Relative Rates of Nucleotide Substitution in Frogs

Accurate estimation of relative mutation rates of mitochondrial DNA (mtDNA) and single-copy nuclear DNA (scnDNA) within lineages contributes to a general understanding of molecular evolutionary processes and facilitates making demographic inferences from population genetic data. The rate of divergence at synonymous sites (K_s) may be used as a surrogate for mutation rate. Such data are available for few organisms and no amphibians. Relative to mammals and birds, amphibian mtDNA is thought to evolve slowly, and the K_s ratio of mtDNA to scnDNA would be expected to be low as well. Relative K_s was estimated from a mitochondrial gene, ND2, and a nuclear gene, c-myc, using both approximate and likelihood methods. Three lineages of congeneric frogs were studied and this ratio was found to be approximately 16, the highest of previously reported ratios. No evidence of a low K_s in the nuclear gene was found: c-myc codon usage was not biased, the K_s was double the intron divergence rate, and the absolute K_s was similar to estimates obtained here for other genes from other frog species. A high K_s in mitochondrial vs. nuclear genes was unexpected in light of previous reports of a slow rate of mtDNA evolution in amphibians. These results highlight the need for further investigation of the effects of life history on mutation rates. Current address (Andrew J. Crawford): Smithsonian Tropical Research Institute, Apartado 2072, Balboa, Ancon, Republic of Panama     

Selective Pressures on <Emphasis Type="Italic">Drosophila</Emphasis> Chemosensory Receptor Genes

The evolution and patterns of selection of genes encoding 10 Drosophila odorant receptors (Or) and the sex pheromone receptor Gr68a were investigated by comparing orthologous sequences across five to eight ecologically diverse species of Drosophila. Using maximum likelihood estimates of dN/dS ratios we show that all 11 genes sampled are under purifying selection, indicating functional constraint. Four of these genes (Or33c, Or42a, Or85e, and Gr68a) may be under positive selection, and if so, there is good evidence that 12 specific amino acid sites may be under positive selection. All of these sites are predicted to be located either in loop regions or just inside membrane spanning regions, and interestingly one of the two sites in Gr68a is in a similar position to a previously described polymorphism in Gr5a that causes a shift in sensitivity to its ligand trehalose. For three Ors, possible evidence for positive selection was detected along a lineage. These include Or22a in the lineage leading to D. mauritiana and Or22b in the lineage leading to D. simulans. This is of interest in light of previous data showing a change in ligand response profile for these species in the sensory neuron (ab3A) which expresses both Or22a and Or22b in D. melanogaster. In summary, while the main chemosensory function and/or structural integrity of these 10 Or genes and Gr68a are evolutionarily preserved, positive selection appears to be acting on some of these genes, at specific sites and along certain lineages, and provides testable hypotheses for further functional experimentation. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. [Reviewing Editor: Dr. David Pollock]     

Drosophila mitochondrial DNA: Conserved sequences in the A+T-rich region and supporting evidence for a secondary structure model of the small ribosomal RNA

Summary The sequence of a segment of theDrosophila virilis mitochondrial DNA (mtDNA) molecule that contains the A+T-rich region, the small rRNA gene, the tRNA^f-met, tRNA^gln, and tRNA^ile genes, and portions of the ND2 and tRNA^val genes is presented and compared with the corresponding segment of theD. yakuba mtDNA molecule. The A+T-rich regions ofD. virilis andD. yakuba contain two correspondingly located sequences of 49 and 276/274 nucleotides that appear to have been conserved during evolution. In each species the replication origin of the mtDNA molecule is calculated to lie within a region that overlaps the larger conserved sequence, and within this overlap is found a potential hairpin structure. Substitutions between the larger conserved sequences of the A+T-rich regions, the small mt-rRNA genes, and the ND2 genes are biased in favor of transversions, 71–97% of which are AT changes. There is a 13.8 times higher frequency of nucleotide differences between the 5 halves than between the 3 halves of theD. virilis andD. yakuba small mt-rRNA genes. Considerations of the effects of observed substitutions and deletion/insertions on possible nucleotide pairing within the small mt-rRNA genes ofD. virilis andD. yakuba strongly support the secondary structure model for theDrosophila small mt-rRNA that we previously proposed.     

