Genome-wide SNPs in the spiny lobster Panulirus homarus reveal a hybrid origin for its subspecies.

BACKGROUND: Evolutionary divergence and speciation often occur at a slower rate in the marine realm due to the higher potential for long-distance reproductive interaction through larval dispersal. One common evolutionary pattern in the Indo-Pacific, is divergence of populations and species at the peripheries of widely-distributed organisms. However, the evolutionary and demographic histories of such divergence are yet to be well understood. Here we address these issues by coupling genome-wide SNP data with mitochondrial DNA sequences to test the patterns of genetic divergence and possible secondary contact among geographically distant populations of the highly valuable spiny lobster Panulirus homarus species complex, distributed widely through the Indo-Pacific, from South Africa to the Marquesas Islands. RESULT: After stringent filtering, 2020 SNPs were used for population genetic and demographic analyses, revealing strong regional structure (FST = 0.148, P < 0001), superficially in accordance with previous analyses. However, detailed demographic analyses supported a much more complex evolutionary history of these populations, including a hybrid origin of a North-West Indian Ocean (NWIO) population, which has previously been discriminated morphologically, but not genetically. The best-supported demographic models suggested that the current genetic relationships among populations were due to a complex series of past divergences followed by asymmetric migration in more recent times. CONCLUSION: Overall, this study suggests that alternating periods of marine divergence and gene flow have driven the current genetic patterns observed in this lobster and may help explain the observed wider patterns of marine species diversity in the Indo-Pacific.

A Gulf in lockdown: How an enforced ban on recreational vessels increased dolphin and fish communication ranges.

From midnight of 26 March 2020, New Zealand became one of the first countries to enter a strict lockdown to combat the spread of COVID-19. The lockdown banned all non-essential services and travel both on land and sea. Overnight, the country's busiest coastal waterway, the Hauraki Gulf Marine Park, became devoid of almost all recreational and non-essential commercial vessels. An almost instant change in the marine soundscape ensued, with ambient sound levels in busy channels dropping nearly threefold the first 12 h. This sudden drop led fish and dolphins to experience an immediate increase in their communication ranges by up to an estimated 65%. Very low vessel activity during the lockdown (indicated by the presence of vessel noise over the day) revealed new insights into cumulative noise effects from vessels on auditory masking. For example, at sites nearer Auckland City, communication ranges increased approximately 18 m (22%) or 50 m (11%) for every 10% decrease in vessel activity for fish and dolphins, respectively. However, further from the city and in deeper water, these communication ranges were increased by approximately 13 m (31%) or 510 m (20%). These new data demonstrate how noise from small vessels can impact underwater soundscapes and how marine animals will have to adapt to ever-growing noise pollution.

The Effect of Sound Frequency and Intensity on Yeast Growth, Fermentation Performance and Volatile Composition of Beer.

This study investigated the impact of varying sound conditions (frequency and intensity) on yeast growth, fermentation performance and production of volatile organic compounds (VOCs) in beer. Fermentations were carried out in plastic bags suspended in large water-filled containers fitted with underwater speakers. Ferments were subjected to either 200-800 or 800-2000 Hz at 124 and 140 dB @ 20 µPa. Headspace solid-phase microextraction (HS-SPME) coupled with gas chromatography-mass spectrometry (GC-MS) was used to identify and measure the relative abundance of the VOCs produced. Sound treatment had significant effects on the number of viable yeast cells in suspension at 10 and 24 h (p < 0.05), with control (silence) samples having the highest cell numbers. For wort gravity, there were significant differences between treatments at 24 and 48 h, with the silence control showing the lowest density before all ferments converged to the same final gravity at 140 h. A total of 33 VOCs were identified in the beer samples, including twelve esters, nine alcohols, three acids, three aldehydes, and six hop-derived compounds. Only the abundance of some alcohols showed any consistent response to the sound treatments. These results show that the application of audible sound via underwater transmission to a beer fermentation elicited limited changes to wort gravity and VOCs during fermentation.

The role of biofouling development in the loss of seed mussels in aquaculture.

