High genetic divergences indicate ancient separation of parthenogenetic lineages of the oribatid mite Platynothrus peltifer (Acari, Oribatida)

Morphological Ontogeny, Ecology, and Biogeography of Fuscozetes fuscipes (Acari, Oribatida, Ceratozetidae)

The systematic status of Fuscozetes Sellnick, 1928, is not clear in the literature. Therefore, the morphological ontogeny of F. fuscipes (C.L. Koch, 1844), the type species of this genus, was investigated and compared with its congeners in this study, and a new diagnosis of Fuscozetes is given. The juveniles of F. fuscipes are light brown, with a brown prodorsum, sclerites, epimeres, and legs. In all juveniles, a humeral organ and a humeral macrosclerite are present. The gastronotum of the larva has 12 pairs of setae (h3 is present), whereas the nymphs have 15 pairs. In the larva, the gastronotal shield is weakly developed, and most gastronotal setae are short except for a slightly longer h2. Most of the gastronotal setae are inserted on the microsclerites except for h3, and several other macrosclerites and many microsclerites are present on the hysterosoma. In the nymphs, the gastronotal shield is well developed, with 10 pairs of setae (d-, l-, and h-series, and p1), and setae p2 and p3 are located on a large posteroventral macrosclerite. In all the instars, femora I and II are oval in cross-section, without a large ventral carina. Mitochondrial COI sequence data revealed a deep split between the Nearctic and Palearctic populations of F. fuscipes, and a less, but significant, divergence within each continent. These strong geographical barriers were contrasted with multiple cases of shared haplotypes over long distances in the Palearctic, indicating high migration rates in modern times.

Molecular and morphometric analyses reveal host-specific cryptic speciation in a mite species, Tetranychus neocaledonicus (Andre, 1933) (Acari: Tetranychidae)

Host- and habitat-induced morphological shape and size variations are common in phytophagous and parasitic taxa. Several integrated morphological and molecular techniques have been commonly used to understand host-induced morpho-cryptic species forms. Compared to other arthropods, cryptic speciation was more common in Acari. This study focused on the host-specific morphological cryptic shape and size variations of Tetranychus neocaledonicus, collected from moringa and cassava hosts. We used geometric morphometric analysis to uncover the shape and size of inter-and intra-spider mite populations, and discovered that host-specific shape and size variations existed in spider mites regardless of sex. Interestingly, there was no phylogenetic signal in spider mites, implying that the morpho-cryptic speciation of T. neocaledonicus is solely based on the host-induced selection. The molecular clock hypothesis was accepted in our CO1 and 18s rRNA phylogeny analyses, and spider mites collected from both hosts were genetically less diverse. We conclude that T. neocaledonicus exhibited morphologically detectable cryptic population diversity in each host but that these populations are evolutionarily young form. Apart from these host-induced variations, we also monitored the impact of the clearing agent (lactic acid) on the shape and size of T. neocaledonicus; from this study, we proved that the clearing agent significantly alters the taxonomically important morphological traits of spider mites irrespective of the mites' sex, as confirmed by multivariate statistical analysis. This is the first study report to investigated the host-induced morphological variations of spider mites and the impact of a clearing agent.

A cytological revisit on parthenogenetic Artemia and the deficiency of a meiosis-specific recombinase DMC1 in the possible transition from bisexuality to parthenogenesis

Although parthenogenesis is widespread in nature and known to have close relationships with bisexuality, the transitional mechanism is poorly understood. Artemia is an ideal model to address this issue because bisexuality and "contagious" obligate parthenogenesis independently exist in its congeneric members. In the present study, we first performed chromosome spreading and immunofluorescence to compare meiotic processes of Artemia adopting two distinct reproductive ways. The results showed that, unlike conventional meiosis in bisexual Artemia, meiosis II in parthenogenic Artemia is entirely absent and anaphase I is followed by a single mitosis-like equational division. Interspecific comparative transcriptomics showed that two central molecules in homologous recombination (HR), Dmc1 and Rad51, exhibited significantly higher expression in bisexual versus parthenogenetic Artemia. qRT-PCR indicated that the expression of both genes peaked at the early oogenesis and gradually decreased afterward. Knocking-down by RNAi of Dmc1 in unfertilized females of bisexual Artemia resulted in a severe deficiency of homologous chromosome pairing and produced univalents at the middle oogenesis stage, which was similar to that of parthenogenic Artemia, while in contrast, silencing Rad51 led to no significant chromosome morphological change. Our results indicated that Dmc1 is vital for HR in bisexual Artemia, and the deficiency of Dmc1 may be correlated with or even possibly one of core factors in the transition from bisexuality to parthenogenesis.

Population Genomic Analyses Suggest a Hybrid Origin, Cryptic Sexuality, and Decay of Genes Regulating Seed Development for the Putatively Strictly Asexual Kingdonia uniflora (Circaeasteraceae, Ranunculales)

Asexual lineages are perceived to be short-lived on evolutionary timescales. Hence, reports for exceptional cases of putative 'ancient asexuals' usually raise questions about the persistence of such species. So far, there have been few studies to solve the mystery in plants. The monotypic Kingdonia dating to the early Eocene, contains only K. uniflora that has no known definitive evidence for sexual reproduction nor records for having congeneric sexual species, raising the possibility that the species has persisted under strict asexuality for a long period of time. Here, we analyze whole genome polymorphism and divergence in K. uniflora. Our results show that K. uniflora is characterized by high allelic heterozygosity and elevated π_N/π_S ratio, in line with theoretical expectations under asexual evolution. Allele frequency spectrum analysis reveals the origin of asexuality in K. uniflora occurred prior to lineage differentiation of the species. Although divergence within K. uniflora individuals exceeds that between populations, the topologies of the two haplotype trees, however, fail to match each other, indicating long-term asexuality is unlikely to account for the high allele divergence and K. uniflora may have a recent hybrid origin. Phi-test shows a statistical probability of recombination for the conflicting phylogenetic signals revealed by the split network, suggesting K. uniflora engages in undetected sexual reproduction. Detection of elevated genetic differentiation and premature stop codons (in some populations) in genes regulating seed development indicates mutational degradation of sexuality-specific genes in K. uniflora. This study unfolds the origin and persistence mechanism of a plant lineage that has been known to reproduce asexually and presents the genomic consequences of lack of sexuality.

