A new maximum size for the family Nomeidae and the third record of a longfin cigarfish, Cubiceps paradoxus (Stromateoidei: Nomeidae) from California, USA.

We report the largest specimen from the stromateoid family Nomeidae. The specimen, measuring 1283 mm total length unpreserved, was caught on hook and line from shore in Port Hueneme, California, USA in June 2019. Despite scavenging damage, the specimen was identified as a longfin cigarfish, Cubiceps paradoxus, using morphological characters and molecular techniques. This is the third record of C. paradoxus from California. We also provide an account of a previously unreported C. paradoxus collected off the US-Mexico Border in 1999 that was examined but not preserved.

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.

Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly.

A natural planktonic bloom of a brown-pigmented photosynthetic green sulfur bacteria (GSB) from the disphotic zone of karstic Lake Banyoles (NE Spain) was studied as a natural enrichment culture from which a nearly complete genome was obtained after metagenomic assembly. We showed in situ a case where horizontal gene transfer (HGT) explained the ecological success of a natural population unveiling ecosystem-specific adaptations. The uncultured brown-pigmented GSB was 99.7% identical in the 16S rRNA gene sequence to its green-pigmented cultured counterpart Chlorobium luteolum DSM 273T. Several differences were detected for ferrous iron acquisition potential, ATP synthesis and gas vesicle formation, although the most striking trait was related to pigment biosynthesis strategy. Chl. luteolum DSM 273T synthesizes bacteriochlorophyll (BChl) c, whereas Chl. luteolum CIII incorporated by HGT a 18-kbp cluster with the genes needed for BChl e and specific carotenoids biosynthesis that provided ecophysiological advantages to successfully colonize the dimly lit waters. We also genomically characterized what we believe to be the first described GSB phage, which based on the metagenomic coverage was likely in an active state of lytic infection. Overall, we observed spread HGT and we unveiled clear evidence for virus-mediated HGT in a natural population of photosynthetic GSB.

Surgeons and suture zones: Hybridization among four surgeonfish species in the Indo-Pacific with variable evolutionary outcomes.

Closely related species can provide valuable insights into evolutionary processes through comparison of their ecology, geographic distribution and the history recorded in their genomes. In the Indo-Pacific, many reef fishes are divided into sister species that come into secondary contact at biogeographic borders, most prominently where Indian Ocean and Pacific Ocean faunas meet. It is unclear whether hybridization in this contact zone represents incomplete speciation, secondary contact, an evolutionary dead-end (for hybrids) or some combination of the above. To address these issues, we conducted comprehensive surveys of two widely-distributed surgeonfish species, Acanthurus leucosternon (N=141) and A. nigricans (N=412), with mtDNA cytochrome b sequences and ten microsatellite loci. These surgeonfishes are found primarily in the Indian and Pacific Oceans, respectively, but overlap at the Christmas and Cocos-Keeling Islands hybrid zone in the eastern Indian Ocean. We also sampled the two other Pacific members of this species complex, A. achilles (N=54) and A. japonicus (N=49), which are known to hybridize with A. nigricans where their ranges overlap. Our results indicate separation between the four species that range from the recent Pleistocene to late Pliocene (235,000-2.25million years ago). The Pacific A. achilles is the most divergent (and possibly ancestral) species with mtDNA dcorr≈0.04, whereas the other two Pacific species (A. japonicus and A. nigricans) are distinguishable only at a population or subspecies level (ΦST=0.6533, P<0.001). Little population structure was observed within species, with evidence of recent population expansion across all four geographic ranges. We detected sharing of mtDNA haplotypes between species and extensive hybridization based on microsatellites, consistent with later generation hybrids but also the effects of allele homoplasy. Despite extensive introgression, 98% of specimens had concordance between mtDNA lineage and species identification based on external morphology, indicating that species integrity may not be eroding. The A. nigricans complex demonstrates a range of outcomes from incomplete speciation to secondary contact to decreasing hybridization with increasing evolutionary depth.

Lepadichthys bilineatus, a new species of clingfish from Oman (Teleostei: Gobiesocidae), with a redescription of Lepadichthys erythraeus Briggs and Link from the Red Sea.

