Nematode small subunit phylogeny correlates with alignment parameters

Morphology and genetic characterization of Physaloptera sibirica Petrow & Gorbunov, 1931 (Spirurida: Physalopteridae), from the hog-badger Arctonyx collaris Cuvier (Carnivora: Mustelidae), with molecular phylogeny of Physalopteridae

BACKGROUND

Nematodes of the family Physalopteridae (Spirurida: Physalopteroidea) commonly parasitize the alimentary canal of all major vertebrate groups. However, many physalopterid species are not adequately described, especially regarding the detailed morphology of the cephalic end. The current genetic database for Physaloptera species is still very limited, which seriously hampers molecular-based species identification. Additionally, the systematic status of some genera and the evolutionary relationships of the subfamilies in the Physalopteridae remain under debate.

METHODS

New morphological data for Physaloptera sibirica was gathered using light and scanning electron microscopy based on newly collected specimens from the hog badger Arctonyx collaris Cuvier (Carnivora: Mustelidae) in China. Six different genetic markers, including nuclear small ribosomal DNA (18S), large ribosomal DNA (28S) and internal transcribed spacer (ITS), mitochondrial cytochrome c oxidase subunit 1 (cox1) and subunit 2 (cox2), and the 12S small subunit ribosomal RNA gene of P. sibirica were sequenced and analyzed for the first time to our knowledge. Additionally, to construct a basic molecular phylogenetic framework for the Physalopteridae, phylogenetic analyses were performed based on the cox1 and 18S + cox1 genes using maximum likelihood (ML) and Bayesian inference (BI) methods.

RESULTS

Scanning electron microscopy (SEM) observation displayed the details of the cephalic structures, deirids, excretory pore, caudal papillae, vulva, phasmids and egg of P. sibirica for the first time to our knowledge. Pairwise comparison of the sequences obtained for P. sibirica did not reveal intraspecific divergence regarding the 18S, 28S, cox1 and 12S genetic markers and a low level of divergence in the ITS (0.16%) and cox2 (2.39%) regions. Maximum likelihood and Bayesian inference analyses showed that the representatives of Physalopteridae formed two major clades (species of Physalopterinae + Thubunaeinae parasitic in terrestrial vertebrates and Proleptinae only occurring in marine or freshwater fishes). Turgida turgida was found nested among representatives of Physaloptera. Physaloptera sibirica clustered together with P. rara. Physalopteroides sp. (Thubunaeinae) formed a sister relationship to the physalopterine Abbreviata caucasica.

CONCLUSIONS

Physaloptera sibirica was redescribed, which is the fourth nematode parasite reported from the hog badger A. collaris, and A. collaris represents a new host for P. sibirica. The phylogenetic results challenged the validity of the subfamily Thubunaeinae and of the genus Turgida and supported dividing the family Physalopteridae into two subfamilies, Physalopterinae and Proleptinae. However, we do not make any immediate systematic changes in the Physalopteridae, because a more rigorous study with broader representation of the Physalopteridae is required. These present findings contribute to morphologically identifying P. sibirica more accurately and provide new insights into the systematics of the Physalopteridae.

Additional data on Spinitectus petterae (Nematoda: Rhabditida) from Clarias gariepinus (Siluriformes: Clariidae) in the Vaal River system: conserved morphology or high intraspecific genetic variability?

Two species of Spinitectus Fourment, 1884 have been recorded from southern Africa, namely Spinitectus polli Campana-Rouget, 1961 and Spinitectus petterae Boomker, 1993, both from the Limpopo River system. Spinitectus petterae was described from North African catfish, Clarias gariepinus (Burchell), whereas S. polli infects squeakers, Synodontis spp. During parasitological surveys in the Vaal River system (Orange River catchment), Spinitectus specimens were collected from C. gariepinus. These systems are adjacent but not connected. Therefore, this study aimed to identify the specimens collected using morphological and molecular techniques. The morphological study included light and scanning electron microscopy of whole specimens and excised spicules. Specimens were genetically characterised using 18S rDNA, 28S rDNA and cox1 mtDNA. Additionally, immature specimens of S. petterae were collected near the type locality. Morphological characteristics were most similar to S. petterae from C. gariepinus, whereas genetic data were dissimilar to all available data for the genus. Additional morphological characteristics noted for S. petterae in the present study were the details of the left and right spicule structure and the porous structures on the pseudolabia. Specimens from the Vaal River system differed from those originally described as S. petterae by additional spines posterior to the third ring, lacking caudal alae and variable total body and male oesophagus length. Based on 18S rDNA, haplotypes from the type locality varied only slightly from the study material, supporting the morphological identification. However, 28S rDNA and, more conspicuously, cox1 mtDNA displayed substantial variation between specimens from these localities, which needs further investigation. Haplotypes generated in the present study were highly dissimilar to those characterised for S. petterae from Tanzania and Egypt. Nevertheless, the nematodes collected from C. gariepinus in the Vaal River system are considered S. petterae. This study expands the geographical distribution and adds additional morphological and genetic information for S. petterae, contributing to the limited knowledge of African species of Spinitectus.

Molecular identification of a new species of Rhigonema (Nematoda: Rhigonematidae) and phylogenetic relationships within the infraorder Rhigonematomorpha

Background

The infraorder Rhigonematomorpha comprises a group of obligate parasitic nematodes of millipedes (Arthropoda: Diplopoda). The current species identification of Rhigonematomorpha nematodes remains mainly based on morphological features, with molecular-based identification still in its infancy. Also, current knowledge of the phylogeny of Rhigonematomorpha is far from comprehensive.

Methods

The morphology of Rhigonematomorpha nematodes belonging to the genus Rhigonema, collected from the millipede Spirobolus bungii Brandt (Diplopoda: Spirobolida) in China, was studied in detail using light and scanning electron microscopy. Five different genetic markers, including the nuclear small ribosomal subunit (18S), internal transcribed spacer (ITS) and large ribosomal subunit (28S) regions and the mitochondrial cox1 and cox2 genes of these Rhigonematomorpha nematodes collected from China and Rhigonema naylae collected from Japan were sequenced and analyzed using Bayesian inference (BI) and Assemble Species by Automatic Partitioning (ASAP) methods. Phylogenetic analyses that included the most comprehensive taxa sampling of Rhigonematomorpha to date were also performed based on the 18S + 28S genes using maximum likelihood (ML) and BI methods.

Results

The specimens of Rhigonema collected from S. bungii in China were identified as a new species, Rhigonema sinense n. sp. Striking variability in tail morphology was observed among individuals of R. sinense n. sp. ASAP analyses based on the 28S, ITS, cox1 and cox2 sequences supported the species partition of R. sinense n. sp. and R. naylae, but showed no evidence that the different morphotypes of R. sinense n. sp. represent distinct genetic lineages. BI analyses also indicated that R. sinense n. sp. represents a separated species from R. naylae based on the cox1 and cox2 genes, but showed that R. naylae nested in samples of R. sinense n. sp. based on the ITS and 28S data. Phylogenetic results showed that the representatives of Rhigonematomorpha formed two large clades. The monophyly of the families Carnoyidae and Ichthyocephalidae and the genus Rhigonema was rejected. The representatives of the family Ransomnematidae clustered together with the family Hethidae with strong support.

Conclusions

A new species of Rhigonematomorpha, R. sinense n. sp. is described based on morphological and molecular evidence. ASAP analyses using 28S, ITS, cox1 and cox2 data indicate the striking variability in tail morphology of R. sinense n. sp. as intraspecific variation, and also suggest that partial 28S, ITS, cox1 and cox2 markers are effective for molecular identification of Rhigonematomorpha nematodes. The phylogenetic results support the traditional classification of Rhigonematomorpha into the two superfamilies Rhigonematoidea and Ransomnematoidea, and indicate that the families Carnoyidae and Ichthyocephalidae and the genus Rhigonema are non-monophyletic. The present phylogeny strongly supports resurrection of the family Brumptaemiliidae, and also indicates that the family Ransomnematidae is sister to the family Hethidae.

