The genetic basis of behavioral isolation between Drosophila mauritiana and D. sechellia

Understanding how species form is a fundamental question in evolutionary biology. Identifying the genetic bases of barriers that prevent gene flow between species provides insight into how speciation occurs. Here, I analyze a poorly understood reproductive isolating barrier, prezygotic reproductive isolation. I perform a genetic analysis of prezygotic isolation between two closely related species of Drosophila, D. mauritiana and D. sechellia. I first confirm the existence of strong behavioral isolation between D. mauritiana females and D. sechellia males. Next, I examine the genetic basis of behavioral isolation by (1) scanning an existing set of introgression lines for chromosomal regions that have a large effect on isolation; and (2) mapping quantitative trait loci (QTL) that underlie behavioral isolation via backcross analysis. In particular, I map QTL that determine whether a hybrid backcross female and a D. sechellia male will mate. I identify a single significant QTL, on the X chromosome, suggesting that few major-effect loci contribute to behavioral isolation between these species. In further work, I refine the map position of the QTL to a small region of the X chromosome.     

Population-based resequencing of experimentally evolved populations reveals the genetic basis of body size variation in Drosophila melanogaster

Body size is a classic quantitative trait with evolutionarily significant variation within many species. Locating the alleles responsible for this variation would help understand the maintenance of variation in body size in particular, as well as quantitative traits in general. However, successful genome-wide association of genotype and phenotype may require very large sample sizes if alleles have low population frequencies or modest effects. As a complementary approach, we propose that population-based resequencing of experimentally evolved populations allows for considerable power to map functional variation. Here, we use this technique to investigate the genetic basis of natural variation in body size in Drosophila melanogaster. Significant differentiation of hundreds of loci in replicate selection populations supports the hypothesis that the genetic basis of body size variation is very polygenic in D. melanogaster. Significantly differentiated variants are limited to single genes at some loci, allowing precise hypotheses to be formed regarding causal polymorphisms, while other significant regions are large and contain many genes. By using significantly associated polymorphisms as a priori candidates in follow-up studies, these data are expected to provide considerable power to determine the genetic basis of natural variation in body size.     

Among‐year variation in selection during early life stages and the genetic basis of fitness in Arabidopsis thaliana

Incomplete information regarding both selection regimes and the genetic basis of fitness limits our understanding of adaptive evolution. Among‐year variation in the genetic basis of fitness is rarely quantified, and estimates of selection are typically based on single components of fitness, thus potentially missing conflicting selection acting during other life‐history stages. Here, we examined among‐year variation in selection on a key life‐history trait and the genetic basis of fitness covering the whole life cycle in the annual plant Arabidopsis thaliana. We planted freshly matured seeds of >200 recombinant inbred lines (RILs) derived from a cross between two locally adapted populations (Italy and Sweden), and both parental genotypes at the native site of the Swedish population in three consecutive years. We quantified selection against the nonlocal Italian genotype, mapped quantitative trait loci (QTL) for fitness and its components, and quantified selection on timing of germination during different life stages. In all 3 years, the local Swedish genotype outperformed the nonlocal Italian genotype. However, both the contribution of early life stages to relative fitness, and the effects of fitness QTL varied among years. Timing of germination was under conflicting selection through seedling establishment vs. adult survival and fecundity, and both the direction and magnitude of net selection varied among years. Our results demonstrate that selection during early life stages and the genetic basis of fitness can vary markedly among years, emphasizing the need for multiyear studies considering the whole life cycle for a full understanding of natural selection and mechanisms maintaining local adaptation.     

Phytotoxicity and distribution of copper in tropical soil amended with sewage sludge and copper sulfate

Abstract

A greenhouse experiment was conducted to evaluate phytotoxicity and distribution of Cu in a tropical soil amended with sewage sludge (Sw) and copper sulfate (CuSO₄.5H₂O). Samples of a clay soil from the State of Paraná, Brazil were collected at depth of 0–20; 20–40 and 40–60 cm, and brought to the laboratory to be properly accommodated in experimental units (PVC tubes). The Cu treatments were performed by the application of Sw (10 t ha-¹) amended with Cu (SB-T), and by CuSO₄. H₂O (WB-T). Lettuce plants were cultivated in the amended soil in order to predict the toxicity of the Cu. The experiment was conducted for 70 days, and then the lettuce plants and soil samples were collected for analysis. A sequential method was used to separate soil Cu into following fractions: exchangeable, amorphous iron oxide bound, crystalline iron oxide bound, organic matter bound and residual bound. The experimental results showed that Fe, Zn, K, P, Cu and organic matter amounts of the soil increased with the treatment SB-T. The toxic phyto-available Cu content in the soil for the lettuce plants was 80.00 mg kg^-1. A percolation study showed that the Cu contents were larger for the first 20 cm of depth, indicating that the metal was not transported down the soil profile. The Cu content of different fractions declined in an order residual > amorphous iron oxide > crystalline iron oxide > organic matter > exchangeable, regardless of treatment performed. Additionally, the Cu contents added from treatments were determined mainly in amorphous iron oxide fraction.     

