Cox1 Sequence Data Research Articles

Interrelationships of Dictyocaulus spp. in Wild Ruminants with Morphological Description of Dictyocaulus cervi n. sp. (Nematoda: Trichostrongyloidea) from Red Deer, Cervus elaphus.

Lungworms from the genus Dictyocaulus cause parasitic bronchitis (dictyocaulosis) characterized by coughing and severe lung pathology in both domestic and wild ruminants. In this study we investigated the interrelationships of Dictyocaulus spp. from European bison (Bison bonasus L.), roe deer (Capreolus capreolus), and red deer (Cervus elaphus) by nucleotide sequence analysis spanning the 18S RNA gene (small subunit [SSU]) and internal transcribed spacer 2 (ITS2) regions of the ribosomal gene array as well as the mitochondrial cytochrome c oxidase subunit 1 (cox1). Molecular analyses of sequence data obtained partly with novel primers from between 10 and 50 specimens from each host were carried out. Bayesian inference analysis revealed that each host species was infected with different genotypes. Analysis of cox1 sequence data showed a diverse genetic background and high evolutionary potential of Dictyocaulus taxa. Data from lungworms of European bison revealed a distinct genotype of Dictyocaulus viviparus, whereas Dictyocaulus capreolus was only found in roe deer. In contrast, red deer were infected with a taxon with unique SSU, ITS2, and cox1 sequences. These results indicate the occurrence of a novel genotype from red deer, which differs significantly from the National Center for Biotechnology Information reference sequence of Dictyocaulus eckerti. The molecular evidence was consistent with a morphological study with description and imaging of Dictyocaulus cervi n. sp. recovered from red deer. Dictyocaulus cervi n. sp. can be distinguished from D. eckerti on the basis of the absence of cervical papillae, the occurrence of a single ring of 4 symmetrical submedian cephalic papillae, length of the tail in females, morphometry of the female reproductive system, and measurements of gubernacula in males. In conclusion, our findings further strengthen the idea that the genetic complexity and diversity among Dictyocaulus lungworms infecting wildlife ruminants is larger than previously believed and warrants further investigation.

Description of Brooksia lacromae sp. nov. (Tunicata, Thaliacea) from the Adriatic Sea

Brooksia lacromae sp. nov. is described from zooplankton material collected at a marine monitoring station in the South Adriatic in the autumn of 2014. The description of both solitary and aggregate forms is given along with 18S rRNA and mitochondrial cox1 sequence data that provides strong evidence that both forms belong to the same species. The described species is morphologically markedly different from B. rostrata (Traustedt, 1893) and B. berneri van Soest, 1975, previously the only two species in the genus Brooksia. Genetic analysis based on 18S rRNA gene confirmed distinctness of B. lacromae sp. nov. from B. rostrata (1.5% uncorrected pairwise distance). The appendicularian Fritillaria helenae Bückmann, 1924, so far known from the Atlantic only, was found in the same samples as B. lacromae sp. nov. Co-occurrence of B. lacromae sp. nov. with an Atlantic appendicularian suggests an Atlantic or Western Mediterranean origin for this new taxon.

Genetic diversity and population genetics of large lungworms (Dictyocaulus, Nematoda) in wild deer in Hungary.

Dictyocaulus nematode worms live as parasites in the lower airways of ungulates and can cause significant disease in both wild and farmed hosts. This study represents the first population genetic analysis of large lungworms in wildlife. Specifically, we quantify genetic variation in Dictyocaulus lungworms from wild deer (red deer, fallow deer and roe deer) in Hungary, based on mitochondrial cytochrome c oxidase subunit 1 (cox1) sequence data, using population genetic and phylogenetic analyses. The studied Dictyocaulus taxa display considerable genetic diversity. At least one cryptic species and a new parasite–host relationship are revealed by our molecular study. Population genetic analyses for Dictyocaulus eckerti revealed high gene flow amongst weakly structured spatial populations that utilise the three host deer species considered here. Our results suggest that D. eckerti is a widespread generalist parasite in ungulates, with a diverse genetic backround and high evolutionary potential. In contrast, evidence of cryptic genetic structure at regional geographic scales was observed for Dictyocaulus capreolus, which infects just one host species, suggesting it is a specialist within the studied area. D. capreolus displayed lower genetic diversity overall, with only moderate gene flow compared to the closely related D. eckerti. We suggest that the differing vagility and dispersal behaviour of hosts are important contributing factors to the population structure of lungworms, and possibly other nematode parasites with single-host life cycles. Our findings are of relevance for the management of lungworms in deer farms and wild deer populations.

