Validation of eDNA as a viable method of detection for dangerous cubozoan jellyfish

Stings from certain species of cubozoan jellyfish are dangerous to humans and their seasonal presence in tropical marine waters poses a significant risk to coastal communities. The detection of cubozoans is difficult due to high spatial and temporal variation in their occurrence and abundance. Environmental DNA (eDNA) has the potential to detect rare species and therefore offers potential to detect cubozoans, not only pelagic medusae, but presence of cryptic polyp life stages. The objective of this study was to validate the use of eDNA as a viable detection method for four cubozoan species (Chironex fleckeri, Copula sivickisi, Carybdea xaymacana, and Carukia barnesi). Species‐specific primers were developed for each of these four cubozoans and an eDNA approach validated utilizing both laboratory and field trials. Laboratory DNA degradation experiments demonstrated that C. sivickisi DNA degraded quickly but could still be detected in sea water for up to 9 days post‐jellyfish removal. Positive detection was found for C. fleckeri, C. xaymacana, and C. sivickisi medusae in the waters surrounding Magnetic Island, Queensland, in the Austral spring/summer (September‐January). Based on visual surveys, there was a poor relationship between concentration of eDNA and abundance of jellyfish. Positive eDNA amplification was also found from water sampled near the substratum when C. sivickisi medusae were out of season and absent. This suggests the eDNA analysis was likely detecting C. sivickisi polyps located within the substratum. Consequently, eDNA is an effective tool to detect both the medusae and likely polyps of cubozoans. This approach provides the means to reduce the risk of envenomation to swimmers and enhance our knowledge of cubozoan ecology

Deep-reef fish communities of the Great Barrier Reef shelf-break: trophic structure and habitat associations

The ecology of habitats along the Great Barrier Reef (GBR) shelf-break has rarely been investigated. Thus, there is little understanding of how associated fishes interact with deeper environments. We examined relationships between deep-reef fish communities and benthic habitat structure. We sampled 48 sites over a large depth gradient (54–260 m) in the central GBR using Baited Remote Underwater Video Stations and multibeam sonar. Fish community composition differed both among multiple shelf-break reefs and habitats within reefs. Epibenthic cover decreased with depth. Deep epibenthic cover included sponges, corals, and macro-algae, with macro-algae present to 194 m. Structural complexity decreased with depth, with more calcified reef, boulders, and bedrock in shallower depths. Deeper sites were flatter and more homogeneous with softer substratum. Habitats were variable within depth strata and were reflected in different fish assemblages among sites and among locations. Overall, fish trophic groups changed with depth and included generalist and benthic carnivores, piscivores, and planktivores while herbivores were rare below 50 m. While depth influenced where trophic groups occurred, site orientation and habitat morphology determined the composition of trophic groups within depths. Future conservation strategies will need to consider the vulnerability of taxa with narrow distributions and habitat requirements in unique shelf-break environments

Data from: Changes in desert avifauna associated with the functional extinction of a terrestrial top predator

We investigated how long-term suppression of populations of a top predator, the dingo Canis dingo, affected composition of sympatric avifauna in Australian deserts, by surveying bird assemblages across ~80 000 km2 of arid dunefields on either side of the Dingo Barrier Fence (DBF; a 5,614 km-long fence separating ecosystems in which dingoes are abundant from ecosystems in which dingoes are functionally extinct). Using fourth-corner modelling, incorporating species’ traits, we identified apparent declines of sedentary birds that nest in low vegetation and small birds that feed primarily on grass seed, and increases in scavenging birds associated with the functional extinction of dingoes. Occupancy differed between sites inside and outside the DBF in 13 bird species. We hypothesise that these differences in bird assemblages across the DBF result, in part, from increases in kangaroos (Macropus spp.) and red foxes (Vulpes vulpes) in arid landscapes where dingoes have been removed. Our study provides evidence that the functional extinction of a large terrestrial predator has had pervasive ecosystem effects, including shifts in composition of avian assemblages

The Great Barrier Reef: biology, environment and management

The Great Barrier Reef Marine Park is 344 400 square kilometres in size and is home to one of the most diverse ecosystems in the world. This comprehensive guide describes the organisms and ecosystems of the Great Barrier Reef, as well as the biological, chemical and physical processes that influence them. Contemporary pressing issues such as climate change, coral bleaching, coral disease and the challenges of coral reef fisheries are also discussed.\ud \ud In addition,the book includes a field guide that will help people to identify the common animals and plants on the reef, then to delve into the book to learn more about the roles the biota play.\ud \ud Beautifully illustrated and with contributions from 33 international experts, The Great Barrier Reef is a must-read for the interested reef tourist, student, researcher and environmental manager. While it has an Australian focus, it can equally be used as a baseline text for most Indo-Pacific coral reefs

Deep-reef fish assemblages of the Great Barrier Reef shelf-break (Australia)

