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Species identification is a key problem throughout the life cycle of marine invertebrates and fishes: from eggs and larvae to adults in ecological research, but also more applied in fisheries research and control, as well as processed seafood products in consumer protection. The application of molecular genetic tools is a powerful method to assign specimens that cannot be identified by morphological character to certain species and also has the potential to be automated, allowing identifying species with highest precision and in large sample sizes. In DNA barcoding a fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene is sequenced and compared with a reference database in order to identify the species. DNA microarrays use a different approach: the DNA of the specimen to be identified is not sequenced, but applied to a DNA chip and hybridises to species-specific probes, which is detected. This has the potential for a high-throughput technology that can analyse even mixed samples, such as plankton hauls or environmental DNA.

DNA microarrays for marine biodiversity studies have been developed and tested in several groups, spanning different applications. They are employed to characterize ecological communities circumventing uncertainties and challenges associated with the conventional techniques of taxonomy employed to characterize these communities. Examples come from identifications of fishes and phytoplankton to monitoring of harmful algae. Although DNA microchips support a great diversity of applications and provide a wealth of findings in functional genomics and environmental studies, limits in ecological applications are known. So far, DNA microarrays used in biodiversity studies provide only qualitative data in terms of presence or absence of the species and its usage is greatly limited in providing the quantitative measurement of environmental samples. Moreover, DNA microarrays are commonly restricted to identify only those species that are targeted by the probes implemented on the chip. In turn, developing a broad spectrum array has technological challenges in terms of probe designing, experimental optimization, and statistical analysis. In this book chapter, we provide a critical assessment on promises and pitfalls of DNA microarrays as tool for marine invertebrate species identification. We implemented a DNA-chip prototype to identify 15 species of marine invertebrates from European Seas, including crustaceans, molluscs, and polychaetes, based on the two mitochondrial markers, cytochrome oxidase subunit I and 16S rRNA. Challenges involved in oligonucleotide probe design, in silico evaluation, and difficulties encountered through hybridization experiments are here explored. Specificity and sensitivity of the probes have also been critically evaluated to verify the suitability of the selected markers for microarray probe design. Since ultimate application of DNA microarray to resolve complex environmental samples is a major challenge, we made an attempt to analyse gut contents of predator fishes. The problems encountered during this analysis, as the presence of target and not target species that could affect the specificity and the sensitivity of the DNA-chip to distinguish low and high abundant target species from a background of non-targets, were explored. We also reviewed advantages and disadvantages of DNA microarray technology compared to other molecular identification methods that recently spread, i.e. DNA barcoding and next generation sequencing. The outcome of the Invertebrate DNA Chip prototype served as a proof-of-concept for the identification of selected marine invertebrates and prey species of demersal fishes by DNA microarray. The potential of such microarrays can encompass several fields of scientific applications in marine biodiversity and ecosystem sciences, as marine ecosystem diversity and environmental monitoring, seafood quality control, and understanding food webs and ecosystem functioning.

Coral reef associated marine invertebrates, such as the blue sea star Linckia laevigata, have a life history with two phases: sedentary adults and planktonic larvae. On the one hand it is hypothesised that the long pelagic larval duration facilitates large distance dispersal. On the other hand, complex oceanographic and geographic characteristics of the Visayan seascape could cause isolation of populations. The study aims to investigate the genetic diversity, genetic population structure and gene flow in L. laevigata to reveal connectivity among populations in the Visayas. The analysis is based on partial sequences (626 bp in length) of the mitochondrial cytochrome oxidase I gene (COI) from 124 individuals collected from five localities in the Visayas. A comparative analysis of these populations with populations from the Indo-Malay Archipelago (IMA) published previously is also presented. Genetic diversity was high (h = 0.98, p = 1.6%) and comparable with preceding studies. Analyses of molecular variance (AMOVA) revealed a lack of spatial population differentiation among sample sites in the Visayas (FST-value = 0.009; P > 0.05). The lack of genetic population structure indicates high gene flow among populations of L. laevigata in the Visayas. Comparative analysis with data from the previous study indicates high connectivity of the Visayas with the central part of the IMA.

The coral reef sea star Linckia laevigata is common on shallow water coral reefs of the Indo-West Pacific. Its large geographic distribution and comprehensive data from previous studies makes it suitable to examine genetic differentiation and connectivity over large geographical scales. Based on partial sequences of the mitochondrial cytochrome oxidase I (COI) gene this study investigates the genetic population structure and connectivity of L. laevigata in the Western Indian Ocean (WIO) and compares it to previous studies in the Indo-Malay-Philippines Archipelago (IMPA). A total of 138 samples were collected from nine locations in the WIO. AMOVA revealed a low but significant ΦST-value of 0.024 for the WIO populations. In the hierarchical AMOVA, the following grouping rejected the hypothesis of panmixia: (1) Kenya (Watamu, Mombasa, Diani) and Tanzanian Island populations (Misali and Jambiani) and (2) the rest of the WIO sites (mainland Tanzania and Madagascar; ΦCT = 0.03). The genetic population structure was stronger and more significant (ΦST = 0.13) in the comparative analysis of WIO and IMPA populations. Three clades were identified in the haplotype network. The strong genetic differentiation (ΦCT = 0.199, P < 0.001) suggests that Indo-West Pacific populations of L. laevigata can be grouped into four biogeographic regions: (1) WIO (2) Eastern Indian Ocean (3) IMPA and (4) Western Pacific. The findings of this study support the existence of a genetic break in the Indo-West Pacific consistent with the effect of lowered sea level during the Pleistocene, which limited gene flow between the Pacific and Indian Ocean.

Illegal, Unreported and Unregulated fishing has had a major role in the overexploitation of global fish populations. In response, international regulations have been imposed and many fisheries have been 'eco-certified' by consumer organizations, but methods for independent control of catch certificates and eco-labels are urgently needed. Here we show that, by using gene-associated single nucleotide polymorphisms, individual marine fish can be assigned back to population of origin with unprecedented high levels of precision. By applying high differentiation single nucleotide polymorphism assays, in four commercial marine fish, on a pan-European scale, we find 93-100% of individuals could be correctly assigned to origin in policy-driven case studies. We show how case-targeted single nucleotide polymorphism assays can be created and forensically validated, using a centrally maintained and publicly available database. Our results demonstrate how application of gene-associated markers will likely revolutionize origin assignment and become highly valuable tools for fighting illegal fishing and mislabelling worldwide.