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Background and Aims: In Central Europe, the drought-tolerant downy oak (Quercus pubescens) is at the northern edge of its natural distribution range, often growing in small and spatially isolated populations. Here, we elucidate how the population genetic structure of Central European Q. pubescens was shaped by geographic barriers, genetic drift and introgression with the closely related sessile oak (Q. petraea)., Methods: 27 Q. pubescens populations from the northern margin of Q. pubescens' natural distribution range were sampled. Based on 16 nuclear microsatellite markers (nSSRs), Bayesian clustering and distance-based analyses were performed to determine the intraspecific genetic structure and to identify genetic barriers. To identify drivers of introgression with Q. petraea, generalised linear models were applied to link levels of introgression with environmental conditions. To track post-glacial migration routes, the spatial distribution of haplotypes based on 8 chloroplast microsatellite markers (cpSSRs) was investigated., Key Results: Based on nSSRs, the study populations of Q. pubescens were divided into a western and an eastern genetic cluster. Within these clusters, more pronounced genetic substructure was observed in the west, probably due to a rugged topography and limited gene flow. Introgression from Q. petraea was more prevalent at wetter and north-exposed sites and in the west. The identified cpSSR haplotypes followed known migration pathways., Conclusions: Our results suggest two late-glacial refugia in or near the southwestern Alps and the southeastern Alps as potential sources for post-glacial migration. Although some genetic exchange is evident in Northern Italy, south of the Alps, the two clusters remain distinct at a large scale. Landscape features and introgression with Q. petraea shaped the genetic substructure at a smaller scale. Our study provides a comprehensive overview of the genetic structure of Q. pubescens in Central Europe, relevant for conservation., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Annals of Botany Company.)

Norway spruce (Picea abies L.) is economically one of the most important conifer species in Europe. Spruce forests are threatened by outbreaks of the bark beetle Ips typographus L., and this will worsen with a projected warmer and drier climate and increased outbreak dynamic following storms. Volatile terpenes and aromatics play pivotal roles in defence of trees, however, little is known about the emission dynamics of these compounds from trees colonized with I. typographus, particularly in dependence on the beetle's developmental stages and colonisation densities. Here, we analysed the emission profiles of volatile organic compounds (VOCs) from spruce logs colonised with low (LDT) and high (HDT) densities of I. typographus from the initial colonisation until the emergence of the next beetle generation. A first VOCs emission peak appeared directly after colonisation and lasted for one week. It mainly consisted of monoterpenoids and most likely reflected the trees' constitutive defence against herbivory. Under HDT, a second emission maximum occurred during the larval stage, whereas under LDT a second peak appeared later during maturation feeding of callow beetles. In contrast to the first peak, sesquiterpenoids, aromatics and oxygenated monoterpenoids dominated the second peak, possibly reflecting the trees' induced defence. Developing beetles seem to face a variety of defence compounds even if the tree has been overwhelmed and colonisation by parental beetles was already successful. The specific release patterns under LDT and HDT might be due to different availability of precursor compounds, depletion of constitutively stored compounds and differences in microbial activities associated with the bark beetles. The present study highlights constitutive defence of spruce trees upon herbivore attack, and the effect of infestation density on the temporal dynamics of induced defence. Particularly the oxygenated monoterpenoid terpinen-4-ol may be used as cue to assess habitat quality and competition by newly arriving beetles., (© The Author(s) 2024. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.)

In many species, polymorphic genomic inversions underlie complex phenotypic polymorphisms and facilitate local adaptation in the face of gene flow. Multiple polymorphic inversions can co-occur in a genome, but the prevalence, evolutionary significance, and limits to complexity of genomic inversion landscapes remain poorly understood. Here, we examine genome-wide genetic variation in one of Europe's most destructive forest pests, the spruce bark beetle Ips typographus, scan for polymorphic inversions, and test whether inversions are associated with key traits in this species. We analyzed 240 individuals from 18 populations across the species' European range and, using a whole-genome resequencing approach, identified 27 polymorphic inversions covering ∼28% of the genome. The inversions vary in size and in levels of intra-inversion recombination, are highly polymorphic across the species range, and often overlap, forming a complex genomic architecture. We found no support for mechanisms such as directional selection, overdominance, and associative overdominance that are often invoked to explain the presence of large inversion polymorphisms in the genome. This suggests that inversions are either neutral or maintained by the combined action of multiple evolutionary forces. We also found that inversions are enriched in odorant receptor genes encoding elements of recognition pathways for host plants, mates, and symbiotic fungi. Our results indicate that the genome of this major forest pest of growing social, political, and economic importance harbors one of the most complex inversion landscapes described to date and raise questions about the limits of intraspecific genomic architecture complexity., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Mixed-species forests are, for multiple reasons, promising options for forest management in Central Europe. However, the extent to which interspecific competition affects tree hydrological processes is not clear. High-resolution dendrometers capture subdaily variations in stem diameter; they can simultaneously monitor stem growth (irreversible changes in diameter) and water status (reversible changes) of individual trees. Using the information on water status, we aimed to assess potential effects of tree species mixture, expressed as local neighborhood identity, on night-time rehydration and water stress. We deployed 112 sensors in pure and mixed forest stands of European beech, Norway spruce and Douglas fir on four sites in the northwestern Germany, measuring stem diameter in 10-min intervals for a period of four years (2019-2022). In a mixture distribution model, we used environmental variables, namely soil matric potential, atmospheric vapor pressure deficit, temperature, precipitation and neighborhood identity to explain night-time rehydration, measured as the daily minimum tree water deficit (TWDmin). TWDmin was used as a daily indicator of water stress and the daily occurrence of sufficient water supply, allowing for stem growth (potential growth). We found that species and neighborhood identity affected night-time rehydration, but the impacts varied depending on soil water availability. While there was no effect at high water availability, increasing drought revealed species-specific patterns. Beech improved night-time rehydration in mixture with Douglas fir, but not in mixture with spruce. Douglas fir, however, only improved rehydration at a smaller share of beech in the neighborhood, while beech dominance tended to reverse this effect. Spruce was adversely affected when mixed with beech. At species level and under dry conditions, we found that night-time rehydration was reduced in all species, but beech had a greater capacity to rehydrate under high to moderate soil water availability than the conifers, even under high atmospheric water demand. Our study gives new insights into neighborhood effects on tree water status and highlights the importance of species-specific characteristics for tree-water relations in mixed-species forests. It shows that drought stress of European beech can be reduced by admixing Douglas fir, which may point towards a strategy to adapt beech stands to climate change., (© The Author(s) 2024. Published by Oxford University Press.)

In forests, a significant proportion of the carbon fixed by trees during photosynthesis is transported belowground along the conducting phloem, so variations in phloem anatomy can lead to variations in transport capacity. Phloem conductance at tree level (Ktree) is also affected by tree height. Both the phloem anatomy and the tree size change during ontogeny, and also differ under different environmental conditions. The goal of our work was to identify the main drivers of variation in Ktree in Scots pine trees growing in natural boreal forests. We conducted a phloem anatomical study and calculated Ktree in trees of three age groups growing in different climatic conditions along a latitudinal gradient from south to north. We found that Ktree was maintained at the same level in actively growing pine trees (25-80-years-old) but increased in old-aged trees (180-190-years-old), possibly reflecting the shift in source-sink relationships of aboveground and belowground parts of trees. Trees of the same age group growing in different climatic conditions demonstrated similar values of Ktree due to coordinated changes in the phloem anatomy and the tree height. In general, the negative influence of tree height on Ktree is offset by the positive influence of phloem width (or trunk diameter) and sieve cell diameter. The exception was young trees growing in the transition zone of the northern taiga subzone to the tundra, where Ktree was the highest in its age group and even exceeded Ktree of middle-aged trees., (© The Author(s) 2024. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Chestnut plants ( Castanea ) are important nut fruit trees worldwide. However, little is known regarding the genetic relationship and evolutionary history of different species within the genus. How modern chestnut plants have developed local adaptation to various climates remains a mystery. The genomic data showed that Castanea henryi first diverged in the Oligocene ~31.56 million years ago, followed by Castanea mollissima, and the divergence between Castanea seguinii and Castanea crenata occurred in the mid-Miocene. Over the last 5 million years, the population of chestnut plants has continued to decline. A combination of selective sweep and environmental association studies was applied to investigate the genomic basis of chestnut adaptation to different climates. Twenty-two candidate genes were associated with temperature and precipitation . We also revealed the molecular mechanism by which CmTOE1 interacts with CmZFP8 and CmGIS3 to promote the formation of non-glandular trichomes for adaptation to low temperature and high altitudes. We found a significant expansion of CER1 genes in Chinese chestnut ( C. mollissima ) and verified the CmERF48 regulation of CmCER1.6 adaptation to drought environments. These results shed light on the East Asian chestnut plants as a monophyletic group that had completed interspecific differentiation in the Miocene, and provided candidate genes for future studies on adaptation to climate change in nut trees., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nanjing Agricultural University.)

