Marine aggregates are an important means of carbon transfers downwards to the deep ocean as well as an important nutritional source for benthic organism communities that are the ultimate recipients of the flux. During these last 10 years, data on size distribution of particulate matter have been collected in different oceanic provinces using an Underwater Video Profiler. The cruise data include simultaneous analyses of particle size distributions as well as additional physical and biological measurements of water properties through the water column. First, size distributions of large aggregates have been compared to simultaneous measurements of particle flux observed in sediment traps. We related sediment trap compositional data to particle size (d) distributions to estimate their vertical fluxes (F) using simple power relationships (F=Ad^b). The spatial resolution of sedimentation processes allowed by the use of in situ particle sizing instruments lead to a more detailed study of the role of physical processes in vertical flux. Second, evolution of the aggregate size distributions with depth was related to overlying primary production and phytoplankton size-distributions on a global scale. A new clustering technique was developed to partition the profiles of aggregate size distributions. Six clusters were isolated. Profiles with a high proportion of large aggregates were found in high-productivity waters while profiles with a high proportion of small aggregates were located in low-productivity waters. The aggregate size and mass flux in the mesopelagic layer were correlated to the nature of primary producers (micro-, nano-, picophytoplankton fractions) and to the amount of integrated chlorophyll a in the euphotic layer using a multiple regression technique on principal components. Finally, a mesoscale area in the North Atlantic Ocean was studied to emphasize the importance of the physical structure of the water column on the horizontal and vertical distribution of particulate matter. The seasonal change in the abundance of aggregates in the upper 1000 m was consistent with changes in the composition and intensity of the particulate flux recorded in sediment traps. In an area dominated by eddies, surface accumulation of aggregates and export down to 1000 m occured at mesoscale distances (<100 km).

Marine aggregates are an important means of carbon transfers downwards to the deep ocean as well as an important nutritional source for benthic organism communities that are the ultimate recipients of the flux. During these last 10 years, data on size distribution of particulate matter have been collected in different oceanic provinces using an Underwater Video Profiler. The cruise data include simultaneous analyses of particle size distributions as well as additional physical and biological measurements of water properties through the water column. First, size distributions of large aggregates have been compared to simultaneous measurements of particle flux observed in sediment traps. We related sediment trap compositional data to particle size (d) distributions to estimate their vertical fluxes (F) using simple power relationships (F=Ad^b). The spatial resolution of sedimentation processes allowed by the use of in situ particle sizing instruments lead to a more detailed study of the role of physical processes in vertical flux. Second, evolution of the aggregate size distributions with depth was related to overlying primary production and phytoplankton size-distributions on a global scale. A new clustering technique was developed to partition the profiles of aggregate size distributions. Six clusters were isolated. Profiles with a high proportion of large aggregates were found in high-productivity waters while profiles with a high proportion of small aggregates were located in low-productivity waters. The aggregate size and mass flux in the mesopelagic layer were correlated to the nature of primary producers (micro-, nano-, picophytoplankton fractions) and to the amount of integrated chlorophyll a in the euphotic layer using a multiple regression technique on principal components. Finally, a mesoscale area in the North Atlantic Ocean was studied to emphasize the importance of the physical structure of the water column on the horizontal and vertical distribution of particulate matter. The seasonal change in the abundance of aggregates in the upper 1000 m was consistent with changes in the composition and intensity of the particulate flux recorded in sediment traps. In an area dominated by eddies, surface accumulation of aggregates and export down to 1000 m occured at mesoscale distances (<100 km).