Graphical Abstract

Gene rearrangements in the mitochondrial genome of ten ascaris species and phylogenetic implications for Ascaridoidea and Heterakoidea families

The Ascaridoidea family and Heterakoidea family are the most common and typical representative of large parasites. Although our understanding of these parasites' diversity has expanded by analyses of some mitochondrial genes, there is limited information on these species' evolutionary rates. Here we determined ten complete mitogenome sequences of five subfamilies of Ascaridoidea and one subfamily of Heterakoidea. The phylogenetic tree divided the Ascaridoidea into six monophyletic major clades, and the divergence time of Heterakoidea family and Ascaridoidea family can be placed during the early Carboniferous Period (300-360 Mya). The reconstruction of the ancestral state showed that the gene orders of all species in Ascaridoidea were conserved, and the Heterakoidea had obvious genome rearrangement. The conserved blocks between them were divided into five and the main types are tandem-duplication/random loss (TDRL). These results will help to better understand the gene rearrangements and evolutionary position of ascaris species.

Phylogenomic Analysis of the Phylum Nematoda: Conflicts and Congruences With Morphology, 18S rRNA, and Mitogenomes

Phylogenetic relationships within many lineages of the phylum Nematoda remain unresolved, despite numerous morphology-based and molecular analyses. We performed several phylogenomic analyses using 286 published genomes and transcriptomes and 19 new transcriptomes by focusing on Trichinellida, Spirurina, Rhabditina, and Tylenchina separately, and by analyzing a selection of species from the whole phylum Nematoda. The phylogeny of Trichinellida supported the division of Trichinella into encapsulated and non-encapsulated species and placed them as sister to Trichuris. The Spirurina subtree supported the clades formed by species from Ascaridomorpha and Spiruromorpha respectively, but did not support Dracunculoidea. The analysis of Tylenchina supported a clade that included all sampled species from Tylenchomorpha and placed it as sister to clades that included sampled species from Cephalobomorpha and Panagrolaimomorpha, supporting the hypothesis that postulates the single origin of the stomatostylet. The Rhabditina subtree placed a clade composed of all sampled species from Diplogastridae as sister to a lineage consisting of paraphyletic Rhabditidae, a single representative of Heterorhabditidae and a clade composed of sampled species belonging to Strongylida. It also strongly supported all suborders within Strongylida. In the phylum-wide analysis, a clade composed of all sampled species belonging to Enoplia were consistently placed as sister to Dorylaimia + Chromadoria. The topology of the Nematoda backbone was consistent with previous studies, including polyphyletic placement of sampled representatives of Monhysterida and Araeolaimida.

Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses?

Alignment is a crucial issue in molecular phylogenetics because different alignment methods can potentially yield very different topologies for individual genes. But it is unclear if the choice of alignment methods remains important in phylogenomic analyses, which incorporate data from hundreds or thousands of genes. For example, problematic biases in alignment might be multiplied across many loci, whereas alignment errors in individual genes might become irrelevant. The issue of alignment trimming (i.e., removing poorly aligned regions or missing data from individual genes) is also poorly explored. Here, we test the impact of 12 different combinations of alignment and trimming methods on phylogenomic analyses. We compare these methods using published phylogenomic data from ultraconserved elements (UCEs) from squamate reptiles (lizards and snakes), birds, and tetrapods. We compare the properties of alignments generated by different alignment and trimming methods (e.g., length, informative sites, missing data). We also test whether these data sets can recover well-established clades when analyzed with concatenated (RAxML) and species-tree methods (ASTRAL-III), using the full data ($\sim $5000 loci) and subsampled data sets (10% and 1% of loci). We show that different alignment and trimming methods can significantly impact various aspects of phylogenomic data sets (e.g., length, informative sites). However, these different methods generally had little impact on the recovery and support values for well-established clades, even across very different numbers of loci. Nevertheless, our results suggest several "best practices" for alignment and trimming. Intriguingly, the choice of phylogenetic methods impacted the phylogenetic results most strongly, with concatenated analyses recovering significantly more well-established clades (with stronger support) than the species-tree analyses. [Alignment; concatenated analysis; phylogenomics; sequence length heterogeneity; species-tree analysis; trimming].

Host specificity and phylogeny of Trichostrongylidae of domestic ruminants in the Guinea savannah of the Adamawa plateau in Cameroon

Gastro-intestinal tracts were examined from thirteen Gudali zebu cattle, ten goats and ten sheep from the Adamawa highland in Northern Cameroon. A total of 28,325 adult helminths were recovered from the abomasa, small and large intestines. Five trichostrongylid genera were identified by their morphology: Haemonchus, Trichostrongylus and Oesophagostomum were predominant in both cattle and small ruminants, whilst Cooperia was only found in cattle both in the abomasum and small intestines. The molecular species identification and the inference of their phylogenetic relationships was based on the analysis of the hypervariable region I of the small subunit 18S rDNA (SSU) and the Second Internal Transcribed Spacer (ITS-2) of 408 adult trichostrongylid worms, which were PCR-amplified, sequenced, and compared with available database entries. Consistent with earlier findings, the SSU was invariable within the Haemonchus and Trichostrongylus genera, confirming the prior classification based on the morphology of the worms, but the ITS-2 was highly inter- and intraspecifically variable and thus allowed to distinguish individual species and to study the haplotype diversity within the different species. In cattle, we report for the first time in Cameroon co-infection with two species of Haemonchus (H. placei and H. similis), together with two species of Cooperia (C. punctata and C. pectinata) and one species of Trichostrongylus (T. axei). In goats and sheep, we found one highly polymorphic clade of Haemonchus contortus and two Trichostrongylus species (T. axei and T. colubriformis). When compared with other Trichostrongylidae from different regions of the world and wildlife, the analysis of haplotypes did not indicate any host and geographical isolation, but a very high haplotype diversity among H. contortus. These findings illustrate the complexity of trichostrongylid populations in domestic ruminants and suggest grazing overlap between domestic and wildlife hosts.

Genomic Analyses Identify Novel Molecular Signatures Specific for the Caenorhabditis and other Nematode Taxa Providing Novel Means for Genetic and Biochemical Studies

The phylum Nematoda encompasses numerous free-living as well as parasitic members, including the widely used animal model Caenorhabditis elegans, with significant impact on human health, agriculture, and environment. In view of the importance of nematodes, it is of much interest to identify novel molecular characteristics that are distinctive features of this phylum, or specific taxonomic groups/clades within it, thereby providing innovative means for diagnostics as well as genetic and biochemical studies. Using genome sequences for 52 available nematodes, a robust phylogenetic tree was constructed based on concatenated sequences of 17 conserved proteins. The branching of species in this tree provides important insights into the evolutionary relationships among the studied nematode species. In parallel, detailed comparative analyses on protein sequences from nematodes (Caenorhabditis) species reported here have identified 52 novel molecular signatures (or synapomorphies) consisting of conserved signature indels (CSIs) in different proteins, which are uniquely shared by the homologs from either all genome-sequenced Caenorhabditis species or a number of higher taxonomic clades of nematodes encompassing this genus. Of these molecular signatures, 39 CSIs in proteins involved in diverse functions are uniquely present in all Caenorhabditis species providing reliable means for distinguishing this group of nematodes in molecular terms. The remainder of the CSIs are specific for a number of higher clades of nematodes and offer important insights into the evolutionary relationships among these species. The structural locations of some of the nematodes-specific CSIs were also mapped in the structural models of the corresponding proteins. All of the studied CSIs are localized within the surface-exposed loops of the proteins suggesting that they may potentially be involved in mediating novel protein-protein or protein-ligand interactions, which are specific for these groups of nematodes. The identified CSIs, due to their exclusivity for the indicated groups, provide reliable means for the identification of species within these nematodes groups in molecular terms. Further, due to the predicted roles of these CSIs in cellular functions, they provide important tools for genetic and biochemical studies in Caenorhabditis and other nematodes.

Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny

Background

Nematodes are among the most diverse and abundant metazoans on Earth, but research on them has been biased toward parasitic taxa and model organisms. Free-living nematodes, particularly from the clades Enoplia and Dorylaimia, have been underrepresented in genome-scale phylogenetic analyses to date, leading to poor resolution of deep relationships within the phylum.

