Intragenomic variation in ITS2 rDNA in the louse of humans, Pediculus humanus: ITS2 is not a suitable marker for population studies in this species

Frontiers Approaches to the Diagnosis of Thrips (Thysanoptera): How Effective Are the Molecular and Electronic Detection Platforms?

Simple Summary

Thrips are important agricultural and forest pests. They cause damage by sucking plant sap and transmitting several plant viruses. Correct identification is the key for epidemiological studies and formulating appropriate management strategies. The application of molecular and electronic detection platforms has improved the morphological character-based diagnosis of thrips species. This article reviews research on molecular and automated identification of thrips species and discusses future research strategies for rapid and high throughput thrips diagnosis.

Abstract

Thrips are insect pests of economically important agricultural, horticultural, and forest crops. They cause damage by sucking plant sap and by transmitting several tospoviruses, ilarviruses, carmoviruses, sobemoviruses, and machlomoviruses. Accurate and timely identification is the key to successful management of thrips species. However, their small size, cryptic nature, presence of color and reproductive morphs, and intraspecies genetic variability make the identification of thrips species challenging. The use of molecular and electronic detection platforms has made thrips identification rapid, precise, sensitive, high throughput, and independent of developmental stages. Multi-locus phylogeny based on mitochondrial, nuclear, and other markers has resolved ambiguities in morphologically indistinguishable thrips species. Microsatellite, RFLP, RAPD, AFLP, and CAPS markers have helped to explain population structure, gene flow, and intraspecies heterogeneity. Recent techniques such as LAMP and RPA have been employed for sensitive and on-site identification of thrips. Artificial neural networks and high throughput diagnostics facilitate automated identification. This review also discusses the potential of pyrosequencing, microarrays, high throughput sequencing, and electronic sensors in delimiting thrips species.

Using the rDNA Internal Transcribed Spacer 1 to Identify the Invasive Pest Rhagoletis cerasi (Diptera: Tephritidae) in North America

The cherry-infesting fruit fly Rhagoletis cerasi Loew is a significant commercial pest in Europe that has recently invaded North America. To date, it has been trapped only in Canada and northwestern counties of New York. It has the potential to spread further and threaten production and movement of cherry commodities. Timely diagnosis of the pest will facilitate surveys and quick response to new detections. Adult morphology of the pest is distinct from other flies in North America. However, when flies are significantly damaged on traps or the immature life stages are found in fruits, molecular methods of identification are important to confirm presence and host-use records. Other than DNA sequencing of genes from flies which takes over a day to complete, there are no timely methods of molecular identification for this pest. In this study, we report the first sequence record of the internal transcribed spacer 1 (ITS1) from R. cerasi and develop two diagnostic tests for the pest based on ITS1 differences among species in North America. The tests use loop-mediated isothermal amplification (LAMP) and multiplex, conventional polymerase chain reaction (mcPCR) technologies that target the same region of the R. cerasi ITS1 sequence. Both tests performed well when tested against collections of R. cerasi from North America and Europe, generating Diagnostic Sensitivity estimates of 98.4-99.5%. Likewise, the tests had relatively high estimates of Diagnostic Specificity (97.8-100%) when tested against Rhagoletis Loew species present in North America that also use cherry as a developmental host.

Evaluation of ITS2 molecular morphometrics effectiveness in species delimitation of Ascomycota - A pilot study

Exploring the secondary structure information of nuclear ribosomal internal transcribed spacer 2 (ITS2) has been a promising approach in species delimitation. However, Compensatory base changes (CBC) concept employed in this approach turns futile when CBC is absent. This prompted us to investigate the utility of insertion/deletion (INDELs) and substitutions in fungal delineation at species level. Upon this rationale, 116 strains representing 97 species, belonging to 6 genera (Colletotrichum, Boeremia, Leptosphaeria, Peyronellaea, Plenodomus and Stagonosporopsis) of Ascomycota were retrieved from Q-bank for molecular morphometric analysis. CBC, INDELs and substitutions between the species of their respective genus were recorded. Most species combinations lacked CBC. Among the substitution events, transitions were predominant. INDELs were less frequent than the substitutions. These evolutionary events were mapped upon the helices to discern species specific variation sites. In 68 species unique variation sites were recognised. The remaining 29 species shared absolute similarity with distinctly named species. The variation sites catalogued in them overlapped with other distinct species and resulted in the blurring of species boundaries. Species specific variation sites recognized in this study are the preliminary results and they could be discerned with absolute confidence when larger datasets encompassing all described species of genera were investigated. They could be of potential use in barcoding fungi at species level. This study also concludes that the ITS2 molecular morphometric analysis is an efficient third dimensional study of the fungal species delimitation. This may help to avoid the false positives in species delimitations and to alleviate the challenges in molecular characterization.

