James Tweedley

Understanding the behavioral strategies that allow freshwater mussels to persist under environmental stress is essential for their conservation, yet burrowing behavior remains poorly quantified. We tested whether valve movement data could be used to detect and characterize burrowing in the endangered Westralunio carteri; a species endemic to a region undergoing severe climatic drying. Mussels from multiple populations were monitored individually under laboratory conditions using Hall effect sensors, and valve movement patterns were analyzed to distinguish between burrowing and non-burrowing behaviors. Burrowing was associated with rapid, high-amplitude valve movements that lengthened as burial progressed, while non-burrowing behaviors showed distinct, slower patterns. These differences indicate that valvometry can reliably identify burrowing behavior, providing a non-invasive method for monitoring mussel activity. This approach has broad applications for ecological research, conservation assessment, and early-warning biomonitoring of imperiled freshwater mussel populations.

The brown-marbled grouper (Epinephelus fuscoguttatus), a high-value species in international trade, has experienced population declines due to intensive fishing. It is one of 12 grouper and snapper species prioritized for management in Saleh Bay, West Nusa Tenggara, Indonesia. This study analyzed catch data (2017–2022) and biological samples (2020–2021) to update key life history parameters, including natural mortality, von Bertalanffy growth parameters, asymptotic length, and size at maturity. Growth was estimated using an ELEFAN-optimized model applied to catch length–frequency data, while maturity was determined through macroscopic examination of gonads. The updated estimates (L50 = 488 mm for both sex; L95 = 568 mm for females and 616 mm for males) were incorporated into a length-based spawning potential ratio (SPR) assessment. Annual SPR values ranged from 0.13 to 0.28, substantially higher than previous estimates of 0.05–0.07, mainly due to the lower L50 used in this study. Despite this improvement, SPR values remain below the management target of 0.30 for groupers and snappers in Saleh Bay. Limited biological samples, particularly the scarcity of larger individuals and males, introduce uncertainty in the estimates. These findings emphasize the value of locally derived life history information and highlight the need for continued biological sampling to refine growth and reproductive parameters and support sustainable fisheries management.

This review examines possible estuarine fish colonisation processes of the Pacific Ocean that started in the Early Jurassic and gained momentum with the break-up of Pangea. Initial colonisation of the newly-created estuaries by fish is likely to have accelerated during the Devonian, with tropical marine families from the Neotethys Sea region using epicontinental seaways between Asia, Australia, India, Arabia, Europe and the Americas to colonise estuaries on these drifting land masses. Analyses of the presence/absence of fish families and species from selected ecoregions around the Pacific Ocean rim showed that estuary-associated fish families on the eastern and western side of the Pacific Ocean separated out at a Bray-Curtis similarity of 41 % but were only ∼5 % similar at the species level. In terms of past and present geodispersal of fish taxa, tropical species may have used ‘island hopping’ to cover the >19 000 km gap between the tropical western and eastern shores of the Pacific. However, most tropical taxa in the eastern Pacific appear to have originated from the Caribbean area of the Western Atlantic and not from the central Western Pacific fish species ‘hotspot’. In contrast, ichthyofaunal colonisation of Western Pacific regions to the north and south of the ‘hotspot’ was facilitated by ocean currents and the more limited distances between estuaries and coastal ecoregions in this part of the Pacific. The cold temperate waters of the Northern and Southern Pacific Ocean would have acted as a barrier to tropical species attempting to use these routes to cross the Pacific Ocean basin. The prevalence of temperate diadromous fish species in both the temperate northern (e.g. Russia and Alaska) and southern (e.g. New Zealand and Patagonia) estuaries is probably a function of local evolutionary trends that favoured such taxa in those particular regions.

