Giant grouper (Epinephelus lanceolatus) is an emerging aquaculture species in Southeast Asia and Australia with limited knowledge of its nutrient requirements and effects of supplements on its physiology. The present study investigated the effects of astaxanthin, vitamin E, and combinations on growth performance, body coloration, and the antioxidant status of juvenile giant grouper. Nine isonitrogenous (crude protein = 65 % ± 0.7 %) and isolipidic (crude lipid = 10 % ± 0.3 %) diets were formulated using a 3 × 3 factorial design, including three levels astaxanthin (0, 75, and 150 mg/kg) and vitamin E (0, 250, and 500 mg/kg), respectively. Each of the nine diets was fed to triplicate groups of 15 giant grouper (18.04 ± 0.92 g) for 30 days. Giant grouper fed the different diets exhibited no significant differences (p > 0.05) in specific growth rate (4.87 %/day - 5.21 %/day). However, dietary astaxanthin supplementation significantly enhanced the redness (a*), yellowness (b*b*), chroma, and hue values of the fin, regardless of the dose supplemented. Giant grouper fed astaxanthin at 75 and 150 mg/kg diet were more yellow and had three times higher b* values than fish fed non-supplemented diets. Further, total antioxidant capacity (TAC; mmol Trolox equivalent) in liver tissues was significantly increased in fish fed any of the astaxanthin-supplemented diets (p ≤ 0.05). In contrast, TAC levels were not affected by vitamin E supplementation. Malondialdehyde (MDA) levels were not significantly (p > 0.05) affected by astaxanthin or vitamin E. Findings from this study will contribute toward a better understanding of the dietary effects of antioxidant and pigment in juvenile giant grouper. We present that dietary treatment can modulate giant grouper pigmentation and may be used in the live fish trade. Further, this study contributes to narrowing the knowledge gap in formulating appropriate diets for giant grouper, which to date is fed diets formulated for other species.

Unravelling the evolutionary history of taxa requires solid delimitation of the traits characterising these. This can be challenging especially in groups with a highly complex taxonomy. The squat lobster family Munididae contains more than 450 species distributed among 21 genera, Munida being the most speciose (similar to 300 species). Previous phylogenetic studies, based on a small part of the diversity of the group, have suggested polyphyletic origins for Munida and the paraphyly of Munididae. Here, we use an integrative approach based on multi-locus phylogenies (two mitochondrial and three nuclear markers) paired with 120 morphological characters, to resolve taxonomic and evolutionary relationships within Munididae. Our study covers similar to 60% of the family's known diversity (over 800 specimens of 291 species belonging to 19 of the 21 genera collected from the Atlantic, Indian and Pacific oceans). Using this information, we confirm the validity of most genera, proposing new ones in cases where the genetic analyses are compatible with morphological characters. Four well-defined munidid clades were recovered, suggesting that new genera should be erected in the currently recognised Munididae (three for the genus Agononida and eleven in Munida), and the genus Grimothea is resurrected. A key to all genera of the family is presented. Molecular clock estimates and ancestral biogeographic area reconstructions complement the taxonomic profiles and suggest some explosive diversification within Munididae during the Cretaceous and the Palaeogene. Further anagenetic events and narrow sympatry accounting for changes in distribution indicate a more limited dispersal capacity than previously considered. Our study unravels how diversification may occur in deep waters and further highlights the importance of the integrative approach in accurately delineating species in understanding the history of a family and the factors driving the evolution.

