39 research outputs found
Biodiversidade e evolução molecular da classe malacostraca
Doutoramento em BiologiaNo actual cenário de perda acelerada de biodiversidade, o nosso
conhecimento dos ecossistemas marinhos, apesar da sua extensão e
complexidade, continua muito inferior ao dos ecossistemas terrestres. A classe
Malacostraca (Arthropoda, Crustacea), um grupo dos mais representativos nos
ecossistemas marinhos, apresenta um elevado nível de diversidade
morfológica e ecológica, mas difícil sua identificação ao nível de espécie
requer frequentemente a ajuda de especialistas em taxonomia. A utilização
recente do “barcoding” (código de barras do ADN), revelou ser um método
rápido e eficaz para a identificação de espécies em diversos grupos de
metazoários, incluindo os Malacostraca. No âmbito desta tese foi construída
uma base de dados de código de barras de ADN envolvendo 132 espécies de
Malacostraca vários locais de amostragem no Atlântico Nordeste e
Mediterrâneo. As sequências de ADN mitocondrial provenientes de 601
espécimes formaram, em 95% dos casos, grupos congruentes com as
identificações baseadas em características morfológicas. No entanto, foi
detectado polimorfismo em seis casos e a divergência intra-específica foi
elevada em exemplares pertencentes a duas espécies morfológicas,
sugerindo, neste caso, a ocorrência de especiação críptica. Este estudo
confirma a utilidade do código de barras de ADN para a identificação de
Malacostraca marinhos. Apesar do sucesso obtido, este método apresenta
alguns problemas, como por exemplo a possível amplificação de
pseudogenes. A ocorrência de pseudogenes e as possíveisabordagens para a
detecção e resolução deste tipo de problemas são discutidas com base em
casos de estudo: análises dos códigos de barras ADN na espécie Goneplax
rhomboides (Crustacea, Decapoda). A análise dos códigos de barras ADN
revelou ainda grupos prioritários de decápodes para estudos taxonómicos e
sistemáticos, nomeadamente os decápodes dos géneros Plesionika e
Pagurus. Neste âmbito são discutidas as relações filogenéticas entre espécies
seleccionadas dos géneros Plesionika e Pagurus.
Este trabalho aponta para várias questões no âmbito da biodiversidade e
evolução molecular da classe Malacostraca que carecem de um maior
esclarecimento, podendo ser considerado como a base para estudo futuros.
Análises filogenéticas adicionais integrando dados morfológicos e moleculares
de um maior número de espécies e de famílias deverão certamente conduzir a
uma melhor avaliação da biodiversidade e da evolução dentro da classe.The biodiversity of many habitats is under threat and although seas cover the
majority of our planet’s surface, far less is known about the biodiversity of
marine environments than that of terrestrial systems. The complexity of its
species and ecosystems is immense.
Marine malacostraca are known as a group with a high level of morphological
and ecological diversity but are difficult to identify by traditional approaches and
usually require the help of highly trained taxonomists. A faster identification
method, DNA barcoding, was found to be an effective tool for species
identification in many metazoan groups including some malacostraca.
Moreover, the generation of a larger comparative database allows additional
insights into the tempo and mode of molecular evolution. Indeed, examination
of diversity at the COI region yields an informative framework to identify and
explore priority issues, demanding in turn a fully integrative approach utilising
additional molecular, distributional and ecological information. Here we expand
the DNA barcode database with a case study involving more than 132
malacostracan species from the Northeast Atlantic Ocean and Mediterranean
Sea. DNA sequences from around 601 specimens grouped into clusters
corresponding to known morphological species in 95% of cases. However
shared polymorphism between sister-species was detected in six species.
