Incompletely resolved phylogenetic trees inflate estimates of phylogenetic conservatism.

The tendency for more closely related species to share similar traits and ecological strategies can be explained by their longer shared evolutionary histories and represents phylogenetic conservatism. How strongly species traits co-vary with phylogeny can significantly impact how we analyze cross-species data and can influence our interpretation of assembly rules in the rapidly expanding field of community phylogenetics. Phylogenetic conservatism is typically quantified by analyzing the distribution of species values on the phylogenetic tree that connects them. Many phylogenetic approaches, however, assume a completely sampled phylogeny: while we have good estimates of deeper phylogenetic relationships for many species-rich groups, such as birds and flowering plants, we often lack information on more recent interspecific relationships (i.e., within a genus). A common solution has been to represent these relationships as polytomies on trees using taxonomy as a guide. Here we show that such trees can dramatically inflate estimates of phylogenetic conservatism quantified using S. P. Blomberg et al.'s K statistic. Using simulations, we show that even randomly generated traits can appear to be phylogenetically conserved on poorly resolved trees. We provide a simple rarefaction-based solution that can reliably retrieve unbiased estimates of K, and we illustrate our method using data on first flowering times from Thoreau's woods (Concord, Massachusetts, USA).

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees.

Phylogenomic databases provide orthology predictions for species with fully sequenced genomes. Although the goal seems well-defined, the content of these databases differs greatly. Seven ortholog databases (Ensembl Compara, eggNOG, HOGENOM, InParanoid, OMA, OrthoDB, Panther) were compared on the basis of reference trees. For three well-conserved protein families, we observed a generally high specificity of orthology assignments for these databases. We show that differences in the completeness of predicted gene relationships and in the phylogenetic information are, for the great majority, not due to the methods used, but to differences in the underlying database concepts. According to our metrics, none of the databases provides a fully correct and comprehensive protein classification. Our results provide a framework for meaningful and systematic comparisons of phylogenomic databases. In the future, a sustainable set of 'Gold standard' phylogenetic trees could provide a robust method for phylogenomic databases to assess their current quality status, measure changes following new database releases and diagnose improvements subsequent to an upgrade of the analysis procedure.

Woodland Improvement and Crop Trees in Iowa, 2005

Vigorous and Healthy woodlands in Iowa have the unique distinction of being able to provide a wealth of benefits for the landowner and residents of the state. Benefits from a healthy forest include timber and wood resources, watershed protection, fragile site protection, wildlife and bird habitat, aesthetics and beauty, and recreational opportunities.

Development of a control alternative for the citrus fruit borer, Ecdytolopha aurantiana (Lepidoptera, Tortricidae): from basic research to the grower

All research steps, developed from 1995 to 2000, to synthesize the sex pheromone of Ecdytolopha aurantiana (Lima, 1927) are described, in order to monitoring this pest that causes losses in the order of 50 million dollars per year to citriculture in the State of São Paulo. The basic researches conducted are described, including the development of an artificial diet for the insect, the study of its temperature and humidity requirements, behavioral studies, and synthesis of the male-attracting substance up to the formulation and distribution of the pheromone to the grower, by means of its commercialization. It is a case of success, at a cost of 50 thousand dollars, involving inter- and multidisciplinary researches, which can be adopted to other insect pests in the country.

Seeing the Wood through the Trees: The Current State of Higher Systematics in the Strepsirhini.

Strepsirhines comprise 10 living or recently extinct families, ≥50% of extant primate families. Their phylogenetic relationships have been intensively studied, but common topologies have only recently emerged; e.g. all recent reconstructions link the Lepilemuridae and Cheirogaleidae. The position of the indriids, however, remains uncertain, and molecular studies have placed them as the sister to every clade except Daubentonia, the preferred sister group of morphologists. The node subtending Afro-Asian lorisids has been similarly elusive. We probed these phylogenetic inconsistencies using a test data set including 20 strepsirhine taxa and 2 outgroups represented by 3,543 mtDNA base pairs, and 43 selected morphological characters, subjecting the data to maximum parsimony, maximum likelihood and Bayesian inference analyses, and reconstructing topology and node ages jointly from the molecular data using relaxed molecular clock analyses. Our permutations yielded compatible but not identical evolutionary histories, and currently popular techniques seem unable to deal adequately with morphological data. We investigated the influence of morphological characters on tree topologies, and examined the effect of taxon sampling in two experiments: (1) we removed the molecular data only for 5 endangered Malagasy taxa to simulate 'extinction leaving a fossil record'; (2) we removed both the sequence and morphological data for these taxa. Topologies were affected more by the inclusion of morphological data only, indicating that palaeontological studies that involve inserting a partial morphological data set into a combined data matrix of extant species should be interpreted with caution. The gap of approximately 10 million years between the daubentoniid divergence and those of the other Malagasy families deserves more study. The apparently contemporaneous divergence of African and non-daubentoniid Malagasy families 40-30 million years ago may be related to regional plume-induced uplift followed by a global period of cooling and drying. © 2013 S. Karger AG, Basel.

