The mitochondrial 12S gene is a suitable marker of populations of Sarcoptes scabiei from wombats, dogs and humans in Australia

Sustaining Transmission in Different Host Species: The Emblematic Case of Sarcoptes scabiei

Some pathogens sustain transmission in multiple different host species, but how this epidemiologically important feat is achieved remains enigmatic. Sarcoptes scabiei is among the most host generalist and successful of mammalian parasites. We synthesize pathogen and host traits that mediate sustained transmission and present cases illustrating three transmission mechanisms (direct, indirect, and combined). The pathogen traits that explain the success of S. scabiei include immune response modulation, on-host movement capacity, off-host seeking behaviors, and environmental persistence. Sociality and host density appear to be key for hosts in which direct transmission dominates, whereas in solitary hosts, the use of shared environments is important for indirect transmission. In social den-using species, combined direct and indirect transmission appears likely. Empirical research rarely considers the mechanisms enabling S. scabiei to become endemic in host species—more often focusing on outbreaks. Our review may illuminate parasites’ adaptation strategies to sustain transmission through varied mechanisms across host species.

Laboratory-based diagnosis of scabies: a review of the current status

Scabies is a neglected tropical disease (NTD) of the skin that is caused by the mite Sarcoptes scabiei. It is considered to be an important public health problem in many regions. The disease is at its most prevalent in low-resource countries where there are overcrowded living conditions coupled with poor hygiene. In some regions, mass drug administration using ivermectin is a key population-based approach to the control of scabies. Before starting a patient on specific treatment, confirming the diagnosis by accurate and rapid identification of the organism is critical. Different laboratory-based techniques for scabies have been developed in the last few decades. These include direct microscopy and histopathology. More recently, serological testing, dermoscopy and different molecular techniques have been developed as diagnostic methods for scabies. To date, none of these, apart from microscopy and dermoscopy, has been translated into routine clinical laboratory practice. A simple point-of-care or laboratory test would provide a rapid and confirmed diagnosis and early institution of effective treatment. In this review we present an update on the laboratory techniques currently in use for the identification of scabies.

Sarcoptic mange: An emerging panzootic in wildlife

Sarcoptic mange, a skin infestation caused by the mite Sarcoptes scabiei, is an emerging disease for some species of wildlife, potentially jeopardizing their welfare and conservation. Sarcoptes scabiei has a near-global distribution facilitated by its forms of transmission and use of a large diversity of host species (many of those with broad geographic distribution). In this review, we synthesize the current knowledge concerning the geographic and host taxonomic distribution of mange in wildlife, the epidemiological connections between species, and the potential threat of sarcoptic mange for wildlife conservation. Recent sarcoptic mange outbreaks in wildlife appear to demonstrate ongoing geographic spread, increase in the number of hosts and increased virulence. Sarcoptic mange has been reported in at least 12 orders, 39 families and 148 species of domestic and wild mammals, making it one of the most generalist ectoparasites of mammals. Taxonomically, the orders with most species found infested so far include Perissodactyla (67% species from the entire order), Artiodactyla (47%), and Diprotodontia (67% from this order). This suggests that new species from these mammal orders are likely to suffer cross-species transmission and be reported positive to sarcoptic mange as surveillance improves. We propose a new agenda for the study of sarcoptic mange in wildlife, including the study of the global phylogeography of S. scabiei, linkages between ecological host traits and sarcoptic mange susceptibility, immunology of individuals and species, development of control strategies in wildlife outbreaks and the effects of global environmental change in the sarcoptic mange system. The ongoing transmission globally and sustained spread among areas and wildlife species make sarcoptic mange an emerging panzootic in wildlife. A better understanding of sarcoptic mange could illuminate the aspects of ecological and evolutionary drivers in cross-species transmission for many emerging diseases.

A review of sarcoptic mange in North American wildlife

The "itch mite" or "mange mite", Sarcoptes scabiei, causes scabies in humans and sarcoptic mange in domestic and free-ranging animals. This mite has a wide host range due to its ability to adapt to new hosts and has been spread across the globe presumably through human expansion. While disease caused by S. scabiei has been very well-studied in humans and domestic animals, there are still numerous gaps in our understanding of this pathogen in free-ranging wildlife. The literature on sarcoptic mange in North American wildlife is particularly limited, which may be due to the relatively limited number of clinically-affected species and lack of severe population impacts seen in other continents. This review article provides a summary of the current knowledge of mange in wildlife, with a focus on the most common clinically-affected species in North America including red foxes (Vulpes vulpes), gray wolves (Canis lupus), coyotes (Canis latrans), and American black bears (Ursus americanus).

Extracting the invisible: obtaining high quality DNA is a challenging task in small arthropods

BACKGROUND

The application of an appropriate extraction method is a relevant factor for the success of all molecular studies.

METHODS

Seven different DNA extraction methods suitable for high-throughput DNA sequencing with very small arthropods were compared by applying nine different protocols: three silica gel based spin methods, two cetyltrimethyl ammonium bromide (CTAB) based ones (one with an additional silica membrane), a protein precipitation method and a method based on a chelating resin (applying different protocols). The quantity (concentration) and quality (degradation, contamination, polymerase chain reaction (PCR) and sequencing success) of the extracted DNA as well as the costs, preparation times, user friendliness, and required supplies were compared across these methods. To assess the DNA quantity, two different DNA concentration measurements were applied. Additionally, the effect of varying amounts of starting material (different body sizes), variable lysis temperatures and mixing during DNA extraction was evaluated.

RESULTS

Although low DNA concentrations were measured for all methods, the results showed that-with the exception of two methods-the PCR success was 100%. However, other parameters show vast differences. The time taken to perform DNA extraction varied from 20 min to 2.5 h (Chelex vs. CTAB) and the costs from 0.02 to 3.46 € (Chelex vs. QIAamp kit) per sample. High quality genomic DNA was only gained from four methods. Results of DNA quantity measurements further indicated that some devices cannot deal with small amounts of DNA and show variant results.

DISCUSSION

In conclusion, using Chelex (chelating resin) turned out as a rapid, low-cost method which can provide high quality DNA for different kinds of molecular investigations.

