Network analyses support the role of prey preferences in shaping resource use patterns within five animal populations

Individual variation is an inherent aspect of animal populations and understanding the mechanisms shaping resource use patterns within populations is crucial to comprehend how individuals partition resources. Theory predicts that differences in prey preferences among consumers and/or differences in the likelihood of adding new resources to their diets are key mechanisms underlying intrapopulation variation in resource use. We developed network models based on optimal diet theory that simulate how individuals consume resources under varying scenarios of individual variation in prey preferences and in the willingness of consuming alternate resources. We then investigated how the structure of individual–resource networks generated under each model compared to the structure of observed networks representing five classical examples of individual diet variation. Our results support the notion that, for the studied populations, individual variation in prey preferences is the major factor explaining patterns in individual–resource networks. In contrast, variation in the willingness of adding prey does not seem to play an important role in shaping patterns of resource use. Individual differences in prey preferences in the studied populations may be generated by complex behavioral rules related to cognitive constraints and experience. Our approach provides a pathway for mapping foraging models into network patterns, which may allow determining the possible mechanisms leading to variation in resource use within populations.     

The role of background selection in shaping patterns of molecular evolution and variation: evidence from variability on the Drosophila X chromosome

In the putatively ancestral population of Drosophila melanogaster, the ratio of silent DNA sequence diversity for X-linked loci to that for autosomal loci is approximately one, instead of the expected "null" value of 3/4. One possible explanation is that background selection (the hitchhiking effect of deleterious mutations) is more effective on the autosomes than on the X chromosome, because of the lack of crossing over in male Drosophila. The expected effects of background selection on neutral variability at sites in the middle of an X chromosome or an autosomal arm were calculated for different models of chromosome organization and methods of approximation, using current estimates of the deleterious mutation rate and distributions of the fitness effects of deleterious mutations. The robustness of the results to different distributions of fitness effects, dominance coefficients, mutation rates, mapping functions, and chromosome size was investigated. The predicted ratio of X-linked to autosomal variability is relatively insensitive to these variables, except for the mutation rate and map length. Provided that the deleterious mutation rate per genome is sufficiently large, it seems likely that background selection can account for the observed X to autosome ratio of variability in the ancestral population of D. melanogaster. The fact that this ratio is much less than one in D. pseudoobscura is also consistent with the model's predictions, since this species has a high rate of crossing over. The results suggest that background selection may play a major role in shaping patterns of molecular evolution and variation.     

The phage-host arms race: shaping the evolution of microbes

Bacteria, the most abundant organisms on the planet, are outnumbered by a factor of 10 to 1 by phages that infect them. Faced with the rapid evolution and turnover of phage particles, bacteria have evolved various mechanisms to evade phage infection and killing, leading to an evolutionary arms race. The extensive co-evolution of both phage and host has resulted in considerable diversity on the part of both bacterial and phage defensive and offensive strategies. Here, we discuss the unique and common features of phage resistance mechanisms and their role in global biodiversity. The commonalities between defense mechanisms suggest avenues for the discovery of novel forms of these mechanisms based on their evolutionary traits.     

Some factors affecting the future composition of UK compound animal feeds

Changes in the livestock compound-feed industry are outlined. It is noted that the change to least-cost formulation of diets manufactured to a strict nutritional specification has increased the economic and biological efficiency with which different types of feed have been utilised by livestock. Nevertheless, the feeding of livestock continues to depend on large quantities of raw materials which are potentially food for humans.A number of reasons are given why crop by-products and other waste materials are not fully utilised by the compound trade, although considerable efforts have been made by the industry to find economic and acceptable alternative raw materials for compound diets. In the case of BOCM Silcock, once a raw material has been successfully evaluated at the Unilever Research Laboratories at Colworth House, extensive development work is conducted at two development farms. Two different procedures are described and illustrated: (i) inclusion of the raw material in question at varying levels in a standard diet to assess effect on performance, and (ii) palatability test work, whereby a bland control-diet is partially replaced by the raw material under test, at levels appropriate to the likely commercial use of the test ingredient.However, the extent to which any waste material is eventually utilised will largely depend on its economic value, relative to the costs of competing raw materials. It appears unlikely that there will be any major availability of new cheap alternatives to cereals in the short term.     

The lipogenic role of leucine in animal skeletal muscles

After incubation of rat, pig and cattle skeletal muscle homogenates with [U-14C]leucine, 80.4%, 37.0% and 57.0% of radioactivity was found in the proteins, 9.4%, 58.7% and 40.9% in the lipids, and 10.2%, 4.3% and 2.1% in 14CO2. This suggests that along-side with utilization in protein synthesis, leucine plays an essential role in lipid synthesis in muscle tissues of agricultural animals. The contribution of [U-14C]leucine to lipogenesis with substrates is greater than that of [U-14C]acetate and [U-14C]glucose in cattle skeletal muscles in vitro and greater than that of [U-14C]acetate in pig muscle. The CO2 production during oxidation of the [U-14C]leucine carbohydrate chain is higher than that during [U-14C]glucose and [U-14C]palmitate oxidation in skeletal muscles of rat and pig. In skeletal muscles of all animal species under study [U-14C]acetate is oxidized far more intensively than the other substrates tested.     

