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Percorrer por autor "Sim-Sim, Manuela"

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  • Building a Portuguese Coalition for Biodiversity Genomics
    Publication . Marques, João Pedro; ALVES, Paulo C; Rosário, Isabel Amorim do; Lopes, Ricardo J.; Moura, Mónica; Meyers, Gene; Sim-Sim, Manuela; Sousa-Santos, C.; Alves, M. Judite; Borges, Paulo A. V.; Brown, Thomas; Carneiro, Miguel; Carrapato, Carlos; Ceríaco, Luis; Ciofi Degli Atti, Claudio; Silva, Luís; Diedericks, Genevieve; Diroma, Maria Angela; Farelo, Liliana; Formenti, Giulio; Gil, Fátima; Grilo, Miguel; Ianucci, Alessio; Leitão, Henrique; Máguas, C.; Mc Cartney, Ann M.; Mendes, Sofia; Moreno, João; Morselli, Marco; Mouton, Alice; Natali, Chiara; Pereira, Fernando; Rego, Rúben; Resendes, Roberto; Roxo, Guilherme; Svardal, Hannes; Trindade, Helena; Vicente, Sara; Winkler, Sylke; Alvarenga, M.; Amaral, Andreia; Antunes, Agostinho; Campos, Paula; Canario, A. V. M.; Castilho, Rita; Castro, Luis Filipe; Crottini, Angelica; Cunha, Mónica; Espregueira Themudo, Gonçalo; Esteves, Pedro; Faria, Rui; Fernandes, Carlos; Ledoux, Jean-Baptiste; Louro, Bruno; Magalhães, Sara; OS, Paulo; Pearson, Gareth; Pimenta, João; Pina-Martins; Santos, Teresa; Serrao, Ester A; Melo-Ferreira, José; Sousa, Vítor
    The diverse physiography of the Portuguese land and marine territory, spanning from continental Europe to the Atlantic archipelagos, has made it an important repository of biodiversity throughout the Pleistocene glacial cycles, leading to a remarkable diversity of species and ecosystems. This rich biodiversity is under threat from anthropogenic drivers, such as climate change, invasive species, land use changes, overexploitation or pathogen (re)emergence. The inventory, characterization and study of biodiversity at inter- and intra-specific levels using genomics is crucial to promote its preservation and recovery by informing biodiversity conservation policies, management measures and research. The participation of researchers from Portuguese institutions in the European Reference Genome Atlas (ERGA) initiative, and its pilot effort to generate reference genomes for European biodiversity, has reinforced the establishment of Biogenome Portugal. This nascent institutional network will connect the national community of researchers in genomics. Here, we describe the Portuguese contribution to ERGA’s pilot effort, which will generate high-quality reference genomes of six species from Portugal that are endemic, iconic and/or endangered, and include plants, insects and vertebrates (fish, birds and mammals) from mainland Portugal or the Azores islands. In addition, we outline the objectives of Biogenome Portugal, which aims to (i) promote scientific collaboration, (ii) contribute to advanced training, (iii) stimulate the participation of institutions and researchers based in Portugal in international biodiversity genomics initiatives, and (iv) contribute to the transfer of knowledge to stakeholders and engaging the public to preserve biodiversity. This initiative will strengthen biodiversity genomics research in Portugal and fuel the genomic inventory of Portuguese eukaryotic species. Such efforts will be critical to the conservation of the country’s rich biodiversity and will contribute to ERGA’s goal of generating reference genomes for European species.
