Randomized Smoothing for Stochastic Optimization

We analyze convergence rates of stochastic optimization procedures for non-smooth convex optimization problems. By combining randomized smoothing techniques with accelerated gradient methods, we obtain convergence rates of stochastic optimization procedures, both in expectation and with high probability, that have optimal dependence on the variance of the gradient estimates. To the best of our knowledge, these are the first variance-based rates for non-smooth optimization. We give several applications of our results to statistical estimation problems, and provide experimental results that demonstrate the effectiveness of the proposed algorithms. We also describe how a combination of our algorithm with recent work on decentralized optimization yields a distributed stochastic optimization algorithm that is order-optimal.Comment: 39 pages, 3 figure

Nocturnality constrains morphological and functional diversity in the eyes of reef fishes

<p>Abstract</p> <p>Background</p> <p>Ambient light levels are often considered to drive the evolution of eye form and function. Diel activity pattern is the main mechanism controlling the visual environment of teleost reef fish, with day-active (diurnal) fish active in well-illuminated conditions, whereas night-active (nocturnal) fish cope with dim light. Physiological optics predicts several specific evolutionary responses to dim-light vision that should be reflected in visual performance features of the eye.</p> <p>Results</p> <p>We analyzed a large comparative dataset on morphological traits of the eyes in 265 species of teleost reef fish in 43 different families. The eye morphology of nocturnal reef teleosts is characterized by a syndrome that indicates better light sensitivity, including large relative eye size, high optical ratio and large, rounded pupils. Improved dim-light image formation comes at the cost of reduced depth of focus and reduction of potential accommodative lens movement. Diurnal teleost reef fish, released from the stringent functional requirements of dim-light vision have much higher morphological and optical diversity than nocturnal species, with large ranges of optical ratio, depth of focus, and lens accommodation.</p> <p>Conclusions</p> <p>Physical characteristics of the environment are an important factor in the evolution and diversification of the vertebrate eye. Both teleost reef fish and terrestrial amniotes meet the functional requirements of dim-light vision with a similar evolutionary response of morphological and optical modifications. The trade-off between improved dim-light vision and reduced optical diversity may be a key factor in explaining the lower trophic diversity of nocturnal reef teleosts.</p

Evolution of Upper Jaw Protrusion Mechanisms in Elasmobranchs

Upper jaw protrusion is a prominent component of the feeding mechanism in most elasmobranchs and has received considerable attention over the years. In this paper, we review what is known of muscle activity during prey capture in elasmobranchs, particularly that of upper jaw protrusion, and evaluate the extent to which functional modifications have evolved through changes in anatomy or patterns of muscle activity. To date, motor activity during feeding has been documented in only four species of elasmobranchs, although they represent the three major elasmobranch groups: Galea (typical sharks); Squalea (dogfish sharks); and Batoidea (skates and rays). Our efforts show that while muscles involved in cranial elevation and lower jaw depression and elevation show a conserved pattern of motor activity and function across species, other muscles show a more variable history. Our observations of elasmobranch upper jaw protrusion mechanisms suggest a mosaic of character changes over the course of evolution that involve anatomical changes in all cases and modifications of muscle activation patterns in some cases. During the evolution of feeding mechanisms of elasmobranchs, there have been two structural changes incorporating a pre-existing motor pattern to yield an unmodified kinematic profile, the original preorbitalis and the descendent preorbitalis. One additional instance of structural modification is accompanied by an alteration in the motor pattern leading to a change in movement pattern, the levator palatoquadrati

Does evolutionary innovation in pharyngeal jaws lead to rapid lineage diversification in labrid fishes?

