Pedro VieiraUniversity of Minho · Centro de Biologia Molecular e Ambiental (CBMA)
Pedro Vieira
BSc, MSc, PhD
About
77
Publications
9,735
Reads
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300
Citations
Citations since 2017
Introduction
Additional affiliations
July 2019 - present
Position
- Bioinformatician
Description
- Project NIS-DNA: https://sites.google.com/view/nis-dna/home?fbclid=IwAR1Z4phzsS1aht-1c8dqjAI5jwxilyWIRTYWf90vCmBmiz0YSoaRZGr9uwY Organizer and tutor of the "R Sessions" https://cbma.uminho.pt/events/rsessions/
September 2018 - May 2019
Position
- Invited Teacher
Description
- Invited teacher of the "Molecular Ecology" course of the Master of Ecology Invited teacher of the "Biogeography" course of the Bachelor of Geography Invited teacher of the "Biodiversity and Global Change" course of the Bachelor of Applied Biology
March 2018 - June 2019
Position
- PostDoc Position
Description
- Project Next-Sea: http://nextsea.org/ https://www.researchgate.net/project/NEXT-SEA-Next-generation-monitoring-of-coastal-ecosystems-in-a-scenario-of-global-change
Education
October 2017 - June 2018
March 2013 - November 2017
September 2010 - December 2011
Publications
Publications (77)
The introduction of non-indigenous species (NIS) is one of the major threats to the integrity of European coastal ecosystems. DNA-based assessments have been increasingly adopted for monitoring NIS. However, the accuracy of DNA-based taxonomic assignments is largely dependent on the completion and reliability of DNA barcode reference libraries. As...
Full-text view-only version of this paper: https://rdcu.be/c3phg. The green phyllodocids Eulalia clavigera and E. viridis are a known European pseudo-cryptic complex, but questions about its distribution and evidence of additional lineages in previous studies call for an investigation of the real diversity within the complex.
We analyze DNA sequenc...
Despite the growing use and potential of DNA metabarcoding to improve and expedite macrozoobenthos monitoring, its employment in Water Framework Directive (WFD) monitoring of transitional ecosystems still remains largely unexplored. In the current study, we addressed this research gap by building upon the biomonitoring network program of the Portug...
Morphologically similar species are often overlooked but molecular techniques have been effective in signalling potential hidden diversity, boosting the documentation of unique evolutionary lineages and ecological diversity. Platynereis dumerilii and Platynereis massiliensis are part of a recognised species complex, where differences in the reprodu...
Updated Gblocks link: http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=gblocks; Updated ABGD link: https://bioinfo.mnhn.fr/abi/public/abgd/abgdweb.html;
Past molecular studies using mtDNA sequences and alloenzymes signalled the existence of at least two cryptic species within the Hediste diversicolor morphotype, in European coasts. Howe...
In marine and coastal ecosystems, the proliferation of non-indigenous species (NIS) is among the top causes of biodiversity loss. Thus, it is essential to prevent the entrance and proliferation of NIS by detecting their presence as early as possible at the most susceptible locations, such as ports and marinas. Molecular techniques, like DNA metabar...
The monitoring of larvae in plankton samples in recreational marinas, ports, or the close vicinities, may provide key information about non-indigenous species (NIS) introduction status or detect their presence at an earlier stage. DNA metabarcoding is a powerful method to assess biodiversity but its efficiency is dependent on the methodologies empl...
DNA metabarcoding is particularly helpful for monitoring taxonomically complex communities and hard to identify morphologically, such as several zoo and ichthyoplankton, which contain eggs and larval stages of unknown species. However, the efficiency of metabarcoding in diversity recovery is dependent on the targeted genetic markers and primers emp...
Despite the growing use and potential of DNA metabarcoding to improve and expedite macrozoobenthos monitoring, its employment in Water Framework Directive (WFD) monitoring of transitional ecosystems still remains largely unexplored and pending proof-of-concept studies. In the current study, we addressed this research gap by building upon the biomon...
Oceanic islands are recognized evolutionary hotspots for terrestrial organisms, but little is known about their impact on marine organisms’ evolution and biogeography. The volcanic archipelagos of Macaronesia occupy a vast and complex region in the Atlantic Ocean and may be particularly suitable to investigate marine island biogeography. In this st...
DOI for the Supplemental Material: https://doi.org/10.6084/m9.figshare.18858224.v1.
Eumida sanguinea is a recognized polychaete species complex which, in previous studies, has been reported to have additional undescribed diversity. We detected nine additional lineages by analysing DNA sequence data (mitochondrial: COI, 16S rRNA and nuclear loci: I...
DNA metabarcoding has great potential to improve marine biomonitoring programs by providing a rapid and accurate assessment of species composition in zoobenthic communities. However, some methodological improvements are still required, especially regarding failed detections, primers efficiency and incompleteness of databases. Here we assessed the e...
The accuracy of specimen identification through DNA barcoding and metabarcoding relies on reference libraries containing records with reliable taxonomy and sequence quality. The considerable growth in barcode data requires stringent data curation, especially in taxonomically difficult groups such as marine invertebrates. A major effort in curating...
