Ecology in the age of DNA barcoding: the resource, the promise and the challenges ahead

Abstract

Ten years after DNA barcoding was initially suggested as a tool to identify species, millions of barcode sequences from more than 1100 species are available in public databases. While several studies have reviewed the methods and potential applications of DNA barcoding, most have focused on species identification and discovery, and relatively few have addressed applications of DNA barcoding data to ecology. These data, and the associated information on the evolutionary histories of taxa that they can provide, offer great opportunities for ecologists to investigate questions that were previously difficult or impossible to address. We present an overview of potential uses of DNA barcoding relevant in the age of ecoinformatics, including applications in community ecology, species invasion, macroevolution, trait evolution, food webs and trophic interactions, metacommunities, and spatial ecology. We also outline some of the challenges and potential advances in DNA barcoding that lie ahead.

Soil phosphorus heterogeneity promotes tree species diversity and phylogenetic clustering in a tropical seasonal rainforest

“…Community phylogenetic analysis provides opportunities to examine possible mechanisms (Brown, 2012; Cavender‐Bares et al., 2009; Joly et al., 2014; Swenson et al., 2007; Willis et al., 2010). Stevens et al.…”

DNA barcodes for ecology, evolution, and conservation

“…With the adoption of NGS technologies in many DNA barcode investigations (e.g., metagenomic applications [13]), uses are already being expanded to answer both applied and basic biological questions. Even if DNA barcodes are not uniformly successful for unambiguous identifications across the entire Tree of Life, ecologists, evolutionary biologists, and conservationists are already adopting DNA barcodes as a tool in their respective fields (e.g., [14,15]). …”

Use of DNA metabarcoding for stomach content analysis in the invasive lionfish Pterois volitans in Puerto Rico

“…Aside from observing this predator−prey interaction in situ, predation can also be documented using visual inspection or, more recently, DNA barcoding to assess biodiversity in diet from gut contents or feces (Sheppard & Harwood 2005). Over a decade has passed since DNA barcoding first proved useful in biodiversity applications (Hebert et al 2003), and has recently been promoted as an ecological tool for addressing issues including a species' invasion potential, trophic interactions, and food webs (Joly et al 2014). With the advancement and lower cost of DNA sequencing and massive growth of reference databases, a metabarcoding approach using next-generation sequencing (NGS) has quickly emerged as a promising method for higherresolution diet analysis , de Barba et al 2014, Deagle et al 2013.…”