    2023Artigo científico Acesso aberto Ver mais
  • Climate threat on the Macaronesian endemic bryophyte flora
    Publication . Patiño, Jairo; Mateo, Rubén G.; Zanatta, Florian; Marquet, Adrien; Aranda, Silvia C.; Borges, Paulo A. V.; Dirkse, Gerard; Gabriel, Rosalina; Gonzalez-Mancebo, Juana M.; Guisan, Antoine; Muñoz, Jesús; Sim-Sim, Manuela; Vanderpoorten, Alain
    Oceanic islands are of fundamental importance for the conservation of biodiversity because they exhibit high endemism rates coupled with fast extinction rates. Nowhere in Europe is this pattern more conspicuous than in the Macaronesian biogeographic region. A large network of protected areas within the region has been developed, but the question of whether these areas will still be climatically suitable for the globally threatened endemic element in the coming decades remains open. Here, we make predictions on the fate of the Macaronesian endemic bryophyte flora in the context of ongoing climate change. The potential distribution of 35 Macaronesian endemic bryophyte species was assessed under present and future climate conditions using an ensemble modelling approach. Projections of the models under different climate change scenarios predicted an average decrease of suitable areas of 62–87% per species and a significant elevational increase by 2070, so that even the commonest species were predicted to fit either the Vulnerable or Endangered IUCN categories. Complete extinctions were foreseen for six of the studied Macaronesian endemic species. Given the uncertainty regarding the capacity of endemic species to track areas of suitable climate within and outside the islands, active management associated to an effective monitoring program is suggested.
    2016-07Artigo científico Acesso aberto Ver mais
  • Climate-driven vicariance and long-distance dispersal explain the Rand Flora pattern in the liverwort Exormotheca pustulosa (Marchantiophyta)
    Publication . Rodrigues, Ana S. B.; Martins, Anabela; Garcia, César Augusto; Sérgio, Cecília; Porley, Ron; Fontinha, Susana; González-Mancebo, Juana M.; Gabriel, Rosalina; Phephu, Nonkululo; Van Roy, Jacques; Dirkse, Gerard; Long, David; Stech, Michael; Patiño, Jairo; Sim-Sim, Manuela
    The ‘Rand flora’ is a biogeographical disjunction which refers to plant lineages occurring at the margins of the African continent and neighbouring oceanic archipelagos. Here, we tested whether the phylogeographical pattern of Exormotheca pustulosa Mitt. was the result of vicariance induced by past climatic changes or the outcome of a series of recent long-distance dispersal events. Two chloroplast markers (rps4-trnF region and psbA-trnH spacer) and one nuclear marker (ITS2) were analysed. Phylogenetic and phylogeographical relationships were inferred as well as divergence time estimates and ancestral areas. Exormotheca possibly originated in Eastern Africa during the Late Oligocene/Early Miocene while Exormotheca putulosa diversified during the Late Miocene. Three main E. pustulosa groups were found: the northern Macaronesia/Western Mediterranean, the South Africa/Saint Helena and the Cape Verde groups. The major splits among these groups occurred during the Late Miocene/Pliocene; diversification was recent, dating back to the Pleistocene. Climate-driven vicariance and subsequent long-distance dispersal events may have shaped the current disjunct distribution of E. pustulosa that corresponds to the Rand Flora pattern. Colonization of Macaronesia seems to have occurred twice by two independent lineages. The evolutionary history of E. pustulosa populations of Cape Verde warrants further study.
    2020-06Artigo científico Acesso restrito Ver mais
  • A comparison of bryophyte diversity in the Macaronesian Islands: island versus habitat approach
    Publication . González-Mancebo, Juana M.; Gabriel, Rosalina; Otto, Rüdiger; Sim-Sim, Manuela; Luís, Leena Margarida; Sérgio, Cecília; Garzón-Machado, Víctor; Aranda, Silvia C.; Capelo, Jorge; Vanderpoorten, Alain
    In this paper, we present a comparison of richness patterns and floristic similarity for bryophytes in the five most important altitudinal habitat types in the Macaronesian islands. We evaluate the importance of different factors discussed in the literature in predicting species diversity applying the traditional island approach and within the framework of the new habitat approach, including area, isolation, climatic factors, geological age and human influence. From the analysis of patterns of bryophyte species distribution for selected habitats across islands and archipelagos, we specifically test the hypothesis that (i) floristic similarity is primarily determined by climatic factors, but not by geographical distance due to high dispersal ability in this species group and (ii) bryophyte richness is best predicted by area, but not by geological age of the habitat due to very low endemicity or speciation rate and high colonization rate.