Consumer Advisory Bulletin, Tree-Trim Tips: Consumer Tips for Iowans with Storm-Damaged Trees, January 2008

The Attorney General’s Consumer Protection Division receives hundreds of calls and consumer complaints every year. Follow these tips to avoid unexpected expense and disappointments. This record is about: International Lottery Schemes: You're the Loser!

Effect of Citrus floral extracts on the foraging behavior of the stingless bee Scaptotrigona pectoralis (Dalla Torre)

Effect of Citrus floral extracts on the foraging behavior of the stingless bee Scaptotrigona pectoralis (Dalla Torre). Stingless bees have an important role as pollinators of many wild and cultivated plant species in tropical regions. Little is known, however, about the interaction between floral fragrances and the foraging behavior of meliponine species. Thus we investigated the chemical composition of the extracts of citric (lemon and orange) flowers and their effects on the foraging behavior of the stingless bee Scaptotrigona pectoralis. We found that each type of flower has its own specific blend of major compounds: limonene (62.9%) for lemon flowers, and farnesol (26.5%), (E)-nerolidol (20.8%), and linalool (12.7%) for orange flowers. In the foraging experiments the S. pectoralis workers were able to use the flower extracts to orient to the food source, overlooking plates baited with hexane only. However, orange flower extracts were seemingly more attractive to these worker bees, maybe because of the particular blend present in it. Our results reveal that these fragrances are very attractive to S. pectoralis, so we can infer that within citric orchards they could be important visitors in the study area; however habitat destruction, overuse of pesticides and the competitive override by managed honeybees might have put at risk their populations and thus the ecological services they provide to us.

Temporal variation in the composition of ant assemblages (Hymenoptera, Formicidae) on trees in the Pantanal floodplain, Mato Grosso do Sul, Brazil

Temporal variation in the composition of ant assemblages (Hymenoptera, Formicidae) on trees in the Pantanal floodplain, Mato Grosso do Sul, Brazil. In this paper we investigate how seasonal flooding influences the composition of assemblages of ants foraging on trees in the Pantanal of Mato Grosso do Sul. During the flood in the Pantanal, a large area is covered by floods that are the main forces that regulate the pattern of diversity in these areas. However, the effects of such natural disturbances in the ant communities are poorly known. In this sense, the objective of this study was to evaluate the effect of temporal variation in assemblages of ants foraging on trees in the Pantanal of Miranda. Samples were collected during a year in two adjacent areas, one who suffered flooding during the wet period and another that did not suffer flooding throughout the year. In 10 sites for each evaluated habitat, five pitfall traps were installed at random in trees 25 m apart from each other. In the habitat with flooding, the highest richness was observed during the flooding period, while there was no significant change in richness in the area that does not suffer flooding. The diversity of species between the two evaluated habitats varied significantly during the two seasons. Most ants sampled belong to species that forage and nest in soil. This suggests that during the flood in flooded habitats, ants that did not migrate to higher areas without flooding adopt the strategy to search for resources in the tree canopy.

