Browsing by Author "Alberto, Filipe"
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- Deep reefs are climatic refugia for genetic diversity of marine forestsPublication . Assis, J.; Coelho, Nelson Castilho; Lamy, Thomas; Valero, Myriam; Alberto, Filipe; Serrão, EsterAimPast climate-driven range shifts shaped intraspecific diversities of species world-wide. Earlier studies, focused on glacial refugia, might have overlooked genetic erosion at lower latitudes associated with warmer periods. For marine species able to colonize deeper waters, depth shifts might be important for local persistence, preventing some latitudinal shifts, analogous to elevational refugia in terrestrial habitats. In this study, we asked whether past latitudinal or depth range shifts explain extant gene pools in Saccorhiza polyschides, a large habitat structuring brown alga distributed from coastal to offshore deep reefs.LocationNorth-east Atlantic and western Mediterranean basin.MethodsGenetic structure and diversity were inferred using seven microsatellite loci, for 27 sites throughout the entire distributional range. Ecological niche modelling (ENM) was performed with and without information about genetic structure (sub-taxon niche structure) to predict distributions for the Last Glacial Maximum (LGM), the warmer Mid-Holocene (MH) and the present.ResultsBoth ENM approaches predicted a wider potential distribution in deeper waters than is presently known, a post-glacial expansion to northern shores and the extirpation of southern edges during the warmer MH. Genetic data corroborated range dynamics, revealing three major genetic groups with current boundaries in the Bay of Biscay and the Lisbon coastal region, pinpointing ancient refugial origins. Despite extensive southern range contraction, the southernmost warmer regions are still the richest in genetic diversity, indicating long-term persistence of large populations. ENMs suggested that this could only have been possible due to stable refugia in deeper reefs.Main conclusionsThe global distribution of gene pools of temperate marine forests is explained by past range shifts that structured both latitudinal glacial refugia and depth refugia during warmer periods. Deep rear edge populations play a fundamental role during periods of extreme climate, allowing persistence and retaining some of the largest genetic diversity pools of the species' distribution.
- Disentangling the Influence of Mutation and Migration in Clonal Seagrasses Using the Genetic Diversity Spectrum for MicrosatellitesPublication . ARNAUD-HAOND, Sophie; Moalic, Yann; Hernandez-Garcia, Emilio; Eguíluz, Víctor M.; Alberto, Filipe; Serrao, Ester A.; Duarte, Carlos M.The recurrent lack of isolation by distance reported at regional scale in seagrass species was recently suggested to stem from stochastic events of large-scale dispersal. We explored the usefulness of phylogenetic information contained in microsatellite loci to test this hypothesis by using the Genetic Diversity Spectrum (GDS) on databases containing, respectively, 7 and 9 microsatellites genotypes for 1541 sampling units of Posidonia oceanica and 1647 of Cymodocea nodosa. The simultaneous increase of microsatellite and geographic distances that emerges reveals a coherent pattern of isolation by distance in contrast to the chaotic pattern previously described using allele frequencies, in particular, for the long-lived P. oceanica. These results suggest that the lack of isolation by distance, rather than the resulting from rare events of large-scale dispersal, reflects at least for some species a stronger influence of mutation over migration at the scale of the distribution range. The global distribution of genetic polymorphism may, therefore, result predominantly from ancient events of step-by-step (re) colonization followed by local recruitment and clonal growth, rather than contemporary gene flow. The analysis of GDS appears useful to unravel the evolutionary forces influencing the dynamics and evolution at distinct temporal and spatial scales by accounting for phylogenetic information borne by microsatellites, under an appropriate mutation model. This finding adds nuance to the generalization of the influence of large-scale dispersal on the dynamics of seagrasses.
