A Model for Transgenerational Imprinting Variation in Complex Traits

Despite the fact that genetic imprinting, i.e., differential expression of the same allele due to its different parental origins, plays a pivotal role in controlling complex traits or diseases, the origin, action and transmission mode of imprinted genes have still remained largely unexplored. We present a new strategy for studying these properties of genetic imprinting with a two-stage reciprocal F mating design, initiated with two contrasting inbred lines. This strategy maps quantitative trait loci that are imprinted (i.e., iQTLs) based on their segregation and transmission across different generations. By incorporating the allelic configuration of an iQTL genotype into a mixture model framework, this strategy provides a path to trace the parental origin of alleles from previous generations. The imprinting effects of iQTLs and their interactions with other traditionally defined genetic effects, expressed in different generations, are estimated and tested by implementing the EM algorithm. The strategy was used to map iQTLs responsible for survival time with four reciprocal F populations and test whether and how the detected iQTLs inherit their imprinting effects into the next generation. The new strategy will provide a tool for quantifying the role of imprinting effects in the creation and maintenance of phenotypic diversity and elucidating a comprehensive picture of the genetic architecture of complex traits and diseases.     

Covariation in Insular Life-history Traits of the Rice Frog(Fejervarya limnocharis)in Eastern China

Although shifts in life-history traits of insular vertebrates, as compared with mainland populations, have been observed in many taxa, few studies have examined the relationships among individual life-history traits on islands. Lifehistory theory also predicts that there is a trade-off between body size and reproductive effort, and between egg size and clutch size. We surveyed the rice frog, Fejervarya limnocharis, on 20 islands within the Zhoushan Archipelago and two nearby sites on the mainland of China to compare differences in life-history traits and to explore relationships among those traits. Rice frog females reached a greater body size on half of the smaller islands among the total 20 surveyed islands, and larger egg size, decreased clutch size and reduced reproductive effort on most of the islands when compared to the two mainland sites. Insular body size was negatively correlated with reproductive effort. There was a negative correlation between egg size and clutch size. Results suggest that life-history theory provides a good explanation for co-variation between body size and reproductive effort, and between egg size and clutch size in rice frogs on the islands.     

A Pleiotropic Nonadditive Model of Variation in Quantitative Traits

A model of mutation-selection-drift balance incorporating pleiotropic and dominance effects of new mutations on quantitative traits and fitness is investigated and used to predict the amount and nature of genetic variation maintained in segregating populations. The model is based on recent information on the joint distribution of mutant effects on bristle traits and fitness in Drosophila melanogaster from experiments on the accumulation of spontaneous and P element-induced mutations. These experiments suggest a leptokurtic distribution of effects with an intermediate correlation between effects on the trait and fitness. Mutants of large effect tend to be partially recessive while those with smaller effect are on average additive, but apparently with very variable gene action. The model is parameterized with two different sets of information derived from P element insertion and spontaneous mutation data, though the latter are not fully known. They differ in the number of mutations per generation which is assumed to affect the trait. Predictions of the variance maintained for bristle number assuming parameters derived from effects of P element insertions, in which the proportion of mutations with an effect on the trait is small, fit reasonably well with experimental observations. The equilibrium genetic variance is nearly independent of the degree of dominance of new mutations. Heritabilities of between 0.4 and 0.6 are predicted with population sizes from 10(4) to 10(6), and most of the variance for the metric trait in segregating populations is due to a small proportion of mutations (about 1% of the total number) with neutral or nearly neutral effects on fitness and intermediate effects on the trait (0.1-0.5σ(P)). Much of the genetic variance is contributed by recessive or partially recessive mutants, but only a small proportion (about 10%) of the genetic variance is dominance variance. The amount of apparent selection on the trait itself generated by the model is very small. If a model is assumed in which all mutation events have an effect on the quantitative trait, the majority of the genetic variance is contributed by deleterious mutations with tiny effects on the trait. If such a model is assumed for viability, the heritability is about 0.1, independent of the population size.     

