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PubMed1999

Fold prediction and evolutionary analysis of the POZ domain: structural and evolutionary relationship with the potassium channel tetramerization domain.

Using iterative database searches, a statistically significant sequence similarity was detected between the POZ (poxvirus and zinc finger) domains found in a variety of proteins involved in animal transcription regulation, cytoskeleton organization, and development, and the tetramerization domain of animal potassium channels. Using the crystal structure of the Aplysia Shaker channel tetramerization domain as a template, the common structure of the POZ domain class was predicted. Examination of the structure resulted in the identification of several structural features and specific amino acid residues that may be involved in conserved protein-protein interactions mediated by the POZ domains as well as those that may contribute to the specificity of these interactions. Phylogenetic analysis of the POZ domains suggests that the common ancestor of the crown group eukaryotes already possessed this domain; POZ domains have undergone independent expansion in plants and in different animal lineages.

Amino Acid Sequence↗
PubMed2004

The evolutionary origin of long-crowing chicken: its evolutionary relationship with fighting cocks disclosed by the mtDNA sequence analysis.

Chickens with exceptionally long crow are often favored all over the world, and connoisseur breeders have bred certain types of chicken exclusively for this trait. In Japan, three chicken varieties have been specifically bred to develop an exceptionally long crow of over 15 s. Although these three long-crowing chickens, Naganakidori, are honored as heritage varieties of Japan, the domestication process and genealogical origin of long-crowing chickens remain unclear. The purpose of this study is to clarify these issues using nucleotide sequences of the mitochondrial DNA D-loop region. Blood samples from a total of nine long-crowing chickens and 74 chickens from 11 Japanese native varieties were collected. DNA sequence data of two Junglefowl species were also collected from the International DNA database (DDBJ /EMBL/GenBank) for use as the outgroup. A phylogenetic tree was then constructed revealing that all three Naganakidori varieties were monophyletic and originated from a fighting cock, a Shamo, for cockfighting. These results suggest that these three long-crowing chickens share a common origin in spite of their conspicuously different characters, and that human cultures favoring long-crowing chickens might have been preceded by a tradition of cockfighting. Moreover, these long-crowing varieties first separated from the fighting cocks of Okinawa, which is geographically closer to Southern China and Indochina than Mainland Japan (Honshu/Kyushu). This implies that Japanese long-crowing chickens were first brought to Mainland Japan as fighting cocks from the surrounding regions of Southern China or Indochina and through Okinawa.

Aggression↗
PubMed2005

Toward a theory of evolutionary computation.

We outline a theory of evolutionary computation using a formal model of evolutionary computation--the Evolutionary Turing Machine--which is introduced as the extension of the Turing Machine model. Evolutionary Turing Machines provide a better and a more complete model for evolutionary computing than conventional Turing Machines, algorithms, and Markov chains. The convergence and convergence rate are defined and investigated in terms of this new model. The sufficient conditions needed for the completeness and optimality of evolutionary search are investigated. In particular, the notion of the total optimality as an instance of the multiobjective optimization of the Universal Evolutionary Turing Machine is introduced. This provides an automatic way to deal with the intractability of evolutionary search by optimizing the quality of solutions and search costs simultaneously. Based on a new model a very flexible classification of optimization problem hardness for the evolutionary techniques is proposed. The expressiveness of evolutionary computation is investigated. We show that the problem of the best evolutionary algorithm is undecidable independently of whether the fitness function is time dependent or fixed. It is demonstrated that the evolutionary computation paradigm is more expressive than Turing Machines, and thus the conventional computer science based on them. We show that an Evolutionary Turing Machine is able to solve nonalgorithmically the halting problem of the Universal Turing Machine and, asymptotically, the best evolutionary algorithm problem. In other words, the best evolutionary algorithm does not exist, but it can be potentially indefinitely approximated using evolutionary techniques.

Algorithms↗