Different Levels Of Selection Research Articles

Friend turned foe: selfish behavior of a spontaneously arising mitochondrial deletion in an experimentally evolved Caenorhabditis elegans population.

Selfish mitochondrial DNA (mtDNA) mutations are variants that can proliferate within cells and enjoy a replication or transmission bias without fitness benefits for the host. mtDNA deletions in Caenorhabditis elegans can reach high heteroplasmic frequencies despite significantly reducing fitness, illustrating how new mtDNA variants can give rise to genetic conflict between different levels of selection and between the nuclear and mitochondrial genomes. During a mutation accumulation experiment in C. elegans, a 1,034-bp deletion originated spontaneously and reached an 81.7% frequency within an experimental evolution line. This heteroplasmic mtDNA deletion, designated as meuDf1, eliminated portions of 2 protein-coding genes (coxIII and nd4) and tRNA-thr in entirety. mtDNA copy number in meuDf1 heteroplasmic individuals was 35% higher than in individuals with wild-type mitochondria. After backcrossing into a common genetic background, the meuDf1 mitotype was associated with reduction in several fitness traits and independent competition experiments found a 40% reduction in composite fitness. Experiments that relaxed individual selection by single individual bottlenecks demonstrated that the deletion-bearing mtDNA possessed a strong transmission bias, thereby qualifying it as a novel selfish mitotype.

Analysis of the genetic diversity of Ayrshire cattle in Russia. Message 2. Genome analysis based on data on the distribution of ROH patterns in Ayrshire cows

BACKGROUND: The analysis of ROH distribution is an important focus of genetic resource conservation programs of cattle. Characterization of ROH-islands allows to identify genetic factors affecting productivity traits of dairy cattle.
 AIM: was to analyze intra-breed genetic diversity and population structure of Ayrshire cattle, based on data on distribution of homozygosity patterns, as well as to identify loci associated with selection intensity and utility traits.
 MATERIALS AND METHODS: ROH distribution data were obtained using whole genome genotyping on Illumina BovineSNP50 (50K) DNA chips (Illumina Inc., USA). The object of the study was the DNA of Ayrshire cows (600 cows), which belonged to farms with different levels of selection and breeding work.
 RESULT: The results of our studies showed a generally similar level of inbredness of the analyzed Ayrshire cattle herds. The homogeneity of the population is confirmed by a large number of animals (72.83%) with FROH values between 0.10 and 0.20. Cluster analysis revealed consolidated groups of individuals, due to their ancestral origins. The discovered ROH-patterns included 268 genes, 32 of which were involved in regulation of the synthesis of protein and fat milk components. The results obtained may be used in breeding programs for Ayrshire cattle in Russia.
 CONCLUSIONS: The Russian population of Ayrshire cattle is distinguished by unique qualities in protein and fat milk composition and genome architecture, while maintaining genetic diversity and insignificant traces of Ayrshire cattle gene pool.

A multi-level modeling approach to guide management of female feral hogs in Great Smoky Mountains National Park

AbstractWe trapped, anesthetized, and fit 16 female feral swine (Sus scrofa) with Global Positioning System (GPS) collars in Great Smoky Mountains National Park (GRSM) to develop predictive summer and winter models for more effective population control efforts. Given the highly diverse habitat and topography in GRSM and the spatial extent of our dataset, we employed Step Selection Function (SSF) to evaluate resource selection at the 3rd-order level and Resource Selection Function (RSF) models at the 2nd-order level for both summer and winter seasons. The summer SSF and RSF models suggested relatively similar levels of selection, whereas the winter models differed by method. We created a straightforward consensus model to better visualize the agreement and constraints of each set of models. In summer, feral swine used lower slopes regardless of elevation, especially those closer to human-dominated spaces such as along paved and gravel roadways. In winter, feral swine maintained preference for lower slopes but preferred oak-dominated forest areas and selection for human development was less than in summer. Wildlife managers can use these models to better focus feral swine surveillance and management in GRSM. Managers can identify areas of high use by season and plan control activities that are both accessible and highly efficient. The combination and consensus framework presented here can be applied to other systems where species’ habitat selection may result in incongruous results across different levels of selection or seasons of interest.

