User:Jasmina Kamberovic/sandbox

Applications
Applications of DNA barcoding include identification of new species, safety assessment of food, identification and assessment of cryptic species, detection of alien species, identification of endangered and threatened species, linking egg and larval stages to adult species, securing intellectual property rights for bioresources, framing global management plans for conservation strategies and elucidate feeding niches. DNA barcode markers can be applied in basic question in systematics, ecology, evolutionary biology and conservation, including community assembly, species interaction networks, taxonomic discovery, and assessing priority areas for environmental protection.

Identification of species
DNA barcoding is a useful tool for species identification, especially when morphological differences between species are limited or absent. Below are mentioned some general applications for species identification with DNA barcoding.


 * Identification of new species, which was for example confirmed in study of birds in North America, revealing deep intraspecific divergences by Hebert et al. 2004.


 * Identification of species where traditional methods are not applicable; an example is the possible identification of groupers causing Ciguatera fish poisoning from meal remnants.


 * Identification of species from cryptic life stages, e.g. larvae for which there is generally little diagnostic character available; used to associate different life  stages (e.g. adult and larval) in many animals.


 * Identifying species listed in Convention on International Trade of Endangered Species (CITES) appendixes for illegal trade monitoring.

Invasive species identification
One way to determine alien specie s is via barcoding. Barcoding can be suitable for detection of species in e.g. border control, where rapid and accurate morphological identification is not possible due to several similar specimens and/or lack of sufficient diagnostic characteristics. Barcoding can also be used to screen an ecosystem for an invasive species, and to distinguish between an invasive species and a native, morphologically similar, species.

Phylogenetic implications
COI DNA barcodes can provide insights into molecular evolution and protein function in animals at different taxonomic scales. The barcoding region COI is informative on recent divergence and useless for estimating old divergence. DNA barcodes allow us to detection not only species, then species interactions and community level of phylogenies.

Delimiting cryptic species
DNA barcoding has been employed as an efficient tool that uses genetic markers in an organism's DNA to enable the identification and recognition of cryptic species. The results of DNA barcoding analyses can be dependent upon the choice of analytical methods used by the investigators, so the process of delimiting cryptic species using DNA barcodes can be as subjective as any other form of taxonomy. Hebert et al.(2004b concluded that Astraptes fulgerator consists of 10 different species in north-western Costa Rica. These results, however, were subsequently challenged by Brower (2006 ), who pointed out numerous serious flaws in the analysis, and concluded that the original data could support no more than the possibility of three to seven cryptic taxa rather than ten cryptic species. The huge genetic investigation regarding the prevalence of cryptic polychaete species within the deep Antarctic benthos was done by Madelaine et al. (2016), uncovering cryptic diversity in 50% of the 15 morphospecies targeted through the comparison of mitochondrial DNA sequences, as well as 10 previously overlooked morphospecies, increasing the total species richness in the sample by 233%.

Diet analysis and food web application
DNA barcoding can be very useful in diet analysis studies, and typically used if it is not possible to identify single specimens found in stomach/fecal contents based on morphological identification. In fecal samples or highly digested stomach contents it is often not possible to distinguish tissue from single species and therefore metabarcoding can be applied instead. Recent advances in molecular techniques allow us to resolve the diet of unstudied taxa. The first study to resolve the species‐level diet of adult odonates based on the metabarcoding method is conducted in southwestern Finland using three different methods for extracting DNA from fecal samples.

Barcoding for food safety
DNA barcoding represents an essential tool to vouch for quality controls of food products, to guarantee food traceability, to safeguard public health, to minimize food piracy, and to valorize local and typical agro-food production systems (http://creativecommons.org/licenses/by/4.0/).

Biomonitoring and ecological assessment
The aim of biomonitoring is to observe the state of the environment and characterize the quality of the environment. The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. The development

of DNA barcoding and metabarcoding could potentially alleviate some of the limitations related to difficulties in morphological identification of bioindicator taxa, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. The first attempts to test the metabarcoding approach to bioassessment are known from Chariton et al. (2010) who studied ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA. The greatest advances is made in England where is metabarcoding based on diatom communities integrated in water quality assessment.