Does Litter Size Variation Affect Models of Terrestrial Carnivore Extinction Risk and Management?

Background

Individual variation in both survival and reproduction has the potential to influence extinction risk. Especially for rare or threatened species, reliable population models should adequately incorporate demographic uncertainty. Here, we focus on an important form of demographic stochasticity: variation in litter sizes. We use terrestrial carnivores as an example taxon, as they are frequently threatened or of economic importance. Since data on intraspecific litter size variation are often sparse, it is unclear what probability distribution should be used to describe the pattern of litter size variation for multiparous carnivores.

Methodology/Principal Findings

We used litter size data on 32 terrestrial carnivore species to test the fit of 12 probability distributions. The influence of these distributions on quasi-extinction probabilities and the probability of successful disease control was then examined for three canid species – the island fox Urocyon littoralis, the red fox Vulpes vulpes, and the African wild dog Lycaon pictus. Best fitting probability distributions differed among the carnivores examined. However, the discretised normal distribution provided the best fit for the majority of species, because variation among litter-sizes was often small. Importantly, however, the outcomes of demographic models were generally robust to the distribution used.

Conclusion/Significance

These results provide reassurance for those using demographic modelling for the management of less studied carnivores in which litter size variation is estimated using data from species with similar reproductive attributes.     

A gene's ability to buffer variation is predicted by its fitness contribution and genetic interactions

Background

Many single-gene knockouts result in increased phenotypic (e.g., morphological) variability among the mutant''s offspring. This has been interpreted as an intrinsic ability of genes to buffer genetic and environmental variation. A phenotypic capacitor is a gene that appears to mask phenotypic variation: when knocked out, the offspring shows more variability than the wild type. Theory predicts that this phenotypic potential should be correlated with a gene''s knockout fitness and its number of negative genetic interactions. Based on experimentally measured phenotypic capacity, it was suggested that knockout fitness was unimportant, but that phenotypic capacitors tend to be hubs in genetic and physical interaction networks.

Methodology/Principal Findings

We re-analyse the available experimental data in a combined model, which includes knockout fitness and network parameters as well as expression level and protein length as predictors of phenotypic potential. Contrary to previous conclusions, we find that the strongest predictor is in fact haploid knockout fitness (responsible for 9% of the variation in phenotypic potential), with an additional contribution from the genetic interaction network (5%); once these two factors are taken into account, protein-protein interactions do not make any additional contribution to the variation in phenotypic potential.

Conclusions/Significance

We conclude that phenotypic potential is not a mysterious “emergent” property of cellular networks. Instead, it is very simply determined by the overall fitness reduction of the organism (which in its compromised state can no longer compensate for multiple factors that contribute to phenotypic variation), and by the number (and presumably nature) of genetic interactions of the knocked-out gene. In this light, Hsp90, the prototypical phenotypic capacitor, may not be representative: typical phenotypic capacitors are not direct “buffers” of variation, but are simply genes encoding central cellular functions.     

Epigenetic variation in plant responses to defence hormones

Background and Aims

There is currently much speculation about the role of epigenetic variation as a determinant of heritable variation in ecologically important plant traits. However, we still know very little about the phenotypic consequences of epigenetic variation, in particular with regard to more complex traits related to biotic interactions.

Methods

Here, a test was carried out to determine whether variation in DNA methylation alone can cause heritable variation in plant growth responses to jasmonic acid and salicylic acid, two key hormones involved in induction of plant defences against herbivores and pathogens. In order to be able to ascribe phenotypic differences to epigenetic variation, the hormone responses were studied of epigenetic recombinant inbred lines (epiRILs) of Arabidopsis thaliana – lines that are highly variable at the level of DNA methylation but nearly identical at the level of DNA sequence.

Key Results

Significant heritable variation was found among epiRILs both in the means of phenotypic traits, including growth rate, and in the degree to which these responded to treatment with jasmonic acid and salicylic acid. Moreover, there was a positive epigenetic correlation between the responses of different epiRILs to the two hormones, suggesting that plant responses to herbivore and pathogen attack may have a similar molecular epigenetic basis.

Conclusions

This study demonstrates that epigenetic variation alone can cause heritable variation in, and thus potentially microevolution of, plant responses to defence hormones. This suggests that part of the variation of plant defences observed in natural populations may be due to underlying epigenetic, rather than entirely genetic, variation.     

