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Cardisoma armatum is a typical member of the Gecarcinidae which show significant behavioral, morphological, physiological, and/or biochemical adaptations permitting extended activities on the land. The special gills (branchiostegal lung) of C. armatum play an important role in maintaining osmotic pressure balance and obtaining oxygen to adapt to the terrestrial environment. However, adaptive molecular mechanisms responding to air exposure in C. armatum are still poorly understood. In this study, transcriptomic analysis and histological analysis were conducted on the gills to test adaptive capabilities over 8 h between the aerial exposure (AE) and the water immersion (WI) group. Differentially expressed genes (DEGs) related to terrestrial adaptation were categorized into four broad categories: ion transport , acid-base balance, energy metabolism and immune response. This is the first research to reveal the molecular mechanism of terrestrial adaptation in C. armatum, and will provide new insight into the molecular genetic basis of terrestrial adaptation in crabs.

Although the representative species of Sesarmidaes, mudflat crab Parasesarma pictum and P. affine, are primarily herbivorous crabs, very little information is available about these transcriptomes. To identify the key genes those are responsible for the digestion systems in these crabs, we investigated transcriptomic profiles of the hepatopancreas in P. pictum and P. affine. Hundreds of unigenes in P. pictum and P. affine were classified related to food digestion and absorption by blast annotation, and many of them were annotated as digestive enzymes that played key roles during food digestion process. Remarkably, we presented the first report that these two Parasesarma genus species had four types of alpha amylase genes and two types of EGs. This transcriptomic information about P. pictum and P. affine will be helpful in further study of crustacean biology and the molecular basis of the herbivorous diet in crabs.

Crabs feed on a wide range of items and display diverse feeding strategies. The primary objective of this study was to investigate 10 digestive enzyme genes in representative crabs to provide insights into the genetic basis of feeding habits among crab functional groups. Crabs were classified into three groups based on their feeding habits: herbivores (HV), omnivores (OV), and carnivores (CV). To test whether crabs' feeding adaptations matched adaptive evolution of digestive enzyme genes, we examined the 10 digestive enzyme genes of 12 crab species based on hepatopancreas transcriptome data. Each of the digestive enzyme genes was compared to orthologous sequences using both nucleotide- (i.e., PAML and Datamonkey) and protein-level (i.e., TreeSAAP) approaches. Positive selection genes were detected in HV crabs (AMYA, APN, and MGAM) and CV crabs (APN, CPB, PNLIP, RISC, TRY, and XPD). Additionally, a series of positive selection sites were localized in important functional regions of these digestive enzyme genes. This is the first study to characterize the molecular basis of crabs' digestive enzyme genes based on functional feeding group. Our data suggest that HV crabs have evolved an enhanced digestion capacity for carbohydrates, and CV crabs have acquired digestion capacity for proteins and lipids.

A thinning study was established in 1967 in moist mixed forests on the Priest River Experimental Forest in northern Idaho, USA. The study design included three thinning intensities: low, moderate, and high intensity (1,976, 988, and 494 trees ha–1). This study examined short-term (11 years) and long-term (50 years) thinning effects on residual stand characteristics, growth, and yield. Since regeneration may occur after thinning, understory change was also addressed. Thinning decreased stand density immediately but improved the growth of residual trees. Shade-tolerant species were favored in all the thinnings and dominated 50 years after thinning. Unthinned stands had higher total and merchantable volume than all thinned stands both 11 years and 50 years post treatment. Regeneration and nontree vegetation richness increased shortly after thinning, whereas nontree vegetation cover decreased sharply 50 years after treatment. The stands developed into multistrata forests with shade-tolerant species in both the overstory and understory. This is contrary to current thinning practice favoring shade-intolerant species, but demonstrates the resilience of moist Northern Rockies forests to partial overstory disturbances. In this study, thinning favoring shade-tolerant species in these mixed forests has a more significant effect on forest structure dynamics than timber production.