Intraspecific divergence was high in specimens belonging to two morphological
species, suggesting the occurrence of cryptic speciation, allowing a rapid
assessment of taxon diversity in groups that have until now received limited
morphological and systematic examination. We highlight taxonomic groups or
species with unusual nucleotide composition or evolutionary rates. Such data
are relevant to strategies for conservation of existing decapod biodiversity, as
well as elucidating the mechanisms and constraints shaping the patterns
observed.This study reconfirms the usefulness of DNA barcoding for the
identification of marine malacostraca, despite complexities that sometimes
arise due to pseudogenes (numts). Here, we study the effect of numts on DNA
barcoding based on barcoding analyses in decapoda species: Goneplax
rhomboides. DNA barcodes reveal priority groups for taxonomic and systematic
focus of decapods. Here we discussed two cases of phylogenetic relationships
among selected species of Plesionika and Pagurus, respectively.
Issues relating to the molecular biodiversity and evolution of the Malacostraca
arising from this study allow identification of future priorities. Further
phylogenetic analyses including morphological and molecular data of selected
families is required, especially encompassing broad geographic and ecological
coverage, will lead to an improved evaluation of the biodiversity and evolution
among selected Malacostraca specie
Multigene Molecular Systematics Confirm Species Status of Morphologically Convergent Pagurus Hermit Crabs
Introduction: In spite of contemporary morphological taxonomy appraisals, apparent high morphological similarity raises uncertainty about the species status of certain Pagurus hermit crabs. This is exemplified between two European species, Pagurus excavatus (Herbst, 1791) and Pagurus alatus (Fabricius 1775), whose species status is still difficult to resolve using morphological criteria alone. Methodology/Principal Findings: To address such ambiguities, we used combinations of Maximum Likelihood (ML) and Bayesian Inference (BI) methods to delineate species boundaries of P. alatus and P. excavatus and formulate an intermediate Pagurus phylogenetic hypothesis, based upon single and concatenated mitochondrial (cytochrome oxidase I [COI]) and nuclear (16S and 28s ribosomal RNA) gene partitions. The molecular data supported the species status of P. excavatus and P. alatus and also clearly resolved two divergent clades within hermit crabs from the Northeast Atlantic Ocean and the Mediterranean Sea. Conclusions/Significance: Despite the abundance and prominent ecological role of hermit crabs, Pagurus, in North East Atlantic Ocean and Mediterranean Sea ecosystems, many important aspects of their taxonomy, biology, systematics and evolution remain poorly explored. The topologies presented here should be regarded as hypotheses that can be incorporated into the robust and integrated understanding of the systematic relationships within and between species of the genus Pagurus inhabiting the Northeast Atlantic Ocean and the Mediterranean Sea
Global cooling as a driver of diversification in a major marine clade
Climate is a strong driver of global diversity and will become increasingly important as human influences drive temperature changes at unprecedented rates. Here we investigate diversification and speciation trends within a diverse group of aquatic crustaceans, the Anomura. We use a phylogenetic framework to demonstrate that speciation rate is correlated with global cooling across the entire tree, in contrast to previous studies. Additionally, we find that marine clades continue to show evidence of increased speciation rates with cooler global temperatures, while the single freshwater clade shows the opposite trend with speciation rates positively correlated to global warming. Our findings suggest that both global cooling and warming lead to diversification and that habitat plays a role in the responses of species to climate change. These results have important implications for our understanding of how extant biota respond to ongoing climate change and are of particular importance for conservation planning of marine ecosystems
Reexamination of the species assignment of Diacavolinia pteropods using DNA barcoding
© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e53889, doi:10.1371/journal.pone.0053889.Thecosome pteropods (Mollusca, Gastropoda) are an ecologically important, diverse, and ubiquitous group of holoplanktonic animals that are the focus of intense research interest due to their external aragonite shell and vulnerability to ocean acidification. Characterizing the response of these animals to low pH and other environmental stressors has been hampered by continued uncertainty in their taxonomic identification. An example of this confusion in species assignment is found in the genus Diacavolinia. All members of this genus were originally indentified as a single species, Cavolinia longirostris, but over the past fifty years the taxonomy has been revisited multiple times; currently the genus comprises 22 different species. This study examines five species of Diacavolinia, including four sampled in the Northeast Atlantic (78 individuals) and one from the Eastern tropical North Pacific (15 individuals). Diacavolina were identified to species based on morphological characteristics according to the current taxonomy, photographed, and then used to determine the sequence of the “DNA barcoding” region of the cytochrome c oxidase subunit I (COI). Specimens from the Atlantic, despite distinct differences in shell morphology, showed polyphyly and a genetic divergence of <3% (K2P distance) whereas the Pacific and Atlantic samples were more distant (~19%). Comparisons of Diacavolinia spp. with other Cavolinia spp. reveal larger distances (~24%). These results indicate that specimens from the Atlantic comprise a single monophyletic species and suggest possible species-level divergence between Atlantic and Pacific populations. The findings support the maintenance of Diacavolinia as a separate genus, yet emphasize the inadequacy of our current taxonomic understanding of pteropods. They highlight the need for accurate species identifications to support estimates of biodiversity, range extent and natural exposure of these planktonic calcifiers to environmental variability; furthermore, the apparent variation of the pteropods shell may have implications for our understanding of the species’ sensitivity to ocean acidification.This material is based upon work supported by the National Science Foundation under Grant Number OCE-0928801. AEM was funded through the WHOI Postdoctoral Scholarship. Support to LBB was provided by the College of Liberal Arts & Sciences, University of Connecticut; and by the Census of Marine Life/Alfred P. Sloan Foundation
The Application of DNA Barcodes for the Identification of Marine Crustaceans from the North Sea and Adjacent Regions
During the last years DNA barcoding has become a popular method of choice for molecular specimen identification. Here we present a comprehensive DNA barcode library of various crustacean taxa found in the North Sea, one of the most extensively studied marine regions of the world. Our data set includes 1,332 barcodes covering 205 species, including taxa of the Amphipoda, Copepoda, Decapoda, Isopoda, Thecostraca, and others. This dataset represents the most extensive DNA barcode library of the Crustacea in terms of species number to date. By using the Barcode of Life Data Systems (BOLD), unique BINs were identified for 198 (96.6%) of the analyzed species. Six species were characterized by two BINs (2.9%), and three BINs were found for the amphipod species Gammarus salinus Spooner, 1947 (0.4%). Intraspecific distances with values higher than 2.2% were revealed for 13 species (6.3%). Exceptionally high distances of up to 14.87% between two distinct but monophyletic clusters were found for the parasitic copepod Caligus elongatus Nordmann, 1832, supporting the results of previous studies that indicated the existence of an overlooked sea louse species. In contrast to these high distances, haplotype-sharing was observed for two decapod spider crab species, Macropodia parva Van Noort & Adema, 1985 and Macropodia rostrata (Linnaeus, 1761), underlining the need for a taxonomic revision of both species. Summarizing the results, our study confirms the application of DNA barcodes as highly effective identification system for the analyzed marine crustaceans of the North Sea and represents an important milestone for modern biodiversity assessment studies using barcode sequence
Systematic and Evolutionary Insights Derived from mtDNA COI Barcode Diversity in the Decapoda (Crustacea: Malacostraca)