Evolutionary Potential of Parthenogenesis-Bisexual Lineages within Triploid Apomictic Thelytoky in Cacopsylla ledi (Flor, 1861) (Hemiptera, Psylloidea) in Fennoscandia

A widely accepted hypothesis is that parthenogenesis is an evolutionary dead end since it is selectively advantageous in the short term only but results in lowered diversification rates. Triploid apomictic parthenogenesis might represent an exception, as in favorable environments, triploid females are able to produce rare males and diploid females. The aim of the present study was to analyze the modes of reproduction and their evolutionary implications in the parthenogenetic psyllid Cacopsylla ledi (Flor, 1861) from Fennoscandia. The cytogenetic assessment of ploidy levels and the analysis of the COI haplotype revealed two geographically separated bisexual lineages implying genuine bisexual populations. The southern lineage occurring south of latitude 65° N in Finland showed a COI haplotype different from that of parthenogenetic triploids in the same population but identical to the haplotype of specimens in a genuine bisexual population in the Czech Republic. This allows us to suggest that bisexuals in southern Fennoscandia represent the original bisexual C. ledi. By contrast, in the northern bisexual lineage north of latitude 65° N, rare males and diploid females carried the same haplotype as triploids in the same population, having been produced by the triploids. In the Kola Peninsula, a genuine bisexual population of presumably rare male/diploid female origin was discovered. As this population is geographically isolated from populations of the ancestral bisexual C. ledi, it can develop into a new bisexual species through peripatric speciation during evolution. Our findings demonstrate that apomictic triploid parthenogenesis is not necessarily an evolutionary dead end but is able to lead to the emergence of a new bisexual species of parthenogenetic origin.

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.

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.

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.

Repeated convergent evolution of parthenogenesis in Acariformes (Acari)

The existence of old species-rich parthenogenetic taxa is a conundrum in evolutionary biology. Such taxa point to ancient parthenogenetic radiations resulting in morphologically distinct species. Ancient parthenogenetic taxa have been proposed to exist in bdelloid rotifers, darwinulid ostracods, and in several taxa of acariform mites (Acariformes, Acari), especially in oribatid mites (Oribatida, Acari). Here, we investigate the diversification of Acariformes and their ancestral mode of reproduction using 18S rRNA. Because parthenogenetic taxa tend to be more frequent in phylogenetically old taxa of Acariformes, we sequenced a wide range of members of this taxon, including early-derivative taxa of Prostigmata, Astigmata, Endeostigmata, and Oribatida. Ancestral character state reconstruction indicated that (a) Acariformes as well as Oribatida evolved from a sexual ancestor, (b) the primary mode of reproduction during evolution of Acariformes was sexual; however, species-rich parthenogenetic taxa radiated independently at least four times (in Brachychthonioidea (Oribatida), Enarthronota (Oribatida), and twice in Nothrina (Oribatida), (c) parthenogenesis additionally evolved frequently in species-poor taxa, for example, Tectocepheus, Oppiella, Rostrozetes, Limnozetes, and Atropacarus, and (d) sexual reproduction likely re-evolved at least three times from species-rich parthenogenetic clusters, in Crotonia (Nothrina), in Mesoplophora/Apoplophora (Mesoplophoridae, Enarthronota), and in Sphaerochthonius/Prototritia (Protoplophoridae, Enarthronota). We discuss possible reasons that favored the frequent diversification of parthenogenetic taxa including the continuous long-term availability of dead organic matter resources as well as generalist feeding of species as indicated by natural variations in stable isotope ratios.

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.

Male Sexual Trait Decay in Two Asexual Springtail Populations Follows Neutral Mutation Accumulation Theory

The transition to asexual reproduction is frequent and widespread across the tree of life and constitutes a major life history change. Without sexual reproduction, selection on sexually selected traits is expected to be weaker or absent, allowing the decay and ultimately loss of sexual traits. In this study, we applied an experimental approach to investigate the decay of reproductive traits under asexuality in two asexual populations of the springtail Folsomia candida. Specifically, we compared several key male sexual traits of a sexual population and two distinct parthenogenetic lines. To allow direct comparisons between sexual and asexual individuals we first determined a suite of life history characteristics in the sexual F. candida population, which performs an indirect transfer of sperm packages (spermatophores).To investigate the decay of male sexual traits under asexuality we measured the size of spermatophores, quantified the amount of sperm DNA material, and tested spermatophore attractiveness to females in all three populations. The amount of sperm DNA material in the sperm droplets and the attractiveness of spermatophores were lower in the asexual lines compared to the sexual population. However, the two asexual lines differed in the extent of decay of these traits. Our results are consistent with predictions from neutral mutation accumulation theory, and thus suggest this to be the main evolutionary process underlying the decay of male traits in F. candida.

Male phenotypes in a female framework: Evidence for degeneration in sperm produced by male snails from asexual lineages

How changes in selective regimes affect trait evolution is an important open biological question. We take advantage of naturally occurring and repeated transitions from sexual to asexual reproduction in a New Zealand freshwater snail species, Potamopyrgus antipodarum, to address how evolution in an asexual context-including the potential for relaxed selection on male-specific traits-influences sperm morphology. The occasional production of male offspring by the otherwise all-female asexual P. antipodarum lineages affords a unique and powerful opportunity to assess the fate of sperm traits in a context where males are exceedingly rare. These comparisons revealed that the sperm produced by 'asexual' males are markedly distinct from sexual counterparts. We also found that the asexual male sperm harboured markedly higher phenotypic variation and was much more likely to be morphologically abnormal. Together, these data suggest that transitions to asexual reproduction might be irreversible, at least in part because male function is likely to be compromised. These results are also consistent with a scenario where relaxed selection and/or mutation accumulation in the absence of sex translates into rapid trait degeneration.

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.

