Linked Genes for Calmodulin and E2 Ubiquitin-Conjugating Enzyme in Trichomonas vaginalis

ABSTRACT In searching the genomes of early-diverging protists to study whether the possession of calmodulin is ancestral to all eukaryotes, the gene for calmodulin was identified in Trichomonas vaginalis. This flagellate is a member of the Parabasalia, one of the earliest lineages of recognized eukaryotes to have diverged. This sequence was used to isolate a homologous 1.250-kb fragment from the T. vaginalis genome by inverse polymerase chain reaction. This fragment was also completely sequenced and shown to contain the 3' end of the single-copy calmodulin gene and the 3' end of a gene encoding a protein with high similarity to E2 ubiquitin-conjugating enzymes, a family which has previously only been identified in animals, plants, and fungi. Phylogenetic analysis of 50 members of the E2 family distinguishes at least nine separate subfamilies one of which includes the T. vaginalis E2-homologue and an uncharacterized gene from yeast chromosome XII.     

Evidence of a latitudinal gradient in spider diversity in Australian cotton

The most common explanation for species diversity increasing towards the tropics is the corresponding increase in habitats (spatial heterogeneity). Consequently, a monoculture (like cotton in Australia) which is grown along a latitudinal gradient, should have the same degree of species diversity throughout its range. We tested to see if diversity in a dominant cotton community (spiders) changed with latitude, and if the community was structurally identical in different parts of Australia. We sampled seven sites extending over 20° of latitude. At each site we sampled 1–3 fields 3–5 times during the cotton growing season using pitfall traps and beatsheets, recording all the spiders collected to family. We found that spider communities in cotton are diverse, including a large range of foraging guilds, making them suitable for a conservation biological control programme. We also found that spider diversity increased from high to low latitudes, and the communities were different, even though the spiders were in the same monocultural habitat. Spider beatsheet communities around Australia were dominated by different families, and responded differently to seasonal changes, indicating that different pest groups would be targeted at different locations. These results show that diversity can increase from high to low latitudes, even if spatial heterogeneity is held constant, and that other factors external to the cotton crop are influencing spider species composition. Other models which may account for the latitudinal gradient, such as non‐equilibrium regional processes, are discussed.     

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

Gene co‐expression analysis has emerged in the past 5 years as a powerful tool for gene function prediction. In essence, co‐expression analysis asks the question ‘what are the genes that are co‐expressed, that is, those that show similar expression profiles across many experiments, with my gene of interest?’. Genes that are highly co‐expressed may be involved in the biological process or processes of the query gene. This review describes the tools that are available for performing such analyses, how each of these perform, and also discusses statistical issues including how normalization of gene expression data can influence co‐expression results, calculation of co‐expression scores and P values, and the influence of data sets used for co‐expression analysis. Finally, examples from the literature will be presented, wherein co‐expression has been used to corroborate and discover various aspects of plant biology.     

Hatching asynchrony and growth trade‐offs within domesticated and wild zebra finch,Taeniopygia guttata,broods

The Australian zebra finch, Taeniopygia guttata, is a widely used model organism, yet few studies have compared domesticated and wild birds with the aim of examining its relevance as an evolutionary model species. Domestic and wild broods hatch over approximately 4 and 2 days, respectively, which is important given that nestlings can fledge after as little as 12 days, although 16–18 days is common. We aimed to evaluate the extent to which the greater hatching asynchrony in domestic stock may effect reproductive success through greater variance in size hierarchies, variance in within‐brood growth rates, and partial brood mortality. Therefore, by simultaneously controlling brood sizes and experimentally manipulating hatching intervals in both domesticated and wild birds, we investigated the consequences of hatching intervals for fledging success and nestling growth patterns, as well as trade‐offs. Fledging success was similarly high in domestic and wild broods of either hatching pattern. Nonetheless, between‐brood analyses revealed that domestic nestlings had significantly higher masses, larger skeletal characters, and longer wings than their wild counterparts, although wild nestlings had comparable wing lengths at the pre‐fledging stage. Moreover, within‐brood analyses revealed only negligible differences between domestic and wild nestlings, and larger effects of hatching order and hatching pattern. Therefore, despite significant differences in the hatching intervals, and the ultimate size achieved by nestlings, the domestication process does not appear to have significantly altered nestling growth trade‐offs. The present study provides reassuring evidence that studies involving domesticated zebra finches, or other domesticated model organisms, may provide reasonable adaptive explanations in behavioural and evolutionary ecology. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 763–773.     

