Evolution of ruminant Sarcocystis (Sporozoa) parasites based on small subunit rDNA sequences

Protozoan Parasites of Sarcocystis spp. in Rodents from Commercial Orchards

Small mammals are an important group of wildlife that can transmit pathogens to humans and animals. There is a lack of comprehensive studies on the protozoan parasites of the genus Sarcocystis in agricultural areas. The aim of the current research was to evaluate the prevalence of Sarcocystis spp., and to identify the parasite species found in the skeletal muscles of rodents and insectivores from commercial orchards. A total of 679 muscle samples from small mammals, mainly rodents (n = 674), belonging to eight species were examined. Muscle samples were pooled into groups, then digested, and the presence of the Sarcocystis species was confirmed by molecular methods. The examined parasites were determined in five rodent species, Apodemus agrarius, A. flavicollis, Clethrionomys glareolus, Microtus arvalis, and M. oeconomus. The prevalence of Sarcocystis spp. was low: 2.23% in voles and 0.79% in mice. Based on a sequence comparison of cox1 and 28S rDNA, four species were identified: S. myodes, Sarcocystis cf. strixi, Sarcocystis sp. Rod1, and Sarcocystis sp. Rod2. This is the first report of S. myodes in A. agrarius, A. flavicollis, and M. arvalis. The identified species were most closely related to Sarcocystis spp., and were transmitted by predatory mammals and birds. Future studies are needed to describe the species morphologically, as well as to define the host spectrum and to evaluate their possible pathogenicity.

Molecular phylogeny of Sarcocystis fayeri (Apicomplexa: Sarcocystidae) from the domestic horse Equus caballus based on 18S rRNA gene sequences and its prevalence

Sarcocystosis is a parasitic disease caused by an intracellular protozoan parasite Sarcocystis belonging to the phylum Apicomplexa. These parasites have a requisite two-host life cycle. Recently, there are many Sarcocystis species that identified morphologically. In the present study, diaphragmatic muscle samples from the domestic horse (Equus caballus) were examined for Sarcocystis infection. The natural infection with sarcocysts was recorded to be 62·5% for only microcysts in the infected muscles. Molecular analysis using the 18S rRNA gene was conducted to swiftly and accurately identify the recovered species. Studies on the expression of the 18S rRNA gene have confirmed that the present parasite isolates belong to the Sarcocystis genus. The sequence data showed significant identities (>80%) with archived gene sequences from species within the Sarcocystidae family, and a dendrogram showing the phylogenetic relationship was constructed. The most closely related species were the previously described Sarcocystis fayeri and Sarcocystis bertrami. The current data showed that the present species was identified as S. fayeri and deposited in GenBank (accession number MF614956.1). This study highlights the importance of the genetic data in the exact taxonomy within sarcocystid species.

Detection of Sarcocystis aucheniae in blood of llama using a duplex semi-nested PCR assay and its association with cyst infestation

The protozoon Sarcocystis aucheniae is the causative agent of South American camelid (SAC) sarcocystosis. Infections are characterized by the presence of cysts in muscles which are in size and appearance similar to rice grains. As consumption of insufficiently cooked infected meat produces gastroenteritis, cyst-containing SAC meat is confiscated by sanitary authorities or depreciated with serious economic consequences for SAC breeders. In this work, a duplex semi-nested PCR was designed to simultaneously detect parasite and llama DNA in host blood samples. Species-specific regions of S. aucheniae 18S rRNA gene and Lama glama 16S mitochondrial gene were amplified, yielding bands of 583 and 257 bp, respectively, and separated by gel electrophoresis. The method proved to be highly sensitive, with a detection limit lower than one parasite per milliliter blood, and the inclusion of primers to detect llama-specific DNA resulted useful as a methodological control. Blood samples collected from llamas of Argentina and Bolivia (n = 225) were analyzed using this method, and 18.7 % resulted positive for S. aucheniae. No correlation was found between PCR results and llama age, sex or the finding of macroscopic cysts in meat after slaughter. Lack of molecular detection in the blood of some llamas harboring macrocysts suggests that parasite circulation in the bloodstream after encystment is under the detection threshold of the test or even absent, while PCR positive results in cyst-infested animals suggests that prior exposure to the parasite does not impede subsequent infections. The described method can be useful to detect active foci of infection, to assess the effectiveness of parasiticide treatments, and for the surveillance and tracing of definitive hosts.

First molecular characterization and morphological aspects of Sarcocystis fusiformis infecting water buffalo Bubalus bubalis in Egypt

Fresh muscle samples from water buffalo (Bubalus bubalis) aged 2-15, from Giza Province, Egypt; were examined for Sarcocystis infection. Macroscopic ovoid sarcocysts embedded in the muscle tissues of the examined buffaloes were detected; they measured 152-230 (210 ± 7) μm in length and 37-119 (95 ± 3) μm in width. The esophagus was the most infected organ followed by the diaphragm, and tongue, while the heart muscles were the least infected. The cyst cavity was compartmentalized by septa derived from the ground substance located under the primary cyst wall. Using transmission electron microscopy, the primary cyst wall bordered sarcocysts were determined to be 0.08-0.22 μm in thickness, raised from the parasitophorous vacuolar membrane, and surrounded by a secondary cyst wall of host origin. The primary cyst wall had irregular wall folds with numerous cauliflower-like projections of variable sizes and shapes accompanied by knob-like electron-dense elevations. 18S rRNA gene expression studies confirmed that the present parasite isolates belonged to the genus Sarcocystis. The sequence data showed significant identities (>90%) with archived gene sequences from many Eimeriidae organisms, and a dendogram showing the phylogenetic relationship was constructed. The most closely related species was Sarcocystis fusiformis KR186117, with an identity percentage of 98%. The recovered sequences were deposited in the GenBank under the accession number MG572125. The present study, to our knowledge, is the first collective ultrastructural and molecular study that confirmed the taxonomy of sarcocysts isolated from water buffaloes in Egypt as Sarcocystis fusiformis.

