Distribution and genetic diversity of the parasitic dinoflagellate Amoebophrya in coastal waters of China

Amoebophrya is an obligate endoparasite infecting wide ranges of marine organisms in coastal and oceanic waters. The parasitoid has received growing attention, due to its enormous genetic diversity in seawaters and suppressive effects on the growth of host dinoflagellates. Harmful algal blooms (HABs) caused by planktonic dinoflagellates have significantly impacted the coastal environment and mariculture in China. Series of studies have been conducted to reveal the occurrence mechanism and negative impacts of HABs in past decades, while the factors contributing to the recession of HABs have rarely been studied. Thus, the host range, prevalence and diversity of Amoebophrya along the coastline of China were systemically investigated to facilitate future studies on the ecological roles of the parasitoid. Overall, 10 dinoflagellate taxa were found to be infected by Amoebophrya spp., and the prevalence ranged from 0.03% to 2.50%. Sequencing of environmental genomic DNA revealed substantial diversity and significant regional heterogeneity of Amoebophryidae sequences derived from 12 coastal bays, while no significant correlation was observed among geographical locations. Phylogenetic analyses of 18S rDNA sequences derived from individual Amoebophrya-infected cells indicated the host divergence of the parasitoid and lend credence to the multiple species assumption. The results further revealed the broad host range, wide distribution and substantial diversity of Amoebophrya in the coastal waters of China, that should not be neglected in future studies on the succession of HABs, as well as the ecological significance of this parasitoid in marine microbial food webs.     

Host range limitation caused by incomplete host regulation in an aphid parasitoid

Defining host ranges in parasitoid insects is important both from a theoretical and an applied point of view. Based on the literature, some species seem able to use a wide range of hosts, while field studies indicate possible local host specialization. In koinobiont endoparasitoid species, such specialization could involve physiological processes. We tested the ability of two strains of the cosmopolitan and polyphagous parasitoid Diaeretiella rapae, to develop in three of its recorded aphid host species. Both strains produced high parasitism rates on the cabbage aphid Brevicoryne brassicae and the green peach aphid Myzus persicae but almost no progeny on the cherry-oat aphid Rhopalosiphum padi. This last species was less attacked by female parasitoids. Moreover, parasitoid eggs and larvae were smaller than in the two other host aphid species and their development was delayed. This abnormal development appeared to be due to an incomplete host regulation process, probably related to the low number and the size of teratocytes produced by D. rapae in R. padi individuals. Such a failure as far as gaining control of the host's metabolism is concerned could play an important role in shaping the host range of parasitoid insects, leading to local variation of the host spectrum in populations from various geographical areas.     

Evaluating the Ribosomal Internal Transcribed Spacer (ITS) as a Candidate Dinoflagellate Barcode Marker

Background

DNA barcoding offers an efficient way to determine species identification and to measure biodiversity. For dinoflagellates, an ancient alveolate group of about 2000 described extant species, DNA barcoding studies have revealed large amounts of unrecognized species diversity, most of which is not represented in culture collections. To date, two mitochondrial gene markers, Cytochrome Oxidase I (COI) and Cytochrome b oxidase (COB), have been used to assess DNA barcoding in dinoflagellates, and both failed to amplify all taxa and suffered from low resolution. Nevertheless, both genes yielded many examples of morphospecies showing cryptic speciation and morphologically distinct named species being genetically similar, highlighting the need for a common marker. For example, a large number of cultured Symbiodinium strains have neither taxonomic identification, nor a common measure of diversity that can be used to compare this genus to other dinoflagellates.

Methodology/Principal Findings

The purpose of this study was to evaluate the Internal Transcribed Spacer units 1 and 2 (ITS) of the rDNA operon, as a high resolution marker for distinguishing species dinoflagellates in culture. In our study, from 78 different species, the ITS barcode clearly differentiated species from genera and could identify 96% of strains to a known species or sub-genus grouping. 8.3% showed evidence of being cryptic species. A quarter of strains identified had no previous species identification. The greatest levels of hidden biodiversity came from Scrippsiella and the Pfiesteriaceae family, whilst Heterocapsa strains showed a high level of mismatch to their given species name.

Conclusions/Significance

The ITS marker was successful in confirming species, revealing hidden diversity in culture collections. This marker, however, may have limited use for environmental barcoding due to paralogues, the potential for unidentifiable chimaeras and priming across taxa. In these cases ITS would serve well in combination with other markers or for specific taxon studies.     