Analysis of the Genetic Parameters for Dairy Linear Appraisal and Zoometric Traits: A Tool to Enhance the Applicability of Murciano-Granadina Goats Major Areas Evaluation System

Selection for zoometrics defines individuals' productive longevity, endurance, enhanced productive abilities and consequently, their long-term profitability. When zoometric analysis is aimed at large highly selected populations or in those at different levels of selection, linear appraisal systems (LAS) provide a timely response. This study estimates genetic and phenotypic parameters for zoometric/LAS traits in Murciano-Granadina goats, estimating genetic and phenotypic correlations among all traits, and determining whether major area selection would be appropriate or if adaptability strategies may need to be followed. Heritability estimates for the zoometric/LAS traits were low to high, ranging from 0.09 to 0.43, and the accuracy of estimation has improved after decades, rendering standard errors negligible. Scale inversion of specific traits may need to be performed before major areas selection strategies are implemented. Genetic and phenotypic correlations suggests that negative selection against thicker bones and higher rear insertion heights indirectly results in the optimization of selection practices in the rest of the traits, especially those in the structure, capacity and mammary system major areas. The integration and implementation of the strategies proposed within the Murciano-Granadina breeding program maximizes selection opportunities and the sustainable international competitiveness of the Murciano-Granadina goat in the dairy goat breed panorama.

Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis

Codon and amino acid usage were associated with almost every aspect of microbial life. However, how the environment may impact the codon and amino acid choice of microbial communities at the habitat level is not clearly understood. Therefore, in this study, we analyzed codon and amino acid usage patterns of a large number of environmental samples collected from diverse ecological niches. Our results suggested that samples derived from similar environmental niches, in general, show overall similar codon and amino acid distribution as compared to samples from other habitats. To substantiate the relative impact of the environment, we considered several factors, such as their similarity in GC content, or in functional or taxonomic abundance. Our analysis demonstrated that none of these factors can fully explain the trends that we observed at the codon or amino acid level implying a direct environmental influence on them. Further, our analysis demonstrated different levels of selection on codon bias in different microbial communities with the highest bias in host-associated environments such as the digestive system or oral samples and the lowest level of selection in soil and water samples. Considering a large number of metagenomic samples here we showed that microorganisms collected from similar environmental backgrounds exhibit similar patterns of codon and amino acid usage irrespective of the location or time from where the samples were collected. Thus our study suggested a direct impact of the environment on codon and amino usage of microorganisms that cannot be explained considering the influence of other factors.

Motivation(s) from control: response-effect contingency and confirmation of sensorimotor predictions reinforce different levels of selection.

Humans and other animals live in dynamic environments. To reliably manipulate the environment and attain their goals they would benefit from a constant modification of motor-responding based on responses' current effect on the current environment. It is argued that this is exactly what is achieved by a mechanism that reinforces responses which have led to accurate sensorimotor predictions. We further show that evaluations of a response's effectiveness can occur simultaneously, driven by at least two different processes, each relying on different statistical properties of the feedback and affecting a different level of responding. Specifically, we show the continuous effect of (a) a sensorimotor process sensitive only to the conditional probability of effects given that the agent acted on the environment (i.e., action-effects) and of (b) a more abstract judgement or inference that is also sensitive to the conditional probabilities of occurrence of feedback given no action by the agent (i.e., inaction-effects). The latter process seems to guide action selection (e.g., should I act?) while the former the manner of the action's execution. This study is the first to show that different evaluation processes of a response's effectiveness influence different levels of responding.

Nutrient status shapes selfish mitochondrial genome dynamics across different levels of selection.

