Tree rings reveal the transient risk of extinction hidden inside climate envelope forecasts.

Given the importance of climate in shaping species' geographic distributions, climate change poses an existential threat to biodiversity. Climate envelope modeling, the predominant approach used to quantify this threat, presumes that individuals in populations respond to climate variability and change according to species-level responses inferred from spatial occurrence data-such that individuals at the cool edge of a species' distribution should benefit from warming (the "leading edge"), whereas individuals at the warm edge should suffer (the "trailing edge"). Using 1,558 tree-ring time series of an aridland pine (Pinus edulis) collected at 977 locations across the species' distribution, we found that trees everywhere grow less in warmer-than-average and drier-than-average years. Ubiquitous negative temperature sensitivity indicates that individuals across the entire distribution should suffer with warming-the entire distribution is a trailing edge. Species-level responses to spatial climate variation are opposite in sign to individual-scale responses to time-varying climate for approximately half the species' distribution with respect to temperature and the majority of the species' distribution with respect to precipitation. These findings, added to evidence from the literature for scale-dependent climate responses in hundreds of species, suggest that correlative, equilibrium-based range forecasts may fail to accurately represent how individuals in populations will be impacted by changing climate. A scale-dependent view of the impact of climate change on biodiversity highlights the transient risk of extinction hidden inside climate envelope forecasts and the importance of evolution in rescuing species from extinction whenever local climate variability and change exceeds individual-scale climate tolerances.

Declining tree growth resilience mediates subsequent forest mortality in the US Mountain West.

Climate change-triggered forest die-off is an increasing threat to global forests and carbon sequestration but remains extremely challenging to predict. Tree growth resilience metrics have been proposed as measurable proxies of tree susceptibility to mortality. However, it remains unclear whether tree growth resilience can improve predictions of stand-level mortality. Here, we use an extensive tree-ring dataset collected at ~3000 permanent forest inventory plots, spanning 13 dominant species across the US Mountain West, where forests have experienced strong drought and extensive die-off has been observed in the past two decades, to test the hypothesis that tree growth resilience to drought can explain and improve predictions of observed stand-level mortality. We found substantial increases in growth variability and temporal autocorrelation as well declining drought resistance and resilience for a number of species over the second half of the 20th century. Declining resilience and low tree growth were strongly associated with cross- and within-species patterns of mortality. Resilience metrics had similar explicative power compared to climate and stand structure, but the covariance structure among predictors implied that the effect of tree resilience on mortality could partially be explained by stand and climate variables. We conclude that tree growth resilience offers highly valuable insights on tree physiology by integrating the effect of stressors on forest mortality but may have only moderate potential to improve large-scale projections of forest die-off under climate change.

Polyploidy and growth-defense tradeoffs in natural populations of western quaking Aspen.

Polyploidy, the expression of more than two sets of chromosomes, is common in plants, and is thought to influence plant trait expression and drive plant species evolution. The degree to which polyploidy influences interactions among physiological processes such as growth and defense in natural populations through its effect on phenotypic variability is poorly understood. We link broad plant genotypic features (including polyploidy) to phenotypic expression of growth and chemical defense in natural populations of quaking aspen (Populus tremuloides) to examine patterns in resource allocation that might drive growth-defense tradeoffs. Quaking aspen are capable of rapid growth, and are also a primary food plant for a large range of herbivores, including insects and ungulates. While often diploid, aspen can exhibit polyploidy as triploid clones. We tested for the effect of genotype, cytotype (ploidy level, divided between diploids and triploids), and ramet age on relationships between growth and leaf chemistry across natural aspen clones in northern Utah. Substantial genotype variability in growth and leaf chemistry occurred across both cytotypes. Phenolic glycosides, but not condensed tannins, were negatively related to growth. Ramet age was also negatively related to growth. Phenolic glycosides were negatively related to condensed tannins, but only for the diploid clones. Triploid clones exhibited ~ 20% higher levels of phenolic glycosides than diploids. Growth in quaking aspen was likely sacrificed for the production of phenolic glycosides. Our study underscores the importance of considering polyploidy, genetic variability, and ramet age in understanding growth-defense tradeoffs in natural populations of clonal organisms, such as quaking aspen.

