scholarly journals Host shifts result in parallel genetic changes when viruses evolve in closely related species

2017 ◽  
Author(s):  
Ben Longdon ◽  
Jonathan P Day ◽  
Joel M Alves ◽  
Sophia CL Smith ◽  
Thomas M Houslay ◽  
...  
Keyword(s):  
Host Species ◽  
Related Species ◽  
Rna Virus ◽  
Parallel Evolution ◽  
Emerging Infectious Diseases ◽  
New Host ◽  
Closely Related Species ◽  
Genetic Changes ◽  
Host Shifts ◽  
Novel Host

AbstractHost shifts, where a pathogen invades and establishes in a new host species, are a major source of emerging infectious diseases. They frequently occur between related host species and often rely on the pathogen evolving adaptations that increase their fitness in the novel host species. To investigate genetic changes in novel hosts, we experimentally evolved replicate lineages of an RNA virus (Drosophila C Virus) in 19 different species of Drosophilidae and deep sequenced the viral genomes. We found a strong pattern of parallel evolution, where viral lineages from the same host were genetically more similar to each other than to lineages from other host species. When we compared viruses that had evolved in different host species, we found that parallel genetic changes were more likely to occur if the two host species were closely related. This suggests that when a virus adapts to one host it might also become better adapted to closely related host species. This may explain in part why host shifts tend to occur between related species, and may mean that when a new pathogen appears in a given species, closely related species may become vulnerable to the new disease.

scholarly journals Rapid divergence in independent aspects of the compatibility phenotype in the Spiroplasma/Drosophila interaction

2021 ◽  
Author(s):  
Joanne S. Griffin ◽  
Michael Gerth ◽  
Gregory D. D. Hurst
Keyword(s):  
Vertical Transmission ◽  
Host Species ◽  
High Efficiency ◽  
Host Shift ◽  
Direct Selection ◽  
New Host ◽  
Host Shifts ◽  
Species Pairs ◽  
Novel Host ◽  
Rapid Divergence

AbstractHeritable symbionts represent important components of host biology, both as antagonistic reproductive parasites and as beneficial protective partners. An important component of heritable microbes’ biology is their ability to establish in new host species, a process equivalent to a host shift for an infectiously transmitted parasite or pathogen. For a host shift to occur, the symbiont must be compatible with the host: it must not cause excess pathology, must have good vertical transmission, and possess a drive phenotype that enables spread. Classically, compatibility has been considered a declining function of genetic distance between novel and ancestral host species. Here we investigate the evolutionary lability of compatibility to heritable microbes by comparing the capacity for a symbiont to establish in two novel host species equally related to the ancestral host. Compatibility of the protective Spiroplasma from D. hydei with D. simulans and D. melanogaster was tested. The Spiroplasma had contrasting compatibility in these two host species. The transinfection showed pathology and low vertical transmission in D. melanogaster but was asymptomatic and transmitted with high efficiency in D. simulans. These results were not affected by the presence/absence of Wolbachia in either of the two species. The pattern of protection was not congruent with that for pathology/transmission, with protection being weaker in the D. simulans, the host in which Spiroplasma was asymptomatic and transmitted well. Further work indicated pathological interactions occurred in D. sechellia and D. yakuba, indicating that D. simulans was unusual in being able to carry the symbiont without damage. The differing compatibility of the symbiont with these closely related host species emphasises first the rapidity with which host-symbiont compatibility evolves despite compatibility itself not being subject to direct selection, and second the independence of the different components of compatibility (pathology, transmission, protection). This requirement to fit three different independently evolving aspects of compatibility, if commonly observed, is likely to be a major feature limiting the rate of host shifts. Moving forward, the variation between sibling species pairs observed above provides an opportunity to identify the mechanisms behind variable compatibility between closely related host species, which will drive hypotheses as to the evolutionary drivers of compatibility variation.