Genetic variability of wildlife-derived Sarcoptes scabiei determined by the ribosomal ITS-2 and mitochondrial 16S genes

Infestation by the ectoparasitic mite Sarcoptes scabiei (Acari: Sarcoptidae) has important implications for global wildlife conservation and both animal and human health. Ribosomal and mitochondrial DNA sequences of parasites are useful to determine genetic diversity and to describe their likely dynamic evolution. In this study, we described the genetic diversity of S. scabiei individuals collected from wild animals in China by sequencing the ribosomal ITS-2 and mitochondrial 16S rRNA genes. A total of 13 Sarcoptes isolates of wildlife, coupled with one of rabbit origin, were subjected to genetic characteristics. After cloning and sequencing, 14 ITS-2 sequences and 12 16S rRNA sequences were obtained and analyzed. Further analysis of haplotype network and population genetic structure revealed that there were 79 haplotypes in ITS-2 (main haplotype H2) and 31 haplotypes in 16S rRNA (main haplotype C10). The phylogenetic trees showed some partial clustering by location and host, and the analysis of gene polymorphism may prompt that all isolates of S. scabiei have a similar origin. We speculate that the genetic evolution of S. scabiei may be related with that of the hosts, but more research is necessary to better understand the host-parasite co-evolutionary relationship in S. scabiei. These results provide new insights into understanding the population genetics and evolutionary biology of S. scabiei and therefore a better understanding of controlling its infestation pathways worldwide.

Expanded Molecular Typing of Sarcoptes scabiei Provides Further Evidence of Disease Spillover Events in the Epidemiology of Sarcoptic Mange in Australian Marsupials

The invasive ectoparasite Sarcoptes scabiei affects the welfare and conservation of Australian marsupials. Molecular data suggest that spillover from other hosts may be responsible for the emergence of this infectious disease, but the scale of such studies is limited. We performed expanded molecular typing of the S. scabiei mitochondrial cox1 gene from 81 skin scrapings from infested wombats ( Vombatus ursinus), koalas ( Phascolarctos cinereus), red foxes ( Vulpes vulpes), and dogs ( Canis lupus familiaris) across Australia. Combined with existing S. scabiei sequences, our analysis revealed 16 haplotypes among Australian animals, sharing between 93.3% and 99.7% sequence similarity. While some sequences were unique to specific hosts or to Australia, key haplotypes could be detected across several marsupial hosts as well as to wild or domestic canids in Australia. We identified 43 cox1 haplotypes with many Australian haplotypes identical to S. scabiei mites from inside and outside Europe. We concluded that multiple introduction events were plausible explanations to the origin and emergence of this parasite into Australian marsupials and that disease spillover from canids was likely. Together, our greatly expanded S. scabiei sequence dataset provided a more nuanced picture of both spillover and sustained intraspecific transmission for this important parasite.

Mitochondrial genome sequencing reveals potential origins of the scabies mite Sarcoptes scabiei infesting two iconic Australian marsupials

BACKGROUND

Debilitating skin infestations caused by the mite, Sarcoptes scabiei, have a profound impact on human and animal health globally. In Australia, this impact is evident across different segments of Australian society, with a growing recognition that it can contribute to rapid declines of native Australian marsupials. Cross-host transmission has been suggested to play a significant role in the epidemiology and origin of mite infestations in different species but a chronic lack of genetic resources has made further inferences difficult. To investigate the origins and molecular epidemiology of S. scabiei in Australian wildlife, we sequenced the mitochondrial genomes of S. scabiei from diseased wombats (Vombatus ursinus) and koalas (Phascolarctos cinereus) spanning New South Wales, Victoria and Tasmania, and compared them with the recently sequenced mitochondrial genome sequences of S. scabiei from humans.

RESULTS

We found unique S. scabiei haplotypes among individual wombat and koala hosts with high sequence similarity (99.1% - 100%). Phylogenetic analysis of near full-length mitochondrial genomes revealed three clades of S. scabiei (one human and two marsupial), with no apparent geographic or host species pattern, suggestive of multiple introductions. The availability of additional mitochondrial gene sequences also enabled a re-evaluation of a range of putative molecular markers of S. scabiei, revealing that cox1 is the most informative gene for molecular epidemiological investigations. Utilising this gene target, we provide additional evidence to support cross-host transmission between different animal hosts.

CONCLUSIONS

Our results suggest a history of parasite invasion through colonisation of Australia from hosts across the globe and the potential for cross-host transmission being a common feature of the epidemiology of this neglected pathogen. If this is the case, comparable patterns may exist elsewhere in the 'New World'. This work provides a basis for expanded molecular studies into mange epidemiology in humans and animals in Australia and other geographic regions.

Sarcoptic mange in wombats-A review and future research directions

Sarcoptic mange is caused by the mite Sarcoptes scabiei and has recently been recognized as an emerging infectious disease of wildlife worldwide. The mite is one of the main causes of population decline in southern hairy-nosed (Lasiorhinus latifrons) and bare-nosed wombats (Vombatus ursinus). This review focuses on Sarcoptes scabiei infestations in wombats and provides insights into why the disease may be so prevalent in wombats. Current treatment practices and trials conducted in the field to reduce the incidence of sarcoptic mange in wombats are described and critically reviewed. Current and potential future avenues of research are discussed.

DNA barcoding for molecular identification of Demodex based on mitochondrial genes

There has been no widely accepted DNA barcode for species identification of Demodex. In this study, we attempted to solve this issue. First, mitochondrial cox1-5' and 12S gene fragments of Demodex folloculorum, D. brevis, D. canis, and D. caprae were amplified, cloned, and sequenced for the first time; intra/interspecific divergences were computed and phylogenetic trees were reconstructed. Then, divergence frequency distribution plots of those two gene fragments were drawn together with mtDNA cox1-middle region and 16S obtained in previous studies. Finally, their identification efficiency was evaluated by comparing barcoding gap. Results indicated that 12S had the higher identification efficiency. Specifically, for cox1-5' region of the four Demodex species, intraspecific divergences were less than 2.0%, and interspecific divergences were 21.1-31.0%; for 12S, intraspecific divergences were less than 1.4%, and interspecific divergences were 20.8-26.9%. The phylogenetic trees demonstrated that the four Demodex species clustered separately, and divergence frequency distribution plot showed that the largest intraspecific divergence of 12S (1.4%) was less than cox1-5' region (2.0%), cox1-middle region (3.1%), and 16S (2.8%). The barcoding gap of 12S was 19.4%, larger than cox1-5' region (19.1%), cox1-middle region (11.3%), and 16S (13.0%); the interspecific divergence span of 12S was 6.2%, smaller than cox1-5' region (10.0%), cox1-middle region (14.1%), and 16S (11.4%). Moreover, 12S has a moderate length (517 bp) for sequencing at once. Therefore, we proposed mtDNA 12S was more suitable than cox1 and 16S to be a DNA barcode for classification and identification of Demodex at lower category level.

