A set of nematode rRNA cistron databases and a primer assessment tool to enable more flexible and comprehensive metabarcoding.

The ITS-2-rRNA has been particularly useful for nematode metabarcoding but does not resolve all phylogenetic relationships, and reference sequences are not available for many nematode species. This is a particular issue when metabarcoding complex communities such as wildlife parasites or terrestrial and aquatic free-living nematode communities. We have used markerDB to produce four databases of distinct regions of the rRNA cistron: the 18S rRNA gene, the 28S rRNA gene, the ITS-1 intergenic spacer and the region spanning ITS-1_5.8S_ITS-2. These databases comprise 2645, 254, 13,461 and 10,107 unique full-length sequences representing 1391, 204, 1837 and 1322 nematode species, respectively. The comparative analysis illustrates the complementary value but also reveals a better representation of Clade III, IV and V than Clade I and Clade II nematodes in each case. Although the ITS-1 database includes the largest number of unique full-length sequences, the 18S rRNA database provides the widest taxonomic coverage. We also developed PrimerTC, a tool to assess primer sequence conservation across any reference sequence database, and have applied it to evaluate a large number of previously published rRNA cistron primers. We identified sets of primers that currently provide the broadest taxonomic coverage for each rRNA marker across the nematode phylum. These new resources will facilitate more comprehensive metabarcoding of nematode communities using either short-read or long-read sequencing platforms. Further, PrimerTC is available as a simple WebApp to guide or assess PCR primer design for any genetic marker and/or taxonomic group beyond the nematode phylum.

Phylogenetic assessment of some Palearctic Allocreadium spp. (Trematoda, Gorgoderoidea: Allocreadiidae).

The genus Allocreadium is a group of digenetic trematodes whose adult representatives mainly parasitize the intestines of freshwater fishes. The aim of this research is to reconstruct the phylogeny of four Palearctic species of this genus, Allocreadium dogieli, Allocreadium isoporum, Allocreadium papilligerum, and Allocreadium sp. ex Oreoleuciscus potanini from Mongolia. The DNA sequences of the 28S rRNA gene and the rDNA ITS2 region were obtained and then analyzed for phylogenetic inference. The analysis is complemented with the morphological descriptions for all four species. Phylogenetic analyses show that the newly obtained isolate of A. isoporum appeared to be genetically similar to previously obtained isolates of A. isoporum. Allocreadium dogieli probably belongs to the same evolutionary lineage of Allocreadium as A. crassum, while A. papilligerum to the same evolutionary lineage as Alocreadium transversale ex Cobitis taenia from Lithuania, but the detailed species composition of these lineages requires further elucidation. Allocreadium sp. was genetically close to Allocreadium sp. ex P. phoxinus from Primorski Krai, Russia, and a group of these Allocreadium had a sister relationship with Allocreadium khankaiensis. Our findings contradict some recent hypotheses about the phylogeography of Allocreadium spp.

First molecular assessment of two digenean parasites of the lancehead snake Bothrops moojeni Hoge, 1966 (Serpentes, Viperidae) in Brazil.

Two digenean species, Infidum infidum Faria, 1910 (Dicrocoeliidae) and Travtrema stenocotyle Cohn, 1902 (Plagiorchiidae), were collected in the large pit viper Bothrops moojeni Hoge, 1966 from Reserva Particular do Patrimônio Natural Cisalpina, municipality of Brasilândia, Mato Grosso do Sul State, Brazil. In this study, we provide the first molecular characterisation using the 28S rDNA and phylogenetic position data of these two common digeneans from B. moojeni. The molecular framework revealed topologies with strongly supported clades using maximum likelihood and Bayesian inference methods, positioned I. infidum among Plagiorchiidae and not among Dicrocoeliidae as expected and T. stenocotyle (Plagiorchiidae) surprisingly grouped as a sister group to Allassogonoporidae, Microphallidae, Pleurogenidae, and Prosthogonimidae, not related to plagiorchids. Our molecular phylogenetic data showed that these species may not correspond to their assigned families and encourage future studies on the systematic of these understudied groups.

Morphological redescription and phylogenetic assessment of Spauligodon aspiculus (Oxyuroidea: Pharyngodonidae) infecting the white-spotted gecko, Tarentola annularis (Squamata: Gekkonidae).