    2013-12Documento de conferência Acesso aberto Ver mais
  • Explaining the «anomalous» distribution of Echinodium Jur. (Bryopsida) : independent evolution in Macaronesia and Australasia
    Publication . Stech, Michael; Sim-Sim, Manuela; Esquível, M. Glória; Fontinha, Susana; Tangney, Ray; Lobo, Carlos; Gabriel, Rosalina; Quandt, Dietmar
    The peculiar disjunction between Macaronesia and Australasia of the morphologically isolated pleurocarpous moss genus Echinodium is one of the most prominent questions in bryology. Echinodium as traditionally circumscribed comprises six extant species, four restricted to the Macaronesian archipelagos and two confined to the Australasian/Pacific regions. Molecular phylogenetic analyses based on plastid trnLUAA intron and nuclear ribosomal ITS sequences indicate that Echinodium is polyphyletic and split into three groups. Three of the four Macaronesian species (E. spinosum and the single island endemics E. renauldii and E. setigerum) are closely related to each other and treated as Echinodium s.str. (Echinodiaceae). Further clarification of the relationships of Echinodium s.str. with Orthostichella, a segregate of Lembophyllaceae, is needed. The remaining Macaronesian species, E. prolixum, is transferred to Isothecium (Lembophyllaceae); this systematic position is also strongly supported by leaf characters. The two Australasian species, E. hispidum and E. umbrosum, are molecularly unrelated to the Macaronesian species and are transferred to Thamnobryum in the Neckeraceae. While the molecular data suggest that the peculiar distribution pattern of ‘Echinodium’ is an artefact, the striking morphological similarity observed in Macaronesian and Australasian species cannot be dismissed. Possible explanations are: (i) parallel morphological evolution of the ‘Echinodium habit’ in Macaronesia and Australasia, or (ii) retention of a set of plesiomorphic characters in non-related groups in relict habitats, the Macaronesian laurel forest and the austral temperate rain forests, respectively. Of these hypotheses, the evolutionary parallelism hypothesis seems more plausible for several reasons, which are discussed.
    2008-10-31Artigo científico Acesso aberto Ver mais
  • The moss Homalothecium mandonii as a model for assessing bryophyte response to climate change in Macaronesia
    Publication . Vanderpoorten, Alain; Mateo, Rúben G.; Sim-Sim, Manuela; Ruas, Sara; Dirkse, Gerard; Gabriel, Rosalina; Borges, Paulo A. V.; González-Mancebo, Juana M.; Calvo, Silvia; Patiño, Jairo
    Os briófitos possuem características ecofisiológicas e biológicas únicas que os tornam excelentes indicadores das alterações climáticas. Com o auxílio de modelos de nicho ecológico, analisou-se em que medida as alterações climáticas podem afectar a brioflora endémica da Macaronésia, em particular o musgo Homalothecium mandonii. A projecção do nicho actual desta espécie sobre as camadas macroclimáticas da última glaciação máxima, indicam que a área de distribuição da espécie seria superior em cerca de 200% relativamente à área actual. As projecções paleoclimáticas identificam ainda que a região noroeste de África e a Península Ibérica possuem condições climáticas favoráveis ao desenvolvimento desta espécie, sugerindo que se poderá tratar de um paleoendemismo. Em conformidade com observações prévias, os resultados obtidos sugerem que a Macaronésia representa um refúgio para as espécies actualmente extintas de zonas continentais. No entanto, as projecções do nicho climático da espécie para o futuro, predizem um declínio da área favorável de 29-53% em 2080. Tais predicções sugerem então que o papel de refúgio climático que a Macaronésia tem desempenhado se encontra fortemente ameaçado como resultado das alterações climáticas em curso.
    2014Artigo científico Acesso aberto Ver mais
  • Observations on Riccia sorocarpa Bisch. subsp. erythrophora R.M.Schust. ex Konstant. & L.Söderstr. and its occurrence in Portugal and the Azores
    Publication . Sérgio, Cecília; Gabriel, Rosalina; Sim-Sim, Manuela; Martins, Anabela; Porley, Ron; Garcia, César Augusto
    INTRODUCTION: Recent bryological research in Portugal has revealed the occurrence of a littleknown segregate of the Riccia sorocarpa group, representing the first record for mainland Portugal and the Azores of Riccia sorocarpa Bisch. subsp. erythrophora R.M.Schust. ex Konstant. & L.Söderstr. New data are presented on the taxonomy and phytogeography of this globally rare taxon. METHODS: A revision of approximately 200 samples of Riccia sorocarpa s.l. from selected Portuguese herbaria, together with some recent field collections, was carried out, based on the results of light and scanning electron microscopy. KEY RESULTS AND CONCLUSIONS: Our findings confirm that Riccia sorocarpa subsp. erythrophora is a distinct subspecies, and show that morphological differences of the thallus, primarily the violet-red purple bases of the ventral scales, are the most important characters for its delimitation. Scanning electron micrographs of spores of this taxon are presented for the first time. Phytogeographically, our data significantly extend the known distribution of the subspecies.
