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.

     

The mitochondrial genome sequence of Enterobius vermicularis (Nematoda: Oxyurida)--an idiosyncratic gene order and phylogenetic information for chromadorean nematodes

The complete mitochondrial genome sequence was determined for the human pinworm Enterobius vermicularis (Oxyurida: Nematoda) and used to infer its phylogenetic relationship to other major groups of chromadorean nematodes. The E. vermicularis genome is a 14,010-bp circular DNA molecule that encodes 36 genes (12 proteins, 22 tRNAs, and 2 rRNAs). This mtDNA genome lacks atp8, as reported for almost all other nematode species investigated. Phylogenetic analyses (maximum parsimony, maximum likelihood, neighbor joining, and Bayesian inference) of nucleotide sequences for the 12 protein-coding genes of 25 nematode species placed E. vermicularis, a representative of the order Oxyurida, as sister to the main Ascaridida+Rhabditida group. Tree topology comparisons using statistical tests rejected an alternative hypothesis favoring a closer relationship among Ascaridida, Spirurida, and Oxyurida, which has been supported from most studies based on nuclear ribosomal DNA sequences. Unlike the relatively conserved gene arrangement found for most chromadorean taxa, E. vermicularis mtDNA gene order is very unique, not sharing similarity to any other nematode species reported to date. This lack of gene order similarity may represent idiosyncratic gene rearrangements unique to this specific lineage of the oxyurids. To more fully understand the extent of gene rearrangement and its evolutionary significance within the nematode phylogenetic framework, additional mitochondrial genomes representing a greater evolutionary diversity of species must be characterized.     

The evolution of tissue migration in parasitic nematodes (Nematoda: Strongylida) inferred from a protein-coding mitochondrial gene

Polymerase chain reaction was used to amplify and sequence a 710-bp region of the mtDNA protein-encoding gene, cytochrome c oxidase subunit I, in nine nematodes belonging to the order Strongylida, one nematode from the order Rhabditida and two nematodes from the order Ascaridida. This study tested the hypothesis that in the Strongylida, tissue migration in orally infecting nematodes reflects a legacy of skin penetrating strategies of host infection that were retained after an oral route of infection became established (percutaneous transmission model). Phylogenetic analyses (NJ, MP, ML) consistently produced a single tree topology with two clades within the Strongylida, one containing nematodes that incorporated tissue migration as part of their life cycles, and the other containing nematodes with no tissue migration. Our analysis concluded that the ancestral Strongylida possessed skin penetrating and tissue migrating characters that were modified as members of the group progressed along one of two evolutionary pathways. In one pathway, skin penetration was lost but tissue migration was retained as the nematodes evolved an oral infection route. In the other, both skin penetration and tissue migration characters were lost as the nematodes evolved an oral infection route. These data support the hypothesis of percutaneous transmission as being ancestral in the Strongylida.     

An ecological law and its macroecological consequences as revealed by studies of relationships between host densities and parasite prevalence

Epidemiological models predict a positive relationship between host population density and abundance of macroparasites. Here I lest these by a comparative study. I used data on communities of four groups of parasites inhabiting the gastrointestinal tract of mammals, nematodes of the orders Oxyurida. Ascarida. Enoplida and Spirurida. respectively. The data came from 44 mammalian species and represent examination of 16886 individual hosts. I studied average prevalence of all nematodes within an order in a host species, a measure of community level abundance, and considered the potential confounding effects of host body weight, fecundity, age at maturity and diet. Host population density was positively correlated with parasite prevalence within the order Oxyurida, where all species have direct life cycles. Considering the effects of other variables did not change this. This supports the assumption that parasite transmission rate generally is a positive function of host population density_: It also strengthens the hypothesis that host densities generally act as important determinants of species richness among directly transmitted parasites and suggests that negative influence of such parasites on host population growth rate increase with increasing host population density among host species. Within the other three nematode orders, where a substantial number of the species have indirect life cycles, no relationships between prevalence and host population density were seen, Again. considering the effects of other variables did not affect this conclusion. This suggests that host population density is a poor predictor of species richness of indirectly transmitted parasites and that effects of such parasites on host population dynamics do not scale with host densities among species of hosts.     