Thirty white-spotted geckos, Tarentola annularis, from the South Sinai desert in Egypt, were examined for helminth parasites. Spauligodon aspiculus was observed to infect 19 geckos with 63.33% as a prevalence of parasitic infection. The present nematode species is separated from congeners by morphological and metrical characteristics such as lateral alae, aspinose filamentous tail, and no spicule, and three pairs of caudal papillae with posterior pair excluded from envelopment by the caudal alae in the male worms, and knobbed eggs, and postbulbar vulva in females. It compared morphometrically with other Spauligodon species described previously and showed few differences in measurements. Molecular characterization based on the partial 28S rRNA nuclear ribosomal gene sequence showed that there was a close identity, up to 72%, with other sequences retrieved from GenBank. Phylogenetic analysis showed that the parasite sequence in conjunction with existing data facilitates the investigation of the placement of this pharyngodonid species within Oxyuridae. The present species is deeply embedded in the genus Spauligodon with close relationships to previously described Spauligodon nicolauensis (gb| JN619349.1, and JF829243.1) as more related sister taxa. This study highlights the importance of combining genetic and morphological data with taxonomy in pharyngodonid species.

Morphological description and phylogenetic assessment of 28S rRNA for Thelandros chalcidiae sp. nov. from Chalcides ocellatus.

Thelandros is a genus of oxyurid nematodes which parasitize both omnivorous and herbivorous hosts. Thelandros chalcidiae sp. nov. is a new taxa described from the large intestine of the ocellated skink, Chalcides ocellatus, from the South Sinai Desert in Egypt. The recovered parasite species was examined at both morphological and molecular levels in order to determine the exact taxonomic position within Pharyngodonidae family. The current pharyngodonid species is characterized by a mouth opening bounded by three bilobed lips; male worms are characterized by the presence of two pairs of cloacal papillae (pre- and adcloacal) and one single caudal papillae (postcloacal) and caudal alae in an auricular form and females with post-equatorial vulva, amphidelphic ovary in which anterior ovary extended to level of excretory pore and posterior ovary extended posteriorly up anal opening. The recovered nematodes were compared with other known species from different hosts and it was found to be morphologically different from them. Molecular characterization based on the partial 28S rRNA nuclear ribosomal gene sequence showed sequence identities ≥ 83.15% with taxa under family Pharyngodonidae, 74.84-87.37% with Oxyuridae, 80.54% with Heteroxynematidae, and 75.98-77.72% with Thelastomatidea. Phylogenetic analysis showed that parasite sequence in conjunction with existing data facilitate placement of this species within Oxyurida. The present species is deeply embedded in genus Thelandros with close relationships to previously described Thelandros sp. and T. galloti in same taxon. This study highlighted importance of combining morphological and genetic data with taxonomy in pharyngodonid species.

Morphology and Molecular Characterization of Parabronema smithii (Cobbold, 1882) (Nematoda: Habronematidae) from Wild Asian Elephant (Elephas maximus maximus) of Sri Lanka.

PURPOSE: The aim of the present study was to carry out a detailed study of morphological features and to determine the phylogenetic position of Parabronema smithii (Cobbold, 1882) found in wild elephants in Sri Lanka. METHODS: Adult worms were collected from stomach ulcers at postmortem examination of wild elephants in the Udawalawe National Park, Sri Lanka. The detailed morphology of P. smithii was studied using light microscopy and, for the first time, scanning electron microscopy. Fifteen morphological characteristics were investigated. The phylogenetic analysis was conducted using the second internal transcribed spacer region (ITS2), and portions of the large subunit ribosomal DNA (28S) and cytochrome c oxidase subunit 1 (cox1). Furthermore, the present study provides a comparison of morphology and morphometrics of Parabronema species that occur in different hosts. CONCLUSION: Parabronema smithii isolated from wild elephants exhibited the key morphological features. Phylogenetic analysis of selected genes revealed that P. smithii is closely associated with P. skrjabini and Habronema spp. Findings of the present study enhance our understanding of the biology and taxonomy of P. smithii in wild elephant in Sri Lanka and will contribute to future phylogeographic studies.

Phylogenetic Relationships of Cardiocephaloides spp. (Digenea, Diplostomoidea) and the Genetic Characterization of Cardiocephaloides physalis from Magellanic Penguin, Spheniscus magellanicus, in Chile.

