A population of a nematode species belonging to the genus Oscheius was isolated in western Uttar Pradesh, India. Morphological and morphometrical studies on this species showed its high similarity with six species described previously from Pakistan (Oscheius citri, O. cobbi, O. cynodonti, O. esculentus, O. punctatus and O. sacchari). The molecular analysis of the ITS1-5.8S-ITS2 rDNA sequences of the Indian population and the six species described from Pakistan showed that all the sequences are almost identical. Thus, based on morphological and molecular characteristics, all of the six above-mentioned Pakistani species and Indian strain do not differ from each other, hence can be considered synonyms. The correct name for this taxon is the first described species O. citri. Additionally, the phylogenetic analysis of the 18S rDNA and the 28S rDNA sequences showed that Oscheius citri is sister to the clade formed by O. chongmingensis and O. rugaoensis from China. The high similarity of morphological and morphometric characteristics of O. citri and other species, O. maqbooli, O. nadarajani, O. niazii, O. shamimi and O. siddiqii, suggest their conspecificity; however, lack of molecular data for these species does not allow this hypothesis to be tested.

The principal goal of our study was to test whether ecologically and chemically different populations of lichens in the Physconia muscigena group belong to a single, or multiple, species. We used sequence data from three markers (ITS rDNA, mtSSU rDNA and TEF1-α) for the reconstruction of phylogenetic trees based on a sampling of mostly European and Canadian populations of P. muscigena (Ach.) Poelt, P. muscigena var. bayeri (Nádv.) Poelt and P. isidiomuscigena Essl. In addition, we sought any possible geographical or ecological trends among chemotypes and haplotypes. Results show that: 1) sequence data of ITS rDNA and TEF1-α show large genetic variation in the Physconia muscigena group, which does not correlate with geographical distribution or thallus chemistry; 2) Physconia muscigena var. bayeri and P. isidiomuscigena appear undifferentiated with P. muscigena in our phylogenetic trees, and the three species cannot be distinguished on the basis of ITS rDNA, mtSSU rDNA and TEF1-α sequences. We therefore synonymized Physconia muscigena var. bayeri with P. muscigena and we recombine P. isidiomuscigena as a variety of P. muscigena.

A new species of Creptotrematina Yamaguti, 1954 was collected from characid fishes, Astyanax fasciatus (Cuvier, 1819) and Astyanax lacustris Lucerna & Soares, 2016 from the Batalha River in the State of Sao Paulo, Brazil. The new species most closely resembles Creptotrematina aguirrepequenoi, but differs by the elongated shape of vitelline follicles, the extension of these follicles in the posterior end of body and the fact that they are not confluent. The morphological differences were confirmed through molecular data. Three specimens were sequenced, and molecular analyses were based on the internal transcribed spacers 2 and D1–D3 domains of the 28S ribosomal RNA gene. The obtained topologies showed the new species as a sister taxon of C. aguirrepequenoi, a species originally described from Astyanax mexicanus in Mexico, and later found in Astyanax aeneus in Costa Rica. Isolates of the new species are reciprocally monophyletic, and genetic distance values are similar to those observed in other species pairs within Allocreadiidae. These findings corroborate that the genus Creptotrematina is mostly a parasite of characids, and widely extended across the Americas, with representative species occurring between Argentina and northern Mexico.

Species identification based on the morphometry of opisthaptoral hard parts, in combination with internal transcribed spacer ribosomal DNA (ITS rDNA) region sequences, confirmed the presence of four viviparous Gyrodactylus von Nordman, 1832 (Plathyhelminthes, Monogenea) species on Nototheniid fish from the Prince Gustav Channel (Weddell Sea, Antarctica). Gyrodactylus antarcticus Gusev, 1967 was found mostly on Trematomus newnesi Boulenger (93 specimens) but also on T. bernacchii Boulenger (one specimen), the latter representing a new host record for this species. Gyrodactylus byrdi Hargis & Dillon, 1968 and G. coriicepsi Rokicka, Lumme & Ziętara, 2009 were recorded on their type hosts, T. newnesi and Notothenia coriiceps Richardson, respectively. Gyrodactylus wilkesi Hargis & Dillon, 1968 was found mostly on the fins of T. bernacchii (29 specimens), but also on T. hansoni Boulenger (one specimen) and T. newnesi (three specimens). The finding of G. wilkesi on T. newnesi represents a new host record. The low number of Gyrodactylus specimens may indicate an accidental infection. The occurence of all four Gyrodactylus species in the Prince Gustav Channel represents a new locality record. According to phylogentic methods, the newly redescribed monogeneans belong to the Antarctic lineage, forming a sister group to North American and European marine Gyrodactylus species, and consist of two species groups, one comprising G. coriicepsi and G. nudifronsi Rokicka, Lumme & Ziętara, 2009, and the other G. anarcticus and G. wilkesi.

