Cryptic diversity in the genus <Emphasis Type="Italic">Adineta</Emphasis> Hudson &; Gosse, 1886 (Rotifera: Bdelloidea: Adinetidae): a DNA taxonomy approach

Cryptic species are continuously discovered in rotifers using different methods to delineate these units of diversity. DNA taxonomy is the most effective method taxonomists have to untie potential cryptic taxa. Here, we estimate hidden diversity in a genus of bdelloid rotifers, Adineta. We analyse cryptic diversity using a coalescent approach to infer evolutionarily significant units from a phylogenetic tree obtained from cytochrome oxidase I sequences. Cryptic diversity was measured for eight traditional species and from several additional undetermined populations. Taxonomic inflation of up to 36 taxa was found in A. vaga from DNA taxonomy. As observed in other microscopic organisms, cryptic taxa within each traditional species were not geographically isolated, but had significantly narrower ecological niches than expected by chance alone.     

On the reality and recognisability of asexual organisms: morphological analysis of the masticatory apparatus of bdelloid rotifers

Species concepts and definitions have been a long-standing debate in evolutionary biology since before Darwin, and almost all proposed solutions are based upon grouping and clustering, with species conceived as somehow biological distinct entities, originated and maintained mainly by reproductive isolation. Lacking reproductive exchange, asexual organisms such as bdelloid rotifers, the best-supported clade of so-called 'ancient asexuals', pose an interesting challenge to debates over the reality of species. However, few data are available on bdelloid rotifers. The only evidence has been that bdelloid species have been more consistently recognised than in their sister sexual group, the monogonont rotifers, across successive taxonomic treatments, but this is confounded by the much lesser degree of taxonomic interest in bdelloids. We applied geometric morphometrics analyses on shape and size of hard masticatory pieces, named trophi, of 1420 bdelloids, belonging to 48 populations of eight traditional species, to test the hypothesis of recognisability of bdelloids. Our morphological analysis confirms that traditional bdelloid species are separated distinct entities, possessing trophi morphologies divided by gaps between taxa, similar to patterns of morphological features in sexually reproducing organisms. In common with most microscopic understudied organisms, bdelloid rotifers harbour much previously undescribed diversity: we found significant differences in trophi morphology within traditional species, revealing the existence of cryptic taxa, similar to those also found in facultatively sexual monogonont rotifers. We confirm that recognisability in bdelloids is not qualitatively different from other small understudied animals such as monogononts, and that sexual versus asexual reproduction does not lead to differences in morphological diversity patterns, as previously suggested based on interpretation of taxonomic revisions.     

Inconsistent estimates of diversity between traditional and DNA taxonomy in bdelloid rotifers

Microscopic animals offer great potential in the analysis of spatial patterns of diversity, as they may provide different scenarios for biogeography and macroecology, but understanding diversity of microscopic animals is hampered by lack of comprehensive data on species distribution and by unreliable taxonomy. DNA taxonomy may prove useful in obtaining reliable data in the future, but we still do not know to what extent traditional and DNA taxonomy can be comparable for microscopic organisms. In this paper, we compare analyses and estimates of diversity at the level of species assemblage between traditional and DNA taxonomy for a group of moss-dwelling microscopic animals, bdelloid rotifers. The results are straightforward: Traditional species identification underestimates diversity by factors of 2 at the local and 2.5 at the regional scale. We discuss the results in the framework of current hypotheses on the distribution of microscopic animals.     

落叶生境蛭态轮虫物种多样性及四种中国新记录种

为研究落叶生境蛭态轮虫物种多样性, 对中国8省28个落叶样品进行了调查, 采样范围涵盖中国热带、亚热带及温带地区, 海拔高度从3 m到1500 m不等, 共记录蛭态轮虫3科8属29种, 其中中国新记录属1属, 中国新记录种4种, 将中国蛭态轮虫记录由88种增加到92种。研究获取了新记录种跛足突盘轮虫(Bradyscela clauda Bryce, 1893)的COⅠ序列, 与基因库中同科物种的COⅠ基因序列聚类比对, 证明了跛足突盘轮虫的遗传位置。结果表明, 落叶生境蛭态轮虫物种多样性较高。因此, 在调查苔藓和土壤等生境的同时, 应加强对落叶生境的研究力度, 以期发现更多的蛭态轮虫新记录种、特有种和新种。     

A carnivorous bdelloid rotifer, Abrochtha carnivora n.sp.

