Plant species richness in Fennoscandia: evaluating the relative importance of climate and history

In Fennoscandia, the species richness of vascular plants in 75 × 75 km squares is highly correlated with geographical (latitude and longitude) and climatic variables (accumulated respiration sum, mean January temperature, and mean July temperature). When generalised additive models (GAM) are used, over 80% of the variation in richness can be statistically explained by geography and climate. Even though climate has such a high explanatory power we present several arguments for interpreting these results with care. Climate has no ecologically sound explanatory power when the variation due to latitude and longitude is accounted for, and the strongest latitudinal gradient in summer temperature is in an area where the latitudinal gradient in species richness is absent. We discuss the role that Holocene history might have on the variation in species richness, and argue that history and climate should be considered simultaneously when explaining the observed patterns in the geographical variation of species richness.     

Greenbeards in yeast: an undergraduate laboratory exercise to teach the genetics of cooperation

Recent years have seen a dramatic increase in our understanding of the social behaviour of microbes. Here, we take advantage of these developments to present an undergraduate laboratory exercise that uses the cooperative flocculating behaviour of yeast (Saccharomyces sp.) to introduce the concept of inclusive fitness and teach the genetics of cooperation. Students generate their own data using co-cultures of various yeast strains and perform statistical analyses to test whether kin selection or greenbeard effects determine the cooperative flocculating behaviour. The lab has run successfully for two consecutive years in a second year course with some 1, 200 students per year at the University of Toronto, Canada. We discuss the benefits of using microbes to teach social evolution, describe the set-up and learning outcomes of the laboratory exercise, and then outline possible extension and variants of the lab. In addition to providing students with the opportunity to use a model organism to study social behaviour, students are also taught common laboratory skills, such as replica plating and sterile techniques. Ultimately, while the genetics of cooperation has traditionally been taught through computer simulations and evolutionary games, this exercise demonstrates a way to experimentally introduce the topic.     

Identification and characterization of novel ERC‐55 interacting proteins: Evidence for the existence of several ERC‐55 splicing variants; including the cytosolic ERC‐55‐C

ERC‐55, encoded from RCN2, is localized in the ER and belongs to the CREC protein family. ERC‐55 is involved in various diseases and abnormal cell behavior, however, the function is not well defined and it has controversially been reported to interact with a cytosolic protein, the vitamin D receptor. We have used a number of proteomic techniques to further our functional understanding of ERC‐55. By affinity purification, we observed interaction with a large variety of proteins, including those secreted and localized outside of the secretory pathway, in the cytosol and also in various organelles. We confirm the existence of several ERC‐55 splicing variants including ERC‐55‐C localized in the cytosol in association with the cytoskeleton. Localization was verified by immunoelectron microscopy and sub‐cellular fractionation. Interaction of lactoferrin, S100P, calcyclin (S100A6), peroxiredoxin‐6, kininogen and lysozyme with ERC‐55 was further studied in vitro by SPR experiments. Interaction of S100P requires [Ca²⁺] of ～10^?7 M or greater, while calcyclin interaction requires [Ca²⁺] of >10^?5 M. Interaction with peroxiredoxin‐6 is independent of Ca²⁺. Co‐localization of lactoferrin, S100P and calcyclin with ERC‐55 in the perinuclear area was analyzed by fluorescence confocal microscopy. The functional variety of the interacting proteins indicates a broad spectrum of ERC‐55 activities such as immunity, redox homeostasis, cell cycle regulation and coagulation.     

Niche conservatism as an emerging principle in ecology and conservation biology

The diversity of life is ultimately generated by evolution, and much attention has focused on the rapid evolution of ecological traits. Yet, the tendency for many ecological traits to instead remain similar over time [niche conservatism (NC)] has many consequences for the fundamental patterns and processes studied in ecology and conservation biology. Here, we describe the mounting evidence for the importance of NC to major topics in ecology (e.g. species richness, ecosystem function) and conservation (e.g. climate change, invasive species). We also review other areas where it may be important but has generally been overlooked, in both ecology (e.g. food webs, disease ecology, mutualistic interactions) and conservation (e.g. habitat modification). We summarize methods for testing for NC, and suggest that a commonly used and advocated method (involving a test for phylogenetic signal) is potentially problematic, and describe alternative approaches. We suggest that considering NC: (1) focuses attention on the within‐species processes that cause traits to be conserved over time, (2) emphasizes connections between questions and research areas that are not obviously related (e.g. invasives, global warming, tropical richness), and (3) suggests new areas for research (e.g. why are some clades largely nocturnal? why do related species share diseases?).     

The science of emotion as a multidisciplinary research paradigm

I discuss the emergence of a science of emotion and argue that research in this domain requires an appreciation of the organization of emotional processes at different levels as postulated by social neuroscience. Emotions cannot be understood without relying on a program of multidisciplinary research. Local multidisciplinarity cannot be achieved without a programmatic framework that takes three issues into account (1) the relationship of multiple levels of emotions and connected processes, (2) the mutually informative study of humans, animals, and artificial systems, and (3) the dynamic nature of emotions in a dynamic systems approach. Illustrations for my arguments are provided relating to facial expressions of humans.     

