Molecular Evolution at the Cytochrome Oxidase Subunit 2 Gene Among Divergent Populations of the Intertidal Copepod, Tigriopus californicus

The longest mitochondrial protein in metazoans is encoded by the male-transmitted mitogenome of the bivalve Scrobicularia plana

Cytochrome c oxidase subunit II (COX2) is one of the three mitochondrially encoded proteins of the complex IV of the respiratory chain that catalyses the reduction of oxygen to water. The cox2 gene spans about 690 base pairs in most animal species and produces a protein composed of approximately 230 amino acids. We discovered an extreme departure from this pattern in the male-transmitted mitogenome of the bivalve Scrobicularia plana with doubly uniparental inheritance (DUI) of mitochondrial DNA (mtDNA), which possesses an important in-frame insertion of approximately 4.8 kb in its cox2 gene. This feature—an enlarged male cox2 gene—is found in many species with DUI; the COX2 protein can be up to 420 amino acids long. Through RT-PCRs, immunoassays and comparative genetics, the evolution and functionality of this insertion in S. plana were characterized. The in-frame insertion is conserved among individuals from different populations and bears the signature of purifying selection seemingly indicating maintenance of functionality. Its transcription and translation were confirmed: this gene produces a polypeptide of 1892 amino acids, making it the largest metazoan COX2 protein known to date. We hypothesize that these extreme modifications in the COX2 protein affect the metabolism of mitochondria containing the male-transmitted mtDNA in Scrobicularia plana.

Genetic diversity of Paramecium species on the basis of multiple loci analysis and ITS secondary structure models

Among ciliates, Paramecium has become a privileged model for the study of "species problem" particularly in the case of the "Paramecium aurelia complex" that has been intensely investigated. Despite extensive studies, the taxonomy of Paramecium is still challenging. The major problem is an uneven sampling of Paramecium with relatively few representatives of each species. To investigate species from the less discovered region (Pakistan), 10 isolates of Paramecium species including a standing-alone FT8 strain previously isolated by some of us were subjected to molecular characterization. Fragments of 18S recombinant DNA (rDNA), ITS1-5.8S-ITS2-5'LSU rDNA, cytochrome c oxidase subunit II, and hsp70 genes were used as molecular markers for phylogenetic analysis of particular isolates. The nucleotide sequences of polymerase chain reaction products of all markers were compared with the available sequences of relevant markers of other Paramecium species from GenBank. Phylogenetic trees based on all molecular markers showed that all the nine strains had a very close relationship with Paramecium primaurelia except for the FT8 strain. FT8 consistently showed its unique position in comparison to all other species in the phylogenetic trees. Available sequences of internal transcribed spacer 1 (ITS1) and ITS2 and some other ciliate sequences from GenBank were used for the construction of secondary models. Two highly conserved helices supported by compensatory base changes among all ciliates of ITS2 secondary structures were found similar to other eukaryotes. Therefore, the most conserved 120 to 180 base pairs regions were identified for their comparative studies. We found that out of the three helices in ITS1 structure, helix B was more conserved in Paramecium species. Despite various substitutions in the primary sequence, it was observed that secondary structures of ITS1 and ITS2 could be helpful in interpreting the phylogenetic relationships both at species as well as at generic level.

Neotropical Monogenoidea. 58. Three new species of Gyrodactylus (Gyrodactylidae) from Scleromystax spp. (Callichthyidae) and the proposal of COII gene as an additional fragment for barcoding gyrodactylids

Based on molecular markers (COII and ITS1-ITS2) and morphological data, we describe three new Neotropical species of Gyrodactylus von Nordmann, 1832 from Scleromystax barbatus (Quoy et Gaimard) and Scleromystax macropterus (Regan) from southern Brazil. The three new species can be distinguished from each other by sequences of both molecular markers and morphology of hooks and anchors. Gyrodactylus bueni sp. n. is characterised by having hook with shaft curved, heel straight, shelf straight, toe pointed, anchor with superficial root slender, elongate and male copulatory organ armed with two rows of spinelets. Gyrodactylus major sp. n. presents hook with shaft, point curved, proximal shaft straight, heel convex, shelf convex, toe concave, anchor with superficial root robust and male copulatory organ armed with two rows of spinelets. Gyrodactylus scleromystaci sp. n. presents hook with shaft, point recurved, heel convex, shelf convex, toe pointed, anchor with superficial root curved and male copulatory organ armed with two rows of spinelets. These species appear to be closely related to other species of Gyrodactylus known from other species of Callichthyidae. These new species, however, differ by the comparative morphology of the haptoral hard structures and molecular data. Comparative analysis of sequences from these species of Gyrodactylus suggests that the COII gene may represent an important marker for the taxonomy of species of Gyrodactylidae and, perhaps, for species of other lineages of Monogenoidea.

