55 research outputs found
Compensatory evolution and the origins of innovations
Cryptic genetic sequences have attenuated effects on phenotypes. In the
classic view, relaxed selection allows cryptic genetic diversity to build up
across individuals in a population, providing alleles that may later contribute
to adaptation when co-opted - e.g. following a mutation increasing expression
from a low, attenuated baseline. This view is described, for example, by the
metaphor of the spread of a population across a neutral network in genotype
space. As an alternative view, consider the fact that most phenotypic traits
are affected by multiple sequences, including cryptic ones. Even in a strictly
clonal population, the co-option of cryptic sequences at different loci may
have different phenotypic effects and offer the population multiple adaptive
possibilities. Here, we model the evolution of quantitative phenotypic
characters encoded by cryptic sequences, and compare the relative contributions
of genetic diversity and of variation across sites to the phenotypic potential
of a population. We show that most of the phenotypic variation accessible
through co-option would exist even in populations with no polymorphism. This is
made possible by a history of compensatory evolution, whereby the phenotypic
effect of a cryptic mutation at one site was balanced by mutations elsewhere in
the genome, leading to a diversity of cryptic effect sizes across sites rather
than across individuals. Cryptic sequences might accelerate adaptation and
facilitate large phenotypic changes even in the absence of genetic diversity,
as traditionally defined in terms of alternative alleles
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Feed-forward regulation adaptively evolves via dynamics rather than topology when there is intrinsic noise
In transcriptional regulatory networks (TRNs), a canonical 3-node feed-forward loop (FFL) is hypothesized to evolve to filter out short spurious signals. We test this adaptive hypothesis against a novel null evolutionary model. Our mutational model captures the intrinsically high prevalence of weak affinity transcription factor binding sites. We also capture stochasticity and delays in gene expression that distort external signals and intrinsically generate noise. Functional FFLs evolve readily under selection for the hypothesized function but not in negative controls. Interestingly, a 4-node "diamond" motif also emerges as a short spurious signal filter. The diamond uses expression dynamics rather than path length to provide fast and slow pathways. When there is no idealized external spurious signal to filter out, but only internally generated noise, only the diamond and not the FFL evolves. While our results support the adaptive hypothesis, we also show that non-adaptive factors, including the intrinsic expression dynamics, matter.University of Arizona; Pew Scholarship; John Templeton Foundation [39667]; National Institutes of Health [R35GM118170, R01GM076041]Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]
Hsp90 depletion goes wild
Hsp90 reveals phenotypic variation in the laboratory, but is Hsp90 depletion important in the wild? Recent work from Chen and Wagner in BMC Evolutionary Biology has discovered a naturally occurring Drosophila allele that downregulates Hsp90, creating sensitivity to cryptic genetic variation. Laboratory studies suggest that the exact magnitude of Hsp90 downregulation is important. Extreme Hsp90 depletion might reactivate transposable elements and/or induce aneuploidy, in addition to revealing cryptic genetic variation
Digital contact tracing/notification for SARS-CoV-2: navigating six points of failure
Digital contact tracing/notification was initially hailed as a promising
strategy to combat SARS-CoV-2, but in most jurisdictions it did not live up to
its promise. To avert a given transmission event, both parties must have
adopted the tech, it must detect the contact, the primary case must be promptly
diagnosed, notifications must be triggered, and the secondary case must change
their behavior to avoid the focal tertiary transmission event. If we
approximate these as independent events, achieving a 26% reduction in R(t)
would require 80% success rates at each of these six points of failure. Here we
review the six failure rates experienced by a variety of digital contact
tracing/notification schemes, including Singapore's TraceTogether, India's
Aarogya Setu, and leading implementations of the Google Apple Exposure
Notification system. This leads to a number of recommendations, e.g. that
tracing/notification apps be multi-functional and integrated with testing,
manual contact tracing, and the gathering of critical scientific data, and that
the narrative be framed in terms of user autonomy rather than user privacy
Complex Adaptations Can Drive the Evolution of the Capacitor [PSI+], Even with Realistic Rates of Yeast Sex
The [PSI+] prion may enhance evolvability by revealing previously cryptic genetic variation, but it is unclear whether such evolvability properties could be favored by natural selection. Sex inhibits the evolution of other putative evolvability mechanisms, such as mutator alleles. This paper explores whether sex also prevents natural selection from favoring modifier alleles that facilitate [PSI+] formation. Sex may permit the spread of “cheater” alleles that acquire the benefits of [PSI+] through mating without incurring the cost of producing [PSI+] at times when it is not adaptive. Using recent quantitative estimates of the frequency of sex in Saccharomyces paradoxus, we calculate that natural selection for evolvability can drive the evolution of the [PSI+] system, so long as yeast populations occasionally require complex adaptations involving synergistic epistasis between two loci. If adaptations are always simple and require substitution at only a single locus, then the [PSI+] system is not favored by natural selection. Obligate sex might inhibit the evolution of [PSI+]-like systems in other species
Evolutionary Capacitance May Be Favored by Natural Selection
Evolutionary capacitors phenotypically reveal a stock of cryptic genetic variation in a reversible fashion. The sudden and reversible revelation of a range of variation is fundamentally different from the gradual introduction of variation by mutation. Here I study the invasion dynamics of modifiers of revelation. A modifier with the optimal rate of revelation m(opt) has a higher probability of invading any other population than of being counterinvaded. m(opt) varies with the population size N and the rate θ at which environmental change makes revelation adaptive. For small populations less than a minimum cutoff N(min), all revelation is selected against. N(min) is typically quite small and increases only weakly, with θ(−1/2). For large populations with N > 1/θ, m(opt) is ∼1/N. Selection for the optimum is highly effective and increases in effectiveness with larger N ≫ 1/θ. For intermediate values of N, m(opt) is typically a little less than θ and is only weakly favored over less frequent revelation. The model is analogous to a two-locus model for the evolution of a mutator allele. It is a fully stochastic model and so is able to show that selection for revelation can be strong enough to overcome random drift
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