Lepadichthys bilineatus is described as a new species of gobiesocid fish from a single specimen, 23.5 mm in standard length, collected from 1.5 m in a tidepool on the southeastern coast of Oman. It is distinct from other Lepadichthys species in having the following combination of characters: dorsal-fin rays 16; anal-fin rays 13; pectoral-fin rays 23; principal caudal-fin rays 10; gill rakers 10 on second and third arch; head large, its length 3.1 in SL; body depth 8.0 in SL; disc single; disc length 6.6 in SL; disc width 6.5 in SL; color in alcohol uniform tan; color when fresh: body grayish blue, grading to brownish red posteriorly; head dark brown dorsally, abruptly pale yellowish below eye, with two whitish lines extending posteriorly and slightly ventrally from eye. Lepadichthys erythraeus, a species thus far known only from the Red Sea , is redescribed based on additional diagnostic characteristics and color photos.

Genomic and proteomic characterization of "Candidatus Nitrosopelagicus brevis": an ammonia-oxidizing archaeon from the open ocean.

Thaumarchaeota are among the most abundant microbial cells in the ocean, but difficulty in cultivating marine Thaumarchaeota has hindered investigation into the physiological and evolutionary basis of their success. We report here a closed genome assembled from a highly enriched culture of the ammonia-oxidizing pelagic thaumarchaeon CN25, originating from the open ocean. The CN25 genome exhibits strong evidence of genome streamlining, including a 1.23-Mbp genome, a high coding density, and a low number of paralogous genes. Proteomic analysis recovered nearly 70% of the predicted proteins encoded by the genome, demonstrating that a high fraction of the genome is translated. In contrast to other minimal marine microbes that acquire, rather than synthesize, cofactors, CN25 encodes and expresses near-complete biosynthetic pathways for multiple vitamins. Metagenomic fragment recruitment indicated the presence of DNA sequences >90% identical to the CN25 genome throughout the oligotrophic ocean. We propose the provisional name "Candidatus Nitrosopelagicus brevis" str. CN25 for this minimalist marine thaumarchaeon and suggest it as a potential model system for understanding archaeal adaptation to the open ocean.

Anampses viridis Valenciennes 1840 (Pisces: Labridae)--a case of taxonomic con- fusion and mistaken extinction.

Anampses viridis Valenciennes 1840 is known from only three specimens collected from Mauritius, and despite intensive sampling, the species has not been seen or reported since it was originally described. This apparent failure to 'rediscover' A. viridis at Mauritius has led to speculation that it is extinct, and the species has been widely cited as an example of a marine fish extinction. Far from being extinct, Anampses viridis has been taxonomically confused and actually is the adult male (terminal phase) colour form and a junior synonym of A. caeruleopunctatus Rüppell 1829, a species that is common and widespread throughout the Indo-West Pacific region.

Phylogeography of two closely related Indo-Pacific butterflyfishes reveals divergent evolutionary histories and discordant results from mtDNA and microsatellites.

Marine biogeographic barriers can have unpredictable consequences, even among closely related species. To resolve phylogeographic patterns for Indo-Pacific reef fauna, we conducted range-wide surveys of sister species, the scrawled butterflyfish (Chaetodon meyeri; N = 134) and the ornate butterflyfish (Chaetodon ornatissimus; N = 296), using mitochondrial DNA cytochrome b sequences and 10 microsatellite loci. The former is distributed primarily in the Indian Ocean but also extends to the Line Islands in the Central Pacific, whereas the latter is distributed primarily in the Central-West Pacific (including Hawaii and French Polynesia) but extends to the eastern margin of the Indian Ocean. Analyses of molecular variance and Bayesian STRUCTURE results revealed 1 range-wide group for C. meyeri and 3 groups for C. ornatissimus: 1) eastern Indian Ocean and western Pacific, 2) Central Pacific, and 3) Hawaii. Estimates of the last population expansion were much more recent for C. meyeri (61 500 to 95 000 years) versus C. ornatissimus (184 700 to 286 300 years). Despite similarities in ecology, morphology, life history, and a broadly overlapping distribution, these sister species have divergent patterns of dispersal and corresponding evolutionary history. The mtDNA and microsatellite markers did not provide concordant results within 1 of our study species (C. meyeri), or in 7 out of 12 other cases of marine fishes in the published literature. This discordance renews caution in relying on one or a few markers for reconstructing historical demography.