Hybridization events between Schistosoma species (Digenea, Platyhelminthes) are reported with increasing frequency, largely due to improved access to molecular tools. Nevertheless, little is known about the distribution and frequency of hybrid schistosomes in nature. Screening for hybrids on a large scale is complicated by the need for nuclear and mitochondrial sequence information, precluding a ‘simple’ barcoding approach. Here we aimed to determine and understand the spatiotemporal distribution of Schistosoma haematobium × Schistosoma bovis hybrids in the Senegal River Basin. From ten villages, distributed over the four main water basins, we genotyped a total of 1236 schistosome larvae collected from human urine samples using a partial mitochondrial cox1 fragment; a subset of 268 parasites was also genotyped using ITS rDNA. Hybrid schistosomes were unevenly distributed, with substantially higher numbers in villages bordering Lac de Guiers than in villages from the Lampsar River and the Middle Valley of the Senegal River. The frequency of hybrids per village was not linked with the prevalence of urinary schistosomiasis in that village. However, we did find a significant positive association between the frequency of hybrids per village and the prevalence of Schistosoma mansoni. We discuss the potential consequences of adopting a barcoding approach when studying hybrids in nature.

Bacidina mendax, described here as a new lichen species, appears to be common and widespread, at least in Central Europe. Analyses of the ITS rDNA region and the morphology of specimens showed an intraspecific variation in the new taxon. It differs from B. neosquamulosa in the lack of a subsquamulose thallus, and from B. caligans in its longer and only slightly curved to apically hooked conidia and lack of a granular (sorediate) thallus. Since ITS rDNA data support the inclusion of Bacidia pycnidiata Czarnota & Coppins in the genus Bacidina, a new combination is proposed.

Cladonia is one of the largest lichen-forming ascomycete genera. It was formerly divided into ten sections, three of which, Crustaceae (Cladina), Tenues, and Impexae, are called the reindeer lichens. While previous studies have elucidated the relationships between species and sections, they often examined only one or a few specimens of each species in the analysis. This study examined the monophyly of selected members of sections Crustaceae, Tenues, and Impexae and their relationships in the genus Cladonia using the internal transcribed spacer region of the nuclear ribosomal DNA (ITS rDNA) and the mitochondrial small subunit gene of the mitochondrial ribosomal DNA (mtSSU). The phylogenetic tree contained four clades, two representing species in section Impexae, one representing species that belong to sections Crustaceae and Tenues, and one clade with C. arbuscula and related species. Five of 22 species, C. pycnoclada, C. stellaris, C. evansii, C. ciliata and C. subtenuis, showed monophyly in the phylogenetic tree; some of these 5 species have been shown previously to be monophyletic. The thallus branching pattern was interpreted as an important heritable character using the mtSSU network. Three duplets of paraphyletic species were further examined using ITS rDNA haplotype networks and AMOVA analysis. The results for the species duplets showed some mixing of haplotypes but the AMOVA analysis provided support for species separation within the duplets. While the evidence supports distinct species, further study is needed to conclusively show separate species in these duplets.

Micarea soralifera sp. nov., a new sorediate species belonging to the M. prasina group, is characterized by soralia developing directly from the endoxylic thallus or small external areoles, as well as the presence of micareic acid. Phylogenetic analyses of mtSSU rDNA sequences have shown that its closest relative is M. subviridescens. ITS rDNA sequence, a marker proposed as the universal barcoding region of fungi, was generated from the holotype.

