Anemonefish are an emerging group of model organisms for studying genetic, ecological, evolutionary, and developmental traits of coral reef fish. The yellowtail clownfish Amphiprion clarkii possesses species-specific characteristics such as inter-species co-habitation, high intra-species color variation, no anemone specificity, and a broad geographic distribution, that can increase our understanding of anemonefish evolutionary history, behavioral strategies, fish-anemone symbiosis, and color pattern evolution. Despite its position as an emerging model species, the genome of A. clarkii is yet to be published. Using PacBio long-read sequencing and Hi-C chromatin capture technology, we generated a high-quality chromosome-scale genome assembly initially comprised of 1,840 contigs with an N50 of 1,203,211 bp. These contigs were successfully anchored into 24 chromosomes of 843,582,782 bp and annotated with 25,050 protein-coding genes encompassing 97.0% of conserved actinopterygian genes, making the quality and completeness of this genome the highest amongst all published anemonefish genomes to date. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further analyses revealed higher copy numbers of erbb3b (a gene involved in melanocyte development) in A. clarkii compared to other anemonefish, thus suggesting a possible link between erbb3b and the natural melanism polymorphism observed in A. clarkii. The publication of this high-quality genome, along with A. clarkii’s many unique traits, position this species as an ideal model organism for addressing scientific questions across a range of disciplines.

Coastal urbanisation is a widespread phenomenon throughout the world and is often linked to increased erosion. Small Pacific islands are not spared from this issue, which is of great importance in the context of climate change. The French Polynesian island of Bora Bora was used as a case study to investigate the historical evolution of its coastline classification and position from 1955 to 2019. A time series of very high-resolution aerial imagery was processed to highlight the changes of the island’s coastline. The overall length of natural shores, including beaches, decreased by 46% from 1955 to 2019 while human-made shores such as seawalls increased by 476%, and as of 2019 represented 61% of the coastline. This evolution alters sedimentary processes: the time series of aerial images highlights increased erosion in the vicinity of seawalls and embankments, leading to the incremental need to construct additional walls. In addition, the gradual removal of natural shoreline types modifies landscapes and may negatively impact marine biodiversity. Through documenting coastal changes to Bora Bora over time, this study highlights the impacts of human-made structures on erosional processes and underscores the need for sustainable coastal management plans in French Polynesia.

Understanding the processes that shape biodiversity is essential for effective environmental management. Across the world’s coral reefs, algal farming damselfish (Stegastes sp.) modify the surrounding benthic community through their creation of algae “farms”. Using a long-term monitoring dataset (2005–2019) from Moorea Island, French Polynesia, we investigated whether the density of dusky damselfish (Stegastes nigricans) is associated with benthic habitat composition, the density of predators and/or competitors, and whether the survey area was inside or outside of a Marine Protected Area (MPA). We found no evidence that benthic cover or number of competitors were associated with dusky damselfish densities, both inside and outside MPAs. In contrast, fluctuations in dusky damselfish densities were negatively associated with the density of predators (e.g. Serranidae, Muraenidae and Scorpaenidae) in the preceding year in non-MPA areas, and both within and outside of MPAs when predator densities were high (2005–2010). These results suggest that healthy predator populations may be important for regulating the abundances of keystone species, such as algal farming damselfish, especially when predator densities are high.