Factors shaping the evolution of colour patterns in Australian agamid lizards (Agamidae): a comparative study

Identifying general patterns of adaptive coloration in animals can help to elucidate the evolutionary processes that generate them. We examined the evolution of colour patterns in Australian agamid lizards, a morphologically and ecologically diverse group that relies primarily on visual communication. We tested whether certain types of colour (yellow–reds and black) were likely to be used as sexual signals, as indicated by their association with indices of sexual selection, namely, sexual dichromatism and sexual dimorphism in body size and head shape. We then tested whether sexually dichromatic colours are associated with specific patterns (uniform, mottled, striped, blotched, reticulated) or ecological variables such as habitat openness, arboreality, and substrate type. The presence of yellow–red on lateral and ventral body regions and black on ventral body regions was significantly more common in males than females. Lateral yellow–red in males was associated with the total extent of sexual dichromatism and size dimorphism, whereas ventral yellow–red was associated with sexual dichromatism. Both lateral and ventral yellow–red were associated with uniform patterning, suggesting that sexual signals in male agamid lizards may often comprise uniform patches or flushes of yellow–red. Although ventral black coloration was more prevalent on males (i.e. strongly sexually dichromatic), it was not associated with indices of sexual selection, suggesting that, in agamid lizards, yellow–red coloration is more likely to be sexually selected than black. Sexually dichromatic coloration was not strongly associated with any of the ecological variables measured. We found some associations, however, between female dorsal patterns and ecological variables, suggesting that female patterns are influenced by natural selection. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 101–112.     

The nature of protein domain evolution: shaping the interaction network

The proteomes that make up the collection of proteins in contemporary organisms evolved through recombination and duplication of a limited set of domains. These protein domains are essentially the main components of globular proteins and are the most principal level at which protein function and protein interactions can be understood. An important aspect of domain evolution is their atomic structure and biochemical function, which are both specified by the information in the amino acid sequence. Changes in this information may bring about new folds, functions and protein architectures. With the present and still increasing wealth of sequences and annotation data brought about by genomics, new evolutionary relationships are constantly being revealed, unknown structures modeled and phylogenies inferred. Such investigations not only help predict the function of newly discovered proteins, but also assist in mapping unforeseen pathways of evolution and reveal crucial, co-evolving inter- and intra-molecular interactions. In turn this will help us describe how protein domains shaped cellular interaction networks and the dynamics with which they are regulated in the cell. Additionally, these studies can be used for the design of new and optimized protein domains for therapy. In this review, we aim to describe the basic concepts of protein domain evolution and illustrate recent developments in molecular evolution that have provided valuable new insights in the field of comparative genomics and protein interaction networks.     

The animal in the genome: comparative genomics and evolution

Comparisons between completely sequenced metazoan genomes have generally emphasized how similar their encoded protein content is, even when the comparison is between phyla. Given the manifest differences between phyla and, in particular, intuitive notions that some animals are more complex than others, this creates something of a paradox. Simplistic explanations have included arguments such as increased numbers of genes; greater numbers of protein products produced through alternative splicing; increased numbers of regulatory non-coding RNAs and increased complexity of the cis-regulatory code. An obvious value of complete genome sequences lies in their ability to provide us with inventories of such components. I examine progress being made in linking genome content to the pattern of animal evolution, and argue that the gap between genomic and phenotypic complexity can only be understood through the totality of interacting components.     

The evolution of animal microRNA function

MicroRNAs (miRNAs) are a large class of small RNAs that function as negative gene regulators in eukaryotes. They regulate diverse biological processes, and bioinformatics data indicate that each miRNA can control hundreds of gene targets, underscoring the potential influence of miRNAs on almost every genetic pathway. In addition to the roles in ontogeny, recent evidence has suggested the possibility that miRNAs have huge impacts on animal phylogeny. The dramatically expanding repertoire of miRNAs and their targets appears to be associated with major body-plan innovations as well as the emergence of phenotypic variation in closely related species. Research in the area of miRNA phylogenetic conservation and diversity suggests that miRNAs play important roles in animal evolution, by driving phenotypic variation during development.     

The theory of games and the evolution of animal conflicts

The evolution of behaviour patterns used in animal conflicts is discussed, using models based on the theory of games. The paper extends arguments used by Maynard Smith &; Price (1973) showing that ritualized behaviour can evolve by individual selection. The concept of an evolutionarily stable strategy, or ESS, is defined. Two types of ritualized contests are distinguished, “tournaments” and “displays”; the latter, defined as contests without physical contact in which victory goes to the contestant which continues longer, are analyzed in detail. Three main conclusions are drawn. The degree of persistence should be very variable, either between individuals or for the same individual at different times; a negative exponential distribution of persistence times is predicted. Individuals should display with constant intensity, independent of how much longer they will in fact continue. An initial asymmetry in the conditions of a contest can be used to settle it, even if it is irrelevant to the outcome of a more protracted conflict if one were to take place.