Commentary: The promise of ecological developmental biology.
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Adaptation, Physiological↗
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Humans and primates: New model organisms for evolutionary developmental biology?
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Animals↗
Fifty years later: I. Michael Lerner's Genetic homeostasis (1954)--a valiant attempt to integrate genes, organisms and environment.
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Adaptation, Biological↗
Evolutionary innovations in the fossil record: the intersection of ecology, development, and macroevolution.
The origins of evolutionary innovations have been intensively studied, but relatively little is known about their large-scale ecological patterns. For post-Paleozoic benthic marine invertebrates, which have the richest and most densely sampled fossil record, order-level taxa tend to appear first in onshore, disturbed habitats, even in groups that are now exclusively deep-water (so that present-day distributions are not reliable indicators of original environments). New results presented here show that the onshore-origination pattern is robust to shifts in taxonomic methods and to new paleontological discoveries, and the few available studies suggest that this pattern can also be seen in terms of excursions in morphospace or the acquisition of derived character states, without reference to taxonomic categories. The environmental pattern at high levels contrasts significantly with the origin of low-level novelties (such as defined genera and families) in crinoids, echinoids, and bryozoans, where first appearances tend to conform to their clade-specific bathymetric diversity gradients. This discordance seems to eliminate potential driving mechanisms that simply scale up within-population genetic or ecological processes. Little is known about the factors that promote the onshore-offshore expansion of orders across the continental shelf, or that drive some clades to abandon ancestral habitats for an exclusively deep-water distribution. The origin of evolutionary innovation must ultimately reside in developmental changes, but the onshore-origination bias could emerge from two different dynamics: the pattern could be primarily genetic and developmental, i.e., innovations truly arise onshore; or primarily ecological, i.e., innovations arise randomly but preferentially survive onshore. Whatever the ultimate driving mechanisms, these macroevolutionary patterns show that theories of large-scale evolutionary novelty must include an ecological dimension.
Animals↗
RNAs everywhere: genome-wide annotation of structured RNAs.
Starting with the discovery of microRNAs and the advent of genome-wide transcriptomics, non-protein-coding transcripts have moved from a fringe topic to a central field research in molecular biology. In this contribution we review the state of the art of "computational RNomics", i.e., the bioinformatics approaches to genome-wide RNA annotation. Instead of rehashing results from recently published surveys in detail, we focus here on the open problem in the field, namely (functional) annotation of the plethora of putative RNAs. A series of exploratory studies are used to provide non-trivial examples for the discussion of some of the difficulties.
Biological Evolution↗
The use of evolutionary biology concepts for genome annotation.
The past decade has seen the completion of numerous whole-genome sequencing projects, began with bacterial genomes and continued with eukaryotic species from different phyla: fungi, plants and animals. Besides, more biological information are produced and are shared thanks to information exchange systems, and more biological concepts, as well as more bioinformatics tools, are available. In this article, we will describe how the evolutionary biology concepts, as well as computer science, are useful for a better understanding of biology in general and genome annotation in particular. The genome annotation process consists of taking the raw DNA produced, for example, by the genome sequencing projects, adding the layers of analysis and interpretation necessary to extract its biological significance and placing it in the context of our understanding of biological processes. Genome annotation is a multistep process falling into two broad categories: structural and functional annotation.
Amino Acid Sequence↗
Editorial: A new series of vignettes on the history of evolutionary developmental biology.
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Biological Evolution↗
Homology in comparative, molecular, and evolutionary developmental biology: the radiation of a concept.
The present paper analyzes the use and understanding of the homology concept across different biological disciplines. It is argued that in its history, the homology concept underwent a sort of adaptive radiation. Once it migrated from comparative anatomy into new biological fields, the homology concept changed in accordance with the theoretical aims and interests of these disciplines. The paper gives a case study of the theoretical role that homology plays in comparative and evolutionary biology, in molecular biology, and in evolutionary developmental biology. It is shown that the concept or variant of homology preferred by a particular biological field is used to bring about items of biological knowledge that are characteristic for this field. A particular branch of biology uses its homology concept to pursue its specific theoretical goals.
Adaptation, Biological↗
Evolutionary analysis of HIV-1 protease inhibitors: Methods for design of inhibitors that evade resistance.
