Estimation of pairwise relatedness between individuals and characterization of isolation-by-distance processes using dominant genetic markers

A new estimator of the pairwise relatedness coefficient between individuals adapted to dominant genetic markers is developed. This estimator does not assume genotypes to be in Hardy-Weinberg proportions but requires a knowledge of the departure from these proportions (i.e. the inbreeding coefficient). Simulations show that the estimator provides accurate estimates, except for some particular types of individual pairs such as full-sibs, and performs better than a previously developed estimator. When comparing marker-based relatedness estimates with pedigree expectations, a new approach to account for the change of the reference population is developed and shown to perform satisfactorily. Simulations also illustrate that this new relatedness estimator can be used to characterize isolation by distance within populations, leading to essentially unbiased estimates of the neighbourhood size. In this context, the estimator appears fairly robust to moderate errors made on the assumed inbreeding coefficient. The analysis of real data sets suggests that dominant markers (random amplified polymorphic DNA, amplified fragment length polymorphism) may be as valuable as co-dominant markers (microsatellites) in studying microgeographic isolation-by-distance processes. It is argued that the estimators developed should find major applications, notably for conservation biology.     

Assessment of genetic structure within and among Bulgarian populations of the common ash (Fraxinus excelsior L.)

We analysed genetic variation within and between populations of the common ash from Bulgaria in order to extract biological information useful in the context of conservation management of eastern European genetic resources of noble hardwood species. A total of 321 trees from three regions of Bulgaria were typed at six highly polymorphic microsatellite loci. Analysis of within-population inbreeding suggests an upper boundary value of 2.7% for the selfing rate. Significant spatial genetic structure consistent with models of isolation by distance was detected within four out of 10 populations as well as among populations. Estimates of neighbourhood size in the range 38-126 individual trees were obtained based on spatial genetic structure analyses at either the intrapopulation or interpopulation level. Differentiation among populations explained only about 8.7% of total genetic diversity. These results are discussed in comparison with data from social broad-leaved species such as oak and beech.     

Metapopulation dynamics with quasi-local competition

Stepping-stone models for the ecological dynamics of metapopulations are often used to address general questions about the effects of spatial structure on the nature and complexity of population fluctuations. Such models describe an ensemble of local and spatially isolated habitat patches that are connected through dispersal. Reproduction and hence the dynamics in a given local population depend on the density of that local population, and a fraction of every local population disperses to neighboring patches. In such models, interesting dynamic phenomena, e.g. the persistence of locally unstable predator-prey interactions, are only observed if the local dynamics in an isolated patch exhibit non-equilibrium behavior. Therefore, the scope of these models is limited. Here we extend these models by making the biologically plausible assumption that reproductive success in a given local habitat not only depends on the density of the local population living in that habitat, but also on the densities of neighboring local populations. This would occur if competition for resources occurs between neighboring populations, e.g. due to foraging in neighboring habitats. With this assumption of quasi-local competition the dynamics of the model change completely. The main difference is that even if the dynamics of the local populations have a stable equilibrium in isolation, the spatially uniform equilibrium in which all local populations are at their carrying capacity becomes unstable if the strength of quasi-local competition reaches a critical level, which can be calculated analytically. In this case the metapopulation reaches a new stable state, which is, however, not spatially uniform anymore and instead results in an irregular spatial pattern of local population abundance. For large metapopulations, a huge number of different, spatially non-uniform equilibrium states coexist as attractors of the metapopulation dynamics, so that the final state of the system depends critically on the initial conditions. The existence of a large number of attractors has important consequences when environmental noise is introduced into the model. Then the metapopulation performs a random walk in the space of all attractors. This leads to large and complicated population fluctuations whose power spectrum obeys a red-shifted power law. Our theory reiterates the potential importance of spatial structure for ecological processes and proposes new mechanisms for the emergence of non-uniform spatial patterns of abundance and for the persistence of complicated temporal population fluctuations.     

Equilibrium structure and stability in a frequency-dependent,two-population diploid model

We investigate the equilibrium structure for an evolutionary genetic model in discrete time involving two monoecious populations subject to intraspecific and interspecific random pairwise interactions. A characterization for local stability of an equilibrium is found, related to the proximity of this equilibrium with evolutionarily stable strategies (ESS). This extends to a multi-population framework a principle initially proposed for single populations, which states that the mean population strategy at a locally stable equilibrium is as close as possible to an ESS.     

Antagonism between local dispersal and self-incompatibility systems in a continuous plant population

Many self-incompatible plant species exist in continuous populations in which individuals disperse locally. Local dispersal of pollen and seeds facilitates inbreeding because pollen pools are likely to contain relatives. Self-incompatibility promotes outbreeding because relatives are likely to carry incompatible alleles. Therefore, populations can experience an antagonism between these forces. In this study, a novel computational model is used to explore the effects of this antagonism on gene flow, allelic diversity, neighbourhood sizes, and identity by descent. I confirm that this antagonism is sensitive to dispersal levels and linkage. However, the results suggest that there is little to no difference between the effects of gametophytic and sporophytic self-incompatibility systems (GSI and SSI) on unlinked loci. More importantly, both GSI and SSI affect unlinked loci in a manner similar to obligate outcrossing without mating types. This suggests that the primary evolutionary impact of self-incompatibility systems may be to prevent selfing, and prevention of biparental inbreeding might be a beneficial side-effect.     