Sarcocystosis in South American camelids: The state of play revisited

Members of the genus Sarcocystis (Apicomplexa: Sarcocystidae) are intracellular protozoan parasites that infect a wide range of domestic and wild animals, resulting in economic losses in production animals worldwide. Sarcocystis spp. have indirect life-cycles where canids and felids serve as main definitive hosts while a range of domestic and wild animals serve as intermediate hosts, including South American camelids (SACs) such as alpacas, llamas and guanacos. These animals primarily occur in South American countries on Andean, elevated plains but in recent years, alpacas and llamas have become emerging animal industries in other parts of the world such as Australia, Europe and the USA due to their high-quality fiber, meat and hides. For instance, alpaca meat is becoming popular in many parts of the world due to its lower cholesterol content than other red meat, thereby it has the potential of a valuable product for both local and international markets. However, SAC meat can be degraded and/or even condemned due to the presence of macroscopic sarcocysts in skeletal muscles, leading to significant economic losses to farmers. The infection is generally asymptomatic, though highly pathogenic or even fatal Sarcocystis infections have also been reported in alpacas and llamas. Despite the economic importance of sarcocystosis in SACs, little is known about the life-cycle of parasites involved, disease transmission, epidemiology, pathogenesis, diagnosis, control and public health significance. This review article provides an in-depth analysis of the existing knowledge on the taxonomy, epidemiology, clinicopathology and diagnosis of Sarcocystis in SACs, highlights knowledge gaps and proposes future areas of research that could contribute to our better understanding of sarcocystosis in these animals.

Examination of Sarcocystis spp. of giant snakes from Australia and Southeast Asia confirms presence of a known pathogen - Sarcocystis nesbitti

We examined Sarcocystis spp. in giant snakes from the Indo-Australian Archipelago and Australia using a combination of morphological (size of sporocyst) and molecular analyses. We amplified by PCR nuclear 18S rDNA from single sporocysts in order to detect mixed infections and unequivocally assign the retrieved sequences to the corresponding parasite stage. Sarcocystis infection was generally high across the study area, with 78 (68%) of 115 examined pythons being infected by one or more Sarcocystis spp. Among 18 randomly chosen, sporocyst-positive samples (11 from Southeast Asia, 7 from Northern Australia) the only Sarcocystis species detected in Southeast Asian snakes was S. singaporensis (in reticulated pythons), which was absent from all Australian samples. We distinguished three different Sarcocystis spp. in the Australian sample set; two were excreted by scrub pythons and one by the spotted python. The sequence of the latter is an undescribed species phylogenetically related to S. lacertae. Of the two Sarcocystis species found in scrub pythons, one showed an 18S rRNA gene sequence similar to S. zamani, which is described from Australia for the first time. The second sequence was identical/similar to that of S. nesbitti, a known human pathogen that was held responsible for outbreaks of disease among tourists in Malaysia. The potential presence of S. nesbitti in Australia challenges the current hypothesis of a snake-primate life cycle, and would have implications for human health in the region. Further molecular and biological characterizations are required to confirm species identity and determine whether or not the Australian isolate has the same zoonotic potential as its Malaysian counterpart. Finally, the absence of S. nesbitti in samples from reticulated pythons (which were reported to be definitive hosts), coupled with our phylogenetic analyses, suggest that alternative snake hosts may be responsible for transmitting this parasite in Malaysia.

Sarcocystis entzerothi n. sp. from the European roe deer (Capreolus capreolus)

In the present study, we describe Sarcocystis entzerothi n. sp. from the European roe deer (Capreolus capreolus) based on the microscopical and DNA analysis. By light microscopy (LM), cysts of S. entzerothi were spindle-shaped with pointed tips, 950-1900 × 70-150 μm in size and had 5-6 μm long finger-like cyst wall protrusions. Cyst wall of S. entzerothi by transmission electron microscopy (TEM) was type 10a-like; villar protrusions were up to 1.2 μm wide, densely packed, lying about 0.1 μm between each other, had profuse microgranules and microfilaments, parasitophorous vacuolar membrane had many minute invaginations, and the ground substance layer measured up to 0.4 μm. This species is morphologically similar to Sarcocystis silva, previously found in the roe deer and the moose (Alces alces). By LM, cysts of S. silva were cigar-shaped with blunted tips, measured 1000-1500 × 130-184 μm, and had 7-8 μm long finger-like cyst wall protrusions. Under TEM, S. silva had no clear differences from S. entzerothi in their cyst wall ultrastructure. Having examined six roe deer hunted in Lithuania, cysts of S. entzerothi and S. silva were identified in four and two animals, respectively. These two Sarcocystis species could be morphologically differentiated according to the shape of the cysts and the length of protrusions. The species examined showed 95.6-96.1 % and 85.6-86.9 % sequence identity within 18S ribosomal DNA (rDNA) and cox1, respectively, and therefore they could be clearly distinguished by means of molecular methods. It should be noted that in the 18S rDNA phylogenetic tree, S. entzerothi from the roe deer was placed together with one sequence of Sarcocystis sp. from the Lithuanian red deer (Cervus elaphus) demonstrating the same species. Based on 18S rDNA and cox1 sequences, S. entzerothi was more closely related to Sarcocystis species transmitted via felids than canids.

Sarcocystis masoni, n. sp. (Apicomplexa: Sarcocystidae), and redescription of Sarcocystis aucheniae from llama (Lama glama), guanaco (Lama guanicoe) and alpaca (Vicugna pacos)

There is considerable confusion concerning the species of Sarcocystis in South American camelids (SAC). Several species names have been used; however, proper descriptions are lacking. In the present paper, we redescribe the macroscopic sarcocyst forming Sarcocystis aucheniae and describe and propose a new name, Sarcocystis masoni for the microscopic sarcocyst forming species. Muscles samples were obtained from llamas (Lama glama) and guanacos (Lama guanicoe) from Argentina and from alpacas (Vicugna pacos) and llamas from Peru. Individual sarcocysts were processed by optical and electron microscopy, and molecular studies. Microscopic sarcocysts of S. masoni were up to 800 µm long and 35–95 µm wide, the sarcocyst wall was 2·5–3·5 µm thick, and had conical to cylindrical villar protrusions (vp) with several microtubules. Each vp had 11 or more rows of knob-like projections. Seven 18S rRNA gene sequences obtained from sarcocysts revealed 95–96% identity with other Sarcocystis spp. sequences reported in the GenBank. Sarcocysts of S. aucheniae were macroscopic, up to 1·2 cm long and surrounded by a dense and laminar 50 µm thick secondary cyst wall. The sarcocyst wall was up to 10 µm thick, and had branched vp, appearing like cauliflower. Comparison of the 11 sequences obtained from individual macroscopic cysts evidenced a 98–99% of sequence homology with other S. aucheniae sequences. In conclusion, 2 morphologically and molecularly different Sarcocystis species, S. masoni (microscopic cysts) and S. aucheniae (macroscopic cysts), were identified affecting different SAC from Argentina and Peru.

