Spirochaete genome identified in red abalone sample represents a novel genus Candidatus Haliotispira gen. nov. within the order Spirochaetales.

A fully assembled spirochaete genome was identified as a contaminating scaffold in our red abalone (Haliotis rufescens) genome assembly. In this paper, we describe the analysis of this bacterial genome. The assembled spirochaete genome is 3.25 Mb in size with 48.5 mol% G+C content. The proteomes of 38 species were compared with the spirochaete genome and it was discovered to form an independent branch within the family Spirochaetaceae on the phylogenetic tree. The comparison of 16S rRNA sequences and average nucleotide identity scores between the spirochaete genome with known species of different families in Spirochaetia indicate that it is an unknown species. Further, the percentage of conserved proteins compared to neighbouring taxa confirm that it does not belong to a known genus within Spirochaetaceae. We propose the name Candidatus Haliotispira prima gen. nov., sp. nov. based on its taxonomic placement and origin. We also tested for the presence of this species in different species of abalone and found that it is also present in white abalone (Haliotis sorenseni). In addition, we highlight the need for better classification of taxa within the class Spirochaetia.

Adaptive markers distinguish North and South Pacific Albacore amid low population differentiation.

Albacore (Thunnus alalunga) support an economically valuable global fishery, but surprisingly little is known about the population structure of this highly migratory species. Physical tagging data suggest that Albacore from the North and South Pacific Ocean are separate stocks, but results from previous genetic studies did not support this two stock hypothesis. In addition, observed biological differences among juveniles suggest that there may be population substructure in the North Pacific. We used double-digest restriction site-associated DNA sequencing to assess population structure among 308 Albacore caught in 12 sample areas across the Pacific Ocean (10 North, 2 South). Since Albacore are highly migratory and spawning areas are unknown, sample groups were not assumed to be equivalent to populations and the genetic data were analyzed iteratively. We tested for putatively adaptive differences among groups and for genetic variation associated with sex. Results indicated that Albacore in the North and South Pacific can be distinguished using 84 putatively adaptive loci, but not using the remaining 12,788 presumed neutral sites. However, two individuals likely represent F1 hybrids between the North and South Pacific populations, and 43 Albacore potentially exhibit lower degrees of mixed ancestry. In addition, four or five cross-hemisphere migrants were potentially identified. No genetic evidence was found for population substructure within the North Pacific, and no loci appeared to distinguish males from females. Potential functions for the putatively adaptive loci were identified, but an annotated Albacore genome is required for further exploration. Future research should try to locate spawning areas so that life history, demography, and genetic population structure can be linked and spatiotemporal patterns can be investigated.

Stable isotope turnover rates and fractionation in captive California yellowtail (Seriola dorsalis): insights for application to field studies.

Stable isotope analysis (SIA) measurements from long-term captivity studies provide required parameters for interpretation of consumer SIA data. We raised young-of-the-year (14-19 cm) California yellowtail (Seriola dorsalis) on a low δ15N and δ13C diet (pellet aquaculture feed) for 525 days, then switched to a high δ15N and δ13C diet (mackerel and squid) for 753 days. Yellowtail muscle was sequentially sampled from each individual after the diet switch (0 to 753 days) and analyzed for δ15N and δ13C, allowing for calculation of diet-tissue discrimination factors (DTDFs) from two isotopically different diets (low δ15N and δ13C: pellets; high δ15N and δ13C: fish/squid) and turnover rates of 15N and 13C. DTDFs were diet dependent: Δ15N = 5.1‰, Δ13C = 3.6‰ for pellets and Δ15N = 2.6‰, Δ13C = 1.3‰ for fish/squid. Half-life estimates from 15N and 13C turnover rates for pooled yellowtail were 181 days and 341 days, respectively, but varied considerably by individual (15N: 99-239 d; 13C: 158-899 d). Quantifying DTDFs supports isotopic approaches to field data that assume isotopic steady-state conditions (e.g., mixing models for diet reconstruction). Characterizing and quantifying turnover rates allow for estimates of diet/habitat shifts and "isotopic clock" approaches, and observed inter-individual variability suggests the need for large datasets in field studies. We provide diet-dependent DTDFs and growth effects on turnover rates, and associated error around these parameters, for application to field-collected SIA data from other large teleosts.

An Annotated Genome for Haliotis rufescens (Red Abalone) and Resequenced Green, Pink, Pinto, Black, and White Abalone Species.

