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Journal of Virology, April 2004, p. 3244-3251, Vol. 78, No. 7
0022-538X/04/$08.00+0 DOI: 10.1128/JVI.78.7.3244-3251.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
and Jenny S. Cory2,
Department of Biological Sciences, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ,1 Molecular Ecology and Biocontrol Group, NERC Centre for Ecology and Hydrology, Oxford OX1 3SR, United Kingdom2
Received 23 July 2003/ Accepted 10 December 2003
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The family Baculoviridae comprises a diverse group of arthropod-specific DNA viruses. They have been reported worldwide from over 600 host species (37), mostly from insects of the order Lepidoptera but also from the orders Diptera, Hymenoptera, and the crustacean order Decapoda (6, 16). The family Baculoviridae is currently subdivided into two genera based on several criteria, including the morphology of the occlusion bodies (OBs) and on mechanisms of nucleocapsid envelopment in infected cells (6). The genus Nucleopolyhedrovirus (NPV) is characterized by viruses forming polyhedral OBs, each containing many virions formed within the nucleus (49), whereas viruses of the genus Granulovirus (GV) typically produce ovoid OBs, with a single virion formed in the nucleocytoplasmic milieu (58). GVs have been described solely from lepidopteran hosts, whereas NPVs have been isolated from a wider range of arthropods. However, the taxonomic status of nonlepidopteran baculoviruses is still uncertain (6). Baculovirus phylogenies have usually been based on individual gene sequences. The polyhedrin/granulin (polh) gene, encoding the major matrix protein of the OBs, has been the most widely used (5, 7, 14, 34, 60), but other genes, such as DNA polymerase, egt, gp41, chitinase, cathepsin, and lef2, have also been utilized (7, 8, 10, 12, 29, 30, 34, 42). In general, these studies agree that the lepidopteran NPVs and GVs constitute distinct, well-defined groups (7, 14, 23, 24, 60).
Almost all phylogenetic studies have been based on sequences from lepidopteran baculoviruses. Mostly because of the rarity of the samples, little work has been done to try to investigate the position of nonlepidopteran baculoviruses. Resolving the relationships between viruses isolated from Hymenoptera, Diptera, and Lepidoptera would greatly enhance our understanding of the evolution of the virus family Baculoviridae. Early amino acid sequencing of the polyhedrin protein of Neodiprion sertifer NPV (NeseNPV) showed that the polh sequence of this hymenopteran virus is quite divergent from that of the lepidopteran viruses, including NPVs and GVs (50). This result has been confirmed by determination of the complete DNA sequence of the gene (60). These phylogenies based on the OB protein imply that the hymenopteran virus is from an ancient lineage. More recently, phylogenetic analyses based on the p74 and DNA polymerase genes, including sequences from the dipteran virus Culex nigripalpus NPV (CuniNPV), also showed that this virus is very divergent from the lepidopteran viruses and that it is more ancestral (41). Similar results were obtained based on complete genome phylogenetic analyses (24). There are currently no baculovirus phylogenies including viruses from the three insect orders.
A comparison of nine complete genome sequences and their study in an evolutionary framework highlighted the genes that were most suitable for phylogenetic studies (23). Among them, two genes conserved in all the baculovirus genomes were chosen for the present study to address the phylogenetic relationships within the Baculoviridae. The gene lef-8 encodes a subunit of the baculovirus RNA polymerase, and ac22 encodes a per os infectivity factor (pif-2) (44). The polh gene was not considered for this study primarily because CuniNPV does not harbor a homologue of this gene (1). This suggests that other divergent baculoviruses might not possess a homologue of polh to encode their major OB protein. At the time of carrying out the analysis, 18 sequences, including that of CuniNPV, were available from the database for lef-8 and ac22. We supplemented this information with 22 novel sequences for these two genes from lepidopteran and hymenopteran baculoviruses. This allowed the reconstruction of phylogenetic trees including baculoviruses isolated from hosts of the arthropod orders Lepidoptera, Hymenoptera, and Diptera to improve our understanding of the early evolution of the virus family Baculoviridae.
Traditionally, two competing evolutionary hypotheses have been put forward to explain the current host distribution of the baculoviruses (16). The first hypothesis states that baculoviruses could have evolved within one group of arthropods, such as the Lepidoptera, and switched to other insect groups (48). The second proposes that the association between baculoviruses and their hosts dates back to the origin of insects or even arthropods and that they coevolved during evolutionary time with the viruses colonizing the insect orders as they arose (by cocladogenesis) (16). We propose to examine these two hypotheses in this study with the reconstruction of a baculovirus phylogeny including, for the first time, viruses from three distinct insect orders.
Furthermore, this study might shed new lights on the interrelationships between baculoviruses and question the phylogenetic validity of the present classification of the Baculoviridae, which divides the family into two genera.