Drug-resistant strains are rapidly selected during AIDS therapy because of the high rate of mutation in HIV. In this report, we present an evolutionary simulation method for analysis of viral mutation and its use for optimization of HIV-1 protease drugs to improve their robustness in the face of resistance mutation. We first present an analysis of the range of resistant mutants that produce viable viruses by using a volume-based viral fitness model. Then, we analyze how this range of mutant proteases allows development of resistance to an optimal inhibitor previously designed by computational coevolution techniques. Finally, we evaluate the resistance patterns of commercially available drugs, and we discuss how resistance might be overcome by optimizing the size of specific side-chains of these inhibitors.
Acquired Immunodeficiency Syndrome↗
Necessary and sufficient conditions for evolutionary suicide.
Evolutionary suicide is an evolutionary process where a viable population adapts in such a way that it can no longer persist. It has already been found that a discontinuous transition to extinction is a necessary condition for suicide. Here we present necessary and sufficient conditions, concerning the bifurcation point, for suicide to occur. Evolutionary suicide has been found in structured metapopulation models. Here we show that suicide can occur also in unstructured population models. Moreover, a structured model does not guarantee the possibility of suicide: we show that suicide cannot occur in age-structured population models of the Gurtin-MacCamy type. The point is that the mutant's fitness must explicitly depend not only on the environmental interaction variable, but also on the resident strategy.
Adaptation, Biological↗
Co-operation and defection: playing the field in virus dynamics.
A previous model (Szathmáry, 1992) is further developed for the dynamics of standard (V) and defective interfering (DI) viruses. The crucial retained element is the incorporation of population structure in the form of a complete distribution of cells infected by particles differing in number. New elements are: the non-linear shared benefit from the contribution of Vs to the group of viruses infecting the same cell (synergistic at low numbers, diminishing returns at high numbers, respectively); a dynamics for the total number of particles (V and DI); and the possibility of extinction if the frequency of Vs is small enough. In evolutionary genetical terms this is a frequency- and density-dependent evolutionary game. A crucial result is retained: coexistence of Vs and DIs is possible provided the multiplicity of infection (hence the size of the coinfection group) is large enough. Phase portraits and vector-field plots for a continuous-time and numerical solutions for a corresponding discrete-time case are presented. The latter reflect the basic features of serial, undiluted passage. The causes for two possible means of extinction (low initial frequency of Vs, and very high vigour of Vs) are revealed: the appearance of high amplitude fluctuations. Coexistence can apparently be ensured by stable points, periodic behaviour, or strange attractors. The paper clarifies the dynamical background of cycles found experimentally in V-DI systems.
Biological Evolution↗
Evolutionary predictions from invariant physical measures of dynamic processes.
The invariant physical measure of a dynamic process comprises the information necessary to compute statistical quantities of the system. It allows us to replace time averages over the system's trajectory by integrals over state-space. In particular, it allows us to compute the long-term growth rate of a fluctuating population and hence to make evolutionary predictions. This is explained here using a one-dimensional difference equation. The invariant physical measure reflects three types of selection in this model: K-selection when the resident has a stable equilibrium; r-selection when the resident exhibits complex dynamics; and c-selection, i.e. selection for lower complexity when the resident undergoes large fluctuations. For all three evolutionary scenarios the interaction of the physical measure with the higher moments of the distribution of offspring numbers is crucial. It is also shown how stochastic noise can affect the invariant physical measure and the evolutionary predictions made from it.
Animals↗
On the nearest neighbour interchange distance between evolutionary trees.
We present some new results on a well-known distance measure between evolutionary trees. The trees we consider are free 3-trees having n leaves labeled 0,...,n - 1 (representing species), and n - 2 internal nodes of degree 3. The distance between two trees is the minimum number of nearest neighbour interchange (NNI) operations required to transform one into the other. First, we improve an upper bound on the nni-distance between two arbitrary n-node trees from 4n log n (Culik & Wood, 1982, Inf. Pro. Letts. 15, 39-42) to n log n. Second, we present a counterexample disproving several theorems in (Waterman & Smith, 1978, J. theor. Biol. 73, 789-800). Roughly speaking, finding an equal partition between two trees does not imply decomposability of the distance finding problem. Third, we present a polynomial-time approximation algorithm that, given two trees, finds a transformation between them of length O(log n) times their distance. We also present some results of computations we performed on small size trees.
Algorithms↗
Addition of Darwin's third dimension to phyletic trees.
