Chromosome-Level Assembly of the Southern Rock Bream (Oplegnathus fasciatus) Genome Using PacBio and Hi-C Technologies

The Rock Bream (Oplegnathus fasciatus) is an economically important rocky reef fish of the Northwest Pacific Ocean. In recent years, it has been cultivated as an important edible fish in coastal areas of China. Despite its economic importance, genome-wide adaptions of domesticated O. fasciatus are largely unknown. Here we report a chromosome-level reference genome of female O. fasciatus (from the southern population in the subtropical region) using the PacBio single molecule sequencing technique (SMRT) and High-through chromosome conformation capture (Hi-C) technologies. The genome was assembled into 120 contigs with a total length of 732.95 Mb and a contig N50 length of 27.33 Mb. After chromosome-level scaffolding, 24 chromosomes with a total length of 723.22 Mb were constructed. Moreover, a total of 27,015 protein-coding genes and 5,880 ncRNAs were annotated in the reference genome. This reference genome of O. fasciatus will provide an important resource not only for basic ecological and population genetic studies but also for dissect artificial selection mechanisms in marine aquaculture.

Rocky reef biodiversity survey: Punta Pardelas, Argentina

Temperate rocky reefs in the SW Atlantic are productive areas that support highly diverse communities of invertebrates, algae and fishes. Rocky outcrops form complex structures which offer a diversity of microhabitats that lead to a great variety of co-existing species. Subtidal biodiversity within the Natural Protected Area Península Valdés is largely unexplored and studies are mainly limited to fish. A total of 560 high definition photoquadrats from seven rocky reefs (1-25 m depth) at Punta Pardelas were obtained during March 2019. In total, 4491 occurrences were recorded and identified to phyla (n = 2), superclasses (n = 1), classes (n = 5), subclasses (n = 2), orders (n = 2), families (n = 1), subfamilies (n = 1), genera (n = 10) and species (n = 43) levels. This dataset was developed to provide a baseline inventory of Punta Pardelas inside the Natural Protected Area, that was only partially reported more than 50 years ago. Such data represent the first step towards monitoring these less-accessible ecosystems. Most of the available information about Atlantic Patagonian marine biodiversity is related to rocky intertidal communities or rocky reef fish communities. Despite having more than 4000 km of coastline, in the last 20 years only four studies have focused on subtidal benthic communities from shallow rocky reefs in Argentina (Genzano et al. 2011, Rechimont et al. 2013, Bravo et al. 2015, Bravo et al. 2020a). However, none of them described the epi-benthic community of different surface orientations on the rocky reefs. This dataset includes several surface orientations (i.e. horizontal, vertical, overhang and cave floor) and their microhabitats. We found almost double the number of taxa previously reported for the area. Through stratified sampling of different surface orientations, we recorded species that are often overlooked and thus registered as part of the existing biodiversity. For example, overhang surfaces in our study showed a unique assemblage and a great diversity of sponges. This work will be valuable as baseline information that is currently out of date in Nuevo Gulf rocky reefs.

Species richness and identity both determine the biomass of global reef fish communities

Changing biodiversity alters ecosystem functioning in nature, but the degree to which this relationship depends on the taxonomic identities rather than the number of species remains untested at broad scales. Here, we partition the effects of declining species richness and changing community composition on fish community biomass across >3000 coral and rocky reef sites globally. We find that high biodiversity is 5.7x more important in maximizing biomass than the remaining influence of other ecological and environmental factors. Differences in fish community biomass across space are equally driven by both reductions in the total number of species and the disproportionate loss of larger-than-average species, which is exacerbated at sites impacted by humans. Our results confirm that sustaining biomass and associated ecosystem functions requires protecting diversity, most importantly of multiple large-bodied species in areas subject to strong human influences.

