driftsel: an R package for detecting signals of natural selection in quantitative traits

Approaches and tools to differentiate between natural selection and genetic drift as causes of population differentiation are of frequent demand in evolutionary biology. Based on the approach of Ovaskainen et al. (2011), we have developed an R package (driftsel ) that can be used to differentiate between stabilizing selection, diversifying selection and random genetic drift as causes of population differentiation in quantitative traits when neutral marker and quantitative genetic data are available. Apart from illustrating the use of this method and the interpretation of results using simulated data, we apply the package on data from three‐spined sticklebacks (Gasterosteus aculeatus) to highlight its virtues. driftsel can also be used to perform usual quantitative genetic analyses in common‐garden study designs.     

The effect of isozyme selection on metric characters in an interspecific backcross of tomato — basis of an early screening procedure

Summary The extent of correlation was estimated between isozyme genotypes and the four widely segregating characters — leaf segment W/L ratio, stigma exsertion, fruit weight, and seed weight — in the first backcross of F₁ Lycopersicon esculentum x Solanum pennellii to the former parent. The inbred parents differ in their alleles at the 12 tested isozymic loci, which are known to mark a minimum of eight of the twelve tomato chromosomes. Based on the isozyme data, a mean heterozygosity value, ¯H, was calculated which estimates the proportion of pennillii alleles in each individual. Correlations between mean heterozygosity and observed levels of each quantitative trait were highly significant and positive or negative as expected from the relative parental values. Plants with the lowest mean heterozygosity — i.e., closest to the esculentum zymotype also had mean values closest to those of this parent amongst the whole backcross population for each of the quantitative traits.Bivariate and multiple regression analysis was used to evaluate the ability of isozymes vs diagnostic morphological characters to estimate the portion of recurrent parent genes carried in each backcross individual. The results suggest that isozyme data gives better estimates than single diagnostic morphological characters and approach the level obtained by combinations of three morphological traits. Since electrophoretic determinations are made on small seedlings, selection at that stage can effect great savings of space and effort by greatly deminishing the size of the population needed at maturity. As such, isozyme selection would precede morphological selection but not replace it, thus the predictive value of these biochemical markers as well as diagnostic morphological characters could be obtained.     

Efficient QTL detection for nonhost resistance in wild lettuce: backcross inbred lines versus F2 population

In plants, several population types [F₂, recombinant inbred lines, backcross inbred lines (BILs), etc.] are used for quantitative trait locus (QTL) analyses. However, dissection of the trait of interest and subsequent confirmation by introgression of QTLs for breeding purposes has not been as successful as that predicted from theoretical calculations. More practical knowledge of different QTL mapping approaches is needed. In this recent study, we describe the detection and mapping of quantitative resistances to downy mildew in a set of 29 BILs of cultivated lettuce (L. sativa) containing genome segments introgressed from wild lettuce (L. saligna). Introgression regions that are associated with quantitative resistance are considered to harbor a QTL. Furthermore, we compare this with results from an already existing F₂ population derived from the same parents. We identified six QTLs in our BIL approach compared to only three in the F₂ approach, while there were two QTLs in common. We performed a simulation study based on our actual data to help us interpret them. This revealed that two newly detected QTLs in the BILs had gone unnoticed in the F₂, due to a combination of recessiveness of the trait and skewed segregation, causing a deficit of the wild species alleles. This study clearly illustrates the added value of extended genetic studies on two different population types (BILs and F₂) to dissect complex genetic traits.     

