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Naiara Rodriguez-Ezpeleta

Naiara Rodriguez-Ezpeleta
AZTI · Marine Research Division

PhD

About

165
Publications
52,953
Reads
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4,788
Citations
Citations since 2017
52 Research Items
2919 Citations
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20172018201920202021202220230100200300400500600
20172018201920202021202220230100200300400500600
Introduction
Skills and Expertise
Additional affiliations
December 2011 - present
AZTI
Position
  • Senior Researcher
October 2008 - December 2011
Center for Cooperative Research in Biosciences
Position
  • Bioinformatics Platform Specialist
July 2007 - September 2008
Newcastle University

Publications

Publications (165)
Preprint
Expectations are high regarding the potential of eDNA metabarcoding for diversity monitoring. To make this approach suitable for this purpose, the completeness and accuracy of reference databases used for taxonomic assignment of eDNA sequences are among the challenges to be tackled. Yet, despite ongoing efforts to increase coverage of reference dat...
Article
Seafood traceability represents a major goal for regulators and fishing industries worldwide who seek to prevent commercial fraud, protect marine resources and ensure consumer safety. Genetic approaches can be used to trace the provenance of seafood based on the ability of DNA markers to assign samples back to their population of origin. Here, we h...
Preprint
Full-text available
In a recent study, Blanco-Fernandez et al. applied molecular tools to authenticate fish products and conclude evidence of 'worrying international fraud'. They revealed mislabeling in recognizable and unrecognizable fish products labeled as anchovy, hake and tuna commercialized by European companies. Their analyses consisted on extracting DNA from t...
Article
Full-text available
Understanding population connectivity within a species as well as potential interactions with its close relatives is crucial to define management units and to derive efficient management actions. However, although genetics can reveal mismatches between biological and management units and other relevant but hidden information such as species misiden...
Article
Full-text available
Establishing the foundations for a sustainable use of deep‐sea resources relies on increasing knowledge on this inaccessible ecosystem, which is challenging with traditional methods. The analysis of environmental DNA (eDNA) emerges as an alternative, but it has been scarcely applied to deep‐sea fish. Here, we have analyzed the fish eDNA contained i...
Article
Full-text available
In a recent paper, “Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring,” Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra‐organismal DNA from macro‐organisms. We agree with this...
Article
Full-text available
The chemical composition of otoliths (earbones) can provide valuable information about stock structure and connectivity patterns among marine fish. For that, chemical signatures must be sufficiently distinct to allow accurate classification of an unknown fish to their area of origin. Here we have examined the suitability of otolith microchemistry a...
Preprint
Full-text available
The deep-sea remains among the most unknown ecosystems on Earth despite its relevant role in carbon sequestration and increasing threat due to interest by fishing and mining industries. This, together with the recent discovery that the upper layer of this ecosystem (mesopelagic zone) harbors about 90% of the fish biomass on Earth, claims for a deep...
Preprint
Full-text available
Genetics analyses can reveal mismatches between biological and management units and thus prevent derived ineffective management actions that could lead to serious consequences for fisheries management. Additionally, genetics could reveal other relevant but hidden information such as species misidentification or hybridization. Here, we have assessed...
Article
Full-text available
Science-based management of marine fisheries and effective ecosystem monitoring both require the analysis of large amounts of often complex and difficult to collect information. Legislation also increasingly requires the attainment of good environmental status, which again demands collection of data to enable efficient monitoring and management of...
Preprint
Full-text available
In a recent paper, “Environmental DNA: What’s behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring”, Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra-organismal DNA from macro-organisms. We agree with this...
Preprint
In a recent paper, “Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring”, Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra-organismal DNA from macro-organisms. We agree with this...
Article
Science-based management of marine fisheries and effective ecosystem monitoring both require the analysis of large amounts of often complex and difficult to collect information. Legislation also increasingly requires the attainment of good environmental status, which again demands collection of data to enable efficient monitoring and management of...