<p>Abstract</p> <p>Background</p> <p>Major modifications to the pharyngeal jaw apparatus are widely regarded as a recurring evolutionary key innovation that has enabled adaptive radiation in many species-rich clades of percomorph fishes. However one of the central predictions of this hypothesis, that the acquisition of a modified pharyngeal jaw apparatus will be positively correlated with explosive lineage diversification, has never been tested. We applied comparative methods to a new time-calibrated phylogeny of labrid fishes to test whether diversification rates shifted at two scales where major pharyngeal jaw innovations have evolved: across all of Labridae and within the subclade of parrotfishes.</p> <p>Results</p> <p>Diversification patterns within early labrids did not reflect rapid initial radiation. Much of modern labrid diversity stems from two recent rapid diversification events; one within julidine fishes and the other with the origin of the most species-rich clade of reef-associated parrotfishes. A secondary pharyngeal jaw innovation was correlated with rapid diversification within the parrotfishes. However diversification rate shifts within parrotfishes are more strongly correlated with the evolution of extreme dichromatism than with pharyngeal jaw modifications.</p> <p>Conclusion</p> <p>The temporal lag between pharyngeal jaw modifications and changes in diversification rates casts doubt on the key innovation hypothesis as a simple explanation for much of the richness seen in labrids and scarines. Although the possession of a secondarily modified PJA was correlated with increased diversification rates, this pattern is better explained by the evolution of extreme dichromatism (and other social and behavioral characters relating to sexual selection) within <it>Scarus </it>and <it>Chlorurus</it>. The PJA-innovation hypothesis also fails to explain the most dominant aspect of labrid lineage diversification, the radiation of the julidines. We suggest that pharyngeal jaws might have played a more important role in enabling morphological evolution of the feeding apparatus in labrids and scarines rather than in accelerating lineage diversification.</p

Global ecological success of Thalassoma fishes in extreme coral reef habitats

Phenotypic adaptations can allow organisms to relax abiotic selection and facilitate their ecological success in challenging habitats, yet we have relatively little data for the prevalence of this phenomenon at macroecological scales. Using data on the relative abundance of coral reef wrasses and parrotfishes (f. Labridae) spread across three ocean basins and the Red Sea, we reveal the consistent global dominance of extreme wave-swept habitats by fishes in the genus Thalassoma, with abundances up to 15 times higher than any other labrid. A key locomotor modification-a winged pectoral fin that facilitates efficient underwater flight in high-flow environments-is likely to have underpinned this global success, as numerical dominance by Thalassoma was contingent upon the presence of high-intensity wave energy. The ecological success of the most abundant species also varied with species richness and the presence of congeneric competitors. While several fish taxa have independently evolved winged pectoral fins, Thalassoma appears to have combined efficient high-speed swimming (to relax abiotic selection) with trophic versatility (to maximize exploitation of rich resources) to exploit and dominate extreme coral reef habitats around the world

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. Although the Early Cretaceous (ca 135 Ma) divergence of living cichlids demanded by the vicariance model now represents a key calibration for teleost molecular clocks, this putative split pre-dates the oldest cichlid fossils by nearly 90 Myr. Here, we provide independent palaeontological and relaxed-molecular-clock estimates for the time of cichlid origin that collectively reject the antiquity of the group required by the Gondwanan vicariance scenario. The distribution of cichlid fossil horizons, the age of stratigraphically consistent outgroup lineages to cichlids and relaxed-clock analysis of a DNA sequence dataset consisting of 10 nuclear genes all deliver overlapping estimates for crown cichlid origin centred on the Palaeocene (ca 65-57 Ma), substantially post-dating the tectonic fragmentation of Gondwana. Our results provide a revised macroevolutionary time scale for cichlids, imply a role for dispersal in generating the observed geographical distribution of this important model clade and add to a growing debate that questions the dominance of the vicariance paradigm of historical biogeography

Effect of forecast skill on management of the Oregon coast coho salmon (Oncorhynchus kisutch) fishery

