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The complete sequence of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3, has been determined by assembling the sequences of the physical map-based contigs of fosmid clones and of long polymerase chain reaction (PCR) products which were used for gap-filling. The entire length of the genome was 1,738,505 bp. The authenticity of the entire genome sequence was supported by restriction analysis of long PCR products, which were directly amplified from the genomic DNA. As the potential protein-coding regions, a total of 2061 open reading frames (ORFs) were assigned, and by similarity search against public databases, 406 (19.7%) were related to genes with putative function and 453 (22.0%) to the sequences registered but with unknown function. The remaining 1202 ORFs (58.3%) did not show any significant similarity to the sequences in the databases. Sequence comparison among the assigned ORFs in the genome provided evidence that a considerable number of ORFs were generated by sequence duplication. By similarity search, 11 ORFs were assumed to contain the intein elements. The RNA genes identified were a single 16S-23S rRNA operon, two 5S rRNA genes and 46 tRNA genes including two with the intron structure. All the assigned ORFs and RNA coding regions occupied 91.25% of the whole genome. The data presented in this paper are available on the internet at http:@www.nite.go.jp.

For assessing the degree of population subdivision, and therefore the extent to which group selection might favor an altruistic trait, an appropriate measure is Nei's GST, defined by (F0-F)/(1-F). F0 is the probability that two alleles drawn from the same group are identical in state and F is the probability for two alleles drawn at random from the entire population. These probabilities can be assessed from molecular polymorphisms. GST has a number of properties that make it useful for empirical studies. When the mutation rate is small relative to the migration rate and the reciprocal of the group size, GST depends mainly on the absolute number of migrants per generation, moves rapidly to near equilibrium, and is independent of the number of alleles. The relative homogenizing effect of migration in the island and stepping-stone models is not as different as might be expected; one immigrant chosen randomly from the rest of the population is only one to two times as effective as one from a neighboring group, appreciably exceeding 2 only when there are 1000 or more groups. The use of molecular data to estimate the degree of population subdivision may permit testable predictions of the extent of altruistic behavior.

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