Patterns of habitat affinity and Austral/Holarctic parallelism in dictynoid spiders (Araneae:Entelegynae)

2010 ◽  
Vol 24 (3) ◽  
pp. 238 ◽  
Author(s):  
Joseph C. Spagna ◽  
Sarah C. Crews ◽  
Rosemary G. Gillespie
Keyword(s):  
18S Rrna ◽  
Single Gene ◽  
Histone H3 ◽  
Rrna Gene ◽  
28S Rrna ◽  
Gene Trees ◽  
Terrestrial Environment ◽  
Alkaline Salt ◽  
Doublet Model ◽  
Combined Data

The ability to survive in a terrestrial environment was a major evolutionary hurdle for animals that, once passed, allowed the diversification of most arthropod and vertebrate lineages. Return to a truly aquatic lifestyle has occurred only rarely among terrestrial lineages, and is generally associated with modifications of the respiratory system to conserve oxygen and allow extended periods of apnea. Among chelicerates, in particular spiders, where the circulatory system also serves as a hydrostatic skeleton, very few taxa have exploited aquatic environments, though these environments are abundant and range from freshwater ponds to the marine intertidal and relictual (salt) lakes. The traditional systematic positions of the taxa inhabiting these environments are controversial. Partitioned Bayesian analysis using a doublet model for stems in the nearly complete 18S rRNA gene (~1800 nt) and in the D2 and D3 regions of the 28S rRNA gene (~690 nt), and standard models for loops and full protein-coding histone H3 (349 nt) partitions (totalling 3133 bp when aligned) of dictynoid spiders and related lineages revealed that the only truly aquatic spider species, Argyroneta aquatica (Clerck, 1767) (Cybaeidae Banks, 1892), belongs in a clade containing other taxa with unusual habitat affinities related to an aquatic existence, including occupation of semi-aquatic (intertidal) areas (Desidae Pocock, 1985: Paratheuma spp.) and highly alkaline salt-crusts (Dictynidae O. Pickard-Cambridge, 1871: Saltonia incerta (Banks, 1898)). In a contrasting pattern, other spiders that also occupy intertidal zones, including some other members of the family Desidae (Desis spp., Badumna longinqua (L. Koch, 1867)), are an independently derived clade found primarily in the southern hemisphere. Use of the doublet model reduced some branch-support values in the single-gene trees for rRNA data, but resulted in a robust combined-data phylogeny from 18S rRNA, 28S rRNA, and histone H3. This combination of results – reduction in support in single-gene trees and gain in support in combined-data trees –is consistent with use of the doublet model reducing problematic signal from non-independent base pairs in individual data partitions, resulting in improved resolution in the combined-data analyses.

scholarly journals Evolutionary relationships among Massospora spp. (Entomophthorales), obligate pathogens of cicadas

2019 ◽  
Author(s):  
Angie M. Macias ◽  
David M. Geiser ◽  
Jason E. Stajich ◽  
Piotr Łukasik ◽  
Claudio Veloso ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Single Gene ◽  
Elongation Factor ◽  
Phylogenetic Inference ◽  
Monophyletic Group ◽  
Evolutionary Relationships ◽  
Rrna Gene ◽  
28S Rrna ◽  
Gene Trees ◽  
Morphological Studies