Re-classification of Pheopolykrikos hartmannii as Polykrikos (Dinophyceae) based partly on the ultrastructure of complex extrusomes

Athecate, pseudocolony-forming dinoflagellates have been classified within two genera of polykrikoids, Polykrikos and Pheopolykrikos, and different views about the boundaries and composition of these genera have been expressed in the literature. The photosynthetic polykrikoid Pheopolykrikos hartmannii, for instance, was originally described within Polykrikos and is now known to branch closely with several Polykrikos species in molecular phylogenetic analyses of ribosomal gene sequences. In this study, we report the first ultrastructural data for this species and demonstrate that Ph. hartmannii has all of the features that characterize the genus Polykrikos, including the synapomorphic “taeniocyst-nematocyst complex”. We also demonstrate that the ultrastructure of the chloroplasts in Ph. hartmannii conforms to the usual peridinin-containing chloroplasts of most photosynthetic dinoflagellates, which improves inferences about the origin(s) and evolution of photosynthesis within the genus. After taking into account all of the ultrastructural data on polykrikoids presented here and in the literature, this species is re-classified to its original status as Polykrikos hartmannii.     

Host range of a newly introduced parasitoid, Binodoxys communis among common aphid species in Hawaii

Binodoxys communis (Gahan) (Hymenoptera:Braconidae), a parasitoid of aphids originally from China, was introduced into Hawaii and evaluated in the laboratory for its ability to detect, accept, oviposit and develop in Aphis gossypii reared on two host plants, plus five other common aphid species. The parasitoid was able to detect all six aphid species and to successfully sting five species, with highest preference for those in the genus Aphis. Aphis species were highly suitable for parasitoid development. Other species were only marginally suitable. Parasitoids spent less time searching on plants of less acceptable aphids. Aphid defensive behaviors did not affect oviposition success, but did lengthen the parasitoid’s handling time of several aphid species. Host acceptance was positively correlated with host suitability, yet one unsuitable host was readily accepted for oviposition.     

Convergence and Divergence in Direct and Indirect Life-History Traits of Closely Related Parasitoids (Braconidae: Microgastrinae)

Closely related species in nature often show similarities in suites of direct and indirect traits that reveal aspects of their phylogenetic history. Here we tested how common descent affects trait evolution in several closely related parasitoid species in the genera Cotesia and Microplitis (Hymenoptera: Braconidae: Microgastrinae) by comparing development, resource use and allocation into reproduction and maintenance. Parasitoids in these genera exhibit traits, like haemolymph feeding as larvae and external pupation that are rare in most parasitoid lineages. The growth of parasitized hosts was reduced by 90 % compared with healthy hosts, and maximum host size depended to a large extent on adult parasitoid size. Development time was longer in the more generalist parasitoids than in the specialists. Adult body mass was sexually dimorphic in all Cotesia species, with females being larger, but not in Microplitis spp. In contrast, in one of the Microplitis species males were found to be the larger sex. Egg load dynamics during the first 6 days after emergence were highly variable but egg number was typically higher in Cotesia spp. compared to Microplitis spp. Longevity in the various species was only greater in female than in male wasps in two Microplitis sp. There was a clear inverse relationship between resource use and allocation, e.g. maximum egg load and longevity, in these parasitoids. Our results reveal that adaptation to constraints imposed by host quality and availability has resulted in trait convergence and divergence at the species, genus and subfamily level.     

Parasites and phytoplankton, with special emphasis on dinoflagellate infections

Planktonic members of most algal groups are known to harbor intracellular symbionts, including viruses, bacteria, fungi, and protozoa. Among the dinoflagellates, viral and bacterial associations were recognized a quarter century ago, yet their impact on host populations remains largely unresolved. By contrast, fungal and protozoan infections of dinoflagellates are well documented and generally viewed as playing major roles in host population dynamics. Our understanding of fungal parasites is largely based on studies for freshwater diatoms and dinoflagellates, although fungal infections are known for some marine phytoplankton. In freshwater systems, fungal chytrids have been linked to mass mortalities of host organisms, suppression or retardation of phytoplankton blooms, and selective effects on species composition leading to successional changes in plankton communities. Parasitic dinoflagellates of the genus Amoebophrya and the newly described Perkinsozoa, Parvilucifera infectans, are widely distributed in coastal waters of the world where they commonly infect photosynthetic and heterotrophic dinoflagellates. Recent work indicates that these parasites can have significant impacts on host physiology, behavior, and bloom dynamics. Thus, parasitism needs to be carefully considered in developing concepts about plankton dynamics and the flow of material in marine food webs.     

