Species boundaries and host range of tortoise mites (Uropodoidea) phoretic on bark beetles (Scolytinae), using morphometric and molecular markers

Cryptic diversity within the Poecilochirus carabi mite species complex phoretic on Nicrophorus burying beetles: Phylogeny, biogeography, and host specificity

Coevolution is often considered a major driver of speciation, but evidence for this claim is not always found because diversity might be cryptic. When morphological divergence is low, molecular data are needed to uncover diversity. This is often the case in mites, which are known for their extensive and often cryptic diversity. We studied mites of the genus Poecilochirus that are phoretic on burying beetles (Silphidae: Nicrophorus). Poecilochirus taxonomy is poorly understood. Most studies on this genus focus on the evolutionary ecology of Poecilochirus carabi sensu lato, a complex of at least two biological species. Based on molecular data of 230 specimens from 43 locations worldwide, we identified 24 genetic clusters that may represent species. We estimate that these mites began to diversify during the Paleogene, when the clade containing P. subterraneus branched off and the remaining mites diverged into two further clades. One clade resembles P. monospinosus. The other clade contains 17 genetic clusters resembling P. carabi s.l.. Among these are P. carabi sensu stricto, P. necrophori, and potentially many additional cryptic species. Our analyses suggest that these clades were formed in the Miocene by large-scale geographic separation; co-speciation of mites with the host beetles can be largely ruled out. Diversification also seems to have happened on a smaller scale, potentially due to adaptation to specific hosts or local abiotic conditions, causing some clusters to specialize on certain beetle species. Our results suggest that biodiversity in this genus was generated by multiple interacting forces shaping the tangled webs of life.

Feeding design in free-living mesostigmatid chelicerae (Acari: Anactinotrichida)

A model based upon mechanics is used in a re-analysis of historical acarine morphological work augmented by an extra seven zoophagous mesostigmatid species. This review shows that predatory mesostigmatids do have cheliceral designs with clear rational purposes. Almost invariably within an overall body size class, the switch in predatory style from a worm-like prey feeding ('crushing/mashing' kill) functional group to a micro-arthropod feeding ('active prey cutting/slicing/slashing' kill) functional group is matched by: an increased cheliceral reach, a bigger chelal gape, a larger morphologically estimated chelal crunch force, and a drop in the adductive lever arm velocity ratio of the chela. Small size matters. Several uropodines (Eviphis ostrinus, the omnivore Trachytes aegrota, Urodiaspis tecta and, Uropoda orbicularis) have more elongate chelicerae (greater reach) than their chelal gape would suggest, even allowing for allometry across mesostigmatids. They may be: plesiosaur-like high-speed strikers of prey, scavenging carrion feeders (like long-necked vultures), probing/burrowing crevice feeders of cryptic nematodes, or small morsel/fragmentary food feeders. Some uropodoids have chelicerae and chelae which probably work like a construction-site mechanical excavator-digger with its small bucket. Possible hoeing/bulldozing, spore-cracking and tiny sabre-tooth cat-like striking actions are discussed for others. Subtle changes lead small mesostigmatids to be predator-scavengers (mesocarnivores) or to be predator-fungivores (hypocarnivores). Some uropodines (e.g., the worm-like prey feeder Alliphis siculus and, Uropoda orbicularis) show chelae similar in design to astigmatids and cryptostigmatids indicating possible facultative saprophagy. Scale matters-obligate predatory designs (hypercarnivory) start for mesostigmatids with chelal gape > 150 μm and cheliceral reach > 350 μm (i.e., about 500-650 μm in body size). Commonality of trophic design in these larger species with solifugids is indicated. Veigaia species with low chelal velocity ratio and other morphological strengthening specialisms, appear specially adapted in a concerted way for predating active soft and fast moving springtails (Collembola). Veigaia cerva shows a markedly bigger chelal gape than its cheliceral reach would proportionately infer suggesting it is a crocodile-like sit-and-wait or ambush predator par excellence. A small chelal gape, low cheliceral reach, moderate velocity ratio variant of the worm-like feeding habit design is supported for phytoseiid pollenophagy. Evidence for a resource partitioning model in the evolution of gnathosomal development is found. A comparison to crustacean claws and vertebrate mandibles is made. Alliphis siculus and Rhodacarus strenzkei are surprisingly powerful mega-cephalics for their small size. Parasitids show a canid-like trophic design. The chelicera of the nematophagous Alliphis halleri shows felid-like features. Glyphtholaspis confusa has hyaena-like cheliceral dentition. The latter species has a markedly smaller chelal gape than its cheliceral reach would suggest proportionately, which together with a high chelal velocity ratio and a high estimated chelal crunch force matches a power specialism of feeding on immobile tough fly eggs/pupae by crushing (durophagy). A consideration of gnathosomal orientation is made. Predatory specialisms appear to often match genera especially in larger mesostigmatids, which may scale quite differently. Comparison to holothyrids and opilioacarids indicates that the cheliceral chelae of the former are cutting-style and those of the latter are crushing-style. A simple validated easy-to-use '2:1 on' predictive algorithm of feeding habit type is included based on a strength-speed tradeoff in chelal velocity ratio for ecologists to test in the field.