Variation in Coding (NADH Dehydrogenase Subunits 2, 3, and 6) and Noncoding Intergenic Spacer Regions of the Mitochondrial Genome in Octocorallia (Cnidaria: Anthozoa)

Low rates of evolution in cnidarian mitochondrial genes such as COI and 16S rDNA have hindered molecular systematic studies in this important invertebrate group. We sequenced fragments of 3 mitochondrial protein-coding genes (NADH dehydrogenase subunits ND2, ND3 and ND6) as well as the COI-COII intergenic spacer, the longest noncoding region found in the octocoral mitochondrial genome, to determine if any of these regions contain levels of variation sufficient for reconstruction of phylogenetic relationships among genera of the anthozoan subclass Octocorallia. Within and between the soft coral families Alcyoniidae and Xeniidae, sequence divergence in the genes ND2 (539 bp), ND3 (102 bp), and ND6 (444 bp) ranged from 0.5% to 12%, with the greatest pairwise distances between the 2 families. The COI-COII intergenic spacer varied in length from 106 to 122 bp, and pairwise sequence divergence values ranged from 0% to 20.4%. Phylogenetic trees constructed using each region separately were poorly resolved. Better phylogenetic resolution was obtained in a combined analysis using all 3 protein-coding regions (1085 bp total). Although relationships among some pairs of species and genera were well supported in the combined analysis, the base of the alcyoniid family tree remained an unresolved polytomy. We conclude that variation in the NADH subunit coding regions is adequate to resolve phylogenetic relationships among families and some genera of Octocorallia, but insufficient for most species - or population-level studies. Although the COI-COII intergenic spacer exhibits greater variability than the protein-coding regions and may contain useful species-specific markers, its short length limits its phylogenetic utility.     

Molecular Evolution of a Small Gene Family of Wound Inducible Kunitz Trypsin Inhibitors in Populus

Maximum likelihood models of codon substitutions were used to analyze the molecular evolution of a Kunitz trypsin inhibitor (KTI) gene family in Populus and Salix. The methods support previous assertions that the KTI genes comprise a rapidly evolving gene family. Models that allow for codon specific estimates of the ratio of nonsynonymous to synonymous substitutions (ω) among sites detect positive Darwinian selection at several sites in the KTI protein. In addition, branch-specific maximum likelihood models show that there is significant heterogeneity in ω among branches of the KTI phylogeny. In particular, ω is substantially higher following duplication than speciation. There is also evidence for significant rate heterogeneity following gene duplication, suggesting different evolutionary rates in newly arisen gene duplicates. The results indicate uneven evolutionary rates both between sites in the KTI protein and among different lineages in the KTI phylogeny, which is incompatible with a neutral model of sequence evolution. [Reviewing Editor: Dr. Willie J. Swanson]     

Comparative Genomics of Mitochondrial DNA in Drosophila simulans

The current study compares the nucleotide variation among 22 complete mitochondrial genomes of the three distinct Drosophila simulans haplotypes with intron 1 of the alcohol dehydrogenase-related locus. This is the first study to investigate the sequence variation of multiple complete mitochondrial genomes within distinct mitochondrial haplotypes of a single species. Patterns of variation suggest distinct forces are influencing the evolution of mitochondrial DNA (mtDNA) and autosomal DNA in D. simulans. First, there is little variation within each mtDNA haplotype but strong differentiation among them. In contrast, there is no support for differentiation of the mitochondrial haplotypes at the autosomal locus. Second, there is a significant deficiency of mitochondrial variation in each haplotype relative to the autosomal locus. Third, the ratio of nonsynonymous to synonymous substitutions is not equal in all branches of the well-resolved phylogeny. There is an excess of nonsynonymous substitutions relative to synonymous substitutions within each D. simulans haplotype. This result is similar to that previously observed within the mtDNA of distinct species. A single evolutionary force may be causally linked to the observed patterns of mtDNA variation—a rickettsia-like microorganism, Wolbachia pipientis, which is known to directly influence mitochondrial evolution but have a less direct influence on autosomal loci. Received: 16 September 1999 / Accepted: 14 March 2000     