Finding the molecular basis of complex genetic variation in humans and mice

I survey the state of the art in complex trait analysis, including the use of new experimental and computational technologies and resources becoming available, and the challenges facing us. I also discuss how the prospects of rodent model systems compare with association mapping in humans.     

Cadmium and copper uptake and translocation in five willow (Salix L.) species

The efficacy for phytoremediation of five willow species was tested by experimental copper and cadmium uptake in a greenhouse hydroponic system. Five treatments included two concentrations (5 and 25 microM for each metal) and a control. Metal concentrations in solution as well as solution uptake were monitored. Metal resistance was assessed through effects on the dry weight of roots and shoots. The willow species tested were generally resistant of increased Cu and Cd content. Metal accumulation was found in all plant organs of all species. Growth and transpiration were not decreased by 5 microM of copper and 25 microM of cadmium in the solution for most species. 25 microM copper caused injury and reduced the dry weight for all species after 21 d. Salix nigra was highly resistant of both Cu and Cd and accumulated more metals than other species. Future field study should be conducted to confirm the findings and feasibility of the phytoremediation technology using those species.     

取食重金属铜对棕尾别麻蝇亲代及子代生长发育与繁殖的影响

为了评估取食含重金属铜饲料对棕尾别麻蝇Boettcherisca peregrine亲代及子代的生长发育与繁殖的影响,在室内给棕尾别麻蝇初产幼虫饲喂含不同浓度（200, 400,800和1 600 µg/g）Cu²⁺的饲料直至化蛹,并对亲代和子代的生长发育和繁殖有关指标进行了观察和分析。结果表明：低浓度的Cu²⁺（200 µg/g）对其体重和体长起促进作用,但对幼虫历期、化蛹率、蛹历期、羽化率、性比、交配率和产仔量无显著作用;较高浓度的Cu²⁺ 则有抑制作用,且Cu²⁺处理浓度越高,亲代幼虫、蛹和雌雄成虫的体重越轻,幼虫和蛹的体长越短,化蛹率、羽化率、交配率和产仔量越低,幼虫历期和蛹期越长,成虫寿命越短。但Cu²⁺处理对成虫性比则无显著的影响。相比之下,经Cu²⁺处理后雌虫所产的子代若不再经Cu²⁺处理,其子代生存、生长发育与繁殖则基本不受影响,说明Cu²⁺对亲代的影响不能遗传至子代。此外,还探讨了该蝇亲代与子代体内Cu²⁺含量在其变态过程中的变化。     

The genetic basis of quantitative variation in susceptibility of Arabidopsis thaliana to Pseudomonas syringae (Pst DC3000): evidence for a new genetic factor of large effect

* Pathogens represent an important threat to plant communities and agriculture, and can shape many aspects of plant evolution. Natural variation in plant disease susceptibility is typically quantitative, yet studies on the molecular basis of disease resistance have focused mainly on qualitative variation. * Here we investigated the genetic architecture of quantitative susceptibility to the bacterium Pseudomonas syringae by performing a quantitative trait locus (QTL) analysis on the F2 progeny of two natural accessions of Arabidopsis thaliana under two nutrient treatments. * We found that a single QTL explains most of the variation (77%) in susceptibility between accessions Columbia (Col-0) and San Feliu-2 (Sf-2), and its effect is independent of nutrients. The Sf-2 allele at this QTL is dominant and can reduce the bacterial population size by 31-fold, much like a classical resistance (R) gene. However, minor QTLs, whose effects are altered by nutrient treatment, were also detected. * Surprisingly, we found that none of the QTLs for susceptibility had any effect on fruit production, suggesting that the use of resistance genes for crop improvement and evolutionary analysis of plant-pathogen interactions requires caution.     