Unravelling the evolutionary history of taxa requires solid delimitation of the traits characterising these. This can be challenging especially in groups with a highly complex taxonomy. The squat lobster family Munididae contains more than 450 species distributed among 21 genera, Munida being the most speciose (~300 species). Previous phylogenetic studies, based on a small part of the diversity of the group, have suggested polyphyletic origins for Munida and the paraphyly of Munididae. Here, we use an integrative approach based on multi-locus phylogenies (two mitochondrial and three nuclear markers) paired with 120 morphological characters, to resolve taxonomic and evolutionary relationships within Munididae. Our study covers ~60% of the family’s known diversity (over 800 specimens of 291 species belonging to 19 of the 21 genera collected from the Atlantic, Indian and Pacific oceans). Using this information, we confirm the validity of most genera, proposing new ones in cases where the genetic analyses are compatible with morphological characters. Four well-defined munidid clades were recovered, suggesting that new genera should be erected in the currently recognised Munididae (three for the genus Agononida and eleven in Munida), and the genus Grimothea is resurrected. A key to all genera of the family is presented. Molecular clock estimates and ancestral biogeographic area reconstructions complement the taxonomic profiles and suggest some explosive diversification within Munididae during the Cretaceous and the Palaeogene. Further anagenetic events and narrow sympatry accounting for changes in distribution indicate a more limited dispersal capacity than previously considered. Our study unravels how diversification may occur in deep waters and further highlights the importance of the integrative approach in accurately delineating species in understanding the history of a family and the factors driving the evolution. ZooBank LSID: urn:lsid:zoobank.org:pub:16A61C4A-8D96-4372-820F-8EBDF179B43C

This study reports on new squat lobsters of the genus Munida collected during recent surveys of Australia’s continental margins. We report on 33 species of Munida including seven new species and 14 new range extensions for Australia. More than 500 specimens were collected, mostly from the western continental margin of Australia, but also including a new species from deep water (>2000 m) off Tasmania. We provide new data on the colour patterns of some species and include molecular data from two mitochondrial markers (16S rRNA and COI) to support the taxonomic status of the new species.

Marine invertebrates harbour a complex suite of bacterial and archaeal symbionts, a subset of which are probably linked to host health and homeostasis. Within a complex microbiome it can be difficult to tease apart beneficial or parasitic symbionts from nonessential commensal or transient microorganisms; however, one approach is to detect strong cophylogenetic patterns between microbial lineages and their respective hosts. We employed the Procrustean approach to cophylogeny (PACo) on 16S rRNA gene derived microbial community profiles paired with COI, 18S rRNA and ITS1 host phylogenies. Second, we undertook a network analysis to identify groups of microbes that were co-occurring within our host species. Across 12 coral, 10 octocoral and five sponge species, each host group and their core microbiota (50% prevalence within host species replicates) had a significant fit to the cophylogenetic model. Independent assessment of each microbial genus and family found that bacteria and archaea affiliated to Endozoicomonadaceae, Spirochaetaceae and Nitrosopumilaceae have the strongest cophylogenetic signals. Further, local Moran's I measure of spatial autocorrelation identified 14 ASVs, including Endozoicomonadaceae and Spirochaetaceae, whose distributions were significantly clustered by host phylogeny. Four co-occurring subnetworks were identified, each of which was dominant in a different host group. Endozoicomonadaceae and Spirochaetaceae ASVs were abundant among the subnetworks, particularly one subnetwork that was exclusively comprised of these two bacterial families and dominated the octocoral microbiota. Our results disentangle key microbial interactions that occur within complex microbiomes and reveal long-standing, essential microbial symbioses in coral reef invertebrates.

Microbiome assemblages of plants and animals often show a degree of correlation with host phylogeny; an eco-evolutionary pattern known as phylosymbiosis. Using 16S rRNA gene sequencing to profile the microbiome, paired with COI, 18S rRNA and ITS1 host phylogenies, phylosymbiosis was investigated in four groups of coral reef invertebrates (scleractinian corals, octocorals, sponges and ascidians). We tested three commonly used metrics to evaluate the extent of phylosymbiosis: (a) intraspecific versus interspecific microbiome variation, (b) topological comparisons between host phylogeny and hierarchical clustering (dendrogram) of host-associated microbial communities, and (c) correlation of host phylogenetic distance with microbial community dissimilarity. In all instances, intraspecific variation in microbiome composition was significantly lower than interspecific variation. Similarly, topological congruency between host phylogeny and the associated microbial dendrogram was more significant than would be expected by chance across all groups, except when using unweighted UniFrac distance (compared with weighted UniFrac and Bray-Curtis dissimilarity). Interestingly, all but the ascidians showed a significant positive correlation between host phylogenetic distance and associated microbial dissimilarity. Our findings provide new perspectives on the diverse nature of marine phylosymbioses and the complex roles of the microbiome in the evolution of marine invertebrates.

