Population structure of the invasive forest pathogen Hymenoscyphus pseudoalbidus

Understanding the genetic diversity and structure of invasive pathogens in source and in introduced areas is crucial to the revelation of hidden biological features of an organism, to the reconstruction of the course of invasions and to the establishment of effective control measures. Hymenoscyphus pseudoalbidus (anamorph: Chalara fraxinea) is an invasive and highly destructive fungal pathogen found on common ash Fraxinus excelsior in Europe and is native to East Asia. To gain insights into its dispersal mechanisms and history of invasion, we used microsatellite markers and characterized the genetic structure and diversity of H. pseudoalbidus populations at three spatial levels: (i) between Europe and Japan, (ii) in Europe and (iii) at the epidemic's front in Switzerland. Phylogenetic and network analysis demonstrated that individuals from both regions are conspecific. However, populations from Japan harboured a higher genetic diversity and were genetically differentiated from European ones. No evident population structure was found among the 1208 European strains using Bayesian and multivariate clustering analysis. Only the distribution of genetic diversity in space, pairwise population differentiation (G_ST) and the spatial analysis of principal components revealed a faint geographical pattern around Europe. A significant allele deficiency in most European populations pointed to a recent genetic bottleneck, whereas no pattern of isolation by distance was found. Our data suggest that H. pseudoalbidus was introduced just once by at least two individuals. The potential source region of H. pseudoalbidus is vast, and further investigations are required for a more accurate localization of the source population.     

The effects of rainfall on different components of seasonal fecundity in a tropical forest passerine

Seasonal fecundity is a composite metric that is determined by component parameters such as clutch size, nest survival and re‐nesting probability. Many of these component parameters are known to vary with environmental conditions, in particular rainfall prior to or during the breeding season. In some species, seasonal fecundity is positively related to rainfall, but little is known about which component parameters of seasonal fecundity respond most strongly to rainfall. We used intensive nest monitoring of a multi‐brooded tropical forest passerine, the Montserrat Oriole Icterus oberi, to examine the effects of rainfall during the pre‐breeding season on component parameters of annual fecundity. We monitored all nests of a total of 42 pairs over 5 years in which rainfall varied substantially. We then related clutch size, nest survival, onset and length of the breeding season, re‐nesting probability and re‐nesting interval to pre‐breeding season rainfall using generalized linear mixed models that accounted for random variation across sites and individual pairs, and incorporated other variables known to affect the response. Higher pre‐breeding season rainfall led to an increase in clutch size and a decrease in re‐nesting interval, but nest survival, re‐nesting probability and length of the breeding season were not affected by variation in rainfall. The onset of the breeding season was delayed in very dry years. We conclude that higher rainfall is likely to increase food availability and thus body condition of female Montserrat Orioles, leading to an increase in fecundity due to larger clutch sizes.     

Microbat responses to forest decline

Tree declines have been recorded across forests and woodlands on most continents, causing tree mortality over thousands of square kilometres, yet the impact of tree declines upon mammals have only rarely been quantified. Once the dominant tree over the western parts of the Swan Coastal Plain in Western Australia, tuart (Eucalyptus gomphocephala) forest has been reduced to less than a third of its former range through clearing for agriculture and urban development. Additionally, over the last 30 years, the remnant population has been heavily impacted by a decline that has an unknown cause, but is likely related to a root pathogen coupled with abiotic factors (reduced rainfall, increased salinity and elevated temperatures). Tuart decline is evident as marked canopy dieback, replacement with epicormic growth and increasing bare branches, while leaf litter is lost from the tree surrounds. We examined the effect of tuart decline and other vegetation measures upon bat activity using auditory monitoring. Vegetation structure was correlated with Vespertilionidae bat activity. Falsistrellus mackenziei were more likely to forage around healthy canopies (activity positively correlated with tuart crown density and negatively correlated with tuart crown dieback). By contrast, the other three taxa were more often encountered in declining rather than healthy tuart sites. Chalinolobus gouldii was positively associated with tuart crown dieback. Activity of Vespadelus regulus and Nyctophilus spp. (species not distinguishable from their calls) were significantly positively correlated with an open tall canopy (positively with cover of plants >10 m tall and negatively with overall canopy cover density). There were no vegetation measurements that were strong predictors of activity of two Molossidae species (Ozimops kitcheneri and Austronomus australis), which intercept insects above the forest canopy. This study clearly reveals different factors influencing the activity of bat taxa, which are likely related to where they feed and their manoeuvrability around tree canopies.     