The diel vertical migration (DVM) and feeding periodicity of myctophids (lanternfishes) were studied in the high-latitude Masfjorden, Norway, and the tropical Red Sea. In Masfjorden, a bottom-mounted echo sounder permitted continuous studies throughout the year, and revealed a diverse seasonal DVM behavior. During spring and summer, when zooplankton peaks in the epipelagic zone, migrating glacier lanternfish performed normal DVM (NDVM), ascending to the epipelagic zone during night and residing below ~200m during daytime. During autumn and winter, when Calanus overwinters between ~150–300 m, migrating glacier lanternfish mainly performed inverse DVM (IDVM), ascending to feed on Calanus in mid-waters during daytime. Non migrating (NoDVM) individuals were present all year below ~300 m in Masfjorden. In the Red Sea, where zooplankton has an epipelagic distribution, the whole population of skinnycheek lanternfish performed NDVM, feeding in the epipelagic zone at night, while residing at ~500–750 m during daytime. The warm waters of the Red Sea were hypothesized to limit the time individuals can stay in the mesopelagic zone without migrating to feed in the epipelagic layers. The DVM behavior of myctophids largely seemed to relate to the distribution of zooplankton, and it was hypothesized that NDVM will prevail with epipelagic distribution of prey, while IDVM and NoDVM are common in areas where zooplankton migrate seasonally to mesopelagic depths. Potential predators were continuously present, found to apparently attack glacier lanternfish, at mesopelagic depth in Masfjorden. Thus, myctophids are under threat of predation even at mesopelagic depth.

Orientador: Prof. Dr. Otto Müller Patrão de Oliveira / Coorientador: Prof. Dr. Renato Mitsuo Nagata / Dissertação (mestrado) - Universidade Federal do ABC, Programa de Pós-Graduação em Evolução e Diversidade, São Bernardo do Campo, 2017. / Com uma grande extensão de costa marítima, o Brasil apresenta diversas lacunas no conhecimento acerca da faunística, ecologia e biogeografia de diversos grupos zoológicos. Para as regiões mesopelágicas e batipelágicas a escassez de informação é ainda mais marcante em especial para os grupos do chamado zooplâncton gelatinoso. Dentre os organismos marinhos gelatinosos, os Hydrozoa são um dos grupos mais abundantes e diversos no plâncton. Como predadores, constituem um importante elo na teia trófica pelágica, podendo potencialmente afetar a distribuição e abundância de espécies de interesse econômico e consequentemente impactar algumas atividades humanas. Assim, o conhecimento acerca da diversidade e distribuição dos hidrozoários planctônicos tende a contribuir para estudos e planejamentos nas áreas de pesca e conservação de ambientes marinhos. O objetivo do presente estudo foi de caracterizar a diversidade e a distribuição dos hidrozoários da plataforma continental e o talude (até 3000m de profundidade) da Bacia de Campos, oriundas das campanhas realizadas pelo projeto HABITATS, durante o período chuvoso e seco de 2009. Os dados foram analisados procurando inferir as relações entre a composição e diversidade das espécies com as massas de água características da região. Foram analisadas 645 amostras sendo divididas em 303 amostras de hidromedusas e 342 amostras de sifonóforos totalizando 28.926 espécimes de Hydrozoa, correspondendo a 73 espécies das quais 44 são sifonóforos. Todas as espécies encontradas já haviam sido previamente registradas no litoral brasileiro. As espécies Aglaura hemistoma, Diphyes bojani, Eudoxoides spiralis, Liriope tetraphyla e Muggiaea kochii foram as espécies dominantes. As espécies Aglaura hemistoma e Diphyes bojani foram encontradas em todas as massas de água analisadas, em ambos os períodos, com significativas contribuições para a composição das comunidades de todas as massas de água. Foi possível correlacionar as espécies Aglaura hemistoma, Liriope tetraphylla e Corymorpha gracilis com a Água Tropical (AT), enquanto as espécies Sminthea eurygaster, Amphogona apicata e Lensia conoidea foram indicativas da Água Central do Atlântico Sul (ACAS), e por fim, Lensia havock e Halicreas minimum foram indicativas da Água Intermediária Antártica (AIA). Quanto a comunidade de sifonóforos, a AT foi caracterizada pela presença de Muggiaea kochii, Diphyes bojani, Abylopsis tetragona, Abylopsis eschscholtzii, Eudoxoides spiralis, Bassia bassensis e Chelophyes appendiculata. A espécie M. kochi caracterizou as regiões mais rasas da plataforma e teve abundâncias decrescentes em direção às regiões de maior profundidade. Em geral, as variáveis ambientais tiveram baixa explicação (aproximadamente 10%) para a variabilidade das densidades da comunidade de hidrozoários planctônicos. As maiores correlações entre as variáveis ambientais e as densidades de sifonóforos foram observadas na AT, em que explicaram aproximadamente 40% da variação da comunidade. Dessa forma, os sifonóforos tiveram uma melhor correlação com a variabilidade ambiental do que as hidromedusas para a AT. No geral, as espécies de sifonóforos tiveram suas distribuições mais restritas a determinadas massas de água, enquanto para as hidromedusas as preferências por massas de água não foram tão claras. Mesmo com a baixa correlação