Phylogenetic information content of Copepoda ribosomal DNA repeat units: ITS1 and ITS2 impact

The utility of various regions of the ribosomal repeat unit for phylogenetic analysis was examined in 16 species representing four families, nine genera, and two orders of the subclass Copepoda (Crustacea). Fragments approximately 2000 bp in length containing the ribosomal DNA (rDNA) 18S and 28S gene fragments, the 5.8S gene, and the internal transcribed spacer regions I and II (ITS1 and ITS2) were amplified and analyzed. The DAMBE (Data Analysis in Molecular Biology and Evolution) software was used to analyze the saturation of nucleotide substitutions; this test revealed the suitability of both the 28S gene fragment and the ITS1/ITS2 rDNA regions for the reconstruction of phylogenetic trees. Distance (minimum evolution) and probabilistic (maximum likelihood, Bayesian) analyses of the data revealed that the 28S rDNA and the ITS1 and ITS2 regions are informative markers for inferring phylogenetic relationships among families of copepods and within the Cyclopidae family and associated genera. Split-graph analysis of concatenated ITS1/ITS2 rDNA regions of cyclopoid copepods suggested that the Mesocyclops, Thermocyclops, and Macrocyclops genera share complex evolutionary relationships. This study revealed that the ITS1 and ITS2 regions potentially represent different phylogenetic signals.

Animal mitochondria, positive selection and cyto-nuclear coevolution: insights from pulmonates

Pulmonate snails have remarkably high levels of mtDNA polymorphism within species and divergence between species, making them an interesting group for the study of mutation and selection on mitochondrial genomes. The availability of sequence data from most major lineages – collected largely for studies of phylogeography - provides an opportunity to perform several tests of selection that may provide general insights into the evolutionary forces that have produced this unusual pattern. Several protein coding mtDNA datasets of pulmonates were analyzed towards this direction. Two different methods for the detection of positive selection were used, one based on phylogeny, and the other on the McDonald-Kreitman test. The cyto-nuclear coevolution hypothesis, often implicated to account for the high levels of mtDNA divergence of some organisms, was also addressed by assessing the divergence pattern exhibited by a nuclear gene. The McDonald-Kreitman test indicated multiple signs of positive selection in the mtDNA genes, but was significantly biased when sequence divergence was high. The phylogenetic method identified five mtDNA datasets as affected by positive selection. In the nuclear gene, the McDonald-Kreitman test provided no significant results, whereas the phylogenetic method identified positive selection as likely present. Overall, our findings indicate that: 1) slim support for the cyto-nuclear coevolution hypothesis is present, 2) the elevated rates of mtDNA polymorphims and divergence in pulmonates do not appear to be due to pervasive positive selection, 3) more stringent tests show that spurious positive selection is uncovered when distant taxa are compared and 4) there are significant examples of positive selection acting in some cases, so it appears that mtDNA evolution in pulmonates can escape from strict deleterious evolution suggested by the Muller’s ratchet effect.

An Incompatibility between a mitochondrial tRNA and its nuclear-encoded tRNA synthetase compromises development and fitness in Drosophila

Mitochondrial transcription, translation, and respiration require interactions between genes encoded in two distinct genomes, generating the potential for mutations in nuclear and mitochondrial genomes to interact epistatically and cause incompatibilities that decrease fitness. Mitochondrial-nuclear epistasis for fitness has been documented within and between populations and species of diverse taxa, but rarely has the genetic or mechanistic basis of these mitochondrial–nuclear interactions been elucidated, limiting our understanding of which genes harbor variants causing mitochondrial–nuclear disruption and of the pathways and processes that are impacted by mitochondrial–nuclear coevolution. Here we identify an amino acid polymorphism in the Drosophila melanogaster nuclear-encoded mitochondrial tyrosyl–tRNA synthetase that interacts epistatically with a polymorphism in the D. simulans mitochondrial-encoded tRNA^Tyr to significantly delay development, compromise bristle formation, and decrease fecundity. The incompatible genotype specifically decreases the activities of oxidative phosphorylation complexes I, III, and IV that contain mitochondrial-encoded subunits. Combined with the identity of the interacting alleles, this pattern indicates that mitochondrial protein translation is affected by this interaction. Our findings suggest that interactions between mitochondrial tRNAs and their nuclear-encoded tRNA synthetases may be targets of compensatory molecular evolution. Human mitochondrial diseases are often genetically complex and variable in penetrance, and the mitochondrial–nuclear interaction we document provides a plausible mechanism to explain this complexity.

