RESUMO
Genetic non-invasive sampling (gNIS) is a critical tool for population genetics studies, supporting conservation efforts while imposing minimal impacts on wildlife. However, gNIS often presents variable levels of DNA degradation and non-endogenous contamination, which can incur considerable processing costs. Furthermore, the use of restriction-site-associated DNA sequencing methods (RADseq) for assessing thousands of genetic markers introduces the challenge of obtaining large sets of shared loci with similar coverage across multiple individuals. Here, we present an approach to handling large-scale gNIS-based datasets using data from the spotted hyena population inhabiting the Ngorongoro Crater in Tanzania. We generated 3RADseq data for more than a thousand individuals, mostly from faecal mucus samples collected non-invasively and varying in DNA degradation and contamination level. Using small-scale sequencing, we screened samples for endogenous DNA content, removed highly contaminated samples, confirmed overlap fragment length between libraries, and balanced individual representation in a sequencing pool. We evaluated the impact of (1) DNA degradation and contamination of non-invasive samples, (2) PCR duplicates and (3) different SNP filters on genotype accuracy based on Mendelian error estimated for parent-offspring trio datasets. Our results showed that when balanced for sequencing depth, contaminated samples presented similar genotype error rates to those of non-contaminated samples. We also showed that PCR duplicates and different SNP filters impact genotype accuracy. In summary, we showed the potential of using gNIS for large-scale genetic monitoring based on SNPs and demonstrated how to improve control over library preparation by using a weighted re-pooling strategy that considers the endogenous DNA content.
RESUMO
RATIONALE: A genetic component may be involved in different stages of the progression of drug addiction. Heroin users escalate unit doses and frequency of self-administration events over time. Rats that self-administer drugs of abuse over extended sessions escalate the amount of drug infused over days. OBJECTIVES: Using a recently developed model of extended-access self-administration allowing for subject-controlled dose escalation of the unit dose, thus potentially escalating the unit dose and number of infusions, we compared for the first time two genetically different inbred rat strains, Fischer and Lewis. METHODS: Extended (18 h/day) self-administration lasted for 14 days. Rats had access to two active levers associated with two different unit doses of heroin. If a rat showed preference for the higher unit dose, then the available doses were escalated in the following session. Four heroin unit doses were available (20, 50, 125, 250 µg/kg per infusion). RESULTS: Fischer rats did not escalate the unit dose of heroin self-administered; daily amount of heroin administered remained low, with a mean daily intake of 1.27 ± 0.22 mg/kg per session. In marked contrast, Lewis rats escalated the total daily amount of heroin self-administered from 3.94 ± 0.82 mg/kg on day 1 to 8.95 ± 2.2 mg/kg on day 14; almost half of the subjects preferred a higher heroin dose than Fischer rats. CONCLUSION: These data are consistent with the hypothesis that Lewis rats are prone to opiate taking and escalation, and are in agreement with our previous data obtained with cocaine.
