Inferring population connectivity across the range of distribution of the stiletto shrimp Artemesia longinaris Spence Bate, 1888 (Decapoda, Penaeidae) from DNA barcoding: implications for fishery management

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

DNA barcoding in pencilfishes (lebiasinidae: nannostomus) reveals cryptic diversity across the brazilian Amazon

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

DNA Barcoding em Utricularia (Lentibulariaceae)

Pós-graduação em Agronomia (Genética e Melhoramento de Plantas) - FCAV

The Gracilariaceae Germplasm Bank of the University of So Paulo, Brazil-a DNA barcoding approach

The University of So Paulo Gracilariaceae Germplasm Bank has 50 strains collected mostly in Brazil, but also elsewhere in the world. This bank has been used as a source of material for research developed locally and abroad. With over 200 species, some of which have high economic value, the family Gracilariaceae has been extensively studied. Nonetheless, taxonomic problems still persist by the existence of cryptic species, phenotypic plasticity, and broad geographic distribution. In the case of algae kept in culture for long periods of time, the identification is even more problematic as a consequence of considerable morphological modification. Thus, the use of molecular markers has been shown to be an efficient tool to elucidate taxonomic issues in the group. In this work, we sequenced the 5'-end of the cox1 gene for 41 strains and the universal plastid amplicon (UPA) plastid region for 45 strains, covering all 50 strains in the bank. In addition, the rbcL for representatives of the cox1/UPA clusters was sequenced for 14 strains. The original species identification based on morphology was compared with the molecular data obtained in this work, resulting in the identification of 13 different species. Our analyses indicate that cox1 and UPA are suitable markers for the delineation of species of Gracilariales in the germplasm bank. The addition of DNA barcode tags to the samples in the Gracilariaceae germplasm bank and the molecular identification of the species will make this bank even more useful for future research as the species can be easily traced and confirmed.

Two new species of Hudsonimyia Roback, 1979 (Diptera: Chironomidae: Tanypodinae) from Neotropical Region unveiled by morphology and DNA barcoding

Two new species of Hudsonimyia Roback, 1979 (Diptera: Chironomidae: Tanypodinae) are described and illustrated as male, pupa and larva. The generic diagnosis of pupa is emended and keys to males, pupae and larvae of known species are provided. The different life stages for one of the described species were associated by DNA barcodes.

Will a DNA barcoding approach be useful to identify Porphyra species (Bangiales, Rhodophyta)?

This paper is part of an extensive study on the biodiversity of the macroalgal flora of So Paulo state, SE Brazil. Previous assessments were based only on morphological descriptions. Here, we tested the effectiveness of DNA barcoding, in comparison with morphological observations for the recognition and cataloging of species. The focus of this study is the genus Porphyra, which is a conspicuous component of the upper intertidal on rocky shores of this region. With five currently accepted species, we have sequenced three short markers: cox1, cox2-3 spacer and UPA to establish the first DNA barcode database for the Porphyra species from the Brazilian coast. The three markers, although with different evolution rates, recovered a cryptic species (Porphyra sp. 77), grouped two different species (Porphyra drewiana and Porphyra spiralis) that are being synonymized, and finally indicated that varieties within P. acanthophora and P. spiralis are merely morphological, with no sequence divergence in the studied molecular markers.

