The theory on and software simulating large-scale genomic data for genotype-by-environment interactions

Background With the emphasis on analysing genotype-by-environment interactions within the framework of genomic selection and genome-wide association analysis, there is an increasing demand for reliable tools that can be used to simulate large-scale genomic data in order to assess related approaches. Results We proposed a theory to simulate large-scale genomic data on genotype-by-environment interactions and added this new function to our developed tool GPOPSIM. Additionally, a simulated threshold trait with large-scale genomic data was also added. The validation of the simulated data indicated that GPOSPIM2.0 is an efficient tool for mimicking the phenotypic data of quantitative traits, threshold traits, and genetically correlated traits with large-scale genomic data while taking genotype-by-environment interactions into account. Conclusions This tool is useful for assessing genotype-by-environment interactions and threshold traits methods.

Captive-bred populations of a partially migratory salmonid fish are unlikely to maintain migratory polymorphism in natural habitats

Variation in life history is fundamental to the long-term persistence of populations and species. Partial migration, in which both migratory and resident individuals are maintained in a population, is commonly found across animal taxa. However, human-induced habitat fragmentation continues to cause a rapid decline in the migratory phenotype in many natural populations. Using field and hatchery experiments, we demonstrated that despite both migrants and residents being maintained in captive environments, few individuals of the red-spotted masu salmon, Oncorhynchus masou ishikawae , became migrants in natural streams when released prior to the migration decision. Released fish rarely reached the threshold body size necessary to become migrants in natural streams, presumably owing to lower growth rates in natural than in captive environments. The decision to migrate is often considered a threshold trait in salmonids and other animal taxa. Our findings highlight the need for management programmes that acknowledge the effects of the environment on the determination of the migratory phenotypes of partially migratory species when releasing captive-bred individuals prior to their migratory decisions.

To accept or reject heterospecific mates: behavioural decisions underlying premating isolation

Premating isolation in animals involves decision-making processes that affect whether individuals accept or reject heterospecific mates. An integrative understanding of the behavioural processes underlying heterospecific acceptance can clarify the conditions under which premating isolation evolves. As an illustration, we review how Reeve's (Reeve 1989 Am. Nat. 133 , 407–435. ( doi:10.1086/284926 )) acceptance threshold model can help make sense of patterns of premating isolation in nature. This model derives a threshold trait value for acceptance for rejection of recipients of an action (e.g. mating) based on the fitness consequences of these decisions. We show that the maintenance of partial reproductive isolation can be an outcome of optimal acceptance thresholds, even in the face of reinforcement. We also use this model to clarify how the composition of multispecies communities can shape premating isolation. The acceptance threshold model can also be viewed as the behavioural underpinning of reproductive character displacement and cascading reinforcement. Finally, we highlight potential limitations of the acceptance threshold model with respect to investigating the role of sexual selection in speciation, and we propose that integration of behavioural models in speciation research will help us gain a full picture of the mechanisms underlying premating isolation. This article is part of the theme issue ‘Signal detection theory in recognition systems: from evolving models to experimental tests’.

How migratory populations become resident

Migratory behaviour is rapidly changing in response to recent environmental changes, yet it is difficult to predict how migration will evolve in the future. To understand what determines the rate of adaptive evolutionary change in migratory behaviour, we simulated the evolution of residency using an individual-based threshold model, which allows for variation in selection, number of genes, environmental effects and assortative mating. Our model indicates that the recent reduction in migratory activity found in a population of Eurasian blackcaps ( Sylvia atricapilla ) is only compatible with this trait being under strong directional selection, in which residents have the highest fitness and fitness declines exponentially with migration distance. All other factors had minor effects on the adaptive response. Under this form of selection, a completely migratory population will become partially migratory in 6 and completely resident in 98 generations, demonstrating the persistence of partial migration, even under strong directional selection. Resident populations will preserve large amounts of cryptic genetic variation, particularly if migration is controlled by a large number of genes with small effects. This model can be used to realistically simulate the evolution of any threshold trait, including semi-continuous traits like migration, for predicting evolutionary response to natural selection in the wild.

Resistance Risk Evaluated by Metaflumizone Selection and the Effects on Toxicities Over Other Insecticides in Spodoptera exigua (Lepidoptera: Noctuidae)

Metaflumizone is a novel semicarbazone insecticide. It functions as a sodium channel blocker insecticide (SCBI) with excellent insecticidal activity on most economically important lepidopterous pests. This study assessed the resistance risk of Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae) to metaflumizone in the laboratory and the effects of metaflumizone selection on toxicities to other insecticides. Spodoptera exigua collected from a field population at Huizhou in 2012 were successively challenged by metaflumizone to evaluate the risk of resistance evolution. Twelve generations of selection increased resistance to metaflumizone by 3.4-fold and threshold trait analysis revealed that the realized heritability (h2) of this resistance was 0.086. When h2 was equal to 0.086 and 90% of individuals were killed at each generation, LC50 to metaflumizone increased by 10-fold after 15 generations. The selection by metaflumizone did not increase the resistance to indoxacarb, chlorantraniliprole, spinosad, methomyl, or endosulfan, suggesting a lack of cross-resistance. However, metaflumizone challenge upheld the recession of resistance to emamectin benzoate, chlorfluazuron, and tebufenozide. The block of resistance drops by metaflumizone exposure implied a possible cross-resistance between metaflumizone and these three insecticides. These results contribute to integrated resistance management of S. exigua.

