Multiple new species: Cryptic diversity in the widespread mite species Cymbaeremaeus cymba (Oribatida, Cymbaeremaeidae)

“Jack‐of‐all‐trades” is parthenogenetic

Sex is evolutionarily more costly than parthenogenesis, evolutionary ecologists therefore wonder why sex is much more frequent than parthenogenesis in the majority of animal lineages. Intriguingly, parthenogenetic individuals and species are as common as or even more common than sexuals in some major and putative ancient animal lineages such as oribatid mites and rotifers. Here, we analyzed oribatid mites (Acari: Oribatida) as a model group because these mites are ancient (early Paleozoic), widely distributed around the globe, and include a high number of parthenogenetic species, which often co‐exist with sexual oribatid mite species. There is evidence that the reproductive mode is phylogenetically conserved in oribatid mites, which makes them an ideal model to test hypotheses on the relationship between reproductive mode and species' ecological strategies. We used oribatid mites to test the frozen niche variation hypothesis; we hypothesized that parthenogenetic oribatid mites occupy narrow specialized ecological niches. We used the geographic range of species as a proxy for specialization as specialized species typically do have narrower geographic ranges than generalistic species. After correcting for phylogenetic signal in reproductive mode and demonstrating that geographic range size has no phylogenetic signal, we found that parthenogenetic lineages have a higher probability to have broader geographic ranges than sexual species arguing against the frozen niche variation hypothesis. Rather, the results suggest that parthenogenetic oribatid mite species are more generalistic than sexual species supporting the general‐purpose genotype hypothesis. The reason why parthenogenetic oribatid mite species are generalists with wide geographic range sizes might be that they are of ancient origin reflecting that they adapted to varying environmental conditions during evolutionary history. Overall, our findings indicate that parthenogenetic oribatid mite species possess a widely adapted general‐purpose genotype and therefore might be viewed as “Jack‐of‐all‐trades.”

A closer look reveals hidden diversity in the intertidal Caribbean Fortuyniidae (Acari, Oribatida)

A molecular genetic and morphometric investigation revealed the supposedly widespread Caribbean and Western Atlantic intertidal oribatid mite species Fortuynia atlantica to comprise at least two different species. Although there are no distinct morphological differences separating these taxa, COI and 18S sequence divergence data, as well as different species delimitation analyses, clearly identify the two species. Fortuynia atlantica is distributed in the northern Caribbean and the Western Atlantic and the new Fortuynia antillea sp. nov. is presently endemic to Barbados. Vicariance is supposed to be responsible for their genetic diversification and stabilizing selection caused by the extreme intertidal environment is suggested to be the reason for the found morphological stasis. The genetic structure of Fortuynia atlantica indicates that Bermudian populations are derived from the northern Caribbean and thus support the theory of dispersal by drifting on the Gulf Stream. Haplotype network data suggest that Bermudian and Bahamian populations were largely shaped by colonization, expansion and extinction events caused by dramatic sea level changes during the Pleistocene. A preliminary phylogenetic analysis based on 18S gene sequences indicates that the globally distributed genus Fortuynia may be a monophyletic group, whereas Caribbean and Western Atlantic members are distinctly separated from the Indo-Pacific and Western Pacific species.

DNA Barcoding Reveals Generalization and Host Overlap in Hummingbird Flower Mites: Implications for the Mating Rendezvous Hypothesis

AbstractHummingbird flower mites are assumed to monopolize single host plant species owing to sexual selection for unique mating rendezvous sites. We tested the main assumption of the mating rendezvous hypothesis-extreme host specialization-by reconstructing interactions among tropical hummingbird flower mites and their host plants using DNA barcoding and taxonomic identifications. We collected 10,654 mites from 489 flowers. We extracted DNA from 1,928 mite specimens and amplified the cytochrome c oxidase I (CO1) DNA barcode. We analyzed the network structure to assess the degree of generalization or specialization of mites to their host plants. We recorded 18 species of hummingbird flower mites from three genera (Proctolaelaps, Rhinoseius, and Tropicoseius) interacting with 14 species of plants. We found that generalist mites are common, and congeneric mite species often share host plants. Our results challenge the assumption of strict specialization that supports this system as an example of mating rendezvous evolution.