载畜率对短花针茅荒漠草原灌木及其邻近土壤养分含量的影响

草地灌丛化现象在草地生态系统上广泛发生。放牧是人类利用草原的重要方式,通过分析不同载畜率下荒漠草原灌木种群及其邻近土壤养分含量的变化,可研究放牧干扰下不同灌木种群的耐牧特性,对深入了解荒漠草原植物群落演替机制具有重要意义。以荒漠草原灌木小叶锦鸡儿(Caragana microphylla)、半灌木驼绒藜(Ceratoides latens)及小半灌木冷蒿(Artemisia frigida)和木地肤(Kochia prostrata)(下称为“灌木”)为研究对象,探究不同载畜率下各个灌木种群的密度、高度、盖度及地上生物量(下称为“数量特征值”)及其邻近土壤养分含量。结果表明:冷蒿的数量特征值均随着载畜率的增加而降低,其他植物种群的数量特征值均在CK或LG区出现最大值,且不同灌木邻近土壤养分含量随着土壤深度的增加而下降(P < 0.05)。不同灌木邻近土壤全氮含量随着载畜率增加而下降;冷蒿邻近有机碳含量在CK区最高,小叶锦鸡儿邻近速效磷含量在HG区最高,其余灌木邻近有机碳、速效磷含量在LG区最高。灌木种群数量特征与土壤养分的关系为:土壤有机碳与冷蒿和驼绒藜的高度、盖度、地上生物量呈正相关,土壤速效磷与木地肤高度、地上生物量呈显著负相关。因此,载畜率均会对灌木植物种群的数量特征值及其邻近土壤养分含量产生影响。     

Quantitative and qualitative transitions of methanogen community structure during the batch anaerobic digestion of cheese-processing wastewater

Qualitative and quantitative shifts in methanogen community structure, associated with process performance data, were investigated during the batch anaerobic digestion of a cheese-processing wastewater, whey permeate. Denaturing gradient gel electrophoresis (DGGE) and real-time PCR techniques were applied to obtain qualitative and quantitative microbial data sets, respectively, based on methanogen 16S rRNA genes. Throughout the operation, dynamic variations in both qualitative and quantitative community structures were observed, with repeated shifts in dominance between the aceticlastic Methanosarcinaceae (suggested mainly by the detection of a Methanosarcina-like population) and the hydrogenotrophic Methanomicrobiales (suggested mainly by the detection of a Methanofollis-like population). This trend corresponded well to the diauxic utilization of acetate and longer-chain fatty acids (C₃–C₆), mainly propionate. Joint-plot non-metric multidimensional scaling (NMS) analysis demonstrated that the qualitative and quantitative community shifts had significant correlations with the composition of residual organic acids and the methane production rate, respectively. This suggests the potential use of microbial community shift analysis as an indicative tool for diagnosing anaerobic digestion processes. The results suggest that more attention should be directed to quantitative, as well as qualitative, approaches for a better understanding of anaerobic digestion, particularly in terms of biogas production efficiency, under dynamic and transitional conditions.     

BRINGING HABITAT INFORMATION INTO STATISTICAL TESTS OF LOCAL ADAPTATION IN QUANTITATIVE TRAITS: A CASE STUDY OF NINE‐SPINED STICKLEBACKS

Detection of footprints of historical natural selection on quantitative traits in cross‐sectional data sets is challenging, especially when the number of populations to be compared is small and the populations are subject to strong random genetic drift. We extend a recent Bayesian multivariate approach to differentiate between selective and neutral causes of population differentiation by the inclusion of habitat information. The extended framework allows one to test for signals of selection in two ways: by comparing the patterns of population differentiation in quantitative traits and in neutral loci, and by comparing the similarity of habitats and phenotypes. We illustrate the framework using data on variation of eight morphological and behavioral traits among four populations of nine‐spined sticklebacks (Pungitius pungitius). In spite of the strong signal of genetic drift in the study system (average F_ST = 0.35 in neutral markers), strong footprints of adaptive population differentiation were uncovered both in morphological and behavioral traits. The results give quantitative support for earlier qualitative assessments, which have attributed the observed differentiation to adaptive divergence in response to differing ecological conditions in pond and marine habitats.     

EXAMINATION OF TWO DIMENSIONAL SPATIAL PATTERN OF PERIPHYTIC DIATOMS USING AN ADHESIVE SURFICIAL PEEL TECHNIQUE1

A simple surficial peel technique using adhesive tape was developed for quantitative removal of haptobenthic diatom communities from topographically simple substrata. The method combines high removal efficiency with low peel distortion, permitting the use of spatial statistics to test whether populations are distributed in the peel randomly or form aggregated or uniform patterns. Using this technique, the microdistribution of Cocconeis placentula Ehr. on a smooth acrylic rod was examined. Using conventional nearest neighbor analyses, a clonal population of C. placentula. characterized by an indentation of the value margin, was significantly aggregated, whereas the overall C. placentula population was uniform or aggregated depending on whether the method of analysis allowed for cell size. Using refined nearest neighbor analysis, the indented population was aggregated, and the overall population was random at distances greater than cell size. The results suggest that the indented clone was weakly motile following cell division and that its directional bearing was random.     

