Hemocyanin gene family evolution in spiders (Araneae), with implications for phylogenetic relationships and divergence times in the infraorder Mygalomorphae

Hemocyanins are multimeric copper-containing hemolymph proteins involved in oxygen binding and transport in all major arthropod lineages. Most arachnids have seven primary subunits (encoded by paralogous genes a–g), which combine to form a 24-mer (4 × 6) quaternary structure. Within some spider lineages, however, hemocyanin evolution has been a dynamic process with extensive paralog duplication and loss. We have obtained hemocyanin gene sequences from numerous representatives of the spider infraorders Mygalomorphae and Araneomorphae in order to infer the evolution of the hemocyanin gene family and estimate spider relationships using these conserved loci. Our hemocyanin gene tree is largely consistent with the previous hypotheses of paralog relationships based on immunological studies, but reveals some discrepancies in which paralog types have been lost or duplicated in specific spider lineages. Analyses of concatenated hemocyanin sequences resolved deep nodes in the spider phylogeny and recovered a number of clades that are supported by other molecular studies, particularly for mygalomorph taxa. The concatenated data set is also used to estimate dates of higher-level spider divergences and suggests that the diversification of extant mygalomorphs preceded that of extant araneomorphs. Spiders are diverse in behavior and respiratory morphology, and our results are beneficial for comparative analyses of spider respiration. Lastly, the conserved hemocyanin sequences allow for the inference of spider relationships and ancient divergence dates.     

Analysis of genetic variability and relationships among Mentha L. using the limonene synthase gene, LS

The genus Mentha comprises a group of aromatic plants with worldwide distribution. Because of frequent interspecific hybridization, the genetic relationships within the genus are not clearly understood. Limonene synthase, which catalyses the first committed step in the essential oil monoterpene biosynthetic pathway, is considered to be a possible rate limiting enzyme. With the homology-based cloning method, primers were designed according to cDNA sequence to amplify full-length DNA sequences in 13 Mentha samples from five species, using Perilla as an outgroup. Analyses of gene structure, length variation, GC-content, Ts/Tv ratio and evolutionary diversity were carried out. Consensus phylogenetic trees were obtained using maximum likelihood, neighbor-joining, and maximum parsimony, respectively, based on the full-length genomic DNA sequences, complete ORF coding sequences and predicted amino acid sequences. The results presented here based on the sequence of MhLS provide the first credibly supported genetic relationships for Mentha, which enables a basis for further mint taxonomy, cultivation and breeding.     

Phylogenetics of Escallonia (Escalloniaceae) based on plastid DNA sequence data

Escallonia (Escalloniaceae) is a New World genus of c. 39 species distributed mainly in the South American highlands. Plastid DNA sequence data from the intergenic spacers trnS‐trnG and 3′ trnV‐ndhC and the ndhF gene for 32 species were used to examine the relationships among species and related genera and to analyse the relationship between phylogeny and the geographical distribution of the species. Maximum parsimony and Bayesian inference were employed to analyse the data. The sister relationship of Escallonia to Forgesia and Valdivia was corroborated. We recovered five strongly supported clades that are geographically structured, suggesting that the evolutionary history of the genus may be linked to historical processes, including the uplift of mountainous systems in South America. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 442–451.     

Responses of epidermal cell turgor pressure and photosynthetic activity of leaves of the atmospheric epiphyte Tillandsia usneoides (Bromeliaceae) after exposure to high humidity

It has been well-established that many epiphytic bromeliads of the atmospheric-type morphology, i.e., with leaf surfaces completely covered by large, overlapping, multicellular trichomes, are capable of absorbing water vapor from the atmosphere when air humidity increases. It is much less clear, however, whether this absorption of water vapor can hydrate the living cells of the leaves and, as a consequence, enhance physiological processes in such cells. The goal of this research was to determine if the absorption of atmospheric water vapor by the atmospheric epiphyte Tillandsia usneoides results in an increase in turgor pressure in leaf epidermal cells that subtend the large trichomes, and, by using chlorophyll fluorescence techniques, to determine if the absorption of atmospheric water vapor by leaves of this epiphyte results in increased photosynthetic activity. Results of measurements on living cells of attached leaves of this epiphytic bromeliad, using a pressure probe and of whole-shoot fluorescence imaging analyses clearly illustrated that the turgor pressure of leaf epidermal cells did not increase, and the photosynthetic activity of leaves did not increase, following exposure of the leaves to high humidity air. These results experimentally demonstrate, for the first time, that the absorption of water vapor following increases in atmospheric humidity in atmospheric epiphytic bromeliads is mostly likely a physical phenomenon resulting from hydration of non-living leaf structures, e.g., trichomes, and has no physiological significance for the plant's living tissues.     

Application of Artificial Bee Colony Algorithm to Maximum Likelihood DOA Estimation

Maximum Likelihood (ML) method has an excellent performance for Direction-Of-Arrival (DOA) estimation, but a multidimensional nonlinear solution search is required which complicates the computation and prevents the method from practical use. To reduce the high computational burden of ML method and make it more suitable to engineering applications, we apply the Artificial Bee Colony (ABC) algorithm to maximize the likelihood function for DOA estimation. As a recently proposed bio-inspired computing algorithm, ABC algorithm is originally used to optimize multivariable functions by imitating the behavior of bee colony finding excellent nectar sources in the nature environment. It offers an excellent alternative to the conventional methods in ML-DOA estimation. The performance of ABC-based ML and other popular meta-heuristic-based ML methods for DOA estimation are compared for various scenarios of convergence, Signal-to-Noise Ratio (SNR), and number of iterations. The computation loads of ABC-based ML and the conventional ML methods for DOA estimation are also investigated. Simulation results demonstrate that the proposed ABC based method is more efficient in computation and statistical performance than other ML-based DOA estimation methods.     

