Swatting Flies: Biting Insects as Non-Invasive Samplers for Mammalian Population Genomics.

Area of Science:

• Wildlife genetics
• Genomics
• Conservation biology

Background:

• Next-generation sequencing (NGS) advances enable DNA analysis from novel sources for wildlife studies.
• Current applications predominantly focus on mitochondrial DNA for species identification, with population genetics analyses being infrequent.
• NGS's capacity for indiscriminate DNA fragment detection theoretically allows whole genome sequencing from environmental samples.

Purpose of the Study:

• To investigate the feasibility of recovering whole genome sequences of wild animals from blood-feeding insects.
• To compare the efficacy of short-read sequencing (Illumina) and adaptive sampling of long-read sequencing (Oxford Nanopore Technology) for obtaining host genomic data from pooled tsetse flies.

Main Methods:

• Utilized pooled tsetse flies as a source of wild animal DNA.
• Employed both short-read (Illumina) and long-read (Oxford Nanopore Technology with adaptive sampling) sequencing platforms.
• Compared the proportion of host DNA recovered after removing insect DNA reads.

Main Results:

• The majority of short-read data (85%-99%) consisted of tsetse fly DNA, with adaptive sampling showing limited impact.
• After removing tsetse fly DNA, remaining reads predominantly mapped to the expected dominant host.
• Genomic data for elephants, warthogs, and giraffes were recovered more reliably than for buffalo, indicating host-specific biases.
• Over 300,000 single nucleotide polymorphisms (SNPs) were identified in elephant DNA, enabling population genetic parameter estimation.

Conclusions:

• Whole genome data from certain wild mammals can be successfully recovered from blood-feeding insects.
• This approach holds significant potential for advancing population genetics studies in wildlife, especially for species where traditional sample collection is challenging.