Abstract
The emerging field of ecological genomics contains several broad research areas. Comparative genomic and conservation genetic analyses are providing great insight into adaptive processes, species bottlenecks, population dynamics and areas of conservation priority. Now the same technological advances in high-throughput sequencing, coupled with taxonomically broad sequence repositories, are providing greater resolution and fundamentally new insights into functional ecology. In particular, we now have the capacity in some systems to rapidly identify thousands of species-level interactions using non-invasive methods based on the detection of trace DNA. This represents a powerful tool for conservation biology, for example allowing the identification of species with particularly inflexible niches and the investigation of food-webs or interaction networks with unusual or vulnerable dynamics. As they develop, these analyses will no doubt provide significant advances in the field of restoration ecology and the identification of appropriate locations for species reintroduction, as well as highlighting species at ecological risk. Here, I describe emerging patterns that have come from the various initial model systems, the advantages and limitations of the technique and key areas where these methods may significantly advance our empirical and applied conservation practices.
Highlights
Species’ interactions are the basis of ecosystem functioning and the provision of ecosystem services (Keesing et al 2010; Kunz et al 2011)
When applied to species interactions, these methods deliver an unprecedented level of insight into ecological networks, making it possible to simultaneously assess thousands of interactions and providing a powerful tool for Molecular detection of interactions conservation biology
The fact that even in a species-poor high arctic web, adding the missing components detected by molecular means yielded fundamentally new conclusions has vast implications for global assessments of ecosystem dynamics and how resilient or vulnerable they may be to disruption. This is important in conservation biology as we evaluate vulnerable species and ecosystems and prioritize areas for protection and intervention
Summary
Species’ interactions are the basis of ecosystem functioning and the provision of ecosystem services (Keesing et al 2010; Kunz et al 2011). In the analysis of marine prey in macaroni penguins (Deagle et al 2007), a combination of 16S, 18S and 28S targets were used which allowed the authors to detect euphausiids, fish, amphipods and cephalopods in the diet of these sea birds during chick rearing As this is a very broad potential taxonomic assemblage to cope with, a multiregion conserved primer approach is key, but within that diet, there is taxonomic ambiguity because these regions are not efficient at species resolution. The ultimate methodological achievement in this field will be to generate an accurate and repeatable measure of abundance or biomass within a sample This is important in conservation biology when we wish to know that an interaction occurred, for example did the shrew eat beetle species A, but how often and in what quantities relative to other prey. There are a variety of cases where these methods are already providing extensive conservation insights
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