Abalone are one of the few marine taxa where aquaculture production dominates the global market as a result of increasing demand and declining natural stocks from overexploitation and disease. To better understand abalone biology, aid in conservation efforts for endangered abalone species, and gain insight into sustainable aquaculture, we created a draft genome of the red abalone (Haliotis rufescens). The approach to this genome draft included initial assembly using raw Illumina and PacBio sequencing data with MaSuRCA, before scaffolding using sequencing data generated from Chicago library preparations with HiRise2. This assembly approach resulted in 8,371 scaffolds and total length of 1.498 Gb; the N50 was 1.895 Mb, and the longest scaffold was 13.2 Mb. Gene models were predicted, using MAKER2, from RNA-Seq data and all related expressed sequence tags and proteins from NCBI; this resulted in 57,785 genes with an average length of 8,255 bp. In addition, single nucleotide polymorphisms were called on Illumina short-sequencing reads from five other eastern Pacific abalone species: the green (H. fulgens), pink (H. corrugata), pinto (H. kamtschatkana), black (H. cracherodii), and white (H. sorenseni) abalone. Phylogenetic relationships largely follow patterns detected by previous studies based on 1,784,991 high-quality single nucleotide polymorphisms. Among the six abalone species examined, the endangered white abalone appears to harbor the lowest levels of heterozygosity. This draft genome assembly and the sequencing data provide a foundation for genome-enabled aquaculture improvement for red abalone, and for genome-guided conservation efforts for the other five species and, in particular, for the endangered white and black abalone.

Erratum: KAREN E. UNDERKOFFLER, MEAGAN A. LUERS, JOHN R. HYDE MATTHEW T. CRAIG (2018) A taxonomic review of Lampris guttatus (Brünnich 1788) (Lampridiformes; Lampridae) with descriptions of three new species. Zootaxa, 4413: 551-565.

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A taxonomic review of Lampris guttatus (Brünnich 1788) Lampridiformes; Lampridae) with descriptions of three new species.

The genus Lampris (Lampridae) currently comprises two species, Lampris guttatus (Brünnich 1788) and L. immaculatus (Gilchrist 1905) commonly known as Opah and Southern Opah, respectively. Hyde et al. (2014) presented DNA sequence data which revealed the presence of five distinct, monophyletic lineages within L. guttatus. In this paper, we present morphological and meristic data supporting the presence of five species previously subsumed within L. guttatus (Brünnich 1788). We restrict Lampris guttatus (Brünnich 1788), resurrect L. lauta (Lowe 1838), and describe three new species of Lampris. A key to the species of Lampris is provided.

Insights into teleost sex determination from the Seriola dorsalis genome assembly.

BACKGROUND: The assembly and annotation of a genome is a valuable resource for a species, with applications ranging from conservation genomics to gene discovery. Genomic resource development is especially important for species in culture, such as the California Yellowtail (Seriola dorsalis), the likely candidate for the establishment of commercial offshore aquaculture production in southern California. Genomic resource development for this species will improve the understanding of sex and other phenotypic traits, and allow for rapid increases in genetic improvement for and economic gain in culture production. RESULTS: We describe the assembly and annotation of the S. dorsalis genome, and present resequencing data from 45 male and 45 female wild-caught S. dorsalis used to identify a sex-determining region and marker in this species. The genome assembly captured approximately 93% of the total 685 MB genome with an average coverage depth of 180×. Using the assembled genome, resequencing data from the 90 fish were aligned to place boundaries on the sex-determining region. Sex-specific markers were developed based on a female-specific, 61 nucleotide deletion identified in that region. We hypothesize that Estradiol 17-beta-dehydrogenase is the putative sex-determining gene and propose a plausible genetic mechanism for ZW sex determination in S. dorsalis involving a female-specific deletion of a transcription factor binding motif that may be targeted by Sox3. CONCLUSIONS: Understanding the mechanism of sex determination and development of assays to determine sex is critical both for management of wild fisheries and for development of efficient and sustainable aquaculture practices. In addition, this genome assembly for S. dorsalis will be a substantial resource for a variety of future research applications.

Larval abundances of rockfishes that were historically targeted by fishing increased over 16 years in association with a large marine protected area.