Article
Skipjack (Katsuwonus pelamis), yellowfin (Thunnus albacares) and bigeye (Thunnus obesus) tuna are the target species of tropical tuna fisheries in the Indian Ocean, with high commercial value in the international market. High fishing pressure over the past three decades has raised concerns about their sustainability. Understanding life history stra...
Article
Based on collaboration with the Greenlandic fishing fleet, we document the presence of Atlantic bluefin tuna (Thunnus thynnus) in most years from 2012 to 2018 in the waters east of Greenland (northern Irminger Sea). In total, 84 individuals have been registered as bycatch in the commercial fisheries in Greenland waters, which indicates that the fir...
Technical Report
Full-text available
The ICES Working Group on Application of Genetics in Fisheries and Aquaculture (WGAGFA) is composed of 51 members from 17 ICES Member States. There is a high level of commitment by the WGAGFA members to their group: During the WGAGFA cycle 2018 to 2020, the annual working group meetings were attended in average by 26 delegates from 11 ICES Member S...
Article
Autonomous Reef Monitoring Structures (ARMS) have been applied worldwide to characterize the critical yet frequently overlooked biodiversity patterns of marine benthic organisms. In order to disentangle the relevance of environmental factors in benthic patterns, here, through standardized metabarcoding protocols, we analyse sessile and mobile (<2 m...
Article
Full-text available
Atlantic bluefin tuna (Thunnus thynnus) from the two main spawning populations in the Mediterranean and Gulf of Mexico occur together in the western, central and eastern Atlantic. Stock composition of catches from mixing areas is uncertain, presenting a major challenge to the sustainable management of the fisheries. This study combines genetic and...
Article
Full-text available
Current methods for monitoring marine fish (including bony fishes and elasmobranchs) diversity mostly rely on trawling surveys, which are invasive, costly, and time‐consuming. Moreover, these methods are selective, targeting a subset of species at the time, and can be inaccessible to certain areas. Here, we used environmental DNA (eDNA), the DNA pr...
Article
Full-text available
Monitoring introduction and spread of nonindigenous species via maritime transport and performing risk assessments require port biological baseline surveys. Yet, the comprehensiveness of these surveys is often compromised by the large number of habitats present in a port, the seasonal variability, and the time-consuming morphological approach used...
Preprint
Full-text available
Current methods for monitoring marine fish diversity mostly rely on trawling surveys, which are invasive, costly and time-consuming. Moreover, these methods are selective, targeting a subset of species at the time, and can be inaccessible to certain areas. Here, we explore the potential of environmental DNA (eDNA), the DNA present in the water colu...
Article
Non-indigenous species are introduced worldwide with ballast water (BW). To prevent further introductions, oceanic BW exchange and BW treatment systems are utilized, but their performance needs to be evaluated. To that aim, characterizing BW communities is essential but usually relies on exhaustive sampling and morphological taxonomic identificatio...
Article
Full-text available
Despite its economic importance, the population structure of the European hake, Merluccius merluccius, is unresolved, and the species is assessed based on two stocks (northern and southern) separated by the Capbreton Canyon. In order to shed light into the European hake population structure, we used Restriction-site-Associated DNA sequencing (RAD-s...
Preprint
Full-text available
Monitoring introduction and spread of non-indigenous species via maritime transport and performing risk assessments require port biological baseline surveys. Yet, the comprehensiveness of these surveys is often compromised by the large number of habitats present in a port, the seasonal variability and the time-consuming morphological approach used...
Article
Effective sustainable management of marine fisheries requires that assessed management units (that is, fish stocks) correspond to biological populations. This issue has long been discussed in the context of Atlantic bluefin tuna (ABFT, Thunnus thynnus) management, which currently considers two unmixed stocks but does not take into account how indiv...
Article
Full-text available
Restriction site-associated DNA sequencing (RAD-seq) has become a powerful and widely used tool in molecular ecology studies as it allows to cost-effectively recover thousands of polymorphic sites across individuals of non-model organisms. However, its successful implementation in population genetics relies on correct data processing that would min...
