Repeated, long-distance migrations by a philopatric predator targeting highly contrasting ecosystems.

Long-distance movements of animals are an important driver of population spatial dynamics and determine the extent of overlap with area-focused human activities, such as fishing. Despite global concerns of declining shark populations, a major limitation in assessments of population trends or spatial management options is the lack of information on their long-term migratory behaviour. For a large marine predator, the tiger shark Galeocerdo cuvier, we show from individuals satellite-tracked for multiple years (up to 1101 days) that adult males undertake annually repeated, round-trip migrations of over 7,500 km in the northwest Atlantic.

Diagnosing domoic acid toxicosis in the California sea lion (Zalophus californianus) using behavioral criteria: A novel approach.

Domoic acid toxicosis in the California sea lion (Zalophus californianus) is difficult to diagnose using presence of toxin alone because the duration of domoic acid presence in blood and urine is generally less than 48 hr following exposure. Because domoic acid toxicosis is often suggested by presentation of behavioral abnormalities, we asked whether assessment of behavior might be useful for diagnostic purposes. We developed an ethogram to categorize behavioral data collected via continuous focal animal sampling.

SmileFinder: a resampling-based approach to evaluate signatures of selection from genome-wide sets of matching allele frequency data in two or more diploid populations.

Background: Adaptive alleles may rise in frequency as a consequence of positive selection, creating a pattern of decreased variation in the neighboring loci, known as a selective sweep. When the region containing this pattern is compared to another population with no history of selection, a rise in variance of allele frequencies between populations is observed. One challenge presented by large genome-wide datasets is the ability to differentiate between patterns that are remnants of natural selection from those expected to arise at random and/or as a consequence of selectively neutral demographic forces acting in the population.

Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis.

High-resolution genetic maps are essential for fine mapping of complex traits, genome assembly, and comparative genomic analysis. Single-nucleotide polymorphisms (SNPs) are the primary molecular markers used for genetic map construction. In this study, we identified 13,362 SNPs evenly distributed across the Japanese flounder (Paralichthys olivaceus) genome.

Genetic ancestry of the extinct Javan and Bali tigers.

The Bali (Panthera tigris balica) and Javan (P. t. sondaica) tigers are recognized as distinct tiger subspecies that went extinct in the 1940s and 1980s, respectively.

Population structure and dispersal of the coral-excavating sponge Cliona delitrix.

Some excavating sponges of the genus Cliona compete with live reef corals, often killing and bioeroding entire colonies. Important aspects affecting distribution of these species, such as dispersal capability and population structure, remain largely unknown. Thus, the aim of this study was to determine levels of genetic connectivity and dispersal of Cliona delitrix across the Greater Caribbean (Caribbean Sea, Bahamas and Florida), to understand current patterns and possible future trends in their distribution and effects on coral reefs.

Time-dependent bidirectional effects of chronic caffeine on functional recovery of the dorsal light reflex after hemilabyrinthectomy in the goldfish Carassius auratus.

Caffeine works through a variety of complex mechanisms to exert an often bidirectional set of functional and structural neurological changes in vertebrates. We investigated the effects of chronic caffeine exposure on functional recovery of the dorsal light reflex (DLR) in hemilabyrinthectomized common goldfish, Carassius auratus. In this lesion model, the unilateral removal of the vestibular organs results in a temporary loss of gravitationally modulated postural control which is quantifiable via the DLR.

The birds of Genome10K.

Everyone loves the birds of the world. From their haunting songs and majesty of flight to dazzling plumage and mating rituals, bird watchers - both amateurs and professionals - have marveled for centuries at their considerable adaptations. Now, we are offered a special treat with the publication of a series of papers in dedicated issues of Science, Genome Biology and GigaScience (which also included pre-publication data release).

Hurricanes accelerated the Florida-Bahamas lionfish invasion.

