Phylogenetic diversity and cosymbiosis in the bioluminescent symbioses of "Photobacterium mandapamensis"

"Photobacterium mandapamensis" (proposed name) and Photobacterium leiognathi are closely related, phenotypically similar marine bacteria that form bioluminescent symbioses with marine animals. Despite their similarity, however, these bacteria can be distinguished phylogenetically by sequence divergence of their luminescence genes, luxCDAB(F)E, by the presence (P. mandapamensis) or the absence (P. leiognathi) of luxF and, as shown here, by the sequence divergence of genes involved in the synthesis of riboflavin, ribBHA. To gain insight into the possibility that P. mandapamensis and P. leiognathi are ecologically distinct, we used these phylogenetic criteria to determine the incidence of P. mandapamensis as a bioluminescent symbiont of marine animals. Five fish species, Acropoma japonicum (Perciformes, Acropomatidae), Photopectoralis panayensis and Photopectoralis bindus (Perciformes, Leiognathidae), Siphamia versicolor (Perciformes, Apogonidae), and Gadella jordani (Gadiformes, Moridae), were found to harbor P. mandapamensis in their light organs. Specimens of A. japonicus, P. panayensis, and P. bindus harbored P. mandapamensis and P. leiognathi together as cosymbionts of the same light organ. Regardless of cosymbiosis, P. mandapamensis was the predominant symbiont of A. japonicum, and it was the apparently exclusive symbiont of S. versicolor and G. jordani. In contrast, P. leiognathi was found to be the predominant symbiont of P. panayensis and P. bindus, and it appears to be the exclusive symbiont of other leiognathid fishes and a loliginid squid. A phylogenetic test for cospeciation revealed no evidence of codivergence between P. mandapamensis and its host fishes, indicating that coevolution apparently is not the basis for this bacterium's host preferences. These results, which are the first report of bacterial cosymbiosis in fish light organs and the first demonstration that P. leiognathi is not the exclusive light organ symbiont of leiognathid fishes, demonstrate that the host species ranges of P. mandapamensis and P. leiognathi are substantially distinct. The host range difference underscores possible differences in the environmental distributions and physiologies of these two bacterial species.     

Productivity links morphology,symbiont specificity and bleaching in the evolution of Caribbean octocoral symbioses

Many cnidarians host endosymbiotic dinoflagellates from the genus Symbiodinium. It is generally assumed that the symbiosis is mutualistic, where the host benefits from symbiont photosynthesis while providing protection and photosynthetic substrates. Diverse assemblages of symbiotic gorgonian octocorals can be found in hard bottom communities throughout the Caribbean. While current research has focused on the phylo- and population genetics of gorgonian symbiont types and their photo-physiology, relatively less work has focused on biogeochemical benefits conferred to the host and how these benefits vary across host species. Here we examine this symbiosis among 11 gorgonian species collected in Bocas del Toro, Panama. By coupling light and dark bottle incubations (P/R) with ¹³C-bicarbonate tracers, we quantified the link between holobiont oxygen metabolism with carbon assimilation and translocation from symbiont to host. Our data show that P/R varied among species, and was correlated with colony morphology and polyp size. Sea fans and sea plumes were net autotrophs (P/R>1.5), while nine species of sea rods were net heterotrophs with most below compensation (P/R<1.0). ¹³C assimilation corroborated the P/R results, and maximum δ¹³C_host values were strongly correlated with polyp size, indicating higher productivity by colonies with high polyp SA:V. A survey of gorgonian-Symbiodinium associations revealed that productive species maintain specialized, obligate symbioses and are more resistant to coral bleaching, whereas generalist and facultative associations are common among sea rods that have higher bleaching sensitivities. Overall, productivity and polyp size had strong phylogenetic signals with carbon fixation and polyp size showing evidence of trait covariance.     