scholarly journals Host shifts result in parallel genetic changes when viruses evolve in closely related species

2018 ◽  
Vol 14 (4) ◽  
pp. e1006951 ◽  
Author(s):  
Ben Longdon ◽  
Jonathan P. Day ◽  
Joel M. Alves ◽  
Sophia C. L. Smith ◽  
Thomas M. Houslay ◽  
...  
Keyword(s):  
Related Species ◽  
Closely Related Species ◽  
Genetic Changes ◽  
Host Shifts

scholarly journals Virulence mismatches in index hosts shape the outcomes of cross-species transmission

2020 ◽  
Vol 117 (46) ◽  
pp. 28859-28866 ◽  
Author(s):  
Nardus Mollentze ◽  
Daniel G. Streicker ◽  
Pablo R. Murcia ◽  
Katie Hampson ◽  
Roman Biek
Keyword(s):  
Rabies Virus ◽  
Host Species ◽  
Single Infection ◽  
Limiting Factor ◽  
New Host ◽  
Host Shifts ◽  
Complex Interactions ◽  
Dead End ◽  
Novel Host ◽  
Meta Analyses

Whether a pathogen entering a new host species results in a single infection or in onward transmission, and potentially an outbreak, depends upon the progression of infection in the index case. Although index infections are rarely observable in nature, experimental inoculations of pathogens into novel host species provide a rich and largely unexploited data source for meta-analyses to identify the host and pathogen determinants of variability in infection outcomes. We analyzed the progressions of 514 experimental cross-species inoculations of rabies virus, a widespread zoonosis which in nature exhibits both dead-end infections and varying levels of sustained transmission in novel hosts. Inoculations originating from bats rather than carnivores, and from warmer- to cooler-bodied species caused infections with shorter incubation periods that were associated with diminished virus excretion. Inoculations between distantly related hosts tended to result in shorter clinical disease periods, which are also expected to impede onward transmission. All effects were modulated by infection dose. Taken together, these results suggest that as host species become more dissimilar, increased virulence might act as a limiting factor preventing onward transmission. These results can explain observed constraints on rabies virus host shifts, describe a previously unrecognized role of host body temperature, and provide a potential explanation for host shifts being less likely between genetically distant species. More generally, our study highlights meta-analyses of experimental infections as a tractable approach to quantify the complex interactions between virus, reservoir, and novel host that shape the outcome of cross-species transmission.

scholarly journals Dynamics of viral index infections in novel hosts

2020 ◽  
Author(s):  
Nardus Mollentze ◽  
Daniel G. Streicker ◽  
Pablo R. Murcia ◽  
Katie Hampson ◽  
Roman Biek
Keyword(s):  
Rabies Virus ◽  
Host Species ◽  
Host Shift ◽  
Single Infection ◽  
Limiting Factor ◽  
New Host ◽  
Host Shifts ◽  
Virus Excretion ◽  
Novel Host ◽  
Meta Analyses

AbstractWhether a pathogen entering a new host species results in a single infection or in onward transmission, and potentially an outbreak, depends upon the progression of infection in the index case. Although index infections are rarely observable in nature, experimental inoculations of pathogens into novel host species have a long history in biomedical research. This provides a rich and largely unexploited data source for meta-analyses to identify the host and pathogen determinants of variability in infection outcomes. Here, we analysed the progressions of 514 experimental cross-species inoculations of rabies virus, a widespread zoonotic pathogen which in nature exhibits both dead end infections and varying levels of sustained transmission in novel hosts. Inoculations originating from bats rather than carnivores, and from warmer to cooler-bodied species caused infections with shorter incubation periods that were associated with diminished virus excretion. Inoculations between distantly related hosts tended to result in shorter clinical disease periods, which will also impede transmission. All effects were modulated by infection dose and together suggest that increased virulence as host species become more dissimilar is the limiting factor preventing onward transmission. These results explain observed constraints on rabies virus host shifts, allow us to evaluate the risk of novel reservoirs establishing, and give mechanistic insights into why host shifts are less likely between genetically distant species. More generally, our study highlights meta-analyses of experimental infections as a tractable approach to quantify the complex interactions between virus, reservoir, and novel host that shape the outcome of cross-species transmission.Significance statementEmerging disease epidemics often result from a pathogen establishing transmission in a novel host species. However, most cross-species transmissions fail to establish in the newly infected species for reasons that remain poorly understood. Examining cross-species inoculations involving rabies, a widespread viral zoonosis, we show that mismatches in virulence, which are predictable from host and viral factors, make sustained transmission in the novel host less likely. In particular, disease progression was accelerated and virus excretion decreased when the reservoir and novel host were physiologically or genetically more dissimilar. These mechanistic insights help to explain and predict host shift events and highlight meta-analyses of existing experimental inoculation data as a powerful and generalisable approach for understanding the dynamics of index infections in novel species.

