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The aim of this study was to examine gender stereotyping by pre-school children in selecting a picture book cover and assigning gender to animal characters in illustrations. We aimed to explore which gender children would assign to bear characters, when these are portrayed in different more or less gender stereotyped activities, occupations or emotional states. Furthermore, we analysed the criteria on which the children based their decision. The sample included 71 children aged 5-6 years. The findings showed that children's selection of their favourite cover was consistent with gender stereotypes; most children picked the cover stereotypical of their gender. Similarly, the children's assigning of gender to bear characters was consistent with gender stereotypes as well. The criteria they used when determining gender of a bear character could be categorized into three broader categories referring to the appearance of the bears; colours used and gender roles present in child's environment.

Pigeons performed a delayed matching-to-sample task in which large or small reinforcers for correct remembering were signaled during the retention interval. Accuracy was low when small reinforcers were signaled, and high when large reinforcers were signaled (the signaled magnitude effect). When the reinforcer-size cue was switched from small to large partway through the retention interval, accuracy accordingly changed from low to high. The opposite happened when the cue was switched from large to small. This dissociation of forgetting from the passage of time raises the possibility that remembering is delay-specific. The reversal of the signaled magnitude effect during the retention interval is consistent with an attentional account in which the stimulus control of remembering is influenced by extraneous events. (Contains 4 figures.)

Twelve rats made repeated choices on an adjusting-delay schedule between a smaller reinforcer (A) that was delivered immediately after a response and a larger reinforcer (B) that was delivered after a delay which increased or decreased by 20% depending on the subject's choices in successive blocks of trials. In two phases of the experiment (100 sessions and 40 sessions), reinforcer sizes were selected which enabled theoretical parameters expressing the rate of delay discounting and sensitivity to reinforcer size to be estimated from the ratio of the indifference delays obtained in the two phases. Indifference delays, calculated from adjusting delays in the last 10 sessions of each phase, were shorter when the sizes of A and B were 14 and 25 [mu]l of a 0.6 M sucrose solution than when they were 25 and 100 [mu]l of the same solution. The ratio of the indifference delays was significantly smaller than that predicted on the basis of an assumed linear relation between reinforcer size and instantaneous reinforcer value, consistent with a previous proposal that this relation may be hyperbolic in form. Estimates of the rate of delay discounting based on the ratio of the two indifference delays (mean, 0.08 s[superscript -1]) were similar to values obtained previously using different intertemporal choice protocols. Estimates of the size-sensitivity parameter (mean 113 [mu]l) were similar to estimates recently derived from performance on progressive-ratio schedules. In both phases of the experiment, adjusting delays in successive blocks of trials were analyzed using the Fourier transform. The power spectrum obtained from individual rats had a dominant frequency that corresponded to a period of oscillation of the adjusting delay between 30 and 100 trial blocks (mean, 78). Power in the dominant frequency band was highest in the early sessions of the first phase and declined with extended training. It is suggested that this experimental protocol may have utility in neurobehoral studies of intertemporal choice. (Contains 9 figures.)

Orally and later in written form, stories have been used to identify and reinforce the values of a culture. The parables of the Bible and the vocalization of articulate animals in Aesop fables continue to be used to teach morals to children. While the majority of existing research investigates the effective use of animals as a tool in character and values education, limited research has been done regarding the benefits of using articulate animals to teach leadership education and to promote the wise selection of leaders. The purpose of this pilot study will be to qualitatively test the theory that students who read and discuss selections from modern fantasy that identify specific articulate animals as role models or bullies will respond differently to questions posed in whole-group discussion. The random selection of middle-school students engaged in followership training will read and discuss the roles of specific animals in selected children's literature. During whole group discussion, responses will be observed and recorded, noting differences to the following two questions: "Are followers responsible for the actions of a leader?" and "Is a bully a leader?" (Contains 25 footnotes.)

Eight pigeons responded in a three-component concurrent-chains procedure, with either independent or dependent initial links. Relative probability and immediacy of reinforcement in the terminal links were both varied, and outcomes on individual trials (reinforcement or nonreinforcement) were either signaled or unsignaled. Terminal-link fixed-time schedules were varied across components within conditions to yield immediacy ratios of 1:2, 1:1 and 2:1. The probabilities of reinforcement were varied across conditions to yield reinforcer ratios of 1:5, 1:2, 2:1 and 5:1. Results showed that a model based on the generalized matching law provided a good description of response allocation, accounting for 92% of the variance overall. As expected, sensitivity to probability was greater in the unsignaled conditions. However, sensitivity to immediacy was also greater in the unsignaled conditions, suggesting that the effect of signaling terminal-link outcomes may not be limited to probability but apply to reinforcer variables in general. The effects of signaling can be explained in terms of conditioned reinforcement added to each alternative's outcomes in the matching law. There was some evidence for an interaction between reinforcer probability and immediacy, particularly for the dependent-schedules group, such that sensitivity to immediacy was greater at moderate rather than extreme reinforcer ratios. However, further analysis suggested that this could have been due to a ceiling effect on response allocation imposed by dependent scheduling. Overall, the present results show that the generalized matching law can provide a useful account of choice between outcomes that vary in both probability and immediacy of reinforcement. (Contains 4 tables and 7 figures.)

Although newborns have surprised scientists with their learning skills, proficiency on concurrent schedules of reinforcement requires (in effect) the ability to integrate and compare behavior-consequence relations over time. Can very young animals obey the quantitative relation that applies to such repeated choices, the generalized matching law? The provenance of the skill is not well understood, and this study provides the first investigation of matching in neonates. Northern bobwhite ("Colinus virginianus") hatchlings pecked left and right targets on a touchscreen for heat delivery on a concurrent variable-interval reinforcement schedule. Within 5 days after hatching, the chicks showed sensitivity levels significantly greater than zero, but short of typical adult levels. However, stable sequential patterns emerged almost immediately, including a consistent choose-rich tendency after unreinforced responses, one that entails some degree of temporal integration. These exploratory data suggest that the basic ability to match develops quickly in this precocial species, but that more extensive experience may be required to achieve the higher sensitivities typically seen in adults. (Contains 6 figures and 1 footnote.)

Grace and McLean (2006) proposed a decision model for acquisition of choice in concurrent chains which assumes that after reinforcement in a terminal link, subjects make a discrimination whether the preceding reinforcer delay was short or long relative to a criterion. Their model was subsequently extended by Christensen and Grace (2008, 2009a, 2009b) to include effects of initial- and terminal-link duration on choice. We show that an expression for steady-state responding can be derived from the decision model, which enables a model for choice that provides an account of archival data that is equal or superior to the contextual choice model (Grace, 1994) and hyperbolic value-added model (Mazur, 2001) in terms of goodness of fit, parsimony, and parameter invariance. The success of the steady-state decision model validates the strategy of understanding acquisition phenomena as a bridge toward explaining choice at the molar level. (Contains 2 tables, 2 figures and 2 footnotes.)