Phylogeny and distribution of the genus Pikea (Gigartinales, Rhodophyta) with special reference to P. yoshizakii from Korea

:Four species have been described in the genus Pikea (Dumontiaceae, Gigartinales): three species from North America and one species from Japan. However, the phylogeny and species delimitation in Pikea remain poorly resolved. Here we provide both rbcL and cox1 sequences for all species of Pikea, including the type of P. pinnata and a paratype of P. robusta. Our data reveal that P. californica, P. pinnata and P. yoshizakii are distinct in both data sets, but P. robusta is synonymous with the earlier-described P. pinnata. Morphological and molecular data show that Pikea from Korea is identical to P. yoshizakii and that the previous report of P. californica in Korea is a misidentification. The genus Pikea is well resolved in the main clade of the Dumontiaceae. This is the first study on the phylogeny of Pikea using rbcL and cox1 sequence data.

Genetic characterization of livestock and human hydatid cyst isolates from northwest Iran, using the mitochondrial cox1 gene sequence.

Cystic echinococcosis (CE), caused by larval stages of the tapeworm Echinococcus granulosus, is one of the most important zoonoses distributed worldwide. Genotype analysis of the parasite isolates from various hosts is required to better understand the host specificity and transmission routes. The aim of this study was to identify the genotypes of E. granulosus isolated from humans and domestic animals from northwest of Iran (Zanjan Province) using the mitochondrial cox1 gene sequence. A total of 86 hydatid cysts including 49 sheep and 28 cattle isolates from the slaughterhouse and nine human isolates from surgical wards of local hospitals were collected. The isolates were subjected to DNA extraction, PCR amplification, and sequence. Eighty-two (95.35%) isolates, including 47 sheep, 26 cattle, and all nine human isolates, were determined as G1 genotype, and the remaining four (4.65%), including two sheep and two cattle isolates, were identified as G3 genotype. From the cox1 sequence data, 13 different haplotypes (10 G1s and three G3s) were detected and named as EGH1-EGH13 (GenBank accession numbers, KP859559-KP859571). EGH1 was the major variant among the haplotypes, and it was identified in 46 (53.49%) isolates (31 sheep, 14 cattle, and one human). Alignment of the partial cox1 sequences showed 12 point mutations including seven (58.3%) synonymous and five (41.7%) non-synonymous substitutions. Based on the results, G1 was the major genotype of E. granulosus in northwest of Iran affecting sheep, cattle, and humans. In addition, a minor group of G3 genotype was found to be circulating in this region.

Disentangling Peronospora on Papaver: phylogenetics, taxonomy, nomenclature and host range of downy mildew of opium poppy (Papaver somniferum) and related species.

Based on sequence data from ITS rDNA, cox1 and cox2, six Peronospora species are recognised as phylogenetically distinct on various Papaver species. The host ranges of the four already described species P. arborescens, P. argemones, P. cristata and P. meconopsidis are clarified. Based on sequence data and morphology, two new species, P. apula and P. somniferi, are described from Papaver apulum and P. somniferum, respectively. The second Peronospora species parasitizing Papaver somniferum, that was only recently recorded as Peronospora cristata from Tasmania, is shown to represent a distinct taxon, P. meconopsidis, originally described from Meconopsis cambrica. It is shown that P. meconopsidis on Papaver somniferum is also present and widespread in Europe and Asia, but has been overlooked due to confusion with P. somniferi and due to less prominent, localized disease symptoms. Oospores are reported for the first time for P. meconopsidis from Asian collections on Papaver somniferum. Morphological descriptions, illustrations and a key are provided for all described Peronospora species on Papaver. cox1 and cox2 sequence data are confirmed as equally good barcoding loci for reliable Peronospora species identification, whereas ITS rDNA does sometimes not resolve species boundaries. Molecular phylogenetic data reveal high host specificity of Peronospora on Papaver, which has the important phytopathological implication that wild Papaver spp. cannot play any role as primary inoculum source for downy mildew epidemics in cultivated opium poppy crops.