The ancient symbiosis between two prokaryotes that gave rise to the eukaryotic cell has required genomic cooperation for at least a billion years. Eukaryotic cells respire through the coordinated expression of their nuclear and mitochondrial genomes, both of which encode the proteins and RNAs required for mitochondrial transcription, translation, and aerobic respiration. Genetic interactions between these genomes are hypothesized to influence the effects of mitochondrial mutations on disease and drive mitochondrial–nuclear coevolution. Here we characterize the molecular cause and the cellular and organismal consequences of a mitochondrial–nuclear interaction in Drosophila between naturally occurring mutations in a mitochondrial tRNA and a nuclear-encoded tRNA synthetase. These mutations have little effect on their own; but, when combined, they severely compromise development and reproduction. tRNA synthetases attach the appropriate amino acid onto their cognate tRNA, and this reaction is required for efficient and accurate protein synthesis. We show that disruption of this interaction compromises mitochondrial function, providing hypotheses for the variable penetrance of diseases associated with mitochondrial tRNAs and for which pathways and processes are likely to be affected by mitochondrial–nuclear interactions.

Fine-scale genetic breaks driven by historical range dynamics and ongoing density-barrier effects in the estuarine seaweed Fucus ceranoides L

BACKGROUND

Factors promoting the emergence of sharp phylogeographic breaks include restricted dispersal, habitat discontinuity, physical barriers, disruptive selection, mating incompatibility, genetic surfing and secondary contact. Disentangling the role of each in any particular system can be difficult, especially when species are evenly distributed across transition zones and dispersal barriers are not evident. The estuarine seaweed Fucus ceranoides provides a good example of highly differentiated populations along its most persistent distributional range at the present rear edge of the species distribution, in NW Iberia. Intrinsic dispersal restrictions are obvious in this species, but have not prevented F. ceranoides from vastly expanding its range northwards following the last glaciation, implying that additional factors are responsible for the lack of connectivity between neighbouring southern populations. In this study we analyze 22 consecutive populations of F. ceranoides along NW Iberia to investigate the processes generating and maintaining the observed high levels of regional genetic divergence.

RESULTS

Variation at seven microsatellite loci and at mtDNA spacer sequences was concordant in revealing that Iberian F. ceranoides is composed of three divergent genetic clusters displaying nearly disjunct geographical distributions. Structure and AFC analyses detected two populations with an admixed nuclear background. Haplotypic diversity was high in the W sector and very low in the N sector. Within each genetic cluster, population structure was also pervasive, although shallower.

CONCLUSIONS

The deep divergence between sectors coupled with the lack of support for a role of oceanographic barriers in defining the location of breaks suggested 1) that the parapatric genetic sectors result from the regional reassembly of formerly vicariant sub-populations, and 2) that the genetic discontinuities at secondary contact zones (and elsewhere) are maintained despite normal migration rates. We conclude that colonization and immigration, as sources of gene-flow, have very different genetic effects. Migration between established populations is effectively too low to prevent their differentiation by drift or to smooth historical differences inherited from the colonization process. F. ceranoides, but possibly low-dispersal species in general, appear to be unified to a large extent by historical, non-equilibrium processes of extinction and colonization, rather than by contemporary patterns of gene flow.

DNA barcoding of marine metazoa

More than 230,000 known species representing 31 metazoan phyla populate the world's oceans. Perhaps another 1,000,000 or more species remain to be discovered. There is reason for concern that species extinctions may out-pace discovery, especially in diverse and endangered marine habitats such as coral reefs. DNA barcodes (i.e., short DNA sequences for species recognition and discrimination) are useful tools to accelerate species-level analysis of marine biodiversity and to facilitate conservation efforts. This review focuses on the usual barcode region for metazoans: a approximately 648 base-pair region of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Barcodes have also been used for population genetic and phylogeographic analysis, identification of prey in gut contents, detection of invasive species, forensics, and seafood safety. More controversially, barcodes have been used to delimit species boundaries, reveal cryptic species, and discover new species. Emerging frontiers are the use of barcodes for rapid and increasingly automated biodiversity assessment by high-throughput sequencing, including environmental barcoding and the use of barcodes to detect species for which formal identification or scientific naming may never be possible.