Adding Tree Rings to North America's National Forest Inventories: An Essential Tool to Guide Drawdown of Atmospheric CO2.

Tree-ring time series provide long-term, annually resolved information on the growth of trees. When sampled in a systematic context, tree-ring data can be scaled to estimate the forest carbon capture and storage of landscapes, biomes, and-ultimately-the globe. A systematic effort to sample tree rings in national forest inventories would yield unprecedented temporal and spatial resolution of forest carbon dynamics and help resolve key scientific uncertainties, which we highlight in terms of evidence for forest greening (enhanced growth) versus browning (reduced growth, increased mortality). We describe jump-starting a tree-ring collection across the continent of North America, given the commitments of Canada, the United States, and Mexico to visit forest inventory plots, along with existing legacy collections. Failing to do so would be a missed opportunity to help chart an evidence-based path toward meeting national commitments to reduce net greenhouse gas emissions, urgently needed for climate stabilization and repair.

MASTREE+: Time-series of plant reproductive effort from six continents.

Significant gaps remain in understanding the response of plant reproduction to environmental change. This is partly because measuring reproduction in long-lived plants requires direct observation over many years and such datasets have rarely been made publicly available. Here we introduce MASTREE+, a data set that collates reproductive time-series data from across the globe and makes these data freely available to the community. MASTREE+ includes 73,828 georeferenced observations of annual reproduction (e.g. seed and fruit counts) in perennial plant populations worldwide. These observations consist of 5971 population-level time-series from 974 species in 66 countries. The mean and median time-series length is 12.4 and 10 years respectively, and the data set includes 1122 series that extend over at least two decades (≥20 years of observations). For a subset of well-studied species, MASTREE+ includes extensive replication of time-series across geographical and climatic gradients. Here we describe the open-access data set, available as a.csv file, and we introduce an associated web-based app for data exploration. MASTREE+ will provide the basis for improved understanding of the response of long-lived plant reproduction to environmental change. Additionally, MASTREE+ will enable investigation of the ecology and evolution of reproductive strategies in perennial plants, and the role of plant reproduction as a driver of ecosystem dynamics.

Aún existen importantes vacíos en la comprensión de la respuesta reproductiva de las plantas al cambio medioambiental, en parte, porque su monitoreo en especies de plantas longevas requiere una observación directa durante muchos años, y estos conjuntos de datos rara vez han estado disponibles. Aquí presentamos a MASTREE +, una base de datos que recopila series de tiempo de la reproducción de las plantas de todo el planeta, poniendo a disposición estos datos de libre acceso para la comunidad científica. MASTREE + incluye 73.828 puntos de observación de la reproducción anual georreferenciados (ej. conteos de semillas y frutos) en poblaciones de plantas perennes en todo el mundo. Estas observaciones consisten en 5971 series temporales a nivel de población provenientes de 974 especies en 66 países. La mediana de la duración de las series de tiempo es de 10 años (media = 12.4 años) y el conjunto de datos incluye 1.122 series de al menos dos décadas (≥20 años de observaciones). Para un subconjunto de especies bien estudiadas, MASTREE +incluye un amplio conjunto de series temporales replicadas en gradientes geográficos y climáticos. Describimos el conjunto de datos de acceso abierto disponible como un archivo.csv y presentamos una aplicación web asociada para la exploración de datos. MASTREE+ proporcionará la base para mejorar la comprensión sobre la respuesta reproductiva de plantas longevas al cambio medioambiental. Además, MASTREE+ facilitará los avances en la investigación de la ecología y la evolución de las estrategias reproductivas en plantas perennes y el papel de la reproducción vegetal como determinante de la dinámica de ecosistemas.

Ecological forecasting of tree growth: Regional fusion of tree-ring and forest inventory data to quantify drivers and characterize uncertainty.