Nematode transmission patterns

The transmission of nematode parasites of vertebrates is reviewed with special reference to the phenomena of monoxeny, heteroxeny, paratenesis, and precocity. Monoxeny is divided into 2 types. Primary monoxeny assumes that there was never an intermediate host in the transmission. Secondary monoxeny assumes the loss of an intermediate host during the course of evolution and its replacement by a tissue phase in the final host. Heteroxeny, or the use of intermediate hosts, is a common feature of many nematode groups. The Spirurida utilize arthropods, the Metastrongyloidea molluscs, and Ascaridida arthropods and vertebrates. Paratenesis, or the use of transport hosts, is a common feature of the transmission of nematode parasites of carnivores. It is postulated that in some instances paratenic hosts have become intermediate hosts and replaced the original intermediate host. Precocity in the development of nematodes in intermediate hosts (including what may have been paratenic hosts) is defined as growth and/or development beyond the expected. Its occurrence among the nematode parasites of vertebrates is reviewed. It is regarded as a transmission strategy which accelerates gamete production in the final host. Precocity could also provide the mechanism for the transfer of a parasite from a predator final host to a prey final host.     

The complete mitochondrial genome of Anisakis simplex (Ascaridida: Nematoda) and phylogenetic implications

We determined the nucleotide sequence of the complete mitochondrial genome of the nematode species Anisakis simplex. The genome is circular, 13,916 bp in size and conforms to the general characteristics of nematode mitochondrial DNAs. The gene arrangement of A. simplex is the same as that of Ascaris suum and almost identical to those of rhabditid species with a minor exception concerning the relative position of the AT-rich and non-coding regions and radically different from those of spirurid species. Along with comparisons of gene arrangement, phylogenetic analyses (maximum parsimony, neighbour joining and maximum likelihood methods) based on concatenated amino acid sequences of 12 protein-coding genes from 13 nematode species provided strong support for the sister-group relationship between Ascaridida and Rhabditida. The Shimodaira-Hasegawa and Templeton's tests both rejected the alternative hypothesis of a closer relationship between Ascaridida and Spirurida. These results contradicted the traditional view of nematode classification and a recent molecular phylogenetic study of 18S rDNA data that assigned Ascaridida and Spirurida as being a sister-group. Mapping of gene arrangement across the phylogenetic tree lead to the assumption that the conserved gene arrangement found in Ascaridida-Rhabditida members might have been acquired after the most recent common ancestor of ascaridid/rhabditid members branched off from the basal stock of the rhabditid lineage.     

Why do larval helminths avoid the gut of intermediate hosts?

In complex life cycles, larval helminths typically migrate from the gut to exploit the tissues of their intermediate hosts. Yet the definitive host's gut is overwhelmingly the most favoured site for adult helminths to release eggs. Vertebrate nematodes with one-host cycles commonly migrate to a site in the host away from the gut before returning to the gut for reproduction; those with complex cycles occupy sites exclusively in the intermediate host's tissues or body spaces, and may or may not show tissue migration before (typically) returning to the gut in the definitive host. We develop models to explain the patterns of exploitation of different host sites, and in particular why larval helminths avoid the intermediate host's gut, and adult helminths favour it. Our models include the survival costs of migration between sites, and maximise fitness (=expected lifetime number of eggs produced by a given helminth propagule) in seeking the optimal strategy (host gut versus host tissue exploitation) under different growth, mortality, transmission and reproductive rates in the gut and tissues (i.e. sites away from the gut). We consider the relative merits of the gut and tissues, and conclude that (i) growth rates are likely to be higher in the tissues, (ii) mortality rates possibly higher in the gut (despite the immunological inertness of the gut lumen), and (iii) that there are very high benefits to egg release in the gut. The models show that these growth and mortality relativities would account for the common life history pattern of avoidance of the intermediate host's gut because the tissues offer a higher growth rate/mortality rate ratio (discounted by the costs of migration), and make a number of testable predictions. Though nematode larvae in paratenic hosts usually migrate to the tissues, unlike larvae in intermediates, they sometimes remain in the gut, which is predicted since in paratenics mortality rate and migration costs alone determine the site to be exploited.     