Differences in Mitochondrial Genome Organization of Cryptococcus Neoformans Strains

The organization of the mitochondrial genomes in two strains belonging in different varieties of Cryptococcus neoformans was analysed. Physical maps of the mtDNA of the IFM5844 (var. neoformans) and IFO410 (var. grubii) strains were constructed by using EcoRI and EcoRV restriction enzymes; functional maps were constructed by hybridization, cloning and sequencing. Most of the genes important in the mitochondrial function (ND1, ND2, ND3, ND4, ND4L, ND5, ND6, ATP6, ATP9, COX1, COX2 and COB) and protein synthesis (SsrRNA and LsrRNA) were localized. We did not find any differences between the strains in the order of these genes. However, they differed significantly in the sizes of the mtDNAs: 32.6 kb for IFM5844, and 24.1 kb for IFO410. This can be attributed to two large regions of the mtDNA. In these regions, differences were found in the numbers of introns in COX1 (no intron in var. grubii, 5 introns in var. neoformans), COB (1 intron in var. grubii, 2 introns in var. neoformans), LsrRNA (no intron in var. grubii, 2 introns in var. neoformans), and ND5 (no intron in var. grubii, 1 intron in var. neoformans) genes. In several introns of the COB and COX1 genes LAGLIDADG motifs were found. Differences were also observed in the nucleotide sequences of some genes and in the sizes and sequences of intergenic regions. The nucleotide sequences of the genes of the IFM and IFO strains were compared with those of the H-99 and JEC 21 strains from the database. Surprisingly high similarities were found between the strains belonging in var. grubii (IFO 410 and H-99) and var. neoformans (IFM 5844 and JEC 21).     

Species-diagnostic markers in <Emphasis Type="Italic">Larix</Emphasis> spp. based on RAPDs and nuclear,cpDNA, and mtDNA gene sequences,and their phylogenetic implications

Genetic markers from the nuclear, chloroplast, and mitochondrial genomes were developed to distinguish unambiguously among four larch species [Larix laricina (Du Roi) K. Koch, Larix decidua (Mill.), Larix kaempferi (Lamb.) Sarg., and Larix sibirica (Ledeb.)] used in intensive forestry in eastern North America. Nine random amplified polymorphic DNA (RAPD) fragments had good diagnostic value, and 3 out of 12 nuclear genes were found to harbor fixed interspecific polymorphisms implicating a total of 17 single nucleotide polymorphisms (SNPs) and 2 indels. The sequencing of five mtDNA introns (cox1-intron1, matR-intron1, nad1-intron b/c, nad3-intron1, and nad5-intron1) and four cpDNA regions (matK, trnL-intron, trnT–trnL and trnL–trnF intergenic spacers) resulted in the identification of 14 sites with fixed interspecific differences among the four species. Including the ten Larix species, one polymorphic site per 47 nucleotide sites sampled was observed for nuclear genes, one per 283 sites for cpDNA, and one per 374 sites for mtDNA. The phylogeny of the genus could be estimated from variation among the ten species detected in two cpDNA intergenic regions and four mtDNA introns. There was congruence between cpDNA and mtDNA phylogenies with three large groups delineated: the North American, North Eurasian, and South Asian taxa. The position of L. sibirica differed between organelle genomes. It was regrouped with South Asian species on the cpDNA tree, but with its North Eurasian congenerics on the mtDNA tree. To simplify the detection of diagnostic DNA sequence polymorphisms among the four main Larix species, cleaved amplified polymorphic sequence (CAPS) assays were developed from the polymorphisms identified in the various genomes. Seventeen primer–enzyme combinations were tested, and six were selected for their high level of informativeness. These new species-specific diagnostic markers should be useful for the certification of larch breeding materials and hybrid stocks used in intensive forestry in the northern hemisphere.     