"Cold spots" in protein cold adaptation: Insights from normalized atomic displacement parameters (B'-factors)

Many analyses published in the last decade suggest that enzymes isolated from cold-adapted organisms are characterized by a higher flexibility of their molecular structure. Recently, it has been argued that all cold-adapted enzymes with catalytic efficiency greater than that of their mesophilic counterparts display local flexibility or rigidity that are likely to cooperate, each acting on specific areas of the enzyme structure. Here we report an analysis of the normalized thermal B-factor distributions in psychrophilic proteins compared with those of their mesophilic and thermophilic counterparts with the aim to detect statistically significant local variations of relative backbone flexibility possibly linked to cold adaptation. We utilized a strategy based mainly on intra-family comparison of local distribution of normalized B-factors. After careful statistical treatment of data, the picture emerging from our results suggests that the distribution of the flexibility in psychrophilic enzymes is locally more heterogeneous than in their respective mesophilic homologues.     

Historical and contemporary gene dispersal in wild carrot (Daucus carota ssp. carota) populations

Background and Aims

Wild carrot is the ancestor of cultivated carrot and is the most important gene pool for carrot breeding. Transgenic carrot may be released into the environment in the future. The aim of the present study was to determine how far a gene can disperse in wild carrot populations, facilitating risk assessment and management of transgene introgression from cultivated to wild carrots and helping to design sampling strategies for germplasm collections.

Methods

Wild carrots were sampled from Meijendel and Alkmaar in The Netherlands and genotyped with 12 microsatellite markers. Spatial autocorrelation analyses were used to detect spatial genetic structures (SGSs). Historical gene dispersal estimates were based on an isolation by distance model. Mating system and contemporary pollen dispersal were estimated using 437 offspring of 20 mothers with different spatial distances and a correlated paternity analysis in the Meijendel population.

Key Results

Significant SGSs are found in both populations and they are not significantly different from each other. Combined SGS analysis indicated significant positive genetic correlations up to 27 m. Historical gene dispersal σ_g and neighbourhood size N_b were estimated to be 4–12 m [95 % confidence interval (CI): 3–25] and 42–73 plants (95 % CI: 28–322) in Meijendel and 10–31 m (95 % CI: 7–∞) and 57–198 plants (95 % CI: 28–∞) in Alkmaar with longer gene dispersal in lower density populations. Contemporary pollen dispersal follows a fat-tailed exponential-power distribution, implying pollen of wild carrots could be dispersed by insects over long distance. The estimated outcrossing rate was 96 %.

Conclusions

SGSs in wild carrots may be the result of high outcrossing, restricted seed dispersal and long-distance pollen dispersal. High outcrossing and long-distance pollen dispersal suggest high frequency of transgene flow might occur from cultivated to wild carrots and that they could easily spread within and between populations.     

Column-switching HPLC–MS/MS analysis of ropivacaine in serum,ultrafiltrate and drainage blood for validating the safety of blood reinfusion

A high-performance liquid chromatography–tandem mass spectrometry (HPLC–MS–MS) method, using back-flush column-switching was developed for total drug concentrations of ropivacaine in serum and drainage blood in the measuring range 0.1–10 μg/mL. Samples were diluted with internal standard (²H₇-ropivacaine) and extraction buffer, centrifuged and injected directly onto a BioTrap 500 MS extraction column. Using a time programmed six-port valve switch, ropivacaine was back-flushed onto a Zorbax SB-Aq analytical column, gradient eluted and finally detected after electro spray ionisation and multiple reaction monitoring (MRM) of the transitions m/z 275 → m/z 126 and m/z 282 → m/z 133 for ropivacaine and ²H₇-ropivacaine, respectively. Accuracy (bias-%) was −1.5 to 5.8% and intermediate precision (C.V.) was 1.4–3.1%. The low sample amount required (10 μL), high specificity and short run time (6 min) makes it very suitable for determination of ropivacaine. Using the same methodology as described above and 200 μL ultrafiltrate, the free drug concentrations of ropivacaine in serum could be precisely determined with a C.V. below 3%. The method was used to investigate the safety of reinfusion of drainage blood after knee and hip arthroplasty when ropivacaine (Naropin^®) was used for local analgesia. Data for 30 patients are summarised.     

多通道局部场电位时变频谱的同步模式及其对行为事件的编码

用时变相干（time-varying coherence）频谱方法分析多通道局部场电位（local field potentials, LFPs）随时间变化的同步模式及其对行为事件的编码。实验数据为行为事件前后3秒的28通道LFPs。分别计算每个通道LFP的功率谱密度（power spectral density, PSD）及多通道LFPs各个特征频段的PSD,选取PSD分布集中的?兹频段为LFPs的特征频段;应用离散二进小波变换获取LFPs的?兹频段分量;从28通道LFPs中选取PSD最大的通道作为参考通道。选取计算窗口为50 ms,从初始点开始计算每个窗口中每个通道LFP及其?兹分量对参考通道的频谱相干分析。移动窗口步长为25 ms,获取多通道LFPs及其?兹分量的时变频谱相干动态分布。研究结果显示,?兹频段分量的PSD占LFPs总功率的71.95%,表明?兹分量是实验中多通道LFPs同步的特征频段;多通道LFPs的?兹分量频谱相干值随时间变化,行为事件点前后1 s的相干值具有显著差别（P＜0.05）,表明多通道LFPs的?兹频段时变频谱相干有效地编码了这一行为事件。