Crusted scabies (sarcoptic mange) in four cats due to Sarcoptes scabiei infestation

Four new cases of sarcoptic mange in cats are described. Two cats resided in areas known to be frequented by foxes, another cohabited with a dog recently diagnosed with sarcoptic mange, while the final cat lived with a mixed breed dog that had been treated for sarcoptic mange 7 months previously. Three cases were diagnosed on the basis of characteristic mite size and morphology in skin scraping from representative lesions, situated on the head (two cases) or head and distal hind limbs (one case). Mites were highly mobile and abundant in all instances, and easily detected also in skin biopsy specimens procured from two cases. Eosinophilic inflammation, hyperkeratosis and parakeratosis were prominent in the tissue sections. In the remaining case, the diagnosis was presumptive, based on characteristic lesions, cohabitation with a canine scabies patient and positive response to scabicide therapy. Pruritus was not a prominent clinical feature in any patient and was considered to be absent in three of the four cases. Lesions in three cats with long-standing disease were reminiscent of crusted scabies (synonym: Norwegian scabies, parakeratotic scabies) as seen in human patients. In three cases, in-contact human carriers developed itchy cutaneous papular lesions. Two cases responded promptly to therapy with systemic avermectin drugs, while one responded to topical treatment with lime sulphur and the remaining cat received both a lime sulphur rinse and ivermectin. Sarcoptic mange should be considered in the differential diagnosis of cats with non-pruritic crusting skin diseases, especially when there is contact with foxes or dogs, and when owners have itchy papular lesions.

The emergence of sarcoptic mange in Australian wildlife: an unresolved debate

Due to its suspected increase in host range and subsequent global diversification, Sarcoptes scabiei has important implications at a global scale for wildlife conservation and animal and human health. The introduction of this pathogen into new locations and hosts has been shown to produce high morbidity and mortality, a situation observed recently in Australian and North American wildlife.

Of the seven native animal species in Australia known to be infested by S. scabiei, the bare-nosed wombat (Vombatus ursinus) suffers the greatest with significant population declines having been observed in New South Wales and Tasmania. The origins of sarcoptic mange in Australian native animals are poorly understood, with the most consistent conclusion being that mange was introduced by settlers and their dogs and subsequently becoming a major burden to native wildlife. Four studies exist addressing the origins of mange in Australia, but all Australian S. scabiei samples derive from only two of these studies. This review highlights this paucity of phylogenetic knowledge of S. scabiei within Australia, and suggests further research is needed to confidently determine the origin, or multiple origins, of this parasite.

At the global scale, numerous genetic studies have attempted to reveal how the host species and host geographic location influence S. scabiei phylogenetics. This review includes an analysis of the global literature, revealing that inconsistent use of gene loci across studies significantly influences phylogenetic inference. Furthermore, by performing a contemporary analytical approach on existing data, it is apparent that (i) new S. scabiei samples, (ii) appropriate gene loci targets, and (iii) advanced phylogenetic approaches are necessary to more confidently comprehend the origins of mange in Australia. Advancing this field of research will aid in understanding the mechanisms of spillover for mange and other parasites globally.

Are humans the initial source of canine mange?

Background

Scabies, or mange as it is called in animals, is an ectoparasitic contagious infestation caused by the mite Sarcoptes scabiei. Sarcoptic mange is an important veterinary disease leading to significant morbidity and mortality in wild and domestic animals. A widely accepted hypothesis, though never substantiated by factual data, suggests that humans were the initial source of the animal contamination. In this study we performed phylogenetic analyses of populations of S. scabiei from humans and from canids to validate or not the hypothesis of a human origin of the mites infecting domestic dogs.

Methods

Mites from dogs and foxes were obtained from three French sites and from other countries. A part of cytochrome c oxidase subunit 1 (cox1) gene was amplified and directly sequenced. Other sequences corresponding to mites from humans, raccoon dogs, foxes, jackal and dogs from various geographical areas were retrieved from GenBank. Phylogenetic analyses were performed using the Otodectes cynotis cox1 sequence as outgroup. Maximum Likelihood and Bayesian Inference analysis approaches were used. To visualize the relationship between the haplotypes, a median joining haplotype network was constructed using Network v4.6 according to host.

Results

Twenty-one haplotypes were observed among mites collected from five different host species, including humans and canids from nine geographical areas. The phylogenetic trees based on Maximum Likelihood and Bayesian Inference analyses showed similar topologies with few differences in node support values. The results were not consistent with a human origin of S. scabiei mites in dogs and, on the contrary, did not exclude the opposite hypothesis of a host switch from dogs to humans.

Conclusions

Phylogenetic relatedness may have an impact in terms of epidemiological control strategy. Our results and other recent studies suggest to re-evaluate the level of transmission between domestic dogs and humans.

Sarcoptes scabiei mites in humans are distributed into three genetically distinct clades

Scabies is an ectoparasitic infestation caused by the mite Sarcoptes scabiei. Currently, S. scabiei is taxonomically divided into different varieties on the basis of host origin. Genetics-based research on scabies has been conducted, but the data on genetic diversity of populations of this mite in humans in Europe are lacking. We evaluated the genetic diversity of populations of S. scabiei. A large series of mites obtained from humans in France and the data of mites from various hosts and geographical areas retrieved from GenBank were included to investigate whether mites are divided into distinct populations. The study of cytochrome c oxidase subunit 1 gene polymorphisms were found to be best suited for phylogenetic analysis. S. scabiei mites were distributed into three genetically distinct clades, with most mites clustering in clades B and C. The Fst value and the Nm value calculated for mites included in clades B and C indicated a strong population structure and a very low gene flow between mites of those clades. The results of the present study not only support the rejection of the hypothesis of panmixia for S. scabiei in humans but also suggest that mites belonging to different clades are genetically isolated. Moreover, the results suggest that the subdivision of S. scabies in varieties according to animal or human hosts is not warranted. In conclusion, S. scabiei mites in humans do not constitute a homogeneous population. Further investigations are now required to assess whether different clinical forms of scabies are associated with particular haplotypes or clades.