Phylogeographic patterns of intertidal arthropods (Acari, Oribatida) from southern Japanese islands reflect paleoclimatic events

The Japanese islands represent one of the world’s biodiversity hotspots. Their geological history and present geography resulted in a high number of endemic species in nearly all major metazoan clades. We investigated the phylogeography of three different intertidal mite species from the Ryukyu islands and southern mainland by means of morphometry and molecular genetics. None of the species represents an endemic, nearly all show distributions ranging over at least the southern and central Ryukyus. Two species, Fortuynia shibai and F. churaumi sp. n. clearly represent sister species that are derived from a common Eastern ancestor. Molecular genetic results indicate that these species separated approx. 3 Ma before the opening of the Okinawa trough, whereas F. shibai most likely showed an ancestral distribution stretching from the central Ryukyus across the Tokara strait to Japanese mainland, whereas F. churaumi probably evolved somewhere south of the Tokara strait. Phylogenetic data further indicates that long periods of isolation resulted in heterogeneous genetic structure but subsequent low sea level stands during Pleistocene allowed recent expansion and gene flow between island populations. Comparing these patterns with those of other animals, these tiny wingless mites apparently show better dispersal abilities than partially volant terrestrial organism groups.

Molecular characterization and genetic diversity of Ornithonyssus sylviarum in chickens (Gallus gallus) from Hainan Island, China

BACKGROUND

The northern fowl mite (NFM), Ornithonyssus sylviarum, is an obligatory hematophagous ectoparasite of birds and one of the most important pests in the poultry industry on several continents. Although NFM poses a serious problem, it remains a neglected pest of poultry in China and other Asian countries. Therefore, a molecular analysis was conducted to provide baseline information on the occurrence, genetic diversity and emergence of NFM in poultry farms from China.

METHODS

This study focused on morphological description and identification of adults based on electron microscopy, molecular sequencing of the mitochondrial cox1 gene and phylogenetic analysis. We have also used the DNA sequences of the cox1 gene to study the genetic diversity, population structure and demographic history. The neutrality tests were used to analyze signatures of historical demographic events.

RESULTS

The mites collected were identified as the northern fowl mite Ornithonyssus sylviarum based on external morphological characterization using electron microscopy. Molecular analysis using a 756-bp long partial fragment of the cox1 gene revealed 99-100% sequence identity with NFM and phylogenetic inferences showed a bootstrap value of 99% indicating a well-supported monophyletic relationship. Molecular diversity indices showed high levels of haplotype diversity dominated by private haplotypes, but low nucleotide divergence between haplotypes. The Tajima's D test and Fu's Fs test showed negative value, indicating deviations from neutrality and both suggested recent population expansion of mite populations supported by a star-like topology of the isolates in the network analysis. Our genetic data are consistent with a single introduction of NFM infestations and the spread of NFM infestation in Hainan poultry farms and a private haplotype dominance, which suggest that infestations are recycled within the farms and transmission routes are limited between farms.

CONCLUSIONS

To our knowledge, this is the first time a molecular report of NFM in chicken from China including other Asian countries using DNA barcoding. The findings have potential implications with respect to understanding the transmission patterns, emergence and populations trends of parasitic infestations of poultry farms that will help for setting the parameters for integrated pest management (IPM) tactics against mite infestations.

The Caribbean enigma: the presence of unusual cryptic diversity in intertidal mites (Arachnida, Acari, Oribatida)

The definition, as well as the existence of cryptic species, is still a subject of controversial debates. Some scientists claim that cryptic diversity is a real phenomenon that should be extensively studied while others argue that cryptic species do not exist as they are nothing more than an incompatibility of species concepts. We investigated the enigmatic case of two widely distributed Caribbean intertidal oribatid mites, Carinozetes bermudensis and Carinozetes mangrovi, consisting of five distinct genetic lineages. Morphological features allowing to clearly distinguish between these lineages are absent, and despite certain congruence with genetic data, comprehensive morphometric analyses also do not show clear separation. Species delimitation analyses based on COI sequence data, on the other hand, suggest five distinct genetic species. Despite the lack of diagnostic characters for these suggested species, the lineages can be classified at least into two morphological groups, the bermudensis and the mangrovi group which can only be distinguished by the arrangement of cuticular ventral carinae. Specimens within a group show nearly identical phenotypes, impeding morphological identification and hence rendering the found diversity cryptic. Stabilizing selection caused by the extreme conditions of the intertidal environment is suggested to be responsible for the found morphological stasis. The genetic lineages show more or less clear geographic patterns; in C. mangrovi, there is a northern, an Antillean, and a Pacific lineage, whereas in C. bermudensis, there is a Bermudian and a Caribbean lineage. In a few places, e.g., the Bahamas and Panama, distributions may overlap. Neither the found biogeographic pattern nor the observed ecological needs could explain the reason for the genetic diversification of Caribbean Carinozetes.

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

The absence of obvious morphological differences between species impedes species identification in many groups of organisms. Such cryptic species appear to be particularly common in small-bodied animals, impacting species richness estimates. In this study we aimed at characterizing the molecular diversity of the Palearctic arboreal oribatid mite species Cymbaeremaeus cymba across large parts of Europe. Phylogenetic analyses of three molecular markers, including the COI barcoding region, identified eight well supported, fairly divergent clades within C. cymba, which we consider to represent distinct species based on molecular species delimitation methods. Intraspecific variation of the COI gene was extremely low in all putative species, contradicting previous assumptions of high intraspecific diversity in oribatid mites. The frequent co-occurrence of two species on a single tree suggests an ecological micro-niche differentiation. Contrary to previous studies on oribatid mites, we find that COI is a good marker for species delimitation and its further use for barcoding of oribatids is highly recommended. Furthermore, we provide descriptions of six new Cymbaeremaeus species and designate a neotype of C. cymba.

Trophic structure of a tropical soil- and litter-dwelling oribatid mite community and consistency of trophic niches across biomes

The trophic positions of the most abundant soil- and litter-dwelling oribatid mite species in a tropical monsoon forest in Dong Nai (Cat Tien) National Park, southern Vietnam, were estimated using stable isotope analysis. Previously published data and Layman's metrics were used to compare the structure of the 'isotopic trophic niches' and the range of resources used by Oribatida in the tropical forest to those observed in temperate forests. The range of trophic levels occupied by oribatid mites, as reflected in their nitrogen isotopic compositions, did not differ between tropical and temperate forests. In contrast, the range of δ¹³C values of oribatid mites in the tropical community was smaller than that typically observed in temperate forests. This was due to the lack of ¹³C-enriched species with strongly calcified integuments. The diversity of trophic niches and the range of resources consumed did not differ between temperate and tropical communities of Oribatida. Moreover, similar δ¹⁵N values were observed for oribatid mite families across temperate and tropical ecosystems, suggesting that the taxonomic system of soil- and litter-dwelling Oribatida is ecologically consistent and supporting the 'taxonomic sufficiency' principle.

