Figure 1 - uploaded by Noëlle F Kümpel
Content may be subject to copyright.
Map showing the study area, the Okapi Faunal Reserve (Réserve de Faune Okapis, RFO), in the Democratic Republic of Congo. All 105 samples with genotypes used in the present study are shown as white open circles.
Source publication
The okapi Okapia johnstoni, a rainforest giraffid endemic to the Democratic Republic of Congo, was recategorized as Endangered on the IUCN Red List in 2013. Historical records and anecdotal reports suggest that a disjunct population of okapi may have occurred south-west of the Congo River but the current distribution and status of the okapi in this...
Citations
... Genomic data for the okapi is still limited to being sequenced from non-invasive sampling strategies (e.g., dung samples) and single molecular markers, such as a few mitochondrial and nuclear genes. Analyses of these verify the presence of okapis south-west of the Congo River [2] and characterize the genetic diversity across their geographic distribution [3]. There are two draft genome assemblies available for the okapi [4][5][6]. ...
The okapi (Okapia johnstoni), or forest giraffe, is the only species in its genus and the only extant sister group of the giraffe within the family Giraffidae. The species is one of the remaining large vertebrates surrounded by mystery because of its elusive behavior as well as the armed conflicts in the region where it occurs, making it difficult to study. Deforestation puts the okapi under constant anthropogenic pressure, and it is currently listed as "Endangered" on the IUCN Red List. Here, we present the first annotated de novo okapi genome assembly based on PacBio continuous long reads, polished with short reads, and anchored into chromosome-scale scaffolds using Hi-C proximity ligation sequencing. The final assembly (TBG_Okapi_asm_v1) has a length of 2.39 Gbp, of which 98% are represented by 28 scaffolds >3.9 Mbp. The contig N50 of 61 Mbp and scaffold N50 of 102 Mbp, together with a BUSCO score of 94.7%, and 23,412 annotated genes, underline the high quality of the assembly. This chromosome-scale genome assembly is a valuable resource for future conservation of the species and comparative genomic studies among the giraffids and other ruminants.
... Genomic data for the okapi is still limited to being sequenced from non-invasive sampling strategies (e.g., dung samples) and single molecular markers, such as a few mitochondrial and nuclear genes. Analyses of these verify the presence of okapis south-west of the Congo River (Stanton et al. 2016) and characterize the genetic diversity across their geographic distribution (Stanton et al. 2014). There are two draft genome assemblies available for the okapi (Agaba et al. 2016;Dudchenko et al. 2017;Chen et al. 2019). ...
The okapi (Okapia johnstoni), or forest giraffe, is the only species in its genus and the only extant sister group of the giraffe within the family Giraffidae. The species is one of the remaining large vertebrates surrounded by mystery because of its elusive behavior as well as the armed conflicts in the region where it occurs, making it difficult to study. Deforestation puts the okapi under constant anthropogenic pressure, and it is currently listed as “Endangered” on the IUCN Red List. Here, we present the first annotated de novo okapi genome assembly based on PacBio continuous long reads, polished with short reads, and anchored into chromosome-scale scaffolds using Hi-C proximity ligation sequencing. The final assembly (TBG_Okapi_asm_v1) has a length of 2.39 Gbp, of which 98% are represented by 28 scaffolds >3.9 Mbp. The contig N50 of 61 Mbp and scaffold N50 of 102 Mbp, together with a BUSCO score of 94.7%, and 23,412 annotated genes, underline the high quality of the assembly. This chromosome-scale genome assembly is a valuable resource for future conservation of the species and comparative genomic studies among the giraffids and other ruminants.
... Being able to identify the sex of samples could benefit agricultural studies on domesticated animals, and could inform conservation initiatives that focus on non-domestic wildlife. Because this method is amenable to low coverage data from low quantity DNA (e.g., ancient or degraded DNA), it can be employed as a non-invasive approach to identifying sex of endangered or rare species, for example, through the analysis of DNA from hair tufts (McKelvey et al. 2006;Stanton et al. 2016) or herbivore scat (Huber et al. 2002). By requiring only minute quantities of DNA as a starting template, the method could be extended to other types of degraded DNA such as archival samples from museum collections (Wandeler et al. 2003;Bi et al. 2013) or forensic samples (Jobling and Gill 2004;Alaeddini et al. 2010). ...
