Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Evolutionary”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,171 records · Page 65Linked to original sources
PubMed2005

Evolutionary emergence of size-structured food webs.

Explaining the structure of terrestrial and aquatic food webs remains one of the most important challenges of ecological theory. Most existing models use emergent properties of food webs, such as diversity and connectance as parameters, to determine other food-web descriptors. Lower-level processes, in particular adaptation (whether by behavioral, developmental, or evolutionary mechanisms), are usually not considered. Here, we show that complex, realistic food webs may emerge by evolution from a single ancestor based on very simple ecological and evolutionary rules. In our model, adaptation acts on body size, whose impact on the metabolism and interactions of organisms is well established. Based on parameters defined at the organism scale, the model predicts emergent properties at the food-web scale. Variations of two key parameters (width of consumption niche and competition intensity) allow very different food-web structures and functionings to emerge, which are similar to those observed in some of the best-documented food webs.

Adaptation, Biological↗
PubMed2005

Evolutionary profiles from the QR factorization of multiple sequence alignments.

We present an algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of the homologous group. The method, based on the multidimensional QR factorization of numerically encoded multiple sequence alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins. We observe a general trend that these smaller, more evolutionarily balanced profiles have comparable and, in many cases, better performance in database searches than conventional profiles containing hundreds of sequences, constructed in an iterative and computationally intensive procedure. For more diverse families or superfamilies, with sequence identity <30%, structural alignments, based purely on the geometry of the protein structures, provide better alignments than pure sequence-based methods. Merging the structure and sequence information allows the construction of accurate profiles for distantly related groups. These structure-based profiles outperformed other sequence-based methods for finding distant homologs and were used to identify a putative class II cysteinyl-tRNA synthetase (CysRS) in several archaea that eluded previous annotation studies. Phylogenetic analysis showed the putative class II CysRSs to be a monophyletic group and homology modeling revealed a constellation of active site residues similar to that in the known class I CysRS.

Algorithms↗
PubMed2005

An evolutionary proteomics approach identifies substrates of the cAMP-dependent protein kinase.

Protein kinases are important mediators of much of the signal transduction that occurs in eukaryotic cells. Unfortunately, the identification of protein kinase substrates has proven to be a difficult task, and we generally know few, if any, of the physiologically relevant targets of any particular kinase. Here, we describe a sequence-based approach that simplified this substrate identification process for the cAMP-dependent protein kinase (PKA) in Saccharomyces cerevisiae. In this method, the evolutionary conservation of all PKA consensus sites in the S. cerevisiae proteome was systematically assessed within a group of related yeasts. The basic premise was that a higher degree of conservation would identify those sites that are functional in vivo. This method identified 44 candidate PKA substrates, 5 of which had been described. A phosphorylation analysis showed that all of the identified candidates were phosphorylated by PKA and that the likelihood of phosphorylation was strongly correlated with the degree of target site conservation. Finally, as proof of principle, the activity of one particular target, Atg1, a key regulator of autophagy, was shown to be controlled by PKA phosphorylation in vivo. These data therefore suggest that this evolutionary proteomics approach identified a number of PKA substrates that had not been uncovered by other methods. Moreover, these data show how this approach could be generally used to identify the physiologically relevant occurrences of any protein motif identified in a eukaryotic proteome.

Autophagy↗
PubMed2005

Genomes, phylogeny, and evolutionary systems biology.

With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics, and computer science are now known as systems biology. Here, I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.

Animals↗
PubMed2005

An evolutionary constraint: strongly disfavored class of change in DNA sequence during divergence of cis-regulatory modules.

