The Roles of Standing Genetic Variation and Evolutionary History in Determining the Evolvability of Anti-Predator Strategies

O'Donnell, Daniel R.; Parigi, Abhijna; Fish, Jordan A.; Dworkin, Ian; Wagner, A.

doi:10.1371/journal.pone.0100163

Cited by 14 publications

(10 citation statements)

References 48 publications

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“…Recent research has revealed long-term effects caused by predators on the evolution of phenotypic traits in D. melanogaster ( Lehmann, Goldman & Dworkin, 2013 ; O’Donnell et al, 2014 ). The presence of predators is known to create changes in a prey’s morphology ( McCollum & Leimberger, 1997 ; Hossie et al, 2010 ) and selection in a prey’s phenotype on factors affecting escape ability ( O’Steen, Cullum & Bennet, 2002 ; Janssens & Stoks, 2014 ).…”

Section: Introductionmentioning

confidence: 99%

Short-term exposure to predation affects body elemental composition, climbing speed and survival ability inDrosophila melanogaster

Krams

Eichler

Trakimas

et al. 2016

PeerJ

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Factors such as temperature, habitat, larval density, food availability and food quality substantially affect organismal development. In addition, risk of predation has a complex impact on the behavioural and morphological life history responses of prey. Responses to predation risk seem to be mediated by physiological stress, which is an adaptation for maintaining homeostasis and improving survivorship during life-threatening situations. We tested whether predator exposure during the larval phase of development has any influence on body elemental composition, energy reserves, body size, climbing speed and survival ability of adult Drosophila melanogaster. Fruit fly larvae were exposed to predation by jumping spiders (Phidippus apacheanus), and the percentage of carbon (C) and nitrogen (N) content, extracted lipids, escape response and survival were measured from predator-exposed and control adult flies. The results revealed predation as an important determinant of adult phenotype formation and survival ability. D. melanogaster reared together with spiders had a higher concentration of body N (but equal body C), a lower body mass and lipid reserves, a higher climbing speed and improved adult survival ability. The results suggest that the potential of predators to affect the development and the adult phenotype of D. melanogaster is high enough to use predators as a more natural stimulus in laboratory experiments when testing, for example, fruit fly memory and learning ability, or when comparing natural populations living under different predation pressures.

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Section: Introductionmentioning

confidence: 99%

Short-term exposure to predation affects body elemental composition, climbing speed and survival ability inDrosophila melanogaster

Krams

Eichler

Trakimas

et al. 2016

PeerJ

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“…The ability to control the mutation rate, genome sizes (the number of instructions in an avidian’s genome), and population size allows an inquiry into the impact of mutation rate and indel spectra on the evolution of genome size. Avida has been previously used to test many evolutionary hypotheses that are difficult to test via biological experimental evolution, such as the evolution of genomic complexity 17 23 , the ‘survival of the flattest’ effect in genotypes evolving at high mutation rates 24 , adaptive radiation 25 , co-evolution as a driving force for higher phenotypic complexity and evolvability 26 , the time-dependent effect of genetic robustness on evolvability 27 , and how standing genetic variation and environment influence evolutionary response to environmental stimuli 28 (among many others). Here we use Avida to investigate genome size evolution because in addition to tracking genome edits and their fitness effects, we can record the evolution of phenotypic traits and thus study the consequences of genome size evolution on phenotypic complexity.…”