Protein–protein interactions of the cytochrome c oxidase DNA barcoding region

Enzymatic amplification of homologous regions of DNA using ‘universal’ polymerase chain reaction primers has provided insight into insect systematics, phylogeography, molecular evolution and species identification. One of the more commonly amplified and sequenced regions is a short region of the cytochrome c oxidase subunit I gene (COI), commonly called the barcoding region. COI is one of three mitochondrial‐encoded subunits of complex IV (Cox) of the electron transport chain. In addition to the mitochondrial subunits there are nine nuclear‐encoded subunits of the complex in Drosophila. Whereas a number of phylogenetic biases associated with this region have been examined and the quaternary structure of Cox has been modelled, the influence of protein–protein interactions on the observed patterns of evolution in this barcoding region of insects has never been examined critically. Using a well‐resolved independently derived phylogeny of 38 Diptera species, we examined the homogeneity of the substitution processes within the barcoding region. We show that, within Diptera, amino acid residues interacting with nuclear‐encoded subunits of Cox are evolving at elevated rates across the phylogeny. Furthermore, we show that codon position two is biased by protein–protein interactions. In contrast, third codon positions provide a less biased estimate of genetic variation in the region. This study highlights the need to examine the potential for systematic bias in DNA barcoding regions as part of the critical assessment of evidence in systematics and in biodiversity assessments.     

The Dictyostelium discoideum mitochondrial genome: A primordial system using the universal code and encoding hydrophilic proteins atypical of metazoan mitochondrial DNA

A 3,345-bp fragment of Dictyostelium discoideum mitochondrial DNA (mtDNA) has been sequenced. This fragment contained the 80-kDa subunit of complex I (NADH:ubiquinone oxidoreductase), encoding a predicted amino acid sequence of 688 residues and a molecular mass of 79,805 daltons which is nuclear encoded in other metazoa. The C-terminus of the D. discoideum complex I gene shared a 10-bp overlap with NADH:ubiquinone oxidoreductase chain 5 (ND5), while 21 by 5 were three tRNA genes (two isoleucine and a histidine) and a further 25 by 5 of these genes is the partial sequence (104 residues) of an unidentified open reading frame (ORF104). Both the 80-kDa subunit and the ORF104 were hydrophilic and highly charged, suggesting they are not membrane associated, unlike most mitochondrially encoded proteins in the metazoa. Sequence analysis of the 80-kDa subunit, its adjacent ND5 gene, and ORF104 indicates the universal stop codon TGA, which codes for tryptophan in nearly all nonplant mtDNA, is either unassigned or coding for a stop codon in D. discoideum. The large size of the mitochondrial genome (54 kb), the lack of intergenic sequence, and the apparent use of the universal code suggest D. discoideum mtDNA may encode many primitive genes that are nuclear encoded in higher organisms.Correspondence to: K.L. WilliamsData deposition: GeneBank     

Evolution of the noncoding regions inDrosophila mitochondrial DNA: Two intergenic regions

The sequences of the mitochondrial DNA (mtDNA) segment containing the two intergenic regions were determined for six species belonging to theDrosophila immigrans species group and compared to the corresponding segments ofDrosophila species which had been studied previously. We found remarkable differences in the evolutionary rates of the two intergenic regions. The Intergenic I region, which lies between thetRNA ^gln and thetRNA ^ile genes, was found to be highly conserved in terms of both size (30 ntp) and nucleotide sequence among the species studied. In contrast, the sequences of the Intergenic II region, which lies between thetRNA ^f-met and thetRNA ^ile genes, showed considerable variation. The size of the Intergenic II region ranged from 0 to 88 ntp, and accurate alignment was possible only among sequences from geographical strains or very closely related species in thenasuta species subgroup. The observed differences in conservation of the two mtDNA intergenic regions are discussed in light of functional constraints on mtDNA sequences.     