The species from Cladonia section Unciales are characterized by the absence of squamules and soredia on the corticate podetia and the presence of usnic acid. Different subspecies, varieties and forms have been distinguished in the type species C. uncialis. In this study, a molecular phylogeny of Cladonia uncialis and members of the traditionally recognized section Unciales, along with additional potentially allied species, was constructed. DNA sequences from three gene loci, namely ITS rDNA, IGS rDNA and ß-tubulin, were analyzed using Maximum Parsimony, Maximum Likelihood, and Bayesian methods. Eleven species were analyzed for the first time using DNA sequence data. Cladonia uncialis subsp. uncialis and subsp. biuncialis were recognized as distinct taxa. The recognition of C. pseudostellata as a species was not supported by the analyses, but it represents a hypothamnolic acid chemotype, which is reported here as new to Europe (Scotland). The presence of subsp. biuncialis in North America (Newfoundland) was substantiated. The subsp. uncialis usually lacks squamatic acid, but in the eastern United States a morph referred to as subsp. uncialis does normally contain that acid. However, this morph did not attain taxonomic recognition based on phylogenetic analyses. All the other taxa formerly included in sect. Unciales turned out to belong to other groups of Cladonia, mainly Amaurocraeae, Borya, Divaricatae, and Perviae. The formerly recognized genus Cladina (reindeer lichens) is non-monophyletic, consisting of three groups within Cladonia, making the concept Cladina even nomenclaturally useless. Alternative topology tests rejected the monophyly of C. pseudostellata, section Unciales and Cladina.

Agonimia flabelliformis sp. nov. (Verrucariaceae, Ascomycota) is described as a new species from the Czech Republic, Germany and Great Britain. Except for the distinctive, flabelliform to minutely coralloid thallus the species mostly resembles A. allobata. It differs from other related species of Agonimia in the absence of cortical papillae and in ascospore size. The distinctness of the new species and its placement within the genus Agonimia is supported by analyses of mitochondrial small subunit ribosomal DNA sequences from several samples of the taxon, and from many other representatives of Verrucariales including newly sequenced A. repleta and A. vouauxii. Additionally, ITS rDNA sequence data supports the distinction of A. flabelliformis from A. allobata. However, A. allobata was found to be highly variable and relationships, as well as the monophyly of taxa within Agonimia, are still unresolved and need further investigation.

Lecanora sorediomarginata Rodrigues, Terrón & Elix sp. nov., described as new to science from Portugal, is characterized morphologically by a crustose whitish-grey to greenish thallus developing soralia from small, marginal warts and chemically by the presence of 3,5-dichloro-2′-O-methylnorstenosporic acid [major], 3,5-dichloro-2′-O-methylanziaic acid [minor], 3,5-dichloro-2′-O-methylnordivaricatic acid [minor], 5-chloro-2′-O-methylanziaic acid [trace], atranorin [minor], chloroatranorin [minor], and usnic acid [trace]. It is chemically similar to L. lividocinerea, to which it shows phylogenetic affinities based on ITS rDNA sequence analysis, and to L. sulphurella. Lecanora sorediomarginata is epiphytic on Pinus pinaster and P. pinea, in pine forests on sand dunes along the Portuguese coast.

Trypanosoma (Megatrypanum) theileri from cattle and trypanosomes of other artiodactyls form a clade of closely related species in analyses using ribosomal sequences. Analysis of polymorphic sequences of a larger number of trypanosomes from broader geographical origins is required to evaluate the clustering of isolates as suggested by previous studies. Here, we determined the sequences of the spliced leader (SL) genes of 21 isolates from cattle and 2 from water buffalo from distant regions of Brazil. Analysis of SL gene repeats revealed that the 5S rRNA gene is inserted within the intergenic region. Phylogeographical patterns inferred using SL sequences showed at least 5 major genotypes of T. theileri distributed in 2 strongly divergent lineages. Lineage TthI comprises genotypes IA and IB from buffalo and cattle, respectively, from the Southeast and Central regions, whereas genotype IC is restricted to cattle from the Southern region. Lineage TthII includes cattle genotypes IIA, which is restricted to the North and Northeast, and IIB, found in the Centre, West, North and Northeast. PCR-RFLP of SL genes revealed valuable markers for genotyping T. theileri. The results of this study emphasize the genetic complexity and corroborate the geographical structuring of T. theileri genotypes found in cattle.