Results

We supplemented publicly available data by sequencing transcriptomes of nine free-living nematodes and two important outgroups and conducted a phylum-wide phylogenomic analysis including a total of 108 nematodes. Analysis of a dataset generated using a conservative orthology inference strategy resulted in a matrix with a high proportion of missing data and moderate to weak support for branching within and placement of Enoplia. A less conservative orthology inference approach recovered more genes and resulted in higher support for the deepest splits within Nematoda, recovering Enoplia as the sister taxon to the rest of Nematoda. Relationships within major clades were similar to those found in previously published studies based on 18S rDNA.

Conclusions

Expanded transcriptome sequencing of free-living nematodes has contributed to better resolution among deep nematode lineages, though the dataset is still strongly biased toward parasites. Inclusion of more free-living nematodes in future phylogenomic analyses will allow a clearer understanding of many interesting aspects of nematode evolution, such as morphological and molecular adaptations to parasitism and whether nematodes originated in a marine or terrestrial environment.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1444-x) contains supplementary material, which is available to authorized users.

PCR detection of Heterakis gallinarum in environmental samples

Heterakis gallinarum is a widely distributed cecal nematode that parasitizes gallinaceous birds including chickens and turkeys. H. gallinarum infection poses a problem for the poultry industry as the nematode egg serves as a vector for the protozoan parasite, Histomonas meleagridis, the causative agent of histomonosis. The only means of detecting H. gallinarum in the environment is microscopic identification of the eggs in soil or feces; however, H. gallinarum eggs are often mistaken for those of Ascaridia galli. Three primer sets were designed from sequences cloned from the H. gallinarum genome to develop a diagnostic PCR. Each of these primer sets amplified a single product from H. gallinarum, but were unable to amplify DNA from H. meleagridis, Ascaridia galli, or Cestode sp. H. gallinarum DNA was amplified from Lumbricus sp. (earthworms) and Alphitobius diaperinus (darkling beetles), confirming that the earthworm acts as a paratenic host for H. gallinarum and suggesting that the darkling beetle may be a carrier for this nematode.

Multiple Sequence Alignment Averaging Improves Phylogeny Reconstruction

The classic methodology of inferring a phylogenetic tree from sequence data is composed of two steps. First, a multiple sequence alignment (MSA) is computed. Then, a tree is reconstructed assuming the MSA is correct. Yet, inferred MSAs were shown to be inaccurate and alignment errors reduce tree inference accuracy. It was previously proposed that filtering unreliable alignment regions can increase the accuracy of tree inference. However, it was also demonstrated that the benefit of this filtering is often obscured by the resulting loss of phylogenetic signal. In this work we explore an approach, in which instead of relying on a single MSA, we generate a large set of alternative MSAs and concatenate them into a single SuperMSA. By doing so, we account for phylogenetic signals contained in columns that are not present in the single MSA computed by alignment algorithms. Using simulations, we demonstrate that this approach results, on average, in more accurate trees compared to 1) using an unfiltered MSA and 2) using a single MSA with weights assigned to columns according to their reliability. Next, we explore in which regions of the MSA space our approach is expected to be beneficial. Finally, we provide a simple criterion for deciding whether or not the extra effort of computing a SuperMSA and inferring a tree from it is beneficial. Based on these assessments, we expect our methodology to be useful for many cases in which diverged sequences are analyzed. The option to generate such a SuperMSA is available at http://guidance.tau.ac.il.

Morphologic Observations and Novel 18S rRNA Sequences of Abbreviata hastaspicula and Abbreviata antarctica from Varanus spp. Lizards in Australia

The nematodes Abbreviata antarctica von Linstow, 1899, and Abbreviata hastaspicula Jones, 1979 , are predominant spirurid nematodes in species of Varanus lizards in Australia. However, genetic knowledge of these two species of nematode is lacking. In this study, nematodes removed from Varanus gouldii were examined using integrated morphologic and molecular methods. We extracted DNA from A. hastaspicula and A. antarctica for PCR and sequencing. Specific 18S small subunit ribosomal RNA (rRNA) primers were designed on the basis of existing 18S rRNA sequences of Physalopterinae strains. Species of Abbreviata, which are closely similar morphologically, may be misidentified, especially the larvae of different species of Abbreviata that cannot be differentiated. The findings of this study will improve the accuracy in identification of A. hastaspicula and A. antarctica, both morphologically and molecularly.

The complete mitochondrial genome of parasitic nematode Camallanus cotti: extreme discontinuity in the rate of mitogenomic architecture evolution within the Chromadorea class

BACKGROUND

Complete mitochondrial genomes are much better suited for the taxonomic identification and phylogenetic studies of nematodes than morphology or traditionally-used molecular markers, but they remain unavailable for the entire Camallanidae family (Chromadorea). As the only published mitogenome in the Camallanina suborder (Dracunculoidea superfamily) exhibited a unique gene order, the other objective of this research was to study the evolution of mitochondrial architecture in the Spirurida order. Thus, we sequenced the complete mitogenome of the Camallanus cotti fish parasite and conducted structural and phylogenomic comparative analyses with all available Spirurida mitogenomes.

RESULTS

The mitogenome is exceptionally large (17,901 bp) among the Chromadorea and, with 46 (pseudo-) genes, exhibits a unique architecture among nematodes. Six protein-coding genes (PCGs) and six tRNAs are duplicated. An additional (seventh) tRNA (Trp) was probably duplicated by the remolding of tRNA-Ser2 (missing). Two pairs of these duplicated PCGs might be functional; three were incomplete and one contained stop codons. Apart from Ala and Asp, all other duplicated tRNAs are conserved and probably functional. Only 19 unique tRNAs were found. Phylogenomic analysis included Gnathostomatidae (Spirurina) in the Camallanina suborder.

CONCLUSIONS

Within the Nematoda, comparable PCG duplications were observed only in the enoplean Mermithidae family, but those result from mitochondrial recombination, whereas characteristics of the studied mitogenome suggest that likely rearrangement mechanisms are either a series of duplications, transpositions and random loss events, or duplication, fragmentation and subsequent reassembly of the mitogenome. We put forward a hypothesis that the evolution of mitogenomic architecture is extremely discontinuous, and that once a long period of stasis in gene order and content has been punctuated by a rearrangement event, such a destabilised mitogenome is much more likely to undergo subsequent rearrangement events, resulting in an exponentially accelerated evolutionary rate of mitogenomic rearrangements. Implications of this model are particularly important for the application of gene order similarity as an additive source of phylogenetic information. Chromadorean nematodes, and particularly Camallanina clade (with C. cotti as an example of extremely accelerated rate of rearrangements), might be a good model to further study this discontinuity in the dynamics of mitogenomic evolution.

Matrotrophy and placentation in invertebrates: a new paradigm

Matrotrophy, the continuous extra-vitelline supply of nutrients from the parent to the progeny during gestation, is one of the masterpieces of nature, contributing to offspring fitness and often correlated with evolutionary diversification. The most elaborate form of matrotrophy-placentotrophy-is well known for its broad occurrence among vertebrates, but the comparative distribution and structural diversity of matrotrophic expression among invertebrates is wanting. In the first comprehensive analysis of matrotrophy across the animal kingdom, we report that regardless of the degree of expression, it is established or inferred in at least 21 of 34 animal phyla, significantly exceeding previous accounts and changing the old paradigm that these phenomena are infrequent among invertebrates. In 10 phyla, matrotrophy is represented by only one or a few species, whereas in 11 it is either not uncommon or widespread and even pervasive. Among invertebrate phyla, Platyhelminthes, Arthropoda and Bryozoa dominate, with 162, 83 and 53 partly or wholly matrotrophic families, respectively. In comparison, Chordata has more than 220 families that include or consist entirely of matrotrophic species. We analysed the distribution of reproductive patterns among and within invertebrate phyla using recently published molecular phylogenies: matrotrophy has seemingly evolved at least 140 times in all major superclades: Parazoa and Eumetazoa, Radiata and Bilateria, Protostomia and Deuterostomia, Lophotrochozoa and Ecdysozoa. In Cycliophora and some Digenea, it may have evolved twice in the same life cycle. The provisioning of developing young is associated with almost all known types of incubation chambers, with matrotrophic viviparity more widespread (20 phyla) than brooding (10 phyla). In nine phyla, both matrotrophic incubation types are present. Matrotrophy is expressed in five nutritive modes, of which histotrophy and placentotrophy are most prevalent. Oophagy, embryophagy and histophagy are rarer, plausibly evolving through heterochronous development of the embryonic mouthparts and digestive system. During gestation, matrotrophic modes can shift, intergrade, and be performed simultaneously. Invertebrate matrotrophic adaptations are less complex structurally than in chordates, but they are more diverse, being formed either by a parent, embryo, or both. In a broad and still preliminary sense, there are indications of trends or grades of evolutionarily increasing complexity of nutritive structures: formation of (i) local zones of enhanced nutritional transport (placental analogues), including specialized parent-offspring cell complexes and various appendages increasing the entire secreting and absorbing surfaces as well as the contact surface between embryo and parent, (ii) compartmentalization of the common incubatory space into more compact and 'isolated' chambers with presumably more effective nutritional relationships, and (iii) internal secretory ('milk') glands. Some placental analogues in onychophorans and arthropods mimic the simplest placental variants in vertebrates, comprising striking examples of convergent evolution acting at all levels-positional, structural and physiological.