A Simple Method to Decode the Complete 18-5.8-28S rRNA Repeated Units of Green Algae by Genome Skimming

Green algae, Chlorella ellipsoidea, Haematococcus pluvialis and Aegagropila linnaei (Phylum Chlorophyta) were simultaneously decoded by a genomic skimming approach within 18-5.8-28S rRNA region. Whole genomic DNAs were isolated from green algae and directly subjected to low coverage genome skimming sequencing. After de novo assembly and mapping, the size of complete 18-5.8-28S rRNA repeated units for three green algae were ranged from 5785 to 6028 bp, which showed high nucleotide diversity (π is around 0.5–0.6) within ITS1 and ITS2 (Internal Transcribed Spacer) regions. Previously, the evolutional diversity of algae has been difficult to decode due to the inability design universal primers that amplify specific marker genes across diverse algal species. In this study, our method provided a rapid and universal approach to decode the 18-5.8-28S rRNA repeat unit in three green algal species. In addition, the completely sequenced 18-5.8-28S rRNA repeated units provided a solid nuclear marker for phylogenetic and evolutionary analysis for green algae for the first time.

Unexpected High Intragenomic Variation in Two of Three Major Pest Thrips Species Does Not Affect Ribosomal Internal Transcribed Spacer 2 (ITS2) Utility for Thrips Identification

The mitochondrial cytochrome oxidase I gene (mtCO1) and the ribosomal internal transcribed spacer 2 region (ITS2) are among the most widely used molecular markers for insect taxonomic characterization. Three economically important species of thrips, Scirtothripsdorsalis, Thripspalmi, and Frankliniellaoccidentalis were selected to examine the extent of intragenomic variation within these two marker regions in the family Thripidae, and determine if this variation would affect the utility of markers in thrips molecular diagnostics. For each species, intragenomic (within individual) variation and intergenomic (among individuals) variation was assessed by cloning and sequencing PCR-amplified copies. Intergenomic variation was generally higher than intragenomic variation except in cases where intergenomic variation was very low, as in mtCO1 from S.dorsalis and F.occidentalis. Intragenomic variation was detected in both markers in all three of the thrips species, however, 2-3 times more intragenomic variation was observed for ITS2 than mtCO1 in both S.dorsalis and T.palmi. Furthermore, levels of intragenomic variation were low for both of the genes in F.occidentalis. In all of the three thrips species, no sex-based clustering of haplotypes was observed in either marker. Unexpected high intragenomic variation in ITS2 for two of three thrips species did not interfere with thrips diagnostics. However, caution should be taken in applying ITS2 to certain studies of S.dorsalis and T.palmi when high levels of intragenomic variation could be problematic or confounding. In such studies, mtCO1 may be a preferable marker. Possible reasons for discrepancies in intragenomic variation among genomic regions are discussed.

Evidence for an African cluster of human head and body lice with variable colors and interbreeding of lice between continents

BACKGROUND

Human head lice and body lice have been classified based on phenotypic characteristics, including geographical source, ecotype (preferred egg laying site hair or clothes), shape and color. More recently, genotypic studies have been based on mitochondrial genes, nuclear genes and intergenic spacers. Mitochondrial genetic analysis reclassified lice into three genotypes (A, B and C). However, no previous study has attempted to correlate both genotypic and phenotypic data.

MATERIALS AND METHODS

Lice were collected in four African countries: Senegal, Burundi, Rwanda and Ethiopia and were photographed to compare their colors. The Multi-Spacer-Typing (MST) method was used to genotype lice belonging to the worldwide Clade A, allowing a comparison of phenotypic and genotypic data.

RESULTS

No congruence between louse color and genotype has been identified. Phylogenetic analysis of the spacer PM2, performed including lice from other sources, showed the existence of an African cluster of human lice. However, the analysis of other spacers suggested that lice from different areas are interbreeding.

CONCLUSIONS

We identified two geotypes of Clade A head and body lice including one that is specifically African, that can be either black or grey and can live on the head or in clothing. We also hypothesized that lice from different areas are interbreeding.