Parviphycus albertanoae sp. nov. (Gelidiales, Rhodophyta) from the Mediterranean Sea

:Parviphycus albertanoae sp. nov. was described from the southern Adriatic Sea, Italy on the basis of morphological and molecular data. The new species formed dense tufts at the upper intertidal level on rocky substrata, exposed to intense wave action. Distinctive morphological characters were compressed upright axes closely arising from short stolons, numerous first-order branches and clavate tetrasporangial sori at main and lateral apices. Phylogenetic analysis of mitochondrial cox1 and plastid rbcL sequence data revealed that P. albertanoae was clearly separated from the congeners of the genus, corroborating the morphological distinctness.

Genetic Differentiation among Maruca vitrata F. (Lepidoptera: Crambidae) Populations on Cultivated Cowpea and Wild Host Plants: Implications for Insect Resistance Management and Biological Control Strategies

Maruca vitrata Fabricius (Lepidoptera: Crambidae) is a polyphagous insect pest that feeds on a variety of leguminous plants in the tropics and subtropics. The contribution of host-associated genetic variation on population structure was investigated using analysis of mitochondrial cytochrome oxidase 1 (cox1) sequence and microsatellite marker data from M. vitrata collected from cultivated cowpea (Vigna unguiculata L. Walp.), and alternative host plants Pueraria phaseoloides (Roxb.) Benth. var. javanica (Benth.) Baker, Loncocarpus sericeus (Poir), and Tephrosia candida (Roxb.). Analyses of microsatellite data revealed a significant global FST estimate of 0.05 (P≤0.001). The program STRUCTURE estimated 2 genotypic clusters (co-ancestries) on the four host plants across 3 geographic locations, but little geographic variation was predicted among genotypes from different geographic locations using analysis of molecular variance (AMOVA; among group variation −0.68%) or F-statistics (F ST Loc = −0.01; P = 0.62). These results were corroborated by mitochondrial haplotype data (φSTLoc = 0.05; P = 0.92). In contrast, genotypes obtained from different host plants showed low but significant levels of genetic variation (F ST Host = 0.04; P = 0.01), which accounted for 4.08% of the total genetic variation, but was not congruent with mitochondrial haplotype analyses (φSTHost = 0.06; P = 0.27). Variation among host plants at a location and host plants among locations showed no consistent evidence for M. vitrata population subdivision. These results suggest that host plants do not significantly influence the genetic structure of M. vitrata, and this has implications for biocontrol agent releases as well as insecticide resistance management (IRM) for M. vitrata in West Africa.

Nesticus dimensis new species, a new troglobitic spider from Turkey (Araneae, Nesticidae), with comments on its phylogenetic relationships.

A new troglobitic spider species, Nesticus dimensis n. sp. (felmale male), inhabiting the Dim Cave of Alanya (Antalya Prov., Turkey) is diagnosed and described. The new species belongs to the Eastern Mediterranean Nesticus Group, which includes N. eremita and N. speluncarum as the most common and widespread species along with N. arenstorffi and N. henderickxi. Evolutionary relationships of the taxa belonging to this group of species are discussed on the basis of morphological and molecular data (using cox1, rrnL and H3 gene sequence data).

Molecular species discovery in the diatom Sellaphora and its congruence with mating trials.

