Mining various genomic resources to resolve old alpha-taxonomy questions: A test of the species hypothesis of the Proteocephalus longicollis species complex (Cestoda: Platyhelminthes) from salmonid fishes

High-throughput sequencing strategies became commonly employed to study non-model parasites, but the corresponding genomes and transcriptomes were seldom mined following the original publication. Similar to the data generated with genome skimming techniques based on shallow-depth shotgun genomes, various genomic and transcriptomic resources can be screened for useful molecular phylogenetic markers traditionally characterised with Sanger sequencing. Here, we provide an example of a strategy using reduced-representation genomic as well as transcriptomic data to obtain broad insights into the molecular diversity of the cestode Proteocephalus longicollis, a common parasite of salmonids distributed throughout the Holarctic region. We extract popular mitochondrial and nuclear ribosomal markers from various genomic resources for hundreds of parasite specimens from multiple European whitefish populations and compare those with Proteocephalus representatives from other species of salmonids and various geographical regions. In contrast with the previous morphology-based assessments, molecular phylogeny reveals a high degree of genetic divergence between Proteocephalus isolates from different salmonids, contrastingly low genetic differentiation within the parasite's populations hosted by the European whitefish (Coregonus lavaretus species complex), and a sister species relationship of Proteocephalus from European whitefish and Proteocephalus percae, a parasite of European perch (Perca fluviatilis). Proteocephalus spp. from North American lake whitefish, brown trout and Arctic charr each formed clearly distinct lineages. These results advance our understanding of the interrelationships of the Proteocephalus-aggregate, a well-recognized clade of Holarctic freshwater fish proteocephalids, and support resurrection of some of the nominal species of Proteocephalus, including Proteocephalus exiguus La Rue, 1911 from North American coregonids and Proteocephalus fallax La Rue, 1911 from European C. lavaretus, reserving Proteocephalus longicollis (Zeder, 1800) exclusively for parasites of Salmo trutta.

Archigetes Leuckart, 1878 (Cestoda, Caryophyllidea): diversity of enigmatic fish tapeworms with monoxenic life cycles

The caryophyllidean genus Archigetes Leuckart, 1878 is unique among all tapeworms in that its species can mature in invertebrate hosts (Oligochaeta), i.e., have a monoxenic (direct) life cycle. All five species were described as progenetic plerocercoids in oligochaetes and two of them also as adults from cypriniform fishes. Two species, A. sieboldi Leuckart, 1878 and A. iowensis Calentine, 1962, were found in North America in non-native common carp (Cyprinus carpio). A molecular study of caryophyllideans from the southern United States has revealed the occurrence of three new species in native freshwater fishes (Catostomidae, Ictiobinae): Archigetes loculotruncatus n. sp. from Ictiobus bubalus, I. niger and Carpiodes cyprinus is the largest representative of the genus and differs by a loculotruncate scolex. Archigetes megacephalus n. sp. from Ictiobus niger, I. bubalus and I. cyprinellus is characterised by a prominent, bothrioloculodiscate scolex. Archigetes vadosus n. sp. from I. bubalus is typified by a globular scolex with very shallow loculi; it differs from the closely related A. sieboldi in the shape of the body, with a distinct neck region and a scolex wider than the remaining body. Archigetes iowensis Calentine, 1962 becomes a junior synonym of Paraglaridacris limnodrili (Yamaguti, 1934). The generic diagnosis of Archigetes is amended and a key to identification of North American taxa is provided. Species of Archigetes and Paraglaridacris differ from each other most conspicuously in the structure of the ovary, which is follicular in Archigetes versus compact in Paraglaridacris.

Molecular evidence of three closely related species of Biacetabulum Hunter, 1927 (Cestoda: Caryophyllidea): a case of recent speciation in different fish hosts (Catostomidae)?