Quantitative morphometrical analysis of a North African population of <Emphasis Type="Italic">Drosophila melanogaster</Emphasis>: sexual dimorphism,and comparison with European populations

Genetic variability of quantitative traits was investigated in aMoroccan population of Drosophila melanogaster, with an isofemale line design. Results were compared with data previously obtained from French populations. Although the environmental and thermal conditions are very different in France and Morocco, only two significant differences were observed: a shorter wing and a lighter abdomen pigmentation in Morocco. It is, therefore, concluded that Moroccan D. melanogaster are quite typical temperate flies, belonging to the Palaearctic region, and very different from the ancestral Afrotropical populations. Almost all traits were genetically variable, as shown by significant intraclass correlations among lines. Genetic correlations were highly significant among three size-related traits, while much lower between size and bristle numbers. Fluctuating asymmetry was greater for abdominal bristles than for sternopleural bristles. Sex dimorphism, analysed as a female/male ratio, was identical in French and Moroccan populations. Examination of the thorax length/thorax width ratio showed that the thorax is more elongated in females. Sexual dimorphism of wing length was significantly more correlated to thorax width than to thorax length. The results illustrate the value of measuring numerous quantitative traits on the same flies for characterizing the genetic architecture of a natural population. In several cases, and especially for genetic correlations, some interesting suggestions could be made, which should be confirmed, or invalidated, by more extensive investigations.     

Microbial growth dynamics on the basis of individual budgets

The popular theories for microbial dynamics by Monod, Pirt and Droop are shown to be special cases of a model for individual budgets, in which growth and maintenance are on the expense of reserve materials. The dynamics of reserve materials is a first order process with a relaxation time proportional to cell length; maintenance is proportional to cell volume, and uptake, which depends hyperbolically on substrate density, is proportional to cell volume as well. Because of the latter, population dynamics depends on the behaviour of the individuals in a simple way, such that the cell volume distribution has no quantitative effect.When uptake is proportional to the surface area of the cell, which is realistic from a physical point of view, the relation between the individual level and the population one becomes more complicated and the cell size and shape distribution affects population dynamics. It is shown how the changing shape of rods modifies uptake and, consequently, growth.The concept of energy conductance, defined as the ratio, of the maximum surface area specific uptake and the volume specific energy reserve has been introduced in the analysis of microbial dynamics. The first tentative results indicate that the value for E. coli is close to the mean value for a wide variety of animals.Properties of the model for cell suspension at constant substrate densities are analyzed and tested against a variety of experimental data from the literature on both the individual and the population level.     

Mammalian herbivores reveal marked genetic divergence among populations of an endangered plant species

Quantitative genetically based traits in dominant and keystone tree species can have extended effects on other biota and also on ecosystem processes. This has direct implications for managed plant systems, where choice of genetic stock in conservation or commercial plantings will affect the ecological and evolutionary trajectory of the associated biotic communities. Hence an understanding of genetic variation in quantitative traits, especially those that relate directly to fitness, should be incorporated into the management of species. In plants, quantitative traits such as foliar defences that mediate the complexity of biotic interactions (e.g. herbivory), may be key fitness traits to consider in the management of gene pools of species that are of high conservation value. In this paper we examine the interactions of an endangered eucalypt species, Eucalyptus morrisbyi and a marsupial herbivore, the common brushtail possum Trichosurus vulpecula. We investigate the genetic variability of resistance of plants sourced from two populations and genetic variability in foliage defences as key quantitative traits that may be essential for survival of this eucalypt species. Trichosurus vulpecula detect clear genetic divergence in the two E. morrisbyi populations as evidenced by their browsing preferences in the field. In addition, trees from the more susceptible population (Calverts Hill) suffered fitness consequences with lower flowering than trees from the more resistant population (Risdon Hills). Field feeding preferences were confirmed in captive feeding trials arguing differences were due to foliar attributes consistent with the genetic‐based differences observed in key chemical and physical foliage traits. Biotic interactions such as herbivory may affect populations of rare plant species. Results of this study highlight the need to understand the degree of genetic differentiation of resistance to herbivores and in the quantitative traits mediating these interactions in species of high conservation value, as these traits affect the adaptive potential of populations.     