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TABLE 1. Baculoviruses included in this study
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TABLE 2. Degenerate oligonucleotide primers used for amplification of a diverse range of baculoviruses
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Maximum-likelihood (ML) analyses were performed in PAUP*, version 4.0b10 (52). Each alignment was analyzed by using a statistical model-fitting approach implemented in MODELTEST, version 3.06, to choose between substitution models (45, 46). The selected models were used to calculate a tree by using the neighbor-joining method under ML distances. This tree was then used to start an ML heuristic search including branch swapping by nearest-neighbor interchange to find shorter trees.
Bayesian phylogenetic analyses of the combined data set were conducted with MrBayes, version 3.0b4 (26). Five Markov chains were run for 1 million generations, and the ML parameters were estimated for each gene partition in every analysis. Trees were sampled every 100th generation; 1,000 trees obtained in the early phase of the analysis were discarded before computing the consensus of the remaining 9,001 trees to assess the posterior probability of each node.
The robustness of the tree topologies was also evaluated by bootstrap analysis under the following conditions: ML heuristic searches with 100 replicates and maximum-parsimony (MP) methods with 1,000 replicates. For the MP reconstructions, uninformative characters were excluded from the data matrices, the trees were built by stepwise addition, and tree bisection reconnection branch swapping was performed to find the best MP tree at each replication step. Differences in tree topologies were assessed by using one-tailed Kishino-Hasegawa (KH) and Shimodaira-Hasegawa (SH) tests implemented for ML tree scores in PAUP* (52).
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For the Lef-8 & Ac22 data set, the best-fit model of evolution selected by MODELTEST (45) was characterized by 9.4% of invariable sites (I) and a gamma shape parameter (G = 1.317%), which reflects the heterogeneity of variation rates across sites, and the substitution model had variable transition rates (A<>G = 2.08; T<>C = 2.82). The tree obtained from the combined alignment (Fig. 1, T1) showed the lepidopteran NPVs divided into two groups and the sawfly viruses with CuniNPV clearly separated from the GVs. However, it also showed that the GVs might be paraphyletic (i.e., split within the tree). To test whether this was strongly supported by the data, ML heuristic searches were performed again to find the most likely tree (T2) under the constraint that the GVs should be monophyletic (enforcing that the GVs should all derive from a single common ancestor). To measure the significance of the differences between T1 and T2, KH and SH tests were performed. The constrained tree (T2) had a likelihood value (-lnL = 19,508.2) only marginally lower than that of the best tree (T1) (-lnL = 19,507.9; delta = 0.32). The KH and SH tests, used to assess the differences between the topologies of T1 and T2, showed that they were not significantly different (KH: P = 0.416; SH: P = 0.975; P value showing a significant difference with best tree, <0.05). This indicates that T2 represents a hypothesis for the evolution of these viruses that is equivalent to that presented by T1. Therefore, in view of the present classification and phylogeny of the baculoviruses, we believe that T2 represents a satisfactory hypothesis for the phylogeny of the baculoviruses. Bayesian phylogenetic analysis further confirmed this evolutionary hypothesis, as the majority rule consensus tree derived from this analysis showed the monophyly of the GVs. The topology of the Bayesian consensus tree was also found to be not significantly different from T1 or T2 by KH and SH tests (data not shown).
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FIG. 1. ML trees obtained from the Lef-8 & Ac22 data set. T1, unconstrained tree; T2, GV monophyletic constraint tree. The trees were found by a heuristic search starting with neighbor joining and nearest-neighbor interchange branch swapping. Virus abbreviations are shown in Table 1.
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FIG. 2. Robustness of the Lef-8 & Ac22 ML tree (T2). Numbers in roman type (ML/MP ratio of >50) indicate bootstrap scores obtained by the ML method with 100 replicates. The second number, when present, indicates the score obtained by the MP method with 1,000 replicates. Numbers in bold italic type indicate the Bayesian posterior probabilities of the nodes.
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The phylogenetic analyses described here include baculoviruses from hosts of the arthropod orders Lepidoptera, Diptera, and Hymenoptera. They indicate that there are at least three, and possibly four, distinct groups of baculoviruses (Fig. 3A). The lepidopteran NPVs clearly form a discrete group, which is distinct from the rest of the baculoviruses. The branch leading to this group is quite long (l = 0.26) (Fig. 3A) and well supported by high bootstrap values and Bayesian posterior probabilities. The GVs, however, appear to be more genetically diverse than the NPVs, and the branch leading to the group is comparatively short (l = 0.03) and poorly supported (Fig. 2 and 3A). This suggests that the GVs are a much older group than the lepidopteran NPVs, that the sampling of the GVs was wider, or that both groups speciate at different speeds. Furthermore, the phylogeny shows that neither the dipteran virus nor the hymenopteran viruses belong to either the GVs or the lepidopteran NPVs. The branch separating the lepidopteran from the nonlepidopteran baculoviruses is long (l = 0.36) (Fig. 3A) and well supported. The branch lengths between the mosquito virus and the sawfly viruses are also large (l = 0.88 and 0.54) (Fig. 3A). This suggests that hymenopteran and dipteran baculoviruses probably belong to distinct and separate groups. The members of the Baculoviridae appear to be clearly divided according to the classification of their hosts.
