Non-monophyly of the monogeneans?

Complete mitochondrial genomes of Dactylogyrus crucifer and Dactylogyrus zandti reveal distinct patterns of codon usage within Dactylogyrus

Monogeneans of the genus Dactylogyrus Diesing, 1850, the largest genus in the family Dactylogyridae, mostly parasitize the gills of cyprinoid hosts; however, only 3 Dactylogyrus' mitochondrial genomes (mitogenomes) are studied so far. The aim of this research is to extend our understanding of the mitogenomes of Dactylogyrus. We sequenced the mitogenomes of D. crucifer and D. zandti isolated from Rutilus rutilus and Abramis brama orientalis in northwest China, and then we compared these mitogenomes with other monogeneans. We used Illumina NovaSeq to sequence the entire mitochondrial genomes of D. crucifer and D. zandti and characterized the mitogenomes to understand the gene structure, gene identity, the secondary structures of the 22 tRNA genes, and relative synonymous codon usage. We used the analytic Bayesian Information and Maximum Likelihood methods to determine their associated phylogenetic trees. The mitogenomes of D. crucifer and D. zandti were 14,403 and 18,584 bp, respectively. Organization and positioning of these genes were in accordance with Dactylogyrus lamellatus and Dactylogyrus tuba. The nucleotide composition of Dactylogyridae was different from other families of Monogenea, and the A+T count of genus Dactylogyrus (54 - 58.4 %) was lower than other genus species of the family Dactylogyridea (63.9 - 78.4 %) in protein-coding genes. Dactylogyrus members displayed a codon usage bias. The relative synonymous codon used by Dactylogyrus was not conserved and was lower than other monogeneans. The codon use patterns of closely-related species isolated from closely-related hosts were identical. Phylogenetic analyses using mitogenomic dataset produced Dactylogyrus isolated from host subfamily Leuciscinae formed a sister-group. Our results contributed significantly to an increased database of mitogenomes, more than 50 %, for Dactylogyrus that may help future studies of mitochondrial genes and codon uses for the analysis of monogenean phylogenetics.

Strong mitonuclear discordance in the phylogeny of Neodermata and evolutionary rates of Polyopisthocotylea

The genomic evolution of Polyopisthocotylea remains poorly understood in comparison to the remaining three classes of Neodermata: Monopisthocotylea, Cestoda, and Trematoda. Moreover, the evolutionary sequence of major events in the phylogeny of Neodermata remains unresolved. Herein we sequenced the mitogenome and transcriptome of the polyopisthocotylean Diplorchis sp., and conducted comparative evolutionary analyses using nuclear (nDNA) and mitochondrial (mtDNA) genomic datasets of Neodermata. We found strong mitonuclear discordance in the phylogeny of Neodermata. Polyopisthocotylea exhibited striking mitonuclear discordance in relative evolutionary rates: the fastest-evolving mtDNA in Neodermata and a comparatively slowly-evolving nDNA genome. This was largely attributable to its very long stem branch in mtDNA topologies, not exhibited by the nDNA data. We found indications that the fast evolution of mitochondrial genomes of Polyopisthocotylea may be driven both by relaxed purifying selection pressures and elevated levels of directional selection. We identified mitochondria-associated genes encoded in the nuclear genome: they exhibited unique evolutionary rates, but not correlated with the evolutionary rate of mtDNA, and there is no evidence for compensatory evolution (they evolved slower than the rest of the genome). Finally, there appears to exist an exceptionally large (≈6.3 kb) nuclear mitochondrial DNA segment (numt) in the nuclear genome of newly sequenced Diplorchis sp. A 3'-end segment of the 16S rRNA gene encoded by the numt was expressed, suggesting that this gene acquired novel, regulatory functions after the transposition to the nuclear genome. In conclusion, Polyopisthocotylea appears to be the lineage with the fastest-evolving mtDNA sequences among all of Bilateria, but most of the substitutions were accumulated deep in the evolutionary history of this lineage. As the nuclear genome does not exhibit a similar pattern, the circumstances underpinning this evolutionary phenomenon remain a mystery.

