Phylogenetic review of the comb-tooth blenny genus Hypleurochilus in the northwest Atlantic and Gulf of Mexico.

As some of the smallest vertebrates, yet largest producers of consumed reef biomass, cryptobenthic reef fishes serve a disproportionate role in reef ecosystems and are one of the most poorly understood groups of fish. The blenny genera Hypleurochilus and Parablennius are currently considered paraphyletic and the interrelationships of Parablennius have been the focus of recent phylogenetic studies. However, the interrelationships of Hypleurochilus remain understudied.

Phylogenomics and biogeography of arid-adapted Chlamydogobius goby fishes.

The progressive aridification of the Australian continent from ∼ 20 million years ago posed severe challenges for the persistence of its resident biota. A key question involves the role of refugial habitats - specifically, their ability to mediate the effects of habitat loss and fragmentation, and their potential to shape opportunities for allopatric speciation. With freshwater species, for example, the patchiness, or absence, of water will constrain distributions.

The complete mitogenomes of the spinyhead blenny, (chaenopsidae) and the lofty triplefin, (Tripterygiidae).

The blennies, (Chaenopsidae) and (Tripterygiidae) are representative members of two families spanning the deepest node of the Blennioidei tree. The mitogenomes of 16,507 bp for and 16,529 bp for each consisted of 37 genes and one control loop region. Phylogenetic analysis confirmed the placement of Chaenopsidae and Tripterygiidae within the Blenniiformes, however, there was instability in the placement of the triplefins between reconstruction methods, likely due to low taxon sampling.

Reevaluating claims of ecological speciation in .

Allopatry has traditionally been viewed as the primary driver of speciation in marine taxa, but the geography of the marine environment and the larval dispersal capabilities of many marine organisms render this view somewhat questionable. In marine fishes, one of the earliest and most highly cited empirical examples of ecological speciation with gene flow is the slippery dick wrasse, . Evidence for this cryptic or incipient speciation event was primarily in the form of a deep divergence in a single mitochondrial locus between the northern and southern Gulf of Mexico, combined with a finding that these two haplotypes were associated with different habitat types ("tropical" vs.

Acanthemblemaria aceroi, a new species of tube blenny from the Caribbean coast of South America with notes on Acanthemblemaria johnsoni (Teleostei: Chaenopsidae).

Acanthemblemaria aceroi new species is described from the upwelling region of the Caribbean coasts of Venezuela and Colombia. It differs from its closest relative, Acanthemblemaria rivasi Stephens, 1970, known from Panama and Costa Rica, in the posterior extent of the infraorbitals, details of head spination, and unique COI sequences. The description of Acanthemblemaria johnsonsi Almany Baldwin, 1996, heretofore known only from Tobago, is expanded based on specimens from islands offshore of eastern Venezuela.

Draft Genome Sequences of 38 Serratia marcescens Isolates Associated with Acroporid Serratiosis.

is a Gram-negative bacterium causally linked to acroporid serratiosis, a form of white pox disease implicated in the decline of elkhorn corals. We report draft genomes of 38 isolates collected from host and nonhost sources. The availability of these genomes will aid future analyses of acroporid serratiosis.

New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset.

Percomorph fishes represent over 17,100 species, including several model organisms and species of economic importance. Despite continuous advances in the resolution of the percomorph Tree of Life, resolution of the sister lineage to Percomorpha remains inconsistent but restricted to a small number of candidate lineages. Here we use an anchored hybrid enrichment (AHE) dataset of 132 loci with over 99,000 base pairs to identify the sister lineage of percomorph fishes.

Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye.

Background: Flatfish cranial asymmetry represents one of the most remarkable morphological innovations among vertebrates, and has fueled vigorous debate on the manner and rate at which strikingly divergent phenotypes evolve. A surprising result of many recent molecular phylogenetic studies is the lack of support for flatfish monophyly, where increasingly larger DNA datasets of up to 23 loci have either yielded a weakly supported flatfish clade or indicated the group is polyphyletic. Lack of resolution for flatfish relationships has been attributed to analytical limitations for dealing with processes such as nucleotide non-stationarity and incomplete lineage sorting (ILS).

Cryptic species diversity in sub-Antarctic islands: A case study of Lepidonotothen.

The marine fauna of the Southern Ocean is well known for an impressive adaptive radiation of fishes, the notothenioids. However, when compared to other marine areas, the frigid waters of the Southern Ocean also contain a seemingly large proportion of cryptic species. The documented instances of speciation in the absence of morphological change are largely observed in invertebrate taxa, in particular around peri- and sub-Antarctic islands such as South Georgia, which has been dubbed a cryptic species hotspot.

Molecular phylogeny of Percomorpha resolves Trichonotus as the sister lineage to Gobioidei (Teleostei: Gobiiformes) and confirms the polyphyly of Trachinoidei.

The percomorph fish clade Gobiiformes is a worldwide, tropical and temperate radiation with species occupying nearly all aquatic, and some semi-terrestrial, habitats. Early molecular phylogenetic studies led to the discovery of Gobiiformes, which contains Gobioidei, the gobies and sleepers, and a clade (Apogonoidei) consisting of Apogonidae and Kurtus, the cardinalfishes and nurseryfishes. Gobioidei is consistently resolved as monophyletic in molecular studies, and includes eight families whose members range from waterfall climbing stream gobies to several prominent lineages inhabiting coral reefs.

Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment.

Background: The past decade has witnessed remarkable progress towards resolution of the Tree of Life. However, despite the increased use of genomic scale datasets, some phylogenetic relationships remain difficult to resolve. Here we employ anchored phylogenomics to capture 107 nuclear loci in 29 species of acanthomorph teleost fishes, with 25 of these species sampled from the recently delimited clade Ovalentaria.