Morphologic and molecular characteristics of Sarcocystis atraii n. sp. (Apicomplexa: Sarcocystidae) infecting the common coot (Fulica atra) from Egypt

A single morphologic type of Sarcocystis cysts found in two out of 43 examined common coots, Fulica atra, is considered to represent a new species for which the name Sarcocystis atraii n. sp. is proposed and its description is provided. Coots were hunted from the vicinity of Brolos Lake located at KafrElsheikh province, Egypt. The structural morphology of the revealed sarcocysts was described using light and transmission electron microscopy. Sarcocysts were found in the leg and thigh muscles. The cysts were microscopic and measured 165-850 μm in length × 50-85 μm in width. Histologically; the sarcocyst wall was wavy and had minute undulations. Ultrastructurally, it measured 1-3 μm in thickness and possessed many mushroom-like villar protrusions sometimes originating from other mushroom-like villar protrusions that measured approximately 0.5-2 μm in length and up to 2 μm in width, with the presence of electron dense ground substance of 300 nm to 1 μm thick. The bradyzoites were elongated, banana-shaped and measured 7.5-14 × 1.5-2.5 μm, with centrally or terminally located nuclei. The ultrastructural features of the cyst wall belonged to type 24. On the basis of sequencing and phylogenic analyses for 18S rRNA , 28S rRNA genes and ITS-1 region; S. atraii n. sp. is considered a genetically distinct species, being most closely related to avian Sarcocystis spp. whose definitive hosts are predatory mammals.

TreSpEx-Detection of Misleading Signal in Phylogenetic Reconstructions Based on Tree Information

Phylogenies of species or genes are commonplace nowadays in many areas of comparative biological studies. However, for phylogenetic reconstructions one must refer to artificial signals such as paralogy, long-branch attraction, saturation, or conflict between different datasets. These signals might eventually mislead the reconstruction even in phylogenomic studies employing hundreds of genes. Unfortunately, there has been no program allowing the detection of such effects in combination with an implementation into automatic process pipelines. TreSpEx (Tree Space Explorer) now combines different approaches (including statistical tests), which utilize tree-based information like nodal support or patristic distances (PDs) to identify misleading signals. The program enables the parallel analysis of hundreds of trees and/or predefined gene partitions, and being command-line driven, it can be integrated into automatic process pipelines. TreSpEx is implemented in Perl and supported on Linux, Mac OS X, and MS Windows. Source code, binaries, and additional material are freely available at http://www.annelida.de/research/bioinformatics/software.html.

Prevalence and molecular characterization of Sarcocystis species in water buffaloes (Bubalus bubalus) in Egypt

The present study was planned to investigate the prevalence of Sarcocystis spp. among slaughtered water buffaloes (Bubalus bubalis) at Alexandria province, Egypt. Three hundred blood samples were collected from slaughtered buffaloes (5-7 years old). Two techniques were used to evaluate the seroprevalence of Sarcocystis spp., enzyme-linked immunosorbent assay (ELISA) and indirect haemagglutination assay (IHA). It was revealed that 203 (67.6 %) and 191 (63.6 %) of the tested serum samples were seropositive to Sarcocystis spp. by ELISA and IHA, respectively. The results of sensitivity and specificity of IHA relative to ELISA were 94 and 100 %, respectively. For molecular characterization of inter- and intra-species genetic polymorphism within Egyptian isolates of Sarcocystis spp. of water buffaloes, polymerase chain reaction (PCR) and polymerase chain reaction-restriction length polymorphisms (PCR-RFLPs) were performed on four macroscopic isolates. The isolates represented two different geographical regions of Egypt, Alexandria and Assuit provinces. Alexandria isolates (large and small-sized cyst of the same host) and Assuit isolates (large and small-sized cyst of the same host) were used. The 18S rDNA of the macroscopic cysts were characterized, in tandem, by four restriction endonucleases, RsaI, MboI, SspI and DraI. RsaI and MboI enzymes did not show any restriction sites for all isolates, leaving the amplified fragments without cutting. SspI showed two fragments in Alexandria and Assuit small-sized isolates cut by the enzyme at 600-700-bp fragments, while Alexandria and Assuit large-sized cysts amplicons were not digested by this enzyme. The fourth enzyme, DraI, cut the PCR product of Alexandria large-sized cysts into two fragments (420-780 bp), while Assuit large-sized amplicon was not cut. It could be concluded that there was a far distance between the two local isolates (small and large sized), but there were no differences between the large-sized isolates.

Genetic assemblage of Sarcocystis spp. in Malaysian snakes

Background

Sarcocystis species are protozoan parasites with a wide host range including snakes. Although there were several reports of Sarcocytis species in snakes, their distribution and prevalence are still not fully explored.

Methods

In this study, fecal specimens of several snake species in Malaysia were examined for the presence of Sarcocystis by PCR of 18S rDNA sequence. Microscopy examination of the fecal specimens for sporocysts was not carried as it was difficult to determine the species of the infecting Sarcocystis.

Results

Of the 28 snake fecal specimens, 7 were positive by PCR. BLASTn and phylogenetic analyses of the amplified 18S rDNA sequences revealed the snakes were infected with either S. nesbitti, S. singaporensis, S. zuoi or undefined Sarcocystis species.

Conclusion

This study is the first to report Sarcocystis infection in a cobra, and S. nesbitti in a reticulated python.

