2. Biodiversity

Bony fishes (class Osteichthyes) are characterised by having skeletons made from bone instead of cartilage. Found in many habitats, from intertidal areas to the open ocean, bony fishes have a major role in both the ecological and economic values of the Reef (Sections 5.4.2 and 5.4.3). Approximately 1625 species are found in the Region, and the majority (1468) are classed as coral reef species.³¹⁸ 

As with other species and groups, bony fish have strong associations with their habitat and the surrounding environmental conditions.³⁶⁴ As a result, current trends of habitat degradation are having flow-on effects, such as a trend towards species that are ecological generalists.³⁶⁵ Understanding the strength of habitat associations is essential for anticipating how the functional roles of fish may be affected by current and future environmental change.^366,367 Since 2019, understanding of how species composition of fish assemblages varies with changing habitat and environmental conditions has advanced considerably.^252,366,368 This information is vital for understanding the functional make up and subsequent ecological role(s) of fish assemblages.^140,369 Moreover, there are subsequent and reciprocal effects on ecological processes, such as food availability, recruitment and predation (Chapter 3). 

Effects are not consistent between species; while some highly specialised species will decline, others may persist (for example, the lemon damselfish, which can use different habitats, such as dead substrata), ³⁷⁰ though this can result in functional loss.³⁶⁵ Indeed, over time summary metrics, such as abundance and species richness, may recover or even appear quite stable but can mask changes to species composition.^371,372 Under future climate scenarios, fishes that already live close to the upper limit of their thermal tolerance (for example, some estuarine species) may be exposed to greater thermal stress.³⁷³ Models predict the range of suitable habitat for some important fishery species (such as juvenile red throat emperor, dusky flathead and blue threadfin salmon) will substantially reduce. Conversely, some species (for example, the flowery rockcod and barred javelin) may increase their distribution, benefiting from increased prey availability.³⁶⁸

Understanding of the effects of ocean warming on the condition of individual bony fishes has increased since the previous report. Development during elevated temperatures can lead to larvae depleting yolk reserves faster ³⁷⁴ and significant reductions in size of juveniles.^374,375 This is of particular concern because peak recruitment periods for juvenile fishes occur during the warmer months in the Region, a time of year when periods of elevated sea surface temperature (including marine heatwaves) are more likely. Transgenerational acclimatisation (that is, conditions experienced by both current and previous generations) can influence future offspring in some bony fish. For example, in the spiny chromis exposure of both parents and grandparents to elevated temperatures improved the aerobic capacity of offspring.³⁷⁶

Current extraction rates for some bony fish species in the Region are considered sustainable, though there are concerns for others (Section 5.4). Importantly, recent research into archival data has provided quantitative historical catch-rate estimates for two species, giant grouper (a protected species in recent times) and barramundi.^51,377 Investigations like this assist with recognition and avoidance of shifting baseline syndromes. 

Microplastic contamination may harm bony fish resulting in cellular stress,³⁷⁸ hormonal imbalances ³⁷⁹ and behavioural traits that may reduce survival.³⁸⁰ Microplastics enter bony fish mainly through ingestion (planktivorous species ³⁸¹) and other pathways (such as passive uptake through the gills ³⁸² or trophic transfer ³⁸³). In general, microplastic loads across the Region are low compared to more densely populated areas of the country.³⁸⁴ Since 2019, spikes in microplastic loads have been associated with seasonal and localised weather events. This issue has the potential to increase in the Region over time as coastal populations grow. 

Long-term monitoring of 3 key fish groups (butterflyfish, parrotfish and surgeonfish) across the Region has identified some changes in mean abundance across reefs surveyed since 2009 (Figure 2.9). Butterflyfish, which rely heavily on coral and other invertebrates for food, have shown possible increases since 2018–19 at the Cooktown–Lizard Island, Cairns and Townsville reefs, the Swain Reefs and offshore Whitsundays reefs. The increase seen in 2016–17 for Capricorn Bunker group reefs has persisted. Abundances of surgeonfish and parrotfish, which feed on a combination of microorganisms that live on or within calcareous substrata,³⁸⁵ have been more variable over time. A trend of slowly increasing parrotfish abundance may be emerging in the Capricorn Bunker group over the long term, while reefs in the Pompeys and around Townsville (mid-shelf and offshore) have shown an overall increase in numbers since 2019–20. Since 2019, patterns in surgeonfish abundance have been variable across surveyed reefs. For instance, surgeonfish abundance has generally decreased in the offshore Whitsundays reefs since 2016–17 (apart from in 2022, when an increase was recorded) and are now below the 2008–09 level. In contrast, numbers of surgeonfish at Swain Reefs and in the Capricorn Bunker group have increased since 2019. 

Changes in the mean abundance of some bony fishes have been observed since 2019 and over the longer term. Trends vary between species groups and regions, and both increases and declines have been observed. In some cases, the observed changes may reflect natural fluctuations in populations. Climate change, habitat degradation and targeted extraction are exerting pressure on bony fishes, and having varying effects in different species and functional groups.