AbstractThe fungal genus Massospora (Zoopagomycota: Entomophthorales) includes more than a dozen obligate, sexually transmissible pathogenic species that infect cicadas (Hemiptera) worldwide. At least two species are known to produce psychoactive compounds during infection, which has garnered considerable interest for this enigmatic genus. As with many Entomophthorales, the evolutionary relationships and host associations of Massospora spp. are not well understood. The acquisition of M. diceroproctae from Arizona, M. tettigatis from Chile, and M. platypediae from California and Colorado provided an opportunity to conduct molecular phylogenetic analyses and morphological studies to investigate if these fungi represent a monophyletic group and delimit species boundaries. In a three-locus phylogenetic analysis including the D1–D2 domains of the nuclear 28S rRNA gene (28S), elongation factor 1 alpha-like (EFL), and beta-tubulin (BTUB), Massospora was resolved in a strongly supported monophyletic group containing four well-supported genealogically exclusive lineages, based on two of three methods of phylogenetic inference. There was incongruence among the single-gene trees: two methods of phylogenetic inference recovered trees with either the same topology as the 3-gene concatenated tree (EFL), or a basal polytomy (28S, BTUB). Massospora levispora and M. platypediae isolates formed a single lineage in all analyses and are synonymized here as M. levispora. Massospora diceroproctae was sister to M. cicadina in all three single-gene trees and on an extremely long branch relative to the other Massospora, and even the outgroup taxa, which may reflect an accelerated rate of molecular evolution and/or incomplete taxa sampling. The results of the morphological study presented here indicate that spore measurements may not be phylogenetically or diagnostically informative. Despite recent advances in understanding the ecology of Massospora, much about its host range and diversity remains unexplored. The emerging phylogenetic framework can provide a foundation for exploring co-evolutionary relationships with cicada hosts and the evolution of behavior-altering compounds.

The molecular systematics of blowflies and screwworm flies (Diptera: Calliphoridae) using 28S rRNA, COX1 and EF-1α: insights into the evolution of dipteran parasitism

Parasitology ◽  
2011 ◽  
Vol 138 (13) ◽  
pp. 1760-1777 ◽  
Author(s):  
LAURA M. McDONAGH ◽  
JAMIE R. STEVENS
Keyword(s):  
Sequence Data ◽  
Single Gene ◽  
Nuclear Gene ◽  
Evolutionary Status ◽  
28S Rrna ◽  
Gene Trees ◽  
Data Set ◽  
Protein Coding ◽  
Nucleotide Sequence Data ◽  
The Family

SUMMARYThe Calliphoridae include some of the most economically significant myiasis-causing flies in the world – blowflies and screwworm flies – with many being notorious for their parasitism of livestock. However, despite more than 50 years of research, key taxonomic relationships within the family remain unresolved. This study utilizes nucleotide sequence data from the protein-coding genes COX1 (mitochondrial) and EF1α (nuclear), and the 28S rRNA (nuclear) gene, from 57 blowfly taxa to improve resolution of key evolutionary relationships within the family Calliphoridae. Bayesian phylogenetic inference was carried out for each single-gene data set, demonstrating significant topological difference between the three gene trees. Nevertheless, all gene trees supported a Calliphorinae-Luciliinae subfamily sister-lineage, with respect to Chrysomyinae. In addition, this study also elucidates the taxonomic and evolutionary status of several less well-studied groups, including the genus Bengalia (either within Calliphoridae or as a separate sister-family), genus Onesia (as a sister-genera to, or sub-genera within, Calliphora), genus Dyscritomyia and Lucilia bufonivora, a specialised parasite of frogs and toads. The occurrence of cross-species hybridisation within Calliphoridae is also further explored, focusing on the two economically significant species Lucilia cuprina and Lucilia sericata. In summary, this study represents the most comprehensive molecular phylogenetic analysis of family Calliphoridae undertaken to date.

Morphological and molecular characterization of Mermisnigrescens Dujardin, (Nematoda: Mermithidae) parasitizing the introduced European earwig (Dermaptera: Forficulidae) in New Zealand

2014 ◽  
Vol 89 (3) ◽  
pp. 267-276 ◽  
Author(s):  
B. Presswell ◽  
S. Evans ◽  
R. Poulin ◽  
F. Jorge
Keyword(s):  
New Zealand ◽  
18S Rrna ◽  
Sequence Data ◽  
18S Rrna Gene ◽  
Parasitic Nematodes ◽  
Rrna Gene ◽  
28S Rrna ◽  
Forficula Auricularia ◽  
Adult Females ◽  
European Earwig