Isotopic insight into host–endosymbiont relationships in Liolaemid lizards

Nitrogen isotopes have been widely used to investigate trophic levels in ecological systems. Isotopic enrichment of 2–5‰ occurs with trophic level increases in food webs. Host–parasite relationships deviate from traditional food webs in that parasites are minimally enriched relative to their hosts. Although this host–parasite enrichment pattern has been shown in multiple systems, few studies have used isotopic relationships to examine other potential symbioses. We examined the relationship between two gut-nematodes and their lizard hosts. One species, Physaloptera retusa, is a documented parasite in the stomach, whereas the relationship of the other species, Parapharyngodon riojensis (pinworms), to the host is putatively commensalistic or mutualistic. Based on the established trophic enrichments, we predicted that, relative to host tissue, parasitic nematodes would be minimally enriched (0–1‰), whereas pinworms, either as commensals or mutualists, would be significantly enriched by 2–5‰. We measured the ¹⁵N values of food, digesta, gut tissue, and nematodes of eight lizard species in the family Liolaemidae. Parasitic worms were enriched 1±0.2‰ relative to host tissue, while the average enrichment value for pinworms relative to gut tissue was 6.7±0.2‰. The results support previous findings that isotopic fractionation in a host–parasite system is lower than traditional food webs. Additionally, the larger enrichment of pinworms relative to known parasites suggests that they are not parasitic and may be several trophic levels beyond the host.     

The origins and evolutionary expansion of the Strongylida (Nematoda)

The Strongylida are thought to have arisen from free-living rhabditoid nematodes, but the relationships between the major groupings within the Strongylida, the Strongylina, the Metastrongylina, Trichostrongylina and the Ancylostomatina are far from clear in spite of the abundance of morphological data now available for analysis. Evolutionary mechanisms including co-evolution, host switching, host dispersal, use of intermediate hosts, various sites of localisation within the definitive host and modifications of life-cycle strategies appear to have been utilised in the expansion of the Strongylida, with different mechanisms predominating in different families or superfamilies. Co-evolution appears to have been a major mode of evolution in the Strongylina, in contrast to the Trichostrongylina, which have used host dispersal and host-switching to great advantage. The phylogeny of the Ancylostomatina shows little association with host evolution, but does match the feeding preferences of the hosts. The Metastrongylina have utilised intermediate hosts and life cycle modifications including a shift to extra-intestinal sites as major means of diversification, in contrast to the other sub-orders. The review, while indicating much progress in our understanding of the phylogeny of the Strongylida, also reveals that enormous gaps still exist, and emphasises the tentative nature of many of the phylogenetic hypotheses tendered to date.     

Parasites in Captive Animals: A Review of Studies in Some European Zoos

There are a number of specific characteristics in the system parasites–zoos and lots of studies in this connection have been carried out. In the present work a literature review of the parasitological investigations performed in some European zoos is presented. The summing-up and analyses of the literature data gave us grounds for drawing the following conclusions: Helminths represent the most frequently reported parasites in the animals inhabiting Europe's zoos. According to the frequency of the reports the most widely-spread among the helminths are the nematodes, followed by the cestodes and trematodes. The nematodes are most often represented by those of the Ascaridida order followed by Strongylida, Enoplida (Trichuridae, Capillariidae), Oxyurida and Rhabditida. Protozoa rank second after the nematodes according to the frequency of reports. The ones affecting the gastrointestinal tract and developing without intermediary hosts are most often established (Cryptosporidium, Giardia, Eimeria). Often parasites causing zoonoses are recorded in the zoo animals. Most often these are primates with the nematodes from the genera Trichuris, Ascaris, Strongyloides and Enterobius being the most common zoonoses agents.     

南极鱼类后生动物寄生虫研究进展: 线虫、绦虫与桡足类

极端的环境造就了南极独特的生物群体, 其中鱼类是南大洋生态系统中最具多样性的脊椎动物, 也是许多寄生虫的中间或终末宿主。南极鱼类寄生虫种类丰富, 是南大洋海洋生物多样性的重要组成部分。探究南极鱼类及其寄生虫的营养关系可为阐释南极海洋生态系统功能及其变动提供重要的生态数据。虽然关于南极鱼类寄生虫的研究已有一百多年的历史, 但这些研究主要集中在寄生虫的种类鉴定、区系调查和组织病理等方面。由于南极鱼类寄生虫研究跨度时间长、地域范围广, 相关研究较为零散。文章综述了南极鱼类寄生线虫、绦虫以及桡足类的种类组成、宿主范围和地理分布等方面的研究, 并对今后开展南极鱼类寄生虫研究工作提出了展望。     

Parasitism of Molluscs by Nematodes: Types of Associations and Evolutionary Trends