The evolution of endoparasitism and complex life cycles in parasitic platyhelminths

Within flatworms, the vast majority of parasitism is innate to Neodermata, the most derived and diversified group of the phylum Platyhelminthes.1,2 The four major lineages of Neodermata maintain various combinations of life strategies.3 They include both externally (ecto-) and internally feeding (endo-) parasites. Some lineages complete their life cycles directly by infecting a single host, whereas others succeed only through serial infections of multiple hosts of various vertebrate and invertebrate groups. Food sources and modes of digestion add further combinatorial layers to the often incompletely understood mosaic of neodermatan life histories. Their evolutionary trajectories have remained molecularly unresolved because of conflicting evolutionary inferences and a lack of genomic data.4 Here, we generated transcriptomes for nine early branching neodermatan representatives and performed detailed phylogenomic analyses to address these critical gaps. Polyopisthocotylea, mostly hematophagous ectoparasites, form a group with the mostly hematophagous but endoparasitic trematodes (Trematoda), rather than sharing a common ancestor with Monopisthocotylea, ectoparasitic epithelial feeders. Phylogenetic placement of the highly specialized endoparasitic Cestoda alters depending on the model. Regardless of this uncertainty, this study brings an unconventional perspective on the evolution of platyhelminth parasitism, rejecting a common origin for the endoparasitic lifestyle intrinsic to cestodes and trematodes. Instead, our data indicate that complex life cycles and invasion of vertebrates' gut lumen, the hallmark features of these parasites, evolved independently within Neodermata. We propose the demise of the traditionally recognized class Monogenea and the promotion of its two subclasses to the class level as Monopisthocotyla new class and Polyopisthocotyla new class.

Exploring Evolutionary Relationships within Neodermata Using Putative Orthologous Groups of Proteins, with Emphasis on Peptidases

The phylogenetic relationships within Neodermata were examined based on putative orthologous groups of proteins (OGPs) from 11 species of Monogenea, Trematoda, and Cestoda. The dataset included OGPs from BUSCO and OMA. Additionally, peptidases were identified and evaluated as phylogenetic markers. Phylogenies were inferred using the maximum likelihood method. A network analysis and a hierarchical grouping analysis of the principal components (HCPC) of orthologous groups of peptidases were performed. The phylogenetic analyses showed the monopisthocotylean monogeneans as the sister-group of cestodes, and the polyopisthocotylean monogeneans as the sister-group of trematodes. However, the sister-group relationship between Monopisthocotylea and Cestoda was not statistically well supported. The network analysis and HCPC also showed a cluster formed by polyopisthocotyleans and trematodes. The present study supports the non-monophyly of Monogenea. An analysis of mutation rates indicated that secreted peptidases and inhibitors, and those with multiple copies, are under positive selection pressure, which could explain the expansion of some families such as C01, C19, I02, and S01. Whilst not definitive, our study presents another point of view in the discussion of the evolution of Neodermata, and we hope that our data drive further discussion and debate on this intriguing topic.

Spermiogenesis and spermatozoon ultrastructure in basal polyopisthocotylean monogeneans, Hexabothriidae and Chimaericolidae, and their significance for the phylogeny of the Monogenea

