Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates

As species richness varies along the tree of life, there is a great interest in identifying factors that affect the rates by which lineages speciate or go extinct. To this end, theoretical biologists have developed a suite of phylogenetic comparative methods that aim to identify where shifts in diversification rates had occurred along a phylogeny and whether they are associated with some traits. Using these methods, numerous studies have predicted that speciation and extinction rates vary across the tree of life. In this study, we show that asymmetric rates of sequence evolution lead to systematic biases in the inferred phylogeny, which in turn lead to erroneous inferences regarding lineage diversification patterns. The results demonstrate that as the asymmetry in sequence evolution rates increases, so does the tendency to select more complicated models that include the possibility of diversification rate shifts. These results thus suggest that any inference regarding shifts in diversification pattern should be treated with great caution, at least until any biases regarding the molecular substitution rate have been ruled out.     

Accelerating microbial iron cycling promotes re-cementation of surface crusts in iron ore regions

Accelerating microbial iron cycling is an innovative environmentally responsible strategy for mine remediation. In the present study, we extend the application of microbial iron cycling in environmental remediation, to include biocementation for the aggregation and stabilization of mine wastes. Microbial iron reduction was promoted monthly for 10 months in crushed canga (a by-product from iron ore mining, dominated by crystalline iron oxides) in 1 m³ containers. Ferrous iron concentrations reached 445 ppm in treatments and diverse lineages of the candidate phyla radiation dominated pore waters, implicating them in fermentation and/or metal cycling in this system. After a 6-month evaporation period, iron-rich cements had formed between grains and 20-cm aggregates were recoverable from treatments throughout the 1-m depth profile, while material from untreated and water-only controls remained unconsolidated. Canga-adapted plants seeded into one of the treatments germinated and grew well. Therefore, application of this geobiotechnology offers promise for stabilization of mine wastes, as well as re-formation of surface crusts that underpin unique and threatened plant ecosystems in iron ore regions.     

Length–mass allometry in snakes

Body size and body shape are tightly related to an animal's physiology, ecology and life history, and, as such, play a major role in understanding ecological and evolutionary phenomena. Because organisms have different shapes, only a uniform proxy of size, such as mass, may be suitable for comparisons between taxa. Unfortunately, snake masses are rarely reported in the literature. On the basis of 423 species of snakes in 10 families, we developed clade‐specific equations for the estimation of snake masses from snout–vent lengths and total lengths. We found that snout–vent lengths predict masses better than total lengths. By examining the effects of phylogeny, as well as ecological and life history traits on the relationship between mass and length, we found that viviparous species are heavier than oviparous species, and diurnal species are heavier than nocturnal species. Furthermore, microhabitat preferences profoundly influence body shape: arboreal snakes are lighter than terrestrial snakes, whereas aquatic snakes are heavier than terrestrial snakes of a similar length. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ●● , ●●–●●.     

Root-to-Root Travel of the Beneficial Bacterium Azospirillum brasilense

The root-to-root travel of the beneficial bacterium Azospirillum brasilense on wheat and soybean roots in agar, sand, and light-textured soil was monitored. We used a motile wild-type (Mot⁺) strain and a motility-deficient (Mot^-) strain which was derived from the wild-type strain. The colonization levels of inoculated roots were similar for the two strains. Mot⁺ cells moved from inoculated roots (either natural or artificial roots in agar, sand, or light-textured soil) to noninoculated roots, where they formed a band-type colonization composed of bacterial aggregates encircling a limited part of the root, regardless of the plant species. The Mot^- strain did not move toward noninoculated roots of either plant species and usually stayed at the inoculation site and root tips. The effect of attractants and repellents was the primary factor governing the motility of Mot⁺ cells in the presence of adequate water. We propose that interroot travel of A. brasilense is an essential preliminary step in the root-bacterium recognition mechanism. Bacterial motility might have a general role in getting Azospirillum cells to the site where firmer attachment favors colonization of the root system. Azospirillum travel toward plants is a nonspecific active process which is not directly dependent on nutrient deficiency but is a consequence of a nonspecific bacterial chemotaxis, influenced by the balance between attractants and possibly repellents leaked by the root.     

Temporal, spatial and hormonal regulation of the S-adenosylmethionine synthetase gene in petunia

Gibberellic acid (GA₃) promotes corolla elongation and pigmentation in petunia flowers. We have previously shown that G.A₃ induces pigmentation by activating specific genes of the anthocyanin biosynthetic pathway. The aim of the present work was to examine whether GA₃ induces also the expression of genes from other metabolic pathways in petunia corollas that may be associated with growth. Recently we reported the cloning of the petunia sam gene coding for S -adenosylmethionine synthetase (SAM-S). In the present work we show that sam expression is induced by GA₃ in both corollas and stems. The expression of the gene was correlated with corolla elongation. GA₃ and the cylokinin, N -6-benzyladenine (BA) promoted corolla growth and sam expression, whereas abscisic acid (ABA) inhibited corolla elongation and repressed sam mRNA accumulation. An analysis of sam expression in stems indicated a high level in young, elongating internodes and a very low level in the mature, non-elongating stem zone. The results of the present study show that the effect of GA₃ on gene expression in the corolla of petunia, is not restricted to the anthocyanin biosynthetic pathway, they also suggest a possible role for sam in GA₃-induced corolla and stem elongation.     

Neuronal recruitment in adult zebra finch brain during a reproductive cycle

Previous studies suggest that adult neurogenesis and neuronal replacement are related to the acquisition of new information. The present study supports this hypothesis by showing that there is an increase in new neuron recruitment in brains of adult male and female zebra finches that coincides with the need to memorize vocalizations of nestlings before they fledge. We counted [(3)H]-Thymidine labeled neurons 40 days after [(3)H]-Thymidine injections. These counts were made in the parents' brains at the time eggs hatched, at the time juveniles fledged and still needed parental care, and at the time juveniles were already independent. We focused on nidopallium caudale (NC), a brain region which plays a role in sound processing. Recruitment of new NC neurons increased at the time the young fledged, followed by a significant decrease when the young reached independence. We suggest that this increase enables parents to recognize their own young when they are still dependent on parental feeding, yet easily lost among other fledglings in the colony. We saw no such increase in neuronal recruitment in the olfactory bulb, suggesting anatomical specificity for the effect seen in NC. We also found a preliminary, positive correlation between number of fledglings and number of new NC neurons in the parents' brain at fledging, suggesting that the number of neurons recruited is sensitive to the number of young fledged.