Environmental DNA Biomonitoring Reveals Seasonal Patterns in Coral Reef Fish Community Structure

Coral reef fish populations are declining due to multiple factors including habitat destruction, overfishing, and climate change. While these can include seasonal impact, seasonal changes can also be a confounding factor, so that seasonal monitoring is essential for detecting true temporal changes in fish community abundance and composition. However, seasonal monitoring is rarely implemented. The aim of this study was to detect the seasonal patterns of coral reef fish community structure around Tidung Kecil Island, Indonesia, using eDNA metabarcoding (eDNA) and underwater visual census (UVC). The UVC identified 32 species belonging to 10 families in the rainy season and 29 species belonging to 7 families in the dry seasons. The eDNA metabarcoding identified 209 species belonging to 56 families and 27 species belonging to 17 families in the rainy and dry seasons, respectively. Based on eDNA metabarcoding data, coral reef fish abundance and community composition differed significantly between seasons (Mann Whitney, p<0.01), while the UVC method did not detect these seasonal differences (Mann Whitney, p>0.05). UVC and eDNA data both showed a predominance of omnivorous fishes in the rainy season and carnivorous fishes in the dry season. Ecological indices did not differ significantly between seasons for either method, although the species making the highest contributions to the similarity (SIMPER) analysis differed between methods. Overall, this study confirms the premise that eDNA metabarcoding can be an effective tool for monitoring seasonal variation in coral reef fish communities.

Reproductive timing and investment decisions of a protogynous hermaphroditic coral reef fish species

<p>Life-history theory suggests that an organism must balance its available energy between two competing physiological processes to maximize fitness: reproduction and somatic growth. Energetic trade-offs are a fundamental concept of life history theory and form the basis of intra- and inter-specific variation in life-history strategies. In fishes, reproduction-growth trade-offs are an essential component of life-history optimization. This is particularly true for species with protogynous sex- change (the most common reproductive mode among coral reef fish species), where reproductive success rapidly and disproportionally increases with body size/ corresponding social status. In such systems, lifetime fitness is inherently linked to patterns of growth and energy allocation strategies determined by an individual’s size-specific rank within the dominance hierarchy. However, energy allocation strategies in a protogynous species may not only be a function of body size. Coral reef fish species are exposed to extremely variable environmental conditions and this can favour the evolution of strategies that utilize good times and avoid disadvantageous times for reproduction. Consequently, size- specific parental investment decisions may vary greatly in time and space according to environmental cues. My thesis focuses on the protogynous reef fish, Thalassoma hardwicke (the sixbar wrasse), which is extremely abundant on shallow coral reefs throughout the Indo-Pacific region. Specifically, I evaluate patterns of spawning and reproductive investment as a function of body size, social status, lunar phase and other environmental parameters. I address the question of whether females/males of differing size make different fitness-related decisions when away from spawning sites, and I evaluate context-dependency in these decisions. Finally, I will attempt to reconstruct the developmental histories (e.g., larval growth rates) of individuals from otoliths to evaluate potential relationships between developmental histories and fitness attributes.</p>

Reproductive timing and investment decisions of a protogynous hermaphroditic coral reef fish species

<p>Life-history theory suggests that an organism must balance its available energy between two competing physiological processes to maximize fitness: reproduction and somatic growth. Energetic trade-offs are a fundamental concept of life history theory and form the basis of intra- and inter-specific variation in life-history strategies. In fishes, reproduction-growth trade-offs are an essential component of life-history optimization. This is particularly true for species with protogynous sex- change (the most common reproductive mode among coral reef fish species), where reproductive success rapidly and disproportionally increases with body size/ corresponding social status. In such systems, lifetime fitness is inherently linked to patterns of growth and energy allocation strategies determined by an individual’s size-specific rank within the dominance hierarchy. However, energy allocation strategies in a protogynous species may not only be a function of body size. Coral reef fish species are exposed to extremely variable environmental conditions and this can favour the evolution of strategies that utilize good times and avoid disadvantageous times for reproduction. Consequently, size- specific parental investment decisions may vary greatly in time and space according to environmental cues. My thesis focuses on the protogynous reef fish, Thalassoma hardwicke (the sixbar wrasse), which is extremely abundant on shallow coral reefs throughout the Indo-Pacific region. Specifically, I evaluate patterns of spawning and reproductive investment as a function of body size, social status, lunar phase and other environmental parameters. I address the question of whether females/males of differing size make different fitness-related decisions when away from spawning sites, and I evaluate context-dependency in these decisions. Finally, I will attempt to reconstruct the developmental histories (e.g., larval growth rates) of individuals from otoliths to evaluate potential relationships between developmental histories and fitness attributes.</p>

The alternative splicing landscape of a coral reef fish during a marine heatwave

Alternative splicing is a molecular mechanism that enables a single gene to encode multiple transcripts and proteins by post-transcriptional modification of pre-RNA molecules. Changes in the splicing scheme of genes can lead to modifications of the transcriptome and the proteome. This mechanism can enable organisms to respond to environmental fluctuations. In this study, we investigated patterns of alternative splicing in the liver of the coral reef fish Acanthochromis polyacanthus in response to the 2016 marine heatwave on the Great Barrier Reef. The differentially spliced (DS; n=40) genes during the onset of the heatwave (i.e. 29.49°C or +1°C from average) were related to essential cellular functions such as the MAPK signaling system, Ca(2+) binding and homeostasis. With the persistence of the heatwave for a period of one month (February to March), 21 DS genes were detected, suggesting that acute warming during the onset of the heatwave is more influential on alternative splicing than the continued exposure to elevated temperatures. After the heatwave, the water temperature cooled to ~24.96°C, and fish showed differential splicing of genes related to cyto-protection and post-damage recovery (n=26). Two-thirds of the DS genes detected across the heatwave were also differentially expressed, revealing that the two molecular mechanisms act together in A. polyacanthus to cope with the acute thermal change. This study exemplifies how splicing patterns of a coral reef fish can be modified by marine heatwaves. Alternative splicing could therefore be a potential mechanism to adjust cellular physiological states under thermal stress and aid coral reef fishes in their response to more frequent acute thermal fluctuations in upcoming decades.