Hydraulic acclimation to shading in boreal conifers of varying shade tolerance

The purpose of this study was to determine how shading affects the hydraulic and wood‐anatomical characteristics of four boreal conifers (Pinus banksiana, Pinus contorta, Picea glauca and Picea mariana) that differ in shade tolerance. Plants were grown in an open field and under a deciduous‐dominated overstory for 6 years. Sapwood‐ and leaf‐area specific conductivity, vulnerability curves, and anatomical measurements (light and scanning electron microscopy) were made on leading shoots from six to nine trees of each treatment combination. There was no difference in sapwood‐area specific conductivity between open‐grown and understory conifers, although two of four species had larger tracheid diameters in the open. Shaded conifers appeared to compensate for small diameter tracheids by changes in pit membrane structure. Scanning electron microscopy revealed that understory conifers had thinner margo strands, greater maximum pore size in the margo, and more torus extensions. All of these trends may contribute to inadequate sealing of the torus. This is supported by the fact that all species showed increased vulnerability to cavitation when grown in the understory. Although evaporative demand in an understory environment is low, a rapid change into fully exposed conditions could be detrimental for shaded conifers.     

Effect of fire on benthic algal assemblage structure and recolonization in intermittent streams

Abstract: Dry biofilm on rocks and other substrata forms an important drought refuge for benthic algae in intermittent streams following the cessation of flow. This dry biofilm is potentially susceptible to disturbance from bushfires, including direct burning and/or scorching and damage from radiant heat, particularly when streams are dry. Therefore, damage to dry biofilms by fire has the potential to influence algal recolonization and assemblage structure in intermittent streams following commencement of flow. The influence of fire on benthic algal assemblages and recolonization was examined in intermittent streams of the Grampians National Park, Victoria, Australia, using a field survey and manipulative field experiment. The field survey compared assemblages in two intermittent streams within a recently burnt area (within 5 months of the fire) with two intermittent streams within an unburnt area. The two burnt streams were still flowing during the fire so most biofilms were not likely to be directly exposed to flames. Considerable site‐to‐site and stream‐to‐stream variation was detected during the field survey, which may have obscured potential differences attributable to indirect effects of the fire. The manipulative field experiment occurred in two intermittent streams and consisted of five treatments chosen to replicate various characteristics of bushfires that may influence dry biofilms: dry biofilm exposed directly to fire; dry biofilm exposed to radiant heat; dry biofilm exposed to ash; and two procedural controls. After exposure to the different treatments, rocks were replaced in the streams and algae were sampled 7 days after flow commenced. Differences occurred across treatments, but treatment differences were inconsistent across the two streams. For example, direct exposure to fire reduced the abundance of recolonizing algae and altered assemblage structure in both streams, while radiant heat had an effect on assemblage structure in one stream only. The manipulative field experiment is likely to have represented the intensity of a small bushfire only. Nonetheless, significant differences across treatments were detected, so these experimental results suggest that fire can damage dry biofilms, and hence, influence algal recolonization and assemblage structure in intermittent streams.     

The importance of energetic versus pelvic constraints on reproductive allocation by the eastern fence lizard (Sceloporus undulatus)

In ectothermic species, females often produce larger eggs in colder environments. Models based on energetic constraints suggest that this pattern is an adaptation to compensate for the slower growth of offspring in the cold. Yet, females in cold environments also tend to be larger than females in warm environments. Consequently, thermal clines in egg size could be caused by pelvic constraints, which stem from the inability of large eggs to pass through a small pelvic aperture. Models based on energetic constraints and models based on pelvic constraints predict similar relationships between maternal size and egg size. However, pelvic constraints should produce these relationships both within and among populations, whereas energetic constraints would not necessarily do so. If pelvic constraints are important, we might also expect small females to compensate by producing eggs that are relatively rich in lipids (i.e. high energy density). The present study aimed to assess whether energetic or pelvic constraints generate geographical variation in egg size of the lizard Sceloporus undulatus . Pelvic width is very highly correlated with body length in S. undulatus , making maternal size a suitable measure of pelvic constraint. Although maternal size and egg mass (dry and wet) covaried among populations, these variables were generally not related within populations. Energetic density of eggs tended to increase with decreasing egg mass (dry and wet), but this relationship was strongest in populations where no relationship between maternal size and egg mass was observed. Our results do not support the pelvic constraint model and thus indicate energetic constraints play a greater role in generating geographical variation in egg size.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 513–521.     

Landscapes of Settlement in Northern Iceland: Historical Ecology of Human Impact and Climate Fluctuation on the Millennial Scale

Early settlement in the North Atlantic produced complex interactions of culture and nature. The sustained program of interdisciplinary collaboration is intended to focus on ninth- to 13th-century sites and landscapes in the highland interior lake basin of Mývatn in Iceland and to contribute a long-term perspective to larger issues of sustainable resource use, soil erosion, and the historical ecology of global change.