Robust ecological forecasting of tree growth under future climate conditions is critical to anticipate future forest carbon storage and flux. Here, we apply three ingredients of ecological forecasting that are key to improving forecast skill: data fusion, confronting model predictions with new data, and partitioning forecast uncertainty. Specifically, we present the first fusion of tree-ring and forest inventory data within a Bayesian state-space model at a multi-site, regional scale, focusing on Pinus ponderosa var. brachyptera in the southwestern US. Leveraging the complementarity of these two data sources, we parsed the ecological complexity of tree growth into the effects of climate, tree size, stand density, site quality, and their interactions, and quantified uncertainties associated with these effects. New measurements of trees, an ongoing process in forest inventories, were used to confront forecasts of tree diameter with observations, and evaluate alternative tree growth models. We forecasted tree diameter and increment in response to an ensemble of climate change projections, and separated forecast uncertainty into four different causes: initial conditions, parameters, climate drivers, and process error. We found a strong negative effect of fall-spring maximum temperature, and a positive effect of water-year precipitation on tree growth. Furthermore, tree vulnerability to climate stress increases with greater competition, with tree size, and at poor sites. Under future climate scenarios, we forecast increment declines of 22%-117%, while the combined effect of climate and size-related trends results in a 56%-91% decline. Partitioning of forecast uncertainty showed that diameter forecast uncertainty is primarily caused by parameter and initial conditions uncertainty, but increment forecast uncertainty is mostly caused by process error and climate driver uncertainty. This fusion of tree-ring and forest inventory data lays the foundation for robust ecological forecasting of aboveground biomass and carbon accounting at tree, plot, and regional scales, including iterative improvement of model skill.

Climate-driven, but dynamic and complex? A reconciliation of competing hypotheses for species' distributions.

Estimates of the percentage of species "committed to extinction" by climate change range from 15% to 37%. The question is whether factors other than climate need to be included in models predicting species' range change. We created demographic range models that include climate vs. climate-plus-competition, evaluating their influence on the geographic distribution of Pinus edulis, a pine endemic to the semiarid southwestern U.S. Analyses of data on 23,426 trees in 1941 forest inventory plots support the inclusion of competition in range models. However, climate and competition together only partially explain this species' distribution. Instead, the evidence suggests that climate affects other range-limiting processes, including landscape-scale, spatial processes such as disturbances and antagonistic biotic interactions. Complex effects of climate on species distributions-through indirect effects, interactions, and feedbacks-are likely to cause sudden changes in abundance and distribution that are not predictable from a climate-only perspective.

Spruce beetle outbreak was not driven by drought stress: Evidence from a tree-ring iso-demographic approach indicates temperatures were more important.

Climate change has amplified eruptive bark beetle outbreaks over recent decades, including spruce beetle (Dendroctonus rufipennis). However, for projecting future bark beetle dynamics there is a critical lack of evidence to differentiate how outbreaks have been promoted by direct effects of warmer temperatures on beetle life cycles versus indirect effects of drought on host susceptibility. To diagnose whether drought-induced host-weakening was important to beetle attack success we used an iso-demographic approach in Engelmann spruce (Picea engelmannii) forests that experienced widespread mortality caused by spruce beetle outbreaks in the 1990s, during a prolonged drought across the central and southern Rocky Mountain region. We determined tree death date demography during this outbreak to differentiate early- and late-dying trees in stands distributed across a landscape within this larger regional mortality event. To directly test for a role of drought stress during outbreak initiation we determined whether early-dying trees had greater sensitivity of tree-ring carbon isotope discrimination (∆13 C) to drought compared to late-dying trees. Rather, evidence indicated the abundance and size of host trees may have modified ∆13 C responses to drought. ∆13 C sensitivity to drought did not differ among early- versus late-dying trees, which runs contrary to previously proposed links between spruce beetle outbreaks and drought. Overall, our results provide strong support for the view that irruptive spruce beetle outbreaks across North America have primarily been driven by warming-amplified beetle life cycles whereas drought-weakened host defenses appear to have been a distant secondary driver of these major disturbance events.

Stable or seral? Fire-driven alternative states in aspen forests of western North America.