First detection of Sarcoptes scabiei from domesticated pig (Sus scrofa) and genetic characterization of S. scabiei from pet, farm and wild hosts in Israel

In this report we describe for the first time the detection of Sarcoptes scabiei type suis mites on domestic pigs in Israel and examine its genetic variation compared with S. sabiei from other hosts. Microscopic examination of skin samples from S. scabiei-infested pigs (Sus scrofa domesticus) revealed all developmental stages of S. scabiei. To detect genetic differences between S. scabiei from different hosts, samples obtained from pig, rabbits (Orictolagus cuniculus), fox (Vulpes vulpes), jackal (Canis aureus) and hedgehog (Erinaceus concolor) were compared with GenBank-annotated sequences of three genetic markers. Segments from the following genes were examined: cytochrome C oxidase subunit 1 (COX1), glutathione-S-transferase 1 (GST1), and voltage-sensitive sodium channel (VSSC). COX1 analysis did not show correlation between host preference and genetic identity. However, GST1 and VSSC had a higher percentage of identical sites within S. scabiei type suis sequences, compared with samples from other hosts. Taking into account the limited numbers of GST1 and VSSC sequences available for comparison, this high similarity between sequences of geographically-distant, but host-related populations, may suggest that different host preference is at least partially correlated with genetic differences. This finding may help in future studies of the factors that drive host preferences in this parasite.

The Complete Mitochondrial Genome of the Beet Webworm, Spoladea recurvalis (Lepidoptera: Crambidae) and Its Phylogenetic Implications

The complete mitochondrial genome (mitogenome) of the beet webworm, Spoladea recurvalis has been sequenced. The circular genome is 15,273 bp in size, encoding 13 protein-coding genes (PCGs), two rRNA genes, and 22 tRNA genes and containing a control region with gene order and orientation identical to that of other ditrysian lepidopteran mitogenomes. The nucleotide composition of the mitogenome shows a high A+T content of 80.9%, and the AT skewness is slightly negative (-0.023). All PCGs start with the typical ATN codons, except for COX1, which may start with the CGA codon. Nine of 13 PCGs have the common stop codon TAA; however, COX1, COX2 and ND5 utilize the T nucleotide and ND4 utilizes TA nucleotides as incomplete termination codons. All tRNAs genes are folded into the typical cloverleaf structure of mitochondrial tRNAs, except for the tRNA^Ser(AGY) gene, in which the DHU arm fails to form a stable stem-loop structure. A total of 157 bp intergenic spacers are scattered in 17 regions. The overlapping sequences are 42 bp in total and found in eight different locations. The 329 bp AT-rich region is comprised of non-repetitive sequences, including the motif ATAG, which is followed by a 14 bp poly-T stretch, a (AT₁₁ microsatellite-like repeat, which is adjacent to the motif ATTTA, and a 9 bp poly-A, which is immediately upstream from the tRNA^Met gene. Phylogenetic analysis, based on 13 PCGs and 13 PCGs+2 rRNAs using Bayesian inference and Maximum likelihood methods, show that the classification position of Pyraloidea is inconsistent with the traditional classification. Hesperioidea is placed within the Papilionoidea rather than as a sister group to it. The Pyraloidea is placed within the Macrolepidoptera with other superfamilies instead of the Papilionoidea.

Development of Conventional and Real-Time Quantitative PCR Assays for Diagnosis and Monitoring of Scabies

Scabies remains the most prevalent, endemic, and neglected ectoparasitic infestation globally and can cause institutional outbreaks. The sensitivity of routine microscopy for demonstration of Sarcoptes scabiei mites or eggs in skin scrapings is only about 50%. Except for three studies using conventional or two-tube nested PCR on a small number of cases, no systematic study has been performed to improve the laboratory diagnosis of this important infection. We developed a conventional and a real-time quantitative PCR (qPCR) assay based on the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene of S. scabiei. The cox1 gene is relatively well conserved, with its sequence having no high levels of similarity to the sequences of other human skin mites, pathogenic zoonotic mites, or common house dust mite species. This mitochondrial gene is also present in large quantities in arthropod cells, potentially improving the sensitivity of a PCR-based assay. In our study, both assays were specific and were more sensitive than microscopy in diagnosing scabies, with positive and negative predictive values of 100%. The S. scabiei DNA copy number in the microscopy-positive specimens was significantly higher than that in the microscopy-negative specimens (median S. scabiei DNA copy number, 3.604 versus 2.457 log10 copies per reaction; P = 0.0213). In the patient with crusted scabies, the qPCR assay performed on lesional skin swabs instead of scrapings revealed that the parasite DNA load took about 2 weeks to become negative after treatment. The utility of using lesional skin swabs as an alternative sample for diagnosis of scabies by PCR should be further evaluated.

Wombats acquired scabies from humans and/or dogs from outside Australia

According to previous studies, Sarcoptes mites of wombats were relatively recently introduced into Australia by colonizers and/or their dogs. However, that affirmation has been called into question due to apparent flaws in the design of the phylogenetic studies. With the aim of providing a definitive answer to this question, a part of the mitochondrial gene coding for 12S rRNA of S. scabiei mites from 23 humans and one dog collected in France was sequenced and a phylogenetic analysis including the sequences previously deposited in Genbank was performed. Phylogenetic analysis did not show host segregation or geographical isolation of the mites. Conversely, the present work suggested that mange in wombats is indeed due to the introduction of S. scabiei into Australia by immigrating individuals and/or their companion animals.

Population identification of Sarcoptes hominis and Sarcoptes canis in China using DNA sequences

There has been no consistent conclusion on whether Sarcoptes mites parasitizing in humans and animals are the same species. To identify Sarcoptes (S.) hominis and S. canis in China, gDNA was extracted from individual mites (five from patients with scabies and five from dogs with mange) for amplification of rDNA ITS2, mtDNA 16S, and cox1 fragment sequences. Then, the sequences obtained were aligned with those from different hosts and geographical locations retrieved from GenBank and sequence analyses were conducted. Phylogenetic trees based on 317-bp mtDNA cox1 showed five distinctive branches (species) of Sarcoptes mites, four for S. hominis (S. hominis Chinese, S. nr. hominis Chinese, S. hominis Australian, and S. hominis Panamanian) and one for S. animal (S. animal). S. animal included mites from nine animal species, with S. canis China, S. canis Australia, and S. canis USA clustering as a subbranch. Further sequence divergence analysis revealed no overlap between intraspecific (≤ 2.6 %) and interspecific (2.6-10.5 %) divergences in 317-bp mtDNA cox1. However, overlap was detected between intra- and interspecific divergences in 311-bp rDNA ITS2 or 275-bp mtDNA 16S when the divergences exceeded 1.0 %, which resulted in failure in identification of Sarcoptes. The results showed that the 317-bp mtDNA cox1 could be used as a DNA barcode for molecular identification of Sarcoptes mites. In addition, geographical isolation was observed between S. hominis Chinese, S. hominis Australian, and S. hominis Panamanian, but not between all S. canis. S. canis and the other S. animal belonged to the same species.