Unearthing soil arthropod diversity through DNA metabarcoding

DNA metabarcoding has the potential to greatly advance understanding of soil biodiversity, but this approach has seen limited application for the most abundant and species-rich group of soil fauna-the arthropods. This study begins to address this gap by comparing information on species composition recovered from metabarcoding two types of bulk samples (specimens, soil) from a temperate zone site and from bulk soil samples collected at eight sites in the Arctic. Analysis of 22 samples (3 specimen, 19 soil) revealed 410 arthropod OTUs belonging to 112 families, 25 orders, and nine classes. Studies at the temperate zone site revealed little overlap in species composition between soil and specimen samples, but more overlap at higher taxonomic levels (families, orders) and congruent patterns of α- and β-diversity. Expansion of soil analyses to the Arctic revealed locally rich, highly dissimilar, and spatially structured assemblages compatible with dispersal limited and environmentally driven assembly. The current study demonstrates that DNA metabarcoding of bulk soil enables rapid, large-scale assessments of soil arthropod diversity. However, deep sequence coverage is required to adequately capture the species present in these samples, and expansion of the DNA barcode reference library is necessary to improve taxonomic resolution of the sequences recovered through this approach.

Hidden biodiversity in microarthropods (Acari, Oribatida, Eremaeoidea, Caleremaeus)

A challenge for taxonomists all over the world and across all taxonomic groups is recognizing and delimiting species, and cryptic species are even more challenging. However, an accurate identification is fundamental for all biological studies from ecology to conversation biology. We used a multidisciplinary approach including genetics as well as morphological and ecological data to assess if an easily recognizable, widely distributed and euryoecious mite taxon represents one and the same species. According to phylogenetic (based on mitochondrial and nuclear genes) and species delimitation analyses, five distinct putative species were detected and supported by high genetic distances. These genetic lineages correlate well with ecological data, and each species could be associated to its own (micro)habitat. Subsequently, slight morphological differences were found and provide additional evidence that five different species occur in Central and Southern Europe. The minuteness and the characteristic habitus of Caleremaeus monilipes tempted to neglect potential higher species diversity. This problem might concern several other "well-known" euryoecious microarthropods. Five new species of the genus Caleremaeus are described, namely Caleremaeus mentobellus sp. nov., C. lignophilus sp. nov., C. alpinus sp. nov., C. elevatus sp. nov., and C. hispanicus sp. nov. Additionally, a morphological evaluation of C. monilipes is presented.

DNA barcodes enable higher taxonomic assignments in the Acari

Although mites (Acari) are abundant in many terrestrial and freshwater ecosystems, their diversity is poorly understood. Since most mite species can be distinguished by variation in the DNA barcode region of cytochrome c oxidase I, the Barcode Index Number (BIN) system provides a reliable species proxy that facilitates large-scale surveys. Such analysis reveals many new BINs that can only be identified as Acari until they are examined by a taxonomic specialist. This study demonstrates that the Barcode of Life Datasystem's identification engine (BOLD ID) generally delivers correct ordinal and family assignments from both full-length DNA barcodes and their truncated versions gathered in metabarcoding studies. This result was demonstrated by examining BOLD ID's capacity to assign 7021 mite BINs to their correct order (4) and family (189). Identification success improved with sequence length and taxon coverage but varied among orders indicating the need for lineage-specific thresholds. A strict sequence similarity threshold (86.6%) prevented all ordinal misassignments and allowed the identification of 78.6% of the 7021 BINs. However, higher thresholds were required to eliminate family misassignments for Sarcoptiformes (89.9%), and Trombidiformes (91.4%), consequently reducing the proportion of BINs identified to 68.6%. Lineages with low barcode coverage in the reference library should be prioritized for barcode library expansion to improve assignment success.

A taxonomist's nightmare - Cryptic diversity in Caribbean intertidal arthropods (Arachnida, Acari, Oribatida)

There has been a long controversy about what defines a species and how to delimitate them which resulted in the existence of more than two dozen different species concepts. Recent research on so-called "cryptic species" heated up this debate as some scientists argue that these cryptic species are only a result of incompatible species concepts. While this may be true, we should keep in mind that all concepts are nothing more than human constructs and that the phenomenon of high phenotypic similarity despite reproductive isolation is real. To investigate and understand this phenomenon it is important to classify and name cryptic species as it allows to communicate them with other fields of science that use Linnaean binomials. To provide a common framework for the description of cryptic species, we propose a possible protocol of how to formally name and describe these taxa in practice. The most important point of this protocol is to explain which species concept was used to delimitate the cryptic taxon. As a model, we present the case of the allegedly widespread Caribbean intertidal mite Thalassozetes barbara, which in fact consists of seven phenotypically very similar but genetically distinct species. All species are island or short-range endemics with poor dispersal abilities that have evolved in geographic isolation. Stabilizing selection caused by the extreme conditions of the intertidal environment is suggested to be responsible for the morphological stasis of this cryptic species complex.