Sex identification of ancient animal biological remains can benefit our understanding of historical population structure, demography and social behavior. Traditional methods for sex identification (e.g. osteological and morphometric comparisons) may be ineffective when animal remains are not well preserved, when sex distinguishing characteristics have not yet developed, or where organisms do not exhibit sex-associated phenotypic dimorphisms. Here we adapt a method developed for human sex determination so that it can be used to identify the sex of ancient and modern animal taxa. The method identifies sex by calculating the ratio of DNA reads aligning to the X chromosome to DNA reads aligning to autosomes (termed the Rx ratio). We tested the accuracy of this method using low coverage genomes from 15 modern elephants ( Loxodonta africana ) for which sex was known. We then applied this method to ancient elephant ivory samples for which sex was unknown, and describe how this method can be further adapted to the genomes of other taxa. This method may be especially useful when only low-coverage genomic data is obtainable. Furthermore, because this method relies on only the X and not the Y chromosome, it can be used to determine the sex of organisms for which a reference genome was obtained from a female or for which only the X chromosome is reported. Such taxa include the domestic cat, sheep, goat, and horse; and non-domesticated animals such as the Sumatran orangutan, western lowland gorilla and meerkat.
... A metodologia de amostragem não invasiva é empregada sobretudo em animais de difícil captura, como os que apresentam grandes áreas de vida, baixa densidade, atividade noturna e hábitos elusivos. Animais com as características mencionadas e ainda em risco de extinção são ainda mais favorecidos com este tipo de amostragem, evitando o estresse para o animal e o risco de sua perda durante o manejo (STANTON, 2016;VELLI, 2015;WALKER, 2016;WHEAT, 2016). ...
O estudo genético de animais de difícil acesso, com hábitos elusivos e noturnos tem sido facilitado por meio das análises genéticas não invasivas, por exemplo, utilizando fezes obtidas no campo. Este tipo de amostra se torna ainda mais importante quando se trabalha com animais ameaçados, permitindo obter dados populacionais de demografa,
razão sexual, parentesco, diversidade genética, diferenciação populacional e fluxo gênico.
Muitos felinos se encontram atualmente ameaçados ou vulneráveis, principalmente
devido à fragmentação e redução de habitats. Populações isoladas diminuem o fluxo gênico com outras populações e podem aumentar a taxa de deriva genética e endogamia, podendo a longo prazo serem extintas no ambiente natural. Por isso, técnicas de amostragem não invasiva de felinos estão sendo cada vez mais utilizadas,
com o intuito de detectar dados populacionais que possam ajudar na conservação estas
espécies. Este capítulo apresenta aspectos básicos da Genética da Conservação e um
levantamento de estudos de casos em felinos brasileiros, que usaram amostragem não
invasiva para obter informações fundamentais sobre a ecologia, biologia e genética, como subsídio para a conservação e preservação em longo prazo desses animais.
... A metodologia de amostragem não invasiva é empregada sobretudo em animais de difícil captura, como os que apresentam grandes áreas de vida, baixa densidade, atividade noturna e hábitos elusivos. Animais com as características mencionadas e ainda em risco de extinção são ainda mais favorecidos com este tipo de amostragem, evitando o estresse para o animal e o risco de sua perda durante o manejo (STANTON, 2016;VELLI, 2015;WALKER, 2016;WHEAT, 2016). ...
... For genetic testing the most commonly used sample is blood or tissue however, these can be difficult to acquire from animals and it is invasive. There is much debate on the ethics of conducting genetic research on stored tissue samples (Clayton et al., 1995, Cambon-Thomsen, 2004, McGuire and Beskow, 2010 (Bayes et al., 2000, Ernest et al., 2000, Frantz et al., 2003, Parsons et al., 2005, Bowkett et al., 2009, Kierepka et al., 2016, Stanton et al., 2016. Vidya and Sukumar (2005a) reported the development of a successful and reliable method for the detection of microsatellites from Asian elephant dung. ...