Lifestyle-Based Approaches Provide Insights into Body Size Variation Across Environmental Gradients in Anurans

Body size of organisms as a fitness-related phenotype has evolved in response to local conditions, often through the size-dependent thermoregulatory mechanisms. The direction and degree of this response should depend on animals’ lifestyle in terms of the preference for terrestrial or aquatic conditions, especially so for adult anurans that differ in lifestyle among species but all must maintain certain body temperatures for metabolism. It may be expected that anuran species frequently exposed to terrestrial environments characterized by fluctuant thermal conditions are more plastic in body size along thermal gradients than those highly relaying on aquatic environments where thermal conditions are relatively stable. We test this prediction using both interspecific and intraspecific data. With anurans in China as the model organisms, we show that across terrestrial species but not aquatic species, body size decreases with increasing ambient temperature. From the published literature worldwide, we summarized that more terrestrial versus fewer aquatic species follow the predicted ecogeographical size patterns. In addition, both interspecific and intraspecific data reveal that arboreal anurans do not exhibit the size cline, probably because relatively warm climates experienced by these species impose weak selective pressures on heat conservation or adaptation to tree-climbing constrains the variation in body size. Our finding highlights the importance of taking lifestyle into account when assessing macroevolutionary trends in body size for anurans in particular and ectothermic taxa in general.     

Interpreting Geographic Variation in Life-History Traits

The geographic variation in the length of the larval periodand the size at metamorphosis of the wood frog,Rana sylvatica,is examined for populations in the tundra of Canada, the mountainsof Virginia, and the lowlands of Maryland. We argue that theobserved differences in developmental plasticity, heriisbilitiesand genetic covariances of traits among localities result fromdifferential selection pressures in each environment, and arerelated to the physiological constraints inherent in developmentand to the degree of compromise between the timing and sizeat metamorphosis allowed in each environment. In Maryland populationsfitness has been maximized by evolutionary changes in size alone;body size in this population is canalized, has low heritabilityand is highly correlated with juvenile survival relative todevelopmental time. In Canada, minimum developmental time yieldsmaximum fitness; the length of the larval period in this populationis canalized and genetically monomorphic relative to body size.In contrast, fitness in the Virginia populations has been determinedby correlated and pleiotropic effects of genes on both developmentaltime and larval body size, and both traits are equally canalized,affect juvenile survivorship equally and display moderate heritabilities.These results stress the importance of interpreting variationin life-history traits relative to constraints inherent in developmentand those imposed by the environment. Heritability and survivorshipdata support the general notion that fitness traits should havelow levels of additive genetic variation, but also suggest thatantagonistic pleiotropy may act to preserve genetic variationin fitness traits under simultaneous selection, and cautionagainst inferring evolutionary importance of individual traitswithout considering the possible presence of pleiotropy.     

Selection for Antimicrobial Peptide Diversity in Frogs Leads to Gene Duplication and Low Allelic Variation

Antimicrobial peptides are highly diverse pathogen-killing molecules. In many taxa, their evolution is characterized by positive selection and frequent gene duplication. It has been proposed that genes encoding antimicrobial peptides might be subject to balancing selection and/or an enhanced mutation rate, but these hypotheses have not been well evaluated because allelic variation has rarely been studied at antimicrobial peptide loci. We present an evolutionary analysis of novel antimicrobial peptide genes from leopard frogs, Rana. Our results demonstrate that a single genome contains multiple homologous copies, among which there is an excess of nonsynonymous nucleotide site divergence relative to that expected from synonymous site divergence. Thus, we confirm the trends of recurrent duplication and positive selection. Allelic variation is quite low relative to interspecies divergence, indicating a recent positive selective sweep with no evidence of balancing selection. Repeated gene duplication, rather than a balanced maintenance of divergent allelic variants at individual loci, appears to be how frogs have responded to selection for a diverse suite of antimicrobial peptides. Our data also support a pattern of enhanced synonymous site substitution in the mature peptide region of the gene, but we cannot conclude that this is due to an elevated mutation rate.     

Differential Evolution of Advertisement Call Traits in Dart-Poison Frogs (Anura: Dendrobatidae)

The ability to recognise and discriminate between heterospecific and conspecific individuals plays an essential role in mate choice, reproductive isolation and thus species diversification. Many animals discriminate based on advertisement calls, whose evolution may be driven by a variety of forces such as natural selection, sexual selection or stochastic processes. The relative importance of stochastic processes acting on a given trait is usually correlated with its phylogenetic signal. Mate-recognition signals are complex traits composed of multiple features that could potentially respond independently to evolutionary forces. The advertisement call of anurans is used in species recognition and mate choice. In this study, we estimate the phylogenetic signal for body size and a suite of traits describing the male advertisement call from dart-poison frogs (Anura: Dendrobatidae). We found a surprisingly high phylogenetic signal for all call traits. In addition, call traits varied in their degree of phylogenetic signal, suggesting that evolutionary forces have been acting differently on different traits. Pulse duration showed the strongest phylogenetic signal. Peak frequency and body size were correlated and presented high phylogenetic signal indicating that the evolution of one trait may be driving or constraining the other. Since most variation in call traits can be explained by the phylogenetic history of the species, we cannot reject the hypothesis that stochastic processes account for significant evolutionary divergence in frog calls.     