AbstractParasitic nematodes of the family Mermithidae were found to be infecting the introduced European earwig Forficula auricularia (Dermaptera: Forficulidae) in Dunedin, South Island, New Zealand. Adult females were later collected from various garden plants while depositing eggs. These mermithid specimens were identified morphologically as Mermis nigrescens Dujardin, 1842. A genetic distance of 0.7% between these specimens and a M. nigrescens isolate from Canada (18S rRNA gene), suggests that they have diverged genetically, but there are currently no available comparable sequences for the European M. nigrescens. Two additional nuclear fragments were also amplified, the 28S rRNA and the ribosomal DNA first internal transcribed spacer (ITS1), providing a basis for future studies. Bearing in mind the morphological similarity with other reported M. nigrescens and the lack of sequence data from other parts of the world, we retain the name M.nigrescens, and suggest that the species may be found to represent a complex of cryptic species when more worldwide data are available. Herein, we present a brief description of the post-parasitic worms and adult females, along with an inferred phylogeny using 18S rRNA gene sequences.

scholarly journals Молекулярно-генетическая изменчивость генов 18S-rRNA и 28S-rRNA у цестод рода Bothriocephalus Rud., 1808 (Cestoda: Bothriocephalidea) из рыб Чёрного моря

2020 ◽  
Author(s):  
Yu.V. Slynko ◽  
T.A. Polyakova ◽  
E.E. Slynko
Keyword(s):  
Black Sea ◽  
18S Rrna ◽  
Molecular Genetic Analysis ◽  
The Body ◽  
The Black Sea ◽  
Rrna Gene ◽  
28S Rrna ◽  
Crimean Peninsula ◽  
Nucleotide Variability ◽  
Scorpaena Porcus

Проведён молекулярно-генетический анализ фрагментов двух генов 18S-rRNA (длиной 568 п.н.) и 28S-rRNA (длиной 312 п.н.) цестод рода Bothriocephalus Rud., 1808, паразитирующих у скорпены Scorpaena porcus (Linnaeus, 1758) и у черноморской камбалы Scophthalmus maeoticus (Pallas, 1814), обитающих в Чёрном море. Материал был собран в северной части Чёрного моря возле побережья Крымского полуострова. Пробы тела паразитов фиксировали в 96 этаноле. В результате, как по каждому гену в отдельности, так и при их объединении установлено, что образец, извлечённый из скорпены (деп. в NCBI MH011407 18S-rRNA и MH000375 28S-rRNA), надёжно идентифицируется, как относящийся к кладе, содержащей B. timii, B. scorpii и B. australis, р-расстояние между нашим образцом и другими видами этой группы не превышает 1,6. Остальные три образца MH011408, MH011409, MH011410 (для гена 18s-rRNA) и MH000376 (для гена 28s-rRNA) сформировали отдельную кладу, состоящую из двух субклад: одна включает образцы МН011409 и МН011410, другая образец МН011408 (указаны только регистрационные номера для гена 18s-rRNA). Следует также отметить, что виды Bothriocephalus timii и Bothriocephalus scorpii дистанцированы всего лишь на 0,5, а Bothriocephalus timii и Bothriocephalus australis на 0,6. Гаплотипы вида Bothriocephalus claviceps составили внешнюю группу, р-расстояние от которого всех, как наших образцов, так и рассматриваемых видов комплекса scorpio , не опускалось ниже 26,3. Вместе с тем, дистанцированность объединённых гаплотипов цестод из черноморской камбалы на уровне 45 р-расстояний, а также значения бутстрепа позволяют полагать их близнецовыми видами (или подвидами) в пределах рода, по аналогии с генами мтДНК. В результате анализа нуклеотидной изменчивости данных фрагментов генов подтверждена принадлежность рассматриваемых экземпляров к роду Bothriocephalus, и они идентифицированы как виды, входящие в комплекс видов Bothriocephalus scorpii .Molecular genetic analysis of fragments of the two genes 18S-rRNA (568 bps long) and 28S-rRNA (312 bps long) cestodes of the genus Bothriocephalus Rud., 1808, parasitizing in Scorpaena porcus (Linnaeus, 1758) and at the Black Sea flounder Scophthalmus maeoticus (Pallas, 1814) living in the Black Sea. Material was collected in the northern Black Sea off the coast of the Crimean Peninsula. Samples of the body of parasites were fixed in 96 ethanol. As a result it was established both for each gene individually and when combining them that the sample extracted from scorpion ( in NCBI MH011407 18S-rRNA and MH000375 28S-rRNA) is reliably identified as referring to clade containing B. timii, B. scorpii and B. australis, the p-distance between our sample and other species of this group does not exceed 1.6. The remaining three samples MH011408, MH011409, MH011410 (for the 18s-rRNA gene) and MH000376 (for the 28s-rRNA gene) formed a separate clade which consists of two subclades: one includes samples MH011409 and MH011410 the other sample MH011408 (only registration numbers are indicated for MH011408 gene 18s-rRNA). It should also be noted that the species Bothriocephalus timii and Bothriocephalus scorpii are only 0.5 apart while Bothriocephalus timii and Bothriocephalus australis are 0.6 apart. Haplotypes of the species Bothriocephalus claviceps constituted an external group, the p-distance from which of all both our samples and the species of the scorpio complex under consideration did not fall below 26.3. At the same time the distance between the combined haplotypes of cestodes from the Black Sea flounder at the level of 45 p-distances as well as bootstrap values allow us to consider them to be twin species (or subspecies) within the genus by analogy with mtDNA genes. An analysis of the nucleotide variability of these gene fragments confirmed the affiliation of the examined species to the genus Bothriocephalus and they were identified as species forming part of the complex of species Bothriocephalus scorpii.