Background: Decapods are the most recognizable of all crustaceans and comprise a dominant group of benthic invertebrates of the continental shelf and slope, including many species of economic importance. Of the 17635 morphologically described Decapoda species, only 5.4% are represented by COI barcode region sequences. It therefore remains a challenge to compile regional databases that identify and analyse the extent and patterns of decapod diversity throughout the world. Methodology/Principal Findings: We contributed 101 decapod species from the North East Atlantic, the Gulf of Cadiz and the Mediterranean Sea, of which 81 species represent novel COI records. Within the newly-generated dataset, 3.6% of the species barcodes conflicted with the assigned morphological taxonomic identification, highlighting both the apparent taxonomic ambiguity among certain groups, and the need for an accelerated and independent taxonomic approach. Using the combined COI barcode projects from the Barcode of Life Database, we provide the most comprehensive COI data set so far examined for the Order (1572 sequences of 528 species, 213 genera, and 67 families). Patterns within families show a general predicted molecular hierarchy, but the scale of divergence at each taxonomic level appears to vary extensively between families. The range values of mean K2P distance observed were: within species 0.285% to 1.375%, within genus 6.376% to 20.924% and within family 11.392% to 25.617%. Nucleotide composition varied greatly across decapods, ranging from 30.8 % to 49.4 % GC content. Conclusions/Significance: Decapod biological diversity was quantified by identifying putative cryptic species allowing a rapid assessment of taxon diversity in groups that have until now received limited morphological and systematic examination. We highlight taxonomic groups or species with unusual nucleotide composition or evolutionary rates. Such data are relevant to strategies for conservation of existing decapod biodiversity, as well as elucidating the mechanisms and constraints shaping the patterns observed.FCT - SFRH/BD/25568/ 2006EC FP6 - GOCE-CT-2005-511234 HERMESFCT - PTDC/MAR/69892/2006 LusomarBo
Lawson criterion for ignition exceeded in an inertial fusion experiment
For more than half a century, researchers around the world have been engaged in attempts to achieve fusion ignition as a proof of principle of various fusion concepts. Following the Lawson criterion, an ignited plasma is one where the fusion heating power is high enough to overcome all the physical processes that cool the fusion plasma, creating a positive thermodynamic feedback loop with rapidly increasing temperature. In inertially confined fusion, ignition is a state where the fusion plasma can begin "burn propagation" into surrounding cold fuel, enabling the possibility of high energy gain. While "scientific breakeven" (i.e., unity target gain) has not yet been achieved (here target gain is 0.72, 1.37 MJ of fusion for 1.92 MJ of laser energy), this Letter reports the first controlled fusion experiment, using laser indirect drive, on the National Ignition Facility to produce capsule gain (here 5.8) and reach ignition by nine different formulations of the Lawson criterion
Caracterização qualitativa do fenómeno de afloramento costeiro de verão na Região de Aveiro
Mestrado em Ciências das Zonas CosteirasO fenómeno de afloramento costeiro é um processo hidrodinâmico
importante que ocorre na costa portuguesa entre os meses de Abril a
Outubro. O afloramento costeiro, é provocado pela acção do vento quando
sopra no sentido Norte-Sul paralelamente à costa Oeste de Portugal
Continental promovendo a ascensão de águas frias e ricas em nutrientes.
O objectivo deste trabalho é caracterizar qualitativamente o fenómeno de
afloramento costeiro de Verão na Região de Aveiro com a utilização de um
modelo Ecológico 3D (COHERENS) e de imagens satélite SeaSTAR (sensor
SeaWiFS).
O modelo foi inicializado com dados biológicos, químicos e físicos e forçado
com dados da estação de meteorologia da Universidade de Aveiro.
Realizaram-se 3 cenários para avaliar: o contributo do vento (sem maré); o
contributo do sentido do vento a uma velocidade constante (vento constante
de 5.2 m.s-1 de NW ou SW). A comparação dos diferentes cenários sugere
uma contribuição nítida do vento NW para o desenvolvimento do
afloramento costeiro na região de Aveiro durante o Verão, com menores
temperaturas e maiores concentrações de clorofila a junto à costa. O
contributo da maré é mínimo em relação ao vento.
Foram usadas para complementar o estudo, imagens SeaWiFS da região de
Aveiro durante o período de Primavera e Verão de 2001 a 2003 obtidas pela
Universidade dos Açores. Através da análise das imagens foi possível
identificar padrões complexos da distribuição em mesoscala de pigmentos
fitoplanctónicos, dinamicamente associados à ocorrência de afloramento
costeiro.
Tanto os dados do modelo como as imagens satélite demonstram: variações
térmicas de superfície são na ordem dos 2.0ºC, com as menores
temperaturas a ocorrer junto à costa (15.5ºC); as concentrações de Clorofila
a são máximas (3.5 mgCloa.m-3) junto à costa e mínimas ao largo (0.5
mgCloa.m-3). O modelo simula também a forte deplecção de nitratos à
superfície apresentando valores máximos (14 mmol N. m-3) junto ao fundo.