Sperm ultrastructure provides morphological characters useful for understanding phylogeny; no study was available for two basal branches of the Polyopisthocotylea, the Chimaericolidea and Diclybothriidea. We describe here spermiogenesis and sperm in Chimaericola leptogaster (Chimaericolidae) and Rajonchocotyle emarginata (Hexabothriidae), and sperm in Callorhynchocotyle callorhynchi (Hexabothriidae). Spermiogenesis in C. leptogaster and R. emarginata shows the usual pattern of most Polyopisthocotylea with typical zones of differentiation and proximo-distal fusion of the flagella. In all three species, the structure of the spermatozoon is biflagellate, with two incorporated trepaxonematan 9 + "1" axonemes and a posterior nucleus. However, unexpected structures were also seen. An alleged synapomorphy of the Polyopisthocotylea is the presence of a continuous row of longitudinal microtubules in the nuclear region. The sperm of C. leptogaster has a posterior part with a single axoneme, and the part with the nucleus is devoid of the continuous row of microtubules. The spermatozoon of R. emarginata has an anterior region with membrane ornamentation, and posterior lateral microtubules are absent. The spermatozoon of C. callorhynchi has transverse sections with only dorsal and ventral microtubules, and its posterior part shows flat sections containing a single axoneme and the nucleus. These findings have important implications for phylogeny and for the definition of synapomorphies in the Neodermata. We point out a series of discrepancies between actual data and interpretation of character states in the matrix of a phylogeny of the Monogenea. Our main conclusion is that the synapomorphy "lateral microtubules in the principal region of the spermatozoon" does not define the Polyopisthocotylea but is restricted to the Mazocraeidea.

Sequencing, characterization and phylogenomics of the complete mitochondrial genome of Dactylogyrus lamellatus (Monogenea: Dactylogyridae)

Despite the worldwide distribution and pathogenicity of monogenean parasites belonging to the largest helminth genus, Dactylogyrus, there are no complete Dactylogyrinae (subfamily) mitogenomes published to date. In order to fill this knowledge gap, we have sequenced and characterized the complete mitogenome of Dactylogyrus lamellatus, a common parasite on the gills of grass carp (Ctenopharyngodon idella). The circular mitogenome is 15,187 bp in size, containing the standard 22 tRNA genes, 2 rRNA genes, 12 protein-encoding genes and a long non-coding region (NCR). There are two highly repetitive regions in the NCR. We have used concatenated nucleotide sequences of all 36 genes to perform the phylogenetic analysis using Bayesian inference and maximum likelihood approaches. As expected, the two dactylogyrids, D. lamellatus (Dactylogyrinae) and Tetrancistrum nebulosi (Ancyrocephalinae), were closely related to each other. These two formed a sister group with Capsalidae, and this cluster finally formed a further sister group with Gyrodactylidae. Phylogenetic affinity between Dactylogyrinae and Ancyrocephalinae was further confirmed by the similarity in their gene arrangement. The sequencing of the first Dactylogyrinae, along with a more suitable selection of outgroups, has enabled us to infer a much better phylogenetic resolution than recent mitogenomic studies. However, as many lineages of the class Monogenea remain underrepresented or not represented at all, a much larger number of mitogenome sequences will have to be available in order to infer the evolutionary relationships among the monogeneans fully, and with certainty.

Advances in Spermatological Characters in the Digenea: Review and Proposal of Spermatozoa Models and Their Phylogenetic Importance

The wide biodiversity and economic importance of digeneans have motivated a great deal of research in the last decade, focussing on their phylogenetic positions. Molecular research was instrumental for our understanding of phylogeny in the Digenea, but spermatological studies have also provided many results, which are potentially useful for phylogeny; however, the complete spermatological data set has never been reviewed in a whole phylogenetic perspective. Spermatological data are now available for more than 100 species, belonging to 15 superfamilies and 46 families. In this paper, we try to summarize the current knowledge about sperm structure in the digeneans and propose a classification of digenean spermatozoa into five basic models. The main ultrastructural characters used are (1) the type of axoneme, (2) the lateral expansion, (3) the association 'external ornamentation of the plasma membrane + cortical microtubules', (4) the field of cortical microtubules and its number, (5) the location of the external ornamentation, (6) the location of the maximum number of cortical microtubules and (7) the number of mitochondria. We also outline the most interesting features for phylogenetic inference and their possible value in the context of digenean systematics, phylogeny and evolution. Associations between sperm models and superfamilies were found as follows: Type 1 in the Schistosomatoidea; Type 2 in the Hemiuroidea; Type 3 in the Opecoeloidea, Lepocreadioidea, Haploporoidea and Opisthorchioidea; Type 4 in the Gorgoderoidea, Microphalloidea, Plagiorchioidea and Gymnophalloidea; Type 5 in the Echinostomatoidea, Microscaphidioidea, Paramphistomoidea, Pronocephaloidea and Brachylaimoidea.