Although there are no confirmed fossil records of mollusc parasitic nematodes, diverse associations of more than 108 described nematode species with slugs and snails provide a fertile ground for speculation of how mollusc parasitism evolved in nematodes. Current phylogenic resolution suggests that molluscs have been independently acquired as hosts on a number of occasions. However, molluscs are significant as hosts for only two major groups of nematodes: as intermediate hosts for metastrongyloids and as definitive hosts for a number of rhabditids. Of the 61 species of nematodes known to use molluscs as intermediate hosts, 49 belong to Metastrongyloidea (Order Strongylida); of the 47 species of nematodes that use molluscs as definitive hosts, 33 belong to the Order Rhabditida. Recent phylogenetic hypotheses have been unable to resolve whether metastrongyloids are sister taxa to those rhabditids that use molluscs as definitive hosts. Although most rhabditid nematodes have been reported not to kill their mollusc hosts prior to their reproduction, some species are pathogenic. In fact, infective juveniles of Phasmarhabditis hermaphrodita vector a lethal bacterium into the slug host in which they reproduce. This life cycle is remarkably similar to the entomopathogenic nematodes in the families Steinernematidae and Heterorhabditidae. Also, the discoveries of Alloionema and Pellioditis in slugs are interesting, as these species have been speculated to represent the ancestral forms of the entomopathogenic nematodes. Development of the infective stage appears to be an important step toward the acquisition of molluscs as definitive hosts, and the association with specific bacteria may have arisen in conjunction with the evolution of necromeny.     

Population structure and genetic diversity analysis in Gynaikothrips uzeli (Zimerman, 1909) (Thysanoptera: Phlaeothripidae) by RAPD markers

Thrips are small insects (0.5-3.0 mm) with distinct habits and life histories characterized by haplodiploid sex determination. In general, low levels of genetic diversity have been reported in haplodiploid insects, although most reports focus on the order Hymenoptera. Therefore, we used RAPD markers to evaluate the structure and both inter- and intra-population genetic variability of Gynaikothrips uzeli (Thysanoptera: Phlaeothripidae). Six populations, three from Paraná state, southern Brazil, and three from Bahia, northeastern Brazil, were studied. Similarly to other haplodiploid insects, the genetic diversity of G. uzeli was reduced. This result is putatively related to the haplodiploid sex determination system, which yields little genetic variation, and to ecological traits of the studied species, such as the low dispersal abilities and life mode in leaf galls. All individuals were homogeneously clustered in their respective collection sites, forming two main groups in which populations from similar environments were more closely related. The analyzed populations were highly structured, and the genetic variation was higher among than within populations.     

The evolutionary expansion of the Spirurida

The possible origins of the 12 superfamilies of the Spirurida are considered, based on comparative morphology, host and geographic distributions. The available evidence suggests a complex origin of these nematodes, some families being derived from the Seuratoidea, and others from the Cosmocercoidea (Ascaridida). The spirurid radiation is an old one and seems to have occurred primarily in the Secondary or early Tertiary eras. Since then, expansion has occurred with host capture as a prominent mechanism. The Dracunculoidea Procamallanidae and Camallanidae are probably derived from the Chitwoodchabaudiidae and the Rictularioidea from the Schneidernematidae. The Seuratidae may have given rise to the Gnathostomatoidea, the Physalopteroidea, the Thelazioidea, the Habronematoidea, the Spiruroidea and the Acuarioidea. The filarioid nematodes appear to have several origins with the Diplotriaenoidea derived from the Spiruroidea, while constituents of the Aproctoidea derived from the Cystidicolinae, the Seuratoidea and the Spiruroidea. The Filarioidea are thought to have arisen from the Spiruroidea and the Thelazioidea. The evolution of tissue parasitism as a secondary phenomenon is considered in various groups.     

Human activity can influence the gut microbiota of Darwin's finches in the Galapagos Islands

The gut microbiota of animal hosts can be influenced by environmental factors, such as unnatural food items that are introduced by humans. Over the past 30 years, human presence has grown exponentially in the Galapagos Islands, which are home to endemic Darwin's finches. Consequently, humans have changed the environment and diet of Darwin's finches, which in turn, could affect their gut microbiota. In this study, we compared the gut microbiota of two species of Darwin's finches, small ground finches (Geospiza fuliginosa) and medium ground finches (Geospiza fortis), across sites with and without human presence, where finches prefer human‐processed and natural food, respectively. We predicted that: (a) finch microbiota would differ between sites with and without humans due to differences in diet, and (b) gut microbiota of each finch species would be most similar where finches have the highest niche overlap (areas with humans) compared to the lowest niche overlap (areas without humans). We found that gut bacterial community structure differed across sites and host species. Gut bacterial diversity was most distinct between the two species at the site with human presence compared to the site without human presence, which contradicted our predictions. Within host species, medium ground finches had lower bacterial diversity at the site with human presence compared to the site without human presence and bacterial diversity of small ground finches did not differ between sites. Our results show that the gut microbiota of Darwin's finches is affected differently across sites with varying human presence.     

