Acclimation of photosynthetic temperature optima of temperate and boreal tree species in response to experimental forest warming

Rising temperatures caused by climate change could negatively alter plant ecosystems if temperatures exceed optimal temperatures for carbon gain. Such changes may threaten temperature‐sensitive species, causing local extinctions and range migrations. This study examined the optimal temperature of net photosynthesis (T_opt) of two boreal and four temperate deciduous tree species grown in the field in northern Minnesota, United States under two contrasting temperature regimes. We hypothesized that T_opt would be higher in temperate than co‐occurring boreal species, with temperate species exhibiting greater plasticity in T_opt, resulting in better acclimation to elevated temperatures. The chamberless experiment, located at two sites in both open and understory conditions, continuously warmed plants and soils during three growing seasons. Results show a modest, but significant shift in T_opt of 1.1 ± 0.21 °C on average for plants subjected to a mean 2.9 ± 0.01 °C warming during midday hours in summer, and shifts with warming were unrelated to species native ranges. The 1.1 °C shift in T_opt with 2.9 °C warming might be interpreted as suggesting limited capacity to shift temperature response functions to better match changes in temperature. However, T_opt of warmed plants was as well‐matched with prior midday temperatures as T_opt of plants in the ambient treatment, and T_opt in both treatments was at a level where realized photosynthesis was within 90–95% of maximum. These results suggest that seedlings of all species were close to optimizing photosynthetic temperature responses, and equally so in both temperature treatments. Our study suggests that temperate and boreal species have considerable capacity to match their photosynthetic temperature response functions to prevailing growing season temperatures that occur today and to those that will likely occur in the coming decades under climate change.     

Comparative genomics of the social amoebae <Emphasis Type="Italic">Dictyostelium discoideum</Emphasis> and <Emphasis Type="Italic">Dictyostelium purpureum</Emphasis>

Background

The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum.

Results

We have produced a draft genome sequence of another group dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. The assembly (8.41 × coverage) comprises 799 scaffolds totaling 33.0 Mb, comparable to the D. discoideum genome size. Sequence comparisons suggest that these two dictyostelids shared a common ancestor approximately 400 million years ago. In spite of this divergence, most orthologs reside in small clusters of conserved synteny. Comparative analyses revealed a core set of orthologous genes that illuminate dictyostelid physiology, as well as differences in gene family content. Interesting patterns of gene conservation and divergence are also evident, suggesting function differences; some protein families, such as the histidine kinases, have undergone little functional change, whereas others, such as the polyketide synthases, have undergone extensive diversification. The abundant amino acid homopolymers encoded in both genomes are generally not found in homologous positions within proteins, so they are unlikely to derive from ancestral DNA triplet repeats. Genes involved in the social stage evolved more rapidly than others, consistent with either relaxed selection or accelerated evolution due to social conflict.

Conclusions

The findings from this new genome sequence and comparative analysis shed light on the biology and evolution of the Dictyostelia.

     

Motivations,success, and cost of coral reef restoration

Coral reef restoration is an increasingly important part of tropical marine conservation. Information about what motivates coral reef restoration as well as its success and cost is not well understood but is needed to inform restoration decisions. We systematically review and synthesize data from mostly scientific studies published in peer‐reviewed and gray literature on the motivations for coral reef restoration, the variables measured, outcomes reported, the cost per hectare of the restoration project, the survival of restored corals, the duration of the project, and its overall spatial extent depending on the restoration technique employed. The main motivation to restore coral reefs for the projects assessed was to further our ecological knowledge and improve restoration techniques, with coral growth, productivity, and survival being the main variables measured. The median project cost was 400,000 US$/ha (2010 US$), ranging from 6,000 US$/ha for the nursery phase of coral gardening to 4,000,000 US$/ha for substrate addition to build an artificial reef. Restoration projects were mostly of short duration (1–2 years) and over small spatial extents (0.01 ha or 108 m²). Median reported survival of restored corals was 60.9%. Future research to survey practitioners who do not publish their discoveries would complement this work. Our findings and database provide critical data to inform future research in coral reef restoration.     

