Correlating viral phenotypes with phylogeny: Accounting for phylogenetic uncertainty

Parker, Joe; Rambaut, Andrew; Pybus, Oliver G.

doi:10.1016/j.meegid.2007.08.001

Cited by 411 publications

(433 citation statements)

References 37 publications

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“…Maximum-likelihood phylogenies of each sequence subset [Capsid ORF, noncoding region, partial replication-associated protein ORF, and all regions concatenated (partial BFDV genome)] were inferred using MEGA (46). The program BaTS (Bayesian Tip-association Significance testing) was used to test for a host species association among the phylogenetic tips using all known BFDV sequences from endemic Australian host species but also among P. elegans subspecies in a separate analysis (47). MrBayes was used to produce a posterior set of trees to be used in BaTS (48).…”

Section: Methodsmentioning

confidence: 99%

Phylogenetic analysis of beak and feather disease virus across a host ring-species complex

Eastwood¹,

Berg²,

Ribot³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Pathogens have been hypothesized to play a major role in host diversity and speciation. Susceptibility of hybrid hosts to pathogens is thought to be a common phenomenon that could promote host population divergence and subsequently speciation. However, few studies have tested for pathogen infection across animal hybrid zones while testing for codivergence of the pathogens in the hybridizing host complex. Over 8 y, we studied natural infection by a rapidly evolving single-strand DNA virus, beak and feather diseases virus (BFDV), which infects parrots, exploiting a host-ring species complex (Platycercus elegans) in Australia. We found that host subspecies and their hybrids varied strikingly in both BFDV prevalence and load: both hybrid and phenotypically intermediate subspecies had lower prevalence and load compared with parental subspecies, while controlling for host age, sex, longitude and latitude, as well as temporal effects. We sequenced viral isolates throughout the range, which revealed patterns of genomic variation analogous to Mayr's ring-species hypothesis, to our knowledge for the first time in any host-pathogen system. Viral phylogeny, geographic location, intraspecific host density, and parrot community diversity and composition did not explain the differences in BFDV prevalence or load between subpopulations. Overall, our analyses suggest that functional host responses to infection, or force of infection, differ between subspecies and hybrids. Our findings highlight the role of host hybridization and clines in altering host-pathogen interactions, dynamics that can have important implications for models of speciation with gene flow, and offer insights into how pathogens may adapt to diverging host populations.psittacine circovirus | host-pathogen coevolution | heterosis | sympatric speciation | crimson rosella

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Section: Methodsmentioning

confidence: 99%

Phylogenetic analysis of beak and feather disease virus across a host ring-species complex

Eastwood¹,

Berg²,

Ribot³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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“…To establish whether shared colour patterns are randomly distributed on each phylogeny or if they might be attributed to phylogenetic relationships (that is, common descent), we used a Bayesian approach to compare our observed distribution of colour forms on each phylogeny with a null, random distribution using program BaTS (Bayesian Tip-association Significance testing 40 ). BaTS tests for significant phylogeny-trait correlations and accounts for phylogenetic uncertainty by integrating over the entire collection of post burn-in trees generated by the MrBayes analysis of each data set.…”

Section: Methodsmentioning

confidence: 99%

Repeated evolution in overlapping mimicry rings among North American velvet ants

et al. 2012

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Müllerian mimicry, in which two or more harmful species share a similar appearance for mutual benefit, is a widely appreciated, yet relatively uncommon natural phenomenon. Although Müllerian mimicry occurs in vertebrates, most studies are focused on tropical, herbivorous invertebrates. Here we identify a large Müllerian mimicry complex in North American velvet ants (Hymenoptera: Mutillidae). These are conspicuous, diurnal parasitoids of bees and wasps that defend themselves with a powerful sting. We investigate morphological and genetic variation and ask whether morphological similarities are the result of convergent evolution or shared ancestry. We find that 65 species in the velvet ant genus Dasymutilla can be placed into one of six morphologically distinct and geographically delimited mimicry rings. Müllerian colour patterns are primarily the result of independent evolution rather than shared, phylogenetic history. These convergent colour syndromes represent one of the largest known Müllerian mimicry complexes yet identified, particularly in the Northern Hemisphere.

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“…The MC statistic assesses the association between specific hosts and viruses by estimating the size of the largest cluster of viruses using the same reservoir hosts. These analyses were performed using the program BaTS v0.90 beta (33), which calculates empirical distributions of these statistics from the credible sample (posterior distribution) of trees provided by the Bayesian phylogenetic analyses (described previously). The significance of association statistics was assessed by randomizing the host-virus associations 1,000 times and recalculating the statistics across the distribution of trees to estimate null distributions.…”

Section: Methodsmentioning

confidence: 99%

Family level phylogenies reveal modes of macroevolution in RNA viruses

Kitchen

Shackelton

Holmes

2010

Proc. Natl. Acad. Sci. U.S.A.

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Despite advances in understanding the patterns and processes of microevolution in RNA viruses, little is known about the determinants of viral diversification at the macroevolutionary scale. In particular, the processes by which viral lineages assigned as different "species" are generated remain largely uncharacterized. To address this issue, we use a robust phylogenetic approach to analyze patterns of lineage diversification in five representative families of RNA viruses. We ask whether the process of lineage diversification primarily occurs when viruses infect new host species, either through cross-species transmission or codivergence, and which are defined here as analogous to allopatric speciation in animals, or by acquiring new niches within the same host species, analogous to sympatric speciation. By mapping probable primary host species onto family level viral phylogenies, we reveal a strong clustering among viral lineages that infect groups of closely related host species. Although this is consistent with lineage diversification within individual hosts, we argue that this pattern more likely represents strong biases in our knowledge of viral biodiversity, because we also find that better-sampled human viruses rarely cluster together. Hence, although closely related viruses tend to infect related host species, it is unlikely that they often infect the same host species, such that evolutionary constraints hinder lineage diversification within individual host species. We conclude that the colonization of new but related host species may represent the principle mode of macroevolution in RNA viruses.emergence | molecular evolution | host jumping

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Correlating viral phenotypes with phylogeny: Accounting for phylogenetic uncertainty

Cited by 411 publications

References 37 publications

Phylogenetic analysis of beak and feather disease virus across a host ring-species complex

Phylogenetic analysis of beak and feather disease virus across a host ring-species complex

Repeated evolution in overlapping mimicry rings among North American velvet ants

Family level phylogenies reveal modes of macroevolution in RNA viruses

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