Shorea robusta (Dipterocarpaceae), commonly known as Sal, is an economically and culturally important timber species, known to contain a wide spectrum of polyphenols, polysaccharides, and other secondary metabolites in the tissues, which can interfere with the extraction of high-quality genomic DNA. In order to screen simple sequence repeat (SSR) markers and carry out other DNA-based analyses for this species in our laboratory, a high-throughput DNA extraction methodology was needed. Hence, we have optimized a simple, rapid, safe, and reliable high-throughput protocol for DNA extraction suitable for both fresh and dry leaves. The standardized protocol delivered good DNA yield of ∼1500 µg from 1 g of leaf tissue, with purity indicated by a 260 nm/280 nm absorbance ratio ranging from 1.70 to 1.91, which validated the suitability of extracted DNA and revealed reduced levels of contaminants. Additionally, the protocol that we developed was found to be suitable for polymerase chain reaction (PCR) amplification using microsatellite markers. Genome-wide characterization with SSR markers has been established in S. robusta , which further validates the protocol and its usefulness in DNA-based studies across the genus and/or family., Competing Interests: None declared., (© The Author(s) 2023. Published by Oxford University Press.)

Infection with the necrotrophic fungus Diplodia sapinea (Fr.) Fuckel is among the economically and ecologically most devastating diseases of conifers in the northern hemisphere and is accelerated by global climate change. This study aims to characterize the changes mediated by D. sapinea infection on its pine host (Pinus sylvestris L.) that lead to the death of its needles. For this purpose, we performed an indoor infection experiment and inoculated shoot tips of pine seedlings with virulent D. sapinea. The consequences for foliar traits, including the phytohormone profile, were characterized at both the metabolite and transcriptome level. Our results showed that D. sapinea infection strongly affected foliar levels of most phytohormones and impaired a multitude of other metabolic and structural foliar traits, such as reactive oxygen species scavenging. Transcriptome analysis revealed that these changes are partially mediated via modified gene expression by fungal exposure. Diplodia sapinea appears to overcome the defense reactions of its pine host by reprogramming gene expression and post-transcriptional controls that determine essential foliar metabolic traits such as the phytohormone profile, cell wall composition and antioxidative system., (© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Coscinium fenestratum is a medicinally significant critically endangered plant found in Western Ghats of India. The leaf spot and blight was observed in Kerala during 2021 with disease incidence of 40% in 20 assessed plants in 0.6 hectare. The associated fungus was isolated on potato dextrose agar medium. A total of six morpho-culturally identical isolates were isolated and morphologically identified. Based on morpho-cultural features, the fungus was identified at genus level as Lasiodiplodia sp., which was further authentically confirmed as Lasiodiplodia theobromae by molecular identification with a representative isolate (KFRIMCC 089) using multigene (ITS, LSU, SSU, TEF1-α, and TUB2) sequence analysis and concatenated phylogenetic analysis (ITS-TEF1-α-TUB2). Pathogenicity tests were also assessed in vitro and in vivo using mycelial disc and spore suspension of L. theobromae, and the isolated fungus's pathogenic behaviour was confirmed after re-isolation and morpho-cultural features. Literature survey reveals that there are no reports of L. theobromae on C. fenestratum from all over the world. Hence, C. fenestratum is being firstly reported as a new host record for L. theobromae from India., (© The Author(s) 2023. Published by Oxford University Press on behalf of Applied Microbiology International.)

Hylurgus ligniperda (F.) and Hylastes ater (Paykull) are secondary bark beetles that have successfully spread beyond their native range, particularly into Pinus spp. plantations in the Southern Hemisphere. They feed on the phloem and cambial regions of highly stressed and recently dead Pinus spp. Here H. ligniperda and H. ater egg, larval, and pupal survival and development rates were modeled. Survival was variably influenced by temperatures depending on the life stage, but general trends were for H. ligniperda to tolerate warmer temperatures in comparison to H. ater. Nonlinear models showed 26, 29, and 34°C are the optimal temperature (maximum development rates) for the development of eggs, larvae, and pupae of H. ligniperda. In contrast, optimal temperature predictions were lower for H. ater, with estimates of 26, 22, and 23°C for the development of eggs, larvae, and pupae, respectively. H. ligniperda pre-imaginal stages were more tolerant to high temperatures, and H. ater pre-imaginal stages were more tolerant to low temperatures. Understanding the thermal requirements and limits for development for these two pests can assist in modeling emergence times, their current and potential species distribution and have potential phytosanitary applications., (© The Author(s) 2022. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Background and Aims: Upscaling carbon allocation requires knowledge of the variability at the scales at which data are collected and applied. Trees exhibit different growth rates and timings of wood formation. However, the factors explaining these differences remain undetermined, making samplings and estimations of the growth dynamics a complicated task, habitually based on technical rather than statistical reasons. This study explored the variability in xylem phenology among 159 balsam firs [Abies balsamea (L.) Mill.]., Methods: Wood microcores were collected weekly from April to October 2018 in a natural stand in Quebec, Canada, to detect cambial activity and wood formation timings. We tested spatial autocorrelation, tree size and cell production rates as explanatory variables of xylem phenology. We assessed sample size and margin of error for wood phenology assessment at different confidence levels., Key Results: Xylem formation lasted between 40 and 110 d, producing between 12 and 93 cells. No effect of spatial proximity or size of individuals was detected on the timings of xylem phenology. Trees with larger cell production rates showed a longer growing season, starting xylem differentiation earlier and ending later. A sample size of 23 trees produced estimates of xylem phenology at a confidence level of 95 % with a margin of error of 1 week., Conclusions: This study highlighted the high variability in the timings of wood formation among trees within an area of 1 km2. The correlation between the number of new xylem cells and the growing season length suggests a close connection between the processes of wood formation and carbon sequestration. However, the causes of the observed differences in xylem phenology remain partially unresolved. We point out the need to carefully consider sample size when assessing xylem phenology to explore the reasons underlying this variability and to allow reliable upscaling of carbon allocation in forests., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Insect herbivory is a dominant interaction across virtually all ecosystems globally and has dramatic effects on plant function such as reduced photosynthesis activity and increased levels of defenses. However, most previous work assessing the link between insect herbivory, photosynthesis and plant defenses has been performed on cultivated model plant species, neglecting a full understanding of patterns in natural systems. In this study, we performed a field experiment to investigate the effects of herbivory by a generalist foliar feeding insect (Lymantria dispar) and leaf mechanical damage on multiple leaf traits associated with defense against herbivory and photosynthesis activity on two sympatric oak species with contrasting leaf habit (the evergreen Quercus coccifera L. and the deciduous Quercus pubescens Willd). Our results showed that, although herbivory treatments and oak species did not strongly affect photosynthesis and dark respiration, these two factors exerted interactive effects. Insect herbivory and mechanical damage (vs control) decreased photosynthesis activity for Q. coccifera but not for Q. pubescens. Insect herbivory and mechanical damage tended to increase chemical (increased flavonoid and lignin concentration) defenses, but these effects were stronger for Q. pubescens. Overall, this study shows that two congeneric oak species with contrasting leaf habit differ in their photosynthetic and defensive responses to insect herbivory. While the evergreen oak species followed a more conservative strategy (reduced photosynthesis and higher physical defenses), the deciduous oak species followed a more acquisitive strategy (maintained photosynthesis and higher chemical defenses)., (© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

The integration of genomic data into genetic evaluations can facilitate the rapid selection of superior genotypes and accelerate the breeding cycle in trees. In this study, 390 trees from 74 control-pollinated families were genotyped using a 36K Axiom SNP array. A total of 15,624 high-quality SNPs were used to develop genomic prediction models for mammalian bark stripping, tree height, and selected primary and secondary chemical compounds in the bark. Genetic parameters from different genomic prediction methods-single-trait best linear unbiased prediction based on a marker-based relationship matrix (genomic best linear unbiased prediction), multitrait single-step genomic best linear unbiased prediction, which integrated the marker-based and pedigree-based relationship matrices (single-step genomic best linear unbiased prediction) and the single-trait generalized ridge regression-were compared to equivalent single- or multitrait pedigree-based approaches (ABLUP). The influence of the statistical distribution of data on the genetic parameters was assessed. Results indicated that the heritability estimates were increased nearly 2-fold with genomic models compared to the equivalent pedigree-based models. Predictive accuracy of the single-step genomic best linear unbiased prediction was higher than the ABLUP for most traits. Allowing for heterogeneity in marker effects through the use of generalized ridge regression did not markedly improve predictive ability over genomic best linear unbiased prediction, arguing that most of the chemical traits are modulated by many genes with small effects. Overall, the traits with low pedigree-based heritability benefited more from genomic models compared to the traits with high pedigree-based heritability. There was no evidence that data skewness or the presence of outliers affected the genomic or pedigree-based genetic estimates., (© The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America.)

