Biological Sciences Faculty Publications Copyright (c) 2013 University of Rhode Island All rights reserved. http://digitalcommons.uri.edu/bio_facpubs Recent documents in Biological Sciences Faculty Publications en-us Mon, 20 May 2013 09:10:40 PDT 3600 Notes on the Marine Algae of the Bermudas. 8. Further Additions to the Flora, Including Griffithsia aestivana sp. nov. (Ceramiaceae, Rhodophyta) and an Update on the Alien Cystoseira compressa (Sargassaceae, Heterokontophyta) http://digitalcommons.uri.edu/bio_facpubs/22 http://digitalcommons.uri.edu/bio_facpubs/22 Mon, 25 Mar 2013 08:34:31 PDT Griffithsia aestivana sp. nov. is described as an endemic from Bermuda. Vegetatively, it is most similar to G. capitata from the eastern Atlantic Ocean, but the two differ in overall size and in the tetrasporic state. Eleven other marine algal taxa are reported from Bermuda for the first time: Anadyomene howei, Struvea elegans, Cladophoropsis macromeres, Derbesia turbinata, Caulerpa racemosa var. lamourouxii, Halimeda discoidea, Chrysymenia nodulosa, Gloiocladia iyoensis, Dasya caraibica, Chondrophycus iridescens and Polysiphonia scopulorum. All except D. turbinata represent new northern limits of distribution in the North Atlantic Ocean. In addition, recent Bermuda collections of the alien Mediterranean Cystoseira compressa and the rarely found Womersleyella setacea are detailed.

]]> Craig W. Schneider et al. Suction Generation in White-Spotted Bamboo Sharks Chiloscyllium Plagiosum http://digitalcommons.uri.edu/bio_facpubs/20 http://digitalcommons.uri.edu/bio_facpubs/20 Thu, 14 Mar 2013 13:15:24 PDT After the divergence of chondrichthyans and teleostomes, the structure of the feeding apparatus also diverged leading to alterations in the suction mechanism. In this study we investigated the mechanism for suction generation during feeding in whitespotted bamboo sharks, Chiloscyllium plagiosum and compared it with that in teleosts. The internal movement of cranial elements and pressure in the buccal, hyoid and pharyngeal cavities that are directly responsible for suction generation was quantified using sonomicrometry and pressure transducers. Backward stepwise multiple linear regressions were used to explore the relationship between expansion and pressure, accounting for 60–96% of the variation in pressure among capture events. The progression of anterior to posterior expansion in the buccal, hyoid and pharyngeal cavities is accompanied by the sequential onset of subambient pressure in these cavities as prey is drawn into the mouth. Gape opening triggers the onset of subambient pressure in the oropharyngeal cavities. Peak gape area coincides with peak subambient buccal pressure. Increased velocity of hyoid area expansion is primarily responsible for generating peak subambient pressure in the buccal and hyoid regions. Pharyngeal expansion appears to function as a sink to receive water influx from the mouth, much like that of compensatory suction in bidirectional aquatic feeders. Interestingly, C. plagiosum generates large suction pressures while paradoxically compressing the buccal cavity laterally, delaying the time to peak pressure. This represents a fundamental difference from the mechanism used to generate suction in teleost fishes. Interestingly, pressure in the three cavities peaks in the posterior to anterior direction. The complex shape changes that the buccal cavity undergoes indicate that, as in teleosts, unsteady flow predominates during suction feeding. Several kinematic variables function together, with great variation over long gape cycles to generate the low subambient pressures used by C. plagiosum to capture prey.

]]> Cheryl D. Wilga et al. Function of the Heterocercal Tail in Sharks: Quantitative Wake Dynamics During Steady Horizontal Swimming and Vertical Maneuvering http://digitalcommons.uri.edu/bio_facpubs/21 http://digitalcommons.uri.edu/bio_facpubs/21 Thu, 14 Mar 2013 13:15:24 PDT The function of the heterocercal tail in sharks has long been debated in the literature. Previous kinematic data have supported the classical theory which proposes that the beating of the heterocercal caudal fin during steady horizontal locomotion pushes posteroventrally on the water, generating a reactive force directed anterodorsally and causing rotation around the center of mass. An alternative model suggests that the heterocercal shark tail functions to direct reaction forces through the center of mass. In this paper, we quantify the function of the tail in two species of shark and compare shark tail function with previous hydrodynamic data on the heterocercal tail of sturgeon Acipenser transmontanus. To address the two models of shark heterocercal tail function, we applied the technique of digital particle image velocimetry (DPIV) to quantify the wake of two species of shark swimming in a flow tank. Both steady horizontal locomotion and vertical maneuvering were analyzed. We used DPIV with both horizontal and vertical light sheet orientations to quantify patterns of wake velocity and vorticity behind the heterocercal tail of leopard sharks (Triakis semifasciata) and bamboo sharks (Chiloscyllium punctatum) swimming at 1.0 Ls–1, where L is total body length. Two synchronized high-speed video cameras allowed simultaneous measurement of shark body position and wake structure. We measured the orientation of tail vortices shed into the wake and the orientation of the central jet through the core of these vortices relative to body orientation. Analysis of flow geometry indicates that the tail of both leopard and bamboo shark generates strongly tilted vortex rings with a mean jet angle of approximately 30 ° below horizontal during steady horizontal swimming. The corresponding angle of the reaction force is much greater than body angle (mean 11 °) and the angle of the path of motion of the center of mass (mean approximately 0 °), thus strongly supporting the classical model of heterocercal tail function for steady horizontal locomotion. Vortex jet angle varies significantly with body angle changes during vertical maneuvering, but sharks show no evidence of active reorientation of jet angle relative to body angle, as was seen in a previous study on the function of sturgeon tail. Vortex jet orientation is significantly more inclined than the relatively horizontal jet generated by sturgeon tail vortex rings, demonstrating substantial differences in function in the heterocercal tails of sharks and sturgeon. We present a summary of forces on a swimming shark integrating data obtained here on the tail with previous data on pectoral fin and body function. Body orientation plays a critical role in the overall force balance and compensates for torques generated by the tail. The pectoral fins do not generate lift during steady horizontal locomotion, but play an important hydrodynamic role during vertical maneuvering.