Integrated Bayesian species delimitation and morphological diagnostics of chorioptic mange mites (Acariformes: Psoroptidae: Chorioptes)

The external morphology of adult and immature stages of mange mites of the genus Chorioptes was investigated with the aid of light and scanning electron microscopy. A molecular phylogeny of this genus was inferred based on six genes (18S, 28S rDNA, EF1-α, SRP54, HSP70, and CO1). The validity of four species (Ch. bovis, Ch. panda, Ch. texanus, and Ch. sweatmani sp. nov. described from the moose from Sweden, Finland, and Russia) was confirmed based on morphology and a Bayesian species delimitation analysis incorporating both gene tree uncertainties and incomplete lineage sorting via the coalescent process model in BPP. Sequence data for Ch. crewei and Ch. mydaus was not available but their morphology strongly suggests their validity. The six valid Chorioptes species are diagnosed using type and non-type specimens, and a key to species is provided. Ch. sweatmani differs from closely related Ch. texanus by the following features: in males, the body length, including the gnathosoma, is 380-405 μm (vs. 220-295 in Ch. texanus), the idiosoma is 3-4 times longer than setae cp (vs. 1.3-1.6 times longer), legs III are approximately three times longer than setae sRIII (vs. 1.8-2 times longer), the apical spur of tarsus III is curved (vs. straight), a spur near seta fIII base is not developed (vs. small but distinct); in females, setae h2 are 1.4-1.5 times shorter than legs IV (vs. about two times longer). Hosts and distribution records of Chorioptes species are summarized.

Preliminary molecular characterizations of Sarcoptes scaibiei (Acari: Sarcoptidae) from farm animals in Egypt

Little is known about the genetic diversity of Sarcoptes scabiei mites in farm animals in Egypt. In this study, we characterized S. scabiei in 25 skin scrapes from water buffalo, cattle, sheep, and rabbits at the nuclear marker ITS2 and mitochondrial markers COX1 and 16S rRNA. Sequences of the ITS2 showed no host segregation or geographical isolation, whereas those of the mitochondrial COX1 and 16S rRNA genes indicated the presence of both host-adapted and geographically segregated populations of S. scabiei. Host adaptation may limit inter-species transmission of. S. scabiei, thus restrict gene flow among S. scabiei from different hosts. This is the first report on the molecular characterization of sarcoptic mites in Egypt. Further genetic studies involving larger numbers of specimens, especially those from humans and companion animals, are needed to understand the molecular epidemiology of sarcoptic mange in Egypt.

Advances in studies of disease-navigating webs: Sarcoptes scabiei as a case study

The discipline of epidemiology is the study of the patterns, causes and effects of health and disease conditions in defined anima populations. It is the key to evidence-based medicine, which is one of the cornerstones of public health. One of the important facets of epidemiology is disease-navigating webs (disease-NW) through which zoonotic and multi-host parasites in general move from one host to another. Epidemiology in this context includes (i) classical epidemiological approaches based on the statistical analysis of disease prevalence and distribution and, more recently, (ii) genetic approaches with approximations of disease-agent population genetics. Both approaches, classical epidemiology and population genetics, are useful for studying disease-NW. However, both have strengths and weaknesses when applied separately, which, unfortunately, is too often current practice. In this paper, we use Sarcoptes scabiei mite epidemiology as a case study to show how important an integrated approach can be in understanding disease-NW and subsequent disease control.

Complete mitochondrial genome recovered from the gut metagenome of overwintering monarch butterflies, Danaus plexippus (L.) (Lepidoptera: Nymphalidae, Danainae)

We present a 15,314 bp mitochondrial genome (mitogenome) sequence from monarch butterflies overwintering in Mexico. The complete mitogenome was generated by next generation sequencing techniques and was reconstructed by iterative assembly of reads from a metagenomic study of pooled butterfly gut DNA. The mitogenome codes for 13 putative protein coding genes, 22 tRNA genes, the large and small rRNA genes, and contains the A + T-rich sequence corresponding to the control region. The consensus sequence presented here has a depth of coverage of 142-fold and only three putative single nucleotide polymorphisms could be detected. The recovered D. plexippus mitogenome represents the second analyzed for the subfamily Danainae and accordingly, the closest available sequenced mitogenome was found to be the one corresponding to Euploea mulciber (Lepidoptera: Nymphalidae, Danainae).

Land-use change and emerging infectious disease on an island continent

A more rigorous and nuanced understanding of land-use change (LUC) as a driver of emerging infectious disease (EID) is required. Here we examine post hunter-gatherer LUC as a driver of infectious disease in one biogeographical region with a compressed and documented history--continental Australia. We do this by examining land-use and native vegetation change (LUCC) associations with infectious disease emergence identified through a systematic (1973-2010) and historical (1788-1973) review of infectious disease literature of humans and animals. We find that 22% (20) of the systematically reviewed EIDs are associated with LUCC, most frequently where natural landscapes have been removed or replaced with agriculture, plantations, livestock or urban development. Historical clustering of vector-borne, zoonotic and environmental disease emergence also follows major periods of extensive land clearing. These advanced stages of LUCC are accompanied by changes in the distribution and density of hosts and vectors, at varying scales and chronology. This review of infectious disease emergence in one continent provides valuable insight into the association between accelerated global LUC and concurrent accelerated infectious disease emergence.