The likelihood of extinction of iconic and dominant herbivores and detritivores of coral reefs: the parrotfishes and surgeonfishes.

Parrotfishes and surgeonfishes perform important functional roles in the dynamics of coral reef systems. This is a consequence of their varied feeding behaviors ranging from targeted consumption of living plant material (primarily surgeonfishes) to feeding on detrital aggregates that are either scraped from the reef surface or excavated from the deeper reef substratum (primarily parrotfishes). Increased fishing pressure and widespread habitat destruction have led to population declines for several species of these two groups. Species-specific data on global distribution, population status, life history characteristics, and major threats were compiled for each of the 179 known species of parrotfishes and surgeonfishes to determine the likelihood of extinction of each species under the Categories and Criteria of the IUCN Red List of Threatened Species. Due in part to the extensive distributions of most species and the life history traits exhibited in these two families, only three (1.7%) of the species are listed at an elevated risk of global extinction. The majority of the parrotfishes and surgeonfishes (86%) are listed as Least Concern, 10% are listed as Data Deficient and 1% are listed as Near Threatened. The risk of localized extinction, however, is higher in some areas, particularly in the Coral Triangle region. The relatively low proportion of species globally listed in threatened Categories is highly encouraging, and some conservation successes are attributed to concentrated conservation efforts. However, with the growing realization of man's profound impact on the planet, conservation actions such as improved marine reserve networks, more stringent fishing regulations, and continued monitoring of the population status at the species and community levels are imperative for the prevention of species loss in these groups of important and iconic coral reef fishes.

Phylogeography of the reef fish Cephalopholis argus (Epinephelidae) indicates Pleistocene isolation across the Indo-Pacific Barrier with contemporary overlap in The Coral Triangle.

BACKGROUND: The Coral Triangle (CT), bounded by the Philippines, the Malay Peninsula, and New Guinea, is the epicenter of marine biodiversity. Hypotheses that explain the source of this rich biodiversity include 1) the center of origin, 2) the center of accumulation, and 3) the region of overlap. Here we contribute to the debate with a phylogeographic survey of a widely distributed reef fish, the Peacock Grouper (Cephalopholis argus; Epinephelidae) at 21 locations (N = 550) using DNA sequence data from mtDNA cytochrome b and two nuclear introns (gonadotropin-releasing hormone and S7 ribosomal protein). RESULTS: Population structure was significant (ΦST = 0.297, P < 0.001; FST = 0.078, P < 0.001; FST = 0.099, P < 0.001 for the three loci, respectively) among five regions: French Polynesia, the central-west Pacific (Line Islands to northeastern Australia), Indo-Pacific boundary (Bali and Rowley Shoals), eastern Indian Ocean (Cocos/Keeling and Christmas Island), and western Indian Ocean (Diego Garcia, Oman, and Seychelles). A strong signal of isolation by distance was detected in both mtDNA (r = 0.749, P = 0.001) and the combined nuclear loci (r = 0.715, P < 0.001). We detected evidence of population expansion with migration toward the CT. Two clusters of haplotypes were detected in the mtDNA data (d = 0.008), corresponding to the Pacific and Indian Oceans, with a low level of introgression observed outside a mixing zone at the Pacific-Indian boundary. CONCLUSIONS: We conclude that the Indo-Pacific Barrier, operating during low sea level associated with glaciation, defines the primary phylogeographic pattern in this species. These data support a scenario of isolation on the scale of 105 year glacial cycles, followed by population expansion toward the CT, and overlap of divergent lineages at the Pacific-Indian boundary. This pattern of isolation, divergence, and subsequent overlap likely contributes to species richness at the adjacent CT and is consistent with the region of overlap hypothesis.

Not All Larvae Stay Close to Home: Insights into Marine Population Connectivity with a Focus on the Brown Surgeonfish (Acanthurus nigrofuscus).