Mitochondrial genomes of Heterakis gallinae and Heterakis beramporia support that they belong to the infraorder Ascaridomorpha

Heterakis gallinae and Heterakis beramporia are the most prevalent nematode infecting native chicken breed, causing major economic losses. In the present study, the complete mitochondrial genomes (mt) of H. gallinae and H. beramporia were amplified by long-PCR and then sequenced. The complete mt genomes of H. gallinae and H. beramporia were 13,973bp and 14,012bp in size, respectively. Both mt genomes contain 12 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. All genes are transcribed in the same direction and the gene arrangement is identical to Ascaridia spp. Phylogenetic analysis based on the 12 protein-coding genes revealed that the family Heterakidae (represented by H. gallinae and H. beramporia) was more closely related to the infraorder Ascaridomorpha than it was to the infraorder Oxyuridomorpha. The present study determined the complete mt genome sequences for two Heterakis species, providing useful markers for studying the systematics, population genetics, and molecular epidemiology of these Heterakis parasites.

Nuclear and mitochondrial genes for inferring Trichuris phylogeny

Nucleotide sequences of the triose phosphate isomerase (TPI) gene (624 bp) and mitochondrial cytochrome b (cob) gene (520 bp) were obtained by PCR and evaluated for utility in inferring the phylogenetic relationships among Trichuris species. Published sequences of one other nuclear gene (18S or SSU rRNA, 1816-1846 bp) and one additional mitochondrial (mtDNA) gene (cytochrome oxidase 1, cox1, 342 bp) were also analyzed. Maximum likelihood and Bayesian inference methods were used to infer phylogenies for each gene separately but also for the combined mitochondrial data (two genes), the combined nuclear data (two genes), and the total evidence (four gene) dataset. Few Trichuris clades were uniformly resolved across separate analyses of individual genes. For the mtDNA, the cob gene trees had greater phylogenetic resolution and tended to have higher support values than the cox1 analyses. For nuclear genes, the SSU gene trees had slightly greater resolution and support values than the TPI analyses, but TPI was the only gene with reliable support for the deepest nodes in the tree. Combined analyses of genes yielded strongly supported clades in most cases, with the exception of the relationship among Trichuris clades 1, 2, and 3, which showed conflicting results between nuclear and mitochondrial genes. Both the TPI and cob genes proved valuable for inferring Trichuris relationships, with greatest resolution and support values achieved through combined analysis of multiple genes. Based on the phylogeny of the combined analysis of nuclear and mitochondrial genes, parsimony mapping of definitive host utilization depicts artiodactyls as the ancestral hosts for these Trichuris, with host-shifts into primates, rodents, and Carnivora.

A new Cosmocercoides species (Nematoda: Cosmocercidae), C. tonkinensis n. sp., in the scale-bellied tree lizard (Acanthosaura lepidogaster) from Vietnam

A new cosmocercid nematode species, Cosmocercoides tonkinensis n. sp., is described from the scale-bellied tree lizard (Acanthosaura lepidogaster) in the northern and central parts of Vietnam. The new species is characterized by medium-sized male worms (4.2-5.1 mm in length and 0.34-0.37 mm in width) relative to known members of the genus, with lateral alae, two sharply pointed spicules of equal length (0.22-0.26 mm in length), a gubernaculum (0.113-0.122 mm in length), 16 or 17 pairs of caudal rosettes, and the presence of somatic papillae. Female worms are slightly larger than male worms (5.3-5.5 mm in length and 0.32-0.42 mm in width), with the vulva situated at 3/5 from the anterior end, and elliptical embryonated eggs, 0.064- 0.084 mm long by 0.040-0.048 mm wide. From 19 recorded species of the genus, the morphology of C. tonkinensis n. sp. is closest to C. multipapillata, C. bufonis, and C. pulcher reported from toads and frogs in East Asia. The present new species is differentiated from them by the number of caudal rosettes, tail length relative to body length, presence of somatic papillae and lateral alae, and embryonated eggs. Furthermore, after C. variabilis in North America and C. sauria in Brazil, this new species is only the third species to be recorded from a reptilian host. The 18S ribosomal RNA gene (rDNA) of the new species is almost identical to that of C. dukae infecting land snails and slugs in North America. Between the present new species and C. pulcher from a toad (Bufo japonicus) in Japan, remarkably fewer nucleotide changes were noticed in the 18S to 28S rDNA including the internal transcribed spacer regions. The molecular phylogenetic position of the genus Cosmocercoides is briefly discussed.

Tradeoff between robustness and elaboration in carotenoid networks produces cycles of avian color diversification

Background

Resolution of the link between micro- and macroevolution calls for comparing both processes on the same deterministic landscape, such as genomic, metabolic or fitness networks. We apply this perspective to the evolution of carotenoid pigmentation that produces spectacular diversity in avian colors and show that basic structural properties of the underlying carotenoid metabolic network are reflected in global patterns of elaboration and diversification in color displays. Birds color themselves by consuming and metabolizing several dietary carotenoids from the environment. Such fundamental dependency on the most upstream external compounds should intrinsically constrain sustained evolutionary elongation of multi-step metabolic pathways needed for color elaboration unless the metabolic network gains robustness – the ability to synthesize the same carotenoid from an additional dietary starting point.

Results

We found that gains and losses of metabolic robustness were associated with evolutionary cycles of elaboration and stasis in expressed carotenoids in birds. Lack of metabolic robustness constrained lineage’s metabolic explorations to the immediate biochemical vicinity of their ecologically distinct dietary carotenoids, whereas gains of robustness repeatedly resulted in sustained elongation of metabolic pathways on evolutionary time scales and corresponding color elaboration.

Conclusions

The structural link between length and robustness in metabolic pathways may explain periodic convergence of phylogenetically distant and ecologically distinct species in expressed carotenoid pigmentation; account for stasis in carotenoid colors in some ecological lineages; and show how the connectivity of the underlying metabolic network provides a mechanistic link between microevolutionary elaboration and macroevolutionary diversification.

Reviewers

This article was reviewed by Junhyong Kim, Eugene Koonin, and Fyodor Kondrashov. For complete reports, see the Reviewers’ reports section.

Electronic supplementary material

The online version of this article (doi:10.1186/s13062-015-0073-6) contains supplementary material, which is available to authorized users.

Evolution of Feeding Structures in the Marine Nematode Order Enoplida

Marine nematodes of the order Enoplida may represent the earliest lineage of nematodes and have a variety of fixed and movable feeding structures in their stomas. This study used an 18S ribosomal RNA phylogeny of the orders Enoplida and Triplonchida (subclass Enoplia) to explore the evolution of these feeding structures in light of previous hypotheses based solely on morphology. The Enoplida and Triplonchida were found to be paraphyletic, as several taxa currently classified as Triplonchida, such as Rhabdodemania, were found to be part of the Enoplida clade. The position of Rhabdodemania within Enoplida was unclear, but a close relation to Enoplidae and Thoracostomopsidae was not supported, making it unlikely that its movable odontia are homologous with the mandibles of these families. A member of Anticomidae was well-supported as the base of the clade containing Phanodermatidae, Enoplidae, and Thoracostomopsidae, suggesting that taxa with buccal rods and mandibles evolved from nematodes with unarmed stomas. The Phanodermatidae were shown to be more closely related to the Enoplidae and Thoracostomopsidae than were the Leptosomatidae, suggesting that the buccal rods of the phanoderms (rather than the mandibular ridge/odontia complex of the Leptosomatidae), may be the origin of the mandibles.