Copper (Cu2+), which represents a major physiological challenge for crab culture, is ubiquitous in the aquatic culture environment, and gills are the first organs that come into direct contact with the environment. However, the molecular basis of the response of crabs to Cu2+ stress remains unclear. Here, we conducted a transcriptome and differential expression analysis on the gills from Chinese mitten crab unexposed and exposed to Cu2+ for 24 h. The comparative transcriptome analysis identified 2486 differentially expressed genes (DEGs). GO functional analysis and KEGG pathway analysis revealed some DEGs, which were mostly related to immunity, metabolism, osmotic regulation, Cu2+ homeostasis regulation, antioxidant activity, and detoxification process. Some pathways related to humoral and cellular immunity, such as phagosome, peroxisome, lysosome, mTOR signaling pathway, PI3K-Akt signaling pathway, Toll-like receptor signaling pathway, and T cell receptor signaling pathway were enhanced under Cu2+ stress. In addition, Cu2+ stress altered the expression patterns of key phagocytosis and apoptosis genes (lectin, cathepsin L, Rab7, and HSP70), confirming that Cu2+ can induce oxidative stress and eventually even apoptosis. Histological analysis revealed that the copper can induce damage at the cellular level. This comparative transcriptome analysis provides valuable molecular information to aid future study of the immune mechanism of Chinese mitten crab in response to Cu2+ stress and provides a foundation for further understanding of the effects of metal toxicity.

As fatty acids are one of the most crucial biomolecules transferred across the aquatic food webs, they are claimed to be bioindicators of stressors. Among the various environmental stressors, food shortage is of prime importance. Lower food availability can affect fatty acid metabolism of organisms. We investigated the effects of short-term starvation on fatty acid metabolism of Daphnia magna neonates and juveniles. The results revealed that the total fatty acid content in neonates and juveniles of daphnids both rapidly declined within 24 h of starvation, and it remained constant after the following 24 h of starvation. In addition, the fatty acid profiles in neonates or juveniles fed for 24 h were not significantly different from that in the fasting individuals, while the feeding daphnids presented notably higher fatty acid saturation and lower unsaturation in relative to the fasting daphnids within the next 24 h. D. magna neonate increased its special need for C16:1n7 over food transformation, and its C16:1n7 content was elevated the most when fed for 48 h, much higher than the other fatty acids. Time-course changes in fatty acid content in starved D. magna showed that the dietary polyunsaturated α-linolenic acid, i.e. C18:3n3, could be considered as the potential biomarker in either neonates or juveniles to respond to the abiotic food shortage. This study could offer insights into the assessment of food-deprived stress in terms of fatty acid metabolism for distinct ages of cladocerans.

Olfaction plays a central role in mating, spawning, obtaining food and escaping predators, which is essential for survival and reproduction of animals. The nature of the olfactory perception in crabs, which is a major group of crustaceans, has remained elusive. This project aims to explore the molecular mechanism of olfaction in crabs and further improve our understanding of olfactory perception in crustaceans. The olfactory receptors and ingestion-related gene expression in Eriocheir japonica sinensis were studied by transcriptomic techniques. The de novo assembly, annotation and functional evaluation were performed with bioinformatics tools. A series of chemosensory receptors associated with olfaction were identified including 33 EsIRs, 24 EsIGluRs, 58 EsVIGluRs, 1 EsOR and 1 EsGC-D. We found IRs were key odorant receptors demonstrating a specific species evolutionary trend in crustaceans. Furthermore, we identified ORs in E. j. sinensis and Litopenaeus vannamei. The incomplete EsOR and LvOR1 structures implied that ORs exist in crustaceans, and may have been degenerated or even lost in the olfactory evolutionary process. In addition, comparative transcriptome analysises demonstrated two possible olfactory transduction pathways of E. j. sinensis: the cGMP-mediated olfactory pathway related to vegetable odor molecules and the cAMP-mediated olfactory pathway related to meat odor molecules. The above results were consistent with its omnivorous ingestion of E. j. sinensis. Our study revealed the unique olfactory molecular mechanism of omnivorous crabs and provided valuable information for further functional research on the chemoreception mechanisms in crustaceans.

A tree crown is a mass of foliage and significantly correlated to biomass and growth of other parts of a tree. Crown width (CW) is defined as an average of two crown diameters perpendicular to each other, obtained from measurements of four crown radii (crown components). The CW is often used as a covariate predictor in various forest models and therefore, its accurate estimate can be useful for forest management. Although various CW models have been developed so far, all of them lack a detailed investigation of the additivity properties of crown components and inherent correlations among the components and total CW. This study compared three alternative procedures of developing the systems of CW models: nonlinear simultaneous equations (NSE), disaggregated model structure with both one-step proportional weighting system (DMS&OSPWS), and two-step proportional weighting system, and aggregated model structure with one constraint on the total CW. Other two commonly used additivity methods: adjustment in proportion and ordinary least square with separating regression were also evaluated. The comparisons were based on the analyses of data obtained from 2207 trees of Mongolian oak (Quercus mongolica Fisch.) on 116 permanent sample plots located in northern China. Results showed that each method ensured a summation of crown components equal to twice as much as the total CW. The NSE better accounted for the inherent correlations among the crown components and total CW. Out of the model structures evaluated, DMS&OSPWS provided the best performance. This article emphasized more on the methodology and it was expected that the method could be applied by other researchers to develop similar systems of the CW models for other species as well.