Concern about threatened species and ecosystem disservices underpin public willingness to pay for ecological restoration

Public preferences for ecological restoration can be revealed through environmental valuation studies that aim to measure willingness to pay. However, respondents' environmental views will often influence the conclusions drawn from such studies. We conducted a national survey of perceptions of the benefits and perverse outcomes arising from ecological restoration using a dichotomous choice payment card. Using interval regression to estimate willingness to pay, we find that there are respondents who will perceive mostly biodiversity benefits from restoration, with a particular interest in threatened species recovery. We find that this eco‐centric view of the benefits of restoration also increases the dollar amount that respondents are willing to pay to support restoration activities. A proportion of respondents also perceive restoration as having negative impacts, with concerns orientated towards increased fire, decreased farmland productivity, and groundwater availability. Perceptions of the potential effects of restoration on land productivity had a significant negative influence on the amount of money respondents were willing to pay. These findings are useful for targeting outreach in order to garner public support for ecological restoration.     

Classification based upon gene expression data: bias and precision of error rates

MOTIVATION: Gene expression data offer a large number of potentially useful predictors for the classification of tissue samples into classes, such as diseased and non-diseased. The predictive error rate of classifiers can be estimated using methods such as cross-validation. We have investigated issues of interpretation and potential bias in the reporting of error rate estimates. The issues considered here are optimization and selection biases, sampling effects, measures of misclassification rate, baseline error rates, two-level external cross-validation and a novel proposal for detection of bias using the permutation mean. RESULTS: Reporting an optimal estimated error rate incurs an optimization bias. Downward bias of 3-5% was found in an existing study of classification based on gene expression data and may be endemic in similar studies. Using a simulated non-informative dataset and two example datasets from existing studies, we show how bias can be detected through the use of label permutations and avoided using two-level external cross-validation. Some studies avoid optimization bias by using single-level cross-validation and a test set, but error rates can be more accurately estimated via two-level cross-validation. In addition to estimating the simple overall error rate, we recommend reporting class error rates plus where possible the conditional risk incorporating prior class probabilities and a misclassification cost matrix. We also describe baseline error rates derived from three trivial classifiers which ignore the predictors. AVAILABILITY: R code which implements two-level external cross-validation with the PAMR package, experiment code, dataset details and additional figures are freely available for non-commercial use from http://www.maths.qut.edu.au/profiles/wood/permr.jsp     

A single P-loop glutamate point mutation to either lysine or arginine switches the cation-anion selectivity of the CNGA2 channel

Cyclic nucleotide-gated (CNG) channels play a critical role in olfactory and visual transduction. Site-directed mutagenesis and inside-out patch-clamp recordings were used to investigate ion permeation and selectivity in two mutant homomeric rat olfactory CNGA2 channels expressed in HEK293 cells. A single point mutation of the negatively charged pore loop (P-loop) glutamate (E342) to either a positively charged lysine or arginine resulted in functional channels, which consistently responded to cGMP, although the currents were generally extremely small. The concentration-response curve of the lysine mutant channel was very similar to that of wild-type (WT) channels, suggesting no major structural alteration to the mutant channels. Reversal potential measurements, during cytoplasmic NaCl dilutions, showed that the lysine and the arginine mutations switched the selectivity of the channel from cations (P(Cl)/P(Na) = 0.07 [WT]) to anions (P(Cl)/P(Na) = 14 [Lys] or 10 [Arg]). Relative anion permeability sequences for the two mutant channels, measured with bi-ionic substitutions, were NO(3)(-) > I(-) > Br(-) > Cl(-) > F(-) > acetate(-), the same as those obtained for anion-selective GABA and glycine channels. The mutant channels also seem to have an extremely small single-channel conductance, measured using noise analysis of about 1-2 pS, compared to a WT value of about 29 pS. The results showed that it is predominantly the charge of the E342 residue in the P-loop, rather than the pore helix dipoles, which controls the cation-anion selectivity of this channel. However, the outward rectification displayed by both mutant channels in symmetrical NaCl solutions suggests that the negative ends of the pore helix dipoles may play a role in reducing the outward movement of Cl(-) ions through these anion-selective channels. These results have potential implications for the determinants of anion-cation selectivity in the large family of P-loop-containing channels.