Inferring landscape effects on dispersal from genetic distances: how far can we go?

Functional connectivity affects demography and gene dynamics in fragmented populations. Besides species-specific dispersal ability, the connectivity between local populations is affected by the landscape elements encountered during dispersal. Documenting these effects is thus a central issue for the conservation and management of fragmented populations. In this study, we compare the power and accuracy of three methods (partial correlations, regressions and Approximate Bayesian Computations) that use genetic distances to infer the effect of landscape upon dispersal. We use stochastic individual-based simulations of fragmented populations surrounded by landscape elements that differ in their permeability to dispersal. The power and accuracy of all three methods are good when there is a strong contrast between the permeability of different landscape elements. The power and accuracy can be further improved by restricting analyses to adjacent pairs of populations. Landscape elements that strongly impede dispersal are the easiest to identify. However, power and accuracy decrease drastically when landscape complexity increases and the contrast between the permeability of landscape elements decreases. We provide guidelines for future studies and underline the needs to evaluate or develop approaches that are more powerful.     

Deciding on a new home: how do honeybees agree?

A swarm of honeybees (Apis mellifera) is capable of selecting one nest-site when faced with a choice of several. We adapt classical mathematical models of disease, information and competing beliefs to such decision-making processes. We show that the collective decision may be arrived at without the necessity for any bee to make any comparison between sites.     

Is horizontal transmission really a problem for phylogenetic comparative methods? A simulation study using continuous cultural traits

Phylogenetic comparative methods (PCMs) provide a potentially powerful toolkit for testing hypotheses about cultural evolution. Here, we build on previous simulation work to assess the effect horizontal transmission between cultures has on the ability of both phylogenetic and non-phylogenetic methods to make inferences about trait evolution. We found that the mode of horizontal transmission of traits has important consequences for both methods. Where traits were horizontally transmitted separately, PCMs accurately reported when trait evolution was not correlated even at the highest levels of horizontal transmission. By contrast, linear regression analyses often incorrectly concluded that traits were correlated. Where simulated trait evolution was not correlated and traits were horizontally transmitted as a pair, both methods inferred increased levels of positive correlation with increasing horizontal transmission. Where simulated trait evolution was correlated, increasing rates of separate horizontal transmission led to decreasing levels of inferred correlation for both methods, but increasing rates of paired horizontal transmission did not. Furthermore, the PCM was also able to make accurate inferences about the ancestral state of traits. These results suggest that under certain conditions, PCMs can be robust to the effects of horizontal transmission. We discuss ways that future work can investigate the mode and tempo of horizontal transmission of cultural traits.     

Defense on multiple fronts: how do plants cope with diverse enemies?

Plants have evolved an array of defense mechanisms to protect themselves against the wide variety of pathogens and pests with which they are confronted. Included in these defense mechanisms are inducible responses that are turned on systemically in the plant in response to attempted infection or predation. The two most studied inducible responses are systemic acquired resistance, which provides enhanced resistance to pathogen infection, and the wound response pathway, resulting in enhanced resistance to insect feeding. Recent research suggests that the two pathways are not completely independent, and the induction of one might affect the expression of the other. However, the evidence for cross-talk between different induced defense response pathways is somewhat confusing, and at times contradictory. Here, we review recent advances in our understanding of how the different pathways might interact.     

Adolescents with childhood-onset GHD: how do we get them to peak bone mass?

The development of osteoporosis, with its attendant risk of fragility fracture, is in part related to the peak bone mass (PBM) achieved in early adulthood. Adolescence is a critical time for the acquisition of bone mass, with around 40% of skeletal mass being accrued during pubertal maturation. Growth hormone (GH) plays an integral role in the achievement of PBM after completion of linear growth, and several recent studies have suggested that GH replacement should continue in individuals with childhood-onset GHD until PBM has been attained - irrespective of the height achieved. In those with severe GHD after growth and pubertal development are complete, a seamless transition of GH therapy into adult life may be preferable to allowing a gap in GH treatment. The 'window of opportunity' concept for achieving PBM will, nevertheless, continue to be challenged by GHD teenagers who may resent the seamless continuation of GH replacement beyond adolescence. Preparation for this possibility should therefore begin during childhood, with all GHD teenagers being encouraged to remain on GH therapy until at least their mid-20s.     

Finding a match: how do homologous sequences get together for recombination?