QTL and quantitative genetic analysis of beak morphology reveals patterns of standing genetic variation in an Estrildid finch

The intra- and interspecific diversity of avian beak morphologies is one of the most compelling examples for the power of natural selection acting on a morphological trait. The development and diversification of the beak have also become a textbook example for evolutionary developmental biology, and variation in expression levels of several genes is known to causally affect beak shape. However, until now, no genomic polymorphisms have been identified, which are related to beak morphology in birds. QTL mapping does reveal the location of causal polymorphisms, albeit with poor spatial resolution. Here, we estimate heritability and genetic correlations for beak length, depth and width and perform a QTL linkage analysis for these traits based on 1404 informative single-nucleotide polymorphisms genotyped in a four-generation pedigree of 992 captive zebra finches (Taeniopygia guttata). Beak size, relative to body size, was sexually dimorphic (larger in males). Heritability estimates ranged from 0.47 for beak length to 0.74 for beak width. QTL mapping revealed four to five regions of significant or suggestive genome-wide linkage for each of the three beak dimensions (nine different regions in total). Eight out of 11 genes known to influence beak morphology are located in these nine peak regions. Five QTL do not cover known candidates demonstrating that yet unknown genes or regulatory elements may influence beak morphology in the zebra finch.     

Quantitative trait locus mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogen Zymoseptoria tritici

We conducted a comprehensive analysis of virulence in the fungal wheat pathogen Zymoseptoria tritici using quantitative trait locus (QTL) mapping. High‐throughput phenotyping based on automated image analysis allowed the measurement of pathogen virulence on a scale and with a precision that was not previously possible. Across two mapping populations encompassing more than 520 progeny, 540 710 pycnidia were counted and their sizes and grey values were measured. A significant correlation was found between pycnidia size and both spore size and number. Precise measurements of percentage leaf area covered by lesions provided a quantitative measure of host damage. Combining these large and accurate phenotypic datasets with a dense panel of restriction site‐associated DNA sequencing (RADseq) genetic markers enabled us to genetically dissect pathogen virulence into components related to host damage and those related to pathogen reproduction. We showed that different components of virulence can be under separate genetic control. Large‐ and small‐effect QTLs were identified for all traits, with some QTLs specific to mapping populations, cultivars and traits and other QTLs shared among traits within the same mapping population. We associated the presence of four accessory chromosomes with small, but significant, increases in several virulence traits, providing the first evidence for a meaningful function associated with accessory chromosomes in this organism. A large‐effect QTL involved in host specialization was identified on chromosome 7, leading to the identification of candidate genes having a large effect on virulence.     

Effects of sample size,number of markers,and allelic richness on the detection of spatial genetic pattern

The influence of study design on the ability to detect the effects of landscape pattern on gene flow is one of the most pressing methodological gaps in landscape genetic research. To investigate the effect of study design on landscape genetics inference, we used a spatially‐explicit, individual‐based program to simulate gene flow in a spatially continuous population inhabiting a landscape with gradual spatial changes in resistance to movement. We simulated a wide range of combinations of number of loci, number of alleles per locus and number of individuals sampled from the population. We assessed how these three aspects of study design influenced the statistical power to successfully identify the generating process among competing hypotheses of isolation‐by‐distance, isolation‐by‐barrier, and isolation‐by‐landscape resistance using a causal modelling approach with partial Mantel tests. We modelled the statistical power to identify the generating process as a response surface for equilibrium and non‐equilibrium conditions after introduction of isolation‐by‐landscape resistance. All three variables (loci, alleles and sampled individuals) affect the power of causal modelling, but to different degrees. Stronger partial Mantel r correlations between landscape distances and genetic distances were found when more loci were used and when loci were more variable, which makes comparisons of effect size between studies difficult. Number of individuals did not affect the accuracy through mean equilibrium partial Mantel r, but larger samples decreased the uncertainty (increasing the precision) of equilibrium partial Mantel r estimates. We conclude that amplifying more (and more variable) loci is likely to increase the power of landscape genetic inferences more than increasing number of individuals.     

Strength of Cu-efflux response in Escherichia coli coordinates metal resistance in Caenorhabditis elegans and contributes to the severity of environmental toxicity

