The Cotesia sesamiae story: insight into host-range evolution in a Hymenoptera parasitoid and implication for its use in biological control programs.

This review covers nearly 20 years of studies on the ecology, physiology and genetics of the Hymenoptera Cotesia sesamiae, an African parasitoid of Lepidoptera that reduces populations of common maize borers in East and South Africa. The first part of the review presents studies based on sampling of C. sesamiae from maize crops in Kenya. From this agrosystem including one host plant and three main host borer species, studies revealed two genetically differentiated populations of C. sesamiae species adapted to their local host community, and showed that their differentiation involved the joint evolution of virulence genes and sensory mechanisms of host acceptance, reinforced by reproductive incompatibility due to Wolbachia infection status and natural inbreeding. In the second part, we consider the larger ecosystem of wild Poales plant species hosting many Lepidoptera stem borer species that are potential hosts for C. sesamiae. The hypothesis of other host-adapted C. sesamiae populations was investigated based on a large sampling of stem borer larvae on various Poales across sub-Saharan Africa. The sampling provided information on the respective contribution of local hosts, biogeography and Wolbachia in the genetic structure of C. sesamiae populations. Molecular evolution analyses highlighted that several bracovirus genes were under positive selection, some of them being under different selection pressure in C. sesamiae populations adapted to different hosts. This suggests that C. sesamiae host races result from co-evolution acting at the local scale on different bracovirus genes. The third part considers the mechanisms driving specialization. C. sesamiae host races are more or less host-specialized. This character is crucial for efficient and environmentally-safe use of natural enemies for biological control of pests. One method to get an insight in the evolutionary stability of host-parasite associations is to characterize the phylogenetic relationships between the so-called host-races. Based on the construction of a phylogeny of C. sesamiae samples from various host- and plant species, we revealed three main lineages. Mechanisms of differentiation are discussed with regard to the geography and ecology of the samples. One of the lineage presented all the hallmarks of a distinct species, which has been morphologically described and is now studied in the perspective of being used as biological control agent against Sesamia nonagrioides Lefèbvre (Lepidoptera: Noctuidae), a major maize pest in West Africa and Mediterranean countries (see Benoist et al. 2017). The fourth part reviews past and present use of C. sesamiae in biological control, and points out the interest of such molecular ecology studies to reconcile biodiversity and food security stakes in future biological control.

On the classification and nomenclature of baculoviruses: a proposal for revision.

Recent evidence from genome sequence analyses demands a substantial revision of the taxonomy and classification of the family Baculoviridae. Comparisons of 29 baculovirus genomes indicated that baculovirus phylogeny followed the classification of the hosts more closely than morphological traits that have previously been used for classification of this virus family. On this basis, dipteran- and hymenopteran-specific nucleopolyhedroviruses (NPV) should be separated from lepidopteran-specific NPVs and accommodated into different genera. We propose a new classification and nomenclature for the genera within the baculovirus family. According to this proposal the updated classification should include four genera: Alphabaculovirus (lepidopteran-specific NPV), Betabaculovirus (lepidopteran-specific Granuloviruses), Gammabaculovirus (hymenopteran-specific NPV) and Deltabaculovirus (dipteran-specific NPV).

Phylogenetic relationships of Echinostoma Rudolphi, 1809 (Digenea: Echinostomatidae) and related genera re-assessed via DNA and morphological analyses.

In order to investigate the relationships within the Echinostomatidae two data sets of gene sequences were analysed. The first consisted of all previously published ND1 sequences (20) together with 17 new sequences. The latter represented six species from the cosmopolitan genera Echinostoma, Echinoparyphium, Hypoderaeum and Isthmiophora. The second data-set of ITS sequences again included all previously published sequences (12) and three new sequences from species of Echinostoma, Echinoparyphium and Isthmiophora. All new isolates, as well as voucher material from five previously sequenced isolates, were identified on the basis of morphological characters. The phylogenetic trees inferred from the ND1 data set helped to clarify the generic affiliation of all isolates and confirmed the morphological identifications. The only exception was Echinoparyphium aconiatum, whose current position in the genus Echinoparyphium was not supported by the sequence data. Although the ITS data provided insufficient resolution for an unequivocal solution to the relationships within the genus Echinostoma, it supported the identification of Echinoparyphium ellisi and the distinct species status of three isolates of Echinostoma revolutum as predicted from the ND1 data.

Use of whole genome sequence data to infer baculovirus phylogeny.

Several phylogenetic methods based on whole genome sequence data were evaluated using data from nine complete baculovirus genomes. The utility of three independent character sets was assessed. The first data set comprised the sequences of the 63 genes common to these viruses. The second set of characters was based on gene order, and phylogenies were inferred using both breakpoint distance analysis and a novel method developed here, termed neighbor pair analysis. The third set recorded gene content by scoring gene presence or absence in each genome. All three data sets yielded phylogenies supporting the separation of the Nucleopolyhedrovirus (NPV) and Granulovirus (GV) genera, the division of the NPVs into groups I and II, and species relationships within group I NPVs. Generation of phylogenies based on the combined sequences of all 63 shared genes proved to be the most effective approach to resolving the relationships among the group II NPVs and the GVs. The history of gene acquisitions and losses that have accompanied baculovirus diversification was visualized by mapping the gene content data onto the phylogenetic tree. This analysis highlighted the fluid nature of baculovirus genomes, with evidence of frequent genome rearrangements and multiple gene content changes during their evolution. Of more than 416 genes identified in the genomes analyzed, only 63 are present in all nine genomes, and 200 genes are found only in a single genome. Despite this fluidity, the whole genome-based methods we describe are sufficiently powerful to recover the underlying phylogeny of the viruses.