Decades of research into homologous recombination have unravelled many of the details concerning the transfer of information between two homologous sequences. By contrast, the processes by which the interacting molecules initially colocalize are largely unknown. How can two homologous needles find each other in the genomic haystack? Is homologous pairing the result of a damage-induced homology search, or is it an enduring and general feature of the genomic architecture that facilitates homologous recombination whenever and wherever damage occurs? This Review presents the homologous-pairing enigma, delineates our current understanding of the process and offers guidelines for future research.     

Commentary: do we have a consistent terminology for species diversity? We are on the way

A consistent terminology for species diversity is subject of an ongoing debate. Recently Tuomisto (Oecologia 164:853–860, 2010) stated that a consistent terminology for diversity already exists. The paper comments on recent papers by ourselves (Jurasinski et al. Oecologia 159:15–26, 2009) and by Moreno and Rodriguez (Oecologia 163:279–282, 2010). Both started from Whittaker’s diversity concept to discuss the ambiguities of the terminology and propose a new, more consistent terminology that is based on the different approaches to diversity analysis. In contrast, Tuomisto adheres to a strict school of thinking and derives a diversity framework in the sense of Whittaker (alpha, beta, gamma) from the conceptual definition of diversity itself. A third group of papers discusses appropriate methods for the analysis of the variation in species composition. Here, we support the idea that alpha, beta and gamma diversity should be used in a strict sense that is based only on the conceptual definition of diversity. We accordingly extend and modify our terminological concept for species diversity. All approaches to the analysis and quantification of species composition and diversity can be assigned to three abstraction levels (species composition, variation in species composition,and variation in variation in species composition) and two scale levels (sample scale, aggregation scale). All methods that investigate the variation in species composition across scale levels evaluate beta relation with beta diversity being just one form of beta relation, which is calculated by dividing gamma diversity of order q by the appropriate alpha diversity of the same order. In contrast, differentiation refers to a pairwise calculation of resemblance in species composition. It is restricted to sample scale and is therefore most often only an intermediate step of analysis. Many ecological questions can be addressed either by direct analysis of the variation in species composition using raw data approaches or by further analysis of differentiation datasets on aggregation scale with or without respect to an external gradient.     

Qualitative and quantitative behavioral traits in a community of furcocercariae trematodes: tools for species separation?

Many trematode cercariae show distinct behavioral features, which have commonly been used in species identification in combination with morphological characteristics. However, information regarding cercariae behavior has often not been quantified in detail, or it is scattered in the literature, which is why the appropriate level of precision in behavioral identity, particularly in groups of cercariae species showing considerable morphological overlap, has not been properly established. In this study, we investigated one such group, the furcocercariae trematodes, by studying their behavior in a community consisting of 8 species (Diplostomum pseudospathaceum, Ichthyocotylurus variegatus, Cotylurus brevis, Cercaria spinulosa, Australapatemom sp., Australapatemom burti, Sanguinicola sp., and Bilharziella polonica) in central Finland. Our aim was not to develop an identification formula on the basis of behavior but to investigate and propose characteristic measurements applicable in separation of cercariae species. We used a 2-level approach, first recording qualitative behavioral traits of the cercariae, including swimming type and resting position; and, second, more detailed quantitative behavioral characteristics, such as resting time, swimming time, and swimming speed. Essentially, species showing a 2-phase behavior were distinguishable according to qualitative traits (resting position), whereas with those showing continuous swimming behavior, a combination of qualitative and quantitative traits (swimming speed) was required. These results suggest that characteristics of cercariae behavior can not only be used in species identification but also in general life history comparisons investigating details of the cercariae transmission.     

The costs of using unauthenticated, over-passaged cell lines: how much more data do we need?

Increasing data demonstrate that cellular cross-contamination, misidentified cell lines, and the use of cultures at high-passage levels contribute to the generation of erroneous and misleading results as well as wasted research funds. Contamination of cell lines by other lines has been recognized and documented back to the 1950s. Based on submissions to major cell repositories in the last decade, it is estimated that between 18% and 36% of cell lines may be contaminated or misidentified. More recently, problems surrounding practices of over-subculturing cells are being identified. As a result of selective pressures and genetic drift, cell lines, when kept in culture too long, exhibit reduced or altered key functions and often no longer represent reliable models of their original source material. A review of papers showing significant experimental variances between low- and high-passage cell culture numbers, as well as contaminated lines, makes a strong case for using verified, tested cell lines at low- or defined passage numbers. In the absence of cell culture guidelines, mandates from the National Institutes of Health (NIH) and other funding agencies or journal requirements, it becomes the responsibility of the scientific community to perform due diligence to ensure the integrity of cell cultures used in research.     

Measures to reduce population fragmentation by roads: what has worked and how do we know?