Monozoic tapeworms (Caryophyllidea) are dominant components of parasite communities of suckers (Catostomidae) in North America, with Biacetabulum Hunter, 1927 representing one of the more species-rich genera. Molecular (28S rDNA) and morphological (including scanning electron microscopy and histology) evaluation of newly collected tapeworms from different fish hosts revealed the existence of four similar (and three closely related) species of Biacetabulum. These four species differ from their congeners by having a long body (up to 48 mm long) with a very long, slender neck (its length represents ≥30% of total body length), a large, globular scolex with a prominent central acetabulum-like loculus on the dorsal and ventral sides, two pairs of shallow lateral loculi and a distinct, slightly convex apical disc, and a cirrus-sac that is situated between the anterior arms of the ovarian wings. Taken together, the morphological and molecular data and the host associations of these species provide evidence of their host specificity. Biacetabulum isaureae n. sp. occurs in notch clip redhorse, Moxostoma collapsum, in South Carolina (USA), B. longicollum n. sp. in silver redhorse, Moxostoma anisurum (type host), and golden redhorse, M. erythrurum, in Manitoba (Canada) and West Virginia (USA), B. overstreeti n. sp. in a spotted sucker, Minytrema melanops, in Mississippi, and B. hypentelii n. sp. in northern hogsucker, Hypentelium nigricans, in Tennessee (USA). The new species differ from each other in the number of postovarian vitelline follicles, the posterior extent of preovarian vitelline follicles and relative size of the cirrus sac.

Disentangling taxonomy of Biacetabulum (Cestoda, Caryophyllidea), parasites of catostomid fishes in North America: proposal of Megancestus gen. n. to accommodate B. carpiodi

A new genus, Megancestus n. gen., is proposed to accommodate the caryophyllidean tapeworm Biacetabulum carpiodi Mackiewicz, 1969 from carpsuckers and quillback (Carpiodes spp.) in North America. This species is not closely related to other species of Biacetabulum Hunter, 1927 and is transferred to a newly erected genus. This new genus is typified by the possession of a small body (total length of 3.1-7.5 mm) with a scolex that bears a pair of large acetabulum-like loculi, two pairs of shallow lateral loculi, and a slightly convex apical disc, testes arranged in one or two layers, oval, thick-walled cirrus-sac, well-developed external seminal vesicle, separate gonopores, H-shaped ovary, few median vitelline follicles, and the uterus extending by a single loop anterior to the cirrus-sac. Megancestus differs from all Nearctic caryophyllidean genera (family Capingentidae), including Biacetabulum, by vitelline follicles dorsal to the ovary that connect the preovarian and postovarian vitelline fields. The most closely related Hunterella Mackiewicz et McCrae, 1962 differs by shape of the scolex (tholate, i.e., devoid of any loculi), dumbbell-shaped ovary and the uterus not extending anterior to the cirrus-sac. Megancestus carpiodi (Mackiewicz, 1969) n. comb. is the only species of the genus and it is a stenoxenous parasite, which has been found only in the river carpsucker (Carpiodes carpio-type host), quillback (Carpiodes cyprinus) and highfin carpsucker (Carpiodes velifer) (Catostomidae: Ictiobinae) in the lower and middle Mississippi basin.

Characterization and phylogenomics of the complete mitochondrial genome of the polyzoic cestode Gangesia oligonchis (Platyhelminthes: Onchoproteocephalidea)

The order Onchoproteocephalidea (Eucestoda) was recently erected to accommodate the hook-bearing tetraphyllideans and the proteocephalideans, which are characterized by internal proglottization and a tetra-acetabulate scolex. The recognized subfamilies in the Proteocephalidae appeared to be non-monophyletic based on 28S recombinant DNA (rDNA) sequence data. Other molecular markers with higher phylogenetic resolution, such as large mitochondrial DNA fragments and multiple genes, are obviously needed. Thus the mitochondrial genome of Gangesia oligonchis, belonging to the putative earliest diverging group of the Proteocephalidae, was sequenced. The circular mitogenome of G. oligonchis was 13,958 bp in size, and contained the standard 36 genes: 22 transfer RNA genes, two rRNA genes and 12 protein-coding genes, as well as two major non-coding regions. A short NCR and a large NCR (lNCR) region were 216 bp and 419 bp in size, respectively. Highly repetitive regions in the lNCR region were detected with that of 11 repeat units. The mitogenome of G. oligonchis shared 71.1% nucleotide identity with Testudotaenia sp. WL-2016. Phylogenetic analyses of the complete mitochondrial genomes with Bayesian inference and maximum likelihood methods indicated that G. oligonchis formed a sister clade with Testudotaenia sp. WL-2016 with maximum support. The ordinal topology is (Caryophyllidea, (Diphyllobothriidea, (Bothriocephalidea, (Onchoproteocephalidea, Cyclophyllidea)))). The mitogenomic gene arrangement of G. oligonchis was identical to that of Testudotaenia sp. WL-2016. Both mitogenomic and nuclear sequence data for many more taxa are required to effectively explore the inter-relationships among the Onchoproteocephalidea.

