Comparing evolvabilities: common errors surrounding the calculation and use of coefficients of additive genetic variation

In 1992, David Houle showed that measures of additive genetic variation standardized by the trait mean, CV(A) (the coefficient of additive genetic variation) and its square (I(A) ), are suitable measures of evolvability. CV(A) has been used widely to compare patterns of genetic variation. However, the use of CV(A) s for comparative purposes relies critically on the correct calculation of this parameter. We reviewed a sample of quantitative genetic studies, focusing on sire models, and found that 45% of studies use incorrect methods for calculating CV(A) and that practices that render these coefficients meaningless are frequent. This may have important consequences for conclusions drawn from comparative studies. Our results are suggestive of a broader problem because miscalculation of the additive genetic variance from a sire model is prevalent among the studies sampled, implying that other important quantitative genetic parameters might also often be estimated incorrectly. We discuss the most prominent issues affecting the use of CV(A) and I(A) , including scale effects, data transformation, and the comparison of traits with different dimensions. Our aim is to increase awareness of the potential mistakes surrounding the calculation and use of evolvabilities, and to compile general guidelines for calculating, reporting, and interpreting these useful measures in future studies.     

Spatio-temporal patterns of habitat use in voles and shrews modified by density, season and predators

1.?Although the intrinsic habitat preferences of a species can be considered to be fixed, the realized habitat use depends on the prevailing abiotic and biotic conditions. Often the core habitats are occupied by dense and stable populations, while marginal habitats become occupied only at times of high density. In a community of interacting species, habitat uses of different species become inter-related, for example an increased density of a strong competitor forcing a weaker competitor to use more marginal habitats. 2.?We studied the spatio-temporal distribution patterns of three common small mammal species, the bank vole Myodes glareolus; the field vole Microtus agrestis; and the common shrew Sorex araneus, in a 4-year trapping study carried out on six large islands, each containing a mixture of three main habitat types (forest, field and clear-cut). We experimentally released least weasels (Mustela n. nivalis) to some of the islands to see how the focal species respond to increased predation pressure. 3.?Both vole species were largely restricted to their core habitats (bank voles to forests and field voles to fields) at times of low population density. With increasing density, the relative habitat use of both species increased in the clear-cut areas. The common shrew was a generalist in its habitat use at all population densities. 4.?The release of the weasels changed the habitat use of all study species. 5.?The vole species showed a stronger aggregated pattern than the common shrew, especially at low population density. The vole aggregations remained in the same localities between seasons, except in the case of bank voles after the weasels were released. 6.?Bank voles and field voles avoided each other at high density. 7.?We conclude that intrinsically differential habitat requirements and flexibility to modify habitat use facilitate the coexistence of the two competing vole species in mosaic landscapes consisting of boreal forests and open habitats.     

Context dependency and metacommunity structuring in boreal headwater streams

We studied the relative importance of spatial and environmental factors as determinants of algal, bryophyte, and macroinvertebrate metacommunities in two boreal drainage basins differing in spatial extent. We used eigenfunction spatial analysis to model the spatial relationships among sites and distance‐based redundancy analysis to partition the variability in biotic communities between the spatial filters generated through spatial eigenfunction analysis and the environmental factors measured in the field. In the smaller study area, each metacommunity was structured mostly by environmental factors. This was evidenced by the fact that either the pure environmental effect was significant or environmental factors were strongly spatially structured. In the larger study area, only pure environmental effects were significant. These findings suggest that the environmental control prevails in boreal headwater streams. However, our findings also suggest that the specific details of the community‐environment and community–space relationships are dependent on the focal organism group and drainage basin.     

The relationship between species richness and evenness: a meta-analysis of studies across aquatic ecosystems

Biological diversity comprises both species richness, i.e., the number of species in a community, and evenness, measuring how similar species are in their abundances. The relationship between species richness and evenness (RRE) across communities remains, however, a controversial issue in ecology because no consistent pattern has been reported. We conducted a systematic meta-review of RRE in aquatic ecosystems along regional to continental gradients and across trophic groups, differing in body size by 13 orders of magnitude. Hypotheses that RRE responded to latitudinal and scale variability across trophic groups were tested by regression analyses. Significant correlations of species richness and evenness only existed in 71 out of 229 datasets. Among the RRE, 89 were negative and 140 were positive. RRE did not vary with latitude but showed a positive response to scale. In a meta-analysis with ecosystem type as a single explaining variable, RRE did not vary among ecosystem types, i.e. between marine and freshwater. Finally, autotrophs had more positive RRE than heterotrophs. The weak RRE in many aquatic datasets suggests that richness and evenness often reflect independent components of biodiversity, highlighting that richness alone may be an incomplete surrogate for biodiversity. Our results further elucidate that RRE is driven by organismal and environmental properties, both of which must be considered to gain a deeper understanding of large-scale patterns of biodiversity.     