Processing of truncated mouse or human rRNA transcribed from ribosomal minigenes transfected into mouse cells

1994 ◽  
Vol 14 (6) ◽  
pp. 4044-4056
Author(s):  
K V Hadjiolova ◽  
A Normann ◽  
J Cavaillé ◽  
E Soupène ◽  
S Mazan ◽  
...  
Keyword(s):  
18S Rrna ◽  
Processing System ◽  
Rrna Genes ◽  
In Vitro Assays ◽  
Rrna Gene ◽  
28S Rrna ◽  
Rrna Processing ◽  
Mouse Cells

The processing of pre-rRNA in eukaryotic cells involves a complex pattern of nucleolytic reactions taking place in preribosomes with the participation of several nonribosomal proteins and small nuclear RNAs. The mechanism of these reactions remains largely unknown, mainly because of the absence of faithful in vitro assays for most processing steps. We have developed a pre-rRNA processing system using the transient expression of ribosomal minigenes transfected into cultured mouse cells. Truncated mouse or human rRNA genes are faithfully transcribed under the control of mouse promoter and terminator signals. The fate of these transcripts is analyzed by the use of reporter sequences flanking the rRNA gene inserts. Both mouse and human transcripts, containing the 3' end of 18S rRNA-encoding DNA (rDNA), internal transcribed spacer (ITS) 1, 5.8S rDNA, ITS 2, and the 5' end of 28S rDNA, are processed predominantly to molecules coterminal with the natural mature rRNAs plus minor products corresponding to cleavages within ITS 1 and ITS 2. To delineate cis-acting signals in pre-rRNA processing, we studied series of more truncated human-mouse minigenes. A faithful processing at the 18S rRNA/ITS 1 junction can be observed with transcripts containing only the 60 3'-terminal nucleotides of 18S rRNA and the 533 proximal nucleotides of ITS 1. However, further truncation of 18S rRNA (to 8 nucleotides) or of ITS 1 (to 48 nucleotides) abolishes the cleavage of the transcript. Processing at the ITS 2/28S rRNA junction is observed with truncated transcripts lacking the 5.8S rRNA plus a major part of ITS 2 and containing only 502 nucleotides of 28S rRNA. However, further truncation of the 28S rRNA segment to 217 nucleotides abolishes processing. Minigene transcripts containing most internal sequences of either ITS 1 or ITS 2, but devoid of ITS/mature rRNA junctions, are not processed, suggesting that the cleavages in vivo within either ITS segment are dependent on the presence in cis of mature rRNA sequences. These results show that the major cis signals for pre-rRNA processing at the 18S rRNA/ITS 1 or the ITS2/28S rRNA junction involve solely a limited critical length of the respective mature rRNA and adjacent spacer sequences.