Assessing ecological patterns in Wellington south coast's nearshore rocky-reef communities for resource conservation and management

<p>Many coastal marine communities are increasingly affected by terrestrial and maritime human activities and growing coastal populations. Protection of coastal assets and the sustainable use of coastal resources requires knowledge of nearshore benthic community status; the environmental processes that structure and connect them; the quality, abundance, and distribution of physical habitat; essential habitat for species requiring protective measures, and the spatio-temporal scales at which these patterns and processes occur. To assess the status of Wellington South Coast’s (WSC) rocky-reef assemblages prior to the enactment of the Taputeranga Marine Reserve in 2009, two annual baseline surveys were conducted during the austral summers of 2007/08 and 2008/09. These surveys evaluated the biotic and abiotic components of the assemblages in terms of diversity, abundance distribution, and size-class frequency patterns of key macroalgal and mobile macro-invertebrate species. These results were analysed to develop recommendations for best post-reserve monitoring practices, including the identification of “indicator” species for rapid yet representative field surveys to assess structural and status changes. In combination with patterns described by a previous pre-reserve baseline survey series (2000) that focussed on a reduced list of macro-algal and mobile macro-invertebrate species, this final pre-reserve survey forms the basis of a historical dataset for WSC rocky reefs that can be used for long-term monitoring of ecosystem shifts due to the new reserve and to possible changes caused by anthropogenic activity or altered natural processes. These aims were addressed by collecting information directly at local/site scale and remotely, at the larger area scale. Dived baseline surveys quantified nearshore WSC rocky-reef epibenthic assemblages at 9 sites at depths ranging from 5-13.6m and at a mean distance from shore = 113m. A survey design that included three sites west of the pending marine reserve, three sites to the east, and three sites within the designated reserve was selected to permit later BACI analyses of post-reserve changes. Species surveyed were those commonly encountered during daylight on exposed surfaces and in accessible crevices and belonged to one of three epibenthic groups: macro-algae (48 species), mobile macro-invertebrates (36 species), and sessile macro-invertebrates (30 morphotypes). These surveys did not include epizoa or smaller, cryptic newly recruited macro-invertebrates. Sessile macro-invertebrate cover was only logged if >0.1%/m2. To gauge possible spatio-temporal patterns in primary productivity as a measure of ecosystem function, biomass and plant size were measured semiannually (winter, summer) for dominant kelp and fucoid species and for two key recreationally and commercially important mobile macro-invertebrate species (sea urchin and abalone). Predictive regression equations developed from wet weight and plant size can be used for future non-destructive estimates of local primary productivity and in trophic modelling. [...] This mapping data forms the basis of a legacy dataset that will assist with monitoring changes in the integrity of critical physical habitat and associated biotic cover. It has also demonstrated that representative descriptions of both biotic and abiotic benthic components can be achieved with a minimum of sampling points and by using the quicker semi-quantitative visual analysis of video. These data can also be used to ground-truth a recently-completed multi-beam acoustic survey of the area. This work has used the approach of landscape ecology, which explains patterns in community structure, function, status and biophysical causes from a spatial perspective, to study biophysical patterns in WSC epibenthic rocky-reef communities. The work identified a high degree of spatial and temporal variation within the abiotic and biotic community within and outside of the reserve area and the limited availability of preferred habitat. The work also identified the need to include indicator species in monitoring to improve the chance of detecting impacted assemblages. These results, and the development of non-destructive sampling tools for assessing ecosystem status, are relevant locally and nationally for resource managers.</p>

Assessing ecological patterns in Wellington south coast's nearshore rocky-reef communities for resource conservation and management