Senescent stem-galls in trees of Eremanthus erythropappus as a resource for arboreal ants

Senescent stem-galls in trees of Eremanthus erythropappus as a resource for arboreal ants. Members of the dipteran families Tephritidae and Cecidomyiidae are inducers of stem-galls in Eremanthus erythropappus (DC.) MacLeish (Asteraceae), a tree common in the state of Minas Gerais, Brazil. When senescent, these galls become available to other organisms, such as ants. The present study describes a community of ants having benefitted from this process of ecosystem-engineering. The colonies in question inhabit the senescent stem-galls of trees of E. erythropappus and were examined in view of answering the following questions: i) whether the presence of stem-galls had any bearing on the richness, composition, or size of the ant colonies therein; and ii) whether the ants displayed any preferences regarding the shape and/or size of the galls. The study was conducted in populations of E. erythropappus trees near the city of Ouro Preto, MG. A total of 227 galls were collected, 14% of which were occupied by ants, belonging to eight different species. Half of the species occupied galls of both morphotypes (fusiform and globular), although we observed a marked preference for larger, globular shapes. Overall, our results showed the galls to be an effective and abundant resource, helping to maintain the diversity of the ants in the canopy. We also observed the occurrence of outstations and polydomic nests, although an in-depth examination of the influence of galls on this type of structuring has not been investigated.

Fósforo adicionado e fungos micorrízicos arbusculares no crescimento e nutrição mineral de limoeiro-cravo [Citrus limonia (L.) OSBECK]

Visando estudar a influência de fósforo adicionado e fungos micorrízicos arbusculares (FMAs) no crescimento e nutrição mineral de limoeiro-cravo, instalou-se um experimento em casa de vegetação, com delineamento inteiramente casualizado, em esquema fatorial 6 x 3, sendo os fatores: (a) seis doses de P (0, 50, 100, 150, 200 e 250 mg kg-1 de substrato) e (b) duas espécies de FMAs (Glomus etunicatum e G. intraradices) e um controle sem FMA, com três repetições, em vasos de 1,7 dm³ de substrato. Após cinco meses do transplantio das mudas de limoeiro-cravo, avaliaram-se a altura, diâmetro do caule, matéria seca da parte aérea das plantas, nutrientes acumulados na parte aérea e percentagem de colonização radicular. No substrato, avaliaram-se o comprimento de micélio extra-radicular ativo (MEA) e total (MET) de FMAs. O porta-enxerto limoeiro-cravo apresentou alta dependência micorrízica na absorção dos nutrientes, quando inoculado com G. intraradices, o que resultou em maior altura, diâmetro de caule e matéria seca da parte aérea das plantas. Apenas essa espécie de FMA formou micorriza com o hospedeiro, com valores de colonização radicular inversamente proporcionais às doses de P adicionado. Houve aumento de MEA e MET com o aumento das doses de P, com alta correlação entre o primeiro e a absorção de nutrientes. Apesar de não colonizar o hospedeiro, a infestação com G. etunicatum resultou em valores de MEA e MET superiores aos do controle, indicando, talvez, capacidade saprofítica desse fungo para sobreviver no substrato.

Within-plot subsampling of trees for assessment in progeny trials of Scots pine

Summary

Organic material decomposition and nutrient dynamics in a mulch system enriched with leguminous trees in the Amazon

The new techniques proposed for agriculture in the Amazon region include rotational fallow systems enriched with leguminous trees and the replacement of biomass burning by mulching. Decomposition and nutrient release from mulch were studied using fine-mesh litterbags with five different leguminous species and the natural fallow vegetation as control. Samples from each treatment were analyzed for total C, N, P, K, Ca, Mg, lignin, cellulose content and soluble polyphenol at different sampling times over the course of one year. The decomposition rate constant varied with species and time. Weight loss from the decomposed litter bag material after 96 days was 30.1 % for Acacia angustissima, 32.7 % for Sclerolobium paniculatum, 33.9 % for Iinga edulis and the Fallow vegetation, 45.2 % for Acacia mangium and 63.6 % for Clitoria racemosa. Immobilization of N and P was observed in all studied treatments. Nitrogen mineralization was negatively correlated with phenol, C-to-N ratio, lignin + phenol/N ratio, and phenol/phosphorus ratios and with N content in the litterbag material. After 362 days of field incubation, an average (of all treatments), 3.3 % K, 32.2 % Ca and 22.4 % Mg remained in the mulch. Results confirm that low quality and high amount of organic C as mulch application are limiting for the quantity of energy available for microorganisms and increase the nutrient immobilization for biomass decomposition, which results in competition for nutrients with the crop plants.

Properties of top soil and the relationship between soil and trees in a boreal Scots pine stand

Summary