Data from: Molecular phylogenetic reconstruction of the endemic Asian salamander family Hynobiidae (Amphibia, Caudata).

The salamander family Hynobiidae contains over 50 species and has been the
subject of a number of molecular phylo-genetic investigations aimed at
reconstructing branches across the entire family. In general, studies
using the greatest amount of sequence data have used reduced taxon
sampling, while the study with the greatest taxon sampling has used a
limited sequence data set. Here, we provide insights into the phylogenetic
history of the Hynobiidae using both dense taxon sampling and a large
mitochondrial DNA sequence data set. We report exclusive new mitochondrial
DNA data of 2566 aligned bases (with 151 excluded sites, of included sites
1157 are variable with 957 parsimony informative). This is sampled from
two genic regions encoding a 12S–16S region (the 3’ end of 12S rRNA,
tRNAVAl, and the 5’ end of 16S rRNA), and a ND2–COI region (ND2, tRNATrp,
tRNAAla, tRNAAsn, the origin for light strand replication—OL, tRNACys,
tRNATyr, and the 5’ end of COI). Analyses using parsimony, Bayesian, and
maximum likelihood optimality criteria produce similar phylogenetic trees,
with discordant branches generally receiving low levels of branch support.
Monophyly of the Hynobiidae is strongly supported across all analyses, as
is the sister relationship and deep divergence between the genus
Onychodactylus with all remaining hynobiids. Within this latter grouping
our phylogenetic results identify six clades that are relatively divergent
from one another, but for which there is minimal support for their
phy-logenetic placement. This includes the genus Batrachuperus, the genus
Hynobius, the genus Pachyhynobius, the genus Salamandrella, a clade
containing the genera Ranodon and Paradactylodon, and a clade containing
the genera Liua and Pseudohynobius. This latter clade receives low
bootstrap support in the parsimony analysis, but is consistent across all
three analytical methods. Our results also clarify a number of
well-supported relationships within the larger Batrachu-perus and Hynobius
clades. While the relationships identified in this study do much to
clarify the phylogenetic history of the Hynobiidae, the poor resolution
among major hynobiid clades, and the contrast of mtDNA-derived
relationships with recent phylogenetic results from a small number of
nuclear genes, highlights the need for continued phylogenetic study with
larger numbers of nuclear loci.