Diego Fontaneto

The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna

Molecular tools have revolutionized the exploration of biodiversity, especially in organisms for which traditional taxonomy is difficult, such as for microscopic animals (meiofauna). Environmental (eDNA) metabarcode surveys of DNA extracted from sediment samples are increasingly popular for surveying biodiversity. Most eDNA surveys use the nuclear gene-encoding small-subunit rDNA gene (18S) as a marker; however, different markers and metrics used for delimiting species have not yet been evaluated against each other or against morphologically defined species (morphospecies). We assessed more than 12,000 meiofaunal sequences of 18S and of the main alternatively used marker [Cytochrome c oxidase subunit I (COI) mtDNA] belonging to 55 datasets covering three taxonomic ranks. Our results show that 18S reduced diversity estimates by a factor of 0.4 relative to morphospecies, whereas COI increased diversity estimates by a factor of 7.6. Moreover, estimates of species richness using COI were robust among three of four commonly used delimitation metrics, whereas estimates using 18S varied widely with the different metrics. We show that meiofaunal diversity has been greatly underestimated by 18S eDNA surveys and that the use of COI provides a better estimate of diversity. The suitability of COI is supported by cross-mating experiments in the literature and evolutionary analyses of discreteness in patterns of genetic variation. Furthermore its splitting of morphospecies is expected from documented levels of cryptic taxa in exemplar meiofauna. We recommend against using 18S as a marker for biodiversity surveys and suggest that use of COI for eDNA surveys could provide more accurate estimates of species richness in the future.

Extreme levels of hidden diversity in microscopic animals (Rotifera) revealed by DNA taxonomy

Knowledge and estimates of species richness at all scales are biased both by our understanding of the evolutionary processes shaping diversity and by the methods used to delineate the basic units of diversity. DNA taxonomy shows that diversity may be underestimated by traditional taxonomy, especially for microscopic animals. The effects of such hidden diversity are usually overlooked in ecological studies. Here, we estimate hidden diversity in bdelloid rotifers, a group of microscopic animals. We analyse cryptic diversity using a coalescent approach to infer taxonomical units from phylogenetic trees. Cryptic diversity was measured for eight traditional species of bdelloid rotifers and the results compared to that of the monogonont rotifer Brachionus plicatilis species complex, which is well studied and for which cross-mating experiments have been performed to explicitly define some of the species boundaries. A taxonomic inflation of up to 34 potential cryptic taxa was found in bdelloids. Cryptic taxa within each traditional species may be spatially isolated, but do not have narrower ecological niches. The species deemed as generalists exhibit the highest cryptic diversity. Cryptic diversity based on molecular characterization is commonly found in animals; nevertheless, the amount of cryptic diversity in bdelloids is much higher than in other groups analysed so far, maybe because of their peculiar parthenogenetic reproduction, other than microscopic size. We discuss this hypothesis in the light of the available empirical evidence from other groups of microscopic invertebrates, such as tardigrades and mites, which share size, habitat heterogeneity, potential for dispersal, and/or parthenogenetic reproduction.

Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data

Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The generalised mixed Yule coalescent (GMYC) and the Poisson tree process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes. Here, we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2000 separate species delimitation analyses across 16 empirical data sets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods. The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification. Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees for obtaining species hypotheses.

Disentangling the morphological stasis in two rotifer species of the Brachionus plicatilis species complex

The taxonomic uncertainty surrounding cryptic species complexes has traditionally been resolved using lengthy experimental approaches, while, since the advent of PCR based techniques the number of cryptic species described in a variety of taxa is increasing steadily. Here we formally describe a new rotifer species of the Brachionus plicatilis complex: Brachionus manjavacas n.sp., disentangling what was known as a morphological stasis. Detailed morphological analyses demonstrated significant differences in body shape and size between B. manjavacas and B. plicatilis s.s., analysed by geometric morphometrics; unfortunately these statistical differences are not taxonomically reliable because of wide overlaps. Size and asymmetry of masticatory apparatus, named trophi, observed by SEM, gave similar results, with taxonomic ambiguity. Only the shape of small pieces of the trophi, named satellites, were consistently different between the species. On a strictly classical taxonomical basis it is absolutely useful to name new species on morphological bases, as we did, and to assess their status as distinct entities. Nevertheless, the two species are broadly similar; therefore, we do not suggest using the small differences in shape of satellites of trophi to identify the species for further ecological studies, but to continue discriminating them on genetic marker bases.