Invasion strategies in clonal aquatic plants: are phenotypic differences caused by phenotypic plasticity or local adaptation?

Background and Aims

The successful spread of invasive plants in new environments is often linked to multiple introductions and a diverse gene pool that facilitates local adaptation to variable environmental conditions. For clonal plants, however, phenotypic plasticity may be equally important. Here the primary adaptive strategy in three non-native, clonally reproducing macrophytes (Egeria densa, Elodea canadensis and Lagarosiphon major) in New Zealand freshwaters were examined and an attempt was made to link observed differences in plant morphology to local variation in habitat conditions.

Methods

Field populations with a large phenotypic variety were sampled in a range of lakes and streams with different chemical and physical properties. The phenotypic plasticity of the species before and after cultivation was studied in a common garden growth experiment, and the genetic diversity of these same populations was also quantified.

Key Results

For all three species, greater variation in plant characteristics was found before they were grown in standardized conditions. Moreover, field populations displayed remarkably little genetic variation and there was little interaction between habitat conditions and plant morphological characteristics.

Conclusions

The results indicate that at the current stage of spread into New Zealand, the primary adaptive strategy of these three invasive macrophytes is phenotypic plasticity. However, while limited, the possibility that genetic diversity between populations may facilitate ecotypic differentiation in the future cannot be excluded. These results thus indicate that invasive clonal aquatic plants adapt to new introduced areas by phenotypic plasticity. Inorganic carbon, nitrogen and phosphorous were important in controlling plant size of E. canadensis and L. major, but no other relationships between plant characteristics and habitat conditions were apparent. This implies that within-species differences in plant size can be explained by local nutrient conditions. All together this strongly suggests that invasive clonal aquatic plants adapt to a wide range of habitats in introduced areas by phenotypic plasticity rather than local adaptation.     

Human Mammary Epithelial Cells Exhibit a Bimodal Correlated Random Walk Pattern

Background

Organisms, at scales ranging from unicellular to mammals, have been known to exhibit foraging behavior described by random walks whose segments confirm to Lévy or exponential distributions. For the first time, we present evidence that single cells (mammary epithelial cells) that exist in multi-cellular organisms (humans) follow a bimodal correlated random walk (BCRW).

Methodology/Principal Findings

Cellular tracks of MCF-10A pBabe, neuN and neuT random migration on 2-D plastic substrates, analyzed using bimodal analysis, were found to reveal the BCRW pattern. We find two types of exponentially distributed correlated flights (corresponding to what we refer to as the directional and re-orientation phases) each having its own correlation between move step-lengths within flights. The exponential distribution of flight lengths was confirmed using different analysis methods (logarithmic binning with normalization, survival frequency plots and maximum likelihood estimation).

Conclusions/Significance

Because of the presence of non-uniform turn angle distribution of move step-lengths within a flight and two different types of flights, we propose that the epithelial random walk is a BCRW comprising of two alternating modes with varying degree of correlations, rather than a simple persistent random walk. A BCRW model rather than a simple persistent random walk correctly matches the super-diffusivity in the cell migration paths as indicated by simulations based on the BCRW model.     

Seed dormancy distribution: explanatory ecological factors

Background and Aims

Knowledge of those traits that vary with latitude should be helpful in predicting how they may evolve locally under climate change. In the sea beet Beta vulgaris ssp. maritima, seed dormancy largely controls the timing of germination, is highly heritable and varies geographically; it is therefore thought to be selected by climate. The aim here was to characterize the variation in seed dormancy among sea beet populations across the French distribution area, as well as the ecological factors in situ that are correlated with and that could therefore select for seed dormancy. The relative importance of genetic inheritance vs. non-genetic variation is also evaluated.

Methods

The proportions of dormant seeds from 85 natural populations encompassing different climates over the whole French distribution area were measured under controlled conditions. Germination phenology was observed in a common garden experiment. Dormancy variation of seeds collected in situ was compared with that of seeds collected on plants grown in the greenhouse.