Individual tree growth models are flexible and commonly used to represent growth dynamics for heterogeneous and structurally complex uneven-aged stands. Besides traditional statistical models, the rapid development of nonparametric and nonlinear machine learning methods, such as random forest (RF), boosted regression tree (BRT), cubist (Cubist) and multivariate adaptive regression splines (MARS), provides a new way for predicting individual tree growth. However, the application of these approaches to individual tree growth modelling is still limited and short of a comparison of their performance. The objectives of this study were to compare and evaluate the performance of the RF, BRT, Cubist and MARS models for modelling the individual tree diameter growth based on tree size, competition, site condition and climate factors for larch&ndash, spruce&ndash, fir mixed forests in northeast China. Totally, 16,619 observations from long-term sample plots were used. Based on tenfold cross-validation, we found that the RF, BRT and Cubist models had a distinct advantage over the MARS model in predicting individual tree diameter growth. The Cubist model ranked the highest in terms of model performance (RMSEcv [0.1351 cm], MAEcv [0.0972 cm] and R2cv [0.5734]), followed by BRT and RF models, whereas the MARS ranked the lowest (RMSEcv [0.1462 cm], MAEcv [0.1086 cm] and R2cv [0.4993]). Relative importance of predictors determined from the RF and BRT models demonstrated that the competition and tree size were the main drivers to diameter growth, and climate had limited capacity in explaining the variation in tree diameter growth at local scale. In general, the RF, BRT and Cubist models are effective and powerful modelling methods for predicting the individual tree diameter growth.

International audience; AbstractKey messageNatural regeneration patterns of conifer species were studied. Seedling regeneration follows patterns responding to stand structure and site condition factors along shade and drought tolerance gradients. Our findings can assist in adaptive forest management for maintaining sustainable regeneration and plant biodiversity.ContextSeedling regeneration can vary with stand factors of overstory trees and understory non-tree vegetation and site conditions.AimsNatural seedling regeneration patterns of coniferous species were investigated using Forest Inventory and Analysis (FIA) data of 10 common species across the Inland Northwest, USA.MethodsZero-inflated negative binomial models were developed to understand the responses of natural regeneration to stand factors and site conditions.ResultsSeedling occurrence varies along shade and drought tolerance gradients responding to stand structure and site conditions. Two moderate shade-tolerant species of different drought tolerance contributed as a transition. Strong response patterns were revealed for seedling density, in which seedling density was improved with the presence of conspecific trees while limited by competition, especially from the understory vegetation layer.ConclusionOverstory structure and understory vegetation could improve or hinder natural regeneration of coniferous tree species given different shade tolerance and site conditions. Our findings can be effectively implemented in adaptive forest management for maintaining sustainable regeneration of specific conifers in broad temperate mixed forests.

We investigated the variability of the relationships between climate and tree-ring growth along an altitudinal gradient and the temporal instability of the relationships under warming for Changbai larch ( Larix olgensis Henry) in northeast of China. Growth response of trees to climate has been found to vary with elevation, but their relationships might also be altered with ongoing global climate change. We developed residual chronologies of tree-ring growth parameters at three sites to investigate variability of the interactions between climate and tree-ring growth for Changbai larch (Larix olgensis Henry) along an altitudinal gradient on the northern slopes of the Changbai Mountains area in Northeastern China. The results indicate that temperature and precipitation are linked differently to the formation of the annual ring width of Changbai larch at different elevations. Tree-ring density of Changbai larch is mainly positively associated with temperature while negatively responding to precipitation. The relationships between temperature and tree-ring growth became unstable, however, after the notable warming of the late 1980s in the study area. Tree-ring width decreased at low elevation under drought stress, whereas showed more positive sensitivity to warming at higher altitudes. We found that the tree-ring density relationship with temperature also became unstable under the rising temperature regime. These findings could be applied in simulating tree-ring growth and forest distribution under various climatic and environmental scenarios.

In this study, the complete 15,662 bp mitochondrial genome was determined from Uca borealis using next-generation sequencing technology. It consists of 13 protein-coding genes, 22 tRNAs, 2 ribosoma...

