Background: Paedocypris, a highly developmentally truncated fish from peat swamp forests in Southeast Asia, comprises the world's smallest vertebrate. Although clearly a cyprinid fish, a hypothesis about its phylogenetic position among the subfamilies of this largest teleost family, with over 2400 species, does not exist. Here we present a phylogenetic analyses of 227 cypriniform taxa, including 213 cyprinids, based upon complete mitochondrial DNA cytochrome b nucleotide sequences in order to determine the phylogenetic position of Paedocypris and to study the evolution of miniaturization among cyprinids.
Results: Our analyses reveal a strongly supported sister group relationship (clade C) between Paedocypris and Sundadanio, another developmentally truncated miniature cyprinid. Clade C was resolved as sister group of a larger clade characterized by small rasborine taxa (clade D). We found that miniaturised taxa are more numerous in the rasborine clade A, formed by clades C and D, than in any other cyprinid clade. The consensus cytb in cyprinids includes 380 amino acids and an incomplete T-- stop codon. We noted that a few cyprinids mostly rasborine taxa placed within clade A had either a TAA or TAG stop codon, 376, 378, or 381 amino acids, and up to 10 base pairs (bp) of noncoding region before the 5' end of the tRNA-Thr. Our relaxed molecular clock estimates revealed high divergence times for the Sundadanio and Paedocypris clades and provide a first temporal framework for the evolution of miniaturization among cyprinids.
Conclusion: Paedocypris belongs to a clade (Rasborinae clade A) that shows recurrent miniaturization, including both taxa characterized by developmental truncation and by proportioned dwarfism. Its closest relative is another miniaturized taxon, the genus Sundadanio. We conclude that the miniaturized cyprinids with remarkable morphological novelties, like Paedocypris and Danionella, are at the same time the most developmentally truncated taxa. The miniaturized cyprinids with no or few developmental truncations like Boraras, Microrasbora, and Horadandia show no such evolutionary novelties.