Key Results

The proportions of dormant seeds in the greenhouse were highly variable, covering almost the entire range from 0 to 1, and followed a geographical pattern from lower dormancy at high latitudes to high dormancy at low latitudes. The distribution of dormancy was positively correlated with yearly temperatures, especially summer temperatures. Minimum temperatures in winter did not significantly explain the trait variation. The genetic component of the total variation was significant and is probably completed by an important adjustment to the local conditions brought about by maternal adaptive phenotypic plasticity.

Conclusions

Dormancy in sea beet could be interpreted as a way to limit summer germination and spread germination over the first autumn and spring or following autumns. This highly heritable trait has the potential to evolve in the relatively near future because of climate change.     

Modification of flower architecture during early stages in the evolution of self-fertilization

Background and Aims

The evolution of selfing from outcrossing is characterized by a series of morphological changes to flowers culminating in the selfing syndrome. However, which morphological traits initiate increased self-pollination and which are accumulated after self-fertilization establishes is poorly understood. Because the expression of floral traits may depend on the conditions experienced by an individual during flower development, investigation of changes in mating system should also account for environmental and developmental factors. Here, early stages in the evolution of self-pollination are investigated by comparing floral traits among Brazilian populations of Eichhornia paniculata (Pontederiaceae), an annual aquatic that displays variation in selfing rates associated with the breakdown of tristyly to semi-homostyly.

Methods

Thirty-one Brazilian populations under uniform glasshouse conditions were compared to investigate genetic and environmental influences on flower size and stigma–anther separation (herkogamy), two traits that commonly vary in association with transitions to selfing. Within-plant variation in herkogamy was also examined and plants grown under contrasting environmental conditions were compared to examine to what extent this trait exhibits phenotypic plasticity.

Key Results

In E. paniculata a reduction in herkogamy is the principal modification initiating the evolution of selfing. Significantly, reduced herkogamy was restricted to the mid-styled morph and occurred independently of flower size. Significant genetic variation for herkogamy was detected among populations and families, including genotypes exhibiting developmental instability of stamen position with bimodal distributions of herkogamy values. Cloned genets exposed to contrasting growth conditions demonstrated environmental control of herkogamy and genotypic differences in plasticity of this trait.

Conclusions

The ability to modify herkogamy independently of other floral traits, genetic variation in the environmental sensitivity of herkogamy, and the production of modified and unmodified flowers within some individuals, reveal the potential for dynamic control of the mating system in a species that commonly confronts heterogeneous aquatic environments.Key words: Eichhornia paniculata, expressivity, flower morphology, herkogamy, phenotypic plasticity, pleiotropy, population variation, self-fertilization, stigma–anther separation, outcrossing, tristyly     

Venous Thromboembolism in an Industrial North American City: Temporal Distribution and Association with Particulate Matter Air Pollution

Background

Emerging evidence, mainly from Europe and Asia, indicates that venous thromboembolism (VTE) occurs most often in winter. Factors implicated in such seasonality are low temperature-mediated exacerbation of coagulation and high levels of particulate matter (PM) air pollution. However, in contrast to most European and Asian cities, particulate matter pollution peaks in the summer in many North American cities.

Objectives

We aimed to exploit this geographical difference and examine the temporal distribution of VTE in a cold-weather, North American city, Detroit, with a summer PM peak. Our goal was thereby to resolve the influence of temperature and PM levels on VTE.

Methods

Our retrospective, analytical semi-ecological study used chart review to confirm 1,907 acute, ambulatory VTE cases, divided them by location (Detroit versus suburban), and plotted monthly VTE frequency distributions. We used Environmental Protection Agency data to determine the temporal distribution of PM pollution components in Detroit. Suburban PM air pollution is presumed negligible and therefore not monitored.

Results

Acute VTE cases in Detroit (1,490) exhibited a summer peak (June 24^th) and differed from both a uniform distribution (P<0.01) and also that of 1,123 no-VTE cases (P<0.02). Levels of 10 µm diameter PM and coarse particle (2.5 to 10 µm) PM also exhibited summer peaks versus a winter peak for 2.5 µm diameter PM. Contrary to their urban counterparts, suburban cases of acute VTE (417) showed no monthly variation.