A synopsis of gall midges associated with conifers,with description of a new species of the genus <Emphasis Type="Italic">Kaltenbachiola</Emphasis> Hedicke (Diptera,Cecidomyiidae: Lasiopterinae) from Yakutia,damaging cones of the Siberian spruce (<Emphasis Type="Italic">Picea obovata</Emphasis>)

The world fauna comprises 134 species from 52 genera of gall midges associated with plants of the order Pinales (3 families, 16 genera and 74 species); 14 genera are specific to Pinales. The distribution of genera and species of gall midges over host plant taxa is described. The Holarctic genus Kaltenbachiola comprises four species all developing in the spruce (Picea spp.) cones. Earlier, K. strobi (Winnertz), widely distributed in Europe, was the only species known in the Palaearctic. A new species Kaltenbachiola anastasiae sp. n. is described, which damages cones of Picea obovata in Central Yakutia. The phylogenetic relationships of Kaltenbachiola with close genera specific to Pinales are characterized, and an updated diagnosis of the genus with additional morphometric parameters and keys to the pine-specific genera of the tribe Dasineurini and to species of the genus Kaltenbachiola are given. The host associations and specific traits of biology and distribution of Kaltenbachiola species are considered.     

Molecular Phylogeny of Parvilucifera prorocentri (Alveolata, Myzozoa): Insights into Perkinsid Character Evolution

ABSTRACT. Perkinsids and colpodellids are lineages that diverged near the origins of dinoflagellates and apicomplexans, respectively, and provide compelling insights into the earliest stages of alveolate evolution. Perkinsids, including Perkinsus and Parvilucifera , are intracellular parasites of animals and dinoflagellates and possess traits also known in syndineans, dinokaryotes (mainly free living dinoflagellates), and colpodellids. An improved understanding of perkinsid biodiversity and phylogeny is expected to shed considerable light on the evolutionary origins of syndineans and dinokaryotes as well as the cellular identities of environmental sequences derived from marine and freshwater habitats. Accordingly, the small subunit (SSU) rDNA sequence from Parvilucifera prorocentri , a tube-forming intracellular parasite of the marine benthic dinoflagellate Prorocentrum fukuyoi , was determined. Molecular phylogenetic analyses demonstrated, with very high statistical support, that P. prorocentri branched as a sister lineage to a divergent clade consisting of Parvilucifera infectans and Parvilucifera sinerae . The entire Parvilucifera clade was nested within a more inclusive and modestly supported clade consisting of Perkinsus and several environmental sequences. Because P. prorocentri possessed a novel combination of ultrastructural features known in Perkinsus, Parvilucifera , and/or syndineans (i.e. germ tubes, trichocysts, and a syndinean-like nucleus), establishing the molecular phylogenetic position of this species enabled us to build a more comprehensive framework for understanding the earliest stages in the evolution of myzozoans.     

Characterization of <Emphasis Type="Italic">Penicillium</Emphasis> Species by Ribosomal DNA Sequencing and BOX,ERIC and REP-PCR Analysis

The genus Penicillium is one of the largest and widely distributed fungal genera described to date. As a result, its taxonomic classification and species discrimination within this genus has become complicated. In this study, 52 isolates that belonged to the Penicillum genus and other related genera were characterized using two DNA-based methods: (i) analysis of the nucleotide sequences of internal transcribed spacers in ribosomal DNA and (ii) analysis of DNA fingerprints that were generated by polymerase chain reactions with specific primers for enterobacterial repetitive intergenic consensus (ERIC) and repetitive extragenic palindromic (REP) sequences, and BOX elements. Using both methods, Penicillium species were discriminated from other fungal genera. Furthermore, Penicillium species that include strains which are used as biocontrol agents, such as P. glabrum, P. purpurogenum, and P. oxalicum, could be distinguished from other Penicillium species using these techniques. Based on our findings, we propose that a polyphasic approach that includes analysis of the nucleotide sequences of ribosomal DNA and detecting the presence of highly conserved, repeated nucleotide sequences can be used to determine the genetic relationships between different Penicillium species. Furthermore, we propose that our results can be used as a start point to develop a strategy to monitor the environmental presence of particular strains of Penicillium species when they are used as biocontrol agents.     