A multiplex real-time polymerase chain reaction assay to diagnose Epiphyas postvittana (Lepidoptera: Tortricidae)

A molecular assay for diagnosis of light brown apple moth, Epiphyas postvittana (Walker) (Lepidoptera: Tortricidae), in North America is reported. The assay multiplexes two TaqMan real-time polymerase chain reaction (RT-PCR) probe systems that are designed to target DNA segments of the internal transcribed spacer region 2 (ITS2) and 18S rRNA gene. The RT-PCR probe designed for the 18S target recognizes a DNA sequence conserved in all of the moths included in the study and functions as a control in the assay. The second probe recognizes a segment of the ITS2 specifically found in E. postvittana and not found in the other moths included in the study, i.e., this segment is not conserved. Inclusion of the two markers in a single multiplex reaction did not affect assay performance. The assay was tested against 637 moths representing > 90 taxa in 15 tribes in all three subfamilies in the Tortricidae. The assay generated no false negatives based on analysis of 355 E. postvittana collected from California, Hawaii, England, New Zealand, and Australia. Analysis of a data set including 282 moths representing 41 genera generated no false positives. Only three inconclusive results were generated from the 637 samples. Spike experiments demonstrated that DNA contamination in the assay can affect samples differently. Contaminated samples analyzed with the ITS2 RT-PCR assay and DNA barcode methodology by using the cytochrome oxidase I gene can generate contradictory diagnoses.

Two different size classes of 5S rDNA units coexisting in the same tandem array in the razor clam Ensis macha: is this region suitable for phylogeographic studies?

For a study of 5S ribosomal genes (rDNA) in the razor clam Ensis macha, the 5S rDNA region was amplified and sequenced. Two variants, so-called type I or short repeat (approximately 430 bp) and type II or long repeat (approximately 735 bp), appeared to be the main components of the 5S rDNA of this species. Their spacers differed markedly, both in length and nucleotide composition. The organization of the two variants was investigated by amplifying the genomic DNA with primers based on the sequence of the type I and type II spacers. PCR amplification products with primers EMLbF and EMSbR showed that the long and short repeats are associated within the same tandem array, suggesting an intermixed arrangement of both spacers. Nevertheless, amplifications carried out with inverse primers EMSinvF/R and EMLinvF/R revealed that some short and long repeats are contiguous in the same tandem array. This is the first report of the coexistence of two variable spacers in the same tandem array in bivalve mollusks.

Do molecules matter more than morphology? Promises and pitfalls in parasites

Systematics involves resolving both the taxonomy and phylogenetic placement of organisms. We review the advantages and disadvantages of the two kinds of information commonly used for such inferences – morphological and molecular data – as applied to the systematics of metazoan parasites generally, with special attention to the malaria parasites. The problems that potentially confound the use of morphology in parasites include challenges to consistent specimen preservation, plasticity of features depending on hosts or other environmental factors, and morphological convergence. Molecular characters such as DNA sequences present an alternative data source and are particularly useful when not all the parasite's life stages are present or when parasitaemia is low. Nonetheless, molecular data can bring challenges that include troublesome DNA isolation, paralogous gene copies, difficulty in developing molecular markers, and preferential amplification in mixed species infections. Given the differential benefits and shortcomings of both molecular and morphological characters, both should be implemented in parasite taxonomy and phylogenetics.

Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus

Regions of rDNA are commonly used to infer phylogenetic relationships among fungal species and as DNA barcodes for identification. These regions occur in large tandem arrays, and concerted evolution is believed to reduce intragenomic variation among copies within these arrays, although some variation still might exist. Phylogenetic studies typically use consensus sequencing, which effectively conceals most intragenomic variation, but cloned sequences containing intragenomic variation are becoming prevalent in DNA databases. To understand effects of using cloned rDNA sequences in phylogenetic analyses we amplified and cloned the ITS region from pure cultures of six Laetiporus species and one Wolfiporia species (Basidiomycota, Polyporales). An average of 66 clones were selected randomly and sequenced from 21 cultures, producing a total of 1399 interpretable sequences. Significant variation (≥ 5% variation in sequence similarity) was observed among ITS copies within six cultures from three species clades (L. cincinnatus, L. sp. clade J, and Wolfiporia dilatohypha) and phylogenetic analyses with the cloned sequences produced different trees relative to analyses with consensus sequences. Cloned sequences from L. cincinnatus fell into more than one species clade and numerous cloned L. cincinnatus sequences fell into entirely new clades, which if analyzed on their own most likely would be recognized as "undescribed" or "novel" taxa. The use of a 95% cut off for defining operational taxonomic units (OTUs) produced seven Laetiporus OTUs with consensus ITS sequences and 20 OTUs with cloned ITS sequences. The use of cloned rDNA sequences might be problematic in fungal phylogenetic analyses, as well as in fungal bar-coding initiatives and efforts to detect fungal pathogens in environmental samples.