]]> C. D. Wilga et al. LOCOMOTION IN STURGEON: FUNCTION OF THE PECTORAL FINS http://digitalcommons.uri.edu/bio_facpubs/19 http://digitalcommons.uri.edu/bio_facpubs/19 Thu, 14 Mar 2013 13:10:21 PDT Pectoral fins are one of the major features of locomotor design in ray-finned fishes and exhibit a well-documented phylogenetic transition from basal to derived clades. In percomorph fishes, the pectoral fins are often used to generate propulsive force via oscillatory movements, and pectoral fin propulsion in this relatively derived clade has been analyzed extensively. However, in the plesiomorphic pectoral fin condition, exemplified by sturgeon, pectoral fins extend laterally from the body in a generally horizontal orientation, have been assumed to generate lift to balance lift forces and moments produced by the heterocercal tail, and are not oscillated to generate propulsive force. The proposal that pectoral fins in fishes such as sturgeon generate lift during horizontal locomotion has never been tested experimentally in freely swimming fishes. In this paper, we examine the function of pectoral fins in sturgeon swimming at speeds from 0.5–3.0 Ls-1, where L is total body length. Sturgeon were studied during steady horizontal locomotion as well as while sinking and rising in the water column. Pectoral fin function was quantified using three-dimensional kinematics to measure the orientation of the fin surface, digital particle image velocimetry (DPIV) was used to describe flow in the wake of the fin and to estimate force exerted on the water, and electromyography was used to assess pectoral fin muscle function. Sturgeon (size range 25–32cm total length) swam horizontally using continuous undulations of the body with a positive body angle that decreased from a mean of 20 ° at 0.5 Ls-1 to 0 ° at 3.0Ls-1. Both the angle of the body and the pectoral fin surface angle changed significantly when sturgeon moved vertically in the water column. Three-dimensional kinematic analysis showed that during steady horizontal swimming the pectoral fins are oriented with a negative angle of attack predicted to generate no significant lift. This result was confirmed by DPIV analysis of the pectoral fin wake, which only revealed fin vortices, and hence force generation, during maneuvering. The orientation of the pectoral fins estimated by a two-dimensional analysis alone is greatly in error and may have contributed to previous suggestions that the pectoral fins are oriented to generate lift. Combined electromyographic and kinematic data showed that the posterior half of the pectoral fin is actively moved as a flap to reorient the head and body to initiate rising and sinking movements. A new force balance for swimming sturgeon is proposed for steady swimming and vertical maneuvering. During steady locomotion, the pectoral fins generate no lift and the positive body angle to the flow is used both to generate lift and to balance moments around the center of mass. To initiate rising or sinking, the posterior portion of the pectoral fins is actively moved ventrally or dorsally, respectively, initiating a starting vortex that, in turn, induces a pitching moment reorienting the body in the flow. Adjustments to body angle initiated by the pectoral fins serve as the primary means by which moments are balanced.

]]> C. D. Wilga et al. FEEDING MECHANISM OF THE ATLANTIC GUITARFISH RHINOBATOS LENTIGINOSUS: MODULATION OF KINEMATIC AND MOTOR ACTIVITY http://digitalcommons.uri.edu/bio_facpubs/18 http://digitalcommons.uri.edu/bio_facpubs/18 Thu, 14 Mar 2013 13:10:19 PDT The kinematics and muscle activity pattern of the head and jaws during feeding in the Atlantic guitarfish Rhinobatos lentiginosus are described and quantified using high-speed video and electromyography to test hypotheses regarding the conservation and modulation of the feeding mechanism. Prey is captured by the guitarfish using suction. Suction capture, bite manipulation and suction transport behaviors in the guitarfish are similar to one another in the relative sequence of kinematic and motor activity, but can be distinguished from one another by variation in absolute muscle activation time, in the presence or absence of muscle activity and in the duration of muscle activity. A novel compression transport behavior was observed that is strikingly different from the other feeding behaviors and has not been described previously in elasmobranchs. The mechanism of upper jaw protrusion in the guitarfish differs from that described in other elasmobranchs. Muscle function and motor pattern during feeding are similar in the plesiomorphic cranial muscles in the guitarfish and the spiny dogfish probably because of their shared ancestral morphology. Modulation in recruitment of jaw and hyoid depressor muscles among feeding behaviors in the guitarfish may be a consequence of duplication of muscles and decoupling of the jaws and hyoid apparatus in batoids.