Biochemical, kinetic, and in silico characterization of DING protein purified from probiotic lactic acid bacteria Pediococcus acidilactici NCDC 252

DING proteins are intriguing proteins characterized by conserved N-terminal sequence. In spite of unusually high sequence conservation even between distantly related species, DING proteins exhibit outstanding functional diversity. An extracellular caseinolytic alkaline enzyme was purified to homogeneity from a probiotic lactic acid bacteria Pediococcus acidilactici NCDC 252 using a simple procedure involving ammonium sulphate precipitation and gel filtration chromatography. This was purified 45.72-fold with a yield and specific activity of 43.5 % and 250 U/mg, respectively. The calculated molecular weight was 38.7 and 38.9 kDa by MALDI and SDS-PAGE, respectively, and pI was 7.77. The enzyme exhibited optimal activity at pH 8.0 and 40 °C. It was considerably stable up to pH 12. For casein, the enzyme had K m of 20 μM with V max of 26 U/ml. The enzyme was resistant to organic solvents but sensitive to DTNB and EDTA that confirmed it as thiol protein with involvement of metal ions in catalysis. Its tryptic peptide fragments showed 95 % similarity with eukaryotic DING, i.e., human phosphate binding protein (HPBP). Homology-based structure evaluation using HBPB as template revealed both to be structurally conserved and also possessing conserved phosphate binding motifs.

Phylogenetics and systematics of Angiostrongylus lungworms and related taxa (Nematoda: Metastrongyloidea) inferred from the nuclear small subunit (SSU) ribosomal DNA sequences

The Angiostrongylus lungworms are of public health and veterinary concern in many countries. At the family level, the Angiostrongylus lungworms have been included in the family Angiostrongylidae or the family Metastrongylidae. The present study was undertaken to determine the usefulness and suitability of the nuclear 18S (small subunit, SSU) rDNA sequences for differentiating various taxa of the genus Angiostrongylus, as well as to determine the systematics and phylogenetic relationship of Angiostrongylus species and other metastrongyloid taxa. This study revealed six 18S (SSU) haplotypes in A. cantonensis, indicating considerable genetic diversity. The uncorrected pairwise ‘p’ distances among A. cantonensis ranged from 0 to 0.86%. The 18S (SSU) rDNA sequences unequivocally distinguished the five Angiostrongylus species, confirmed the close relationship of A. cantonensis and A. malaysiensis and that of A. costaricensis and A. dujardini, and were consistent with the family status of Angiostrongylidae and Metastrongylidae. In all cases, the congeneric metastrongyloid species clustered together. There was no supporting evidence to include the genus Skrjabingylus as a member of Metastrongylidae. The genera Aelurostrongylus and Didelphostrongylus were not recovered with Angiostrongylus, indicating polyphyly of the Angiostrongylidae. Of the currently recognized families of Metastrongyloidea, only Crenosomatidae appeared to be monophyletic. In view of the unsettled questions regarding the phylogenetic relationships of various taxa of the metastrongyloid worms, further analyses using more markers and more taxa are warranted.

Phylogenetic study of Class Armophorea (Alveolata, Ciliophora) based on 18S-rDNA data

The 18S rDNA phylogeny of Class Armophorea, a group of anaerobic ciliates, is proposed based on an analysis of 44 sequences (out of 195) retrieved from the NCBI/GenBank database. Emphasis was placed on the use of two nucleotide alignment criteria that involved variation in the gap-opening and gap-extension parameters and the use of rRNA secondary structure to orientate multiple-alignment. A sensitivity analysis of 76 data sets was run to assess the effect of variations in indel parameters on tree topologies. Bayesian inference, maximum likelihood and maximum parsimony phylogenetic analyses were used to explore how different analytic frameworks influenced the resulting hypotheses. A sensitivity analysis revealed that the relationships among higher taxa of the Intramacronucleata were dependent upon how indels were determined during multiple-alignment of nucleotides. The phylogenetic analyses rejected the monophyly of the Armophorea most of the time and consistently indicated that the Metopidae and Nyctotheridae were related to the Litostomatea. There was no consensus on the placement of the Caenomorphidae, which could be a sister group of the Metopidae + Nyctorheridae, or could have diverged at the base of the Spirotrichea branch or the Intramacronucleata tree.

Gene discovery, evolutionary affinity and molecular detection of Oxyspirura petrowi, an eye worm parasite of game birds

Background

Oxyspirura petrowi appears to be emerging as a nematode parasite that could negatively impact Northern Bobwhite quail individuals and populations within Texas and other regions of the United States. Despite this eye worm's potential importance in the conservation of wild quail, little is known about the general biology and genome composition of O. petrowi. To fill the knowledge gap, we performed a small scale random genome sequence survey, sequenced its 18S rRNA and the intergenic region between the 18S and 28S rRNA genes, studied its phylogenetic affinity, and developed a PCR protocol for the detection of this eye worm.

Results

We have generated ~240 kb of genome sequence data derived from 348 clones by a random genome survey of an O. petrowi genomic library. The eye worm genome is AT-rich (i.e., 62.2% AT-content), and contains a high number of microsatellite sequences. The discovered genes encode a wide-range of proteins including hypothetical proteins, enzymes, nematode-specific proteins. Phylogenetic analysis based on 18S rRNA sequences indicate that the Spiruroidea is paraphyletic, in which Oxyspirura and its closely related species are sisters to the filarial nematodes. We have also developed a PCR protocol based on the ITS2 sequence that allows sensitive and specific detection of eye worm DNA in feces. Using this newly developed protocol, we have determined that ~28% to 33% of the fecal samples collected from Northern Bobwhites and Scaled Quail in Texas in the spring of 2013 are O. petrowi positive.

Conclusions

The O. petrowi genome is rich in microsatellite sequences that may be used in future genotyping and molecular fingerprinting analysis. This eye worm is evolutionarily close to the filarial nematodes, implying that therapeutic strategies for filariasis such as Loa loa would be referential in developing treatments for the Thelazoidea parasites. Our qPCR-based survey has confirmed that O. petrowi infection is of potential concern to quail managers in Texas.

Assessing phylogenetic relationships among galliformes: a multigene phylogeny with expanded taxon sampling in Phasianidae

Galliform birds (relatives of the chicken and turkey) have attracted substantial attention due to their importance to society and value as model systems. This makes understanding the evolutionary history of Galliformes, especially the species-rich family Phasianidae, particularly interesting and important for comparative studies in this group. Previous studies have differed in their conclusions regarding galliform phylogeny. Some of these studies have suggested that specific clades within this order underwent rapid radiations, potentially leading to the observed difficulty in resolving their phylogenetic relationships. Here we presented analyses of six nuclear intron sequences and two mitochondrial regions, an amount of sequence data larger than many previous studies, and expanded taxon sampling by collecting data from 88 galliform species and four anseriform outgroups. Our results corroborated recent studies describing relationships among the major families, and provided further evidence that the traditional division of the largest family, the Phasianidae into two major groups ("pheasants" and "partridges") is not valid. Within the Phasianidae, relationships among many genera have varied among studies and there has been little consensus for the placement of many taxa. Using this large dataset, with substantial sampling within the Phasianidae, we obtained strong bootstrap support to confirm some previously hypothesized relationships and we were able to exclude others. In addition, we added the first nuclear sequence data for the partridge and quail genera Ammoperdix, Caloperdix, Excalfactoria, and Margaroperdix, placing these taxa in the galliform tree of life with confidence. Despite the novel insights obtained by combining increased sampling of taxa and loci, our results suggest that additional data collection will be necessary to solve the remaining uncertainties.

Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals

Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions.

