DNA barcoding of Corsican mayflies (Ephemeroptera) with implications on biogeography, systematics and biodiversity

Mayflies (Ephemeroptera) are known to generally present a high degree of insular endemism: half of the 28 species known from Corsica and Sardinia are considered as endemic. We sequenced the DNA barcode (a fragment of the mitochondrial COI gene) of 349 specimens from 50 localities in Corsica, Sardinia, continental Europe and North Africa. We reconstructed gene trees of eight genera or species groups representing the main mayfly families. Alternative topologies were built to test if our reconstructions suggested a single or multiple Corsican/Sardinian colonization event(s) in each genus or species group. A molecular clock calibrated with different evolution rates was used to try to link speciation processes with geological events. Our results confirm the high degree of endemism of Corsican and Sardinian mayflies and the close relationship between these two faunas. Moreover, we have evidence that the mayfly diversity of the two islands is highly underestimated as at least six new putative species occur on the two islands. We demonstrated that the Corsican and Sardinian mayfly fauna reveals a complex history mainly related to geological events. The Messinian Salinity Crisis, which is thought to have reduced marine barriers, thus facilitating gene flow between insular and continental populations, was detected as the most important event in the speciation of most lineages. Vicariance processes related to the split and rotation of the Corso-Sardinian microplate had a minor impact as they involved only two genera with limited dispersal and ecological range. Colonization events posterior to the Messinian Salinity Crisis had only marginal effects as we had indication of recent gene flow only in two clades. With very limited recent gene flow and a high degree of endemism, mayflies from Corsica and Sardinia present all the criteria for conservation prioritization.

Occurrence of inorganic arsenic in edible Shiitake (Lentinula edodes) products

The present study reports arsenic speciation analysis in edible Shiitake (Lentinula edodes) products. The study focused on the extraction, and accurate quantification of inorganic arsenic (iAs), the most toxic form of arsenic, which was selectively separated and determined using anion exchange LC-ICPMS. A wide variety of edible Shiitake products (fresh mushrooms, food supplements, canned and dehydrated) were purchased and analysed. A cultivated Shiitake grown under controlled conditions was also analysed. The extraction method showed satisfactory extraction efficiencies (>90%) and column recoveries (>85%) for all samples. Arsenic speciation revealed that iAs was the major As compound up to 1.38 mg As per kg dm (with a mean percentage of 84% of the total arsenic) and other organoarsenicals were found as minor species. Shiitake products had high proportions of iAs and therefore should not be ignored as potential contributors to dietary iAs exposure in populations with a high intake of Shiitake products.

The role of clade competition in the diversification of North American canids.

The history of biodiversity is characterized by a continual replacement of branches in the tree of life. The rise and demise of these branches (clades) are ultimately determined by changes in speciation and extinction rates, often interpreted as a response to varying abiotic and biotic factors. However, understanding the relative importance of these factors remains a major challenge in evolutionary biology. Here we analyze the rich North American fossil record of the dog family Canidae and of other carnivores to tease apart the roles of competition, body size evolution, and climate change on the sequential replacement of three canid subfamilies (two of which have gone extinct). We develop a novel Bayesian analytic framework to show that competition from multiple carnivore clades successively drove the demise and replacement of the two extinct canid subfamilies by increasing their extinction rates and suppressing their speciation. Competitive effects have likely come from ecologically similar species from both canid and felid clades. These results imply that competition among entire clades, generally considered a rare process, can play a more substantial role than climate change and body size evolution in determining the sequential rise and decline of clades.

Molecular phylogenetics and temporal diversification in the genus Aeromonas based on the sequences of five housekeeping genes

Several approaches have been developed to estimate both the relative and absolute rates of speciation and extinction within clades based on molecular phylogenetic reconstructions of evolutionary relationships, according to an underlying model of diversification. However, the macroevolutionary models established for eukaryotes have scarcely been used with prokaryotes. We have investigated the rate and pattern of cladogenesis in the genus Aeromonas (γ-Proteobacteria, Proteobacteria, Bacteria) using the sequences of five housekeeping genes and an uncorrelated relaxed-clock approach. To our knowledge, until now this analysis has never been applied to all the species described in a bacterial genus and thus opens up the possibility of establishing models of speciation from sequence data commonly used in phylogenetic studies of prokaryotes. Our results suggest that the genus Aeromonas began to diverge between 248 and 266 million years ago, exhibiting a constant divergence rate through the Phanerozoic, which could be described as a pure birth process.

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.