PURPOSE: Cardiocephaloides is a small genus of strigeid digeneans with an essentially cosmopolitan distribution. Most members of Cardiocephaloides are found in larid birds, however, Cardiocephaloides physalis is an exception and parasitizes penguins in some coastal regions of South America and South Africa. No prior molecular phylogenetic studies have included DNA sequence data of C. physalis. Herein, we provide molecular phylogenetic analyses of Cardiocephaloides using DNA sequences from five species of these strigeids. METHODS: Adult Cardiocephaloides spp. were obtained from larid birds and penguins collected from 3 biogeographical realms (Palearctic, Nearctic and Neotropics). We have generated sequences of the complete ITS region and partial 28S gene of the nuclear ribosomal DNA, along with partial sequences of the mitochondrial CO1 gene for C. physalis, C. medioconiger and the type species of the genus, C. longicollis and used them for phylogenetic inference. RESULTS: Cardiocephaloides spp. appeared as a 100% supported clade in the phylogenetic tree based on 28S sequences. The position of C. physalis varied between the phylogenetic trees based on the relatively conservative 28S gene on one hand, and variable ITS1 and COI sequences on the other. Cardiocephaloides physalis was nested within the clade of Cardiocephaloides spp. in the 28S tree and appeared as the sister group to the remaining members of the genus in the ITS1 region and COI trees. We detected 0.4-1.6% interspecific divergence in 28S, 1.9-6.9% in the ITS region and 8.7-11.8% in CO1 sequences of Cardiocephaloides spp. Our 28S sequence of C. physalis from South America and a shorter sequence from Africa available in the GenBank were identical. CONCLUSION: Cardiocephaloides as represented in the currently available dataset is monophyletic with C. physalis parasitism in penguins likely resulting from a secondary host-switching event. Identical 28S sequences of C. physalis from South America and Africa cautiously confirm the broad distribution of this species, although comparison of faster mutating genes (e. g., CO1) is recommended for a better substantiated conclusion.

An integrative taxonomic assessment of Procamallanus (Spirocamallanus) huacraensis (Nematoda: Camallanidae), infecting the freshwater catfish Trichomycterus spegazzinii (Siluriformes: Trichomycteridae) in Argentina.

Procamallanus (Spirocamallanus) huacraensis infecting the catfish Trichomycterus spegazzinii from Escoipe River, Salta province (Argentina), is redescribed and genetically characterised for the first time, based on three genetic markers (nuclear 18S and 28S rRNA; cytochrome c oxidase subunit I [cox1] mtDNA). The phylogeny of Camallanidae was also discussed. Morphological evaluation of P. (S.) huacraensis using light and scanning electron microscopy revealed the previously undescribed features: location of deirids, accurate morphology of larvae (L1) and ovijector in females, as well as phasmids in males. Differences were found comparing the newly collected material and the type specimens, probably because the original description lacked detailing. Unfortunately, type specimens of P. (S.) huacraensis were no available for loan. The results of morphological and genetic analyses supported the validity of P. (S.) huacraensis. Inconsistencies regarding the taxonomic identification of species of Camallanidae in GenBank database were noted. Based on the current genetic database of Camallanidae, phylogenetic reconstructions using the 18S rRNA sequences were most consistent, due to the inclusion of higher number of taxa. Procamallanus (S.) huacraensis appeared as sister group of P. (S.) rarus, also isolated from a catfish in a neighbouring region. The order and habitat of hosts were also similar within some well-supported parasite lineages, but without common geographic origin. However, it is still premature to make definitive affirmations regarding the role of such features in the phylogenetic patterns of Camallanidae, given the scarcity of genetic data. The phylogenetic reconstructions also confirmed the artificiality of the morphology-based systematics of the family.

First description of the male of Philometroides acreanensis and phylogenetic assessment of Philometridae (Nematoda: Dracunculoidea) suggest instability of some taxa.

