Evolution of duplicate control regions in the mitochondrial genomes of metazoa: A case study with Australasian Ixodes ticks

To investigate the evolution pattern and phylogenetic utility of duplicate control regions (CRs) in mitochondrial (mt) genomes, we sequenced the entire mt genomes of three Ixodes species and part of the mt genomes of another I I species. All the species from the Australasian lineage have duplicate CRs, whereas the other species have one CR. Sequence analyses indicate that the two CRs of the Australasian Ixodes ticks have evolved in concert in each species. In addition to the Australasian Ixodes ticks, species from seven other lineages of metazoa also have mt genomes with duplicate CRs. Accumulated mtDNA sequence data from these metazoans and two recent experiments on replication of mt genomes in human cell lines with duplicate CRs allowed us to re-examine four intriguing questions about the presence of duplicate CRs in the mt genomes of metazoa: (1) Why do some mt genomes, but not others, have duplicate CRs? (2) How did mt genomes with duplicate CRs evolve? (3) How could the nucleotide sequences of duplicate CRs remain identical or very similar over evolutionary time? (4) Are duplicate CRs phylogenetic markers? It appears that mt genomes with duplicate CRs have a selective advantage in replication over mt genomes with one CR. Tandem duplication followed by deletion of genes is the most plausible mechanism for the generation of mt genomes with duplicate CRs. Once duplicate CRs occur in an mt genome, they tend to evolve in concert, probably by gene conversion. However, there are lineages where gene conversion may not always occur, and, thus, the two CRs may evolve independently in these lineages. Duplicate CRs have much potential as phylogenetic markers at low taxonomic levels, such as within genera, within families, or among families, but not at high taxonomic levels, such as among orders.

Intragenomic variation in ITS2 rDNA in the louse of humans, Pediculus humanus: ITS2 is not a suitable marker for population studies in this species

The two internal transcribed spacers (ITS) of ribosomal DNA are often used as markers of populations of insects. We studied the ITS2 of the head lice and body lice of humans, to determine whether this gene is a suitable marker of populations of these insects. ITS2 sequences were amplified by PCR from lice from four different countries: Australia, China, Japan and the USA. Direct cycle-sequencing of some of these PCR products gave equivocal nucleotide chromatograms. This indicated that some lice had more than one ITS2 sequence, so we cloned PCR products from these lice. Temperature gradient gel electrophoresis (TGGE) revealed that 50 of the 67 clones we screened had different nucleotide sequences. All lice had several ITS2 types, including those with unequivocal chromatograms. A phylogenetic tree of 15 different ITS2 sequences showed that the sequences from individual lice were not monophyletic. We conclude that the ITS2 is not a useful marker of populations for Pediculus humanus.

Recurrent gains and losses of large (84-109 bp) repeats in the rDNA internal transcribed spacer 2 (ITS2) of rhipicephaline ticks

We studied the internal transcribed spacer 2 (ITS2) in twenty-two spp. of ticks from the subfamily Rhipicephalinae. A 104-109 base pair (bp) region was Imperfectly repeated In most ticks studied. Mapping the number of repeat copies on to a phylogeny from the ITS2 showed that there have been many Independent gains and losses of repeats. Comparison of the sequences of the repeat copies Indicated that in most taxa concerted evolution had played little if any role in the evolution of these regions, as the copies clustered by sequence position rather than species, In our putative secondary structure, each repeat copy can fold into a distinct and almost identical stem-loop complex; a gain or loss of a repeat copy apparently does not impair the function of the ITS2 in these ticks.