Early detection of bark- and wood-boring beetles is critical to support the eradication of recently established populations in novel regions. Flight intercept traps baited with semiochemical lures are essential for surveillance and population monitoring of introduced insects. We present laboratory and field data to test potential improvements in trap sensitivity to detect Hylastes ater (Paykull), Hylurgus ligniperda (Fabricius) (Coleoptera:Scolytinae), and Arhopalus ferus (Mulsant) (Coleoptera:Cerambycidae). We evaluated the effects of type and permeability of plastic material on release rates of host-plant volatiles and the addition of the pheromone racemic E-fuscumol on beetle species catch within an exotic Pinus radiata (D. Don) plantation forest. We trapped 228,278 H. ligniperda, 91 H. ater, and 2,504 A. ferus over two experiments. Our results show strong attraction of H. ligniperda to host-plant volatiles with a positive relationship between increased release rates and trap catch. H. ater follows this trend, with attraction to ethanol and (-)-β-pinene. H. ligniperda was more strongly attracted to host volatiles than H. ater, the average ratio between baited and unbaited traps being 51.25:1 and 3.75:1, respectively for each species. There was no effect of host-plant volatiles or release rate on A. ferus catch, but a weak attraction by A. ferus to racemic E-fuscumol. Overall, we demonstrate species-specific differences in Coleoptera attraction to host-plant volatile release rates and semiochemical blends. Results demonstrate mechanisms to improve trap catch of H. ligniperda and H. ater. Racemic E-fuscumol shows some promise for A. ferus, but further investigation is required to determine whether chirality affects attraction., (© The Author(s) 2021. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Peatlands both accumulate carbon and release methane, but their broad range in environmental conditions means that the diversity of microorganisms responsible for carbon cycling is still uncertain. Here, we describe a community analysis of methanogenic archaea responsible for methane production in 17 peatlands from 36 to 53 N latitude across the eastern half of North America, including three metal-contaminated sites. Methanogenic community structure was analysed through Illumina amplicon sequencing of the mcrA gene. Whether metal-contaminated sites were included or not, metal concentrations in peat were a primary driver of methanogenic community composition, particularly nickel, a trace element required in the F430 cofactor in methyl-coenzyme M reductase that is also toxic at high concentrations. Copper was also a strong predictor, likely due to inhibition at toxic levels and/or to cooccurrence with nickel, since copper enzymes are not known to be present in anaerobic archaea. The methanogenic groups Methanocellales and Methanosarcinales were prevalent in peatlands with low nickel concentrations, while Methanomicrobiales and Methanomassiliicoccales were abundant in peatlands with higher nickel concentrations. Results suggest that peat-associated trace metals are predictors of methanogenic communities in peatlands., (© The Author(s) 2021. Published by Oxford University Press on behalf of FEMS.)

Understanding local adaptation has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating systems, and demographic histories. We evaluated signatures of local adaptation in European aspen (Populus tremula) across Europe by means of whole-genome resequencing of a collection of 411 individual trees. We dissected admixture patterns between aspen lineages and observed a strong genomic mosaicism in Scandinavian trees, evidencing different colonization trajectories into the peninsula from Russia, Central and Western Europe. As a consequence of the secondary contacts between populations after the last glacial maximum, we detected an adaptive introgression event in a genome region of ∼500 kb in chromosome 10, harboring a large-effect locus that has previously been shown to contribute to adaptation to the short growing seasons characteristic of Northern Scandinavia. Demographic simulations and ancestry inference suggest an Eastern origin-probably Russian-of the adaptive Nordic allele which nowadays is present in a homozygous state at the north of Scandinavia. The strength of introgression and positive selection signatures in this region is a unique feature in the genome. Furthermore, we detected signals of balancing selection, shared across regional populations, that highlight the importance of standing variation as a primary source of alleles that facilitate local adaptation. Our results, therefore, emphasize the importance of migration-selection balance underlying the genetic architecture of key adaptive quantitative traits., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Mesophyll conductance (gm) determines the diffusion of CO2 from the substomatal cavities to the site of carboxylation in the chloroplasts and represents a critical component of the diffusive limitation of photosynthesis. In this study, we evaluated the average effect sizes of different environmental constraints on gm in Populus spp., a forest tree model. We collected raw data of 815 A-Ci response curves from 26 datasets to estimate gm, using a single curve-fitting method to alleviate method-related bias. We performed a meta-analysis to assess the effects of different abiotic stresses on gm. We found a significant increase in gm from the bottom to the top of the canopy that was concomitant with the increase of maximum rate of carboxylation and light-saturated photosynthetic rate (Amax). gm was positively associated with increases in soil moisture and nutrient availability, but was insensitive to increasing soil copper concentration and did not vary with atmospheric CO2 concentration. Our results showed that gm was strongly related to Amax and to a lesser extent to stomatal conductance (gs). Moreover, a negative exponential relationship was obtained between gm and specific leaf area, which may be used to scale-up gm within the canopy., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Experimental Biology.)

Aim: To design and assess a novel protocol that employs isothermal titration calorimetry (ITC) for rapid detection of extended-spectrum β-lactamase (ESBL)-producers in clinical pathogens., Methods and Results: A total of 69 clinical Enterobacteriaceae isolates were examined in the new ESBL-ITC test by examining the heat profiles associated with enzyme hydrolysis of different substrates (imipenem, cefotaxime and clavulanic acid). The presence of β-lactamase genes in the bacteria tested was confirmed by PCR and DNA sequencing. Comparative analysis between ESBL-ITC and conventional minimum inhibitory concentrations (MIC)/combined disk method (CDM) showed high agreement between the two assays. However, the ESBL-ITC test had a remarkable advantage of providing testing result within 1 h, in comparison to the 32-48 h required by MIC/CDM., Conclusions: The ESBL-ITC test developed in this work offers a new option for rapid and accurate detection of ESBL-producers., Significance and Impact of the Study: Timely detection of ESBL-producers is vital to guide the decision-making process in clinical treatment as well as in hospital-infection control. The new ESBL-ITC test provides a rapid phenotypic assay that can be further adapted for clinical diagnosis of ESBL-producing pathogens., (© 2020 The Society for Applied Microbiology.)

Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree-species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree-species tree discordance; genomics; information theory.]., (© The Author(s) 2020. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.)