The male of Philometroides acreanensis, parasitic in the anterior intestine external wall of the freshwater catfish Pimelodus blochii, from the Brazilian Amazon, is described for the first time. Additional data on the morphology of females is given. The new morphological data strengthened the validity of the species as well as its first genetic characterization, using three nuclear genetic markers (18S and 28S of the rDNA and ITS1-58S-ITS2), confirmed the high genetic resemblance of male and female specimens. Philometroides acreanensis shows morphological features of the generic diagnosis of Neophilometroides, Alinema, Philometra and Philometroides. Phylogenetic analyses using sequences of the18S rDNA from representatives of Dracunculoidea confirmed the validity of P. acreanensis and its close relatedness with Alinema rather than with other genera. The validity of Philonemidae was confirmed, as was the monophyly of Philometridae and Clavinema. However, Dentiphilometra, Philometra and Philometroides appear not to be monophyletic. Host taxa, habitat and geographic occurrence seem to have some relationship with the evolutionary traits of certain phylogenetic assemblages of philometrids, which were highly supported in the phylogentic reconstructions. Even though interesting aspects of the phylogeny and taxonomy of Philometridae came to light, further integrative approaches should be used that include additional genetic markers, due to the loose boundaries between some genera as observed here.

Phylogenetic assessment of Chromocyphellaceae (Agaricineae, Basidiomycota) and a new lamellate species of Chromocyphella.

Cyphelloid fungi represent a polyphyletic assemblage of reduced agarics, including the brown-spored family Chromocyphellaceae. In order to elucidate the phylogenetic position of Chromocyphellaceae, newly generated sequences of Chromocyphella were included in a multigene alignment of the Agaricineae and phylogenetically analyzed. The current analyses show that the Chromocyphella muscicola specimen used to phylogenetically place Chromocyphellaceae in its original description was misidentified and that the Chromocyphellaceae nests in the Hymenogastraceae, Chromocyphella being sister to Flammula. Chromocyphella is emended, including now a new species with lamellate and stipitate basidiomata, C. lamellata. The name Cymbella crouanii, type species of Chromocyphella, is lecto- and epitypified. Our analyses support a new origin of cyphelloid fungi. The shift to a cyphelloid basidioma from an agaric ancestor is suggested to have occurred in two evolutionary steps in Chromocyphella, an initial reduction in basidioma size and a subsequent loss of lamellae and stipe.

Molecular phylogenetics and biogeography of the ambush bugs (Hemiptera: Reduviidae: Phymatinae).

The ambush bugs (Heteroptera: Reduviidae: Phymatinae) are a diverse clade of predators known for their cryptic hunting behavior and morphologically diverse raptorial forelegs. Despite their striking appearance, role as pollinator predators, and intriguing biogeographic distribution, phylogenetic relationships within Phymatinae are largely unknown and the evolutionary history of the subfamily has remained in the dark. We here utilize the most extensive molecular phylogeny of ambush bugs to date, generated from a 3328 base pair molecular dataset, to refine our understanding of phymatine relationships, estimate dates of divergence (BEAST 2), and uncover historical biogeographic patterns (S-DIVA and DEC). This taxon set (39 species of Phymatinae and six outgroups) allowed reevaluation of the proposed sister group of Phymatinae and tribal-level relationships within the group, and for the first time proposes species-level relationships within Phymata Latreille, the largest genus of ambush bugs (∼109spp.). Available evidence suggests that Phymata originated in the Neotropical region, with subsequent dispersals to the Nearctic and Palearctic regions. This study provides a framework for future research investigating the evolutionary history of ambush bugs, as well as ecological and microevolutionary investigations.

Redescription and Molecular Assessment of Relationships Among Three Species of Echeneibothrium (Rhinebothriidea: Echeneibothriidae) Parasitizing the Yellownose Skate, Dipturus chilensis, in Chile.

