Morphological and molecular characters of Scutellonema brachyurus () from South Africa.
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ABSTRACT:
SUBMITTER: Shokoohi E
PROVIDER: S-EPMC8039989 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The construction of morphological character matrices is central to paleontological systematic study, which extracts paleontological information from fossils. Although the word information has been repeatedly mentioned in a wide array of paleontological systematic studies, its meaning has rarely been clarified nor specifically defined. It is important, however, to establish a standard to measure paleontological information because fossils are hardly complete, rendering the recognition of homologous and homoplastic structures difficult. Here, based on information theory, we show the deep connections between paleontological systematic study and communication system engineering. Information is defined as the decrease of uncertainty and it is the information in morphological characters that allows distinguishing operational taxonomic units (OTUs) and reconstructing evolutionary history. We propose that concepts in communication system engineering such as source coding and channel coding, correspond to the construction of diagnostic features and the entire character matrices in paleontological studies. The two coding strategies should be distinguished following typical communication system engineering, because they serve dual purposes. With character matrices from six different vertebrate groups, we analyzed their information properties including source entropy, mutual information, and channel capacity. Estimation of channel capacity shows character saturation of all matrices in transmitting paleontological information, indicating that, due to the presence of noise, oversampling characters not only increases the burden in character scoring, but also may decrease quality of matrices. We further test the use of information entropy, which measures how informative a variable is, as a character weighting criterion in parsimony-based systematic studies. The results show high consistency with existing knowledge with both good resolution and interpretability.
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Project description:The aim of this study was to compare the transcriptional response to TB in regions of different incidence / prevalence.
2010-08-11 | GSE19442 | GEO
Project description:A vast polychaete fauna is hidden behind complexes of cryptic and pseudo-cryptic species, which has greatly hindered our understanding of species diversity in several regions worldwide. Among the eunicids, Marphysa sanguinea Montagu, 1813 is a typical example, recorded in three oceans and with various species considered its junior synonyms. In South Africa, specimens previously misidentified as M. sanguinea are now known as Marphysa elityeni Lewis & Karageorgopoulos, 2008. Of the six Marphysa Quatrefages, 1865a species recorded from the same region, three have their distributions restricted to South Africa while the others are considered to have worldwide distributions. Here, we evaluated the taxonomic status of the indigenous M. elityeni and investigated the presence of the widespread species Marphysa macintoshi Crossland, 1903 and Marphysa depressa Schmarda, 1861 in South Africa using morphological and molecular data. Our results reveal that M. elityeni is a junior synonym of Marphysa haemasoma, a species previously described from South Africa which is herein reinstated as a valid species. Both M. macintoshi and M. depressa are not present in South Africa and their status as being distributed worldwide deserves further investigation. Marphysa durbanensis Day, 1934 and the new species described here, M. sherlockae n. sp., had been misidentified as M. macintoshi and M. depressa respectively. Thus, the number of Marphysa species with distributions restricted to South Africa increased from three to five. This study reiterates the importance of implementing an integrated taxonomic framework to unravel local biodiversity.
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Project description:Two populations of a Butlerius species were recovered from compost in two gardens in Potchefstroom, North-West Province, South Africa. Although the genus has previously been reported from South Africa, no species of the genus has ever been identified in the country. Based on morphological, morphometric, and molecular studies, the specimens were identified as Butlerius butleri and are herein reported for the first time from South Africa. The South African specimens are 1,082 to 1,423 µm long, a = 40.8 to 47.6; b = 4.7 to 5.8; c = 4.0 to 6.0; c' = 117 to 16.3; V = 44 to 47%. Cuticle with evenly spaced punctations. Reproductive system didelphic, amphidelphic, both branches equal in length. Four large glands opening into proximal part of uterus. Males with prominent sphincter present in mid-region of vas deferens. Spicules 36 to 43 μm long, gubernaculum 23 to 31 µm long, nine pairs of genital papillae, three pre-cloacal and six post-cloacal, formula: v1, v2, v3d/v4, ad, ph, v5, 6, 7, pd. The v5, 6, 7 clusters greatly separated, left subventral group at level of phasmid, right subventral group at level of posterior dorsal papilla. Although there were some differences, the South African populations of the species compare well to all know descriptions of the species. Phylogenetic analysis based on partial small subunit (SSU) rDNA sequences showed that both South African populations of B. butleri are in a maximally supported sister relation with an Iranian population of this species. Based on large subunit (LSU) rDNA sequences, the two populations of B. butleri clustered together in a well-supported clade.