]]> Cheryl D. Wilga et al. DUROPHAGY IN SHARKS: FEEDING MECHANICS OF THE HAMMERHEADSPHYRNA TIBURO http://digitalcommons.uri.edu/bio_facpubs/17 http://digitalcommons.uri.edu/bio_facpubs/17 Thu, 14 Mar 2013 13:10:18 PDT This study investigates the motor pattern and head movements during feeding of a durophagus shark, the bonnethead Sphyrna tiburo, using electromyography and simultaneous high-speed video. Sphyrna tiburo feeds almost exclusively on hard-shelled crabs, with shrimp and fish taken occasionally. It captures crabs by ram feeding, then processes or reduces the prey by crushing it between molariform teeth, finally transporting the prey by suction for swallowing. The prey-crushing mechanism is distinct from that of ram or bite capture and suction transport. This crushing mechanism is accomplished by altering the duration of jaw adductor muscle activity and modifying jaw kinematics by the addition of a second jaw-closing phase. In crushing events, motor activity of the jaw adductor muscles continues (biting of the prey occurs as the jaws close and continues after the jaws have closed) throughout a second jaw-closing phase, unlike capture and transport events during which motor activity (biting) ceases at jaw closure. Sphyrna tiburo is able to take advantage of a resource (hard prey) that is not readily available to most sharks by utilizing a suite of durophagous characteristics: molariform teeth, a modified jaw protrusor muscle, altered jaw adductor activity and modified jaw kinematics. Sphyrna tiburo is a specialist feeder on crab prey as demonstrated by the lack of differences in kinematic or motor patterns when offered prey of differing hardness and its apparent lack of ability to modulate its behavior when feeding on other prey. Functional patterns are altered and coupled with modifications in dental and jaw morphology to produce diverse crushing behaviors in elasmobranchs.

]]> Cheryl D. Wilga et al. CONSERVATION AND VARIATION IN THE FEEDING MECHANISM OF THE SPINY DOGFISH SQUALUS ACANTHIAS http://digitalcommons.uri.edu/bio_facpubs/16 http://digitalcommons.uri.edu/bio_facpubs/16 Thu, 14 Mar 2013 13:10:17 PDT Changes in the feeding mechanism with feeding behavior were investigated using high-speed video and electromyography to examine the kinematics and motor pattern of prey capture, manipulation and transport in the spiny dogfish Squalus acanthias (Squalidae: Squaliformes). In this study, Squalus acanthias used both suction and ram behaviors to capture and manipulate prey, while only suction was used to transport prey. The basic kinematic feeding sequence observed in other aquatic-feeding lower vertebrates is conserved in the spiny dogfish. Prey capture, bite manipulation and suction transport events are characterized by a common pattern of head movements and motor activity, but are distinguishable by differences in duration and relative timing. In general, capture events are longer in duration than manipulation and transport events, as found in other aquatic-feeding lower vertebrates. Numerous individual effects were found, indicating that individual sharks are capable of varying head movements and motor activity among successful feeding events. Upper jaw protrusion in the spiny dogfish is not restricted by its orbitostylic jaw suspension; rather, the upper jaw is protruded by 30 % of its head length, considerably more than in the lemon shark Negaprion brevirostris (Carcharhinidae: Carcharhiniformes) (18 %) with its hyostylic jaw suspension. One function of upper jaw protrusion is to assist in jaw closure by protruding the upper jaw as well as elevating the lower jaw to close the gape, thus decreasing the time to jaw closure. The mechanism of upper jaw protrusion was found to differ between squaliform and carcharhiniform sharks. Whereas the levator palatoquadrati muscle assists in retracting the upper jaw in the spiny dogfish, it assists in protruding the upper jaw in the lemon shark. This study represents the first comprehensive electromyographic and kinematic analysis of the feeding mechanism in a squaliform shark.