Without effective homeostatic systems in place, excess copper (Cu) is universally toxic to organisms. While increased utilization of anthropogenic Cu in the environment has driven the diversification of Cu-resistance systems within enterobacteria, little research has focused on how this change in bacterial architecture impacts host organisms that need to maintain their own Cu homeostasis. Therefore, we utilized a simplified host–microbe system to determine whether the efficiency of one bacterial Cu-resistance system, increasing Cu-efflux capacity via the ubiquitous CusRS two-component system, contributes to the availability and subsequent toxicity of Cu in host Caenorhabditis elegans nematode. We found that a fully functional Cu-efflux system in bacteria increased the severity of Cu toxicity in host nematodes without increasing the C. elegans Cu-body burden. Instead, increased Cu toxicity in the host was associated with reduced expression of a protective metal stress-response gene, numr-1, in the posterior pharynx of nematodes where pharyngeal grinding breaks apart ingested bacteria before passing into the digestive tract. The spatial localization of numr-1 transgene activation and loss of bacterially dependent Cu-resistance in nematodes without an effective numr-1 response support the hypothesis that numr-1 is responsive to the bacterial Cu-efflux capacity. We propose that the bacterial Cu-efflux capacity acts as a robust spatial determinant for a host’s response to chronic Cu stress.     

Genetic analysis of extended life span in Drosophila melanogaster I. RAPD screen for genetic divergence between selected and control lines

Using lines selected for long life by Luckinbill and his co-workers, we screened two selected and two control lines for allelic frequency differences at 1200 randomly chosen RAPD marker loci. Twenty-three marker loci showed frequency differences in excess of 80%, and five were greater than 90%. Age-specific effects of the five most differentiated loci were estimated by collecting complete survival data in segregating backcross populations. Alleles at four of the five marker loci were associated with significant extension of life span in males, while two marker loci had significant effects in females. Eighty percent of the total selection response in males can be explained by the identified QTL's, under the assumption of additivity. The N14+ marker allele accounted for a 12-day life span extension in males, but had little effect in females. Both sex-limited and sex-shared effects were observed. Analysis of age-specific mortality rates suggests that life span extension occurs by a combination of genetic factors that moderate both the level of mortality and the rate at which mortality increases with age. This revised version was published online in July 2006 with corrections to the Cover Date.     

Intraspecific genetic variation in host vigour,viral load and disease tolerance during Drosophila C virus infection

Genetic variation for resistance and disease tolerance has been described in a range of species. In Drosophila melanogaster, genetic variation in mortality following systemic Drosophila C virus (DCV) infection is driven by large-effect polymorphisms in the restriction factor pastrel (pst). However, it is unclear if pst contributes to disease tolerance. We investigated systemic DCV challenges spanning nine orders of magnitude, in males and females of 10 Drosophila Genetic Reference Panel lines carrying either a susceptible (S) or resistant (R) pst allele. We find among-line variation in fly survival, viral load and disease tolerance measured both as the ability to maintain survival (mortality tolerance) and reproduction (fecundity tolerance). We further uncover novel effects of pst on host vigour, as flies carrying the R allele exhibited higher survival and fecundity even in the absence of infection. Finally, we found significant genetic variation in the expression of the JAK-STAT ligand upd3 and the epigenetic regulator of JAK-STAT G9a. However, while G9a has been previously shown to mediate tolerance of DCV infection, we found no correlation between the expression of either upd3 or G9a on fly tolerance or resistance. Our work highlights the importance of both resistance and tolerance in viral defence.     

Genome‐wide SNP analysis reveals a genetic basis for sea‐age variation in a wild population of Atlantic salmon (Salmo salar)

Delaying sexual maturation can lead to larger body size and higher reproductive success, but carries an increased risk of death before reproducing. Classical life history theory predicts that trade‐offs between reproductive success and survival should lead to the evolution of an optimal strategy in a given population. However, variation in mating strategies generally persists, and in general, there remains a poor understanding of genetic and physiological mechanisms underlying this variation. One extreme case of this is in the Atlantic salmon (Salmo salar), which can show variation in the age at which they return from their marine migration to spawn (i.e. their ‘sea age’). This results in large size differences between strategies, with direct implications for individual fitness. Here, we used an Illumina Infinium SNP array to identify regions of the genome associated with variation in sea age in a large population of Atlantic salmon in Northern Europe, implementing individual‐based genome‐wide association studies (GWAS) and population‐based F_ST outlier analyses. We identified several regions of the genome which vary in association with phenotype and/or selection between sea ages, with nearby genes having functions related to muscle development, metabolism, immune response and mate choice. In addition, we found that individuals of different sea ages belong to different, yet sympatric populations in this system, indicating that reproductive isolation may be driven by divergence between stable strategies. Overall, this study demonstrates how genome‐wide methodologies can be integrated with samples collected from wild, structured populations to understand their ecology and evolution in a natural context.     

