Mitochondrial DNA polymorphisms and sperm motility in Mytilus edulis (Bivalvia: Mytilidae)

The system of mitochondrial DNA (mtDNA) inheritance in Mytilus and other bivalves, termed doubly uniparental inheritance (DUI), is novel among animals. Males pass on their male transmitted (M-type) mtDNA from fathers to their sons whereas females pass on their female transmitted (F-type) mtDNA from mothers to both sons and daughters. Thus, Mytilus males contain two distinct types of mtDNA. Interestingly, sperm contains only the paternal mtDNA. Phylogenetic analysis has shown that some female types have been able to switch their route of inheritance. These "recently masculinized" mitochondrial genomes behave as a typical M-type in that they are transmitted from generation to generation through sperm. Because the "recently masculinized" and "standard" male mitotypes in M. edulis exhibit approximately 8.7% amino acid sequence divergence, we hypothesized that these differences could affect mitochondrial, and hence sperm, functions. Furthermore, since recently masculinized mitotypes have been shown to replace standard male types periodically over evolutionary timescales, we tested the hypothesis that sperm swimming speeds would be greater for males with recently masculinized M-type genomes. Sperm activity was videotaped, digitized and tracked. A linear mixed effects model found no significant difference in linear velocities or curvilinear speeds between the mitotypes suggesting that swimming speeds are similar for both in the period shortly after spawning.     

Characterization of a mitochondrial ORF from the gender-associated mtDNAs of Mytilus spp. (Bivalvia: Mytilidae): identification of the "missing" ATPase 8 gene

Bivalve species are characterized by extraordinary variability in terms of mitochondrial (mt) genome size, gene arrangement and tRNA gene number. Many species are thought to lack the mitochondrial protein-coding gene atp8. Of these species, the Mytilidae appears to be the only known taxon with doubly uniparental inheritance of mtDNA that does not possess the atp8 gene. This raises the question as to whether mytilids have completely lost the ATP8 protein, whether the gene has been transferred to the nucleus or whether they possess a highly modified version of the gene/protein that has led to its lack of annotation. In the present study, we re-investigated all complete (or nearly complete) F and M mytilid mt genomes previously sequenced for the presence of conserved open reading frames (ORFs) that might code for ATP8 and/or have other functional importance in these bivalves. We also revised the annotations of all available complete mitochondrial genomes of bivalves and nematodes that are thought to lack atp8 in an attempt to detect it. Our results indicate that a novel mytilid ORF of significant length (i.e., the ORF is >85 amino acids in length), with complete start and stop codons, is a candidate for the atp8 gene: (1) it possesses a pattern of evolution expected for a protein-coding gene evolving under purifying selection (i.e., the 3rd>1st>2nd codon pattern of evolution), (2) it is actively transcribed in Mytilus species, (3) it has one predicted transmembrane helix (as do other metazoan ATP8 proteins), (4) it has conserved functional motifs and (5), comparisons of its amino acid sequence with ATP8 sequences of other molluscan or bivalve species reveal similar hydropathy profiles. Furthermore, our revised annotations also confirmed the mt presence of atp8 in almost all bivalve species and in one nematode species. Our results thus support recognizing the presence of ATPase 8 in most bivalves mt genomes (if not all) rather than the continued characterization of these genomes as lacking this gene.     

Tissue-specific expression of male-transmitted mitochondrial DNA and its implications for rates of molecular evolution in Mytilus mussels (Bivalvia: Mytilidae).

Mytilus and other bivalves exhibit an unusual system of mitochondrial DNA (mtDNA) transmission termed doubly uniparental inheritance (DUI). Specifically, males transmit the mtDNA they have received from their fathers to their sons. Females transmit their mother's mtDNA to both sons and daughters. Males are normally heteroplasmic and females are normally homoplasmic, but not exclusively. This system is associated with an unusual pattern of molecular evolution. Male-transmitted mtDNA (M type) evolves faster than female-transmitted (F type) mtDNA. Relatively relaxed selection on the M type has been proposed as an explanation for this phenomenon. To further evaluate the selective forces acting upon the M-type genome, we used RT-PCR to determine where it is expressed. M-type mtDNA expression was detected in all gonad samples and in 50% of somatic tissues of males, and in a single female tissue. F-type mtDNA expression was detected in all female tissues, all male somatic tissues, and all but one male gonad sample. We argue that the expression of M-type mtDNA in male somatic and male gonad tissues has implications for the strength of selection acting upon it.     