Mating system shifts and transposable element evolution in the plant genus Capsella

Background

Despite having predominately deleterious fitness effects, transposable elements (TEs) are major constituents of eukaryote genomes in general and of plant genomes in particular. Although the proportion of the genome made up of TEs varies at least four-fold across plants, the relative importance of the evolutionary forces shaping variation in TE abundance and distributions across taxa remains unclear. Under several theoretical models, mating system plays an important role in governing the evolutionary dynamics of TEs. Here, we use the recently sequenced Capsella rubella reference genome and short-read whole genome sequencing of multiple individuals to quantify abundance, genome distributions, and population frequencies of TEs in three recently diverged species of differing mating system, two self-compatible species (C. rubella and C. orientalis) and their self-incompatible outcrossing relative, C. grandiflora.

Results

We detect different dynamics of TE evolution in our two self-compatible species; C. rubella shows a small increase in transposon copy number, while C. orientalis shows a substantial decrease relative to C. grandiflora. The direction of this change in copy number is genome wide and consistent across transposon classes. For insertions near genes, however, we detect the highest abundances in C. grandiflora. Finally, we also find differences in the population frequency distributions across the three species.

Conclusion

Overall, our results suggest that the evolution of selfing may have different effects on TE evolution on a short and on a long timescale. Moreover, cross-species comparisons of transposon abundance are sensitive to reference genome bias, and efforts to control for this bias are key when making comparisons across species.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-602) contains supplementary material, which is available to authorized users.     

A model for habitat selection and species distribution derived from central place foraging theory

We have developed a habitat selection model based on central place foraging theory. An individual’s decision to include a patch in its habitat depends on the marginal fitness contribution of that patch, which is characterized by its quality and distance to the central place. The essence of the model we have developed is a fitness isocline which is a function of patch quality and travel time to the patch. It has two parameters: the maximum travel distance to a patch of infinite quality and a coefficient that appropriately scales quality by travel time. Patches falling below the isocline will have positive marginal fitness values and should be included in the habitat. The maximum travel distance depends on the availability and quality of patches, as well as on the forager’s life history, whereas the scaling parameter mostly depends on life history properties. Using the model, we derived a landscape quality metric (which can be thought of as a connectivity measure) that sums the values of available habitat in the landscape around a central place. We then fitted the two parameters to foraging data on breeding white storks (Ciconia ciconia) and estimated landscape quality, which correlated strongly with reproductive success. Landscape quality was then calculated for a larger region where re-introduction of the species is currently going on in order to demonstrate how this model can also be regarded as a species distribution model. In conclusion, we have built a general habitat selection model for central place foragers and a novel way of estimating landscape quality based on a behaviorally scaled connectivity metric.     

On the ecology of Thelypteris limbosperma in W Norway. The distribution in relation to climatic factors

In 31 selected districts in W Norway the vertical distribution of Thelypteris limbosperma has been recorded. Special attention has been paid to the area within which T. limbosperma occurs as a dominant in the vegetation. Both horizontal and vertical distribution areas are related to climatic factors, namely the mean temperature of the wannest and coldest months, precipitation and humidity conditions expressed by Martonnes aridity index. Correlations between the distribution of T. limbosperma and these parameters have been elucidated. In oceanic districts correlations exist between the vertical distribution limits and the mean temperature of the warmest month, t. max = 14.2°C and 10.3°C. In suboceanic districts correlations are with t. min = -5.3°C, P = 121 mm; and H = 87.0. In districts where H < 60 the fern is sparce or missing.     

Upward shift in elevational plant species ranges in Sikkilsdalen,central Norway

Phytosociological studies can be an important tool to detect temporal vegetation changes in response to global climate change. In this study, we present the results of a resurvey of a plot‐based phytosociological study from Sikkilsdalen, central Norway, originally executed between 1922 and 1932. By using a detailed phytosociological study we are able to investigate several aspects of elevational shifts in species ranges. Here we tested for upward and downward shifts in observed upper and lower distribution limits of species, as well as changes in species optima along an elevational gradient, and related the observed range shifts to species traits that could explain the observed trends. More species shifted upwards than downwards, independently of whether we were investigating shifts in species’ upper or lower distribution ranges or in species optima. However, shifts in species upper range margins changed independently of their lower range margins. Linking different species traits to the magnitude of shifts we found that species with a higher preference for prolonged snow cover shifted upwards more in their upper elevational limits and in their optima than species that prefer a shorter snow cover, whereas no species traits were correlated with the magnitude of changes in lower limits. The observed change in species ranges concord both with studies on other mountains in the region and with studies from other alpine areas. Furthermore, our study indicates that different factors are influencing species ranges at the upper and lower range limits. Increased precipitation rates and increased temperatures are considered the most important factors for the observed changes, probably mainly through altering the pattern in snow cover dynamics in the area.