Fishes of the order Cypriniformes are almost completely restricted to freshwater bodies and number > 3400 species placed in 5 families, each with poorly defined subfamilies and/or tribes. The present study represents the first attempt toward resolution of the higher-level relationships of the world's largest freshwater-fish clade based on whole mitochondrial (mt) genome sequences from 53 cypriniforms (including 46 newly determined sequences) plus 6 outgroups. Unambiguously aligned, concatenated mt genome sequences (14,563 bp) were divided into 5 partitions (first, second, and third codon positions of the protein-coding genes, rRNA genes, and tRNA genes), and partitioned Bayesian analyses were conducted, with protein-coding genes being treated in 3 different manners (all positions included; third codon positions converted into purine [R] and pyrimidine [Y] [RY-coding]; third codon positions excluded). The resultant phylogenies strongly supported monophyly of the Cypriniformes as well as that of the families Cyprinidae, Catostomidae, and a clade comprising Balitoridae + Cobitidae, with the 2 latter loach families being reciprocally paraphyletic. Although all of the data sets yielded nearly identical tree topologies with regard to the shallower relationships, deeper relationships among the 4 major clades (the above 3 major clades plus Gyrinocheilidae, represented by a single species Gyrinocheilus aymonieri in this study), were incongruent depending on the data sets. Treatment of the rapidly saturated third codon-position transitions appeared to be a source of such incongruities, and we advocate that RY-coding, which takes only transversions into account, effectively removes this likely "noise" from the data set and avoids the apparent lack of signal by retaining all available positions in the data set.

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Chromosome substitution series are useful tools for precise mapping of quantitative trait loci (QTLs) and for the evaluation of gene action as a single factor or in the case of gene interactions. In this study, we produced reciprocal sets of chromosome segment substitution lines (CSSLs) between Asominori (Japonica) and IR24 (Indica) in cultivated rice, Oryza sativa L. A set of chromosome segment substitution lines carries a single or a few donor chromosome segments overlapping with neighboring segments in a uniform genetic background. Reciprocal sets were developed by repeated backcrossing to respective recurrent parents and DNA markerassisted selections. The sets consisted of a series of 70 lines of Asominori CSSLs with IR24 genetic background (designated as 'IAS') and a series of 91 lines of IR24 CSSLs with Asominori genetic background (designated as 'AIS'). These substitution series represented most of the genome of the donor parents on the alien genetic backgrounds. Each of the substitution lines was nearly isogenic to the recurrent parent: the average proportions of recurrent parent's genome were 93 % and 91 % in the IAS and AIS, respectively. Consistent reciprocal QTL effects for heading date and grain size were observed in both IAS and AIS. The reciprocal substitution set appeared to be an efficient and systematic method for QTL precision analysis.