Genetics and taxonomy of Chilean smooth-shelled mussels, Mytilus spp. (Bivalvia: Mytilidae)

It has been previously established that native smooth-shelled mussels in southern South America possess close evolutionary affinities with Northern-Hemisphere Mytilus edulis L. 1758 (McDonald et al. (1991) [5]). This result has since been challenged by authors claiming that Chilean mussels should be considered a local subspecies of M. galloprovincialis Lmk. 1819. Moreover, morphological, physiological, ecotoxicological and molecular genetic studies on Chilean smooth-shelled mussels still frequently refer to ‘M. chilensis’ Hupé 1854, even though the previous discovery of alien M. galloprovincialis and considerable heterogeneity in shell morphology among samples collected along the Chilean shores raise concerns that different Mytilus spp. species might have been included under ‘M. chilensis’. Here we reviewed the molecular and morphological data available on smooth-shelled mussels from Chile in an attempt to clarify both their genetic composition and their taxonomic status. Using multivariate analysis on sample × allozyme-frequency matrices, we confirmed the widespread occurrence of the Southern-Hemisphere form of M. edulis along the shores from the North Patagonia region of Chile to the southern tip of the South American continent. The populations sampled in southern central Chile showed some evidence of slight introgression from Southern-Hemisphere M. galloprovincialis. Morphological characterization of a sample from Dichato in southern central Chile was consistent with its previous genetic identification as Mediterranean M. galloprovincialis. The occurrence of Southern-Hemisphere M. galloprovincialis in Punta Arenas at the southern tip of the South American continent was also reported. Southern-Hemisphere M. edulis, including native Chilean smooth-shelled Mytilus, should be assigned subspecific rank and named M. edulis platensis d’Orbigny 1846.     

A mitochondrial phylogeography of Brachidontes variabilis (Bivalvia: Mytilidae) reveals three cryptic species

This study examined genetic variation across the range of Brachidontes variabilis to produce a molecular phylogeography. Neighbour joining (NJ), minimum evolution (ME) and maximum parsimony (MP) trees based on partial mitochondrial DNA sequences of 16S-rDNA and cytochrome oxidase (COI) genes revealed three monophyletic clades: (1) Brachidontes pharaonis s.l. from the Mediterranean Sea and the Red Sea; (2) B. variabilis from the Indian Ocean; (3) B. variabilis from the western Pacific Ocean. Although the three clades have never been differentiated by malacologists employing conventional morphological keys, they should be ascribed to the taxonomic rank of species. The nucleotide divergences between Brachidontes lineages (between 10.3% and 23.2%) were substantially higher than the divergence between congeneric Mytilus species (2.3–6.7%) and corresponded to interspecific divergences found in other bivalvia, indicating that they should be considered three different species. Analysis of the 16S-rDNA sequences revealed heteroplasmy, indicating dual uniparental inheritance (DUI) of mtDNA in the species of Brachidontes collected in the Indian Ocean, but not in the species in the Pacific nor in the species in the Red Sea and the Mediterranean Sea. When we employed the conventional estimate of the rate of mitochondrial sequence divergence (2% per million years), the divergence times for the three monophyletic lineages were 6–11 Myr for the Indian Ocean and Pacific Ocean Brachidontes sp. and 6.5–9 Myr for the Red Sea and Indian Ocean Brachidontes sp . Thus, these species diverged from one another during the Miocene (23.8–5.3 Myr). We infer that a common ancestor of the three Brachidontes species probably had an Indo-Pacific distribution and that vicariance events, linked to Pleistocene glaciations first and then to the opening of the Red Sea, produced three monophyletic lineages.     

Direct evidence for homologous recombination in mussel (Mytilus galloprovincialis) mitochondrial DNA.

