Browsing by Author "Afonso, Carlos"
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- Chromosome-level genome of the venomous snail Kalloconus canariensis: a valuable model for venomics and comparative genomicsPublication . Herráez-Pérez, Ana; Pardos-Blas, José Ramón; Afonso, Carlos; Tenorio, Manuel J; Zardoya, RafaelBackground: Genomes are powerful resources to understand the evolutionary mechanisms underpinning the origin and diversification of the venoms of cone snails (Conidae: Caenogastropoda) and could aid in the development of novel drugs. Findings: Here, we used PacBio continuous long reads and Omni-C data to assemble the chromosome-level genome of Kalloconus canariensis, a vermivorous cone endemic to the Canary Islands. The final genome size was 2.87 Gb, with a N50 of 79.75 Mb and 91% of the reads located into the 35 largest scaffolds. Up to 55.80% of the genome was annotated as repetitive regions, being class I of transposable elements (16.65%) predominant. The annotation estimated 34,287 gene models. Comparative analysis of this genome with the 2 cone snail genomes released to date (Dendroconus betulinus and Lautoconus ventricosus) revealed similar genome sizes and organization, although chromosome sizes tended to be shorter in K. canariensis. Phylogenetic relationships within subclass Caenogastropoda were recovered with strong statistical support. The family Conidae was recovered as a clade, with K. canariensis plus L. ventricosus sister to D. betulinus. Conclusions: Despite the great diversity of cone snails ( >900 species) and their venoms (hundreds of peptides per species), only 2 recently reported genomes are available for the group. The high-quality chromosome-level assembly of K. canariensis will be a valuable reference for studying the origin and evolution of conotoxin genes as well as whole-genome duplication events during gastropod evolution.
- Co-design of a marine protected area zoning and the lessons learned from itPublication . e Costa, Horta; Guimarães, M. Helena; Rangel, Mafalda; Ressurreição, Adriana; Monteiro, Pedro; Oliveira, Frederico; Bentes, Luis; Sales Henriques, Nuno; Sousa, Inês; Alexandre, Sofia; Pontes, João; Afonso, Carlos; Belackova, Adela; Marçalo, Ana; Cardoso-Andrade, Mariana; Correia, António José; Lobo, Vanda; Gonçalves, Emanuel J.; Pitta e Cunha, Tiago; Gonçalves, Jorge Manuel SantosMarine Protected Areas (MPAs) are a tool to safeguard marine natural systems, yet their effectiveness depends on how well they are integrated into the existing socioeconomic context. Stakeholder engagement in MPA design can contribute to increasing integration. This study focuses on the co-design of an MPA between researchers, public administration, the private sector, and non-governmental organizations. The proposed MPA is in Portugal and includes an area that is a hotspot for biodiversity and economic activities. This is the first MPA proposal in mainland Portugal co-designed using a participatory approach. This study highlights the steps of the zoning process and synthesizes the eight main lessons learned, useful for other cases, particularly for relatively small coastal MPAs with multiple socioeconomic activities. Three zoning proposals were developed and discussed within the participatory process. The proposals considered the best scientific and local knowledge available and were defined using ecological, socioeconomic, and shape-area guiding principles. In an iterative manner and following a participatory approach, compromises with stakeholders were achieved, and a final proposal, scientifically sound and socially accepted by most stakeholders, was delivered to the government. The final zoning plan will achieve ambitious conservation goals, including the largest fully protected area to be declared in mainland Portugal, while minimizing the impacts on the existing economic activities and promoting its sustainability. This process resulted in valuable lessons that may be applied elsewhere and guide future MPA implementation or rezoning of existing ones. These transdisciplinary and participatory processes can be time and resource-consuming but are vital for ensuring MPA effectiveness.
