Mitogenomic evidence of population differentiation of thorny skate, Amblyraja radiata, in the North Atlantic.

Management of thorny skate (Amblyraja radiata) in the Northwest Atlantic has posed a conservation dilemma for several decades due to the species' lack of response to strong conservation efforts in the US Gulf of Maine and the Canadian Scotian Shelf, confusion over the relationship between two reproductive size morphs of differing life histories that are sympatric in the Northwest Atlantic, and conflicting data on regional population connectivity throughout the species' broader range. To better assess potential A. radiata regional population differentiation and genetic links to life-history variation, we analysed complete mitochondrial genome sequences from 527 specimens collected across the species' North Atlantic geographic range, with particular emphasis on the Northwest Atlantic region. A high level of genetic diversity was evident across the North Atlantic, but significant genetic differentiation was identified between specimens inhabiting the Northwest (Gulf of Maine and Newfoundland) and Northeast (Greenland, Iceland, North Sea, and Arctic Circle) Atlantic. In the Northwest Atlantic, significant differentiation between the Gulf of Maine and Newfoundland regions was revealed; however, the overall level of differentiation was very low. No genetic difference was identified between the large and small reproductive morphs. The results of this study advance our understanding of A. radiata population structure in the North Atlantic but do not resolve all the questions confounding our understanding of the species' biology and evolutionary history.

Architectural and ultrastructural features of tessellated calcified cartilage in modern and extinct chondrichthyan fishes.

Tessellated calcified cartilage (TCC) is a distinctive kind of biomineralized perichondral tissue found in many modern and extinct chondrichthyans (sharks, rays, chimaeroids and their extinct allies). Customarily, this feature has been treated somewhat superficially in phylogenetic analyses, often as a single "defining" character of a chondrichthyan clade. TCC is actually a complex hard tissue with numerous distinctive attributes, but its use as a character complex for phylogenetic analysis has not yet been optimized. This study attempts to improve this situation by presenting new terminology for certain aspects of tesseral architecture, including single-monolayered, multiple-monolayered, polylayered and voussoir tesserae; new histological data, including thin sections of TCC in several Palaeozoic taxa, and new proposals for ways in which various characters and states (many of which are defined here for the first time) could be applied in future phylogenetic analyses of chondrichthyan fishes. It can be concluded that many, but not all, of the unique attributes of modern TCC evolved by the Early Devonian (ca. 400 before present (bp)). The globular calcified cartilage reported in Silurian sinacanthids and the so-called subtessellated perichondral biomineralization (with irregular and ill-defined geometries of a layer or layers of calcified cartilage blocks) of certain extinct "acanthodians" (e.g., Climatius, Ischnacanthus, Cheiracanthus) could represent evolutionary precursors of TCC, which seems to characterize only part of the chondrichthyan total group. It is hypothesized that heavily biomineralized "layer-cake" TCC in certain Palaeozoic chondrichthyans perhaps served a dual physiological role, as a phosphate sink and in providing increased skeletal density in very large (>7 m) Devonian-Permian marine sharks such as ctenacanths and as an adaptation to calcium-deficient environments among Permo-Carboniferous non-marine sharks such as xenacanths. By contrast, the equivalent tissue in modern elasmobranchs probably serves only to reinforce regions of cartilage (mostly in the jaws) subjected to high loading. It is also noted that much of the variation observed in tesseral architecture (including localized remodelling), ultrastructure and histology in modern and extinct chondrichthyans is confined to the perichondrally facing cap zone (where Type-1 collagen matrix predominates in modern TCC), whereas the main body of the tessera (where Type-2 collagen matrix predominates) exhibits comparatively little evidence of remodelling and histological or structural variation.

Pattern and timing of diversification in the African freshwater fish genus Distichodus (Characiformes: Distichodontidae).