To develop a comparative phylogeographic framework to understand the origins, evolution, taxonomic richness, and distribution of Australian demersal fish endemics in the context of the Indo‐West Pacific (IWP).

ABSTRACT Accidental oil spills from shipping and during extraction can threaten marine biota, particularly coral reef species which are already under pressure from anthropogenic disturbances. Marine sponges are an important structural and functional component of coral reef ecosystems; however, despite their ecological importance, little is known about how sponges and their microbial symbionts respond to petroleum products. Here, we use a systems biology-based approach to assess the effects of water-accommodated fractions (WAF) of crude oil, chemically enhanced water-accommodated fractions of crude oil (CWAF), and dispersant (Corexit EC9500A) on the survival, metamorphosis, gene expression, and microbial symbiosis of the abundant reef sponge Rhopaloeides odorabile in larval laboratory-based assays. Larval survival was unaffected by the 100% WAF treatment (107 μg liter−1 polycyclic aromatic hydrocarbon [PAH]), whereas significant decreases in metamorphosis were observed at 13% WAF (13.9 μg liter−1 PAH). The CWAF and dispersant treatments were more toxic, with decreases in metamorphosis identified at 0.8% (0.58 μg liter−1 PAH) and 1.6% (38 mg liter−1 Corexit EC9500A), respectively. In addition to the negative impact on larval settlement, significant changes in host gene expression and disruptions to the microbiome were evident, with microbial shifts detected at the lowest treatment level (1.6% WAF; 1.7 μg liter−1 PAH), including a significant reduction in the relative abundance of a previously described thaumarchaeal symbiont. The responsiveness of the R. odorabile microbial community to the lowest level of hydrocarbon treatment highlights the utility of the sponge microbiome as a sensitive marker for exposure to crude oils and dispersants. IMPORTANCE Larvae of the sponge R. odorabile survived exposure to high concentrations of petroleum hydrocarbons; however, their ability to settle and metamorphose was adversely affected at environmentally relevant concentrations, and these effects were paralleled by marked changes in sponge gene expression and preceded by disruption of the symbiotic microbiome. Given the ecological importance of sponges, uncontrolled hydrocarbon releases from shipping accidents or production could affect sponge recruitment, which would have concomitant consequences for reef ecosystem function. Author Video: An author video summary of this article is available.

The red algal genus Asparagopsis (Bonnemaisoniaceae) is a significant resource for bioactive natural products. However, prior to domestication for commercial production, we need to understand the potential variation in growth and concentration of natural products between isolates of Asparagopsis and, beyond that, how these traits are affected by environmental conditions. Ten isolates of Asparagopsis taxiformis were collected from tropical and warm-temperate regions in Queensland, Australia, and identified by molecular barcoding of the mitochondrial intergenic spacer (cox2–3 spacer). The isolates were cultured at three temperatures ranging from the minimum of the warm-temperate region to the maximum of the tropical region. Growth rates and the concentration of natural products varied between the region of origin, between isolates within region and between temperatures. Growth differed by up to 50% between isolates, whereas the concentration of natural products differed more than tenfold. Growth rates were highest at the minimum temperature of 20.2°C, irrespective of region of origin, and were lowest at the maximum temperature of 28.1°C. Natural products were threefold higher in tropical isolates, and this variation was not correlated to growth. Consequently, targeting isolates with high concentrations of natural products should be the primary strategy for the domestication of Asparagopsis for biotechnology applications.