]]> Cheryl D. Wilga et al. LIFE AT STABLE LOW OXYGEN LEVELS: ADAPTATIONS OF ANIMALS TO OCEANIC OXYGEN MINIMUM LAYERS http://digitalcommons.uri.edu/bio_facpubs/15 http://digitalcommons.uri.edu/bio_facpubs/15 Tue, 12 Mar 2013 08:40:23 PDT Zones of minimum oxygen level are found at intermediate depths in most of the world’s oceans and, although the oxygen partial pressure in some of these ‘oxygen minimum layers’ is only a fraction of a kilopascal, populations of pelagic metazoans exist there. These oxygen minimum layers are areas of the water column and the associated benthos with stable conditions of continuously low oxygen level and low temperature at intermediate depths (400–1000 m depth) over vast areas. Off California, where PO2at the oxygen minimum is 0.8 kPa, there are abundant populations of animals both in the water column and on the bottom. Farther to the south in the eastern tropical Pacific, oxygen partial pressures of less than approximately 0.4 kPa result in very low biomasses and diversity of animals at minimum layer depths. At the minimum oxygen levels found off California, most animals which inhabit the minimum zones appear to support their routine metabolic demands via aerobic metabolism. They do this by being very effective at removing oxygen from water. Among the adaptations of pelagic crustaceans to these conditions are: (1) enhanced ventilatory abilities, (2) enhanced percentage removal of O2 from the ventilatory stream, (3) large gill surface areas, (4) short diffusion distances from the water to the blood, and (5) hemocyanin respiratory proteins with a very high affinity for O2, high cooperativity and large Bohr effects. The lower O2 consumption rates of many deeper-living species are also functionally adaptive in that they facilitate aerobic survival at low PO2. However, they are not adaptations to the minimum layer, since similarly low rates are found in the same and comparable species living at the same depths in regions without well-developed minima, and these animals are unable to survive at the low PO2values of the minima. While anaerobic metabolism may be important for metabolic rates above the routine level for most animals in the minimum layer, there is little evidence for the use of sustained anaerobiosis in the species studied. In summary, given the stable presence of very low O2 levels in the minima, the primary adaptations of animals living within them are those that support aerobic metabolism by giving the animals remarkable abilities to extract O2 from water. These abilities are notably better than those of animals adapted to unstable hypoxic environments, such as intertidal mudflats, while the latter animals rely to a much greater extent on anaerobiosis and perhaps on metabolic suppression to survive periods of anoxia.

]]> James J. Childress et al. FLIGHT OF THE VAMPIRE: ONTOGENETIC GAIT-TRANSITION IN VAMPYROTEUTHIS INFERNALIS (CEPHALOPODA: VAMPYROMORPHA) http://digitalcommons.uri.edu/bio_facpubs/14 http://digitalcommons.uri.edu/bio_facpubs/14 Tue, 12 Mar 2013 08:40:20 PDT Vampyroteuthis infernalis is a cosmopolitan cephalopod that lives in the oxygen minimum layer between 600 and 800 m depth. Morphometric and physiological studies have indicated that V. infernalis has little capacity for jet propulsion and has the lowest metabolic rate ever measured for a cephalopod. Because fin swimming is inherently more efficient than jet propulsion, some of the reduction in energy usage relative to other cephalopods may result from the use of fins as the primary means of propulsion. V. infernalis undergoes a rapid metamorphosis which consists of changes in the position, size and shape of the fins. This suggests that there are changes in the selective factors affecting locomotion through ontogeny. The present study describes these changes in relation to models for underwater ‘flight’. Citrate synthase (CS) and octopine dehydrogenase (ODH) activities, indicative of aerobic and anaerobic metabolism, respectively, were measured in fin, mantle and arm tissue across a range of body size of four orders of magnitude. The low enzymatic activities in both posterior and anterior fin tissue and the relatively high activity in mantle muscle prior to metamorphosis indicate that jet propulsion using mantle contraction is the primary means of propulsion in juvenile V. infernalis. The increase in CS activity with size after metamorphosis suggests an increased use of the fins for lift-based propulsion. Fin swimming appears to be the primary means of propulsion at all adult sizes. The negative allometry of CS activity in mantle and arm muscle is consistent with the scaling of oxygen consumption previously measured for V. infernalis and with the scaling of aerobic metabolism observed in most animals. The unusual positive allometry of fin muscle CS activity suggests that the use of fins is either relatively more important or more costly in larger animals. Positive scaling of ODH activity in all tissues suggests that fin propulsion, jet propulsion and medusoid ‘bell-swimming’ are all important for burst escape responses. Enzyme activities in Cirrothauma murrayi are consistent with finswimming observed from submersibles, while those in Opisthoteuthis californiana suggest a strong reliance on medusoid swimming using the arms. The transition from jet propulsion to paired-fin ‘flight’ with increasing body size in Vampyroteuthis infernalis appears functionally to be an ontogenetic ‘gait-transition’.

]]> Brad A. Seibel et al. Recalculated diet and daily ration of the shortfin mako ( Isurus oxyrinchus ), with a focus on quantifying predation on bluefish (Pomatomus saltatrix) in the northwest Atlantic Ocean http://digitalcommons.uri.edu/bio_facpubs/13 http://digitalcommons.uri.edu/bio_facpubs/13 Tue, 12 Mar 2013 08:35:16 PDT The diet and daily ration of the shortfin mako (Isurus oxyrinchus) in the northwest Atlantic were re-examined to determine whether fluctuations in prey abundance and availability are ref lected in these two biological variables. During the summers of 2001 and 2002, stomach content data were collected from fishing tournaments along the northeast coast of the United States. These data were quantified by using four diet indices and were compared to index calculations from historical diet data collected from 1972 through 1983. Bluefish (Pomatomus saltatrix) were the predominant prey in the 1972–83 and 2001–02 diets, accounting for 92.6% of the current diet by weight and 86.9% of the historical diet by volume. From the 2001– 02 diet data, daily ration was estimated and it indicated that shortfin makos must consume roughly 4.6% of their body weight per day to fulfill energetic demands. The daily energetic requirement was broken down by using a calculated energy content for the current diet of 4909 KJ/kg. Based on the proportional energy of bluefish in the diet by weight, an average shortfin mako consumes roughly 500 kg of bluefish per year off the northeast coast of the United States. The results are discussed in relation to the potential effect of intense shortfin mako predation on bluefish abundance in the region.