Genotyping of human lice suggests multiple emergencies of body lice from local head louse populations

Background

Genetic analyses of human lice have shown that the current taxonomic classification of head lice (Pediculus humanus capitis) and body lice (Pediculus humanus humanus) does not reflect their phylogenetic organization. Three phylotypes of head lice A, B and C exist but body lice have been observed only in phylotype A. Head and body lice have different behaviours and only the latter have been involved in outbreaks of infectious diseases including epidemic typhus, trench fever and louse borne recurrent fever. Recent studies suggest that body lice arose several times from head louse populations.

Methods and Findings

By introducing a new genotyping technique, sequencing variable intergenic spacers which were selected from louse genomic sequence, we were able to evaluate the genotypic distribution of 207 human lice. Sequence variation of two intergenic spacers, S2 and S5, discriminated the 207 lice into 148 genotypes and sequence variation of another two intergenic spacers, PM1 and PM2, discriminated 174 lice into 77 genotypes. Concatenation of the four intergenic spacers discriminated a panel of 97 lice into 96 genotypes. These intergenic spacer sequence types were relatively specific geographically, and enabled us to identify two clusters in France, one cluster in Central Africa (where a large body louse outbreak has been observed) and one cluster in Russia. Interestingly, head and body lice were not genetically differentiated.

Conclusions

We propose a hypothesis for the emergence of body lice, and suggest that humans with both low hygiene and head louse infestations provide an opportunity for head louse variants, able to ingest a larger blood meal (a required characteristic of body lice), to colonize clothing. If this hypothesis is ultimately supported, it would help to explain why poor human hygiene often coincides with outbreaks of body lice. Additionally, if head lice act as a reservoir for body lice, and that any social degradation in human populations may allow the formation of new populations of body lice, then head louse populations are potentially a greater threat to humans than previously assumed.

While being phenotypically and physiologically different, human head and body lice are indistinguishable based on mitochondrial and nuclear genes. As protein-coding genes are too conserved to provide significant genetic diversity, we performed strain-typing of a large collection of human head and body lice using variable intergenic spacer sequences. Ninety-seven human lice were classified into ninety-six genotypes based on four intergenic spacer sequences. Genotypic and phylogenetic analyses using these sequences suggested that human head and body lice are still indistinguishable. We hypothesized that the phenotypic and physiological differences between human head and body lice are controlled by very limited mutations. Under conditions of poor hygiene, head lice can propagate very quickly. Some of them will colonize clothing, producing a body louse variant (genetic or phenetic), which can lead to an epidemic. Lice collected in Rwanda and Burundi, where outbreaks of louse-borne diseases have been recently reported, are grouped tightly into a cluster and those collected from homeless people in France were also grouped into a cluster with lice collected in French non-homeless people. Our strain-typing approach based on highly variable intergenic spacers may be helpful to elucidate louse evolution and to survey louse-borne diseases.

Analysis of ITS1 and ITS2 sequences in Ensis razor shells: suitability as molecular markers at the population and species levels, and evolution of these ribosomal DNA spacers

Internal transcribed spacer 1 and 2 (ITS1 and ITS2) sequences were analysed in Ensis razor shells (Mollusca: Bivalvia: Pharidae). We aimed to (1) test ITS1 and ITS2 as molecular markers at the population level in the successful alien E. directus (Conrad, 1843); (2) test these spacers at the species level in E. directus and three other Ensis species, E. siliqua (L., 1758), E. macha (Molina, 1782), and E. magnus (Schumacher, 1817); and (3) analyse the evolutionary processes that may be shaping Ensis ITS1 and ITS2 extant variation. In E. directus, despite the intragenomic divergence detected, ITS1 and ITS2 were informative in differentiating the geographic areas considered (Denmark and Canada) by means of both the insertion-deletion polymorphism and the nucleotide polymorphism. In this species, the 5.8S ribosomal gene (5.8S) showed scarce polymorphism. At the species level, maximum parsimony and maximum likelihood analyses revealed that ITS1 and ITS2 may be suitable to reconstruct Ensis phylogenetic relationships. Finally, the evolutionary models that best fit the long-term evolution of Ensis ITS1–5.8S–ITS2 are discussed. A mixed process of concerted evolution, birth-and-death evolution, and selection is chosen as an option that may reconcile the long-term evolution of Ensis ITS1–5.8S–ITS2 and 5S ribosomal DNA.

Molecular phylogeography of Culex quinquefasciatus mosquitoes in central Bangladesh

Mosquitoes in the Culex pipiens complex are a major vector of numerous parasitic and arboviral diseases. Here we report the phylogeography of a prevalent Culex mosquito, Cx. quinquefasciatus, from three locations in Bangladesh: Dhaka, Savar and Mymensingh. Sequence analysis of the genes encoding mitochondrial cytochrome oxidase subunit II, nuclear elongation factor-1 alpha, and acetylcholinesterase-2 revealed the lack of a population genetic structure among the three locations. Moreover, the highly divergent ribosomal internal transcribed spacer 2 suggests that this locus has not evolved in concert. The results further show evidence of historical introgression of internal transcribed spacer 2 from Cx. pipiens to Cx. quinquefasciatus of Bangladesh, and that the introgression occurred before Cx. quinquefasciatus had dispersed within this region. The study also reveals historical population expansion in this region, followed by a post-expansion Wolbachia sweep.