Many diatom and other microbial eukaryote morphospecies consist of a variable number of (pseudo)cryptic species, with obvious consequences for such fields as biogeography and community ecology. Here, we investigated the species limits of morphologically similar small-celled strains of the model diatom Sellaphora from the United Kingdom and Australia, using cox1 mitochondrial and rbcL chloroplast gene sequences. Based on cox1 sequence data, the sequenced strains belonged to six closely related lineages, presumably species, of which one corresponds to the previously described S. auldreekie D.G. Mann & S.M. McDonald. Although rbcL displayed less sequence variation, the same six lineages were also recovered in an rbcL phylogeny of the genus. Molecular species discovery was compared to mating trials involving three of the lineages, showing that they were reproductively isolated. Incomplete evidence from a fourth lineage suggested that it too was reproductively isolated. A posteriori examination of light microscope morphology revealed no simple metrics or presence/absence characters that could consistently separate all species of the auldreekie complex, even though some do differ in pole width or stria density. While it is premature to make conclusions about their biogeography, it is obvious that a number of cryptic Sellaphora species thus far undetected in the UK are easily found at several localities in warm-temperate Australia.

Ancyronyx Erichson, 1847 (Coleoptera, Elmidae) from Mindoro, Philippines, with description of the larvae and two new species using DNA sequences for the assignment of the developmental stages

Ancyronyx buhid sp. n. and Ancyronyx tamaraw sp. n. are described based on adults and larvae, matched using their cox1 or cob DNA sequence data. Additional records of Ancyronyx schillhammeri Jäch, 1994 and Ancyronyx minerva Freitag & Jäch, 2007 from Mindoro are listed. The previously unknown larva of Ancyronyx schillhammeri is also described here, aided by cox1 data. The new species and larval stages are described in detail and illustrated by SEM and stacked microscopic images. Keys to the adult and larval Ancyronyx species of Mindoro and an updated checklist of Philippine Ancyronyx species are provided. The usefulness as bioindicators, the phylogenetic relationships and biogeographic aspects affecting the distribution patterns are briefly discussed.

Revision of Australian Matini diving beetles based on morphological and molecular data (Coleoptera, Dytiscidae, Matinae), with description of a new species

Morphological characters and mitochondrial DNA sequence data were used to revise the Australian diving beetles in the genera Allomatus Mouchamps, 1964 and Batrachomatus Clark, 1863. As a result of these studies Allomatus syn. n. is synonymised with Batrachomatus, and Allomatus nannup Watts, 1978 from SW Australia and Allomatus wilsoni Mouchamps, 1964 from SE Victoria are transferred to Batrachomatus. The four Australian Matini species knownso far are re-described, and Batrachomatus larsoni sp. n. from the Windsor Tableland in NE Queensland is described. After more than 40 years Batrachomatus wilsoni has been re-discovered in two rivers in Victoria. We delineate the species using traditionally employed morphological structures such as in the male genitalia and body size, shape and colour pattern, as well as mitochondrial cox1 sequence data for 20 individuals. Important species characters (median lobes, parameres and colour patterns) were illustrated. We provide an identification key and outline distribution and habitat preferences of each species. All Australian Matini are lotic, inhabiting permanent and intermittent streams, creeks and rivers.

Host specificity of parasitic gastropods of the genusAnnulobalcisHabe, 1965 (Mollusca, Gastropoda, Eulimidae) from crinoids in Vietnam, with descriptions of four new species

ABSTRACT Parasitic gastropods of the genus Annulobalcis Habe, 1965 (family Eulimidae), associated with the crinoids (comatulids) are common in Nhatrang Bay (Southern Vietnam). Morphological examination of Annulobalcis specimens, collected in this area revealed four distinct forms, significantly different also in host specificity. Mitochondrial cox1 sequence data have shown these forms to comprise four distinct species, their relationships are discussed. As a result of morphological and molecular studies, four new species of the genus Annulobalcis are described: A. albus n. sp., A. wareni n. sp., A. maculatus n. sp., and A. vinarius n. sp. The three former species appeared to be strictly species specific in their choice of host (parasitizing a single host species each), while the latter was found on a number of hosts, although mostly on a single species. Speciation in relation to host specificity of Annulobalcis is discussed.

