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opencc-zeroDec 2018View details →

Data from: Contrasting processes drive ophiuroid phylodiversity across shallow and deep seafloors

Our knowledge of the distribution and evolution of deep-sea life is limited, impeding our ability to identify priority areas for conservation. Here we analyse, for the first time, large integrated phylogenomic and distributional datasets of seafloor fauna from sea surface to abyss and equator to pole of the Southern Hemisphere for an entire class of invertebrates (Ophiuroidea). We find that latitudinal diversity gradients are assembled through contrasting evolutionary processes for shallow (0-200 m) and deep (> 200 m) seas. The shallow-water tropical-temperate realm broadly reflects a tropical diversification-driven process but with exchange in both directions. Diversification rates are reversed for the realm containing the deep sea and Antarctica, being highest at polar and lowest at tropical latitudes, and net exchange is from high to low latitudes. The tropical upper bathyal (200-700 m deep), with its rich ancient phylodiversity, is characterised by relatively low diversification and moderate immigration rates. Conversely, the young specialised Antarctic fauna is inferred to be rebounding from regional extinction associated with the rapid cooling of polar waters over the mid-Cenozoic.

opencc-zeroMay 2019View details →

Data from: Seasonal contrasts in individual consistency of oriental honey buzzards' migration

Individual consistency in migration can shine light on the mechanisms of migration. Most studies reported that birds are more consistent in the timing than in the routes or stopover sites during migration, but some specialist species showed the opposite patterns, being more consistent in spatial than temporal aspects of migration. One possible explanation for this contrast is that specialists rely on particular food or habitat resources, which restrict the migratory routes they can take, leading to high spatial consistency. If this is the case, the effect of specialist foraging should become apparent only when birds forage, instead of fasting and flying continuously. To test this effect, we analysed individual consistency in migration of the oriental honey buzzard (Pernis ptilorhynchus), a specialist raptor that feeds on honeybees and wasps, using a long-term tracking data set. As honey buzzards make extended stopovers during which they forage in spring but not in autumn, the spatial consistency should be higher in spring than in autumn. Honey buzzards were highly consistent in both their migratory routes and stopover sites in Southeast Asia, but only during spring migration. Our results highlight an important link between species' migratory consistency and foraging ecology.

opencc-zeroDec 2013View details →

Data from: Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles

Comparative analysis is a potentially powerful approach to study the effects of ecological traits on genetic variation and rate of evolution across species. However, the lack of suitable datasets means that comparative studies of correlates of genetic traits across an entire clade have been rare. Here, we use a large DNA-barcode dataset (5062 sequences) of water beetles to test the effects of species ecology and geographical distribution on genetic variation within species and rates of molecular evolution across species. We investigated species traits predicted to influence their genetic characteristics, such as surrogate measures of species population size, latitudinal distribution and habitat types, taking phylogeny into account. Genetic variation of cytochrome oxidase I in water beetles was positively correlated with occupancy (numbers of sites of species presence) and negatively with latitude, whereas substitution rates across species depended mainly on habitat types, and running water specialists had the highest rate. These results are consistent with theoretical predictions from nearly-neutral theories of evolution, and suggest that the comparative analysis using large databases can give insights into correlates of genetic variation and molecular evolution.

opencc-zeroAug 2019View details →

Data from: Exposure to opposing temperature extremes causes comparable effects on Cardinium density but contrasting effects on Cardinium-induced cytoplasmic incompatibility

Terrestrial arthropods, including insects, commonly harbor maternally inherited intracellular symbionts that confer benefits to the host or manipulate host reproduction to favor infected female progeny. These symbionts may be especially vulnerable to thermal stress, potentially leading to destabilization of the symbiosis and imposing costs to the host. For example, increased temperatures can reduce the density of a common reproductive manipulator, Wolbachia, and the strength of its crossing incompatibility (cytoplasmic incompatibility, or CI) phenotype. Another manipulative symbiont, Cardinium hertigii, infects ~ 6-10% of Arthropods, and also can induce CI, but there is little homology between the molecular mechanisms of CI induced by Cardinium and Wolbachia. Here we investigated whether temperature disrupts the CI phenotype of Cardinium in a parasitic wasp host, Encarsia suzannae. We examined the effects of both warm (32°C day/ 29°C night) and cool (20°C day/ 17°C night) temperatures on Cardinium CI and found that both types of temperature stress modified aspects of this symbiosis. Warm temperatures reduced symbiont density, pupal developmental time, vertical transmission rate, and the strength of both CI modification and rescue. Cool temperatures also reduced symbiont density, however this resulted in stronger CI, likely due to cool temperatures prolonging the host pupal stage. The opposing effects of cool and warm-mediated reductions in symbiont density on the resulting CI phenotype indicates that CI strength may be independent of density in this system. Temperature stress also modified the CI phenotype only if it occurred during the pupal stage, highlighting the likely importance of this stage for CI induction in this symbiosis.