The efficient seeding of juvenile mussels is critical to the sustainability and profitability of mussel aquaculture. However, seeding mussels is highly inefficient, with many juveniles being lost in the following few months. One possible cause of these losses could be the development of biofouling assemblages. Therefore, the relationships between biofouling accumulation and losses of juveniles were assessed. Losses of juvenile mussels were initially high (42.9-49.1% over approximately one to two weeks), with lower rates of loss over the following four to five months. Biofouling development followed a successional pattern beginning with colonisation by amphipods, subsequent establishment of macroalgae, and the formation of an assemblage dominated by mussels and sessile invertebrates. However, biofouling development did not play a major role in the loss of juveniles. Rather, large-scale losses of mussels occurred shortly after seeding when biofouling was scant, suggesting alternative causes of loss were in operation.

Mechanisms of peripheral phylogeographic divergence in the indo-Pacific: lessons from the spiny lobster Panulirus homarus.

BACKGROUND: There is increasing recognition of the concordance between marine biogeographic and phylogeographic boundaries. However, it is still unclear how population-level divergence translates into species-level divergence, and what are the principal factors that first initiate that divergence, and then maintain reproductive isolation. This study examines the likely forces driving population and lineage divergences in the broadly-distributed Indo-Pacific spiny lobster Panulirus homarus, which has peripheral divergent lineages in the west and east. The study focuses particularly on the West Indian Ocean, which is emerging as a region of unexpected diversity. Mitochondrial control region (mtCR) and COI sequences as well as genotypes of 9 microsatellite loci were examined in 410 individuals from 17 locations grouped into 7 regions from South Africa in the west, and eastward across to Taiwan and the Marquesas Islands. Phylogenetic and population-level analyses were used to test the significance and timing of divergences and describe the genetic relationships among populations. RESULTS: Analyses of the mtCR revealed high levels of divergence among the seven regions (ФST = 0.594, P < 0.001). Microsatellite analyses also revealed significant divergence among regions, but at a much lower level (FST = 0.066, P < 0.001). The results reveal different patterns of mtCR v. nDNA divergence between the two distinct peripheral lineages: a subspecies in South Africa and Madagascar, and a phylogeographically diverged population in the Marquesas. The results also expose a number of other more fine-scale population divergences, particularly in the Indian Ocean. CONCLUSIONS: The divergence of peripheral lineages in the west and east of the species' range appear to have been initiated and maintained by very different processes. The pattern of mitochondrial and nuclear divergence of the western lineage, implicates processes of parapatric isolation, secondary contact and introgression, and suggests possible maintenance through adaptation and behavioural reproductive isolation. In contrast, the eastern lineage appears to have diverged through a rare colonisation event, maintained through long-term isolation, and matches expectations of the core-periphery hypothesis. The process of active peripheral speciation may be a common force in the Indo-Pacific that helps drive some of the regions' recognized biogeographic boundaries.

Effects of Underwater Turbine Noise on Crab Larval Metamorphosis.

The development of marine tidal turbines has advanced at a rapid rate over the last decade but with little detailed understanding of the potential noise impacts on invertebrates. Previous research has shown that underwater reef noise plays an important role in mediating metamorphosis in many larval crabs and fishes. New research suggests that underwater estuarine noise may also mediate metamorphosis in estuarine crab larvae and that the noise emitted from underwater tidal and sea-based wind turbines may significantly influence larval metamorphosis in estuarine crabs.

Vessel Noise Promotes Hull Fouling.

Fouling of submerged vessel hulls due to the rapid settlement of algae and invertebrates is a longstanding and costly problem. It is widely thought that the presence of extensive vacant surfaces on vessel hulls is responsible for the rapid attachment and growth of biofouling. We investigated whether noise from vessels in port could also be involved in promoting the settlement and growth of common biofouling organisms on vessel hulls. Three important biofouling species exhibited significantly faster development and settlement and better survival when exposed to vessel noise compared with control species. The extent of these responses appeared to vary in relation to the intensity of the vessel noise and may help to explain differences in biofouling observed on vessel hulls.