Article
The use of genomic approaches to assist with biodiversity estimations is an alternative to traditional biomonitoring, which is very time-consuming and costly. In response to the high demand for quick community descriptions, DNA metabarcoding can simultaneously assign taxonomy to hundreds of samples rapidly and at low cost. However, the technique ha...
Article
Full-text available
Environmental factors can influence diversity and population structure in marine species and accurate understanding of this influence can both improve fisheries management and help predict responses to environmental change. We used 7163 SNPs derived from restriction site-associated DNA sequencing genotyped in 245 individuals of the economically imp...
Article
Full-text available
The Atlantic bluefin tuna is a highly migratory species emblematic of the challenges associated with shared fisheries management. In an effort to resolve the species’ stock dynamics, a genome-wide search for spatially informative single nucleotide polymorphisms (SNPs) was undertaken, by way of sequencing reduced representation libraries. An allele...
Article
Full-text available
Global patterns of planktonic diversity are mainly determined by the dispersal of propagules with ocean currents. However, the role that abundance and body size play in determining spatial patterns of diversity remains unclear. Here we analyse spatial community structure - β-diversity - for several planktonic and nektonic organisms from prokaryotes...
Poster
Full-text available
Comprehensive and reliable DNA barcode reference libraries are essential elements of any DNA-based monitoring tool. Ideally, reference libraries should cover the full sweep of species in the target ecosystem, with a balanced geographic representation of each species distribution range. It is therefore essential to assess the missing taxa and geogra...
Article
Full-text available
Mesopelagic fish are largely abundant poorly studied fish that are still intact, but which, due to their potentially great added value, will be imminently exploited by humans. Therefore, studies that provide information to anticipate the anthropogenic impact on this important resource are urgently needed. In particular, knowledge about their connec...
Article
Full-text available
Ballast water is a main vector of introduction of Harmful Aquatic Organisms and Pathogens, which includes Non-Indigenous Species. Numerous and diversified organisms are transferred daily from a donor to a recipient port. Developed to prevent these introduction events, the International Convention for the Control and Management of Ships' Ballast Wat...
Article
Recruitment of sardine (Sardina pilchardus Walbaum, 1792) and anchovy (Engraulis encrasicolus Linnaeus, 1758) is thought to be regulated by predation of their eggs and larvae. Predators of sardine and anchovy can be identified by visual taxonomic identification of stomach contents, but this method is time consuming, tedious and may underestimate pr...
Article
Full-text available
Aquatic Invasive Alien Species (AIAS) are increasing due to the synergistic effects of climate change and habitat destruction. AIAS can heavily impact biodiversity and human health, causing a loss of ecosystem services; therefore, their control and management have now become a priority, particularly in the light of the new EU regulation 1143/2014 o...
Article
Biotic indices for monitoring marine ecosystems are mostly based on the analysis of benthic macroinvertebrate communities. Due to their high sensitivity to pollution and fast response to environmental changes, bacterial assemblages could complement the information provided by benthic metazoan communities as indicators of human-induced impacts, but...
Presentation
Full-text available
Intraguild predation between small pelagic fish as regulation mechanism of early life stage survival may have a significant effect on inter-annual variations in fish abundance and recruitment variability. For instance, although traditionally linked to physical (e.g. transport, retention) processes, survival of anchovy early life stages in the main...
Technical Report
Full-text available
The Working Group on the Application of Genetics in Fisheries and Mariculture (WGAGFM) met in Olhão, Portugal, 2–5 May 2017. Nineteen participants from 11 countries discussed the four Terms of Reference (ToR) and associated matters. Specifically, there was a focused discussion concerning the proposal by the ICES Science Committee to establish Aquac...
Data
Full-text available
Article
Full-text available
Marine environmental monitoring has tended to focus on site-specific methods of investigation. These traditional methods have low spatial and temporal resolution and are relatively labor intensive per unit area/time that they cover. To implement the Marine Strategy Framework Directive (MSFD), European Member States are required to improve marine mo...