Characterization of the ribosomal RNA gene of Kudoa neothunni (Myxosporea: Multivalvulida) in tunas (Thunnus spp.) and Kudoa scomberi n. sp. in a chub mackerel (Scomber japonicus)

Kudoa neothunni is the first described Kudoa species having six shell valves and polar capsules, previously assigned to the genus Hexacapsula Arai and Matsumoto, 1953. Since its genetic analyses remain to be conducted, the present study characterizes the ribosomal RNA gene (rDNA) using two isolates from a yellowfin tuna (Thunnus albacares) with post-harvest myoliquefaction and a northern bluefin tuna (Thunnus thynnus) without tissue degradation. Spores of the two isolates localized in the myofiber of trunk muscles, forming pseudocysts, and showed typical morphology of K. neothunni with six equal-sized shell valves radially arranged in apical view: spores (n = 15) measuring 9.5-11.4 μm in width, 7.3-8.6 μm in suture width, 8.9-10.9 μm in thickness, and 7.3-7.7 μm in length; and polar capsules measuring 3.6-4.1 μm by 1.8-2.3 μm. In lateral view, the spores were pyramidal in shape without apical protrusions. Their 18S and 5.8S rDNA sequences were essentially identical, but variations in the ITS1 (62.4 % similarity across 757-bp length), ITS2 (66.9 % similarity across 599-bp length), and 28S (99.0 % similarity across 2,245-bp length) rDNA regions existed between the two isolates. On phylogenetic trees based on the 18S or 28S rDNA sequence, K. neothunni formed a clade with Kudoa spp. with more than four shell valves and polar capsules, particularly K. grammatorcyni and K. scomberomori. Semiquadrate spores of a kudoid species with four shell valves and polar capsules were detected from minute cysts (0.30-0.75 mm by 0.20-0.40 mm) embedded in the trunk muscle of a chub mackerel (Scomber japonicus) fished in the Sea of Japan. Morphologically, it resembled K. caudata described from a chub mackerel fished in the southeastern Pacific Ocean off Peru; however, it lacked filamentous projections on the shell valves of spores. Additionally, it morphologically resembled K. thunni described from a yellowfin tuna also fished in the Pacific Ocean; spores (n = 30) measuring 8.2-10.5 μm in width, 7.0-8.8 μm in thickness, and 6.1-6.8 μm in length; and polar capsule measuring 2.5-3.4 μm by 1.3-2.0 μm. The similarities of the 18S and 28S rDNA sequences between these two species were 98.5 % and 96.3 %, respectively. Simultaneously, the dimensions of cysts in the trunk muscle formed by K. thunni are clearly larger than those of the present species from a chub mackerel: 1.3-2.0 mm by 1.1-1.4 mm (n = 14) vs. 0.30-0.75 mm by 0.20-0.40 mm (n = 7), respectively. Thus, Kudoa scomberi n. sp. is proposed for this multivalvulid species found in the chub mackerel.

Comparative analysis of complete mitochondrial genome sequences confirms independent origins of plant-parasitic nematodes

Background

The nematode infraorder Tylenchomorpha (Class Chromadorea) includes plant parasites that are of agricultural and economic importance, as well as insect-associates and fungal feeding species. Among tylenchomorph plant parasites, members of the superfamily Tylenchoidea, such as root-knot nematodes, have great impact on agriculture. Of the five superfamilies within Tylenchomorpha, one (Aphelenchoidea) includes mainly fungal-feeding species, but also some damaging plant pathogens, including certain Bursaphelenchus spp. The evolutionary relationships of tylenchoid and aphelenchoid nematodes have been disputed based on classical morphological features and molecular data. For example, similarities in the structure of the stomatostylet suggested a common evolutionary origin. In contrast, phylogenetic hypotheses based on nuclear SSU ribosomal DNA sequences have revealed paraphyly of Aphelenchoidea, with, for example, fungal-feeding Aphelenchus spp. within Tylenchomorpha, but Bursaphelenchus and Aphelenchoides spp. more closely related to infraorder Panagrolaimomorpha. We investigated phylogenetic relationships of plant-parasitic tylenchoid and aphelenchoid species in the context of other chromadorean nematodes based on comparative analysis of complete mitochondrial genome data, including two newly sequenced genomes from Bursaphelenchus xylophilus (Aphelenchoidea) and Pratylenchus vulnus (Tylenchoidea).

Results

The complete mitochondrial genomes of B. xylophilus and P. vulnus are 14,778 bp and 21,656 bp, respectively, and identical to all other chromadorean nematode mtDNAs in that they contain 36 genes (lacking atp8) encoded in the same direction. Their mitochondrial protein-coding genes are biased toward use of amino acids encoded by T-rich codons, resulting in high A+T richness. Phylogenetic analyses of both nucleotide and amino acid sequence datasets using maximum likelihood and Bayesian methods did not support B. xylophilus as most closely related to Tylenchomorpha (Tylenchoidea). Instead, B. xylophilus, was nested within a strongly supported clade consisting of species from infraorders Rhabditomorpha, Panagrolaimomorpha, Diplogasteromorpha, and Ascaridomorpha. The clade containing sampled Tylenchoidea (P. vulnus, H. glycines, and R. similis) was sister to all analyzed chromadoreans. Comparison of gene arrangement data was also consistent with the phylogenetic relationships as inferred from sequence data. Alternative tree topologies depicting a monophyletic grouping of B. xylophilus (Aphelenchoidea) plus Tylenchoidea, Tylenchoidea plus Diplogasteromorpha (Pristionchus pacificus), or B. xylophilus plus Diplogasteromorpha were significantly worse interpretations of the mtDNA data.

Conclusions

Phylogenetic trees inferred from nucleotide and amino acid sequences of mtDNA coding genes are in agreement that B. xylophilus (the single representative of Aphelenchoidea) is not closely related to Tylenchoidea, indicating that these two groups of plant parasites do not share an exclusive most recent common ancestor, and that certain morphological similarities between these stylet-bearing nematodes must result from convergent evolution. In addition, the exceptionally large mtDNA genome size of P. vulnus, which is the largest among chromadorean nematode mtDNAs sequenced to date, results from lengthy repeated segments in non-coding regions.

A method of alignment masking for refining the phylogenetic signal of multiple sequence alignments

Inaccurate inference of positional homologies in multiple sequence alignments and systematic errors introduced by alignment heuristics obfuscate phylogenetic inference. Alignment masking, the elimination of phylogenetically uninformative or misleading sites from an alignment before phylogenetic analysis, is a common practice in phylogenetic analysis. Although masking is often done manually, automated methods are necessary to handle the much larger data sets being prepared today. In this study, we introduce the concept of subsplits and demonstrate their use in extracting phylogenetic signal from alignments. We design a clustering approach for alignment masking where each cluster contains similar columns-similarity being defined on the basis of compatible subsplits; our approach then identifies noisy clusters and eliminates them. Trees inferred from the columns in the retained clusters are found to be topologically closer to the reference trees. We test our method on numerous standard benchmarks (both synthetic and biological data sets) and compare its performance with other methods of alignment masking. We find that our method can eliminate sites more accurately than other methods, particularly on divergent data, and can improve the topologies of the inferred trees in likelihood-based analyses. Software available upon request from the author.

Molecular genetic conspecificity of Spiculopteragia houdemeri (Schwartz, 1926) and S. andreevae (Dróżdż, 1965) (Nematoda: Ostertagiinae) from wild ruminants in Japan

Male dimorphism of the subfamily Ostertagiinae (Nematoda: Trichostrongylidae) is a well-known phenomenon, and two or more morphotypes of a single species have previously been described as different species. Two Spiculopteragia spp., S. houdemeri (syn. S. yamashitai) and S. andreevae (syn. Rinadia andreevae) recorded in Asian cervids and wild bovids, are considered to represent major and minor morphs of S. houdemeri, respectively, based solely on their co-occurrence in the same host individual along with monomorphic females. In this study, males of morph houdemeri ( = S. houdemeri) and morph andreevae ( = S. andreevae) as well as females with three different vulval ornamentations were collected from sika deer (Cervus nippon) and Japanese serows (Capricornis crispus) distributed on the mainland of Japan. Morphologically characterized worms were subjected to molecular genetic analyses based on the internal transcribed spacer region of the ribosomal RNA gene and a partial region of the cytochrome c oxidase subunit I gene of mitochondrial DNA. Of 181 collected sika deer, 177 (97.8%) and 73 (40.3%) deer harboured males of morphs houdemeri and andreevae, respectively. Worm numbers of the former morph were found to range between 1 and 444 per individual, whereas only 1–25 worms per individual were detected for the latter morph. Five out of six serows harboured 47–71 or 2–9 males of morphs houdemeri and andreevae per individual, respectively. Females with one or two vulval flaps were predominant, but there was a substantial presence of flapless females in both host species. All the morphs of male and female adults had an identical genetic background, thus directly confirming the morphological polymorphism of S. houdemeri.