Long-term evolution of 5S ribosomal DNA seems to be driven by birth-and-death processes and selection in Ensis razor shells (Mollusca: Bivalvia)

A study of nucleotide sequence variation of 5S ribosomal DNA from six Ensis species revealed that several 5S ribosomal DNA variants, based on differences in their nontranscribed spacers (NTS), occur in Ensis genomes. The 5S rRNA gene was not very polymorphic, compared with the NTS region. The phylogenetic analyses performed showed a between-species clustering of 5S ribosomal DNA variants. Sequence divergence levels between variants were very large, revealing a lack of sequence homogenization. These results strongly suggest that the long-term evolution of Ensis 5S ribosomal DNA is driven by birth-and-death processes and selection.

Multiple genes elucidate the evolution of venomous snail-hunting Conus species

The species-rich Cone snails (Conus sp.) are predatory, marine gastropods known for small venom peptides that are valuable for pharmacological research applications. Phylogenetic analyses with mitochondrial rRNA sequences have facilitated peptide discovery. However, these relatively conserved genes leave unresolved the closer relationships among many species. We sequenced 26 internal transcribed spacer 2 (ITS2) sequences from genomic ribosomal DNA to elucidate the evolutionary relationships among molluscivorous species and to piscivorous and vermivorous species. We show that ITS2 sequences are well conserved within species but are sufficiently variable among species to resolve recent divergences. Using Bayesian, maximum likelihood and log-determinant methods, we use the ITS sequences to resolve portions of the tree that could not be resolved using the more conventional mt rRNA sequences. When the ITS2 sequences are added to existing COI and to the more conserved rRNA sequences and then properly modeled, support throughout the tree is increased. This enables us to show finer relationships among the molluscivorous species that reveal three well-supported clades (Conus, Cylinder, and Darioconus) and renders the ITS2 sequences an essential component in advancing the discovery and pharmacological characterization of novel peptides from the venoms of these molluscs.

Populations, hybrids and the systematic concepts of species and subspecies in Chagas disease triatomine vectors inferred from nuclear ribosomal and mitochondrial DNA

In Chagas disease, triatomine vectors are the main target for control measures because of the absence of effective drugs. The broad usefulness of nuclear rDNA and mtDNA sequences explains why triatomine studies using these markers have increased so pronouncedly in recent years. This indicates the appropriateness of an updated review about these molecular markers, concentrating on aspects useful for research on Chagas disease vectors. A comparative analysis is presented on the efficiency, weight of their different characteristics, limitations and problems of each of the different DNA markers in the light of the results obtained in studies on populations, hybrids, subspecies and species of the subfamily Triatominae. The use of a standardized composite haplotype code nomenclature for both nuclear rDNA and mtDNA markers is strongly encouraged to avoid difficulties in comparative studies. Triatomine aspects related to concerted evolution, microsatellites, minisatellites and insertions/deletions in nuclear rDNA and silent/non-silent mutations, pseudogenes and weaknesses of partial sequences in mtDNA are analysed. Introgression and hybrids, nuclear and mitochondrial DNA strengths, and compared evolutionary rates of nuclear rDNA and mtDNA in triatomines are discussed. Many conclusions are obtained thanks to the availability, for the first time in triatomines, of a complete sequence of a protein-coding mtDNA gene as ND1 from very numerous triatomine species covering from different populations of a species up to members belonging to different tribes. The evolutionary rates of each nuclear rDNA marker and mtDNA marker are analysed by comparison at subspecies level (intrapopulational, interpopulational, between morphs, and between subspecies) and species level (close and distant species of the same genus, species of different genera, and species of different tribes). Weaknesses of mtDNA for systematic-taxonomic purposes detected recently and newly in insects and triatomines, respectively, are discussed in detail. Emphasis is given to taxonomic units and biological entities presenting well-known problematics, both from the systematic-taxonomic and/or epidemiological-control points of view, as well as to molecular situations which can give rise to erroneous conclusions. All these aspects constitute the background on which the key question about the systematic concepts of species and subspecies in triatomines is focused. The global purpose is to facilitate future work on triatomines by highlighting present gaps, how better choice the appropriate markers, and marker aspects which should be taken into account. Key characteristics as alpha, CI and transformation rate matrices ought to be obtained and noted to get appropriate results and allow correct interpretations. The main aim is to offer a baseline for future fundamental research on triatomines and applied research on transmission, epidemiology and control measures related to Chagas disease vectors.