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.

Experimental and molecular approximation to microbial niche: trophic interactions between oribatid mites and microfungi in an oligotrophic freshwater system

Mite-fungal interactions play a key role in structuring core ecosystem processes such as nutrient dynamics. Despite their ecological relevance, these cross-kingdom interactions remain poorly understood particularly in extreme environments. Herein, we investigated feeding preferences of a novel genetic lineage of aquatic oribatids obtained from an oligotrophic freshwater system in the Cuatro Ciénegas Basin (CCB) within the Chihuahuan Desert, Mexico. During in vitro diet preference bioassays, transient aquatic microfungi (Aspergillus niger, Talaromyces sp., and Pleosporales sp.) recovered from the same mesocosm samples were offered individually and simultaneously to mites. Gut content was analyzed using classic plating and culture-independent direct PCR (focusing on the fungal barcoding region) methods. Our results indicated that oribatids fed on all tested fungal isolates, yet the profusely developing A. niger was preferentially consumed with all fungal components being digested. This feeding habit is particularly interesting since A. niger has been reported as an unsuitable dietary element for population growth, being consistently avoided by mites in previous laboratory experiments. It is possible that our mites from the CCB have adapted to exploit available resources within this oligotrophic site. This work confirms the trophic relationship between microfungi and mites, two rarely investigated major components of the microbial community, shedding light on the niche dynamics under low-nutrient conditions.

General environmental heterogeneity as the explanation of sexuality? Comparative study shows that ancient asexual taxa are associated with both biotically and abiotically homogeneous environments

Ecological theories of sexual reproduction assume that sexuality is advantageous in certain conditions, for example, in biotically or abiotically more heterogeneous environments. Such theories thus could be tested by comparative studies. However, the published results of these studies are rather unconvincing. Here, we present the results of a new comparative study based exclusively on the ancient asexual clades. The association with biotically or abiotically homogeneous environments in these asexual clades was compared with the same association in their sister, or closely related, sexual clades. Using the conservative definition of ancient asexuals (i.e., age >1 million years), we found eight pairs of taxa of sexual and asexual species, six differing in the heterogeneity of their inhabited environment on the basis of available data. The difference between the environmental type associated with the sexual and asexual species was then compared in an exact binomial test. The results showed that the majority of ancient asexual clades tend to be associated with biotically, abiotically, or both biotically and abiotically more homogeneous environments than their sexual controls. In the exploratory part of the study, we found that the ancient asexuals often have durable resting stages, enabling life in subjectively homogeneous environments, live in the absence of intense biotic interactions, and are very often sedentary, inhabiting benthos, and soil. The consequences of these findings for the ecological theories of sexual reproduction are discussed.

Effective purifying selection in ancient asexual oribatid mites

Sex is beneficial in the long term because it can prevent mutational meltdown through increased effectiveness of selection. This idea is supported by empirical evidence of deleterious mutation accumulation in species with a recent transition to asexuality. Here, we study the effectiveness of purifying selection in oribatid mites which have lost sex millions of years ago and diversified into different families and species while reproducing asexually. We compare the accumulation of deleterious nonsynonymous and synonymous mutations between three asexual and three sexual lineages using transcriptome data. Contrasting studies of young asexual lineages, we find evidence for strong purifying selection that is more effective in asexual as compared to sexual oribatid mite lineages. Our results suggest that large populations likely sustain effective purifying selection and facilitate the escape of mutational meltdown in the absence of sex. Thus, sex per se is not a prerequisite for the long-term persistence of animal lineages.

Asexual reproduction is thought to be an evolutionary dead end in eukaryotes because deleterious mutations will not be purged effectively. Here, Brandt and colleagues show that anciently asexual oribatid mites in fact have reduced accumulation of deleterious mutations compared to their sexual relatives.

The nuclear 28S gene fragment D3 as species marker in oribatid mites (Acari, Oribatida) from German peatlands

To make oribatid mites an applicable tool in monitoring programs it is necessary to find a molecular species marker that allows distinct, rapid and easy species identification. In previous studies, the common barcoding sequence COI showed to be too variable to serve as species marker in oribatid mites. The aim of the present study is to evaluate the potential use of the D3 region of the nuclear 28S rDNA gene for species identification. Therefore, we generated a reference DNA library of 28S D3 to identify specimens of the Oribatida from Germany, with focus on species occurring in peatlands being one of the most endangered habitats in Europe. New DNA sequences were obtained from 325 individuals and 64 species (58 genera, 34 families). By adding 28S D3-sequences from GenBank we altogether analysed 385 sequences from 89 German species, 32 of them restricted to peatlands and further 42 occurring in peatlands occasionally, representing 46 and 33% of the oribatids in German peatlands, respectively. P-distances were measured between species within families as well as for intraspecific divergence. 28S D3 showed low intraspecific genetic p-distances between 0 and 0.5%, interspecific distances within families varied between 0 and 9.7%. Most species pairs within families were further separated by one to four indels in addition to substitutions. Altogether, 93% of all analysed species are clearly delineated by 28S D3. Our study emphasises that 28S D3 rDNA is a useful barcode for the identification of oribatid mite specimens and represents an important step in building-up a comprehensive barcode library to allow metabarcoding analyses of environmental peatland samples for Oribatida in Germany as well as in Central Europe.

Genetic structure and distribution of Parisotoma notabilis (Collembola) in Europe: Cryptic diversity, split of lineages and colonization patterns

Climatic and biome changes of the past million years influenced the population structure and genetic diversity of soil-living arthropods in Europe. However, their effects on the genetic structure of widespread and abundant soil animal species such as the Collembola Parisotoma notabilis remain virtually unknown. This generalist and parthenogenetic species is an early colonizer of disturbed habitats and often occurs in human modified environments. To investigate ancient climatic influence and recent distributions on the genetic structure of P. notabilis we analyzed populations on a pan-European scale using three genetic markers differing in substitution rates. The results showed that P. notabilis comprises several genetic lineages with distinct distribution ranges that diverged in the Miocene. Genetic distances of COI between lineages ranged between 15% and 18% and molecular clock estimates suggest Late Miocene divergences considering the standard arthropod rate of 2.3% per my. Compared to other soil-living arthropods like oribatid mites, European lineages of P. notabilis are rather young and genetically uniform. The close association with anthropogenic habitats presumably contributed to rapid spread in Europe.

