Dataset Information

Low STR variability in the threatened marsh deer, Blastocerus dichotomus, detected through amplicon sequencing in non-invasive samples.

ABSTRACT: Blastocerus dichotomus is the largest deer in South America. We have used 25 microsatellite markers detected and genotyped by Next Generation Sequencing to estimate the genetic variability of B. dichotomus in Argentina, where most of its populations are threatened. Primer design was based on the sequence of a shallow partial genome (15,967,456 reads; 16.66% genome coverage, mean depth 1.64) of a single individual. From the thousands of microsatellite loci found, even under high stringency selection, we chose and tested a set of 80 markers on 30 DNA samples extracted from tissue and feces from three Argentinean populations. Heterozygosity levels were low across all loci in all populations (H=0.31 to 0.40). Amplicon sequencing is a fast, easy, and affordable technique that can be very useful for the characterization of microsatellite marker sets for the conservation genetics of non-model organisms. This work is also one of the first ones to use amplicon sequencing in non-invasive samples and represents an important development for the study of threatened species.

SUBMITTER: Wolfenson LI

PROVIDER: S-EPMC9601240 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Low STR variability in the threatened marsh deer, Blastocerus dichotomus, detected through amplicon sequencing in non-invasive samples.

Wolfenson Laura Irene LI McCracken Gregory R GR Ruzzante Daniel E DE Mirol Patricia P Solé-Cava Antonio A

Genetics and molecular biology 20221024 4

Blastocerus dichotomus is the largest deer in South America. We have used 25 microsatellite markers detected and genotyped by Next Generation Sequencing to estimate the genetic variability of B. dichotomus in Argentina, where most of its populations are threatened. Primer design was based on the sequence of a shallow partial genome (15,967,456 reads; 16.66% genome coverage, mean depth 1.64) of a single individual. From the thousands of microsatellite loci found, even under high stringency select ...[more]

PMID: 36288451

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Project description:BackgroundIn an era of unprecedented socio-ecological changes, managing wildlife health demands high-quality data collection and the engagement of local communities. Blastocerus dichotomus, the largest South American deer, is Vulnerable to extinction mainly due to habitat loss. Diseases have been recognised as a potential threat, and winter mortality has been historically described in marsh deer populations from Argentina. Field difficulties have, however, prevented in-depth studies of their health status.ResultsBetween May 2014 and April 2017, we investigated marsh deer morbidity and mortality in the two largest populations in Argentina. We collected data by means of a passive surveillance system that involved a network of researchers, field partners (veterinarians, park rangers, and local community), and decision makers. We sampled marsh deer during as well as outside mortality events. A total of 44 marsh deer with different body condition scores were evaluated. We obtained haematology and biochemistry values from animals with good body condition score. Marsh deer with poor body condition had a high burden of the ticks Amblyomma triste and Rhipicephalus microplus. Vector-borne agents such as Theileria cervi, Trypanosoma theileri, Trypanosoma evansi, Ehrlichia chaffeensis, Anaplasma platys, Anaplasma odocoilei, Anaplasma marginale, and Candidatus Anaplasma boleense were also found. Haemonchus spp., Ostertagia spp., and Trichostrongylus spp. were the most frequent gastrointestinal parasites in deer with poor body condition. A Multiple Correspondence Analysis reinforced a possible association of winter period with lower body score condition, high tick loads, infection with E. chaffeensis, and presence of harmful gastrointestinal parasites.ConclusionsOur approach allowed the establishment of a participatory surveillance network of marsh deer morbidity and mortality in Argentina. We report and analyse the first data obtained opportunistically within the framework of this network, providing information on the infectious and parasitic agents in marsh deer populations. The occurrence of Fasciola hepatica and Leptospira interrogans serovar pyrogenes is reported for the first time in wild marsh deer from Argentina. Our data will be useful to improve the interpretation of future mortality events. The field implementation of a surveillance network is key to a holistic approach to wildlife diseases.

Dataset Information

Low STR variability in the threatened marsh deer, Blastocerus dichotomus, detected through amplicon sequencing in non-invasive samples.

Publications

Low STR variability in the threatened marsh deer, Blastocerus dichotomus, detected through amplicon sequencing in non-invasive samples.

Similar Datasets

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