Much progress has recently been made in revising the taxonomic assignments of genera originally classified in the polyphyletic "Tetraphyllidea." Many of these genera, including Echeneibothrium, were accommodated in the order Rhinebothriidea. However, beyond this larger taxonomic action, little work has been conducted on this genus over the past 50 yr. Consequently, the criteria used for characterizing species of Echeneibothrium have lagged behind those typically used in more modern descriptions of elasmobranch-hosted cestode taxa. A series of collecting trips to Chile to obtain cestodes from the yellownose skate, Dipturus chilensis , provided a unique opportunity to apply modern morphological and molecular methods to investigate the 3 species of Echeneibothrium reported parasitizing this skate, specifically Echeneibothrium megalosoma, Echeneibothrium multiloculatum, and Echeneibothrium williamsi. In addition to redescribing all 3 species, using morphological data from light and scanning electron microscopy, maximum likelihood and bayesian inference phylogenetic analyses of the D1-D3 regions of the 28S rDNA gene were conducted to assess their relationships among other echeneibothriids for which comparable data are available. Sequencing of 59 specimens representing these 3 species of Echeneibothrium allowed us to assess the intra- and interspecific variation in the 28S rDNA gene. The redescriptions use standardized terminology for scolex morphology, proglottid anatomy, and microthrix forms and pattern; they also expand on the original descriptions to include data on scolex size, ovary size, vas deferens and vaginal configurations, testes arrangement, and genital pore position. Our morphological work led to a major reinterpretation of the scolex morphology with the recognition that all 3 species bear an apical bothridial sucker, rather than an apical loculus, prompting emendation of the diagnosis for the family Echeneibothriidae. The presence of a band of spinitriches at the apex of the apical modification of the scolex proper seems to represent an important feature for distinguishing the 2 portions of the myzorhynchus across species. Intraspecific variation ranged from 0 to 7 bp across species and interspecific variation ranged from a low of 39-46 bp between E. williamsi and E. multiloculatum to a high of 61-66 bp between E. multiloculatum and E. megalosoma. Phylogenetic analyses indicate that the 3 species of Echeneibothrium hosted by the yellownose skate are not each other's closest relatives, suggesting multiple colonization events of D. chilensis have occurred. Further phylogenetic investigation is also likely to confirm the status of the genus Pseudanthobothrium as a synonym of Echeneibothrium because its species generally group among members of Echeneibothrium.

Molecular and morphological phylogenetics of chelonine parasitoid wasps (Hymenoptera: Braconidae), with a critical assessment of divergence time estimations.

Parasitoid wasps of the subfamily Cheloninae are both species rich and poorly known. Although the taxonomy of Cheloninae appears to be relatively stable, there is no clear understanding of relationships among higher-level taxa. We here applied molecular phylogenetic analyses using three markers (COI, EF1α, 28S) and 37 morphological characters to elucidate the evolution and systematics of these wasps. Analyses were based on 83 specimens representing 13 genera. All genera except Ascogaster, Phanerotoma, and Pseudophanerotoma formed monophyletic groups; Furcidentia (stat. rev.) is raised to generic rank. Neither Chelonus (Chelonus) nor Chelonus (Microchelonus) were recovered as monophyletic, but together formed a monophyletic lineage. The tribes Chelonini and Odontosphaeropygini formed monophyletic groups, but the Phanerotomini sensu Zettel and Pseudophanerotomini were retrieved as either para- or polyphyletic. The genera comprising the former subfamily Adeliinae were confirmed as being nested within the Cheloninae. To estimate the age of the subfamily, we used 16 fossil taxa. Three approaches were compared: fixed-rate dating, node dating, and total-evidence dating, with age estimates differing greatly between the three methods. Shortcomings of each approach in relation to our dataset are discussed, and none of the age estimates is deemed sufficiently reliable. Given that most dating studies use a single method only, in most cases without presenting analyses on the sensitivity to priors, it is likely that numerous age estimates in the literature suffer from a similar lack of robustness. We argue for a more rigorous approach to dating analyses and for a faithful presentation of uncertainties in divergence time estimates. Given the results of the phylogenetic analysis the following taxonomic changes are proposed: Furcidentia Zettel (stat. rev.), previously treated as a subgenus of Pseudophanerotoma Zettel is raised to generic rank; Microchelonus Szépligeti (syn. nov.), variously treated by previous authors, is proposed as a junior synonym of Chelonus Jurine; the following subgenera of Microchelonus - Baculonus Braet & van Achterberg (syn. nov.), Carinichelonus Tobias (syn. nov.) and Scabrichelonus He, Chen & van Achterberg (syn. nov.), are proposed as junior synonyms of Chelonus; a number of new species names are proposed due to homonyms resulting from the above changes and these are listed in the paper.

Molecular analysis of the genera Hapalotrema Looss, 1899 and Learedius Price, 1934 (Digenea: Spirorchiidae) reveals potential cryptic species, with comments on the validity of the genus Learedius.