On the rate of DNA sequence evolution inDrosophila

Summary Analysis of the rate of nucleotide substitution at silent sites inDrosophila genes reveals three main points. First, the silent rate varies (by a factor of two) among nuclear genes; it is inversely related to the degree of codon usage bias, and so selection among synonymous codons appears to constrain the rate of silent substitution in some genes. Second, mitochondrial genes may have evolved only as fast as nuclear genes with weak codon usage bias (and two times faster than nuclear genes with high codon usage bias); this is quite different from the situation in mammals where mitochondrial genes evolve approximately 5–10 times faster than nuclear genes. Third, the absolute rate of substitution at silent sites in nuclear genes inDrosophila is about three times hihger than the average silent rate in mammals.     

Analysis of complete mitochondrial DNA sequences of three members of the Montastraea annularis coral species complex (Cnidaria, Anthozoa, Scleractinia)

Complete mitochondrial nucleotide sequences of two individuals each of Montastraea annularis, Montastraea faveolata, and Montastraea franksi were determined. Gene composition and order differed substantially from the sea anemone Metridium senile, but were identical to that of the phylogenetically distant coral genus Acropora. However, characteristics of the non-coding regions differed between the two scleractinian genera. Among members of the M. annularis complex, only 25 of 16,134 base pair positions were variable. Sixteen of these occurred in one colony of M. franksi, which (together with additional data) indicates the existence of multiple divergent mitochondrial lineages in this species. Overall, rates of evolution for these mitochondrial genomes were extremely slow (0.03–0.04% per million years based on the fossil record of the M. annularis complex). At higher taxonomic levels, patterns of genetic divergence and synonymous/nonsynonymous substitutions suggest non-neutral and unequal rates of evolution between the two lineages to which Montastraea and Acropora belong.     

The Effect of Local Nucleotides on Synonymous Codon Usage in the Honeybee (<Emphasis Type="Italic">Apis mellifera</Emphasis> L.) Genome

Using all currently predicted coding regions in the honeybee genome, a novel form of synonymous codon bias is presented that affects the usage of particular codons dependent on the surrounding nucleotides in the coding region. Nucleotides at the third codon site are correlated, dependent on their weak (adenine [A] or thyamine [T]) versus strong (guanine [G] or cytosine [C]) status, to nucleotides on the first codon site which are dependent on their purine (A/G) versus pyrimidine (C/T) status. In particular, for adjacent third and first site nucleotides, weak–pyrimidine and strong–purine nucleotide combinations occur much more frequently than the underabundant weak–purine and strong–pyrimidine nucleotide combinations. Since a similar effect is also found in the noncoding regions, but is present for all adjacent nucleotides, this coding effect is most likely due to a genome-wide context-dependent mutation error correcting mechanism in combination with selective constraints on adjacent first and second nucleotide pairs within codons. The position-dependent relationship of synonymous codon usage is evidence for a novel form of codon position bias which utilizes the redundancy in the genetic code to minimize the effect of nucleotide mutations within coding regions. [Reviewing Editor: Dr. Brian Morton]     

The complete mitochondrial genome structure of snow leopard <Emphasis Type="Italic">Panthera uncia</Emphasis>