Description of Sarcocystis turdusi sp. nov. from the common blackbird (Turdus merula)

Cysts of Sarcocystis species were found in 24 of 44 (54·5%) examined blackbirds (Turdus merula). Under the light microscope, only 1 morphological type of cyst was found in all birds investigated. Ribbon-shaped cysts were long (the largest fragment found amounted to 7 mm) and of different thickness (25–206 μm). A cyst wall reached up to 3·5 μm and had finger-like protrusions. Under the transmission electron microscope, a single cyst isolated from 1 blackbird was studied. The cyst wall was 2·5–4·4 μm thick, had club- or irregularly-shaped and sometimes branched protrusions that differed in size. The content of cysts was divided into large chambers by septa. Orange segment-shaped cystozoites were 6·2 × 1·4 (5·5–7·2 × 1·2–1·5) μm. This type of cyst wall has never been described in Sarcocystis species isolated from birds, thus far. The results of 18S rDNA, 28S rDNA and ITS–1 region sequences showed that S. turdusi was most closely related to S. columbae, S. calchasi, S. wobeseri, S. cornixi and Sarcocystis sp. ex Accipiter nisus parasitizing birds. Phylogenetic results suggest that predatory birds are the most probable definitive hosts of S. turdusi.

Ultrastructural and molecular characterization of Sarcocystis isolated from camel (Camelus dromedarius) in Iran

Sarcocystis cameli was first described in one-humped camels (Camelus dromedarius), and it is the only species which have so far reported in camels. Although more than 150 species of Sarcocystis were described in various animals, only a few data on camel Sarcocystis ultrastructure were published, and this report is the first for molecular information (DNA sequence and RLFP digestion pattern). The main objective of the present work is to characterize Sarcocystis isolated from camels by electron microscopy and PCR-RFLP methods. Muscle samples were taken from the fresh esophagus, diaphragm, skeletal muscles, and heart of one-humped camels (C. dromedarius) slaughtered in abattoirs of Tehran and Ghazvin provinces, Iran. The dissection and trypsin digestion techniques were applied for the detection of the cysts. The infected samples were fixed in glutaraldehyde and/or frozen at -20°C until use for ultrastructural and molecular studies, respectively. The ultrastructural and molecular studies were carried out contemporaneously. The 18S rRNA gene of the parasites was amplified by PCR. The PCR products were cloned into a pTZ57R/T and sequenced. In addition, the PCR products were digested separately with each of the four restriction enzymes for RFLP. Our results indicated that only microcysts were observed in muscle samples. The microcysts were white, elongated, spindled, and a few spiral-shaped, with mean size 260 × 75 μm which are identical with S. cameli. The ultrastructure of microcyst wall had many non-branched finger-like protrusions irregularly folded. There was a 600-bp specific band amplified after PCR with specific primers. The molecular data for camel Sarcocystis is reported for the first time in Iran and the world.

The red fox (Vulpes vulpes) and the arctic fox (Vulpes lagopus) are definitive hosts of Sarcocystis alces and Sarcocystis hjorti from moose (Alces alces)

The aim of this study was to determine whether foxes might act as definitive hosts of Sarcocystis alces in moose. In 2 experiments, 6 silver foxes (Vulpes vulpes) and 6 blue foxes (Vulpes lagopus) were fed muscle tissue from moose containing numerous sarcocysts of S. alces, and euthanazed 7-28 days post-infection (p.i.). Intestinal mucosal scrapings and faecal samples were screened microscopically for Sarcocystis oocysts/sporocysts, which were identified to species by means of species-specific primers and sequence analysis targeting the ssu rRNA gene. All foxes in both experiments became infected with Sarcocystis; the oocysts were fully sporulated by 14 days p.i., containing sporocysts measuring 14-15 x 10 microm. Molecular identification revealed that the oocysts/sporocysts belonged to 2 species, S. alces and Sarcocystis hjorti, although sarcocysts of S. hjorti were only identified in moose subsequent to the infection of foxes. In the first experiment, all 8 foxes also became infected with a Hammondia sp. derived from moose, shedding unsporulated, subspherical oocysts, measuring 10-12 microm in diameter, from 6-7 days p.i. onwards. The study proved that canids (the red fox and arctic fox) are definitive hosts for S. alces and S. hjorti, as had been inferred from the phylogenetic position of these species.

Sarcocystis in Norwegian roe deer (Capreolus capreolus): molecular and morphological identification of Sarcocystis oviformis n. sp. and Sarcocystis gracilis and their phylogenetic relationship with other Sarcocystis species

Fresh muscle tissue from six roe deer from Southeastern Norway was examined for sarcocysts. Cysts were excised and morphologically classified by light microscopy, and some cysts were further examined by scanning electron microscopy or DNA amplification and sequencing of the small subunit (ssu) rRNA gene. Two Sarcocystis species, Sarcocystis gracilis and Sarcocystis oviformis n. sp., were found and described by morphological and molecular methods. S. gracilis was found in all animals, whereas S. oviformis was found in only one roe deer. Polymerase chain reaction identification was necessary for definitive species identification, since cysts of S. gracilis varied in surface structure and since cysts of both S. gracilis and S. oviformis were morphologically indistinguishable from sarcocysts in other cervidae. Phylogenetic analyses based on complete ssu rRNA gene sequences revealed a close relationship between S. gracilis and other canine-transmitted Sarcocystis species, whereas S. oviformis formed a well-supported group with Sarcocystis hardangeri of reindeer and Sarcocystis ovalis of moose.

Sarcocystis in moose (Alces alces): molecular identification and phylogeny of six Sarcocystis species in moose, and a morphological description of three new species

Muscle tissues from 34 moose from Southeastern Norway and two moose from Canada were examined. Sarcocysts were excised and morphologically classified by light microscopy, and some cysts were further examined by scanning electron microscopy or DNA amplification and sequencing at the small subunit (ssu) rRNA gene. In Norwegian moose, three sarcocyst types were recognized, yet five Sarcocystis species were found by sequence analysis. New names were proposed for three species which could be characterised by both morphological and molecular methods, i.e., Sarcocystis alces, Sarcocystis ovalis, and Sarcocystis scandinavica. S. alces was the most prevalent species, whereas S. scandinavica and the two unnamed species were rare and might either use another principal intermediate host or a rare definitive host. The five species in Norwegian moose were different from Sarcocystis alceslatrans isolated from a Canadian moose. Phylogenetic analyses based on complete ssu rRNA gene sequences revealed a close relationship between the six Sarcocystis species from moose and species from reindeer and Sika deer. We conclude that molecular methods are necessary for unequivocal species identification, as different cervid hosts harbour morphologically indistinguishable sarcocysts.