Neobenedenia melleni Parasite of Red Snapper, Lutjanus erythropterus, with Regression Statistical Analysis between Fish Length, Temperature, and Parasitic Intensity in Infected Fish, Cultured at Jerejak Island, Penang, Malaysia

The fish parasites collected from Lutjanus erythropterus fish species showed a correlation with parasitic intensity, fish size, and temperature, and statistical model summary was produced using SPSS version 20, statistical software. Statistical model summary concluded that among the variables which significantly predict the prevalence of Neobenedenia melleni parasites are fish length and water temperature, both significant at 1% and 5%. Furthermore, the increase in one unit of fish length, holding other variables constant, increases the prevalence of parasite by approximately 1 (0.7≈1) unit. Also, increasing the temperature from 32°C to 33°C will positively increase the number of parasites by approximately 0.32 units, holding other variables constant. The model can be summarized as estimated number of Neobenedenia melleni parasites = 8.2 + 0.7 ⁎ (fish length) + 0.32 ⁎ (water temperature). Next, this study has also shown the DNA sequence and parasitic morphology of Neobenedenia melleni. Nucleotide sequence for 18s ribosomal gene RNA in this study showed 99% similarity with N. melleni EU707804.1 from GenBank. Finally, all the sequence of Neobenedenia melleni in this study was deposited in GenBank with accession numbers of KU843501, KU843502, KU843503, and KU843504.

Comparative genomics of flatworms (platyhelminthes) reveals shared genomic features of ecto- and endoparastic neodermata

The ectoparasitic Monogenea comprise a major part of the obligate parasitic flatworm diversity. Although genomic adaptations to parasitism have been studied in the endoparasitic tapeworms (Cestoda) and flukes (Trematoda), no representative of the Monogenea has been investigated yet. We present the high-quality draft genome of Gyrodactylus salaris, an economically important monogenean ectoparasite of wild Atlantic salmon (Salmo salar). A total of 15,488 gene models were identified, of which 7,102 were functionally annotated. The controversial phylogenetic relationships within the obligate parasitic Neodermata were resolved in a phylogenomic analysis using 1,719 gene models (alignment length of >500,000 amino acids) for a set of 16 metazoan taxa. The Monogenea were found basal to the Cestoda and Trematoda, which implies ectoparasitism being plesiomorphic within the Neodermata and strongly supports a common origin of complex life cycles. Comparative analysis of seven parasitic flatworm genomes identified shared genomic features for the ecto- and endoparasitic lineages, such as a substantial reduction of the core bilaterian gene complement, including the homeodomain-containing genes, and a loss of the piwi and vasa genes, which are considered essential for animal development. Furthermore, the shared loss of functional fatty acid biosynthesis pathways and the absence of peroxisomes, the latter organelles presumed ubiquitous in eukaryotes except for parasitic protozoans, were inferred. The draft genome of G. salaris opens for future in-depth analyses of pathogenicity and host specificity of poorly characterized G. salaris strains, and will enhance studies addressing the genomics of host–parasite interactions and speciation in the highly diverse monogenean flatworms.

Excretory system of representatives from family Diplozoidae (Monogenea)

Diplozoons are representatives of blood-feeding ectoparasites from the family Diplozoidae (Polyopisthocotylea, Monogenea). Although these worms have been the subject of numerous taxonomical, phylogenetic, and ecological studies, the detailed study of their excretory system has remained relatively neglected. Our observations focused on the morphological and ultrastructural features of the excretory apparatus of four diplozoid species: Diplozoon paradoxum, Eudiplozoon nipponicum, Paradiplozoon bliccae, and Paradiplozoon homoion. Observations were obtained using two microscope methods: light microscopy, equipped with differential interference contrast (Nomarski DIC) and transmission electron microscopy (TEM). The ultrastructure of two basic compartments which forms the excretory apparatus, flame cells with filtration apparatus, and canal cells forming the protonephridial ducts is revealed in this study. A unique consecutive sequence of longitudinal semi-thin sections of the excretory pore of E. nipponicum is visualized there for the first time.