Geographic Variation in Male Sexual Signals in Strawberry Poison Frogs (Dendrobates pumilio)

In this paper, we compare the advertisement calls of 207 neotropical strawberry poison frogs (Dendrobates pumilio) collected in 21 localities along a transect from northern Costa Rica to western Panama. Populations varied most in call duration and call rate, while pulse rate and duty cycle were less variable. Multivariate analyses showed that call variation followed a cline with higher call rates, shorter calls, lower duty cycles and higher pulse rates in the southeast. Body size decreased towards the southeast and explained most variation in dominant frequency, as well as some residual variation in call rate. We conclude that a combination of geography and morphology is largely responsible for call variation within this species. Two inferred bio‐acoustic groups were roughly in accordance with two genetic groups, geographically separated in central Costa Rica. However, genetic distances among populations did not co‐vary with call dissimilarity after correction for geographic distances. Thus, differences in calls between genetic groups are probably mainly a result of clinal variation. These findings agree with the general observation that bio‐acoustic variation is often not (highly) associated with genetic divergence. Moreover, colour polymorphism observed among Panamanian populations was not reflected in a higher variability in call parameters relative to the monomorphic Costa Rican populations.     

A Review of Spatial Variation of Inorganic Nitrogen (N) Wet Deposition in China

Atmospheric nitrogen (N) deposition (N_dep), an important component of the global N cycle, has increased sharply in recent decades in China. Although there were already some studies on N_dep on a national scale, there were some gaps on the magnitude and the spatial patterns of N_dep. In this study, a national-scale N_dep pattern was constructed based on 139 published papers from 2003 to 2014 and the effects of precipitation (P), energy consumption (E) and N fertilizer use (F_N) on spatial patterns of N_dep were analyzed. The wet deposition flux of NH₄⁺-N, NO₃^--N and total N_dep was 6.83, 5.35 and 12.18 kg ha^-1 a^-1, respectively. N_dep exhibited a decreasing gradient from southeast to northwest of China. Through accuracy assessment of the spatial N_dep distribution and comparisons with other studies, the spatial N_dep distribution by Lu and Tian and this study both gained high accuracy. A strong exponential function was found between P and N_dep, F_N and N_dep and E and N_dep, and P and F_N had higher contribution than E on the spatial variation of N_dep. Fossil fuel combustion was the main contributor for NO₃^--N (86.0%) and biomass burning contributed 5.4% on the deposition of NO₃^--N. The ion of NH₄⁺ was mainly from agricultural activities (85.9%) and fossil fuel combustion (6.0%). Overall, N_dep in China might be considerably affected by the high emissions of NO_x and NH₃ from fossil fuel combustion and agricultural activities.     

Sluggish Movement and Repugnant Odor Are Positively Interacting Insect Defensive Traits in Encounters with Frogs

Sluggish movement is common in chemically defended insects. We have recently shown that sluggish movement can be beneficial to prey when it fails to release the attack response of an ambush (=motion-oriented) predator. Here, we test the hypothesis that sluggish movement and chemical defense (i.e., repugnant odor) together are more defensive than either alone. We manipulated the movement and odor of lubber grasshoppers to produce four prey types: (1) sluggish-moving and high odor, (2) sluggish-moving and low odor, (3) fast-moving and high odor, and (4) fast-moving and low odor. We then offered these prey to frogs. In two independent experiments, frogs attacked prey type 1 (i.e., sluggish-moving and high-odor prey) significantly later than they attacked the other prey types. Hence, the defenses of sluggish movement and repugnant odor can act together to produce a prey that is better defended than prey with either defense alone. This may help explain why these two traits commonly cooccur in insects.     

Evidence for Genetic Variation in Human Mate Preferences for Sexually Dimorphic Physical Traits

Intersexual selection has been proposed as an important force in shaping a number of morphological traits that differ between human populations and/or between the sexes. Important to these accounts is the source of mate preferences for such traits, but this has not been investigated. In a large sample of twins, we assess forced-choice, dichotomous mate preferences for height, skin colour, hair colour and length, chest hair, facial hair, and breast size. Across the traits, identical twins reported more similar preferences than nonidentical twins, suggesting genetic effects. However, the relative magnitude of estimated genetic and environmental effects differed greatly and significantly between different trait preferences, with heritability estimates ranging from zero to 57%.     