The DNA of functional cis-regulatory modules displays extensive sequence conservation in comparisons of genomes from modestly distant species. Patches of sequence that are several hundred base pairs in length within these modules are often seen to be 80-95% identical, although the flanking sequence cannot even be aligned. However, it is unlikely that base pairs located between the transcription factor target sites of cis-regulatory modules have sequence-dependent function, and the mechanism that constrains evolutionary change within cis-regulatory modules is incompletely understood. We chose five functionally characterized cis-regulatory modules from the Strongylocentrotus purpuratus (sea urchin) genome and obtained orthologous regulatory and flanking sequences from a bacterial artificial chromosome genome library of a congener, Strongylocentrotus franciscanus. As expected, single-nucleotide substitutions and small indels occur freely at many positions within the regulatory modules of these two species, as they do outside the regulatory modules. However, large indels (>20 bp) are statistically almost absent within the regulatory modules, although they are common in flanking intergenic or intronic sequence. The result helps to explain the patterns of evolutionary sequence divergence characteristic of cis-regulatory DNA.

Animals↗
PubMed2006

Historical contingency and the purported uniqueness of evolutionary innovations.

Many events in the history of life are thought to be singular, that is, without parallels, analogs, or homologs in time and space. These claims imply that history is profoundly contingent in that independent origins of life in the universe will spawn radically different histories. If, however, most innovations arose more than once on Earth, histories would be predictable and replicable at the scale of functional roles and directions of adaptive change. Times of origin of 23 purportedly unique evolutionary innovations are significantly more ancient than the times of first instantiation of 55 innovations that evolved more than once, implying that the early phases of life's history were less replicable than later phases or that the appearance of singularity results from information loss through time. Indirect support for information loss comes from the distribution of sizes of clades in which the same minor, geologically recent innovation has arisen multiple times. For three repeated molluscan innovations, 28-71% of instantiations are represented by clades of five or fewer species. Such small clades would be undetectable in the early history of life. Purportedly unique innovations either arose from the union and integration of previously independent components or belong to classes of functionally similar innovations. Claims of singularity are therefore not well supported by the available evidence. Details of initial conditions, evolutionary pathways, phenotypes, and timing are contingent, but important ecological, functional, and directional aspects of the history of life are replicable and predictable.

Animals↗
PubMed2006

The group covariance effect and fitness trade-offs during evolutionary transitions in individuality.

Transforming our understanding of life is the realization that evolution occurs not only among individuals within populations but also through the integration of groups of preexisting individuals into a new higher-level individual, that is, through evolutionary transitions in individuality. During evolutionary transitions (such as during the origin of gene networks, bacteria-like cells, eukaryotic cells, multicellular organisms, and societies), fitness must be reorganized; specifically, it must be transferred from the lower- to the higher-level units and partitioned among the lower-level units that specialize in the fitness components of the new higher-level individual. This paper studies the role of fitness trade-offs in fitness reorganization, the evolution of cooperation, and the conversion of a group into a new individual during the origin of multicellular life. Specifically, this study shows that the fitness of the group is augmented over the average fitness of its members according to a covariance effect. This covariance effect appears to be one of the first emergent properties of the group and a general aspect of groups with multiplicative properties that are themselves averages of properties of lower-level units. The covariance effect allows groups to break through the constraints that govern their members, and this effect likely applies to group dynamics in other fields.

Animals↗
PubMed2006

Evaluation of mortality trajectories in evolutionary biodemography.

An important task in evolutionary biodemography is to determine the schedule of survival and reproduction as the outcome of natural selection acting on life histories. We do this by using a model in which the state of the organism is characterized by mass and accumulated damage, both of which are affected by activity and which affect the rate of mortality. Focusing on growth during the juvenile period, we determine the level of activity that maximizes reproductive value. Given this, we are able to project forward and determine the trajectory of mortality for an individual following the optimal life history, given the physiological and reproductive parameters. We show that there are two main classes of juvenile mortality trajectories: U-shaped (such as recently reported for prereproductive humans) and steadily declining and we are able to connect the shape of the mortality trajectory with the physiological and reproductive parameters characterizing the life history. Our work shows the importance of state in models of evolutionary biodemography and the power of modern computational methods to illuminate biological process.

Aging↗
PubMed2006

Evolutionary trade-off between weapons and testes.