Pigeons were presented with a concurrent-chains schedule in which the total time to primary reinforcement was equated for the two alternatives (VI 30 s VI 60 s vs. VI 60 s VI 30 s). In one set of conditions, the terminal links were signaled by the same stimulus, and in another set of conditions they were signaled by different stimuli. Choice was in favor of the shorter terminal link when the terminal links were differentially signaled but in favor of the shorter initial link (and longer terminal link) when the terminal links shared the same stimulus. Preference reversed regularly with reversals of the stimulus condition and was unrelated to the discrimination between the two terminal links during the nondifferential stimulus condition. The present results suggest that the relative value of the terminal-link stimuli and the relative rate of conditioned reinforcer presentation are important influences on choice behavior, and that models of conditioned reinforcement need to include both factors. (Contains 2 figures and 2 tables.)

Learning by repetition engages distinct cognitive strategies whose contributions are adjusted with experience. Early in learning, performance relies upon flexible, attentive strategies. With extended practice, inflexible, automatic strategies emerge. This transition is thought fundamental to habit formation and applies to human and animal cognition. In the context of spatial navigation, place strategies are flexible, typically employed early in training, and rely on the spatial arrangement of landmarks to locate a goal. Response strategies are inflexible, become dominant after overtraining, and utilize fixed motor sequences. Although these strategies can operate independently, they have also been shown to interact. However, since previous work has focused on single-choice learning, if and how these strategies interact across sequential choices remains unclear. To test strategy interactions across sequential choices, we utilized various two-choice spatial navigation tasks administered on the Opposing Ts maze, an apparatus for rodents that permits experimental control over strategy recruitment. We found that when a second choice required spatial working memory, the transition to response navigation on the first choice was blocked. Control experiments specified this effect to the cognitive aspects of the secondary task. In addition, response navigation, once established on a single choice, was not reversed by subsequent introduction of a secondary choice reliant on spatial working memory. These results demonstrate that performance strategies interact across choices, highlighting the sensitivity of strategy use to the cognitive demands of subsequent actions, an influence from which overtrained rigid actions may be protected.

Two experiments were conducted to compare choices between sequences of reinforcers in pigeon (Experiment 1) and human (Experiment 2) subjects, using functionally analogous procedures. The subjects made pairwise choices among 3 sequence types, all of which provided the same overall reinforcement rate, but differed in their temporal patterning. Token reinforcement schedules were used in both experiments and the type of exchange schedule varied across blocks of sessions. Some conditions permitted immediate exchange of tokens for consumable reinforcers (food for pigeons, video access for humans); in other conditions, tokens accumulated and were exchanged for consumable reinforcers only at the end of the sequence. Choice patterns in the immediate-exchange conditions were generally similar across species, with both pigeons and humans preferring sequences with the shortest delay to the initial reinforcer in the series. The results are broadly consistent with models of temporal discounting expanded to include the impact of sequences of delayed reinforcers acting in parallel from the time of the choice. Preferences were less consistent with discounting models in the delayed exchange conditions. Questionnaire data gathered at the end of the experiment were consistent with prior results of questionnaire studies, but showed no straightforward relation to the observed choice patterns, urging caution in the extrapolation of results from one decision-making domain to the other. (Contains 2 tables and 8 figures.)

Museum games can be a powerful meaning-making experience for players, but only if we understand that what makes games fun is also what makes them meaningful. Renowned game designer Sid Meier ("Civilization", "Railroad Tycoon", "Pirates") famously defined a good game as "a series of interesting choices." What makes choices interesting? The same things that make them meaningful: consequences, context, and a savvy appeal to human psychology. When designed well, these choices can make even mundane content meaningful. So imagine the possibilities when we use the stuff of museums--art, science, history, and technology--as our content and context. Whether creating a game or a simpler activity, we can draw on principles of game design to weave a series of interesting choices that honors our real-world content while engaging visitors in thoughtful ways. This article considers that most common type of "game"--the quiz--before analyzing the board game "Monopoly" for attributes of interesting choices, and finally discusses how those attributes are built into several games for cultural institutions. (Contains 9 notes.)

In four experiments, we investigated whether masked stimuli in priming experiments are subjected to early or to late selection. In Experiment 1, participants classified four target-pictures as being small or large. In line with early selection accounts, prime-pictures with a different perceptual appearance as the experienced targets did not elicit congruency effect. In Experiment 2, 40 targets all depicting animals were presented. Results were in line with late selections assumptions because novel animal primes but not novel primes form different semantic categories yielded congruency effects. In Experiment 3, the targets were chosen such that there is a second semantic feature that covaried with the required response. Here, novel primes picturing small animals did not influence target responses with regard to the instructed size classification, but with regard to their affiliation to the category animal.In Experiment 4, small and large pictures from two categories were presented. Category match did not influence priming, ruling out that feature overlap contaminated the former results. The results indicate that participants' prestimulus expectations determine in which stage in the processing-stream masked stimuli are selected. (Contains 5 figures and 6 footnotes.)

Previous research with the radial maze has found evidence that rats can remember both places that they have already been (retrospective coding) and places they have yet to visit (prospective coding; Cook, R. G., Brown, M. F., & Riley, D. A. (1985). Flexible memory processing by rats: Use of prospective and retrospective information in the radial maze. "Journal of Experimental Psychology: Animal Behaviour Processes, 11", 453-469). Such "dual coding" also has been found in pigeons using a radial maze analog in which insertion of a delay at different points during a trial affects performance differentially depending on where in the trial it is inserted. When a delay is interpolated either early or late in a trial, there is minimal disruption of performance compared with when it is interpolated in the middle of the trial. However, the analysis required with this procedure requires the assumption that if errors made on control trials are subtracted from errors made in delay trials, the remaining errors can be directly attributed to the delay. But errors may also be attributed to the changing criterion for making a response as the trial proceeds. Furthermore, the animal's tendency to choose alternatives in a systematic order may also affect its need to remember the sequence of choices made (and yet to be made) on each trial. In the present research, we avoided having to make this assumption by giving the pigeons a two-alternative choice at the time of testing and by randomly determining for the pigeon the order of predelay choices on each trial. This change in procedure resulted in comparable performance as a function of where in the trial the test occurred on both control and delay trials. The effect of the delay was to produce a general decrement in performance independent of where it occurred in the trial. (Contains 4 figures.)

The purpose of this study was to examine effects of "d"-amphetamine on choice controlled by reinforcement delay. Eight pigeons responded under a concurrent-chains procedure in which one terminal-link schedule was always fixed- interval 8 s, and the other terminal-link schedule changed from session to session between fixed-interval 4 s and fixed-interval 16 s according to a 31-step pseudorandom binary sequence. After sufficient exposure to these contingencies (at least once through the pseudorandom binary sequence), the pigeons acquired a preference for the shorter reinforcement delay within each session. Estimates of the sensitivity to reinforcement immediacy were similar to those obtained in previous studies. For all pigeons, at least one dose of "d"-amphetamine attenuated preference and, hence, decreased estimates of sensitivity to reinforcement immediacy; in most cases, this effect occurred without a change in overall response rates. In many cases, the reduced sensitivity to reinforcement delay produced by "d"-amphetamine resulted primarily from a decrease in the asymptotic level of preference achieved within the session; in some cases, "d"-amphetamine produced complete indifference. These findings suggest that a reduction in the sensitivity to reinforcement delay may be an important behavioral mechanism of the effects of psychomotor stimulants. (Contains 2 tables and 8 figures.)

