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PubMed1998

Evolutionary classification of homeodomains.

PURPOSE AND METHODS: We performed multiple comparisons between available amino acid (aa) sequences of homeodomain(HOM)-containing proteins from a wide spectrum of animals to create an evolutionary classification of the proteins. RESULTS: Based on results of statistical and special computational analyses of over 500 homeodomain aa sequences (HOMs) a novel system of concepts describing complex structural correlations between homologous proteins is proposed. This system includes such notions as differentiated isofunctionality of aa, chemotype, stereotype, local functional motifs, gradual conservativeness of aa positions, and group-specific domain patterns, as well as major categories of the evolutionary classification of HOMs (Division, Type, Branch, Class, Family, Series, Variety, Sort). Using this approach, a complete structural systematics of HOMs belonging to proteomes of eukaryotic animals is proposed. CONCLUSIONS: The proposed structural classification of HOMs is in full agreement with the bulk of experimental data revealing complex functional similarities and differences among HOMs in terms of their expression patterns in developing embryos. It turn, this classification can provide answers regarding homology among homeodomains when experimental data are conflicting.

Amino Acid Sequence↗
PubMed2004

On Maxwell's demons and the origin of evolutionary variations: an internalist perspective.

This paper defends an internalist perspective of selection based on the hypothesis that considers living evolutionary units as Maxwell's demons (MD) or Zurek's Information Gathering and Using Systems (IGUS). Individuals are considered as IGUS that extract work by means of measuring and recording processes. Interactions or measurements convert uncertainty about the environment (Shannon's information, H) into internalized information in the form of a compressed record (Chaitin's algorithmic complexity, K). The requirements of the model and the limitations inherent to its formalization are discussed. This approach offers an alternative view to the causes of evolutionary variations which goes beyond the classical Lamarckian-Darwinian controversy. I argue that random variations only apply near-to-equilibrium at the time organisms have attained structural closure, and that a speed up of mutation rates that facilitates the production of directed variations occurs far-from-equilibrium due to organisms' openness to the surrounding conditions. However, real organisms are located somewhere between the above two cases and thus, operate at an intermediate stage where there is a maximum efficiency of H/K conversion. In consequence, IGUS keep their autonomy and evolving capacity by compromising between external circumstances and inner constraints. This compromise is made possible by closure regulation. Likewise, this model explains why nature has favored the selection of agents capable of selectively recording a partial description of their environment.

Biological Evolution↗
PubMed1999

Toward an evolutionary taxonomy of treatable conditions.

The definition of disorder as a harmful dysfunction (J. C. Wakefield, 1999) is a useful concept, anchored in the recognition that the evolved human architecture consists of a collection of functional mechanisms that may potentially be impaired and whose impairment may be harmful. Because natural selection organized each mechanism to solve a distinct adaptive problem under ancestral conditions, the criteria for whether a mechanism is dysfunctional are supplied by whether the mechanism has become impaired in performing its ancestral function. Because evolutionary function and dysfunction diverge markedly from normal human standards of value, many dysfunctions are beneficial, whereas various mechanisms that are performing their evolved function may cause disturbing outcomes. For this reason, many conditions in addition to disorders may require treatment, and the authors attempt to sketch an evolutionary taxonomy of treatable conditions.

Biological Evolution↗
PubMed2003

Fictions and facts about evolutionary approaches to human behavior: comment on Lickliter and Honeycutt (2003).

Six misconceptions about evolutionary approaches to human behavior are exposed. Evidence is adduced to support the assertions that evolutionary approaches do not (a) adopt a reductionistic "gene-centered" level of analysis, (b) assume that natural selection is the only process that creates and designs ontogenetic processes and phenotypic outcomes, (c) assume that genes are the only agents responsible for the transgenerational inheritance of phenotypic traits and characteristics, (d) assume that genes are self-contained and impervious to extragenetic influences, (e) posit a strong form of genetic determinism, or (f) pay lip service to the role of the environment. Building straw men and knocking them down is an inherently destructive enterprise; integrating different approaches is a more constructive way of contributing to the growth of knowledge.