Adult blood flukes of the genera Hapalotrema Looss, 1899 and Learedius Price, 1934 were collected from turtles off Queensland and the Hawaiian Islands. Specimens were identified as Hapalotrema pambanensis Mehrotra, 1973, H. synorchis Luhman, 1935, H. postorchis Rao, 1976 and Learedius learedi Price, 1934 on the basis of morphology. No major morphological differences were found between specimens from this study and previously published descriptions. DNA was also extracted and sequences obtained using custom spirorchiid-specific primers for the ITS2 and 28S rDNA regions, in order to confirm species identification and investigate phylogenetic relationships. Intraspecific genetic variation was generally low. However the ITS2 region of H. postorchis and to a lesser extent that of L. learedi showed considerable variation between specimens from the Pacific and Atlantic oceans. Further studies will be required to determine whether this variation should be considered inter- or intra-specific. Maximum likelihood phylogenetic analyses were completed for both sequenced genes. Learedius learedi was unequivocally nested among species of Hapalotrema, suggesting that the status of the genus Learedius may need to be reassessed.

A new species of Plectognathotrema Layman, 1930 (Trematoda: Zoogonidae) from an Australian monacanthid, with a molecular assessment of the phylogenetic position of the genus.

During helminthological examinations of teleost fishes of Ningaloo Reef, Western Australia, a new species of the enigmatic genus Plectognathotrema Layman, 1930 was discovered infecting the pot-bellied leatherjacket Pseudomonacanthus peroni (Hollard). The new species, Plectognathotrema kamegaii n. sp., is formally described, and the status of its four congeners is reviewed. Plectognathotrema hydrolagi Olson, Hanson & Pratt, 1970 is not recognised within the genus, as it differs greatly from its congeners in the form and arrangement of the vitellarium, testes and uterus, and in that it was described from a holocephalan. Plectognathotrema cephalopore Layman, 1930 and P. tsushimaense Kamegai, 1970 are morphologically similar, were described from the same host species and from close geographical localities and are considered synonymous. The new taxon is most similar to P. cephalopore, but differs from it in being much smaller and possessing a distinctly larger oral sucker relative to its body size. The generation of novel partial 28S ribosomal DNA sequences allowed a phylogenetic assessment of the genus and demonstrated that Plectognathotrema clearly belongs in the Zoogonidae Odhner, 1902, rather than in the Fellodistomidae Nicoll, 1909, where it is currently assigned. With the inclusion of Plectognathotrema in the Zoogonidae, there are now three zoogonid genera for which the species are restricted to monacanthid teleosts, i.e. Cephaloporus Yamaguti, 1934, Plectognathotrema and Yamagutiplectognathotrema Parukhin, 1977. Species of these genera share pronounced morphological and ecological affinities and a previously synonymised subfamily, the Cephaloporinae Yamaguti, 1934, is resurrected for them. The host specificity of these trematodes is commented upon.

The phylogenetic position of the Loimoidae Price, 1936 (Monogenoidea: Monocotylidea) based on analyses of partial rDNA sequences and morphological data.

Phylogenetic analyses of partial sequences of 18S and 28S rDNA of some monogenoids, including monocotylids and a specimen of Loimosina sp. collected from a hammerhead shark off Brazil, indicated that the Loimoidae (as represented by the specimen of Loimosina sp.) represents an in-group taxon of the Monocotylidae. In all analyses, the Loimoidae fell within a major monocotylid clade including species of the Heterocotylinae, Decacotylinae, and Monocotylinae. The Loimoidae formed a terminal clade with two heterocotyline species, Troglocephalus rhinobatidis and Neoheterocotyle rhinobatis, for which it represented the sister taxon. The following morphological characters supported the clade comprising the Loimoidae, Heterocotylinae, Decacotylinae and Monocotylinae: single vagina present, presence of a narrow deep anchor root, and presence of a marginal haptoral membrane. The presence of cephalic pits was identified as a putative synapomorphy for the clade (Loimoidae (T. rhinobatidis, N. rhinobatis)). Although rDNA sequence data support the rejection of the Loimoidae and incorporating its species into the Monocotylidae, this action was not recommended pending a full phylogenetic analysis of morphological data.

A molecular phylogenetic assessment of the genus Gyromitra in North America.