我国林蛙的研究概况和开展环渤海区域林蛙多样性研究的意义

林蛙是一个复杂多样的类群,我国现有13种,历来是两栖动物分类学和系统学研究的热点之一。本文简要概述了我国林蛙研究的历史及其近10年来的最新研究成果。同时,结合作者近年来的研究,提出环渤海区域是我围林蛙的一个分化中心和热点地区。开展该区域林蛙研究具有重要的科学意义。     

Analysis of Some Two-Locus Systems for Traits Exhibiting Continuous Variation

Some generalized two-locus, major-gene models for traits exhibiting continuous expression are investigated. Conditions of gametic equilibria are stated as functions of the parameters characterizing the within phenotypic-genotypic distributions. Selection is stabilizing in favor of an optimum phenotype. It is established that an increase in the phenotypic variance facilitates stability of a central polymorphic state with tighter linkage. Also, with increased phenotypic variance in an additive two-locus selection model, a Hardy-Weinberg type of equilibrium will be less central. The rate of convergence, in this case, is slowed down with an augmented environmental background.     

Individual Variation in Advertisement Calls of Territorial Male Green Frogs, Rana clamitans: Implications for Individual Discrimination

Individuals of many territorial species discriminate between familiar territorial neighbors and unfamiliar strangers based on individual differences in acoustic signals. Many anuran amphibians are territorial and use primarily acoustic communication during social interactions, but evidence for acoustically mediated individual discrimination is available only for one species. As a first step in research designed to investigate individual discrimination in a second species of territorial frog, we examined patterns of within-male and among-male variability in 198 advertisement calls of 20 male green frogs, Rana clamitans . The aim was to determine which acoustic properties could be used by males to recognize their territorial neighbors and to estimate limits of reliability afforded by these properties for identifying different neighbors. All of the call properties that we examined exhibited significant inter-individual variation. Discriminant function analyses assigned between 52% and 100% of calls to the correct individual, depending on sample size and the call properties included in the model. This suggests that there is sufficient among-male variability to statistically identify individuals by their advertisement calls. The call properties of fundamental frequency and dominant frequency contributed the most towards discrimination among individuals. Based on their natural history and behavior and the results reported here, we suggest that male green frogs likely discriminate between strangers and adjacently territorial neighbors based on individual variation in advertisement calls.     

Phenotypic Plasticity in Life-history Traits and Feeding Appendages in Two Species of Daphnia Fed a Natural Phytoplankton Assemblage

The ability of two cladoceran species – Daphnia pulicaria and D. mendotae – to utilize a natural phytoplankton assemblage dominated by cyanobacteria was investigated experimentally. Reference animals were fed high quality green algae. The natural phytoplankton assemblage originated from Oneida Lake (NY, USA). Both cladoceran species occur in the lake, but their densities vary temporally. As expected, lake phytoplankton were a poor food source. Fecundity decreased, and age at first reproduction and offspring size increased. The magnitude of these effects varied between and within species. The increase in offspring size differs from studies using toxic cyanobacterial strains, but agrees with expectations on adaptive responses to low food availability. Both species performed equally on the lake phytoplankton, but D. pulicaria appeared to be the superior species in the high quality food treatment.     

A Review of Thermotherapy to Free Plant Materials from Pathogens,Especially Seeds from Bacteria

Treating planting materials with heat is a one-century-old method of disease control that has proved to be efficient against various pathogenic microorganisms. Thermotherapy, simple in principle, consists in heat treatment of plant parts at temperature/time regimes that kill the conserved pathogen and that are only slightly injurious to the host. Heat is applied mainly by water, air, or vapor.

A large variety of plant parts can be heat treated: Whole tree, scions, vitroplants, seedlings, stalks, cuttings, sprouts, cut flowers, seeds, bulbs, tubers, corms, or fruit and vegetables in storage. The target pathogenic microorganisms are mainly fungi, viruses, and bacteria. Many studies show the success of reducing diseases by heat. Thermotherapy also is the main means, associated with meristem and tip culture, of producing virus-free explants from infected mother-plants.

Most bacterial diseases of annual plants are seed-borne. Seed-transmission provides numerous foci of primary infection in the field and only a relatively small amount of infested seeds is sufficient to promote serious disease outbreaks. To disinfect seeds, authors mainly use hot water and hot air treatments. Satisfactory control has been obtained for several bacterial diseases (on tomato, tobacco, rice, barley, cucumber, Crucifers, pumpkin, guar, and cotton), mostly caused by the genera Xanthomonas and Pseudomonas. Thermotherapy is more difficult to use with large seeds of legumes, such as pea, bean, or soybean, because a significant decrease of germination is often obtained before the bacteria have been totally killed. The success of thermotherapy may be improved by combination with chemicals at the seed stage, by sprays during plant growth, or by replacing water with nonaqueous fluids.