Vocalisations of the bigeye Pempheris adspersa: characteristics, source level and active space.

Fish sounds are an important biological component of the underwater soundscape. Understanding species-specific sounds and their associated behaviour is critical for determining how animals use the biological component of the soundscape. Using both field and laboratory experiments, we describe the sound production of a nocturnal planktivore, Pempheris adspersa (New Zealand bigeye), and provide calculations for the potential effective distance of the sound for intraspecific communication. Bigeye vocalisations recorded in the field were confirmed as such by tank recordings. They can be described as popping sounds, with individual pops of short duration (7.9±0.3 ms) and a peak frequency of 405±12 Hz. Sound production varied during a 24 h period, with peak vocalisation activity occurring during the night, when the fish are most active. The source level of the bigeye vocalisation was 115.8±0.2 dB re. 1 µPa at 1 m, which is relatively quiet compared with other soniferous fish. Effective calling range, or active space, depended on both season and lunar phase, with a maximum calling distance of 31.6 m and a minimum of 0.6 m. The bigeyes' nocturnal behaviour, characteristics of their vocalisation, source level and the spatial scale of its active space reported in the current study demonstrate the potential for fish vocalisations to function effectively as contact calls for maintaining school cohesion in darkness.

Inducers of settlement and moulting in post-larval spiny lobster.

The rapid and often remote location of suitable habitats used by migrating organisms is often critical to their subsequent recruitment, fitness and survival, and this includes in the marine environment. However, for the non-feeding post-larval stage of spiny lobsters, effective settlement cues for habitat selection are critical to their success but are poorly described. Therefore, the current study examined whether acoustic and substrate cues have the potential to shorten the time to moulting and affect their subsequent nutritional condition in the pueruli of the southern spiny lobster, Jasus edwardsii. Individuals moulted to first instar juveniles up to 38% faster when exposed to the underwater sound from two types of typical settlement habitat (coastal kelp- and urchin-dominated reefs) compared to those with no underwater sound. The settlement delay in the post-larvae without underwater sound also resulted in juveniles in poorer survival and nutritional condition as measured by their protein and lipid contents. In a separate experiment, post-larvae presented with seaweed and rock substrates were found to complete settlement and moult to juvenile by as much as 20% faster compared to those on the sand and control treatments. Overall, the results are the first to demonstrate that the pueruli of J. edwardsii have the ability to detect and respond to underwater sound, as well as determining that both acoustic and substrate cues play a role in modulating physiological development during settlement.

Recruitment of the parasitic pea crab Nepinnotheres novaezelandiae into green-lipped mussels Perna canaliculus.

Pea crab species are globally ubiquitous parasites of marine bivalves including several major aquaculture species. However, little is known about the environmental factors that affect their recruitment into aquacultured mussels. The effect of depth and distance from shore on the recruitment of the parasitic pea crab Nepinnotheres novaezelandiae into New Zealand green-lipped mussels Perna canaliculus was examined with a field experiment. The incidence of pea crab infection of mussels over 295 d was nearly double when deployed at 5-10 m depth (1.97%) compared to 20-30 m depth (0.96%), although it was not significantly different due to the overall low period prevalence in the experimental population. The sex ratio of crabs recovered was significantly skewed towards females with a ratio of 1:14 (χ = 11.3, p < 0.001). Infection with pea crabs was found to significantly reduce final mussel shell height on average by 28% (21.0 mm) over 295 d (Mann-Whitney U = 6.0, p < 0.0001). This study confirms that parasitism of green-lipped mussels by pea crabs has a significant impact on the growth of the mussels and suggests that the incidence of pea crabs will be higher in shallower water and when mussels are in closer proximity to the shore. With no control methods available for preventing pea crab infection, these results suggest that moving mussel farms offshore has the potential to reduce the incidence of pea crabs in mussels and warrants larger-scale assessment.

Fouling in your own nest: vessel noise increases biofouling.