Behavior↗
PubMed2003

Dynamical evolutionary psychology: individual decision rules and emergent social norms.

A new theory integrating evolutionary and dynamical approaches is proposed. Following evolutionary models, psychological mechanisms are conceived as conditional decision rules designed to address fundamental problems confronted by human ancestors, with qualitatively different decision rules serving different problem domains and individual differences in decision rules as a function of adaptive and random variation. Following dynamical models, decision mechanisms within individuals are assumed to unfold in dynamic interplay with decision mechanisms of others in social networks. Decision mechanisms in different domains have different dynamic outcomes and lead to different sociospatial geometries. Three series of simulations examining trade-offs in cooperation and mating decisions illustratehow individual decision mechanisms and group dynamics mutually constrain one another, and offer insights about gene-culture interactions.

Adaptation, Psychological↗
PubMed1998

The ParaHox gene cluster is an evolutionary sister of the Hox gene cluster.

Genes of the Hox cluster are restricted to the animal kingdom and play a central role in axial patterning in divergent animal phyla. Despite its evolutionary and developmental significance, the origin of the Hox gene cluster is obscure. The consensus is that a primordial Hox cluster arose by tandem gene duplication close to animal origins. Several homeobox genes with high sequence identity to Hox genes are found outside the Hox cluster and are known as 'dispersed' Hox-like genes; these genes may have been transposed away from an expanding cluster. Here we show that three of these dispersed homeobox genes form a novel gene cluster in the cephalochordate amphioxus. We argue that this 'ParaHox' gene cluster is an ancient paralogue (evolutionary sister) of the Hox gene cluster; the two gene clusters arose by duplication of a ProtoHox gene cluster. Furthermore, we show that amphioxus ParaHox genes have co-linear developmental expression patterns in anterior, middle and posterior tissues. We propose that the origin of distinct Hox and ParaHox genes by gene-cluster duplication facilitated an increase in body complexity during the Cambrian explosion.

Amino Acid Sequence↗
PubMed2001

Evolutionary radiations and convergences in the structural organization of mammalian brains.

The sizes of mammalian brain components seem to be mostly related to the sizes of the whole brain (and body), suggesting a one-dimensional scale of encephalization. Previous multivariate study of such data concludes that evolutionary selection for enlargement of any one brain part is constrained to selection for a concerted enlargement of the whole brain. However, interactions between structurally related pairs of brain parts confirm reports of differential change in brain nuclei, and imply mosaic rather than concerted evolution. Here we analyse a large number of variables simultaneously using multi-dimensional methods. We show that the relative proportions of different systems of functionally integrated brain structures vary independently between different mammalian orders, demonstrating separate evolutionary radiations in mammalian brain organization. Within each major order we identify clusters of unrelated species that occupy similar behavioural niches and have convergently evolved similar brain proportions. We conclude that within orders, mosaic brain organization is caused by selective adaptation, whereas between orders it suggests an interplay between selection and constraints.

Adaptation, Physiological↗
PubMed2001

Evolutionary analyses of the human genome.

The completion of the human genome will greatly accelerate the development of a new branch of science--evolutionary genomics. We can now directly address important questions about the evolutionary history of human genes and their regulatory sequences. Computational analyses of the human genome will reveal the number of genes and repetitive elements, the extent of gene duplication and compositional heterogeneity in the human genome, and the extent of domain shuffling and domain sharing among proteins. Here we present some first glimpses of these features.

Conserved Sequence↗
PubMed2001

An evolutionary scaling law for the primate visual system and its basis in cortical function.