When no efficient chemicals are known to control a disease, treating seeds by heat may be of great interest. However, the method requires studies to determine the most appropriate kind of heat for a particular plant part, and the optimal combination of time and temperature of exposure to use for the best efficiency with the least damage to the host.     

Population Variation in Continuously Varying Traits as an Ecological Genetics Problem

The niche variation hypothesis is an adaptive explanation forvariation within populations and for, the differences in variationbetween populations in morphological, physiological or behavioraltraits. It has received only partial support from empiricaltests and has been criticized on theoretical grounds. Recentquantitative genetic models have made an advance by exploringthe effects of mutation, migration, mating pattern and selectionon phenotypic variance. These models are reviewed and theirmost important features are integrated in a new model. In thismodel population variation is in a state of balance betweenthe opposing forces of mutation and immigration, which tendto elevate variation, and selection and possibly genetic drifttending to decrease it. Populations exhibiting different levelsof variation are interpereted as having different equilibriumpoints, and it is the task of empirical studies to determinethe relative magnitudes of the opposing factors. An exampleis given from studies of Darwin's finches. Geospiza fortis variesmore than G. scandens on Isla Daphne Major, Galápagos,in several morphological traits including beak and body size.This is explained, assuming equal mutation rates in the twospecies, as the result of more frequent genetic input to theG. fortis population, through occasional hybridization withimmigrant G. fuliginosa, and relaxed stabilizing selection.Stabilizing selection is less intense on G.fortis than on G.scandens because the G. fortis population has a broader niche;there is both a within-phenotype and betweenphenotype componentto the broad niche of G. fortis. The success of theory in explainingpopulation variation is discussed, and it is concluded thatempirical studies lag far behind theory.     

Dominance Genetic Variation Contributes Little to the Missing Heritability for Human Complex Traits

For human complex traits, non-additive genetic variation has been invoked to explain “missing heritability,” but its discovery is often neglected in genome-wide association studies. Here we propose a method of using SNP data to partition and estimate the proportion of phenotypic variance attributed to additive and dominance genetic variation at all SNPs (hSNP2 and δSNP2) in unrelated individuals based on an orthogonal model where the estimate of hSNP2 is independent of that of δSNP2. With this method, we analyzed 79 quantitative traits in 6,715 unrelated European Americans. The estimate of δSNP2 averaged across all the 79 quantitative traits was 0.03, approximately a fifth of that for additive variation (average hSNP2 = 0.15). There were a few traits that showed substantial estimates of δSNP2, none of which were replicated in a larger sample of 11,965 individuals. We further performed genome-wide association analyses of the 79 quantitative traits and detected SNPs with genome-wide significant dominance effects only at the ABO locus for factor VIII and von Willebrand factor. All these results suggest that dominance variation at common SNPs explains only a small fraction of phenotypic variation for human complex traits and contributes little to the missing narrow-sense heritability problem.     

Elevation-Related Variation in Leaf Stomatal Traits as a Function of Plant Functional Type: Evidence from Changbai Mountain,China

Understanding the variation in stomatal characteristics in relation to climatic gradients can reveal the adaptation strategies of plants, and help us to predict their responses to future climate changes. In this study, we investigated stomatal density (SD) and stomatal length (SL) in 150 plant species along an elevation gradient (540–2357 m) in Changbai Mountain, China, and explored the patterns and drivers of stomatal characteristics across species and plant functional types (PFTs: trees, shrubs, and herbs). The average values of SD and SL for all species combined were 156 mm^–2 and 35 µm, respectively. SD was higher in trees (224 mm^–2) than in shrubs (156 mm^–2) or herbs (124 mm^–2), and SL was largest in herbs (37 µm). SD was negatively correlated with SL in all species and PFTs (P<0.01). The relationship between stomatal characteristics and elevation differed among PFTs. In trees, SD decreased and SL increased with elevation; in shrubs and herbs, SD initially increased and then decreased. Elevation-related differences in SL were not significant. PFT explained 7.20–17.6% of the total variation in SD and SL; the contributions of CO₂ partial pressure (), precipitation, and soil water content (SWC) were weak (0.02–2.28%). Our findings suggest that elevation-related patterns of stomatal characteristics in leaves are primarily a function of PFT, and highlight the importance of differences among PFTs in modeling gas exchange in terrestrial ecosystems under global climate change.