<p>Many coastal marine communities are increasingly affected by terrestrial and maritime human activities and growing coastal populations. Protection of coastal assets and the sustainable use of coastal resources requires knowledge of nearshore benthic community status; the environmental processes that structure and connect them; the quality, abundance, and distribution of physical habitat; essential habitat for species requiring protective measures, and the spatio-temporal scales at which these patterns and processes occur. To assess the status of Wellington South Coast’s (WSC) rocky-reef assemblages prior to the enactment of the Taputeranga Marine Reserve in 2009, two annual baseline surveys were conducted during the austral summers of 2007/08 and 2008/09. These surveys evaluated the biotic and abiotic components of the assemblages in terms of diversity, abundance distribution, and size-class frequency patterns of key macroalgal and mobile macro-invertebrate species. These results were analysed to develop recommendations for best post-reserve monitoring practices, including the identification of “indicator” species for rapid yet representative field surveys to assess structural and status changes. In combination with patterns described by a previous pre-reserve baseline survey series (2000) that focussed on a reduced list of macro-algal and mobile macro-invertebrate species, this final pre-reserve survey forms the basis of a historical dataset for WSC rocky reefs that can be used for long-term monitoring of ecosystem shifts due to the new reserve and to possible changes caused by anthropogenic activity or altered natural processes. These aims were addressed by collecting information directly at local/site scale and remotely, at the larger area scale. Dived baseline surveys quantified nearshore WSC rocky-reef epibenthic assemblages at 9 sites at depths ranging from 5-13.6m and at a mean distance from shore = 113m. A survey design that included three sites west of the pending marine reserve, three sites to the east, and three sites within the designated reserve was selected to permit later BACI analyses of post-reserve changes. Species surveyed were those commonly encountered during daylight on exposed surfaces and in accessible crevices and belonged to one of three epibenthic groups: macro-algae (48 species), mobile macro-invertebrates (36 species), and sessile macro-invertebrates (30 morphotypes). These surveys did not include epizoa or smaller, cryptic newly recruited macro-invertebrates. Sessile macro-invertebrate cover was only logged if >0.1%/m2. To gauge possible spatio-temporal patterns in primary productivity as a measure of ecosystem function, biomass and plant size were measured semiannually (winter, summer) for dominant kelp and fucoid species and for two key recreationally and commercially important mobile macro-invertebrate species (sea urchin and abalone). Predictive regression equations developed from wet weight and plant size can be used for future non-destructive estimates of local primary productivity and in trophic modelling. [...] This mapping data forms the basis of a legacy dataset that will assist with monitoring changes in the integrity of critical physical habitat and associated biotic cover. It has also demonstrated that representative descriptions of both biotic and abiotic benthic components can be achieved with a minimum of sampling points and by using the quicker semi-quantitative visual analysis of video. These data can also be used to ground-truth a recently-completed multi-beam acoustic survey of the area. This work has used the approach of landscape ecology, which explains patterns in community structure, function, status and biophysical causes from a spatial perspective, to study biophysical patterns in WSC epibenthic rocky-reef communities. The work identified a high degree of spatial and temporal variation within the abiotic and biotic community within and outside of the reserve area and the limited availability of preferred habitat. The work also identified the need to include indicator species in monitoring to improve the chance of detecting impacted assemblages. These results, and the development of non-destructive sampling tools for assessing ecosystem status, are relevant locally and nationally for resource managers.</p>

