Automated identification of conserved synteny after whole-genome duplication.

An important objective for inferring the evolutionary history of gene families is the determination of orthologies and paralogies. Lineage-specific paralog loss following whole-genome duplication events can cause anciently related homologs to appear in some assays as orthologs. Conserved synteny-the tendency of neighboring genes to retain their relative positions and orders on chromosomes over evolutionary time-can help resolve such errors.

Inferring ancestral gene order.

To explain the evolutionary mechanisms by which populations of organisms change over time, it is necessary to first understand the pathways by which genomes have changed over time. Understanding genome evolution requires comparing modern genomes with ancestral genomes, which thus necessitates the reconstruction of those ancestral genomes. This chapter describes automated approaches to infer the nature of ancestral genomes from modern sequenced genomes.

Aligning sequences by minimum description length.

This paper presents a new information theoretic framework for aligning sequences in bioinformatics. A transmitter compresses a set of sequences by constructing a regular expression that describes the regions of similarity in the sequences. To retrieve the original set of sequences, a receiver generates all strings that match the expression.

Anticodon-dependent conservation of bacterial tRNA gene sequences.

The residues in tRNA that account for its tertiary fold and for its specific aminoacylation are well understood. In contrast, relatively little is known about the residues in tRNA that dictate its ability to transit the different sites of the ribosome. Yet protein synthesis cannot occur unless tRNA properly engages with the ribosome.

A neural network model of chemotaxis predicts functions of synaptic connections in the nematode Caenorhabditis elegans.

The anatomical connectivity of the nervous system of the nematode Caenorhabditis elegans has been almost completely described, but determination of the neurophysiological basis of behavior in this system is just beginning. Here we used an optimization algorithm to search for patterns of connectivity sufficient to compute the sensorimotor transformation underlying C. elegans chemotaxis, a simple form of spatial orientation behavior in which turning probability is modulated by the rate of change of chemical concentration.

The origins of genome complexity.

Complete genomic sequences from diverse phylogenetic lineages reveal notable increases in genome complexity from prokaryotes to multicellular eukaryotes. The changes include gradual increases in gene number, resulting from the retention of duplicate genes, and more abrupt increases in the abundance of spliceosomal introns and mobile genetic elements. We argue that many of these modifications emerged passively in response to the long-term population-size reductions that accompanied increases in organism size.

The evolutionary demography of duplicate genes.

Although gene duplication has generally been viewed as a necessary source of material for the origin of evolutionary novelties, the rates of origin, loss, and preservation of gene duplicates are not well understood. Applying steady-state demographic techniques to the age distributions of duplicate genes censused in seven completely sequenced genomes, we estimate the average rate of duplication of a eukaryotic gene to be on the order of 0.01/ gene/million years, which is of the same order of magnitude as the mutation rate per nucleotide site.