Herpesviruses are ubiquitous and are found worldwide, most animal species can be infected with multiple herpesviruses. Some cause clinical disease and others remain symptomatic throughout life. Herpesviruses are found in both captive and wild animals including Asian elephants (Elephas maximus). Elephant Endothelioltropic Herpesvirus (EEHV) has been reported in both captive and wild Asian elephants, with a number of cases being reported in North America, Europe and Asia. It has been suggested that EEHV is associated with haemorrhagic disease, which has been attributed to a number of Asian elephant deaths, affecting mostly juveniles and calves. Clinical signs can vary from weight loss, lethargy, depression, cyanosis of the tongue and sudden death. Molecular testing using qPCR has enabled the detection of individual variants of EEHV, this thesis investigates the EEHV1 variant. EEHV1 has been highlighted as the variant that is more frequently associated with deaths. This thesis includes five studies investigating different aspects of EEHV. Including, the relationship between pregnancy and EEHV viral shedding, the use of an amended human protocol for culturing endothelial cells, EEHV tissue tropism, a potential genetic or familial link between EEHV associated deaths and the detection of potential co-pathogens. The main findings from this thesis include: 1) the use of a longitudinal study investigating a potential link between the physiological stress of pregnancy and EEHV viral shedding. This study suggested there was no link between pregnancy and EEHV viral shedding however other stressors may be involved. 2) Using an amended human umbilical vein endothelial cell protocol, the culture of Asian elephant endothelial cells was successful. The cells from this study may be used in subsequent drug testing and vaccine development. 3) Quantitative PCR was used to determine EEHV1 tropism in tissues from two deaths associated with the virus. Tropism appeared to be for the heart and liver. 4) This thesis provides results from a preliminary study into a potential link between EEHV associated deaths. The data from an Asian elephant genogram shows there is the possibility of a genetic or familial link, which requires further investigation. 5) A number of tissues from deaths associated with EEHV and or death from other causes were investigated for the presence of potential co-pathogens, including the presence of encephalomyocarditis virus (EMCV), using microarray technology. The results indicated there were no co-pathogens present in the tissues. This thesis adds to the current published data, and includes the first known preliminary study investigating a potential genetic link between elephant deaths due to EEHV.
... Finding, capturing, and sampling wild koalas is costly in both time and money, while sampling sick or injured animals may bias sampling toward areas of increased human presence. However, the increasing use of noninvasive sampling has allowed for cheaper, easier genetic sampling across a range of species (e.g., okapi (Okapia johnstoni) (Stanton et al., 2016), wolves (Canis lupus) (Scandura, 2005;Stenglein, Waits, Ausband, Zager, & Mack, 2011), Spanish imperial eagles (Aquila adalberti) (Horváth, Martínez-Cruz, Negro, Kalmár, & Godoy, 2005)), and more recently koalas (Wedrowicz, Karsa, Mosse, & Hogan, 2013). ...
Maintaining genetic diversity is a crucial component in conserving threatened species. For the iconic Australian koala, there is little genetic information on wild populations that is not either skewed by biased sampling methods (e.g., sampling effort skewed toward urban areas) or of limited usefulness due to low numbers of microsatellites used. The ability to genotype DNA extracted from koala scats using next-generation sequencing technology will not only help resolve location sample bias but also improve the accuracy and scope of genetic analyses (e.g., neutral vs. adaptive genetic diversity, inbreeding, and effective population size). Here, we present the successful SNP genotyping (1272 SNP loci) of koala DNA extracted from scat, using a proprietary DArTseq™ protocol. We compare genotype results from two-day-old scat DNA and 14-day-old scat DNA to a blood DNA template, to test accuracy of scat genotyping. We find that DNA from fresher scat results in fewer loci with missing information than DNA from older scat; however, 14-day-old scat can still provide useful genetic information, depending on the research question. We also find that a subset of 209 conserved loci can accurately identify individual koalas, even from older scat samples. In addition, we find that DNA sequences identified from scat samples through the DArTseq™ process can provide genetic identification of koala diet species, bacterial and viral pathogens, and parasitic organisms.
... Les crottes d'éléphants sont facilement reconnaissables, mais il y a plusieurs espèces d'ongulés sympatriques dans cette région qui produisent des crottes en forme de boulettes, dont le bongo, le sitatunga, plusieurs espèces de céphalophes et deux espèces de cochons sauvages. Les équipes et les gardes bien formées en suivi de la faune peuvent généralement faire la différence entre des crottes d'okapi et celles d'autres animaux (Stanton et al. 2014a), mais il y a la possibilité d'erreurs d'identification par le personnel non formés ; ainsi les crottes d'okapi enregistrées au cours des patrouilles sont parfois susceptibles d'appartenir à d'autres espèces. ...