Altered Gene Response to Aflatoxin B1 in the Spleens of Susceptible and Resistant Turkeys

Susceptibility and/or resistance to aflatoxin B1 (AFB1) is a threshold trait governed principally by glutathione S transferase (GST)-mediated detoxification. In poultry, domesticated turkeys are highly sensitive to AFB1, most likely due to dysfunction in hepatic GSTs. In contrast, wild turkeys are comparatively resistant to aflatoxicosis due to the presence of functional hepatic GSTAs and other possible physiological and immunological interactions. The underlying genetic basis for the disparate GST function in turkeys is unknown as are the broader molecular interactions that control the systemic response. This study quantifies the effects of dietary AFB1 on gene expression in the turkey spleen, specifically contrasting genetically distinct domesticated (DT, susceptible) and Eastern wild (EW, resistant) birds. Male turkey poults were subjected to a short-term AFB1 treatment protocol with feed supplemented with 320 ppb AFB1 beginning on day 15 of age and continuing for 14 days. Spleen tissues were harvested and subjected to deep RNA sequencing and transcriptome analysis. Analysis of differential gene expression found the effects of AFB1 treatment on the spleen transcriptomes considerably more prominent in the DT birds compared to EW. However, expression of the differentially expressed genes (DEGs) was directionally biased, with the majority showing higher expression in EW (i.e., down-regulation in DT). Significantly altered pathways included FXR/RXR and LXR/RXR activation, coagulation system, prothrombin activation, acute phase response, and atherosclerosis signaling. Differential extra-hepatic expression of acute phase protein genes was confirmed by quantitative real time PCR (qRT-PCR) in the original experiment and additional turkey lines. Results demonstrate that wild turkeys possess a capacity to more effectively respond to AFB1 exposure.

Evaluating benefits of stocking on sockeye recovery projections in a nutrient-enhanced mixed life history population

Dam construction often blocks migration of anadromous sockeye salmon (Oncorhynchus nerka), resulting in a residualized population that is often managed as landlocked kokanee. Anadromy resumes when a reconnection to the ocean is established; however, there may be selective pressure acting on threshold trait(s) affecting smolt timing and probability. While there may be interest in predicting persistence of anadromous and residual sockeye forms, this is difficult because the heritability of smolting in these populations is poorly known. We develop a fully density-dependent age-structured model to project abundances for both anadromous and resident sockeye. The model considers trophic interactions due to nutrient variation and the density-dependent consequences for smolting and adult returns. Moreover, it asks how each life history type will persist if a hatchery were used to promote anadromous sockeye through artificial selection. We show hatchery supplementation is unlikely to impact anadromous or resident sockeye significantly, although there is substantial prediction uncertainty suggested in projections. Our study suggests that providing passage for previous land-locked anadromous populations will lead to the return of anadromous fish in the short term, but long-term prospects are far from certain.

Short-term Changes in the Mean: 2. Truncation and Threshold Selection

The selection intensity, the mean change in a trait within a generation expressed in phenotypic standard deviations, provides an important metric for comparing the strength of selection over designs. Further, under truncation selection (only individuals above some threshold leave offspring), the selection intensity is a function of the fraction saved, and hence the breeder's equation is often expressed in terms of the selection intensity. An important special case of truncation selection is a threshold trait, wherein an individual only expresses a particular phenotype when its underlying liability value exceeds some threshold. This chapter examines selection on such traits, and generalizes this binary-trait setting (with binomial residuals) to other classes of discrete traits, wherein some underling linear model (generating the threshold) is this transformed via a generalized linear mixed model into an observed trait value.

Torus Mandibularis: Etiology and Bioarcheological Utility

Torus mandibularis is a non-metric traitcommonly recorded in bioarcheological investigationand often included in the battery of non-metric traitsused to analyse biological distance among populations.However, there is considerable debate regarding theetiology of the trait, with genetic and environmentalfactors both having been posited as the primary factorin torus development. This study of 498 individuals,drawn from eight archeological samples, investigatesthe variation in torus frequency in different groups asdefined by sample, age, sex, and measures of functionalstress. Frequencies varied significantly among bothsamples and dental attrition categories, supportingthe idea that mandibular tori are a threshold trait,influenced by both genetic and environmental factors.Results of this study suggest the utility of mandibulartori in bioarchaeology may lie outside of biodistanceanalyses that rely on the high heritability quotient ofnon-metric traits to establish population distances.

Fitness consequences of threshold trait expression subject to environmental cues

Most cases of alternative reproductive tactics (ARTs) are thought to represent conditional strategies, whereby high-status males express highly competitive phenotypes, whereas males below a certain status threshold resort to sneaky tactics. The underlying evolutionarily stable strategy (ESS) model assumes that males of high competitive ability achieve higher fitness when expressing the territorial phenotype, whereas the less competitive males are more fit as sneakers, caused by fitness functions for the ARTs having different slopes and intersecting at a threshold value of competitive ability. The model, however, is notoriously difficult to test as it requires access to low-status territorials and high-status sneakers, that rarely occur in nature. Here, we test the conditional ESS in the androdimorphic acarid mite Sancassania berlesei , where large males tend to develop into an armoured, aggressive ‘fighter’ morph, while small males become unarmoured, non-aggressive ‘scramblers’. In addition to body size, male morph is affected by pheromones produced by big populations, with fighters being suppressed in dense colonies. By manipulating pheromone concentration, we obtained high-status scramblers and low-status fighters. We also estimated status- and size-dependent fitness functions for male morphs across a range of population sizes. Fighters had the highest fitness in small populations and their fitness declined with increasing density, whereas the reverse was true for scramblers, providing support for condition-dependent ESS with respect to demography. However, whereas male fitness increased with body size, the fitness functions did not differ significantly between morphs. Thus, although we found evidence for the intersection of morph fitness functions with respect to demography, we did not find such an intersection in relation to male body size. Our results highlight how demography can exert selection pressures shaping the evolution of the conditional strategy in species with ARTs.