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At least 1,261 records · Page 70Linked to original sources
PubMed2003

The challenge of constructing large phylogenetic trees.

The amount of sequence data available to reconstruct the evolutionary history of genes and species has increased 20-fold in the past decade. Consequently the size of phylogenetic analyses has grown as well, and phylogenetic methods, algorithms and their implementations have struggled to keep pace. Computational and other challenges raised by this burgeoning database emerge at several stages of analysis, from the optimal assembly of large data matrices from sequence databases, to the efficient construction of trees from these large matrices and the piece-wise assembly of 'supertrees' from those trees in turn. A final challenge is posed by the difficulty of visualizing and making inferences from trees that might soon routinely contain thousands of species.

Algorithms↗
PubMed2006

Evolutionary trace report_maker: a new type of service for comparative analysis of proteins.

: Evolutionary trace report_maker offers a new type of service for researchers investigating the function of novel proteins. It pools, from different sources, information about protein sequence, structure and elementary annotation, and to that background superimposes inference about the evolutionary behavior of individual residues, using real-valued evolutionary trace method. As its only input it takes a Protein Data Bank identifier or UniProt accession number, and returns a human-readable document in PDF format, supplemented by the original data needed to reproduce the results quoted in the report.

Algorithms↗
PubMed2007

Negotiation of mutualism: rhizobia and legumes.

The evolution and persistence of biological cooperation have been an important puzzle in evolutionary theory. Here, we suggest a new approach based on bargaining theory to tackle the question. We present a mechanistic model for negotiation of benefits between a nitrogen-fixing nodule and a legume plant. To that end, we first derive growth rates for the nodule and plant from metabolic models of each as a function of material fluxes between them. We use these growth rates as pay-off functions in the negotiation process, which is analogous to collective bargaining between a firm and a workers' union. Our model predicts that negotiations lead to the Nash bargaining solution, maximizing the product of players' pay-offs. This work introduces elements of cooperative game theory into the field of mutualistic interactions. In the discussion of the paper, we argue for the benefits of such an approach in studying the question of biological cooperation.

Biological Evolution↗
PubMed1996

Evolution teaching.

Explore the source record for details and available documents.

Biological Evolution↗
PubMed2005

The liabilities of mobility: a selection pressure for the transition to consciousness in animal evolution.

The issue of the biological origin of consciousness is linked to that of its function. One source of evidence in this regard is the contrast between the types of information that are and are not included within its compass. Consciousness presents us with a stable arena for our actions-the world-but excludes awareness of the multiple sensory and sensorimotor transformations through which the image of that world is extracted from the confounding influence of self-produced motion of multiple receptor arrays mounted on multijointed and swivelling body parts. Likewise excluded are the complex orchestrations of thousands of muscle movements routinely involved in the pursuit of our goals. This suggests that consciousness arose as a solution to problems in the logistics of decision making in mobile animals with centralized brains, and has correspondingly ancient roots.

Animals↗
PubMed1993

Calibrating rates of early Cambrian evolution.

An explosive episode of biological diversification occurred near the beginning of the Cambrian period. Evolutionary rates in the Cambrian have been difficult to quantify accurately because of a lack of high-precision ages. Currently, uranium-lead zircon geochronology is the most powerful method for dating rocks of Cambrian age. Uranium-lead zircon data from lower Cambrian rocks located in northeast Siberia indicate that the Cambrian period began at approximately 544 million years ago and that its oldest (Manykaian) stage lasted no less than 10 million years. Other data indicate that the Tommotian and Atdabanian stages together lasted only 5 to 10 million years. The resulting compression of Early Cambrian time accentuates the rapidity of both the faunal diversification and subsequent Cambrian turnover.

Biological Evolution↗