The complete mitochondrial genome (mtDNA) of snow leopard Panthera uncia was obtained by using the polymerase chain reaction (PCR) technique based on the PCR fragments of 30 primers we designed. The entire mtDNA sequence was 16 773 base pairs (bp) in length, and the base composition was: A—5,357 bp (31.9%); C—4,444 bp (26.5%); G—2,428 bp (14.5%); T—4,544 bp (27.1%). The structural characteristics [0] of the P. uncia mitochondrial genome were highly similar to these of Felis catus, Acinonyx jubatus, Neofelis nebulosa and other mammals. However, we found several distinctive features of the mitochondrial genome of Panthera unica. First, the termination codon of COIII was TAA, which differed from those of F. catus, A. jubatus and N. nebulosa. Second, tRNA^{Ser (AGY)}, which lacked the ‘‘DHU’’ arm, could not be folded into the typical cloverleaf-shaped structure. Third, in the control region, a long repetitive sequence in RS-2 (32 bp) region was found with 2 repeats while one short repetitive segment (9 bp) was found with 15 repeats in the RS-3 region. We performed phylogenetic analysis based on a 3 816 bp concatenated sequence of 12S rRNA, 16S rRNA, ND2, ND4, ND5, Cyt b and ATP8 for P. uncia and other related species, the result indicated that P. uncia and P. leo were the sister species, which was different from the previous findings.     

Phylogeography of southern Asian Dolly Varden char <Emphasis Type="Italic">Salvelinus malma krascheninnikovi</Emphasis>: Genealogical analysis of mitochondrial DNA

Phylogeography of southern Asian Dolly Varden char was studied using the data on mtDNA variation (regions ND1/ND2, ND5/ND6, and Cytb/D loop) obtained using PCR-RFLP analysis. Analysis of contemporary population genetic structure showed that Salvelinus malma krascheninnikovi throughout the whole species range was characterized by high population differentiation in combination with rather small differences between the populations from remote regions. The genealogy of mtDNA haplotypes was reconstructed and nested clade analysis of geographical distances was performed. Geographical distribution of mtDNA haplotypes of S. m. krascheninnikovi was explained by population genetic processes (restricted gene flow), as well as by historical demographic events (range expansion and fragmentation). It was demonstrated that the main demographic events were associated with cyclic processes of the geological formation of the Sea of Japan and adjacent territories. Furthermore, genealogical tree of S. m. krascheninnikovi contained the traces of secondary contact between isolated phylogeographical lineages.     

Substitution rates in hepatitis delta virus

Substitution rates were estimated for the coding and noncoding regions of the hepatitis delta virus (HDV). The estimated rates of synonymous substitution in HDV were lower than the rates of substitution at nonsynonymous sites and in the noncoding region. HDV has lower synonymous substitution rates than the hepatitis C virus, though both are RNA viruses. The relatively low rate of synonymous substitution in HDV may be due to a strong preference of G and C nucleotides at third codon positions. Variation in substitution rate among HDV lineages may be correlated with the clinical development of the HDV-induced hepatitis. The phylogenetic tree inferred for 24 HDV strains reveals similarities between lineages isolated from the same geographic region. Correspondence to: W.-H. Li     

Evolutionary History and Mode of the <Emphasis Type="Italic">amylase</Emphasis> Multigene Family in <Emphasis Type="Italic">Drosophila</Emphasis>

Previous studies indicate that the tandemly repeated members of the amylase (Amy) gene family evolved in a concerted manner in the melanogaster subgroup and in some other species. In this paper, we analyzed all of the 49 active and complete Amy gene sequences in Drosophila, mostly from subgenus Sophophora. Phylogenetic analysis indicated that the two types of diverged Amy genes in the Drosophila montium subgroup and Drosophila ananassae, which are located in distant chromosomal regions from each other, originated independently in different evolutionary lineages of the melanogaster group after the split of the obscura and melanogaster groups. One of the two clusters was lost after duplication in the melanogaster subgroup. Given the time, 24.9 mya, of divergence between the obscura and the melanogaster groups (Russo et al. 1995), the two duplication events were estimated to occur at about 13.96 ± 1.93 and 12.38 ± 1.76 mya in the montium subgroup and D. ananassae, respectively. An accelerated rate of amino acid changes was not observed in either lineage after these gene duplications. However, the G+C contents at the third codon positions (GC3) decreased significantly along one of the two Amy clusters both in the montium subgroup and in D. ananassae right after gene duplication. Furthermore, one of the two types of the Amy genes with a lower GC3 content has lost a specific regulatory element within the montium subgroup species and D. ananassae. While the tandemly repeated members evolved in a concerted manner, the two types of diverged Amy genes in Drosophila experienced frequent gene duplication, gene loss, and divergent evolution following the model of a birth-and-death process.     