Abstract. Here we describe a new bdelloid rotifer, Abrochtha carnivora n.sp., that preys on other bdelloids and monogonont rotifers. This is the first report of predatory behavior in bdelloids. Despite this extraordinary behavior, A. carnivora displays no major structural deviation from the standard body plan for members of the bdelloid family Philodinavidae: body with head (with ciliated corona), trunk, and foot, mastax with ramate trophi. The finding of such a carnivorous species, unique for the class, appears to contradict the common assumption that the wholly parthenogenetic bdelloids are evolutionary dead-ends.     

Bdelloid rotifers: ‘sleeping beauties’ and ‘evolutionary scandals’, but not only

Bdelloid rotifers are mostly known for two peculiarities, continuous parthenogenetic reproduction and dormancy in response to habitat desiccation, a phenomenon named anhydrobiosis. These uncommon traits earned them the names of ‘evolutionary scandals’ and ‘sleeping beauties’, respectively. Relevant aspects of bdelloid biology have recently been described that connect parthenogenesis to anhydrobiosis and that might account for their evolutionary survival in spite of the conservative reproduction. In the present study, I explore recent literature, in the attempt to disentangle the apparent incongruency between the apomictic reproduction and the presumed long-term evolutionary survival of bdelloid species. Recent results remarkably improved our knowledge of bdelloid population biology, genetics, and molecular biology. The most relevant findings concern (i) acquisition of foreign genes through horizontal transfer, (ii) presence of divergent sequences possibly corresponding to ancient gene duplications and (iii) capacity to escape parasites: events that appear to be connected with dormancy. I also address the results of recent studies on the relationships between bdelloids and other rotifers, including acanthocephalans, in an attempt to highlight similarities and differences that should be clarified to better understand phylogenetic relationship among the Rotifera sensu lato.

     

The Necessity of DNA Taxonomy to Reveal Cryptic Diversity and Spatial Distribution of Meiofauna,with a Focus on Nemertea

Meiofauna represent one of the most abundant and diverse communities in marine benthic ecosystems. However, an accurate assessment of diversity at the level of species has been and remains challenging for these microscopic organisms. Therefore, for many taxa, especially the soft body forms such as nemerteans, which often lack clear diagnostic morphological traits, DNA taxonomy is an effective means to assess species diversity. Morphological taxonomy of Nemertea is well documented as complicated by scarcity of unambiguous character states and compromised by diagnoses of a majority of species (and higher clades) being inadequate or based on ambiguous characters and character states. Therefore, recent studies have advocated for the primacy of molecular tools to solve the taxonomy of this group. DNA taxonomy uncovers possible hidden cryptic species, provides a coherent means to systematize taxa in definite clades, and also reveals possible biogeographic patterns. Here, we analyze diversity of nemertean species by considering the barcode region of the mitochondrial gene Cytochrome Oxidase subunit I (COI) and different species delineation approaches in order to infer evolutionarily significant units. In the aim to uncover actual diversity of meiofaunal nemerteans across different sites in Central America, COI sequences were obtained for specimens assigned here to the genera Cephalothrix, Ototyphlonemertes, and Tetrastemma-like worms, each commonly encountered in our sampling. Additional genetic, taxonomic, and geographic data of other specimens belonging to these genera were added from GenBank. Results are consistent across different DNA taxonomy approaches, and revealed (i) the presence of several hidden cryptic species and (ii) numerous potential misidentifications due to traditional taxonomy. (iii) We additionally test a possible biogeographic pattern of taxonomic units revealed by this study, and, except for a few cases, the putative species seem not to be widely distributed, in contrast to what traditional taxonomy would suggest for the recognized morphotypes.     