]]> Anthony D. Wood et al. Fluid Dynamics of Feeding Behaviour in White-Spotted Bamboo Sharks http://digitalcommons.uri.edu/bio_facpubs/12 http://digitalcommons.uri.edu/bio_facpubs/12 Tue, 12 Mar 2013 08:20:23 PDT Although the motor control of feeding is presumed to be generally conserved, some fishes are capable of modulating the feeding behaviour in response to prey type and or prey size. This led to the ʻfeeding modulation hypothesisʼ, which states that rapid suction strikes are pre-programmed stereotyped events that proceed to completion once initiated regardless of sensory input. If this hypothesis holds true, successful strikes should be indistinguishable from unsuccessful strikes owing to a lack of feedback control in specialized suction feeding fishes. The hydrodynamics of suction feeding in white-spotted bamboo sharks (Chiloscyllium plagiosum) was studied in three behaviours: successful strikes, intraoral transports of prey and unsuccessful strikes. The area of the fluid velocity region around the head of feeding sharks was quantified using time-resolved digital particle image velocimetry (DPIV). The maximal size of the fluid velocity region is 56% larger in successful strikes than unsuccessful strikes (10.79cm2 vs 6.90cm2), but they do not differ in duration, indicating that strikes are modulated based on some aspect of the prey or simply as a result of decreased effort on the part of the predator. The hydrodynamic profiles of successful and unsuccessful strikes differ after 21 ms, a period probably too short to provide time to react through feedback control. The predator-to-prey distance is larger in missed strikes compared with successful strikes, indicating that insufficient suction is generated to compensate for the increased distance. An accuracy index distinguishes unsuccessful strikes (–0.26) from successful strikes (0.45 to 0.61). Successful strikes occur primarily between the horizontal axis of the mouth and the dorsal boundary of the ingested parcel of water, and missed prey are closer to the boundary or beyond. Suction transports are shorter in duration than suction strikes but have similar maximal fluid velocity areas to move the prey through the oropharyngeal cavity into the oesophagus (54ms vs 67ms).

]]> Sandra Nauwelaerts et al. THREE-DIMENSIONAL KINEMATICS AND WAKE STRUCTURE OF THE PECTORALFINS DURING LOCOMOTION IN LEOPARD SHARKS TRIAKIS SEMIFASCIATA http://digitalcommons.uri.edu/bio_facpubs/11 http://digitalcommons.uri.edu/bio_facpubs/11 Tue, 12 Mar 2013 08:20:22 PDT The classical theory of locomotion in sharks proposes that shark pectoral fins are oriented to generate lift forces that balance the moment produced by the oscillating heterocercal tail. Accordingly, previous studies of shark locomotion have used fixed-wing aircraft as a model assuming that sharks have similar stability and control mechanisms. However, unlike airplanes, sharks are propelled by undulations of the body and tail and have considerable control of pectoral fin motion. In this paper, we use a new approach to examine the function of the pectoral fins of leopard sharks, Triakis semifasciata, during steady horizontal swimming at speeds of 0.5–2.0 l s-1, where l is total body length, and during vertical maneuvering (rising and sinking) in the water column. The planar orientation of the pectoral fin was measured using threedimensional kinematics, while fluid flow in the wake of the pectoral fin and forces exerted on the water by the fin were quantified using digital particle image velocimetry (DPIV). Steady horizontal swimming in leopard sharks is characterized by continuous undulations of the body with a positive body tilt to the flow that decreases from a mean of 11 ° to 0.6 ° with increasing flow speeds from 0.5 to 2.0 l s-1. Three-dimensional analysis showed that, during steady horizontal locomotion, the pectoral fins are cambered, concave downwards, at a negative angle of attack that we predict to generate no significant lift. Leopard shark pectoral fins are also oriented at a substantial negative dihedral angle that amplifies roll moments and hence promotes rapid changes in body position. Vortices shed from the trailing edge of the pectoral fin were detected only during vertical maneuvering. Starting vortices are produced when the posterior plane of the pectoral fin is actively flipped upwards or downwards to initiate rising or sinking, respectively, in the water column. The starting vortex produced by the pectoral fin induces a pitching moment that reorients the body relative to the flow. Body and pectoral fin surface angle are altered significantly when leopard sharks change vertical position in the water column. Thus, locomotion in leopard sharks is not analogous to flight in fixed-wing aircraft. Instead, a new force balance for swimming leopard sharks is proposed for steady swimming and maneuvering. Total force balance on the body is adjusted by altering the body angle during steady swimming as well as during vertical maneuvering, while the pectoral fins appear to be critical for initiating maneuvering behaviors, but not for lift production during steady horizontal locomotion.

