Coupling of bacterial endosymbiont and host mitochondrial genomes in the hydrothermal vent clam Calyptogena magnifica

The hydrothermal vent clam Calyptogena magnifica (Bivalvia: Vesicomyidae) depends for its nutrition on sulfur-oxidizing symbiotic bacteria housed in its gill tissues. This symbiont is transmitted vertically between generations via the clam's eggs; however, it remains uncertain whether occasionally symbionts are horizontally transmitted or acquired from the environment. If symbionts are transmitted strictly vertically through the egg cytoplasm, inheritance of symbiont lineages should behave as if coupled to the host's maternally inherited mitochondrial DNA. This coupling would be obscured, however, with low rates of horizontal or environmental transfers, the equivalent of recombination between host lineages. Population genetic analyses of C. magnifica clams and associated symbionts from eastern Pacific hydrothermal vents clearly supported the hypothesis of strictly maternal cotransmission. Host mitochondrial and symbiont DNA sequences were coupled in a clam population that was polymorphic for both genetic markers. These markers were not similarly coupled with sequence variation at a nuclear gene locus, as expected for a randomly mating sexual population. Phylogenetic analysis of the two cytoplasmic genes also revealed no evidence for recombination. The tight association between vesicomyid clams and their vertically transmitted bacterial endosymbionts is phylogenetically very young (<50 million years) and may serve as a model for the origin and evolution of eukaryotic organelles.     

Diversifying selection in a parasitoid's symbiotic virus among genes involved in inhibiting host immunity

During parasitization of their hosts some insect parasitoids deliver resident viruses which encode genes that must be expressed in the host for successful parasitization. Among these viruses the Campoletis sonorensis Ichnovirus has been well studied and encodes a cys-motif gene family implicated in disruption of host immunity and other physiological systems. Members of this gene family encode one or more intercystine-knot structural motifs in which the non-cysteine residues of the motif are variable. We analyzed patterns of synonymous and non-synonymous substitution within the cys-motif to investigate the evolution of this gene family and the likelihood of virus-host gene coevolution. Maximum likelihood techniques suggest positive selection acts on 8 of 51 codons in the aligned cysteine-rich region. Although the detected positive selection was not strong, it likely contributes to the diversification of this gene family. Comparison of selection pressure relative to tertiary structure of the VHv1.1 cys-motif protein suggests that the hypervariable sites are exposed. Furthermore, invariant residues in the motif exhibit a region-specific pattern of codon bias, suggesting there are unusual mechanisms of effecting selection pressure at work in this system, though the mechanism has yet to be studied. The positive selection and duplication of both the gene family and the cys-motif implies either selection is driving the molecular radiation of immune suppressive genes toward novel hosts, or molecular coevolution with host targets.Novel nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession numbers AY033945, AY197489, AY197490, AY197491, AY197492, AY197493 and AY197494     

Natural adaptation and human selection of northeast African sheep genomes

African sheep manifest diverse but distinct physio-anatomical traits, which are the outcomes of natural- and human-driven selection. Here, we generated 34.8 million variants from 150 indigenous northeast African sheep genomes sequenced at an average depth of ～54× for 130 samples (Ethiopia, Libya) and ～20× for 20 samples (Sudan). These represented sheep from diverse environments, tail morphology and post-Neolithic introductions to Africa. Phylogenetic and model-based admixture analysis provided evidence of four genetic groups corresponding to altitudinal geographic origins, tail morphotypes and possible historical introduction and dispersal of the species into and across the continent. Running admixture at higher levels of K (6 ≤ K ≤ 25), revealed cryptic levels of genome intermixing as well as distinct genetic backgrounds in some populations. Comparative genomic analysis identified targets of selection that spanned conserved haplotype structures overlapping clusters of genes and gene families. These were related to hypoxia responses, ear morphology, caudal vertebrae and tail skeleton length, and tail fat-depot structures. Our findings provide novel insights underpinning morphological variation and response to human-driven selection and environmental adaptation in African indigenous sheep.     