Population Genetics of the Red Rock Lobster, Jasus edwardsii

<p>Understanding patterns of gene flow across a species range is a vital component of an effective fisheries management strategy. The advent of highly polymorphic microsatellite markers has facilitated the detection of fine-scale patterns of genetic differentiation at levels below the resolving power of earlier techniques. This has triggered the wide-spread re-examination of population structure for a number of commercially targeted species. The aims of thesis were to re-investigate patterns of gene flow of the red rock lobster Jasus edwardsii throughout New Zealand and across the Tasman Sea using novel microsatellite markers. Jasus edwardsii is a keystone species of subtidal rocky reef system and supports lucrative export markets in both Australia and New Zealand. Eight highly polymorphic microsatellite markers were developed from 454 sequence data and screened across a Wellington south coast population to obtain basic diversity indices. All loci were polymorphic with the number of alleles per locus ranging from 6-39. Observed and expected heterozygosity ranged from 0.563-0.937 and 0.583-0.961, respectively. There were no significant deviations from Hardy-Weinberg equilibrium following standard Bonferroni corrections. The loci were used in a population analysis of J. edwardsii that spanned 10 degrees of latitude and stretched 3,500 km across the South Pacific. The analysis rejected the null-hypothesis of panmixia based on earlier mDNA analysis and revealed significant population structure (FST=0.011, RST=0.028) at a wide range of scales. Stewart Island was determined to have the highest levels of genetic differentiation of all populations sampled suggesting a high degree of reproductive isolation and self-recruitment. This study also identified high levels of asymmetric gene flow from Australia to New Zealand indicating a historical source-sink relationship between the two countries. Results from the genetic analysis were consistent with results from oceanographic dispersal models and it is likely that the genetic results reflect historical and contemporary patterns of Jasus edwardsii dispersal and recruitment throughout its range.</p>

Population Genetics of the Red Rock Lobster, Jasus edwardsii

<p>Understanding patterns of gene flow across a species range is a vital component of an effective fisheries management strategy. The advent of highly polymorphic microsatellite markers has facilitated the detection of fine-scale patterns of genetic differentiation at levels below the resolving power of earlier techniques. This has triggered the wide-spread re-examination of population structure for a number of commercially targeted species. The aims of thesis were to re-investigate patterns of gene flow of the red rock lobster Jasus edwardsii throughout New Zealand and across the Tasman Sea using novel microsatellite markers. Jasus edwardsii is a keystone species of subtidal rocky reef system and supports lucrative export markets in both Australia and New Zealand. Eight highly polymorphic microsatellite markers were developed from 454 sequence data and screened across a Wellington south coast population to obtain basic diversity indices. All loci were polymorphic with the number of alleles per locus ranging from 6-39. Observed and expected heterozygosity ranged from 0.563-0.937 and 0.583-0.961, respectively. There were no significant deviations from Hardy-Weinberg equilibrium following standard Bonferroni corrections. The loci were used in a population analysis of J. edwardsii that spanned 10 degrees of latitude and stretched 3,500 km across the South Pacific. The analysis rejected the null-hypothesis of panmixia based on earlier mDNA analysis and revealed significant population structure (FST=0.011, RST=0.028) at a wide range of scales. Stewart Island was determined to have the highest levels of genetic differentiation of all populations sampled suggesting a high degree of reproductive isolation and self-recruitment. This study also identified high levels of asymmetric gene flow from Australia to New Zealand indicating a historical source-sink relationship between the two countries. Results from the genetic analysis were consistent with results from oceanographic dispersal models and it is likely that the genetic results reflect historical and contemporary patterns of Jasus edwardsii dispersal and recruitment throughout its range.</p>

Quantitative Ecological Impact Assessments using Natural Abundance Carbon and Nitrogen Stable Isotope Signatures