Comparison of genetic differentiation at marker loci and quantitative traits

The comparison of the degree of differentiation in neutral marker loci and genes coding quantitative traits with standardized and equivalent measures of genetic differentiation (F_ST and Q_ST, respectively) can provide insights into two important but seldom explored questions in evolutionary genetics: (i) what is the relative importance of random genetic drift and directional natural selection as causes of population differentiation in quantitative traits, and (ii) does the degree of divergence in neutral marker loci predict the degree of divergence in genes coding quantitative traits? Examination of data from 18 independent studies of plants and animals using both standard statistical and meta‐analytical methods revealed a number of interesting points. First, the degree of differentiation in quantitative traits (Q_ST) typically exceeds that observed in neutral marker genes (F_ST), suggesting a prominent role for natural selection in accounting for patterns of quantitative trait differentiation among contemporary populations. Second, the F_ST – Q_ST difference is more pronounced for allozyme markers and morphological traits, than for other kinds of molecular markers and life‐history traits. Third, very few studies reveal situations were Q_ST < F_ST, suggesting that selection pressures, and hence optimal phenotypes, in different populations of the same species are unlikely to be often similar. Fourth, there is a strong correlation between Q_ST and F_ST indices across the different studies for allozyme (r=0.81), microsatellite (r=0.87) and combined (r=0.75) marker data, suggesting that the degree of genetic differentiation in neutral marker loci is closely predictive of the degree of differentiation in loci coding quantitative traits. However, these interpretations are subject to a number of assumptions about the data and methods used to derive the estimates of population differentiation in the two sets of traits.     

An alternative to Lotka-Volterra competition in coarse-grained environments

Competition in a coarse-grained heterogeneous environment is considered. It is assumed that each individual adjust has position within the macrohabitat so as to try to maximize a utility whose value is a function of position within the habitat and of the population density at that position. Robust qualitative conclusions concerning the resulting population behavior relate niche breadth, niche shift, and resource partitioning to changes in population numbers. In particular populations avoid competition by reducing coarse-grained niche overlap so that overlap is a measure not of the degree of competition but of its absence. Specific models of exploitation or interference competition give specific quantitative results which are summarized. Competition equations are derived from underlying models which imply Lotka-Volterra equations in a fine-grained environment (MacArthur, R., and Levins, R. 1967. Amer. Natur.101, 377–385) but which are nonlinear in per capita growth in a coarse-grained one. The findings are relevant to theoretical studies of competition, limiting similarity, species packing, and the evolution of niche position as well as to practical problems of data analysis and resource management. The extension to predator-prey interactions is outlined.     

Quantifying the contribution of immigration to population dynamics: a review of methods,evidence and perspectives in birds and mammals