A hallmark of mammalian brain evolution is the disproportionate increase in neocortical size as compared with subcortical structures. Because primary visual cortex (V1) is the most thoroughly understood cortical region, the visual system provides an excellent model in which to investigate the evolutionary expansion of neocortex. I have compared the numbers of neurons in the visual thalamus (lateral geniculate nucleus; LGN) and area V1 across primate species. Here I find that the number of V1 neurons increases as the 3/2 power of the number of LGN neurons. As a consequence of this scaling law, the human, for example, uses four times as many V1 neurons per LGN neuron (356) to process visual information as does a tarsier (87). I argue that the 3/2 power relationship is a natural consequence of the organization of V1, together with the requirement that spatial resolution in V1 should parallel the maximum resolution provided by the LGN. The additional observation that thalamus/neocortex follows the same evolutionary scaling law as LGN/V1 may suggest that neocortex generally conforms to the same organizational principle as V1.

Animals↗
PubMed2001

Evolutionary computation.

Evolution does not require DNA, or even living organisms. In computer science, the field known as 'evolutionary computation' uses evolution as an algorithmic tool, implementing random variation, reproduction and selection by altering and moving data within a computer. This harnesses the power of evolution as an alternative to the more traditional ways to design software or hardware. Research into evolutionary computation should be of interest to geneticists, as evolved programs often reveal properties - such as robustness and non-expressed DNA - that are analogous to many biological phenomena.

Algorithms↗
PubMed1995

Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily.

The sequences of proteins from ancient organisms can be reconstructed from the sequences of their descendants by a procedure that assumes that the descendant proteins arose from the extinct ancestor by the smallest number of independent evolutionary events ('parsimony'). The reconstructed sequences can then be prepared in the laboratory and studied. Thirteen ancient ribonucleases (RNases) have been reconstructed as intermediates in the evolution of the RNase protein family in artiodactyls (the mammal order that includes pig, camel, deer, sheep and ox). The properties of the reconstructed proteins suggest that parsimony yields plausible ancient sequences. Going back in time, a significant change in behaviour, namely a fivefold increase in catalytic activity against double-stranded RNA, appears in the RNase reconstructed for the founding ancestor of the artiodactyl lineage, which lived about 40 million years ago. This corresponds to the period when ruminant digestion arose in the artiodactyls, suggests that contemporary artiodactyl digestive RNases arose from a non-digestive ancestor, and illustrates how evolutionary reconstructions can help in the understanding of physiological function within a protein family.

Amino Acid Sequence↗
PubMed1995

The major evolutionary transitions.

There is no theoretical reason to expect evolutionary lineages to increase in complexity with time, and no empirical evidence that they do so. Nevertheless, eukaryotic cells are more complex than prokaryotic ones, animals and plants are more complex than protists, and so on. This increase in complexity may have been achieved as a result of a series of major evolutionary transitions. These involved changes in the way information is stored and transmitted.

Animals↗
PubMed1996

Non-mutualistic yucca moths and their evolutionary consequences.

Interspecific mutualisms are regarded as having evolved from antagonistic or commensalistic interactions, with most mutualisms remaining facultative but some having coevolved into obligate reciprocal dependency. Underlying mutualism is an intrinsic conflict between the parties, in that each is under selection for increased exploitation of the other. Theoretical models suggest that this conflict is a source of evolutionary instability, and that evolution of 'cheating' by one party may lead to reciprocal extinction. Here we present phylogenic evidence for reversal of an obligate mutualism: within the yucca moth complex, distinct cheater species derived from obligate pollinators inflict a heavy cost on their yucca hosts by laying their eggs but not pollinating the yucca. Phylogenetic data show the cheaters to have existed for a long time. Coexisting pollinators and cheaters are not sister taxa, supporting predictions that evolution of cheating within a single pollinator is evolutionarily unstable. Several lines of evidence support a hypothesis that host shifts preceded the reversal of obligate mutualism. Host or partner shifts is a mechanism that can provide a route of evolutionary escape among obligate mutualists in general.

Animals↗
PubMed1999

Incorporating rules for responding into evolutionary games.