Genetic structure and distribution of Gelidium elegans (Gelidiales, Rhodophyta) in Korea based on mitochondrial cox1 sequence data

Gelidium elegans Kützing is commonly found in Korea, China, and Japan, and is the economically most important agarophyte in the northwest Pacific. To assess the genetic structure of the Korean species, we analyzed 1200 base pairs of the mitochondrial cox1 gene from 272 individuals collected from 36 locations. A total of 34 haplotypes were found, most of which were unique, including 27 (79%) ‘private’ haplotypes. The nucleotide and haplotype diversities of cox1 within G. elegans were 0.711±0.028 (H) and 0.00736±0.00038 (π), respectively. The distribution of cox1 haplotypes, pairwise FST values, results of neutrality tests, AMOVA, and mismatch distribution revealed the existence of a deep genetic break between central Pacific Japan and all the other locations, corresponding to the surface seawater current patterns as well as the genetic signature of potential demographic expansion.

Two novel and potentially endemic species of Phytophthora associated with episodic dieback of Kwongan vegetation in the south‐west of Western Australia

Two novel homothallic species of Phytophthora causing dieback of Kwongan vegetation in south‐west Western Australia are described here as Phytophthora arenaria sp. nov. and Phytophthora constricta sp. nov. DNA sequencing of the ITS rDNA and cox1 gene confirmed that P. arenaria and P. constricta are unique species residing in ITS clades 4 and 9, respectively. Phytophthora arenaria has been isolated from vegetation occurring on the northern sandplains which are warmer and drier than the southern sandplains from which P. constricta has been predominantly isolated, and both species appear morphologically and physiologically well adapted to the ecosystems in which they occur. Both species have been associated mainly with dead and dying Banksia species and the pathogenicity of both P. arenaria and P. constricta to Banksia attenuata was confirmed in this study. The combination of unique DNA sequences, including considerable variation in cox1 sequence data, thick oospore walls and physiological characteristics that appear to be adaptations favouring survival in the harsh Kwongan ecosystem suggest that these species may be endemic to Western Australia.

A simultaneous journal / wiki publication and dissemination of a new species description: Neobidessodes darwiniensis sp. n. from northern Australia (Coleoptera, Dytiscidae, Bidessini)

Here, we describe a new Australian species in journal format and simultaneously open the description in a wiki format on the www.species-id.net. The wiki format will always link to the fixed original journal description of the taxon, however it permits future edits and additions to species' taxonomy and biology. The diving beetle Neobidessodes darwiniensis sp. n. (Coleoptera: Dytiscidae, Bidessini) is described based on a single female, collected in a rest pool of the Harriet Creek in the Darwin Area, Northern Territory. Within Neobidessodes the new species is well characterized by its elongate oval body with rounded sides, short and stout segments of antennae, length of body and dorsal surface coloration. In addition to external morphology, we used mitochondrial cox1 sequence data to support generic assignment and to delineate the new species from other Australian Bidessini including all other known Neobidessodes. Illustrations based on digital images are provided here and as online resources. A modified key is provided. Altogether ten species of the genus are now known worldwide, nine from Australia and one from New Guinea.

Reconciling phylogeography and ecological niche models for New Zealand beetles: Looking beyond glacial refugia

Mitochondrial DNA (cox1) sequence data and recently developed coalescent phylogeography models were used to construct geo-spatial histories for the New Zealand fungus beetles Epistranus lawsoni and Pristoderus bakewelli (Zopheridae). These methods utilize continuous-time Markov chains and Bayesian stochastic search variable selection incorporated in BEAST to identify historical dispersal patterns via ancestral state reconstruction. Ecological niche models (ENMs) were incorporated to reconstruct the potential geographic distribution of each species during the Last Glacial Maximum (LGM). Coalescent analyses suggest a North Island origin for E. lawsoni, with gene flow predominately north–south between adjacent regions. ENMs for E. lawsoni indicated glacial refugia in coastal regions of both main islands, consistent with phylogenetic patterns but at odds with the coalescent dates, which implicate much older topographic events. Dispersal matrices revealed patterns of gene flow consistent with projected refugia, suggesting long-term South Island survival with population vicariance around the Southern Alps. Phylogeographic relationships are more ambiguous for P. bakewelli, although long-term survival on both main islands is evident. Divergence dates for both species are consistent with the topographic evolution of New Zealand over the last 10Ma, whereas the signature of the LGM is less apparent in the time-scaled phylogeny.