Gyromitra is a widespread genus of macroscopic apothecial ascomycetes whose taxa may be mycorrhizal, saprophytic or parasitic. Nuclear ribosomal 28S large subunit sequence data from 35 specimens from North America, along with sequences available in GenBank, were used in maximum-parsimony, maximum-likelihood and Bayesian analyses to reconstruct a phylogeny of Gyromitra in North America. Gyromitra sensu lato forms a monophyletic group within the Discinaceae composed of five distinct subgenera and 11 well supported clades that include Discina, Hydnotrya and Pseudorhizina. A new subgenus is proposed to accommodate G. californica and G. sphaerospora.

Molecular assessment of apicomplexan parasites in the snake Psammophis from North Africa: do multiple parasite lineages reflect the final vertebrate host diet?

The Apicomplexa are intracellular pathogens of animals, with the Coccidia being the largest group. Among these are the hemogregarines, which include some of the most common hemoparasites found in reptiles. Several studies have reported a possible pattern of prey-predator transmission for some of these parasites. Snakes from the Mediterranean region have been found to be parasitized with Hepatozoon spp. similar to those in lacertids and gekkonids, supporting the prey-predator transmission hypothesis. Here we analyzed specimens of the saurophagous genus Psammophis from North Africa, an ecologically different region. Through molecular analysis of tissue samples we detected 3 different apicomplexan parasites: Caryospora, Sarcocystis, and Hepatozoon. Caryospora was detected in a Forskål's sand snake Psammophis schokari from Algeria, constituting the first time these parasites have been detected from a tissue sample through molecular screening. The obtained Sarcocystis phylogeny does not reflect the relationships of their final hosts, with the parasites identified from snakes forming at least 3 unrelated groups, indicating that it is still premature to predict definitive host based on the phylogeny of these parasites. Three unrelated lineages of Hepatozoon parasites were identified in Psammophis, each closely related to lineages previously identified from different lizard groups, on which these snakes feed. This once again indicates that diet might be a key element in transmission, at least for Hepatozoon species of saurophagous snakes.

Molecular identification of human hookworm infections in economically disadvantaged communities in Peninsular Malaysia.

Species identification of human hookworm infections among eight communities in rural areas of Peninsular Malaysia was determined during 2009-2011. Fecal samples were examined by microscopy and subsequently, the internal transcribed spacer 2 and 28S ribosomal RNA region of Necator americanus and Ancylostoma spp. were sequenced. Overall, 9.1% (58 of 634) were identified positive by microscopy for hookworm infection, and 47 (81.0%) of 58 were successfully amplified and sequenced. Sequence comparison found that N. americanus (87.2%) was the most predominant hookworm identified, followed by Ancylostoma ceylanicum (23.4%). No A. duodenale infection was detected in this study. Detection of A. ceylanicum in humans highlighted the zoonotic transmission among humans living near dogs. Thus, implementation of effective control measures for hookworm infections in future should seriously consider this zoonotic implication.

Phylogenetic signal and noise: predicting the power of a data set to resolve phylogeny.

A principal objective for phylogenetic experimental design is to predict the power of a data set to resolve nodes in a phylogenetic tree. However, proactively assessing the potential for phylogenetic noise compared with signal in a candidate data set has been a formidable challenge. Understanding the impact of collection of additional sequence data to resolve recalcitrant internodes at diverse historical times will facilitate increasingly accurate and cost-effective phylogenetic research. Here, we derive theory based on the fundamental unit of the phylogenetic tree, the quartet, that applies estimates of the state space and the rates of evolution of characters in a data set to predict phylogenetic signal and phylogenetic noise and therefore to predict the power to resolve internodes. We develop and implement a Monte Carlo approach to estimating power to resolve as well as deriving a nearly equivalent faster deterministic calculation. These approaches are applied to describe the distribution of potential signal, polytomy, or noise for two example data sets, one recent (cytochrome c oxidase I and 28S ribosomal rRNA sequences from Diplazontinae parasitoid wasps) and one deep (eight nuclear genes and a phylogenomic sequence for diverse microbial eukaryotes including Stramenopiles, Alveolata, and Rhizaria). The predicted power of resolution for the loci analyzed is consistent with the historic use of the genes in phylogenetics.