In this study, we demonstrate how perturbations to the Florida Current caused by hurricanes are relevant to the spread of invasive lionfish from Florida to the Bahamas. Without such perturbations, this current represents a potential barrier to the transport of planktonic lionfish eggs and larvae across the Straits of Florida. We further show that once lionfish became established in the Bahamas, hurricanes significantly hastened their spread through the island chain.

Evolutionary genomics and adaptive evolution of the Hedgehog gene family (Shh, Ihh and Dhh) in vertebrates.

The Hedgehog (Hh) gene family codes for a class of secreted proteins composed of two active domains that act as signalling molecules during embryo development, namely for the development of the nervous and skeletal systems and the formation of the testis cord. While only one Hh gene is found typically in invertebrate genomes, most vertebrates species have three (Sonic hedgehog--Shh; Indian hedgehog--Ihh; and Desert hedgehog--Dhh), each with different expression patterns and functions, which likely helped promote the increasing complexity of vertebrates and their successful diversification. In this study, we used comparative genomic and adaptive evolutionary analyses to characterize the evolution of the Hh genes in vertebrates following the two major whole genome duplication (WGD) events.

Whole-genome analyses resolve early branches in the tree of life of modern birds.

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species.

Comparative genomics reveals insights into avian genome evolution and adaptation.

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss.

Comparative population genetics and evolutionary history of two commonly misidentified billfishes of management and conservation concern.

Background: Misidentifications between exploited species may lead to inaccuracies in population assessments, with potentially irreversible conservation ramifications if overexploitation of either species is occurring. A notable showcase is provided by the realization that the roundscale spearfish (Tetrapturus georgii), a recently validated species, has been historically misidentified as the morphologically very similar and severely overfished white marlin (Kajikia albida) (IUCN listing: Vulnerable). In effect, no information exists on the population status and evolutionary history of the enigmatic roundscale spearfish, a large, highly vagile and broadly distributed pelagic species.

Phylogenetic and transcriptomic analyses reveal the evolution of bioluminescence and light detection in marine deep-sea shrimps of the family Oplophoridae (Crustacea: Decapoda).

Bioluminescence is essential to the survival of many organisms, particularly in the deep sea where light is limited. Shrimp of the family Oplophoridae exhibit a remarkable mechanism of bioluminescence in the form of a secretion used for predatory defense. Three of the ten genera possess an additional mode of bioluminescence in the form of light-emitting organs called photophores.

Two distinct microbial communities revealed in the sponge Cinachyrella.

Marine sponges are vital components of benthic and coral reef ecosystems, providing shelter and nutrition for many organisms. In addition, sponges act as an essential carbon and nutrient link between the pelagic and benthic environment by filtering large quantities of seawater. Many sponge species harbor a diverse microbial community (including Archaea, Bacteria and Eukaryotes), which can constitute up to 50% of the sponge biomass.

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication.

Little is known about the genetic changes that distinguish domestic cat populations from their wild progenitors. Here we describe a high-quality domestic cat reference genome assembly and comparative inferences made with other cat breeds, wildcats, and other mammals. Based upon these comparisons, we identified positively selected genes enriched for genes involved in lipid metabolism that underpin adaptations to a hypercarnivorous diet.

GWATCH: a web platform for automated gene association discovery analysis.

Background: As genome-wide sequence analyses for complex human disease determinants are expanding, it is increasingly necessary to develop strategies to promote discovery and validation of potential disease-gene associations.

Findings: Here we present a dynamic web-based platform - GWATCH - that automates and facilitates four steps in genetic epidemiological discovery: 1) Rapid gene association search and discovery analysis of large genome-wide datasets; 2) Expanded visual display of gene associations for genome-wide variants (SNPs, indels, CNVs), including Manhattan plots, 2D and 3D snapshots of any gene region, and a dynamic genome browser illustrating gene association chromosomal regions; 3) Real-time validation/replication of candidate or putative genes suggested from other sources, limiting Bonferroni genome-wide association study (GWAS) penalties; 4) Open data release and sharing by eliminating privacy constraints (The National Human Genome Research Institute (NHGRI) Institutional Review Board (IRB), informed consent, The Health Insurance Portability and Accountability Act (HIPAA) of 1996 etc.) on unabridged results, which allows for open access comparative and meta-analysis.

