12,487 research outputs found
A simple model of unbounded evolutionary versatility as a largest-scale trend in organismal evolution
The idea that there are any large-scale trends in the evolution of biological organisms is highly controversial. It is commonly believed, for example, that there is a large-scale trend in evolution towards increasing complexity, but empirical and theoretical arguments undermine this belief. Natural selection results in organisms that are well adapted to their local environments, but it is not clear how local adaptation can produce a global trend. In this paper, I present a simple computational model, in which local adaptation to a randomly changing environment results in a global trend towards increasing evolutionary versatility. In this model, for evolutionary versatility to increase without bound, the environment must be highly dynamic. The model also shows that unbounded evolutionary versatility implies an accelerating evolutionary pace. I believe that unbounded increase in evolutionary versatility is a large-scale trend in evolution. I discuss some of the testable predictions about organismal evolution that are suggested by the model
Inference of Ancestral Recombination Graphs through Topological Data Analysis
The recent explosion of genomic data has underscored the need for
interpretable and comprehensive analyses that can capture complex phylogenetic
relationships within and across species. Recombination, reassortment and
horizontal gene transfer constitute examples of pervasive biological phenomena
that cannot be captured by tree-like representations. Starting from hundreds of
genomes, we are interested in the reconstruction of potential evolutionary
histories leading to the observed data. Ancestral recombination graphs
represent potential histories that explicitly accommodate recombination and
mutation events across orthologous genomes. However, they are computationally
costly to reconstruct, usually being infeasible for more than few tens of
genomes. Recently, Topological Data Analysis (TDA) methods have been proposed
as robust and scalable methods that can capture the genetic scale and frequency
of recombination. We build upon previous TDA developments for detecting and
quantifying recombination, and present a novel framework that can be applied to
hundreds of genomes and can be interpreted in terms of minimal histories of
mutation and recombination events, quantifying the scales and identifying the
genomic locations of recombinations. We implement this framework in a software
package, called TARGet, and apply it to several examples, including small
migration between different populations, human recombination, and horizontal
evolution in finches inhabiting the Gal\'apagos Islands.Comment: 33 pages, 12 figures. The accompanying software, instructions and
example files used in the manuscript can be obtained from
https://github.com/RabadanLab/TARGe
Genetic Algorithms for the Imitation of Genomic Styles in Protein Backtranslation
Several technological applications require the translation of a protein into
a nucleic acid that codes for it (``backtranslation''). The degeneracy of the
genetic code makes this translation ambiguous; moreover, not every translation
is equally viable. The common answer to this problem is the imitation of the
codon usage of the target species. Here we discuss several other features of
coding sequences (``coding statistics'') that are relevant for the ``genomic
style'' of different species. A genetic algorithm is then used to obtain
backtranslations that mimic these styles, by minimizing the difference in the
coding statistics. Possible improvements and applications are discussed.Comment: 17 pages, 13 figures. Submitted to Theor. Comp. Scienc
Biological evolution through mutation, selection, and drift: An introductory review
Motivated by present activities in (statistical) physics directed towards
biological evolution, we review the interplay of three evolutionary forces:
mutation, selection, and genetic drift. The review addresses itself to
physicists and intends to bridge the gap between the biological and the
physical literature. We first clarify the terminology and recapitulate the
basic models of population genetics, which describe the evolution of the
composition of a population under the joint action of the various evolutionary
forces. Building on these foundations, we specify the ingredients explicitly,
namely, the various mutation models and fitness landscapes. We then review
recent developments concerning models of mutational degradation. These predict
upper limits for the mutation rate above which mutation can no longer be
controlled by selection, the most important phenomena being error thresholds,
Muller's ratchet, and mutational meltdowns. Error thresholds are deterministic
phenomena, whereas Muller's ratchet requires the stochastic component brought
about by finite population size. Mutational meltdowns additionally rely on an
explicit model of population dynamics, and describe the extinction of
populations. Special emphasis is put on the mutual relationship between these
phenomena. Finally, a few connections with the process of molecular evolution
are established.Comment: 62 pages, 6 figures, many reference
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
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