The assumption that animal mitochondrial DNA (mtDNA) does not undergo homologous recombination is based on indirect evidence, yet it has had an important influence on our understanding of mtDNA repair and mutation accumulation (and thus mitochondrial disease and aging) and on biohistorical inferences made from population data. Recently, several studies have suggested recombination in primate mtDNA on the basis of patterns of frequency distribution and linkage associations of mtDNA mutations in human populations, but others have failed to produce similar evidence. Here, we provide direct evidence for homologous mtDNA recombination in mussels, where heteroplasmy is the rule in males. Our results indicate a high rate of mtDNA recombination. Coupled with the observation that mammalian mitochondria contain the enzymes needed for the catalysis of homologous recombination, these findings suggest that animal mtDNA molecules may recombine regularly and that the extent to which this generates new haplotypes may depend only on the frequency of biparental inheritance of the mitochondrial genome. This generalization must, however, await evidence from animal species with typical maternal mtDNA inheritance.     

First record of the microsporidian parasite Steinhausia mytilovum in Mytilus sp. (Bivalvia: Mytilidae) from France

Steinhausia mytilovum is a globally distributed microsporidian parasite which infects the oocytes of the blue mussels Mytilus edulis and M. galloprovincialis. Despite the intensive monitoring effort made on mussel populations, the parasite has not previously been reported in France. We report herein on the occurrence of S. mytilovum in Mytilus sp. from 1 cultured and 2 natural populations on the northern coast of France, thus extending the parasite's known distribution northwards. We also report on the observation in 1989 of S. mytilovum in M. galloprovincialis from the Golfe de Fos area in the Mediterranean Sea (South of France). S. mytilovum was observed in the European hybrid zone between M. edulis and M. galloprovincialis, which therefore renders the exact taxonomic status of the infected hosts unknown. The prevalence of the parasite was low, which suggests that its effect on mussel populations was probably limited.     

Comparative analysis of gender-associated complete mitochondrial genomes in marine mussels (Mytilus spp.)

Marine mussels of the genus Mytilus have an unusual mode of mitochondrial DNA (mtDNA) transmission termed doubly uniparental inheritance (DUI). Female mussels are homoplasmic for the F mitotype, which is inherited maternally, while males are usually heteroplasmic, carrying a mixture of the maternal F mitotype and the paternally inherited M genome. Two classes of M genomes have been observed: "standard" M genomes and "recently masculinized" M genomes. The latter are more similar to F genomes at the sequence level but are transmitted paternally like standard M genomes. In this study we report the complete sequences of two standard male M. edulis and one recently masculinized male M. trossulus mitochondrial genome. A comparative analysis, including the previously sequenced M. edulis F and M. galloprovincialis F and M mtDNAs, reveals that these genomes are identical in gene order, but highly divergent in nucleotide and amino acid sequence. The large amount (>20%) of nucleotide substitutions that fall in coding regions implies that there are several amino acid replacements between the F and M genomes, which likely have an impact on the structural and functional properties of the mitochondrial proteome. Correlation of the divergence rate of different protein-coding genes indicates that mtDNA-encoded proteins of the M genome are still under selective constraints, although less highly than genes of the F genome. The mosaic F/M control region of the masculinized F genome provides evidence for lineage-specific sequences that may be responsible for the different mode of transmission genetics. This analysis shows the value of comparative genomics to better understand the mechanisms of maintenance and segregation of mtDNA sequence variants in mytilid mussels.     