Interpopulation patterns of divergence and selection across the transcriptome of the copepod Tigriopus californicus

The accumulation of genetic incompatibilities between isolated populations is thought to lead to the evolution of intrinsic postzygotic isolation. The molecular basis for these mechanisms, however, remains poorly understood. The intertidal copepod Tigriopus californicus provides unique opportunities for addressing mechanistic questions regarding the early stages of speciation; hybrids between highly divergent populations are fertile and viable, but exhibit reduced fitness at the F(2) or later generations. Given the current scarcity of genomic information in taxa at incipient stages of reproductive isolation, we utilize high-throughout 454 pyrosequencing to characterize a substantial fraction of protein-coding regions (the transcriptome) of T. californicus. Our sequencing effort was divided equally between two divergent populations in order to estimate levels of divergence and to reveal patterns of selection across the transcriptome. Assembly of sequences generated over 40,000 putatively unique transcripts (unigenes) for each population, 19,622 of which were orthologous between populations. BLAST searches of public databases determined protein identity and functional features for 15,402 and 12,670 unigenes, respectively. Based on rates of nonsynonymous and synonymous substitutions in 5897 interpopulation orthologs (those >150 bp and with at least 2X coverage), we identified 229 potential targets of positive selection. Many of these genes are predicted to be involved in several metabolic processes, and to function in hydrolase, peptidase and binding activities. The library of T. californicus coding regions, annotated with their predicted functions and level of divergence, will serve as an invaluable resource for elucidating molecular mechanisms underlying the early stages of speciation.

Cytoplasmic phylogeny and evidence of cyto-nuclear co-adaptation in Arabidopsis thaliana

In recent years Arabidopsis thaliana has become a model species for genomic variability and adaptation studies. Although impressive quantities of data have been gathered on the nuclear genomic diversity of this species, little has been published regarding its cytoplasmic diversity. We analyzed the diversity of plastid (pt) and mitochondrial (mt) genomes among 95 accessions, covering most Arabidopsis geographic origins. Four intergenic regions of the pt genome were sequenced, and a total of 68 polymorphisms and 65 pt haplotypes were identified. Several strategies were developed to identify mt polymorphisms among a subset of 14 accessions. Fifteen polymorphisms were further developed as PCR-based markers and used to analyze the whole set of 95 accessions. Using statistical parsimony, we built pt and mt phylogenetic networks of haplotype groups. To root the pt network, the pt intergenic regions of two related Arabidopsis species, Arabidopsis lyrata and Arabidopsis arenosa, were also sequenced. The mt and pt phylogenies are highly congruent and could be combined into a single cytoplasmic phylogeny. To estimate whether co-adaptation between nuclear and cytoplasmic genomes exists in A. thaliana, we tested the germination capacity in challenging conditions of 27 pairs of reciprocal F(2) families. We found that the cytoplasm donor had a significant effect on the germination capacity of some F(2) families.

Investigations of fine-scale phylogeography in Tigriopus californicus reveal historical patterns of population divergence

Background

The intertidal copepod Tigriopus californicus is a model for studying the process of genetic divergence in allopatry and for probing the nature of genetic changes that lead to reproductive isolation. Although previous studies have revealed a pattern of remarkably high levels of genetic divergence between the populations of this species at several spatial scales, it is not clear what types of historical processes are responsible. Particularly lacking are data that can yield insights into population history from the finest scales of geographic resolution.

Results

Sequence variation in both cytochrome b (CYTB, mtDNA) and the rieske iron-sulfur protein (RISP, nuclear) are examined at a fine scale within four different regions for populations of T. californicus. High levels of genetic divergence are seen for both genes at the broader scale, and genetic subdivision is apparent at nearly all scales in these populations for these two genes. Patterns of polymorphism and divergence in both CYTB and RISP suggest that selection may be leading to non-neutral evolution of these genes in several cases but a pervasive pattern of neither selection nor coadaptation is seen for these markers.