A support vector machine based test for incongruence between sets of trees in tree space

BACKGROUND

The increased use of multi-locus data sets for phylogenetic reconstruction has increased the need to determine whether a set of gene trees significantly deviate from the phylogenetic patterns of other genes. Such unusual gene trees may have been influenced by other evolutionary processes such as selection, gene duplication, or horizontal gene transfer.

RESULTS

Motivated by this problem we propose a nonparametric goodness-of-fit test for two empirical distributions of gene trees, and we developed the software GeneOut to estimate a p-value for the test. Our approach maps trees into a multi-dimensional vector space and then applies support vector machines (SVMs) to measure the separation between two sets of pre-defined trees. We use a permutation test to assess the significance of the SVM separation. To demonstrate the performance of GeneOut, we applied it to the comparison of gene trees simulated within different species trees across a range of species tree depths. Applied directly to sets of simulated gene trees with large sample sizes, GeneOut was able to detect very small differences between two set of gene trees generated under different species trees. Our statistical test can also include tree reconstruction into its test framework through a variety of phylogenetic optimality criteria. When applied to DNA sequence data simulated from different sets of gene trees, results in the form of receiver operating characteristic (ROC) curves indicated that GeneOut performed well in the detection of differences between sets of trees with different distributions in a multi-dimensional space. Furthermore, it controlled false positive and false negative rates very well, indicating a high degree of accuracy.

CONCLUSIONS

The non-parametric nature of our statistical test provides fast and efficient analyses, and makes it an applicable test for any scenario where evolutionary or other factors can lead to trees with different multi-dimensional distributions. The software GeneOut is freely available under the GNU public license.

Three novel myxobolid species of genera Henneguya and Myxobolus (Myxosporea: Bivalvulida) from marine fish in Japan

Myxosporean genera Henneguya and Myxobolus (Bivalvulida: Myxobolidae) are closely related in morphology and molecular phylogeny, speciose with approximately 1,000 nominal species. The majority of them are recorded from freshwater fish worldwide, and few are known from marine fish. In this study, three myxobolid spp. are described from marine fish around Japan. Two novel Henneguya spp., Henneguya ogawai sp. n. and Henneguya yokoyamai sp. n., are described from two black sea breams (Acanthopagrus schlegelii) fished in the Inland Sea (Setonaikai), Japan. Plasmodia of the former species were localized in the esophageal or intestinal wall, and those of the latter species were in the wall of the gall bladder and peritoneum. Spore development in plasmodia of these two species was synchronous. The spore body of H. ogawai sp. n. was 11.0 (8.9-12.2) μm in length, 6.9 (6.3-7.5) μm in width, 5.9 (5.2-6.6) μm in thickness, with a bifurcated caudal process of equal length, 10.0 (8.4-12.7) μm long; total spore length, 21.1 (19.2-23.4) μm. It contained two polar capsule, 4.3 (3.8-5.2) × 1.9 (1.4-2.3) μm. The spore body of H. yokoyamai sp. n. was 11.0 (10.1-13.7) μm in length, 7.1 (6.6-7.5) μm in width, and 5.6 (4.5-6.4) μm in thickness, with a bifurcated caudal process of equal length, 14.1 (10.8-17.0) μm long; total spore length, 25.0 (21.9-29.2) μm. It contained two polar capsules, 3.7 (3.1-4.2) × 2.0 (1.8-2.4) μm. A novel Myxobolus sp., Myxobolus machidai sp. n., is described from a spotted knifejaw (Oplegnathus punctatus) fished in the Sea of Japan, off Shimonoseki, Yamaguchi Prefecture, Japan. Plasmodia were embedded in the esophageal wall. Its round spore was small in size, 9.0 (8.1-9.4) μm in length, 7.8 (7.5-8.3) μm in width, and 5.5 (5.1-6.0) μm in thickness. It contained two polar capsules, 3.5 (3.2-3.8) × 2.3 (2.2-2.5) μm. Spore development in a plasmodium was asynchronous. Nucleotide sequencing of the small subunit ribosomal RNA gene (SSU rDNA) of these two novel Henneguya spp. revealed a close phylogenetic relationship with the marine clade of Henneguya spp.; however, they were distinct in morphology and SSU rDNA sequence from any known species. M. machidai sp. n. was grouped with freshwater Henneguya spp. in a phylogenetic tree based on the SSU rDNA, distant from a known marine clade of Myxobolus spp. reported mainly from the Mediterranean Sea. This is the first record of Henneguya-Myxobolus spp. from natural marine water in Japan.

Testing hypotheses about the sister group of the passeriformes using an independent 30-locus data set

Although many phylogenetic studies have focused on developing hypotheses about relationships, advances in data collection and computation have increased the feasibility of collecting large independent data sets to rigorously test controversial hypotheses or carefully assess artifacts that may be misleading. One such relationship in need of independent evaluation is the position of Passeriformes (perching birds) in avian phylogeny. This order comprises more than half of all extant birds, and it includes one of the most important avian model systems (the zebra finch). Recent large-scale studies using morphology, mitochondrial, and nuclear sequence data have generated very different hypotheses about the sister group of Passeriformes, and all conflict with an older hypothesis generated using DNA-DNA hybridization. We used novel data from 30 nuclear loci, primarily introns, for 28 taxa to evaluate five major a priori hypotheses regarding the phylogenetic position of Passeriformes. Although previous studies have suggested that nuclear introns are ideal for the resolution of ancient avian relationships, introns have also been criticized because of the potential for alignment ambiguities and the loss of signal due to saturation. To examine these issues, we generated multiple alignments using several alignment programs, varying alignment parameters, and using guide trees that reflected the different a priori hypotheses. Although different alignments and analyses yielded slightly different results, our analyses excluded all but one of the five a priori hypotheses. In many cases, the passerines were sister to the Psittaciformes (parrots), and taxa were members of a larger clade that includes Falconidae (falcons) and Cariamidae (seriemas). However, the position of Coliiformes (mousebirds) was highly unstable in our analyses of 30 loci, and this represented the primary source of incongruence among analyses. Mousebirds were united with passerines or parrots in some analyses, suggesting an additional hypothesis that needs to be considered in future studies. There was no clear evidence that base-compositional convergence, saturation, or long-branch attraction affected our conclusions. These results provide independent evidence excluding four major hypotheses about the position of passerines, allowing the extensive studies on this group to be placed in a more rigorous evolutionary framework.

Monophyly of clade III nematodes is not supported by phylogenetic analysis of complete mitochondrial genome sequences

Background

The orders Ascaridida, Oxyurida, and Spirurida represent major components of zooparasitic nematode diversity, including many species of veterinary and medical importance. Phylum-wide nematode phylogenetic hypotheses have mainly been based on nuclear rDNA sequences, but more recently complete mitochondrial (mtDNA) gene sequences have provided another source of molecular information to evaluate relationships. Although there is much agreement between nuclear rDNA and mtDNA phylogenies, relationships among certain major clades are different. In this study we report that mtDNA sequences do not support the monophyly of Ascaridida, Oxyurida and Spirurida (clade III) in contrast to results for nuclear rDNA. Results from mtDNA genomes show promise as an additional independently evolving genome for developing phylogenetic hypotheses for nematodes, although substantially increased taxon sampling is needed for enhanced comparative value with nuclear rDNA. Ultimately, topological incongruence (and congruence) between nuclear rDNA and mtDNA phylogenetic hypotheses will need to be tested relative to additional independent loci that provide appropriate levels of resolution.