Revision of Acanthotaenia von Linstow, 1903 (Cestoda: Proteocephalidae), parasites of monitors (Varanus spp.), based on morphological and molecular data

A morphological and molecular phylogenetic study of proteocephalid tapeworms of the genus Acanthotaenia von Linstow, 1903, parasites of monitors (Varanidae), was carried out. The type species, A. shipleyi von Linstow, 1903, which was originally described based on an immature specimen from Sri Lanka, is redescribed based on new material from the type host, Varanus salvator, in Sri Lanka, Malaysia, and Vietnam, and its neotype is designated. In addition, Acanthotaenia susanae n. sp. is described from Varanus nebulosus in Vietnam. The new species differs from congeners by the large size of the scolex, width of the rostellum and the number of testes. New molecular data (sequences of lsrDNA and cox1) revealed Acanthotaenia paraphyletic with the inclusion of Australotaenia bunthangi de Chambrier & Scholz, 2012, a parasite of Enhydris enhydris (Ophidia: Homalopsidae) in Cambodia. Molecular data confirm a wide distribution of A. shipleyi (isolates from Malaysia and Vietnam were almost identical) and indicate a strict host specificity (oioxeny) of individual species of the genus. Type specimens of four species made it possible to supplement their morphological descriptions. A survey of all species of Acanthotaenia recognised as valid is presented and the following taxonomic changes are proposed: Acanthotaenia pythonis Wahid, 1968 described from the green python, Morelia viridis, in a zoo, is transferred to Kapsulotaenia as Kapsulotaenia pythonis (Wahid, 1968) n. comb., because it possesses intrauterine eggs grouped in capsules. Acanthotaenia gracilis (Beddard, 1913) from Varanus varius in Australia is considered to be species inquirenda because its original descriptions did not contain sufficient data for adequate circumscription and differentiation from congeners and type material was not available. Generic diagnosis of Acanthotaenia is amended and a key to its seven species is provided.

Comparative mitogenomics supports synonymy of the genera Ligula and Digramma (Cestoda: Diphyllobothriidae)

Background

After observing differences in the number of reproductive complexes per proglottid within the genus Ligula, the genus Digramma was erected. However, the validity of Digramma has been previously questioned due to a low variability in the cox1, nad1 and ITS rDNA sequences between the two genera. We undertook a study to greatly increase the amount of sequence data available for resolution of this question by sequencing and characterizing the complete mitogenomes of Digramma interrupta and Ligula intestinalis.

Results

The circular mtDNA molecules of Digramma interrupta and Ligula intestinalis are 13,685 bp and 13,621 bp in size, respectively, both comprising 12 PCGs, 22 tRNA genes, two rRNA genes, and two mNCRs. Both mitogenomes exhibit the same gene order and share 92.7% nucleotide identity, compared with 85.8–86.5% to the most closely related genus Dibothriocephalus. Each gene from D. interrupta and L. intestinalis is almost of the same size, and the sequence identity ranges from 87.5% (trnD) to 100% (trnH, trnQ and trnV). NCR2 sequences of D. interrupta and L. intestinalis are 249 bp and 183 bp in length, respectively, which contributes to the main difference in length between their complete mitogenomes. A sliding window analysis of the 12 PCGs and two rRNAs indicated nucleotide diversity to be higher in nad5, nad6, nad2, nad4 and cox3, whereas the most conserved genes were rrnL and rrnS. Lower sequence identity was also found in nad2, nad4, nad5, nad6 and cox3 genes between the two diphyllobothriids. Within the Diphyllobothriidae, phylogenetic analysis indicated Ligula and Digramma to be most closely related to one another, forming a sister group with Dibothriocephalus.