Invasive and non-invasive lineages in Xenostrobus (Bivalvia: Mytilidae)

The mussel genus Xenostrobus comprises eight named extant species from the Indo-West Pacific, including Xenostrobus inconstans, Xenostrobus pulex and Xenostrobus securis from Australia, the latter two also occurring in New Zealand. Xenostrobus species are predominantly restricted to estuaries or sheltered marine habitats although X. pulex inhabits the rocky intertidal on open coasts. Xenostrobus has recently been suggested to be congeneric with the freshwater invasive species Limnoperna fortunei. Xenostrobus securis is itself invasive in the Far East and Europe. This study employed DNA sequences from cytochrome c oxidase (COI), the D1 expansion region of 28S rRNA and the internal transcribed spacers of the ribosomal cistrons to investigate species relationships and habitat transitions in Australasian Xenostrobus. It is unlikely that Xenostrobus and Limnoperna are congeneric as their COI sequences are very different. There was unexpected complexity in defining Xenostrobus species. Xenostrobus pulex from New Zealand is probably a distinct species to the Australian taxon of that name with the name X. neozelanicus available for that taxon. Xenostrobus inconstans and Australian X. pulex were not reciprocally monophyletic in COI analyses. The phylogeography of the COI haplotypes of X. securis suggests that it may be a cryptic species complex, although this possibility could not be confirmed by sequences of the other genes.     

Nonneutral evolution and differential mutation rate of gender-associated mitochondrial DNA lineages in the marine mussel Mytilus.

Mussels have two types of mitochondrial DNA (mtDNA). The M type is transmitted paternally, and the F type is transmitted maternally. To test hypotheses of the molecular evolution of both mtDNA genomes, 50 nucleotide sequences were obtained for 396 bp of the COIII gene of European populations of Mytilus edulis and the Atlantic and Mediterranean forms of M. galloprovincialis. Analysis based on the proportion of synonymous and nonsynonymous substitutions indicate that mtDNA is evolving in a non-neutral and complex fashion. Previous studies on American mussels demonstrated that the F genome experiences a higher purifying selection and that the M genome evolves faster. Here we show that these patterns also hold in European populations. However, in contrast to American populations, where an excess of replacement substitution between F and M lineages has been reported, a significant excess of replacement polymorphism within mtDNA lineages is observed in European populations of M. galloprovincialis. European populations also show an excess of replacement polymorphism within the F but not within the M genome with respect to American M. trossulus, as well as a consistent pattern of excess of rare variants in both F and M genomes. These results are consistent with a nearly neutral model of molecular evolution and a recent relaxation of selective constraints on European mtDNA. Levels of diversity are significantly higher for the M than F genome, and the M genome also accumulates synonymous and nonsynonymous substitutions at a higher rate, in contrast with earlier reports where no difference for the synonymous rate was observed. It is suggested that a subtle balance between relaxed selection and a higher mutation rate explains the faster evolutionary rate of the M lineage.     

Features of the shell morphology of Mytilus trossulus (Bivalvia: Mytilidae) in the fouling of the alga Sargassum pallidum (Phaeophyceae: Sargassaceae)

The features of ontogenetic variation in the shell shape of the bivalve Mytilus trossulus were studied based on material that was collected from different biotopes in the Vostok Bay of the Sea of Japan in 2011. It was revealed that the mollusks had different shell shapes in rock populations and in foulings of artificial substrates but all the developmental changes fall within formerly recorded peculiarities. It is shown that significant deviations from the typical form of the shell are characteristic to mollusks from the fouling of thalli of the brown algae Sargassum pallidum that inhabit shallow water at surf-exposed rocky headlands. The mollusks from this biotope were characterized by numerous traces of deformations of the shell, an atypically skewed growth of the rear edge, and a significant excess (20–25%) of the width over the shell height. It was revealed that the recorded features of shell morphology are apparently associated with features of mussel habitation in an environment with active hydrodynamics.     

The Reaction of Mytilus trossulus Larvae (Bivalvia,Mytilidae) to Desalination and Increase of Water Column Temperature

Under homogeneous salinity and temperature conditions and uniform daylight, the early larvae of the Pacific mussel Mytilus trossulus (blastulae and trochophores) accumulated in the uppermost layer of water column, while the late larvae tend to concentrate at the bottom. In a water column with a temperature or salinity gradient, the early larvae accumulated at the surface even when the salinity and temperature conditions were incompatible with their life activity. The distribution of the late larvae was different as they were able to leave water of unfavorable temperature and salinity and accumulate at the bottom.     

