Cryptic Plasmodium inui and P. fieldi infections among symptomatic malaria patients in Thailand

BACKGROUND

Some nonhuman primate Plasmodium species including P. knowlesi and P. cynomolgi can cross-transmit from macaque natural hosts to humans under natural infection. This study aims to retrospectively explore other simian Plasmodium species in the blood samples of symptomatic malaria patients in Thailand.

METHODS

A total of 5271 blood samples from acute febrile patients from 5 malaria endemic provinces and 1015 blood samples from long-tailed and pig-tailed macaques from 3 locations were examined for Plasmodium species by microscopy and species-specific polymerase chain reaction. The Plasmodium mitochondrial cytochrome oxidase 1 (COX1) gene was analyzed by amplicon deep sequencing as well as Sanger sequencing from recombinant plasmid clones to reaffirm and characterize P. inui and P. fieldi.

RESULTS

Besides human malaria, P. knowlesi, P. cynomolgi, P. inui and P. fieldi infections were diagnosed in 15, 21, 19 and 3 patients, respectively. Most P. inui and all P. fieldi infected patients had simultaneous infections with other Plasmodium species, and seemed to be responsive to chloroquine or artemisinin-mefloquine. P. inui was the most prevalent species among macaque populations. Phylogenetic analysis of the COX1 sequences from human and macaque isolates reveals the genetic diversity of P. inui and suggests that multiple parasite strains have been incriminated in human infections.

CONCLUSIONS

Both P. inui and P. fieldi could establish infection in humans under natural transmission. Despite occurring at a low prevalence and mostly co-existing with other Plasmodium species, P. inui infections in humans have a wide distribution in Thailand.

Intraspecies Variation in Tetrahymena rostrata

Two distinct isolates of the facultative parasite, Tetrahymena rostrata were compared, identifying and utilising markers that are useful for studying clonal variation within the species were identified and utilised. The sequences of mitochondrial genomes and several nuclear genes were determined using Illumina short read sequencing. The two T. rostrata isolates had similar morphology. The linear mitogenomes had the gene content and organisation typical of the Tetrahymena genus, comprising 8 tRNA genes, 6 ribosomal RNA genes and 45 protein coding sequences (CDS), twenty-two of which had known function. The two isolates had nucleotide identity within common nuclear markers encoded within the histone H3 and H4 and small subunit ribosomal RNA genes and differed by only 2–4 nucleotides in a region of the characterised actin genes. Variation was observed in several mitochondrial genes and was used to determine intraspecies variation and may reflect the natural history of T. rostrata from different hosts or the geographic origins of the isolates.

Molecular, morphometric and digital automated identification of three Diaphorina species (Hemiptera: Liviidae)

Diaphorina is a species-rich genus, native to the tropics and subtropics of the Old World, particularly of more arid regions. One of the species, Diaphorina citri, is the economically most important pest of citrus. Diaphorina species are morphologically similar which makes their identification difficult. In this study, the accuracy of DNA barcoding, using mitochondrial cytochrome c oxidase subunit 1 (COI), geometric morphometrics of the forewing and digital image processing methods were tested for identification of the three Diaphorina species: D. chobauti, D. citri and D. zygophylli. Moreover, the published COI sequences of D. citri, D. communis and D. lycii obtained from Genbank were used for cluster analyses. DNA barcodes for D. chobauti and D. zygophylli are deposited in Genbank for the first time. The results of the molecular and geometric morphometric analyses are congruent and place D. chobauti as the sister taxon of the other Diaphorina species. The geometric morphometric analysis shows that in D. zygophylli the fore margin is slightly curved proximally and sharply bent distally, while in D. chobauti and D. citri it is straight proximally and weakly bent distally. The results of digital image processing show that the distribution of the dark pattern differs consistently in the three studied species.

Habitat requirements affect genetic variation in three species of mayfly (Ephemeroptera, Baetidae) from South Africa

This study investigates genetic diversity in three species of Ephemeroptera, one eurytopic and therefore widespread (Afroptilumsudafricanum) and two stenotopic and thus endemic (Demoreptusnatalensis and Demoreptuscapensis) species, all of which co-occur in the southern Great Escarpment, South Africa. Mitochondrial DNA was analysed to compare the genetic diversity between the habitat generalist and the two habitat specialists. Afroptilumsudafricanum showed no indication of population genetic structure due to geographic location, while both Demoreptus species revealed clear genetic differentiation between geographic localities and catchments, evident from phylogenetic analyses and high F_ST values from AMOVA. In addition, the phylogenetic analyses indicate some deeper haplotype divergences within A.sudafricanum and Demoreptus that merit taxonomic attention. These results give important insight into evolutionary processes occurring through habitat specialisation and population isolation. Further research and sampling across a wider geographic setting that includes both major mountain blocks of the Escarpment and lowland non-Escarpment sites will allow for refined understanding of biodiversity and associated habitat preferences, and illuminate comparative inferences into gene flow and cryptic speciation.