It has long been recognized that male mating competition is responsible for the evolution of weaponry for mate acquisition. However, when females mate with more than one male, competition between males can continue after mating in the form of sperm competition. Theory predicts that males should increase their investment in sperm production as sperm competition is increased, but it assumes that males face a trade-off between sperm production and other life-history traits such as mate acquisition. Here, we use a genus of horned beetle, Onthophagus, to examine the trade-off between investment in testes required for fertilizations and investment in weapons used to obtain matings. In a within-species study, we prevented males from developing horns and found that these males grew larger and invested relatively more in testes growth than did males allowed to grow horns. Among species, there was no general relationship between the relative sizes of horns and testes. However, the allometric slope of horn size on body size was negatively associated with the allometric slope of testes size on body size. We suggest that this reflects meaningful evolutionary changes in the developmental mechanisms regulating trait growth, specifically in the degree of nutrition-dependent phenotypic plasticity versus canalization of traits. Finally, we show how this resource allocation trade-off has influenced the evolutionary diversification of weapons, revealing a rich interplay between developmental trade-offs and both pre- and postmating mechanisms of sexual competition.

Animals↗
PubMed2007

Improved evolutionary optimization from genetically adaptive multimethod search.

In the last few decades, evolutionary algorithms have emerged as a revolutionary approach for solving search and optimization problems involving multiple conflicting objectives. Beyond their ability to search intractably large spaces for multiple solutions, these algorithms are able to maintain a diverse population of solutions and exploit similarities of solutions by recombination. However, existing theory and numerical experiments have demonstrated that it is impossible to develop a single algorithm for population evolution that is always efficient for a diverse set of optimization problems. Here we show that significant improvements in the efficiency of evolutionary search can be achieved by running multiple optimization algorithms simultaneously using new concepts of global information sharing and genetically adaptive offspring creation. We call this approach a multialgorithm, genetically adaptive multiobjective, or AMALGAM, method, to evoke the image of a procedure that merges the strengths of different optimization algorithms. Benchmark results using a set of well known multiobjective test problems show that AMALGAM approaches a factor of 10 improvement over current optimization algorithms for the more complex, higher dimensional problems. The AMALGAM method provides new opportunities for solving previously intractable optimization problems.

Algorithms↗
PubMed2003

Natural variation in human membrane transporter genes reveals evolutionary and functional constraints.

Membrane transporters maintain cellular and organismal homeostasis by importing nutrients and exporting toxic compounds. Transporters also play a crucial role in drug response, serving as drug targets and setting drug levels. As part of a pharmacogenetics project, we screened exons and flanking intronic regions for variation in a set of 24 membrane transporter genes (96 kb; 57% coding) in 247 DNA samples from ethnically diverse populations. We identified 680 single nucleotide polymorphisms (SNPs), of which 175 were synonymous and 155 caused amino acid changes, and 29 small insertions and deletions. Amino acid diversity (pi(NS)) in transmembrane domains (TMDs) was significantly lower than in loop domains, suggesting that TMDs have special functional constraints. This difference was especially striking in the ATP-binding cassette superfamily and did not parallel evolutionary conservation: there was little variation in the TMDs, even in evolutionarily unconserved residues. We used allele frequency distribution to evaluate different scoring systems (Grantham, blosum62, SIFT, and evolutionarily conservedevolutionarily unconserved) for their ability to predict which SNPs affect function. Our underlying assumption was that alleles that are functionally deleterious will be selected against and thus under represented at high frequencies and over represented at low frequencies. We found that evolutionary conservation of orthologous sequences, as assessed by evolutionarily conservedevolutionarily unconserved and SIFT, was the best predictor of allele frequency distribution and hence of function. European Americans had an excess of high frequency alleles in comparison to African Americans, consistent with a historic bottleneck. In addition, African Americans exhibited a much higher frequency of population specific medium-frequency alleles than did European Americans.