Constraining the Deep Origin of Parasitic Flatworms and Host-Interactions with Fossil Evidence

Novel fossil discoveries have contributed to our understanding of the evolutionary appearance of parasitism in flatworms. Furthermore, genetic analyses with greater coverage have shifted our views on the coevolution of parasitic flatworms and their hosts. The putative record of parasitic flatworms is consistent with extant host associations and so can be used to put constraints on the evolutionary origin of the parasites themselves. The future lies in new molecular clock analyses combined with additional discoveries of exceptionally preserved flatworms associated with hosts and coprolites. Besides direct evidence, the host fossil record and biogeography have the potential to constrain their evolutionary history, albeit with caution needed to avoid circularity, and a need for calibrations to be implemented in the most conservative way. This might result in imprecise, but accurate divergence estimates for the evolution of parasitic flatworms.

Nuclear genomic signals of the 'microturbellarian' roots of platyhelminth evolutionary innovation

Flatworms number among the most diverse invertebrate phyla and represent the most biomedically significant branch of the major bilaterian clade Spiralia, but to date, deep evolutionary relationships within this group have been studied using only a single locus (the rRNA operon), leaving the origins of many key clades unclear. In this study, using a survey of genomes and transcriptomes representing all free-living flatworm orders, we provide resolution of platyhelminth interrelationships based on hundreds of nuclear protein-coding genes, exploring phylogenetic signal through concatenation as well as recently developed consensus approaches. These analyses robustly support a modern hypothesis of flatworm phylogeny, one which emphasizes the primacy of the often-overlooked 'microturbellarian' groups in understanding the major evolutionary transitions within Platyhelminthes: perhaps most notably, we propose a novel scenario for the interrelationships between free-living and vertebrate-parasitic flatworms, providing new opportunities to shed light on the origins and biological consequences of parasitism in these iconic invertebrates.

The monogenean which lost its clamps

Ectoparasites face a daily challenge: to remain attached to their hosts. Polyopisthocotylean monogeneans usually attach to the surface of fish gills using highly specialized structures, the sclerotized clamps. In the original description of the protomicrocotylid species Lethacotyle fijiensis, described 60 years ago, the clamps were considered to be absent but few specimens were available and this observation was later questioned. In addition, genera within the family Protomicrocotylidae have either clamps of the “gastrocotylid” or the “microcotylid” types; this puzzled systematists because these clamp types are characteristic of distinct, major groups. Discovery of another, new, species of the genus Lethacotyle, has allowed us to explore the nature of the attachment structures in protomicrocotylids. Lethacotyle vera n. sp. is described from the gills of the carangid Caranx papuensis off New Caledonia. It is distinguished from Lethacotyle fijiensis, the only other species of the genus, by the length of the male copulatory spines. Sequences of 28S rDNA were used to build a tree, in which Lethacotyle vera grouped with other protomicrocotylids. The identity of the host fish was confirmed with COI barcodes. We observed that protomicrocotylids have specialized structures associated with their attachment organ, such as lateral flaps and transverse striations, which are not known in other monogeneans. We thus hypothesized that the clamps in protomicrocotylids were sequentially lost during evolution, coinciding with the development of other attachment structures. To test the hypothesis, we calculated the surfaces of clamps and body in 120 species of gastrocotylinean monogeneans, based on published descriptions. The ratio of clamp surface: body surface was the lowest in protomicrocotylids. We conclude that clamps in protomicrocotylids are vestigial organs, and that occurrence of “gastrocotylid” and simpler “microcotylid” clamps within the same family are steps in an evolutionary sequence, leading to the absence of these attributes in species of Lethacotyle.