Phylogenetic codivergence supports coevolution of mimetic Heliconius butterflies

The unpalatable and warning-patterned butterflies Heliconius erato and Heliconius melpomene provide the best studied example of mutualistic Müllerian mimicry, thought-but rarely demonstrated-to promote coevolution. Some of the strongest available evidence for coevolution comes from phylogenetic codivergence, the parallel divergence of ecologically associated lineages. Early evolutionary reconstructions suggested codivergence between mimetic populations of H. erato and H. melpomene, and this was initially hailed as one of the most striking known cases of coevolution. However, subsequent molecular phylogenetic analyses found discrepancies in phylogenetic branching patterns and timing (topological and temporal incongruence) that argued against codivergence. We present the first explicit cophylogenetic test of codivergence between mimetic populations of H. erato and H. melpomene, and re-examine the timing of these radiations. We find statistically significant topological congruence between multilocus coalescent population phylogenies of H. erato and H. melpomene. Cophylogenetic historical reconstructions support repeated codivergence of mimetic populations, from the base of the sampled radiations. Pairwise distance correlation tests, based on our coalescent analyses plus recently published AFLP and wing colour pattern gene data, also suggest that the phylogenies of H. erato and H. melpomene show significant topological congruence. Divergence time estimates, based on a Bayesian coalescent model, suggest that the evolutionary radiations of H. erato and H. melpomene occurred over the same time period, and are compatible with a series of temporally congruent codivergence events. Our results suggest that differences in within-species genetic divergence are the result of a greater overall effective population size for H. erato relative to H. melpomene and do not imply incongruence in the timing of their phylogenetic radiations. Repeated codivergence between Müllerian co-mimics, predicted to exert mutual selection pressures, strongly suggests coevolution. Our results therefore support a history of reciprocal coevolution between Müllerian co-mimics characterised by phylogenetic codivergence and parallel phenotypic change.     

Geographical variation in host–ant specificity of the parasitic butterfly Maculinea alcon in Denmark

Abstract  1. Maculinea alcon uses three different species of Myrmica host ants along a north–south gradient in Europe. Based on this geographical variation in host ant use, Elmes et al . (1994) suggested that M. alcon might consist of three or more cryptic species or host races, each using a single and different host-ant species.
2. Population-specific differences in allozyme genotypes of M. alcon in Denmark ( Gadeberg & Boomsma, 1997 ) have suggested that genetically differentiated forms may occur in a gradient across Denmark, possibly in relation to the use of different host ants.
3. It was found that two host-ant species are indeed used as hosts in Denmark, but not in a clear-cut north–south gradient. Furthermore, specificity was not complete for many M. alcon populations. Of five populations investigated in detail, one used primarily M. rubra as a host, another exclusively used M. ruginodis , while the other three populations used both ant species. No population in Denmark used M. scabrinodis as a host, although this species was present in the habitat and is known to be a host in central and southern Europe.
4. In terms of number of parasites per nest and number of nests parasitised, M. rubra seems to be a more suitable host in populations where two host species are used simultaneously. Host-ant species has an influence on caterpillar size but this varies geographically. Analyses of pupae did not, however, show size differences between M. alcon raised in M. rubra and M. ruginodis nests.
5. The geographical mosaic of host specificity and demography of M. alcon in Denmark probably reflects the co-evolution of M. alcon with two alternative host species. This system therefore provides an interesting opportunity for studying details of the evolution of parasite specificity and the dynamics of host-race formation.     

Limited geographic distribution of certain strains of the bioluminescent symbiont Photobacterium leiognathi

Photobacterium leiognathi is a facultative bioluminescent symbiont of marine animals. Strains of P.?leiognathi that are merodiploid for the luminescence genes (lux-rib operon) have been previously obtained only from Japan. In contrast, strains bearing a single lux-rib operon have been obtained from all the areas sampled in Japan and the western Pacific. In this study, we tested whether distribution of merodiploid P.?leiognathi is limited by physical barriers in the environment, or because fish in the western Pacific preferentially form symbiosis with bacteria bearing a single lux-rib operon. We collected light organ symbionts from Secutor indicius, a fish species that is typically found in the western Pacific and has only recently expanded its geographic range to Japan. We found that all S.?indicius specimens collected from Japan formed symbiosis only with single lux-rib operon-bearing strains, although fish from other species collected from the same geographic area frequently contained merodiploid strains. This result shows that S.?indicius were preferentially colonized by bacteria bearing a single lux-rib operon and suggests that the limited geographic distribution of merodiploid P.?leiognathi can be attributed to preferential colonization of fish species found in the western Pacific by strains bearing only a single lux-rib operon.     

