The systematics of the viviparid freshwater snail genus Margarya endemic to the ancient lakes of Yunnan, China, is revised based on comparative analyses of morphological features, including shell, operculum, radula, and genital anatomy, and molecular phylogenetic analyses of partial sequences of the mitochondrial 16S rDNA (16S) and cytochrome c oxidase subunit I (COI) genes, as well as the nuclear Internal Transcribed Spacer 2 (ITS2). The taxonomic utility of key anatomical and morphological features in this group is evaluated. The genus Margarya as delimited previously is split into three genera in order to retain monophyletic taxa: (1) Margaryas.s., consisting of four species, i.e. the type species Margarya melanioides plus Margaryafrancheti, Margaryaoxytropoides, and Margaryamonodi; (2) the previously introduced subgenus Tchangmargarya is elevated to an independent genus containing two species, Tchangmargarya yangtsunghaiensis and the new species Tchangmargarya multilabiata sp. nov.; and (3) a new genus, Anularya gen. nov., is described, also containing two species, i.e. Anularya mansuyi and Anularya bicostata. Molecular phylogenies based on analyses of three gene fragments have identical topologies, supporting the monophyly of these genera. The sister group of Margarya s.s. is Cipangopaludina, whereas the sister group of Anularya is Sinotaia; Tchangmargarya is sister to a clade containing all the aforementioned groups. Features of the operculum and the right male tentacle (penis) are particularly informative on the generic level, whereas shell and radular characters are especially useful to differentiate species. The phylogenetic relationships recovered here are consistent with orogenic patterns of the Yunnan Mountains. Changes in the river system and water area of ancient lakes caused by tectonic activities probably play an important role in speciation and shaping the current pattern of species distribution in Yunnan.
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