Evolutionarily stable infection by a male-killing endosymbiont in Drosophila innubila: molecular evidence from the host and parasite genomes

Maternally inherited microbes that spread via male-killing are common pathogens of insects, yet very little is known about the evolutionary duration of these associations. The few examples to date indicate very recent, and thus potentially transient, infections. A male-killing strain of Wolbachia has recently been discovered in natural populations of Drosophila innubila. The population-level effects of this infection are significant: approximately 35% of females are infected, infected females produce very strongly female-biased sex ratios, and the resulting population-level sex ratio is significantly female biased. Using data on infection prevalence and Wolbachia transmission rates, infected cytoplasmic lineages are estimated to experience a approximately 5% selective advantage relative to uninfected lineages. The evolutionary history of this infection was explored by surveying patterns of polymorphism in both the host and parasite genomes, comparing the Wolbachia wsp gene and the host mtDNA COI gene to five host nuclear genes. Molecular data suggest that this male-killing infection is evolutionarily old, a conclusion supported with a simple model of parasite and mtDNA transmission dynamics. Despite a large effective population size of the host species and strong selection to evolve resistance, the D. innubila-Wolbachia association is likely at a stable equilibrium that is maintained by imperfect maternal transmission of the bacteria rather than partial resistance in the host species.     

An endosymbiont positively modulates ornithine decarboxylase in host trypanosomatids

Some trypanosomatids, such as Crithidia deanei, are endosymbiont-containing species. Aposymbiotic strains are obtained after antibiotic treatment, revealing interesting aspects of this symbiotic association. Ornithine decarboxylase (ODC) promotes polyamine biosynthesis and contributes to cell proliferation. Here, we show that ODC activity is higher in endosymbiont-bearing trypanosomatids than in aposymbiotic cells, but isolated endosymbionts did not display this enzyme activity. Intriguingly, expressed levels of ODC were similar in both strains, suggesting that ODC is positively modulated in endosymbiont-bearing cells. When the aposymbiotic strain was grown in conditioned medium, obtained after cultivation of the endosymbiont-bearing strain, cellular proliferation as well as ODC activity and localization were similar to that observed in the endosymbiont-containing trypanosomatids. Furthermore, dialyzed-heated medium and trypsin treatment reduced ODC activity of the aposymbiont strain. Taken together, these data indicate that the endosymbiont can enhance the protozoan ODC activity by providing factors of protein nature, which increase the host polyamine metabolism.     

The evolution of endosymbiont density in doubly infected host species

Multiple infection of individual hosts with several species or strains of maternally inherited endosymbionts is commonly observed in animals, especially insects. Here, we address theoretically the effect of co-infection on the optimal density of the endosymbionts in doubly infected hosts. Our analysis is based on the observation that a maternally inherited double infection is only stable if doubly infected females produce more doubly infected daughters than singly infected or uninfected females produce daughters. We consider both a general model and a model involving two endosymbionts inducing bidirectional cytoplasmic incompatibility (CI). We demonstrate that the optimal replication rate of endosymbionts in doubly infected hosts can be expected to be similar to or below the optimal replication rate in singly infected hosts. This is in contrast to some theoretical predictions for horizontally transmitted parasites and stems from the two strains of endosymbionts having coupled fitness. We discuss our results with respect to recent empirical results on endosymbiont densities, the evolution of CI-inducing bacteria and, more generally, the evolution of cooperation through direct fitness benefits.     