entre as variáveis ambientais e os hidrozoários foi possível ampliar o conhecimento acerca da distribuição vertical das espécies, além de caracterizar possíveis correlações das espécies com as principais variáveis ambientais. / With a large extension, the Brazilian coast has several gaps on the knowledge of faunistic, ecology and biogeography of some zoological groups. For the mesopelagic and bathypelagic regions, the scarcity of information is even more evident, especially for the gelatinous zooplankton. Among the marine gelatinous organisms, hydrozoans are one of the most abundant and diverse groups in the plankton. As predators, they comprise an important link in the pelagic trophic web, potentially affecting the distribution and abundance of species of economic interest, consequently, affecting human activities. Thus, the knowledge about planktonic hydrozoans diversity and distribution contribute to studies on fisheries and conservation of marine environment. The aim of this study was to describe the diversity and distribution of hydrozoans over the continental shelf and slope (until 3000m deep) of the Campos Basin (RJ), from campaigns performed by the HABITATS project, during the rainy and dry seasons of 2009. The data was analyzed aiming to infer the possible relationships between species composition and diversity with the local water masses. A total of 645 samples were analyzed divided in 303 samples of hydromedusae and 342 samples of Siphonophorae totalizing 28,926 specimens of Hydrozoa, corresponding to 73 species, 44 of siphonophores and 29 hydromedusae. All species found have previous records for the Brazilian coast. Aglaura hemistoma, Diphyes bojani, Eudoxoides spiralis, Liriope tetraphylla and Muggiaea kochii were the dominant species. The species Aglaura hemistoma and Diphyes bojani were present in all analyzed water masses, in both seasons, with significant contribution for the community composition of all water masses. Furthermore, the species A. hemistoma, L. tetraphylla and Corymorpha gracilis were associated with the Tropical water (TW), while Sminthea eurygaster, Amphogona apicata and Lensia conoidea were indicative of the South Atlantic Central Water (SACW), and finally Lensia havock and Halicreas minimum were indicative of Antartic Intermediate Water (AAIW). The Siphonophorae community in TW was characterized by the presence of M. kochii, D. bojani, Abylopsis tetragona, Abylopsis eschscholtzii, E. spiralis, Bassia bassensis and Chelophyes appendiculata. The species M. kochii characterized shallow continental shelf waters with decreasing abundance toward deeper regions. In general, environmental variables had low explanation (about 10%) to the variability in the densities of planktonic hydrozoans community. The highest correlation between environmental variables and the siphonophores densities were found in TW, which explained nearly 40% of the community variation. Siphonophorae were better environment indicative than the hydromedusa to TW. Therefore, the siphonophores had higher correlation with environmental variability than hydromedusae in the TW. Overall, the Siphonophorae species had their distribution restrict to determined water masses while the hydromedusae preferences for water masses were unclear. Even with the low correlation between the environmental variables and the Hydrozoa species was possible do increase the actual knowledge about species vertical distribution, besides characterizing possible relationships of the species with the main environmental variables.

The nighttime distribution of vertically migrating mesopelagic fish in relation to nocturnal light was studied during a circumglobal survey, in the Red Sea, and in a fjord at high latitude. The study was based on data derived from ship borne echo sounders (circumglobal and the Red Sea) as well as using upward looking echo sounders mounted on the bottom (Masfjorden, Norway). We also applied a numerical model for analyzing diel vertical migration patterns. The effect of the lunar cycle was the focus in studies at low latitudes, while seasonal changes in nocturnal light climate was in focus at high latitude. Lunar phase significantly affected the distribution of mesopelagic fish at the global scale and in the Red Sea. During nights near full moon, scattering layers of mesopelagic fish distributed deeper than during darker phases of the moon. At high latitude, mesopelagic fish switched its behavior along with seasonal changes in nocturnal lights. In autumn, the population of the studied fish (Maurolicus mueleri) formed separated layers. Juveniles performed normal diel vertical migration followed by midnight sinking, with midnight sinking mainly related to temperature minima and also for avoiding predators. Meanwhile the adults did not migrate vertically, reducing foraging but increasing the adult survival. From late winter to mid-Spring, interrupted ascents behavior was noted in the afternoon. Predator avoidance, satiation, and finding temperature optimum might be the reason behind interrupted ascents. At lighter nights in mid-summer, M. muelleri took on schooling behavior, likely as an anti-predator behavior permitting access to the upper waters in the absence of darkness.