With the ongoing crisis of biodiversity loss and limited resources for conservation, the concept of biodiversity hotspots has been useful in determining conservation priority areas. However, there has been limited research into how temporal variability in biodiversity may influence conservation area prioritization. To address this information gap, we present an approach to evaluate the temporal consistency of biodiversity hotspots in large marine ecosystems. Using a large scale, public monitoring dataset collected over an eight year period off the US Pacific Coast, we developed a methodological approach for avoiding biases associated with hotspot delineation. We aggregated benthic fish species data from research trawls and calculated mean hotspot thresholds for fish species richness and Shannon’s diversity indices over the eight year dataset. We used a spatial frequency distribution method to assign hotspot designations to the grid cells annually. We found no areas containing consistently high biodiversity through the entire study period based on the mean thresholds, and no grid cell was designated as a hotspot for greater than 50% of the time-series. To test if our approach was sensitive to sampling effort and the geographic extent of the survey, we followed a similar routine for the northern region of the survey area. Our finding of low consistency in benthic fish biodiversity hotspots over time was upheld, regardless of biodiversity metric used, whether thresholds were calculated per year or across all years, or the spatial extent for which we calculated thresholds and identified hotspots. Our results suggest that static measures of benthic fish biodiversity off the US West Coast are insufficient for identification of hotspots and that long-term data are required to appropriately identify patterns of high temporal variability in biodiversity for these highly mobile taxa. Given that ecological communities are responding to a changing climate and other environmental perturbations, our work highlights the need for scientists and conservation managers to consider both spatial and temporal dynamics when designating biodiversity hotspots.

Inorganic phosphorus (SRP) concentrations in the subtropical North Atlantic are some of the lowest in the global ocean and have been hypothesized to constrain primary production. Based upon data from several transect cruises in this region, it has been hypothesized that dissolved organic phosphorus (DOP) supports a significant fraction of primary production in the subtropical North Atlantic. In this study, a time-series of phosphorus biogeochemistry is presented for the Bermuda Atlantic Time-series Study site, including rates of phosphorus export. Most parameters have a seasonal pattern, although year-over-year variability in the seasonal pattern is substantial, likely due to differences in external forcing. Suspended particulate phosphorus exhibits a seasonal maximum during the spring bloom, despite the absence of a seasonal peak in SRP. However, DOP concentrations are at an annual maximum prior to the winter/spring bloom and decline over the course of the spring bloom while whole community alkaline phosphatase activities are highest. As a result of DOP bioavailability, the growth of particles during the spring bloom occurs in Redfield proportions, though particles exported from the euphotic zone show rapid and significant remineralization of phosphorus within the first 50 m below the euphotic zone. Based upon DOP data from transect cruises in this region, the southward cross gyral flux of DOP is estimated to support ~25% of annual primary production and ~100% of phosphorus export. These estimates are consistent with other research in the subtropical North Atlantic and reinforce the hypothesis that while the subtropics may be phosphorus stressed (a physiological response to low inorganic phosphorus), utilization of the DOP pool allows production and accumulation of microbial biomass at Redfield proportions.

While there is a persistent inverse relationship between latitude and species diversity across many taxa and ecosystems, deviations from this norm offer an opportunity to understand the conditions that contribute to large-scale diversity patterns. Marine systems, in particular, provide such an opportunity, as marine diversity does not always follow a strict latitudinal gradient, perhaps because several hypothesized drivers of the latitudinal diversity gradient are uncorrelated in marine systems. We used a large scale public monitoring dataset collected over an eight year period to examine benthic marine faunal biodiversity patterns for the continental shelf (55-183 m depth) and slope habitats (184-1280 m depth) off the US West Coast (47°20'N-32°40'N). We specifically asked whether marine biodiversity followed a strict latitudinal gradient, and if these latitudinal patterns varied across depth, in different benthic substrates, and over ecological time scales. Further, we subdivided our study area into three smaller regions to test whether coast-wide patterns of biodiversity held at regional scales, where local oceanographic processes tend to influence community structure and function. Overall, we found complex patterns of biodiversity on both the coast-wide and regional scales that differed by taxonomic group. Importantly, marine biodiversity was not always highest at low latitudes. We found that latitude, depth, substrate, and year were all important descriptors of fish and invertebrate diversity. Invertebrate richness and taxonomic diversity were highest at high latitudes and in deeper waters. Fish richness also increased with latitude, but exhibited a hump-shaped relationship with depth, increasing with depth up to the continental shelf break, ~200 m depth, and then decreasing in deeper waters. We found relationships between fish taxonomic and functional diversity and latitude, depth, substrate, and time at the regional scale, but not at the coast-wide scale, suggesting that coast-wide patterns can obscure important correlates at smaller scales. Our study provides insight into complex diversity patterns of the deep water soft substrate benthic ecosystems off the US West Coast.