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confidence: 99%

Evolution of Genome Size in Asexual Digital Organisms

Gupta¹,

LaBar²,

Miyagi³

et al. 2016

Sci Rep

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Genome sizes have evolved to vary widely, from 250 bases in viroids to 670 billion bases in some amoebas. This remarkable variation in genome size is the outcome of complex interactions between various evolutionary factors such as mutation rate and population size. While comparative genomics has uncovered how some of these evolutionary factors influence genome size, we still do not understand what drives genome size evolution. Specifically, it is not clear how the primordial mutational processes of base substitutions, insertions, and deletions influence genome size evolution in asexual organisms. Here, we use digital evolution to investigate genome size evolution by tracking genome edits and their fitness effects in real time. In agreement with empirical data, we find that mutation rate is inversely correlated with genome size in asexual populations. We show that at low point mutation rate, insertions are significantly more beneficial than deletions, driving genome expansion and the acquisition of phenotypic complexity. Conversely, the high mutational load experienced at high mutation rates inhibits genome growth, forcing the genomes to compress their genetic information. Our analyses suggest that the inverse relationship between mutation rate and genome size is a result of the tradeoff between evolving phenotypic innovation and limiting the mutational load.Genome sizes evolve by various mechanisms, some of which are common to all domains of life (insertions and deletions) while others are seen in some taxonomic groups more than others (horizontal gene transfer in bacteria and transposable element activity in eukaryotes). While one might think that genome expansion leads to the acquisition of more protein-coding genes and functions, genome size does not strongly correlate with organismal complexity (the C-value paradox). Whole-genome sequencing data provide some explanation for this paradox: appreciable variation in eukaryotic genome sizes has been attributed to ploidy 1 , and to an expansion of non-coding DNA such as introns, intergenic regions, and repeats 2 . Yet, genome size also positively correlates with the number of protein-coding genes 2 , suggesting that larger genome size is a prerequisite for gaining new genes that could lead to phenotypic innovation.The point mutation rate, relative frequencies of insertions and deletions (indels), and population size are three factors seen across the tree of life that are thought to influence genome size evolution. The negative correlation between genome size and point mutation rate is observed in all living organisms, from viruses to Homo sapiens 3 . However, a recent analysis based on more taxa found that this inverse relationship holds true only for prokaryotes and viruses, and that genome size and mutation rate are instead positively correlated in eukaryotes 4 . A high point mutation rate forces viruses to maintain small genome sizes in an effort to limit the number of deleterious mutations 5 . This selection pressure to reduce genome size is so strong that vir...

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“…), and antipredator strategies (Fish et al. ) have all been studied in Avida. Our understanding of kin inclusivity (Johnson et al.…”

Section: Methodsmentioning

confidence: 99%

“…Avida is an established system in the study of many biological phenomena. The evolution of phenomena such as quorum sensing (Beckman et al 2012), division of labor , ecological networks (Fortuna et al 2013), multicellularity (Hessel and Goings 2013), prey intelligence , and antipredator strategies (Fish et al 2014) have all been studied in Avida. Our understanding of kin inclusivity (Johnson et al 2014), host-parasite coevolution (Zaman et al 2011), diversity in response to resource availability (Walker and Ofria 2012), recapitulation theory (Clune et al 2012), temporal polyethism (Goldsby et al 2012), and ecological and mutation-order speciation (Anderson and Harmon 2014) has been improved through studies in Avida.…”

Section: Avidamentioning

confidence: 99%

Context matters: sexual signaling loss in digital organisms

Weigel

Testa

Peer

et al. 2015

Ecology and Evolution

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Sexual signals are important in attracting and choosing mates; however, these signals and their associated preferences are often costly and frequently lost. Despite the prevalence of signaling system loss in many taxa, the factors leading to signal loss remain poorly understood. Here, we test the hypothesis that complexity in signal loss scenarios is due to the context-dependent nature of the many factors affecting signal loss itself. Using the Avida digital life platform, we evolved 50 replicates of ∼250 lineages, each with a unique combination of parameters, including whether signaling is obligate or facultative; genetic linkage between signaling and receiving genes; population size; and strength of preference for signals. Each of these factors ostensibly plays a crucial role in signal loss, but was found to do so only under specific conditions. Under obligate signaling, genetic linkage, but not population size, influenced signal loss; under facultative signaling, genetic linkage does not have significant influence. Somewhat surprisingly, only a total loss of preference in the obligate signaling populations led to total signal loss, indicating that even a modest amount of preference is enough to maintain signaling systems. Strength of preference proved to be the strongest single force preventing signal loss, as it consistently overcame the potential effects of drift within our study. Our findings suggest that signaling loss is often dependent on not just preference for signals, population size, and genetic linkage, but also whether signals are required to initiate mating. These data provide an understanding of the factors (and their interactions) that may facilitate the maintenance of sexual signals.

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The Roles of Standing Genetic Variation and Evolutionary History in Determining the Evolvability of Anti-Predator Strategies

Cited by 14 publications

References 48 publications

Short-term exposure to predation affects body elemental composition, climbing speed and survival ability inDrosophila melanogaster

Short-term exposure to predation affects body elemental composition, climbing speed and survival ability inDrosophila melanogaster

Evolution of Genome Size in Asexual Digital Organisms

Context matters: sexual signaling loss in digital organisms

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