Revision of Coronostrongylus (Nematoda : Strongyloidea) parasitic in the stomachs of macropodid marsupials

2002 ◽  
Vol 16 (6) ◽  
pp. 893 ◽  
Author(s):  
I. Beveridge
Keyword(s):  
Papua New Guinea ◽  
Host Species ◽  
Related Species ◽  
New Guinea ◽  
Nematode Species ◽  
Closely Related Species ◽  
Nematode Genus ◽  
Eastern Australia ◽  
Wide Range ◽  
Species Occurrences

The monotypic nematode genus Coronostrongylus Johnston & Mawson, 1939 from the stomachs of macropodid marsupials was reviewed and was found to consist of a least seven closely related species. Coronostrongylus coronatus Johnston & Mawson, 1939 is found most commonly in Macropus rufogriseus, but occurs occasionally in M. dorsalis, M. parryi and Petrogale inornata. Coronostrongylus johnsoni, sp. nov. is most commonly found in M. dorsalis, but occurs also in M. rufogriseus, M. parma, Thylogale stigmatica, Petrogale godmani and P. brachyotis. Coronostrongylus barkeri, sp. nov. is most prevalent in Onychogalea unguifera, but occurs also in M. rufus, M. robustus and P. brachyotis. Coronostrongylus closei, sp. nov. is restricted to Petrogale persephone. Coronostrongylus sharmani, sp. nov. occurs only in rock wallabies from eastern Australia: P.�coenensis, P. godmani and P. mareeba; C. spratti, sp. nov. occurs in P. inornata and P. assimilis. Coronostrongylus spearei, sp. nov. is restricted to Papua New Guinea where it is found in Dorcopsulus vanhearni, Dorcopsis hageni and D. muelleri. Although all of the nematode species occur in one principal host species or a series of closely related host species, occurrences in geographically disjunct areas and in phylogenetically distant hosts are features of C. coronatus, C. barkeri, sp. nov. and C. johnsoni, sp. nov. The occurrence of seven closely related nematode species found in a wide range of macropodid host species is more readily accounted for by a hypothesis involving multiple colonisations of hosts than by the hypothesis of co-speciation.

Altitudinal Variation in, and Morphological Divergence between, Three Related Species of Grasshopper, Praxibulus sp., Kosciuscola cognatus and K. usitatus (Orthoptera:Acrididae)

1980 ◽  
Vol 28 (1) ◽  
pp. 103 ◽  
Author(s):  
NA Campbell ◽  
JM Dearn
Keyword(s):  
Related Species ◽  
Character Displacement ◽  
Altitudinal Variation ◽  
Multivariate Statistical ◽  
Closely Related Species ◽  
Genetic Changes ◽  
Parallel Change ◽  
Variable Character ◽  
Multivariate Statistical Approach ◽  
Species Specific