Future climate scenarios for the boreal zone project increasing temperatures and precipitation, as well as extreme weather events such as heavy rain during the growing season. This can result in more frequent short-term waterlogging (WL) leading to unfavorable conditions for tree roots. In addition, it is decisive whether short-term WL periods during the growing season occur continuously or periodically. We assessed the effects of short-termed WL on 4-year-old Scots pine (Pinus sylvestris L.) saplings after shoot elongation started. Waterlogging (WL) lasted either continuously for 2.5 weeks (ContWL) or noncontinuously for 5 weeks, consisting of three repeated 1-week-interval WL periods (IntWL). Both treatments resulted in the same duration of soil anoxia. We studied soil gases, root and shoot growth and physiology, and root survival probability and longevity during the experiment. In the final harvest, we determined shoot and root biomass and hydraulic conductance and electrical impedance spectra of the root systems. Soil CO2 and CH4 concentrations increased immediately after WL onset and O2 decreased until anoxia. Waterlogging decreased fine root survival probability, but there was no difference between WL treatments. Shoot growth suffered more from ContWL and root growth more from IntWL. Needle concentrations of pinitol increased in the WL saplings, indicating stress. No WL effects were observed in photosynthesis and chlorophyll fluorescence. Increased starch concentration in needles by WL may be due to damaged roots and thus a missing belowground sink. Electrical impedance indicated suffering of WL saplings, although root hydraulic conductance did not differ between the treatments. Oxidative stress of short-term and interval WL can have long-lasting effects on shoot and root growth and the physiology of Scots pine. We conclude that even short-term WL during the growing season is a stress factor, which will probably increase in the future and can affect carbon allocation and dynamics in boreal forests., (© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Past research suggests climate change will cause the climate envelopes of various tree species to shift to higher latitudes and can lead to a northward migration of trees. However, the success and scope of the migration are likely affected by factors that are not contained in the climate envelope, such as photoperiod and interactive effects of multiple environmental factors, and these effects are currently not well understood. In this study, we investigated the interactive effects of CO2 concentrations ([CO2]), photoperiod and soil moisture on the morphological and physiological traits of Populus tremuloides Michx. We grew seedlings under two levels of [CO2] (ambient [CO2] (AC) 400 vs elevated [CO2] (EC) 1000 μmol mol-1), four photoperiod regimes (growing season photoperiods at 48 (seed origin), 52, 55 and 58°N latitude) and two soil moisture regimes (high soil moisture (HSM) vs low soil moisture (LSM), -2 MPa) for two growing seasons in greenhouses. Both morphological and physiological responses were observed. Low soil moisture reduced leaf size, total leaf area and height growth by 33, 46 and 12%, respectively, and increased root/shoot ratio by 20%. The smaller leaf area and increased root/shoot ratio allowed the seedlings in LSM to maintain higher the maximum rate of Rubisco carboxylation (Vcmax) and the maximum rate of electron transport for RuBP regeneration (Jmax) than control seedlings (55 and 83% higher in July, 52 and 70% in August, respectively). Photoperiod and [CO2] modified responses to LSM and LSM altered responses to photoperiod and [CO2], e.g., the August photosynthetic rate was 44% higher in LSM than in HSM under EC but no such a difference existed under AC. The increase in Vcmax and Jmax in response to LSM varied with photoperiod (Vcmax: 36% at 52°N, 22% at 55°N, 47% at 58°N; Jmax: 29% at 52°N, 21% at 55°N, 45% at 58°N). Stomatal conductance and its reduction in response to LSM declined with increasing photoperiod, which can have significant implications for soil moisture effect on northward migration. This study highlights the need to consider the complex interactions of [CO2], photoperiod and soil moisture when planning assisted migration or predicting the natural migration of boreal forests in the future., (© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permission@oup.com.)

Background and Aims: Biotic and abiotic stressors can cause different defoliation patterns within trees. Foliar pathogens of conifers commonly prefer older needles and infection with defoliation that progresses from the bottom crown to the top. The functional role of the lower crown of trees is a key question to address the impact of defoliation caused by foliar pathogens., Methods: A 2 year artificial defoliation experiment was performed using two genotypes of grafted Pinus radiata to investigate the effects of lower-crown defoliation on carbon (C) assimilation and allocation. Grafts received one of the following treatments in consecutive years: control-control, control-defoliated, defoliated-control and defoliated-defoliated., Results: No upregulation of photosynthesis either biochemically or through stomatal control was observed in response to defoliation. The root:shoot ratio and leaf mass were not affected by any treatment, suggesting prioritization of crown regrowth following defoliation. In genotype B, defoliation appeared to impose C shortage and caused reduced above-ground growth and sugar storage in roots, while in genotype A, neither growth nor storage was altered. Root C storage in genotype B decreased only transiently and recovered over the second growing season., Conclusions: In genotype A, the contribution of the lower crown to the whole-tree C uptake appears to be negligible, presumably conferring resilience to foliar pathogens affecting the lower crown. Our results suggest that there is no C limitation after lower-crown defoliation in P. radiata grafts. Further, our findings imply genotype-specific defoliation tolerance in P. radiata., (© The Author(s) 2020. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

The pine processionary moth, Thaumetopoea pityocampa (Denis and Schiffermüller), is an important insect in the Mediterranean region, as it defoliates pines and its urticating hairs can cause allergic reactions in humans and animals. Moreover, this species exhibits an interesting genetic structure as recently a distinct East-North African mtDNA lineage ('ENA clade') has been described. This clade has been recently detected in Greek populations where it has currently expanded its range by replacing the 'endemic' T. pityocampa lineages. Here, we report new data on the rapid spread of 'ENA clade' in the Greek island Evoia in only a few years. As the underlying mechanisms of the 'ENA clade' range expansion has not been studied so far, we screened T. pityocampa for an infection with the heritable bacterial endosymbionts Wolbachia (Bacteria: Anaplasmataceae), Cardinium (Bacteria: Bacteroidaceae), Rickettsia (Bacteria: Rickettsiaceae) and Spiroplasma (Bacteria: Spiroplasmataceae). These bacteria can manipulate the reproduction of infected hosts, something that could potentially explain the rapid spread of 'ENA clade' lineage. Therefore, we screened 28 individuals that exhibited T. pityocampa 'ENA clade' and 'endemic' T. pityocampa haplotypes from nine populations scattered all over Greece. None of them was infected with any of the four endosymbionts, suggesting that these bacteria do not cause reproductive manipulations in T. pityocampa lineages and, thus, other factors should be explored in future research efforts., (© The Author(s) 2019. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Carbon allocation plays a key role in ecosystem dynamics and plant adaptation to changing environmental conditions. Hence, proper description of this process in vegetation models is crucial for the simulations of the impact of climate change on carbon cycling in forests. Here we review how carbon allocation modelling is currently implemented in 31 contrasting models to identify the main gaps compared with our theoretical and empirical understanding of carbon allocation. A hybrid approach based on combining several principles and/or types of carbon allocation modelling prevailed in the examined models, while physiologically more sophisticated approaches were used less often than empirical ones. The analysis revealed that, although the number of carbon allocation studies over the past 10 years has substantially increased, some background processes are still insufficiently understood and some issues in models are frequently poorly represented, oversimplified or even omitted. Hence, current challenges for carbon allocation modelling in forest ecosystems are (i) to overcome remaining limits in process understanding, particularly regarding the impact of disturbances on carbon allocation, accumulation and utilization of nonstructural carbohydrates, and carbon use by symbionts, and (ii) to implement existing knowledge of carbon allocation into defence, regeneration and improved resource uptake in order to better account for changing environmental conditions., (© The Author(s) 2019. Published by Oxford University Press.)

Phloem transport is the process by which plants internally distribute assimilates. The loading of assimilates near the photosynthetic source is responsible for generating enough osmotic pressure to drive sap flow towards the sink tissues where assimilates are consumed. Phloem loading is variable and subject to a diurnal cycle. It is dominated by photosynthesis during the day and by degradation of leaf starch to sugars at night. Most studies ignore the effect of the loading cycle on transport and assume that sugar flow operates at equilibrium. In this study, phloem transport was simulated for three successive days using a finite element model of time-dependent Münch-Horwitz equations. The spatial and temporal distributions of phloem pressure, sucrose concentration, sap velocity and sucrose flux were predicted for five different time variations in sucrose loading. Results showed that periodic loading induces an alternance of two distinct transport phases: one with high pressure, concentration and sucrose flux magnitudes and another with low magnitudes. In contrast, phloem water velocity remained remarkably stable. The alternating phases persisted over time and, under source-driven variation, transport did not reach steady-state conditions for the tested configuration. However, the impact of loading dynamics on transport was mitigated by pathway effects. Oscillations were not only delayed as one travelled away from the source, their amplitude was also reduced over distance. That behaviour stabilized the supply of sucrose to the sink, which continued at moderate levels during the dark cycles. This finding suggests that transport would assist night conversion of starch to sugars in the leaf to prevent carbon starvation at distant sinks in the early morning. The propagation velocity of pressure/concentration waves in phloem was predicted to vary by a factor up to 2.5 depending on the time series chosen to describe the dynamics of loading. Finally, the model predicted that up to 87% of the amount of sucrose loaded over 48 h would be unloaded under time-dependent loading, whereas only 76% would under constant-rate loading. This additional efficiency was periodic. It did not increase significantly the overall efficiency of the system but could be responsible for inducing rhythms in sink activity., (© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Sustainable crop production for a rapidly growing human population is one of the current challenges faced by the agricultural sector. However, many of the chemical agents used in agriculture can be hazardous to humans, non-targeted organism and environment. Plant growth promoting rhizobacteria have demonstrated a role in promoting plant growth and health under various stress conditions including disease. Unfortunately, bacterial viability degrades due to temperature and other environmental factors (Bashan et al., Plant Soil 378: 1-33, 2014). Encapsulation of bacteria into core-shell biopolymers is one of the promising techniques to overcome the problem. This study deals with the encapsulation of Bacillus salmalaya 139SI using simple double coating biopolymer technique which consist of brown rice protein/alginate and 0·5% low molecular weight chitosan of pH 4 and 6. The influence of biopolymer to bacteria mass ratio and the chitosan pH on the encapsulation process, physic-chemical, morphology and bioactivity properties of encapsulated B. salmalaya 139SI have been studied systematically. Based on the analysis of physico-chemical, morphology and bioactivity properties, B. salmalaya 139S1 encapsulated using double coating encapsulation technology has promising viability pre- and postfreeze-drying with excellent encapsulation yields of 99·7 and 89·3% respectively. SIGNIFICANCE AND IMPACT OF THE STUDY: The need of a simple yet effective way of encapsulating plant growth promoting rhizobacteria is crucial to further improve their benefits to global sustainable agriculture practice. Effective encapsulation allows for protection, controlled release and function of the micro-organism, as well as providing a longer shelf life for the product. This research report offers an innovative yet simple way of encapsulating using double coating technology with environmentally friendly biopolymers that could degrade and provide nutrients when in soil. Importantly, the bioactivity of the bacteria is maintained upon encapsulation., (© 2018 The Society for Applied Microbiology.)