Diversity and specificity of Caribbean sponge–zoanthid symbioses: a foundation for understanding the adaptive significance of symbioses and generating hypotheses about higher-order systematics

The diversity and specificity of symbiotic associations may be useful in revealing the underlying ecology of symbioses and evolutionary relationships of symbiotic species. Symbioses between coral reef sponges and zoanthids are widespread and common in the greater Caribbean region, although the diversity and specificity of the species involved have only been explored at a few sites and the adaptive significance has only been examined for three combinations. We identified extensive diversity among sponges that associate with zoanthids by compiling sponge–zoanthid species associations from field surveys, the literature, and museum collections, and examined the patterns of specificity at multiple levels of sponge and zoanthid taxonomy. The results obtained indicate that facultative sponges are highly specific to the species of their partners whereas obligate zoanthids are not. The patterns of specificity among sponges and zoanthids suggest that many of these associations are not likely to be parasitic. Sponges harbouring photosynthetic endosymbionts associate at a disproportionately high frequency with zoanthids that harbour photosynthetic endosymbionts. Zoanthids embed in the surfaces of sponges to various degrees, resulting in a range of intimacy that negatively correlates with the number of hosts and polyp volume of zoanthids. Dendrograms based on the similarity among associations are largely consistent with current hypotheses of sponge higher-order systematics, but inconsistent with the current hypotheses of zoanthid systematics, and they highlight the potential utility of ecological characters in systematic analyses.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 695–711.     

Phylogenetic consequences of symbioses: Eukarya and Eubacteria are not monophyletic taxa.

In the past systematists have not been concerned with distinguishing the different phylogenetic histories for symbiont taxa that have merged within a composite taxon, or holobiont. I suggest that symbionts can retain their status as discrete taxa and that their independent histories can be included in phylogenetic analyses intending to discover monophyletic groups. Use of reticulate branches to include independent histories for different symbionts, incorporates our improving understanding of evolution and provides greater accuracy in denoting monophyletic groups. In an expanded view, a monophyletic group includes only and all the descendants of the merged-symbionts' common ancestor. Holobiont taxa will have constituent symbionts included in different monophyletic groups and there will be a reduction in the number of monophyletic groups recognized, particularly at higher taxonomic levels. As a consequence of considering symbioses in phylogenetic analyses, the proposed taxa Eubacteria and Eukarya are seen to be non-monophyletic, and, thus, poor indicators of evolutionary history.     

Coevolutionary interactions in a host–parasite system

Interactions between parasitic cuckoos and their hosts represent a classic example of coevolution, where adaptations in the parasite to exploit the host select for defences, which in turn select for new parasite adaptations. Current interactions between the two parties may be at an evolutionary equilibrium or, alternatively, a coevolutionary arms race may be taking place. By taking into account the effect of gene flow in 15 European magpie ( Pica pica ) populations, we studied the coevolutionary interactions with its brood parasite, the great spotted cuckoo ( Clamator glandarius ). Our results suggest that, in Europe, magpies and cuckoos are engaged in an ongoing coevolutionary process because, despite controlling for the large amounts of gene flow among different magpie populations, we still found a positive relationship between host defence (i.e. foreign egg recognition and rejection) and parasite selection pressure.     

Phylogenomic analysis of seal lice reveals codivergence with their hosts

Lice are considered a model system for studying the process of cospeciation because they are obligate and permanent parasites and are often highly host‐specific. Among lice, species in the family Echinophthiriidae Enderlein (Anoplura) are unique in that they infest mammalian hosts with an amphibious lifestyle, i.e. pinnipeds and the river otter. There is evidence that the ancestor of this group infested the terrestrial ancestor of pinnipeds, which suggests these parasites coevolved with their hosts during the transition to marine environments. However, there has been no previous study investigating the phylogenetic relationships among sucking lice parasitizing seals and sea lions. To uncover the evolutionary history of these parasites, we obtained genomic data for Antarctophthirus microchir Trouessart and Neumann (from two hosts), Antarctophthirus carlinii Leonardi et al., Antarctophthirus lobodontis Enderlein, Antarctophthirus ogmorhini Enderlein, Lepidophthirus macrorhini Enderlein, and Proechinophthirus fluctus Ferris. From genomic sequence reads, we assembled > 1000 nuclear genes and used these data to infer a phylogenetic tree for these lice. We also used the assembled genes in combination with read‐mapping to estimate heterozygosity and effective population size from individual lice. Our analysis supports the monophyly of lice from pinnipeds and uncovers phylogenetic relationships within the group. Surprisingly, we found that A. carlinii, A. lobodontis, and A. ogmorhini have very little genetic divergence among them, whereas the divergence between different geographic representatives of A. microchir indicate that they are possibly different species. Nevertheless, our phylogeny of Echinophthiriidae suggests that these lice have consistently codiverged with their hosts with minimal host switching. Population genomic metrics indicate that louse effective population size is linked to host demographics, which further highlights the close association between pinnipeds and their lice.     