A three-dimensional (3D) approach for visualizing the phyletic relationship of living animals is proposed and developed as an alternative to current two-dimensional (2D) evolutionary trees. The 3D tree enhances visualization and qualitative analysis since it simultaneously provides topological (tree-structure) and spatial information (based upon genetically measured distances). However, the meaning of the third dimension, particularly its relationship to temporal processes, and further quantitative analyses emerge as open questions. Our method consists of two phases. First, a 3D representation of the genetic relationships of a related group of extant animals is produced using an optimization algorithm developed here. Second, linear connections are added to suggest a visual representation of the differing evolutionary trajectories of the organisms involved on the basis of a 2D tree algorithm. The method is applied to a set of distantly related Caenophidian snakes, and the resulting relationships are analysed. The discussions here are meant to stimulate the generation of 3D trees in the goal of complementing standard 2D views and, perhaps ultimately, improving our classification of evolutionary relationships.
Algorithms↗
Effect of time delay and evolutionarily stable strategy.
In this paper, a simple two-phenotype model with time delay is investigated. The main results are that: (i) the stability of the interior equilibrium point of the pure strategy model not only depends on the property of the payoff matrix but also the effect of time delay; (ii) the conditions of the evolutionarily stable strategy in the two-phenotype model with time delay are completely identical with the conditions in the two-phenotype model with no time delay; and (iii) a mixed evolutionarily stable strategy can be an unstable equilibrium state of the population in the two-phenotype model with time delay.
Animals↗
Self-organized criticality in spatial evolutionary game theory.
Self-organized criticality is an important framework for understanding the emergence of scale-free natural phenomena. Cellular automata provide simple interesting models in which to study self-organized criticality. We consider the dynamics of a new class of cellular automata which are constructed as natural spatial extensions of evolutionary game theory. This construction yields a discrete one-parameter family of cellular automata. We show that there is a range of parameter values for which this system exhibits complex dynamics with long range correlations between states in both time and space. In this region the dynamics evolve to a self-organized critical state in which structures exist on all time and length scales, and the relevant statistical measures have power law behaviour.
Animals↗
Coevolutionary chase in two-species systems with applications to mimicry.
We study a general dynamical model describing coevolution of two haploid populations with two alleles at a single locus under weak linear symmetric frequency-dependent selection. A novel and more realistic element of our modeling approach is that both species are allowed to evolve. We analyse conditions for "evolutionary chase" between two phenotypically similar species in which one species evolves to decrease its resemblance with the other species while this other species evolves to increase its resemblance with the first species. We apply our results to a series of simple population genetics models describing classical Müllerian and Batesian mimicries as well as intermediate cases. We show that one of the most important factors influencing the plausibility of non-equilibrium dynamics in systems of mimicry is the relationship between the strength of between-species and within-species interactions. This indicates that this relationship should be the focus of both experimental and theoretical work. Our results suggest that systematic studies of frequencies of different mimicry morphs through time may be very useful.
Animals↗
Evolutionarily stable leaf area production in plant populations.
Using an analytical model, it was shown that for a given amount of nitrogen in the canopy of a stand (N(T)), there exists an evolutionarily stable leaf area index (ES-LAI), and therefore an evolutionarily stable average leaf nitrogen content (n(ES)(av);n(ES)(av) =N(T)/ES-LAI), at which no individual plant in the stand can increase its photosynthesis by changing its leaf area. It was also shown that this ES-LAI is always greater than the optimal LAI that maximizes photosynthesis per unit N(T) of the stand. This illustrates that the canopy structure that maximizes photosynthesis of a population is not the same as the canopy structure that maximizes photosynthesis of individuals within a population. It was further derived that the ES-LAI at given N(T) increases with the ratio between the light-saturated photosynthesis and the N content per unit leaf area (leaf-PPNUE) and that it decreases with the canopy extinction coefficient for light (K(L)), the light availability and the apparent quantum yield (phi). These hypotheses were tested by comparing calculated ES-LAI and n(ES)(av) values to actual LAIs and leaf N contents measured for stands of a large variety of herbaceous plants. There was a close correspondence between the calculated and measured values. As predicted by the model, plants with high leaf-PPNUEs produced more leaf area per unit nitrogen than those with low leaf-PPNUEs while plants with horizontal leaves, forming stands with higher K(L) values, produced less leaf area than those with more vertically inclined leaves. These results suggest that maximization of individual plant photosynthesis per unit of nitrogen plays an important role in determining leaf area production of plants and the resulting canopy structure of stands of vegetation. They further suggest this optimization to be a mechanism by which leaf traits such as leaf-PPNUE and leaf inclination angle are causally related to structural characteristics of the population, i.e. the leaf area index of the stand.
Biological Evolution↗