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Although coral reef health across the globe is declining as a result of anthropogenic impacts, relatively little is known of how environmental variability influences reef organisms other than corals and fish. Sponges are an important component of coral reef fauna that perform many important functional roles and changes in their abundance and diversity as a result of environmental change has the potential to affect overall reef ecosystem functioning. In this study, we examined patterns of sponge biodiversity and abundance across a range of environments to assess the potential key drivers of differences in benthic community structure. We found that sponge assemblages were significantly different across the study sites, but were dominated by one species Lamellodysidea herbacea (42% of all sponges patches recorded) and that the differential rate of sediment deposition was the most important variable driving differences in abundance patterns. Lamellodysidea herbacea abundance was positively associated with sedimentation rates, while total sponge abundance excluding Lamellodysidea herbacea was negatively associated with rates of sedimentation. Overall variation in sponge assemblage composition was correlated with a number of variables although each variable explained only a small amount of the overall variation. Although sponge abundance remained similar across environments, diversity was negatively affected by sedimentation, with the most sedimented sites being dominated by a single sponge species. Our study shows how some sponge species are able to tolerate high levels of sediment and that any transition of coral reefs to more sedimented states may result in a shift to a low diversity sponge dominated system, which is likely to have subsequent effects on ecosystem functioning.

Declines in coral abundance have been linked to increased sedimentation at many locations across the world and at some of these locations there have been subsequent increases in sponge abundance. These shifts appear counterintuitive as sponges are suspension feeders and many rely on photosymbionts for carbon. At a sedimented reef in Indonesia (Wakatobi) corals have declined and the photoautotrophic sponge Lamellodysidea herbacea is now abundant. We hypothesise that this is partly due to L. herbacea’s ability to clear its tissues of high levels of settled-sediment and compensate for associated metabolic demands by altering its respiration rate. Negligible detrimental effects to sponge tissue were observed after treatments up to five times the sedimentation rate of the highly sedimented reef. Rapid sediment clearance occurred that was potentially aided by mucus production. Finally, high sediment exposure caused an immediate reduction in respiration rate, likely due to reduced pumping to prevent clogging, whereas sustained high sedimentation caused an increase in respiration rate, potentially due to the energetic cost of mucus production. Our study provides evidence that some sponges can tolerate environments that appear unsuitable to many corals and with increased sedimentation this acclimation may support further transitions to sponge dominated reefs in the future.

Coral reefs across the world are under threat from a range of stressors, and while there has been considerable focus on the impacts of these stressors on corals, far less is known about their effect on other reef organisms. The 1997–8 El-Niño Southern Oscillation (ENSO) had notable and severe impacts on coral reefs worldwide, but not all reef organisms were negatively impacted by this large-scale event. Here we describe how the sponge fauna at Bahia, Brazil was influenced by the 1997–8 ENSO event. Sponge assemblages from three contrasting reef habitats (reef tops, walls and shallow banks) at four sites were assessed annually from 1995 to 2011. The within-habitat sponge diversity did not vary significantly across the study period; however, there was a significant increase in density in all habitats. Multivariate analyses revealed no significant difference in sponge assemblage composition (ANOSIM) between pre- and post-ENSO years for any of the habitats, suggesting that neither the 1997–8 nor any subsequent smaller ENSO events have had any measurable impact on the reef sponge assemblage. Importantly, this is in marked contrast to the results previously reported for a suite of other taxa (including corals, echinoderms, bryozoans, and ascidians), which all suffered mass mortalities as a result of the ENSO event. Our results suggest that of all reef taxa, sponges have the potential to be resilient to large-scale thermal stress events and we hypothesize that sponges might be less affected by projected increases in sea surface temperature compared to other major groups of reef organisms.

Understanding patterns of connectivity and adaptive divergence is crucial for supporting conservation and sustainable management of harvested species. This study utilised single nucleotide polymorphisms (SNPs) to investigate spatially explicit patterns of genetic structure, gene flow and adaptive divergence in the commercially important southern rock lobster Jasus edwardsii across New Zealand (NZ), a species with a 2‐year pelagic larval duration. Using neutral (1608 SNPs) and outlier (250 SNPs) panels, genetic analyses revealed significant population differentiation between J. edwardsii individuals collected from one site in Tasmania (Australia) and those from 22 sites in NZ, supporting earlier findings indicating substantial genetic variation between the two stocks. Within NZ, neutral markers revealed a high degree of genetic connectivity of J. edwardsii, but also subtle genetic differentiation of one northern site only. In contrast, analysis of outlier markers identified three genetically differentiated regions within NZ: the Northeast (NE), Northwest (NW) and Southern (S) groups. Migration models indicated bidirectional but asymmetrical gene flow amongst these groups (S → NW → NE), consistent with larval dispersal and settlement models. Patterns of genetic structure at the outlier loci were strongly correlated with the environmental variables ‘carbonate concentration’, ‘roughness at the seafloor’ and ‘sea surface temperature’ across NZ, which may contribute to differential settlement and survival of J. edwardsii. These findings demonstrate complex patterns of connectivity and the influence of environment factors on genetic structure and local genetic adaptative divergence of J. edwardsii despite its very high dispersal potential. The population genomic and connectivity findings support the current spatially explicit management regime of the rock lobster fishery in New Zealand, and the seascape genomic findings may be of value to the fishery in responding to new or enhanced patterns of environmental variability driven by climate change or to the development of a new aquaculture industry.