Nephroma occultum is a COSEWIC listed cyanolichen of “Special Concern”. It is endemic to old-growth cedar-hemlock forests in western North America. This is the first study to place N. occultum into a phylogenetic framework using nucleotide sequence and secondary structure data. It also addresses the phylogenetic relationship between N. occultum and N. arcticum. Analysis of fungal Internal Transcribed Spacer (ITS) ribosomal DNA (rDNA) produced four major clades. The cyanobacterial transfer RNALeu intron (tRNALeu) from N. occultum was separated from that of N. isidiosum and fell between the Eurasian and North American epiphytic taxa. Examination of length and complexity of the folded secondary structures revealed different trends in the ITS1 and ITS2 rRNA regions. Even though N. occultum is endemic to North America, it seems more closely related to South American temperate rainforest species than to the sympatric N. arcticum. Nephroma occultum is alone among the studied species of Peltigerales in having an exceptionally long ITS1 region, and a different tRNALeu intron DNA sequence of the photobiont suggesting association with a unique genotype of Nostoc. It may be argued that the fitness of N. occultum may be influenced by the complex ITS1 RNA structure, a unique photobiont genotype undergoing a genetic bottleneck, no sexual reproduction to generate variation, and the inability to associate with different photobionts to adapt to changing habitats.

Primers are presented to amplify an intron-containing portion of the actin type I locus from Asterochloris algae. The amount of variation and phylogenetic resolution provided by the ITS rDNA are compared with that from the actin locus. The number of variable and parsimony-informative sites within the actin locus was drastically higher than that of the ITS. Phylogenetic analyses of the ITS resulted in poorly resolved trees with low support values. In contrast, phylogenetic analyses of the actin locus yielded trees with better support and resolution. It is concluded that the actin type I introns will be useful for studies investigating species concepts and population genetics.

The genetic diversity of photobionts in the lichen Protoparmeliopsis muralis was examined to determine the identity of the photobiont and the level of selectivity for the photobiont by the mycobiont. Forty ITS rDNA sequences of photobionts from thirty nine specimens of Protoparmeliopsis muralis have been determined. The photobiont species were identified both by direct comparison with the available sequences and by phylogenetic analysis. The sequences obtained from P. muralis specimens belonged to different Trebouxia clades. The most common photobionts were T. incrustata and an unidentified lineage, here named as “muralis I”. Less common photobionts were T. asymmetrica and T. gigantea. Two unidentified Trebouxia spp. and a photobiont that belonged to the clade that includes T. impressa, T. flava and T. potteri were also found to be associated with P. muralis. Such flexibility has not been reported to date. Moreover, two different photobionts were found in a single specimen. They belonged to the T. gigantea clade and “muralis I” lineage. The low level of selectivity with respect to the photobiont may constitute an important aspect in that Protoparmeliopsis muralis is one of the most successful urban lichens in the world.

The taxonomic position of the Neuropogon group, as inferred from the morphology of representative species of the group and ITS sequences from Usnea antarctica and U. sphacelata, is discussed. Morphological observations revealed that the Neuropogon group does not have annular-pseudocyphellae, which are characteristic of the subgenus Dolichousnea, or a fistulose axis, which is characteristic of the subgenus Eumitria. In addition, the hypothecium of Neuropogon is thin, and the iodine reaction in the axis is negative. These features are consistent with those of the subgenus Usnea. Within the subgenus Usnea, Neuropogon is morphologically distinct from sections Usnea and Ceratinae (i.e. having a sphacelata-type cortex, black pigmentation of the upper thallus and a dark brown apothecial disc). The molecular data suggest that U. antarctica and U. sphacelata are members of the subgenus Usnea and are less closely related to subgenera Dolichousnea and Eumitria. The morphological and molecular phylogenetic analysis suggest that the Neuropogon group is a member of the subgenus Usnea at the level of a section, and the appropriate name for this group is subgenus Usnea section Neuropogon (Nees & Flot.) Mont.