Globally billions of dollars are spent each year on attempting to reduce marine biofouling on commercial vessels, largely because it results in higher fuel costs due to increased hydrodynamic drag. Biofouling has been long assumed to be primarily due to the availability of vacant space on the surface of the hull. Here, it is shown that the addition of the noise emitted through a vessel's hull in port increases the settlement and growth of biofouling organisms within four weeks of clean surfaces being placed in the sea. More than twice as many bryozoans, oysters, calcareous tube worms and barnacles settled and established on surfaces with vessel noise compared to those without. Likewise, individuals from three species grew significantly larger in size in the presence of vessel noise. The results demonstrate that vessel noise in port is promoting biofouling on hulls and that underwater sound plays a much wider ecological role in the marine environment than was previously considered possible.

Examining the inorganic elemental composition of lobster phyllosoma (Panulirus ornatus) with X-ray fluorescence microscopy.

The ornate spiny rock lobster, Panulirus ornatus, is an attractive candidate for aquaculture. The larval stages of spiny lobsters, known as phyllosoma, are complex with many developmental stages. Very little is known about the inorganic element composition of phyllosoma. In this study, a novel method using synchrotron X-ray fluorescence microscopy (XFM) was applied to investigate the distributions of metals potassium (K), calcium (Ca), copper (Cu), zinc (Zn), the metalloid arsenic (As), and nonmetal bromine (Br) within individual phyllosoma at stages 3, 4, and 8 of their development. For the first time, 1 µm resolution synchrotron XFM images of whole phyllosoma as well as closer examinations of their eyes, mouths, setae, and tails were obtained. Elements accumulated in certain locations within phyllosoma, providing insight into their likely biological role for these organisms. This information may be useful for the application of dietary supplementation in the future to closed larval cycle lobster aquaculture operations.

Identifying the source populations supplying a vital economic marine species for the New Zealand aquaculture industry.

Aquaculture of New Zealand's endemic green-lipped mussel (Perna canaliculus) is an industry valued at NZ$ 336 M per annum and is ~ 80% reliant on the natural supply of wild mussel spat harvested at a single location-Te Oneroa-a-Tohe-Ninety Mile Beach (NMB)-in northern New Zealand. Despite the economic and ecological importance of this spat supply, little is known about the population connectivity of green-lipped mussels in this region or the location of the source population(s). In this study, we used a biophysical model to simulate the two-stage dispersal process of P. canaliculus. A combination of backward and forward tracking experiments was used to identify primary settlement areas and putative source populations. The model was then used to estimate the local connectivity, revealing two geographic regions of connectivity in northern New Zealand, with limited larval exchange between them. Although secondary dispersal can double the dispersal distance, our simulations show that spat collected at NMB originate from neighbouring mussel beds, with large contributions from beds located at Ahipara (southern end of NMB). These results provide information that may be used to help monitor and protect these important source populations to ensure the ongoing success of the New Zealand mussel aquaculture industry.

Location, location, location: finding a suitable home among the noise.

While sound is a useful cue for guiding the onshore orientation of larvae because it travels long distances underwater, it also has the potential to convey valuable information about the quality and type of the habitat at the source. Here, we provide, to our knowledge, the first evidence that settlement-stage coastal crab species can interpret and show a strong settlement and metamorphosis response to habitat-related differences in natural underwater sound. Laboratory- and field-based experiments demonstrated that time to metamorphosis in the settlement-stage larvae of common coastal crab species varied in response to different underwater sound signatures produced by different habitat types. The megalopae of five species of both temperate and tropical crabs showed a significant decrease in time to metamorphosis, when exposed to sound from their optimal settlement habitat type compared with other habitat types. These results indicate that sounds emanating from specific underwater habitats may play a major role in determining spatial patterns of recruitment in coastal crab species.

Biological characteristics of parasitic Nepinnotheres novaezelandiae within a Perna canaliculus farm.