opencc-zeroDec 2018View details →

Data from: Decreased brain connectivity in smoking contrasts with increased connectivity in drinking

In a group of 831 participants from the general population in the Human Connectome Project, smokers exhibited low overall functional connectivity, and more specifically of the lateral orbitofrontal cortex which is associated with non-reward mechanisms, the adjacent inferior frontal gyrus, and the precuneus. Participants who drank a high amount had overall increases in resting state functional connectivity, and specific increases in reward-related systems including the medial orbitofrontal cortex and the cingulate cortex. Increased impulsivity was found in smokers, associated with decreased functional connectivity of the non-reward-related lateral orbitofrontal cortex; and increased impulsivity was found in high amount drinkers, associated with increased functional connectivity of the reward-related medial orbitofrontal cortex. The main findings were cross-validated in an independent longitudinal dataset with 1176 participants, IMAGEN. Further, the functional connectivities in 14-year-old non-smokers (and also in female low-drinkers) were related to who would smoke or drink at age 19. An implication is that these differences in brain functional connectivities play a role in smoking and drinking, together with other factors.

opencc-zeroDec 2013View details →

Data from: Free-living bacterial communities associated with tubeworm (Ridgeia piscesae) aggregations in contrasting diffuse flow hydrothermal vent habitats at the Main Endeavour Field, Juan de Fuca Ridge

We systematically studied free-living bacterial diversity within aggregations of the vestimentiferan tubeworm Ridgeia piscesae sampled from two contrasting flow regimes (High Flow and Low Flow) in the Endeavour Hydrothermal Vents Marine Protected Area (MPA) on the Juan de Fuca Ridge (Northeast Pacific). Eight samples of particulate detritus were recovered from paired tubeworm grabs from four vent sites. Most sequences (454 tag and Sanger methods) were affiliated to the Epsilonproteobacteria, and the sulfur-oxidizing genus Sulfurovum was dominant in all samples. Gammaproteobacteria were also detected, mainly in Low Flow sequence libraries, and were affiliated with known methanotrophs and decomposers. The cooccurrence of sulfur reducers from the Deltaproteobac- teria and the Epsilonproteobacteria suggests internal sulfur cycling within these habitats. Other phyla detected included Bacteroidetes, Actinobacteria, Chloroflexi, Firmicutes, Planctomycetes, Verrucomicrobia, and Deinococcus–Thermus. Statisti- cally significant relationships between sequence library composition and habitat type suggest a predictable pattern for High Flow and Low Flow environments. Most sequences significantly more represented in High Flow libraries were related to sulfur and hydrogen oxidizers, while mainly heterotrophic groups were more represented in Low Flow libraries. Differences in temperature, avail- able energy for metabolism, and stability between High Flow and Low Flow habitats potentially explain their distinct bacterial communities.

opencc-zeroJun 2021View details →

Data from: Contrasting effects of land cover on nesting habitat use and reproductive output for bumble bees

<a name="_Hlk64216363">Understanding habitat quality is central to understanding the distributions of species on the landscape, as well as to conserving and restoring at-risk species. Although it is well-known that many species require different resources throughout their life cycles, pollinator conservation efforts focus almost exclusively on forage resources. In this study, we evaluate nesting habitat for bumble bees by locating nests directly on the landscape. We compared colony density and colony reproductive output for Bombus impatiens, the common eastern bumble bee, across three different land cover types (hay fields, meadows, and forests). We also assessed nesting habitat associations for all Bombus nests located during surveys to tease apart species-specific patterns of habitat use. We found that B. impatiens nested under the ground in two natural land cover types, forests and meadows, but found no B. impatiens nests in hay fields. Though B. impatiens nested at similar densities in both meadows and forests, colonies in forests had much higher reproductive output. </a>In contrast, B. griseocollis tended to nest on the surface of the ground and was almost always found in meadows. B. perplexis was the only species to nest in all three habitat types, including hay fields. For some bumble bee species in this system, meadows, the habitat type with abundant forage resources, may be sufficient to maintain them throughout their life cycles. However, B. impatiens might benefit from heterogeneous landscapes with forests and meadows. Results for B. impatiens emphasize the longstanding notion that habitat use is not always positively correlated with habitat quality (as measured by reproductive output). Our results also show that habitat selection by bumble bees at one spatial scale may be influenced by resources at other scales. Finally, we demonstrate the feasibility of direct nest searches for understanding bumble bee distribution and ecology.