Results

For this comparative phylogenetic study, we determined the complete mitochondrial genome sequences of three nematode species, Cucullanus robustus (13,972 bp) representing Ascaridida, Wellcomia siamensis (14,128 bp) representing Oxyurida, and Heliconema longissimum (13,610 bp) representing Spirurida. These new sequences were used along with 33 published nematode mitochondrial genomes to investigate phylogenetic relationships among chromadorean orders. Phylogenetic analyses of both nucleotide and amino acid sequence datasets support the hypothesis that Ascaridida is nested within Rhabditida. The position of Oxyurida within Chromadorea varies among analyses; in most analyses this order is sister to the Ascaridida plus Rhabditida clade, with representative Spirurida forming a distinct clade, however, in one case Oxyurida is sister to Spirurida. Ascaridida, Oxyurida, and Spirurida (the sampled clade III taxa) do not form a monophyletic group based on complete mitochondrial DNA sequences. Tree topology tests revealed that constraining clade III taxa to be monophyletic, given the mtDNA datasets analyzed, was a significantly worse result.

Conclusion

The phylogenetic hypotheses from comparative analysis of the complete mitochondrial genome data (analysis of nucleotide and amino acid datasets, and nucleotide data excluding 3^rd positions) indicates that nematodes representing Ascaridida, Oxyurida and Spirurida do not share an exclusive most recent common ancestor, in contrast to published results based on nuclear ribosomal DNA. Overall, mtDNA genome data provides reliable support for nematode relationships that often corroborates findings based on nuclear rDNA. It is anticipated that additional taxonomic sampling will provide a wealth of information on mitochondrial genome evolution and sequence data for developing phylogenetic hypotheses for the phylum Nematoda.

Kudoa iwatai and two novel Kudoa spp., K. trachuri n. sp. and K. thunni n. sp. (Myxosporea: Multivalvulida), from daily consumed marine fish in western Japan

Infection of marine fish by certain myxosporean species of the genus Kudoa results in unsightly cyst formation in the trunk muscle or post-mortem myoliquefaction, causing a great economic loss to aquaculture industries, capture fisheries, and fish dealers. In addition, consumers encountering unsightly Kudoa cysts in fish fillets believe them to be unknown foreign materials acquired during processing. To identify prevalent Kudoa spp. encountered in daily life by the Japanese population, fresh fish slices (sashimi) or fish fillets with whitish spots were collected during a 7-month period (May to December 2008) at local markets in the city of Yamaguchi, western Japan. Kudoa cysts were found in three Japanese seaperches (Lateolabrax japonicus), two black sea bream (Acanthopagrus schlegelii), two Japanese jack mackerel (Trachurus japonicus), and one albacore (Thunnus alalunga). Kudoa iwatai was identified in all the examined Japanese seaperch and black sea bream from Japan's Inland Sea, as assessed by morphology and genetic analysis of the 18S and 28S ribosomal RNA gene (rDNA). Kudoa trachuri n. sp. from two Japanese jack mackerel fished in the Japanese Sea off Nagasaki and Kudoa thunni n. sp. from one albacore fished in the Pacific Ocean had a spore, which was semiquadrate in shape in apical views and ovoid in lateral views, with four equal shell valves and drop-like polar capsules. Scanning electron microscopy revealed that these three Kudoa species had different types of small projections at the apex of each valve. The 18S and 28S rDNA sequences of K. trachuri n. sp. and K. thunni n. sp. were found to be closely related to those of Kudoa crumena; however, these sequences were distinct in each of the species, which additionally exhibited different morphological features.

Kudoa septempunctata n. sp. (Myxosporea: Multivalvulida) from an aquacultured olive flounder (Paralichthys olivaceus) imported from Korea

A new myxosporean species, Kudoa septempunctata n. sp. (Myxosporea: Multivalvulida), is described from the trunk muscles of an aquacultured olive flounder (Paralichthys olivaceus) imported from Korea. This species formed pseudocysts in the myofiber without inflammatory reactions, and the infection was not evident macroscopically. Spores of the new species were irregularly stellate in apical view, with the majority having seven unequal valves, each with a polar capsule of variable size (the remaining spores had six valves and polar capsules). The spores had dimensions of: width 11.8 (11.1-13.1); thickness 9.4 (8.9-10.0); length 8.5 (7.9-8.9); polar capsule length 4.6 (3.7-5.3); and polar capsule width 2.4 (2.2-2.8; mean with range in parentheses; n = 10; all measurements in micrometers). Scanning electron microscopy of the spores revealed unequal positioning of the seven valves without a definite center, rounded posterior ends of valves, and tiny projections at the apex of each valve. The small subunit ribosomal RNA gene (SSU rDNA) sequence of the new species was closely related to Kudoa spp. with five or more valves, particularly Kudoa thalassomi (97.6% identity) recorded from the trunk muscles of a moon wrasse (Thalassoma lunare) around the Australian continent. However, the latter species has six valves with a pointed edge and six polar capsules of a uniform size. The new species was also distinct from all presently known Kudoa spp. with seven valves and polar capsules, i.e. Kudoa yasunagai and Kudoa lethrini, regarding tissue tropism (trunk muscles versus brain), spore shape or external appendages, and SSU rDNA sequence.

Resolving phylogenetic incongruence to articulate homology and phenotypic evolution: a case study from Nematoda

Modern morphology-based systematics, including questions of incongruence with molecular data, emphasizes analysis over similarity criteria to assess homology. Yet detailed examination of a few key characters, using new tools and processes such as computerized, three-dimensional ultrastructural reconstruction of cell complexes, can resolve apparent incongruence by re-examining primary homologies. In nematodes of Tylenchomorpha, a parasitic feeding phenotype is thus reconciled with immediate free-living outgroups. Closer inspection of morphology reveals phenotypes congruent with molecular-based phylogeny and points to a new locus of homology in mouthparts. In nematode models, the study of individually homologous cells reveals a conserved modality of evolution among dissimilar feeding apparati adapted to divergent lifestyles. Conservatism of cellular components, consistent with that of other body systems, allows meaningful comparative morphology in difficult groups of microscopic organisms. The advent of phylogenomics is synergistic with morphology in systematics, providing an honest test of homology in the evolution of phenotype.

Comparative, three-dimensional anterior sensory reconstruction of Aphelenchus avenae (nematoda: Tylenchomorpha)

The anterior sensory anatomy (not including amphids) of the nematode Aphelenchus avenae (Tylenchomorpha) has been three-dimensionally reconstructed from serial, transmission electron microscopy thin sections. Models, showing detailed morphology and spatial relationships of cuticular sensilla and internal sensory receptors, are the first computerized reconstruction of sensory structures of a Tylenchomorpha nematode. Results are analyzed with respect to similarly detailed reconstructions of Rhabditida outgroup nematodes, Acrobeles complexus (Cephalobomorpha) and Caenorhabditis elegans (Rhabditomorpha). Homologies identified in A. avenae demonstrate the general conservation of the anterior sensory system between freeliving nematodes and the largely plant parasitic Tylenchomorpha. A higher degree of similarity is shown between A. avenae and A. complexus, with common features including: the presence of a second, internal outer labial dendrite (OL1); a second cephalic dendrite in the female (CEP2/CEM); an accessory process loop of inner labial dendrite 1; and terminus morphology and epidermal associations of internal sensory receptors BAG and URX. Unique to A. avenae is a pair of peripheral, lateral neurons of unknown homology but with axial positions and intercellular relationships nearly identical to the "posterior branches" of URX in A. complexus. Knowledge of homologies and connectivity of anterior sensory structures provides a basis for expansion of the experimental behavioral model of C. elegans to the economically important nematodes of Tylenchomorpha.

Heartworm biology, treatment, and control

This article is a review of the systematics, taxonomy, biology, prevention, control, and treatment of the canine heartworm, Dirofilaria immitus. This filarioid parasite remains one of the most important and dangerous diseases of the dog throughout the United States. The geographic range of the parasite is expanding, and in many parts of the country it has emerged as a threat to canine welfare only in the last 50 or so years. The article also discusses the pathophysiological mechanisms behind the disease induced, the means for diagnosing the disease, and the means of assessing the success of therapy. The treatment of potential complications of heartworm infection, such as post-adulticide thromboembolism, eosinophilic granulomatous pneumonitis, and caval syndrome, is also discussed.