Spatial gradients in species diversity of microscopic animals: the case of bdelloid rotifers at high altitude

Aim Organisms smaller than 2 mm appear not to follow the spatial patterns in richness and diversity commonly observed in macroscopic organisms. We describe spatial patterns in species diversity in a group of microscopic organisms, bdelloid rotifers, living in moss and lichen patches, in order to test the hypotheses of no relationship between species richness and composition and spatial gradients, suggested by previously published patterns in microscopic organisms. Location Moss and lichen patches as habitats for bdelloids, on high‐elevation peaks at altitudes between 2984 and 4527 m a.s.l. across the Italian, French and Swiss Alps, with distances among sample sites ranging from 1 m to 420 km, in comparison with lower‐elevation samples at altitudes from 850 to 1810 m a.s.l. Methods We sampled species assemblages of bdelloid rotifers living in isolated moss and lichen patches in 47 sites. We described the observed α, β and γ diversities; the heterogeneity of species assemblages; and the estimated number of species (incidence‐based coverage estimator). Patterns in species distribution were analysed at three different levels: (1) habitat, comparing species richness on moss and lichen substrates, testing differences in α diversity and heterogeneity (anova ), species composition (analysis of similarities test), and γ diversity (rarefaction curves); (2) altitude, comparing the observed richness with previously published data from locations well below 2000 m; and (3) distances between sites, correlating the matrix of Jaccard dissimilarities and the matrix of geographical distances with a Mantel test. Results Both species richness and species composition of bdelloid rotifers differed significantly between mosses and lichens at high elevations, but no difference was found in the heterogeneity of species assemblages. Alpha diversity was significantly lower at high‐elevation than at low‐elevation sites, but the estimated number of species was not reduced when compared with sites at low elevations. Geographical distance between sites had no effect on species composition in either mosses or lichens. The distribution of species was highly heterogeneous, with a low similarity among assemblages. Main conclusions As expected, bdelloids appear to occupy habitats selectively. The altitudinal gradient in species richness for bdelloid rotifers is limited to a decrease in α diversity only; such a decrease is not caused by a lower number of species (low γ diversity) being able to tolerate harsh conditions, and high‐altitude species are not a subset of species living at lower elevations. The observed values of α, β and γ diversity at high altitudes in the Alps are compatible with the scenario of a very low number of available propagules because of the low density of patches of favourable habitat. Our results suggest that the geographical distribution of animals, and therefore biodiversity patterns, may be strongly influenced by animal size, as small organisms such as bdelloids appear to show spatial patterns that differ from those known in larger animals. Differences in body size should be taken into account carefully in future studies of biodiversity patterns.     

Molecular evidence for broad-scale distributions in bdelloid rotifers: everything is not everywhere but most things are very widespread

The Baas-Becking's hypothesis, also known by the term 'everything is everywhere' (EisE), states that microscopic organisms such as bacteria and protists are globally distributed and do not show biogeographical patterns, due to their high dispersal potential. We tested the prediction of the EisE hypothesis on bdelloid rotifers, microscopic animals similar to protists in size and ecology that present one of the best cases among animals for the plausibility of global dispersal. Geographical range sizes and patterns of isolation by distance were estimated for global collections of the genera Adineta and Rotaria, using different taxonomic units: (i) traditional species based on morphology, (ii) the most inclusive monophyletic lineages from a cytochrome oxidase I phylogeny comprising just a single traditional species, and (iii) genetic clusters indicative of independently evolving lineages. Although there are cases of truly cosmopolitan distribution, even at the most finely resolved taxonomic level, most genetic clusters are distributed at continental or lower scales. Nevertheless, although 'everything is not everywhere', bdelloid rotifers do display broad distributions typical of those of other microscopic organisms. Broad dispersal and large population sizes might be factors lessening the evolutionary cost of long-term abstinence from sexual reproduction in this famous group of obligate parthenogens.     

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

Theories on the evolution and maintenance of sex are challenged by the existence of ancient parthenogenetic lineages such as bdelloid rotifers and darwinulid ostracods. It has been proposed that several parthenogenetic and speciose taxa of oribatid mites (Acari) also have an ancient origin. We used nucleotide sequences of the mitochondrial gene cytochrome oxidase I to estimate the age of the parthenogenetic oribatid mite species Platynothrus peltifer. Sixty-five specimens from 16 sites in North America, Europe and Asia were analysed. Seven major clades were identified. Within-clade genetic distances were below 2 % similar to the total intraspecific genetic diversity of most organisms. However, distances between clades averaged 56 % with a maximum of 125 %. We conclude that P. peltifer, as it is currently conceived, has existed for perhaps 100 million years, has an extant distribution that results from continental drift rather than dispersal and was subject to several cryptic speciations.     