- Comparative transcriptomics of the venoms of continental and insular radiations of West African conesPublication . Abalde, Samuel; Tenorio, Manuel J.; Afonso, Carlos; Zardoya, RafaelThe transcriptomes of the venom glands of 13 closely related species of vermivorous cones endemic to West Africa from generaAfriconusandVarioconuswere sequenced and venom repertoires compared within a phylogenetic framework using oneKalloconusspecies as outgroup. The total number of conotoxin precursors per species varied between 108 and 221. Individuals of the same species shared about one-fourth of the total conotoxin precursors. The number of common sequences was drastically reduced in the pairwise comparisons between closely related species, and the phylogenetical signal was totally eroded at the inter-generic level (no sequence was identified as shared derived), due to the intrinsic high variability of these secreted peptides. A common set of four conotoxin precursor superfamilies (T, O1, O2 and M) was expanded in all studied cone species, and thus, they are considered the basic venom toolkit for hunting and defense in the West African vermivorous cone snails. Maximum-likelihood ancestral character reconstructions inferred shared conotoxin precursors preferentially at internal nodes close to the tips of the phylogeny (between individuals and between closely related species) as well as in the common ancestor ofVarioconus. Besides the common toolkit, the two genera showed significantly distinct catalogues of conotoxin precursors in terms of type of superfamilies present and the abundance of members per superfamily, but had similar relative expression levels indicating functional convergence. Differential expression comparisons between vermivorous and piscivorous cones highlighted the importance of the A and S superfamilies for fish hunting and defense.
- Conotoxin diversity in Chelyconus ermineus (Born, 1778) and the convergent origin of Piscivory in the Atlantic and Indo-Pacific conesPublication . Abalde, Samuel; Tenorio, Manuel J.; Afonso, Carlos; Zardoya, RafaelThe transcriptome of the venom duct of the Atlantic piscivorous cone species Chelyconus ermineus (Born, 1778) was determined. The venom repertoire of this species includes at least 378 conotoxin precursors, which could be ascribed to 33 known and 22 new (unassigned) protein superfamilies, respectively. Most abundant superfamilies were T, W, O1, M, O2, and Z, accounting for 57% of all detected diversity. A total of three individuals were sequenced showing considerable intraspecific variation: each individual had many exclusive conotoxin precursors, and only 20% of all inferred mature peptides were common to all individuals. Three different regions (distal, medium, and proximal with respect to the venom bulb) of the venom duct were analyzed independently. Diversity (in terms of number of distinct members) of conotoxin precursor superfamilies increased toward the distal region whereas transcripts detected toward the proximal region showed higher expression levels. Only the superfamilies A and I3 showed statistically significant differential expression across regions of the venom duct. Sequences belonging to the alpha (motor cabal) and kappa (lightning-strike cabal) subfamilies of the superfamily A were mainly detected in the proximal region of the venom duct. The mature peptides of the alpha subfamily had the α4/4 cysteine spacing pattern, which has been shown to selectively target muscle nicotinic-acetylcholine receptors, ultimately producing paralysis. This function is performed by mature peptides having a α3/5 cysteine spacing pattern in piscivorous cone species from the Indo-Pacific region, thereby supporting a convergent evolution of piscivory in cones.
- Engaging and legitimizing communities: co-designing a community-based marine protected areaPublication . Rangel, Mafalda; Horta e Costa, Barbara; Guimarães, Mª Helena; Ressurreição, Adriana; Monteiro, Pedro; Oliveira, Frederico; Bentes, Luis; Sales Henriques, Nuno; Sousa, Inês; Ferreira Alexandre, Teresa Sofia; Pontes, João; Afonso, Carlos; Belackova, Adela; Marçalo, Ana; Cardoso-Andrade, Mariana; Cortês, António; Correia, António José; Lobo, Vanda; Gonçalves, Emanuel J.; Cunha, Tiago Pitta e; Gonçalves, Jorge Manuel SantosMarine Protected Areas are increasingly used as tools to preserve marine habitats and biodiversity worldwide. Nonetheless, creating MPAs in densely populated multi-use coastal areas comes with intrinsic conflict potential, since protection and economic development are not always hand-in-hand and local users might disagree with the designation of such conservation tools. The use of inclusive and transparent participatory processes to co-design such MPAs can be seen as a way of protecting biodiversity while acknowledging the needs of local users and building conservation tools that fit both purposes. Here we describe a participatory process developed to codesign a Marine Protected Area of Community Interest in a biodiversity, fishing and tourism hotspot in the Algarve (southern Portugal) where the majority of involved stakeholders (96 %) endorsed the final MPA proposal. The methodology and tools used are described in detail, lessons learned are critically analysed and a roadmap to be used in other realities is provided. Evidences collected show that the approach developed allows conservation and economic activities to share the same ground and advocate for the same goals in preserving coastal marine habitats.