    2022-08Artigo científico Acesso aberto Ver mais
  • Stone-stacking as a looming threat to rock-dwelling biodiversity
    Publication . Rocha, Ricardo; Borges, Paulo A. V.; Cardoso, Pedro; Kusrini, Mirza D.; Martín-Esquivel, José L.; Menezes, Dilia; Ferreira, Mário Mota; Nunes, Sara F.; Órfão, Inês; Gonçalves, Catarina Serra; Sim-Sim, Manuela; Sepúlveda, Pedro; Teixeira, Dinarte; Traveset, Anna
    This letter to the editor describes the surge of “photo-friendly” stacks of stones as an emerging tourism-associated threat to rock-dwelling biodiversity.
    2020Artigo científico Acesso aberto Ver mais
  • Terrestrial and freshwater biodiversity of the Madeira and Selvagens archipelagos
    Publication . Borges, Paulo A. V.; Abreu, Cristina; Aguiar, António F.; Carvalho, Palmira; Fontinha, Susana; Jardim, Roberto; Melo, Ireneia; Oliveira, Paulo; Sequeira, Miguel M.; Sérgio, Cecília; Serrano, Artur R. M.; Sim-Sim, Manuela; Vieira, Paulo
    As ilhas atlânticas dos Açores, Madeira, Selvagens, Canárias e Cabo Verde constituem uma das regiões da Europa mais ricas em diversidade de fungos, plantas e animais. Desde 2004 que a inventariação detalhada da diversidade destas ilhas tem sido um dos principais objectivos dos projectos ATLÂNTICO e BIONATURA (incluídos no projecto EU INTERREG IIIB). Este livro é a mais recente contribuição destes projectos, apresentando uma lista de todos os fungos, flora e fauna terrestre conhecida, incluindo a dulçaquícola, para dois arquipélagos atlânticos (Madeira e Selvagens). A lista abrange o arquipélago da Madeira, constituído por duas ilhas de maiores dimensões (Madeira e Porto Santo) e três pequenas, cujo conjunto constitui as Desertas (Ilhéu Chão, Deserta Grande e Bugio), e ainda o arquipélago das Selvagens, formado por duas pequenas ilhas (Selvagem Grande e Selvagem Pequena) e um ilhéu (Ilhéu de Fora).
    2008Capítulo de livro Acesso aberto Ver mais
  • The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics
    Publication . Mc Cartney, Ann M.; Formenti, Giulio; Mouton, Alice; De Panis, Diego; Marins, Luísa S.; Leitão, Henrique G.; Diedericks, Genevieve; Kirangwa, Joseph; Morselli, Marco; Salces-Ortiz, Judit; Escudero, Nuria; Iannucci, Alessio; Natali, Chiara; Svardal, Hannes; Fernández, Rosa; De Pooter, Tim; Joris, Geert; Strazisar, Mojca; Wood, Jonathan M. D.; Herron, Katie E.; Seehausen, Ole; Watts, Phillip C.; Shaw, Felix; Davey, Robert P.; Minotto, Alice; Fernández, José M.; Böhne, Astrid; Alegria, Carla; Alioto, Tyler; Alves, Paulo C.; Amorim, Isabel R.; Aury, Jean-Marc; Backstrom, Niclas; Baldrian, Petr; Baltrunaite, Laima; Barta, Endre; BedHom, Bertrand; Belser, Caroline; Bergsten, Johannes; Bertrand, Laurie; Bilandija, Helena; Binzer-Panchal, Mahesh; Bista, Iliana; Blaxter, Mark; Borges, Paulo A. V.; Dias, Guilherme