The mitochondrial genetic diversity, distribution and invasive potential of multiple cryptic operational taxonomic units ( OTU s) of the red invasive seaweed Asparagopsis were assessed by studying introduced Mediterranean and Hawaiian populations. Invasive behavior of each Asparagopsis OTU was inferred from phylogeographic reconstructions, past historical demographic dynamics, recent range expansion assessments and future distributional predictions obtained from demographic models. Genealogical networks resolved Asparagopsis gametophytes and tetrasporophytes into four A. taxiformis and one A. armata cryptic OTU s. Falkenbergia isolates of A. taxiformis L3 were recovered for the first time in the western Mediterranean Sea and represent a new introduction for this area. Neutrality statistics supported past range expansion for A. taxiformis L1 and L2 in Hawaii. On the other hand, extreme geographic expansion and an increase in effective population size were found only for A. taxiformis L2 in the western Mediterranean Sea. Distribution models predicted shifts of the climatically suitable areas and population expansion for A. armata L1 and A. taxiformis L1 and L2. Our integrated study confirms a high invasive risk for A. taxiformis L1 and L2 in temperate and tropical areas. Despite the differences in predictions among modelling approaches, a number of regions were identified as zones with high invasion risk for A. taxiformis L2. Since range shifts are likely climate‐driven phenomena, future invasive behavior cannot be excluded for the rest of the lineages.

Six species of Paramunida are reported from the continental margin of north-western Australia. Three species are new to science: Paramunida christinae sp. nov., P. ioannis sp. nov., and P. spiniantennata sp. nov. Two species are reported for the first time from Australian waters, P. evexa Macpherson, 1996 and P. tricarinata (Alcock, 1894). These species were confirmed by molecular evidence from the mitochondrial markers ND1 and 16S. We also examine phylogenetic relationships within the genus, and provide an identification key for all known Paramunida species.

Six species of Paramunida are reported from the continental margin of north-western Australia. Three species are new to science: Paramunida christinae sp. nov., P. ioannis sp. nov., and P. spiniantennata sp. nov. Two species are reported for the first time from Australian waters, P. evexa Macpherson, 1996 and P. tricarinata (Alcock, 1894). These species were confirmed by molecular evidence from the mitochondrial markers ND1 and 16S. We also examine phylogenetic relationships within the genus, and provide an identification key for all known Paramunida species.

Six species of Paramunida are reported from the continental margin of north-western Australia. Three species are new to science: Paramunida christinae sp. nov., P. ioannis sp. nov., and P. spiniantennata sp. nov. Two species are reported for the first time from Australian waters, P. evexa Macpherson, 1996 and P. tricarinata (Alcock, 1894). These species were confirmed by molecular evidence from the mitochondrial markers ND1 and 16S. We also examine phylogenetic relationships within the genus, and provide an identification key for all known Paramunida species.

The red seaweed Asparagopsis taxiformis embodies five cryptic mitochondrial lineages (lineage 1–5) introduced worldwide as a consequence of human mediated transport and climate change. We compared globally collected mitochondrial cox2‐3 intergenic spacer sequences with sequences produced from multiple Australian locations and South Korea to identify Asparagopsis lineages and to reveal cryptic introductions. We report A. taxiformis lineage 4 from Cocos (Keeling) Islands, Australia, and the highly invasive Indo‐Pacific Mediterranean lineage 2 from South Korea and Lord Howe Island, Australia. Phylogeographic analysis showed a clear haplotype and geographic separation between western Australian and Great Barrier Reef (GBR) isolates belonging to the recently described lineage 5. The same lineage, however, was characterized by a substantial genetic and geographic break between the majority of Australian specimens and Asparagopsis collections from South Solitary Island, Southern GBR, Lord Howe Island, Kermadec Islands, Norfolk Island, New Caledonia and French Polynesia. The disjunct geographic distribution and sequence divergence between these two groups supports the recognition of a sixth cryptic A. taxiformis mitochondrial lineage. As climatic changes accelerate the relocation of biota and offer novel niches for colonization, periodic surveys for early detection of cryptic invasive seaweeds will be critical in determining whether eradication or effective containment of the aliens are feasible.