G. Gergely, H. Bekkering, and I. Kiraly (2002) showed that 14-month-old infants imitate rationally, copying an adult's unusual action more often when it was freely chosen than when it was forced by some constraint. This suggests that infants understand others' intentions as rational choices of action plans. It is important to test whether apes also understand others' intentions in this way. In each of the current 3 studies, a comparison group of 14-month-olds used a tool more often when a demonstrator freely chose to use it than when she had to use it, but apes generally used the tool equally often in both conditions (orangutans were an exception). Only some apes thus show an understanding of others' intentions as rational choices of action plans.

Four bonobos, seven gorillas, and six orangutans were presented with two small rectangular boards on a platform. One of the boards had a piece of food under it so that it acquired an inclined orientation whereas the other remained flat on the platform. Subjects preferentially selected the inclined board. In another experiment, subjects were initially presented with two inclined boards and a transformation took place in which one of the boards fell flat to the platform while the other remained inclined. Subjects also preferred the board that remained inclined. Two additional experiments highlighted some of the possible limitations of their reasoning in this task. Presented with two inclined boards, one of which was visibly supported by a piece of wood, they failed to systematically select the unsupported one whose only reason for being inclined was the presence of the reward. Another experiment presented two rewards in each trial (instead of the customary one) in one of the following two combinations: large banana vs. small carrot or small banana vs. large carrot. Prior to the test, E presented both rewards to the subject and then hid each of them under one of the boards so that both boards were differentially inclined due to the different sizes of the rewards involved. Although subjects selected the board that showed a greater inclination (thus securing the larger reward), they disregarded the type of food that was involved. This often meant that they chose the large carrot over the small banana even though they reversed such a choice when the rewards were not occluded by the boards. Providing subjects with a "reminder" of the type of reward hidden under the boards did not alter the original results. There was no evidence of learning throughout the various experiments and control tests ruled out the possibility of inadvertent cuing by the experimenter, poor performance due to a lack of motivation, or good performance due to a predisposition to select objects with sloped surfaces. It is concluded that subjects made some inferences about the reason for the inclined orientation of the boards, and not simply associated an inclined orientation with the presence of the reward.

Pigeons responded in a successive-encounters procedure that consisted of a search state, a choice state, and a handling state. The search state was either a fixed-interval or mixed-interval schedule presented on the center key of a three-key chamber. Upon completion of the search state, the choice state was presented, in which the center key was off and the two side keys were lit. A pigeon could either accept a delay followed by food (by pecking the right key) or reject this option and return to the search state (by pecking the left key). During the choice state, a red right key represented the long alternative (a long handling delay followed by food), and a green right key represented the short alternative (a short handling delay followed by food). In some conditions, both the short and long alternatives were fixed-time schedules, and in other conditions both were mixed-time schedules. Contrary to the predictions of both optimal foraging theory and delay-reduction theory, the percentage of trials on which pigeons accepted the long alternative depended on whether the search and handling schedules were fixed or mixed. They were more likely to accept the long alternative when the search states were fixed-interval rather than mixed-interval schedules, and more likely to reject the long alternative when the handling states were fixed-time rather than mixed-time schedules. This pattern of results was in qualitative agreement with the predictions of the hyperbolic-decay model, which states that the value of a reinforcer is inversely related to the delay between a choice response and reinforcer delivery. (Contains 1 table and 6 figures.)

Six pigeons were trained on a procedure in which seven components arranged different food-delivery ratios on concurrent variable-interval schedules each session. The components were unsignaled, lasted for 10 food deliveries, and occurred in random order with a 60-s blackout between components. The schedules were arranged using a switching-key procedure in which two responses on a center key changed the schedules and associated stimuli on two side keys. In Experiment 1, over five conditions, an increasing proportion of food deliveries accompanied by a magazine light was replaced with the presentation of the magazine light only. Local analyses of preference showed preference pulses toward the alternative that had just produced either a food-plus-magazine-light or magazine-light-only presentation, but pulses after food deliveries were always greater than those after magazine lights. Increasing proportions of magazine lights did not change the size of preference pulses after food or magazine-light presentations. Experiment 2 investigated the effects of correlations between food ratios and magazine-light ratios: In Condition 6, magazine-light ratios in components were inversely correlated (-1.0) with food ratios, and in Condition 7, magazine-light ratios were uncorrelated with food ratios. In Conditions 8 and 9, pecks also produced occasional 2.5-s flashes of a green keylight. In Condition 8, food and magazine-light ratios were correlated 1.0 whereas food and green-key ratios were correlated -1.0. In Condition 9, food and green-key ratios were correlated 1.0 whereas food and magazine-light ratios were correlated -1.0. Preference pulses toward alternatives after magazine lights and green keys depended on the correlation between these event ratios and the food ratios: If the ratios were correlated +1.0, positive preference pulses resulted; if the correlation was -1.0, preference pulses were negative. These results suggest that the Law of Effect has more to do with events signaling consequences than with strengthening responses. (Contains 1 table and 9 figures.)

We investigated the effects of discriminative stimuli on choice in a highly variable environment using a procedure in which multiple two-key concurrent VI VI components changed every 10 reinforcers and were signaled by differential flashes of red and yellow keylights. Across conditions, five pigeons were exposed to a number of different combinations of the following component reinforcer ratios: 27:1, 9:1, 3:1, 1:1, 1:3, 1:9, 1:27. Overall, there was clear control by the component signals in that preference, early in components and particularly before any reinforcers had been delivered, was ordinally related to the signaled reinforcer ratios. In conditions in which only two components arranged unequal reinforcer ratios (e.g., 27:1 and 1:27) with the remaining components arranging 1:1 reinforcer ratios, preference before the first reinforcer in a component showed peak shift in that the most extreme preference did not occur in the unequal reinforcer-ratio components, but in 1:1 components further towards the ends of the stimulus dimension. The contingency-discriminability model (Davison & Nevin, 1999) was fitted to the data and provided an excellent description of the interactions between stimulus and reinforcer effects in a highly variable environment. (Contains 3 tables and 11 figures.)