Beyond barcoding: a mitochondrial genomics approach to molecular phylogenetics and diagnostics of blowflies (Diptera: Calliphoridae)

Members of the Calliphoridae (blowflies) are significant for medical and veterinary management, due to the ability of some species to consume living flesh as larvae, and for forensic investigations due to the ability of others to develop in corpses. Due to the difficulty of accurately identifying larval blowflies to species there is a need for DNA-based diagnostics for this family, however the widely used DNA-barcoding marker, cox1, has been shown to fail for several groups within this family. Additionally, many phylogenetic relationships within the Calliphoridae are still unresolved, particularly deeper level relationships. Sequencing whole mt genomes has been demonstrated both as an effective method for identifying the most informative diagnostic markers and for resolving phylogenetic relationships. Twenty-seven complete, or nearly so, mt genomes were sequenced representing 13 species, seven genera and four calliphorid subfamilies and a member of the related family Tachinidae. PCR and sequencing primers developed for sequencing one calliphorid species could be reused to sequence related species within the same superfamily with success rates ranging from 61% to 100%, demonstrating the speed and efficiency with which an mt genome dataset can be assembled. Comparison of molecular divergences for each of the 13 protein-coding genes and 2 ribosomal RNA genes, at a range of taxonomic scales identified novel targets for developing as diagnostic markers which were 117-200% more variable than the markers which have been used previously in calliphorids. Phylogenetic analysis of whole mt genome sequences resulted in much stronger support for family and subfamily-level relationships. The Calliphoridae are polyphyletic, with the Polleninae more closely related to the Tachinidae, and the Sarcophagidae are the sister group of the remaining calliphorids. Within the Calliphoridae, there was strong support for the monophyly of the Chrysomyinae and Luciliinae and for the sister-grouping of Luciliinae with Calliphorinae. Relationships within Chrysomya were not well resolved. Whole mt genome data, supported the previously demonstrated paraphyly of Lucilia cuprina with respect to L. sericata and allowed us to conclude that it is due to hybrid introgression prior to the last common ancestor of modern sericata populations, rather than due to recent hybridisation, nuclear pseudogenes or incomplete lineage sorting.

RAPD-SCAR marker and genetic relationship analysis of three Demodex species (Acari: Demodicidae)

For a long time, classification of Demodex mites has been mainly based on their hosts and phenotype characteristics. The study was the first to conduct molecular identification and genetic relationship analysis for six isolates of three Demodex species by random amplified polymorphic DNA (RAPD) and sequence-characterized amplified region (SCAR) marker. Totally, 239 DNA fragments were amplified from six Demodex isolates with 10 random primers in RAPD, of which 165 were polymorphic. Using a single primer, at least five fragments and at most 40 in the six isolates were amplified, whereas within a single isolate, a range of 35-49 fragments were amplified. DNA fingerprints of primers CZ 1-9 revealed intra- and interspecies difference in six Demodex isolates, whereas primer CZ 10 only revealed interspecies difference. The genetic distance and dendrogram showed the intraspecific genetic distances were closer than the interspecific genetic distances. The interspecific genetic distances of Demodex folliculorum and Demodex canis (0.7931-0.8140) were shorter than that of Demodex brevis and D. canis (0.8182-0.8987). The RAPD-SCAR marker displayed primer CZ 10 could be applied to identify the three Demodex species. The 479-bp fragment was specific for D. brevis, and the 261-bp fragment was specific for D. canis. The conclusion was that the RAPD-SCAR multi-marker was effective in molecular identification of three Demodex species. The genetic relationship between D. folliculorum and D. canis was nearer than that between D. folliculorum and D. brevis.

Sarcoptes-World Molecular Network (Sarcoptes-WMN): integrating research on scabies

Parasites threaten human and animal health globally. It is estimated that more than 60% of people on planet Earth carry at least one parasite, many of them several different species. Unfortunately, parasite studies suffer from duplications and inconsistencies between different investigator groups. Hence, groups need to collaborate in an integrated manner in areas including parasite control, improved therapy strategies, diagnostic and surveillance tools, and public awareness. Parasite studies will be better served if there is coordinated management of field data and samples across multidisciplinary approach plans, among academic and non-academic organizations worldwide. In this paper we report the first 'Living organism-World Molecular Network', with the cooperation of 167 parasitologists from 88 countries on all continents. This integrative approach, the 'Sarcoptes-World Molecular Network', seeks to harmonize Sarcoptes epidemiology, diagnosis, treatment, and molecular studies from all over the world, with the aim of decreasing mite infestations in humans and animals.

Parasite zoonoses and wildlife: emerging issues

The role of wildlife as important sources, reservoirs and amplifiers of emerging human and domestic livestock pathogens, in addition to well recognized zoonoses of public health significance, has gained considerable attention in recent years. However, there has been little attention given to the transmission and impacts of pathogens of human origin, particularly protozoan, helminth and arthropod parasites, on wildlife. Substantial advances in molecular technologies are greatly improving our ability to follow parasite flow among host species and populations and revealing valuable insights about the interactions between cycles of transmission. Here we present several case studies of parasite emergence, or risk of emergence, in wildlife, as a result of contact with humans or anthropogenic activities. For some of these parasites, there is growing evidence of the serious consequences of infection on wildlife survival, whereas for others, there is a paucity of information about their impact.

Effectiveness of the postponed isolation (post-frozen isolation) method for PCR-quality Sarcoptes mite gDNA

The aim of the present study was to assess whether individual Sarcoptes mites collected from frozen skin ('postponed isolation' method) are suitable sources of PCR-quality genomic DNA, and to test the effectiveness of this method in comparison with the 'direct isolation' method, often used through force of habit. Hundreds of single Sarcoptes scabiei samples, resulting from direct (live) or postponed (post-frozen) isolation, were tested using a approximately 450 bp product (ITS-2) and multi-locus 10x genotyping with microsatellite markers. No statistical difference in yield of soluble DNA was found between the two isolation methods. Nevertheless, 19% of the reactions were classified as failed preparations in the direct isolation method, whereas the rate of unsuccessful reactions was 34% in the postponed isolation method. Consequently, post-frozen isolation is suitable and recommendable for Sarcoptes mite gDNA preparation, particularly when performing a balancing act among safety, practicability and profitability. These results have implications for mite collection for DNA extraction, and hence the needed wider leap of Sarcoptes into the genetic era.