Conclusions

Owing to higher nucleotide diversity, the genes nad2, nad4, nad5, nad6 and cox3 should be considered optimal candidates to use as molecular markers for population genetics and species identification between the two closely related species. The phylogenetic results in combination with the comparative analysis of the two mitogenomes, consistently support the congeneric status of L. intestinalis and D. interrupta.

Electronic supplementary material

The online version of this article (10.1186/s13071-018-2910-9) contains supplementary material, which is available to authorized users.

MACROEVOLUTIONARY PATTERNS OF MORPHOLOGICAL DIVERSIFICATION AMONG PARASITIC FLATWORMS (PLATYHELMINTHES: CERCOMERIA)

Patterns of parasite morphological diversification were investigated using a morphological data base for the parasitic platyhelminths comprising 1,459 characters analyzed using phylogenetic systematic methods. Only 10.8% of the 1,882 character transformations are losses, casting doubt on views that parasites are secondarily simplified and exhibit degenerate evolution. Chi-squared analysis indicates that character loss in the Digenea and Monogenea occurs in proportion to total change and is disproportionately lower within the Eucestoda. In the Digenea fewer female characters and more male characters have been lost than expected by the total number of characters in that group, and more male and more nonreproductive characters have been lost in proportion to their distribution across groups. In the Monogenea fewer nonreproductive and more larval characters have been lost than expected within the group, and female character loss is high relative to other groups. In the Eucestoda fewer female and more larval characters have been lost than expected within the group, whereas loss of male and nonreproductive character is low, and loss of larval characters is high, compared to the other groups. Patterns of character loss result partially from characters that show repeated (homoplasious) loss in different groups. High consistency index and low homoplasy slope ratio values indicate that the parasitic platyhelminths show unusually low levels of homoplasy, casting doubt on views that parasite morphology is unusually adaptively plastic. Homoplasy within the monogeneans occurs in proportion to overall character change, is slightly higher than expected in the digeneans, and is much lower than expected within the eucestodes. Homoplasy occurs less often than expected in larval characters, and more often than expected in nonreproductive characters in the Digenea. Monogeneans show more homoplasy than expected for larval characters both within and among groups. Eucestodes show fewer homoplasious male and nonreproductive, and more homoplasious larval, characters than expected within the group, and higher homoplasy in larval characters and lower homoplasy in female and nonreproductive characters among groups.

A large 28S rDNA-based phylogeny confirms the limitations of established morphological characters for classification of proteocephalidean tapeworms (Platyhelminthes, Cestoda)

Proteocephalidean tapeworms form a diverse group of parasites currently known from 315 valid species. Most of the diversity of adult proteocephalideans can be found in freshwater fishes (predominantly catfishes), a large proportion infects reptiles, but only a few infect amphibians, and a single species has been found to parasitize possums. Although they have a cosmopolitan distribution, a large proportion of taxa are exclusively found in South America. We analyzed the largest proteocephalidean cestode molecular dataset to date comprising more than 100 species (30 new), including representatives from 54 genera (80%) and all subfamilies, thus significantly improving upon previous works to develop a molecular phylogeny for the group. The Old World origin of proteocephalideans is confirmed, with their more recent expansion in South America. The earliest diverging lineages are composed of Acanthotaeniinae and Gangesiinae but most of the presently recognized subfamilies (and genera) appear not to be monophyletic; a deep systematic reorganization of the order is thus needed and the present subfamilial system should be abandoned. The main characters on which the classical systematics of the group has been built, such as scolex morphology or relative position of genital organs in relation to the longitudinal musculature, are of limited value, as demonstrated by the very weak support for morphologically-defined subfamilies. However, new characters, such as the pattern of uterus development, relative ovary size, and egg structure have been identified, which may be useful in defining phylogenetically well-supported subgroups. A strongly supported lineage infecting various snakes from a wide geographical distribution was found. Although several improvements over previous works regarding phylogenetic resolution and taxon coverage were achieved in this study, the major polytomy in our tree, composed largely of siluriform parasites from the Neotropics, remained unresolved and possibly reflects a rapid radiation. The genus Spasskyellina Freze, 1965 is resurrected for three species of Monticellia bearing spinitriches on the margins of their suckers.