Polymerase chain reaction amplifications for the rl6S, COI, and COIII
were carried out using QIAGEN protocol.
Character conflict between partitions as measured by Mickevich and Farris's (1981) Incongruence Length Difference was low, in particular for the COIII
and 16S datasets.
Table III.- Results of site model on COIII
, ND3, ND4 and ND5 genes.
The sequences of Octopus mimus included in this study were 4 for COI, 6 for COIII
, and 2 for r16S, and these were taken from Soller et al.
As with the common features of other bony fishes (Miya et al., 2003; Cheng et al., 2012), three reading-frames overlap were noted on the same strand: ATPase8 and ATPase6 overlapped by 4 nucleotides, ATPase6 and COIII
overlapped by 1 nucleotide, and ND4L and ND4 overlapped by 7 nucleotides (Supplementary Table I).
This fragment (ND3/COIII region) consists of a large portion of the NADH subunit 3 gene, the complete COIII
gene (Sweijd 1999) and five transfer RNA genes (Maynard et al.
There appeared to be some crude relationship between the length of a gene and its chance of leading to a tree identical to the whole-genome tree; indeed, only one gene less than 1111 bp (COIII
, 785 bp) gave a tree identical to the whole-genome tree (Table I).
After preliminary DNA sequence analyses of insert fragment ends, a 1.5-kb insert that contained the COIII
gene was chosen for complete DNA sequence analysis.
Partial sequences of mtDNA genes, such as cytochrome oxidase I (COI), cytochrome oxidase III (COIII
), and 16S rRNA, have proved to be important tools in intraspecific and interspecific phylogenetic studies of Cephalopoda and other mollusks (Akasaki et al., 2006; He et al., 2016; Mao et al., 2016; Wang et al., 2016).
Two restriction fragment-length polymorphisms (RFLP) in the COI and COIII
mitochondrial genes (mtDNA) have previously shown high frequencies (composite haplotype BB) in the DEBY line relative to native Chesapeake Bay oysters (Reeb & Avise 1990, Hare et al.
A total of 656 base pairs of mtDNA was sequenced for each individual beetle, including a 190 bp portion of the COIII
gene corresponding to bp 5021 and 5210 of the D.