Interactions between the toxicity of the heavy metals cadmium,copper, zinc in combinations and the detoxifying role of calcium in the brown algaCystoseira barbata

The toxicity of three heavy metals, Cd, Cu and Zn, and the detoxifying role of Ca have been studied for the brown algaCystoseira barbata formaaurentia after a 4-week laboratory culture. The experimental design was based upon a complete factorial design 2^k, which seems to be the first time it has been used in algal physiology. It was demonstrated that these three elements, applied jointly, act on weight-growth, chlorophyll a, c and carotenoid synthesis and Cd, Cu and Zn uptake. Cd and Zn act in synergy or in antagony, depending on their exogenous concentrations, on chlorophyll a and on carotenoid synthesis. Zn is antagonistic towards Cd and Cu on weight-growth in the combination Cd-Cu-Zn. From different element combinations, the protective role of Ca appears evident on weight-growth (Cd-Zn-Ca and Cu-Ca), chlorophyll a (Cd-Cu-Ca and Cu-Zn-Ca), chlorophyll c (Cd-Ca), carotenoid synthesis (Cd-Cu-Ca and Cu-Zn-Ca), Cd and Cu uptake (Cd-Cu-Ca) and Zn uptake (Cu-Zn-Ca). This role is confirmed by cytological investigations. This is apparently the first report concerning a Ca interaction with toxicity of heavy metals applied in combinations. However, the mechanisms of tolerance remain unknown.     

Thiol pools and glutathione redox ratios as possible indicators of copper toxicity in the green macroalgae Enteromorpha spp. from the Scheldt Estuary (SW Netherlands,Belgium) and Thermaikos Gulf (Greece,N Aegean Sea)

Defence mechanisms against Cu toxicity were examined in two dominant Enteromorpha species from two coastal water types. The macroalgae were collected at three locations in the eulittoral of the Scheldt Estuary (Netherlands, Belgium) and the Thermaikos Gulf (Greece). For 10 days E. prolifera (Scheldt) and E. linza (Thermaikos) were incubated in seawater media of different salinities: 6, 9, 23 psu and 25, 30, 35 psu, respectively. In one series, media were enriched with 100 μg Cu l-1; responses were compared with those in controls with no extra Cu added. Enteromorpha, which is frequently used as a monitor species for heavy metal contamination, had relatively high Cu tissue levels (0.5–3.8 μmol Cu gdwt-1). Cu levels in E. prolifera controls (Scheldt) decreased with salinity; this was not the case with Cu levels in E. linza controls (Thermaikos). During the 10-d incubation algal protein contents and tissue Cu were rather stable. In E. linza (Thermaikos) algal protein contents were significantly lower than those of E. prolifera (Scheldt), although there was no indication for nitrogen limitation in E. linza. E. linza also had much lower glutathione pools than E. prolifera. Only under acute Cu stress (metal addition) did E. prolifera synthesise metal-binding thiols (phytochelatins). Phytochelatin pools are not suitable as an indicator of the Cu levels in these algae. The glutathione redox ratio GSH:(GSH + 0.5GSSG) was used as an indicator of (Cu-induced) oxidative stress. In E. prolifera (Scheldt) this ratio decreased with algal Cu content (P <0.05), from ~0.5 to ~0.2. The average glutathione ratios in Enteromorpha from the Scheldt and Thermaikos showed some oxidative stress induction with increasing algal Cu contents, however more clearly if Cu was added. As this redox ratio can also be influenced by environmental factors such as irradiance and desiccation, it may not be useful as an indicator for Cu-induced oxidative stress in situ. This revised version was published online in September 2006 with corrections to the Cover Date.     

Natural variation in the genetic architecture of a host-parasite interaction in the bumblebee Bombus terrestris

The genetic architecture of fitness-relevant traits in natural populations is a topic that has remained almost untouched by quantitative genetics. Given the importance of parasitism for the host's fitness, we used QTL mapping to study the genetic architecture of traits relevant for host-parasite interactions in the trypanosome parasite, Crithidia bombi and its host, Bombus terrestris. The three traits analysed were the parasite's infection intensity, the strength of the general immune response (measured as the encapsulation of a novel antigen) and body size. The genetic architecture of these traits was examined in three natural, unmanipulated mapping populations of B. terrestris. Our results indicate that the intracolonial phenotypic variation of all three traits is based on a network of QTLs and epistatic interactions. While these networks are similar between mapping populations in complexity and number of QTLs, as well as in their epistatic interactions, the variability in the position of QTL and the interacting loci was high. Only one QTL for body size was plausibly found in at least two populations. QTLs for encapsulation and Crithidia infection intensity were located on the same linkage groups.