BACKGROUND: Distichodus is a clade of tropical freshwater fishes currently comprising 25 named species distributed continent-wide throughout the Nilo-Sudan and most Sub-Saharan drainages. This study investigates the phylogenetic relationships, timing of diversification, and biogeographic history of the genus from a taxonomically comprehensive mutilocus dataset analyzed using Maximum Likelihood and Bayesian methods of phylogenetic inference, coalescence-based species-tree estimation, divergence time estimation, and inference of geographic range evolution. RESULTS: Analyses of comparative DNA sequence data in a phylogenetic context reveal the existence of two major clades of similar species-level diversity and provide support for the monophyletic status of most sampled species. Biogeographic reconstruction on a time-scaled phylogeny suggest that the origins of the genus date back to the late Oligocene and that current geographic distributions are the result of a Congo Basin origin followed by dispersal and range expansion into adjacent ichthyofaunal provinces at different times during the evolutionary history of the group. CONCLUSIONS: We present the most comprehensive phylogenetic, chronological, and biogeographic treatment yet conducted for the genus. The few instances of species paraphyly (D. teugelsi, D. fasciolatus) revealed by the resulting phylogenies are likely a consequence of post-divergence introgressive hybridization and/or incomplete lineage sorting due to recent speciation. Historical biogeographic findings are both in agreement and conflict with previous studies of other continent-wide African freshwater fish genera, suggesting a complex scenario for the assemblage of Africa's continental ichthyofaunal communities.

A new Western North Atlantic Ocean kitefin shark (Squaliformes: Dalatiidae) from the Gulf of Mexico.

A new species of kitefin shark (Squaliformes; Dalatiidae) is described from the Gulf of Mexico (Western North Atlantic Ocean) based on five diagnostic features not seen on the only other known Mollisquama specimen, the holotype of Mollisquama parini Dolganov which was captured in the Eastern South Pacific Ocean. The new species, Mollisquama mississippiensis sp. nov., is distinguished from its congener by a putative pit organ located ventrally just posterior of the lower jaw margin center, photophores irregularly distributed along many areas of the body, 16 distinct ventral-abdominal photophore aggregations, and two differences associated with the dentition. Other potential distinguishing features are 10 fewer vertebrae than Mollisquama parini and six morphometric proportional differences that exceeded +/- 20% from the holotype.

Measuring inferential importance of taxa using taxon influence indices.

Assessing the importance of different taxa for inferring evolutionary history is a critical, but underutilized, aspect of systematics. Quantifying the importance of all taxa within a dataset provides an empirical measurement that can establish a ranking of extant taxa for ecological study and/or quantify the relative importance of newly announced or redescribed specimens to enable the disentangling of novelty and inferential influence. Here, we illustrate the use of taxon influence indices through analysis of both molecular and morphological datasets, introducing a modified Bayesian approach to the taxon influence index that accounts for model and topological uncertainty. Quantification of taxon influence using the Bayesian approach produced clear rankings for both dataset types. Bayesian taxon rankings differed from maximum likelihood (ML)-derived rankings from a mitogenomic dataset, and the highest ranking taxa exhibited the largest interquartile range in influence estimate, suggesting variance in the estimate must be taken into account when the ranking of taxa is the feature of interest. Application of the Bayesian taxon influence index to a recent morphological analysis of the Tully Monster (Tullimonstrum) reveals that it exhibits consistently low inferential importance across two recent treatments of the taxon with alternative character codings. These results lend support to the idea that taxon influence indices may be robust to character coding and therefore effective for morphological analyses. These results underscore a need for the development of approaches to, and application of, taxon influence analyses both for the purpose of establishing robust rankings for future inquiry and for explicitly quantifying the importance of individual taxa. Quantifying the importance of individual taxa refocuses debates in morphological studies from questions of character choice/significance and taxon sampling to explicitly analytical techniques, and guides discussion of the context of new discoveries.

Cranial morphology in Mollisquama sp. (Squaliformes; Dalatiidae) and patterns of cranial evolution in dalatiid sharks.

Dalatiid sharks are members of a family of predominantly small, midwater meso- and bathypelagic chondrichthyans. The family is notable for both its number of monotypic genera and high morphological disparity. Three of the seven dalatiid genera are known only from holotype specimens (Mollisquama parini) or from only a handful of specimens (Euprotomicroides zantedeschia, Heteroscymnoides marleyi), with the only detailed anatomical work consistent across all taxa being studies of dentition. Here, we present detailed anatomical description of the second-ever specimen of Mollisquama (Mollisquama sp.) covering chondrocranial, jaw, dental, and muscular anatomy, derived from a phase-contrast synchrotron microtomographic scan. Mollisquama sp. is unique among dalatiids in possessing a deep carinal process, extending ventrally from the bar between the subethmoid region and basal angle in squaloid sharks, containing a large fenestra infiltrated by the suborbitalis muscle. Mollisquama sp. also exhibits additional possibly diagnostic features, including a planar configuration of the labial cartilages and the absence of labial folds; a pad-like orbital process on the palatoquadrate; and the origination of the suborbitalis muscle solely on the carina, rather than the intraorbital wall. Character optimization of anatomical data onto a phylogeny of dalatiid sharks suggests Mollisquama sp. to be among the most specialized in the family, expanding the existing dalatiid morphospace. However, the functional significance of such transformations remains unclear. Synchrotron-derived data, which do not require chemical pretreatment of specimens, may elucidate soft-tissue functional correlates in future studies of undersampled taxa, such as dalatiids.