Changes in structure of over‐ and midstory tree species in a Mediterranean‐type forest after an extreme drought‐associated heatwave

Worldwide, extreme climatic events such as drought and heatwaves are associated with forest mortality. However, the precise drivers of tree mortality at individual and stand levels vary considerably, with substantial gaps in knowledge across studies in biomes and continents. In 2010–2011, a drought‐associated heatwave occurred in south‐western Australia and drove sudden and rapid forest canopy collapse. Working in the Northern Jarrah (Eucalyptus marginata) Forest, we quantified the response of key overstory (E. marginata, Corymbia calophylla) and midstory (Banksia grandis, Allocasuarina fraseriana) tree species to the extreme climate event. Using transects spanning a gradient of drought impacts (minimal (50–100 m), transitional (100–150 m) and severe (30–60 m)), tree species mortality in relation to stand characteristics (stand basal area and stem density) and edaphic factors (soil depth) was determined. We show differential mortality between the two overstory species and the two midstory species corresponding to the drought‐associated heatwave. The dominant overstory species, E. marginata, had significantly higher mortality (~19%) than C. calophylla (~7%) in the severe zone. The midstory species, B. grandis, demonstrated substantially higher mortality (~59%) than A. fraseriana (~4%) in the transitional zone. Banksia grandis exhibited a substantial shift in structure in response to the drought‐associated heatwave in relation to tree size, basal area and soil depth. This study illustrates the role of climate extremes in driving ecosystem change and highlights the critical need to identify and quantify the resulting impact to help predict future forest die‐off events and to underpin forest management and conservation.     

Tree growth variation in the tropical forest: understanding effects of temperature,rainfall and CO2

Tropical forest responses to climatic variability have important consequences for global carbon cycling, but are poorly understood. As empirical, correlative studies cannot disentangle the interactive effects of climatic variables on tree growth, we used a tree growth model (IBTREE) to unravel the climate effects on different physiological pathways and in turn on stem growth variation. We parameterized the model for canopy trees of Toona ciliata (Meliaceae) from a Thai monsoon forest and compared predicted and measured variation from a tree‐ring study over a 30‐year period. We used historical climatic variation of minimum and maximum day temperature, precipitation and carbon dioxide (CO₂) in different combinations to estimate the contribution of each climate factor in explaining the inter‐annual variation in stem growth. Running the model with only variation in maximum temperature and rainfall yielded stem growth patterns that explained almost 70% of the observed inter‐annual variation in stem growth. Our results show that maximum temperature had a strong negative effect on the stem growth by increasing respiration, reducing stomatal conductance and thus mitigating a higher transpiration demand, and – to a lesser extent – by directly reducing photosynthesis. Although stem growth was rather weakly sensitive to rain, stem growth variation responded strongly and positively to rainfall variation owing to the strong inter‐annual fluctuations in rainfall. Minimum temperature and atmospheric CO₂ concentration did not significantly contribute to explaining the inter‐annual variation in stem growth. Our innovative approach – combining a simulation model with historical data on tree‐ring growth and climate – allowed disentangling the effects of strongly correlated climate variables on growth through different physiological pathways. Similar studies on different species and in different forest types are needed to further improve our understanding of the sensitivity of tropical tree growth to climatic variability and change.     

Substrate modification for enhanced native forest restoration,Reefton

Restoration of postmining substrates to native forest is a standard requirement of resource consents for mine sites located within areas of native forest in New Zealand. Unweathered waste rock presents significant challenges for plant growth, and past research highlights the importance of replacing soil as part of restoration. However, replacing soil with its horizon structure intact or even obtaining sufficient soil for restoration can be a challenge in some situations. In this paper, we describe the results of two trials undertaken at the OceanaGold Ltd. open‐cast gold mine in Reefton to explore the influence of substrate conditions on the growth of native forest seedlings. We show that beech (Nothofagus) seedlings grown on A‐horizon soil grew significantly better than those grown on soil mixed with waste rock, and both grew significantly better than plants grown just on waste rock. In the second trial, we show that bark chips are not a good substitute for soil. These results confirm the importance of having the correct substrate for successful native forest restoration.     