While estimates of connectivity are important for effective management, few such estimates are available for reef invertebrates other than for corals. Barrel sponges are one of the largest and most conspicuous members of the coral reef fauna across the Indo-Pacific and given their large size, longevity and ability to process large volumes of water, they have a major role in reef functioning. Here we used a panel of microsatellite markers to characterise the genetic structure of two barrel sponge species, Xestospongia testudinaria and a currently undescribed Xestospongia species. We sampled across seven populations in the Wakatobi Marine National Park, SE Sulawesi (Indonesia) spanning a spatial scale of approximately 2 to 70 km, and present the first estimates of demographic connectivity for coral reef sponges. Genetic analyses showed high levels of genetic differentiation between all populations for both species, but contrasting patterns of genetic structuring for the two species. Autocorrelation analyses showed the likely dispersal distances of both species to be in the order of 60 and 140 m for Xestopongia sp. and Xestospongia testudinaria, respectively, which was supported by assignment tests that showed high levels of self-recruitment (>80%). We also found consistently high inbreeding coefficients across all populations for both species. Our study highlights the potential susceptibility of barrel sponges to environmental perturbations because they are generally long-lived, slow growing, have small population sizes and are likely to be reliant on self-recruitment. Surprisingly, despite these features we actually found the highest abundance of both barrel sponge species (although they were generally smaller) at a site that has been severely impacted by humans over the last fifty years. This suggests that barrel sponges exhibit environmental adaptation to declining environmental quality and has important implications for the management and conservation of these important reef species.

Temperate mesophotic ecosystems (TMEs) have the potential to act as climate refugia for shallower benthic species impacted by environmental change. However, the extent to which mesophotic ecosystems might provide an ecological refuge, particularly for key functional groups like sponges, remains poorly known in temperate systems. Our study investigates sponge assemblage structure across a depth gradient at the Poor Knights Islands Marine Reserve, New Zealand, to assess the potential for mesophotic depths to act as ecological refuges for species inhabiting shallow water in the scenarios where mesophotic depths avoid shallower disturbances. Using ROV and SCUBA‐based image surveys across three sites, sponge abundance data were collected from depths spanning 5 to 65 m. Assemblage composition, species richness, and depth‐dependent abundance patterns were analysed using nMDS, PERMANOVA, and linear regression. Results revealed high beta diversity across depths, with sponge assemblages strongly structured by depth. The majority of sponge operational taxonomic units (OTUs) were restricted to either shallow (< 30 m) or mesophotic (> 30 m) zones, with between 26.4 and 32.7% of OTUs shared between both, and a total of 18 sponge OTUs found in multiple depths in each zone across all three sites. Depth related abundance patterns tended to be species specific, meaning the potential for any refuge effect will likely also vary between species depending on their local abundance. Our findings highlight the vertical structuring of sponge assemblages and suggest that, while TMEs may offer some refuge potential to specific species in scenarios where mesophotic habitats avoid disturbances experienced by shallow species, the benefits won't apply to entire sponge assemblages.