DNA↗
PubMed2001

Rapid plant diversification: planning for an evolutionary future.

Systematic conservation planning is a branch of conservation biology that seeks to identify spatially explicit options for the preservation of biodiversity. Alternative systems of conservation areas are predictions about effective ways of promoting the persistence of biodiversity; therefore, they should consider not only biodiversity pattern but also the ecological and evolutionary processes that maintain and generate species. Most research and application, however, has focused on pattern representation only. This paper outlines the development of a conservation system designed to preserve biodiversity pattern and process in the context of a rapidly changing environment. The study area is the Cape Floristic Region (CFR), a biodiversity hotspot of global significance, located in southwestern Africa. This region has experienced rapid (post-Pliocene) ecological diversification of many plant lineages; there are numerous genera with large clusters of closely related species (flocks) that have subdivided habitats at a very fine scale. The challenge is to design conservation systems that will preserve both the pattern of large numbers of species and various natural processes, including the potential for lineage turnover. We outline an approach for designing a system of conservation areas to incorporate the spatial components of the evolutionary processes that maintain and generate biodiversity in the CFR. We discuss the difficulty of assessing the requirements for pattern versus process representation in the face of ongoing threats to biodiversity, the difficulty of testing the predictions of alternative conservation systems, and the widespread need in conservation planning to incorporate and set targets for the spatial components (or surrogates) of processes.

Biological Evolution↗
PubMed2002

The evolutionary history of methicillin-resistant Staphylococcus aureus (MRSA).

Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of hospital-acquired infections that are becoming increasingly difficult to combat because of emerging resistance to all current antibiotic classes. The evolutionary origins of MRSA are poorly understood, no rational nomenclature exists, and there is no consensus on the number of major MRSA clones or the relatedness of clones described from different countries. We resolve all of these issues and provide a more thorough and precise analysis of the evolution of MRSA clones than has previously been possible. Using multilocus sequence typing and an algorithm, BURST, we analyzed an international collection of 912 MRSA and methicillin-susceptible S. aureus (MSSA) isolates. We identified 11 major MRSA clones within five groups of related genotypes. The putative ancestral genotype of each group and the most parsimonious patterns of descent of isolates from each ancestor were inferred by using BURST, which, together with analysis of the methicillin resistance genes, established the likely evolutionary origins of each major MRSA clone, the genotype of the original MRSA clone and its MSSA progenitor, and the extent of acquisition and horizontal movement of the methicillin resistance genes. Major MRSA clones have arisen repeatedly from successful epidemic MSSA strains, and isolates with decreased susceptibility to vancomycin, the antibiotic of last resort, are arising from some of these major MRSA clones, highlighting a depressing progression of increasing drug resistance within a small number of ecologically successful S. aureus genotypes.

Alleles↗
PubMed2001

Evolutionary self-organization of cell-free genetic coding.

Genetic encoding provides a generic construction scheme for biomolecular functions. This paper addresses the key problem of coevolution and exploitation of the multiple components necessary to implement a replicable genetic encoding scheme. Extending earlier results on multicomponent replication, the necessity of spatial structure for the evolutionary stabilization of the genetic coding system is established. An individual-based stochastic model of interacting molecules in three-dimensional space is presented that allows the evolution of genetic coding to be analyzed explicitly. A massively parallel configurable computer (NGEN) is used to implement the model, on the time scale of millions of generations, directly in electronic hardware. The spatial correlations between components of the genetic coding system are analyzed and found to be essential for evolutionary stability.

Animals↗
PubMed2002

Hotspots and the conservation of evolutionary history.

Species diversity is unevenly distributed across the globe, with terrestrial diversity concentrated in a few restricted biodiversity hotspots. These areas are associated with high losses of primary vegetation and increased human population density, resulting in growing numbers of threatened species. We show that conservation of these hotspots is critical because they harbor even greater amounts of evolutionary history than expected by species numbers alone. We used supertrees for carnivores and primates to estimate that nearly 70% of the total amount of evolutionary history represented in these groups is found in 25 biodiversity hotspots.