The highly rearranged mitochondrial genome of the plague thrips, Thrips imaginis (Insecta : thysanoptera): Convergence of two novel gene boundaries and an extraordinary arrangement of rRNA genes

To help understand the mechanisms of gene rearrangement in the mitochondrial (mt) genomes of hemipteroid insects, we sequenced the mt genome of the plague thrips, Thrips imaginis (Thysanoptera). This genome is circular, 15,407 by long, and has many unusual features, including (1) rRNA genes inverted and distant from one another, (2) an extra gene for tRNA-Ser, (3) a tRNA-Val lacking a D-arm, (4) two pseudo-tRNA genes, (5) duplicate control regions, and (6) translocations and/or inversions of 24 of the 37 genes. The mechanism of rRNA gene transcription in T. imaginis may be different from that of other arthropods since the two rRNA genes have inverted and are distant from one another. Further, the rRNA genes are not adjacent or even close to either of the two control regions. Tandem duplication and deletion is a plausible model for the evolution of duplicate control regions and for the gene translocations, but intramitochondrial recombination may account for the gene inversions in T. imaginis. All the 18 genes between control regions #1 and #2 have translocated and/or inverted, whereas only six of the 20 genes outside this region have translocated and/or inverted. Moreover, the extra tRNA gene and the two pseudo-tRNA genes are either in this region or immediately adjacent to one of the control regions. These observations suggest that tandem duplication and deletion may be facilitated by the duplicate control regions and may have occurred a number of times in the lineage leading to T. imaginis. T. imaginis shares two novel gene boundaries with a lepidopsocid species from another order of hemipteroid insects, the Psocoptera. The evidence available suggests that these shared gene boundaries evolved by convergence and thus are not informative for the interordinal phylogeny of hemipteroid insects. We discuss the potential of hemipteroid insects as a model system for studies of the evolution of animal rut genomes and outline some fundamental questions that may be addressed with this system.

The use and implications of ribosomal DNA sequencing for the discrimination of digenean species

In just over a decade, the use of molecular approaches for the recognition of parasites has become commonplace. For trematodes, the internal transcribed spacer region of ribosomal DNA (ITS rDNA) has become the default region of choice. Here, we review the findings of 63 studies that report ITS rDNA sequence data for about 155 digenean species from 19 families, and then review the levels of variation that have been reported and how the variation has been interpreted. Overall, complete ITS sequences (or ITS1 or ITS2 regions alone) usually distinguish trematode species clearly, including combinations for which morphology gives ambiguous results. Closely related species may have few base differences and in at least one convincing case the ITS2 sequences of two good species are identical. In some cases, the ITS1 region gives greater resolution than the ITS2 because of the presence of variable repeat units that are generally lacking in the ITS2. Intraspecific variation is usually low and frequently apparently absent. Information on geographical variation of digeneans is limited but at least some of the reported variation probably reflects the presence of multiple species. Despite the accepted dogma that concerted evolution makes the individual representative of the entire species, a significant number of studies have reported at least some intraspecific variation. The significance of such variation is difficult to assess a posteriori, but it seems likely that identification and sequencing errors account for some of it and failure to recognise separate species may also be significant. Some reported variation clearly requires further analysis. The use of a yardstick to determine when separate species should be recognised is flawed. Instead, we argue that consistent genetic differences that are associated with consistent morphological or biological traits should be considered the marker for separate species. We propose a generalised approach to the use of rDNA to distinguish trematode species.

Molecular mechanisms for the variation of mitochondrial gene content and gene arrangement among chigger mites of the genus Leptotrombidium (Acari : Acariformes)

The gene content of a mitochondrial (mt) genome, i.e., 37 genes and a large noncoding region (LNR), is usually conserved in Metazoa. The arrangement of these genes and the LNR is generally conserved at low taxonomic levels but varies substantially at high levels. We report here a variation in mt gene content and gene arrangement among chigger mites of the genus Leptotrombidium. We found previously that the mt genome of Leptotrombidium pallidum has an extra gene for large-subunit rRNA (rrnL), a pseudo-gene for small-subunit rRNA (PrrnS), and three extra LNRs, additional to the 37 genes and an LNR typical of Metazoa. Further, the arrangement of mt genes of L. pallidum differs drastically from that of the hypothetical ancestor of the arthropods. To find to what extent the novel gene content and gene arrangement occurred in Leptotrombidium, we sequenced the entire or partial mt genomes of three other species, L. akamushi, L. deliense, and L. fletcheri. These three species share the arrangement of all genes with L. pallidum, except trnQ (for tRNA-glutamine). Unlike L. pallidum, however, these three species do not have extra rrnL or PrrnS and have only one extra LNR. By comparison between Leptotrombidium species and the ancestor of the arthropods, we propose that (1) the type of mt genome present in L. pallidum evolved from the type present in the other three Leptotrombidium species, and (2) three molecular mechanisms were involved in the evolution of mt gene content and gene arrangement in Leptotrombidium species.