Morphological variation between and within the closely related species Praxibuius sp.. Kosciuscola cognatus and K. usiratus has been examined along three independent altitudinal transects, by a multivariate statistical approach. The analyses, which were restricted to males. show that there is complete morphological separation between the three species. Moreover. there are species-specific patterns of character correlation which are consistent and relatively invariant within species, and do not exhibit altitudinal variation. The results suggest that there exist both distinct invariant species-specific character patterns and variable character patterns showing intraspecific variation. It is concluded that speciation in these grasshoppers could have involved genetic changes quite distinct from those involved in local intraspecific adaptation. Two further results are: first. evidence has been obtained for character displacement between Kosciuscola cognaius and Praxibulus sp. in an area of extensive sympatry: second. populations of K. cognatus along one transect, with a karyotype intermediate between typical K. cognatus and X usiiatus, show a parallel change in morphology towards that characteristic of K. usiiatus.

scholarly journals Excessive Parallelism in Protein Evolution of Lake Baikal Amphipod Species Flock

2020 ◽  
Vol 12 (9) ◽  
pp. 1493-1503
Author(s):  
Valentina Burskaia ◽  
Sergey Naumenko ◽  
Mikhail Schelkunov ◽  
Daria Bedulina ◽  
Tatyana Neretina ◽  
...  
Keyword(s):  
Amino Acid ◽  
Lake Baikal ◽  
Related Species ◽  
Parallel Evolution ◽  
Amino Acid Level ◽  
Species Flock ◽  
Amphipod Species ◽  
Closely Related Species ◽  
Epistatic Interactions ◽  
Synonymous Sites

Abstract Repeated emergence of similar adaptations is often explained by parallel evolution of underlying genes. However, evidence of parallel evolution at amino acid level is limited. When the analyzed species are highly divergent, this can be due to epistatic interactions underlying the dynamic nature of the amino acid preferences: The same amino acid substitution may have different phenotypic effects on different genetic backgrounds. Distantly related species also often inhabit radically different environments, which makes the emergence of parallel adaptations less likely. Here, we hypothesize that parallel molecular adaptations are more prevalent between closely related species. We analyze the rate of parallel evolution in genome-size sets of orthologous genes in three groups of species with widely ranging levels of divergence: 46 species of the relatively recent lake Baikal amphipod radiation, a species flock of very closely related cichlids, and a set of significantly more divergent vertebrates. Strikingly, in genes of amphipods, the rate of parallel substitutions at nonsynonymous sites exceeded that at synonymous sites, suggesting rampant selection driving parallel adaptation. At sites of parallel substitutions, the intraspecies polymorphism is low, suggesting that parallelism has been driven by positive selection and is therefore adaptive. By contrast, in cichlids, the rate of nonsynonymous parallel evolution was similar to that at synonymous sites, whereas in vertebrates, this rate was lower than that at synonymous sites, indicating that in these groups of species, parallel substitutions are mainly fixed by drift.

scholarly journals Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints

2013 ◽  
Vol 368 (1614) ◽  
pp. 20120196 ◽  
Author(s):  
Nuno Rodrigues Faria ◽  
Marc A. Suchard ◽  
Andrew Rambaut ◽  
Daniel G. Streicker ◽  
Philippe Lemey
Keyword(s):  
Rabies Virus ◽  
Host Species ◽  
Bayesian Model Averaging ◽  
Model Averaging ◽  
Viral Gene ◽  
Human Pathogens ◽  
New Host ◽  
Discrete State ◽  
Transition Processes ◽  
Host Shifts