Aim
DNA metabarcoding has great potential to improve biomonitoring in island's marine ecosystems, which are highly vulnerable to global change and non-indigenous species (NIS) introductions. However, the depth and accuracy of the taxonomic identifications are mainly dependent on reference libraries containing representative and reliable sequences f...
The identification of patterns and mechanisms behind species’ distribution is one of the major challenges in ecology, having important outcomes for the conservation and management of ecosystems. This is especially true for those components of biodiversity providing essential ecosystem functions and for which standard surveys may underestimate their...
Oceanic islands are recognized evolutionary hotspots for terrestrial organisms, but little is known about their impact on marine organisms' evolution and biogeography. The volcanic archipelagos of Macaronesia occupy a vast and complex region which is particularly suitable to investigate marine island biogeography.
In this study, we used mitochondri...
The polychaete genusLaeonereis(Annelida, Nereididae) occurs over a broad geographic range and extends nearly across the entire Atlantic coast of America, from the USA to Uruguay. Despite the research efforts to clarify its diversity and systematics, mostly by morphological and ecological evidence, there is still uncertainty, mainly concerning the s...
The identification of the patterns and mechanisms behind species’ distribution is one of the major challenges in ecology, having also important outcomes for the conservation and management of ecosystems. This is especially true for those components of biodiversity providing essential ecosystem functions and for which standard surveys may underestim...
The accuracy of the identification of unknown specimens using DNA barcoding and metabarcoding relies on reference libraries containing records with reliable taxonomy and sequence quality. A rampant growth in barcode data led to a stringent need for data curation, especially in taxonomically difficult groups such as marine invertebrates. A major eff...
Recent studies reporting complexes of cryptic or pseudo-cryptic species with narrow geographic distributions have been challenging the cosmopolitan status of a fair number of marine benthic invertebrates. Morphologically similar species are often overlooked but molecular techniques have been extremely effective in signalling potential hidden divers...
DNA metabarcoding has been widely used in biodiversity assessments as a complement to traditional morphology-based techniques. This technique is useful for the early detection and surveillance of non-indigenous species (NIS) in aquatic ecosystems. When introduced to new locations, NIS can establish, and become invasive, which may cause severe alter...
Biodiversity studies greatly benefit from molecular tools, such as DNA metabarcoding, which provides an effective identification tool in biomonitoring and conservation programmes. The accuracy of species‐level assignment, and consequent taxonomic coverage, relies on comprehensive DNA barcode reference libraries. The role of these libraries is to su...
DNA metabarcoding has the capacity to bolster current biodiversity assessment techniques, including the early detection and monitoring of non-indigenous species (NIS). However, the success of this approach is greatly dependent on the availability, taxonomic coverage and reliability of reference sequences in genetic databases, whose deficiencies can...
In coastal ecosystems, non-indigenous species (NIS) are recognized as a major threat to biodiversity, ecosystem functioning and socio-economic activities. Here we present a systematic review on the use of metabarcoding for NIS surveillance in marine and coastal ecosystems, through the analysis of 42 publications. Metabarcoding has been mainly appli...
Meiofauna organisms play an important role in ecological, trophic and sedimentary processes in estuarine ecosystems. Recently, the application of environmental DNA (eDNA) for investigating meiofauna in different environments, improved the accessibility to its diversity and composition in a scale, frequency and depth previously unattainable. Neverth...
Automated system to assess the quality and reliability of reference libraries
In coastal ecosystems, non-indigenous species (NIS) are recognized as a major threat to biodiversity, ecosystem functioning and socio-economic activities. Here we present a systematic review on the use of metabarcoding for NIS surveillance in marine and coastal ecosystems, through the analysis of 42 publications. Metabarcoding has been mainly appli...
DNA metabarcoding provides a rapid and effective identification tool of macroinvertebrate species. The accuracy of species-level assignment, and consequent taxonomic coverage, relies on comprehensive DNA barcode reference libraries, which, due to incompleteness, are currently a recognized limitation for metabarcoding applications. In this study, we...
We report on two new lineages of the Eumida sanguinea complex from Great Britain and describe one of them as a new species using a multilocus approach, including the mitochondrial DNA COI‐5P and the nuclear markers ITS (ITS1, 5.8S rRNA and ITS2) and 28S rRNA. The molecular analysis placed Eumida mackiei sp. nov. in a monophyletic clade with 19.1% (...
Meiofaunal organisms play a key role in estuarine ecosystems, being responsible for significant ecological processes. However, meiofauna constitutes a particularly difficult community to be monitored through conventional morphology-based approaches. New emerging tools, such as DNA metabarcoding, facilitate the access to these communities and provid...
Polychaetes are common in coastal and estuarine environments worldwide and constitute one of the most complex groups of marine invertebrates. The morpho-physiology of the female reproductive system (FRS) can be understood by using histological tools to describe reproductive cycle and gametogenesis paths and, among other purposes, aiming to identify...