SOUL homologs constitute a heme-binding protein superfamily putatively involved in heme and tetrapyrrole metabolisms associated with a number of physiological processes. Despite their omnipresence across the tree of life and the biochemical characterization of many SOUL members, their functional role and the evolutionary events leading to such remarkable protein repertoire still remain cryptic. To explore SOUL evolution, we apply a computational phylogenetic approach, including a relevant number of SOUL homologs, to identify paralog forms and reconstruct their genealogy across the tree of life and within species. In animal lineages, multiple gene duplication or loss events and paralog functional specializations underlie SOUL evolution from the dawn of ancestral echinoderm and mollusc SOUL forms. In photosynthetic organisms, SOUL evolution is linked to the endosymbiosis events leading to plastid acquisition in eukaryotes. Derivative features, such as the F2L peptide and BH3 domain, evolved in vertebrates and provided innovative functionality to support immune response and apoptosis. The evolution of elements such as the N-terminal protein domain DUF2358, the His42 residue, or the tetrapyrrole heme-binding site is modern, and their functional implications still unresolved. This study represents the first in-depth analysis of SOUL protein evolution and provides novel insights in the understanding of their obscure physiological role.

The unrivalled level of biodiversity across the tropical Indo-Australian Archipelago (IAA) has been the subject of wide debate. Attempts to understand its origins have focussed on the timing of speciation, rates of diversification and the directionality of colonisation across geographical and climatic gradients in an array of marine groups. We investigate origins and evolution in the Choerodon tuskfishes, a group of labrids whose centre of diversity coincides with this region. Mitochondrial (COI, 16S) and nuclear (RAG2, Tmo4c4) molecular phylogenies and biogeographic analyses, coupled with molecular clock dating, were inferred from 19 of the 23 valid Choerodon species. Two additional, undescribed Choerodon species were also included, showing reciprocal monophyly in both genomes, confirming their species level status. Choerodon diverged from their ancestral sister group, the Odacines, at the onset of the Miocene, coinciding with the collision of the Australian and Eurasian Plates when extensive areas of shallow-water habitat formed. Despite subsequent evolutionary patterns being partially obscured by overlapping distribution ranges between many species and a lack of clear evidence for climatically driven lineage divergences, our data support an evolutionary scenario of peripheral endemics budding from once widespread populations across this biodiversity hotspot. Interestingly, these peripheral endemics tend to occupy more specialised reef or non-reef habitats whereas widespread groups appear to generally take advantage of both reef and non-reef environments. Our results are discussed in light of the most accredited hypotheses proposed to explain species richness in the IAA, with some support for processes such as centrifugal speciation.

Marine fungi are an understudied group of eukaryotic microorganisms characterized by unresolved genealogies and unstable classification. Whereas DNA barcoding via the nuclear ribosomal internal transcribed spacer (ITS) provides a robust and rapid tool for fungal species delineation, accurate classification of fungi is often arduous given the large number of partial or unknown barcodes and misidentified isolates deposited in public databases. This situation is perpetuated by a paucity of cultivable fungal strains available for phylogenetic research linked to these data sets. We analyze ITS barcodes produced from a subsample (290) of 1781 cultured isolates of marine-derived fungi in the Bioresources Library located at the Australian Institute of Marine Science (AIMS). Our analysis revealed high levels of under-explored fungal diversity. The majority of isolates were ascomycetes including representatives of the subclasses Eurotiomycetidae, Hypocreomycetidae, Sordariomycetidae, Pleosporomycetidae, Dothideomycetidae, Xylariomycetidae and Saccharomycetidae. The phylum Basidiomycota was represented by isolates affiliated with the genera Tritirachium and Tilletiopsis. BLAST searches revealed 26 unknown OTUs and 50 isolates corresponding to previously uncultured, unidentified fungal clones. This study makes a significant addition to the availability of barcoded, culturable marine-derived fungi for detailed future genomic and physiological studies. We also demonstrate the influence of commonly used alignment algorithms and genetic distance measures on the accuracy and comparability of estimating Operational Taxonomic Units (OTUs) by the automatic barcode gap finder (ABGD) method. Large scale biodiversity screening programs that combine datasets using algorithmic OTU delineation pipelines need to ensure compatible algorithms have been used because the algorithm matters.