La modélisation en écologie est aujourd'hui une pratique scientifique de premier plan. Portée par l'avancement technologique, les modèles utilisés en sciences de l'environnement présentent une complexité grandissante. La complexification des modèles est une nécessité pour une variété d'études, mais elle peut être une source d'incompréhension, voire d'erreurs. Savoir gérer son implémentation apparaît donc nécessaire. Fort de ce constat, deux approches complémentaires se sont distinguées et furent étudiées dans ce travail de thèse. D'une part, il est possible de gérer la complexité a priori, en contraignant directement les hypothèses de construction et le formalisme du modèle par l'utilisation d'un cadre théorique. Une illustration de l'utilisation d'un schéma théorique, la théorie des Budgets Dynamiques d'Énergie, présente comment une description précise de l'effet des ultraviolets fut adjointe à un modèle de l'endosymbiose corallienne. Cette étude met en lumière leur possible rôle dans le blanchiment des coraux scléractiniaires. La gestion de la complexité pouvant aussi s'opérer a posteriori, c'est à dire une fois l'étape de construction passée. Ainsi, une méthodologie d'analyse statistique des sorties de modèles ayant pour but de permettre leur simplification fut établie. À titre d'exemple, cette méthode a été appliquée sur un modèle à micro-échelle de l'écosystème mésopélagique. Ne plus avoir la possibilité d'entreprendre une approche analytique de son modèle n'est donc pas une fatalité pour qui veut maitriser son outil, car une multitude d'approches permettent d'obtenir des informations toutes aussi intéressantes. / Ecological modelling is nowadays a leading topic. the models used in environmental science turn to be more and more complex. Driven by technological advancement, the models used in environmental sciences are increasingly complex. The complexity of models is a need for a variety of studies, but it can also be a source of misunderstanding, or even errors. How to manage its implementation is therefore necessary. With this in mind, two complementary approaches have been studied in this thesis. On the one hand, it is possible to manage the complexity textit a priori, by directly constraining the construction assumptions and formalism of the model using a theo- retical framework. An illustration of the use of a theoretical framework, the theory of Dynamic Energy Budgets, shows how an accurate description of the effect of ultraviolet was added to a model of scleractinian corals. This study enlightened their possible role in coral bleaching events. Managing complexity can also be carried out textit a posteriori, ie once the construc- tion phase is done. Thus, a simplification methodology using a statistical analysis of the model outputs was established . As an example, this method was applied on a micro- scale model of the mesopelagic ecosystem. Eventually, not being able of pursuing an analytical approach of the model is not inevitable for those who want to still mastering their model, it exists a multitude of tool who brings equally interesting informations.

Mesopelagic (open ocean, 200-1000 m depth) fishes are important consumers of zooplankton and are prey of oceanic predators. Some mesopelagic fishes (e.g., myctophids and stomiids) undertake a diel vertical migration where they ascend to the near-surface waters during the night to feed and descend into the depths during the day to avoid predators. Other mesopelagic fishes (e.g., Sternoptyx spp.) do not vertically migrate and remain at deep depths throughout the day. While in the epipelagic zone (surface – 200 m depth), vertically migrating fishes become prey to upper-trophic level predators, such as: tunas and billfishes. Benthic fishes (e.g., macrourids) often vertically migrate as well, ascending into the pelagic zone to feed on pelagic organisms. Fishes of different depths and vertical migration habits likely have a different ecological role in food webs. The relationship between parasites and gut contents provides insights into ecological processes occurring within assemblages, as prey items are often vectors for parasites. This study examined the differences between the prey items present in the gastrointestinal cavity and parasites of 26 mesopelagic fish species in the Gulf of Mexico. Results showed that based on the proportionally dominant prey items per species, six different feeding guilds existed within this assemblage, five based on planktivory: copepodivores, predators of copepods and other zooplankton, predators of copepods and euphausiids, gelatinivores, generalists, crustacean decapodivores, and upper-trophic level predators. Larger fishes preyed on larger prey items and harbored more parasites. Sigmops elongatus exhibited an ontogenetic diet shift at 75 mm standard length, progressing from eating primarily copepods at small sizes to eating primarily euphausiids at large sizes. Compared to similar studies, this study revealed a higher parasitic infestation by trematodes, an endoparasite (parasite within the host) class often restricted to nearshore hosts, in Gulf of Mexico fishes. Helicometrina nimia, the dominant parasite of the gempylid Nealotus tripes, has not previously been recorded in hosts below 200 m depth, suggesting a foodweb pathway that transitions from nearshore to offshore. These data can be used to develop and refine models aimed at understanding ecosystem structure and connectivity.