Phylogenetic relationships among Eimeria spp. (Apicomplexa, Eimeriidae) infecting rabbits: evolutionary significance of biological and morphological features

Monophyly of all 11 valid Eimeria species from rabbits (Oryctolagus cuniculus Linnaeus, 1758) was revealed based on nuclear 18S rDNA sequence data. This finding implies that these species, which vary considerably in terms of their morphology and biology, diversified on a single host or several closely related species. Phylogenetic analysis divided rabbit Eimeria species into 2 sister lineages, corresponding to the presence/absence of the oocyst residuum. Other morphological or biological traits (oocyst shape and size, presence/absence of oocyst inner structures, pathogenicity, infection site, pre-patent and patent periods, sporulation time, and number of asexual generations) do not explicitly correlate with the phylogeny of rabbit coccidia.

Data congruence, paedomorphosis and salamanders

BACKGROUND

The retention of ancestral juvenile characters by adult stages of descendants is called paedomorphosis. However, this process can mislead phylogenetic analyses based on morphological data, even in combination with molecular data, because the assessment if a character is primary absent or secondary lost is difficult. Thus, the detection of incongruence between morphological and molecular data is necessary to investigate the reliability of simultaneous analyses. Different methods have been proposed to detect data congruence or incongruence. Five of them (PABA, PBS, NDI, LILD, DRI) are used herein to assess incongruence between morphological and molecular data in a case study addressing salamander phylogeny, which comprises several supposedly paedomorphic taxa. Therefore, previously published data sets were compiled herein. Furthermore, two strategies ameliorating effects of paedomorphosis on phylogenetic studies were tested herein using a statistical rigor. Additionally, efficiency of the different methods to assess incongruence was analyzed using this empirical data set. Finally, a test statistic is presented for all these methods except DRI.

RESULTS

The addition of morphological data to molecular data results in both different positions of three of the four paedomorphic taxa and strong incongruence, but treating the morphological data using different strategies ameliorating the negative impact of paedomorphosis revokes these changes and minimizes the conflict. Of these strategies the strategy to just exclude paedomorphic character traits seem to be most beneficial. Of the three molecular partitions analyzed herein the RAG1 partition seems to be the most suitable to resolve deep salamander phylogeny. The rRNA and mtDNA partition are either too conserved or too variable, respectively. Of the different methods to detect incongruence, the NDI and PABA approaches are more conservative in the indication of incongruence than LILD and PBS.

CONCLUSION

Paedomorphosis induces strong conflicts and can mislead the phylogenetic analyses even in combined analyses. However, different strategies are efficiently minimizing these problems. Though the exploration of different methods to detect incongruence is preferable NDI and PABA are more conservative than the others and NDI is computational less extensive than PABA.

Genetic characterisation of six Sarcocystis species from reindeer (Rangifer tarandus tarandus) in Norway based on the small subunit rRNA gene

Six Sarcocystis species, i.e. Sarcocystis grueneri, Sarcocystis rangi, Sarcocystis tarandivulpes, Sarcocystis hardangeri, Sarcocystis rangiferi and Sarcocystis tarandi have previously been described from reindeer based on sarcocyst morphology. In order to validate and expand the species descriptions, the complete small subunit (ssu) rRNA gene was sequenced and used to genetically characterise the six species. The aim was to reveal possible genetic variation in the ssu rRNA gene within each Sarcocystis species, between the species from reindeer, but also between the reindeer species and related Sarcocystis species characterised in other studies. Muscle tissue from the heart and diaphragm was sampled from 18 adult semi-domesticated reindeer at a field abattoir in northern Norway. Sarcocysts were excised from the tissue and classified into one of the six known Sarcocystis species based on their morphology. Two cysts of each of the six species from two different animals were randomly selected for further DNA analyses. The complete ssu rRNA gene was amplified by the polymerase chain reaction (PCR) and subsequently sequenced. The complete ssu rRNA gene sequences were used to compare the six species with each other and with other previously sequenced Sarcocystis species retrieved from GenBank. There was little sequence variation between two isolates of the same species, but the six species differed from each other by insertions, deletions and single nucleotide polymorphisms (SNPs), mainly located in variable regions of the gene. The identity between the six species from reindeer was approximately the same as when other Sarcocystis species using a different intermediate host were compared with each other. This study supported previous findings of reindeer being the intermediate host for at least six Sarcocystis species and the results also indicated the existence of certain nucleotide positions within the ssu rRNA gene that are unique to Sarcocystis species with a canine definitive host.

Phylogenetic analyses of parasites in the new millennium

Phylogenetic analysis has changed greatly in the last decade, and the most important themes in that change are reviewed here. Sequence data have become the most common source of phylogenetic information. This means that explicit models for evolutionary processes have been developed in a likelihood context, which allow more realistic data analyses. These models are becoming increasingly complex, both for nucleotides and for amino acid sequences, and so all such models need to be quantitatively assessed for each data set, to find the most appropriate one for use in any particular tree-building analysis. Bayesian analysis has been developed for tree-building and is greatly increasing in popularity. This is because a good heuristic strategy exists, which allows large data sets to be analyzed with complex evolutionary models in a practical time. Perhaps the most disappointing aspect of tree interpretation is the ongoing confusion between rooted and unrooted trees, while the effect of taxon and character sampling is often overlooked when constructing a phylogeny (especially in parasitology). The review finishes with a detailed consideration of the analysis of a multi-gene data set for several dozen taxa of Cryptosporidium (Apicomplexa), illustrating many of the theoretical and practical points highlighted in the review.

The current status of the small subunit rRNA phylogeny of the coccidia (Sporozoa)

There is no current comprehensive assessment of the molecular phylogeny of the coccidia, as all recently published papers either deal with subsets of the taxa or sequence data, or provide non-robust analyses. Here, we present a comprehensive and consistent phylogenetic analysis of the available data for the small-subunit ribosomal RNA gene sequence, including a number of taxa not previously studied, based on a Bayesian tree-building analysis and the covariotide model of evolution. The assumptions of the analysis have been rigorously tested, and the benefits and limitations highlighted. Our results provide support for a number of prior conclusions, including the monophyly of the families Sarcocystidae (cyst-forming coccidia) and Eimeriidae (oocyst-forming coccidia), but with bird-host Isospora species in the Eimeriidae and mammal-host species in the Sarcocystidae. However, it is clear that a number of previously reported relationships are dependent on the evolutionary model chosen, such as the placements of Goussia janae, Lankesterella minimia and Caryospora bigenetica. Our results also confirm the monophyly of the subfamilies Toxoplasmatinae and Sarcocystinae, but only some of the previously reported groups within these subfamilies are supported by our analysis. Similarly, only some of the previously reported groups within the Eimeriidae are supported by our analysis, and the genus Eimeria is clearly paraphyletic. There are unambiguous patterns of host-parasite relationship within the coccidia, as most of the well-supported groups have a consistent and restricted range of hosts, with the exception of the Toxoplasmatinae. Furthermore, the previously reported groups for which we found no support all have a diverse range of unrelated hosts, confirming that these are unlikely to be natural groups. The most interesting unaddressed questions may relate to Isospora, which has the fewest available sequences and host-parasite relationships apparently not as straightforward as elsewhere within the suborder.