Problem statement
Large-scale global initiatives aiming to acquire a comprehensive catalogue of all living species and tackle the different biodiversity knowledge shortfalls (Hortal et al., 2012), have promoted the generation of vast amounts of DNA sequence data. The use of DNA barcodes as a universal system for DNA-based species identification, na...
Meiobenthic organisms are key components of estuarine environments, providing invaluable functions and services. In particular, meiofaunal organisms participate actively in nutrient cycles and energy flux, supporting higher trophic levels, as well as the stabilization of sediments. Due to their small size (between 30 µm and 1mm) and high dispersal...
https://doi.org/10.1139/gen-2019-0083
Genome, 2019, 62(6): 372
Background: DNA metabarcoding provides a practical approach to investigate communities hard to track through traditional morphological approaches as, for instance, the estuarine meiofauna. In this study, we examined the patterns of small-scale spatial variation of meiofaunal communiti...
Diversification and speciation of terrestrial organisms is anticipated in oceanic islands such as Macaronesia, a group of Atlantic islands that have remained unconnected to continental landmasses. Hitherto, the diversification of marine organisms in oceanic islands, especially those with low vagility, has received little direct empirical analysis u...
The Northeast Atlantic (NEA) is an important and complex biogeographic region with a very rich marine fauna. However, little is known about the role of the Macaronesian islands in the evolutionary history and diversification of marine invertebrates in the NEA. Among the amphipods, the members of the family Hyalidae are particularly common and abund...
Meiofaunal communities play a key role in estuarine ecosystems, being responsible for significant trophic, ecological and sedimentary processes. However, meiofauna constitutes a particularly difficult community to be monitored through conventional morphology-based approaches. New emerging tools, such as DNA metabarcoding, facilitate the access to t...
DNA barcode reference library for marine amphipods
DNA barcode reference library for the superorder Peracarida
Sphaeromatid isopods, such as Dynamene, are common and abundant members of the invertebrate fauna of littoral and shallow sublittoral substrates. Six species of Dynamene occur in the northern hemisphere. Only two species exist outside this range, in Australia. The distribution of the various species in the NE Atlantic-Black Sea axis has been contro...
Material examined in this study
List of locations where Dynamene specimens were recorded in this study
Benthic communities play a key role in the maintenance of ocean and coastal ecosystems’ processes. Supplementary information is required to increase knowledge about their structure, in order to improve conservation strategies for threatened species. Assessing structure and diversity of these communities can be rather challenging, due to technical d...
Marine Protected Areas (MPA) help in the preservation of endangered habitats and species, and constitute effective tools for the management of populations of commercially important species. Molecular tools are emerging as fundamental methodologies for assisting the delineation MPAs boundaries, providing important data on genetic diversity, rare hap...
Peracarida is a Superorder of the subphylum Crustacea and one of the most diverse and widely distributed groups of crustaceans. In marine coasts, peracaridean species are among the most ecologically important invertebrates, with high relevance in trophic interactions and constituting one of the dominant groups and key components of marine benthic c...
Problem statement
Peracarida is a Superorder of the subphylum Crustacea and one of the most diverse and widely distributed groups of crustaceans. In marine coasts, peracaridean species are among the most ecologically important invertebrates, with high relevance in trophic interactions and constituting one of the dominant groups and key components o...
Acknowledgements Costa FO, deWaard JR, Boutillier J, Ratnasingham S, Dooh RT, Hajibabaei M, Hebert PDN (2007) Biological identifications through DNA barcodes: the case of Crustacea. Can J Fish Aquat Sci 64: 272- 295.
Lobo J, Costa PM, Teixeira MAL, Ferreira MSG., Costa MH, Costa FOC (2013) Enhanced primers for amplification of DNA barcodes from a b...
Understanding the spatial patterns of species and genetic diversity has been one of the main focuses in ecology. It is important to explore the evolutionary processes related to the origin of a species, and the factors influencing its genetic structure. The use of a standard system, like the DNA barcode, can assist in the identification and discrim...
Distribution and genetic diversity of Dynamene
The resistance of malaria parasites to available drugs continues to grow, and this makes the need for new antimalarial therapies pressing. Aminoacyl-tRNA synthetases (ARSs) are essential enzymes and well-established antibacterial targets and so constitute a promising set of targets for the development of new antimalarials. Despite their potential a...
This work aimed to investigate the association of the carriage of plasmid-mediated quinolone resistance (PMQR) genes, the virulence potential encoded in pathogenicity islands (PAIs) and the phylogenetic background in Escherichia coli strains isolated from waters of diverse origin. Antimicrobial susceptibilities were determined by the disc diffusion...
Questions
Questions (2)
Hi to all.
We (Pedro Vieira (Portugal) and David Holdich (England)) are currently studying the distribution of the sphaeromatid isopod, Dynamene, on European and N. African Atlantic coasts, as well as the Mediterranean, Adriatic, Black and Red Seas. If you have any material of this genus that you would be prepared to let us examine then we would be very grateful.
Thank you in advance, Pedro
I need some help with the identification of this group of isopodes.