Patterns of Diversity in Soft-Bodied Meiofauna: Dispersal Ability and Body Size Matter

Background Biogeographical and macroecological principles are derived from patterns of distribution in large organisms, whereas microscopic ones have often been considered uninteresting, because of their supposed wide distribution. Here, after reporting the results of an intensive faunistic survey of marine microscopic animals (meiofauna) in Northern Sardinia, we test for the effect of body size, dispersal ability, and habitat features on the patterns of distribution of several groups. Methodology/Principal Findings As a dataset we use the results of a workshop held at La Maddalena (Sardinia, Italy) in September 2010, aimed at studying selected taxa of soft-bodied meiofauna (Acoela, Annelida, Gastrotricha, Nemertodermatida, Platyhelminthes and Rotifera), in conjunction with data on the same taxa obtained during a previous workshop hosted at Tjärnö (Western Sweden) in September 2007. Using linear mixed effects models and model averaging while accounting for sampling bias and potential pseudoreplication, we found evidence that: (1) meiofaunal groups with more restricted distribution are the ones with low dispersal potential; (2) meiofaunal groups with higher probability of finding new species for science are the ones with low dispersal potential; (3) the proportion of the global species pool of each meiofaunal group present in each area at the regional scale is negatively related to body size, and positively related to their occurrence in the endobenthic habitat. Conclusion/Significance Our macroecological analysis of meiofauna, in the framework of the ubiquity hypothesis for microscopic organisms, indicates that not only body size but mostly dispersal ability and also occurrence in the endobenthic habitat are important correlates of diversity for these understudied animals, with different importance at different spatial scales. Furthermore, since the Western Mediterranean is one of the best-studied areas in the world, the large number of undescribed species (37%) highlights that the census of marine meiofauna is still very far from being complete.

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

The Baas‐Beckings 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.

Biogeography of microscopic organisms : is everything small everywhere?

Preface Part I. Theoretical Framework: 1. Why biogeography of microorganisms? Diego Fontaneto and Juliet Brodie 2. Historical biogeography, microbial endemism and the role of classification: everything is endemic David M. Williams Part II. Prokaryotes: 3. Biogeography of prokaryotes Donnabella C. Lacap, Maggie C. Y. Lau and Stephen B. Pointing 4. Thermophilic bacteria in cool soils: metabolic activity and mechanisms of dispersal Roger Marchant, Ibrahim M. Banat and Andrea Franzetti Part III. Unicellular Eukaryotes: 5. Dispersal of protists: the role of cysts and human introductions Wilhelm Foissner 6. Everything is everywhere: a twenty-first century de-/reconstruction with respect to protists David Bass and Jens Boenigk 7. Arcellinida testate amoebae (Arcellinida: Amoebozoa): model of organisms for assessing microbial biogeography Thierry J. Heger, Enrique Lara and Edward A. D. Mitchell 8. Everything is not everywhere: the distribution of cactophilic yeast Philip F. Ganter Part IV. Pluricellular Eukaryotes: 9. Coalescent analyses reveal contrasting patterns of intercontinental gene flow in arctic-alpine and boreal-temperate fungi Jozsef Geml 10. Biogeography and phylogeography of lichen fungi and their photobiont Silke Werth 11. Biogeography of mosses and allies: does size matter? Nagore G. Medina, Isabel Draper and Francisco Lara 12. Dispersal limitation or habitat quality - what shapes the distribution ranges of ferns? Hanno Schaefer 13. Ubiquity of microscopic animals? Evidence from the morphological approach in species identification Tom Artois, Diego Fontaneto, William D. Hummon, Sandra J. McInnes, M. Antonio Todaro, Martin V. Sorensen and Aldo Zullini 14. Molecular approach to micrometazoans: are they here, there and everywhere? Noemi Guil Lopez Part V. Processes: 15. Microbes as a test of biogeographical principles David G. Jenkins, Kim A. Medley and Rima B. Franklin 16. A metacommunity perspective on the phylo- and biogeography of small organisms Luc De Meester 17. Geographical variation in the diversity of microbial communities: research directions and prospects for experimental biogeography Joaquin Hortal Index.