Geochronology of weathering and landscape evolution, Dugald River valley, NW Queensland, Australia

40Ar/39Ar laser incremental heating analyses of individual grains of supergene jarosite, alunite, and cryptomelane from weathering profiles in the Dugald River area, Queensland, Australia, show a strong positive correlation between a sample’s age and its elevation. We analyzed 125 grains extracted from 35 hand specimens collected from weathering profiles at 11 sites located at 3 distinct elevations. The highest elevation profile hosts the oldest supergene minerals, whereas progressively younger samples occur at lower positions in the landscape. The highest elevation sampling sites (three sites), located on top of an elongated mesa (255 to 275 m elevation), yield ages in the 16 to 12 Ma range. Samples from an intermediate elevation site (225 to 230 m elevation) yield ages in the 6 to 4 Ma range. Samples collected at the lowest elevation sites (200 to 220 m elevation) yield ages in the 2.2 to 0.8 Ma interval. Grains of supergene alunite, jarosite, and cryptomelane analyzed from individual single hand specimens yield reproducible results, confirming the suitability of these minerals to 40Ar/39Ar geochronology. Multiple samples collected from the same site also yield reproducible results, indicating that the ages measured are true precipitation ages for the samples analyzed. Different sites, up to 3 km apart, sampled from weathering profiles at the same elevation again yield reproducible results. The consistency of results confirms that 40Ar/39Ar geochronology of supergene jarosite, alunite, and cryptomelane yields ages of formation of weathering profiles, providing a reliable numerical basis for differentiating and correlating these profiles. The age versus elevation relationship obtained suggest that the stepped landscapes in the Dugald River area record a progressive downward migration of a relatively flat weathering front. The steps in the landscape result from differential erosion of previously weathered bedrock displaying different susceptibility to weathering and contrasting resistance to erosion. Combined, the age versus elevation relationships measured yield a weathering rate of 3.8 m. Myr−1 (for the past 15 Ma) if a descending subhorizontal weathering front is assumed. The results also permit the calculation of the erosion rate of the more easily weathered and eroded lithologies, assuming an initially flat landscape as proposed in models of episodic landscape development. The average erosion rate for the past 15 Ma is 3.3 m. Myr−1, consistent with erosion rates obtained by cosmogenic isotope studies in the region.

Thermal effects in the evolution of initially layered mantle material

A simplified model for anisotropic mantle convection based on a novel class of rheologies, originally developed for folding instabilities in multilayered rock (MUHLHAUS et al., 2002), is extended ¨ through the introduction of a thermal anisotropy dependent on the local layering. To examine the effect of the thermal anisotropy on the evolution of mantle material, a parallel implementation of this model was undertaken using the Escript modelling toolkit and the Finley finite-element computational kernel (DAVIES et al., 2004). For the cases studied, there appears too little if any effect. For comparative purposes, the effects of anisotropic shear viscosity and the introduced thermal anisotropy are also presented. These results contribute to the characterization of viscous anisotropic mantle convection subject to variation in thermal conductivities and shear viscosities.

Evolution of Wolbachia pipientis transmission dynamics in insects

Wolbachia pipientis is an intracellular bacterial parasite of arthropods that enhances its transmission by manipulating host reproduction, most commonly by inducing cytoplasmic incompatibility. The discovery of isolates with modified cytoplasmic incompatibility phenotypes and others with novel virulence properties is an indication of the potential breadth of evolutionary strategies employed by Wolbachia.