DNA barcoding taxonomy and diversity of the Mediterranean sharks and rays

Elasmobranchs are an important by-catch of commercial fisheries targeting bony fishes. Fisheries targeting sharks are rare, but usually almost all specimen bycatched are marketed. They risk extinction if current fishing pressure continues (Ferretti et al., 2008). Accurate species identification is critical for the design of sustainable fisheries and appropriate management plans, especially since not all species are equally sensitive to fishing pressure (Walker & Hislop 1998). The identification of species constitutes the first basic step for biodiversity monitoring and conservation (Dayrat B et al., 2005). More recently, mtDNA sequencing has also been used for species identification and its use has become widespread under the DNA Barcode initiative (e.g. Hebert et al. 2003a, 2003b; Ward et al. 2005, 2008a; Moura et al 2008; Steinke et al. 2009). The aims of this work were: 1) identify sharks and skates species using DNA barcode; 2) compare species of different provenance; 3) use DNA barcode for misidentified species. Using DNA barcode 15 species of sharks (Alopias vulpinus, Centrophorus granulosus, Cetorhinus maximus, Dalatias licha, Etmopterus spinax, Galeorhinus galeus, Galeus melastomus, Heptranchias perlo, Hexanchus griseus, Mustelus mustelus, Mustelus punctulatus, Oxynotus centrina, Scyliorhinus canicula Squalus acanthias, Squalus blainville), 1 species of chimaera (Chimaera monstrosa) and 21 species of rays/skayes (Dasyatis centroura, Dasyatis pastinaca, Dasyatis sp., Dipturus nidarosiensis, Dipturus oxyrinchus, Leucoraja circularis, Leucoraja melitensis, Myliobatis aquila, Pteromylaeus bovinus, Pteroplatytrygon violacea, Raja asterias, Raja brachyura, Raja clavata, Raja miraletus, Raja montagui, Raja radula, Raja polystigma, Raja undulata, Rostroraja alba, Torpedo marmorata, Torpedo nobiliana, Torpedo torpedo) was identified.

Assessing the Phylogenetic Utility of DNA Barcoding Using the New Zealand Cicada Genus Kikihia

DNA Barcoding (Hebert et al. 2003) has the potential to revolutionize the process of identifying and cataloguing biodiversity; however, significant controversy surrounds some of the proposed applications. In the seven years since DNA barcoding was introduced, the Web of Science records more than 600 studies that have weighed the pros and cons of this procedure. Unfortunately, the scientific community has been unable to come to any consensus on what threshold to use to differentiate species or even whether the barcoding region provides enough information to serve as an accurate species identification tool. The purpose of my thesis is to analyze mitochondrial DNA (mtDNA) barcoding’s potential to identify known species and provide a well-resolved phylogeny for the New Zealand cicada genus Kikihia. In order to do this, I created a phylogenetic tree for species in the genus Kikihia based solely on the barcoding region and compared it to a phylogeny previously created by Marshall et al. (2008) that benefits from information from other mtDNA and nuclear genes as well as species-specific song data. I determined how well the barcoding region delimits species that have been recognized based on morphology and song. In addition, I looked at the effect of sampling on the success of barcoding studies. I analyzed subsets of a larger, more densely sampled dataset for the Kikihia Muta Group to determine which aspects of my sampling strategy led to the most accurate identifications. Since DNA barcoding would by definition have problems in diagnosing hybrid individuals, I studied two species (K. “murihikua” and K. angusta) that are known to hybridize. Individuals that were not obvious hybrids (determined by morphology) were selected for the case study. Phylogenetic analysis of the barcoding region revealed insights into the reasons these two species could not be successfully differentiated using barcoding alone.

DNA barcoding identifies a cosmopolitan diet in the ocean sunfish

The ocean sunfish (Mola mola) is the world’s heaviest bony fish reaching a body mass of up to 2.3 tonnes. However, the prey M. mola consumes to fuel this prodigious growth remains poorly known. Sunfish were thought to be obligate gelatinous plankton feeders, but recent studies suggest a more generalist diet. In this study, through molecular barcoding and for the first time, the diet of sunfish in the north-east Atlantic Ocean was characterised. Overall, DNA from the diet content of 57 individuals was successfully amplified, identifying 41 different prey items. Sunfish fed mainly on crustaceans and teleosts, with cnidarians comprising only 16% of the consumed prey. Although no adult fishes were sampled, we found evidence for an ontogenetic shift in the diet, with smaller individuals feeding mainly on small crustaceans and teleost fish, whereas the diet of larger fish included more cnidarian species. Our results confirm that smaller sunfish feed predominantly on benthic and on coastal pelagic species, whereas larger fish depend on pelagic prey. Therefore, sunfish is a generalist predator with a greater diversity of links in coastal food webs than previously realised. Its removal as fisheries’ bycatch may have wider reaching ecological consequences, potentially disrupting coastal trophic interactions.