Invasions by insects introduced via international trade continue to cause worldwide impacts. Surveillance programs using traps baited with host volatiles and pheromones can detect incursions of nonnative species. We report on two experiments executed to determine if attractants for several insect species can be combined without compromising trap catches and detection ability of target species. In the first experiment, we tested the effect of bark beetle pheromones (plus α-pinene) and trap contact with foliage on trap catches of the brown marmorated stink bug Halyomorpha halys Stål (Hemiptera: Pentatomidae) in traps baited with a mixture of bisabolenes and methyl (E,E,Z)-2,4,6-decatrienoate. Trap capture of H. halys adults was greater in traps not in contact with foliage, and the bark beetle pheromones ipsenol and ipsdienol did not affect trap capture of H. halys. In the second experiment, we tested the effects of multi-lure interactions among the primary host attractants α-pinene and ethanol, and the pheromones monochamol, ipsenol, ipsdienol, lanierone, and the H. halys compounds, on trap captures of various forest and agricultural insect pests. Specifically, we targeted Monochamus spp. (Coleoptera: Cerambycidae), Ips spp. (Coleoptera: Scolytinae) and H. halys. We found that a combination of all lures did not catch significantly lower numbers of Monochamus carolinensis Olivier, Monochamus scutellatus Say (Coleoptera: Cerambycidae), and Ips pini Say (Coleoptera: Scolytidae) than lure combinations missing components although removal of both lanierone and ipsdienol somewhat increased catches of Ips grandicollis Eichhoff (Coleoptera: Curculionidae). Our results support the use of traps baited with a full combination of these attractants in surveillance programs. This should reduce costs and increase detection rates of a wider range of conifer forest pests and H. halys.

Teak (Tectona grandis L. f.) is one of the precious bench mark tropical hardwood having qualities of durability, strength and visual pleasantries. Natural teak populations harbour a variety of characteristics that determine their economic, ecological and environmental importance. Sequencing of whole nuclear genome of teak provides a platform for functional analyses and development of genomic tools in applied tree improvement. A draft genome of 317 Mb was assembled at 151× coverage and annotated 36, 172 protein-coding genes. Approximately about 11.18% of the genome was repetitive. Microsatellites or simple sequence repeats (SSRs) are undoubtedly the most informative markers in genotyping, genetics and applied breeding applications. We generated 182,712 SSRs at the whole genome level, of which, 170,574 perfect SSRs were found; 16,252 perfect SSRs showed in silico polymorphisms across six genotypes suggesting their promising use in genetic conservation and tree improvement programmes. Genomic SSR markers developed in this study have high potential in advancing conservation and management of teak genetic resources. Phylogenetic studies confirmed the taxonomic position of the genus Tectona within the family Lamiaceae. Interestingly, estimation of divergence time inferred that the Miocene origin of the Tectona genus to be around 21.4508 million years ago.

Background and Aims: Anisotropic cell elongation depends on cell wall relaxation and cellulose microfibril arrangement. The aim of this study was to characterize the molecular function of AtDICE1 encoding a novel transmembrane protein involved in anisotropic cell elongation in Arabidopsis., Methods: Phenotypic characterizations of transgenic Arabidopsis plants mis-regulating AtDICE1 expression with different pharmacological treatments were made, and biochemical, cell biological and transcriptome analyses were performed., Key Results: Upregulation of AtDICE1 in Arabidopsis (35S::AtDICE1) resulted in severe dwarfism, probably caused by defects in anisotropic cell elongation. Epidermal cell swelling was evident in all tissues, and abnormal secondary wall thickenings were observed in pith cells of stems. These phenotypes were reproduced not only by inducible expression of AtDICE1 but also by overexpression of its poplar homologue in Arabidopsis. RNA interference suppression lines of AtDICE1 resulted in no observable phenotypic changes. Interestingly, wild-type plants treated with isoxaben, a cellulose biosynthesis inhibitor, phenocopied the 35S::AtDICE1 plants, suggesting that cellulose biosynthesis was compromised in the 35S::AtDICE1 plants. Indeed, disturbed cortical microtubule arrangements in 35S::AtDICE1/GFP-TuA6 plants were observed, and the cellulose content was significantly reduced in 35S::AtDICE1 plants. A promoter::GUS analysis showed that AtDICE1 is mainly expressed in vascular tissue, and transient expression of GFP:AtDICE1 in tobacco suggests that AtDICE1 is probably localized in the endoplasmic reticulum (ER). In addition, the external N-terminal conserved domain of AtDICE1 was found to be necessary for AtDICE1 function. Whole transcriptome analyses of 35S::AtDICE1 revealed that many genes involved in cell wall modification and stress/defence responses were mis-regulated., Conclusions: AtDICE1, a novel ER-localized transmembrane protein, may contribute to anisotropic cell elongation in the formation of vascular tissue by affecting cellulose biosynthesis.

A phenotype-based screening of the T1 transgenic Arabidopsis population transformed by overexpression constructs of the entire poplar MYB transcription factor family found that overexpression of a poplar MYB transcription factor, PtrMYB012, in Arabidopsis resulted in upwardly curled rosette leaves, dwarfism and male sterility. Sequence analysis identified that PtrMYB012 is homologous to the Arabidopsis GAMYB genes (e.g., AtMYB65 and AtMYB33). Gene expression analysis revealed that PtrMYB012 is specifically expressed in floral tissues, especially in male catkins, similar to AtMYB65. It was well known that Arabidopsis GAMYBs are negatively regulated by microRNA159 (miR159) during vegetative growth; thus, the typical phenotypes of upwardly curled leaves, dwarfism and male sterility were only shown in overexpression of GAMYBs with mutations in the miR159 target sequence. To confirm our phenotypic consequences, we independently re-produced transgenic Arabidopsis plants overexpressing PtrMYB012 without mutations in the miR159 target sequence. The resulting 35 S::PtrMYB012 Arabidopsis plants phenocopied the previous transgenic Arabidopsis plants, suggesting that PtrMYB012 is probably not a target of Arabidopsis miR159 despite containing the conserved miR159 target sequence. To gain further insight, we produced transgenic poplars overexpressing the intact PtrMYB012. As a result, no conspicuous phenotype was found in 35 S::PtrMYB012 poplar plants. These results suggest that PtrMYB012 transcripts are down-regulated by miR159 in poplar but not in Arabidopsis. Indeed, subsequent 5'-RACE analysis confirmed that PtrMYB012 transcripts are completely degraded in poplar, probably by miR159, but not in Arabidopsis. These results suggest that species-specific family members of miR159 are important for the regulation of normal growth and development in plants.

In the present work, we sampled individuals of the processionary pine moth, Thaumetopoea pityocampa (Denis and Schiffermüller; Lepidoptera: Notodontidae) from different areas of Greece between 2014 and 2016. These samples were sequenced for a 760-bp long mtDNA COI locus and the haplotypes retrieved clearly showed that the occurrence of T. pityocampa in Greece is being considerably restricted, with only 8 individuals out of the 221 exhibiting T. pityocampa haplotypes and the rest being identified as T. pityocampa ENA clade haplotypes. To that, one haplotype in particular exhibited the highest abundance and broadest geographic distribution, occurring both in mainland and on islands. Our data suggest a rather recent and rapid population expansion of the ENA clade in Greece and a concomitant recent displacement of T. pityocampa. It thus seems that the relation between T. pityocampa and T. pityocampa ENA clade needs to be further and thorough analyzed before the taxonomic status of T. pityocampa ENA clade can be concluded with confidence.