Spermatological characteristics of Pleurogenidae (Digenea) inferred from the ultrastructural study of Pleurogenes claviger, Pleurogenoides medians and Prosotocus confusus

The present work constitutes the first ultrastructural analysis of the spermatozoon in the Pleurogenidae, with the study of three species belonging to three of the 16 genera included in this family, namely Pleurogenes claviger, Pleurogenoides medians and Prosotocus confusus. The mature spermatozoa of these pleurogenids present two axonemes of the 9+“1” trepaxonematan pattern, a nucleus, two mitochondria, two bundles of parallel cortical microtubules, external ornamentation, spine-like bodies and granules of glycogen. The organization of these characters in the sperm cell is similar in the three species. Thus, the anterior spermatozoon extremity is filiform and a continuous and submembranous layer of parallel cortical microtubules surrounds the axonemes at their anterior end. The posterior spermatozoon extremity exhibits the second axoneme and corresponds to the Cryptogonimidean type of Quilichini et al. (2010). Slight differences were noted between the spermatozoon of P. confusus and those of the two remaining species in the location of mitochondria.

An annotated list of fish parasites (Isopoda, Copepoda, Monogenea, Digenea, Cestoda, Nematoda) collected from Snappers and Bream (Lutjanidae, Nemipteridae, Caesionidae) in New Caledonia confirms high parasite biodiversity on coral reef fish

BACKGROUND

Coral reefs are areas of maximum biodiversity, but the parasites of coral reef fishes, and especially their species richness, are not well known. Over an 8-year period, parasites were collected from 24 species of Lutjanidae, Nemipteridae and Caesionidae off New Caledonia, South Pacific.

RESULTS

Host-parasite and parasite-host lists are provided, with a total of 207 host-parasite combinations and 58 parasite species identified at the species level, with 27 new host records. Results are presented for isopods, copepods, monogeneans, digeneans, cestodes and nematodes. When results are restricted to well-sampled reef fish species (sample size > 30), the number of host-parasite combinations is 20-25 per fish species, and the number of parasites identified at the species level is 9-13 per fish species. Lutjanids include reef-associated fish and deeper sea fish from the outer slopes of the coral reef: fish from both milieus were compared. Surprisingly, parasite biodiversity was higher in deeper sea fish than in reef fish (host-parasite combinations: 12.50 vs 10.13, number of species per fish 3.75 vs 3.00); however, we identified four biases which diminish the validity of this comparison. Finally, these results and previously published results allow us to propose a generalization of parasite biodiversity for four major families of reef-associated fishes (Lutjanidae, Nemipteridae, Serranidae and Lethrinidae): well-sampled fish have a mean of 20 host-parasite combinations per fish species, and the number of parasites identified at the species level is 10 per fish species.

CONCLUSIONS

Since all precautions have been taken to minimize taxon numbers, it is safe to affirm than the number of fish parasites is at least ten times the number of fish species in coral reefs, for species of similar size or larger than the species in the four families studied; this is a major improvement to our estimate of biodiversity in coral reefs. Our results suggest that extinction of a coral reef fish species would eventually result in the coextinction of at least ten species of parasites.

Ultrastructural characteristics of the protonephridial terminal organ and associated ducts of adult specimens of the Aspidogastrea, Digenea and Monogenea, with comments on the relationships between these groups