Conclusion

The use of sequence data at a fine-scale of resolution in this species has provided novel insights into the processes that have resulted in the accumulation of genetic divergence among populations. This divergence is likely to result from an interplay between a limited dispersal ability for this copepod and the temporal instability of copepod habitat. Both shorter-term processes such as the extinction/recolonization dynamics of copepod pools and longer-term processes such as geological uplift of coastline and sea level changes appear to have impacted the patterns of differentiation. Some patterns of sequence variation are consistent with selection acting upon the loci used in this study; however, it appears that most phylogeographic patterns are the result of history and not selection on these genes in this species.

Role-reversal of gender-associated mitochondrial DNA affects mitochondrial function in Mytilus edulis (Bivalvia: Mytilidae)

Mussel species of the genus Mytilus possess an unusual system of mitochondrial DNA (mtDNA) transmission termed doubly uniparental inheritance. They are characterized by the presence of two highly divergent gender-associated mtDNA genomes (often with>20 and>10% divergences in DNA and amino acid sequences, respectively) that are inherited either maternally (F mtDNA) or paternally (M mtDNA). Females are typically homoplasmic for the F mtDNA and males are heteroplasmic with the F mtDNA being most common in all tissues except the gonad that is dominated by the M mtDNA. Collectively, males are polymorphic for two classes of M mtDNAs known as the "standard male" and "recently masculinized" M types (SM and RM, respectively). The coding portions of the RM mtDNA genome differ from the SM mtDNA by as much as the maternally inherited F mtDNA genome differs from the SM type. Because the SM and RM types exhibit considerable amino acid sequence divergence, we hypothesized that these differences could affect mitochondrial respiratory chain complex enzyme activities. To test this hypothesis, the activity of the major mitochondrial respiratory chain complexes (complexes II, I+III and IV) as well as the activity of citrate synthase were measured on gonad samples from males containing either the SM or RM mtDNA. Our data demonstrate that the mitochondrial subunits encoded by the RM mtDNA are associated with higher enzymatic activities than the gene products of the SM mtDNA.

Extreme primary and secondary protein structure variability in the chimeric male-transmitted cytochrome c oxidase subunit II protein in freshwater mussels: evidence for an elevated amino acid substitution rate in the face of domain-specific purifying selection

BACKGROUND

Freshwater unionoidean bivalves, and species representing two marine bivalve orders (Mytiloida and Veneroida), exhibit a mode of mtDNA inheritance involving distinct maternal (F) and paternal (M) transmission routes concomitant with highly divergent gender-associated mtDNA genomes. Additionally, male unionoidean bivalves have a approximately 550 bp 3' coding extension to the cox2 gene (Mcox2e), that is apparently absent from all other metazoan taxa.

RESULTS

Our molecular sequence analyses of MCOX2e indicate that both the primary and secondary structures of the MCOX2e region are evolving much faster than other regions of the F and M COX2-COX1 gene junction. The near N-terminus approximately 2/3 of the MCOX2e region contains an interspecifically variable number of predicted transmembrane helices (TMH) and interhelical loops (IHL) whereas the C-terminus approximately 1/3 is relatively conserved and hydrophilic while containing conserved functional motifs. MCOX2e displays an overall pattern of purifying selection that leads to the preservation of TMH/IHL and C-terminus tail sub-regions. However, 14 amino acid positions in the MCOX2e TMH/IHL sub-region might be targeted by diversifying selection, each representing a site where there exists interspecific variation for the constituent amino acids residing in a TMH or IHL.

CONCLUSION

Our results indicate that Mcox2e is unique to unionoidean bivalves, likely the result of a single insertion event that took place over 65 MYA and that MCOX2e is functional. The predicted TMH number, length and position variability likely stems from substitution-based processes rather than the typically implicated insertion/deletion events. MCOX2e has relatively high rates of primary and secondary structure evolution, with some amino acid residues potentially subjected to site-specific positive selection, yet an overall pattern of purifying selection leading to the preservation of the TMH/IHL and hydrophilic C-terminus tail subregions. The more conserved C-terminus tail (relative to the TMH/IHL sub-region of MCOX2e) is likely biologically active because it contains functional motifs. The rapid evolution of primary and secondary structure in MCOX2e, combined with the action of both positive and purifying selection, provide supporting evidence for the hypothesis that MCOX2e has a novel reproductive function within unionoidean bivalves. All tolled, our data indicate that unionoidean bivalve MCOX2 is the first reported chimeric animal mtDNA-encoded protein.