Application of propylene glycol in DNA-based studies of invertebrates

High-throughput sequencing (HTS) studies on invertebrates commonly use ethanol as the main sample fixative (upon collection) and preservative (for storage and curation). However, alternative agents exists, which should not be automatically neglected when studies are newly designed. This review provides an overview of the application of propylene glycol (PG) in DNA-based studies of invertebrates, thus to stimulate an evidence-based discussion.

The use of PG in DNA-based studies of invertebrates is still limited (n = 79), but a steady increase has been visible since 2011. Most studies used PG as a fixative for passive trapping (73%) and performed Sanger sequencing (66%; e.g. DNA barcoding). More recently, HTS setups joined the field (11%). Terrestrial Coleoptera (30%) and Diptera (20%) were the most studied groups. Very often, information on the grade of PG used (75%) or storage conditions (duration, temperature) were lacking. This rendered direct comparisons of study results difficult, and highlight the need for further systematic studies on these subjects.

When compared to absolute ethanol, PG can be more widely and cheaply acquired (e.g. as an antifreeze, 13% of studies). It also enables longer trapping intervals, being especially relevant at remote or hard-to-reach places. Shipping of PG-conserved samples is regarded as risk-free and is authorised, pinpointing its potential for larger trapping programs or citizen science projects. Its property to retain flexibility of morphological characters as well as to lead to a reduced shrinkage effect was especially appraised by integrative study designs. Finally, the so far limited application of PG in the context of HTS showed promising results for short read amplicon sequencing and reduced representation methods. Knowledge of the influence of PG fixation and storage for long(er) read HTS setups is currently unavailable.

Given our review results and taking difficulties of direct methodological comparisons into account, future DNA-based studies of invertebrates should on a case-by-case basis critically scrutinise if the application of PG in their anticipated study design can be of benefit.

Unexpected diversity in the host-generalist oribatid mite Paraleius leontonychus (Oribatida, Scheloribatidae) phoretic on Palearctic bark beetles

Bark beetles are feared as pests in forestry but they also support a large number of other taxa that exploit the beetles and their galleries. Among arthropods, mites are the largest taxon associated with bark beetles. Many of these mites are phoretic and often involved in complex interactions with the beetles and other organisms. Within the oribatid mite family Scheloribatidae, only two of the three nominal species of Paraleius have been frequently found in galleries of bark beetles and on the beetles themselves. One of the species, P. leontonychus, has a wide distribution range spanning over three ecozones of the world and is believed to be a host generalist, reported from numerous bark beetle and tree species. In the present study, phylogenetic analyses of one mitochondrial and two nuclear genes identified six well supported, fairly divergent clades within P. leontonychus which we consider to represent distinct species based on molecular species delimitation methods and largely congruent clustering in mitochondrial and nuclear gene trees. These species do not tend to be strictly host specific and might occur syntopically. Moreover, mito-nuclear discordance indicates a case of past hybridization/introgression among distinct Paraleius species, the first case of interspecific hybridization reported in mites other than ticks.

Phoretic mite communities associated with bark beetles in the maritime and stone pine forests of Setúbal, Portugal

The phoretic mite communities of prominent bark beetle pests associated with pine stands of southern Portugal were sampled to determine whether they vary across bark beetle species and stand type. Bark beetles were sampled for mites from two primary (aggressive) bark beetle species (Ips sexdentatus and Orthotomicus erosus) and the most common secondary species (Hylurgus ligniperda) in maritime pine (Pinus pinaster) and stone pine (Pinus pinea) in the Setúbal province of Portugal. Twelve mite species, spanning diverse ecological roles, are found associated with these bark beetle systems. The relative abundances of the 12 species that make up the phoretic mite communities of maritime and stone pine varied significantly between host beetle species as well as between stand type, indicating that the phoretic host and dominant tree type are important drivers of mite community composition. The functional roles of these mites are outlined and their ecological significance in pine forest ecosystems is discussed.