The world's smallest fishes belong to the genus Paedocypris. These miniature fishes are endemic to an extreme habitat: the peat swamp forests in Southeast Asia, characterized by highly acidic blackwater. This threatened habitat is home to a large array of fishes, including a number of miniaturized but also developmentally truncated species. Especially the genus Paedocypris is characterized by profound, organism-wide developmental truncation, resulting in sexually mature individuals of <8 mm in length with a larval phenotype. Here, we report on evolutionary simplification in the genomes of two species of the dwarf minnow genus Paedocypris using whole-genome sequencing. The two species feature unprecedented Hox gene loss and genome reduction in association with their massive developmental truncation. We also show how other genes involved in the development of musculature, nervous system, and skeleton have been lost in Paedocypris, mirroring its highly progenetic phenotype. Further, our analyses suggest two mechanisms responsible for the genome streamlining in Paedocypris in relation to other Cypriniformes: severe intron shortening and reduced repeat content. As the first report on the genomic sequence of a vertebrate species with organism-wide developmental truncation, the results of our work enhance our understanding of genome evolution and how genotypes are translated to phenotypes. In addition, as a naturally simplified system closely related to zebrafish, Paedocypris provides novel insights into vertebrate development.

Kalopanax septemlobus, commonly named the castor aralia tree, is a highly valued woody medicinal tree belonging to the family Araliaceae. Kalopanax septemlobus contains approximately 15 triterpenoid saponins primarily constituted of hederagenin aglycones. Hederagenin is a representative precursor for hemolytic saponin in plants. In the present study, transcriptome analysis was performed to discover genes involved in hederagenin saponin biosynthesis in K. septemlobus. De novo assembly generated 82,698 unique sequences, including 17,747 contigs and 64,951 singletons, following 454 pyrosequencing. Oxidosqualene cyclases (OSCs) are enzymes that catalyze the formation of diverse triterpene skeletons from 2,3-oxidosqualene. Heterologous expression of an OSC sequence in yeast revealed that KsBAS is a β-amyrin synthase gene. Cytochrome P450 genes (CYPs) make up a supergene family in the plant genome and play a key role in the biosynthesis of sapogenin aglycones. In total, 95 contigs and 110 singletons annotated as CYPs were obtained by sequencing the K. septemlobus transcriptome. By heterologous expression in yeast, we found that CYP716A94 was β-amyrin 28-oxidase involved in oleanolic acid production from β-amyrin, and CYP72A397 was oleanolic acid 23-hydroxylase involved in hederagenin production from oleanolic acid. Engineered yeast co-expressing KsBAS, CYP716A94 and CYP72A397 produced hederagenin. Kalopanax septemlobus CYP72A397 is a novel CYP enzyme that synthesizes hederagenin aglycone from oleanolic acid as a single product. In conclusion, we characterized three genes participating in sequential steps for hederagenin biosynthesis from β-amyrin, which are likely to play a major role in hederagenin saponin biosynthesis in K. septemlobus.

Douglas fir (Pseudotsuga menziesii) is a conifer species that stores large amounts of terpenoids, mainly monoterpenoids in resin ducts of various tissues. The effects of drought on stored leaf terpenoid concentrations in trees are scarcely studied and published data are partially controversial, since reduced, unaffected or elevated terpenoid contents due to drought have been reported. Even less is known on the effect of drought on root terpenoids. In the present work, we investigated the effect of reduced water availability on the terpenoid content in roots and needles of Douglas fir seedlings. Two contrasting Douglas fir provenances were studied: an interior provenance (var. glauca) with assumed higher drought resistance, and a coastal provenance (var. menziesii) with assumed lower drought resistance. We tested the hypothesis that both provenances show specific patterns of stored terpenoids and that the patterns will change in response to drought in both, needles and roots. We further expected stronger changes in the less drought tolerant coastal provenance. For this purpose, we performed an experiment under controlled conditions, in which the trees were exposed to moderate and severe drought stress. According to our expectations, the study revealed clear provenance-specific terpenoid patterns in needles. However, such patterns were not detected in the roots. Drought slightly increased the needle terpenoid contents of the coastal but not of the interior provenance. We also observed increased terpenoid abundance mainly in roots of the moderately stressed coastal provenance. Overall, from the observed provenance-specific reactions with increased terpenoid levels in trees of the coastal origin in response to drought, we conclude on functions of terpenoids for abiotic stress tolerance that might be fulfilled by other, constitutively expressed mechanisms in drought-adapted interior provenances., (© The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Southeast (SE) Asia is 1 of the most biodiverse regions in the world, and it holds approximately 20% of all mammal species. Despite this, the majority of SE Asia's genetic diversity is still poorly characterized. The growing interest in using environmental DNA to assess and monitor SE Asian species, in particular threatened mammals-has created the urgent need to expand the available reference database of mitochondrial barcode and complete mitogenome sequences. We have partially addressed this need by generating 72 new mitogenome sequences reconstructed from DNA isolated from a range of historical and modern tissue samples. Approximately 55 gigabases of raw sequence were generated. From this data, we assembled 72 complete mitogenome sequences, with an average depth of coverage of ×102.9 and ×55.2 for modern samples and historical samples, respectively. This dataset represents 52 species, of which 30 species had no previous mitogenome data available. The mitogenomes were geotagged to their sampling location, where known, to display a detailed geographical distribution of the species. Our new database of 52 taxa will strongly enhance the utility of environmental DNA approaches for monitoring mammals in SE Asia as it greatly increases the likelihoods that identification of metabarcoding sequencing reads can be assigned to reference sequences. This magnifies the confidence in species detections and thus allows more robust surveys and monitoring programmes of SE Asia's threatened mammal biodiversity. The extensive collections of historical samples from SE Asia in western and SE Asian museums should serve as additional valuable material to further enrich this reference database., (© The Author 2017. Published by Oxford University Press.)

Bamboo and rattan are widely grown for manufacturing, horticulture, and agroforestry. Bamboo and rattan production might help reduce poverty, boost economic growth, mitigate climate change, and protect the natural environment. Despite progress in research, sufficient molecular and genomic resources to study these species are lacking. We launched the Genome Atlas of Bamboo and Rattan (GABR) project, a comprehensive, coordinated international effort to accelerate understanding of bamboo and rattan genetics through genome analysis. GABR includes 2 core subprojects: Bamboo-T1K (Transcriptomes of 1000 Bamboos) and Rattan-G5 (Genomes of 5 Rattans), and several other subprojects. Here we describe the organization, directions, and status of GABR., (© The Authors 2017. Published by Oxford University Press.)

Aphids in the pine-feeding Nearctic genus Essigella (Sternorrhyncha, Aphididae, Lachninae) have been introduced in Europe, North Africa, Oceania, and South America. Mitochondrial, nuclear, and endosymbiont DNA sequences of 12 introduced populations from three continents confirm they all belong to Essigella californica (Essig, 1909). Intron sequence variation of the nuclear gene EF-1α has revealed the existence of four distinct groups. Group I gathers one population from China, where the species is newly reported, and several from Europe (France and Italy); Group II is represented by one population from Argentina; Group III includes two populations from Southern Australia with one from New Zealand; and Group IV corresponds to five populations from Eastern and South-Eastern Australia. These results indicate that introduced populations of E. californica have at least four source populations. They also show that intron variation of EF-1α can be a method to discriminate populations of asexually reproducing aphids., (© The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