Better fisheries management is often given as one justification for research on improving forecasts of fish survival. However, the value gained from expected improvements in forecast skill in terms of achieving management goals is rarely quantified as part of research objectives. Using Monte Carlo simulations of population dynamics, we assessed the effect of forecast skill under two strategies for managing Oregon coast natural (OCN) coho salmon (Oncorhynchus kisutch). The first, or status quo, strategy is currently being used to rebuild threatened OCN coho populations. This strategy determines harvest based on both a forecasted marine survival rate and parental spawner abundance. The second strategy relies on a forecast of preharvest adult abundance to achieve a constant spawner escapement target. Performance of the status quo strategy was largely insensitive to forecast skill, while the second strategy showed sensitivity that varied with escapement target and specific performance metric. The results imply that effort towards improving forecasts is not justifiable solely on the basis of improved management under the status quo strategy, though it may be were the management strategy altered.Une meilleure gestion des ressources halieutiques est une des raisons communément évoquées pour justifier les recherches sur l’amélioration de la capacité de prévision de la survie du poisson. Cela dit, la quantification de la valeur dé-coulant des améliorations attendues de la capacité de prévision pour ce qui est de l’atteinte des objectifs de gestion est rare- ment incluse dans les objectifs de recherche. En utilisant des simulations de Monte Carlo de la dynamique des populations, nous avons évalué l’effet de la capacité de prévision dans le contexte de deux stratégies de gestion du saumon coho (Onco-rhynchus kisutch) naturel de la côte de l’Oregon (OCN). La première stratégie, celle du statu quo, est actuellement utilisée pour reconstituer les populations menacées de saumon coho OCN. Selon cette stratégie, la récolte est établie en fonction des prévisions concernant le taux de survie en mer et l’abondance de géniteurs parentaux. La deuxième stratégie repose sur la prévision de l’abondance des adultes avant la récolte pour en arriver à une cible d’échappée de géniteurs constante. Le ren-dement de la stratégie du statu quo s’est avéré peu sensible à la capacité de prévision, alors que la sensibilité de la deuxième stratégie variait selon la cible d’échappée et le paramètre de mesure du rendement utilisé. Ces résultats indiquent que l’amé-lioration de la gestion dans le contexte d’une approche axée sur le statu quo ne justifie pas, à elle seule, les efforts visant l’amélioration des prévisions, mais que ces efforts pourraient être justifiés si la stratégie de gestion était modifiée

Reevaluating claims of ecological speciation in Halichoeres bivittatus

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, Halichoeres bivittatus. 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. “subtropical”) in the Florida Keys and Bermuda, where they overlap. Here, we examine habitat assortment in the Florida Keys using a broader sampling of populations and habitat types than were available for the original study. We find no evidence to support the claim that haplotype frequencies differ between habitat types, and little evidence to support any differences between populations in the Keys. These results undermine claims of ecological speciation with gene flow in Halichoeres bivittatus. Future claims of this type should be supported by multiple lines of evidence that illuminate potential mechanisms and allow researchers to rule out alternative explanations for spatial patterns of genetic differences

Face Masks and Cough Etiquette Reduce the Cough Aerosol Concentration of Pseudomonas aeruginosa in People with Cystic Fibrosis

People with cystic fibrosis (CF) generate Pseudomonas aeruginosa in droplet nuclei during coughing. The use of surgical masks has been recommended in healthcare settings to minimize pathogen transmission between patients with CF.To determine if face masks and cough etiquette reduce viable P. aeruginosa aerosolized during coughing.Twenty-five adults with CF and chronic P. aeruginosa infection were recruited. Participants performed six talking and coughing maneuvers, with or without face masks (surgical and N95) and hand covering the mouth when coughing (cough etiquette) in an aerosol-sampling device. An Andersen Cascade Impactor was used to sample the aerosol at 2 meters from each participant. Quantitative sputum and aerosol bacterial cultures were performed, and participants rated the mask comfort levels during the cough maneuvers.During uncovered coughing (reference maneuver), 19 of 25 (76%) participants produced aerosols containing P. aeruginosa, with a positive correlation found between sputum P. aeruginosa concentration (measured as cfu/ml) and aerosol P. aeruginosa colony-forming units. There was a reduction in aerosol P. aeruginosa load during coughing with a surgical mask, coughing with an N95 mask, and cough etiquette compared with uncovered coughing (P