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Thomás Banha

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Projeto de formação discente
Ronaldo Bastos Francini Filho
Rafael Almeida Magris
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Descrição do projeto

The Great Amazon Reef System: biodiversity, knowledge gaps, and conservation
Mesophotic ecosystems (MEs) are important transition environments between shallow coral reefs and the deep sea, harboring many species of ecological and economical importance. The Great Amazon Reef System (GARS) is a mesophotic reef system that flourishes below the Amazon River Plume that has an important role as a transition between the Caribbean and South Atlantic biogeographical Provinces. Evidence for the existence of a reef environment below the Amazon-Orinoco Plume (AOP) is available since the 1970s, but the GARS was thoroughly described only recently. The AOP acts as a biogeographic filter between the Caribbean and Brazil, with some species being able to cross the AOP, probably passing through the GARS. The functional traits that facilitate the migration of species are known mostly to reef fish, but little is known about the traits of benthic organisms such as macroalgae and invertebrates, even though their relevance to the construction and functioning environments such as the GARS. Also, the Amazon coast has the largest continuous mangrove belt in the world and holds more than half of the mangrove area from Brazil. This sheltered, shallow ecosystem is known as a nursery for larvae and juveniles from economic and ecologically important species, which in the future end up migrating to deeper ecosystems. In a scenario where a recently described, understudied environment is already threatened by eminent oil exploration, science-oriented management actions are crucial. The delimitation of priority areas for conservation is necessary to preserve the reef system, the biota within, and the population that relies on the GARS. Here we aim to study the newly described GARS, making a systematic review of the knowledge available for the area, analyzing its biodiversity and the role of AOP as a biological filter, and take the first steps towards the conservation of the GARS, reconciling preservation of the biodiversity and economic activities. Our specific objectives are (i) to identify trends of the research on mesophotic reefs worldwide, with a particular focus on knowledge gaps for the GARS; (ii) to perform a multi-taxa analysis to identify traits allowing the biota to transition through the AOP filter; (iii) analyze the cross-shelf distribution of organisms inhabiting the GARS, comparing to other mesophotic/turbid reef environments; (iv) identify transitional habitats and evaluate the ontogenetic migration of GARS species; and (v) propose priority areas for conservation, considering the oil and gas exploitation activities, fisheries and other uses in the region.
Amazon River plume; Mesophotic reef; Ontogenetic migration; Systematic conservation planning; topic modeling
To identify gaps and trends in scientific research in the GARS area, we will use an automated text analysis known as topic modeling. This method is often applied in social science but in recent years has become more used in biological sciences (Syed et al. 2018; Luiz et al. 2019; McCallen et al. 2019; Andrew et al. 2021). We will search articles found in Clarivate Analytics Web of Science using the following string (i.e., word combination): ((mesophotic OR shelf-edge) AND (reef OR ecosystem OR coral)) OR ("deep* reef"). The analysis will follow the methods from Luiz et al. (2019), using latent Dirichlet allocation (LDA) modeling to identify common topics in which the papers are grouped. Using the R package “ldatuning” (Murzintcev, 2014) we will estimate the most preferable number of topics for the model and define the number according to the optimization method proposed by Deveaud et al. (2014). To fit the best LDA model we will use the R package “topicmodels” (Hornik & Grün, 2011). Following the approach of Luiz et al. (2019), we will identify topics with increasing (hot topic) and decreasing (cold topic) popularity, topic specificity/generality (if they co-occur with other topics), and the research gaps concerning the mesophotic ecosystem and subsequently the GARS.
The functional traits of reef fish are widely studied (Luiz et al 2012; Luiz et al 2019; Mazzei et al 2021; McLean et al 2021), while the studies of benthic organisms traits are increasing in the last years (Lam-Gordillo et al 2020a, b). Here, we aim to assess the role of the AOP filter for the community, using a cross-taxa approach (Sunday et al. 2015; MacLean et al. 2017), encompassing species from the Caribbean and Brazil, including those from the GARS. To assess the role of the AOP as a filter, we will evaluate which traits allow organisms to cross the AOP, by analyzing the relationship between species traits and their distribution using generalized linear mixed-effects models (Luiz et al. 2012).
Adapting the methods from Tamir et al. (2019), we plan to do belt transects at stratified according to depth (every 10m), following the boat drift line, parallel to the shoreline. We will also film as detailed as possible the sites where the individuals of interest were registered. Footage acquired in previous cruises will be analyzed together with the videos acquired by this project. The data to be analyzed comprises videos from shallow areas (60m), taken using a double Deep Worker submarine and ROVs (see Francini-Filho et al. 2018).
L. purpureus will be used as a model organism to investigate the ontogenetic migration of species from the coast to the GARS. Individuals will be sampled across-shelf, targeting a wide range of length, covering juveniles and adults, to assess the ontogenetic shifts of habitat use, which is observed in other snappers (Aburto-Oropeza et al. 2009; Tanaka et al 2011). Additionally, we will also perform stable isotope analysis of otoliths to support the data on ontogenetic migration (Gillanders 2005; Wallace et al. 2014).
The data gathered by this Ph.D. project and other research in the region will contribute to an effective MPA network design (Mills et al. 2010), aiming to reconcile sustainable economic activities and biodiversity conservation. Using the R package prioritizr (Hanson et al., 2017; Magris et al. 2020), we will assemble data on species distribution, threats, and connectivity to support the definition of the PACs, covering the distribution of the species among the different habitats, allowing the species connectivity between them.
Bibliography Review - May 2022 to Dec 2024
Data Acquisition - May 2022 to Aug 2024
Topic Modeling - May 2022 to Apr 2023
Cross-shelf - May 2022 to Dec 2023
Trait Analyses - Sep 2022 to Aug 2024
Ontogenetic migration analyses - Jan 2023 to Aug 2024
Systematic Planning - Jan 2024 to Aug 2025
Qualification - Sep 2023 to Dec 2023
Research project abroad - Jan 2024 to Apr 2025
Courses - May 2022 to Dec 2023
Thesis deposit - Sep 2025 to Dec 2025


Laboratório de Ecologia e Conservação Marinha (LabEco-Mar), coordenado pelo Prof. Ronaldo B. Francini Filho
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