Molecular characterisation of two known species of Paratylenchus Micoletzky, 1922 from Iran with notes on the validity of Paratylenchus audriellus Brown, 1959

Nematology ◽  
2016 ◽  
Vol 18 (5) ◽  
pp. 591-604 ◽  
Author(s):  
Mehrab Esmaeili ◽  
Ramin Heydari ◽  
Pablo Castillo ◽  
Mozhgan Ziaie Bidhendi ◽  
Juan E. Palomares-Rius
Keyword(s):  
18S Rrna ◽  
First Record ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
28S Rrna ◽  
Molecular Characterisation ◽  
Female Tail ◽  
Valid Taxon ◽  
Two Populations ◽  
Partial 18S

During a survey on pin nematodes in western Iran, two populations of Paratylenchus audriellus and Paratylenchus tenuicaudatus were collected and subsequently analysed morphologically and molecularly. Paratylenchus audriellus is characterised by the long stylet (48-61 μm) and the typical female tail with a characteristic claw-like process with sharply pointed terminus. To our knowledge, the Iranian population of P. tenuicaudatus is the first record from Iran. The molecular characterisation of P. audriellus nematodes using the D2-D3 of 28S rRNA and the partial 18S rRNA gene sequences revealed that this species is clearly separated from P. straeleni and should be considered as a valid taxon.

Morphological and molecular characterisation of Caloosia longicaudata (Loos, 1948) Siddiqi & Goodey, 1963 (Nematoda: Caloosiidae) from Maui, the Hawaiian Islands with notes on some species of the genus

Nematology ◽  
2011 ◽  
Vol 13 (4) ◽  
pp. 381-393 ◽  
Author(s):  
Esther van den Berg ◽  
Sergei Subbotin ◽  
Louwrens Tiedt
Keyword(s):  
18S Rrna ◽  
Hawaiian Islands ◽  
Rrna Gene ◽  
28S Rrna ◽  
Molecular Characterisation ◽  
Diagnostic Pcr ◽  
Rflp Profile ◽  
First Time ◽  
Partial 18S ◽  
Scanning Electron

AbstractCaloosia longicaudata is described from Maui, the Hawaiian Islands, for the first time and both sexes are characterised morphologically using light and scanning electron microscopy. Molecular characterisation of C. longicaudata using the D2-D3 domain of 28S rRNA, partial 18S rRNA and ITS rRNA gene sequences is also provided. The phylogenetic relationships of this species with other representatives of the suborder Criconematina are presented and discussed. A diagnostic PCR-ITS-RFLP profile for C. longicaudata is given together with an identification table for eight species of Caloosia. Caloosia langola n. comb. is transferred to the genus and C. shorai is synonymised with H. psidii.

scholarly journals Sequencing and Analysis of Fungal rRNA Operons for Development of Broad-Range Fungal PCR Assays

2009 ◽  
Vol 75 (6) ◽  
pp. 1559-1565 ◽  
Author(s):  
Prasanna D. Khot ◽  
Daisy L. Ko ◽  
David N. Fredricks
Keyword(s):  
Fungal Pathogens ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Internal Transcribed Spacers ◽  
Rrna Gene ◽  
28S Rrna ◽  
28S Rrna Gene ◽  
Fungal Dna ◽  
Pcr Assays ◽  
Distance Matrices