Transmission electron microscopical observations were made on the protonephridial terminal organ and associated ducts of three adult trematodes, the aspidogastrean Aspidogaster limacoides Diesing, 1835 and the digeneans Azygia lucii (Müller, 1776) and Phyllodistomum angulatum Linstow, 1907, and the monogenean Ancyrocephalus paradoxus Creplin, 1839. Previously unreported ultrastructural details of the terminal organ of adult trematodes include multiple contact sites (septate junctions and zonulae adherentes) between the membranes of the terminal and adjacent canal cells. Septate junctions traverse the epithelial cytoplasm of the canal wall, and the same type of septate junctions are observed within the cytoplasmic cord at the level of the tip of the flame tuft in both longitudinal and oblique sections of all three trematode species studied. In the monopisthocotylean Ancyrocephalus paradoxus, the absence of any junctions in the cytoplasmic cord and the presence of septate junction within all of the protonephridial ducts are reported. On the basis of the small number of monogenean species in which these features have been studied, in relation to the size of the group, there seems to be a high diversity in some characters of the protonephridial terminal organ. The study confirms that the Aspidogastrea and Digenea possess the same morphology of their protonephridial terminal organ and, although this differs slightly from that of most members of the Monogenea so far studied, it supports previous views on the close relationship of these groups.

Field preservation of monogenean parasites for molecular and morphological analyses

In the present work we examined the efficacy of three different chemical solutions (EtOH 70%, DMSO-NaCl solution, and Longmire buffer) in field preservation of fish gills to be subsequently screened for monogenean specimens destined to morphological and molecular analyses. Degree of difficulty in collecting monogeneans from gills, morphological state of parasites, integrity of their DNA and reliability of sequence reading were observed and qualitatively compared to those of gills and parasites stored in 5% formalin and 99% ethanol. Data were collected over a period of 2 months. Storage in Longmire buffer resulted in dissociation of gills and parasites, while both DMSO and 70% ethanol provided a fine physical and molecular preservation of gills and monogeneans, allowing rapid collection of parasites from lamellae, and easy extraction, amplification and sequencing of parasitic DNA.

Advances and Trends in the Molecular Systematics of the Parasitic Platyhelminthes

The application of molecular systematics to the parasitic Platyhelminthes (Cestoda, Digenea and Monogenea) over the last decade has advanced our understanding of their interrelationships and evolution substantially. Here we review the current state of play and the early works that led to the molecular-based hypotheses that now predominate in the field; advances in their systematics, taxonomy, classification and phylogeny, as well as trends in species circumscription, molecular targets and analytical methods are discussed for each of the three major parasitic groups. A by-product of this effort has been an ever increasing number of parasitic flatworms characterized genetically, and the useful application of these data to the diagnosis of animal and human pathogens, and to the elucidation of life histories are presented. The final section considers future directions in the field, including taxon sampling, molecular targets of choice, and the current and future utility of mitochondrial and nuclear genomics in systematic study.

Phylogeny and classification of the Digenea (Platyhelminthes: Trematoda)

Complete small subunit ribosomal RNA gene (ssrDNA) and partial (D1-D3) large subunit ribosomal RNA gene (lsrDNA) sequences were used to estimate the phylogeny of the Digenea via maximum parsimony and Bayesian inference. Here we contribute 80 new ssrDNA and 124 new lsrDNA sequences. Fully complementary data sets of the two genes were assembled from newly generated and previously published sequences and comprised 163 digenean taxa representing 77 nominal families and seven aspidogastrean outgroup taxa representing three families. Analyses were conducted on the genes independently as well as combined and separate analyses including only the higher plagiorchiidan taxa were performed using a reduced-taxon alignment including additional characters that could not be otherwise unambiguously aligned. The combined data analyses yielded the most strongly supported results and differences between the two methods of analysis were primarily in their degree of resolution. The Bayesian analysis including all taxa and characters, and incorporating a model of nucleotide substitution (general-time-reversible with among-site rate heterogeneity), was considered the best estimate of the phylogeny and was used to evaluate their classification and evolution. In broad terms, the Digenea forms a dichotomy that is split between a lineage leading to the Brachylaimoidea, Diplostomoidea and Schistosomatoidea (collectively the Diplostomida nomen novum (nom. nov.)) and the remainder of the Digenea (the Plagiorchiida), in which the Bivesiculata nom. nov. and Transversotremata nom. nov. form the two most basal lineages, followed by the Hemiurata. The remainder of the Plagiorchiida forms a large number of independent lineages leading to the crown clade Xiphidiata nom. nov. that comprises the Allocreadioidea, Gorgoderoidea, Microphalloidea and Plagiorchioidea, which are united by the presence of a penetrating stylet in their cercariae. Although a majority of families and to a lesser degree, superfamilies are supported as currently defined, the traditional divisions of the Echinostomida, Plagiorchiida and Strigeida were found to comprise non-natural assemblages. Therefore, the membership of established higher taxa are emended, new taxa erected and a revised, phylogenetically based classification proposed and discussed in light of ontogeny, morphology and taxonomic history.

