Combining methods for non-invasive fecal DNA enables whole genome and
metagenomic analyses in wildlife biologyAlida de Flamingh, Yasuko Ishida,
Patrícia Pečnerová, Sahara Vilchis, Hans R. Siegismund, Rudi J. van Aarde,
Ripan S. Malhi & Alfred L. RocaFrontiers in Genetics12 January 2023Abstract
Non-invasive biological samples benefit studies that investigate rare,
elusive, endangered, or dangerous species. Integrating genomic techniques
that use non-invasive biological sampling with advances in computational
approaches can benefit and inform wildlife conservation and management.
Here, we used non-invasive fecal DNA samples to generate low- to
medium-coverage genomes (e.g., >90% of the complete nuclear genome at six
X-fold coverage) and metagenomic sequences, combining widely available and
accessible DNA collection cards with commonly used DNA extraction and
library building approaches. DNA preservation cards are easy to transport
and can be stored non-refrigerated, avoiding cumbersome or costly sample
methods. The genomic library construction and shotgun sequencing approach
did not require enrichment or targeted DNA amplification. The utility and
potential of the data generated was demonstrated through genome scale and
metagenomic analyses of zoo and free-ranging African savanna elephants
(Loxodonta africana). Fecal samples collected from free-ranging individuals
contained an average of 12.41% (5.54–21.65%) endogenous elephant DNA.
Clustering of these elephants with others from the same geographic region
was demonstrated by a principal component analysis of genetic variation
using nuclear genome-wide SNPs. Metagenomic analyses identified taxa that
included Loxodonta, green plants, fungi, arthropods, bacteria, viruses and
archaea, showcasing the utility of this approach for addressing
complementary questions based on host-associated DNA, e.g., pathogen and
parasite identification. The molecular and bioinformatic analyses presented
here contributes towards the expansion and application of genomic
techniques to conservation science and practice.
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