Animals↗
PubMed1972

Nonmathematical concepts of selection, evolutionary energy, and levels of evolution.

The place of mathematics in hypotheticodeductive processes and in biological research is discussed. (Natural) Selection is defined and described as differential elimination of performed sets at any level. Sets and acting sets are groups of units (themselves sets of smaller units) at any level that may or do interact. A pseudomathematical equation describes directional change (evolution) in sets at any level. Selection is the ram of evolution; it cannot generate, but can only direct, evolutionary energy. The energy of evolution is derived from molecular or chemical levels, is transmitted upwards through the increasingly complex sets of sets that form living systems, and is turned in directions determined by the sum of selective processes, at different levels, which may either supplement or oppose each other. All evolutionary processes conform to the pseudomathematical equation referred to above, use energy as described above, and have a P/OE (ratio of programming to open-endedness) that cannot be measured, but can be related to other P/OE values. Phylogeny and ontogeny are compared as processes af directional change with set selection. Stages in the evolution of multi-cellular individuals are suggested, and are essentially the same as stages in the evolution of some multi-individual insect societies. Thinking is considered as a part of ontogeny involving an irreversible, nonrepetitive process of set selection in the brain.

Biological Evolution↗
PubMed1975

Slow evolutionary loss of the potential for interspecific hybridization in birds: a manifestation of slow regulatory evolution.

Birds have lost the potential for interspecific hybridization slowly. This inference emerges from protein comparisons made on 36 pairs of bird species capable of hybridization. Micro-complement fixation tests show that hybridizable pairs of bird species differ by an average of 12 units of albumin immunological distance and 25 units of transferrin immunological distance. As these proteins evolve at a known and rather steady rate, it is inferred that the average hybridization species pair diverged from a common ancestor about 22 million years ago. The corresponding period for frog species pairs capable of hybridization is about 21 million years, while for hybridizable placental mammals it is only 2 to 3 million years. Thus birds resemble frogs in having lost the potential for interspecific hybridization about 10 times as slowly as have mammals. Birds have also been evolving very slowly at the anatomical level, particularly within the last 25 million years, according to Simpson, Romer, and many other vertebrate zoologists. In this respect they resemble frogs and differ from placental mammals, which have been undergoing unusually rapid anatomical evolution. Chromosomal evolution is also thought to have proceeded very slowly in both birds and frogs, relative to mammals. The above observations are consistent with the hypothesis that evolutionary changes in regulatory systems, that is, changes in the patterns of gene expression, provide the basis for both anatomical evolution and the evolutionary loss of hybridization potential.

Animals↗
PubMed1978

Evolutionary adaptation of membranes to temperature.

The "fluidity" of brain synaptosomal membrane preparations of arctic and hot-springs fish species, two temperature water fish species acclimated to different seasonal temperatures, and two mammals was estimated using the fluorescence polarization technique. At all measurement temperatures, the fluidity decreased in the order: arctic sculpin, 5 degrees-acclimated goldfish, 25 degrees-acclimated goldfish, desert pupfish, and rat. This correlated with increasing adaptation or body (i.e., cellular) temperatures of 0 degrees, 5 degrees, 25 degrees, 34 degrees, and 37 degrees and suggested a partial compensation of membrane fluidity for environmental temperature that occurs over the evolutionary time period as well as during laboratory (seasonal) acclimation. Evolutionary adaptation of relatively stenothermal species to constant thermal environments resulted in a more complete compensation than laboratory (seasonal) acclimation. Each compensation is accompanied by differences in the saturation of membrane phosphoglycerides. At increased cellular temperatures the proportion of saturated fatty acids increased and the unsaturation index decreased; the correlation between these indices and the measured expression of membrane dynamic structure was highly significant. It is concluded that the homeoviscous compensation of synaptic membrane function is an important component of temperature adaptation.

Adaptation, Physiological↗