Climate–human interactions contributed to historical forest recruitment dynamics in Mediterranean subalpine ecosystems

Long‐term tree recruitment dynamics of subalpine forests mainly depend on temperature changes, but little is known about the feedbacks between historical land use and climate. Here, we analyze a southern European, millennium‐long dataset of tree recruitment from three high‐elevation pine forests located in Mediterranean mountains (Pyrenees, northeastern Spain; Pollino, southern Italy; and Mt. Smolikas, northern Greece). We identify synchronized recruitment peaks in the late 15th and early 16th centuries, following prolonged periods of societal and climate instability. Major European population crises in the 14th and 15th centuries associated with recurrent famines, the Black Death pandemic, and political turmoil are likely to have reduced the deforestation of subalpine environments and caused widespread rewilding. We suggest that a distinct cold phase in the Little Ice Age around 1450 ce could also have accelerated the cessation of grazing pressure, particularly in the Pyrenees, where the demographic crisis was less severe. Most pronounced in the Pyrenees, the enhanced pine recruitment from around 1500–1550 ce coincides with temporarily warmer temperatures associated with a positive phase of the North Atlantic Oscillation. We diagnose that a mixture of human and climate factors has influenced past forest recruitment dynamics in Mediterranean subalpine ecosystems. Our results highlight how complex human–climate interactions shaped forest dynamics during pre‐industrial times and provide historical analogies to recent rewilding.     

Molecular Analysis of ORF6, ORF7 and ORF8 of Beet yellows virus Iranian Isolate

Beet yellows virus (BYV), a member of the Closteroviridae family, is one of the most important sugar beet yellowing viruses. The nine ORFs of BYV genome encode different proteins required for BYV life cycle. We sequenced a part of the genome of BYV Iranian isolate consisting of ORF6, ORF7 and ORF8. The primer pair BYVA/Z was used for amplification of this region in RT‐PCR. The amplicon (1615 bp) was cloned and sequenced. Comparisons showed the amplified segment is corresponding to ORF6, ORF7 and ORF8 of BYV genome encoding coat protein, p20 and p21 proteins, respectively. The ORF7 of BYV Iranian isolate overlaps with ORF6 and ORF8 in four and 26 nucleotides at 5′ and 3′ ends, respectively. The ORF7 of Iranian isolate of BYV was sequenced completely. However, approximately 24 nt. from the beginning of ORF6 and 23 nt. from end of ORF8, including the stop codon, were not determined. ORF6, ORF7 and ORF8 showed the highest similarity at nucleotide (98.3, 99.4 and 99.2%) and amino acid (97.4, 98.9 and 100%) sequence levels, with BYV Ukrainian isolate. Phylogenetic analysis of the deduced amino acid sequences of ORF6, ORF7 and ORF8 revealed closer relationship of Iranian isolate of BYV with BYV Ukrainian isolate than other BYV isolates available at GenBank.     

A metabolic signature for long life in the Caenorhabditis elegans Mit mutants

Mit mutations that disrupt function of the mitochondrial electron transport chain can, inexplicably, prolong Caenorhabditis elegans lifespan. In this study we use a metabolomics approach to identify an ensemble of mitochondrial‐derived α‐ketoacids and α‐hydroxyacids that are produced by long‐lived Mit mutants but not by other long‐lived mutants or by short‐lived mitochondrial mutants. We show that accumulation of these compounds is dependent on concerted inhibition of three α‐ketoacid dehydrogenases that share dihydrolipoamide dehydrogenase (DLD) as a common subunit, a protein previously linked in humans with increased risk of Alzheimer's disease. When the expression of DLD in wild‐type animals was reduced using RNA interference we observed an unprecedented effect on lifespan – as RNAi dosage was increased lifespan was significantly shortened, but, at higher doses, it was significantly lengthened, suggesting that DLD plays a unique role in modulating length of life. Our findings provide novel insight into the origin of the Mit phenotype.     

Dampening effects of long‐term experimental drought on growth and mortality rates of a Holm oak forest