Sarcoptes mite from collection to DNA extraction: the lost realm of the neglected parasite

Sarcoptes mite from collection to DNA extraction forms the cornerstone for studies on Sarcoptes scabiei. Whilst the new science era took a shy leap into the different facets of mite studies, the cornerstone was almost entirely neglected. Mite collection, cleaning, storage and DNA extraction were, basically, humble attempts to extrapolate, adapt, modify or 'pirate' those existing methods to the peculiarities of Sarcoptes research. These aspects usually constituted few lines, bashfully mentioned, in the materials and methods section of some papers, which arose in unique problems concerning cost-effectiveness, time profitability, safety and even worse, the credibility of the results, creating contradictory conclusions in some cases. This 'noisy' situation encouraged us to collect, classify and review, for the first time to our knowledge, some aspects relating to studies on Sarcoptes mite from collection to DNA extraction, which will be useful for further studies on Sarcoptes, and have implications for the effective control of the diseases Sarcoptes mite causes. Further studies are needed, especially to compare the profitability, safety, sensibility and specificity of the different methods of this neglected realm of the ubiquitous ectoparasite.

Sarcoptic mange in southern hairy-nosed wombats (Lasiorhinus latifrons): distribution and prevalence in the Murraylands of South Australia

This study examined the history, prevalence and distribution of sarcoptic mange in southern hairy-nosed wombats (Lasiorhinus latifrons) in the Murraylands, South Australia. Results from a survey suggested that there had been a long history of sporadic mange outbreaks, with 43% of 85 respondents indicating that they had seen diseased animals. There was a concentration of positive sightings (59%) in the vicinity of one town, Swan Reach. A total of 67 wombats was also caught on three pastoral properties; 0% (n = 21), 4% (n = 21) and 76% (n = 23) were found to have mange at each respective site. Diseased wombats presented with erythema, parakeratosis and alopecia and had lower median condition, subcutaneous fat and higher bone prominence scores than healthy animals. Severely diseased adult wombats had an average bodyweight that was 9.86 kg lower than those without mange. Infected animals suffered higher mortality, with a rate of ~37% in eight months on one property. It is suggested that mange may have a significant effect on southern hairy-nosed wombats and outbreaks could result in the decline and/or possible extinction of small, isolated populations. Population management initiatives, including suspending culling quotas in infected populations, should thus be considered.

The complete mitochondrial genome of the sexual oribatid mite Steganacarus magnus: genome rearrangements and loss of tRNAs

Background

Complete mitochondrial (mt) genomes and the gene rearrangements therein are increasingly used as molecular markers for investigating phylogenetic relationships, especially for elucidating deep splits. Contributing to the complete mt genomes of arthropods, especially Arachnida, available so far, we provide the first complete mt genome of a sarcoptiform mite species, the sexually reproducing oribatid mite Steganacarus magnus (Acari, Oribatida) which was determined by sequencing of long PCR products.

Results

The mt genome of S. magnus lacks 16 tRNAs, only those for leucine, histidine, proline, tryptophan, glutamine and serine are present. Within those tRNAs only tRNA-His and tRNA-Pro have kept their original position, the others are translocated. Furthermore, the mt genome of S. magnus consists of 13,818 bp and it is composed of 13 protein-coding genes and two genes for the ribosomal RNA subunits that are typically found in metazoan mt genomes. The gene order in S. magnus differs from the hypothetical ancestral chelicerate arrangement as conserved in Limulus polyphemus: instead of nad1-rrnL-rrnS-LNR-nad2 (tRNAs excluded) S. magnus is nad2-rrnL-nad1-rrnS-LNR. Phylogenetic analyses of a concatenated amino acid dataset of all mt protein-coding genes of 28 arthropod species suggest a sister-group relationship of sarcoptiform and prostigmatid mites (S. magnus and Leptotrombidium).

Conclusion

The mt gene arrangement of S. magnus differs from the hypothetical ground plan of arthropods and from that of other mites further contributing to the variety of mt gene arrangements found in Arachnida. The unexpected lack of tRNAs is enigmatic, probably showing that the loss of mt genes is an ongoing evolutionary process. For solving phylogenetic relationships of oribatid mite lineages and their position within Acari further complete mt genomes are needed.

The complete mitochondrial genome of the tobacco hornworm, Manduca sexta, (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths

The entire mitochondrial genome of the tobacco hornworm, Manduca sexta (Lepidoptera: Spinghidae) was sequenced -- a circular molecular 15516 bp in size. The arrangement of the protein coding genes (PCGs) was the same as that found in the ancestral insect, however Manduca possessed the derived tRNA arrangement of CR-M-I-Q which has been found in all Lepidoptera sequenced to date. Additionally, Manduca, like all lepidopteran mt genomes, has numerous large intergenic spacer regions and microsatellite-like repeat regions. Nucleotide composition is highly A+T biased, and the lepidopterans have the second most biased nucleotide composition of the insect orders after Hymenoptera. Secondary structural features of the PCGs identified in other Lepidoptera were present but highly modified by the presence of microsatellite-like repeat regions which may significantly alter their function in the post-transcriptional modification of pre-mRNAs. Secondary structure models of the ribosomal RNA genes of Manduca are presented and are similar to those proposed for other insect orders. Conserved regions were identified within non-translated spacer regions which correspond to sites for the origin and termination of replication and transcription. Comparisons of gene variability across the order suggest that the mitochondrial genes most frequently used in phylogenetic analysis of the Lepidoptera, cox1 and cox2, are amongst the least variable genes in the genome and phylogenetic resolution could be improved by using alternative, higher variability genes such as nad2, nad3, nad4 and nad5.

Mitochondrial genomic comparisons of the subterranean termites from the Genus Reticulitermes (Insecta: Isoptera: Rhinotermitidae)

Termites of the genus Reticulitermes are some of the most significant pests of structural timber and tree farming in the northern hemisphere, causing losses in the billions of dollars annually because of direct damage and termite control costs. This group has been frequently targeted for population genetic, phylogenetic, and species limit studies, most of which use mitochondrial (mt) genes; however, only a small fraction of the genome has been sequenced. The entire mt genome was sequenced for the eastern North American members of Reticulitermes: R. flavipes, R. santonensis, R. virginicus, and R. hageni. The mt genome has the same gene content and organization as that found in most insect species; however, the nucleotide composition and skew are highly biased (AT% low, strong A- and C-skew). Both the protein-coding and transfer RNA genes show high absolute levels of nucleotide substitution, suggesting that the high rates of mutation within Reticulitermes inferred from analyses of single mt genes are a general characteristic of the entire mt genome. The AT-rich or control region has a remarkable structure not previously observed in insect mt genomes. The majority of the control region is made up of 2 sets of repeat units, typically with 2 full and 1 partial copies of both the A (or small; 186 bp) and B (or large; 552 bp) repeats. The partial repeat units overlap by 36 bp. The size, location, and degree of overlap for the partial repeat units correspond to highly conserved stem/loop structures within the repeat units, suggesting that these structures are involved in the replication-mediated processes that govern repeat-unit evolution within mt genomes. Finally, molecular variation within the mt gene regions was compared with previous regions used in molecular diagnostics or phylogenetics of Reticulitermes. High numbers of single nucleotide polymorphisms were found in each of the mt genes, and some of the highest variability was found in gene regions that have not previously been investigated in this group. The whole mt genome sequence can thus be used to predict useful regions for future investigation.