Parasitic dinoflagellates and ellobiopsids (Ellobiopsidae) of the coastal waters of the sea of Japan

Five species of parasitic dinoflagellates of the genera Protoodinium, Paulsenella, Duboscquella, Syndinium, and Dissodinium and two species of ellobiopsids of the genus Ellobiopsis are described. Figures and distribution data are provided. All species, except for Dissodinium pseudolunula Swift ex Elbrachter et Drebes, are first records for the Russia Far-Eastern seas.     

Interactions between ant species increase arrival rates of an ant parasitoid

Behaviours or traits associated with aggression and communication may increase an animal's conspicuousness to predators or parasitoids. Most examples of this come from instances of aggression or communication within a species. We tested whether interspecific encounters between ants enhance the host location success of a parasitoid (Diptera: Phoridae) that attacks ants in the genus Linepithema. At food resources recruited to by Linepithema, parasitoid discovery rates were lower when Linepithema was alone than when other ant species were present. In experimentally controlled encounters, parasitoid discovery rates were elevated when Linepithema confronted an ant species that elicited use of chemicals, but not when it confronted an ant species that primarily elicited physical aggression. These results indicate that phorid parasitoids of Linepithema use the ant's chemicals as host location cues. Because Linepithema is known to abandon food resources in the presence of its phorid parasitoids, its use of chemicals during interspecific encounters may diminish its competitive success when phorids are nearby. Copyright 2003 Published by Elsevier Science Ltd on behalf of The Association for the Study of Animal Behaviour.      

A molecular phylogeny of Basidiophora reveals several apparently host-specific lineages on Astereae

The genus Basidiophora has long been thought to contain only two species, Basidiophora entospora and Basidiophora kellermanii, the latter of which was transferred to a newly described monotypic genus, Benua, at the end of the twentieth century, leaving Basidiophora monotypic, despite its vast host range, including a member of the Eupatoriae and several genera in the subfamily Asteroideae of the Asteraceae. Using historic herbarium specimens, we demonstrate that while Benua kellermanii is genetically highly homogenous, at least seven distinct phylogenetic lineages exist within Basidiophora, which, based on sequence divergence, most likely constitute hitherto overlooked cryptic species. As the specimens from Symphyotrichum novae-angliae formed a well-supported clade with little variation, we consider Peronospora simplex described on this host as an independent species, which is transferred to the genus Basidiophora in this study. The phylogeny of the pathogens corresponds well to the phylogeny of the respective hosts, which is unusual in downy mildews and might hint at clade-limited colonisation and subsequent radiation to closely related hosts of Astereae or even suggest a co-evolution scenario. Our findings provide further evidence that species with assumed broad host ranges should be thoroughly evaluated with respect to their phylogenetic relationships, especially in biotrophic genera with only limited morphological diversity. In some cases, host specificity of genetically divergent lineages might be the only phenotypic trait remaining for species delimitation. Future detailed morphological comparisons are needed to reveal if the seemingly cryptic species of Basidiophora can be distinguished based on subtle morphological characteristics.     

Genome-based taxonomy of genera Halomicrobium and Halosiccatus,and description of Halomicrobium salinisoli sp. nov

The genera Halosiccatus and Halomicrobium are the most closely related genera within the family Haloarculaceae (class Halobacteria). All species of these two genera are closely related to each other in phylogenetic analyses based on their 16S rRNA gene sequences, and also using the sequences of four housekeeping genes. The genus Halosiccatus was proposed based on inferred phylogeny using only one of the three distinct 16S rRNA genes detected in strain DC8^T, while Halomicrobium zhouii, one of three species of Halomicrobium, was omitted from the reference species used in these analyses. The related 16S rRNA gene sequence similarities of type strains of Halomicrobium katesii and Halomicrobium mukohataei were as high as 99.5%–99.7%, much higher than the threshold values proposed as species boundaries. These issues could have resulted in taxonomic inaccuracies in the genera Halosiccatus and Halomicrobium, and a thorough study was undertaken to clarify the status of all species in both genera. Based on phylogenetic and phylogenomic analyses, the current four species of the two genera form a single clade with high bootstrap confidence, indicating that the genus Halosiccatus should be merged with Halomicrobium. Halomicrobium katesii Kharroub et al. 2008 is proposed as a later heterotypic synonym of Halomicrobium mukohataei (Ihara et al. 1997) Oren et al. 2002. An additional species is also described (strains LT50^T and TH30), and was isolated from different Gobi saline soil samples of Tarim Basin, Xinjiang, China. Phenotypic, chemotaxonomic, genomic and phylogenetic properties indicated that strains LT50^T (=CGMCC 1.15187^T = JCM 30837^T) and TH30 (=CGMCC 1.15189 = JCM 30839) represent a novel species of the genus Halomicrobium, for which the name Halomicrobium salinisoli sp. nov. is proposed.     