ABSTRACT rRNA genes are attractive targets for developing PCR assays targeting human fungal pathogens. Most studies have focused on the 18S rRNA gene, internal transcribed spacers, and the 5′ end of the 28S rRNA gene. An approximately 2,900-bp region of the 28S rRNA gene remains largely unexplored because sequences of many medically relevant fungi are either unavailable or undefined in genomic databases. The internal transcribed spacers and 28S rRNA gene of nine medically and phylogenetically important fungi were sequenced. In addition, 42 sequences from this region were acquired from public databases, resulting in an alignment of 51 fungal sequences spanning 30 fungal genera. For the nearly 3,950-bp region from the 3′ end of 18S rRNA gene to the 3′ end of the 28S rRNA gene, 27 broad-range PCR primers were designed such that their sequence homology with the human rRNA gene was minimal. All 62 possible amplicons in the size range from 75 to 400 bp from 27 primers were screened using fungal genomic DNA from 26 species spanning 14 genera. Eleven of the 62 amplicons did not cross-react with 1 μg/PCR human DNA but simultaneously amplified 10 fg of fungal DNA. Phylogenetic distance matrices were calculated for regions covered by these 11 amplicons based on 51 fungi. Two of these 11 amplicons successfully amplified 30 fg of fungal DNA from 25 of 26 fungi and provided the most phylogenetic information for species identification based on the distance matrices. These PCR assays hold promise for detection and identification of fungal pathogens in human tissues.

A new dagger nematode, Xiphinema poasense n. sp. (Nematoda: Longidoridae), from Costa Rica

Nematology ◽  
2018 ◽  
Vol 20 (3) ◽  
pp. 235-252 ◽  
Author(s):  
Ingrid Varela-Benavides ◽  
Walter Peraza-Padilla ◽  
Carolina Cantalapiedra-Navarrete ◽  
Juan E. Palomares-Rius ◽  
Pablo Castillo ◽  
...  
Keyword(s):  
Costa Rica ◽  
18S Rrna ◽  
Mitochondrial Gene ◽  
The Body ◽  
Wild Plants ◽  
Rrna Gene ◽  
28S Rrna ◽  
Body Contour ◽  
Genital Branch ◽  
Partial 18S

A new dagger nematode,Xiphinema poasensen. sp., is described and illustrated from three populations extracted from soil associated with a combined plantation ofEucalyptussp.,Cupressussp. andPennisetumsp. and wild plants from a tropical pre-montane forest in Costa Rica. The new dagger nematode is characterised by a moderate body size 2612 (2416-3042) μm long, a rounded lip region 15.0 (13.5-16.5) μm broad, separated from the body contour by a shallow depression, amphidial fovea large, stirrup-shaped, a very long odontostyle (175 (164-188) μm), stylet guiding ring located 167 (136-181) μm from anterior end, vulva situated anterior to mid-body (36-40%), anterior genital branch complete but strongly reduced, without uterine differentiation, female tail short, hemispherical to convex-conoid with a c′ ratio = 0.7 (0.6-0.8) and bearing two pairs of caudal pores, and male absent. Integrative diagnosis was completed with molecular data using D2-D3 expansion segments of 28S rRNA, ITS1 region, partial 18S-rRNA and the partial mitochondrial gene cytochrome c oxidase subunit 1 (coxI). The phylogenetic relationships based on D2-D3 segments of this species with otherXiphinemaspp. of theX.non-americanumgroup indicated thatX. poasensen. sp. clustered with other species with a reduced anterior genital branch from the morphospecies Group 2,viz.,X. costaricenseandX. krugi. However, the phylogeny ofcoxIand partial 18S rRNA gene revealed that the new species did not cluster withXiphinemaspecies having the anterior genital branch absent or reduced (i.e., morphospecies Groups 1 and 2, respectively).

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