This study explores the accuracy and reliability of species detection from soil samples, using Rosche GS-FLX high-throughput sequencing, coupled with 16S mitochondrial DNA (mtDNA) metabarcoding. Study sites at safari parks, zoological gardens and farms were selected due to detailed records of the presence of exotic species. This framework was used to monitor how edaphic and biotic factors influence taphonomic processes of ‘dirt’ DNA originating from free-ranging vertebrate species.
The measured Vertebrate species richness inferred from ‘dirt’ DNA in surface soil, was improved by increasing the sample density and spatial scale, rather than increasing the amount of soil processed from individual soil samples. Intriguingly, the relative proportions of mammal ‘dirt’ DNA haplotypes identified in the soil surface more closely reflects the total biomass of the species on site, rather than the individual populations census size. However, animal behavior was observed to bias biodiversity estimates at the sampled scale, and one species, which had recently been introduced, was not detected.
Additionally, the use of marker DNA molecules in high-throughput sequencing experiments, allows between sample comparisons of relative haplotype frequencies. This approach was used to explore different sediment types for their susceptibility to DNA leaching, and general guidelines are defined as to when leaching is likely to affect diversity estimates from ancient sediments. A better understanding of this process, leading to the incorrect temporal association of results, is important for the analysis of sediment ancient DNA (sedaDNA) obtained from ancient environmental samples.
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