Toward absolute abundance for conservation applications: Estimating the number of contributors via microhaplotype genotyping of mixed-DNA samples.

Molecular methods including metabarcoding and quantitative polymerase chain reaction have shown promise for estimating species abundance by quantifying the concentration of genetic material in field samples. However, the relationship between specimen abundance and detectable concentrations of genetic material is often variable in practice. DNA mixture analysis represents an alternative approach to quantify specimen abundance based on the presence of unique alleles in a sample. The DNA mixture approach provides novel opportunities to inform ecology and conservation by estimating the absolute abundance of target taxa through molecular methods; yet, the challenges associated with genotyping many highly variable markers in mixed-DNA samples have prevented its widespread use. To advance molecular approaches for abundance estimation, we explored the utility of microhaplotypes for DNA mixture analysis by applying a 125-marker panel to 1179 Chinook salmon (Oncorhynchus tshawytscha) smolts from the Sacramento-San Joaquin Delta, California, USA. We assessed the accuracy of DNA mixture analysis through a combination of mock mixtures containing DNA from up to 20 smolts and a trophic ecological application enumerating smolts in predator diets. Mock DNA mixtures of up to 10 smolts could reliably be resolved using microhaplotypes, and increasing the panel size would likely facilitate the identification of more individuals. However, while analysis of predator gastrointestinal tract contents indicated DNA mixture analysis could discern the presence of multiple prey items, poor and variable DNA quality prevented accurate genotyping and abundance estimation. Our results indicate that DNA mixture analysis can perform well with high-quality DNA, but methodological improvements in genotyping degraded DNA are necessary before this approach can be used on marginal-quality samples.

Campsites, forest fires, and entry point distance affect earthworm abundance in the Boundary Waters Canoe Area Wilderness.

Factors controlling the spread of invasive earthworms in Minnesota's Boundary Waters Canoe Area Wilderness are poorly known. Believed to have been introduced by anglers who use them as bait, invasive earthworms can alter the physical and chemical properties of soil and modify forest plant communities. To examine factors influencing earthworm distribution and abundance, we sampled 38 islands across five lakes to assess the effects of campsites, fire and entry point distance on earthworm density, biomass and species richness. We hypothesized that all three parameters would be greater on islands with campsites, lower on burned islands and would decrease with distance from the wilderness entry point. In addition to sampling earthworms, we collected soil cores to examine soil organic matter and recorded ground and vegetation cover. Campsite presence was the single most important factor affecting sampled earthworm communities; density, biomass and species richness were all higher on islands having campsites. Fire was associated with reduced earthworm density, but had no direct effects on earthworm biomass or species richness. Fire influenced earthworm biomass primarily through its negative relationship to groundcover and through an interaction with entry point distance. Entry point distance itself affected earthworm density and biomass. For islands with campsites, earthworm biomass increased with distance from the entry point.