Evolutionary relationships among cyst-forming coccidia Sarcocystis spp. (Alveolata: Apicomplexa: Coccidea) in endemic African tree vipers and perspective for evolution of heteroxenous life cycle

Cyst-forming coccidia of the genus Sarcocystis (Alveolata: Apicomplexa: Coccidea) parasitize vertebrates worldwide. Data from the small subunit rRNA genes (SSU) and the D2 domain of the large subunit rRNA genes were used to reconstruct phylogeny for all species in the Sarcocystidae for which sequences are currently available. We have focused on the evolutionary history of species that circulate between snakes as definitive hosts and rodents as intermediate hosts. Trees were reconstructed using maximum parsimony, minimum evolution, maximum likelihood and the bayesian phylogenetics. Our reconstructions support monophyly of Sarcocystidae but fail to robustly resolve the relationship within clades. Using a concatenated dataset of available rDNAs, the "isosporoid" coccidia Neospora, Toxoplasma, Besnoitia, Isospora and Hyaloklossia form a sister group to the monophyletic Sarcocystis. Moreover, we show that Sarcocystis from arboreal vipers of the genus Atheris, which are endemic to the mountain rain forests of the Equatorial Africa, are monophyletic, with sister species parasitizing the desert viper Pseudocerastes persicus from the Near East. We report the co-evolution of Sarcocystis spp. with their final snake hosts. The geological history of the African continent, mountain ranges, forests and general SSU rDNA rates were used to construct a linearized tree. Possible origin of the heteroxenous life cycle of Sarcocystis is discussed.

Phylogeny of gregarines (Apicomplexa) as inferred from small-subunit rDNA and beta-tubulin

Gregarines are thought to be deep-branching apicomplexans. Accordingly, a robust inference of gregarine phylogeny is crucial to any interpretation of apicomplexan evolution, but molecular sequences from gregarines are restricted to a small number of small-subunit (SSU) rDNA sequences from derived taxa. This work examines the usefulness of SSU rDNA and beta-tubulin sequences for inferring gregarine phylogeny. SSU rRNA genes from Lecudina (Mingazzini) sp., Monocystis agilis Stein, Leidyana migrator Clopton and Gregarina polymorpha Dufour, as well as the beta-tubulin gene from Leidyana migrator, were sequenced. The results of phylogenetic analyses of alveolate taxa using both genes were consistent with an early origin of gregarines and the putative 'sister' relationship between gregarines and Cryptosporidium, but neither phylogeny was strongly supported. In addition, two SSU rDNA sequences from unidentified marine eukaryotes were found to branch among the gregarines: one was a sequence derived from the haemolymph parasite of the giant clam, Tridacna crocea, and the other was a sequence misattributed to the foraminiferan Ammonium beccarii. In all of our analyses, the SSU rDNA sequence from Colpodella sp. clustered weakly with the apicomplexans, which is consistent with ultrastructural data. Altogether, the exact position of gregarines with respect to Cryptosporidium and other apicomplexans remains to be confirmed, but the congruence of SSU rDNA and beta-tubulin trees with one another and with morphological data does suggest that further sampling of molecular data will eventually put gregarine diversity into a phylogenetic context.

Dog shedding oocysts of Neospora caninum: PCR diagnosis and molecular phylogenetic approach

Results of molecular determination of a dog isolate of Neospora caninum in the Czech Republic are presented. Colorless bisporocystic oocysts measuring 10-13 micro m x 10-11 micro m were recovered from feces and used for DNA isolation. A diagnostic PCR procedure using previously described molecular methods was performed to determine the species. The N. caninum species-specific primers based on the Nc 5 region produced a positive result, while primers specific for Hammondia heydorni rDNA internal transcribed spacer 1 (ITS1) was negative. Sequencing and phylogenetic comparison of ITS1 rDNA and the D2 domain of the large subunit rDNA (D2 LSU) determined our isolate to be N. caninum. Phylogenetic analysis of closely related genera Toxoplasma, Neospora and Hammondia based on ITS1 and D2 LSU robustly distinguished three clades: (i). Toxoplasma gondii + Hammondia hammondi, (ii). N. caninum + Neospora hughesi, and (iii). H. heydorni. Based on phylogenetic relationships we propose three acceptable suggestions to solve the problem of taxonomy of these genera.

Characterization of Sarcocystis species in domestic animals using a PCR-RFLP analysis of variation in the 18S rRNA gene: a cost-effective and simple technique for routine species identification

Thirteen restriction endonucleases were used to investigate nuclotide sequence variation in the 18S rRNA DNA of 88 individuals from ten Sarcocystis taxa collected as cysts from their intermediate hosts, swine, cattle and water buffalo. A DNA sequence of approximately 900 bp was used. A total of 26 electromorphs were detected. The electromorphs were sorted into seven different haplotypes that coincided with the six named species and an unidentified species from cattle. These findings support those of our morphological examinations, which suggested that the taxa resembling Sarcocystis hirsuta, S. hominis, both found in water buffalo, and S. sinensis found in cattle, are not new species but are in fact S. hirsuta and S. hominis as found in cattle, and S. sinensis as found in water buffalo; this finding supports the idea that these species can utilize both cattle and water buffalo as intermediate hosts and are not restricted to one or the other host group as previously thought. PCR-RFLP resolved by agarose gel electrophoresis is shown to be an easy and rapid method of discriminating between these species.