<p>The use of delta15N and delta13C signatures to infer sources of enrichment in ecological systems relies on predictability in the transfer of delta15N and delta13C ratios. This thesis examines patterns of delta15N and delta13C change as pools of nitrogen and carbon move from a sewage effluent discharge into organisms in an adjacent coastal rocky reef community (Titahi Bay, New Zealand). These changes and their mechanisms are examined in the broader context of current research using carbon and nitrogen stable isotope ratios in marine ecology, with particular reference to impact assessment. Firstly this thesis examines the assimilation of nitrogen and carbon isotopes in Ulva sp. under varying light conditions and nitrogen source (e.g., nitrate or ammonium). In a field study, algae grown at depth and under lower light conditions showed comparatively lighter nitrogen isotope signatures relative to the predicted concentration of available 15N-enriched sewage nitrogen. In a complementary laboratory experiment, results from manipulated light availability and N source (either nitrate or ammonium, in equivalent molar concentrations) suggest that: 1) low-light conditions can produce algae with lighter nitrogen isotope signatures; and 2) this effect was more pronounced for ammonium (3.7 per mil difference between high light and low light treatments) than for nitrate (0.6 per mil difference between high light and low light treatments) sources. Stable carbon isotope ratios (delta13C) of Ulva sp.grown in conditions of low nitrogen availability were shown to be generally lower than those grown in nitrogen rich conditions in both field and laboratory studies. Where nitrogen supply was sufficient for growth, low light conditions also produced generally lower delta13C signatures than high light conditions. Experimental trials with a uniform dissolved inorganic carbon source and altered light and nitrogen enrichment levels produced delta 13C levels in Ulva sp. tissue that spanned the recorded delta13C ranges of many common algal species; -5.99 per mil (high light, with added ammonium and phosphate) to -17.61 per mil (high light without nutrient additions). Chapter 3 of this study examines the growth response of Ulva sp. to surplus nitrate and ammonium (the two most common forms of nitrogen available to plants in seawater), under light limited conditions. Ulva sp. experienced a temporary reduction in growth rate and nitrogen assimilation capacity (shown in tissue nitrogen indices) when grown on nitrate, relative to ammonium. The magnitude and the temporary nature of these results suggest that in natural populations the relative proportion of nitrate or ammonium available is unlikely to significantly affect the growth capacity of Ulva sp. In chapter 4, I use delta13C and delta15N signatures to separately trace the dissolved and particulate fractions of sewage effluent dispersal onto a rocky reef community. Delta15N signatures from tissue of the macroalga Carpophyllum maschalocarpum, and the herbivorous isopod Amphoroidea media tracked the distribution and signature of DIN from a sewage treatment plant that generated heavy delta15N signatures. Delta13C signatures from tissue of the filter-feeding half-crab Petrolisthes elongatus tracked the distribution and signature of suspended sewage particulate organic matter.</p>

Quantitative Ecological Impact Assessments using Natural Abundance Carbon and Nitrogen Stable Isotope Signatures

<p>The use of delta15N and delta13C signatures to infer sources of enrichment in ecological systems relies on predictability in the transfer of delta15N and delta13C ratios. This thesis examines patterns of delta15N and delta13C change as pools of nitrogen and carbon move from a sewage effluent discharge into organisms in an adjacent coastal rocky reef community (Titahi Bay, New Zealand). These changes and their mechanisms are examined in the broader context of current research using carbon and nitrogen stable isotope ratios in marine ecology, with particular reference to impact assessment. Firstly this thesis examines the assimilation of nitrogen and carbon isotopes in Ulva sp. under varying light conditions and nitrogen source (e.g., nitrate or ammonium). In a field study, algae grown at depth and under lower light conditions showed comparatively lighter nitrogen isotope signatures relative to the predicted concentration of available 15N-enriched sewage nitrogen. In a complementary laboratory experiment, results from manipulated light availability and N source (either nitrate or ammonium, in equivalent molar concentrations) suggest that: 1) low-light conditions can produce algae with lighter nitrogen isotope signatures; and 2) this effect was more pronounced for ammonium (3.7 per mil difference between high light and low light treatments) than for nitrate (0.6 per mil difference between high light and low light treatments) sources. Stable carbon isotope ratios (delta13C) of Ulva sp.grown in conditions of low nitrogen availability were shown to be generally lower than those grown in nitrogen rich conditions in both field and laboratory studies. Where nitrogen supply was sufficient for growth, low light conditions also produced generally lower delta13C signatures than high light conditions. Experimental trials with a uniform dissolved inorganic carbon source and altered light and nitrogen enrichment levels produced delta 13C levels in Ulva sp. tissue that spanned the recorded delta13C ranges of many common algal species; -5.99 per mil (high light, with added ammonium and phosphate) to -17.61 per mil (high light without nutrient additions). Chapter 3 of this study examines the growth response of Ulva sp. to surplus nitrate and ammonium (the two most common forms of nitrogen available to plants in seawater), under light limited conditions. Ulva sp. experienced a temporary reduction in growth rate and nitrogen assimilation capacity (shown in tissue nitrogen indices) when grown on nitrate, relative to ammonium. The magnitude and the temporary nature of these results suggest that in natural populations the relative proportion of nitrate or ammonium available is unlikely to significantly affect the growth capacity of Ulva sp. In chapter 4, I use delta13C and delta15N signatures to separately trace the dissolved and particulate fractions of sewage effluent dispersal onto a rocky reef community. Delta15N signatures from tissue of the macroalga Carpophyllum maschalocarpum, and the herbivorous isopod Amphoroidea media tracked the distribution and signature of DIN from a sewage treatment plant that generated heavy delta15N signatures. Delta13C signatures from tissue of the filter-feeding half-crab Petrolisthes elongatus tracked the distribution and signature of suspended sewage particulate organic matter.</p>