Pea crabs are commercially significant parasites in the aquaculture production of bivalves in many parts of the world. However, there is scant information available on the biology of these important parasites in aquaculture. The population structure, sex ratio, and breeding status were determined for the pea crab Nepinnotheres novaezelandiae residing in a typical green-lipped mussel Perna canaliculus farm in New Zealand. Of the 324 crabs randomly sampled, there were significantly more female (82.4%) than male (17.6%) crabs found. The vast majority of crabs (87.0%) were sexually mature and of these, females comprised 86.4% and males 13.6%. However, the sex ratio of immature crabs was relatively even, suggesting that male crabs may have higher mortality while searching for mates. Crab size was highly variable, indicating that recruitment to mussels in the farm was continuous. Carapace width ranged from 4.00 to 11.5 mm, with males tending to be smaller with a mean (±SE) carapace width of 6.31 ± 0.16 mm versus females with a carapace width of 8.03 ± 0.06 mm. The crabs did not show any preference for parasitizing mussels of different sexes. Despite the fact that the mussels were only 10 mo old, most female crabs were sexually mature (Stage V) and 89.3% were gravid. The mean (±SE) clutch size was 2592 ± 579 and clutch size was directly associated with female carapace width. The mussel farm pea crab population was estimated at 126390 ± 14144 individuals, including 93000 gravid females carrying a total of over 241 million eggs. Overall, the results show that pea crabs rapidly colonize farmed mussels and mature quickly to establish a significant breeding population within the mussel farm, with larval output capable of infecting nearby mussel farms as well as wild populations of bivalves.

Natural heavy metal concentrations in seawater as a possible cause of low survival of larval mussels.

BACKGROUND: A period of seismic activity starting in 2010 coincided with a decline in commercial catches of wild seed mussels in a major aquaculture production region of New Zealand. Analyses of over 40 years of mussel seed catch data from in the Pelorus and Kenepuru Sounds, confirmed a marked decline since 2010 in catches of the preferred, green-lipped mussel (Perna canaliculus), the larvae of which is known to have low tolerance of heavy metals in seawater. METHODS: Heavy metal mean concentrations were measured throughout the Pelorus and Kenepuru Sounds. The concentrations ranged from < 0.60-3.24, < 16.94-74.35, < 1.47-4.00, 2.23-19.02, 1.86-3.29 and 0.12-0.52 µg L-1 for Cr, Fe, Cu, Zn, As, and Cd, respectively. Seawater from six locations in the Sounds, historically associated with high commercial catches of settling mussel larvae, was used for experimental rearing of green-lipped mussel larvae. RESULTS: No mussel embryos survived when incubated in these seawater samples. The mean concentrations of Cr, Fe, As, and Cd were significantly higher in the seawater from the Sounds than in the hatchery seawater. A higher concentration of one or a combination of these heavy metals could be the cause of the poor larval survival. These findings could be crucial for the sustainability of mussel farming in the area.

Genetic and particle modelling approaches to assessing population connectivity in a deep sea lobster.

The emergence of high resolution population genetic techniques, such as genotyping-by-sequencing (GBS), in combination with recent advances in particle modelling of larval dispersal in marine organisms, can deliver powerful new insights to support fisheries conservation and management. In this study, we used this combination to investigate the population connectivity of a commercial deep sea lobster species, the New Zealand scampi, Metanephrops challengeri, which ranges across a vast area of seafloor around New Zealand. This species has limited dispersal capabilities, including larvae with weak swimming abilities and short pelagic duration, while the reptant juvenile/adult stages of the lifecycle are obligate burrow dwellers with limited home ranges. Ninety-one individuals, collected from five scampi fishery management areas around New Zealand, were genotyped using GBS. Using 983 haplotypic genomic loci, three genetically distinct groups were identified: eastern, southern and western. These groups showed significant genetic differentiation with clear source-sink dynamics. The direction of gene flow inferred from the genomic data largely reflected the hydrodynamic particle modelling of ocean current flow around New Zealand. The modelled dispersal during pelagic larval phase highlights the strong connectivity among eastern sampling locations and explains the low genetic differentiation detected among these sampled areas. Our results highlight the value of using a transdisciplinary approach in the inference of connectivity among populations for informing conservation and fishery management.

Biodegradable chelating agent improves the survival of early larvae for shellfish aquaculture.

