PACo: A Novel Procrustes Application to Cophylogenetic Analysis

Balbuena, Juan Antonio; Míguez-Lozano, Raúl; Blasco‐Costa, Isabel

doi:10.1371/journal.pone.0061048

Cited by 259 publications

(358 citation statements)

References 67 publications

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“…The distance between sequences was calculated based on the number of base differences per site between sequences using pairwise comparisons with 1,000 bootstraps; this simple method was applied, since most distance methods are comparable and give similar estimates (63)(64)(65). Cophylogeny was tested with the tick COI tree and the FLE tree using the Procrustes Approach to Co-phylogeny (PACo) (66) in R version 3.3.1 (https://www.R-project.org/), with the vegan and ape packages (67,68).…”

Section: Methodsmentioning

confidence: 99%

Francisella-Like Endosymbionts and Rickettsia Species in Local and Imported Hyalomma Ticks

Azagi

Klement

Perlman

et al. 2017

Appl Environ Microbiol

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Hyalomma ticks (Acari: Ixodidae) are hosts for Francisella-like endosymbionts (FLE) and may serve as vectors of zoonotic disease agents. This study aimed to provide an initial characterization of the interaction between Hyalomma and FLE and to determine the prevalence of pathogenic Rickettsia in these ticks. Hyalomma marginatum, Hyalomma rufipes, Hyalomma dromedarii, Hyalomma aegyptium, and Hyalomma excavatum ticks, identified morphologically and molecularly, were collected from different hosts and locations representing the distribution of the genus Hyalomma in Israel, as well as from migratory birds. A high prevalence of FLE was found in all Hyalomma species (90.6%), as well as efficient maternal transmission of FLE (91.8%), and the localization of FLE in Malpighian tubules, ovaries, and salivary glands in H. marginatum. Furthermore, we demonstrated strong cophylogeny between FLE and their host species. Contrary to FLE, the prevalence of Rickettsia ranged from 2.4% to 81.3% and was significantly different between Hyalomma species, with a higher prevalence in ticks collected from migratory birds. Using ompA gene sequences, most of the Rickettsia spp. were similar to Rickettsia aeschlimannii, while a few were similar to Rickettsia africae of the spotted fever group (SFG). Given their zoonotic importance, 249 ticks were tested for Crimean Congo hemorrhagic fever virus infection, and all were negative. The results imply that Hyalomma and FLE have obligatory symbiotic interactions, indicating a potential SFG Rickettsia zoonosis risk. A further understanding of the possible influence of FLE on Hyalomma development, as well as on its infection with Rickettsia pathogens, may lead to novel ways to control tick-borne zoonoses.IMPORTANCE This study shows that Francisella-like endosymbionts were ubiquitous in Hyalomma, were maternally transmitted, and cospeciated with their hosts. These findings imply that the interaction between FLE and Hyalomma is of an obligatory nature. It provides an example of an integrative taxonomy approach to simply differentiate among species infesting the same host and to identify nymphal and larval stages to be used in further studies. In addition, it shows the potential of imported Hyalomma ticks to serve as a vector for spotted fever group rickettsiae. The information gathered in this study can be further implemented in the development of symbiont-based disease control strategies for the benefit of human health.

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Section: Methodsmentioning

confidence: 99%

Francisella-Like Endosymbionts and Rickettsia Species in Local and Imported Hyalomma Ticks

Azagi

Klement

Perlman

et al. 2017

Appl Environ Microbiol

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“…We generated a third matrix for host-parasite links, which allows for multiple linkages among bat species and Bartonella genotypes. Two methods were used to measure the fit between bat and bartonella tree topologies through the matrix of host-parasite linkages, ParaFit (Legendre et al, 2002) and the Procrustean Approach to Cophylogeny (PACo) (Balbuena et al, 2013). Both methods decompose distance matrices of host and parasite phylogenies into principal components and combine those principal components with the matrix of host-parasite associations.…”

Section: Methodsmentioning

confidence: 99%

“…We hypothesize that significant patterns of evolutionary codivergence with hosts, phylogeography, and divergent adaptation to hosts and vectors can all be found in bat bartonellae, although they may have varying degrees of importance in the formation of distinct Bartonella lineages. We first use global fit methods (Balbuena et al, 2013; Legendre et al, 2002) to look for significant patterns of phylogeography, evolutionary codivergence with bat hosts, and divergent adaptation to bats and vectors. We add to this analysis a linear model that can test the relative influence of codivergence and host sympatry on the evolution of Bartonella in bats.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic and geographic patterns of bartonella host shifts among bat species

