Data S1 Phylogenetic trees for the pooled sample of Murina gracilis and M. recondita
Previous phylogenetic reconstructions of mtDNA sequences from 12 Murina species
suggested a putative sister relationship between M. gracilis and M. recondita, although these
analyses included only a few individuals of these two taxa (Kuo 2004). To confirm this
relationship with larger sample sizes, here we applied maximum parsimony (MP) and Bayesian
phylogenetic analyses to the newly generated concatenated sequences of Cyt-b and COI for both
M. gracilis and M. recondita. To root our trees, we also included a sample of a continental
species, M. eleryi, which was obtained from Hungarian Natural History Museum (HNHM) and
represents a specimen (ID: 2007.28.2) collected from Vietnam (Bac Kan Province: Kim Hy
Nature Reserve: 22°14.849’N, 105°58.376’E); sequences of Cyt-b and COI for this single sample
were obtained following the protocols described in the text.
MP analysis was performed with the program TNT 1.1 (Goloboff et al. 2008) where all nucleotide
substitutions were weighted equally, and heuristic searches for the most parsimonious tree were
performed based on ten replicates of random addition of sequences, each followed by a tree
bisection recombination (TBR) tree search. Clade support was assessed by bootstrapping (1000
replicates); for each bootstrap replicate, tree searching was performed with one random sequence
addition followed by TBR. Bayesian analysis was implemented in MrBayes 3.1.2 (Ronquist &
Huelsenbeck 2003). Following Shapiro et al. (2006), we partitioned the concatenated sequence,
into the first plus second codon positions, together termed CP12, and the third codon position,
termed CP3. The nucleotide substitution process was specified as HKY+I+G for CP12, and
GTR+G for CP3, both of which were selected a priori by applying the
maximum-likelihood-based algorithm coupled with the Akaike Information Criterion (AIC)
implemented in jModelTest 0.1.1 (Posada 2008). For Bayesian simulations, two independent
runs of Metropolis-coupling Markov chain Monte Carlo (MC3) were performed, each with seven
heated chains (temperature parameter = 0.1) and with a burn-in of 0.2 million iterations followed
by a sampling phase of 0.8 million iterations (100 iterations per sample).
The resulting phylogenetic trees indicated a reciprocal monophyletic relationship between M.
gracilis and M. recondita, with the clades comprising M. gracilis and M. recondita supported
by MP bootstrap values of 94 and 100, respectively, and posterior probabilities of 0.91 and
1.00, respectively. Based on this finding, we separated these taxa in subsequent analyses of
haplotype phylogenetic relationships (see main manuscript). For these we used network rather
than tree-based reconstructions, because of the advantages offered by the former approach for
analysing intra-specific relationships when ancestral haplotypes are still present in the
populations (Posada & Crandall 2001).
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