]]> C. D. Wilga et al. Modeling the Consequences of Thermal Trait Variation for the Cane Toad Invasion of Australia http://digitalcommons.uri.edu/bio_facpubs/10 http://digitalcommons.uri.edu/bio_facpubs/10 Mon, 25 Feb 2013 11:45:15 PST Mechanistic species distribution models (SDMs) are ideally suited for predicting the nonnative distributions of invasive species, but require accurate parameteri? zation of key functional traits. Importantly, any ability of the invader to acclimate or adapt rapidly to local conditions must be incorporated. Our field and laboratory studies measured phenotypic variation and tested for plasticity in the thermal sensitivity of locomotor performance and low-temperature tolerance of adult cane toads Bufo marinus in eastern Australia. We used a biophysical model to explore the adaptive significance of this variation and how it affected distribution predictions. Laboratory trials showed that geographic differences in low-temperature tolerance (i.e., the critical thermal minimum; CTMin) of field caught toads reflect thermal acclimation, whereas populations differed in the thermal dependence of locomotor performance even after acclimation. Incorporating low-temperature tolerance as a dimension of the fundamental niche reduced the predicted southern distribution. To test whether these factors predicted to be range limiting were consistent with reduced performance for individuals, we used the biophysical model and daily climate data to conduct "virtual transplants." These models predicted that acclimation reduced cold stress by 32-100% for toads sheltering near the ground surface; toads inside burrows could remain above their CTMin, but the required burrow depth increased with latitude. Low temperature tolerance of the adult phase may constrain the southern range limit of the cane toad in Australia, and plasticity in this trait may have facilitated the southward range expansion.

]]> Jason J. Kolbe et al. Molecular Investigation Reveals Epi/Endophytic Extrageneric Kelp (Laminariales, Phaeophyceae) Gametophytes Colonizing Lessoniopsis Littoralis Thalli http://digitalcommons.uri.edu/bio_facpubs/9 http://digitalcommons.uri.edu/bio_facpubs/9 Mon, 25 Feb 2013 11:40:18 PST A recent molecular investigation of kelp systematics revealed mitochondrial sequences that gave phylogenies inconsistent with those based on nuclear and chloroplast sequences for the species Lessoniopsis littoralis. Sequence from the mitochondrial nad6 region placed L. littoralis in the middle of a clade of Alaria species in our trees, whereas Rubisco and nuclear ribosomal DNA sequences resolved L. littoralis within the Alariaceae, but distinct from Alaria. To resolve these conflicting results, the nad6 region was sequenced from additional samples of L. littoralis. The resulting data variously placed L. littoralis with Macrocystis integrifolia, Nereocystis luetkeana, and an additional Alaria isolate. A series of hypotheses were devised and explored to effectively exclude introgression via hybridization as a viable explanation for our observations. Rather, molecular and microscopy data revealed that gametophytes of Alaria, Macrocystis and Nereocystis epi/endophytically, colonize the older portions of the thallus of L. littoralis. A substantial primer mismatch, unique to L. littoralis, was uncovered subsequently explaining why nad6 sequences from only Alaria, Macrocystis and Nereocystis were amplified from L. littoralis sporophyte samples, although the DNA from the gametophytes likely represented only a small percentage of the total DNA extracted.

]]> Christopher E. Lane et al. Extensive Conserved Synteny of Genes Between the Karyotypes of <i>Manduca sexta</i> and <i>Bombyx mori</i> Revealed by BAC-FISH Mapping http://digitalcommons.uri.edu/bio_facpubs/8 http://digitalcommons.uri.edu/bio_facpubs/8 Wed, 05 Sep 2012 07:20:16 PDT Background: Genome sequencing projects have been completed for several species representing four highly diverged holometabolous insect orders, Diptera, Hymenoptera, Coleoptera, and Lepidoptera. The striking evolutionary diversity of insects argues a need for efficient methods to apply genome information from such models to genetically uncharacterized species. Constructing conserved synteny maps plays a crucial role in this task. Here, we demonstrate the use of fluorescence in situ hybridization with bacterial artificial chromosome probes as a powerful tool for physical mapping of genes and comparative genome analysis in Lepidoptera, which have numerous and morphologically uniform holokinetic chromosomes.

Methodology/Principal Findings: We isolated 214 clones containing 159 orthologs of well conserved single-copy genes of a sequenced lepidopteran model, the silkworm, Bombyx mori, from a BAC library of a sphingid with an unexplored genome, the tobacco hornworm, Manduca sexta. We then constructed a BAC-FISH karyotype identifying all 28 chromosomes of M. sexta by mapping 124 loci using the corresponding BAC clones. BAC probes from three M. sexta chromosomes also generated clear signals on the corresponding chromosomes of the convolvulus hawk moth, Agrius convolvuli, which belongs to the same subfamily, Sphinginae, as M. sexta.

Conclusions/Significance: Comparison of the M. sexta BAC physical map with the linkage map and genome sequence of B. mori pointed to extensive conserved synteny including conserved gene order in most chromosomes. Only a few rearrangements, including three inversions, three translocations, and two fission/fusion events were estimated to have occurred after the divergence of Bombycidae and Sphingidae. These results add to accumulating evidence for the stability of lepidopteran genomes. Generating signals on A. convolvuli chromosomes using heterologous M. sexta probes demonstrated that BAC-FISH with orthologous sequences can be used for karyotyping a wide range of related and genetically uncharacterized species, significantly extending the ability to develop synteny maps for comparative and functional genomics.