The toxicity of heavy metals commonly impacts the survival of crustacean and bivalve larvae in hatchery culture, and this has led to the widespread use of EDTA to decrease this toxicity. Since EDTA has a very poor biodegradability leading to potential persistent environmental effects, alternative methods to prevent heavy metal toxicity to shellfish larvae are needed. EDDS is a biodegradable potential alternative to EDTA for this application and was tested as a treatment of the seawater used for rearing aquaculture Greenshell™ mussel (Perna canaliculus) larval embryos in this study. Mussel embryos reared with EDTA or EDDS had significantly better survival than without. The concentrations and spatial distributions of heavy metals in D-veliger larvae as determined by Inductively Coupled Plasma Mass Spectrometry (ICP-MS) and X-ray Fluorescence Microscopy (XFM) suggested that chelating agents increased the levels of calcium in larvae while they reduced the concentration of zinc. In addition, where decreased accumulation of the other heavy metals was not observed, chelating agents affected their distribution within the larvae, especially for copper and arsenic. This is the first study to test the use of EDDS for aquaculture hatchery application and shows that EDDS is an effective biodegradable alternative to EDTA that can mitigate the effects of heavy metals for shellfish larval rearing.

Examining the role of ethylenediaminetetraacetic acid (EDTA) in larval shellfish production in seawater contaminated with heavy metals.

Heavy metal pollution is a concern in many coastal locations where it is frequently deleterious to the survival of young shellfish. Consequently, a great number of commercial shellfish hatcheries around the world rely on the addition of ethylenediaminetetraacetic acid (EDTA) to seawater to ensure successful larval production. Despite the importance of this practice to global shellfish production the mode of action of EDTA in larval production remains undetermined. It is assumed EDTA chelates heavy metals in seawater preventing interference in larval development. Larval mussels (Perna canaliculus) raised in seawater with 3 µM EDTA had a 15 fold higher yield than those without EDTA. The concentration and spatial arrangement of heavy metals in larvae as determined by Inductively Coupled Plasma Mass Spectrometry (ICPMS) and X-ray Fluorescence Microscopy (XFM) was consistent with reduced bioavailability of several metals, especially copper and zinc. This is the first study to confirm the effectiveness of EDTA for managing metal pollution commonly encountered in coastal shellfish hatcheries.

Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding.

Deep sea lobsters are highly valued for seafood and provide the basis of important commercial fisheries in many parts of the world. Despite their economic significance, relatively little is known about their natural diets. Microscopic analyses of foregut content in some species have suffered from low taxonomic resolution, with many of the dietary items difficult to reliably identify as their tissue is easily digested. DNA metabarcoding has the potential to provide greater taxonomic resolution of the diet of the New Zealand scampi (Metanephrops challengeri) through the identification of gut contents, but a number of methodological concerns need to be overcome first to ensure optimum DNA metabarcoding results. In this study, a range of methodological parameters were tested to determine the optimum protocols for DNA metabarcoding, and provide a first view of M. challengeri diet. Several PCR protocols were tested, using two universal primer pairs targeting the 18S rRNA and COI genes, on DNA extracted from both frozen and ethanol preserved samples for both foregut and hindgut digesta. The selection of appropriate DNA polymerases, buffers and methods for reducing PCR inhibitors (including the use of BSA) were found to be critical. Amplification from frozen or ethanol preserved gut contents appeared similarly dependable. The COI gene was found to be more effective than 18S rRNA gene for identifying large eukaryotic taxa from the digesta; however, it was less successfully amplified. The 18S rRNA gene was more easily amplified, but identified mostly smaller marine organisms such as plankton and parasites. This preliminary analysis of the diet of M. challengeri identified a range of species (13,541 reads identified as diet), which included the ghost shark (Hydrolagus novaezealandiae), silver warehou (Seriolella punctata), tall sea pen (Funiculina quadrangularis) and the salp (Ihlea racovitzai), suggesting that they have a varied diet, with a high reliance on scavenging a diverse range of pelagic and benthic species from the seafloor.