European mistletoe (Viscum album L.) has largely infested Central European forests and causes high mortality probability particularly in dry years. However, little information is available about the consequences of mistletoe infestation for metabolic processes in bark and wood of its host, despite their important roles in infestation defense. We analyzed the tissue hydration, carbohydrate composition, phytohormone profile, reactive oxygen species and anti-oxidant levels in bark and wood of Scots pines (Pinus sylvestris L.), as dependent on mistletoe infestation. As a consequence of mistletoe infestation, host bark and wood showed impaired hydration and reduced total carbon content. In the bark, soluble sugar and lignin contents increased, apparently at the expense of holo-cellulose. Hydrogen peroxide accumulation was accompanied by increased glutathione and decreased reduced ascorbic acid levels. Mistletoe infestation mediated alteration of the phytohormone profile in bark and wood of its host. Cytokinins, jasmonic acid and abscisic acid levels increased in both tissues, whereas salicylic acid and indole-3-acetic acid, which were only detected in the bark, declined. The present results show that mistletoe infestation affects both the host's anti-oxidative defense system and the phytohormone profile after establishment of the xylem tapping haustorium. The significance of these processes for the development of the woody mistletoe stem and the haustorium is discussed., (© The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Maximization of genetic gain in forest tree breeding programs is contingent on the accuracy of the predicted breeding values and precision of the estimated genetic parameters. We investigated the effect of the combined use of contemporary pedigree information and genomic relatedness estimates on the accuracy of predicted breeding values and precision of estimated genetic parameters, as well as rankings of selection candidates, using single-step genomic evaluation (HBLUP). In this study, two traits with diverse heritabilities [tree height (HT) and wood density (WD)] were assessed at various levels of family genotyping efforts (0, 25, 50, 75, and 100%) from a population of white spruce ( Picea glauca ) consisting of 1694 trees from 214 open-pollinated families, representing 43 provenances in Québec, Canada. The results revealed that HBLUP bivariate analysis is effective in reducing the known bias in heritability estimates of open-pollinated populations, as it exposes hidden relatedness, potential pedigree errors, and inbreeding. The addition of genomic information in the analysis considerably improved the accuracy in breeding value estimates by accounting for both Mendelian sampling and historical coancestry that were not captured by the contemporary pedigree alone. Increasing family genotyping efforts were associated with continuous improvement in model fit, precision of genetic parameters, and breeding value accuracy. Yet, improvements were observed even at minimal genotyping effort, indicating that even modest genotyping effort is effective in improving genetic evaluation. The combined utilization of both pedigree and genomic information may be a cost-effective approach to increase the accuracy of breeding values in forest tree breeding programs where shallow pedigrees and large testing populations are the norm., (Copyright © 2017 Ratcliffe et al.)

An assemblage of tree species with different crown properties creates heterogeneous environments at the canopy level. Changes of functional leaf traits are expected, especially those related to light interception and photosynthesis. Chlorophyll a fluorescence (ChlF) properties in dark-adapted leaves, specific leaf area, leaf nitrogen content (N) and carbon isotope composition (δ13C) were measured on Picea abies (L.) H.Karst., Pinus sylvestris L. and Betula pendula Roth. in monospecific and mixed boreal forests in Europe, in order to test whether they were affected by stand species richness and composition. Photosynthetic efficiency, assessed by induced emission of leaf ChlF, was positively influenced in B. pendula by species richness, whereas P. abies showed higher photosynthetic efficiency in monospecific stands. Pinus sylvestris had different responses when it coexisted with P. abies or B. pendula. The presence of B. pendula, but not of P. abies, in the forest had a positive effect on the efficiency of photosynthetic electron transport and N in P. sylvestris needles, and the photosynthetic responses were positively correlated with an increase of leaf δ13C. These effects on P. sylvestris may be related to high light availability at the canopy level due to the less dense canopy of B. pendula. The different light requirements of coexisting species was the most important factor affecting the distribution of foliage in the canopy, driving the physiological responses of the mixed species. Future research directions claim to enhance the informative potential of the methods to analyse the responses of pure and mixed forests to environmental factors, including a broader set of plant species' functional traits and physiological responses., (© The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Current recommendations for applying the antiaggregation pheromone 3-methylcyclohex-2-en-1-one (MCH) to protect live trees from Douglas-fir beetle, Dendroctonus pseudotsugae Hopkins, infestation are to space individual passive releasers (MCH bubble capsules) on a 12- by 12-m grid throughout areas to be protected. Previous field studies and a theoretical study using a puff dispersion model to predict pheromone concentrations have shown that releasers emitting higher rates of MCH spaced farther apart may be as effective as the established standard treatment. During 2012 and 2013, we tested higher release rates of MCH at correspondingly wider spacings to keep the total amount of MCH released per unit area equal in all treatments. In 2012 near Challis, ID, treatments included the established standard release rate and spacing, four and six times the standard release rate at correspondingly wider spacings, and an untreated control. In 2013 near Ketchum, ID, treatments included the established standard release rate and spacing, five and seven times the standard release rate at correspondingly wider spacings, and an untreated control. Results from both years indicated that all MCH treatments were equally effective in reducing Douglas-fir beetle infestation. Using higher release rate formulations at wider spacings will reduce labor costs of installing MCH treatments, and, in cases where it is necessary, retrieving the releasers as well. In addition to reducing labor costs, the revised treatment protocol may increase the feasibility of treating areas that currently may not be possible due to treatment costs., (© The Authors 2016. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Anthocyanins are a group of colorful and bioactive natural pigments with important physiological and ecological functions in plants. We found an MYB transcription factor (PtrMYB119) from Populus trichocarpa that positively regulates anthocyanin production when expressed under the control of the CaMV 35S promoter in transgenic Arabidopsis Amino acid sequence analysis revealed that PtrMYB119 is highly homologous to Arabidopsis PAP1 (PRODUCTION OF ANTHOCYANIN PIGMENT1), a well-known transcriptional activator of anthocyanin biosynthesis. Independently produced transgenic poplars overexpressing PtrMYB119 or PtrMYB120 (a paralogous gene to PtrMYB119) (i.e., 35S::PtrMYB119 and 35S::PtrMYB120, respectively) showed elevated accumulation of anthocyanins in the whole plants, including leaf, stem and even root tissues. Using a reverse-phase high-performance liquid chromatography, we confirmed that the majority of the accumulated anthocyanin in our transgenic poplar is cyanidin-3-O-glucoside. Gene expression analyses revealed that most of the genes involved in the anthocyanin biosynthetic pathway were highly upregulated in 35S::PtrMYB119 poplars compared with the nontransformed control poplar. Among these genes, expression of PtrCHS1 (Chalcone Synthase1) and PtrANS2 (Anthocyanin Synthase2), which catalyze the initial and last steps of anthocyanin biosynthesis, respectively, was upregulated by up to 350-fold. Subsequent transient activation assays confirmed that PtrMYB119 activated the transcription of both PtrCHS1 and PtrANS2 Interestingly, expression of MYB182, a repressor of both anthocyanin and proanthocyanidin (PA) biosynthesis, was largely suppressed in 35S::PtrMYB119 poplars, while expression of MYB134, an activator of PA biosynthesis, was not changed significantly. More interestingly, high-level accumulation of anthocyanins in 35S::PtrMYB119 poplars did not have an adverse effect on plant growth. Taken together, our results demonstrate that PtrMYB119 and PtrMYB120 function as transcriptional activators of anthocyanin accumulation in both Arabidopsis and poplar., (© The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Every species has certain habitat requirements, which may be altered by interactions with other co-occurring species. These interactions are mostly ignored in predictive models trying to identify key habitat variables correlated with species population abundance/occurrence. We investigated how the structure of the urban landscape, food resources, potential competitors, predators, and interaction between these factors influence the abundance of house sparrow Passer domesticus and the tree sparrow P. montanus in sixty 25 ha plots distributed randomly across residential areas of the city of Poznań (Poland). The abundance of the house sparrow was positively correlated with the abundance of pigeons but negatively correlated with human-related food resources. There were significant interaction terms between abundances of other urban species and habitat variables in statistical models. For example, the abundance of house sparrow was negatively correlated with the abundance of corvids and tree sparrows but only when food resources were low. The abundance of tree sparrows positively correlated with density of streets and the distance from the city center. The abundance of this species positively correlated with the abundance of corvids when food resources were low but negatively correlated at low covers of green area. Our study indicates that associations between food resources, habitat covers, and the relative abundance of two sparrow species are altered by the abundance of other urban species. Competition, niche separation and social facilitation may be responsible for these interactive effects. Thus, biotic interactions should be included not only as an additive effect but also as an interaction term between abundance and habitat variables in statistical models predicting species abundance and occurrence.

Carrying capacity is 1 driver of wildlife population dynamics. Although in previous studies carrying capacity was considered to be a fixed entity, it may differ among locations due to environmental variation. The factors underlying variability in carrying capacity, however, have rarely been examined. Here, we investigated spatial heterogeneity in the carrying capacity of Japanese sika deer ( Cervus nippon ) from 2005 to 2014 in Yamanashi Prefecture, central Japan (mesh with grid cells of 5.5×4.6 km) by state-space modeling. Both carrying capacity and density dependence differed greatly among cells. Estimated carrying capacities ranged from 1.34 to 98.4 deer/km 2 . According to estimated population dynamics, grid cells with larger proportions of artificial grassland and deciduous forest were subject to lower density dependence and higher carrying capacity. We conclude that population dynamics of ungulates may vary spatially through spatial variation in carrying capacity and that the density level for controlling ungulate abundance should be based on the current density level relative to the carrying capacity for each area.