Evidence of weak habitat specialisation in microscopic animals

Macroecology and biogeography of microscopic organisms (any living organism smaller than 2 mm) are quickly developing into fruitful research areas. Microscopic organisms also offer the potential for testing predictions and models derived from observations on larger organisms due to the feasibility of performing lab and mesocosm experiments. However, more empirical knowledge on the similarities and differences between micro- and macro-organisms is needed to ascertain how much of the results obtained from the former can be generalised to the latter. One potential misconception, based mostly on anedoctal evidence rather than explicit tests, is that microscopic organisms may have wider ecological tolerance and a lower degree of habitat specialisation than large organisms. Here we explicitly test this hypothesis within the framework of metacommunity theory, by studying host specificify in the assemblages of bdelloid rotifers (animals about 350 μm in body length) living in different species of lichens in Sweden. Using several regression-based and ANOVA analyses and controlling for both spatial structure and the kind of substrate the lichen grow over (bark vs rock), we found evidence of significant but weak species-specific associations between bdelloids and lichens, a wide overlap in species composition between lichens, and wide ecological tolerance for most bdelloid species. This confirms that microscopic organisms such as bdelloids have a lower degree of habitat specialisation than larger organisms, although this happens in a complex scenario of ecological processes, where source-sink dynamics and geographic distances seem to have no effect on species composition at the analysed scale.     

Using DNA taxonomy to investigate the ecological determinants of plankton diversity: explaining the occurrence of Synchaeta spp. (Rotifera,Monogononta) in mountain lakes

1. The occurrence of unresolved complexes of cryptic species may hinder the identification of the main ecological drivers of biodiversity when different cryptic taxa have different ecological requirements. 2. We assessed factors influencing the occurrence of Synchaeta species (monogonont rotifers) in 17 waterbodies of the Trentino‐South Tyrol region in the Eastern Alps. To do so, we compared the results of using unresolved complexes of cryptic species, as is common practice in limnological studies based on morphological taxonomy, and having resolved cryptic complexes, made possible by DNA taxonomy. 3. To identify cryptic species, we used the generalised mixed Yule coalescent (GMYC) model. We investigated the relationship between the environment and the occurrence of Synchaeta spp. by multivariate ordination using two definitions of the units of diversity, namely (i) unresolved species complexes (morphospecies) and (ii) putative cryptic species (GMYC entities). Our expectation was that resolving complexes of cryptic species could provide more information than using morphospecies. 4. As expected, DNA taxonomy provided greater taxonomic resolution than morphological taxonomy. Further, environmental‐based multivariate ordination on cryptic species explained a significantly higher proportion of variance than that based on morphospecies. Occurrence of GMYC entities was related to total phosphorus (TP), whereas no relationship could be found between morphospecies and the environment. Moreover, different cryptic species within the same morphospecies showed different, and even opposite, preferences for TP. In addition, the wide geographical distribution of haplotypes and cryptic species indicated the absence of barriers to dispersal in Synchaeta.     

Patterns of diversity in microscopic animals: are they comparable to those in protists or in larger animals?

Aim General patterns of biodiversity, such as latitudinal gradients and species‐area relationships, are found consistently in a wide range of organisms, but recent results for protist diversity suggest that organisms shorter than 2 mm do not display such patterns. We tested this prediction in bdelloid rotifers, pluricellular metazoans smaller than 2 mm, but with size and ecology comparable to protists. Location A single valley in northern Italy was surveyed in detail and compared to all available faunistic data on bdelloids worldwide. Methods We analysed 171 local assemblages of bdelloid rotifers living in 5 systems of dry mosses and submerged mosses in running water and in lakes. We compared patterns of alpha, beta, and gamma diversity, and nestedness of metacommunities, with those known from protists and larger organisms. Results Bdelloid rotifers showed low local species richness (alpha diversity), with strong habitat selection, as observed in larger organisms. The number of species differed among systems, with a higher number of species in dry than in aquatic mosses. There was no hierarchical structure or exclusion of species in the metacommunity pattern within each system. Local diversity for the entire valley was surprisingly high compared with worldwide bdelloid diversity, similar to observed patterns in protists. Main Conclusions Bdelloid rotifers have some of the peculiarities of protist biodiversity, although at slightly different spatial scales, thus confirming the idea of a major change in biodiversity patterns among organisms shorter than 2 mm. However, bdelloids show stronger habitat selection than protists. We suggest two possible explanations for the observed patterns: (1) dispersal is very rare, and not all bdelloid clones are arriving everywhere; and (2) dispersal is effective in displacing propagules, but environmental heterogeneity is very high and prevents many species from colonizing a given patch of moss.     