McKee

Hayman

Kosoy

et al. 2016

Infection, Genetics and Evolution

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The influence of factors contributing to parasite diversity in individual hosts and communities are increasingly studied, but there has been less focus on the dominant processes leading to parasite diversification. Using bartonella infections in bats as a model system, we explored the influence of three processes that can contribute to bartonella diversification and lineage formation: (1) spatial correlation in the invasion and transmission of bartonella among bats (phylogeography); (2) divergent adaptation of bartonellae to bat hosts and arthropod vectors; and (3) evolutionary codivergence between bats and bartonellae. Using a combination of global fit techniques and ancestral state reconstruction, we found that codivergence appears to be the dominant process leading to diversification of bartonella in bats, with lineages of bartonellae corresponding to separate bat suborders, superfamilies, and families. Furthermore, we estimated the rates at which bartonellae shift bat hosts across taxonomic scales (suborders, superfamilies, and families) and found that transition rates decrease with increasing taxonomic distance, providing support for a mechanism that can contribute to the observed evolutionary congruence between bats and their associated bartonellae. While bartonella diversification is associated with host sympatry, the influence of this factor is minor compared to the influence of codivergence and there is a clear indication that some bartonella lineages span multiple regions, particularly between Africa and Southeast Asia. Divergent adaptation of bartonellae to bat hosts and arthropod vectors is apparent and can dilute the overall pattern of codivergence, however its importance in the formation of Bartonella lineages in bats is small relative to codivergence. We argue that exploring all three of these processes yields a more complete understanding of bat-bartonella relationships and the evolution of the genus Bartonella, generally. Application of these methods to other infectious bacteria and viruses could uncover common processes that lead to parasite diversification and the formation of host-parasite relationships.

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“…The e i 2 ’s and their 95% confidence intervals were estimated using a jackknife method. Each i th link is replaced by 0 (i.e., we eliminate that specific host-parasite association from our matrix), then we estimate the e i 2 squared residual for each host-parasite link to assess its contribution to the global cospeciation fit; and those links that contribute relatively little to m 2 XY likely represent coevolutionary links [see [49] for more details].…”

Section: Methodsmentioning

confidence: 99%

Different meal, same flavor: cospeciation and host switching of haemosporidian parasites in some non-passerine birds

Santiago‐Alarcon

Rodríguez-Ferraro

Parker

et al. 2014

Parasites & Vectors

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BackgroundPrevious studies have shown that haemosporidian parasites (Haemoproteus (Parahaemoproteus) and Plasmodium) infecting passerine birds have an evolutionary history of host switching with little cospeciation, in particular at low taxonomic levels (e.g., below the family level), which is suggested as the main speciation mechanism of this group of parasites. Recent studies have characterized diverse clades of haemosporidian parasites (H. (Haemoproteus) and H. (Parahaemoproteus)) infecting non-passerine birds (e.g., Columbiformes, Pelecaniiformes). Here, we explore the cospeciation history of H. (Haemoproteus) and H. (Parahaemoproteus) parasites with their non-passerine hosts.MethodsWe sequenced the mtDNA cyt b gene of both haemosporidian parasites and their avian non-passerine hosts. We built Bayesian phylogenetic hypotheses and created concensus phylograms that were subsequently used to conduct cospeciation analyses. We used both a global cospeciation test, PACo, and an event-cost algorithm implemented in CoRe-PA.ResultsThe global test suggests that H. (Haemoproteus) and H. (Parahaemoproteus) parasites have a diversification history dominated by cospeciation events particularly at the family level. Host-parasite links from the PACo analysis show that host switching events are common within families (i.e., among genera and among species within genera), and occasionally across different orders (e.g., Columbiformes to Pelecaniiformes). Event-cost analyses show that haemosporidian coevolutionary history is dominated by host switching and some codivergence, but with duplication events also present. Genetic lineages unique to raptor species (e.g., FALC11) commonly switch between Falconiformes and Strigiformes.ConclusionsOur results corroborate previous findings that have detected a global cospeciation signal at the family taxonomic level, and they also support a history of frequent switching closer to the tips of the host phylogeny, which seems to be the main diversification mechanism of haemosporidians. Such dynamic host-parasite associations are relevant to the epidemiology of emerging diseases because low parasite host specificity is a prerequisite for the emergence of novel diseases. The evidence on host distributions suggests that haemosporidian parasites have the potential to rapidly develop novel host-associations. This pattern has also been recorded in fish-monogenean interactions, suggesting a general diversification mechanism for parasites when host choice is not restricted by ecological barriers.

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PACo: A Novel Procrustes Application to Cophylogenetic Analysis

Cited by 259 publications

References 67 publications

Francisella-Like Endosymbionts and Rickettsia Species in Local and Imported Hyalomma Ticks

Francisella-Like Endosymbionts and Rickettsia Species in Local and Imported Hyalomma Ticks

Phylogenetic and geographic patterns of bartonella host shifts among bat species

Different meal, same flavor: cospeciation and host switching of haemosporidian parasites in some non-passerine birds

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