Evolution of heteroneuran Lepidoptera (Insecta) and the utility of dopa decarboxylase for Cretaceous-age phylogenetics

This study tests the utility of the nuclear gene encoding dopa decarboxylase (DDC) for recovering Cretaceous‐age divergences within the lepidopteran clade Heteroneura, which contains 98% of lepidopteran species. A 709‐bp fragment of DDC has been sequenced in 32 species, including representatives of all major lineages of Heteroneura plus outgroups from more basal lepidopteran groups and the related order Trichoptera. Pairwise divergences across the first and second codon positions and amino acids increase with depth throughout the taxonomic hierarchy, indicating that non‐synonymous substitutions are not fully saturated; whereas, divergences across the third codon position level off at the family to superfamily level. Inclusion of non‐neolepidopteran outgroups results in phylogeny estimates that contradict well established groups, almost surely due to sparse taxon sampling and high character divergence. When these taxa and an equivalently divergent basal ditrysian are excluded, DDC trees show nearly complete recovery of ten uncontroversial basal heteroneuran ‘test clades’ of family rank and higher, about half with strong bootstrap support. Thus, DDC clearly carries phylogenetic signal at these levels. Bootstrap support for resolution of the controversial relationships among the five main heteroneuran groups (four monotrysian superfamilies plus Ditrysia) is individually low, but two of three previous hypotheses were statistically rejected overall by DDC. DDC trees within the primitive heteroneuran superfamily Incurvarioidea, though modestly supported, closely resemble a previous morphological hypothesis, while removing the requirement for reversal in a possible ‘key adaptation’, the larval case. Taxon overlap with a previous mtDNA study of Prodoxidae (Incurvarioidea), which includes much‐ studied mutualist pollinators, permits a comparison of substitution rates with the conservative mitochondrial COI+COII region, as well as combined‐data re‐examination of generic reltionships. Non‐synonymous substitution is about 25% slower in DDC than in COI+COII, though synonymous substitution is faster. With additional taxon sampling, and in combination with other genes, DDC promises to be a powerful tool for reconstructing among‐superfamily relationships within Lepidoptera and probably other insect groups.     

Nucleotide diversity in the mitochondrial and nuclear compartments of <Emphasis Type="Italic">Chlamydomonas reinhardtii</Emphasis>: investigating the origins of genome architecture

Background  

The magnitude of intronic and intergenic DNA can vary substantially both within and among evolutionary lineages; however, the forces responsible for this disparity in genome compactness are conjectural. One explanation, termed the mutational-burden hypothesis, posits that genome compactness is primarily driven by two nonadaptive processes: mutation and random genetic drift – the effects of which can be discerned by measuring the nucleotide diversity at silent sites (π_silent), defined as noncoding sites and the synonymous sites of protein-coding regions. The mutational-burden hypothesis holds that π_silent is negatively correlated to genome compactness. We used the model organism Chlamydomonas reinhardtii, which has a streamlined, coding-dense mitochondrial genome and an noncompact, intron-rich nuclear genome, to investigate the mutational-burden hypothesis. For measuring π_silent we sequenced the complete mitochondrial genome and portions of 7 nuclear genes from 7 geographical isolates of C. reinhardtii.