As important centres for biological diversity, aspen forests are essential to the function and aesthetics of montane ecosystems in western North America. Aspen stands are maintained by a nuanced relationship with wildfire, although in recent decades aspen mortality has increased. The need to understand the baseline environmental conditions that favour aspen is clear; however, long-term fire history reconstructions are rare due to the scarcity of natural archives in dry montane settings. Here, we analyse a high-resolution lake sediment record from southwestern, Utah, USA to quantify the compositional and burning conditions that promote stable (or seral) aspen forests. Our results show that aspen presence is negatively correlated with subalpine fir and that severe fires tend to promote persistent and diverse aspen ecosystems over centennial timescales. This information improves our understanding of aspen disturbance ecology and identifies the circumstances where critical transitions in montane forests may occur.

Sampling bias overestimates climate change impacts on forest growth in the southwestern United States.

Climate-tree growth relationships recorded in annual growth rings have recently been the basis for projecting climate change impacts on forests. However, most trees and sample sites represented in the International Tree-Ring Data Bank (ITRDB) were chosen to maximize climate signal and are characterized by marginal growing conditions not representative of the larger forest ecosystem. We evaluate the magnitude of this potential bias using a spatially unbiased tree-ring network collected by the USFS Forest Inventory and Analysis (FIA) program. We show that U.S. Southwest ITRDB samples overestimate regional forest climate sensitivity by 41-59%, because ITRDB trees were sampled at warmer and drier locations, both at the macro- and micro-site scale, and are systematically older compared to the FIA collection. Although there are uncertainties associated with our statistical approach, projection based on representative FIA samples suggests 29% less of a climate change-induced growth decrease compared to projection based on climate-sensitive ITRDB samples.

Early and specific gene expression triggered by rice resistance gene Pi33 in response to infection by ACE1 avirulent blast fungus.

* Our view of genes involved in rice disease resistance is far from complete. Here we used a gene-for-gene relationship corresponding to the interaction between atypical avirulence gene ACE1 from Magnaporthe grisea and rice resistance gene Pi33 to better characterize early rice defence responses induced during such interaction. * Rice genes differentially expressed during early stages of Pi33/ACE1 interaction were identified using DNA chip-based differential hybridization and QRT-PCR survey of the expression of known and putative regulators of disease resistance. * One hundred genes were identified as induced or repressed during rice defence response, 80% of which are novel, including resistance gene analogues. Pi33/ACE1 interaction also triggered the up-regulation of classical PR defence genes and a massive down-regulation of chlorophyll a/b binding genes. Most of these differentially expressed genes were induced or repressed earlier in Pi33/ACE1 interaction than in the gene-for-gene interaction involving Nipponbare resistant cultivar. * Besides demonstrating that an ACE1/Pi33 interaction induced classical and specific expression patterns, this work provides a list of new genes likely to be involved in rice disease resistance.

Whole-genome comparison between Photorhabdus strains to identify genomic regions involved in the specificity of nematode interaction.

The bacterium Photorhabdus establishes a highly specific association with Heterorhabditis, its nematode host. Photorhabdus strains associated with Heterorhabditis bacteriophora or Heterorhabditis megidis were compared using a Photorhabdus DNA microarray. We describe 31 regions belonging to the Photorhabdus flexible gene pool. Distribution analysis of regions among the Photorhabdus genus identified loci possibly involved in nematode specificity.

Cloning and functional expression in yeast of a cDNA coding for an obtusifoliol 14alpha-demethylase (CYP51) in wheat.

Screening of a wheat cDNA library with an heterologous CYP81B1 probe from Helianthus tuberosus led to the isolation of a partial cDNA coding a protein with all the characteristics of a typical P450 with high homology (32-39% identity) to the fungal and mammalian CYP51s. Extensive screening of several wheat cDNA libraries isolated a longer cDNA (W516) coding a peptide of 453 amino acids. Alignment of W516 with other P450 sequences revealed that it was missing a segment corresponding to the N-terminal membrane anchor of the protein. The corresponding segment from the yeast lanosterol 14alpha-demethylase was linked to the partial wheat cDNA and the chimera expressed in Saccharomyces cerevisiae. Compared to microsomes from control yeasts, membranes of yeast expressing the chimera catalysed 14alpha-demethylation of obtusifoliol with an increased efficiency relative to lanosterol demethylase activity. W516 is thus a plant member of the most ancient and conserved P450 family, CYP51.

Analysis of kafirin promoter activity in transgenic tobacco seeds.