opencc-zeroDec 2017View details →

Data from: Roads to isolation: similar genomic history patterns in two species of freshwater crabs with contrasting environmental tolerances and range sizes

Freshwater species often show high levels of endemism and risk of extinction owing to their limited dispersal abilities. This is exemplified by the stenotopic freshwater crab, Johora singaporensis which is one of the world's 100 most threatened species, and currently inhabits less than 0.01 km2 of five low order hill streams within the highly urbanized island city‐state of Singapore. We compared populations of J. singaporensis with that of the non‐threatened, widespread, abundant, and eurytopic freshwater crab, Parathelphusa maculata, and found surprisingly high congruence between their population genomic histories. Based on 2,617 and 2,470 genome‐wide SNPs mined via the double‐digest restriction‐associated DNA sequencing method for ~90 individuals of J. singaporensis and P. maculata, respectively, the populations are strongly isolated (FST = 0.146–0.371), have low genetic diversity for both species (also for COI), and show signatures of recent genetic bottlenecks. The most genetically isolated populations for both species are separated from other populations by one of the oldest roads in Singapore. These results suggest that anthropogenic developments may have impacted stream‐dependent species in a uniform manner, regardless of ubiquity, habitat preference, or dispersal modes of the species. While signs of inbreeding were not detected for the critically endangered species, the genetic distinctiveness and low diversity of the populations call for genetic rescue and connecting corridors between the remaining fragments of the natural habitat.

opencc-by-4.0Jul 2021View details →

Impacts of City Shape on Rainfall in Contrasting Environments

WRF-LES simulation of rainfall over inland and costal environment. Results here are under the quasi-equilibrium state.

FIGURE 7 in Morphological and phylogenetic characterization of seven species of Vaucheria (Xanthophyceae), including two new species, from contrasting habitats in New Zealand

FIGURE 7. Light micrographs and illustration of Vaucheria litorea antheridia (E5A). A, C, F. Long cylindrical antheridia with short conical papillae and subtended by a wall bound cavity in a sympodial cluster. B. Wall bound cavity subtending an antheridium (arrow). D, E. Large terminal pore of an antheridium (arrow). E. Sperm material being ejected from pore. G, H. Lateral conical papillae in antheridium (arrows). Scale bars = 200 µm (A, C, F), 100 µm (B, D, E, G, H).

FIGURE 3 in Morphological and phylogenetic characterization of seven species of Vaucheria (Xanthophyceae), including two new species, from contrasting habitats in New Zealand

FIGURE 3. Light micrographs and illustration of Vaucheria bursata reproductive structures. A, E. UCVFW1. G. UCVFW2. C, D. UCVFW3. B. UCVFW4. H, I. UCVFW5. G. Two oogonia either side of a developing antheridium. I. Two sets of antheridia and oogonia side by side. Scale bars = 50 µm.

FIGURE 6 in Morphological and phylogenetic characterization of seven species of Vaucheria (Xanthophyceae), including two new species, from contrasting habitats in New Zealand

FIGURE 6. Light micrographs and illustrations of Vaucheria aestuarii reproductive structures (G7). A, C, D, F, G. Clavate oogonia with mass of protoplasm left behind by mature oospore (arrows), note there is no wall bound cavity subtending the oogonia. E. Long cylindrical antheridia with short cylindrical- conical papillae (arrows) in a monopodial cluster, subtended by a wall bound cavity. H. Antheridium with a wall bound cavity (arrow). I. Antheridia in a monopodial cluster, note 2 wall bound cavities (arrows) in a single antheridium separated by a mass of sperm. Bars = 50 µm.