Article
Full-text available
Metabarcoding is an accurate and cost-effective technique that allows for simultaneous taxonomic identification of multiple environmental samples. Application of this technique to marine benthic macroinvertebrate biodiversity assessment for biomonitoring purposes requires standardization of laboratory and data analysis procedures. In this context,...
Presentation
Intraguild predation between small pelagic fish as regulation mechanism of early life stage survival (e.g. top-down control) may have a significant effect on inter-annual variations in fish abundance and recruitment variability. For instance, although traditionally linked to physical (e.g. transport, retention) processes, survival of anchovy early...
Presentation
Intraguild predation between small pelagic fish as regulation mechanism of early life stage survival (e.g. top-down control) may have a significant effect on inter-annual variations in fish abundance and recruitment variability. For instance, although traditionally linked to physical (e.g. transport, retention) processes, survival of anchovy early...
Article
Full-text available
Understanding patterns of dispersal and connectivity among marine populations can directly inform fisheries conservation and management. Advances in high-throughput sequencing offer new opportunities for estimating marine connectivity. We used Restriction-site Associated DNA sequencing to examine dispersal and realized connectivity in the sea scall...
Chapter
Full-text available
This protocol details the analysis of Illumina MiSeq amplicon libraries derived from marine benthic macroinvertebrate samples and based on two barcodes of the mitochondrial cytochrome oxidase 1 (CO1) gene: a “short region,” covered by overlapping forward and reverse reads and a “long region” for which forward and reverse reads do not overlap. Aside...
Poster
Full-text available
Sardines (Sardina pilchardus) and anchovies (Engraulis encrasicolus) are small pelagic species inhabiting the Bay of Biscay. Due to their high commercial value, significant effort is devoted to understand the factors affecting the recruitment of these species, which is partly regulated by mortality of their eggs and larvae, predated by other organi...
Article
Full-text available
Characterization of biodiversity has been extensively used to confidently monitor and assess environmental status. Yet, visual morphology, traditionally and widely used for species identification in coastal and marine ecosystem communities, is tedious and entails limitations. Metabarcoding coupled with high-throughput sequencing (HTS) represents an...
Article
Full-text available
Although species from the genus Thunnus include some of the most commercially important and most severely overexploited fishes, the phylogeny of this genus is still unresolved, hampering evolutionary and traceability studies that could help improve conservation and management strategies for these species. Previous attempts based on mitochondrial an...
Article
Full-text available
Characterization of biodiversity has been extensively used to confidently monitor and assess environmental status. Yet, visual morphology, traditionally and widely used for species identification in coastal and marine ecosystem communities, is tedious and entails limitations. Metabarcoding coupled with high-throughput sequencing (HTS) represents an...
Article
Full-text available
Metabarcoding (large-scale taxonomic identification of complex samples via analysis of one or few orthologous DNA regions, called barcodes) is revolutionizing analysis of biodiversity of marine zooplankton assemblages. Metabarcoding relies on high-throughput DNA sequencing (HTS) technologies, which yield millions of DNA sequences in parallel and al...
Article
Full-text available
Restriction-site associated DNA sequencing (RAD-seq) and related methods are revolutionizing the field of population genomics in non-model organisms as they allow generating an unprecedented number of single nucleotide polymorphisms (SNPs) even when no genomic information is available. Yet, RAD-seq data analyses rely on assumptions on nature and nu...
Article
Full-text available
Traditional and emerging human activities are increasingly putting pressures on marine ecosystems and impacting their ability to sustain ecological and human communities. To evaluate the health status of marine ecosystems we need a science-based, integrated Ecosystem Approach, that incorporates knowledge of ecosystem function and services provided...
Conference Paper
Full-text available
A genotyping-by-sequencing approach was used to discover single nucleotide polymorphisms (SNPs) throughout the Atlantic bluefin tuna (Thunnus thynnus) genome while simultaneously analyzing the species' population structuring using 723 individuals captured between 2007-2013 from fourteen locations throughout the species' range, including several pre...