4,398 research outputs found
Supply-driven evolution: mutation bias and trait-fitness distributions can drive macro-evolutionary dynamics
Many well-documented macro-evolutionary phenomena still challenge current evolutionary theory. Examples include long-term evolutionary trends, major transitions in evolution, conservation of certain biological features such as hox genes, and the episodic creation of new taxa. Here, we present a framework that may explain these phenomena. We do so by introducing a probabilistic relationship between trait value and reproductive fitness. This integration allows mutation bias to become a robust driver of long-term evolutionary trends against environmental bias, in a way that is consistent with all current evolutionary theories. In cases where mutation bias is strong, such as when detrimental mutations are more common than beneficial mutations, a regime called “supply-driven” evolution can arise. This regime can explain the irreversible persistence of higher structural hierarchies, which happens in the major transitions in evolution. We further generalize this result in the long-term dynamics of phenotype spaces. We show how mutations that open new phenotype spaces can become frozen in time. At the same time, new possibilities may be observed as a burst in the creation of new taxa
The biased evolution of generation time
Many life-history traits, like the age at maturity or adult longevity, are
important determinants of the generation time. For instance, semelparous
species whose adults reproduce once and die have shorter generation times than
iteroparous species that reproduce on several occasions. A shorter generation
time ensures a higher growth rate in stable environments where resources are in
excess, and is therefore a positively selected feature in this (rarely met)
situation. In a stable and limiting environment, all combination of traits (or
strategies) that produce the same number of viable offspring on average are
strictly neutral even when their generation times differ. We first study the
evolution of life-history strategies with different generation times in this
context, and show that those with the longest generation time represent the
most likely evolutionary outcomes. Indeed, strategies with longer generation
times generate fewer mutants per time unit, which makes them less likely to be
replaced within a given time period. This `turnover bias' inevitably exists and
favors the evolution of strategies with long generation times. Its real impact,
however, should depend on the strength and direction of other evolutionary
forces; selection for short generation times, for instance, may oppose turnover
bias. Likewise, the evolutionary outcome depends on the strength of such
selection and population size, comparably to other biases acting on the
occurrence of mutations.Comment: Now we also study the evolution of development duration, suggesting
that turnover bias is involved in the evolutionary dynamics of any trait
linked with the generation tim
Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data
Background. A large number of algorithms is being developed to reconstruct
evolutionary models of individual tumours from genome sequencing data. Most
methods can analyze multiple samples collected either through bulk multi-region
sequencing experiments or the sequencing of individual cancer cells. However,
rarely the same method can support both data types.
Results. We introduce TRaIT, a computational framework to infer mutational
graphs that model the accumulation of multiple types of somatic alterations
driving tumour evolution. Compared to other tools, TRaIT supports multi-region
and single-cell sequencing data within the same statistical framework, and
delivers expressive models that capture many complex evolutionary phenomena.
TRaIT improves accuracy, robustness to data-specific errors and computational
complexity compared to competing methods.
Conclusions. We show that the application of TRaIT to single-cell and
multi-region cancer datasets can produce accurate and reliable models of
single-tumour evolution, quantify the extent of intra-tumour heterogeneity and
generate new testable experimental hypotheses
The implications of shared identity on indirect reciprocity
The ability to sustain indirect reciprocity is an example of collective intelligence. It is increasingly relevant to future technology and autonomous machines that need to function in a coalition. Indirect reciprocity involves providing benefit to others without guaranteeing a future return. The identity through which an agent presents itself to others is fundamental, as this is how the reputation of an agent is considered. In this paper, we examine the sharing of identity between agents, which is an important and frequently overlooked issue when considering indirect reciprocity. We model an agent's identity using traits, which can be shared with other agents, and offer a basis for an agent to change their identity. Through this approach, we determine how shared identity affects cooperation, and the conditions through which cooperation can be sustained. This also helps us to understand how and why behavioural strategies involving identity function are put in place, such as whitewashing. The framework offers the opportunity to assess the interplay between the sharing of traits and the cost, in terms of reduced cooperation and opportunities for shirkers to benefit
From genotypes to organisms: state-of-the-art and perspectives of a cornerstone in evolutionary dynamics
Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map. Though we are still far from achieving a complete picture of these relationships, our current understanding of simpler questions, such as the structure induced in the space of genotypes by sequences mapped to molecular structures, has revealed important facts that deeply affect the dynamical description of evolutionary processes. Empirical evidence supporting the fundamental relevance of features such as phenotypic bias is mounting as well, while the synthesis of conceptual and experimental progress leads to questioning current assumptions on the nature of evolutionary dynamics-cancer progression models or synthetic biology approaches being notable examples. This work delves with a critical and constructive attitude into our current knowledge of how genotypes map onto molecular phenotypes and organismal functions, and discusses theoretical and empirical avenues to broaden and improve this comprehension. As a final goal, this community should aim at deriving an updated picture of evolutionary processes soundly relying on the structural properties of genotype spaces, as revealed by modern techniques of molecular and functional analysis
From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics
Understanding how genotypes map onto phenotypes, fitness, and eventually
organisms is arguably the next major missing piece in a fully predictive theory
of evolution. We refer to this generally as the problem of the
genotype-phenotype map. Though we are still far from achieving a complete
picture of these relationships, our current understanding of simpler questions,
such as the structure induced in the space of genotypes by sequences mapped to
molecular structures, has revealed important facts that deeply affect the
dynamical description of evolutionary processes. Empirical evidence supporting
the fundamental relevance of features such as phenotypic bias is mounting as
well, while the synthesis of conceptual and experimental progress leads to
questioning current assumptions on the nature of evolutionary dynamics-cancer
progression models or synthetic biology approaches being notable examples. This
work delves into a critical and constructive attitude in our current knowledge
of how genotypes map onto molecular phenotypes and organismal functions, and
discusses theoretical and empirical avenues to broaden and improve this
comprehension. As a final goal, this community should aim at deriving an
updated picture of evolutionary processes soundly relying on the structural
properties of genotype spaces, as revealed by modern techniques of molecular
and functional analysis.Comment: 111 pages, 11 figures uses elsarticle latex clas
Inference of natural selection from ancient DNA.
Evolutionary processes, including selection, can be indirectly inferred based on patterns of genomic variation among contemporary populations or species. However, this often requires unrealistic assumptions of ancestral demography and selective regimes. Sequencing ancient DNA from temporally spaced samples can inform about past selection processes, as time series data allow direct quantification of population parameters collected before, during, and after genetic changes driven by selection. In this Comment and Opinion, we advocate for the inclusion of temporal sampling and the generation of paleogenomic datasets in evolutionary biology, and highlight some of the recent advances that have yet to be broadly applied by evolutionary biologists. In doing so, we consider the expected signatures of balancing, purifying, and positive selection in time series data, and detail how this can advance our understanding of the chronology and tempo of genomic change driven by selection. However, we also recognize the limitations of such data, which can suffer from postmortem damage, fragmentation, low coverage, and typically low sample size. We therefore highlight the many assumptions and considerations associated with analyzing paleogenomic data and the assumptions associated with analytical methods
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A framework for how environment contributes to cancer risk
Evolutionary theory explains why metazoan species are largely protected against the negative fitness effects of cancers. Nevertheless, cancer is often observed at high incidence across a range of species. Although there are many challenges to quantifying cancer epidemiology and assessing its causes, we claim that most modern-day cancer in animals - and humans in particular - are due to environments deviating from central tendencies of distributions that have prevailed during cancer resistance evolution. Such novel environmental conditions may be natural and/or of anthropogenic origin, and may interface with cancer risk in numerous ways, broadly classifiable as those: increasing organism body size and/or life span, disrupting processes within the organism, and affecting germline. We argue that anthropogenic influences, in particular, explain much of the present-day cancer risk across life, including in humans. Based on a literature survey of animal species and a parameterised mathematical model for humans, we suggest that combined risks of all cancers in a population beyond c. 5% can be explained to some extent by the influence of novel environments. Our framework provides a basis for understanding how natural environmental variation and human activity impact cancer risk, with potential implications for species ecology
High-speed detection of emergent market clustering via an unsupervised parallel genetic algorithm
We implement a master-slave parallel genetic algorithm (PGA) with a bespoke
log-likelihood fitness function to identify emergent clusters within price
evolutions. We use graphics processing units (GPUs) to implement a PGA and
visualise the results using disjoint minimal spanning trees (MSTs). We
demonstrate that our GPU PGA, implemented on a commercially available general
purpose GPU, is able to recover stock clusters in sub-second speed, based on a
subset of stocks in the South African market. This represents a pragmatic
choice for low-cost, scalable parallel computing and is significantly faster
than a prototype serial implementation in an optimised C-based
fourth-generation programming language, although the results are not directly
comparable due to compiler differences. Combined with fast online intraday
correlation matrix estimation from high frequency data for cluster
identification, the proposed implementation offers cost-effective,
near-real-time risk assessment for financial practitioners.Comment: 10 pages, 5 figures, 4 tables, More thorough discussion of
implementatio
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