Este trabalho salienta a importância dos estudos multidisciplinares com
utilização de metodologias distintas (modelo e dados de satélites) para um
melhor conhecimento dos fenómenos de afloramento costeiro.Coastal upwelling is one of the most important hydrodynamic processes that
occur in Portuguese coasts between April and October. This process is
induced by the wind when it blows parallel to the Portuguese coast and
towards the south, promoting the upwelling of cold waters rich in nutrients.
The main objective of this work is to characterize qualitatively the summer
coastal upwelling near the Aveiro region, by using a 3D Ecological model
(COHERENS) and SeaSTAR satellite (sensor SeaWiFS) images.
This model was initialized with biological, chemical and physical data and was
forced with meteorological data obtained at meteorology station at the
University of Aveiro. Three scenarios were studied: with wind effect (without
tide); wind at a constant speed (5.2 m.s-1 from NW and from SW. Comparison
of the different scenarios suggest a strong contribution of the NW wind for the
development of summer coastal upwelling near the Aveiro region, with lower
temperatures and higher chlorophyll a concentrations near the coast.
Contribution of the tide is minimum compared with the one from the wind.
To complement the study, SeaWiFS images for the Aveiro region were used
during spring and summer months of 2001 to 2003 obtained at the University
of the Azores. Results show complex patterns of mesoscale distribution of
phytoplankton, dynamically linked to the occurrence of coastal upwelling.
The model and satellite images data demonstrate: temperature variation on
the surface of the order of 2.0ºC, with lower temperatures (15.5ºC) and
maximum chlorophyll a concentrations near the coast (3.5 mgChla.m-3).
Minimum chlorophyll a concentrations are found offshore (0.5 mgChla.m-3).
The model simulates also strong surface nitrate depletion with maximum
values found on the bottom (14 mmol N.m-3).
This work promotes the importance of multidisciplinary studies that use
different methodologies such as; modelling and satellite images data with the
purpose to better understand the hydrodynamic processes of coastal
upwelling
Investigating the molecular systematic relationships amongst selected Plesionika (Decapoda: Pandalidae) from the Northeast Atlantic and Mediterranean Sea
Despite the high number of species and ecological diversity of pandalid shrimps, there has been no previous attempt to resolve evolutionary relationships of several genera using molecular tools. Although mitochondrial DNA cytochrome oxidase I (COI) is widely used in barcoding studies to delimit species boundaries, additional insights into phylogenetic affinities can be obtained, especially when used in combination with data from additional genes. The knowledge of molecular diversity is essential to understand phylogenetic relationships and will help systematic clarifications. Based on partial fragments of the 16S and COI genes, we have focused specifically on addressing the systematic relationships of the economically and ecologically important shrimp genus Plesionika within a framework of five genera from within the Pandalidae. Our results showed that species within Plesionika are substantially divergent when compared with other genera, exhibiting the highest average nucleotide divergence, with 0.1123 and 0.0846 in COI and 16S genes, respectively. In addition, sequence divergence was found to vary greatly within the genus Plesionika (COI/16S): 0.0247/0.0016 between Plesionika antigai and Plesionika heterocarpus and 0.1616/0.098 between Plesionika heterocarpus and Plesionika edwardsii. We did not find amino acid sequence divergence between P. heterocarpus and P. antigai compared with P. heterocarpus and P. edwardsii (8.10%, K2P distance). Three species of Plesionika (P. antigai, P. heterocarpus and Plesionika scopifera) appear well separated from other Plesionika species in both maximum likelihood and Bayesian analyses. The present study confirms the utility of COI over 16S as a genetic marker to resolve relationships between different species of Plesionika from the Northeast Atlantic and Mediterranean Sea, in addition to species delimitation. The findings highlight the need to further review paraphyly within Plesionika in an attempt to recognize a concordance in the evolutionary history of Plesionika with major ecological and geological events