What's in a name: the taxonomic status of human head and body lice

Human head lice (Anoplura: Pediculidae: Pediculus) are pandemic, parasitizing countless school children worldwide due to the evolution of insecticide resistance, and human body (clothing) lice are responsible for the deaths of millions as a result of vectoring several deadly bacterial pathogens. Despite the obvious impact these lice have had on their human hosts, it is unclear whether head and body lice represent two morphological forms of a single species or two distinct species. To assess the taxonomic status of head and body lice, we provide a synthesis of publicly available molecular data in GenBank, and we compare phylogenetic and population genetic methods using the most diverse geographic and molecular sampling presently available. Our analyses find reticulated networks, gene flow, and a lack of reciprocal monophyly, all of which indicate that head and body lice do not represent genetically distinct evolutionary units. Based on these findings, as well as inconsistencies of morphological, behavioral, and ecological variability between head and body lice, we contend that no known species concept would recognize these louse morphotypes as separate species. We recommend recognizing head and body lice as morphotypes of a single species, Pediculus humanus, until compelling new data and analyses (preferably analyses of fast evolving nuclear markers in a coalescent framework) indicate otherwise.

Deep genetic divergences among Indo-Pacific populations of the coral reef sponge Leucetta chagosensis (Leucettidae): founder effects, vicariance, or both?

Background

An increasing number of studies demonstrate that genetic differentiation and speciation in the sea occur over much smaller spatial scales than previously appreciated given the wide distribution range of many morphologically defined coral reef invertebrate species and the presumed dispersal-enhancing qualities of ocean currents. However, knowledge about the processes that lead to population divergence and speciation is often lacking despite being essential for the understanding, conservation, and management of marine biodiversity. Sponges, a highly diverse, ecologically and economically important reef-invertebrate taxon, exhibit spatial trends in the Indo-West Pacific that are not universally reflected in other marine phyla. So far, however, processes generating those unexpected patterns are not understood.

Results

We unraveled the phylogeographic structure of the widespread Indo-Pacific coral reef sponge Leucetta chagosensis across its known geographic range using two nuclear markers: the rDNA internal transcribed spacers (ITS 1&2) and a fragment of the 28S gene, as well as the second intron of the ATP synthetase beta subunit-gene (ATPSb-iII). This enabled the detection of several deeply divergent clades congruent over both loci, one containing specimens from the Indian Ocean (Red Sea and Maldives), another one from the Philippines, and two other large and substructured NW Pacific and SW Pacific clades with an area of overlap in the Great Barrier Reef/Coral Sea. Reciprocally monophyletic populations were observed from the Philippines, Red Sea, Maldives, Japan, Samoa, and Polynesia, demonstrating long-standing isolation. Populations along the South Equatorial Current in the south-western Pacific showed isolation-by-distance effects. Overall, the results pointed towards stepping-stone dispersal with some putative long-distance exchange, consistent with expectations from low dispersal capabilities.

Conclusion

We argue that both founder and vicariance events during the late Pliocene and Pleistocene were responsible to varying degrees for generating the deep phylogeographic structure. This structure was perpetuated largely as a result of the life history of L. chagosensis, resulting in high levels of regional isolation. Reciprocally monophyletic populations constitute putative sibling (cryptic) species, while population para- and polyphyly may indicate incipient speciation processes. The genetic diversity and biodiversity of tropical Indo-Pacific sponges appears to be substantially underestimated since the high level of genetic divergence is not necessarily manifested at the morphological level.

Host‐symbiont interactions of the primary endosymbiont of human head and body lice

The first mycetome was discovered more than 340 yr ago in the human louse. Despite the remarkable biology and medical and social importance of human lice, its primary endosymbiont has eluded identification and characterization. Here, we report the host-symbiont interaction of the mycetomic bacterium of the head louse Pediculus humanus capitis and the body louse P. h. humanus. The endosymbiont represents a new bacterial lineage in the gamma-Proteobacteria. Its closest sequenced relative is Arsenophonus nasoniae, from which it differs by more than 10%. A. nasoniae is a male-killing endosymbiont of jewel wasps. Using microdissection and multiphoton confocal microscopy, we show the remarkable interaction of this bacterium with its host. This endosymbiont is unique because it occupies sequentially four different mycetomes during the development of its host, undergoes three cycles of proliferation, changes in length from 2-4 microm to more than 100 microm, and has two extracellular migrations, during one of which the endosymbionts have to outrun its host's immune cells. The host and its symbiont have evolved one of the most complex interactions: two provisional or transitory mycetomes, a main mycetome and a paired filial mycetome. Despite the close relatedness of body and head lice, differences are present in the mycetomic provisioning and the immunological response.