Acari of Canada

Summaries of taxonomic knowledge are provided for all acarine groups in Canada, accompanied by references to relevant publications, changes in classification at the family level since 1979, and notes on biology relevant to estimating their diversity. Nearly 3000 described species from 269 families are recorded in the country, representing a 56% increase from the 1917 species reported by Lindquist et al. (1979). An additional 42 families are known from Canada only from material identified to family- or genus-level. Of the total 311 families known in Canada, 69 are newly recorded since 1979, excluding apparent new records due solely to classification changes. This substantial progress is most evident in Oribatida and Hydrachnidia, for which many regional checklists and family-level revisions have been published. Except for recent taxonomic leaps in a few other groups, particularly of symbiotic mites (Astigmata: feather mites; Mesostigmata: Rhinonyssidae), knowledge remains limited for most other taxa, for which most species records are unpublished and may require verification. Taxonomic revisions are greatly needed for a large majority of families in Canada. Based in part on species recorded in adjacent areas of the USA and on hosts known to be present here, we conservatively estimate that nearly 10,000 species of mites occur in Canada, but the actual number could be 15,000 or more. This means that at least 70% of Canada's mite fauna is yet unrecorded. Much work also remains to match existing molecular data with species names, as less than 10% of the ~7500 Barcode Index Numbers for Canadian mites in the Barcode of Life Database are associated with named species. Understudied hosts and terrestrial and aquatic habitats require investigation across Canada to uncover new species and to clarify geographic and ecological distributions of known species.

Comparative phylogeography of parasitic Laelaps mites contribute new insights into the specialist-generalist variation hypothesis (SGVH)

Background

The specialist-generalist variation hypothesis (SGVH) in parasites suggests that, due to patchiness in habitat (host availability), specialist species will show more subdivided population structure when compared to generalist species. In addition, since specialist species are more prone to local stochastic extinction events with their hosts, they will show lower levels of intraspecific genetic diversity when compared to more generalist.

Results

To test the wider applicability of the SGVH we compared 337 cytochrome oxidase I mitochondrial DNA and 268 nuclear tropomyosin DNA sequenced fragments derived from two co-distributed Laelaps mite species and compared the data to 294 COI mtDNA sequences derived from the respective hosts Rhabdomys dilectus, R. bechuanae, Mastomys coucha and M. natalensis. In support of the SGVH, the generalist L. muricola was characterized by a high mtDNA haplotypic diversity of 0.97 (±0.00) and a low level of population differentiation (mtDNA F_st = 0.56, p < 0.05; nuDNA F_st = 0.33, P < 0.05) while the specialist L. giganteus was overall characterized by a lower haplotypic diversity of 0.77 (±0.03) and comparatively higher levels of population differentiation (mtDNA F_st = 0.87, P < 0.05; nuDNA F_st = 0.48, P < 0.05). When the two specialist L. giganteus lineages, which occur on two different Rhabdomys species, are respectively compared to the generalist parasite, L. muricola, the SGVH is not fully supported. One of the specialist L. giganteus species occurring on R. dilectus shows similar low levels of population differentiation (mtDNA F_st = 0.53, P < 0.05; nuDNA F_st = 0.12, P < 0.05) than that found for the generalist L. muricola. This finding can be correlated to differences in host dispersal: R. bechuanae populations are characterized by a differentiated mtDNA F_st of 0.79 (P < 0.05) while R. dilectus populations are less structured with a mtDNA F_st = 0.18 (P < 0.05).

Conclusions

These findings suggest that in ectoparasites, host specificity and the vagility of the host are both important drivers for parasite dispersal. It is proposed that the SGHV hypothesis should also incorporate reference to host dispersal since in our case only the specialist species who occur on less mobile hosts showed more subdivided population structure when compared to generalist species.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1245-7) contains supplementary material, which is available to authorized users.

Host species exploitation and discrimination by animal parasites

Parasite species often show differential fitness on different host species. We developed an equation-based model to explore conditions favouring host species exploitation and discrimination. In our model, diploid infective stages randomly encountered hosts of two species; the parasite's relative fitness in exploiting each host species, and its ability to discriminate between them, was determined by the parasite's genotype at two independent diallelic loci. Relative host species frequency determined allele frequencies at the exploitation locus, whereas differential fitness and combined host density determined frequency of discrimination alleles. The model predicts instances where populations contain mixes of discriminatory and non-discriminatory infective stages. Also, non-discriminatory parasites should evolve when differential fitness is low to moderate and when combined host densities are low, but not so low as to cause parasite extinction. A corollary is that parasite discrimination (and host-specificity) increases with higher combined host densities. Instances in nature where parasites fail to discriminate when differential fitness is extreme could be explained by one host species evolving resistance, following from earlier selection for parasite non-discrimination. Similar results overall were obtained for haploid extensions of the model. Our model emulates multi-host associations and has implications for understanding broadening of host species ranges by parasites.This article is part of the themed issue 'Opening the black box: re-examining the ecology and evolution of parasite transmission'.