- Dispersal, sex ad clonality in the marine environment: population genetic structure of the seagrass Cymodocea nodosa on Mediterranean and Atlantic coastsPublication . Alberto, Filipe; Serrão, Ester; Duarte, Carlos M.As angióspermicas marinhas, vulgarmente denominadas ervas marinhas, são um grupo de monocotiledóneas que crescem nas águas costeiras e ambientes estuarinos de todos os mares do mundo com a excepção da Antártida. Todas as ervas marinhas apresentam um crescimento populacional que depende do balanço entre reprodução sexuada e crescimento clonal. A espécie modelo desta tese, a erva marinha Cymodocea nodosa, é uma planta dióica caracterizada por um crescimento clonal rápido e produção de sementes posicionadas junto ao rizoma materno. A espécie apresenta uma distribuição geográfica repartida pela bacia Mediterrânica e Atlântico Norte, desde o estuário do Sado até ao banco de Arguin na Mauritânia, assim como no Arquipélago Canário e ilha da Madeira. O âmbito desta tese é o estudo da genética populacional desta planta clonal através da análise de marcadores microsatéllites que são aqui inicialmente caracterizados. Estas ferramentas foram utilizadas ao longo deste trabalho para responder a uma série de questões organizadas segundo uma escala espacial e evolutiva crescente. Inicialmente são colocadas questões relacionadas com a capacidade de distinguir a individualidade genética, uma questão essencial em estudos de organismos clonais. Passamos de seguida para o nível dos processos populacionais onde procuramos compreender se a aparente baixa capacidade de dispersão da espécie se reflecte na sua estrutura genética espacial. De que modo contribuem a reprodução sexual e clonal para a dispersão de genes à escala local? Os resultados revelaram a mais forte estrutura genética jamais encontrada para qualquer erva marinha, apenas comparável com a de ervas terrestres que apresentam auto-fertilização. A estrutura clonal e a fraca dispersão observadas sugerem que a estratégia de recrutamento da espécie deve seguir um modelo de adição constante de plântulas à escala da pradaria, com alta mortalidade inicial. A estrutura genética espacial de uma população necessita de várias gerações para se estabelecer; quais são então os processos (clonais ou sexuais) que determinam o crescimento da espécie nas fases iniciais de colonização, correspondentes ao crescimento e fusão de manchas de vegetação? Através da análise da variação da riqueza genotípica de uma série de manchas de idade variável, e da sua alocação sexual, descobrimos que enquanto que muitas manchas permanecem monoclonais por muitos anos, noutras encontramos um padrão de enriquecimento do número de clones por mancha com o aumento da idade da mancha. Um aumento rápido parece estar associado à fase de fusão de várias manchas formando uma pradaria contínua, como sugere o elevado número de clones e investimento sexual 9 encontrados nesse caso. As manchas compostas por mais do que um clone revelaram ser dominadas por apenas um ou dois clones, contudo e inesperadamente os clones de menor tamanho não eram os filhos dos clones dominantes. Subindo para uma escala geográfica maior, estudámos os níveis de diferenciação genética nas Ilhas Canárias, um sistema caracterizado pelo isolamento geográfico característico dos habitats em ilhas. A estrutura genética de Cymodocea nodosa revelou uma baixa diversidade alélica, provavelmente devido ao efeito de gargalo associado à colonização destas ilhas, e uma alta riqueza genotípica, comprovadora de uma elevada dependência da reprodução sexuada. A diferenciação genética encontrada entre populações é bastante marcada, mesmo para pradarias localizadas na mesma ilha, revelando que o fluxo de genes inter-populacional deve ser bastante reduzido e um sistema dominado pelos efeitos da deriva genética. Finalmente, sempre aumentado a escala geográfica da análise, questionamos qual o efeito da importante barreira geográfica constituída pela transição entre o Oceano Atlântico e o Mar Mediterrâneo nos padrões filogeográficos da espécie. Um total de 16 e 19 pradarias foram amostradas no Atlântico e Mediterrâneo respectivamente. Uma forte diferenciação genética entre populações foi novamente encontrada ao longo da distribuição da espécie, mas neste caso os padrões parecem ser explicados pela vicariância produzida pela história geológica desta região desde o Plioceno e pela colonização ancestral do Atlântico a partir do Mediten-âneo caracterizada por sucessivas reduções do tamanho efectivo da população. Um conjunto bem marcado de alelos específicos de cada bacia apenas pode ser encontrado em conjunto na Ibéria Atlântica, sugerindo esta região como uma zona de contacto secundário. Com base no resultados encontrados aqui são propostas duas zonas como unidades de gestão do ponto de vista evolutivo 1) o grupo constituído pelas ilhas Canárias e Mauritânia, pela grande divergência genética encontrada e 2) a baía de Cádiz pela raridade regional que a sua elevada riqueza genotípica significa no contexto da Cymodocea nodosa na costa Atlântica do Sul da Península Ibérica.
