General properties and phylogenetic utilities of nuclear ribosomal DNA and mitochondrial DNA commonly used in molecular systematics

Abstract

To choose one or more appropriate molecular markers or gene regions for resolving a particular systematic question among the organisms at a certain categorical level is still a very difficult process. The primary goal of this review, therefore, is to provide a theoretical information in choosing one or more molecular markers or gene regions by illustrating general properties and phylogenetic utilities of nuclear ribosomal DNA (rDNA) and mitochondrial DNA (mtDNA) that have been most commonly used for phylogenetic researches. The highly conserved molecular markers and/or gene regions are useful for investigating phylogenetic relationships at higher categorical levels (deep branches of evolutionary history). On the other hand, the hypervariable molecular markers and/or gene regions are useful for elucidating phylogenetic relationships at lower categorical levels (recently diverged branches). In summary, different selective forces have led to the evolution of various molecular markers or gene regions with varying degrees of sequence conservation. Thus, appropriate molecular markers or gene regions should be chosen with even greater caution to deduce true phylogenetic relationships over a broad taxonomic spectrum.

Fig. 1

Schematic diagram of a tandem repeat unit of rDNA.

Fig. 2

Structural organization of the IGS region of a branchiopod crustacean, Charybdis japonica rDNA. The 1,195 bp non-repetitive region 1 and the 813 bp non-repetitive region 2 are marked with numbers in parentheses at the top. The 3,332 bp repetitive region is composed of 4 subrepeats. The tandem array of 960 bp repeat units is represented by various arrow heads. The array of 9 open diamonds represent the 142 bp repeat units. The array of the 3,390 bp repeat unit is represented by open oval. The asterisks indicate the truncated repeat unit. (Courtesy of Ryu et al., 1999)

Fig. 3

Position and orientation of conserved primers on a typical insect mtDNA map. (Courtesy of Roehrdanz and Degrugillier, 1998)

Fig. 4

Phylogenetic tree showing the three domains based on nuclear SSU rRNA sequences. (Courtesy of Woose et al., 1990)

Fig. 5

A. Anterior, ventral surface of Argulus nobilis (top) and anterior portion of Porcephalus crotali (bottom). B. Maximum parsimonious tree (top) showing that the Pentastomida phylogenetic position is within the Crustacea (total tree length=370, CI=0.681, on the basis of 164 informative sites). An annelid was used as an outgroup. The numbers on each branch indicate branch lengths (steps). Relationships (bottom) reconstructed by the method of invariants/operator metrics. Branch lengths are number of transversions/1,000 nucleotides and are to scale. (Courtesy of Abele et al., 1989)

Fig. 6

Phylogenetic position of the phylum Onychophora. Annelids were used as outgroups. (modified after Ballard et al., 1992)

Fig. 7

Mitochondrial DNA gene rearrangements (COI/L(UUR)/COII) supporting sister relationship between crustaceans and insects. (modified after Boore et al., 1998)

Fig. 8

A. Putative nuclear SSU rRNA secondary structure of Hypogastrura dolsana, order Collembola. The two arrows indicate the helices E23-2 to E23-5 in the V4 region and the helix 43 in the V7 region, respectively. These two regions have the highest sequence variability in insect nuclear SSU rDNA. The helix E23-2 and the basal part of the helix 43 were used as anchored pairings for predicting partial secondary structures of all the insect SSU rDNAs accessible from the EMBL data base. The bold lines mark the two regions of anchored pairings. The entire regions of the V4 and V7 are shown in boxes. B. Secondary structure evolution of the helices E23-2 to E23-5 (the V4 region) and the helix 43 (the V7 region) of nuclear SSU rRNA. The paleontological record of major insect subclades according to Kukalova-Peck (1991) is superimposed onto the canonical view of insect phylogeny (Kristensen, 1991). Numbers above branches refer to conspicuous derived character states: (1) ectognathous mouth part, (2) double articulation of mandible, (3) possession of wings, (4) complete metamorphosis, (5) modification of hind wings to halteres, acquisition of a labellum. (Courtesy of Hwang et al., 2000)

Fig. 9

A. Autoradiogram of dot blots made with radiolabeled Anopheles aquasalis-specific oligonucleotide probe and chromosomal DNAs isolated from 9 Anopheles species including A. aquasalis. B. Striped and reprobed with ribosomal DNA of A. smaragdinus to show the presence of equal amounts of chromosomal DNA in each dot. (Courtesy of Perera et al., 1998)