Abstract Tropical mesophotic and sub-mesophotic fish ecology is poorly understood despite increasing vulnerability of deeper fish assemblages. Worldwide there is greater fishing pressure on continental shelf-breaks and the effects of disturbances on deeper fish species have not yet been assessed. Difficult to access, deeper reefs host undocumented fish diversity and abundance. Baited Remote Underwater Video Stations (BRUVS) with lights were used to sample deeper habitats (54–260 m), in the Great Barrier Reef (GBR), Australia. Here we describe fish biodiversity, relative abundance and richness, assessing the prediction that depth would drive assemblage structure in the GBR. Distinct groups of fishes were found with depth whilst overall richness and abundance decreased steeply between 100 and 260 m. Commercially-valuable Lutjanidae species from Pristipomoides and Etelis genera, were absent from shallower depths. Few fish species overlapped between adjacent depth strata, indicating unique assemblages with depth. We also detected new location records and potential new species records. The high biodiversity of fish found in shelf-break environments is poorly appreciated and depth is a strong predictor of assemblage composition. This may pose a challenge for managers of commercial fisheries as distinct depth ranges of taxa may translate to more readily targeted habitats, and therefore, an inherent vulnerability to exploitation

Partially protected areas as a management tool on inshore reefs

Partially Protected Areas (PPAs) are a widely-used management tool, yet comparatively little is known about their effectiveness compared to more commonly studied No-Take Marine Reserves (NTMRs). Here, we examine the efficacy of two kinds of PPAs (with and without spearfishing) within the Great Barrier Reef Marine Park (GBRMP) that are subject to a range of fishing limitations, and assess their utility as a marine park zoning and fisheries management tool. Fish abundance, size, and habitat composition were compared inside PPAs and NTMRs on inshore reefs of the central GBR. Fish abundances were lower inside PPAs relative to adjacent NTMRs for primary fishing targets, with no detectable effects for secondary targets and non-targets, or for species richness. Fish assemblages differed amongst zones, but these variations were minor compared to regional variations in species composition. Partially Protected Areas supported 46%–69% of the relative abundance of total primary targets compared to adjacent NTMRs, with no evident increase in abundance in zones where spearfishing was prohibited. There were no reductions in the size of two key target species: coral trout (Plectropomus spp.) and stripey snapper (Lutjanus carponotatus) inside PPAs, and only stripey snapper had significant reductions in abundance inside PPAs compared to NTMRS. Habitat and biophysical characteristics (especially topographic complexity) were strong drivers of fish abundance, but the relative influence of zone was greater for target species compared to non-targets. This study provides novel data on PPAs and highlights their utility as a spatial management tool in contributing to conservation and fisheries management goals

Bird survey data for dryad

Bird survey data for drya

Aerial photography and machine learning for estimating extremely high flamingo numbers on the Makgadikgadi Pans, Botswana

Monitoring biodiversity over time and space is essential for effective conservation of habitats, processes, and dependent organisms. Estimating large abundances of individuals can be challenging (e.g. birds and mammals), demanding efficient and effective methods. The Makgadikgadi Pans in north-eastern Botswana have high concentrations of breeding and feeding flamingos (Phoenicopterus roseus and Phoeniconaias minor), among the world’s most important breeding sites. No published estimates of flamingos exist since 2009, with historical estimates providing limited details on methods. We developed a semi-supervised machine learning method for counting a large feeding concentration of flamingos (2 June 2019) in aerial photographs from northern Sua Pan of the Makgadikgadi Pans. We also analysed rainfall and flooding frequency and extent, using satellite imagery, estimating likely frequency of these flamingo concentrations. Lastly, we reviewed the site’s global importance as flamingo breeding habitat. Our analysis successfully provided an estimate of 372,172 to 689,473 flamingos, with methods producing over 97 % test accuracy. Uncertainty related primarily to data coverage and collection rather than methodology. This estimate underlined the Makgadikgadi Pans’ significance for flamingos, supported by a high frequency of flooding (>5:10 years). Sua Pan ranked in the top ten breeding sites for the lesser and greater flamingos in the world. These methods can be applied to other large concentrations of flamingos and other animals. Our techniques provide considerable promise for tracking flamingo populations to ensure their protection. We provide code, for use in Google Earth Engine

Breeding Flow Thresholds of Colonial Breeding Waterbirds in the Murray-Darling Basin, Australia

Biodiversity on floodplains is under increasing pressure as demand for water for human needs expands. Understanding how waterbirds respond to river flows feeding floodplain wetlands is critical for successful management. We analysed data on breeding by colonial breeding large waders-Eastern Great Egret Ardea modesta, Intermediate Egret Ardea intermedia, Little Egret Egretta garzetta, Nankeen Night Heron Nycticorax caledonicus, Australian White Ibis Threskiornis molucca, Glossy Ibis Plegadis falcinellus, Straw-necked Ibis Threskiornis spinicollis, and Royal Spoonbill Platalea regia-in response to river flow for three wetlands in the Murray- Darling Basin, Australia. Each wetland, which included Barmah-Millewa, the Macquarie Marshes, and Lake Merreti, has a distinctive geomorphology and hydrology. There were clear consistent thresholds of flow producing a >0.7 probability of attempted breeding by most species when a daily flow threshold was exceeded for 30-50 days. Flow characteristics were highly correlated and thresholds could also be expressed in terms of the total flow volume July-December and peak flow in September or October. Below thresholds, there was zero probability of breeding for most species. These minimum thresholds provide critical information for management of these wetlands. Our approach provides an analytical framework for estimating thresholds for other floodplains