- Genetic homogeneity in the seagrass Cymodocea nodosa at its northern Atlantic limit revealed through RAPDPublication . Alberto, Filipe; Mata, Leonardo; Santos, RuiRandom amplified polymorphic DNA (RAPD) markers were used to analyse the genetic variability of the dioecious seagrass Cymodocea nodosa Ucria (Ascherson) in the Ria Formosa lagoon, Portugal, the species' northern limit in the Atlantic. Three individuals from each of 6 meadows were genotyped with 28 primers. Meadows described previously as having flower marks were compared with meadows where flowers did not occur. A single polymorphic band, specific for one meadow, was observed in a total of 177 fragments. The lack of genetic variability among meadows both with and without flower indicates that flower production is not associated with a higher level of genetic variation. The genetic homogeneity of C, nodosa in the Ria Formosa suggests a founder effect, produced by a single or a limited number of migrants composing the colonising gene pool, This hypothesis is supported by the geographic isolation from other populations as the nearest populations lie more than 300 km away from the Ria Formosa. The lack of reproductive success of C, nodosa in Ria Formosa natural park and its low genetic variability are important factors in the conservation of this species since recolonisation can only occur through vegetative growth.
- Individual-based genetic analyses support asexual hydrochory dispersal in Zostera nolteiPublication . Berković, Buga; Coelho, Nelson; Gouveia, Licínia; Serrao, Ester; Alberto, FilipeDispersal beyond the local patch in clonal plants was typically thought to result from sexual reproduction via seed dispersal. However, evidence for the separation, transport by water, and re-establishment of asexual propagules (asexual hydrochory) is mounting suggesting other important means of dispersal in aquatic plants. Using an unprecedented sampling size and microsatellite genetic identification, we describe the distribution of seagrass clones along tens of km within a coastal lagoon in Southern Portugal. Our spatially explicit individual-based sampling design covered 84 km(2) and collected 3 185 Zostera noltei ramets from 803 sites. We estimated clone age, assuming rhizome elongation as the only mechanism of clone spread, and contrasted it with paleo-oceanographic sea level change. We also studied the association between a source of disturbance and the location of large clones. A total of 16 clones were sampled more than 10 times and the most abundant one was sampled 59 times. The largest distance between two samples from the same clone was 26.4 km and a total of 58 and 10 clones were sampled across more than 2 and 10 km, respectively. The number of extremely large clone sizes, and their old ages when assuming the rhizome elongation as the single causal mechanism, suggests other processes are behind the span of these clones. We discuss how the dispersal of vegetative fragments in a stepping-stone manner might have produced this pattern. We found higher probabilities to sample large clones away from the lagoon inlet, considered a source of disturbance. This study corroborates previous experiments on the success of transport and re-establishment of asexual fragments and supports the hypothesis that asexual hydrochory is responsible for the extent of these clones.
- MsatAllele_1.0: An R package to visualize the binning of microsatellite AllelesPublication . Alberto, FilipeMsatAllele is a computer package built on R to visualize and bin the raw microsatellite allele size distributions. The method is based on the creation of an R database with exported files from the open-source electropherogram peak-reading program STRAND. Contrary to other binning programs, in this program, the bin limits are not fixed and are automatically defined by the data stored in the database. Data manipulation and graphical functions allow to 1) visualize raw allele size variation, allowing the detection of potential scoring errors, strange bin distributions, and unexpected spacing between the bins; 2) bin raw fragment sizes and write bin summary statistics for each locus; and 3) export genotype files with the resulting binned data.