The factors that determine the origin and fate of cross-species transmission events remain unclear for the majority of human pathogens, despite being central for the development of predictive models and assessing the efficacy of prevention strategies. Here, we describe a flexible Bayesian statistical framework to reconstruct virus transmission between different host species based on viral gene sequences, while simultaneously testing and estimating the contribution of several potential predictors of cross-species transmission. Specifically, we use a generalized linear model extension of phylogenetic diffusion to perform Bayesian model averaging over candidate predictors. By further extending this model with branch partitioning, we allow for distinct host transition processes on external and internal branches, thus discriminating between recent cross-species transmissions, many of which are likely to result in dead-end infections, and host shifts that reflect successful onwards transmission in the new host species. Our approach corroborates genetic distance between hosts as a key determinant of both host shifts and cross-species transmissions of rabies virus in North American bats. Furthermore, our results indicate that geographical range overlap is a modest predictor for cross-species transmission, but not for host shifts. Although our evolutionary framework focused on the multi-host reservoir dynamics of bat rabies virus, it is applicable to other pathogens and to other discrete state transition processes.

scholarly journals Parallel evolution of metazoan mitochondrial proteins

2016 ◽  
Author(s):  
Galya V. Klink ◽  
Georgii A. Bazykin
Keyword(s):  
Amino Acid ◽  
Related Species ◽  
Parallel Evolution ◽  
Phylogenetic Reconstruction ◽  
Acid Sites ◽  
Mitochondrial Proteins ◽  
Phylogenetic Distance ◽  
Closely Related Species ◽  
Epistatic Interactions ◽  
The Mean

AbstractAmino acid propensities at amino acid sites change with time due to epistatic interactions or changing environment, affecting the probabilities of fixation of different amino acids. Such changes should lead to an increased rate of homoplasies (reversals, parallelisms, and convergences) at closely related species. Here, we reconstruct the phylogeny of twelve mitochondrial proteins from several thousand metazoan species, and measure the phylogenetic distances between branches at which either the same allele originated repeatedly due to homoplasies, or different alleles originated due to divergent substitutions. The mean phylogenetic distance between parallel substitutions is ∼20% lower than the mean phylogenetic distance between divergent substitutions, indicating that a variant fixed in a species is more likely to be deleterious in a more phylogenetically remote species, compared to a more closely related species. These findings are robust to artefacts of phylogenetic reconstruction or of pooling of sites from different conservation classes or functional groups, and imply that single-position fitness landscapes change at rates similar to rates of amino acid changes.

scholarly journals Susceptibility across host species is independent of dietary protein to carbohydrate ratios

2020 ◽  
Author(s):  
Katherine E Roberts ◽  
Ben Longdon
Keyword(s):  
Viral Load ◽  
Dietary Protein ◽  
Host Species ◽  
Rna Virus ◽  
Ecological Factors ◽  
Host Shift ◽  
Host Susceptibility ◽  
Novel Host ◽  
Host Diet ◽  
Host Parasite

AbstractThe likelihood of a successful host shift of a parasite to a novel host species can be influenced by environmental factors that can act on both the host and parasite. Changes in nutritional resource availability have been shown to alter pathogen susceptibility and the outcome of infection in a range of systems. Here we examined how dietary protein to carbohydrate altered susceptibility in a large cross infection experiment. We infected 27 species of Drosophilidae with an RNA virus on three food types of differing protein to carbohydrate ratios. We then measured how viral load and mortality across species was affected by changes in diet. We found that changes in the protein:carbohydrate in the diet did not alter the outcomes of infection, with strong positive inter-species correlations in both viral load and mortality across diets, suggesting no species by diet interaction. Mortality and viral load were strongly positively correlated, and this association was consistent across diets. This suggests changes in diet may give consistent outcomes across host species, and may not be universally important in determining host susceptibility to pathogens.Impact StatementA successful host shift of a parasite from one susceptible species to a novel host can be influenced by many ecological factors. Changes in host diet can alter the immune response and outcomes of host–parasite interactions and could potentially alter the outcome of a virus host shift. To investigate, we infected 27 species of Drosophilidae with an RNA virus (DCV) across three food types with differing protein to carbohydrate ratios. We then looked at pathogen loads and survival of infected hosts compared to uninfected controls. Changes in the ratio of protein to carbohydrate did not alter susceptibility to DCV across host species.

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