The conceptual basis for a new classification of the coccidia

At the joint meeting of the 8th International Coccidiosis Conference and the Annual Scientific Meeting of the Australian Society for Parasitology in Palm Cove, Australia, in July 2001, a Controversial Roundtable was held on 'New classification of coccidia'. The aim of this Roundtable was to stimulate and encourage discussion and debate on current classification schemes for the group of parasitic protozoa known as the eimeriid coccidia. In the past, such classifications have been based only on phenotypic characters such as morphology, ultrastructure, life cycles, and host specificity. However, over the past 10-15 years, molecular phylogenetic studies on taxa of the eimeriid coccidia have revealed that several of the families, subfamilies, and genera that have been erected based on non-molecular characters are paraphyletic. Therefore, this Roundtable was an important forum for initial discussions on how a new and more comprehensive classification of the eimeriid coccidia, which takes into consideration both phenotypic and molecular characters, can be devised. The stimulus came from invited speakers who gave introductions into selected areas of taxonomy and classification. Following these introductions, a more general discussion with the audience addressed potential steps that may be taken in future work. This review is the immediate outcome of the Roundtable. It describes advantages and disadvantages of the use of phenotypic or molecular characters as the base for taxonomic schemes for eimeriid coccidia. It gives specific examples for drawbacks of current classifications based only on phenotypic characters as well as potential pitfalls associated with the use of only molecular phylogenies. It addresses current controversies as well as rules of taxonomy and nomenclature relevant for the eimeriid coccidia. Finally, it recommends the establishment of an international group of scientists to meet on a regular basis, stimulate further discussions, and give direction on how the final goal, i.e. a proposal for a revised, and widely accepted, classification of the eimeriid coccidia, may be achieved.

Limitations of relative apparent synapomorphy analysis (RASA) for measuring phylogenetic signal

In this paper we use hypothetical and empirical data matrices to evaluate the ability of relative apparent synapomorphy analysis (RASA) to measure phylogenetic signal, select outgroups, and identify terminals subject to long-branch attraction. In all cases, except for equal character-state frequencies, RASA indicated extraordinarily high levels of phylogenetic information for hypothetical data matrices that are uninformative regarding relationships among the terminals. Yet, regardless of the number of characters or character-state frequencies, RASA failed to detect phylogenetic signal for hypothetical matrices with strong phylogenetic signal. In our empirical example, RASA indicated increasing phylogenetic signal for matrices for which the strict consensus of the most parsimonious trees is increasingly poorly resolved, clades are increasingly poorly supported, and for which many relationships are in conflict with more widely sampled analyses. RASA is an ineffective approach to identify outgroup terminal(s) with the most plesiomorphic character states for the ingroup. Our hypothetical example demonstrated that RASA preferred outgroup terminals with increasing numbers of convergent character states with ingroup terminals, and rejected the outgroup terminal with all plesiomorphic character states. Our empirical example demonstrated that RASA, in all three cases examined, selected an ingroup terminal, rather than an outgroup terminal, as the best outgroup. In no case was one of the two outgroup terminals even close to being considered the optimal outgroup by RASA. RASA is an ineffective means of identifying problematic long-branch terminals. In our hypothetical example, RASA indicated a terminal as being a problematic long-branch terminal in spite of the terminal being on a zero-length branch and having no possibility of undergoing long-branch attraction with another terminal. RASA also failed to identify actual problematic long-branch terminals that did undergo long-branch attraction, but only after following Lyons-Weiler and Hoelzer's (1997) three-step process to identify and remove terminals subject to long-branch attraction. We conclude that RASA should not be used for any of these purposes.

Molecular approaches for inferring evolutionary relationships among protistan parasites

Within the diverse group of parasites broadly recognized as protists, there are limited morphological characters that can be used to distinguish species and even fewer characters that can infer evolutionary relationships among species. For this reason, molecular data are commonly used to infer relationships among species and strains. These studies most commonly rely on sequences associated with the ribosomal RNA genes but increasingly other nuclear, mitochondrial or plastid genes are contributing data. Molecular systematics has been invaluable in expanding the range of characters that are available for inferring relationships among protistan taxa. As an adjunct to morphological characters, sequence data allow us to better understand the evolutionary history of this group of parasites and thereby erect a well-supported taxonomic framework that reflects these historical relationships. Importantly, the predictive nature of such a framework can aid the search for therapeutic compounds (e.g. via shared biochemical pathways) and highlight organisms that should be tested for cross-reactivity in immunological or molecular diagnostic methods (e.g. use of the closest relatives to assess test specificity). For emergent and poorly known parasites, molecular characterization and placement within the broader phylogenetic framework can help predict likely life history traits, including possible or likely definitive hosts.

Multiple origin of the dihomoxenous life cycle in sarcosporidia

Although their ssrRNA gene sequences are closely related, the lizard sarcosporidia (Apicomplexa, Sarcocystidae) Sarcocystis lacertae and Sarcocystis gallotiae posses heteroxenous and dihomoxenous life cycles, respectively. When aligned with available sarcosporidian ssrRNA genes, both species constitute a monophyletic clade that is only distantly related with sarcosporidia that have a viperid snake as their definitive host (Sarcocystis sp., Sarcocystis atheridis). To test the phyletic status of the dihomoxenous life style, Sarcocystis rodentifelis and Sarcocystis muris, two dihomoxenous parasites of mammals were included into this study. All studied species group together with former Frenkelia spp., Sarcocystis neurona and related marsupial and bird sarcosporidia in a monophyletic clade. However, the available dataset supports independent appearance of the dihomoxenous life cycle at least twice during the evolution of the Sarcocystidae.

A review of Sarcocystis neurona and equine protozoal myeloencephalitis (EPM)

Equine protozoal myeloencephalitis (EPM) is a serious neurological disease of horses in the Americas. The protozoan most commonly associated with EPM is Sarcocystis neurona. The complete life cycle of S. neurona is unknown, including its natural intermediate host that harbors its sarcocyst. Opossums (Didelphis virginiana, Didelphis albiventris) are its definitive hosts. Horses are considered its aberrant hosts because only schizonts and merozoites (no sarcocysts) are found in horses. EPM-like disease occurs in a variety of mammals including cats, mink, raccoons, skunks, Pacific harbor seals, ponies, and Southern sea otters. Cats can act as an experimental intermediate host harboring the sarcocyst stage after ingesting sporocysts. This paper reviews information on the history, structure, life cycle, biology, pathogenesis, induction of disease in animals, clinical signs, diagnosis, pathology, epidemiology, and treatment of EPM caused by S. neurona.