Conclusions

The summer peak of acute VTE in Detroit indicates that low temperature is not a major factor in VTE pathogenesis. In contrast, concordance of the 10 µm diameter PM, coarse particle, and the Detroit VTE monthly distributions, combined with no monthly suburban VTE variation, is consistent with a role for PM pollution. Furthermore, divergence of the VTE and 2.5 µm PM distributions suggests that particle size may play a role.     

Distribution of calcium (Ca) and magnesium (Mg) in the leaves of Brassica rapa under varying exogenous Ca and Mg supply

Background and Aims

Leafy vegetable Brassica crops are an important source of dietary calcium (Ca) and magnesium (Mg) and represent potential targets for increasing leaf Ca and Mg concentrations through agronomy or breeding. Although the internal distribution of Ca and Mg within leaves affects the accumulation of these elements, such data are not available for Brassica. The aim of this study was to characterize the internal distribution of Ca and Mg in the leaves of a vegetable Brassica and to determine the effects of altered exogenous Ca and Mg supply on this distribution.

Methods

Brassica rapa ssp. trilocularis ‘R-o-18’ was grown at four different Ca:Mg treatments for 21 d in a controlled environment. Concentrations of Ca and Mg were determined in fully expanded leaves using inductively coupled plasma-mass spectrometry (ICP-MS). Internal distributions of Ca and Mg were determined in transverse leaf sections at the base and apex of leaves using energy-dispersive X-ray spectroscopy (EDS) with cryo-scanning electron microscopy (cryo-SEM).

Key Results

Leaf Ca and Mg concentrations were greatest in palisade and spongy mesophyll cells, respectively, although this was dependent on exogenous supply. Calcium accumulation in palisade mesophyll cells was enhanced slightly under high Mg supply; in contrast, Mg accumulation in spongy mesophyll cells was not affected by Ca supply.

Conclusions

The results are consistent with Arabidopsis thaliana and other Brassicaceae, providing phenotypic evidence that conserved mechanisms regulate leaf Ca and Mg distribution at a cellular scale. The future study of Arabidopsis gene orthologues in mutants of this reference B. rapa genotype will improve our understanding of Ca and Mg homeostasis in plants and may provide a model-to-crop translation pathway for targeted breeding.     

Geographical differentiation in floral traits across the distribution range of the Patagonian oil-secreting Calceolaria polyrhiza: do pollinators matter?

Background and Aims

The underlying evolutionary processes of pollinator-driven floral diversification are still poorly understood. According to the Grant–Stebbins model speciation begins with adaptive local differentiation in the response to spatial heterogeneity in pollinators. Although this crucial process links the micro- and macroevolution of floral adaptation, it has received little attention. In this study geographical phenotypic variation was investigated in Patagonian Calceolaria polyrhiza and its pollinators, two oil-collecting bee species that differ in body size and geographical distribution.

Methods

Patterns of phenotypic variation were examined together with their relationships with pollinators and abiotic factors. Six floral and seven vegetative traits were measured in 45 populations distributed across the entire species range. Climatic and edaphic parameters were determined for 25 selected sites, 2–16 bees per site of the most frequent pollinator species were captured, and a critical flower–bee mechanical fitting trait involved in effective pollination was measured. Geographical patterns of phenotypic and environmental variation were examined using uni- and multivariate analyses. Decoupled geographical variation between corolla area and floral traits related to the mechanical fit of pollinators was explored using a Mantel test.

Key Results

The body length of pollinators and the floral traits related to mechanical fit were strongly correlated with each other. Geographical variation of the mechanical-fit-related traits was decoupled from variation in corolla size; the latter had a geographical pattern consistent with that of the vegetative traits and was mainly affected by climatic gradients.

Conclusions

The results are consistent with pollinators playing a key role in shaping floral phenotype at a geographical scale and promoting the differentiation of two floral ecotypes. The relationship between the critical floral-fit-related trait and bee length remained significant even in models that included various environmental variables and an allometric predictor (corolla area). The abiotic environment also has an important role, mainly affecting floral size. Decoupled geographical variation between floral mechanical-fit-related traits and floral size would represent a strategy to maintain plant–pollinator phenotypic matching in this environmentally heterogeneous area.     