Long-term stasis in acariform mites provides evidence for morphologically stable evolution: Molecular vs. morphological differentiation in Linopodes (Acariformes; Prostigmata)

Molecular species delimitation, usually by COI DNA barcoding, shows that cryptic speciation is a common phenomenon observed in most animal phyla. Cryptic species have frequently been observed among all major taxa of mites. The mites of the eupodoid genus Linopodes are cosmopolitan in distribution and are most often found in soil-related habitats. Currently, the genus consists of 22 morphologically similar species, which, in practice, are indistinguishable on the basis of their morphological features. The diagnostic issue of the Linopodes species may be caused by the poor delineation of the species, which need taxonomic revision, or the low morphological variability among cryptic species. In this paper, we present the results of molecular species delimitation carried out using sampled Linopodes populations and the level of morphological inter/intraspecific variation within defined groups. We compared COI, 18S and 28S sequence data together with morphological characters. The molecular delimitation revealed seven well-defined species of Linopodes based on DNA sequences. A well-supported phylogenetic tree revealed the same seven species, while morphological analysis showed negligible phenotypic differentiation among the species revealed. We demonstrate that mites can undergo changes in their DNA accompanied by morphological stasis lasting at least 80 MY.

DNA barcoding of Austrian snow scorpionflies (Mecoptera, Boreidae) reveals potential cryptic diversity in Boreus westwoodi

Background

Snow scorpionflies (genus Boreus) belong to a family of Mecoptera, Boreidae, that has been vastly neglected by entomological researchers due to their shift in seasonality to the winter months. Their activity during this time is regarded as a strategy for predator avoidance and regular sightings on snow fields suggest that this also facilitates dispersal. However, many aspects about snow scorpionflies, especially systematics, taxonomy, distribution of species, phylogenetics and phylogeography have remained fairly unexplored until today. In this study, we fill some of these gaps by generating a reference DNA barcode database for Austrian snow scorpionflies in the frame of the Austrian Barcode of Life initiative and by characterising morphological diversity in the study region.

Methods

Initial species assignment of all 67 specimens was based on male morphological characters previously reported to differ between Boreus species and, for females, the shape of the ovipositor. DNA barcoding of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene was carried out for all 67 samples and served as a basis for BIN assignment, genetic distance calculations, as well as alternative species delimitation analyses (ABGD, GMYC, bGMYC, bPTP) and a statistical parsimony network to infer phylogenetic relationships among individual samples/sampling sites.

Results

Morphological investigations suggested the presence of both Boreus hyemalis and Boreus westwoodi in Austria. DNA barcoding also separated the two species, but resulted in several divergent clades, the paraphyly of B. westwoodi in Austria, and high levels of phylogeographic structure on a small geographic scale. Even though the different molecular species delimitation methods disagreed on the exact number of species, they unequivocally suggested the presence of more than the traditionally recognized two Boreus species in Austria, thus indicating potential cryptic species within the genus Boreus in general and especially in B. westwoodi.

Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis)

In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for gene flow, spatial, and environmental processes that can obfuscate phylogenetic inference and bias species delimitation. As a case study, we sequenced genome-wide exons and introns to evince the processes that underlie the diversification of Philippine Puddle Frogs-a group that is widespread, phenotypically conserved, and exhibits high levels of geographically-based genetic structure. We showed that widely adopted tree- and distance-based approaches inferred up to 20 species, compared to genomic analyses that inferred an optimal number of five distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the five groups and elucidate two specific ways in which gene flow can cause overestimations of species diversity: (1) admixed populations can be inferred as distinct lineages characterized by long branches in phylograms; and (2) admixed lineages can appear to be genetically divergent, even from their parental populations when simple measures of genetic distance are used. We demonstrate that the relationship between mitochondrial and genome-wide nuclear p-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and, consequently, species diversity. Additionally, genetic distance was also biased by spatial and environmental processes. Overall, we showed that high levels of genetic diversity in Philippine Puddle Frogs predominantly comprise metapopulation lineages that arose through complex patterns of admixture, isolation-by-distance, and isolation-by-environment as opposed to species divergence. Our findings suggest that speciation may not be the major process underlying the high levels of hidden diversity observed in many taxonomic groups and that widely-adopted tree- and distance-based methods overestimate species diversity in the presence of gene flow.