Marine protected areas (MPAs) can facilitate recovery of diminished stocks by protecting reproductive adults. To effectively augment fisheries, however, reproductive output must increase within the bounds of MPAs so that larvae can be exported to surrounding areas and seed the region. In response to dramatic declines of rockfishes (Sebastes spp.) in southern California by the late 1990s two large MPAs, the Cowcod Conservation Areas (CCAs), were established in 2001. To evaluate whether the CCAs affected rockfish productivity we evaluated the dynamics of 8 species that were, and 7 that were not, historically targeted by fishing. Abundances of 6/8 targeted and 4/7 non-targeted species increased regionally from 1998 to 2013. These upturns were probably affected by environmental conditions in addition to changes in fishing pressure as the presence of most species correlated negatively with temperature, and temperature was lower than the historic average in 11/15 years. Seventy-five per cent of the targeted, but none of the non-targeted species increased at a greater rate inside than outside the CCAs while controlling for environmental factors. Results indicate that management actions, coupled with favourable environmental conditions, facilitated the resurgence of multiple rockfish species that were targeted by intense fishing effort for decades.

Estimating fish abundance at spawning aggregations from courtship sound levels.

Sound produced by fish spawning aggregations (FSAs) permits the use of passive acoustic methods to identify the timing and location of spawning. However, difficulties in relating sound levels to abundance have impeded the use of passive acoustics to conduct quantitative assessments of biomass. Here we show that models of measured fish sound production versus independently measured fish density can be generated to estimate abundance and biomass from sound levels at FSAs. We compared sound levels produced by spawning Gulf Corvina (Cynoscion othonopterus) with simultaneous measurements of density from active acoustic surveys in the Colorado River Delta, Mexico. During the formation of FSAs, we estimated peak abundance at 1.53 to 1.55 million fish, which equated to a biomass of 2,133 to 2,145 metric tons. Sound levels ranged from 0.02 to 12,738 Pa2, with larger measurements observed on outgoing tides. The relationship between sound levels and densities was variable across the duration of surveys but stabilized during the peak spawning period after high tide to produce a linear relationship. Our results support the use of active acoustic methods to estimate density, abundance, and biomass of fish at FSAs; using appropriately scaled empirical relationships, sound levels can be used to infer these estimates.

Population genomics reveals high gene flow in grass rockfish (Sebastes rastrelliger).

Variation at the genomic level is important for understanding a species' demographic and phylogenetic history, in addition to identifying candidate regions that may be under selection and important to local adaptation. We used restriction-site associated DNA (RAD) sequencing to sample single nucleotide polymorphisms (SNPs) from the grass rockfish genome (Sebastes rastrelliger) to assess range-wide patterns of population structure and test for signatures of selection (i.e. outlier loci). Two different filtering criteria yielded 6572 and 10,393 SNPs that were genotyped in over 70% of 110 individuals from six sampling areas using RAD loci. Global FST across sampling sites is 0.0009-0.002 for all loci. Two methods for the detection of outlier loci failed to identify any outlier loci. Clustering analyses and discriminant analysis of principal components were not able to detect any population structure in our dataset. These results suggest high levels of gene flow for this species across its range and that this level of gene flow makes it difficult to detect outlier loci in the current dataset.

Animal physiology. Whole-body endothermy in a mesopelagic fish, the opah, Lampris guttatus.

Endothermy (the metabolic production and retention of heat to warm body temperature above ambient) enhances physiological function, and whole-body endothermy generally sets mammals and birds apart from other animals. Here, we describe a whole-body form of endothermy in a fish, the opah (Lampris guttatus), that produces heat through the constant "flapping" of wing-like pectoral fins and minimizes heat loss through a series of counter-current heat exchangers within its gills. Unlike other fish, opah distribute warmed blood throughout the body, including to the heart, enhancing physiological performance and buffering internal organ function while foraging in the cold, nutrient-rich waters below the ocean thermocline.

DNA barcoding provides support for a cryptic species complex within the globally distributed and fishery important opah (Lampris guttatus).

The cornerstone of fisheries management relies on a solid taxonomic base and an understanding of how animals can be grouped into coherent management units. Surprisingly, little is known about the basic biology and ecology of opah (Lampris guttatus), a globally distributed species that is commercially exploited and regionally common in the North Pacific. Recent efforts to collect life history data on this species uncovered evidence of two North Pacific morphotypes. Sequencing of the mitochondrial cytochrome c oxidase I gene (655 bp) for these morphotypes and other specimens collected worldwide (n = 480) produced five strongly diverged and well-supported clades. Additional sequence data from the cytochrome b gene (1141 bp) as well as the nuclear recombination activating gene 1 (1323 bp) corroborated these results, suggesting these five clades probably represent separate species. Our conclusion that opah is a complex of five separate species has implications for management and indicates a need to gather additional data on these poorly understood fishes.