Mitochondrial genomes of parasitic arthropods: implications for studies of population genetics and evolution

Over 39000 species of arthropods parasitize humans, domestic animals and wildlife. Despite their medical, veterinary and economic importance, most aspects of the population genetics and evolution of the vast majority of parasitic arthropods are poorly understood. Mitochondrial genomes are a rich source of markers for studies of population genetics and evolution. These markers include (1) nucleotide sequences of each of the 37 mitochondrial genes and non-coding regions; (2) concatenated nucleotide sequences of 2 or more genes; and (3) genomic features, such as gene duplications, gene rearrangements, and changes in gene content and secondary structures of RNAs. To date, the mitochondrial genomes of over 700 species of multi-cellular animals have been sequenced entirely, however, only 24 of these species are parasitic arthropods. Of the mitochondrial genome markers, only the nucleotide sequences of 4 mitochondrial genes,cox1,cob,rrnSandrrnL, have been well explored in population genetic and evolutionary studies of parasitic arthropods whereas the sequences of the other 33 genes, and various genomic features have not. We review current knowledge of the mitochondrial genomes of parasitic arthropods, summarize applications of mitochondrial genes and genomic features in population genetic and evolutionary studies, and highlight prospects for future research.

Navigating parasite webs and parasite flow: emerging and re-emerging parasitic zoonoses of wildlife origin

Wildlife are now recognised as an important source of emerging human pathogens, including parasites. This paper discusses the linkages between wildlife, people, zoonotic parasites and the ecosystems in which they co-exist, revisits definitions for 'emerging' and 're-emerging', and lists zoonotic parasites that can be acquired from wildlife including, for some, estimates of the associated global human health burdens. The paper also introduces the concepts of 'parasite webs' and 'parasite flow', provides a context for parasites, relative to other infectious agents, as causes of emerging human disease, and discusses drivers of disease emergence and re-emergence, especially changes in biodiversity and climate. Angiostrongylus cantonensis in the Caribbean and the southern United States, Baylisascaris procyonis in California and Georgia, Plasmodium knowlesi in Sarawak, Malaysia, Human African Trypanosomiasis, Sarcoptes scabiei in carnivores, and Cryptosporidium, Giardia and Toxoplasma in marine ecosystems are presented as examples of wildlife-derived zoonotic parasites of particular recent interest. An ecological approach to disease is promoted, as is a need for an increased profile for this approach in undergraduate and graduate education in the health sciences. Synergy among scientists and disciplines is identified as critical for the study of parasites and parasitic disease in wildlife populations. Recent advances in techniques for the investigation of parasite fauna of wildlife are presented and monitoring and surveillance systems for wildlife disease are discussed. Some of the limitations inherent in predictions for the emergence and re-emergence of infection and disease associated with zoonotic parasites of wildlife are identified. The importance of public awareness and public education in the prevention and control of emerging and re-emerging zoonotic infection and disease are emphasised. Finally, some thoughts for the future are presented.

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.

Molecular identification of pathogenic house dust mites using 12S rRNA sequences

House dust mites are microarthropods implicated in the cause of allergic diseases. Currently, there is no phylogenetic analysis of dust mites based on genomic or mitochondrial DNA (mtDNA) evidence. For the first time, we report evolutionary relationships based on partial mtDNA 12S rRNA sequences among the four dust mite families Pyroglyphidae (Dermatophagoides pteronyssinus), Glycyphagoidea (Glycyphagus privatus), Acaridae (Aleuroglyphus ovatus), and Echimyopodidae (Blomia tropicalis). Thirteen sequence variants were obtained and phylogenetic analysis showed two monophyletic clades composed of two species each. Contrary to current taxonomic classification, the Acaridae clustered in a monophyletic group with the Pyroglyphidae. Considering the current difficulties in identifying these medically important species for the purpose of eradication and treatment, it is significant that sequence data are capable of discriminating between species belonging to different families of dust mites.

Testing the hypothesis of recent population expansions in nematode parasites of human-associated hosts

It has been predicted that parasites of human-associated organisms (eg humans, domestic pets, farm animals, agricultural and silvicultural plants) are more likely to show rapid recent population expansions than are parasites of other hosts. Here, we directly test the generality of this demographic prediction for species of parasitic nematodes that currently have mitochondrial sequence data available in the literature or the public-access genetic databases. Of the 23 host/parasite combinations analysed, there are seven human-associated parasite species with expanding populations and three without, and there are three non-human-associated parasite species with expanding populations and 10 without. This statistically significant pattern confirms the prediction. However, it is likely that the situation is more complicated than the simple hypothesis test suggests, and those species that do not fit the predicted general pattern provide interesting insights into other evolutionary processes that influence the historical population genetics of host-parasite relationships. These processes include the effects of postglacial migrations, evolutionary relationships and possibly life-history characteristics. Furthermore, the analysis highlights the limitations of this form of bioinformatic data-mining, in comparison to controlled experimental hypothesis tests.

Networks in phylogenetic analysis: new tools for population biology

Phylogenetic analysis has changed greatly in the past decade, including the more widespread appreciation of the idea that evolutionary histories are not always tree-like, and may, thus, be best represented as reticulated networks rather than as strictly dichotomous trees. Reconstructing such histories in the absence of a bifurcating speciation process is even more difficult than the usual procedure, and a range of alternative strategies have been developed. There seem to be two basic uses for a network model of evolution: the display of real but unobservable evolutionary events (i.e. a hypothesis of the true phylogenetic history), and the display of character conflict within the data itself (i.e. a summary of the data). These two general approaches are briefly reviewed here, and the strengths and weaknesses of the different implementations are compared and contrasted. Each network methodology seems to have limitations in terms of how it responds to increasing complexity (e.g. conflict) in the data, and therefore each is likely to be more appropriate for one of the two uses than for the other. Several examples using parasitological data sets illustrate the uses of networks within the context of population biology.