- First record of Ocinebrina nicolai (Mollusca: Gastropoda: Muricidae: Ocenebrinae) in North-Eastern Atlantic watersPublication . Afonso, Carlos; Bonomolo, Giuseppe; Monteiro, Pedro; Bentes, Luis; Oliveira, Frederico; Veiga, Pedro; Rangel, Mafalda; Sousa, Inês; Leite, Laura; Gonçalves, J. M. S.Ocinebrina nicolai Monterosato, 1884 a marine mollusc belonging to the Muricidae family is reported from Algarve, south coast of Portugal for the first time and is a new record for the biodiversity of the Portuguese malacological fauna and northeastern Atlantic waters. This species with a medium-size shell for the genus (14–16 mm) was initially sampled during a baseline project that studied marine biotopes in the central Algarve region. This short note presents a brief diagnosis of the species, provides local information on geographical distribution, habitat, and compares it with other congeneric species found in Portugal: Ocinebrina aciculata (Lamarck, 1822) and Ocinebrina edwardsii (Payraudeau, 1826).
- Hidden species diversity and mito-nuclear discordance within the Mediterranean cone snail, Lautoconus ventricosusPublication . Abalde, Samuel; Crocetta, Fabio; Tenorio, Manuel J.; D'Aniello, Salvatore; Fassio, Giulia; Rodríguez-Flores, Paula C.; Uribe, Juan E.; Afonso, Carlos; Oliverio, Marco; Zardoya, RafaelThe Mediterranean cone snail, Lautoconus ventricosus, is currently considered a single species inhabiting the whole Mediterranean basin and the adjacent Atlantic coasts. Yet, no population genetic study has assessed its taxonomic status. Here, we collected 245 individuals from 75 localities throughout the Mediterranean Sea and used cox1 barcodes, complete mitochondrial genomes, and genome skims to test whether L. ventricosus represents a complex of cryptic species. The maximum likelihood phylogeny based on complete mitochondrial genomes recovered six main clades (hereby named blue, brown, green, orange, red, and violet) with sufficient sequence divergence to be considered putative species. On the other hand, phylogenomic analyses based on 437 nuclear genes only recovered four out of the six clades: blue and orange clades were thoroughly mixed and the brown one was not recovered. This mito-nuclear discordance revealed instances of incomplete lineage sorting and introgression, and may have caused important differences in the dating of main cladogenetic events. Species delimitation tests proposed the existence of at least three species: green, violet, and red + blue + orange (i.e., cyan). Green plus cyan (with sympatric distributions) and violet, had West and East Mediterranean distributions, respectively, mostly separated by the Siculo-Tunisian biogeographical barrier. Morphometric analyses of the shell using species hypotheses as factor and shell length as covariate showed that the discrimination power of the studied parameters was only 70.2%, reinforcing the cryptic nature of the uncovered species, and the importance of integrative taxonomic approaches considering morphology, ecology, biogeography, and mitochondrial and nuclear population genetic variation.