The Diversity of Coolia spp. (Dinophyceae Ostreopsidaceae) in the Central Great Barrier Reef Region

Background

Dinoflagellates are important primary producers, crucial in marine food webs. Toxic strains, however, are the main causative agents of non-bacterial seafood poisoning, a major concern for public health worldwide. Despite their importance, taxonomic uncertainty within many genera of dinoflagellates is still high. The genus Coolia includes potentially harmful species and the diversity within the genus is just starting to become apparent.

Methodology/Principal Findings

In the current study, cultures were established from strains of Coolia spp. isolated from the central Great Barrier Reef (GBR). Cultures were identified based on thecal plate morphology and analyses of sequences (18S, ITS and 28S) from the nuclear rRNA operon. We report that the central GBR harbors a high diversity of Coolia species, including two species known to be capable of toxin production (C. tropicalis and C. malayensis), as well as the non-toxic C. canariensis. The strain of C. canariensis isolated from the GBR may in fact be a cryptic species, closely related but nevertheless phylogenetically distinct from the strain on which the holotype of C. canariensis was based. We also found evidence of the occurrence of a cryptic species morphologically very similar to both C. malayensis and C. monotis. The consequences of taxonomic confusion within the genus are discussed.

Conclusion/Significance

The central GBR region harbors a previously unreported high diversity of Coolia spp., including two species known to potentially produce toxins. The presence of a cryptic species of unknown toxicity highlights the importance of cryptic diversity within dinoflagellates.     

Description, host-specificity, and strain selectivity of the dinoflagellate parasite Parvilucifera sinerae sp. nov. (Perkinsozoa)

A new species of parasite, Parvilucifera sinerae sp. nov., isolated from a bloom of the toxic dinoflagellate Alexandrium minutum in the harbor of Arenys de Mar (Mediterranean Sea, Spain), is described. This species is morphologically, behaviourally, and genetically (18S rDNA sequence) different from Parvilucifera infectans, until now the only species of the genus Parvilucifera to be genetically analyzed. Sequence analysis of the 18S ribosomal DNA supported P. sinerae as a new species placed within the Perkinsozoa and close to P. infectans. Data on the seasonal occurrence of P. sinerae, its infective rates in natural and laboratory cultures, and intra-species strain-specific resistance are presented. Life-cycle studies in field samples showed that the dinoflagellate resting zygote (resting cyst) was resistant to infection, but the mobile zygote (planozygote) or pellicle stage (temporary cyst) became infected. The effects of light and salinity levels on the growth of P. sinerae were examined, and the results showed that low salinity levels promote both sporangial germination and higher rates of infection. Our findings on this newly described parasite point to a complex host-parasite interaction and provide valuable information that leads to a reconsideration of the biological strategy to control dinoflagellate blooms by means of intentional parasitic infections.     

The Genus Lactobacillus: A Taxonomic Update

Lactic Acid Bacteria (LAB) are a functional group of microorganisms comprising Gram-positive, catalase negative bacteria that produce lactic acid as the major metabolic end-product of carbohydrate fermentation. Among LAB, Lactobacillus is the genus including a high number of GRAS species (Generally Recognized As Safe) and many strains are among the most important bacteria in food microbiology and human nutrition, due to their contribution to fermented food production or their use as probiotics. From a taxonomic point of view, the genus Lactobacillus includes at present (October 2012), 152 validly described species, and it belongs to the family Lactobacillaceae together with genus Pediococcus, with whom it is phylogenetically intermixed. The updated phylogenetic analysis based on 16S rRNA gene sequence revealed that the family is divided into 15 groups of three or more species, 4 couples and 10 single lines of descents. In addition, other taxonomically relevant information for Lactobacillus species was collected. This study aims at updating the taxonomy of the genus Lactobacillus, presenting the phylogenetic structure of the Lactobacillaceae and discussing the clusters as possible nuclei of genera to be described in the future. It is expected that scientists and producers in the field of probiotics could benefit from information reported here about the correct identification procedures and nomenclature of beneficial strains of lactobacilli.     