Spatial dynamics in a host–multiparasitoid community

1. The harlequin bug, a herbivore on bladderpod, is attacked by two specialist egg parasitoids Trissolcus murgantiae and Ooencyrtus johnsonii . Ooencyrtus can out-compete Trissolcus in the laboratory, but coexistence is the norm in field populations. Despite the heavy mortality inflicted by the two parasitoids, the host–parasitoid interaction is persistent in all sites that have been studied in southern California.
2. I manipulated inter-patch distances in a field experiment to determine whether spatial processes drive parasitoid coexistence and/or host–parasitoid dynamics. I first tested the hypothesis that the parasitoids coexist via a dispersal–competition trade-off. Both parasitoid species took significantly longer to colonize isolated patches than well-connected patches, suggesting that they have comparable dispersal abilities. Ooencyrtus did not exclude Trissolcus even when inter-patch distances were reduced to 25–30% of those observed in natural populations. These data suggest that parasitoid coexistence can occur in the absence of a dispersal advantage to the inferior competitor.
3. Since the treatments with isolated vs. well-connected patches did not differ in parasitoid composition, I next asked whether isolation would destabilize, or drive extinct, the host–multiparasitoid interaction. No local extinctions of bugs or parasitoids were observed during the 18-month study period. Bug populations in the isolated patches were no more variable than those in the well-connected patches. In fact, temporal variability in the experimentally isolated patches was comparable to that observed in highly isolated natural populations.
4. These data argue against a strong effect of spatial processes on host–parasitoid dynamics. Local processes may mediate both parasitoid coexistence as well as the host–parasitoid interaction.     

Wolbachia in two insect host–parasitoid communities

Wolbachia form a group of intracellular bacteria that alter reproduction in their arthropod hosts. Two major phylogenetic subdivisions (A and B) of Wolbachia occur. Using a polymerase chain reaction assay we surveyed for the A and B group Wolbachia in 82 insect species from two temperate host–parasitoid communities (food webs) and a general collection of Lepidoptera caught at a light trap. One host–parasitoid community was based around leaf-mining Lepidoptera, and the other around Aphids. We found that: (i) 22.0% of insects sampled were infected with Wolbachia ; and (ii) the prevalence and type (A or B) of Wolbachia infection differed significantly between communities and taxonomic groups. We obtained DNA sequences from the ftsZ gene for the group B Wolbachia found in six leaf-mining species and one of their parasitoids, as well as four of the Lepidoptera caught by a light trap. Taken together, the results of our survey and phylogenetic analyses of the sequence data suggest that host–parasitoid transfer of Wolbachia is not the major route through which the species we have examined become infected. In addition, the Wolbachia strains observed in five leaf-mining species from the same genus were not closely related, indicating that transfer between species has not occurred due to a shared feeding niche or cospeciation.     

Strain diversity and host specificity in a specialized gut symbiont of honeybees and bumblebees

Host‐restricted lineages of gut bacteria often include many closely related strains, but this fine‐scale diversity is rarely investigated. The specialized gut symbiont Snodgrassella alvi has codiversified with honeybees (Apis mellifera) and bumblebees (Bombus) for millions of years. Snodgrassella alvi strains are nearly identical for 16S rRNA gene sequences but have distinct gene repertoires potentially affecting host biology and community interactions. We examined S. alvi strain diversity within and between hosts using deep sequencing both of a single‐copy coding gene (minD) and of the V4 region of the 16S rRNA gene. We sampled workers from domestic and feral A. mellifera colonies and wild‐caught Bombus representing 14 species. Conventional analyses of community profiles, based on the V4 region of the 16S rRNA gene, failed to expose most strain variation. In contrast, the minD analysis revealed extensive strain variation within and between host species and individuals. Snodgrassella alvi strain diversity is significantly higher in A. mellifera than in Bombus, supporting the hypothesis that colony founding by swarms of workers enables retention of more diversity than colony founding by a single queen. Most Bombus individuals (72%) are dominated by a single S. alvi strain, whereas most A. mellifera (86%) possess multiple strains. No S. alvi strains are shared between A. mellifera and Bombus, indicating some host specificity. Among Bombus‐restricted strains, some are restricted to a single host species or subgenus, while others occur in multiple subgenera. Findings demonstrate that strains diversify both within and between host species and can be highly specific or relatively generalized in their host associations.     