A simulation module in the computer program colony for sibship and parentage analysis

A simulation module is built into the software package colony to simulate marker genotype data of individuals with a predefined parentage and sibship structure. The simulated data can then be used to compare the accuracy, robustness and computational efficiency of different methods for sibship and parentage reconstruction, to examine the impact of different parameter options in a software on its accuracy and computational efficiency and to assess the information sufficiency of a given set of markers for a sibship and parentage analysis. This computer note describes the method used for simulating genotype data with a pedigree and its possible applications. The method can quickly generate genotype data for a one‐ or two‐generation pedigree of virtually any complexity with up to 30k offspring, at up to 30k codominant or dominant loci with an arbitrary degree of linkage and a user‐defined mistyping rate. The data can be fed directly into the colony program for analysis by three sibship and parentage reconstruction methods and can also be imported into other programs such as Excel and R. With slight modification, the data can be analysed by other relationship analysis software.     

Paleodistribution modeling suggests glacial refugia in Scandinavia and out‐of‐Tibet range expansion of the Arctic fox

Quaternary glacial cycles have shaped the geographic distributions and evolution of numerous species in the Arctic. Ancient DNA suggests that the Arctic fox went extinct in Europe at the end of the Pleistocene and that Scandinavia was subsequently recolonized from Siberia, indicating inability to track its habitat through space as climate changed. Using ecological niche modeling, we found that climatically suitable conditions for Arctic fox were found in Scandinavia both during the last glacial maximum (LGM) and the mid‐Holocene. Our results are supported by fossil occurrences from the last glacial. Furthermore, the model projection for the LGM, validated with fossil records, suggested an approximate distance of 2000 km between suitable Arctic conditions and the Tibetan Plateau well within the dispersal distance of the species, supporting the recently proposed hypothesis of range expansion from an origin on the Tibetan Plateau to the rest of Eurasia. The fact that the Arctic fox disappeared from Scandinavia despite suitable conditions suggests that extant populations may be more sensitive to climate change than previously thought.     

Linking leaf veins to growth and mortality rates: an example from a subtropical tree community

A fundamental goal in ecology is to link variation in species function to performance, but functional trait–performance investigations have had mixed success. This indicates that less commonly measured functional traits may more clearly elucidate trait–performance relationships. Despite the potential importance of leaf vein traits, which are expected to be related to resource delivery rates and photosynthetic capacity, there are few studies, which examine associations between these traits and demographic performance in communities. Here, we examined the associations between species traits including leaf venation traits and demographic rates (Relative Growth Rate, RGR and mortality) as well as the spatial distributions of traits along soil environment for 54 co‐occurring species in a subtropical forest. Size‐related changes in demographic rates were estimated using a hierarchical Bayesian approach. Next, Kendall's rank correlations were quantified between traits and estimated demographic rates at a given size and between traits and species‐average soil environment. Species with denser venation, smaller areoles, less succulent, or thinner leaves showed higher RGR for a wide range of size classes. Species with leaves of denser veins, larger area, cheaper construction costs or thinner, or low‐density wood were associated with high mortality rates only in small size classes. Lastly, contrary to our expectations, acquisitive traits were not related to resource‐rich edaphic conditions. This study shows that leaf vein traits are weakly, but significantly related to tree demographic performance together with other species traits. Because leaf traits associated with an acquisitive strategy such as denser venation, less succulence, and thinner leaves showed higher growth rate, but similar leaf traits were not associated with mortality, different pathways may shape species growth and survival. This study suggests that we are still not measuring some of key traits related to resource‐use strategies, which dictate the demography and distributions of species.     

Tree diversity,tree height and environmental harshness in eastern and western North America

Does variation in environmental harshness explain local and regional species diversity gradients? We hypothesise that for a given life form like trees, greater harshness leads to a smaller range of traits that are viable and thereby also to lower species diversity. On the basis of a strong dependence of maximum tree height on site productivity and other measures of site quality, we propose maximum tree height as an inverse measure of environmental harshness for trees. Our results show that tree species richness is strongly positively correlated with maximum tree height across multiple spatial scales in forests of both eastern and western North America. Maximum tree height co‐varied with species richness along gradients from benign to harsh environmental conditions, which supports the hypothesis that harshness may be a general mechanism limiting local diversity and explaining diversity gradients within a biogeographic region.     

Availability and toxicity of cadmium to forage grasses grown in contaminated soil

It is important to know the mechanisms for forage development, especially those related to the tolerance of potentially toxic elements, when considering their use in phytoremediation in heavy metal contaminated areas. In this study, we evaluated plant growth, concentration, and the availability of cadmium (Cd) for forage grasses (Panicum maximum Jacq. cv. Aruana and cv. Tanzânia; Brachiaria decumbens cv. Basilisk; Brachiaria brizantha cv. Xaraés and cv. Marandu) cultivated in Cd contaminated soils. The experiments were performed under greenhouse conditions over a 90-day evaluation period, and the Cd rates were 2, 4, and 12 mg/kg of soil. The relative growth rate of the forage grasses decreased as Cd rates increased, and the following descending order of susceptibility was observed: Marandu > Xaraés > Aruana > Tanzânia > Basilisk, with regard to phytotoxicity in these plants. The forage Cd concentration increased in line with increases in the Cd rates. Cd contents extracted by Mehlich-1 and by diethylenetriaminepentaacetic acid presented high positive correlation with forage relative growth. The forage plants did not block Cd entry into the food chain because they were not capable of limiting Cd absorption.