Founder events and pre-glacial divergences shape the genetic structure of European Collembola species

Background

Climate oscillations in the Cenozoic reduced species richness and genetic diversity of terrestrial and aquatic animals and plants in central and northern Europe. The most abundant arthropods in temperate soils are Collembola that live in almost any soil-related habitat. Extant species show little morphological variation to Eocene fossils, suggesting persistence of species in stable habitats for millions of years. Collembola are able to evade adverse climatic conditions by moving into deeper soil layers and are tolerant to frost and draught. If these adaptations sufficed for surviving glacial periods remains open and needs to be investigated in a phylogeographic context, i.e. investigating spatial structure on molecular level. We investigated the molecular variation of three common species of Collembola at a pan-European scale to identify glacial refuges and post-glacial colonization patterns with three genetic markers.

Results

All genes revealed remarkable genetic structure between but not within populations, suggesting density dependent processes for establishment of populations (founder-takes-all principle), which is common for European animals and plants. In contrast to the post-glacial recolonization patterns of many aboveground organisms, divergence times of most geographic lineages indicate preservation of genetic structure since the Miocene.

Conclusions

Collembola survived severe climatic changes including those during Quatenary glaciation and kept high genetic variance across Europe. Likely the buffering of temperature oscilliations in soil and the ability to evade adverse climatic conditions due to cold-tolerance and horizontal migration enabled Collembola to evade strong selective pressure of abiotic forces.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0719-8) contains supplementary material, which is available to authorized users.

Temporal fluctuations in oribatid mites indicate that density-independent factors favour parthenogenetic reproduction

We investigated the oribatid mite density, community structure and the percentage of parthenogenetic individuals in four different forest types across three regions in Germany in 2008 and once again in 2011. We compared temporal (inter-annual) fluctuations in population densities between sexually and parthenogenetically reproducing species of oribatid mites. We hypothesized that population densities in parthenogenetic oribatid mite species fluctuate more than in sexual ones. Further, we expected species composition and dominance of parthenogenetic species to differ between forest types and regions. Oribatid mite community structure did not differ between years but varied with forest type and region, indicating low species turnover in time. As hypothesized, temporal fluctuations were more pronounced in parthenogenetic as compared to sexual species. The percentage of parthenogenetic individuals was significantly higher in coniferous than in beech forests and significantly higher in Schorfheide-Chorin than in Hainich-Dün and Schwäbische Alb. The results indicate that parthenogenetic species flourish if populations are controlled by density-independent factors and dominate at sites were resources are plentiful and easily available, such as coniferous forests, and in regions with more acidic soils and thick organic layers, such as Schorfheide-Chorin. However, historical factors also may have contributed to the increased dominance of parthenogenetic species in the Schorfheide-Chorin, as this region was more heavily glaciated and this may have favoured parthenogenetic species. Overall, our study supports the hypothesis that parthenogenetic species benefit from the lack of density-dependent population control whereas the opposite is true for sexual species.

No Accumulation of Transposable Elements in Asexual Arthropods

Transposable elements (TEs) and other repetitive DNA can accumulate in the absence of recombination, a process contributing to the degeneration of Y-chromosomes and other nonrecombining genome portions. A similar accumulation of repetitive DNA is expected for asexually reproducing species, given their entire genome is effectively nonrecombining. We tested this expectation by comparing the whole-genome TE loads of five asexual arthropod lineages and their sexual relatives, including asexual and sexual lineages of crustaceans (Daphnia water fleas), insects (Leptopilina wasps), and mites (Oribatida). Surprisingly, there was no evidence for increased TE load in genomes of asexual as compared to sexual lineages, neither for all classes of repetitive elements combined nor for specific TE families. Our study therefore suggests that nonrecombining genomes do not accumulate TEs like nonrecombining genomic regions of sexual lineages. Even if a slight but undetected increase of TEs were caused by asexual reproduction, it appears to be negligible compared to variance between species caused by processes unrelated to reproductive mode. It remains to be determined if molecular mechanisms underlying genome regulation in asexuals hamper TE activity. Alternatively, the differences in TE dynamics between nonrecombining genomes in asexual lineages versus nonrecombining genome portions in sexual species might stem from selection for benign TEs in asexual lineages because of the lack of genetic conflict between TEs and their hosts and/or because asexual lineages may only arise from sexual ancestors with particularly low TE loads.

The marbled crayfish as a paradigm for saltational speciation by autopolyploidy and parthenogenesis in animals

The parthenogenetic all-female marbled crayfish is a novel research model and potent invader of freshwater ecosystems. It is a triploid descendant of the sexually reproducing slough crayfish, Procambarus fallax, but its taxonomic status has remained unsettled. By cross-breeding experiments and parentage analysis we show here that marbled crayfish and P. fallax are reproductively separated. Both crayfish copulate readily, suggesting that the reproductive barrier is set at the cytogenetic rather than the behavioural level. Analysis of complete mitochondrial genomes of marbled crayfish from laboratory lineages and wild populations demonstrates genetic identity and indicates a single origin. Flow cytometric comparison of DNA contents of haemocytes and analysis of nuclear microsatellite loci confirm triploidy and suggest autopolyploidisation as its cause. Global DNA methylation is significantly reduced in marbled crayfish implying the involvement of molecular epigenetic mechanisms in its origination. Morphologically, both crayfish are very similar but growth and fecundity are considerably larger in marbled crayfish, making it a different animal with superior fitness. These data and the high probability of a divergent future evolution of the marbled crayfish and P. fallax clusters suggest that marbled crayfish should be considered as an independent asexual species. Our findings also establish the P. fallax-marbled crayfish pair as a novel paradigm for rare chromosomal speciation by autopolyploidy and parthenogenesis in animals and for saltational evolution in general.

Cryptic speciation in the Acari: a function of species lifestyles or our ability to separate species?