Rotifers in saltwater environments, re-evaluation of an inconspicuous taxon

Rotifers are microscopic aquatic animals that comprise more than 1800 species. Most rotifer species live in freshwater and limno-terrestrial habitats, while thalassic environments (brackish+seawater) are thought to host few species. No recent review of saline rotifers is available. Here we report the results of a review of the literature concerning rotifers from saline environments, distinguished into three categories: stenohaline, euryhaline, and haloxenous, and found both in truly marine habitats and/or in inland saline waters. A total of about 200 studies, mentioning fully identified rotifers from saline waters, allowed us to list as many as 443 rotifer taxa at either specific, subspecific and infrasubspecific rank, corresponding to 391 nominal species. Truly thalassic taxa, not found in inland saline waters only, accounted for 289, including the ‘stenohaline’ (143) and the euryhaline (146) ones. As for freshwaters, the majority of the thalassic rotifers inhabit the psammon, or display a benthic–periphytic way of life, while the plankton likewise is less species rich and less abundant. The geographical distribution of the brackish and marine rotifers largely reflects the distribution of rotifer investigators, therefore, no biogeographical analysis can be performed yet. In conclusion, the analysis of literature citing rotifers in salt waters, uncovers an unexpected rotifer fauna: the apparent richness of the group in thalassic environments is worthy of being addressed by further investigations, as many species have been reported only by their description, suggesting either considerable endemism or taxonomic errors.

Is the meiofauna a good indicator for climate change and anthropogenic impacts

Our planet is changing, and one of the most pressing challenges facing the scientific community revolves around understanding how ecological communities respond to global changes. From coastal to deep-sea ecosystems, ecologists are exploring new areas of research to find model organisms that help predict the future of life on our planet. Among the different categories of organisms, meiofauna offer several advantages for the study of marine benthic ecosystems. This paper reviews the advances in the study of meiofauna with regard to climate change and anthropogenic impacts. Four taxonomic groups are valuable for predicting global changes: foraminifers (especially calcareous forms), nematodes, copepods and ostracods. Environmental variables are fundamental in the interpretation of meiofaunal patterns and multistressor experiments are more informative than single stressor ones, revealing complex ecological and biological interactions. Global change has a general negative effect on meiofauna, with important consequences on benthic food webs. However, some meiofaunal species can be favoured by the extreme conditions induced by global change, as they can exhibit remarkable physiological adaptations. This review highlights the need to incorporate studies on taxonomy, genetics and function of meiofaunal taxa into global change impact research.

Fifteen species in one: deciphering the Brachionus plicatilis species complex (Rotifera, Monogononta) through DNA taxonomy

Abstract Understanding patterns and processes in biological diversity is a critical task given current and rapid environmental change. Such knowledge is even more essential when the taxa under consideration are important ecological and evolutionary models. One of these cases is the monogonont rotifer cryptic species complex Brachionus plicatilis, which is by far the most extensively studied group of rotifers, is widely used in aquaculture, and is known to host a large amount of unresolved diversity. Here we collate a dataset of previously available and newly generated sequences of COI and ITS1 for 1273 isolates of the B. plicatilis complex and apply three approaches in DNA taxonomy (i.e. ABGD, PTP, and GMYC) to identify and provide support for the existence of 15 species within the complex. We used these results to explore phylogenetic signal in morphometric and ecological traits, and to understand correlation among the traits using phylogenetic comparative models. Our results support niche conservatism for some traits (e.g. body length) and phylogenetic plasticity for others (e.g. genome size).