Recent reports of localized larval recruitment in predominately small-range fishes are countered by studies that show high genetic connectivity across large oceanic distances. This discrepancy may result from the different timescales over which genetic and demographic processes operate or rather may indicate regular long-distance dispersal in some species. Here, we contribute an analysis of mtDNA cytochrome b diversity in the widely distributed Brown Surgeonfish (Acanthurus nigrofuscus; N = 560), which revealed significant genetic structure only at the extremes of the range (ΦCT = 0.452; P < .001). Collections from Hawaii to the Eastern Indian Ocean comprise one large, undifferentiated population. This pattern of limited genetic subdivision across reefs of the central Indo-Pacific has been observed in a number of large-range reef fishes. Conversely, small-range fishes are often deeply structured over the same area. These findings demonstrate population connectivity differences among species at biogeographic and evolutionary timescales, which likely translates into differences in dispersal ability at ecological and demographic timescales. While interspecific differences in population connectivity complicate the design of management strategies, the integration of multiscale connectivity patterns into marine resource planning will help ensure long-term ecosystem stability by preserving functionally diverse communities.

A phylogenetic test of the size-advantage model: evolutionary changes in mating behavior influence the loss of sex change in a fish lineage.

The size-advantage model asserts that mating behavior influences the incidence and direction of sex change in animals. Selection for protogyny (female to male sex change) occurs in mating systems in which large males monopolize and pair spawn with females; however, gonochorism (no sex change) is favored when adults spawn in groups and sperm competition is present. Despite widespread empirical and theoretical support for the model, these predictions have not been tested within a phylogenetic context. Here we show that the loss of sex change within a lineage of reef fishes is influenced by evolutionary changes in two traits related to their mating behavior: mating group structure and sperm competition intensity. Phylogenetic reconstructions of the reproductive evolution of groupers (Epinephelidae) indicate that protogyny and paired spawning are the ancestral conditions for the lineage; both gonochorism and group spawning evolved independently at least four times in three different genera. Evolutionary transformations from protogyny to gonochorism (loss of sex change) are associated with equivalent transformations in mating group structure from paired to group spawning, and sperm competition is considerably higher in gonochoric species than in protogynous species. These results provide explicit phylogenetic support for predictions of the size-advantage model, demonstrating that selection for protogynous sex change decreases as mating group size and sperm competition intensity increase.

Recent invasion of the tropical Atlantic by an Indo-Pacific coral reef fish.

The last tropical connection between Atlantic and Indian-Pacific habitats closed c. 2 million years ago (Ma), with the onset of cold-water upwelling off southwestern Africa. Yet comparative morphology indicates more recent connections in several taxa, including reef-associated gobies (genus Gnatholepis). Coalescence and phylogenetic analyses of mtDNA cytochrome b sequences demonstrate that Gnatholepis invaded the Atlantic during an interglacial period approximately 145,000 years ago (d = 0.0054), colonizing from the Indian Ocean to the western Atlantic, and subsequently to the central ( approximately 100,000 years ago) and eastern Atlantic ( approximately 30,000 years ago). Census data show a contemporary range expansion in the northeastern Atlantic linked to global warming.

The phylogeny of Paralabrax (Perciformes: Serranidae) and allied taxa inferred from partial 16S and 12S mitochondrial ribosomal DNA sequences.

Partial sequences of 16S and 12S mitochondrial ribosomal DNA were used to examine the phylogenetic relationships of the primarily eastern Pacific genus Paralabrax (Perciformes: Serranidae) and allied taxa. Paralabrax is considered a basal serranine, which is itself considered the basal subfamily in the Serranidae. Multiple serranines reported closely related to Paralabrax from the genera Serranus, Hypoplectrus, Cratinus, and Centropristis were used as outgroups. Species from the remaining two subfamilies, Epinephilinae and Anthiinae, of the Serranidae were also used in the analyses. The tree of the Serranidae was rooted with the families Polyprionidae and Priacanthidae. Paralabrax, the Serranidae, and the Serraninae were monophyletic in this study. Serranus was found to be paraphyletic. Centropristis, formerly considered the sister taxon to Paralabrax, was not closely related in these analyses. Cratinus agassizii, a monotypic genus from the eastern Pacific, was found to be the sister taxon to Paralabrax. There is greater resolution for intergeneric and subfamily relations than interspecific relationships. A single most parsimonious tree for the interspecific relationships of Paralabrax and allied taxa is proposed. This proposed molecular phylogeny is consistent with known biogeographic processes in the eastern Pacific.