Abstract:
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 freeranging
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.
Description:
DATA AVAILABILITY STATEMENT : The genomic data for the zoo and free-ranging elephants in
the study are available on the NCBI Short-Read Archive (SRA)
under bioproject number PRJNA910109, metagenomic result
files for replicate sampling of zoo elephant dung are available
on DRYAD (https://doi.org/10.5061/dryad.80gb5mktv).
Bioinformatic code is available from https://github.com/
adeflamingh/de_Flamingh_et_al_2022_FiG.