Multiple rRNA Variants in a Single Spore of the Microsporidian Nosema bombi

To understand the source of the multiple DNA sequence variants of Nosema bombi ribosomal RNA (rRNA) found in a single bumble bee host, we PCR amplified, cloned, and sequenced the partial rRNA gene from 125 clones, which were derived from four out of 46 spores individually isolated from a single host by laser microdissection. At least two rRNA variants, characterized by either (GTTT)(2) or (GTTT)(3) repeat units within the internal transcribed spacer (ITS) region, were found per spore in approximately equal proportions, variants which were also found in approximately equal proportions in 55 clones of the two DNA extracts of multiple spores from the same host. Firstly, we demonstrate for the first time that DNA sequences can be obtained from single-binucleate microsporidia. Secondly, it appears that concerted evolution has not homogenized the sequences of all rRNA copies within a single N. bombi spore or even within a single nucleus. We thereby demonstrate unequivocally that two or more rRNA sequence variants exist per N. bombi spore, and urge caution in the use of multicopy rRNA genes for population genetic and phylogenetic analysis of this and other Microsporidia unless homologous copies can be reliably typed.

Phylogenetic analysis of Culicoides species from France based on nuclear ITS1-rDNA sequences

Biting midges of the genus Culicoides (Diptera: Ceratopogonidae) play important roles in the transmission of viral diseases affecting wild and domestic ruminants and horses, including Bluetongue (BT) and African horse sickness (AHS) respectively. In southern Europe, BT has been largely transmitted by the classical Afro-Asian vector Culicoides imicola Kieffer. However, other species such as C. obsoletus Meigen, C. scoticus Downs & Kettle and C. pulicaris Linné may also be involved in BTV transmission. As a consequence of the discovery of C. imicola followed by BTV-2 outbreaks on the island of Corsica in October 2000, further studies on these biting midges have been carried out. To better characterize the evolution and phylogenetic relations of Culicoides, molecular analysis in parallel with a morphology-based taxonomic approach were performed. Phylogenetic analyses of French Culicoides species were undertaken using the ribosomal DNA (rDNA) internal transcribed spacer 1 (ITS1) as a molecular target. This region was shown to be useful in understanding evolutionary and genetic relationships between species. Construction of several trees showed that molecular phylogeny within the genus Culicoides correlates not only with morphological-based taxonomy but also with ecological patterns.

Parasite histories and novel phylogenetic tools: Alternative approaches to inferring parasite evolution from molecular markers

Parasitological research is often contingent on the knowledge of the phylogeny/genealogy of the studied group. Although molecular phylogenetics has proved to be a powerful tool in such investigations, its application in the traditional fashion, based on a tree inference from the primary nucleotide sequences may, in many cases, be insufficient or even improper. These limitations are due to a number of factors, such as a scarcity/ambiguity of phylogenetic information in the sequences, an intricacy of gene relationships at low phylogenetic levels, or a lack of criteria when deciding among several competing coevolutionary scenarios. With respect to the importance of a precise and reliable phylogenetic background in many biological studies, attempts are being made to extend molecular phylogenetics with a variety of new data sources and methodologies. In this review, selected approaches potentially applicable to parasitological research are presented and their advantages as well as drawbacks are discussed. These issues include the usage of idiosyncratic markers (unique features with presumably low probability of homoplasy), such as insertion of mobile elements, gene rearrangements and secondary structure features; the problem of ancestral polymorphism and reticulate relationships at low phylogenetic levels; and the utility of a molecular clock to facilitate discrimination among alternative scenarios in host-parasite coevolution.

Intragenomic heterogeneity of internal transcribed spacer rDNA in neotropical malaria vector Anopheles aquasalis (Diptera: Culicidae)

Intragenomic heterogeneity of the internal transcribed spacer (ITS) array was investigated in Anopheles aquasalis Curry mosquitoes from two geographic locations in each of Brazil and Venezuela, and one in Suriname. Polymerase chain reaction-amplified copies of the ITS were cloned and sequenced. The length of the entire array ranged from 782 to 990 bp, with most variation due to microsatellite insertions in ITS1. We detected 40 different ITSL sequences and 15 different ITS2 sequences of the 71 to 72 clones examined. The sequence divergence within localities ranged from 0.002 to 0.043 for ITS1 and from 0 to 0.006 for ITS2. Point mutations were common to both spacer regions, but dinucleotide microsatellite repeats were restricted to ITS1. Sequences from neither ITS1 nor ITS2 had a diagnostic distribution or were informative in distinguishing these populations, providing additional support for the status of An. aquasalis as a single species.