Invasive species display remarkable levels of ecophysiological plasticity, which supports colonization, population establishment and fitness across their introduction range. The red seaweed genus Asparagopsis comprises genetically homogeneous invasive species (A. armata) and cryptic species complexes (A. taxiformis sensu lato) consisting of invasive mitochondrial lineages introduced worldwide. The photosynthetic plasticity of Australian, Mediterranean and Hawaiian Falkenbergia stages (i.e. the tetrasporophytic stage) of A. taxiformis lineages 2, 3 and 4 and Mediterranean isolates of A. armata was assessed by challenging their photosynthetic performance at five different temperatures (12–26 °C). Our aim is to portray the photosynthetic profiles in relation to temperature for each of the aforementioned Asparagopsis OTUs. We additionally test the physiological response of A. taxiformis lineage 2 sampled within its invasive (Mediterranean Sea) and native range (Australia) to identify physiological features associated with invasive strains. Based on photosynthesis optima, Asparagopsis isolates were recovered into a tropical (NL2 and L4) and a temperate (AA, Il2 and L3) group that presented no differences in most photosynthetic parameters at the experimental temperatures, thus indicating a greater physiological plasticity. On the other hand, low Ic values together with an apparent lack of sensitivity in the photosynthetic response to changing temperatures were revealed for the Mediterranean lineage 2, indicative of adaptive benefits that likely support its invasive success compared to the rest of the genus. Our results represent a valuable resource to predict distributional shifts in some of the lineages and to anticipate control programs for lineage 3, potentially invasive.

AbstractUnderstanding the factors that cause population divergence has long been ofinterest to marine biologists in their attempts to interpret the effect of human-mediated vectors. Broadcast-spawning species with limited dispersal capabilityare excellent candidates to measure the present-day patterns of genetic diversity.The tunicate Ciona intestinalis (Ascidiacea) is comprised of a complex ofmorphologically cryptic species that form vigorous aggregates in eutrophic habi-tats (harbors, gulfs and lagoons) where they can compete with the epibenthiccommunity and cause biofouling problems. This study investigated biogeograph-ic variability and migration patterns of C. intestinalis sp. A along NortheastAtlantic and Mediterranean coasts using microsatellite markers. Data presentedhere on 371 specimens collected from 17 populations reveal high genetic poly-morphism, but with a deficit of heterozygote deficiency. Absence of evidence forisolation by distance suggests that the genetic patterns do not reflect the geo-graphic distribution of sampled populations. Substantial gene flow and artificialpotential for dispersal boost high levels of within-population genetic variabilityand prevent genetic differentiation within and between seas. A predominant east-ward migration pattern was revealed by the data set, with very limited opportu-nity for C. intestinalis sp. A to travel westward. This directional movementindicates that other properties (e.g. habitat quality, genetic traits, mating system,life cycle) may cause adaptive divergence at a large biogeographic scale.IntroductionDispersal plays an important role in the biogeographicdistribution of marine organisms, influencing the coloni-zation of new habitats, the connectivity of populationsand ultimately species persistence (Bilton et al. 2001;Grantham et al. 2003). At sea, physical barriers are oftenabsent and water currents may accelerate larval dispersal,determining population homogeneity over large geo-graphic areas (Knutsen et al. 2003; Cowen & Sponaugle2009). In benthic invertebrates, large larval output,increased larval duration and long-distance dispersal mayallow high genetic connectivity thereby mitigating theeffect of genetic drift and inbreeding (Hedgecock 1986),and eventually leading to panmixia. Hydrologic (e.g. pat-terns of marine currents, existence of different watermasses) and ecological barriers (e.g. habitat discontinuity,larval behavior) may hinder long-distance movements(Palumbi 1994; Riginos & Nachman 2001; Bierne et al.2003). Once barriers have been established, internal (e.g.life strategy and larval survival) and external (e.g. envi-ronmental parameters) factors may favor, together with