Evolution occurs and can be conceptualized along a spectrum, bounded on one extreme by the relationships between deep lineages – such as phyla, classes, and orders – and on the other by the molecular dynamics of operational taxonomic units within a species, defined as population genetics. The purpose of this dissertation was to better understand the evolutionary and population dynamics of crustaceans within the Gulf of Mexico. In the second chapter of my dissertation, I provide a guide to best phylogenetic practice while reviewing infraordinal relationships within Decapoda, including the promise held by next-generation sequencing (NGS) approaches such as Anchored Hybrid Enrichment. Chapter III is a phylogenetic study of species relationships within the economically important shrimp genus, Farfantepenaeus, targeting three mitochondrial genes and uncovering an intriguing pattern of latitudinal speciation. As the first inclusive molecular phylogeny of the genus, we find support for the newly described species F. isabelae, but a lack of support for the species status of F. notialis. Additionally, our results suggest the existence of two distinct subspecies of F. brasiliensis. Chapter IV investigates the relative impacts of habitat heterogeneity and the presence of a possible glacial refugium in determining population dynamics of the Giant Deep-Sea Isopod, Bathynomus giganteus in the northern Gulf of Mexico. Through hybrid population genetics/genomics analyses and Bayesian testing of population models, we find strong evidence for habitat heterogeneity determining population dynamics for this charismatic deep-sea invertebrate. Chapter V further investigates the role of environment in determining and maintaining genetic diversity and population connectivity, specifically focused on establishing biological baselines with which we can diagnose health and resilience of the Gulf of Mexico. This was accomplished through a comparative NGS population genomics study of three species of mesopelagic crustaceans: Acanthephyra purpurea, Systellaspis debilis, and Robustosergia robusta. While diversity and connectivity differs in each species, the comparative results bespeak the importance of access to the Gulf Loop Current in determining and maintaining population dynamics. Overall, my work significantly contributes to our knowledge of Crustacea at the phylogenetic- and population genetic-level.

Maurolicus é um gênero representado por peixes mesopelágicos, com elevada biomassa na Zona Econômica Exclusiva sudeste sul brasileira. O material deste estudo provém de arrastos com rede de meia água efetuados com o N/Oc. Atlântico Sul, entre as isóbatas de 100 e 1500 m e entre as latitudes 22° e 35° S, realizados no inverno de 1996; outono de 1997 e primavera de 1997. A análise das características merísticas e morfológicas de 120 exemplares, coletados em 4 pontos distintos, indicou que na região ocorre M. stehmanni Parin & Kobyliansky, 1993. Através da análise da distribuição vertical e horizontal das capturas, verificou-se que a espécie está associada à região de quebra de plataforma continental, permanecendo em profundidades maiores que 200 metros durante o dia, migrando para camadas superiores a noite, com a diminuição da intensidade luminosa. Pela distribuição de freqüência de comprimento e proporção entre jovens e adultos constatou-se que ocorreu recrutamento em todos os períodos estudados. A partir da análise da proporção entre peixes jovens e adultos por comprimento estimou-se o L50médio em 32 mm. As análises da relação gonadossomática, da freqüência dos estádios de maturidade gonadal e do &#8710;K (diferença entre o fator de condição total e somático) indicaram que a espécie apresentou atividade reprodutiva em todas as áreas e épocas analisadas. A relação entre o raio do otólito e o tamanho dos indivíduos é linear, porém não foi possível identificar a periodicidade de formação dos anéis, impossibilitando estimativas adequadas dos parâmetros de crescimento. Aplicando-se a rotina ELEFAN I, do pacote computacional FISAT, aos dados de freqüência de comprimento foi estimado o L&#8734; em 53 mm e k em 