Selecting representative model micro-organisms

Background  

Micro-biological research relies on the use of model organisms that act as representatives of their species or subspecies, these are frequently well-characterized laboratory strains. However, it has often become apparent that the model strain initially chosen does not represent important features of the species. For micro-organisms, the diversity of their genomes is such that even the best possible choice of initial strain for sequencing may not assure that the genome obtained adequately represents the species. To acquire information about a species' genome as efficiently as possible, we require a method to choose strains for analysis on the basis of how well they represent the species.     

The effects of mating design on introgression between chromosomally divergent sunflower species

Population genetic theory suggests that mating designs employing one or more generations of sib-crossing or selfing prior to backcrossing are more effective than backcrossing alone for moving alleles across linkage groups where effective recombination rates are low (e.g., chromosomally divergent linkages). To test this hypothesis, we analyzed the effects of chromosomal structural differences and mating designs on the frequency and genomic distribution of introgressed markers using the domesticated sunflower, Helianthus annuus, and one of its wild relatives, H. petiolaris, as the experimental system. We surveyed 170 progeny, representing the end products of three different mating designs (design I, P-F₁-BC₁-BC₂-F₂-F₃; design II, P-F₁-F₂-BC₁-BC₂-F₃; and design III, P-F₁-F₂-F₃-BC₁-BC₂), for 197 parental RAPD markers of known genomic location. Comparison of observed patterns of introgression with expectations based on simulations of unrestricted introgression revealed that much of the genome was protected from introgression regardless of mating design or chromosomal structural differences. Although the simulations indicated that all markers should introgress into multiple individuals in each of the three mating designs, 20 of 58 (34%) markers from collinear linkage groups, and 112 of 139 (81%) markers from rearranged linkage groups did not introgress. In addition, the average size of introgressed fragments (12.2 cM) was less than half that predicted by theoretical models (26–33 cM). Both of these observations are consistent with strong selection against introgressed linkage blocks, particularly in chromosomally divergent linkages. Nonetheless, mating designs II and III, which employed one and two generations of sib-mating, respectively, prior to backcrossing, were significantly more effective at moving alleles across both collinear and rearranged linkages than mating design I, in which the backcross generations preceded sib-mating. Thus, breeding strategies that include sib-crossing, in combination with backcrossing, should significantly increase the effectiveness of gene transfer across complex genic or chromosomal sterility barriers.     

Modelling expected trout ranges under current and future water temperature regimes in the Eastern Cape,South Africa

Different values have resulted in conflicts between anglers and conservation lobbies in the management of trout in South Africa. Key to the conflict is the demarcation of boundaries to areas in which brown trout Salmo trutta and rainbow trout Oncorhynchus mykiss currently occur, or are likely to establish following stocking for angling. To provide a longer-term perspective on these areas, we developed models to link salmonid biological thermal thresholds to elevation. These, when applied spatially using a digital elevation model with a probability of occurrence model, provided the basis for estimating potentially available thermal habitat for these two cold water species. Here, we acknowledge that other variables (stocking history; river connectivity) also play a role in understanding trout distributions. Using a simple scenario of an increase in mean daily water temperatures of 2 °C, we demonstrated that both brown and rainbow trout are likely to exhibit considerable range reductions in the future. Because it is possible that these range restrictions will result in an increasing desire to introduce trout into areas above their current distribution limits for the maintenance of angling opportunities, conservation managers should prioritise these areas, with management interventions seeking to understand what will help to limit introductions.     

Within-clutch variation in offspring sex determined by differences in sire body size: cryptic mate choice in the wild

Sexual selection theory predicts that paternal quality should drive female investment in progeny. We tested whether polyandrous female side-blotched lizards, Uta stansburiana, would adjust within-clutch progeny investment according to sire phenotypes. In two different years, polyandrous females selectively used sperm from larger sires to produce sons and used sperm from smaller sires to produce daughters. This cryptic sperm choice had significant effects on progeny survival to maturity that were consistent with sexually antagonistic effects associated with sire body size. Large sires produced sons with high viability and small sires produced daughters with high viability. These results are consistent with our previous findings that alleles for male body size have different fitness effects in male and female progeny. Breeding experiments in the laboratory indicate that results from the wild are more likely due to female choice than biased sperm production by males. Our results demonstrate highly refined gender-specific female choice for sperm and indicate that sire body size may signal the quality of sons or daughters that a sire will produce.     