Intragenomic variation of the rDNA internal transcribed spacers in sponges (Phylum Porifera): implications for phylogenetic studies

The internal transcribed spacer regions (ITS1 and ITS2) of the tandemly repeated nuclear ribosomal DNA clusters are frequently used as markers for fine scale analyses in diverse animals. In certain taxa, ITS is nearly exclusively used for population level or inter-specific studies, despite the frequent presence of divergent paralogs within individual genomes that can be phylogenetically misleading. For the first time we survey diverse marine sponges to determine the extent and phylogenetic implications of intragenomic polymorphisms (IGPs) exhibited at their ITS loci. We discover that the extent of IGP varies greatly between taxa (with most taxa exhibiting very few) and cannot be predicted by taxonomy. Furthermore, we demonstrate that ITS can be phylogenetically informative between species when moderate levels of IGPs are detected, but that ITS paralogy can interfere with population level studies. We caution against the routine use of ITS in phylogenetic studies of sponges without (1) screening for IGPs in specimens from every population sampled; (2) including all divergent paralogs in phylogenetic analyses; (3) testing ITS data using other single-copy, unlinked loci (such as nuclear introns).

The geographical segregation of human lice preceded that of Pediculus humanus capitis and Pediculus humanus humanus

In order to investigate human-louse phylogeny, we partially sequenced two nuclear (18S rRNA and EF-1 alpha) and one mitochondrial (COI) genes from 155 Pediculus from different geographical origins. The phylogenetic analysis of 18S rRNA and EF-1 alpha sequences showed that human lice were classified into lice from Sub-Saharan Africa and lice from other areas. In both clusters, head and body lice were clearly grouped into two separate clusters. Our results indicate that the earliest divergence within human pediculidae occurred between African lice and other lice, and the divergence between head and body lice was not the result from a single event.

Heterogeneity of ITS1 sequences in the biting midge Culicoides impunctatus (Goetghebuer) suggests a population in Argyll, Scotland, may be genetically distinct

Ribosomal DNA (rDNA) internal transcribed spacer 1 (ITS1) is a useful genomic region for understanding evolutionary and genetic relationships. In the current study, variation in ITS1 from eight Culicoides species was analysed by PCR, DNA restriction analysis, cloning, and sequencing. ITS1 variants were essentially homogenized within a species, as sequences were identical or closely related. However, Culicoides impunctatus ITS1 sequences derived from one (Argyll) of five populations contained considerable genomic diversity. The secondary structure of each ITS1 was computed. The structure aided the production of an accurate alignment and the identification of a large indel. A phylogenetic analysis was performed. Some of the sequences from the diverse Argyll C. impunctatus population were more related to Culicoides imicola, a vector of animal pathogens in the Old World, than they were to the other C. impunctatus sequences. Thus, the rDNA ITS1 regions of individuals in the Argyll C. impunctatus population were not conforming to the general theory of rDNA homogenization through molecular drive.Key words: Culicoides, ITS1, phylogeny, rDNA, secondary structure.

Human lice and their control

Current research on human louse biology has focused on the long-standing debate about speciation of head and body lice but using new tools of DNA and enzyme analysis. These studies have indicated that head and body lice from the same geographical zone may be more closely allied than insects inhabiting the same ecological niche in other regions. However, the majority of research over the past decade has involved clinical aspects including transmission, treatment, and the appearance and identification of resistant strains within populations of lice. Despite advances, there is a need for a better understanding of louse biology, as existing therapies fail and lice remain potential vectors of disease for millions of people.

Transcriptome identification of putative genes involved in protein catabolism and innate immune response in human body louse (Pediculicidae: Pediculus humanus)

Genomics information relating to human body lice is surprisingly scarce, and this has constrained studies of their physiology, immunology and vector biology. To identify novel body louse genes, we used engorged adult lice to generate a cDNA library. Initially, 1152 clones were screened for inserts, edited for removal of vector sequences and base pairs of poor quality, and viewed for splicing variations, gene families and polymorphism. Computational methods identified 506 inferred open reading frames including the first predicted louse defensin. The inferred defensin aligns well with other insect defensins and has highly conserved cysteine residues, as are known for other defensin sequences. Two cysteine and five serine proteinases were categorized according to their inferred catalytic sites. We also discovered seven putative ubiquitin-pathway genes and four iron metabolizing deduced enzymes. Finally, glutathione-S-transferases and cytochrome P450 genes were among the detoxification enzymes found. Results from this first systematic effort to discover human body louse genes should promote further studies in Phthiraptera and lice.