Forests respond to increasing intensities and frequencies of drought by reducing growth and with higher tree mortality rates. Little is known, however, about the long‐term consequences of generally drier conditions and more frequent extreme droughts. A Holm oak forest was exposed to experimental rainfall manipulation for 13 years to study the effect of increasing drought on growth and mortality of the dominant species Quercus ilex, Phillyrea latifolia, and Arbutus unedo. The drought treatment reduced stem growth of A. unedo (?66.5%) and Q. ilex (?17.5%), whereas P. latifolia remained unaffected. Higher stem mortality rates were noticeable in Q. ilex (+42.3%), but not in the other two species. Stem growth was a function of the drought index of early spring in the three species. Stem mortality rates depended on the drought index of winter and spring for Q. ilex and in spring and summer for P. latifolia, but showed no relation to climate in A. unedo. Following a long and intense drought (2005–2006), stem growth of Q. ilex and P. latifolia increased, whereas it decreased in A. unedo. Q. ilex also enhanced its survival after this period. Furthermore, the effect of drought treatment on stem growth in Q. ilex and A. unedo was attenuated as the study progressed. These results highlight the different vulnerabilities of Mediterranean species to more frequent and intense droughts, which may lead to partial species substitution and changes in forest structure and thus in carbon uptake. The response to drought, however, changed over time. Decreased intra‐ and interspecific competition after extreme events with high mortality, together with probable morphological and physiological acclimation to drought during the study period, may, at least in the short term, buffer forests against drier conditions. The long‐term effects of drought consequently deserve more attention, because the ecosystemic responses are unlikely to be stable over time.Nontechnical summaryIn this study, we evaluate the effect of long‐term (13 years) experimental drought on growth and mortality rates of three forest Mediterranean species, and their response to the different intensities and durations of natural drought. We provide evidence for species‐specific responses to drought, what may eventually lead to a partial community shift favoring the more drought‐resistant species. However, we also report a dampening of the treatment effect on the two drought‐sensitive species, which may indicate a potential adaptation to drier conditions at the ecosystem or population level. These results are thus relevant to account for the stabilizing processes that would alter the initial response of ecosystem to drought through changes in plant physiology, morphology, and demography compensation.     

The use of DNA barcodes to estimate phylogenetic diversity in forest communities of southern China

To elucidate potential ecological and evolutionary processes associated with the assembly of plant communities, there is now widespread use of estimates of phylogenetic diversity that are based on a variety of DNA barcode regions and phylogenetic construction methods. However, relatively few studies consider how estimates of phylogenetic diversity may be influenced by single DNA barcodes incorporated into a sequence matrix (conservative regions vs. hypervariable regions) and the use of a backbone family‐level phylogeny. Here, we use general linear mixed‐effects models to examine the influence of different combinations of core DNA barcodes (rbcL, matK, ITS, and ITS2) and phylogeny construction methods on a series of estimates of community phylogenetic diversity for two subtropical forest plots in Guangdong, southern China. We ask: (a) What are the relative influences of single DNA barcodes on estimates phylogenetic diversity metrics? and (b) What is the effect of using a backbone family‐level phylogeny to estimate topology‐based phylogenetic diversity metrics? The combination of more than one barcode (i.e., rbcL + matK + ITS) and the use of a backbone family‐level phylogeny provided the most parsimonious explanation of variation in estimates of phylogenetic diversity. The use of a backbone family‐level phylogeny showed a stronger effect on phylogenetic diversity metrics that are based on tree topology compared to those that are based on branch lengths. In addition, the variation in the estimates of phylogenetic diversity that was explained by the top‐rank models ranged from 0.1% to 31% and was dependent on the type of phylogenetic community structure metric. Our study underscores the importance of incorporating a multilocus DNA barcode and the use of a backbone family‐level phylogeny to infer phylogenetic diversity, where the type of DNA barcode employed and the phylogenetic construction method used can serve as a significant source of variation in estimates of phylogenetic community structure.     

Using ecosystem CO2 measurements to estimate the timing and magnitude of greenhouse gas mitigation potential of forest bioenergy

Forest bioenergy opportunities may be hindered by a long greenhouse gas (GHG) payback time. Estimating this payback time requires the quantification of forest‐atmosphere carbon exchanges, usually through process‐based simulation models. Such models are prone to large uncertainties, especially over long‐term carbon fluxes from dead organic matter pools. We propose the use of whole ecosystem field‐measured CO₂ exchanges obtained from eddy covariance flux towers to assess the GHG mitigation potential of forest biomass projects as a way to implicitly integrate all field‐level CO₂ fluxes and the inter‐annual variability in these fluxes. As an example, we perform the evaluation of a theoretical bioenergy project that uses tree stems as bioenergy feedstock and include multi‐year measurements of net ecosystem exchange (NEE) from forest harvest chronosequences in the boreal forest of Canada to estimate the time dynamics of ecosystem CO₂ exchanges following harvesting. Results from this approach are consistent with previous results using process‐based models and suggest a multi‐decadal payback time for our project. The time for atmospheric carbon debt repayment of bioenergy projects is highly dependent on ecosystem‐level CO₂ exchanges. The use of empirical NEE measurements may provide a direct evaluation of, or at least constraints on, the GHG mitigation potential of forest bioenergy projects.