There are approximately 55,000 described Acari species, accounting for almost half of all known Arachnida species, but total estimated Acari diversity is reckoned to be far greater. One important source of currently hidden Acari diversity is cryptic speciation, which poses challenges to taxonomists documenting biodiversity assessment as well as to researchers in medicine and agriculture. In this review, we revisit the subject of biodiversity in the Acari and investigate what is currently known about cryptic species within this group. Based on a thorough literature search, we show that the probability of occurrence of cryptic species is mainly related to the number of attempts made to detect them. The use of, both, DNA tools and bioassays significantly increased the probability of cryptic species detection. We did not confirm the generally-accepted idea that species lifestyle (i.e. free-living vs. symbiotic) affects the number of cryptic species. To increase detection of cryptic lineages and to understand the processes leading to cryptic speciation in Acari, integrative approaches including multivariate morphometrics, molecular tools, crossing, ecological assays, intensive sampling, and experimental evolution are recommended. We conclude that there is a demonstrable need for future investigations focusing on potentially hidden mite and tick species and addressing evolutionary mechanisms behind cryptic speciation within Acari.

Phylogeny and species delineation in European species of the genus Steganacarus (Acari, Oribatida) using mitochondrial and nuclear markers

Species of the genus Steganacarus are soil-living oribatid mites (Acari, Phthiracaridae) with a ptychoid body. The phylogeny and species status of the species of Steganacarus are not resolved, some authors group all ten German species of Steganacarus within the genus Steganacarus whereas others split them into three subgenera, Steganacarus, Tropacarus and Atropacarus. Additionally, two species, S. magnus and T. carinatus, comprise morphotypes of questionable species status. We investigated the phylogeny and species status of ten European Steganacarus species, i.e. S. applicatus, S. herculeanus, S. magnus forma magna, S. magnus forma anomala, S. spinosus, Tropacarus brevipilus, T. carinatus forma carinata, T. carinatus forma pulcherrima, Atropacarus striculus and Rhacaplacarus ortizi. We used two molecular markers, a 251 bp fragment of the nuclear gene 28S rDNA (D3) and a 477 bp fragment of the mitochondrial COI region. The phylogeny based on a combined analysis of D3 and COI separated four subgenera (Steganacarus, Tropacarus and Atropacarus, Rhacaplacarus) indicating that they form monophyletic groups. The COI region separated all ten species of the genus Steganacarus and showed variation within some species often correlating with the geographic origin of the species. Resolution of the more conserved D3 region was limited, indicating that radiation events are rather recent. Overall, our results indicate that both genes alone cannot be used for phylogeny and barcoding since variation is too low in D3 and too high in COI. However, when used in combination these genes provide reliable insight into the phylogeny, radiation and species status of taxa of the genus Steganacarus.

Evidence for frozen-niche variation in a cosmopolitan parthenogenetic soil mite species (Acari, Oribatida)

Parthenogenetic lineages may colonize marginal areas of the range of related sexual species or coexist with sexual species in the same habitat. Frozen-Niche-Variation and General-Purpose-Genotype are two hypotheses suggesting that competition and interclonal selection result in parthenogenetic populations being either genetically diverse or rather homogeneous. The cosmopolitan parthenogenetic oribatid mite Oppiella nova has a broad ecological phenotype and is omnipresent in a variety of habitats. Morphological variation in body size is prominent in this species and suggests adaptation to distinct environmental conditions. We investigated genetic variance and body size of five independent forest - grassland ecotones. Forests and grasslands were inhabited by distinct genetic lineages with transitional habitats being colonized by both genetic lineages from forest and grassland. Notably, individuals of grasslands were significantly larger than individuals in forests. These differences indicate the presence of specialized genetic lineages specifically adapted to either forests or grasslands which coexist in transitional habitats. Molecular clock estimates suggest that forest and grassland lineages separated 16-6 million years ago, indicating long-term persistence of these lineages in their respective habitat. Long-term persistence, and morphological and genetic divergence imply that drift and environmental factors result in the evolution of distinct parthenogenetic lineages resembling evolution in sexual species. This suggests that parthenogenetic reproduction is not an evolutionary dead end.

Population genetics of bisexual and unisexual populations of the scaly-winged bark louse Echmepteryx hageni (Insecta: Psocoptera)

The scaly-winged bark louse, Echmepteryx hageni, exhibits a unique pattern of co-existence of apparently differnt reproductive modes. Unisexuality is widespread in eastern North America, while sexual populations are restricted to isolated rock out-croppings in southern Illinois and eastern Kentucky. Three of the four nuclear loci examined show greater genetic diversity in the unisexual form compared to the sexual form of E. hageni, in accordance with the pattern previously shown in mitochondrial genetic data. Neutrality tests of the nuclear loci indicate a consistent signal of demographic expansion in asexual populations, but not in sexual populations. There was evidence of inbreeding in the isolated sexual populations at three of the nuclear loci, and one locus had signs of gene specific balancing selection. However, there is no significant genetic differentiation between bisexual and unisexual populations, possibly due to the greater effective population size of nuclear loci relative to mitochondrial loci. The mitochondrial differentiation of E. hageni populations in the northwestern part of their range (Minnesota and Wisconsin) was also not reflected in the nuclear data. We present three hypotheses that may explain the disparity in observed nuclear and mitochondrial genetic diversity between the reproductive forms of E. hageni.

Resource availability as driving factor of the reproductive mode in soil microarthropods (Acari, Oribatida)

The availability of high quality resources is an important factor driving community structure and reproductive mode of animals. Parthenogenetic reproduction prevails when resources are available in excess, whereas sexuality correlates with resource shortage. We investigated the effect of resource availability on the community structure of oribatid mites in a laboratory experiment. Availability of food resources was increased by addition of glucose to leaf litter and reduced by leaching of nutrients from leaf litter. Experimental systems were incubated at three different temperatures to establish different regimes of resource exploitation. Community structure of oribatids and numbers of eggs per female were measured over a period of ten months. We expected the density of oribatid mites to decline in the reduced litter quality treatment but to increase in the glucose treatment. Both effects were assumed to be more pronounced at higher temperatures. We hypothesized sexual species to be less affected than parthenogenetic species by reduced resource quality due to higher genetic diversity allowing more efficient exploitation of limited resources, but to be outnumbered by parthenogenetic species in case of resource addition due to faster reproduction. In contrast to our hypotheses, both sexual and parthenogenetic oribatid mite species responded similarly with their densities declining uniformly during incubation. The parthenogenetic Brachychthoniidae and Tectocepheus dominated early in the experiment but were replaced later by parthenogenetic Desmonomata and Rhysotritia. In parthenogenetic species the number of eggs per female increased during the experiment while the number of eggs in sexual females remained constant or decreased slightly; in general, egg numbers were higher in sexual than in parthenogenetic species. The results indicate that for sustaining oribatid mite populations other resources than litter and associated saprotrophic microorganisms are needed. They also indicate that there are two groups of parthenogenetically reproducing species: exploiters of easily available resources and consumers of leaf litter associated resources.