Diversifying selection of the tumor-growth promoter angiogenin in primate evolution

Diversifying selection drives the rapid differentiation of gene sequences and is one of the main forces behind adaptive evolution. Most genes known to be shaped by diversifying selection are those involved in host-pathogen or male-female interactions characterized as molecular "arms races." Here we report the unexpected detection of diversifying selection in the evolution of a tumor-growth promoter, angiogenin (ANG). A comparison among 11 primate species demonstrates that ANG has a significantly higher rate of nucleotide substitution at nonsynonymous sites than at synonymous sites, a hallmark of positive selection acting at the molecular level. Furthermore, we observed significant charge diversity at the molecular surface, suggesting the presence of selective pressures in the microenvironment of ANG, including its binding molecules. A population survey of ANG in chimpanzees, however, reveals no polymorphism, which may have resulted from a recent selective sweep of a charge-altering substitution in chimpanzee evolution. Functional assays of recombinant ANGs from the human and owl monkey indicate that primate ANGs retain angiogenic activity despite rapid evolution. Our study, together with findings of similar selection in the primate breast cancer suppressor gene, BRCA1, reveals an intriguing phenomenon of unusual selective pressures on, and adaptive evolution of, cancer-related genes in primate evolution.     

Infection density of Wolbachia endosymbiont affected by co-infection and host genotype

Infection density is among the most important factors for understanding the biological effects of Wolbachia and other endosymbionts on their hosts. To gain insight into the mechanisms of infection density regulation, we investigated the adzuki bean beetles Callosobruchus chinensis and their Wolbachia endosymbionts. Double-infected, single-infected and uninfected host strains with controlled nuclear genetic backgrounds were generated by introgression, and infection densities in these strains were evaluated by a quantitative polymerase chain reaction technique. Our study revealed previously unknown aspects of Wolbachia density regulation: (i) the identification of intra-specific host genotypes that affect Wolbachia density differently and (ii) the suppression of Wolbachia density by co-infecting Wolbachia strains. These findings shed new light on symbiont-symbiont and host-symbiont interactions in the Wolbachia-insect endosymbiosis and strongly suggest that Wolbachia density is determined through a complex interaction between host genotype, symbiont genotype and other factors.     

The evolution of mitochondrial genomes in subterranean caviomorph rodents: adaptation against a background of purifying selection

South American tuco-tucos (Ctenomys) and the related coruro (Spalacopus) are two rodent lineages that have independently colonised the subterranean niche. The energetically demanding lifestyles of these species, coupled with the hypoxic atmospheres characteristic of subterranean environments, may have altered the selective regimes on genes encoding proteins related to cellular respiration. Here, we examined the molecular evolution of 13 protein-coding genes in the mitochondrial genome of seven caviomorph rodents, including these two subterranean genera and their above-ground relatives. Using maximum-likelihood and Bayesian approaches, we estimated rates of synonymous (dS) and nonsynonymous (dN) substitutions. We found a significantly higher ω ratio (dN/dS) in subterranean groups as compared to their non-subterranean counterparts in 11 of 13 genes, although no ω ratio was larger than 1. Additionally, we applied a method based on quantitative physicochemical properties to test for positive selection. Amino acid changes implicated in radical structural or functional shifts in the protein property were found to be ubiquitous across the phylogeny, but concentrated in the subterranean lineages. Convergent changes were also found between the subterranean genera used in this study and other mammals adapted to hypoxia. The results of this study suggest a link between niche shifts and weak directional (or episodic) selection at the molecular level against a background of purifying selection.     

The battle of two genomes: genetics of bacterial host/pathogen interactions in mice

Genetic factors strongly determine the outcome of infectious diseases caused by various pathogens. The molecular mechanisms of resistance and susceptibility in humans, however, remains largely unknown. Complex interactions of multiple genes that control the host response to a pathogen further complicate the picture. Animal models have a tremendous potential to dissect the complex genetic system of host–pathogen interaction into single components. This is particularly true for the mouse, which will continue to develop into an invaluable tool in the identification and cloning of host resistance genes. Three main approaches have been taken to establish mouse models for human infectious diseases: 1) Production of mouse mutants by gene targeting; 2) positional cloning of host-resistance genes in mutant mice; and 3) mapping and characterization of quantitative trait loci (QTL) controlling the complex aspects of host–pathogen interactions. The contribution of all three methods to the understanding of infectious diseases in humans will be reviewed in this work, with a special emphasis on the studies of resistance/susceptibility mechanism in bacterial infections. Received: 7 September 2000 / Accepted: 23 November 2000     

