The medaka draft genome and insights into vertebrate genome evolution.

The medaka Oryzias latipes is a small egg-laying freshwater teleost, and has become an excellent model system for developmental genetics and evolutionary biology. The medaka genome is relatively small in size, approximately 800 Mb, and the genome…

The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate…

Constraints in embryonic development are thought to bias the direction of evolution by making some changes less likely, and others more likely, depending on their consequences on ontogeny. Here, we characterize the constraints acting on genome…

HOX genes specify cell fate in the anterior-posterior axis of animal embryos. Invertebrate chordates have one HOX cluster, but mammals have four, suggesting that cluster duplication facilitated the evolution of vertebrate body plans. This report…

Recent analyses indicated that genes with larger effect of knockout or mutation and with larger probability to revert to single copy after whole genome duplication are expressed earlier in development. Here, we further investigate whether tissue…

The surprising variation in the number of Hox clusters and the genomic architecture within vertebrate lineages, especially within the ray-finned fish, reflects a history of duplications and subsequent lineage-specific gene loss. Recent research on…

Background: Comparative genomic studies are revealing frequent gains and losses of whole genes via duplication and pseudogenization. One commonly used method for inferring the number and timing of gene gains and losses reconciles the gene tree for…

The increasing availability of genomic sequences from different vertebrate organisms affords molecular biologists the opportunity to thoroughly in- vestigate phenomena that were only hinted at by more sparse data. The work described in this thesis…

In chordate phylogeny, changes in the nervous system. jaws. and appendages transformed meek filter feeders into fearsome predators(1). Gene duplication is thought to promote such innovation(2). Vertebrate ancestors probably had single copies of…

The recent sequencing of the lizard genome provides a unique opportunity to examine the evolution of vertebrate genomes in a phylogenetic context. The lizard genome contains an extraordinary diversity of active transposable elements that far exceeds…