Phylogenetic characterization of three morphs of mussels (Bivalvia, Mytilidae) inhabiting isolated marine environments in Palau Islands

Marine lakes in the Palau Islands are known to harbor unique marine fauna that have remained isolated since the formation of the lakes after the Last Glacial Maximum. We analyzed mussels from marine lakes located on different islands and conducted morphological, phylogenetic and population genetic characterization to clarify their evolutionary history. The mussels were morphologically classified into three differentiated morphs: NS, ON, and MC. Their common characteristics were consistent with the Brachidontes-Hormomya complex of the Mytilidae family. Phylogenetic analysis based on the nuclear 18S ribosomal RNA gene supported the taxonomic position of the mussels among the Mytilidae. In the mitochondrial cytochrome c oxidase subunit I (COI) gene lineage, NS-and MC-morphs were highly diverged from each other; their estimated time of divergence dates back to the mid-Pleistocene. ON-morph was more closely related to MC-morph, although the shell morphologies of ON- and MC-morphs were easily distinguishable. Population genetic analysis revealed the coexistence of highly diverged haplotypes within a population of ON-morph, indicating introgression of mtDNA among the morphs. Our data suggest that morphological differentiation of marine lake mussels can occur in a relatively short period under different environmental conditions. Thus, the marine lakes provide a unique site for the study of diversification in mussels.     

Size and age composition of populations and growth of Mytilus trossulus (Bivalvia: Mytilidae) in the subtidal area of western Kamchatka

Fairly large Mytilus trossulus beds were found in the subtidal zone at depths to 40 m off the western coast of Kamchatka. The size and age composition of local populations and growth rates of M. trossulus in this region and at Atlasova Island were studied. Significant variability of the shell shape of mollusks was found. In the western Kamchatka subtidal, M. trossulus grew faster than in the northern Kuril Islands and eastern Kamchatka. Mussels attained commercial size (50 mm in shell length) in the fourth year of life in the former case and in the fifth-sixth year in other cases. Mollusks of different ages, from 1 to 8–9 year olds, were present in western Kamchatka populations; i.e., juvenile recruitment takes place regularly, while growth rates vary. Growth and population structure of M. trossulus are discussed in relation to the habitat conditions on the western Kamchatka shelf.     

Genetic variation of Mytilus coruscus Gould (Bivalvia: Mytilidae) populations in the East China Sea inferred from mtDNA COI gene Sequence

In order to characterize the genetic relationship of six populations of Mytilus coruscus Gould in the East China Sea, a 681 bp region of mtDNA COI gene was sequenced and analyzed. Eighty four individuals in total were collected from three cultured populations and three wild populations from three localities of the coast of East China Sea. The sequences from these different populations identified 62 polymorphic sites, which included 41 singleton variable sites and 21 parsimony informative sites that defined 45 distinct haplotypes. Phylogenetic analysis showed that most haplotypes were highly interconnected with each other. Thirty seven of the 45 haplotypes were only found in their own populations, seven were found at two-four localities and only haplotype NO.2 was found in all six populations, indicating that most haplotypes were locally restricted. All haplotypes had shaped two similar branches, each including individuals from all six strains. The results of F_ST values indicated that the genetic distances between populations are not closely associated with their geographic distances.     

A molecular phylogeny of the marine mussel genus Perna (Bivalvia: Mytilidae) based on nuclear (ITS1&2) and mitochondrial (COI) DNA sequences

A molecular phylogeny is presented for marine mussels of the genus Perna, based on nuclear (ITS1,ITS2) and mitochondrial (COI) DNA sequence data. The three generally recognised species (Perna viridis, Perna perna and Perna canaliculus) and one putative species (Perna picta) were each sampled from several locations within their known geographic distributions. A range of phylogenetic analyses was used to investigate the current taxonomic assignments, evolutionary relationships and the biogeographical history of the genus. The different analyses produced similar, well supported topologies and verified the monophyly of the genus with respect to five mytilid outgroup species. P. perna (Atlantic), P. viridis (Indo-West Pacific), and P. canaliculus (New Zealand) each formed distinct clades, confirming their specific status. Putative P. picta from North Africa clustered within the P. perna clade and is not regarded as a separate species. P. perna and P. canaliculus were the most closely related of the three species. Possible biogeographic explanations for the present species distributions are evaluated.     

