TetraploidSNPMap: Software for Linkage Analysis and QTL Mapping in Autotetraploid Populations Using SNP Dosage Data

An earlier software application of ours, TetraploidMap for Windows, enabled linkage analysis and quantitative trait locus interval mapping to be carried out in an experimental cross of an autotetraploid species, using both dominant markers such as amplified fragment length polymorphisms and codominant markers such as simple sequence repeats. The size was limited to 800 markers, and quantitative trait locus mapping was conducted for each parent separately due to the difficulties in obtaining a reliable consensus map for the 2 parents. Modern genotyping technologies now give rise to datasets of thousands of single nucleotide polymorphisms, and these can be scored in autotetraploid species as single nucleotide polymorphism dosages, distinguishing among the heterozygotes AAAB, AABB, and ABBB, rather than simply using the presence or absence of an allele. The dosage data is more informative about recombination and leads to higher density linkage maps. The current program, TetraploidSNPMap, makes full use of the dosage data, and has new facilities for displaying the clustering of single nucleotide polymorphisms, rapid ordering of large numbers of single nucleotide polymorphisms using a multidimensional scaling analysis, and phase calling. It also has new routines for quantitative trait locus mapping based on a hidden Markov model, which use the dosage data to model the effects of alleles from both parents simultaneously. A Windows-based interface facilitates data entry and exploration. It is distributed with a detailed user guide. TetraploidSNPMap is freely available from our GitHub repository

Drought has negative consequences on aphid fitness and plant vigor:Insights from a meta-analysis

Abstract Aphids are abundant in natural and managed vegetation, supporting a diverse community of organisms and causing damage to agricultural crops. Due to a changing climate, periods of drought are anticipated to increase, and the potential consequences of this for aphid–plant interactions are unclear. Using a meta‐analysis and synthesis approach, we aimed to advance understanding of how increased drought incidence will affect this ecologically and economically important insect group and to characterize any potential underlying mechanisms. We used qualitative and quantitative synthesis techniques to determine whether drought stress has a negative, positive, or null effect on aphid fitness and examined these effects in relation to (a) aphid biology, (b) geographical region, and (c) host plant biology. Across all studies, aphid fitness is typically reduced under drought. Subgroup analysis detected no difference in relation to aphid biology, geographical region, or the aphid–plant combination, indicating the negative effect of drought on aphids is potentially universal. Furthermore, drought stress had a negative impact on plant vigor and increased plant concentrations of defensive chemicals, suggesting the observed response of aphids is associated with reduced plant vigor and increased chemical defense in drought‐stressed plants. We propose a conceptual model to predict drought effects on aphid fitness in relation to plant vigor and defense to stimulate further research

Fatigue crack growth prediction in GLARE hybrid laminates

A mechanistic approach for fatigue crack growth prediction in GLARE laminates is presented. Three-dimensional finite element models are used to obtain the mode I stress intensity factor, KI, in the aluminum layers, and the fatigue crack growth rate of monolithic aluminum expressed as a Paris-type power law is used to predict the crack growth rates in the GLARE laminates. The crack growth rates in three different types of GLARE laminates with center-cracked tension configurations under cyclic loads are predicted and compared with experimental results. Qualitatively, the current approach predicts that the crack growth rate remains approximately constant with crack length, which is consistent with experimental observations. The quantitative correlations with the experimental crack growth rates also show excellent agreement. It is also found that the stress intensity factors in the aluminum layers at different through-thickness locations in the GLARE laminates are not identical. The cause and implications of this discrepancy and the advantages of the current approach to predict crack growth rates in generic hybrid laminates are discussed

Disease induced dynamics in host-parasitoid systems: chaos and coexistence

All animals and plants are, to some extent, susceptible to disease caused by varying combinations of parasites, viruses and bacteria. In this paper, we present a mathematical model of interactions between a host, two parasitoids and a pathogen which shows that the presence of an infection can preserve and promote diversity in such multi-species systems. Initially, we use a system of ordinary differential equations to investigate interactions between two species of parasitoids, a host and a host infection. We show that the presence of all four species is necessary for the system as a whole to persist, and that in particular, the presence of the pathogen is necessary for the coexistence of the two parasitoid species. The inclusion of infection induces a wide range of dynamics, including chaos, and these dynamics are robust for a wide range of parameter values. We then extend the model to include spatial effects by introducing random motility (diffusion) of all three species and examine the subsequent spatio-temporal dynamics, including travelling waves and other more complicated heterogeneous behaviour. The computational simulation results of the model suggest that infection in the hosts can blunt the effects of competition between parasitoids, allowing the weaker competitor to survive. Regardless of the nature of the stability of the coexistent steady state of the system, there is an initial period of transient dynamics, the length of which can be extended by an appropriate choice of initial conditions. The existence of these transient dynamics suggests that systems subject to regular restoration to a starting state, such as agro-ecosystems, may be kept in a continual state of dynamic transience, and this has implications for the use of natural enemies to control insect pests, the preservation of biodiversity in farmland habitats and the more general dynamics of disease processes

Combination of genetics and spatial modelling highlights the sensitivity of cod (Gadus morhua) population diversity in the North Sea to distributions of fishing

Conserving genetic diversity in animal populations is important for sustaining their ability to respond to environmental change. However, the ‘between-population’ component of genetic diversity (biocomplexity) is threatened in many exploited populations, particularly marine fish, where harvest management regions may be larger than the spatial extent of genetically distinct sub-populations. Using single nucleotide polymorphism (SNP) data we delineated the geographic limits of three population units of Atlantic cod (Gadus morhua) in northwest European waters. Two of the populations co-habit the North Sea, and trawl survey data showed differing trends in their abundances. We developed a spatial model of these units to simulate population dynamics under spatial patterns of harvesting, Competition between units during the pelagic juvenile stages in the model led to suppression of the more localised northern North Sea (Viking) unit by the more widespread (Dogger) unit, and its premature extinction under some spatial patterns of fishing. Fishery catch limits for cod are set at the scale of the whole North Sea without regard to such sub-population dynamics. Our model offers a method to quantify adjustments to regional fishing mortality rates to strike a balance between maximising sustainable yield and conserving vulnerable populations