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FIG. 3. Evolution of the Baculoviridae. (A) Phylogeny of the baculoviruses, highlighting four main groups of the unrooted tree (T2); numbers indicate branch lengths in substitutions per site. (B) Relationships of the three arthropod orders infected by the baculoviruses shown in panel A (57).
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Unsuccessful attempts were made to obtain sequences from virus isolates from lacewings (Neuroptera, Chrysopa PV-330, and Hemerobius NPV-318 and -440; NERC, CEH) and craneflies (Diptera, Tipula oleracea NPV-35 and -281; NERC, CEH) that had been classified as NPVs (22). These viruses might be extremely divergent baculoviruses beyond the range of our degenerate primers, but these results may also indicate that they belong to other virus families yet to be identified. No samples of crustacean baculoviruses were available for this study. A baculovirus of the shrimp Peneaus monodon is still included in the ICTV tentative baculovirus list (6). A recent morphological description of Monodon baculovirus might correspond to this virus (47). However, the lack of molecular sequences for this virus still casts doubt on its affiliation with the Baculoviridae, especially as another shrimp virus, the white spot syndrome virus, formerly classified as a baculovirus, is in the process of being classified to its own virus family, Nimaviridae, since sequences have become available (55, 56). Thus, it was not possible to confirm the presence of baculoviruses in the Crustacea, nor in insect orders other than Lepidoptera, Diptera, and Hymenoptera.
From the unrooted tree (Fig. 3A), it is possible to envisage a scenario where the GVs could have given rise to all the NPVs (lepidopteran and nonlepidopteran). This would reconcile the phylogeny with the present classification of the baculoviruses into two genera. However, evidence from DNA polymerase phylogenies (41) and comparative genomics studies including GVs, NPVs, and CuniNPV genomes (24) showed that the GVs and lepidopteran NPVs are more closely related to each other than they are to the mosquito virus. This therefore reinforces the idea that in a phylogenetic context the NPV genus might not include viruses from a nonlepidopteran background.
Taxonomic proposals. If the ICTV was to consider using phylogenetic concepts for the classification of baculoviruses, this would require the genera to be monophyletic. This study shows that under the present ICTV classification, the NPV genus is polyphyletic. So from a phylogenetic perspective, CuniNPV and the sawfly NPVs should be removed from the NPV genus and classified under the unclassified baculovirus section. Our evidence would also support a taxonomic proposal to create one or two new genera of baculoviruses. The number of new genera would depend on further evidence to cluster together or keep apart the dipteran and hymenopteran baculoviruses.
BLAST search results showed that NeseNPV345, NeseNPV413, and NeseNPV726 are isolates of the species N. sertifer NPV (taxonomic code 00.006.0.01.017.). The other virus isolated from N. lecontei should still be classified as a separate species, N. lecontei NPV (taxonomic code 00.006.0.01.323.). Comparisons of phylogenetic distances and distinct host ranges (15) suggest that NPVs of G. hercyniae are part of a third distinct species.
Evolution of the Baculoviridae. Among baculovirologists, two views are commonly held for the evolutionary origins of the Baculoviridae (16). The first hypothesis proposes that the baculoviruses originated within the Lepidoptera, with subsequent horizontal transmissions to other insect orders from lepidopteran virus clades (48). The second postulates that the origin of baculoviruses dates back to the origin of arthropods, with the cocladogenesis of the viruses and their hosts (16).
If the first hypothesis was true, a phylogeny including baculoviruses from different orders of hosts would not show any clear clustering of baculoviruses according to host order. It would show nonlepidopteran viruses, either in clusters or singlets, arising within the NPVs or GVs, making lepidopteran NPVs or GVs paraphyletic. The phylogeny of baculoviruses including hosts from three different insect orders (Fig. 3A) seems to reject this hypothesis, as viruses strongly cluster according to the order of insects from which they have been isolated. We believe that our lepidopteran virus sampling is diverse enough to address this question. However, this does not exclude the discovery of a nonlepidopteran baculovirus belonging to the lepidopteran NPVs or GVs.