Pigeons' choice in concurrent chains can adapt to rapidly changing contingencies. Grace, Bragason, and McLean (2003) found that relative initial-link response rate was sensitive to the immediacy ratio in the current session when one of the terminal-link fixed-interval schedules was changed daily according to a pseudorandom binary sequence (e.g., Schofield & Davison, 1997). The present experiment tested whether the degree of variation in delays across sessions had any effect on acquisition rate in Grace et al.'s (2003) rapid-acquisition procedure. In one condition ("minimal variation"), the left terminal link was always fixed-interval 8 s and the right terminal link was either fixed-interval 4 s or fixed-interval 16 s. In the other condition ("maximal variation"), a unique pair of fixed-interval values was used in each session. Responding was sensitive to the current-session immediacy ratio in both conditions, but across subjects there was no systematic difference in sensitivity. These results challenge the view that initial-link responding in the rapid-acquisition procedure is determined by changes in the learned value of the terminal-link stimuli, and suggests instead that a process resembling categorical discrimination may control performance. A decision model based on the assumption that delays are categorized as short or long relative to the history of delays provided a good account of the data and shows promise in being able to explain other choice phenomena. (Contains 10 figures and 2 tables.)

In Experiment 1 with rats, a left lever press led to a 5-s delay and then a possible reinforcer. A right lever press led to an adjusting delay and then a certain reinforcer. This delay was adjusted over trials to estimate an indifference point, or a delay at which the two alternatives were chosen about equally often. Indifference points increased as the probability of reinforcement for the left lever decreased. In some conditions with a 20% chance of food, a light above the left lever was lit during the 5-s delay on all trials, but in other conditions, the light was only lit on those trials that ended with food. Unlike previous results with pigeons, the presence or absence of the delay light on no-food trials had no effect on the rats' indifference points. In other conditions, the rats showed less preference for the 20% alternative when the time between trials was longer. In Experiment 2 with rats, fixed-interval schedules were used instead of simple delays, and the presence or absence of the fixed-interval requirement on no-food trials had no effect on the indifference points. In Experiment 3 with rats and Experiment 4 with pigeons, the animals chose between a fixed-ratio 8 schedule that led to food on 33% of the trials and an adjusting-ratio schedule with food on 100% of the trials. Surprisingly, the rats showed less preference for the 33% alternative in conditions in which the ratio requirement was omitted on no-food trials. For the pigeons, the presence or absence of the ratio requirement on no-food trials had little effect. The results suggest that there may be differences between rats and pigeons in how they respond in choice situations involving delayed and probabilistic reinforcers. (Contains 2 tables and 6 figures.)

Mitochondrial genomes co-evolve with the nuclear genome over evolutionary timescales and are shaped by selection in the female germline. Here we investigate how mismatching between nuclear and mitochondrial ancestry impacts the somatic evolution of the mitochondrial genome in different tissues throughout ageing. We used ultrasensitive duplex sequencing to profile ~2.5 million mitochondrial genomes across five mitochondrial haplotypes and three tissues in young and aged mice, cataloguing ~1.2 million mitochondrial somatic and ultralow-frequency inherited mutations, of which 81,097 are unique. We identify haplotype-specific mutational patterns and several mutational hotspots, including at the light strand origin of replication, which consistently exhibits the highest mutation frequency. We show that rodents exhibit a distinct mitochondrial somatic mutational spectrum compared with primates with a surfeit of reactive oxygen species-associated G > T/C > A mutations, and that somatic mutations in protein-coding genes exhibit signatures of negative selection. Lastly, we identify an extensive enrichment in somatic reversion mutations that re-align mito-nuclear ancestry within an organisms lifespan. Together, our findings demonstrate that mitochondrial genomes are a dynamically evolving subcellular population shaped by somatic mutation and selection throughout organismal lifetimes.

Genomic evidence supports an important role for selection in shaping patterns of introgression along the genome, but frameworks for understanding the evolutionary dynamics within hybrid populations that underlie these patterns have been lacking. Due to the clock-like effect of recombination in hybrids breaking up parental haplotypes, drift and selection produce predictable patterns of ancestry variation at varying spatial genomic scales through time. Here, we develop methods based on the Discrete Wavelet Transform to study the genomic scale of local ancestry variation and its association with recombination rates and show that these methods capture temporal dynamics of drift and genome-wide selection after hybridization. We apply these methods to published datasets from hybrid populations of swordtail fish (Xiphophorus) and baboons (Papio) and to inferred Neanderthal introgression in modern humans. Across systems, upward of 20% of variation in local ancestry at the broadest genomic scales can be attributed to systematic selection against introgressed alleles, consistent with strong selection acting on early-generation hybrids. Signatures of selection at fine genomic scales suggest selection over longer time scales; however, we suggest that our ability to confidently infer selection at fine scales is likely limited by inherent biases in current methods for estimating local ancestry from contiguous segments of genomic similarity. Wavelet approaches will become widely applicable as genomic data from systems with introgression become increasingly available and can help shed light on generalities of the genomic consequences of interspecific hybridization.

Natural selection generally favours phenotypic variability in camouflaged organisms, whereas aposematic organisms are expected to evolve a more uniform warning coloration. However, no comprehensive analysis of the phenotypic consequences of predator selection in aposematic and cryptic species exists. Using state-of-the-art image analysis, we examine 2800 wing images of 82 moth species accessed via three online museum databases. We test whether anti-predator strategy (i.e., camouflage or aposematism) explains intraspecific variation in wing colour and pattern across northern hemisphere moths. In addition, we test two mutually non-exclusive, ecological hypotheses to explain variation in colour pattern: diel-activity or dietary-niche. In this work, taking into account phylogenetic relationships, moth phenotypic variability is best explained by anti-predator strategy with camouflaged moths being more variable in wing patterning than aposematic species.

The host interferon pathway upregulates intrinsic restriction factors in response to viral infection. Many of them block a diverse range of viruses, suggesting that their antiviral functions might have been shaped by multiple viral families during evolution. Host-virus conflicts have led to the rapid adaptation of host and viral proteins at their interaction hotspots. Hence, we can use evolutionary genetic analyses to elucidate antiviral mechanisms and domain functions of restriction factors. Zinc finger antiviral protein (ZAP) is a restriction factor against RNA viruses such as alphaviruses, in addition to other RNA, retro-, and DNA viruses, yet its precise antiviral mechanism is not fully characterized. Previously, an analysis of 13 primate ZAP orthologs identified three positively selected residues in the poly(ADP-ribose) polymerase-like domain. However, selective pressure from ancient alphaviruses and others likely drove ZAP adaptation in a wider representation of mammals. We performed positive selection analyses in 261 mammalian ZAP using more robust methods with complementary strengths and identified seven positively selected sites in all domains of the protein. We generated ZAP inducible cell lines in which the positively selected residues of ZAP are mutated and tested their effects on alphavirus replication and known ZAP activities. Interestingly, the mutant in the second WWE domain of ZAP (N658A) is dramatically better than wild-type ZAP at blocking replication of Sindbis virus and other ZAP-sensitive alphaviruses due to enhanced viral translation inhibition. The N658A mutant is adjacent to the previously reported poly(ADP-ribose) (PAR) binding pocket, but surprisingly has reduced binding to PAR. In summary, the second WWE domain is critical for engineering a more potent ZAP and fluctuations in PAR binding modulate ZAP antiviral activity. Our study has the potential to unravel the role of ADP-ribosylation in the host innate immune defense and viral evolutionary strategies that antagonize this post-translational modification.