Diversification Patterns of Lanternfishes Reveal Multiple Rate Shifts in a Critical Mesopelagic Clade Targeted for Human Exploitation.

The mesopelagic (midwater) and deep-sea environments together comprise over 90% of the volume of the world ocean [1] and provide services that are only recently becoming recognized [2]. One of the most significant of these services relates to midwater fish biomass, recently estimated to be two orders of magnitude larger than the current worldwide fisheries catch [3, 4]. Calls to exploit midwater fish biomass have increased despite warnings about the unknown recovery potential of such organisms [2] and despite existing data suggesting that deep-sea fishes could be classified as endangered [5]. Here, to provide a null model for the respondability of midwater fishes, I use lanternfishes-which comprise the majority of worldwide midwater fish biomass [6]-to examine the diversification response of a critical midwater clade to oceanic changes over evolutionary timescales, including several extinction and turnover events. Using a time-calibrated molecular phylogeny based on seven autosomal protein-coding loci, with over 50% species sampling and three ingroup node calibrations, I show that lanternfishes exhibit a continuously increasing diversification rate, consistent with nonequilibrium speciation dynamics, and three major evolutionary rate shift locations with timing that is similar to those of marine clades in more well-known environments. These results suggest that lanternfish diversification patterns overlapped with major events in the physical partitioning of the ocean volume and that the clade has responded positively to a range of pre-Anthropocene extinction drivers [7]. However, lanternfish respondability to modern extinction drivers-habitat loss and overexploitation-is best addressed with populational and ecological data and remains largely unknown.

A new phylogenetic test for comparing multiple high-dimensional evolutionary rates suggests interplay of evolutionary rates and modularity in lanternfishes (Myctophiformes; Myctophidae).

The interplay between evolutionary rates and modularity influences the evolution of organismal body plans by both promoting and constraining the magnitude and direction of trait response to ecological conditions. However, few studies have examined whether the best-fit hypothesis of modularity is the same as the shape subset with the greatest difference in evolutionary rate. Here, we develop a new phylogenetic comparative method for comparing evolutionary rates among high-dimensional traits, and apply this method to analyze body shape evolution in bioluminescent lanternfishes. We frame the study of evolutionary rates and modularity through analysis of three hypotheses derived from the literature on fish development, biomechanics, and bioluminescent communication. We show that a development-informed partitioning of shape exhibits the greatest evolutionary rate differences among modules, but that a hydrodynamically informed partitioning is the best-fit modularity hypothesis. Furthermore, we show that bioluminescent lateral photophores evolve at a similar rate as, and are strongly integrated with, body shape in lanternfishes. These results suggest that overlapping life-history constraints on development and movement define axes of body shape evolution in lanternfishes, and that the positions of their lateral photophore complexes are likely a passive outcome of the interaction of these ecological pressures.

Seven-locus molecular phylogeny of Myctophiformes (Teleostei; Scopelomorpha) highlights the utility of the order for studies of deep-sea evolution.

Fishes of the order Myctophiformes (Teleostei; Scopelomorpha) comprise over half of all deep-sea biomass, and are a critical component of marine ecosystems worldwide. Members of the family Myctophidae, within Myctophiformes, form the majority of species diversity within the order (∼250 species, 33 genera, 2 subfamilies), and are further known for their diverse bioluminescent traits, comprised of distinct cranial, postcranial, and caudal luminous systems that is perhaps the most elaborate among all vertebrates. These features make myctophids particularly compelling from both economic and scientific perspectives, yet no studies have sampled these fishes at a density appropriate for addressing any questions requiring a phylogenetic hypothesis as input. This study therefore presents a seven-locus molecular phylogeny of the order, sampling over 50% of all nominal myctophid species. This taxon sampling triples the representation of the next most comprehensive analysis, and reveals several new and well-supported hypotheses of relationships, in addition to supporting traditional hypotheses based on combined morphological data. This analysis shows that the slendertailed myctophids Gonichthys, Centrobranchus, Loweina, and Tarletonbeania are rendered non-monophyletic by a polyphyletic Myctophum; the enigmatic, monotypic genus Notolychnus valdiviae is nested within tribe Lampanyctini; the genus Diaphus is divided into at least two clades, with the suborbital (So) group recovered as monophyletic with strong support; and the genera Lampanyctus and Nannobrachium are recovered as non-monophyletic. These molecular results highlight the potential of myctophids as a premier model system for the application of modern comparative methods to studies of deep-sea evolution.