Pseudobacciger cheneyae n. sp. (Digenea: Gymnophalloidea) from Weber’s chromis (Chromis weberi Fowler & Bean) (Perciformes: Pomacentridae) at Lizard Island,Great Barrier Reef,Australia

A new species of digenean, Pseudobacciger cheneyae n. sp., is described from the intestines of Weber’s chromis (Chromis weberi Fowler & Bean) from off Lizard Island, Great Barrier Reef, Australia. This species differs from the three described species of Pseudobacciger Nahhas & Cable, 1964 [P. cablei Madhavi, 1975, P. harengulae Yamaguti, 1938 and P. manteri Nahhas & Cable, 1964] in combinations of the size of the suckers and the length of the caeca. The host of the present species is a perciform (Family Pomacentridae) which contrasts with previous records of the genus which are almost exclusively from clupeiform fishes. The genus Pseudobacciger is presently recognised within the family Faustulidae (Poche, 1926) but phylogenetic analyses of 28S and ITS2 rDNA show that the new species bears no relationship to species of four other faustulid genera (Antorchis Linton, 1911, Bacciger Nicoll, 1924, Paradiscogaster Yamaguti, 1934 and Trigonocryptus Martin, 1958) but that instead it is nested within the Gymnophalloidea (Odhner, 1905) as sister to the Tandanicolidae (Johnston, 1927). This result suggests that the Faustulidae is polyphyletic.     

Phylogenetic relationships among monogenean gill parasites (Dactylogyridea, Ancyrocephalidae) infesting tilapiine hosts (Cichlidae): systematic and evolutionary implications

We studied the systematics of 14 species of monogenean (Ancyrocephalidae) gill parasites from West African tilapiine hosts (Cichlidae) using both morphological and genetic data. With these tools, we were able to: (i) confirm the validity of the previously described morphological parasite species and of the genus Scutogyrus; (ii) propose that some stenoxenous species (i.e., parasite species with more than one host) may be composed of sister species (e.g., Cichlidogyrus tilapiae); (iii) state that the use of the morphology of the haptoral sclerites is more suitable to infer phylogenetic relationships than the morphology of the genitalia (which seems to be more useful to resolve species-level identifications, presumably because of its faster rate of change). These results imply that: (i) the specificity of these monogenean parasites is greater than initially supposed (what were thought to be stenoxenous species may be assemblages of oïoxenous sister species); (ii) related species groups (i.e., “tilapiae,” “halli,” and “tiberianus”) have to be, as genus Scutogyrus, validated within the 54 ancyrocephalid species described from 18 species of tilapiine hosts in West Africa, (iii) the group “tilapiae,” due to its morphology and host range, have to be considered as being the most primitive; (iv) the occurrence of lateral transfers and parallel speciation processes are necessary to describe the repartition of the newly described parasite groups on the three host genera studied (Tilapia, Oreochromis, and Sarotherodon).     

Histories of host shifts and cospeciation among free‐living parasitoids of Rhagoletis flies

Host shifts by specialist insects can lead to reproductive isolation between insect populations that use different hosts, promoting diversification. When both a phytophagous insect and its ancestrally associated parasitoid shift to the same novel host plant, they may cospeciate. However, because adult parasitoids are free living, they can also colonize novel host insects and diversify independent of their ancestral host insect. Although shifts of parasitoids to new insect hosts have been documented in ecological time, the long‐term importance of such shifts to parasitoid diversity has not been evaluated. We used a genus of flies with a history of speciation via host shifting (Rhagoletis [Diptera: Tephritidae]) and three associated hymenopteran parasitoid genera (Diachasma, Coptera and Utetes) to examine cophylogenetic relationships between parasitoids and their host insects. We inferred phylogenies of Rhagoletis, Diachasma, Coptera and Utetes and used distance‐based cophylogenetic methods (ParaFit and PACo) to assess congruence between fly and parasitoid trees. We used an event‐based method with a free‐living parasitoid cost model to reconstruct cophylogenetic histories of each parasitoid genus and Rhagoletis. We found that the current species diversity and host–parasitoid associations between the Rhagoletis flies and parasitoids are the primary result of ancient cospeciation events. Parasitoid shifts to ancestrally unrelated hosts primarily occur near the branch tips, suggesting that host shifts contribute to recent parasitoid species diversity but that these lineages may not persist over longer time periods. Our analyses also stress the importance of biologically informed cost models when investigating the coevolutionary histories of hosts and free‐living parasitoids.