On the fate of sexual traits under asexuality

Environmental shifts and life-history changes may result in formerly adaptive traits becoming non-functional or maladaptive. In the absence of pleiotropy and other constraints, such traits may decay as a consequence of neutral mutation accumulation or selective processes, highlighting the importance of natural selection for adaptations. A suite of traits are expected to lose their adaptive function in asexual organisms derived from sexual ancestors, and the many independent transitions to asexuality allow for comparative studies of parallel trait maintenance versus decay. In addition, because certain traits, notably male-specific traits, are usually not exposed to selection under asexuality, their decay would have to occur as a consequence of drift. Selective processes could drive the decay of traits associated with costs, which may be the case for the majority of sexual traits expressed in females. We review the fate of male and female sexual traits in 93 animal lineages characterized by asexual reproduction, covering a broad taxon range including molluscs, arachnids, diplopods, crustaceans and eleven different hexapod orders. Many asexual lineages are still able occasionally to produce males. These asexually produced males are often largely or even fully functional, revealing that major developmental pathways can remain quiescent and functional over extended time periods. By contrast, for asexual females, there is a parallel and rapid decay of sexual traits, especially of traits related to mate attraction and location, as expected given the considerable costs often associated with the expression of these traits. The level of decay of female sexual traits, in addition to asexual females being unable to fertilize their eggs, would severely impede reversals to sexual reproduction, even in recently derived asexual lineages. More generally, the parallel maintenance versus decay of different trait types across diverse asexual lineages suggests that neutral traits display little or no decay even after extended periods under relaxed selection, while extensive decay for selected traits occurs extremely quickly. These patterns also highlight that adaptations can fix rapidly in natural populations of asexual organisms, in spite of their mode of reproduction.

Multiple lines of evidence on the genetic relatedness of the parthenogenetic and bisexual Haemaphysalis longicornis (Acari: Ixodidae)

As an obligate hematophagous ectoparasite, the hard tick Haemaphysalis longicornis exhibits two reproductive strategies, bisexual reproduction, and obligate parthenogenesis, which have attracted a widespread attention. However, the speciation of parthenogenetic population remained ambiguous due to its similarity in morphology but the remarkable differences in cytogenetics as compared with those of the bisexual ones. In the present study, we explored several new lines of genetic evidence to resolve this controversial issue. The number of the chromosomes in two lineages was checked by classical methods and their total DNA levels were determined utilizing flowcytometry. In addition, the sequences of 12S rDNA, 16S rDNA, cytochrome c oxidase I and II (COI, COII) and internal transcribed spacer-2 (ITS-2) genes were used to assess their phylogenetic relationship. We observed that the chromosome ploidy of bisexual and parthenogenetic H. longicornis collected by our laboratory was diploid and triploid, respectively. Flowcytometry analysis indicated a ratio close to 2:3 in the DNA contents of bisexual to parthenogenetic H. longicornis. Although the chromosome ploidy is different, their gene sequences are extremely similar. Analogous to the intra-species genetic difference of other invertebrates, sequence differences of all loci examined are below 2%. Phylogenetic trees constructed from 12S rDNA, 16S rDNA, COI, and ITS-2 genes revealed that they were all in the same monophyletic clade instead of splitting independently into evolutional branches. Moreover, according to 4× Rule, the K/θ ratio of two reproductive populations calculated based on COI was much smaller than four, strongly supporting that they belong to the same species. Therefore, we conclude that the evolutionary process just disturbs the chromosome ploidy and the sexual determination of parthenogenetic population and that it would be better to consider parthenogenetic H. longicornis as a metapopulation rather than a cryptic species.

Neutral and selection-driven decay of sexual traits in asexual stick insects

Environmental shifts and lifestyle changes may result in formerly adaptive traits becoming non-functional or maladaptive. The subsequent decay of such traits highlights the importance of natural selection for adaptations, yet its causes have rarely been investigated. To study the fate of formerly adaptive traits after lifestyle changes, we evaluated sexual traits in five independently derived asexual lineages, including traits that are specific to males and therefore not exposed to selection. At least four of the asexual lineages retained the capacity to produce males that display normal courtship behaviours and are able to fertilize eggs of females from related sexual species. The maintenance of male traits may stem from pleiotropy, or from these traits only regressing via drift, which may require millions of years to generate phenotypic effects. By contrast, we found parallel decay of sexual traits in females. Asexual females produced altered airborne and contact signals, had modified sperm storage organs, and lost the ability to fertilize their eggs, impeding reversals to sexual reproduction. Female sexual traits were decayed even in recently derived asexuals, suggesting that trait changes following the evolution of asexuality, when they occur, proceed rapidly and are driven by selective processes rather than drift.

Speciation in the asexual realm: is the parthenogenetic weevil Naupactus cervinus a complex of species in statu nascendi?

Population genetic theory shows that asexual organisms may evolve into species, which behave as independent evolutionary units. As a result, they form genotypic clusters separated by deep gaps due to geographic isolation and/or divergent selection. Identification of several genetically divergent groups of weevils embodied in the nominal species Naupactus cervinus deserves further study, in order to test if these lineages are evolving independently. In the present paper we tested if the parthenogenetic weevil N. cervinus, native to South America and broadly distributed throughout the world, contains more than one evolutionary unit. For this purpose, we applied three different approaches, a multilocus phylogenetic analysis, the GMYC approach and the K/θ method. We accomplished these analyses through a survey of mitochondrial (COI and COII genes) and nuclear (ITS1 sequence) genetic variation and morphometric analysis in a sample which included individuals from different locations within the native geographic range of N. cervinus. In addition, we compared the divergence accumulated in this species with that in another weevil of the same tribe (Naupactini) showing identical reproductive mode to see if similar levels of morphological variation matches similar levels of genetic divergence. We report the presence of two independent evolutionary units living in sympatry in forest areas. The incongruence between mitochondrial and nuclear datasets analyzed herein reflects incomplete lineage sorting of the nuclear marker and different evolutionary rates between genomes. Ecological divergence driven by natural selection (sympatry) or secondary contact after geographic isolation (allopatry) might explain the deep gaps in mitochondrial phylogenies. Instead, Wolbachia infection was ruled out as a causal factor for such differentiation. We conclude that N. cervinus is probably a species complex with at least two well differentiated lineages that would represent a cluster of species in statu nascendi.