Quantitative Ecological Impact Assessments using Natural Abundance Carbon and Nitrogen Stable Isotope Signatures

<p>The use of delta15N and delta13C signatures to infer sources of enrichment in ecological systems relies on predictability in the transfer of delta15N and delta13C ratios. This thesis examines patterns of delta15N and delta13C change as pools of nitrogen and carbon move from a sewage effluent discharge into organisms in an adjacent coastal rocky reef community (Titahi Bay, New Zealand). These changes and their mechanisms are examined in the broader context of current research using carbon and nitrogen stable isotope ratios in marine ecology, with particular reference to impact assessment. Firstly this thesis examines the assimilation of nitrogen and carbon isotopes in Ulva sp. under varying light conditions and nitrogen source (e.g., nitrate or ammonium). In a field study, algae grown at depth and under lower light conditions showed comparatively lighter nitrogen isotope signatures relative to the predicted concentration of available 15N-enriched sewage nitrogen. In a complementary laboratory experiment, results from manipulated light availability and N source (either nitrate or ammonium, in equivalent molar concentrations) suggest that: 1) low-light conditions can produce algae with lighter nitrogen isotope signatures; and 2) this effect was more pronounced for ammonium (3.7 per mil difference between high light and low light treatments) than for nitrate (0.6 per mil difference between high light and low light treatments) sources. Stable carbon isotope ratios (delta13C) of Ulva sp.grown in conditions of low nitrogen availability were shown to be generally lower than those grown in nitrogen rich conditions in both field and laboratory studies. Where nitrogen supply was sufficient for growth, low light conditions also produced generally lower delta13C signatures than high light conditions. Experimental trials with a uniform dissolved inorganic carbon source and altered light and nitrogen enrichment levels produced delta 13C levels in Ulva sp. tissue that spanned the recorded delta13C ranges of many common algal species; -5.99 per mil (high light, with added ammonium and phosphate) to -17.61 per mil (high light without nutrient additions). Chapter 3 of this study examines the growth response of Ulva sp. to surplus nitrate and ammonium (the two most common forms of nitrogen available to plants in seawater), under light limited conditions. Ulva sp. experienced a temporary reduction in growth rate and nitrogen assimilation capacity (shown in tissue nitrogen indices) when grown on nitrate, relative to ammonium. The magnitude and the temporary nature of these results suggest that in natural populations the relative proportion of nitrate or ammonium available is unlikely to significantly affect the growth capacity of Ulva sp. In chapter 4, I use delta13C and delta15N signatures to separately trace the dissolved and particulate fractions of sewage effluent dispersal onto a rocky reef community. Delta15N signatures from tissue of the macroalga Carpophyllum maschalocarpum, and the herbivorous isopod Amphoroidea media tracked the distribution and signature of DIN from a sewage treatment plant that generated heavy delta15N signatures. Delta13C signatures from tissue of the filter-feeding half-crab Petrolisthes elongatus tracked the distribution and signature of suspended sewage particulate organic matter.</p>