First genetic evidence that invasive bullhead (Cottus L. 1758) in Scotland is of English origin and the difficulty of resolving the European Cottus species taxonomy

The European bullhead (Cottus gobio) is widely distributed across Europe, and within the UK is native to England and Wales, where it is protected under the Habitats Directive. In Scotland, however, the species is considered invasive and thriving populations are recorded in the Forth and Clyde river catchments, and the Ale Water in the Scottish Borders. The genetic identity of the Scottish populations has not been established. There is also debate about the status of the European bullhead and its validity as single species, a species complex with several unresolved species, or distinct different species in its European distribution range. There is therefore a need to determine the taxonomy and likely source of the novel Scottish populations. Genetic analyses using cytochrome oxidase 1 (COI) mitochondrial DNA sequences were undertaken on specimens from the Forth and Clyde catchments, and combined with the results of morphological characteristics to provide a comprehensive assessment of the taxonomic classification for Scottish bullheads. There was considerable variation in morphological characteristics between populations within Scotland and a wider range of variability than previously recorded for English populations. Genetically the Scottish populations were very closely related to English specimens, supporting the hypothesis of introduction directly from England to Scotland. In terms of broader relationships, Scottish specimens are genetically more closely related to the ostensible species Chabot fluviatile Cottus perifretum, which has been suggested as one of a complex of species across Europe. Morphologically they exhibit characteristics on the spectrum between C. perifretum and C. gobio. There is an urgent need for the clarification of the taxonomy of Cottus sp(p). to avoid confusion in future publications, legislation and management practices relating to bullheads throughout the UK and Europe.

DNA barcoding techniques used to identify the shared ichthyofauna between the Pantanal floodplain and Upper Parana River

The biological invasion process is widely debated topic, as the population depletion of some species and the extinction of others are related to this process. To accelerate the identification of species and to detect non-native forms, new tools are being developed, such as those based on genetic markers. This study aimed to use Barcode DNA methodology to identify fish species that had translocated between the Parana and Paraguay River Basins. Based on a database of two studies that were conducted in these regions, 289 sequences of Cytochrome Oxidase C subunit 1 (COI) were used for General Mixed Youle Coalecent (GMYC) analysis, including 29 morphospecies that were sampled in both river basins. As a result, we observed that while some morphospecies have low variation, demonstrating a recent occupation of the basins, other morphospecies probably represent species complexes. A third of the morphospecies had well-defined lineages but not enough to be treated as different Molecular Operational Taxonomic Units (MOTUs). These results demonstrate that human interventions possibly participated in the distribution of some lineages. However, biogeographical historical processes are also important for the morphospecies distribution. The data suggest that the number of species that are present in these two basins is underestimated and that human actions can irreversibly affect the natural history of the species in these regions.

Combining Tpi and CO1 Genetic Markers to Discriminate Invasive Helicoverpa armigera From Local Helicoverpa zea (Lepidoptera: Noctuidae) Populations in the Southeastern United States

The recent establishment of the Old World pest Helicoverpa armigera (Hübner) into South America has had significant economic consequences and places the rest of the hemisphere at risk, emphasizing the need for improved methods of monitoring. A major complication is that a sibling species endemic to the New World, Helicoverpa zea (Boddie), is morphologically very similar, with the two species capable of producing fertile hybrids in the laboratory. The consequences of such hybridization in the field are uncertain, but could result in significant and unpredictable changes in the timing, range, and pesticide susceptibilities of Helicoverpa infestations. The objective here is to provide new genetic resources applicable to Helicoverpa populations in northern Florida and neighboring states (a region at risk for H. armigera) that can distinguish the two species and possible hybrids. The genetic variability in segments of the mitochondrial cytochrome oxidase 1 (CO1) and the Z-linked triosephosphate isomerase (Tpi) genes were determined for H. zea from the southeastern United States. These were compared to DNA sequences from H. armigera specimens from Morocco, Australia, and Europe. Phylogenetic network analysis showed a clear demarcation between the two species for all gene segments. These results extend earlier studies establishing CO1 as marker for discriminating the Helicoverpa species complex and introduce a new sex-linked genomic marker. The CO1 and Tpi markers in combination provide a more accurate and sensitive method than existing techniques for identifying hybridization between H. zea and H. armigera and could potentially be used to extrapolate the likely source of invasive H. armigera populations.

Inferring the phylogeny of bovidae using mitochondrial DNA sequences: resolving power of individual genes relative to complete genomes

Molecular techniques that assess biodiversity through the analysis of a small segment of mitochondrial genome have been getting wide attention for inferring the mammalian diversity. Due to their highly conserved nature, specific mitochondrial genes offer a promising tool for phylogenetic analysis. However, there is no established criteria for selecting the typical mitochondrial DNA (mtDNA) segments to achieve a greater resolving power. We therefore chose the family Bovidae as a model and compared the tree-topologies resulting from the commonly used and phylogenetically-informative genes including 16S rRNA, 12S rRNA, COI, Cyt b and D-loop with respect to complete mitochondrial genome. The tree topologies from the whole mitochondrial genome of 12 species were not identical albeit similar with those resulting from the five individual genes mentioned above. High bootstrap values were observed for mtDNA compared with that of any single gene. The average pair-wise sequence divergence using different genetic modes was found to be: D-loop (0.229) > Cyt b (0.159) > COI or complete mtDNA (0.143) > 12S rRNA (0.094) > 16S rRNA (0.091). The tree resulting from complete mtDNA clearly separated the 12 taxa of Bovidae into 3 major clusters, one cluster each for subfamily Cervinae and Bovinae and the third cluster comprised the distinctive clades of Caprinae and Antilopinae. However, jumping clades of Antilopinae were observed while using the individual genes. This study showed that Bison bison and Bos Taurus have very close phylogenetic relationship compared to Bubalus bubalis (Bovinae), irrespective of the method used. Our findings suggest that complete mtDNA genome provides most reliable understanding of complex phylogenetic relationships while the reliability of individual gene trees should be verified with high bootstrap support.