Cooperation and cheating are widespread evolutionary strategies. While cheating confers an advantage to individual entities within a group, competition between groups favors cooperation. Selfish or cheater mitochondrial DNA (mtDNA) proliferates within hosts while being selected against at the level of host fitness. How does environment shape cheater dynamics across different selection levels? Focusing on food availability, we address this question using heteroplasmic Caenorhabditis elegans. We find that the proliferation of selfish mtDNA within hosts depends on nutrient status stimulating mtDNA biogenesis in the developing germline. Interestingly, mtDNA biogenesis is not sufficient for this proliferation, which also requires the stress-response transcription factor FoxO/DAF-16. At the level of host fitness, FoxO/DAF-16 also prevents food scarcity from accelerating the selection against selfish mtDNA. This suggests that the ability to cope with nutrient stress can promote host tolerance of cheaters. Our study delineates environmental effects on selfish mtDNA dynamics at different levels of selection.

Lymph node metastases develop through a wider evolutionary bottleneck than distant metastases.

Genetic diversity among metastases is poorly understood but contains important information about disease evolution at secondary sites. Here we investigate inter- and intra-lesion heterogeneity for two types of metastases that associate with different clinical outcomes: lymph node and distant organ metastases in human colorectal cancer. We develop a rigorous mathematical framework for quantifying metastatic phylogenetic diversity. Distant metastases are typically monophyletic and genetically similar to each other. Lymph node metastases, in contrast, display high levels of inter-lesion diversity. We validate these findings by analyzing 317 multi-region biopsies from an independent cohort of 20 patients. We further demonstrate higher levels of intra-lesion heterogeneity in lymph node than in distant metastases. Our results show that fewer primary tumor lineages seed distant metastases than lymph node metastases, indicating that the two sites are subject to different levels of selection. Thus, lymph node and distant metastases develop through fundamentally different evolutionary mechanisms.

Life History Divergence in Livebearing Fishes in Response to Predation: Is There a Microevolution to Macroevolution Barrier?

A central problem in evolutionary biology is to determine whether adaptive phenotypic variation within species (microevolution) ultimately gives rise to new species (macroevolution). Predation environment can select for trait divergence among populations within species. The implied hypothesis is that the selection resulting from predation environment that creates population divergence within species would continue across the speciation boundary such that patterns of divergence after speciation would be a magnified accumulation of the trait variation observed before speciation. In this paper, we test for congruence in the mechanisms of microevolution and macroevolution by comparing the patterns of life history divergence among three closely related species of the livebearer genus Brachyrhaphis (Poeciliidae), namely B. rhabdophora, B. roseni, and B. terrabensis. Within B. rhabdophora, populations occur in either predator or predator-free environments, and have been considered to be at a nascent stage of speciation. Sister species B. roseni and B. terrabensis are segregated into predator and predator-free environments, respectively, and represent a post-speciation comparison. Male and female size at maturity, clutch size, and offspring size (and to a lesser extent reproductive allocation) all diverged according to predation environment and differences were amplified through evolutionary time, i.e., across the speciation boundary. Variation observed among nascent species differentiated by predation environment is a good predictor of variation among established species differentiated by predation environment. We found no evidence for different processes or different levels of selection acting across the speciation boundary, suggesting that macroevolution in these species can be understood as an accumulation of micro-evolutionary changes.

Economic results in the breeding of goats under intensive and extensive systems

The goal of the present study is to establish the economic results from the application of intensive, semi-intensive and extensive systems of breeding. The study included two Bulgarian goat breeds: Bulgarian Dairy White (BDW), with different levels of selection and raised under two different systems, barn and pasture-barn-based, as well as Local Longhair breed goats raised under a pasture-barn system. The data on the productivity, income and expenses were obtained from the financial statements of the farms, and calculated per individual doe. The highest natural, economic and cost-efficiency results were exhibited by the does of the BDW breed, which is bred in a barn all year long. The herd is under strict selection control, with an average dairy capacity of 820 l per doe and fertility of 1.8 goatlings. These goats brought income in the amount of BGN 702.50 per doe, while the expenses were BGN 537.70. Profit with subsidy was reported as BGN 165.85, and without subsidy – BGN 85.85. They achieved cost-efficiency of the income with subsidy amounting to +23.57, and + 13.77 without subsidy, while the expenses were, respectively, +30.84 and + 15.97. Significantly lower values of natural and economic parameters were exhibited by the does of the BDW breed, which were under a pasture-barn system and without selection control. Even though they were lower, profits and cost-efficiency were still positive. Expectedly, the lowest natural and economic parameters were observed in the does of the Bulgarian Local Longhair breed. They registered a loss of BGN 21.39 without subsidy and a profit of BGN 18.61 with a subsidy for animals under selection control. The cost-efficiency of income and expenses without subsidies was negative, whereas with subsidies it was positive, albeit at minimum values.