Phylogenetic host specificity and understanding parasite sharing in primates

Understanding how parasites are transmitted to new species is of great importance for human health, agriculture and conservation. However, it is still unclear why some parasites are shared by many species, while others have only one host. Using a new measure of ‘phylogenetic host specificity’, we find that most primate parasites with more than one host are phylogenetic generalists, infecting less closely related primates than expected. Evolutionary models suggest that phylogenetic host generalism is driven by a mixture of host–parasite cospeciation and lower rates of parasite extinction. We also show that phylogenetic relatedness is important in most analyses, but fails to fully explain patterns of parasite sharing among primates. Host ecology and geographical distribution emerged as key additional factors that influence contacts among hosts to facilitate sharing. Greater understanding of these factors is therefore crucial to improve our ability to predict future infectious disease risks.     

Disturbance‐modulated symbioses in termitophily

Symbiosis, the living‐together of unlike organisms, underlies every major transition in evolution and pervades most ecological dynamics. Among examples of symbioses, the simultaneous occupation of a termite nest by its builder termites and intruding invertebrate species (so‐called termitophily) provides suitable macroscopic scenarios for the study of species coexistence in confined environments. Current evidence on termitophily abounds for dynamics occurring at the interindividual level within the termitarium, but is insufficient for broader scales such as the community and the landscape. Here, we inspect the effects of abiotic disturbance on termitophile presence and function in termitaria at these broader scales. To do so, we censused the termitophile communities inhabiting 30 termitaria of distinct volumes which had been exposed to increasing degrees of fire‐induced disturbance in a savanna‐like ecosystem in southeastern Brazil. We provide evidence that such an abiotic disturbance can ease the living‐together of termitophiles and termites. Putative processes facilitating these symbioses, however, varied according to the invader. For nonsocial invaders, disturbance seemed to boost coexistence with termites via the habitat amelioration that termitaria provided under wildfire, as suggested by the positive correlation between disturbance degree and termitophile abundance and richness. As for social invaders (ants), disturbance seemed to enhance associational defenses with termites, as suggested by the negative correlation between the presence of ant colonies and the richness and abundance of other termitarium‐cohabiting termitophiles. It is then apparent that disturbance‐modulated distinct symbioses in these termite nests.     

Molecular and ecological evidence for species specificity and coevolution in a group of marine algal-bacterial symbioses

The phylogenetic relationships of bacterial symbionts from three gall-bearing species in the marine red algal genus Prionitis (Rhodophyta) were inferred from 16S rDNA sequence analysis and compared to host phylogeny also inferred from sequence comparisons (nuclear ribosomal internal-transcribed-spacer region). Gall formation has been described previously on two species of Prionitis, P. lanceolata (from central California) and P. decipiens (from Peru). This investigation reports gall formation on a third related host, Prionitis filiformis. Phylogenetic analyses based on sequence comparisons place the bacteria as a single lineage within the Roseobacter grouping of the alpha subclass of the division Proteobacteria (99.4 to 98.25% sequence identity among phylotypes). Comparison of symbiont and host molecular phylogenies confirms the presence of three gall-bearing algal lineages and is consistent with the hypothesis that these red seaweeds and their bacterial symbionts are coevolving. The species specificity of these associations was investigated in nature by whole-cell hybridization of gall bacteria and in the laboratory by using cross-inoculation trials. Whole-cell in situ hybridization confirmed that a single bacterial symbiont phylotype is present in galls on each host. In laboratory trials, bacterial symbionts were incapable of inducing galls on alternate hosts (including two non-gall-bearing species). Symbiont-host specificity in Prionitis gall formation indicates an effective ecological separation between these closely related symbiont phylotypes and provides an example of a biological context in which to consider the organismic significance of 16S rDNA sequence variation.