In various organisms, sequencing of selectively bred lines at apparent selection limits has demonstrated that genetic variation can remain at many loci, implying that evolution at the genetic level may continue even if the population mean phenotype remains constant. We compared selection signatures at generations 22 and 61 of the High Runner mouse experiment, which includes 4 replicate lines bred for voluntary wheel-running behavior (HR) and 4 non-selected control (C) lines. Previously, we reported multiple regions of differentiation between the HR and C lines, based on whole-genome sequence data for 10 mice from each line at generation 61, which was >31 generations after selection limits had been reached in all HR lines. Here, we analyzed pooled sequencing data from ~20 mice for each of the 8 lines at generation 22, around when HR lines were reaching limits. Differentiation analyses of allele frequencies at ~4.4 million SNP loci used the regularized T-test and detected 258 differentiated regions with FDR = 0.01. Comparable analyses involving pooling generation 61 individual mouse genotypes into allele frequencies by line produced only 11 such regions, with almost no overlap among the largest and most statistically significant peaks between the two generations. These results implicate a sort of genetic churn that continues at loci relevant for running. Simulations indicate that loss of statistical power due to random genetic drift and sampling error are insufficient to explain the differences in selection signatures. The 13 differentiated regions at generation 22 with strict culling measures include 79 genes related to a wide variety of functions. Gene ontology identified pathways related to olfaction and vomeronasal pathways as being overrepresented, consistent with generation 61 analyses, despite those specific regions differing between generations. Genes Dspp and Rbm24 are also identified as potentially explaining known bone and skeletal muscle differences, respectively, between the linetypes.

Ancestral Coast Salish societies in the Pacific Northwest kept long-haired woolly dogs that were bred and cared for over millennia. However, the dog wool-weaving tradition declined during the 19th century, and the population was lost. In this study, we analyzed genomic and isotopic data from a preserved woolly dog pelt from Mutton, collected in 1859. Mutton is the only known example of an Indigenous North American dog with dominant precolonial ancestry postdating the onset of settler colonialism. We identified candidate genetic variants potentially linked with their distinct woolly phenotype. We integrated these data with interviews from Coast Salish Elders, Knowledge Keepers, and weavers about shared traditional knowledge and memories surrounding woolly dogs, their importance within Coast Salish societies, and how colonial policies led directly to their disappearance.

Aging is a nearly inescapable trait among organisms yet lifespan varies tremendously across different species and spans several orders of magnitude in vertebrates alone. This vast phenotypic diversity is driven by distinct evolutionary trajectories and tradeoffs that are reflected in patterns of diversification and constraint in organismal genomes. Age-specific impacts of selection also shape allele frequencies in populations, thus impacting disease susceptibility and environment-specific mortality risk. Further, the mutational processes that spawn this genetic diversity in both germline and somatic cells are strongly influenced by age and life history. We discuss recent advances in our understanding of the evolution of aging and lifespan at organismal, population, and cellular scales, and highlight outstanding questions that remain unanswered.

Admixture, the exchange of genetic information between distinct source populations, is thought to be a major source of adaptive genetic variation. Unlike mutation events, which periodically generate single alleles, admixture can introduce many selected alleles simultaneously. As such, the effects of linkage between selected alleles may be especially pronounced in admixed populations. However, existing tools for identifying selected mutations within admixed populations only account for selection at a single site, overlooking phenomena such as linkage among proximal selected alleles. Here, we develop and extensively validate a method for identifying and quantifying the individual effects of multiple linked selected sites on a chromosome in admixed populations. Our approach numerically calculates the expected local ancestry landscape in an admixed population for a given multi-locus selection model, and then maximizes the likelihood of the model. After applying this method to admixed populations of Drosophila melanogaster and Passer italiae, we found that the impacts between linked sites may be an important contributor to natural selection in admixed populations. Furthermore, for the situations we considered, the selection coefficients and number of selected sites are overestimated in analyses that do not consider the effects of linkage among selected sites. Our results imply that linkage among selected sites may be an important evolutionary force in admixed populations. This tool provides a powerful generalized method to investigate these crucial phenomena in diverse populations.

BackgroundWorldwide invasion and expansion of Aedes albopictus, an important vector of dengue, chikungunya, and Zika viruses, has become a serious concern in global public health. Chemical insecticides are the primary means currently available to control the mosquito populations. However, long-term and large-scale use of insecticides has selected for resistance in the mosquito that is accompanied by a genetic load that impacts fitness.ResultsA number of laboratory strains representing different resistance mechanisms were isolated and identified from laboratory-derived, deltamethrin-resistant Ae. albopictus recovered in previous work. Resistance levels and fitness costs of the strains were evaluated and compared to characterize the evolution of the resistance genotypes and phenotypes. The heterozygous F1534S mutation (1534F/S) in the voltage gated sodium channel (vgsc) gene product (VGSC), first detected in early stages of resistance evolution, not only confers high-level resistance, but also produces no significant fitness costs, leading to the rapid spread of resistance in the population. This is followed by the increase in frequency of homozygous F1534S (1534S/S) mosquitoes that have significant fitness disadvantages, prompting the emergence of an unlinked I1532T mutation with fewer side effects and a mating advantage better adapted to the selection and reproductive pressures imposed in the experiments. Metabolic resistance with no significant fitness cost and mediating a high-tolerance resistance phenotype may play a dominant role in the subsequent evolution of resistance. The different resistant strains had similar vector competence for dengue virus type-2 (DENV-2). Furthermore, a comparative analysis of vectorial capacity revealed that increased survival due to deltamethrin resistance balanced the negative fitness cost effects and contributed to the risk of dengue virus (DENV) transmission by resistant populations. The progressive evolution of resistance results in mosquitoes with both target-site insensitivity and metabolic resistance with lower fitness costs, which further leads to resistant populations with both high resistance levels and vectorial capacity.ConclusionsThis study reveals a possible mechanism for the evolution of deltamethrin resistance in Aedes albopictus. These findings will help guide practical strategies for insecticide use, resistance management and the prevention and control of mosquito-borne disease.

Croziers paradox suggests that genetic kin recognition will not be evolutionarily stable. The problem is that more common tags (markers) are more likely to be recognized and helped. This causes common tags to increase in frequency, eliminating the genetic variability that is required for genetic kin recognition. Two potential solutions to this problem have been suggested: host-parasite coevolution and multiple social encounters. We show that the host-parasite coevolution hypothesis does not work as commonly assumed. Host-parasite coevolution only stabilizes kin recognition at a parasite resistance locus if parasites adapt rapidly to hosts and cause intermediate or high levels of damage (virulence). Additionally, when kin recognition is stabilized at a parasite resistance locus, this can have an additional cost of making hosts more susceptible to parasites. However, we show that if the genetic architecture is allowed to evolve, meaning natural selection can choose the recognition locus, genetic kin recognition is more likely to be stable. The reason for this is that host-parasite coevolution can maintain tag diversity at another (neutral) locus by genetic hitchhiking, allowing that other locus to be used for genetic kin recognition. These results suggest a way that host-parasite coevolution can resolve Croziers paradox, without making hosts more susceptible to parasites. However, the opportunity for multiple social encounters may provide a more robust resolution of Croziers paradox.