Comparative population genetic analysis of bocaccio rockfish Sebastes paucispinis using anonymous and gene-associated simple sequence repeat loci.

Comparative population genetic analyses of traditional and emergent molecular markers aid in determining appropriate use of new technologies. The bocaccio rockfish Sebastes paucispinis is a high gene-flow marine species off the west coast of North America that experienced strong population decline over the past 3 decades. We used 18 anonymous and 13 gene-associated simple sequence repeat (SSR) loci (expressed sequence tag [EST]-SSRs) to characterize range-wide population structure with temporal replicates. No F(ST)-outliers were detected using the LOSITAN program, suggesting that neither balancing nor divergent selection affected the loci surveyed. Consistent hierarchical structuring of populations by geography or year class was not detected regardless of marker class. The EST-SSRs were less variable than the anonymous SSRs, but no correlation between F(ST) and variation or marker class was observed. General linear model analysis showed that low EST-SSR variation was attributable to low mean repeat number. Comparative genomic analysis with Gasterosteus aculeatus, Takifugu rubripes, and Oryzias latipes showed consistently lower repeat number in EST-SSRs than SSR loci that were not in ESTs. Purifying selection likely imposed functional constraints on EST-SSRs resulting in low repeat numbers that affected diversity estimates but did not affect the observed pattern of population structure.

The origin, evolution, and diversification of rockfishes of the genus Sebastes (Cuvier).

The evolutionary relationships of the livebearing rockfishes of the genus Sebastes have been a point of interest since their original description. With over 65 species found in the northeast Pacific (NEP), 27 in the northwest Pacific (NWP), seven in the Gulf of California (GC), four in the north Atlantic (NA) and at least two in the southern hemisphere (SH), they represent a fascinating lineage for studies of spatial and temporal patterns of dispersal, vicariance and speciation in the marine environment. Previous studies of Sebastes species have attempted to reconstruct their phylogeny using allozyme patterns or portions of a single mitochondrial gene while incompletely sampling the genus, resulting in a partial picture with low statistical support. In this study, genetic analyses using sequence data (5581 characters) from seven mitochondrial genes (cytochrome b, cytochrome c oxidase subunit 1, 12S rRNA, 16S rRNA, tRNA proline, tRNA threonine and the control region) and two nuclear genes (recombination activating gene 2 and internal transcribed spacer 1), along with a near complete sampling of species, have produced a well supported phylogenetic hypothesis of the relationships between Sebastes species as well as clarifying their position within the scorpaenid subfamily, Sebastinae. Though studies of similar magnitude have been conducted at the family and subfamily level, this represents the most detailed and extensive examination of biogeography and marine speciation within a single, widely distributed marine fish genus. Both Bayesian posterior and maximum parsimony analyses produced highly similar phylogenies suggesting an origin for Sebastes at high-latitudes in the NWP. The majority of previously proposed sub-generic groupings based upon morphology are found to be either para- or polyphletic. Using Bayesian-derived genetic distance measures together with rate smoothing techniques, a molecular clock was applied to the phylogeny. The clock-calibrated data suggest that Sebastes originated in the middle Miocene, concordant with fossil data, and began substantial diversification and dispersal in synchrony with high-latitude cooling and establishment of productive upwelling systems across the north Pacific (NP) in the late Miocene. Contrary to contemporary taxonomic criteria that often group Asian and North American species based on common morphology, the molecular phylogenies tend to indicate geographically circumscribed lineages with no evidence for repeated long distance dispersal between disjunct biogeographic provinces (e.g., Asian species nested within a North American lineage). No examples of large-scale glacial vicariance as would be suggested by Asian and North American sibling species were observed. To the contrary, sibling species tended to be in geographic proximity. While occasional long distance dispersal may occur, such as the single colonization of the SH, and thermal barriers presently exist between the NP, NA, GC, and SH taxa, the observable patterns in Sebastes suggest colonization occurs by stepwise invasion of newly available habitat when temperature conditions permit. Colonization events are spread throughout the sub-generic lineages. Vicariant isolation processes may occur on smaller geographic scales perhaps due to local isolating mechanisms such as glacial advance and retreat, sea level change, and ocean currents. Allopatric differences may be enhanced by a tendency for female mate choice and assortative mating in these livebearing species. The ongoing process of thermal advance and retreat is reflected in contemporary patterns of phylogeographic population genetic structure within species and may be enhanced under climate warming.