Roads impede animal movement, which decreases habitat accessibility and reduces gene flow. Ecopassages have been built to mitigate this but there is little research with which to evaluate their effectiveness, owing to the difficulty in accessing results of existing research; the lack of scientific rigor in these studies; and the low priority of connectivity planning in road projects. In this article, we suggest that the imperative for improving studies of ecopassage effectiveness is that road ecology research should be included from the earliest stages of road projects onwards. This would enable before-after-control-impact (BACI) design research, producing useful information for the particular road project as well as rigorous results for use in future road mitigation. Well-designed studies on ecopassage effectiveness could help improve landscape connectivity even with the increasing number and use by traffic of roads.     

Evaluation of extracorporeal shock wave therapy for refractory angina pectoris with quantitative analysis using cardiac magnetic resonance imaging: a short communication

Aims

There is a continuing search for new treatment options in patients who suffer from refractory angina pectoris to improve quality of life. Several studies have recently demonstrated promising results by stimulating angiogenesis using extracorporeal shockwave therapy in these patients. The purpose of this study is to quantitatively analyse the effect of extracorporeal shockwave therapy on myocardial perfusion in patients with refractory angina pectoris.

Methods

We included 15 patients with NYHA class 3–4 of whom 8 patients underwent baseline and follow-up cardiac magnetic resonance imaging (CMR). All patients received 9 shockwave treatments of their ischaemic zone over a period of 3 months.

Results

Quantitative analysis of myocardial perfusion using CMR revealed no significant improvement of myocardial perfusion after treatment (0.80 ± 0.22 vs 0.76 ± 0.31; p = 0.42). However, the total group of 15 patients did experience a significant improvement in NYHA class (p = 0.034) and reduction of nitroglycerin use (p = 0.012).

Conclusion

Although treatment with extracorporeal shockwave was associated with an improvement in NYHA class, we could not observe an improvement in myocardial ischaemic zone and perfusion with CMR. To unravel the exact mechanisms of shockwave treatment, more in vitro and animal studies as well as larger (placebo-controlled) studies are required.

     

Is the abundance of species determined by their functional traits? A new method with a test using plant communities

The relation between functional traits and abundance of species has the potential to provide evidence on the mechanisms that structure local ecological communities. The niche-limitation/limiting-similarity hypothesis, derived from MacArthur and Levins’ original concept, predicts that species that are similar to others in terms of functional traits will suffer greater competition and hence be less abundant. On the other hand, the environment-filtering/habitat-optimum hypothesis predicts that groups of species with functional traits that are close to the optimum for that environment, and are therefore similar to other species, will be more abundant. We propose a new niche-assembly model for predicting the relative abundance of species in communities from their functional traits, which can detect the patterns that would be expected from either of these hypotheses. The model was fitted to eight plant communities sampled in the Lake Ohau district of New Zealand. For seven of the sites, the patterns could not be distinguished from that expected under a null model. However, in one site there was highly significant departure from the null model in the direction expected from the niche-limitation hypothesis. The site was probably the most productive of those examined. It is possible that competition for light rather than belowground resources, or faster recovery from disturbance, allowed greater predictability. Surprisingly, the predictability was seen when just the presences of a species’ neighbours in trait space were taken into account, but not when the potential effects of those neighbours were weighted by their abundance. For three of the four model types, the effects of species on each other were consistently negative: a significant trend. These results contradict the various neutral models of ecological communities.     

Dealing with detection error in site occupancy surveys: what can we do with a single survey?

Aim Site occupancy probabilities of target species are commonly used in various ecological studies, e.g. to monitor current status and trends in biodiversity. Detection error introduces bias in the estimators of site occupancy. Existing methods for estimating occupancy probability in the presence of detection error use replicate surveys. These methods assume population closure, i.e. the site occupancy status remains constant across surveys, and independence between surveys. We present an approach for estimating site occupancy probability in the presence of detection error that requires only a single survey and does not require assumption of population closure or independence. In place of the closure assumption, this method requires covariates that affect detection and occupancy.Methods Penalized maximum-likelihood method was used to estimate the parameters. Estimability of the parameters was checked using data cloning. Parametric boostrapping method was used for computing confidence intervals.Important findings The single-survey approach facilitates analysis of historical datasets where replicate surveys are unavailable, situations where replicate surveys are expensive to conduct and when the assumptions of closure or independence are not met. This method saves significant amounts of time, energy and money in ecological surveys without sacrificing statistical validity. Further, we show that occupancy and habitat suitability are not synonymous and suggest a method to estimate habitat suitability using single-survey data.