The second hypothesis would lead to a phylogeny where the relationships between groups of baculoviruses mirror the evolutionary relationships of insect orders, with the ages of the different baculovirus lineages reflecting those of their hosts. The orders Diptera and Lepidoptera are more closely related to each other than to the Hymenoptera (Fig. 3B) (57). The phylogeny obtained in this study could be consistent with the phylogenetic host tracking of insect orders by baculoviruses, as it is possible to root the tree on the hymenopteran baculovirus branch (Fig. 3A). However, further evidence needs to be gathered before accepting the hypothesis, particularly the comparison of evolutionary rates between baculoviruses and their hosts. From our data set, it is not possible to infer directly a reliable rate of sequence evolution for the baculoviruses, particularly because the genes used in this study do not have any homologues outside of the Baculoviridae.
A third scenario can be suggested for the origin of the baculoviruses. We propose that ancestral baculoviruses were probably able to horizontally infect hosts of different orders, with ancient coevolution between the hosts and pathogens then leading to the progressive specialization of different baculovirus lineages to hosts of different orders. According to this hypothesis, a phylogeny of the baculoviruses would show a clear separation of the viruses infecting different kinds of hosts without necessarily reflecting the evolution of insect orders. The phylogeny obtained in this study supports this hypothesis (Fig. 3A).
The uncertainty of the position of the root in the baculovirus phylogeny does not allow us to completely discard the second hypothesis in favor of the third. Some elements of baculovirus biology suggest that the dipteran baculovirus might belong to the more ancestral lineage, thus favoring the third scenario. The complete genome sequence of the mosquito virus CuniNPV showed that this virus does not possess a polyhedrin gene and that another protein is the major constituent of the OBs (1, 41), whereas polyhedrin sequences have been obtained from sawfly viruses (50, 60). Furthermore, lepidopteran and hymenopteran sawfly larvae share similar feeding ecologies and are often found in the same environment in the wild, i.e., terrestrial plants. They would thus be exposed to each others' viruses, whereas mosquito larvae are aquatic. This suggests that the lepidopteran and hymenopteran viruses could be more closely related to each other than to the mosquito virus. However, the dipteran virus lineage might have undergone a nonorthologous gene displacement for its OB protein.
In terms of pathogenesis and tissue tropism, mosquito and sawfly viruses are more similar to each other than to the lepidopteran GVs or NPVs. These viruses only infect midgut epithelial cells (15, 16, 41), whereas GVs and lepidopteran NPVs generally cause systemic infections, often infecting a wide range of tissues. The restriction of infection to midgut epithelial cells has been proposed as an ancestral characteristic of baculoviruses (16). Only one lepidopteran baculovirus has been found to have a similar pathology, H. brillians GV (17). However, phylogenies including this virus showed that this virus is not basal to the GV group (Fig. 2) and, therefore, that the restriction of infection to the midgut epithelial cells is not an ancestral trait in lepidopteran baculoviruses (5). Thus, it is not possible to conclude whether the mosquito and sawfly viruses are more primitive or more derived than the lepidopteran baculoviruses based on the cell specificity of their infections. Although they were based on smaller taxon sets, previous phylogenetic studies suggested that they were more ancestral than the lepidopteran NPVs or GVs (41, 50, 60).
The relationships of the deeper branches of the baculovirus phylogenies might benefit in the near future from comparative genomic analyses. If sawfly virus genomes were found to be more similar to the lepidopteran baculoviruses, then the mosquito virus could remain at the base of the tree. If they share more genomic features with CuniNPV, then the hymenopteran and dipteran viruses could be grouped together to the exclusion of the lepidopteran baculoviruses. However, if CuniNPV is more similar to the lepidopteran baculoviruses, then the hymenopteran baculoviruses could be the more ancestral lineage. This last option would favor the second theory of early cospeciation between the Baculoviridae and the Arthropoda, as the baculovirus phylogeny would then reflect that of the order of their hosts, although this would need to be correlated with a comparative study of evolutionary rates between hosts and pathogens.
Regardless of the position of the root of the baculovirus tree, the phylogenetic separation of the viruses into groups according to the hosts' classification indicates that baculoviruses have been specialist pathogens of insects since the diversification of the family Baculoviridae. The selection pressure exerted on baculoviruses by their different hosts has promoted their specialization to the point where specific baculovirus lineages are specific to particular kinds of host insects, such as larvae of Lepidoptera, Hymenoptera, and Diptera. These coevolutionary adaptations have constrained the range of possible hosts available to each virus lineage. Over time, this has translated into the phylogenetic pattern that we observe today, where the Baculoviridae from different insect orders belong to different evolutionary lineages.
The Natural Environment Research Council CASE studentship award GT04/99/TS/142 supported E.A.H.
Present address: Syngenta, Jealotts Hill International Research Station, Bracknell, Berkshire RG42 6EY, United Kingdom. ![]()
Present address: Laboratory of Virology, Wageningen University, 6909 PD Wageningen, The Netherlands ![]()
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