0,9 ano-1, indicando que a espécie atinge o tamanho médio da 1 a maturação gonadal em torno do 1º ano de vida. / Maurolicus is a genus of mesopelagic fish very abundant in the south-eastern and south Brazilian Economic Exclusive Zone. The material of this study was sampled by mid water trawl during cruises of R/V Atlântico Sul in winter of 1996, autumn of 1997 and spring of 1997, between 100 and 1500 meters depth, from latitudes of 22° to 35° S. The meristic and morphological analysis of 120 specimens collected in 4 distinctive points, has indicated the occurrence of M. stehmanni Parin & Kobyliansky, 1993 in the area. Through the vertical and horizontal distribution of the catches it was verified that this species is associated with the shelf break, staying in depths higher than 200 m during the day, migrating to lower depths at night as the luminous intensity falls. The length frequency and the proportion between youngs and adults showed that the recruitment occured during the periods surveyed. By means of young-adult proportion by length a value of L50 about 32 mm was estimated. The study of gonadossomatic relationship, gonadal maturity frequency and &#8710;K (difference between total and somatic condition factor) indicated that M. stehmanni presented reproductive activity in the area during all the sampled seasons. There is a linear relationship between the standard length and the otolith radius, however the periodicity of the zone formation was not identified, which did not permit appropriate estimates of the growth parameters. The L&#8734; of 53 mm and k of 0,9 year–1 were estimated using ELEFAN I routine (FISAT) based on length frequency data, indicating that M. stehmanni attains maturity around its first year of life.

A distribuição horizontal e vertical das larvas de peixes mesopelágicos de Phosichthyidae foi descrita a partir de dados amostrados desde a superfície até 200 m de profundidade, e em 5 estratos na coluna de água. As coletas foram realizadas no verão e inverno de 2002, em radiais perpendiculares à costa Sudeste do Brasil, entre o cabo de São Tomé (RJ) e a ilha de São Sebastião (SP). A abundância das larvas (larvas.m²) foi estimada para o material amostrado pela rede Bongô (333 cm) e a densidade (larvas.m³) para a Multi Plankton Sampler (300 cm). No total foram coletadas 538 larvas de Phosichthyidae no verão e 146 no inverno. Duas espécies foram identificadas, Pollichthys mauli e Vinciguerria nimbaria, ambas apresentaram-se distribuídas, preferencialmente, na região oceânica da área de estudo com maiores densidades entre 60 e 80 m de profundidade, onde a temperatura e a salinidade foram superiores a 20°C e 36, respectivamente, estando diretamente relacionados à massa de Água Tropical, transportada pela Corrente do Brasil. Todas as fases de desenvolvimento larval foram capturadas, entretanto, a maioria das larvas estava em pós-flexão da notocorda. Em relação à variação diária, as larvas foram mais abundantes durante a noite. / Horizontal and vertical distribution of mesopelagic Phosichthyidae fish larvae was described based on data sampled collected from the surface up to 200 m depth, and at five stratums on the water column. The sampling was performed in summer and winter, 2002, on perpendiculars transects in southeastern Brazilian Bight, between São Tomé Cape (RJ) and São Sebastião Island (SP). The abundance of larval (larvae.m²) was estimated from sample of Bongo net (333 cm) and the density (larvae.m³) from sample of Multi Plankton Sampler (300 cm). A total of 538 larvae of Phosichthyidae was collected during summer, and 146 in the winter. Two species, Pollichthys mauli and Vinciguerria nimbaria, were identified; both were mainly distributed in the oceanic region of the study area and were more abundant between 60 and 80 m depth, where temperature and salinity were higher than 20°C and 36, respectively, which are directly related with the Tropical Water mass, transported by Brazil Current. All larval stages of development were caught, however, the majority was in postflexion stage. In relation to diel variation, larvae were more abundant during the night.