Changes in mitochondrial genetic codes as phylogenetic characters: two examples from the flatworms.

Shared molecular genetic characteristics other than DNA and protein sequences can provide excellent sources of phylogenetic information, particularly if they are complex and rare and are consequently unlikely to have arisen by chance convergence. We have used two such characters, arising from changes in mitochondrial genetic code, to define a clade within the Platyhelminthes (flatworms), the Rhabditophora. We have sampled 10 distinct classes within the Rhabditophora and find that all have the codon AAA coding for the amino acid Asn rather than the usual Lys and AUA for Ile rather than the usual Met. We find no evidence to support claims that the codon UAA codes for Tyr in the Platyhelminthes rather than the standard stop codon. The Rhabditophora are a very diverse group comprising the majority of the free-living turbellarian taxa and the parasitic Neodermata. In contrast, three other classes of turbellarian flatworm, the Acoela, Nemertodermatida, and Catenulida, have the standard invertebrate assignments for these codons and so are convincingly excluded from the rhabditophoran clade. We have developed a rapid computerized method for analyzing genetic codes and demonstrate the wide phylogenetic distribution of the standard invertebrate code as well as confirming already known metazoan deviations from it (ascidian, vertebrate, echinoderm/hemichordate).

The interrelationships of proseriata (Platyhelminthes: seriata) tested with molecules and morphology.

Proseriate flatworms are common members of the interstitial benthic fauna worldwide, predominantly occupying marine environments. As minute animals, having relatively few characters useful for cladistic analysis, they have been difficult to present in a phylogenetic framework using morphology alone. Here we present a new morphological matrix consisting of 16 putatively homologous characters and two molecular data sets to investigate further this major group of free-living members of the Platyhelminthes. Complete 18S rDNA (representing 277 parsimony-informative characters) from 17 ingroup taxa and partial 28S rDNA spanning variable expansion regions D1 to D3 and D1 to D6 (representing 219 and 361 parsimony-informative characters, respectively) from 27 and 14 ingroup taxa, respectively, were determined and aligned as complementary data sets. Morphological and molecular data sets were analyzed separately and together to determine underlying phylogenetic patterns and to resolve conflict between published scenarios based on morphology alone. The monophyly of the Proseriata cannot be confirmed categorically with any of these data sets. However, the constituent taxa are confirmed as basal members of the Neoophora, and a sister group relationship with Tricladida is rejected. Similarly, the monophyly of one of the two subtaxa of the Proseriata, the Lithophora, could not be confirmed with molecules. Concerning intragroup relationships, we could reject one of the two phylogenetic trees formerly proposed, as well as the clade Otoplanidae + Coelogynoporidae. However, a clade Otoplanidae + Archimonocelididae + Monocelididae (to which the Monotoplanidae belong) was supported, and the position of the genus Calviria shifted from the Archimonocelididae to the Coelogynoporidae.

Acoel flatworms: earliest extant bilaterian Metazoans, not members of Platyhelminthes.

Because of their simple organization the Acoela have been considered to be either primitive bilaterians or descendants of coelomates through secondary loss of derived features. Sequence data of 18S ribosomal DNA genes from non-fast evolving species of acoels and other metazoans reveal that this group does not belong to the Platyhelminthes but represents the extant members of the earliest divergent Bilateria, an interpretation that is supported by recent studies on the embryonic cleavage pattern and nervous system of acoels. This study has implications for understanding the evolution of major body plans, and for perceptions of the Cambrian evolutionary explosion.

Digenean parasites of deep-sea teleosts: a review and case studies of intrageneric phylogenies.

Studies on the digenean parasites of deep-sea (> 200 m depth) teleosts are reviewed and two case study generic phylogenies are presented based on LSU rDNA and ND1 mtDNA sequences. The phylogeny of the lepocreadiid genus Lepidapedon, the most common deep-sea digenean genus, is not clearly resolved as the two gene trees are not compatible. It can be inferred, however, that the genus has radiated in the deeper waters off the continental shelf, mainly in fishes of the gadiform family Macrouridae. Steringophorus, a fellodistomid genus, is better resolved. In this case a deep-sea radiation is also indicated, but the pattern of host-specificity is not clear, with evidence of much host-switching. Results of studies of the parasites of the macrourid fish Coryphaenoides (Nematonurus) armatus from various depths have reinforced recent views on the lack of zoned depth-related communities in the deep-sea. The diversity of deep-sea digeneans is relatively low with only 18 families (of about 60) reported. Little, or nothing, is known from most deep-sea areas and nothing from trenches and mid-ocean ridge systems.

Vintage helminths yield valuable molecules.

Museum and archival collections of parasites are available throughout the world but, although they represent a huge diversity of species and forms, they tend to be used solely for reference to morphology, if at all. As biochemical techniques begin to overcome the problems associated with ancient, degraded and formalin-fixed tissues, the value of such collections increases. Molecular data are now available for rare, elusive and extinct species, as well as those densely sampled for epidemiological, biogeographical or clinical collections. Here, Elisabeth Herniou, Auriol Pearce and Tim Littlewood describe some of the advances and pitfalls associated with retrieving DNA from formalin-fixed helminth material and suggest just some of the new ways that parasitologists can tap into these resources.