Diversifying selection and concerted evolution of a type IV secretion system in Bartonella

We have studied the evolution of a type IV secretion system (T4SS), in Bartonella, which is thought to have changed function from conjugation to erythrocyte adherence following a recent horizontal gene transfer event. The system, called Trw, is unique among T4SSs in that genes encoding both exo- and intracellular components are located within the same duplicated fragment. This provides an opportunity to study the influence of selection on proteins involved in host-pathogen interactions. We sequenced the trw locus from several strains of Bartonella henselae and investigated its evolutionary history by comparisons to other Bartonella species. Several instances of recombination and gene conversion events where detected in the 2- to 5-fold duplicated gene fragments encompassing trwJIH, explaining the homogenization of the anchoring protein TrwI and the divergence of the minor pilus protein TrwJ. A phylogenetic analysis of the 7- to 8-fold duplicated gene coding for the major pilus protein TrwL displayed 2 distinct clades, likely representing a subfunctionalization event. The analyses of the B. henselae strains also identified a recent horizontal transfer event of almost the complete trwL region. We suggest that the switch in function of the T4SS was mediated by the duplication of the genes encoding pilus components and their diversification by combinatorial sequence shuffling within and among genomes. We suggest that the pilus proteins have evolved by diversifying selection to match a divergent set of erythrocyte surface structures, consistent with the trench warfare coevolutionary model.     

A fungal endosymbiont affects host plant recruitment through seed- and litter-mediated mechanisms

1.  Many grass species are associated with maternally transmitted fungal endophytes. Increasing evidence shows that endophytes enhance host plant success under varied conditions, yet studies have rarely considered alternative mechanisms whereby these mutualistic symbionts may affect regeneration from seed.
2.  We performed a microcosm experiment to evaluate whether infection with Neotyphodium occultans affects recruitment in the annual grass Lolium multiflorum either directly, by infecting the seeds, or indirectly, by altering the suitability of recruitment microsites through the litter shed by host plants. Endophyte effects on establishment were tested for different litter depths and watering regimes under natural herbivory by leaf-cutting ants.
3.  Seed infection increased seedling emergence through the litter as well as final recruitment, irrespective of microsite conditions. However, litter produced by infected plants delayed emergence and decreased density of both infected and non-infected grass populations.
4.  Individual plant biomass did not change with seed infection but was increased under deep litter from endophyte-infected plants. Although seed infection did not protect establishing plants from leaf-cutting ants, herbivory was reduced in the presence of deep litter shed by infected plants.
5.  We conclude that fungal endophytes may affect host plant recruitment across subsequent generations not only by infecting the seeds but also through the host's dead remains. While the former effect entailed an advantage to infected plants, litter-mediated effects did not discriminate by infection status, and generally promoted the establishment of fewer and larger plants. Thus hidden foliar symbionts may play an underappreciated role in maintaining host species dominance through the litter produced by prior patch occupants.     

Role of olfaction in host plant selection and local adaptation of a polyphagous herbivore,Eucolaspis Sharp

Host plant cues are known to shape insect–host plant association in many insect groups. More pronounced associations are generally manifested in specialist herbivores, but little is known in generalist herbivores. We used a polyphagous native beetle from New Zealand, bronze beetle, Eucolaspis sp. ‘Hawkes Bay’ (Chrysomelidae: Eumolpinae) to explore the role of olfaction in locating host plants and local adaptation. We also tested the role of other cues in the degree of acceptance or rejection of hosts. Adult Eucolaspis beetles were attracted to fresh leaf volatiles from apple and blackberry (Rosaceae). Male and female beetles responded similarly to olfactory cues of host plants. An indication of evolutionary affiliation was observed in olfactory preferences of geographically isolated conspecific populations. We found that geographically isolated populations of the beetles differ in their olfactory responses and exhibit some degree of local adaptation. However, irrespective of geographical and ecological associations, blackberry was preferred over apple as a feeding plant, and another novel plant, bush lawyer (Rubus australis), was readily accepted by 53.25% of the tested beetles. We show that plant volatiles play an important role in host location by Eucolaspis, but the acceptance or rejection of a particular host could also involve visual and contact cues.     