Evolutionary game theory is concerned with the evolutionarily stable outcomes of the process of natural selection. The theory is especially relevant when the fitness of an organism depends on the behaviour of other members of its population. Here we focus on the interaction between two organisms that have a conflict of interest. The standard approach to such two-player games is to assume that each player chooses a single action and that the evolutionarily stable action of each player is the best given the action of its opponent. We argue that, instead, most two-player games should be modelled as involving a series of interactions in which opponents negotiate the final outcome. Thus we should be concerned with evolutionarily stable negotiation rules rather than evolutionarily stable actions. The evolutionarily stable negotiation rule of each player is the best rule given the rule of its opponent. As we show, the action chosen as a result of the negotiation is not the best action given the action of the opponent. This conclusion necessitates a fundamental change in the way that evolutionary games are modelled.

Animals↗
PubMed2000

An evolutionary bridge to a new protein fold.

Arc repressor bearing the N11L substitution (Arc-N11L) is an evolutionary intermediate between the wild type protein, in which the region surrounding position 11 forms a beta-sheet, and a double mutant 'switch Arc', in which this region is helical. Here, Arc-N11L is shown to be able to adopt either the wild type or mutant conformations. Exchange between these structures occurs on the millisecond time scale in a dynamic equilibrium in which the relative populations of each fold depend on temperature, solvent conditions and ligand binding. The N11L mutation serves as an evolutionary bridge from the beta-sheet to the helical fold because in the mutant, Leu is an integral part of the hydrophobic core of the new structure but can also occupy a surface position in the wild type structure. Conversely, the polar Asn 11 side chain serves as a negative design element in wild type Arc because it cannot be incorporated into the core of the mutant fold.

Amino Acid Sequence↗
PubMed1980

Regulatory gene adaptation: an evolutionary model.

There is increasing support for the notion that changes in regulatory loci have played a major role in eukaryotic evolution. Assuming a model of genetic regulation based upon presently accepted views of the organisation of the eukaryotic genome and basic models of evolutionary genetics, one can provide a context for speculation about the advantages and disadvantages of adaptation via regulatory genes. As additional information is obtained on particular regulatory systems, the evolutionary genetic model can be modified and expanded.

Adaptation, Biological↗
PubMed1996

Evolutionary conservation and molecular characteristics of repetitive sequences of Drosophila koepferae.

Thirteen middle repetitive DNA clones obtained from the genome of Drosophila koepferae have been tested for their evolutionary conservation in the other seven species of the buzzatii and martensis clusters (repleta group). All but two of these clones exhibit qualitatively similar patterns of hybridization in the eight species. The average interspecific hybridization signal is 85 per cent of that found intraspecifically, ranging from 73 to 93 per cent. Partial sequencing of six of these clones has shown sequences related to the retrotransposon Gypsy, first characterized in D. melanogaster, as well as to the Anopheles gambiae LINE elements T1Ag and Q. A fragment of a hitherto unknown, short inverted repeat transposable element has also been found. The evolutionary conservation of repetitive D. koepferae sequences seems to be related to the high proportion of simple DNA and inactive mobile elements in the genome of this species.

Amino Acid Sequence↗
PubMed1978

Nonprogressive, histologically mild membranous glomerulonephritis appearing in all evolutionary phases as histologically "early" membranous glomerulonephritis.

Seven adult patients with idiopathic nephrotic syndrome and with a glomerular histology considered normal but with ultrastructurally provable membranous glomerulonephritis (MNG) were studied. The glomerular lesions were found to represent all ultrastructural evolutionary phases (A,B, and C) of MGN. In patients with serial biopsies, the membranous lesion seemed to have passed through all of its evolutionary phases towards healing (C) without developing spikes or thickening of the glomerular basement membrane (GBM), i.e., the traditional light microscopic characteristics of MGN. This evolution was associated with a benign clinical course. The membranous lesions were associated with a vacuolization visible in obliquely or tangentially cut segments of the GBM in silver-stained paraffin sections. This alteration seemed to be created by irregularities of the argyrophilic lamina densa of the GBM and not by subepithelial deposits, as suggested previously. All seven patients had a remission of the nephrotic syndrome which appeared to be spontaneous and not drug-induced. The amount of proteinuria correlated with the ultrastructural phase of MGN and with the intensity of immunofluorescent staining. In one patient, the latter became negative.

Adrenal Cortex Hormones↗