Spectral sensitivity, luminous sensitivity, and temporal resolution of the visual systems in three sympatric temperate coastal shark species.

We used electroretinography (ERG) to determine spectral and luminous sensitivities, and the temporal resolution (flicker fusion frequency, FFF) in three sympatric (but phylogenetically distant) coastal shark species: Carcharhinus plumbeus (sandbar shark), Mustelus canis (smooth dogfish), and Squalus acanthias (spiny dogfish). Spectral sensitivities were similar (range ~400-600 nm, peak sensitivity ~470 nm), with a high likelihood of rod/cone dichromacy enhancing contrast discrimination. Spiny dogfish were significantly less light sensitive than the other species, whereas their FFF was ~19 Hz at maximum intensities; a value equal to that of sandbar shark and significantly above that of smooth dogfish (~9-12 Hz).

Are lionfish set for a Mediterranean invasion? Modelling explains why this is unlikely to occur.

The Atlantic invasion of Indo-Pacific lionfish (Pterois volitans/P. miles) has been as swift as it has been disastrous. Lionfish are non-native to the Mediterranean, but an invasion is perhaps even more likely than for the Atlantic.

Annotated features of domestic cat - Felis catus genome.

Background: Domestic cats enjoy an extensive veterinary medical surveillance which has described nearly 250 genetic diseases analogous to human disorders. Feline infectious agents offer powerful natural models of deadly human diseases, which include feline immunodeficiency virus, feline sarcoma virus and feline leukemia virus. A rich veterinary literature of feline disease pathogenesis and the demonstration of a highly conserved ancestral mammal genome organization make the cat genome annotation a highly informative resource that facilitates multifaceted research endeavors.

Phylogeny of Comatulidae (Echinodermata: Crinoidea: Comatulida): a new classification and an assessment of morphological characters for crinoid taxonomy.

Comatulidae Fleming, 1828 (previously, and incorrectly, Comasteridae A.H. Clark, 1908a), is a group of feather star crinoids currently divided into four accepted subfamilies, 21 genera and approximately 95 nominal species.

Intranasal dopamine treatment reinstates object-place memory in aged rats.

Following oral or IV administration, dopamine (DA) cannot cross the blood-brain barrier to a significant extent, but can enter the brain when administered via the nasal passages. Intranasal administration of DA was shown to increase extracellular DA in the striatum, to have antidepressant action and to improve attention and working memory in rats. Here we show that aged (22-24 months old) rats are deficient in an object-place learning task, but that this learning/memory is intact and comparable with that of adult rats upon pre-trial administration of 0.

Intraspecific variation in vertical habitat use by tiger sharks (Galeocerdo cuvier) in the western North Atlantic.

Tiger sharks (Galeocerdo cuvier) are a wide ranging, potentially keystone predator species that display a variety of horizontal movement patterns, making use of coastal and pelagic waters. Far less, however, is known about their vertical movements and use of the water column. We used pop-up satellite archival tags with two data sampling rates (high rate and standard rate tags) to investigate the vertical habitat use and diving behavior of tiger sharks tagged on the Puerto Rico-Virgin Islands platform and off Bermuda between 2008 and 2009.

Genetic variations affecting serum carcinoembryonic antigen levels and status of regional lymph nodes in patients with sporadic colorectal cancer from Southern China.

Background: Serum carcinoembryonic antigen (sCEA) level might be an indicator of disease. Indeed, an elevated sCEA level is a prognostic factor in colorectal cancer (CRC) patients. However, the genetic determinants of sCEA level in healthy and CRC population remains unclear.

The air-sea interface and surface stress under tropical cyclones.

Tropical cyclone track prediction is steadily improving, while storm intensity prediction has seen little progress in the last quarter century. Important physics are not yet well understood and implemented in tropical cyclone forecast models. Missing and unresolved physics, especially at the air-sea interface, are among the factors limiting storm predictions.