Co-evolution of plant LTR-retrotransposons and their host genomes

zTransposable elements (TEs), particularly, long terminal repeat retrotransposons (LTR-RTs), are the most abundant DNA components in all plant species that have been investigated, and are largely responsible for plant genome size variation. Although plant genomes have experienced periodic proliferation and/or recent burst of LTRretrotransposons, the majority of LTR-RTs are inactivated by DNA methylation and small RNA-mediated silencing mechanisms, and/or were deleted/truncated by unequal homologous recombination and illegitimate recombination, as suppression mechanisms that counteract genome expansion caused by LTR-RT amplification. LTR-RT DNA is generally enriched in pericentromeric regions of the host genomes, which appears to be the outcomes of preferential insertions of LTR-RTs in these regions and low effectiveness of selection that purges LTR-RT DNA from these regions relative to chromosomal arms. Potential functions of various TEs in their host genomes remain blurry; nevertheless, LTR-RTs have been recognized to play important roles in maintaining chromatin structures and centromere functions and regulation of gene expressions in their host genomes.     

Annotation of selection strengths in viral genomes

MOTIVATION: Viral genomes tend to code in overlapping reading frames to maximize informational content. This may result in atypical codon bias and particular evolutionary constraints. Due to the fast mutation rate of viruses, there is additional strong evidence for varying selection between intra- and intergenomic regions. The presence of multiple coding regions complicates the concept of K(a)/K(s) ratio, and thus begs for an alternative approach when investigating selection strengths. Building on the paper by McCauley and Hein, we develop a method for annotating a viral genome coding in overlapping reading frames. We introduce an evolutionary model capable of accounting for varying levels of selection along the genome, and incorporate it into our prior single sequence HMM methodology, extending it now to a phylogenetic HMM. Given an alignment of several homologous viruses to a reference sequence, we may thus achieve an annotation both of coding regions as well as selection strengths, allowing us to investigate different selection patterns and hypotheses. RESULTS: We illustrate our method by applying it to a multiple alignment of four HIV2 sequences, as well as of three Hepatitis B sequences. We obtain an annotation of the coding regions, as well as a posterior probability for each site of the strength of selection acting on it. From this we may deduce the average posterior selection acting on the different genes. Whilst we are encouraged to see in HIV2, that the known to be conserved genes gag and pol are indeed annotated as such, we also discover several sites of less stringent negative selection within the env gene. To the best of our knowledge, we are the first to subsequently provide a full selection annotation of the Hepatitis B genome by explicitly modelling the evolution within overlapping reading frames, and not relying on simple K(a)/K(s) ratios.     

Biochemical and genetic consequences of gene transfer from endosymbiont to host genome

Summary In the origin of the mitochondrion and plastid, gene transfer from the ancestral endosymbiont to the host was proposed to be a crucial event. For this genic integration to proceed, products of transferred genes had to return to and enter the endosymbionts. The limiting event was the crossing of the barrier presented by the two semipermeable membranes bounding the proto-organelle. In this paper it is suggested that spontaneous transport allowed transferred gene encoded proteins to enter the endosymbionts before receptors evolved. The effects of these events, including the degeneration of the endosymbiont genome, are discussed. Although the presumed gene transfer had profound effects on the metabolic relationships between host and endosymbionts it probably cannot account for all examples of organelle/cytoplasmic isozyme pairs or the absence of amino acid synthetic enzymes in animal cells.