BackgroundRapid adaptation to new environments can facilitate species invasions and range expansions. Understanding the mechanisms of adaptation used by invasive disease vectors in new regions has key implications for mitigating the prevalence and spread of vector-borne disease, although they remain relatively unexplored.ResultsHere, we integrate whole-genome sequencing data from 96 Aedes aegypti mosquitoes collected from various sites in southern and central California with 25 annual topo-climate variables to investigate genome-wide signals of local adaptation among populations. Patterns of population structure, as inferred using principal components and admixture analysis, were consistent with three genetic clusters. Using various landscape genomics approaches, which all remove the confounding effects of shared ancestry on correlations between genetic and environmental variation, we identified 112 genes showing strong signals of local environmental adaptation associated with one or more topo-climate factors. Some of them have known effects in climate adaptation, such as heat-shock proteins, which shows selective sweep and recent positive selection acting on these genomic regions.ConclusionsOur results provide a genome wide perspective on the distribution of adaptive loci and lay the foundation for future work to understand how environmental adaptation in Ae. aegypti impacts the arboviral disease landscape and how such adaptation could help or hinder efforts at population control.

Mutant dynamics in fragmented populations have been studied extensively in evolutionary biology. Yet, open questions remain, both experimentally and theoretically. Some of the fundamental properties predicted by models still need to be addressed experimentally. We contribute to this by using a combination of experiments and theory to investigate the role of migration in mutant distribution. In the case of neutral mutants, while the mean frequency of mutants is not influenced by migration, the probability distribution is. To address this empirically, we performed in vitro experiments, where mixtures of GFP-labelled ("mutant") and non-labelled ("wid-type") murine cells were grown in wells (demes), and migration was mimicked via cell transfer from well to well. In the presence of migration, we observed a change in the skewedness of the distribution of the mutant frequencies in the wells, consistent with previous and our own model predictions. In the presence of de novo mutant production, we used modelling to investigate the level at which disadvantageous mutants are predicted to exist, which has implications for the adaptive potential of the population in case of an environmental change. In panmictic populations, disadvantageous mutants can persist around a steady state, determined by the rate of mutant production and the selective disadvantage (selection-mutation balance). In a fragmented system that consists of demes connected by migration, a steady-state persistence of disadvantageous mutants is also observed, which, however, is fundamentally different from the mutation-selection balance and characterized by higher mutant levels. The increase in mutant frequencies above the selection-mutation balance can be maintained in small ( N

Multicellular life requires altruistic cooperation between cells. The adaptive immune system is a notable exception, wherein germinal center B cells compete vigorously for limiting positive selection signals. Studying primary human lymphomas and developing new mouse models, we found that mutations affecting BTG1 disrupt a critical immune gatekeeper mechanism that strictly limits B cell fitness during antibody affinity maturation. This mechanism converted germinal center B cells into supercompetitors that rapidly outstrip their normal counterparts. This effect was conferred by a small shift in MYC protein induction kinetics but resulted in aggressive invasive lymphomas, which in humans are linked to dire clinical outcomes. Our findings reveal a delicate evolutionary trade-off between natural selection of B cells to provide immunity and potentially dangerous features that recall the more competitive nature of unicellular organisms.

The characteristic properties of the X chromosome, such as male hemizygosity and its unique inheritance pattern, expose it to natural selection in a way that can be different from the autosomes. Here, we investigate the differences in the tempo and mode of adaptation on the X chromosome and autosomes in a population of Drosophila melanogaster. Specifically, we test the hypothesis that due to hemizygosity and a lower effective population size on the X, the relative proportion of hard sweeps, which are expected when adaptation is gradual, compared with soft sweeps, which are expected when adaptation is rapid, is greater on the X than on the autosomes. We quantify the incidence of hard versus soft sweeps in North American D. melanogaster population genomic data with haplotype homozygosity statistics and find an enrichment of the proportion of hard versus soft sweeps on the X chromosome compared with the autosomes, confirming predictions we make from simulations. Understanding these differences may enable a deeper understanding of how important phenotypes arise as well as the impact of fundamental evolutionary parameters on adaptation, such as dominance, sex-specific selection, and sex-biased demography.

All cavefishes, living exclusively in caves across the globe, exhibit similar phenotypic traits, including the characteristic loss of eyes. To understand whether such phenotypic convergence shares similar genomic bases, here we investigated genome-wide evolutionary signatures of cavefish phenotypes by comparing whole-genome sequences of three pairs of cavefishes and their surface fish relatives. Notably, we newly sequenced and generated a whole-genome assembly of the Chinese cavefish Triplophysa rosa. Our comparative analyses revealed several shared features of cavefish genome evolution. Cavefishes had lower mutation rates than their surface fish relatives. In contrast, the ratio of nonsynonymous to synonymous substitutions (ω) was significantly elevated in cavefishes compared to in surface fishes, consistent with the relaxation of purifying selection. In addition, cavefish genomes had an increased mutational load, including mutations that alter protein hydrophobicity profiles, which were considered harmful. Interestingly, however, we found no overlap in positively selected genes among different cavefish lineages, indicating that the phenotypic convergence in cavefishes was not caused by positive selection of the same sets of genes. Analyses of previously identified candidate genes associated with cave phenotypes supported this conclusion. Genes belonging to the lipid metabolism functional ontology were under relaxed purifying selection in all cavefish genomes, which may be associated with the nutrient-poor habitat of cavefishes. Our work reveals previously uncharacterized patterns of cavefish genome evolution and provides comparative insights into the evolution of cave-associated phenotypic traits.

The interaction of evolutionary processes to determine quantitative genetic variation has implications for contemporary and future phenotypic evolution, as well as for our ability to detect causal genetic variants. While theoretical studies have provided robust predictions to discriminate among competing models, empirical assessment of these has been limited. In particular, theory highlights the importance of pleiotropy in resolving observations of selection and mutation, but empirical investigations have typically been limited to few traits. Here, we applied high-dimensional Bayesian Sparse Factor Genetic modeling to gene expression datasets in 2 species, Drosophila melanogaster and Drosophila serrata, to explore the distributions of genetic variance across high-dimensional phenotypic space. Surprisingly, most of the heritable trait covariation was due to few lines (genotypes) with extreme [>3 interquartile ranges (IQR) from the median] values. Intriguingly, while genotypes extreme for a multivariate factor also tended to have a higher proportion of individual traits that were extreme, we also observed genotypes that were extreme for multivariate factors but not for any individual trait. We observed other consistent differences between heritable multivariate factors with outlier lines vs those factors without extreme values, including differences in gene functions. We use these observations to identify further data required to advance our understanding of the evolutionary dynamics and nature of standing genetic variation for quantitative traits.

