Expression of Hairpin-Enriched Mitochondrial DNA in Two Hairworm Species (Nematomorpha).

Nematomorpha (hairworms) is a phylum of parasitic ecdysozoans, best known for infecting arthropods and guiding their hosts toward water, where the parasite can complete its life cycle. Over 350 species of nematomorphs have been described, yet molecular data for the group remain scarce. The few available mitochondrial genomes of nematomorphs are enriched with long inverted repeats, which are embedded in the coding sequences of their genes-a remarkably unusual feature exclusive to this phylum. Here, we obtain and annotate the repeats in the mitochondrial genome of another nematomorph species-Parachordodes pustulosus. Using genomic and transcriptomic libraries, we investigate the impact of inverted repeats on the read coverage of the mitochondrial genome. Pronounced drops in the read coverage coincide with regions containing long inverted repeats, denoting the 'blind spots' of short-fragment sequencing libraries. Phylogenetic inference with the novel data reveals multiple disagreements between the traditional system of Nematomorpha and molecular data, rendering several genera paraphyletic, including Parachordodes.

Distribution of Bacterial Endosymbionts of the Cardinium Clade in Plant-Parasitic Nematodes.

Bacteria of the genus "Candidatus Cardinium" and related organisms composing the Cardinium clade are intracellular endosymbionts frequently occurring in several arthropod groups, freshwater mussels and plant-parasitic nematodes. Phylogenetic analyses based on two gene sequences (16S rRNA and gyrB) showed that the Cardinium clade comprised at least five groups: A, B, C, D and E. In this study, a screening of 142 samples of plant-parasitic nematodes belonging to 93 species from 12 families and two orders using PCR with specific primers and sequencing, revealed bacteria of Cardinium clade in 14 nematode samples belonging to 12 species of cyst nematodes of the family Heteroderidae. Furthermore, in this study, the genome of the Cardinium cHhum from the hop cyst nematode, Heterodera humuli, was also amplified, sequenced and analyzed. The comparisons of the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values for the strain Cardinium cHhum with regard to related organisms with available genomes, combined with the data on 16S rRNA and gyrB gene sequence identities, showed that this strain represents a new candidate species within the genus "Candidatus Paenicardinium". The phylogenetic position of endosymbionts of the Cardinium clade detected in nematode hosts was also compared to known representatives of this clade from other metazoans. Phylogenetic reconstructions based on analysis of 16S rRNA, gyrB, sufB, gloEL, fusA, infB genes and genomes and estimates of genetic distances both indicate that the endosymbiont of the root-lesion nematode Pratylenchus penetrans represented a separate lineage and is designated herein as a new group F. The phylogenetic analysis also confirmed that endosymbionts of ostracods represent the novel group G. Evolutionary relationships of bacterial endosymbionts of the Cardinium clade within invertebrates are presented and discussed.

The re-description of Synoecnemahirsutum Timm, 1959 (Synoecneminae, Ungellidae, Drilonematoidea) from a pheretimoid earthworm in Vietnam with the analysis of its phylogenetic relationships.

Synoecnemahirsutum Timm, 1959 (Ungellidae, Drilonematoidea), found in the body cavity of the pheretimoid earthworm at the border of Laos and Vietnam, was re-described and illustrated. The mitochondrial genome of S.hirsutum obtained with Illumina HiSeq sequencing is the first annotated mitochondrial genome as a representative of the superfamily Drilonematoidea. The phylogeny inferred from the analysis of 12 mitochondrial genes has shown some similarity of S.hirsutum with a cephalobid Acrobeloidesvarius.

Diversity and host associations of Myrsidea chewing lice (Phthiraptera: Menoponidae) in the tropical rainforest of Malaysian Borneo.

The tropical rainforests of Sundaland are a global biodiversity hotspot increasingly threatened by human activities. While parasitic insects are an important component of the ecosystem, their diversity and parasite-host relations are poorly understood in the tropics. We investigated parasites of passerine birds, the chewing lice of the speciose genus MyrsideaWaterston, 1915 (Phthiraptera: Menoponidae) in a natural rainforest community of Malaysian Borneo. Based on morphology, we registered 10 species of lice from 14 bird species of six different host families. This indicated a high degree of host specificity and that the complexity of the system could be underestimated with the potential for cryptic lineages/species to be present. We tested the species boundaries by combining morphological, genetic and host speciation diversity. The phylogenetic relationships of lice were investigated by analyzing the partial mitochondrial cytochrome oxidase I (COI) and the nuclear elongation factor alpha (EF-1α) genes sequences of the species. This revealed a monophyletic group of Myrsidea lineages from seven hosts of the avian family Pycnonotidae, one host of Timaliidae and one host of Pellorneidae. However, species delimitation methods supported the species boundaries hypothesized by morphological studies and confirmed that four species of Myrsidea are not single host specific. Cophylogenetic analysis by both distance-based test ParaFit and event-based method Jane confirmed overall congruence between the phylogenies of Myrsidea and their hosts. In total we recorded three cospeciation events for 14 host-parasite associations. However only one host-parasite link (M. carmenae and their hosts Terpsiphone affinis and Hypothymis azurea) was significant after the multiple testing correction in ParaFit. Four new species are described: Myrsidea carmenae sp.n. ex Hypothymis azurea and Terpsiphone affinis, Myrsidea franciscae sp.n. ex Rhipidura javanica, Myrsidea ramoni sp.n. ex Copsychus malabaricus stricklandii, and Myrsidea victoriae sp.n. ex. Turdinus sepiarius.