Multilocus coalescent species delimitation reveals widespread cryptic differentiation among Drakensberg mountain-living freshwater crabs (Decapoda : Potamonautes)

Cryptic lineages present major challenges for evolutionary and conservation studies, particularly where these lineages remain undiscovered. Freshwater crabs are known to harbour cryptic diversity, in most cases with limited morphological differences. During the present study, we used a multilocus (12S rRNA, 16S rRNA, COI, 28S rRNA, DecapANT and PEPCK) Bayesian species delimitation to examine cryptic diversity within a freshwater crab species complex (Potamonautes clarus/P. depressus). We sampled 25 highland rivers in the Tugela and uMkomazi River drainage systems of the Drakensberg Mountain range, in the KwaZulu–Natal province of South Africa. Our results showed there to be at least eight lineages: six novel potamonautid freshwater crabs, and two described taxa P. clarus and P. depressus. Divergence from the most recent common ancestor occurred between the mid- and late Miocene (12.1 Mya), while divergence within the species complex occurred ~10.3 Mya up until the Holocene (0.11 Mya). The discovery of six novel lineages of freshwater crabs from a seemingly restricted distribution range has conservation implications, but to date most conservation planning strategies have focussed on freshwater vertebrates. By conducting a fine-scale phylogenetic survey using invertebrates, this study provides a platform for the inclusion of freshwater invertebrates in future conservation assessments.

Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens

DNA barcoding is an efficient method to identify specimens and to detect undescribed/cryptic species. Sanger sequencing of individual specimens is the standard approach in generating large-scale DNA barcode libraries and identifying unknowns. However, the Sanger sequencing technology is, in some respects, inferior to next-generation sequencers, which are capable of producing millions of sequence reads simultaneously. Additionally, direct Sanger sequencing of DNA barcode amplicons, as practiced in most DNA barcoding procedures, is hampered by the need for relatively high-target amplicon yield, coamplification of nuclear mitochondrial pseudogenes, confusion with sequences from intracellular endosymbiotic bacteria (e.g. Wolbachia) and instances of intraindividual variability (i.e. heteroplasmy). Any of these situations can lead to failed Sanger sequencing attempts or ambiguity of the generated DNA barcodes. Here, we demonstrate the potential application of next-generation sequencing platforms for parallel acquisition of DNA barcode sequences from hundreds of specimens simultaneously. To facilitate retrieval of sequences obtained from individual specimens, we tag individual specimens during PCR amplification using unique 10-mer oligonucleotides attached to DNA barcoding PCR primers. We employ 454 pyrosequencing to recover full-length DNA barcodes of 190 specimens using 12.5% capacity of a 454 sequencing run (i.e. two lanes of a 16 lane run). We obtained an average of 143 sequence reads for each individual specimen. The sequences produced are full-length DNA barcodes for all but one of the included specimens. In a subset of samples, we also detected Wolbachia, nontarget species, and heteroplasmic sequences. Next-generation sequencing is of great value because of its protocol simplicity, greatly reduced cost per barcode read, faster throughout and added information content.

Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens

DNA barcoding is an efficient method to identify specimens and to detect undescribed/cryptic species. Sanger sequencing of individual specimens is the standard approach in generating large-scale DNA barcode libraries and identifying unknowns. However, the Sanger sequencing technology is, in some respects, inferior to next-generation sequencers, which are capable of producing millions of sequence reads simultaneously. Additionally, direct Sanger sequencing of DNA barcode amplicons, as practiced in most DNA barcoding procedures, is hampered by the need for relatively high-target amplicon yield, coamplification of nuclear mitochondrial pseudogenes, confusion with sequences from intracellular endosymbiotic bacteria (e.g. Wolbachia) and instances of intraindividual variability (i.e. heteroplasmy). Any of these situations can lead to failed Sanger sequencing attempts or ambiguity of the generated DNA barcodes. Here, we demonstrate the potential application of next-generation sequencing platforms for parallel acquisition of DNA barcode sequences from hundreds of specimens simultaneously. To facilitate retrieval of sequences obtained from individual specimens, we tag individual specimens during PCR amplification using unique 10-mer oligonucleotides attached to DNA barcoding PCR primers. We employ 454 pyrosequencing to recover full-length DNA barcodes of 190 specimens using 12.5% capacity of a 454 sequencing run (i.e. two lanes of a 16 lane run). We obtained an average of 143 sequence reads for each individual specimen. The sequences produced are full-length DNA barcodes for all but one of the included specimens. In a subset of samples, we also detected Wolbachia, nontarget species, and heteroplasmic sequences. Next-generation sequencing is of great value because of its protocol simplicity, greatly reduced cost per barcode read, faster throughout and added information content.