Cryptic diversity in the ubiquist species Parisotoma notabilis (Collembola, Isotomidae): a long-used chimeric species?

Parisotoma notabilis is the most common species of Collembola in Europe and is currently designated as ubiquist. This species has been extensively used in numerous studies and is considered as well characterized on a morphological ground. Despite the homogeneity of its morphology, the sequencing of the barcoding fragment (5′ end of COI) for several populations throughout Europe and North America revealed four distinct genetic lineages. The divergence found between these lineages was similar to the genetic distance among other species of the genus Parisotoma included in the analysis. All four lineages have been confirmed by the nuclear gene 28S. This congruence between mitochondrial and nuclear signals, as well as the geographical distribution pattern of lineages observed in Europe, supports the potential specific status of these lineages. Based on specimens from the type locality (Hamburg), the species name was successfully assigned to one of these lineages. This finding raises several problems as Parisotoma notabilis has been widely used in many ecological studies. Accumulation of new data for the different lineages detected, especially ecological information and life history traits, is needed to help resolve this situation.

Cryptic species in putative ancient asexual darwinulids (Crustacea, Ostracoda)

BACKGROUND

Fully asexually reproducing taxa lack outcrossing. Hence, the classic Biological Species Concept cannot be applied.

METHODOLOGY/PRINCIPAL FINDINGS

We used DNA sequences from the mitochondrial COI gene and the nuclear ITS2 region to check species boundaries according to the evolutionary genetic (EG) species concept in five morphospecies in the putative ancient asexual ostracod genera, Penthesilenula and Darwinula, from different continents. We applied two methods for detecting cryptic species, namely the K/θ method and the General Mixed Yule Coalescent model (GMYC). We could confirm the existence of species in all five darwinulid morphospecies and additional cryptic diversity in three morphospecies, namely in Penthesilenula brasiliensis, Darwinula stevensoni and in P. aotearoa. The number of cryptic species within one morphospecies varied between seven (P. brasiliensis), five to six (D. stevensoni) and two (P. aotearoa), respectively, depending on the method used. Cryptic species mainly followed continental distributions. We also found evidence for coexistence at the local scale for Brazilian cryptic species of P. brasiliensis and P. aotearoa. Our ITS2 data confirmed that species exist in darwinulids but detected far less EG species, namely two to three cryptic species in P. brasiliensis and no cryptic species at all in the other darwinulid morphospecies.

CONCLUSIONS/SIGNIFICANCE

Our results clearly demonstrate that both species and cryptic diversity can be recognized in putative ancient asexual ostracods using the EG species concept, and that COI data are more suitable than ITS2 for this purpose. The discovery of up to eight cryptic species within a single morphospecies will significantly increase estimates of biodiversity in this asexual ostracod group. Which factors, other than long-term geographic isolation, are important for speciation processes in these ancient asexuals remains to be investigated.

Population dynamics with a mixed type of sexual and asexual reproduction in a fluctuating environment

BACKGROUND

Carassius gibelio, a cyprinid fish from Eurasia, has the ability to reproduce both sexually and asexually. This fish is also known as an invasive species which colonized almost all continental Europe, most likely originating from Asia and Eastern Europe. Populations of both sexually and asexually reproducing individuals exist in sympatry. In this study we try to elucidate the advantages of such a mixed type of reproduction. We investigate the dynamics of two sympatric populations with sexual and asexual reproduction in a periodically fluctuating environment. We define an individual-based computational model in which genotypes are represented by L loci, and the environment is composed of L resources for which the two populations compete.

RESULTS

Our model demonstrates advantageous population dynamics where the optimal percentage of asexual reproduction depends on selection strength, on the number of selected loci and on the timescale of environmental fluctuations. We show that the sexual reproduction is necessary for "generating" fit genotypes, while the asexual reproduction is suitable for "amplifying" them. The simulations show that the optimal percentage of asexual reproduction increases with the length of the environment stability period and decrease with the strength of the selection and the number of loci.

CONCLUSIONS

In this paper we addressed the advantages of a mixed type of sexual and asexual reproduction in a changing environment and explored the idea that a species that is able to adapt itself to environmental fluctuation can easily colonize a new habitat. Our results could provide a possible explanation for the rapid and efficient invasion of species with a variable ratio of sexual and asexual reproduction such as Carassius gibelio.

Who is eating what: diet assessment using next generation sequencing

The analysis of food webs and their dynamics facilitates understanding of the mechanistic processes behind community ecology and ecosystem functions. Having accurate techniques for determining dietary ranges and components is critical for this endeavour. While visual analyses and early molecular approaches are highly labour intensive and often lack resolution, recent DNA-based approaches potentially provide more accurate methods for dietary studies. A suite of approaches have been used based on the identification of consumed species by characterization of DNA present in gut or faecal samples. In one approach, a standardized DNA region (DNA barcode) is PCR amplified, amplicons are sequenced and then compared to a reference database for identification. Initially, this involved sequencing clones from PCR products, and studies were limited in scale because of the costs and effort required. The recent development of next generation sequencing (NGS) has made this approach much more powerful, by allowing the direct characterization of dozens of samples with several thousand sequences per PCR product, and has the potential to reveal many consumed species simultaneously (DNA metabarcoding). Continual improvement of NGS technologies, on-going decreases in costs and current massive expansion of reference databases make this approach promising. Here we review the power and pitfalls of NGS diet methods. We present the critical factors to take into account when choosing or designing a suitable barcode. Then, we consider both technical and analytical aspects of NGS diet studies. Finally, we discuss the validation of data accuracy including the viability of producing quantitative data.