Molecular and quantitative trait variation within and among small fragmented populations of the endangered plant species Psilopeganum sinense

Background and Aims

Natural selection and genetic drift are important evolutionary forces in determining genetic and phenotypic differentiation in plant populations. The extent to which these two distinct evolutionary forces affect locally adaptive quantitative traits has been well studied in common plant and animal species. However, we know less about how quantitative traits respond to selection pressures and drift in endangered species that have small population sizes and fragmented distributions. To address this question, this study assessed the relative strengths of selection and genetic drift in shaping population differentiation of phenotypic traits in Psilopeganum sinense, a naturally rare and recently endangered plant species.

Methods

Population differentiation at five quantitative traits (Q_ST) obtained from a common garden experiment was compared with differentiation at putatively neutral microsatellite markers (F_ST) in seven populations of P. sinense. Q_ST estimates were derived using a Bayesian hierarchical variance component method.

Key Results

Trait-specific Q_ST values were equal to or lower than F_ST. Neutral genetic diversity was not correlated with quantitative genetic variation within the populations of P. sinense.

Conclusions

Despite the prevalent empirical evidence for Q_ST > F_ST, the results instead suggest a definitive role of stabilizing selection and drift leading to phenotypic differentiation among small populations. Three traits exhibited a significantly lower Q_ST relative to F_ST, suggesting that populations of P. sinense might have experienced stabilizing selection for the same optimal phenotypes despite large geographical distances between populations and habitat fragmentation. For the other two traits, Q_ST estimates were of the same magnitude as F_ST, indicating that divergence in these traits could have been achieved by genetic drift alone. The lack of correlation between molecular marker and quantitative genetic variation suggests that sophisticated considerations are required for the inference of conservation measures of P. sinense from neutral genetic markers.     

The Predictive Performance and Stability of Six Species Distribution Models

Background

Predicting species’ potential geographical range by species distribution models (SDMs) is central to understand their ecological requirements. However, the effects of using different modeling techniques need further investigation. In order to improve the prediction effect, we need to assess the predictive performance and stability of different SDMs.

Methodology

We collected the distribution data of five common tree species (Pinus massoniana, Betula platyphylla, Quercus wutaishanica, Quercus mongolica and Quercus variabilis) and simulated their potential distribution area using 13 environmental variables and six widely used SDMs: BIOCLIM, DOMAIN, MAHAL, RF, MAXENT, and SVM. Each model run was repeated 100 times (trials). We compared the predictive performance by testing the consistency between observations and simulated distributions and assessed the stability by the standard deviation, coefficient of variation, and the 99% confidence interval of Kappa and AUC values.

Results

The mean values of AUC and Kappa from MAHAL, RF, MAXENT, and SVM trials were similar and significantly higher than those from BIOCLIM and DOMAIN trials (p<0.05), while the associated standard deviations and coefficients of variation were larger for BIOCLIM and DOMAIN trials (p<0.05), and the 99% confidence intervals for AUC and Kappa values were narrower for MAHAL, RF, MAXENT, and SVM. Compared to BIOCLIM and DOMAIN, other SDMs (MAHAL, RF, MAXENT, and SVM) had higher prediction accuracy, smaller confidence intervals, and were more stable and less affected by the random variable (randomly selected pseudo-absence points).

Conclusions

According to the prediction performance and stability of SDMs, we can divide these six SDMs into two categories: a high performance and stability group including MAHAL, RF, MAXENT, and SVM, and a low performance and stability group consisting of BIOCLIM, and DOMAIN. We highlight that choosing appropriate SDMs to address a specific problem is an important part of the modeling process.     

Genetic identity affects performance of species in grasslands of different plant diversity: an experiment with Lolium perenne cultivars

Background and Aims

Recent biodiversity research has focused on ecosystem processes, but less is known about responses of populations of individual plant species to changing community diversity and implications of genetic variation within species. To address these issues, effects of plant community diversity on the performance of different cultivars of Lolium perenne were analysed.

Methods

Populations of 15 genetic cultivars of Lolium perenne were established in experimental grasslands varying in richness of species (from 1 to 60) and functional groups (from 1 to 4). Population sizes, mean size of individual plants, biomass of individual shoots and seed production were measured in the first and second growing season after establishment.