]]> Yuji Yasukochi et al. KAIKObase: An integrated silkworm genome database and data mining tool http://digitalcommons.uri.edu/bio_facpubs/7 http://digitalcommons.uri.edu/bio_facpubs/7 Tue, 31 Jul 2012 11:16:00 PDT Background: The silkworm, Bombyx mori, is one of the most economically important insects in many developing countries owing to its large-scale cultivation for silk production. With the development of genomic and biotechnological tools, B. mori has also become an important bioreactor for production of various recombinant proteins of biomedical interest. In 2004, two genome sequencing projects for B. mori were reported independently by Chinese and Japanese teams; however, the datasets were insufficient for building long genomic scaffolds which are essential for unambiguous annotation of the genome. Now, both the datasets have been merged and assembled through a joint collaboration between the two groups.

Description: Integration of the two data sets of silkworm whole-genome-shotgun sequencing by the Japanese and Chinese groups together with newly obtained fosmid- and BAC-end sequences produced the best continuity (~3.7 Mb in N50 scaffold size) among the sequenced insect genomes and provided a high degree of nucleotide coverage (88%) of all 28 chromosomes. In addition, a physical map of BAC contigs constructed by fingerprinting BAC clones and a SNP linkage map constructed using BAC-end sequences were available. In parallel, proteomic data from twodimensional polyacrylamide gel electrophoresis in various tissues and developmental stages were compiled into a silkworm proteome database. Finally, a Bombyx trap database was constructed for documenting insertion positions and expression data of transposon insertion lines.

Conclusion: For efficient usage of genome information for functional studies, genomic sequences, physical and genetic map information and EST data were compiled into KAIKObase, an integrated silkworm genome database which consists of 4 map viewers, a gene viewer, and sequence, keyword and position search systems to display results and data at the level of nucleotide sequence, gene, scaffold and chromosome. Integration of the silkworm proteome database and the Bombyx trap database with KAIKObase led to a high-grade, user-friendly, and comprehensive silkworm genome database which is now available from URL: http://sgp.dna.affrc.go.jp/KAIKObase/.

]]> Michihiko Shimomura et al. Construction and Sequence Sampling of Deep-Coverage Large-Insect BAC Libraries for Three Model Lepidopteran Species http://digitalcommons.uri.edu/bio_facpubs/6 http://digitalcommons.uri.edu/bio_facpubs/6 Mon, 30 Jul 2012 12:43:58 PDT Background: Manduca sexta, Heliothis virescens, and Heliconius erato represent three widely-used insect model species for genomic and fundamental studies in Lepidoptera. Large-insert BAC libraries of these insects are critical resources for many molecular studies, including physical mapping and genome sequencing, but not available to date.

Results: We report the construction and characterization of six large-insert BAC libraries for the three species and sampling sequence analysis of the genomes. The six BAC libraries were constructed with two restriction enzymes, two libraries for each species, and each has an average clone insert size ranging from 152–175 kb. We estimated that the genome coverage of each library ranged from 6–9 ×, with the two combined libraries of each species being equivalent to 13.0–16.3 × haploid genomes. The genome coverage, quality and utility of the libraries were further confirmed by library screening using 6~8 putative single-copy probes. To provide a first glimpse into these genomes, we sequenced and analyzed the BAC ends of ~200 clones randomly selected from the libraries of each species. The data revealed that the genomes are AT-rich, contain relatively small fractions of repeat elements with a majority belonging to the category of low complexity repeats, and are more abundant in retro-elements than DNA transposons. Among the species, the H. erato genome is somewhat more abundant in repeat elements and simple repeats than those of M. sexta and H. virescens. The BLAST analysis of the BAC end sequences suggested that the evolution of the three genomes is widely varied, with the genome of H. virescens being the most conserved as a typical lepidopteran, whereas both genomes of H. erato and M. sexta appear to have evolved significantly, resulting in a higher level of species- or evolutionary lineage-specific sequences.

Conclusion: The high-quality and large-insert BAC libraries of the insects, together with the identified BACs containing genes of interest, provide valuable information, resources and tools for comprehensive understanding and studies of the insect genomes and for addressing many fundamental questions in Lepidoptera. The sample of the genomic sequences provides the first insight into the constitution and evolution of the insect genomes.

]]> Chengcang Wu et al. An Integrated Genetic Linkage Map for Silkworms with Three Parental Combinations and Its Application to the Mapping of Single Genes and QTL http://digitalcommons.uri.edu/bio_facpubs/5 http://digitalcommons.uri.edu/bio_facpubs/5 Mon, 30 Jul 2012 12:39:37 PDT Background: Bombyx mori, the domesticated silkworm, is a well-studied model insect with great economic and scientific significance. Although more than 400 mutations have been described in silkworms, most have not been identified, especially those affecting economically-important traits. Simple sequence repeats (SSRs) are effective and economical tools for mapping traits and genetic improvement. The current SSR linkage map is of low density and contains few polymorphisms. The purpose of this work was to develop a dense and informative linkage map that would assist in the preliminary mapping and dissection of quantitative trait loci (QTL) in a variety of silkworm strains.