Despite the importance of trophic interactions between organisms, and the relationship between primary production and benthic diversity, there have been few studies that have quantified the carbon flow from pelagic to benthic environments as a result of the assemblage level activity of suspension-feeding organisms. In this study, we examine the feeding activity of seven common sponge species from the Taputeranga marine reserve on the south coast of Wellington in New Zealand. We analysed the diet composition, feeding efficiency, pumping rates, and the number of food particles (specifically picoplanktonic prokaryotic cells) retained by sponges. We used this information, combined with abundance estimates of the sponges and estimations of the total amount of food available to sponges in a known volume of water (89,821 m(3)), to estimate: (1) particulate organic carbon (POC) fluxes through sponges as a result of their suspension-feeding activities on picoplankton; and (2) the proportion of the available POC from picoplankton that sponges consume. The most POC acquired by the sponges was from non-photosynthetic bacterial cells (ranging from 0.09 to 4.69 g C d(-1) with varying sponge percentage cover from 0.5 to 5%), followed by Prochlorococcus (0.07 to 3.47 g C d(-1)) and then Synechococcus (0.05 to 2.34 g C d(-1)) cells. Depending on sponge abundance, the amount of POC that sponges consumed as a proportion of the total POC available was 0.2-12.1% for Bac, 0.4-21.3% for Prochlo, and 0.3-15.8% for Synecho. The flux of POC for the whole sponge assemblage, based on the consumption of prokaryotic picoplankton, ranged from 0.07-3.50 g C m(2) d(-1). This study is the first to estimate the contribution of a sponge assemblage (rather than focusing on individual sponge species) to POC flow from three groups of picoplankton in a temperate rocky reef through the feeding activity of sponges and demonstrates the importance of sponges to energy flow in rocky reef environments.

Sponges are functionally important components of global benthic environments and have been proposed as potential winners under future climate scenarios. We review the evidence to support this hypothesis by examining the individual and combined effects of ocean warming (OW) and ocean acidification (OA) on sponges and comparing sponge responses with tolerance thresholds for other benthic organisms. Although sponges are generally tolerant of OA and may even benefit from elevated partial pressure of carbon dioxide, they are often sensitive to seawater temperatures only a few degrees higher than their normal range. Sponge responses to the combined effects of OA and OW are generally more positive than their response to OW alone. We found that sponges are generally less affected by OW or OA than are a number of currently dominant benthic organisms, such as corals. Therefore, sponges are expected to benefit under near-future climate scenarios, although species-specific differences in tolerance will likely shift the sponge assemblage composition toward more resilient species.

While there is now strong evidence that many factors can shape dispersal, the mechanisms influencing connectivity patterns are species‐specific and remain largely unknown for many species with a high dispersal potential. The rock lobsters Jasus tristani and Jasus paulensis have a long pelagic larval duration (up to 20 months) and inhabit seamounts and islands in the southern Atlantic and Indian Oceans, respectively. We used a multidisciplinary approach to assess the genetic relationships between J. tristani and J. paulensis, investigate historic and contemporary gene flow, and inform fisheries management. Using 17,256 neutral single nucleotide polymorphisms we found low but significant genetic differentiation. We show that patterns of connectivity changed over time in accordance with climatic fluctuations. Historic migration estimates showed stronger connectivity from the Indian to the Atlantic Ocean (influenced by the Agulhas Leakage). In contrast, the individual‐based model coupled with contemporary migration estimates inferred from genetic data showed stronger inter‐ocean connectivity in the opposite direction from the Atlantic to the Indian Ocean driven by the Subtropical Front. We suggest that the J. tristani and J. paulensis historical distribution might have extended further north (when water temperatures were lower) resulting in larval dispersal between the ocean basis being more influenced by the Agulhas Leakage than the Subtropical Front. As water temperatures in the region increase in accordance with anthropogenic climate change, a southern shift in the distribution range of J. tristani and J. paulensis could further reduce larval transport from the Indian to the Atlantic Ocean, adding complexity to fisheries management. Using a multidisciplinary approach combining genetic data (SNPs) with individual‐based modelling, we show that patterns of connectivity between rock lobsters Jasus tristani and Jasus paulensis changed over time in accordance with climatic fluctuations. Historical connectivity between the ocean basis was more influenced by the Agulhas Leakage (from the Indian to the Atlantic Ocean) while contemporary connectivity is stronger in the opposite direction from the Atlantic to the Indian Ocean, driven by the Subtropical Front.

Double digest restriction site-associated DNA sequencing (ddRADseq) and target capture sequencing methods are used to explore population and phylogenetic questions in non-model organisms. ddRADseq offers a simple and reliable protocol for population genomic studies, however it can result in a large amount of missing data due to allelic dropout. Target capture sequencing offers an opportunity to increase sequencing coverage with little missing data and consistent orthologous loci across samples, although this approach has generally been applied to conserved markers for deeper evolutionary questions. Here, we combine both methods to generate high quality sequencing data for population genomic studies of all marine lobster species from the genus Jasus . We designed probes based on ddRADseq libraries of two lobster species ( Jasus edwardsii and Sagmariasus verreau xi) and evaluated the captured sequencing data in five other Jasus species. We validated 4,465 polymorphic loci amongst these species using a cost effective sequencing protocol, of which 1,730 were recovered from all species, and 4,026 were present in at least three species. The method was also successfully applied to DNA samples obtained from museum specimens. This data will be further used to assess spatial-temporal genetic variation in Jasus species found in the Southern Hemisphere.