ML and BI trees inferred from the multiple nuclear gene sequences generated identical tree topologies.
Unique taxonomic status for the PNT was confirmed through comparison of multiple nuclear gene sequences, and also supported by evidence from chemotypic diversity.
On the basis of the multiple nuclear gene sequences, Eizirik et al. (2010) proposed a complete molecular phylogeny for 50 different genera representing all carnivoran families and constructed a molecular timescale for the evolution of Carnivora.
In this study, we analyzed multiple nuclear gene sequences of eight species and subspecies of Pseudorasbora, Pseudopungtungia, and Pungtungia residing in China, Japan, and Korea to elucidate their molecular phylogenetic relationships.
Still, the monophyly of Brachiozoa (=Phoronozoa) including brachiopods and phoronids was later independently corroborated by analyses based on rDNA [ 7, 8, 12, 13, 38- 41] and sodium-potassium ATPase α-subunit sequences [ 15], multiple nuclear protein-encoding sequences [ 26, 42], total evidence analyses [ 9, 39, 43] and phylogenomic approaches [ 30, 35].
These analyses rely on a spectrum of molecular data ranging from rDNA sequences [ 6- 16], mitochondrial protein sequences [ 17- 19], single nuclear protein-encoding genes [ 20, 21], Hox genes [ 22, 23], multiple nuclear protein-encoding sequences [ 24, 25] and phylogenomic approaches [ 26- 34].
Whereas some rDNA analyses indicate that brachiopods are paraphyletic and phoronids are the sister group of inarticulate brachiopods [ 38, 40, 41, 44], brachiopods come out as monophyletic in analyses of morphological data [ 2, 4, 9, 39, 43, 45- 47], of multiple nuclear protein-encoding sequences [ 42], and of phylogenomic datasets [ 30, 35].
Further, the entire mitochondrial genome was represented by multiple copies of paralogous nuclear sequences.
Our results, based on multiple nuclear DNA-coded protein sequences from 64 arthropod taxa, including all hexapod orders, six crustacean species (representing three classes), one myriapod, and two chelicerates with both ML and Bayesian inference analyses, support the monophyletic origin of hexapods.
We successfully sequenced multiple nuclear genes, each with multiple copies and multiple alleles, and also sequenced three single-copy chloroplast regions, all in 64 individuals representing 11 species.