Chamaecyparis obtusa essential oil (COE) has been widely used to treat allergic diseases and was suggested to exert anti-inflammatory, antioxidant, and antimicrobial effects. This study evaluated the effects of COE on pain-related behavior and pro-inflammatory cytokines in rats with carrageenan (CGN)-induced arthritis. Reduced dynamic weight load on inflamed joint in voluntarily walking rats was used as the behavior test for arthritic pain; 10% COE-treated group was significantly attenuated pain (6-8 h post-CGN injection) compared to VEH (mineral oil)-treated group. In addition, the protein levels of interleukin (IL)-1β, tumor necrosis factor-α, IL-6 (6-8 h), and cyclooxygenase (COX)-2 (8 h) within the synovial membrane, as well as IL-1β, COX-2 (6-8 h), and IL-6 (5-7 h) within the meniscus, of 10% COE-treated group were significantly reduced. The current results implicate that COE has anti-inflammatory and anti-nociceptive effects on arthritis in rats.

Gibberellins (GAs) are important regulators of plant shoot biomass growth, and GA 20-oxidase (GA20ox) is one of the major regulatory enzymes in the GA biosynthetic pathway. Previously, we showed that the expression levels of a putative GA20ox1 (i.e., PdGA20ox1) in stem tissue of 3-month-old seedlings of 12 families of Pinus densiflora were positively correlated with stem diameter growth across those same families growing in an even-aged 32-year-old pine forest (Park EJ, Lee WY, Kurepin LV, Zhang R, Janzen L, Pharis RP (2015) Plant hormone-assisted early family selection in Pinus densiflora via a retrospective approach. Tree Physiol 35:86-94). To further investigate the molecular function of this gene in the stem wood growth of forest trees, we produced transgenic poplar lines expressing PdGA20ox1 under the control of the 35S promoter (designated as 35S::PdGA20ox1). By age 3 months, most of the 35S::PdGA20ox1 poplar trees were showing an exceptional enhancement of stem wood growth, i.e., up to fourfold increases in stem dry weight, compared with the nontransformed control poplar plants. Significant increases in endogenous GA1, its immediate precursor (GA20) and its catabolite (GA8) in elongating internode tissue accompanied the increased stem growth in the transgenic lines. Additionally, the development of gelatinous fibers occurred in vertically grown stems of the 35S::PdGA20ox1 poplars. An analysis of the cell wall monosaccharide composition of the 35S::PdGA20ox1 poplars showed significant increases in xylose and glucose contents, indicating a qualitative increase in secondary wall depositions. Microarray analyses led us to find a total of 276 probe sets that were upregulated (using threefold as a threshold) in the stem tissues of 35S::PdGA20ox1 poplars relative to the controls. 'Cell organization or biogenesis'- and 'cell wall'-related genes were overrepresented, including many of genes that are involved in cell wall modification. Several transcriptional regulators, which positively regulate cell elongation through GA signaling, were also upregulated. In contrast, genes involved in defense signaling were appreciably downregulated in the 35S::PdGA20ox1 stem tissues, suggesting a growth versus defense trade-off. Taken together, our results suggest that PdGA20ox1 functions to promote stem growth and wood formation in poplar, probably by activating GA signaling while coincidentally depressing defense signaling., (© The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Monochamus saltuarius Gebler is a vector that transmits the pine wood nematode, Bursaphelenchus xylophilus, to Korean white pine, Pinus koraiensis, in Korea. To reduce the damage caused by this nematode in pine forests, timely control measures are needed to suppress the cerambycid beetle population. This study sought to construct a forecasting model to predict beetle emergence based on spring temperature. Logs of Korean white pine were infested with M. saltuarius in 2009, and the infested logs were overwintered. In February 2010, infested logs were then moved into incubators held at constant temperature conditions of 16, 20, 23, 25, 27, 30 or 34°C until all adults had emerged. The developmental rate of the beetles was estimated by linear and nonlinear equations and a forecasting model for emergence of the beetle was constructed by pooling data based on normalized developmental rate. The lower threshold temperature for development was 8.3°C. The forecasting model relatively well predicted the emergence pattern of M. saltuarius collected from four areas in northern Republic of Korea. The median emergence dates predicted by the model were 2.2-5.9 d earlier than the observed median dates., (© The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

In an even-aged pine forest trees can vary considerably in stem size. We examined the basis for this anomaly using a retrospective approach. Twelve open-pollinated families of Pinus densiflora Sieb. et Zucc. were deliberately chosen for their variation in stem volumes at age 32 years. Seedlings obtained from these families were grown to age 6 months under optimal nursery conditions. Endogenous levels of growth hormones (auxin [IAA] and gibberellins [GAs]) and expression of the GA biosynthesis gene, PdGA20ox1, all assessed at age 3 months, were significantly correlated, across family, with seedling stem and/or shoot dry biomass at age 6 months. Retrospective comparisons of seedling growth, seedling stem tissue GA(20) and seedling stem expression levels of PdGA20ox1 were then made, across family, with tree stem growth at age 32 years. Age 6 months length and shoot dry biomass at age 6 months showed positive and significant Pearson's correlations with age 32 years tree stem diameters and a tree stem volume index, as did seedling stem tissue GA(20). Even seedling stem PdGA20ox1 expression levels were positively and near significantly (P = 0.088) correlated with age 32 years tree stem diameters. Auxin and GAs control nursery growth of seedlings at the family level, and this control also extends, for GAs at least, to field growth of older trees. We propose that family differences in PdGA20ox1 gene expression, and thus endogenous GA levels, may explain much of the natural variation seen for tree stem size in even-aged pine forests. If our hypothesis is correct, then the heritable components of variation in tree stem growth capacity should be predictable by hormonal and gene expression profiling. Such profiling, combined with the measurement of seedling phenotypic growth characters, could have the potential to accelerate the early selection of those conifer families that possess traits for inherently rapid stem wood growth., (© The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

In this study, we demonstrated the occurrence of stomatal patchiness and its spatial scale in leaves from various sizes of trees grown in a lowland dipterocarp forest in Peninsular Malaysia. To evaluate the patterns of stomatal behavior, we used three techniques simultaneously to analyze heterobaric or homobaric leaves from five tree species ranging from 0.6 to 31 m in height: (i) diurnal changes in chlorophyll fluorescence imaging, (ii) observation and simulation of leaf gas-exchange rates and (iii) a pressure-infiltration method. Measurements were performed in situ with 1000 or 500 μmol m(-2) s(-1) photosynthetic photon flux density. Diurnal patterns in the spatial distribution of photosynthetic electron transport rate (J) mapped from chlorophyll fluorescence images, a comparison of observed and simulated leaf gas-exchange rates, and the spatial distribution of stomatal apertures obtained from the acid-fuchsin-infiltrated area showed that patchy stomatal closure coupled with severe midday depression of photosynthesis occurred in Neobalanocarpus heimii (King) Ashton, a higher canopy tree with heterobaric leaves due to the higher leaf temperature and vapor pressure deficit. However, subcanopy or understory trees showed uniform stomatal behavior throughout the day, although they also have heterobaric leaves. These results suggest that the occurrence of stomatal patchiness is determined by tree size and/or environmental conditions. The analysis of spatial scale by chlorophyll fluorescence imaging showed that several adjacent anatomical patches (lamina areas bounded by bundle-sheath extensions within the lamina) may co-operate for the distributed patterns of J and stomatal apertures., (© The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Understory plants in tropical forests often experience a low-light environment combined with high CO2 concentration. We hypothesized that the high CO2 concentration may compensate for leaf carbon loss caused by the low light, through increasing light-use efficiency of both steady-state and dynamic photosynthetic properties. To test the hypothesis, we examined CO2 gas exchange in response to an artificial lightfleck in Dipterocarpus sublamellatus Foxw. seedlings under contrasting CO2 conditions: 350 and 700 μmol CO2 mol(-1) air in a tropical rain forest, Pasoh, Malaysia. Total photosynthetic carbon gain from the lightfleck was about double when subjected to the high CO2 when compared with the low CO2 concentration. The increase of light-use efficiency in dynamic photosynthesis contributed 7% of the increased carbon gain, most of which was due to reduction of photosynthetic induction to light increase under the high CO2. The light compensation point of photosynthesis decreased by 58% and the apparent quantum yield increased by 26% at the high CO2 compared with those at the low CO2. The study suggests that high CO2 increases photosynthetic light-use efficiency under both steady-state and fluctuating light conditions, which should be considered in assessing the leaf carbon gain of understory plants in low-light environments., (© The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)