Patterns of reproductive differentiation and reproductive plasticity in the major evolutionary transition to superorganismality.

Major evolutionary transitions in individuality are characterised by the formation of new levels of biological complexity from the cooperation of previously independent lower-level units. The evolution of superorganismality in insects is one such major transition, and is characterised by an extreme division of reproductive labour between ancestrally autonomous units, in the form of queen and worker castes. Here, we discuss the nature of plasticity in the emergence of castes across the major transition to superorganismality in insects. We identify key changes in plasticity which act at different levels of selection: a loss of reproductivity plasticity at the individual level is matched by a gain in plasticity at the colony level. Taking multi-level selection into consideration has important implications for formulating testable hypotheses regarding the nature of plasticity in a major transition from a lower to a higher level of biological complexity.

FURTHER THOUGHTS ON SKINNER’S SELECTIONISM

Early in Skinner’s professional career, he took an important step away from the psychological essentialism that pervades the field of psychology: He observed that the relationship between behavior and its consequences was most orderly when his analytical units embraced the variability that is implicit in all selection contingencies. The view that variability is fundamental, not accidental, is the central difference between selectionism and essentialism. One reason for pursuing analogies among different levels of selection is the extraordinary power of contingencies of selection to explain adaptive complexity in nature. Apparent exceptions to the analogy between behavioral and evolutionary development can be interpreted in terms of directed variation. As an example of directed variation, Skinner’s explicit exposition of the analogy between shaping and natural selection in 1953 might have been inspired, in part, by the work of the British biologist, J. W. S. Pringle (1951).

Multilevel mutation-selection systems and set-valued duals.

A class of measure-valued processes which model multilevel multitype populations undergoing mutation, selection, genetic drift and spatial migration is considered. We investigate the qualitative behaviour of models with multilevel selection and the interaction between the different levels of selection. The basic tools in our analysis include the martingale problem formulation for measure-valued processes and a generalization of the function-valued and set-valued dual representations introduced in Dawson-Greven (Spatial Fleming-Viot models with selection and mutation. Lecture notes in mathematics, vol 2092. Springer, Cham, 2014). The dual is a powerful tool for the analysis of the long-time behaviour of these processes and the study of evolutionary systems which model phenomena including altruism, the emergence of cooperation and more complex interactions.

Effect of Tetracycline Dose and Treatment Mode on Selection of Resistant Coliform Bacteria in Nursery Pigs.

