategic initiatives (Task 5.3). The protocols already optimized and currently under development for the collection and preservation of eDNA samples are reported herein. Moreover, the future directions of sample collection and preservation at InBIO are discussed. This development was made possible through the recruitment of the ERA Chair team (WP2), secondments and Junior Researcher exchanges through the collaboration with international networks (WP3), an enhancement of computational infrastructure at InBIO (WP4) and participation of team members in workshops and conferences (WP6). Together, Deliverables D4.2-D4.5 (this document; Ferreira et al. 2018; Galhardo et al. 2018; Paupério et al. 2018) form a detailed account of the successful deployment of a fully functional eDNA lab under the EnvMetaGen project, and provide a valuable resource for eDNA practitioners in all spheres of the triple-helix model