In white-throated sparrows, two alternative morphs differing in plumage and behavior segregate with a large chromosomal rearrangement. As with sex chromosomes such as the mammalian Y, the rearranged version of chromosome two (ZAL2m) is in a near-constant state of heterozygosity, offering opportunities to investigate both degenerative and selective processes during the early evolutionary stages of supergenes. Here, we generated, synthesized, and analyzed extensive genome-scale data to better understand the forces shaping the evolution of the ZAL2 and ZAL2m chromosomes in this species. We found that features of ZAL2m are consistent with substantially reduced recombination and low levels of degeneration. We also found evidence that selective sweeps took place both on ZAL2m and its standard counterpart, ZAL2, after the rearrangement event. Signatures of positive selection were associated with allelic bias in gene expression, suggesting that antagonistic selection has operated on gene regulation. Finally, we discovered a region exhibiting long-range haplotypes inside the rearrangement on ZAL2m. These haplotypes appear to have been maintained by balancing selection, retaining genetic diversity within the supergene. Together, our analyses illuminate mechanisms contributing to the evolution of a young chromosomal polymorphism, revealing complex selective processes acting concurrently with genetic degeneration to drive the evolution of supergenes.

Genetic admixture is central to primate evolution. We combined 50 years of field observations of immigration and group demography with genomic data from ~9 generations of hybrid baboons to investigate the consequences of admixture in the wild. Despite no obvious fitness costs to hybrids, we found signatures of selection against admixture similar to those described for archaic hominins. These patterns were concentrated near genes where ancestry is strongly associated with gene expression. Our analyses also show that introgression is partially predictable across the genome. This study demonstrates the value of integrating genomic and field data for revealing how "genomic signatures of selection" (e.g., reduced introgression in low-recombination regions) manifest in nature; moreover, it underscores the importance of other primates as living models for human evolution.

Hybridization and subsequent genetic introgression are now known to be common features of the histories of many species, including our own. Following hybridization, selection often purges introgressed DNA genome-wide. While assortative mating can limit hybridization in the first place, it is also known to play an important role in postzygotic selection against hybrids and, thus, the purging of introgressed DNA. However, this role is usually thought of as a direct one: a tendency for mates to be conspecific reduces the sexual fitness of hybrids, reducing the transmission of introgressed ancestry. Here, we explore a second, indirect role of assortative mating as a postzygotic barrier to gene flow. Under assortative mating, parents covary in their ancestry, causing ancestry to be "bundled" in their offspring and later generations. This bundling effect increases ancestry variance in the population, enhancing the efficiency with which postzygotic selection purges introgressed DNA. Using whole-genome simulations, we show that the bundling effect can comprise a substantial portion of mate choice's overall effect as a postzygotic barrier to gene flow. We then derive a simple method for estimating the impact of the bundling effect from standard metrics of assortative mating. Applying this method to data from a diverse set of hybrid zones, we find that the bundling effect increases the purging of introgressed DNA by between 1.2-fold (in a baboon system with weak assortative mating) and 14-fold (in a swordtail system with strong assortative mating). Thus, assortative mating's bundling effect contributes substantially to the genetic isolation of species.

The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1-8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000-30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.

Direct observation of evolution in response to natural environmental change can resolve fundamental questions about adaptation, including its pace, temporal dynamics, and underlying phenotypic and genomic architecture. We tracked the evolution of fitness-associated phenotypes and allele frequencies genome-wide in 10 replicate field populations of Drosophila melanogaster over 10 generations from summer to late fall. Adaptation was evident over each sampling interval (one to four generations), with exceptionally rapid phenotypic adaptation and large allele frequency shifts at many independent loci. The direction and basis of the adaptive response shifted repeatedly over time, consistent with the action of strong and rapidly fluctuating selection. Overall, we found clear phenotypic and genomic evidence of adaptive tracking occurring contemporaneously with environmental change, thus demonstrating the temporally dynamic nature of adaptation.

Many traits responsible for male reproduction evolve quickly, including gene expression phenotypes in germline and somatic male reproductive tissues. Rapid male evolution in polyandrous species is thought to be driven by competition among males for fertilizations and conflicts between male and female fitness interests that manifest in postcopulatory phenotypes. In Drosophila, seminal fluid proteins secreted by three major cell types of the male accessory gland and ejaculatory duct are required for female sperm storage and use, and influence female postcopulatory traits. Recent work has shown that these cell types have overlapping but distinct effects on female postcopulatory biology, yet relatively little is known about their evolutionary properties. Here, we use single-nucleus RNA-Seq of the accessory gland and ejaculatory duct from Drosophila melanogaster and two closely related species to comprehensively describe the cell diversity of these tissues and their transcriptome evolution for the first time. We find that seminal fluid transcripts are strongly partitioned across the major cell types, and expression of many other genes additionally defines each cell type. We also report previously undocumented diversity in main cells. Transcriptome divergence was found to be heterogeneous across cell types and lineages, revealing a complex evolutionary process. Furthermore, protein adaptation varied across cell types, with potential consequences for our understanding of selection on male postcopulatory traits.

Visual sensitivity and body pigmentation are often shaped by both natural selection from the environment and sexual selection from mate choice. One way of quantifying the impact of the environment is by measuring how traits have changed after colonization of a novel habitat. To do this, we studied Poecilia mexicana populations that have repeatedly adapted to extreme sulphidic (H2 S-containing) environments. We measured visual sensitivity using opsin gene expression, as well as body pigmentation, for populations in four independent drainages. Both visual sensitivity and body pigmentation showed significant parallel shifts towards greater medium-wavelength sensitivity and reflectance in sulphidic populations. Altogether we found that sulphidic habitats select for differences in visual sensitivity and pigmentation. Shifts between habitats may be due to both differences in the water's spectral properties and correlated ecological changes.

The first Editor of Evolution was Ernst Mayr. His foreword to the first issue of Evolution published in 1947 framed evolution as a "problem of interaction" that was just beginning to be studied in this broad context. First, I explore progress and prospects on understanding the subsidiary interactions identified by Mayr, including interactions between parts of organisms, between individuals and populations, between species, and between the organism and its abiotic environment. Mayr's overall "problem of interaction" framework is examined in the context of coevolution within and among levels of biological organization. This leads to a comparison in the relative roles of biotic versus abiotic agents of selection and fluctuating versus directional selection, followed by stabilizing selection in shaping the genomic architecture of adaptation. Oligogenic architectures may be typical for traits shaped more by fluctuating selection and biotic selection. Conversely, polygenic architectures may be typical for traits shaped more by directional followed by stabilizing selection and abiotic selection. The distribution of effect sizes and turnover dynamics of adaptive alleles in these scenarios deserves further study. Second, I review two case studies on the evolution of acquired toxicity in animals, one involving cardiac glycosides obtained from plants and one involving bacterial virulence factors horizontally transferred to animals. The approaches used in these studies and the results gained directly flow from Mayr's vision of an evolutionary biology that revolves around the "problem of interaction."