Phylogenetic position of the monogeneans Sundanonchus, Thaparocleidus, and Cichlidogyrus inferred from 28S rDNA sequences

A molecular phylogeny was inferred from newly obtained partial 28S rRNA gene sequences of Sundanonchus micropeltis (Sundanonchidae), Thaparocleidus siamensis and Cichlidogyrus sp. (Ancyrocephalidae), and other already available sequences. Although sequences are lacking for several families, the following phylogenetic relationships could be inferred. The Diplectanidae were the sister-group to a clade including Sundanonchus and the Ancyrocephalidae; Sundanonchus was the sister-group to the Ancyrocephalidae, therefore suggesting validity of the Sundanonchidae, which include this single genus; within the Ancyrocephalidae, Thaparocleidus (Ancylodiscoidinae) was the sister-group to the four other taxa, though with relatively low support, suggesting that the Ancylodiscoidinae are the sister-group to the Ancyrocephalinae.

Phylogeny of the monopisthocotylea and Polyopisthocotylea (Platyhelminthes) inferred from 28S rDNA sequences

This study focuses on the phylogenetic relationships within the Polyopisthocotylea and Monopisthocotylea, two groups that are often grouped within the monogeneans, a group of disputed paraphyly. Phylogenetic analyses were conducted with multiple outgroups chosen according to two hypotheses, a paraphyletic Monogenea or a monophyletic Monogenea, and with three methods, namely maximum parsimony, neighbour joining and maximum likelihood. Sequences used were from the partial domain C1, full domain D1, and partial domain C2 (550 nucleotides, 209 unambiguously aligned sites) from the 28S ribosomal RNA gene for 16 species of monopisthocotyleans, 26 polyopisthocotyleans including six polystomatids, and other Platyhelminthes (61 species in total, 27 new sequences). Results were similar with outgroups corresponding to the two hypotheses. Within the Monopisthocotylea, relationships were: ¿[(Udonella, capsalids), monocotylids], (diplectanids, ancyrocephalids)¿; each of these families was found to be monophyletic and their monophyly was supported by high bootstrap values in neighbour joining and maximum parsimony. Within the Polyopisthocotylea, the polystomatids were the sister-group of all others. Among the latter, Hexabothrium, parasite of chondrichthyans, was the most basal, and the mazocraeids, mainly parasites of clupeomorph teleosts, were the sister-groups of all other studied polyopisthocotyleans, these, mainly parasites of euteleosts, being polytomous.

The phylogenetic position of Udonella (Platyhelminthes)

Phylogenetic analysis of molecular data from complete 18S rRNA and partial 28S rRNA genes, of a variety of platyhelminths, places the enigmatic Udonella caligorum firmly as a monopisthocotylean monogenean. Both maximum parsimony and a modified distance measure, operating under a maximum likelihood model, gave identical solutions for each data set. These data further support morphological evidence from ultrastructural studies indicating the neodermatan affinities of Udonella, namely shared features in sensory receptors, surface tegument, sperm structure and spermiogenesis. The molecular data reject the class Udonellidea and the placement of udonellids as sister-group to the Neodermata. As shown previously with molecular data, the monogeneans appear as a paraphyletic assemblage comprising strongly monophyletic Monopisthocotylea and Polyopisthocotylea. Their relationships with the trematodes and cestodes are not resolved with 28S rDNA or 18S rDNA alone.