Offshore wind farms (OWF) are rapidly emerging as essential infrastructure for transitioning to renewable energy, and this has been particularly important in the waters of China. To evaluate the impact of OWF construction, Ecopath models were developed for an OWF area and, separately, for a nearby control area, using biological and environmental survey data collected in 2022 and 2023. Functional groups were initially categorized into soft-substrate and hard-substrate (turbine monopiles) communities. The results showed that the colonization of turbine monopiles by sessile organisms significantly increased the productivity of most fish functional groups in the OWF area compared to the control. The OWF ecosystem exhibited higher trophic levels, especially for macroinvertebrates and fish, and a more complex food web with enhanced detritus flow than the control area. Mixed trophic impact analysis indicated a shift from a pelagic to a benthic-dominated system following OWF construction. Notably, detritus accounted for 52 % of total system throughput in the OWF area, compared to 38 % in the control area, highlighting a transition toward detritus-based energy flow. Furthermore, the OWF system showed significantly higher values for total system throughput, omnivory index, connectivity, Finn’s cycling index, and ascendency. Overall, the presence of the OWF resulted in significant changes in the trophic flow and system structure, creating a more complex, mature, and stable benthic-dominated ecosystem. These findings indicate that the establishment of OWF enhances both the structural composition and functional dynamics of surrounding marine ecosystems.

Machine learning has opened the door for the automated sorting (classification) of images, holograms and acoustic backscatters of individual plankton, invertebrates, fish and marine mammals. However, this field is complicated by decades of paradoxically promising reports of classifier performance that do not correlate with real-world uptake of this technology in aquatic sciences. Simple metrics of classifier performance are essential for optimizing, evaluating and comparing machine learning classifiers, but a wide variety of metrics and calculation variants have been proposed. Several characteristics of species count data influence metric behavior: severe imbalance and variance, zero-inflation, high class numbers and contamination with non-target classes. This study explores the hidden complexity of classifier performance metrics for species count data using synthetic datasets and simulated classifier outputs. It demonstrates how these data characteristics can severely distort metric values, with seven of eight variants of the most common metric, Accuracy, returning near-perfect scores (up to 98%) even when no instances are correctly classified. Clear recommendations are made for classifier evaluation pitfalls and metric variants to avoid, ultimately finding one variant of the F1-Score (mF1) to be the most suitable single metric, with several important calculation caveats specific to species count data. Due to ambiguous terminology and inconsistent definitions, it is often impossible to identify which variant of a performance metric has been applied in classifier studies. It is vital that authors are intentional and transparent about their metric use to support the vast potential for machine learning to revolutionize the research and monitoring of aquatic environments.

Estuaries are ephemeral ecosystems on geological timescales, with lifespans dictated by their degree of isolation from the ocean (Hodgkin & Hesp, 1998). The south coast of Western Australia has a Mediterranean climate, with rainfall declining and becoming more variable from west to east. Of the ~50 recognised estuaries in south-western Australia, those within the UNESCO-listed Fitzgerald Biosphere (Picture 1) receive amongst the lowest river flow and are often closed from the ocean by a sand bar at their mouths (Tweedley et al., 2016). Prolonged closure and evaporation lead to hypersalinity. Furthermore, catchment land clearing increases sedimentation, which reduces scouring and the duration of any sand bar breach. Combined with secondary salinsation, these impacts increase the magnitude of future hypersalinity (Hoeksema et al., 2018).

We visited estuaries in the Fitzgerald Biosphere in November 2020, after three years of below-average rainfall. Hypersaline conditions, which are known to reduce fish species richness and faunal complexity (Hoeksema et al., 2023), were recorded in all estuaries (55-240 ppt). The prevalence of hypersalinity has presumably acted as a selection pressure, as most native fish and invertebrate species found were highly salt-tolerant (Krispyn et al., 2021). While few fish species globally can survive prolonged exposure to salinities >50 ppt, in south-western Australia five species have been recorded in salinities ≥100 ppt. The prolonged bar closures required to create these environmental conditions reduce the provision of ecosystem goods and services by these estuaries, as they cannot act as nursery areas for marine species, export nutrients to coastal waters, and the reduced faunal assemblage limits food resources for fish and birds (Cronin-O'Reilly et al., 2024). As water evaporates and salinities increase, fish attempt to move into upstream refuges. However, rock and/or sand bars can prevent this movement, generating mortality events.

Climate predictions suggest reductions in winter rainfall and changes in the frequency of summer storms, which would influence bar breaching (Andrys et al., 2017). Sea levels will rise, but as the sand bars can be 5 m high and hundreds of meters long, the effect of wave overtopping may be limited. The combination of climate change and sedimentation may speed up the transition of some estuaries to salt lakes (Tweedley et al., 2024). Understanding the ecology of estuaries in the Fitzgerald Biosphere may inform the management of estuaries further west, and of low-inflow estuarine systems globally (Tweedley et al., 2019).