Sexual selection and alternative mating behaviours generate demographic stochasticity in small populations.

Recent theory predicts that environmental variation and small population size facilitate the coexistence of alternative phenotypes despite unequal mean fitness. However, traditional studies of reproductive strategies often assume that the stability of alternative mating behaviours relies on equal male fitness. We present results from field observations and experimental manipulations of thermal resources on territories demonstrating the coexistence of alternative reproductive behaviours with unequal fitness. The side-blotched lizard Uta stansburiana exhibits two alternative strategies for territoriality: "usurp" and "defend". Paternity analysis revealed significantly greater mean fitness for "usurpers" than "defenders" in our study of natural variation. Moreover, variance in fitness was significantly higher for usurpers on both experimental and natural plots, implying that "usurp" is a risky strategy with potentially large pay-offs or none at all. We show theoretically that significantly higher variance in usurper fitness can allow for coexistence with defenders despite higher mean fitness of usurpers. This coexistence is facilitated by small population size. Our results have general implications for the evolution of alternative strategies and the maintenance of genetic diversity in small populations.     

Correlational selection and the evolution of genomic architecture

We review and discuss the importance of correlational selection (selection for optimal character combinations) in natural populations. If two or more traits subject to multivariate selection are heritable, correlational selection builds favourable genetic correlations through the formation of linkage disequilibrium at underlying loci governing the traits. However, linkage disequilibria built up by correlational selection are expected to decay rapidly (ie, within a few generations), unless correlational selection is strong and chronic. We argue that frequency-dependent biotic interactions that have 'Red Queen dynamics' (eg, host-parasite interactions, predator-prey relationships or intraspecific arms races) often fuel chronic correlational selection, which is strong enough to maintain adaptive genetic correlations of the kind we describe. We illustrate these processes and phenomena using empirical examples from various plant and animal systems, including our own recent work on the evolutionary dynamics of a heritable throat colour polymorphism in the side-blotched lizard Uta stansburiana. In particular, male and female colour morphs of side-blotched lizards cycle on five- and two-generation (year) timescales under the force of strong frequency-dependent selection. Each morph refines the other morph in a Red Queen dynamic. Strong correlational selection gradients among life history, immunological and morphological traits shape the genetic correlations of the side-blotched lizard polymorphism. We discuss the broader evolutionary consequences of the buildup of co-adapted trait complexes within species, such as the implications for speciation processes.     

Testosterone, endurance, and Darwinian fitness: natural and sexual selection on the physiological bases of alternative male behaviors in side-blotched lizards

The mechanistic bases of natural and sexual selection on physiological and behavioral traits were examined in male morphs of three colors of the side-blotched lizard, Uta stansburiana. Orange-throated males are aggressive and defend large territories with many females. Blue-throated males defend smaller territories with fewer females; however, blue-throated males assiduously mate guard females on their territory. Yellow-throated males do not defend a territory, but patrol a large home range. They obtain secretive copulations from females on the territories of dominant males. Males with bright orange throats had higher levels of plasma testosterone (T), endurance, activity, and home range size and concomitantly gained greater control over female home ranges than blue- or yellow-throated males. Experimentally elevating plasma T in yellow- and blue-throated males increased their endurance, activity, home range size, and control over female territories to levels that were seen in unmanipulated orange-throated males that had naturally high plasma T. However, the enhanced performance of orange-throated males is not without costs. Orange-throated males had low survival compared to the other morphs. Finally, some yellow-throated males transformed to a partial blue morphology late in the season and the endurance of these transforming yellow-throated males increased from early to late in the season. In addition, yellow-throated males that transformed to blue also had significantly higher plasma T late in the season compared to the plasma T earlier in the season. T appears to play an important role in the physiological changes that all three color morphs undergo during the process of maturation. In some yellow males, T plays an additional role in plastic changes in behavior and physiology late in the reproductive season. We discuss natural and sexual selection on physiological and behavioral traits that leads to the evolution of steroid regulation in the context of alternative male strategies.     