Review of the millipede genus Orthomorpha Bollman, 1893 (Diplopoda, Polydesmida, Paradoxosomatidae) in Vietnam, with several new records and descriptions of two new species.

The genus Orthomorpha is shown to currently be represented in Vietnam by ten species or varieties, including new records of O. arboricola (Attems, 1937), O. coarctata (de Saussure, 1860), O. rotundicollis (Attems, 1937) and O. scabra Jeekel, 1964, and two new species, O. caramel sp. nov. and O. vietnamica sp. nov. A key to all eight Orthomorpha species and two varieties known to occur in Vietnam is provided. Although the morphological characters that have been traditionally used for Orthomorpha taxonomy are here considered superior to molecular ones, molecular-based phylogenetic relationships and taxon assignments within the tribe Orthomorphini are provisionally analyzed using fragments of the cytochrome c oxidase subunit I (COI) mitochondrial gene. The preferred phylograms, both rooted and unrooted, demonstrate the monophyly of the tribe Orthomorphini, but due to the special, uncertain or even controversial position of O. coarctata, which occurs closer to the genera Antheromorpha and Hylomus, the genus Orthomorpha in current usage appears to be polyphyletic. However, if O. coarctata is to be treated within the monotypic genus Asiomorpha, the monophyly of Orthomorpha becomes manifest. On the other hand, a cautious approach is followed to avoid descriptions of suspicious new taxa/species. Thus, solely because the average genetic distance between O. rodundicollis subrotundicollis var. nov. and O. rodundicollis, as well as that between O. scabra grandis var. nov. and O. scabra, are both found to be negligibly small, the statuses of the sympatric and closest yet morphologically different varieties are treated only as such, i.e., infrasubspecific categories. The apparent discord observed between morphological and molecular data is obviously due to only partial and single-gene topologies used, possibly also to hybridization already known to occur in some closely related and sympatric paradoxosomatid species or even genera.

Coding palindromes in mitochondrial genes of Nematomorpha.

Inverted repeats are common DNA elements, but they rarely overlap with protein-coding sequences due to the ensuing conflict with the structure and function of the encoded protein. We discovered numerous perfect inverted repeats of considerable length (up to 284 bp) embedded within the protein-coding genes in mitochondrial genomes of four Nematomorpha species. Strikingly, both arms of the inverted repeats encode conserved regions of the amino acid sequence. We confirmed enzymatic activity of the respiratory complex I encoded by inverted repeat-containing genes. The nucleotide composition of inverted repeats suggests strong selection at the amino acid level in these regions. We conclude that the inverted repeat-containing genes are transcribed and translated into functional proteins. The survey of available mitochondrial genomes reveals that several other organisms possess similar albeit shorter embedded repeats. Mitochondrial genomes of Nematomorpha demonstrate an extraordinary evolutionary compromise where protein function and stringent secondary structure elements within the coding regions are preserved simultaneously.

Captive individuals of endangered Philippine raptors maintain native feather mites (Acariformes: Pterolichoidea) species.

Endangered species of hosts are coupled with endangered species of parasites, which share the risk of co-extinction. Conservation efforts sometimes include breeding of rare species in captivity. Data on parasites of captive populations of endangered species is scarce and the ability of small numbers of captive host individuals to support the biodiversity of native parasites is limited. Examination of ectosymbionts of the critically endangered Philippine eagles and the endangered Mindanao Hawk-Eagle kept at the Philippine Eagle Center, Philippines, revealed three feather mite species despite regular treatment with insecticide powder. No other ectosymbiont taxa were detected. Studies in morphology and molecular phylogeny of these feather mites based on mitochondrial and nuclear DNA markers indicate that species found were typical for Accipitridae. Three new pterolichoid feather mite species (Acari: Pterolichoidea) were described from two species of eagles (Accipitriformes: Accipitridae) endemic to the Philippines: Hieracolichus philippinensis sp. n. (Gabuciniidae) and Pseudalloptinus pithecophagae sp. n. (Pterolichidae) from the Great Philippine Eagle Pithecophaga jefferyi Ogilvie-Grant, 1896, and Pseudogabucinia nisaeti sp. n. (Kramerellidae) from the Mindanao Hawk-Eagle Nisaetus pinskeri Gould, 1863. The presence of H. philippinensis on P. jefferyi supports the recent finding that the Great Philippine Eagle belongs to the lineage of serpent eagles (Circaetinae) rather than to the Harpy and other eagles.