This study describes the results of a randomized clinical trial investigating the effect of oxytetracycline treatment dose and mode of administration on the selection of antibiotic-resistant coliform bacteria in fecal samples from nursery pigs. Nursery pigs (pigs of 4 to 7 weeks of age) in five pig herds were treated with oxytetracycline for Lawsonia intracellularis-induced diarrhea. Each group was randomly allocated to one of five treatment groups: oral flock treatment with a (i) high (20 mg/kg of body weight), (ii) medium (10 mg/kg), or (iii) low (5 mg/kg) dose, (iv) oral pen-wise (small-group) treatment (10 mg/kg), and (v) individual intramuscular injection treatment (10 mg/kg). All groups were treated once a day for 5 days. In all groups, treatment caused a rise in the numbers and proportions of tetracycline-resistant coliform bacteria right after treatment, followed by a significant drop by the time that the pigs left the nursery unit. The counts and proportions of tetracycline-resistant coliforms did not vary significantly between treatment groups, except immediately after treatment, when the highest treatment dose resulted in the highest number of resistant coliforms. A control group treated with tiamulin did not show significant changes in the numbers or proportions of tetracycline-resistant coliforms. Selection for tetracycline-resistant coliforms was significantly correlated to selection for ampicillin- and sulfonamide-resistant strains but not to selection for cefotaxime-resistant strains. In conclusion, the difference in the dose of oxytetracycline and the way in which the drug was applied did not cause significantly different levels of selection of tetracycline-resistant coliform bacteria under the conditions tested.IMPORTANCE Antimicrobial resistance is a global threat to human health. Treatment of livestock with antimicrobials has a direct impact on this problem, and there is a need to improve the ways that we use antimicrobials in livestock production. We hypothesized that antibiotic resistance development following treatment of diarrhea in nursery pigs could be reduced either by lowering the dose of oxytetracycline or by replacing the commonly used practice of flock treatment with individual or small-group treatments, since this would reduce the number of pigs treated. However, the study showed no significant difference between treatment groups with respect to the number or proportion of tetracycline-resistant coliforms selected. The most important conclusion is that under practical field conditions, there will be no added value, in terms of lowering resistance development, by exchanging flock treatment for individual or small-group treatment of nursery pigs. The reason for the lack of an effect of single-animal treatment is probably that such animals share the environment with treated animals and take up resistant bacteria from the environment.

Levels of selection shaping caste interactions during queen replacement in the honey bee, Apis mellifera

We investigated the different levels of selection that may influence the queen replacement process in honey bees by monitoring queen–queen and worker–queen interactions in queenless observation colonies containing populations of paint-marked workers that were either related or not related to introduced virgin queens experimentally reared to be of low- and high-quality, as estimated by differences in size and potential reproductive capacities. The high-quality queens were more likely to survive and become the new laying queen of their colonies. Queen survival was positively associated with both queen fighting ability and worker–queen interactions. Surviving queens were more aggressive and had greater fighting success. However, surviving queens were not bigger than killed queens nor were they the first queens to emerge, suggesting that queen size and early emergence alone are not the determining factors of queen fighting ability. The worker–queen interaction that was most strongly associated with the outcome of queen replacement was the vibration signal, which is a communication signal that workers perform on virgin queens. Surviving queens were vibrated at rates 3–4 times those experienced by killed queens and a queen’s vibration rate was positively correlated with her fighting ability and the number of rivals killed. Workers showed no consistent preferences for related vs. unrelated queens and the proportion of interactions received from related workers was not associated with any aspect of queen fighting ability and success monitored. Our results suggests that caste interactions during queen replacement have been shaped by both selection acting at the level of the individual queen (which favors higher quality queens with greater fighting ability) and selection acting at the level of the colony (which favors workers directing vibration signals towards queens with greater fighting potential), ultimately resulting in a higher quality queen becoming the new laying queen of the colony. Selection acting at the level of the individual worker through kin selection, which would favor preferential treatment of related queens, did not consistently influence caste interactions or the outcome of the replacement process. Thus, the outcome of queen replacement in honey bees may be determined primarily by a combination of a queen’s inherent fighting ability coupled with the rate at which she receives some interactions (particularly vibration signals) from workers.