Production of high-energy lipids by microalgae may provide a sustainable energy source that can help tackle climate change. However, microalgae engineered to produce more lipids usually grow slowly, leading to reduced overall yields. Unfortunately, culture vessels used to select cells based on growth while maintaining high biomass production, such as well plates, water-in-oil droplet emulsions, and nanowell arrays, do not provide production-relevant environments that cells experience in scaled-up cultures (e.g., bioreactors or outdoor cultivation farms). As a result, strains that are developed in the laboratory may not exhibit the same beneficial phenotypic behavior when transferred to industrial production. Here, we introduce PicoShells, picoliter-scale porous hydrogel compartments, that enable >100,000 individual cells to be compartmentalized, cultured in production-relevant environments, and selected based on growth and bioproduct accumulation traits using standard flow cytometers. PicoShells consist of a hollow inner cavity where cells are encapsulated and a porous outer shell that allows for continuous solution exchange with the external environment. PicoShells allow for cell growth directly in culture environments, such as shaking flasks and bioreactors. We experimentally demonstrate that Chlorella sp., Saccharomyces cerevisiae, and Chinese hamster ovary cells, used for bioproduction, grow to significantly larger colony sizes in PicoShells than in water-in-oil droplet emulsions (P < 0.05). We also demonstrate that PicoShells containing faster dividing and growing Chlorella clonal colonies can be selected using a fluorescence-activated cell sorter and regrown. Using the PicoShell process, we select a Chlorella population that accumulates chlorophyll 8% faster than does an unselected population after a single selection cycle.

Neural crest cell genes control the migration of neural crest cells to multiple parts of developing vertebrate embryos. A recent hypothesis posits that the "domestication syndrome" characteristic of domesticated animals is driven by selection for tameness acting on neural crest cell genes, particularly those affecting cell migration. This is posited to explain why this syndrome involves many disparate phenotypic effects. These effects can be connected to deficits in neural crest cell migration. This hypothesis predicts that patterns of selection on these neural crest cell genes will differ between domesticated species and related wild species. Specifically, it predicts higher levels of positive selection on these genes in domesticated species, relative to closely related wild species. Here we test this prediction in a comparative framework. We obtained DNA sequences from a public database (NCBI) for eleven key neural crest cell genes from a set of thirty domesticated vertebrates and matched close relatives that remain wild. We used the program Contrast-FEL in the software suite HyPhy to compare the number of sites under positive selection (as measured by non-synonymous to synonymous nucleotide substitution rates across codons) between these two types of taxa in a phylogenetic framework. We found that domesticated lineages showed a consistently higher level of positive selection on these key genes, relative to their closely related wild counterparts. In addition, we found support for relaxation of selection and purifying selection. We argue that this result is consistent with an important role for these genes in the domestication syndrome.

Hybrid incompatibilities occur when interactions between opposite ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are "intrinsic," meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis using sequence data are scarce. In this article, we compiled genetic data for F2 hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus aculeatus L.) that were born and raised in either the field (seminatural experimental ponds) or the laboratory (aquaria). Because selection against incompatibilities results in elevated ancestry heterozygosity, we tested the prediction that ancestry heterozygosity will be higher in pond-raised fish compared to those raised in aquaria. We found that ancestry heterozygosity was elevated by approximately 3% in crosses raised in ponds compared to those raised in aquaria. Additional analyses support a phenotypic basis for incompatibility and suggest that environment-specific single-locus heterozygote advantage is not the cause of selection on ancestry heterozygosity. Our study provides evidence that, in stickleback, a coarse-albeit indirect-signal of environment-dependent hybrid incompatibility is reliably detectable and suggests that extrinsic incompatibilities can evolve before intrinsic incompatibilities.

BackgroundA striking aspect of evolution is that it often converges on similar trajectories. Evolutionary convergence can occur in deep time or over short time scales, and is associated with the imposition of similar selective pressures. Repeated convergent events provide a framework to infer the genetic basis of adaptive traits. The current study examines the genetic basis of secondary web loss within web-building spiders (Araneoidea). Specifically, we use a lineage of spiders in the genus Tetragnatha (Tetragnathidae) that has diverged into two clades associated with the relatively recent (5 mya) colonization of, and subsequent adaptive radiation within, the Hawaiian Islands. One clade has adopted a cursorial lifestyle, and the other has retained the ancestral behavior of capturing prey with sticky orb webs. We explore how these behavioral phenotypes are reflected in the morphology of the spinning apparatus and internal silk glands, and the expression of silk genes. Several sister families to the Tetragnathidae have undergone similar web loss, so we also ask whether convergent patterns of selection can be detected in these lineages.ResultsThe cursorial clade has lost spigots associated with the sticky spiral of the orb web. This appears to have been accompanied by loss of silk glands themselves. We generated phylogenies of silk proteins (spidroins), which showed that the transcriptomes of cursorial Tetragnatha contain all major spidroins except for flagelliform. We also found an uncharacterized spidroin that has higher expression in cursorial species. We found evidence for convergent selection acting on this spidroin, as well as genes involved in protein metabolism, in the cursorial Tetragnatha and divergent cursorial lineages in the families Malkaridae and Mimetidae.ConclusionsOur results provide strong evidence that independent web loss events and the associated adoption of a cursorial lifestyle are based on similar genetic mechanisms. Many genes we identified as having evolved convergently are associated with protein synthesis, degradation, and processing, which are processes that play important roles in silk production. This study demonstrates, in the case of independent evolution of web loss, that similar selective pressures act on many of the same genes to produce the same phenotypes and behaviors.

Historically it has been difficult to study the evolution of bacterial small RNAs (sRNAs) across distantly related species. For example, identifying homologs of sRNAs is often difficult in genomes that have undergone multiple structural rearrangements. Also, some types of regulatory sRNAs evolve at rapid rates. The high degree of genomic synteny among divergent host-restricted bacterial lineages, including intracellular symbionts, is conducive to sRNA maintenance and homolog identification. In turn, symbiont genomes can provide us with novel insights into sRNA evolution. Here, we examine the sRNA expression profile of the obligate symbiont of psyllids, Carsonella ruddii, which has one of the smallest cellular genomes described. Using RNA-seq, we identified 36 and 32 antisense sRNAs (asRNAs) expressed by Carsonella from the psyllids Bactericera cockerelli (Carsonella-BC) and Diaphorina citri (Carsonella-DC), respectively. The majority of these asRNAs were associated with genes that are involved in essential amino acid biosynthetic pathways. Eleven of the asRNAs were conserved in both Carsonella lineages and the majority were maintained by selection. Notably, five of the corresponding coding sequences are also the targets of conserved asRNAs in a distantly related insect symbiont, Buchnera. We detected differential expression of two asRNAs for genes involved in arginine and leucine biosynthesis occurring between two distinct Carsonella-BC life stages. Using asRNAs identified in Carsonella, Buchnera, and Profftella which are all endosymbionts, and Escherichia coli, we determined that regions upstream of these asRNAs encode unique conserved patterns of AT/GC richness, GC skew, and sequence motifs which may be involved in asRNA regulation.