| S-EPMC8039983 | biostudies-literature
Project description:Fossils provide our only direct window into evolutionary events in the distant past. Incorporating them into phylogenetic hypotheses of living clades can help time-calibrate divergences, as well as elucidate macroevolutionary dynamics. However, the effect fossils have on phylogenetic reconstruction from morphology remains controversial. The consequences of explicitly incorporating the stratigraphic ages of fossils using tip-dated inference are also unclear. Here, we use simulations to evaluate the performance of inference methods across different levels of fossil sampling and missing data. Our results show that fossil taxa improve phylogenetic analysis of morphological datasets, even when highly fragmentary. Irrespective of inference method, fossils improve the accuracy of phylogenies and increase the number of resolved nodes. They also induce the collapse of ancient and highly uncertain relationships that tend to be incorrectly resolved when sampling only extant taxa. Furthermore, tip-dated analyses under the fossilized birth-death process outperform undated methods of inference, demonstrating that the stratigraphic ages of fossils contain vital phylogenetic information. Fossils help to extract true phylogenetic signals from morphology, an effect that is mediated by both their distinctive morphology and their temporal information, and their incorporation in total-evidence phylogenetics is necessary to faithfully reconstruct evolutionary history.
| S-EPMC8246652 | biostudies-literature
Project description:The aim of this study was to compare the transcriptional response to TB in regions of different incidence / prevalence. Experimental Design: Whole blood collected in tempus tubes from patients with different spectra of TB disease. All patients were sampled prior to the initiation of any antimycobacterial therapy. Active Pulmonary TB: PTB - All patients confirmed by isolation of Mycobacterium Tuberculosis on culture of sputum. Latent TB: LTB - All patients were screened at a tuberculosis clinic. All were positive by Interferon-Gamma Release assay(IGRA); specifically Quantiferon Gold In-Tube Assay (Cellestis, Australia). Latent patients had no clinical, or microbiological evidence of active infection and were asymptomatic. Experimental Variables: Patient group: Active PTB; Latent TB. There are no healthy controls in this dataset as it was being used for validation only. Controls: Latent TB individuals are used as a control for PTB in this dataset since there are few to no unexposed adult controls in Cape Town.
2010-08-11 | E-GEOD-19442 | biostudies-arrayexpress
Project description:BACKGROUND: Trypanosomes are ubiquitous blood parasites of marine and freshwater fishes, typically transmitted by aquatic leeches. Phylogenetic studies have been dominated by examples derived from freshwater fishes, with few marine representatives. Furthermore, life cycle studies on marine fish trypanosomes have focused on those of the northern hemisphere. In this investigation, we have examined the life cycle and molecular taxonomy of a marine fish trypanosome from South Africa. METHODS: To locate trypanosome stages, leeches were removed from fishes captured on the west and south coasts of South Africa, and fish blood films and leech squashes were Giemsa-stained and screened; leeches were also examined histologically. To determine whether trypanosome stages in fishes and leeches were of the same genotype, DNA was extracted from Giemsa-stained fish blood films and leech squashes, and from fish whole blood. Fragments of the 18S rRNA gene were amplified by PCR using trypanosome-specific primers and sequenced. Resulting sequence data were compared with each other and with published trypanosome 18S rDNA sequences, and used for phylogenetic analysis. RESULTS: Trypanosomes were detected in blood films from fishes of the families Clinidae, Blenniidae and Gobiidae. The flagellates ranged in size and staining properties within the films and across fish hosts. In squashes and histological sections of adult and juvenile leeches, identified as Zeylanicobdella arugamensis, trypanosome developmental stages were predominantly slender epimastigotes. Sequence data showed that trypanosomes derived from fishes were identical, irrespective of whether they were small or large forms; sequences derived largely from leech epimastigotes were also identical to those obtained from fish trypanosomes. Fish and leech trypanosome sequences fell into a marine fish aquatic clade, and aligned most closely with two trypanosome sequences from marine fishes off Norway. CONCLUSIONS: Combined morphological and molecular methods indicate that the trypanosomes examined here represent a single pleomorphic species, rather than the three species described originally. This species is identified as Trypanosoma nudigobii Fantham, 1919 with the leech Z. arugamensis as its vector, and T. capigobii Fantham, 1919 and T. blenniclini Fantham, 1930 are regarded as junior synonyms of the species. Phylogenetic analysis establishes its affinity with marine fish trypanosomes off Norway.