Results: Through an analysis of > 50,000 genotypes across new mapping populations, we constructed two new linkage maps covering 27 assigned chromosomes and merged the data with previously reported data sets. The integrated consensus map contains 692 unique SSR sites, improving the density from 6.3 cM in the previous map to 4.8 cM. We also developed 497 confirmed neighboring markers for corresponding low-polymorphism sites, with 244 having polymorphisms. Large-scale statistics on the SSR type were suggestive of highly efficient markers, based upon which we searched 16,462 available genomic scaffolds for SSR loci. With the newly constructed map, we mapped single-gene traits, the QTL of filaments, and a number of ribosomal protein genes.

Conclusion: The integrated map produced in this study is a highly efficient genetic tool for the high-throughput mapping of single genes and QTL. Compared to previous maps, the current map offers a greater number of markers and polymorphisms; thus, it may be used as a resource for marker-assisted breeding.

]]> Shuai Zhan et al. A BAC-Based Integrated Linkage Map of the Silkworm <i>Bombyx mori</i> http://digitalcommons.uri.edu/bio_facpubs/4 http://digitalcommons.uri.edu/bio_facpubs/4 Mon, 30 Jul 2012 12:33:00 PDT Background: In 2004, draft sequences of the model lepidopteran Bombyx mori were reported using whole-genome shotgun sequencing. Because of relatively shallow genome coverage, the silkworm genome remains fragmented, hampering annotation and comparative genome studies. For a more complete genome analysis, we developed extended scaffolds combining physical maps with improved genetic maps.

Results: We mapped 1,755 single nucleotide polymorphism (SNP) markers from bacterial artificial chromosome (BAC) end sequences onto 28 linkage groups using a recombining male backcross population, yielding an average inter-SNP distance of 0.81 cM (about 270 kilobases). We constructed 6,221 contigs by fingerprinting clones from three BAC libraries digested with different restriction enzymes, and assigned a total of 724 single copy genes to them by BLAST (basic local alignment search tool) search of the BAC end sequences and high-density BAC filter hybridization using expressed sequence tags as probes. We assigned 964 additional expressed sequence tags to linkage groups by restriction fragment length polymorphism analysis of a nonrecombining female backcross population. Altogether, 361.1 megabases of BAC contigs and singletons were integrated with a map containing 1,688 independent genes. A test of synteny using Oxford grid analysis with more than 500 silkworm genes revealed six versus 20 silkworm linkage groups containing eight or more orthologs of Apis versus Tribolium, respectively.

Conclusion: The integrated map contains approximately 10% of predicted silkworm genes and has an estimated 76% genome coverage by BACs. This provides a new resource for improved assembly of whole-genome shotgun data, gene annotation and positional cloning, and will serve as a platform for comparative genomics and gene discovery in Lepidoptera and other insects.

]]> Kimiko Yamamoto et al. Complete Sequence and Analysis of the Mitochondrial Genome of <i>Hemiselmis andersenii</i> CCMP644 (Cryptophyceae) http://digitalcommons.uri.edu/bio_facpubs/3 http://digitalcommons.uri.edu/bio_facpubs/3 Mon, 30 Jul 2012 12:14:34 PDT Background: Cryptophytes are an enigmatic group of unicellular eukaryotes with plastids derived by secondary (i.e., eukaryote-eukaryote) endosymbiosis. Cryptophytes are unusual in that they possess four genomes–a host cell-derived nuclear and mitochondrial genome and an endosymbiont-derived plastid and 'nucleomorph' genome. The evolutionary origins of the host and endosymbiont components of cryptophyte algae are at present poorly understood. Thus far, a single complete mitochondrial genome sequence has been determined for the cryptophyte Rhodomonas salina. Here, the second complete mitochondrial genome of the cryptophyte alga Hemiselmis andersenii CCMP644 is presented.

Results: The H. andersenii mtDNA is 60,553 bp in size and encodes 30 structural RNAs and 36 protein-coding genes, all located on the same strand. A prominent feature of the genome is the presence of a ~20 Kbp long intergenic region comprised of numerous tandem and dispersed repeat units of between 22–336 bp. Adjacent to these repeats are 27 copies of palindromic sequences predicted to form stable DNA stem-loop structures. One such stem-loop is located near a GCrich and GC-poor region and may have a regulatory function in replication or transcription. The H. andersenii mtDNA shares a number of features in common with the genome of the cryptophyte Rhodomonas salina, including general architecture, gene content, and the presence of a large repeat region. However, the H. andersenii mtDNA is devoid of inverted repeats and introns, which are present in R. salina. Comparative analyses of the suite of tRNAs encoded in the two genomes reveal that the H. andersenii mtDNA has lost or converted its original trnK(uuu) gene and possesses a trnSderived 'trnK(uuu)', which appears unable to produce a functional tRNA. Mitochondrial protein coding gene phylogenies strongly support a variety of previously established eukaryotic groups, but fail to resolve the relationships among higher-order eukaryotic lineages.

Conclusion: Comparison of the H. andersenii and R. salina mitochondrial genomes reveals a number of cryptophyte-specific genomic features, most notably the presence of a large repeat-rich intergenic region. However, unlike R. salina, the H. andersenii mtDNA does not possess introns and lacks a Lys-tRNA, which is presumably imported from the cytosol.

]]> Eunsoo Kim et al.