A quantitative method to extract moss-dwelling rotifers

One of the difficulties in working with bdelloid rotifers is to extract them from the substratum. In the present paper a method is suggested to separate moss-dwelling bdelloids and other animals quantitatively from their habitat. By this procedure it is possible to identify the entire spectrum of species and to calculate exactly their individual densities per unit area or dry weight of moss.     

On choice of substrate and habitat in bdelzoid rotifers

Information on the distributions of 77 bdelloid rotifers from diverse waters in south and central Sweden was analyzed to reveal their relationships to substrate and habitat. Only two species were reported from plankton, both in low frequency. An artificial substrate, white cotton, was utilized only by few bdelloids, mainly by species with eyes. Only one species occurred at higher frequency on the saprobic substrate Sphaerotilus. Most bdelloids prefer environments rich in oxygen, but some species may be found in soft-bottom sediments. Several species dwell preferentially in diverse habitats of bogs. Some bdelloids have an exceptionally broad ecological range, but even for these is it possible to distinguish a pattern of preference and avoidance.     

SEXUAL SPECIES ARE SEPARATED BY LARGER GENETIC GAPS THAN ASEXUAL SPECIES IN ROTIFERS

Why organisms diversify into discrete species instead of showing a continuum of genotypic and phenotypic forms is an important yet rarely studied question in speciation biology. Does species discreteness come from adaptation to fill discrete niches or from interspecific gaps generated by reproductive isolation? We investigate the importance of reproductive isolation by comparing genetic discreteness, in terms of intra‐ and interspecific variation, between facultatively sexual monogonont rotifers and obligately asexual bdelloid rotifers. We calculated the age (phylogenetic distance) and average pairwise genetic distance (raw distance) within and among evolutionarily significant units of diversity in six bdelloid clades and seven monogonont clades sampled for 4211 individuals in total. We find that monogonont species are more discrete than bdelloid species with respect to divergence between species but exhibit similar levels of intraspecific variation (species cohesiveness). This pattern arises because bdelloids have diversified into discrete genetic clusters at a faster net rate than monogononts. Although sampling biases or differences in ecology that are independent of sexuality might also affect these patterns, the results are consistent with the hypothesis that bdelloids diversified at a faster rate into less discrete species because their diversification does not depend on the evolution of reproductive isolation.     

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.     

Planktonic and periphytic bdelloid rotifers from Thailand reveal a species assemblage with a combination of cosmopolitan and tropical species

The dispersal pattern of microorganisms has been a debated topic in the last decade, because for microscopic organisms with dispersing stages, biogeographic barriers may not exist and geographic distances may have little effect on the probability of their occurrence. In this study we tested whether a group of microscopic animals, the bdelloid rotifers, sampled in a tropical country, could indeed be cosmopolitan, strictly tropical, and/or have endemic species. We sampled freshwater habitats throughout Thailand in dry and rainy seasons between 2014 and 2016, focusing on permanent water bodies, where the prevalence of species producing resting stages acting as propagules for dispersal should be minimal and thus dispersal limitation should exist, with several species being narrowly distributed. We used traditional morphological identification, geometric morphometric analyses on the shape and size of the jaws, and DNA taxonomy to identify species and to quantify the morphological and genetic distances of Thai samples in comparison with data on bdelloids from other areas in the world. We found a total of 12 species of planktonic and periphytic bdelloid rotifers, and all approaches we used, qualitative and quantitative, confirmed a group of nine potentially cosmopolitan species already known from other continents, one tropical oriental species, and two new species with a potentially narrow geographic distribution, one of which we here formally describe. We thus support the idea that for microscopic animals the moderate endemicity hypothesis suggested for protists may also hold true: most of the species we found indeed have a wide geographic distribution, but other species with narrower distributions do exist.

http://zoobank.org/urn:lsid:zoobank.org:pub:3DF5A913-BE6A-4EA4-88FD-C38C0F7AE00A