| S-EPMC3904685 | biostudies-literature
Project description:BACKGROUND:Rhipicephalus microplus, an invasive tick species of Asian origin and the main vector of Babesia species, is considered one of the most widespread ectoparasites of livestock. The tick has spread from its native habitats on translocated livestock to large parts of the tropical world, where it has replaced some of the local populations of Rhipicephalus decoloratus ticks. Although the tick was reported in Uganda 70 years ago, it has not been found in any subsequent surveys. This study was carried out to update the national tick species distribution on livestock in Uganda as a basis for tick and tick-borne disease control, with particular reference to R. microplus. METHODS:The study was carried out in Kadungulu, Serere district, south-eastern Uganda, which is dominated by small scale livestock producers. All the ticks collected from 240 cattle from six villages were identified microscopically. Five R. microplus specimens were further processed for phylogenetic analysis and species confirmation. RESULTS:The predominant tick species found on cattle was Rhipicephalus appendiculatus (86.9 %; n = 16,509). Other species found were Amblyomma variegatum (7.2 %; n = 1377), Rhipicephalus evertsi (2.3 %; n = 434) and R. microplus (3.6 %; n = 687). Phylogenetic analysis of the 12S rRNA, 16S rRNA and ITS2 gene sequences of R. microplus confirmed the morphological identification. CONCLUSIONS:It is concluded that R. microplus has replaced R. decoloratus in the sampled villages in Kadungulu sub-county, since the latter was not any longer found in this area. There is currently no livestock movement policy in force in Uganda, which could possibly limit the further spread of R. microplus ticks. Future surveys, but also retrospective surveys of museum specimens, will reveal the extent of distribution of R. microplus in Uganda and also for how long this tick has been present on livestock without being noticed.
| S-EPMC7118885 | biostudies-literature
Project description:Background. The bacterial foodborne pathogen Campylobacter jejuni is a common cause of acute gastroenteritis and is also associated with the postinfectious neuropathies, Guillain-Barré and Miller Fisher syndromes. This study described the use of multilocus sequence typing and DNA microarrays to examine the genetic content of a collection of South African C. jejuni strains, recovered from patients with enteritis, Guillain-Barré or Miller Fisher syndromes. Methodology/Principal Findings. The comparative genomic analysis by using multilocus sequence typing and DNA microarrays demonstrated that the South African strains with Penner heat-stable (HS) serotype HS:41 were clearly distinct from the other South African strains. Further analysis of the DNA microarray data demonstrated that the serotype HS:41 strains from South African GBS and enteritis patients are highly similar in gene content. Interestingly, the South African HS:41 strains were distinct in gene content when compared to serotype HS:41 strains from other geographical locations due to the presence of genomic islands, referred to as Campylobacter jejuni integrated elements. Only the genomic integrated element CJIE1, a Campylobacter Mu-like prophage, was present in the South African HS:41 strains whereas absent in the closely-related HS:41 strains from Mexico. A more distantly-related HS:41 strain from Canada possessed both genomic integrated elements CJIE1 and CJIE2. Conclusion/Significance. These findings demonstrated that these C. jejuni integrated elements may contribute to the differentiation of closely-related C. jejuni strains. In addition, the presence of bacteriophage-related genes in CJIE1 may probably contribute to increasing the genomic diversity of these C. jejuni strains. This comparative genomic analysis of the foodborne pathogen C. jejuni provides fundamental information that potentially could lead to improved methods for analyzing the epidemiology of disease outbreaks and their sources. Keywords: comparative genomic indexing analysis
