The sequence of the mitochondrial DNA (mtDNA) of the branchiopod crustacean
Daphnia pulex has been completed. It is 15 333 bp with an A + T content of
62.3%, and contains the typical complement of 13 protein-coding, 22 transf
er RNA (tRNA) and two ribosomal RNA (rRNA) genes. Comparison of this sequen
ce with the sequences of the other eight completely sequenced arthropod mtD
NAs showed that gene order and orientation are identical to that of Drosoph
ila but different from Artemia due to the rearrangement of two tRNA genes.
Nucleotide composition, codon usage, and amino acid composition are very si
milar in the crustaceans, but divergent from insects and chelicerates which
show a much higher bias towards AS-T. However, with few exceptions, the mi
tochondrial proteins of Daphnia are more similar to those of the dipteran i
nsects (Drosophila and Anopheles) than to those of Artemia, at both the nuc
leotide and amino acid levels, suggesting that Artemia mtDNA is evolving at
an accelerated rate. These results also show that sequence evolution and t
he evolution of nucleotide composition can be decoupled. Analysis of nucleo
tide substitution patterns in COII showed that there has been an unbiased a
cceleration of the overall substitution rate in Artemia. In contrast, the a
ccelerated substitution rate in Apis is due partly to extreme A+T mutation
pressure. Secondary structures are proposed for the Daphnia tRNAs and rRNAs
. The tRNAs are similar to those of other arthropods but tend to have T Psi
C arms that are only 4 bp long. The rRNA secondary structures are similar
to those proposed for insects except for the absence of a small number of h
elices in Daphnia. Phylogenetic analysis of second codon positions grouped
Daphnia with Artemia, as expected, despite the latter's accelerated diverge
nce rate. In contrast, the unusual pattern of mtDNA divergence in Apis led
to a topology in which the holometabolous insects (Anopheles, Drosophila, A
pis) appeared to be paraphyletic with respect to the hemimetabolous insect,
Locusta, due to the early branching of Apis. (C) 1999 Elsevier Science B.V
. All rights reserved.