Sequences corresponding to 855 bp of 5' promoter region and the transit peptide from lambdaGK.1,a genomic clone encoding a 22 kDa alpha-kafirin seed protein from sorghum, were translationally fused to a cloned beta-glucuronidase (GUS) coding sequence from uidA and transferred to tobacco via Agrobacterium tumefaciens-mediated transformation. No GUS expression was detectable at any stage of growth in stems or leaves of these plants. However, GUS expression was detected in both embryo and endosperm tissues of resulting tobacco seeds 10-15 days after flowering. Dissected tissues indicate endosperm expression was localized within the bulk endosperm and not within the parenchyma cell layer underlying the integument. These studies also demonstrate that within dissected tobacco embryos, expression from the kafirin promoter was restricted to the mesocotyl region.

Characterization of a rice gene family encoding root-specific proteins.

Two cDNA clones (RCc2 and RCc3) corresponding to mRNAs highly expressed only in root tissues of rice (Oryza sativa L.) seedlings were characterized. Respectively, they encode polypeptides of 146 (14.5 kDa) and 133 amino acids (13.4 kDa) that share high (> 70%) sequence similarity with a polypeptide encoded by a cDNA (ZRP3) encoding an mRNA preferentially expressed in young maize roots. Genomic DNA blot analysis revealed that they are members of a small gene family and RCg2, the gene corresponding to RCc2, was isolated. A 1656 bp 5'-upstream sequence of RCg2 was translationally fused to a beta-glucuronidase (GUS) reporter gene and stable introduction of the chimeric construct into rice was confirmed by PCR and genomic DNA blot analyses. Histochemical analysis of transgenic rice plants containing the full-length chimeric gene showed high levels of GUS activity in mature cells and the elongation and maturation zones of primary and secondary roots, and in the root caps, but no GUS activity was detected in root meristematic regions. Surprisingly, high GUS activity was also detected in leaves of the same plants. This raises the possibility that the RCg2 5'-upstream element may not be sufficient for the proper spatial control of root specificity in transgenic rice.

The major biotinyl protein from Pisum sativum seeds covalently binds biotin at a novel site.

Seeds of Pisum sativum contain a biotinyl polypeptide called SBP65 that behaves as a putative sink for the free vitamin, representing more than 90% of the total protein-bound biotin in mature seeds. A cDNA encoding SBP65 was cloned and sequenced. The deduced primary structure of the protein was confirmed by protein sequencing. Peptide sequencing also indicated binding of the biotin to lysine 103. The biotinylation domain of SBP65 differs markedly from that of presently known biotin enzymes. Molecular analysis of the protein sequence reveals an extremely hydrophilic protein containing several repeated motifs. These properties, as well as the temporal and spatial patterns of expression of this protein, suggest that SBP65 belongs to the LEA (late embryogenesis-abundant) group of proteins.

Cyclophilins are encoded by a small gene family in rice.

cDNA clones were isolated and sequenced that encode two related but distinct rice cyclophilins, Cyp1 and Cyp2. The predicted amino acid sequences of each are 72% identical to human T-cell cyclophilin. Genomic DNA gel blot analysis suggests cyclophilins in rice are encoded by a small, 6-10-member gene family. Both Cyp1 and Cyp2 have seven extra amino acid residues in the N-terminal portion of the proteins that are not found in human or other non-plant cyclophilins, suggesting that this is a characteristic of plant cyclophilins. Cyp2 was expressed as 1000 nt transcripts in leaf and root tissues. Cyp1 was expressed as 800 and 900 nt transcripts. Whereas the 900 nt transcript was present in both root and leaf mRNA, the 800 nt transcript was only detectable in root mRNA. A genomic clone of Cyp2 was isolated, sequenced and shown to lack introns. A single transcriptional start site was identified 27 residues downstream of a putative TATA box. The 5' end of the transcript was shown to contain a region rich in adenyl residues (27 of 35). This region would not be conducive to secondary structure formation, which raises the possibility that Cyp2 might be preferentially translated during stress conditions.

Branched-chain-amino-acid biosynthesis in plants: molecular cloning and characterization of the gene encoding acetohydroxy acid isomeroreductase (ketol-acid reductoisomerase) from Arabidopsis thaliana (thale cress).