Mitochondrial cox1 sequence data reliably uncover patterns of insect diversity but suffer from high lineage-idiosyncratic error rates.

BackgroundThe demand for scientific biodiversity data is increasing, but taxonomic expertise is often limited or not available. DNA sequencing is a potential remedy to overcome this taxonomic impediment. Mitochondrial DNA is most commonly used, e.g., for species identification (“DNA barcoding”). Here, we present the first study in arthropods based on a near-complete species sampling of a family-level taxon from the entire Australian region. We aimed to assess how reliably mtDNA data can capture species diversity when many sister species pairs are included. Then, we contrasted phylogenetic subsampling with the hitherto more commonly applied geographical subsampling, where sister species are not necessarily captured.Methodology/Principal FindingsWe sequenced 800 bp cox1 for 1,439 individuals including 260 Australian species (78% species coverage). We used clustering with thresholds of 1 to 10% and general mixed Yule Coalescent (GMYC) analysis for the estimation of species richness. The performance metrics used were taxonomic accuracy and agreement between the morphological and molecular species richness estimation. Clustering (at the 3% level) and GMYC reliably estimated species diversity for single or multiple geographic regions, with an error for larger clades of lower than 10%, thus outperforming parataxonomy. However, the rates of error were higher for some individual genera, with values of up to 45% when very recent species formed nonmonophyletic clusters. Taxonomic accuracy was always lower, with error rates above 20% and a larger variation at the genus level (0 to 70%). Sørensen similarity indices calculated for morphospecies, 3% clusters and GMYC entities for different pairs of localities was consistent among methods and showed expected decrease over distance.Conclusion/Significance Cox1 sequence data are a powerful tool for large-scale species richness estimation, with a great potential for use in ecology and β-diversity studies and for setting conservation priorities. However, error rates can be high in individual lineages.

Parallel habitat‐driven differences in the phylogeographical structure of two independent lineages of Mediterranean saline water beetles

It has been hypothesized that species living in small lentic water bodies, because of the short-term geological persistence of their habitat, should show higher dispersal ability, with increased gene flow among populations and a less pronounced phylogeographical structure. Conversely, lotic species, living in more geologically stable habitats, should show reduced dispersal and an increased phylogeographical structure at the same geographical scales. In this work we tested the influence of habitat type in two groups of aquatic Coleoptera (Nebrioporus ceresyi and Ochthebius notabilis groups, families Dytiscidae and Hydraenidae respectively), each of them with closely related species typical of lotic and lentic saline Western Mediterranean water bodies. We used mitochondrial cox1 sequence data of 453 specimens of 77 populations through the range of nine species to compare a lotic vs. a lentic lineage in each of the two groups. Despite the differences in biology (predators vs. detritivorous) and evolutionary history, in both lotic lineages there was a higher proportion of nucleotide diversity among than within groups of populations, and a faster rate of accumulation of haplotype diversity (as measured by rarefaction curves) than in the lentic lineages. Similarly, lotic lineages had a higher absolute phylogenetic diversity, more remarkable considering their smaller absolute geographical ranges. By comparing closely related species, we were able to show the effect of contrasting habitat preferences in two different groups, in agreement with predictions derived from habitat stability.

Taxonomic revision of Gracilaria “verrucosa” from the Russian Far East based on morphological and molecular data

Abstract Gracilaria “verrucosa” is now regarded an invalid name, with G. gracilis being used in recent studies of the genus from the Russian coast of the East Sea (Sea of Japan). This has created nomenclatural confusion for members of the genus in this region. Here we revise the taxonomy of G. “verrucosa” from Peter the Great Bay (East Sea, Russia) based on morpho-anatomical characters and comparisons of nuclear small subunit rDNA, plastid rbcL and mitochondrial cox1 sequence data. No differences were found between sequences for attached and unattached forms of G. “verrucosa”. Molecular data also indicate that G. “verrucosa” from Peter the Great Bay is conspecific with Gracilaria vermiculophylla from the northwestern Pacific, and the Russian population is closely related to Korean-Japanese populations from the East Sea rather than with populations on the Pacific coast of Japan.