The demography of a population is often reduced to the apparent (or local) survival of individuals and their realised fecundity within a study area defined according to logistical constraints rather than landscape features. Such demographics are then used to infer whether a local population contributes positively to population dynamics across a wider landscape context. Such a simplistic approach ignores a fundamental process underpinning population dynamics: dispersal. Indeed, it has long been accepted that immigration contributed by dispersers that emigrated from neighbouring populations may strongly influence the net growth of a local population. To date however, we lack a clear picture of how widely immigration rate varies both among and within populations, in relation to extrinsic and intrinsic ecological conditions, even for the best‐studied avian and mammalian populations. This empirical knowledge gap precludes the emergence of a sound conceptual framework that ought to inform conservation and population ecology. This review, conducted on both birds and mammals, has thus three complementary objectives. First, we describe and evaluate the relative merits of methods used to quantify immigration and how they relate to widely applicable metrics. We identify two simple and unifying metrics to measure immigration: the immigration rate i_t defined as the ratio of the number of immigrants present in the population at time t + 1 and the total breeding population in year t, and π_t , the proportion of immigrants among new recruits (i.e. new breeders). Two recently developed methods are likely to provide the most valuable data on immigration in the near future: individual parentage (rather than population) assignments based on genetic sampling, and spatially explicit integrated population models combining multiple sources of demographic data (survival, fecundity and population counts). Second, we report on a systematic literature review of studies providing a quantitative measure of immigration. Although the diversity of methods employed precludes detailed analyses, it appears that the number of immigrants exceeds locally born individuals in recruitment for most avian populations (median π_t  = 0.57, N = 45 estimates from 37 studies), a figure twofold higher than estimated for mammalian populations (median π_t  = 0.26, N = 33 estimates from 11 studies). Third, recent quantitative studies reveal that immigration can be the main driver of temporal variation in population growth rates, across a wide array of demographic and spatial contexts. To what extent immigration acts as a regulatory process has however been considered only rarely to date and deserves more attention. Overall, it is likely that most populations benefit from immigrants without necessarily being sink populations. Furthermore, we suggest that quantitative estimates of immigration should be core to future demographic studies and plead for more empirical evidence about the ways in which immigration interacts with local demographic processes to shape population dynamics. Finally, we discuss how to tackle spatial population dynamics by exploring, beyond the classical source–sink framework, the extent to which populations exchange individuals according to spatial scale and type of population distribution throughout the landscape.     

The relationship between neutral lipid reserves and infectivity for hatched and dormant juveniles of Globodera spp.

A quantitative histochemical technique based on scanning microdensitometry has been used to investigate neutral lipid utilisation by hatched and dormant juveniles of Globodera rostochiensis and Globodera pallida. During storage in water at 20°C, hatched juveniles of the two species showed no statistical difference in their rate of lipid utilisation. A semi-logarithmic curve fitted to the pooled data suggests that 50% relative utilisation occurred after 36 ± 4 days of storage. Measurement of the neutral lipid reserves for unhatched juveniles of G. pallida dormant in field soils in Northern England for a maximum of 14 yr showed a reduced rate of metabolism with a 50% loss of neutral lipid reserves after 7·5 ± 1·1 yr. The use of neutral lipid reserves by the hatched, starved juveniles was correlated with their survival and with a loss of both locomotor activity and an ability to infect tomato seedlings. Furthermore, results suggest that a loss of mobility by juveniles from field populations of G. pallida immediately after hatching was more closely related to their neutral lipid reserves than the duration of their dormancy. Infection of plants was also reduced for one population. This suggests that measurement of the neutral lipid reserves of a population may be of value for modifying the economic threshold to take account of changes in infectivity during prolonged rotations.     

Null model analyses of temporal patterns of bird assemblages and their foraging guilds revealed the predominance of positive and random associations

Patterns of species associations have been commonly used to infer interactions among species. If species positively co‐occur, they may form predominantly neutral assemblages, and such patterns suggest a relatively weak role for compensatory dynamics. The main objective of this study was to test this prediction on temporal samples of bird assemblages (n = 19, 10–57 years) by the presence/absence and quantitative null models on assemblage and guild levels. These null model outcomes were further analyzed to evaluate the effects of various data set characteristics on the outcomes of the null models. The analysis of two binary null models in combination with three association indices revealed 20% with significant aggregations, 61% with random associations, and only 19% with significant segregations (n = 95 simulations). The results of the quantitative null model simulations detected more none‐random associations: 61% aggregations, 6% random associations, and 33% segregations (n = 114 simulations). Similarly, quantitative analyses on guild levels showed 58% aggregations, 20% segregations, and 22% random associations (n = 450 simulations). Bayesian GLMs detected that the outcomes of the binary and quantitative null models applied to the assemblage analyses were significantly related to census plot size, whereas the outcomes of the quantitative analyses were also related to the mean population densities of species in the data matrices. In guild‐level analyses, only 9% of the GLMs showed a significant influence of matrix properties (plot size, matrix size, species richness, and mean species population densities) on the null model outcomes. The results did not show the prevalence of negative associations that would have supported compensatory dynamics. Instead, we assume that a similar response of the majority of species to climate‐driven and stochastic factors may be responsible for the revealed predominance of positive associations.     