Distinct phylogeographic patterns in populations of two oribatid mite species from the genus Pantelozetes (Acari, Oribatida, Thyrisomidae) in Central Europe

Oribatid mites are important decomposers of dead organic matter in soils across the world. Their origin dates back at least 380 Mya. Multiple severe climatic changes during Late Pliocene and Pleistocene shaped the migration patterns of these organisms and should be reflected in the genetic variability of their current populations. In this study, we examined the genetic diversity and phylogeographic structure as well as the evolutionary history of populations of two ecologically different oribatid mite species. Pantelozetes cavaticus is a troglophile oribatid mite known mainly from Central European caves, whereas Pantelozetes paolii is a common surface eurytopic species with Holarctic distribution. We used two molecular markers-mitochondrial cytochrome c oxidase subunit I (COI) and the nuclear D3 region of the 28S rDNA gene-to reveal phylogenetic relationships between contemporary populations. Whereas the D3 region showed minimal or no variability within populations, COI appeared to be a relevant marker for population studies. Phylogeographic analysis based on COI detected two lineages of P. cavaticus ('Czech' and 'Slovak'), which separated during the Late Pliocene (2.9 Mya) and revealed the existence of one new species. In contrast, three identified genetic lineages of P. paolii (radiation time 2.9 and 1.2 Mya, respectively) uncovered in this study were found to coexist in the distant sampling localities, suggesting a connection between populations even over long distances.

Patterns of intraspecific morphological variability in soil mites reflect their dispersal ability

The ability to disperse is one of the most important factors influencing the biogeography of species and speciation processes. Highly mobile species have been shown to lack geographic population structures, whereas less mobile species show genetically strongly subdivided populations which are expected to also display at least subtle phenotypic differences. Geometric morphometric methods (GMM) were now used to analyze morphological differences between European populations of a presumed non-phoretic, little mobile mite species in comparison to a highly mobile, phoretic species. The non-phoretic species Scutacarus carinthiacus showed a phenotypic population structure, whereas the phoretic species S. acarorum displayed homogeneity. These different patterns most probably can be explained by different levels of gene flow due to different dispersal abilities of the two species. GMM proved to be a sensitive tool that is especially recommendable for the analysis of (old) museum material and/or specimens in microscopic slides, which are not suitable for molecular genetic analysis.

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.

Discriminating larvae of two syntopic Cychramus species (Coleoptera, Nitidulidae) by means of bar-HRM analysis

Molecular genetic methods are increasingly used to supplement or substitute classical morphology-based species identification. Here, we employ a COI mini-barcode coupled high-resolution melting analysis to quickly, cost-efficiently and reliably determine larvae of two closely related Cychramus (Coleoptera, Nitidulidae) species. Euclidean distance comparison (p < 0.01) and a Welch t-test of the melting point temperatures (p < 0.01) provide highly significant statistical evidence for species specific differences in melting and fluorescence curves, thus allowing the assignment of larvae to either of the two species. This protocol serves as a fast, low-cost and low-tech method to discriminate between pairs or groups of closely related species and can be adapted and applied to various ecological research questions.

Revisiting the Evolution of Arboreal Life in Oribatid Mites

Though mostly soil dwelling, oribatid mites are found in all kind of habitats, with several species exclusively living on trees. Using previously published DNA sequences and eco-morphological data available from the literature, we inferred the number of transitions between soil dwelling to a truly arboreal lifestyle in oribatid mites and the shape evolution of a particular morphological structure of a sense organ (bothridial seta (= sensillus) of a trichobothrium), the shape of which was previously reported to be associated with an arboreal lifestyle. Our data suggest that a truly arboreal lifestyle evolved several times independently in oribatid mites, but much less often than previously proposed in the past. Even though all truly arboreal species indeed seem to possess a capitate sensillus, this character is not exclusive for arboreal taxa. Nonetheless, since all truly arboreal species do have a capitate sensillus, this might be considered an important (pre-)adaptation to a life on trees. We further provide guidelines on how the term “arboreal” should be applied in future mite research and emphasize the importance of exact microhabitat characterization, as this will greatly facilitate comparisons across studies.

Resolving an unnoticed diversity within the Schistura robertsi species complex (Teleostei: Nemacheilidae) using molecules and morphology

The Schistura robertsi species complex is a group of freshwater fish inhabiting streams in southeast Myanmar as well as in western and southern Thailand. In southern Thailand, the distribution exceeds the biogeographically important 'Surat Thani - Krabi line'. The complex is believed to include five described and one undescribed species, but monophyly and systematics of the group have never been studied explicitly. The present study aims to resolve the number of species within the Schistura robertsi group as well as their distribution areas and phylogenetic relations. We analysed mitochondrial and nuclear sequence data of 86 specimens from 47 localities and 18 morphological characters of 193 specimens. The phylogenetic analyses revealed the S. robertsi complex to be monophyletic and to be composed of ten major lineages. Six of them correspond to the known described or undescribed species, but another four newly identified clades reveal the existence of an overlooked diversity within the group. All genetic lineages are statistically highly supported and all are morphologically diagnosable, suggesting that they represent distinct species. The distribution areas of several clades overlap, the cases of direct co-occurrence show no sign of hybridisation.