Contrasting demographic history and phylogeographical patterns in two Indo-Pacific gastropods

Marine species with ranges that span the Indo-Australian Archipelago (IAA) exhibit a range of phylogeographical patterns, most of which are interpreted in the context of vicariance between Indian and Pacific Ocean populations during Pliocene and Pleistocene low sea-level stands. However, patterns often vary among ecologically similar taxa, sometimes even within genera. This study compares phylogeographical patterns in two species of highly dispersive neritid gastropod, Nerita albicilla and Nerita plicata, with nearly sympatric ranges that span the Indo-Pacific. Mitochondrial COI sequences from >1000 individuals from 97 sites reveal similar phylogenies in both species (two divergent clades differing by 3.2% and 2.3%, for N. albicilla and N. plicata, respectively). However, despite ecological similarity and congeneric status, the two species exhibit phylogeographical discordance. N. albicilla has maintained reciprocal monophyly of Indian and Pacific Ocean populations, while N. plicata is panmictic between oceans, but displays a genetic cline in the Central Pacific. Although this difference might be explained by qualitatively different demographic histories, parameter estimates from three coalescent models indicate that both species have high levels of gene flow between demes (2Nem>75), and share a common history of population expansion that is likely associated with cyclical flooding of continental shelves and island lagoons following low sea-level stands. Results indicate that ecologically similar, codistributed species may respond very differently to shared environmental processes, suggesting that relatively minor differences in traits such as pelagic larval duration or microhabitat association may profoundly impact phylogeographical structure.

No evidence for faster male hybrid sterility in population crosses of an intertidal copepod (Tigriopus californicus)

Two different forces are thought to contribute to the rapid accumulation of hybrid male sterility that has been observed in many inter-specific crosses, namely the faster male and the dominance theories. For male heterogametic taxa, both faster male and dominance would work in the same direction to cause the rapid evolution of male sterility; however, for taxa lacking differentiated sex chromosomes only the faster male theory would explain the rapid evolution of male hybrid sterility. It is currently unknown what causes the faster evolution of male sterility, but increased sexual selection on males and the sensitivity of genes involved in male reproduction are two hypotheses that could explain the observation. Here, patterns of hybrid sterility in crosses of genetically divergent copepod populations are examined to test potential mechanisms of faster male evolution. The study species, Tigriopus californicus, lacks differentiated, hemizygous sex chromosomes and appears to have low levels of divergence caused by sexual selection acting upon males. Hybrid sterility does not accumulate more rapidly in males than females in these crosses suggesting that in this taxon male reproductive genes are not inherently more prone to disruption in hybrids.

Three divergent mitochondrial genomes from California populations of the copepod Tigriopus californicus

Previous work on the harpacticoid copepod Tigriopus californicus has focused on the extensive population differentiation in three mtDNA protein coding genes (COXI, COXII, Cytb). In order to get a more complete understanding of mtDNA evolution in this species, we sequenced three complete mitochondrial genomes (one from each of three California populations) and compared them to two published mtDNA genomes from an Asian congener, Tigriopus japonicus. Several features of the mtDNA genome appear to be conserved within the genus: 1) the unique order of the protein coding genes, rRNA genes and most of the tRNA genes, 2) the genome is compact, varying between 14.3 and 14.6 kb, and 3) all genes are encoded on the same strand of the mtDNA. Within T. californicus, extremely high levels of nucleotide divergence (>20%) are observed across much of the mitochondrial genome. Inferred amino acid sequences of the proteins encoded in the mtDNAs also show high levels of divergence; at the extreme, the three ND3 variants in T. californicus showed >25% amino acid substitutions, compared with <3% amino acid divergence at the previously studied COXI locus. Unusual secondary structures make functional assignments of some tRNAs difficult. The only apparent tRNA(trp) in these genomes completely overlaps the 5' end of the 16S rRNA in all three T. californicus mtDNAs. Although not previously noted, this feature is also conserved in T. japonicus mtDNAs; whether this sequence is processed into a functional tRNA has not been determined. The putative control region contains a duplicated segment of different length (from 88 to 155 bp) in each of the T. californicus sequences. In each case, the duplicated segments are not tandem repeats; despite their different lengths, the distance between the start of the first and the start of the second repeat is conserved (520 bp). The functional significance, if any, of this repeat structure remains unknown.

The unusual system of doubly uniparental inheritance of mtDNA: isn't one enough?