Key Results

Population sizes of all cultivars decreased with increasing community species richness. Plant individuals formed fewer shoots with a lower shoot mass in more species-rich plant communities. A large proportion of variation in plant size and relative population growth was attributable to effects of community species and functional group richness, but the inclusion of cultivar identity explained additional 4–7 % of variation. Cultivar identity explained most variation (28–51 %) at the shoot level (biomass of individual tillers and reproductive shoots, seed production, heading stage). Coefficients of variation of the measured variables across plant communities were larger in cultivars with a lower average performance, indicating that this variation was predominantly due to passive growth reductions and not a consequence of larger adaptive plastic responses. No single cultivar performed best in all communities.

Conclusions

The decreasing performance of Lolium perenne in plant communities of increasing species richness suggests a regulation of competitive interactions by species diversity. Genetic variation within species provides a base for larger phenotypic variation and may affect competitive ability. However, heterogeneous biotic environments (= plant communities of different species composition) are important for the maintenance of intra-specific genetic variation.Key words: Biodiversity, competition, genetic variation, growth reduction, Lolium perenne, phenotypic plasticity, species richness     

Plant resource-use strategies: the importance of phenotypic plasticity in response to a productivity gradient for two subalpine species

Background and Aims

Functional traits are indicators of plant interactions with their environment and the resource-use strategies of species can be defined through some key functional traits. The importance of genetic variability and phenotypic plasticity in trait variations in response to a common environmental change was investigated in two subalpine species.

Methods

Two species with contrasted resource-use strategies, Dactylis glomerata and Festuca paniculata, were grown along a productivity gradient in a greenhouse experiment. Functional traits of different genotypes were measured to estimate the relative roles of phenotypic plasticity and genetic variability, and to compare their levels of phenotypic plasticity.

Key Results

Trait variability in the field for the two species is more likely to be the result of phenotypic plasticity rather than of genetic differentiation between populations. The exploitative species D. glomerata expressed an overall higher level of phenotypic plasticity compared with the conservative species F. paniculata. In addition to different amplitudes of phenotypic plasticity, the two species differed in their pattern of response for three functional traits relevant to resource use (specific leaf area, leaf dry matter content and leaf nitrogen content).

Conclusions

Functional trait variability was mainly the result of phenotypic plasticity, with the exploitative species showing greater variability. In addition to average trait values, two species with different resource-use strategies differed in their plastic responses to productivity.     

Analysis of structural diversity in wolf-like canids reveals post-domestication variants

Background

Although a variety of genetic changes have been implicated in causing phenotypic differences among dogs, the role of copy number variants (CNVs) and their impact on phenotypic variation is still poorly understood. Further, very limited knowledge exists on structural variation in the gray wolf, the ancestor of the dog, or other closely related wild canids. Documenting CNVs variation in wild canids is essential to identify ancestral states and variation that may have appeared after domestication.

Results

In this work, we genotyped 1,611 dog CNVs in 23 wolf-like canids (4 purebred dogs, one dingo, 15 gray wolves, one red wolf, one coyote and one golden jackal) to identify CNVs that may have arisen after domestication. We have found an increase in GC-rich regions close to the breakpoints and around 1 kb away from them suggesting that some common motifs might be associated with the formation of CNVs. Among the CNV regions that showed the largest differentiation between dogs and wild canids we found 12 genes, nine of which are related to two known functions associated with dog domestication; growth (PDE4D, CRTC3 and NEB) and neurological function (PDE4D, EML5, ZNF500, SLC6A11, ELAVL2, RGS7 and CTSB).

Conclusions

Our results provide insight into the evolution of structural variation in canines, where recombination is not regulated by PRDM9 due to the inactivation of this gene. We also identified genes within the most differentiated CNV regions between dogs and wolves, which could reflect selection during the domestication process.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-465) contains supplementary material, which is available to authorized users.     

Intraspecific karyotypic polymorphism is highly concordant with allozyme variation in Lysimachia mauritiana (Primulaceae: Myrsinoideae) in Taiwan: implications for the colonization history and dispersal patterns of coastal plants

Background and Aims

Investigating intraspecific karyotypic and genetic variations jointly can provide unique insights into how historical, ecological and cytogenetic factors influence microevolution. A coastal herb, Lysimachia mauritiana, exhibits extensive karyotypic polymorphism and displays a complex cytogeographic pattern across the Ryukyus. To explore whether a similar degree of chromosomal variation exists south of the Ryukyus, and in an attempt to ascertain the mechanisms that may have generated the patterns, comprehensive sampling was conducted in Taiwan.