DNA barcoding identifies a cosmopolitan diet in the ocean sunfish

The ocean sunfish (Mola mola) is the world’s heaviest bony fish reaching a body mass of up to 2.3 tonnes. However, the prey M. mola consumes to fuel this prodigious growth remains poorly known. Sunfish were thought to be obligate gelatinous plankton feeders, but recent studies suggest a more generalist diet. In this study, through molecular barcoding and for the first time, the diet of sunfish in the north-east Atlantic Ocean was characterised. Overall, DNA from the diet content of 57 individuals was successfully amplified, identifying 41 different prey items. Sunfish fed mainly on crustaceans and teleosts, with cnidarians comprising only 16% of the consumed prey. Although no adult fishes were sampled, we found evidence for an ontogenetic shift in the diet, with smaller individuals feeding mainly on small crustaceans and teleost fish, whereas the diet of larger fish included more cnidarian species. Our results confirm that smaller sunfish feed predominantly on benthic and on coastal pelagic species, whereas larger fish depend on pelagic prey. Therefore, sunfish is a generalist predator with a greater diversity of links in coastal food webs than previously realised. Its removal as fisheries’ bycatch may have wider reaching ecological consequences, potentially disrupting coastal trophic interactions.

DNA Barcoding as a tool for Zoological Taxonomy: Identification of bony fish in the Mediterranean Sea

The description of all the species present in nature is a vast task to be fulfilled by using the classical approach of morphological description of the organisms. In recent years, the traditional taxonomy, based primarily on identification keys of species, has shown a number of limitations in the use of the distinctive features in many animal taxa and inconsistencies with the genetic data. Furthermore, the increasing need to get a true estimate of biodiversity has led Zoological Taxonomy to seek new approaches and methodologies to support the traditional methods. The classification procedure has added modern criteriasuch as the evolutionary relationships and the genetic, biochemical and morphological characteristics of the organisms.Until now the Linnean binomial was the only abbreviated code associated with the description of the morphology of a species. The new technologies aim to achieve a short nucleotide sequence of the DNA to be used as an unique and solely label for a particular species, a specific genetic barcode. For both morphological and genetic approaches, skills and experience are required. Taxonomy is one of zoological disciplines that has been benefited from the achievements reached by modern molecular biotechnology. Using a molecular approach it is possible to identify cryptic species, to establish a family relationship between species and their membership of taxonomic categories or to reconstruct the evolutionary history of a taxon.

DNA barcoding: an effective tool to overcome morphological identification constraints in the assessment of the ecological quality

DNA barcoding has the potential to overcome taxonomic challenges in biological community assessments. However, fulfilling that potential requires successful amplification of a large and unbiased portion of the community. In this study, we attempted to identify mitochondrial gene cytochrome c oxidase I (COI) barcodes from 1024 benthic invertebrate specimens belonging to 54 taxa from low salinity environments of the Mira estuary and Torgal riverside (SW Portugal). Up to 17 primer pairs and several reaction conditions were attempted among specimens from all taxa, with amplification success defined as a single band of approximately 658 bp visualized on a pre-cast agarose gel, starting near the 5' end of the COI gene and suitable for sequencing. Amplification success was achieved for 99.6% of the 54 taxa, though no single primer was successful for more than 88.9% of the taxa. However, only 68.5% of the specimens within these taxa successfully amplified. Inhibition factors resulting from a non-purified DNA extracted and inexistence of species-specific primers for COI were pointed as the main reasons for an unsuccessful amplification. These results suggest that DNA barcoding can be an effective tool for application in low salinity environments where taxa such as chironomids and oligochaetes are challenging for morphological identification. Nevertheless, its implementation is not simple, as methods are still being standardized and multiple species

Priming of a DNA metabarcoding approach for species identification and inventory in marine macrobenthic communities

Dissertação de mestrado em Molecular Genetics

Biblioteca de referência de DNA barcodes de bivalves (Mollusca: Bivalvia) e gastrópodes (Mollusca: Gastropoda) da costa Portuguesa

Dissertação de mestrado em Ecologia

DNA barcodes de peixes marinhos da Europa: compilação de uma biblioteca de referência validada e investigação de padrões de divergência genética

Dissertação de mestrado em Ecologia