Mitochondria possess their own genetic material (mitochondrial DNA or mtDNA), whose gene products are involved in mitochondrial respiration and oxidative phosphorylation, transcription, and translation. In animals, mitochondrial DNA is typically transmitted to offspring by the mother alone. The discovery of 'doubly uniparental inheritance' (DUI) of mtDNA in some bivalves has challenged the paradigm of strict maternal inheritance (SMI). In this review, we survey recent advances in our understanding of DUI, which is a peculiar system of cytoplasmic DNA inheritance that involves distinct maternal and paternal routes of mtDNA transmission, a novel extension of a mitochondrial gene (cox2), recombination, and periodic 'role-reversals' of the normally male and female-transmitted mitochondrial genomes. DUI provides a unique opportunity for studying nuclear-cytoplasmic genome interactions and the evolutionary significance of different modes of mitochondrial inheritance.

The copepod Tigriopus: a promising marine model organism for ecotoxicology and environmental genomics

There is an increasing body of evidence to support the significant role of invertebrates in assessing impacts of environmental contaminants on marine ecosystems. Therefore, in recent years massive efforts have been directed to identify viable and ecologically relevant invertebrate toxicity testing models. Tigriopus, a harpacticoid copepod has a number of promising characteristics which make it a candidate worth consideration in such efforts. Tigriopus and other copepods are widely distributed and ecologically important organisms. Their position in marine food chains is very prominent, especially with regard to the transfer of energy. Copepods also play an important role in the transportation of aquatic pollutants across the food chains. In recent years there has been a phenomenal increase in the knowledge base of Tigriopus spp., particularly in the areas of their ecology, geophylogeny, genomics and their behavioural, biochemical and molecular responses following exposure to environmental stressors and chemicals. Sequences of a number of important marker genes have been studied in various Tigriopus spp., notably T. californicus and T. japonicus. These genes belong to normal biophysiological functions (e.g. electron transport system enzymes) as well as stress and toxic chemical exposure responses (heat shock protein 20, glutathione reductase, glutathione S-transferase). Recently, 40,740 expressed sequenced tags (ESTs) from T. japonicus, have been sequenced and of them, 5,673 ESTs showed significant hits (E-value, >1.0E-05) to the red flour beetle Tribolium genome database. Metals and organic pollutants such as antifouling agents, pesticides, polycyclic aromatic hydrocarbons (PAH) and polychrlorinated biphenyls (PCB) have shown reproducible biological responses when tested in Tigriopus spp. Promising results have been obtained when Tigriopus was used for assessment of risk associated with exposure to endocrine-disrupting chemicals (EDCs). Application of environmental gene expression techniques has allowed evaluation of transcriptional changes in T. japonicus with the ultimate aim of understanding the mechanisms of action of environmental stressors. Through a better understanding of toxicological mechanisms, ecotoxicologists may use this ecologically relevant species in risk assessment studies in marine systems. The combination of uses as a whole-animal bioassay and gene expression studies indicate that Tigriopus may serve as an excellent tool to evaluate the impacts of marine pollution throughout the coastal region. The purpose of this review is to illustrate the potential of using Tigriopus to fulfill the niche as an important invertebrate marine model organism for ecotoxicology and environmental genomics. In addition, the knowledge gaps and areas for further studies have also been discussed.

Doubly uniparental inheritance is associated with high polymorphism for rearranged and recombinant control region haplotypes in Baltic Mytilus trossulus

Many bivalve species, including mussels of the genus Mytilus, are unusual in having two mtDNA genomes, one inherited maternally (the F genome) and the other inherited paternally (the M genome). The sequence differences between the genomes are usually great, indicating ancient divergence predating speciation events. However, in Mytilus trossulus from the Baltic, both genomes are similar to the F genome from the closely related M. edulis. This study analyzed the mtDNA control region structure in male and female Baltic M. trossulus mussels. We show that a great diversity of structural rearrangements is present in both sexes. Sperm samples are dominated by recombinant haplotypes with M. edulis M-like control region segments, some having large duplications. By contrast, the rearranged haplotypes that dominate in eggs lack segments from this M genome. The rearrangements can be explained by a combination of tandem duplication, deletion, and intermolecular recombination. An evolutionary pathway leading to the recombinant haplotypes is suggested. The data are also considered in relation to the hypothesis that the M. edulis M-like control region sequence is necessary to confer the paternal role on genomes that are otherwise F-like.