2007-12-19 | GSE9862 | GEO
Project description:Abstract Glinus is a small genus of Molluginaceae with 8–10 species mostly distributed in the tropics of the World. Its composition and evolutionary relationships were poorly studied. A new molecular phylogeny constructed here using nuclear (ITS) and chloroplast (rbcL, trnK-matK) markers confirmed the monophyly of the genus. Based on ITS analysis, the following well-supported lineages are present within Glinus: the G.bainesii lineage is recovered as sister to the remainder of the genus followed by G.oppositifolius. Three other clades are: G.hirtus with G.orygioides; G.radiatus and G.lotoides; the latter is represented by a sample from North America, and G.zambesiacus as sister to G.setiflorus + G.lotoides + G.dictamnoides. On the plastid gene tree, G.bainesii + G.oppositifolius form a sister clade to all other Glinus species. The next clade is formed by G.hirtus and G.orygioides followed by G.radiatus plus an American sample of G.lotoides. The next branch comprises G.setiflorus as sister to G.zambesiacus + G.lotoides + G.dictamnoides. Glinus seems to have originated from Africa around the Late Eocene or Early Miocene, with further radiations to Australia and the Americas during the Late Miocene or Late Pliocene. Compared with the previous limited character set used for the diagnostics, we have found ten new morphological and carpological traits distinguishing Glinus members. In both trees based on nuclear and plastid datasets, the major phylogenetic clades cannot be characterized by the peculiar morphological characters. Many shared character states leading to their contrasting pattern in the multivariate analysis model are interpreted as a high homoplasy in the phylogenetically distant species. We paid special attention to the composition of the genus in Sub-Saharan Africa, a region with the greatest species diversity. Our results provide new insight into the taxonomy of Glinus in this region. Glinuslotoidesvar.virens accepted in many previous works is a synonym of G.dictamnoides that is closely related to G.lotoides based on molecular analysis and morphological characters. The status of the American populations of G.lotoides needs further investigation due to different characters of the specimens from the Old and the New World. Many specimens previously identified as G.lotoidesvar.virens and as the intermediates G.lotoides × G.oppositifolius belong to G.zambesiacussp. nov. and G.hirtuscomb. nov. (? Mollugohirta); the latter species is resurrected from synonymy after 200 years of unacceptance. In some African treatments, G.hirtus was known under the invalidly published name G.dahomensis. Glinuszambesiacus is distributed in the southern and eastern parts of tropical Africa, and G.hirtus previously assumed to be endemic to West Africa is indeed a species with a wide distribution across the tropical part of the continent. Glinusmicrophyllus previously accepted as endemic to West Tropical Africa together with other new synonyms (G.oppositifoliusvar.lanatus, G.herniarioides, Wycliffearotundifolia) is considered here as G.oppositifoliusvar.keenaniicomb. nov. (? Mollugohirtavar.keenanii), a variety found across the entire distribution of G.oppositifolius (Australia, Asia, and Africa). The presence of the American G.radiatus in Africa is not confirmed, and all records of this species belong to G.hirtus. The lectotypes of some names (G.dictamnoides, G.herniarioides, Mollugohirta, M.setiflora, Pharnaceumpentagynum, Wycliffea) as well as a neotype of G.trianthemoides are designated. A new key to the identification of all Glinus species in Sub-Saharan Africa is provided. A checklist is given of all accepted species in this region (G.bainesii, G.hirtus, G.lotoides, G.oppositifolius s.l., G.setiflorus, and G.zambesiacus) with their nomenclature, morphological description and geographical distribution.
| S-EPMC7921084 | biostudies-literature