FIGURE 2. 50 in Morphological and phylogenetic characterization of seven species of Vaucheria (Xanthophyceae), including two new species, from contrasting habitats in New Zealand

FIGURE 2. 50% majority rule consensus tree showing Bayesian phylogenies of Vaucheria strains from different habitats in New Zealand (indicated in bold) based on the phylogenetic analysis of the rbcL gene and partial rbcL-rbcS spacer region. Support numbers and branches are Bayesian posterior probabilities/ Maximum Parsimony bootstrap values. The different taxonomic sections of the strains are as in Andersen and Bailey (2002) and the presence and absence of a gametophore bearing antheridia and oogonia are indicated beside the tree. Scale bar = 0.1 substitutions/site. Substitution model and data sets described in text.

FIGURE 5 in Morphological and phylogenetic characterization of seven species of Vaucheria (Xanthophyceae), including two new species, from contrasting habitats in New Zealand

FIGURE 5. Light micrographs and illustrations of Vaucheria erythrospora reproductive structures (UCVBW1). A–D, H. Two pendant oogonia borne laterally on pedicels to 1 circinate antheridium. E, G. Gametophore with a single oogonia; note distal oogonial cavity (arrow). F. Mature oogonia broken off from gametophore, note characteristic red colouration of the oospore and distal oogonial cavity. Scale bars = 50 µm.

FIGURE 8 in Morphological and phylogenetic characterization of seven species of Vaucheria (Xanthophyceae), including two new species, from contrasting habitats in New Zealand

FIGURE 8. Light micrographs and illustrations of Vaucheria edaphica reproductive structures (UCVT1). A, C, G, I. Gametophore bearing pendent, mostly sessile oogonia with distal prominence and a circinate antheridium, note oospores covering entire portion of oogonium. B, D. Single reniform oogonium with circinate antheridium. E, F. Developing oogonia; note green colouration. J, K, L. Variations of gametophore arrangement. Scale bars = 20 µm.

FIGURE 4 in Morphological and phylogenetic characterization of seven species of Vaucheria (Xanthophyceae), including two new species, from contrasting habitats in New Zealand

FIGURE 4. Light micrographs and illustration of Vaucheria borealis reproductive structures (UCVFW6). A. Antheridium with developing oogonia. B, C, F. Single ovoid oogonia with a horizontal beak and an evenly textured, smooth wall and a circinate antheridium; note reddish colouration of mature oogonial pedicel in C, D. Mature antheridium. E. Mature oogonium with characteristic reddish oospore, smooth wall, horizontal beak (arrows). Scale bars = 20 µm.

FIGURE 1 in Morphological and phylogenetic characterization of seven species of Vaucheria (Xanthophyceae), including two new species, from contrasting habitats in New Zealand

FIGURE 1. Map of the collection sites in Canterbury (black dots). Inset map shows collection site of marine sample, Whangateau Harbour (black dot), Auckland and also the location of the main collection area in Canterbury, New Zealand.

opencc-by-4.0May 2020View details →

Digital breast tomosynthesis and contrast-enhanced dual-energy digital mammography alone and in combination compared to 2D digital synthetized mammography and MR imaging in breast cancer detection and classification

We uploaded the dataset of included patients of manuscript: Petrillo A, Fusco R, Vallone P, Filice S, Granata V, Petrosino T, Rosaria Rubulotta M, Setola SV, Mattace Raso M, Maio F, Raiano C, Siani C, Di Bonito M, Botti G. Digital breast tomosynthesis and contrast-enhanced dual-energy digital mammography alone and in combination compared to 2D digital synthetized mammography and MR imaging in breast cancer detection and classification. Breast J. 2020 May;26(5):860-872. doi: 10.1111/tbj.13739. Epub 2019 Dec 30. PMID: 31886607.

opencc-by-4.0Mar 2020View details →

Evaluation of average glandular dose and investigation of the relationship with compressed breast thickness in dual energy contrast enhanced digital mammography and digital breast tomosynthesis.

We uploaded the average absorbed glandular dose (AGD), compressed breast thickness (CBT) and compression force (CF) values of of Dual energy contrast enhanced digital mammography (CEDM) related to the manuscript: Fusco R, Raiano N, Raiano C, Maio F, Vallone P, Mattace Raso M, Setola SV, Granata V, Rubulotta MR, Barretta ML, Petrosino T, Petrillo A. Evaluation of average glandular dose and investigation of the relationship with compressed breast thickness in dual energy contrast enhanced digital mammography and digital breast tomosynthesis. Eur J Radiol. 2020 May;126:108912. doi: 10.1016/j.ejrad.2020.108912.