Environmental DNA from avian residual saliva in fruits and its potential uses in population genetics

Beyond Biodiversity: Can Environmental DNA (eDNA) Cut it as a Population Genetics Tool?

“…Perhaps one of the biggest obstacles in transitioning from species detection to population genetics using eDNA is assigning sequences to individuals. Previous non-invasive genetic techniques for terrestrial organisms have been able to assume different individuals from separate scats [34,45] or feeding sites [39,40,84]. Additionally, DNA extracted from invertebrate stomachs (iDNA) has also been used to obtain host DNA [28,[85][86][87].…”

“…Degraded DNA samples yielding low quality and/or template can contribute to these challenges, requiring increased replicates, increased PCR cycles, or increased sequencing depth [94,95]. Recent eDNA sampling has shown that allelic variation can be missed in multiple markers depending on extraction and capture methodologies [40]. Therefore, testing methodologies and using multiple markers will be important for reliable, reproducible eDNA capture and amplification in eDNA population genetic studies.…”

“…Phylogenetically, nuDNA may show different patterns of divergence within populations compared to mtDNA data [124,127,129]. Obtaining more markers is easier with nuDNA (e.g., 10's of microsatellites or 10000's of SNPs) and can also help provide the ability to distinguish individuals with similar genetic signatures [40,[130][131][132]. For example, multi-allelic microsatellites could be used, and they have the added advantage of establishing a minimum number of individuals present in an eDNA sample.…”

“…However, we take a narrower view of "environmental sample"; defining eDNA as DNA taken from soil, water, or air, excluding samples from direct individual remains such as fecal matter, hair, or feeding traces [18,34,38]. Direct organismal traces may allow for assignment of genetic data to specific individuals [38][39][40]. From these non-invasive samples, DNA may be used to describe abundance [32][33][34], effective population size [41], density [35], diet [42], and sex of individuals [43,44].…”

Beyond Biodiversity: Can Environmental DNA (eDNA) Cut It as a Population Genetics Tool?

“…” However, we take a narrower view of environmental sample; defining eDNA as DNA taken from soil, water, or air, excluding samples from direct individual remains such as fecal matter, hair, or feeding traces [18,37,41]. Direct organismal traces may allow for assignment of genetic data to specific individuals [41,42,43]. From these non-invasive samples, DNA may be used to describe abundance [35,36,37], effective population size [44], density [38], diet [45], and sex of individuals [46,47].…”