Methods

Karyotypes were analysed at mitotic metaphase for 550 individuals from 42 populations throughout Taiwan Proper and its adjacent islands. In addition, genetic variation was estimated using 12 allozymes (21 loci) of 314 individuals sampled from 12 localities.

Key Results

Four chromosome numbers and eight cytotypes, including four endemic cytotypes, were detected. Cytotype distributions were highly structured geographically, with single cytotypes present in most populations and four major cytotypes dominating the north, east and south of Taiwan and the Penghu Archipelago. Allozyme variation was very low and F-statistics indicated an extremely high level of population differentiation, implying limited gene flow among populations. Cluster analysis of allozyme variation uncovered four geographic groups, each corresponding perfectly to the four dominant cytotypes. The geographic structure of cytotype distribution and allozyme variation probably resulted from severe genetic drift triggered by genetic bottlenecks, suggesting that Taiwanese populations were likely to be derived from four independent founder events. In the few localities with multiple cytotypes, cytogeographic patterns and inferences of chromosomal evolution revealed a trend of northward dispersal, consistent with the course of the Kuroshio Current that has been influential in shaping the coastal biota of the region.

Conclusions

The data elucidate the patterns of colonization and the effects of the Kuroshio Current on the distribution of L. mauritiana in Taiwan. These inferences are highly relevant to other coastal plant species in the region and will stimulate further studies.     

The TNFalpha gene relates to clinical phenotype in alpha-1-antitrypsin deficiency

Background

Genetic variation may underlie phenotypic variation in chronic obstructive pulmonary disease (COPD) in subjects with and without alpha 1 antitrypsin deficiency (AATD). Genotype specific sub-phenotypes are likely and may underlie the poor replication of previous genetic studies. This study investigated subjects with AATD to determine the relationship between specific phenotypes and TNFα polymorphisms.

Methods

424 unrelated subjects of the PiZZ genotype were assessed for history of chronic bronchitis, impairment of lung function and radiological presence of emphysema and bronchiectasis. A subset of subjects with 3 years consecutive lung function data was assessed for decline of lung function. Four single nucleotide polymorphisms (SNPs) tagging TNFα were genotyped using TaqMan^® genotyping technologies and compared between subjects affected by each phenotype and those unaffected. Plasma TNFα levels were measured in all PiZZ subjects.

Results

All SNPs were in Hardy-Weinberg equilibrium. A significant difference in rs361525 genotype (p = 0.01) and allele (p = 0.01) frequency was seen between subjects with and without chronic bronchitis, independent of the presence of other phenotypes. TNFα plasma level showed no phenotypic or genotypic associations.

Conclusion

Variation in TNFα is associated with chronic bronchitis in AATD.     

Effects of Sex on Intra-Individual Variance in Urinary Solutes in Stone-Formers Collected from a Single Clinical Laboratory

Background/Aims

Our work in a rodent model of urinary calcium suggests genetic and gender effects on increased residual variability in urine chemistries. Based on these findings, we hypothesized that sex would similarly be associated with residual variation in human urine solutes. Sex-related effects on residuals might affect the establishment of physiological baselines and error in medical assays.

Methods

We tested the effects of sex on residual variation in urine chemistry by estimating coefficients of variation (CV) for urinary solutes in paired sequential 24-h urines (≤72 hour interval) in 6,758 females and 9,024 males aged 16–80 submitted to a clinical laboratory.

Results

Females had higher CVs than males for urinary phosphorus overall at the False Discovery Rate (P<0.01). There was no effect of sex on CV for calcium (P>0.3). Males had higher CVs for citrate (P<0.01) from ages 16–45 and females higher CVs for citrate (P<0.01) from ages 56–80, suggesting effects of an extant oestral cycle on residual variance.

Conclusions

Our findings indicate the effects of sex on residual variance of the excretion of urinary solutes including phosphorus and citrate; differences in CV by sex might reflect dietary lability, differences in the fidelity of reporting or genetic differentiation in renal solute consistency. Such an effect could complicate medical analysis by the addition of random error to phenotypic assays. Renal analysis might require explicit incorporation of heterogeneity among factorial effects, and for sex in particular.