The impact of shifts in marine biodiversity hotspots on patterns of range evolution: Evidence from the Holocentridae (squirrelfishes and soldierfishes).

One of the most striking biodiversity patterns is the uneven distribution of marine species richness, with species diversity in the Indo-Australian Archipelago (IAA) exceeding all other areas. However, the IAA formed fairly recently, and marine biodiversity hotspots have shifted across nearly half the globe since the Paleogene. Understanding how lineages have responded to shifting biodiversity hotspots represents a necessary historic perspective on the formation and maintenance of global marine biodiversity.

Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting.

Cichlid fishes are a key model system in the study of adaptive radiation, speciation and evolutionary developmental biology. More than 1600 cichlid species inhabit freshwater and marginal marine environments across several southern landmasses. This distributional pattern, combined with parallels between cichlid phylogeny and sequences of Mesozoic continental rifting, has led to the widely accepted hypothesis that cichlids are an ancient group whose major biogeographic patterns arose from Gondwanan vicariance.

Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes.

Spiny-rayed fishes, or acanthomorphs, comprise nearly one-third of all living vertebrates. Despite their dominant role in aquatic ecosystems, the evolutionary history and tempo of acanthomorph diversification is poorly understood. We investigate the pattern of lineage diversification in acanthomorphs by using a well-resolved time-calibrated phylogeny inferred from a nuclear gene supermatrix that includes 520 acanthomorph species and 37 fossil age constraints.

Resolution of ray-finned fish phylogeny and timing of diversification.

Ray-finned fishes make up half of all living vertebrate species. Nearly all ray-finned fishes are teleosts, which include most commercially important fish species, several model organisms for genomics and developmental biology, and the dominant component of marine and freshwater vertebrate faunas. Despite the economic and scientific importance of ray-finned fishes, the lack of a single comprehensive phylogeny with corresponding divergence-time estimates has limited our understanding of the evolution and diversification of this radiation.

The evolution of pharyngognathy: a phylogenetic and functional appraisal of the pharyngeal jaw key innovation in labroid fishes and beyond.

The perciform group Labroidei includes approximately 2600 species and comprises some of the most diverse and successful lineages of teleost fishes. Composed of four major clades, Cichlidae, Labridae (wrasses, parrotfishes, and weed whitings), Pomacentridae (damselfishes), and Embiotocidae (surfperches); labroids have been an icon for studies of biodiversity, adaptive radiation, and sexual selection. The success and diversification of labroids have been largely attributed to the presence of a major innovation in the pharyngeal jaw apparatus, pharyngognathy, which is hypothesized to increase feeding capacity and versatility.

Reconciling molecules and morphology: molecular systematics and biogeography of Neotropical blennies (Acanthemblemaria).

Neotropical reef fish communities are species-poor compared to those of the Indo-West Pacific. An exception to that pattern is the blenny clade Chaenopsidae, one of only three rocky and coral reef fish families largely endemic to the Neotropics. Within the chaenopsids, the genus Acanthemblemaria is the most species-rich and is characterized by elaborate spinous processes on the skull.

A new lysozyme from the eastern oyster, Crassostrea virginica, and a possible evolutionary pathway for i-type lysozymes in bivalves from host defense to digestion.

Background: Lysozymes are enzymes that lyse bacterial cell walls, an activity widely used for host defense but also modified in some instances for digestion. The biochemical and evolutionary changes between these different functional forms has been well-studied in the c-type lysozymes of vertebrates, but less so in the i-type lysozymes prevalent in most invertebrate animals. Some bivalve molluscs possess both defensive and digestive lysozymes.

Nuclear and mitochondrial sequence data reveal and conceal different demographic histories and population genetic processes in Caribbean reef fishes.

Mitochondrial and nuclear sequence data should recover historical demographic events at different temporal scales due to differences in their effective population sizes and substitution rates. This expectation was tested for two closely related coral reef fish, the tube blennies Acanthemblemaria aspera and A. spinosa.

High amino acid diversity and positive selection at a putative coral immunity gene (tachylectin-2).

Background: Genes involved in immune functions, including pathogen recognition and the activation of innate defense pathways, are among the most genetically variable known, and the proteins that they encode are often characterized by high rates of amino acid substitutions, a hallmark of positive selection. The high levels of variation characteristic of immunity genes make them useful tools for conservation genetics. To date, highly variable immunity genes have yet to be found in corals, keystone organisms of the world's most diverse marine ecosystem, the coral reef.

Nuclear sequences reveal mid-range isolation of an imperilled deep-water coral population.

The mitochondrial DNA of corals and their anthozoan kin evolves slowly, with substitution rates about two orders of magnitude lower than in typical bilateral animals. This has impeded the delineation of closely related species and isolated populations in corals, compounding problems caused by high morphological plasticity. Here we characterize rates of divergence and levels of variation for three nuclear gene regions, then use these nuclear sequences as markers to test for population structure in Oculina, a taxonomically confused genus of corals.

Novel espin actin-bundling proteins are localized to Purkinje cell dendritic spines and bind the Src homology 3 adapter protein insulin receptor substrate p53.

We identified a group of actin-binding-bundling proteins that are expressed in cerebellar Purkinje cells (PCs) but are not detected in other neurons of the CNS. These proteins are novel isoforms of the actin-bundling protein espin that arise through the use of a unique site for transcriptional initiation and differential splicing. Light and electron microscopic localization studies demonstrated that these espin isoforms are enriched in the dendritic spines of PCs.