In some estuaries, low inflow and/or isolation from the ocean can result in evapoconcentration and hypersalinity (≥40 ppt). This can create osmoregulatory and energetic challenges for the faunal community, leading to reductions in diversity as more species pass their thresholds. As climate change is increasing the magnitude and duration of hypersaline conditions, we used benthic macroinvertebrate data from 12 estuaries across a Mediterranean climatic region (southwestern Australia) to assess the influence of salinity (0–122 ppt) on the invertebrate fauna. Taxa richness and diversity were highest in salinities between 0 and 39 ppt, peaking at salinities closest to seawater, while total density peaked at 40–49 ppt. Beyond 50 ppt, these measures declined significantly. Community composition changed markedly along the salinity gradient. In lower salinities, communities were diverse, comprising polychaetes, malacostracans, hexapods, ostracods, bivalves, and gastropods. However, in salinities ≥50 ppt, many taxa declined, leading to communities dominated by polychaetes (mainly Capitella spp.) and hexapods (mostly larval chironomids). At 90 ppt, only polychaetes and hexapods remained, and at ≥110 ppt, only the latter taxon persisted. This faunal shift towards insect dominance in hypersaline conditions mirrors observations in other Mediterranean and arid/semi-arid regions, with the resulting communities resembling saline wetlands or salt lakes. This loss of invertebrates can substantially impact ecosystem functioning and trophic pathways, and the findings of this study provide a basis for predicting how these communities will respond to increasing hypersalinity driven by climate change.

Coastal environments and their associated biota provide numerous environmental, economic and societal services. Cockburn Sound, a temperate embayment on the lower west coast of Western Australia, is immensely important for the State and adjacent capital city of Perth. However, urbanisation and associated terrestrial and marine development has the potential to threaten this important ecosystem. This study collated published and unpublished data to review the current state of the ecological resources of Cockburn Sound and describe how they have changed over the past century. Post-WWII, the embayment began undergoing pronounced anthropogenic changes that limited oceanic water exchange, increased nutrient load, modified benthic habitats and increased fishing pressure. The most visual outcome of these changes was substantial eutrophication and the loss of 77% of seagrass habitats. However, the increased primary productivity from elevated nutrient inputs produced high commercial fishery yields of up to ~1,700 t in the early 1990s before improved wastewater regulation and restricted fishing access steadily reduced commercial catches to ~300 t in recent years. Despite substantial anthropogenic-induced changes, Cockburn Sound has remained a diverse and ecologically important area. For example, the embayment is a key spawning area for large aggregations of Snapper, is a breeding and feeding site for seventeen marine bird species (including Little Penguins) and, is frequented by numerous protected species such as pinnipeds, dolphins, and White and Grey Nurse sharks. In recent decades, numerous projects have been initiated to restore parts of Cockburn Sound with mixed success, including seagrass transplantation, deployment of artificial reefs and stocking of key fish species, mainly Snapper. Nevertheless, while still biodiverse, there are signs of considerable ecological stress from escalating anthropogenic pressures and the cumulative impacts of ongoing and future developments, including climate change, which may severely impact the functioning of this important ecosystem.

Starting with the Remane diagram, various conceptual models have been proposed to show how species richness varies along a salinity gradient. However, as relatively few estuaries experience extreme hypersalinity, quantitative data are lacking to evaluate the model. We used data for 1891 samples of benthic macroinvertebrates from 12 estuaries in southwestern Australia (salinity 0–122 ppt) to determine the salinities in which 257 taxa were recorded. The pattern of richness differed from the conceptual models, with relatively few species (≤20%) recorded in freshwater and oligohaline salinities. Richness peaked at 35 ppt (seawater, 44%) before declining precipitously, with 21% and 10% of taxa recorded in hyperhaline salinities of 40 and 48 ppt, respectively. Taxa were recorded across the full salinity range, and several holohaline annelids, crustaceans, and insects were identified. Descriptive statistics and the frequency distribution of each taxon along the salinity gradient are provided. These identify stenohaline taxa and those with different extents of euryhalinity and how the occurrence of these taxa changes with salinity. The results help predict how benthic macroinvertebrate species and assemblages in estuaries in southwestern Australia and other Mediterranean climatic regions may shift due to climate change, particularly increased incidences and magnitude of hypersalinity.