Borges; Bosse, Mirte; Brown, Tom; Bruggmann, Rémy; Buena-Atienza, Elena; Burgin, Josephine; Buzan, Elena; Cariani, Alessia; Casadei, Nicolas; Chiara, Matteo; Chozas, Sergio; Čiampor, Fedor; Crottini, Angelica; Cruaud, Corinne; Cruz, Fernando; Dalen, Love; De Biase, Alessio; del Campo, Javier; Delic, Teo; Dennis, Alice B.; Derks, Martijn F. L.; Diroma, Maria Angela; Djan, Mihajla; Duprat, Simone; Eleftheriadi, Klara; Feulner, Philine G. D.; Flot, Jean-François; Forni, Giobbe; Fosso, Bruno; Fournier, Pascal; Fournier-Chambrillon, Christine; Gabaldon, Toni; Garg, Shilpa; Gissi, Carmela; Giupponi, Luca; Gomez-Garrido, Jessica; González, Josefa; Grilo, Miguel L.; Grüning, Björn; Guerin, Thomas; Guiglielmoni, Nadege; Gut, Marta; Haesler, Marcel P.; Hahn, Christoph; Halpern, Balint; Harrison, Peter W.; Heintz, Julia; Hindrikson, Maris; Höglund, Jacob; Howe, Kerstin; Hughes, Graham M.; Istace, Benjamin; Cock, Mark J.; Janžekovič, Franc; Jonsson, Zophonias O.; Joye-Dind, Sagane; Koskimäki, Janne J.; Krystufek, Boris; Kubacka, Justyna; Kuhl, Heiner; Kusza, Szilvia; Labadie, Karine; Lähteenaro, Meri; Lantz, Henrik; Lavrinienko, Anton; Leclère, Lucas; Lopes, Ricardo Jorge; Madsen, Ole; Magdelenat, Ghislaine; Magoga, Giulia; Manousaki, Tereza; Mappes, Tapio; Marques, Joao Pedro; Redondo, Gemma I. Martinez; Maumus, Florian; McCarthy, Shane A.; Megens, Hendrik-Jan; Melo-Ferreira, Jose; Mendes, Sofia L.; Montagna, Matteo; Moreno, Joao; Mosbech, Mai-Britt; Moura, Mónica; Musilova, Zuzana; Myers, Eugene; Nash, Will J.; Nater, Alexander; Nicholson, Pamela; Niell, Manuel; Nijland, Reindert; Noel, Benjamin; Noren, Karin; Oliveira, Pedro H.; Olsen, Remi-Andre; Ometto, Lino; Oomen, Rebekah A.; Ossowski, Stephan; Palinauskas, Vaidas; Palsson, Snaebjorn; Panibe, Jerome P.; Pauperio, Joana; Pavlek, Martina; Payen, Emilie; Pawlowska, Julia; Pellicer, Jaume; Pesole, Graziano; Pimenta, Joao; Pippel, Martin; Pirttilä, Anna Maria; Poulakakis, Nikos; Rajan, Jeena; M.C. Rego, Rúben; Resendes, Roberto; Resl, Philipp; Riesgo, Ana; Rodin-Morch, Patrik; Soares, Andre E. R.; Fernandes, Carlos Rodriguez; Romeiras, Maria M.; Roxo, Guilherme; Rüber, Lukas; Ruiz-Lopez, Maria Jose; Saarma, Urmas; da Silva, Luis P.; Sim-Sim, Manuela; Soler, Lucile; Sousa, Vitor C.; Santos, Carla Sousa; Spada, Alberto; Stefanovic, Milomir; Steger, Viktor; Stiller, Josefin; Stöck, Matthias; Struck, Torsten H.; Sudasinghe, Hiranya; Tapanainen, Riikka; Tellgren-Roth, Christian; Trindade, Helena; Tukalenko, Yevhen; Urso, Ilenia; Vacherie, Benoit; Van Belleghem, Steven M.; Van Oers, Kees; Vargas-Chavez, Carlos; Velickovic, Nevena; Vella, Noel; Vella, Adriana; Vernesi, Cristiano; Vicente, Sara; Villa, Sara; Pettersson, Olga Vinnere; Volckaert, Filip A. M.; Voros, Judit; Wincker, Patrick; Winkler, Sylke; Ciofi, Claudio; Waterhouse, Robert M.; Mazzoni, Camila J.
    A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.
    2024Artigo científico Acesso aberto Ver mais