A Sizer model for cell differentiation in Arabidopsis thaliana root growth

Plant roots grow due to cell division in the meristem and subsequent cell elongation and differentiation, a tightly coordinated process that ensures growth and adaptation to the changing environment. How the newly formed cells decide to stop elongating becoming fully differentiated is not yet understood. To address this question, we established a novel approach that combines the quantitative phenotypic variability of wild‐type Arabidopsis roots with computational data from mathematical models. Our analyses reveal that primary root growth is consistent with a Sizer mechanism, in which cells sense their length and stop elongating when reaching a threshold value. The local expression of brassinosteroid receptors only in the meristem is sufficient to set this value. Analysis of roots insensitive to BR signaling and of roots with gibberellin biosynthesis inhibited suggests distinct roles of these hormones on cell expansion termination. Overall, our study underscores the value of using computational modeling together with quantitative data to understand root growth.     

Association Tests for a Censored Quantitative Trait and Candidate Genes in Structured Populations with Multilevel Genetic Relatedness

Summary Several statistical methods for detecting associations between quantitative traits and candidate genes in structured populations have been developed for fully observed phenotypes. However, many experiments are concerned with failure‐time phenotypes, which are usually subject to censoring. In this article, we propose statistical methods for detecting associations between a censored quantitative trait and candidate genes in structured populations with complex multiple levels of genetic relatedness among sampled individuals. The proposed methods correct for continuous population stratification using both population structure variables as covariates and the frailty terms attributable to kinship. The relationship between the time‐at‐onset data and genotypic scores at a candidate marker is modeled via a parametric Weibull frailty accelerated failure time (AFT) model as well as a semiparametric frailty AFT model, where the baseline survival function is flexibly modeled as a mixture of Polya trees centered around a family of Weibull distributions. For both parametric and semiparametric models, the frailties are modeled via an intrinsic Gaussian conditional autoregressive prior distribution with the kinship matrix being the adjacency matrix connecting subjects. Simulation studies and applications to the Arabidopsis thaliana line flowering time data sets demonstrated the advantage of the new proposals over existing approaches.     

Determining trophic niche width: an experimental test of the stable isotope approach

Determining the trophic niche width of an animal population and the relative degree to which a generalist population consists of dietary specialists are long‐standing problems of ecology. It has been proposed that the variance of stable isotope values in consumer tissues could be used to quantify trophic niche width of consumer populations. However, this promising idea has not yet been rigorously tested. By conducting controlled laboratory experiments using model consumer populations (Daphnia sp., Crustacea) with controlled diets, we investigated the effect of individual‐ and population‐level specialisation and generalism on consumer δ¹³C mean and variance values. While our experimental data follow general expectations, we extend current qualitative models to quantitative predictions of the dependence of isotopic variance on dietary correlation time, a measure for the typical time over which a consumer changes its diet. This quantitative approach allows us to pinpoint possible procedural pitfalls and critical sources of measurement uncertainty. Our results show that the stable isotope approach represents a powerful method for estimating trophic niche widths, especially when taking the quantitative concept of dietary correlation time into account.     

QUANTIFYING EVOLUTIONARY POTENTIAL OF MARINE FISH LARVAE: HERITABILITY,SELECTION, AND EVOLUTIONARY CONSTRAINTS

For many marine fish, intense larval mortality may provide considerable opportunity for selection, yet much less is known about the evolutionary potential of larval traits. We combined field demographic studies and manipulative experiments to estimate quantitative genetic parameters for both larval size and swimming performance for a natural population of a common coral‐reef fish, the bicolor damselfish (Stegastes partitus). We also examined selection on larval size by synthesizing information from published estimates of selective mortality. We introduce a method that uses the Lande–Arnold framework for examining selection on quantitative traits to empirically reconstruct adaptive landscapes. This method allows the relationship between phenotypic value and fitness components to be described across a broad range of trait values. Our results suggested that despite strong viability selection for large larvae and moderate heritability (h²= 0.29), evolutionary responses of larvae would likely be balanced by reproductive selection favoring mothers that produce more, smaller offspring. Although long‐term evolutionary responses of larval traits may be constrained by size‐number trade‐offs, our results suggest that phenotypic variation in larval size may be an ecologically important source of variability in population dynamics through effects on larval survival and recruitment to benthic populations.