Evolutionary dynamics of HIV at multiple spatial and temporal scales

Infectious diseases remain a formidable challenge to human health, and understanding pathogen evolution is crucial to designing effective therapeutics and control strategies. Here, we review important evolutionary aspects of HIV infection, highlighting the concept of selection at multiple spatial and temporal scales. At the smallest scale, a single cell may be infected by multiple virions competing for intracellular resources. Recombination and phenotypic mixing introduce novel evolutionary dynamics. As the virus spreads between cells in an infected individual, it continually evolves to circumvent the immune system. We discuss evolutionary mechanisms of HIV pathogenesis and progression to AIDS. Viral spread throughout the human population can lead to changes in virulence and the transmission of immune-evading variation. HIV emerged as a human pathogen due to selection occurring between different species, adapting from related viruses of primates. HIV also evolves resistance to antiretroviral drugs within a single infected host, and we explore the possibility for the spread of these strains between hosts, leading to a drug-resistant epidemic. We investigate the role of latency, drug-protected compartments, and direct cell-to-cell transmission on viral evolution. The introduction of an HIV vaccine may select for viral variants that escape vaccine control, both within an individual and throughout the population. Due to the strong selective pressure exerted by HIV-induced morbidity and mortality in many parts of the world, the human population itself may be co-evolving in response to the HIV pandemic. Throughout the paper, we focus on trade-offs between costs and benefits that constrain viral evolution and accentuate how selection pressures differ at different levels of selection.Electronic supplementary materialThe online version of this article (doi:10.1007/s00109-012-0892-1) contains supplementary material, which is available to authorized users.

IMMUNE DEFENSE IN LEAF-CUTTING ANTS: A CROSS-FOSTERING APPROACH

To ameliorate the impact of disease, social insects combine individual innate immune defenses with collective social defenses. This implies that there are different levels of selection acting on investment in immunity, each with their own trade-offs. We present the results of a cross-fostering experiment designed to address the influences of genotype and social rearing environment upon individual and social immune defenses. We used a multiply mating leaf-cutting ant, enabling us to test for patriline effects within a colony, as well as cross-colony matriline effects. The worker's father influenced both individual innate immunity (constitutive antibacterial activity) and the size of the metapleural gland, which secretes antimicrobial compounds and functions in individual and social defense, indicating multiple mating could have important consequences for both defense types. However, the primarily social defense, a Pseudonocardia bacteria that helps to control pathogens in the ants' fungus garden, showed a significant colony of origin by rearing environment interaction, whereby ants that acquired the bacteria of a foster colony obtained a less abundant cover of bacteria: one explanation for this pattern would be co-adaptation between host colonies and their vertically transmitted mutualist. These results illustrate the complexity of the selection pressures that affect the expression of multilevel immune defenses.

Is God an Adaptation?

In this critical notice to Robert Wright’s The Evolution of God, we focus on the question of whether Wright’s God is one which can be said to be an adaptation in a well defined sense. Thus we evaluate the likelihood of different models of adaptive evolution of cultural ideas in their different levels of selection. Our result is an emphasis on the plurality of mechanisms that may lead to adaptation. By way of conclusion we assess epistemologically some of Wright’s more controversial claims concerning the directionality of evolution and moral progress.

The structure of feeding behavior in commercial broiler lines selected for different growth rates

Selection for increased growth rate in livestock is accompanied by increased requirements for food resources. It has been suggested that more intensively selected birds, such as broilers, have altered food intake control mechanisms and may be constantly hungry, due to the high demands of fast growth rates. If this is the case, it would be a major welfare issue. We investigated the hypothesis that more intensive selection for growth in some lines of broilers has altered feeding behavior by analyzing short-term feeding behavior bouts in relation to the roles of hunger and satiety mechanisms in the control of food intake. Using 4 genetic lines, resulting from different levels of selection for growth rate, meal pattern analysis was performed and the bouting of short-term feeding behavior was estimated. All lines showed bouted feeding behavior, although differences in meal size, number of meals, and meal duration were evident across lines. In all lines, the probability of birds starting a new meal was low immediately after finishing the previous meal and increased with time, as expected for feeding behavior governed by hunger and satiety mechanisms. Normal feeding behavior was, therefore, not affected by the intensity of selection. Feeding rate increased with growth rate, suggesting that this may be a consequence of selection. However the other characteristics of feeding behavior, such as meal duration, did not change consistently with higher growth rate. Due to differences between lines in bird size, the number and weight of birds per pen also differed between the lines. The differences in feeding behavior between lines were greatly diminished when weight of birds per square meter was taken into account but were still statistically significant. Overall, it is apparent that even when growth rate and body size have been substantially altered by genetic selection, the underlying normal controls of feeding behavior are conserved in broiler birds.

Siphonophores

Siphonophores