Towards the goal of gaining a better understanding of the molecular mechanisms controlling branched-chain-amino-acid biosynthesis in plants, we have isolated, sequenced and characterized a gene encoding acetohydroxy acid isomero-reductase (ketol-acid reductoisomerase) from Arabidopsis thaliana (thale cress). Comparison between the acetohydroxy acid isomeroreductase cDNA and the genomic sequence has allowed us to determine the exon structure of the coding region. The isolated acetohydroxy acid isomeroreductase gene is distributed over approx. 4.5 kbp and contains nine introns (79-347 bp). The transcriptional start site was found to be 52 bp upstream of the translational initiation site. Southern-blot analysis of A. thaliana genomic DNA shows that the acetohydroxy acid isomeroreductase is encoded by a single-copy gene.

Human cytomegalovirus RNAs immunoprecipitated by multiple systemic lupus erythematosus antisera.

The association of human cytomegalovirus (HCMV) RNAs with ribonucleoprotein particles that react with antibodies from patients with systemic lupus erythematosus was tested by immunoprecipitation with multiple patients' sera. A major late 2.8 kb RNA and several minor RNAs encoded by the HCMV long repeat region were immunoprecipitated from HCMV-infected cells by La, Ro and, much less abundantly, Sm autoimmune antisera. The exact location of these RNAs was determined by high resolution R-loop mapping and found to be between 0.8093 and 0.8189 map units. The 2.8 kb RNA is polyadenylated and associated with polysomes but does not appear to be spliced. Immunoprecipitation was not seen using normal or other autoimmune antisera. In addition, immunoprecipitation was specific to these RNAs in that other abundant HCMV RNAs were not immunoprecipitated. It was also found that the addition of increasing amounts of purified La antigen to infected cell lysates inhibited immunoprecipitation of the 2.8 kb RNA by La antiserum. The data suggest that specific HCMV RNAs may interact with cellular ribonucleoproteins known to be involved in post-transcriptional regulation of gene expression.

Characterization of the kafirin gene family from sorghum reveals extensive homology with zein from maize.

Electrophoretic analysis of translation products of polyadenylated RNA isolated from mid-maturation sorghum seed in the presence of [(35)S]met, [(3)H]leu, or [(3)H]val revealed two major proteins of kDa and 21 kDa. These products were not detected when [(3)H]lys was supplied as the radioactive substrate. Under similar electrophoretic conditions, kafirin (a major seed storage prolamin of sorghum), migrated as two bands of 22 kDa and 19 kDa. Sequence analysis of two cDNA clones (pSK8 and pSKR2) from sorghum seed mRNA revealed them to be highly homologous with each other and to the 22 kDa zeins from maize, suggesting that they represented kafirin cDNAs. Compared with pSKR2, pSK8 had an insertion of 24 nucleotides and a deletion of 24 nucleotides, so that the coding regions were nearly identical in length. The deduced amino acid sequence for these cDNA clones reveals that kafirin, like zein, is rich in glutamine and nonpolar amino acids, but contains no lysine. Both kafirin and zein have a 21 amino acid signal peptide exhibiting 80% homology and eight copies of a repetitive amino acid block in the C-terminal domain with the consensus: infI (supP) LL finP (supA) LN infQ (supP) LALANPAAYLQQQQ.The kafirin cDNAs were used as probes to screen a sorghum genomic library; one genomic clone (λGK.1) was sequenced and found to be very similar (97.8%) to the pSK8 cDNA clone. Clone λGK.1 contains features typical for a functional gene in that the intronless open reading frame encoding 268 amino acids is flanked at the 5' end by sequences corresponding to the CAAT and TATA promoter boxes (positioned at about -60 and -30 bp, respectively, from the transcriptional initiation site), and at the 3' end by a consensus polyadenylation signal. In common with zein genomic clones, kafirin clones contain a 15 basepair consensus sequence centered at postion -320 relative to the transcriptional initiation site. Under similar hybridization conditions, genomic reconstruction analysis using an oligonucleotide probe indicated the presence of less than 20 copies of kafirin per haploid sorghum genome compared with approximatley 140 copies of zein per haploid maize genome.