Are characiform fishes Gondwanan in origin? Insights from a time-scaled molecular phylogeny of the Citharinoidei (Ostariophysi: Characiformes).

Fishes of the order Characiformes are a diverse and economically important teleost clade whose extant members are found exclusively in African and Neotropical freshwaters. Although their transatlantic distribution has been primarily attributed to the Early Cretaceous fragmentation of western Gondwana, vicariance has not been tested with temporal information beyond that contained in their fragmentary fossil record and a recent time-scaled phylogeny focused on the African family Alestidae. Because members of the suborder Citharinoidei constitute the sister lineage to the entire remaining Afro-Neotropical characiform radiation, we inferred a time-calibrated molecular phylogeny of citharinoids using a popular Bayesian approach to molecular dating in order to assess the adequacy of current vicariance hypotheses and shed light on the early biogeographic history of characiform fishes. Given that the only comprehensive phylogenetic treatment of the Citharinoidei has been a morphology-based analysis published over three decades ago, the present study also provided an opportunity to further investigate citharinoid relationships and update the evolutionary framework that has laid the foundations for the current classification of the group. The inferred chronogram is robust to changes in calibration priors and suggests that the origins of citharinoids date back to the Turonian (ca 90 Ma) of the Late Cretaceous. Most modern citharinoid genera, however, appear to have originated and diversified much more recently, mainly during the Miocene. By reconciling molecular-clock- with fossil-based estimates for the origins of the Characiformes, our results provide further support for the hypothesis that attributes the disjunct distribution of the order to the opening of the South Atlantic Ocean. The striking overlap in tempo of diversification and biogeographic patterns between citharinoids and the African-endemic family Alestidae suggests that their evolutionary histories could have been strongly and similarly influenced by Miocene geotectonic events that modified the landscape and produced the drainage pattern of Central Africa seen today.

A new ectoparasitic distichodontid of the genus Eugnathichthys (Characiformes: Citharinoidei) from the Congo basin of central Africa, with a molecular phylogeny for the genus.

A new species of ectoparasitic distichodontid, Eugnathichthys virgatus, is described from localities in the central and western Congo basin. The new species is a fin-eater even at small sizes and, in common with congeners, is capable of biting off sections of heavily ossified fin-rays of large prey species. Prior to the present study, two species were included in this distinctive distichodontid genus: the type species, Eugnathichthys eetveldii, and a second species, E. macroterolepis, both of which are widely distributed throughout much of the Congo basin. Morphologically, E. virgatus is readily distinguished from its two congeners based on a combination of meristic and morphometric attributes. The new species possesses a unique pigmentation pattern, a reduced number of pectoral-fin rays, and a markedly reduced dentition on the fifth ceratobranchial elements of the pharynx, all of which are derived features considered diagnostic for the new species. With molecular data the species is further diagnosed by four apomorphic, non-synonomous nucleotide transitions in two sampled genes (NADH dehydrogenase subunit 2 and glycosyltransferase). Phylogenetic analysis of those mtDNA and ncDNA markers supports a sister-group relationship between E. virgatus and E. eetveldii rather than with E. macroterolepis, the species with which it bears closest phenetic similarity.

Indel information eliminates trivial sequence alignment in maximum likelihood phylogenetic analysis.

Although there has been a recent proliferation in maximum-likelihood (ML)-based tree estimation methods based on a fixed sequence alignment (MSA), little research has been done on incorporating indel information in this traditional framework. We show, using a simple model on a single character example, that a trivial alignment of a different form than that previously identified for parsimony is optimal in ML under standard assumptions treating indels as "missing" data, but that it is not optimal when indels are incorporated into the character alphabet. We show that the optimality of the trivial alignment is not an artefact of simplified theory assumptions by demonstrating that trivial alignment likelihoods of five different multiple sequence alignment datasets exhibit this phenomenon. These results demonstrate the need for use of indel information in likelihood analysis on fixed MSAs, and suggest that caution must be exercised when drawing conclusions from software implementations claiming improvements in likelihood scores under an indels-as-missing assumption. © The Willi Hennig Society 2012.