Experimental excursions on adaptive landscapes: density-dependent selection on egg size

Abstract. Theories of density-dependent natural selection suggest that intraspecific competition will favor juveniles of high competitive ability. Empirical evidence has been provided from laboratory selection experiments, but field studies are lacking due to the logistical difficulties of experimentally manipulating population densities in natural settings. Here, we present data from a decade-long experimental field study of side-blotched lizards, Uta stansburiana that overcomes these difficulties. We tested the hypothesis that density-dependent natural selection causes egg size to increase from early to late clutches in this and many other species. Using a novel combination of environmental manipulations of hatchling density and phenotypic manipulations of egg size, we demonstrate that the nature of selection on egg size changes dramatically in the absence of older competitors. The strength of selection on egg size among later-clutch hatchlings released in areas without competitors from early clutches became almost doubled in magnitude, compared to that among hatchlings released in the presence of older competitors. These experimental findings demonstrate density-dependent natural selection on egg size; however, they contradict the classical idea that egg size increases during the reproductive season because of competition between early and late hatchlings. The results indicate that competitive age or size asymmetries between early and late hatchlings can override within-cohort asymmetries due to egg size. We suggest that competition could be an important mediator of oscillating selection pressures in this and other systems. Finally, we discuss the utility of "double-level," simultaneous experimental manipulation of both phenotypic traits that are targets of selection (e.g., egg size) as well the environmental agents of selection (e.g., population density).     

Corticosterone, locomotor performance, and metabolism in side-blotched lizards (Uta stansburiana)

Elevated levels of circulating corticosterone commonly occur in response to stressors in wild vertebrates. A rise in corticosterone, usually in animals of subordinate rank, results in a variety of effects on behavior and physiology. Behavioral and physiological responses to short-term increases in corticosterone are well studied. In contrast, the effects of chronic elevated levels of corticosterone are poorly understood, particularly in lizards. Here, we examined the long-term effects of exogenous corticosterone on locomotor performance, resting and active metabolic rate, and hematocrit in male side-blotched lizards Uta stansburiana. Corticosterone implantation resulted in higher levels of stamina relative to sham-surgery controls. In addition, lizards with elevated corticosterone exhibited lower resting metabolic rates relative to controls. Corticosterone had no effect on peak activity metabolism but did result in faster recovery times following exhaustive exercise. We suggest that elevated levels of corticosterone in response to dominance interactions promote enhanced locomotor abilities, perhaps as a flight response to avoid agonistic interactions. Furthermore, stressed lizards are characterized by lower resting metabolic rates, which may serve as strategy to conserve energy stores and enhance survival.     

An experimental test of frequency-dependent selection on male mating strategy in the field

We provide field-based experimental evidence for the frequency-dependent nature of the fitness of alternative mating strategies. We manipulated the frequency of genetically determined phenotypic strategies in six wild populations of the side-blotched lizard, Uta stansburiana. The within-population pattern of mating was assessed using nine microsatellite loci to assign paternity. Within populations of the side-blotched lizard exist three colour morphs (orange, blue and yellow) associated with male mating strategy. The frequency of these morphs has previously been found to oscillate over a 4- to 5-year period. We found, as predicted, that the common phenotype lost fitness to its antagonist. The mating patterns of all six populations adhered to a priori predictions that were derived from previous empirical and theoretical observations on this system. We found that the frequency-dependent nature of male fitness could be accounted for by the composition of their competitors at a small local population level, driven by associations within a focal female's social neighbourhood.