Origin of a haplodiploid beetle lineage

The beetle family Scolytidae includes several groups having regular sib-mating and extremely female-biased sex ratios. Two such groups are known to include haplodiploid species: (i) the tribe Xyleborini and (ii) Coccotrypes and related genera within the tribe Dryocoetini. Relationships of these groups have been controversial. We analysed elongation factor 1-α (852 bp) and cytochrome oxidase 1 (1179 bp) sequences for 40 species. The most-parsimonious trees imply a single origin of haplodiploidy uniting Xyleborini (approximately 1200 species) and sib-mating Dryocoetini (approximately 160 species). The sister-group of the haplodiploid clade is the outcrossing genus Dryocoetes. The controversial genus Premnobius is outside the haplodiploid clade. Most haplodiploid scolytids exploit novel resources, ambrosia fungi or seeds, but a few have the ancestral habit of feeding on phloem. Thus, scolytids provide the clearest example of W. D. Hamilton''s scenario for the evolution of haplodiploidy (life under bark leading to inbreeding and hence to female-biased sex ratios through haplodiploidy) and now constitute a unique opportunity to study diplodiploid and haplodiploid sister-lineages in a shared ancestral habitat. There is some evidence of sex determination by maternally inherited endosymbiotic bacteria, which may explain the consistency with which female-biased sex ratios and close inbreeding have been maintained.     

The evolutionary origins of nematodes within the order Strongylida are related to predilection sites within hosts

The evolutionary relationships of the different groups of nematodes within the order Strongylida based on morphological data have been speculative and the subject of conjecture. In this paper, we present a multigene phylogenetic analysis, using sequence data of the 18S and 28S ribosomal RNA genes from representatives of all four suborders and seven superfamilies of the Strongylida, to test existing hypotheses proposed for the relationships of the suborders based on morphological data sets. The results obtained demonstrated that the Strongylida is a monophyletic assemblage, with only the Metastrongylina (but not the other suborders) forming a distinct monophyletic clade. We show that, in contrast to all previous hypotheses, one major lineage comprises taxa which occur exclusively in the pulmonary, circulatory or nervous systems of marsupial and eutherian mammals, whereas a second lineage comprises species occurring in the gastrointestinal tracts or perirenal tissues of vertebrates, or in the lungs of birds. The findings suggest that the predilection site of adult nematodes and host type reflect the evolutionary origin of the different taxonomic groups within the Strongylida.     

Protospirura kaindiensis n. sp. (Spirura: Spiruridae) and other helminths from Pseudohydromys (Muridae: Hydromyinae) from Papua New Guinea

One cestode and 3 species of nematodes are recorded from Pseudohydromys murinus and Pseudohydromys occidentalis (Muridae: Hydromyinae), from Papua New Guinea, for the first time. Heterakis fieldingi (Ascaridida: Heterakidea) has previously been known from Australia. Odilia sp. resembles Odilia praeputialis in the orientation of the synlophe and the number and size of ridges but differs in the length of spicule and lack of a praepuce. Protospirura kaindiensis n. sp. (Spirurida: Spiruridae) is readily distinguished from all other members of the genus by the number and arrangement of caudal papillae and the length of the spicules.     

The Red Queen Process does not Select for High Recombination Rates in Haplodiploid Hosts

One of the main competing theories to describe the evolution of recombination is the Red Queen hypothesis (RQH). Presently, many theoretical analyses of the RQH typically examine fitness interactions in host-parasite frameworks. Less emphasis has been placed on understanding the impact of host ploidy in these systems. In this study, we look to investigate the high observed rates of recombination observed in two common haplodiploid species (Apis mellifera and Bombus terrestris). We compared haplodiploid to diploid host populations under infection with haploid asexual parasites, using a matching allele model. Results from a simulation analysis showed that the Red Queen does not run in haplodiploid hosts and is therefore, probably not responsible for the high recombination rates observed so far in haplodiploid hosts.