Phylogenetic evidence of mitochondrial DNA introgression among pocket gophers in New Mexico (family Geomyidae)

Mitochondrial DNA (mtDNA) variation in the cytochrome b gene was determined for two divergent taxa of pocket gophers, Thomomys bottae actuosus and T. b. ruidosae . These two taxa hybridize in a narrow contact zone, but introgression of nuclear markers such as allozymes or chromosomes does not extend much beyond the hybrid zone (Patton et al. 1979). We found that despite their distinctness, the two subspecies shared very similar mtDNA haplotypes. By a comparison of phylogenetic histories derived from nuclear markers (allozymes) and from mtDNA haplotypes sampled in different populations of T. bottae from New Mexico, we show that apparent similarity is due to an introgression of T. b. ruidosae mtDNA into T. b. actuosus nuclear background. Evidence of introgression is not limited to the present-day contact zone between these two taxa, but extends at least 75 km away from it. The actuosus haplotype coexists along with the ruidosae mtDNA in the Gallinas Mts., which are inhabited by otherwise pure T. b. actuosus , while further north only typical actuosus haplotypes were detected. Of several potential mechanisms which could lead to such a geographical pattern of variation, we argue that a combination of range shifts due to climatic fluctuations, and genetic drift are most likely. Horizontal gene transfers due to hybridization are historical events which seem rather common among pocket gophers. Although they can be identified with careful phylogenetic study using independent data sets, the potential for misinterpreting a gene tree as an organismal tree is great in this and other groups of animals.     

Interspecies transfer of female mitochondrial DNA is coupled with role-reversals and departure from neutrality in the mussel Mytilus trossulus.

Mussels of the genus Mytilus have distinct and highly diverged male and female mitochondrial DNA (mtDNA) genomes with separate routes of inheritance. Previous studies of European populations of Mytilus trossulus demonstrated that 33% of males are heteroplasmic for a second mtDNA genome of increased length and that hybridization with Mytilus edulis does not block mtDNA introgression, in contrast to reports for American populations. Here, we demonstrate that the female mtDNA type of M. edulis has replaced the resident female mtDNA type of European M. trossulus. This is supported by COIII sequence data indicating that the female mtDNA of European M. trossulus is very similar to that of M. edulis and that in phylogenetic trees, the mtDNAs of these two species cluster together but separately from American M. trossulus sequences, the latter not being disturbed by introgressive hybridization. We also provide evidence that the mtDNA genome of increased length found in heteroplasmic males of European M. trossulus derives from a recent partition of an introgressed M. edulis female type into the male route of transmission. Neutrality tests reveal that European populations of M. trossulus display an excess of replacement polymorphism within the female mtDNA type with respect to conspecific American populations, as well as a significant excess of rare variants, of a similar magnitude to those previously reported for the invading European M. edulis mtDNA. Results are consistent with a nearly neutral model of molecular evolution and suggest that selection acting on European M. trossulus mtDNA is largely independent of the nuclear genetic background.     

The largest unassigned regions of the male- and female-transmitted mitochondrial DNAs in Musculista senhousia (Bivalvia Mytilidae)

Musculista senhousia is a marine mussel with doubly uniparental inheritance (DUI) of mitochondria. In this study we analyzed the largest unassigned region (LUR) of its female- and male-transmitted mitochondrial genomes, described their fine characteristics and searched for shared features. Our results suggest that both LURs contain the control region of their respective mitochondrial genomes. The female-transmitted control region is duplicated in tandem, with the two copies evolving in concert. This makes the F-mtDNA of M. senhousia the first Bivalve mitochondrial genome with this feature. We also compared M. senhousia control regions to that of other Mytilidae, and demonstrated that signals for basic mtDNA functions are retained over evolutionary times even among the fast-evolving mitochondrial genomes of DUI species. Finally, we discussed how similarities between female and male LURs may be explained in the context of DUI evolution and if the duplicated female control region might have influenced the DUI system in this species.