Molecular phylogeny of the other tissue coccidia: Lankesterella and Caryospora

Nearly complete sequences were obtained from the 18S rDNA genes of Eimeria falciformis (the type species of the genus), Caryospora bigenetica, and Lankesterella minima. Two clones of the rDNA gene from C. higenetica varied slightly in primary structure. Parsimony-based and maximum likelihood phylogenetic reconstructions with a number of other apicomplexan taxa support 2 major clades within the Eucoccidiorida, i.e., the isosporoid coccidia (consisting of Toxoplasma, Neospora, Isospora [in part], and Sarcocystis spp.) and a second clade containing Lankesterella and Caryospora spp., as well as the eimeriid coccidia (Cyclospora, Isospora [in part], and Eimeria spp.). Our observations suggest that Caryospora spp. may not belong in the family Eimeriidae but rather may be allied with the family Lankesterellidae with which they share molecular and life history similarities. This may be a third lineage of coccidian parasites that has independently evolved a unique heteroxenous transmission strategy.

Molecular phylogeny of Besnoitia and the genetic relationships among Besnoitia of cattle, wildebeest and goats

Knowledge on parasites of the genus Besnoitia is sparse, which are classified in the subfamily Toxoplasmatinae of the phylum Apicomplexa. This arrangement hypotheses that Besnoitia represents the sister group to species such as Toxoplasma gondii and Hammondia hammondi. In order to test this hypothesis, phylogenetic analyses of 18S ribosomal DNA (rDNA) from Besnoitia, Hammondia, Isospora, Frenkelia, Eimeria, Neospora, Sarcocystis and Toxoplasma were performed. The 18S rDNA of Besnoitia besnoiti, Besnoitia jellisoni and Eimeria alabamensis were amplified by PCR and sequenced. Phylogenetic analyses by parsimony and maximum-likelihood methods showed Besnoitia to be reproducibly the sister group to a clade containing Hammondia, Neospora and Toxoplasma. Furthermore, Besnoitia of cattle, wildebeest and goats had identical ITS1 rDNA sequences, which questions the use of the taxon Besnoitia caprae to describe the Besnoitia found in goats.

Effects of sequence alignment and structural domains of ribosomal DNA on phylogeny reconstruction for the protozoan family sarcocystidae

Finding correct species relationships using phylogeny reconstruction based on molecular data is dependent on several empirical and technical factors. These include the choice of DNA sequence from which phylogeny is to be inferred, the establishment of character homology within a sequence alignment, and the phylogeny algorithm used. Nevertheless, sequencing and phylogeny tools provide a way of testing certain hypotheses regarding the relationship among the organisms for which phenotypic characters demonstrate conflicting evolutionary information. The protozoan family Sarcocystidae is one such group for which molecular data have been applied phylogenetically to resolve questionable relationships. However, analyses carried out to date, particularly based on small-subunit ribosomal DNA, have not resolved all of the relationships within this family. Analysis of more than one gene is necessary in order to obtain a robust species signal, and some DNA sequences may not be appropriate in terms of their phylogenetic information content. With this in mind, we tested the informativeness of our chosen molecule, the large-subunit ribosomal DNA (lsu rDNA), by using subdivisions of the sequence in phylogenetic analysis through PAUP, fastDNAml, and neighbor joining. The segments of sequence applied correspond to areas of higher nucleotide variation in a secondary-structure alignment involving 21 taxa. We found that subdivision of the entire lsu rDNA is inappropriate for phylogenetic analysis of the Sarcocystidae. There are limited informative nucleotide sites in the lsu rDNA for certain clades, such as the one encompassing the subfamily Toxoplasmatinae. Consequently, the removal of any segment of the alignment compromises the final tree topology. We also tested the effect of using two different alignment procedures (CLUSTAL W and the structure alignment using DCSE) and three different tree-building methods on the final tree topology. This work shows that congruence between different methods in the formation of clades may be a feature of robust topology; however, a sequence alignment based on primary structure may not be comparing homologous nucleotides even though the expected topology is obtained. Our results support previous findings showing the paraphyly of the current genera Sarcocystis and Hammondia and again bring to question the relationships of Sarcocystis muris, Isospora felis, and Neospora caninum. In addition, results based on phylogenetic analysis of the structure alignment suggest that Sarcocystis zamani and Sarcocystis singaporensis, which have reptilian definitive hosts, are monophyletic with Sarcocystis species using mammalian definitive hosts if the genus Frenkelia is synonymized with Sarcocystis.

Phylogenetic relationships of the genus Frenkelia: a review of its history and new knowledge gained from comparison of large subunit ribosomal ribonucleic acid gene sequences

The different genera currently classified into the family Sarcocystidae include parasites which are of significant medical, veterinary and economic importance. The genus Sarcocystis is the largest within the family Sarcocystidae and consists of species which infect a broad range of animals including mammals, birds and reptiles. Frenkelia, another genus within this family, consists of parasites that use rodents as intermediate hosts and birds of prey as definitive hosts. Both genera follow an almost identical pattern of life cycle, and their life cycle stages are morphologically very similar. However, the relationship between the two genera remains unresolved because previous analyses of phenotypic characters and of small subunit ribosomal ribonucleic acid gene sequences have questioned the validity of the genus Frenkelia or the monophyly of the genus Sarcocystis if Frenkelia was recognised as a valid genus. We therefore subjected the large subunit ribosomal ribonucleic acid gene sequences of representative taxa in these genera to phylogenetic analyses to ascertain a definitive relationship between the two genera. The full length large subunit ribosomal ribonucleic acid gene sequences obtained were aligned using Clustal W and Dedicated Comparative Sequence Editor secondary structure alignments. The Dedicated Comparative Sequence Editor alignment was then split into two data sets, one including helical regions, and one including non-helical regions, in order to determine the more informative sites. Subsequently, all four alignment data sets were subjected to different tree-building algorithms. All of the analyses produced trees supporting the paraphyly of the genus Sarcocystis if Frenkelia was recognised as a valid genus and, thus, call for a revision of the current definition of these genera. However, an alternative, more parsimonious and more appropriate solution to the Sarcocystis/Frenkelia controversy is to synonymise the genus Frenkelia with the genus Sarcocystis.