... De plus, les okapis sont des animaux difficiles à observer en milieu sauvage et leur présence peut facilement ne pas être détectée, en particulier lorsque les densités de population sont faibles. Une aire de répartition provisoire de l'okapi a été construite en combinant les données d'études de terrain récentes et disponibles -utilisant une identification moléculaire de l'espèce lorsque cette information était disponible (Stanton et al. 2014a) -avec les rapports des communautés qui ont confirmé les informations trouvées récemment sur les peaux ou la viande de brousse, et la connaissance de l'aire de répartition historique ; tout ceci couplé à la couverture forestière actuelle et au type d'habitat. Cette aire de répartition -la zone de présence (EOO ; Extent of Occurrence en anglais) -est de 383 190 km² et est représentée par une ligne pointillée sur la Figure 12. ...
... Elephant dung is unmistakable, but there are several sympatric ungulate species in the region which produce pellet dung, including bongo, sitatunga, several duiker species, and two species of wild hog. Well-trained wildlife survey teams and rangers can usually distinguish between the dung of okapi and other species (Stanton et al. 2014a), but there is the possibility of mis-identification by untrained personnel; thus the 'okapi' dung recorded on patrols is likely to sometimes be that of other species. ...
... In addition, okapi are rarely observed and their occurrence can easily go undetected, especially at low densities. A tentative okapi range has been constructed by combining available recent survey data -utilising molecular species identification where this information was available (Stanton et al. 2014a)with community reports which confirmed recent findings of skins or bushmeat, and knowledge of the historic range coupled with present forest cover and habitat type. This range -the Extent of Occurrence (EOO) -is 383,190 km 2 and is shown as a dashed outline on Figure 12. ...
... Very little was known about the biodiversity of this area until surveys were conducted from 2007 to 2009 (Hart 2009a). Exploratory surveys documented okapi presence, with molecular confirmation that dung samples were from okapi (Stanton et al. 2014a), representing an extension of the known present-day range. An estimate of okapi population size is not available, though observations suggest okapi are uncommon (Hart 2009a) and that distribution is localised, with the species occurring only between the Lomami and Tshuapa rivers (J. ...
... Moreover it is currently unknown how genetically representative captive okapi are of wild population genetic diversity and evolutionary history, information that is particularly important in light of its recent reclassification (Mallon et al. 2013). Okapi predominantly occur across central, eastern and northern Democratic Republic of Congo, but also occur at lower density southwest of the Congo River (Stanton et al. 2014a). However no reliable estimates exist for current population size (Mallon et al. 2013). ...
Breeding programs for endangered species increasingly use molecular genetics to inform their management strategies. Molecular approaches can be useful for investigating relatedness, resolving pedigree uncertainties, and for estimating genetic diversity in captive and wild populations. Genetic data can also be used to evaluate the representation of wild population genomes within captive population gene-pools. Maintaining a captive population that is genetically representative of its wild counterpart offers a means of conserving the original evolutionary potential of a species. Okapi, an even-toed ungulate, endemic to the Democratic Republic of Congo, have recently been reclassified as Endangered by the IUCN. We carried out a genetic assessment of the ex-situ okapi (Okapia johnstoni) population, alongside an investigation into the genetic structure of wild populations across their geographic range. We found that while levels of nuclear (12 microsatellite loci) genetic variation in the wild, founder and captive okapi populations were similar, mitochondrial (833 bp of Cyt b, CR, tRNA-Thr and tRNA-Pro) variation within captive okapi was considerably reduced compared to the wild, with 16 % lower haplotype diversity. Further, both nuclear and mitochondrial alleles present in captivity provided only partial representation of those present in the wild. Thirty mitochondrial haplotypes found in the wild were not found in captivity, and two haplotypes found in captivity were not found in the wild, and the patterns of genetic variation at microsatellite loci in our captive samples were considerably different to those of the wild samples. Our study highlights the importance of genetic characterisation of captive populations, even for well-managed ex-situ breeding programs with detailed studbooks. We recommend that the captive US population should be further genetically characterised to guide management of translocations between European and US captive populations.