- Past climate-driven range shifts structuring intraspecific biodiversity levels of the giant kelp (Macrocystis pyrifera) at global scalesPublication . Assis, Jorge; Alberto, Filipe; Macaya, Erasmo C.; Coelho, Nelson; Faugeron, Sylvain; Pearson, Gareth; Ladah, Lydia; Reed, Daniel C.; Raimondi, Peter; Mansilla, Andrés; Brickle, Paul; Zuccarello, Giuseppe C.; Serrao, EsterThe paradigm of past climate-driven range shifts structuring the distribution of marine intraspecific biodiversity lacks replication in biological models exposed to comparable limiting conditions in independent regions. This may lead to confounding effects unlinked to climate drivers. We aim to fill in this gap by asking whether the global distribution of intraspecific biodiversity of giant kelp (Macrocystis pyrifera) is explained by past climate changes occurring across the two hemispheres. We compared the species' population genetic diversity and structure inferred with microsatellite markers, with range shifts and long-term refugial regions predicted with species distribution modelling (SDM) from the last glacial maximum (LGM) to the present. The broad antitropical distribution of Macrocystis pyrifera is composed by six significantly differentiated genetic groups, for which current genetic diversity levels match the expectations of past climate changes. Range shifts from the LGM to the present structured low latitude refugial regions where genetic relics with higher and unique diversity were found (particularly in the Channel Islands of California and in Peru), while post-glacial expansions following similar to 40% range contraction explained extensive regions with homogenous reduced diversity. The estimated effect of past climate-driven range shifts was comparable between hemispheres, largely demonstrating that the distribution of intraspecific marine biodiversity can be structured by comparable evolutionary forces across the global ocean. Additionally, the differentiation and endemicity of regional genetic groups, confers high conservation value to these localized intraspecific biodiversity hotspots of giant kelp forests.
- Recruit survival of Cymodocea nodosa along a depth gradientPublication . Paulo, Diogo; Manent, Pablo; Barrio, Juan M.; Serrão, Ester; Alberto, FilipeClonal plants can reproduce sexually and clonally, expressing different proportions of these different life histories in distinctive environments. In seagrass meadows, light attenuation hinders marine plant colonization in deeper areas of its vertical distribution. Therefore it is expected that the fluorescence maximum quantum yield of seedlings will be higher at deep limits of the meadow relative to shallower depths. We hypothesized that seagrass seedlings experience higher mortality in deeper areas of the meadows than at shallower levels. Our objective was to test survival of seagrass seedlings along a depth gradient in meadows of Cymodocea nodosa in the Canary Islands. Seedlings germinated in laboratory conditions, were transplanted to a natural meadow at three water depths: shallow (5 m), medium (8 m) and deep (12 m). Transplanted seedlings were monitored by measuring maximum quantum yield, leaf length, number of leaves per shoot and survival. Our data suggest that light does not hinder survival of seedlings along the depth gradient of the meadow. Before establishing clonal growth, seedlings in deeper areas had higher survival rates than those in shallow areas. Even though seeds are present at shallow depths and sexual allocation is high, sexual contribution can be lower than expected due to seedling loss.
- Sexual reproduction vs. clonal propagation in the recovery of a seagrass meadow after an extreme weather eventPublication . Paulo, Diogo; Diekmann, Onno; Ramos, Ana; Alberto, Filipe; Serrao, EsterMarine flowering plants can reproduce sexually and clonally, and the relative contribution of these two modes can be dependent on the environmental conditions. Zostera marina, a seagrass widely distributed in the northern hemisphere, can form annual and perennial meadows with different proportions of sexual versus clonal propagation depending on the environmental disturbance regime. We study the hypothesis that the contribution of sexual propagation varies during the recovery of a seagrass meadow. In this case study, we compare the proportion of sexual versus clonal propagation of a perennial Z. marina meadow before its disappearance due to winter storms and after recovery. Before disturbance, genotypic diversity was high, indicating frequent sexual reproduction events likely to create an abundant seed bank. Seedling germination allowed the population to recover after the extreme disturbance. As months passed, seedlings became rare and finally absent, giving place to adult shoots. In an advanced stage of colonization, the shoots colonized the area by vegetative growth, which lowered the genotypic diversity. Despite this reduction over time, the genotypic diversity of the new meadow is still high, demonstrating the importance of sexual reproduction in meadow recovery and persistence.