- Macroinvertebrates associated with macroalgae within integrated multi-trophic aquaculture (IMTA) in earthen ponds: potential for accessory productionPublication . Vieira, Rafael; Mateus, Miguel; Afonso, Carlos; Soares, Florbela; Pousão-Ferreira, Pedro; Gamito, SofiaThe present work aims to evaluate the macroinvertebrate community associated with macroalgae in earthen pond systems to better understand their potential in detritus recycling and as an accessory production. Sampling took place on the settling pond of an aquaculture research station, where macroalgae permanently occurred at high densities. The results suggest differentiation between seasons but not between sites within the settling pond. Seasonal variation was observable in terms of macroinvertebrate density, biomass, and diversity. Two non-indigenous species of invertebrates were found, the crustaceans Grandidierella japonica and Paracerceis sculpta Amphipods were the most abundant group, and their high nutritional value can be exploited. Detritus and the epiphyte layer are the main food items for the invertebrates, reinforcing the advantages of these organisms being present to enhance the recycling of excess detritus and to transfer organic matter to upper trophic levels. These species, naturally present in aquaculture facilities, can improve the water quality and increase the variability of food nutrients for reared species.
- Marxan as a zoning tool for development and economic purposed areas - Aquaculture Management Areas (AMAs)Publication . Sales Henriques, Nuno; Monteiro, Pedro; Bentes, Luis; Oliveira, Frederico; Afonso, Carlos; Gonçalves, Jorge Manuel SantosThe increased number of human activities within the marine environment and the demand for maritime space has increased to a point where in some parts of the globe the demand for maritime space has exceeded the available area. The overlapping objectives and activities have caused severe conflicts among users and with the natural marine environment itself. For that reason, holistic strategies such as Ecosystem Based Management (EBM) and Maritime Spatial Planning (MSP) have been evolved and developed to sustainably manage the marine environment, avoiding conflicts and creating synergies. Spatial analysis tools like Marxan have been used for several years as decision support tools mostly for conservation plans, such as design and establishment of protected areas. In this study we approach the potential of this tool with a different purpose in mind: instead of using the available information of the region for the development of a conservation plan, we used this tool and the available information to select areas to establish Aquaculture Management Areas (AMAs). We also intended to analyse how the existing features of the region would affect the final result of a spatial plan aimed to establish areas for economic and development purposes. We conclude that the use of Marxan can be advantageous to support the planning and development of coastal regions, not only in a conservationist point of view (as it has been mostly used), but also into a developing and economic driven approach. This tool can be particularly useful in regions or situations where there is a large number of stakeholders, ecological and geographical features that could potentially conflict with the establishment, the management and the success of the proposed management areas. (C) 2017 Elsevier Ltd. All rights reserved.
- Mitogenomic phylogeny of cone snails endemic to SenegalPublication . Abalde, Samuel; Tenorio, Manuel J.; Afonso, Carlos; Zardoya, RafaelCone snails attain in Senegal one of their highest peaks of species diversity throughout the continental coast of Western Africa. A total of 15 endemic species have been described, all placed in the genus Lautoconus. While there is ample data regarding the morphology of the shell and the radular tooth of these species, virtually nothing is known regarding the genetic diversity and phylogenetic relationships of one of the most endangered groups of cones. In this work, we determined the complete or near complete (only lacking the control region) mitochondrial (mt) genomes of 17 specimens representing 11 endemic species (Lautoconus belairensis, Lautoconus bruguieresi, Lautoconus cacao, Lautoconus cloveri, Lautoconus cf. echinophilus, Lautoconus guinaicus, Lautoconus hybridus, Lautoconus senegalensis, Lautoconus mercator, Lautoconus taslei, and Lautoconus unifasciatus). We also sequenced the complete mt genome of Lautoconus guanche from the Canary Islands, which has been related to the cones endemic to Senegal. All mt genomes share the same gene arrangement, which conforms to the consensus reported for Conidae, Neogastropoda and Caenogastropoda. Phylogenetic analyses using probabilistic methods recovered three major lineages, whose divergence coincided in time with sea level and ocean current changes as well as temperature fluctuations during the Messinian salinity crisis and the PlioPleistocene transition. Furthermore, the three lineages corresponded to distinct types of radular tooth (robust, small, and elongated), suggesting that dietary specialization could be an additional evolutionary driver in the diversification of the cones endemic to Senegal. The reconstructed phylogeny showed several cases of phenotypic convergence (cryptic species) and questions the validity of some species (ecotypes or phenotypic plasticity), both results having important taxonomic and conservation consequences. (C) 2017 Elsevier Inc. All rights reserved.