DNA family shuffling within the chicken avidin protein family - A shortcut to more powerful protein tools

Avidins represent an interesting group of proteins showing high structural similarity and ligand-binding properties but low similarity in primary structure. In this study, we show that it is possible to create functional chimeric proteins from the avidin protein family when applying DNA family shuffling to the genes of the avidin protein family: avidin, avidin related gene 2 and biotin-binding protein A. The novel chimeric proteins were selected by phage display biopanning against biotin, and the selected enriched proteins were characterized, displaying diverse features distinct from the parental genes, including binding to cysteine.     

Challenges using stable isotopes for estimating trophic levels in marine amphipods

In marine food web studies, stable isotopes of nitrogen (δ¹⁵N) and carbon (δ¹³C) are widely used to estimate organisms’ trophic levels (TL) and carbon sources, respectively. For smaller organisms, whole specimens are commonly analyzed. However, this “bulk method” involves several pitfalls since different tissues may fractionate stable isotopes differently. We compared the δ¹⁵N and δ¹³C values of exoskeleton versus soft tissue, in relation to whole specimens, of three common Arctic amphipods in Svalbard waters: the benthic Anonyx nugax, the sympagic (ice-associated) Gammarus wilkitzkii and the pelagic Themisto libellula. The δ¹⁵N values of the exoskeletons were significantly lower than those of the soft tissues for A. nugax (10.5 ± 0.7‰ vs. 15.7 ± 0.7‰), G. wilkitzkii (3.3 ± 0.3‰ vs. 8.3 ± 0.4‰) and T. libellula (8.6 ± 0.3‰ vs.10.8 ± 0.3‰). The differences in δ¹³C values between exoskeletons and soft tissues were insignificant, except for A. nugax (−21.2 ± 0.2‰ vs. −20.3 ± 0.2‰, respectively). The δ¹⁵N values of whole organisms were between those of the exoskeletons and the soft tissues, being similarly enriched in ¹⁵N as the exoskeletons (except G. wilkitzkii) and depleted in ¹⁵N by 1.2–3.7‰ compared to the soft tissues. The δ¹⁵N-derived TLs of the soft tissues agreed best with the known feeding preferences of the three amphipods, which suggest a potential underestimation of 0.5–1.0 TL when stable isotope analyses are performed on whole crustaceans with thick exoskeletons. The insignificant or small differences in δ¹³C values among exoskeletons, soft tissues and whole specimens, however, suggest low probability for misinterpretations of crustaceans’ primary carbon source in marine ecosystems with distinctly different δ¹³C-carbon sources.     

Dopamine levels in the mosquito Aedes aegypti during adult development, following blood feeding and in response to heat stress

Dopamine, a catecholamine neurotransmitter, is important for insect development and is known to be involved in insect stress responses. In the current study, dopamine was analysed in Aedes aegypti heads by HPLC. We found that immediately after adult emergence, males have significantly higher concentrations of dopamine than females, and that dopamine concentrations decrease with age in both sexes. Dopamine levels increase in females following a blood meal suggesting that dopamine might be involved in ovarian- and/or egg-development. We also found that female mosquitoes have a higher tolerance to a short term thermal stress in a water bath than males up to 44 degrees C, however, both sexes die if exposed to short term temperatures between 44 and 45 degrees C. Finally, we did not find any indication that dopamine levels were associated with short time thermal stress response in female mosquitoes.     

The response regulator ResD modulates virulence gene expression in response to carbohydrates in Listeria monocytogenes

Listeria monocytogenes is a versatile bacterial pathogen that is able to accommodate to diverse environmental and host conditions. Presently, we have identified a L. monocytogenes two-component response regulator, ResD that is required for the repression of virulence gene expression known to occur in the presence of easily fermentable carbohydrates not found inside host organisms. Structurally and functionally, ResD resembles the respiration regulator ResD in Bacillus subtilis as deletion of the L. monocytogenes resD reduces respiration and expression of cydA, encoding a subunit of cytochrome bd. The resD mutation also reduces expression of mptA encoding the EIIABman component of a mannose/glucose-specific PTS system, indicating that ResD controls sugar uptake. This notion was supported by the poor growth of resD mutant cells that was alleviated by excess of selected carbohydrates. Despite the growth deficient phenotype of the mutant in vitro the mutation did not affect intracellular multiplication in epithelial or macrophage cell lines. When examining virulence gene expression we observed traditional induction by charcoal in both mutant and wild-type cells whereas the repression observed in wild-type cells by fermentable carbohydrates did not occur in resD mutant cells. Thus, ResD is a central regulator of L. monocytogenes when present in the external environment.