Musca domestica salivary gland hypertrophy virus, a globally distributed insect virus that infects and sterilizes female houseflies.

The housefly, Musca domestica, is a cosmopolitan pest of livestock and poultry and is of economic, veterinary, and public health importance. Populations of M. domestica are naturally infected with M. domestica salivary gland hypertrophy virus (MdSGHV), a nonoccluded double-stranded DNA virus that inhibits egg production in infected females and is characterized by salivary gland hypertrophy (SGH) symptoms. MdSGHV has been detected in housefly samples from North America, Europe, Asia, the Caribbean, and the southwestern Pacific. In this study, houseflies were collected from various locations and dissected to observe SGH symptoms, and infected gland pairs were collected for MdSGHV isolation and amplification in laboratory-reared houseflies. Differences among the MdSGHV isolates were examined by using molecular and bioassay approaches. Approximately 600-bp nucleotide sequences from each of five open reading frames having homology to genes encoding DNA polymerase and partial homology to the genes encoding four per os infectivity factor proteins (p74, pif-1, pif-2, and pif-3) were selected for phylogenetic analyses. Nucleotide sequences from 16 different geographic isolates were highly homologous, and the polymorphism detected was correlated with geographic source. The virulence of the geographic MdSGHV isolates was evaluated by per os treatment of newly emerged and 24-h-old houseflies with homogenates of infected salivary glands. In all cases, 24-h-old flies displayed a resistance to oral infection that was significantly greater than that displayed by newly eclosed adults. Regardless of the MdSGHV isolate tested, all susceptible insects displayed similar degrees of SGH and complete suppression of oogenesis.

Host age and pathogen dosage impact cyst morphogenesis in the invertebrate pathogenic alga Helicosporidium sp. (Chlorophyta: Trebouxiophyceae).

Helicosporidium sp. is a pathogenic alga that replicates in the hemolymph of various invertebrate hosts. Morphogenesis of the infectious life stage, the cyst, occurs in the infected host, but to date cannot be induced in vitro. Using larvae of the heterologous host Helicoverpa zea, we examined potential factors influencing pathogenicity and in vivo cyst production of the alga and the impact of infection on host survival. Factors tested were cyst dosage administered per os (ranging from 10(2) to 10(5) cysts per larva) and host age at exposure (third, fourth, and fifth larval instar). Cyst production occurred between 7 and 13days after treatment, regardless of host age at treatment. Increasing dosage increased both percent infection and mortality, but cyst production did not track the total infection response. Increasing host age at exposure mitigated dosage effects on infection and mortality and also elevated cyst production in later-treated larvae. Only the highest dosage produced a significant decrease in the overall time to death. Moderate cyst dosages and later host ages were most effective at regenerating Helicosporidium cysts.

Development of the insect pathogenic alga Helicosporidium.

This study examined the morphogenesis and replication dynamics of the different life stages (cysts, filamentous cells, vegetative cells) of Helicosporidium sp., a non-photosynthetic, entomopathogenic alga. The isolate (SjHe) used originated from an infected black fly larva. Filamentous cell transformation into vegetative cells and autosporulation during vegetative cell replication were observed under controlled in vitro conditions. The transformation process was initiated by a partial swelling of the filamentous cell along with the reorganization of the nuclear material. Two subsequent nuclear and cell divisions resulted in the release of 4 rod-shaped daughter cells, which divided into oval to spherical vegetative cells. These underwent several cycles of autosporogenic cell division. Multiple-passaged vegetative cell cultures formed non-motile, adherent cell clusters (palmelloid colonies). Vegetative replication dynamics were also observed in 2 experimental noctuid hosts, Spodoptera exigua and Helicoverpa zea. The average density of helicosporidial cells produced per microliter hemolymph exceeded cell concentrations obtained in vitro by 15- and 46-fold in S. exigua and H. zea, respectively. Cyst morphogenesis was only observed in the hemolymph, whereas no cysts differentiated at various in vitro conditions.