Quest for Orthologs (QfO) is a community effort with the goal to improve and benchmark orthology predictions. As quality assessment assumes prior knowledge on species phylogenies, we investigated the congruency between existing species trees by comparing the relationships of 147 QfO reference organisms from six Tree of Life (ToL)/species tree projects: The National Center for Biotechnology Information (NCBI) taxonomy, Opentree of Life, the sequenced species/species ToL, the 16S ribosomal RNA (rRNA) database, and trees published by Ciccarelli et al. (Ciccarelli FD, et al. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283-1287) and by Huerta-Cepas et al. (Huerta-Cepas J, Marcet-Houben M, Gabaldon T. 2014. A nested phylogenetic reconstruction approach provides scalable resolution in the eukaryotic Tree Of Life. PeerJ PrePrints 2:223) Our study reveals that each species tree suggests a different phylogeny: 87 of the 146 (60%) possible splits of a dichotomous and rooted tree are congruent, while all other splits are incongruent in at least one of the species trees. Topological differences are observed not only at deep speciation events, but also within younger clades, such as Hominidae, Rodentia, Laurasiatheria, or rosids. The evolutionary relationships of 27 archaea and bacteria are highly inconsistent. By assessing 458,108 gene trees from 65 genomes, we show that consistent species topologies are more often supported by gene phylogenies than contradicting ones. The largest concordant species tree includes 77 of the QfO reference organisms at the most. Results are summarized in the form of a consensus ToL (http://swisstree.vital-it.ch/species_tree) that can serve different benchmarking purposes.

Differential growth responses to water balance of coexisting deciduous tree species are linked to wood density in a Bolivian tropical dry forest

A seasonal period of water deficit characterizes tropical dry forests (TDFs). There, sympatric tree species exhibit a diversity of growth rates, functional traits, and responses to drought, suggesting that each species may possess different strategies to grow under different conditions of water availability. The evaluation of the long-term growth responses to changes in the soil water balance should provide an understanding of how and when coexisting tree species respond to water deficit in TDFs. Furthermore, such differential growth responses may be linked to functional traits related to water storage and conductance. We used dendrochronology and climate data to retrospectively assess how the radial growth of seven coexisting deciduous tree species responded to the seasonal soil water balance in a Bolivian TDF. Linear mixed-effects models were used to quantify the relationships between basal area increment and seasonal water balance. We related these relationships with wood density and sapwood production to assess if they affect the growth responses to climate. The growth of all species responded positively to water balance during the wet season, but such responses differed among species as a function of their wood density. For instance, species with a strong growth response to water availability averaged a low wood density which may facilitate the storage of water in the stem. By contrast, species with very dense wood were those whose growth was less sensitive to water availability. Coexisting tree species thus show differential growth responses to changes in soil water balance during the wet season. Our findings also provide a link between wood density, a trait related to the ability of trees to store water in the stem, and wood formation in response to water availability.

Systematics and phylogeography of the Dysdera erythrina species complex (Araneae, Dysderidae) in Sardinia

Sardinia is the second largest island in the Mediterranean and, together with Corsica and nearby mainland areas, one of the top biodiversity hotspots in the region. The origin of Sardinia traces back to the opening of the western Mediterranean in the late Oligocene. This geological event and the subsequent Messinian Salinity Crisis and Pleistocene glacial cycles have had a major impact on local biodiversity. The Dysdera woodlouse hunter spiders are one of the most diverse ground-dweller groups in the Mediterranean. Here we describe the first two species of this genus endemic to Sardinia: Dysdera jana sp. n. and Dysdera shardana sp. n. The two species show contrasting allopatric distribution: D. jana sp. n. is a narrow endemic while D. shardana sp. n. is distributed throughout most of the island. A multi-gene DNA sequence phylogenetic analys based on mitochondrial and nuclear genes supports the close relationships of the new species to the type species of the genus Dysdera erythrina. Age estimates reject Oligocene origin of the new Dysdera species and identify the Messinian Salinity Crises as the most plausible period for the split between Sardinian endemics and their closest relatives. Phylogeographic analysis reveals deep genetic divergences and population structure in Dysdera shardana sp. n., suggesting that restriction to gene flow probably due to environmental factors could explain local speciation events. Taxonomy, phylogeny, DNA sequencing, Mediterranean biogeography, phylogeography

Tracking the ghost of coevolution in specific plant-insect interactions : the case of the pollination system between the globeflower Trollius europaeus and seven european Chiastocheta flies

This study aims at understanding the evolutionary processes at work in specialized species interactions. Prom the macroevolutionary perspective, coevolution among specialized taxa was proposed to be one of the major processes generating biodiversity. We challenge this idea from the theoretical and practical perspective and through a literature review and show that the major hypotheses linking coevolutionary process with macroevolutionary patterns do not necessarily predict lineage co diversification and parallel speciation, limit¬ing the utility of the comparative phylogenenetic approach for investigating coevolution¬ary processes. We also point to the rarity of observed long-term coevolutionary dynamics among lineages and propose that coevolution rather occurs in shorter timescales, followed by ecological fitting. Prom the empirical point, we focus on the nursery pollination interaction between the European globeflower Trollius europaeus (Ranunculaceae) and its associated Chiastocheta flies (Anthomyiidae; Diptera) as a model system of evolution and maintenance of special¬ized interactions. The flies are obligate parasites of the seeds, but also pollinate the plant - it was thus proposed that both species are mutually dependent. Contrasting with the paradigm used for two decades of research on this system, we show that the female fitness component of the plant is similar in the populations with and without Chiastocheta. The plant is thus not exclusively dependent on the flies for reproduction. We discuss this result in the context of the factors responsible for the evolution of mutualistic systems. Understanding the evolution of a biological system requires understanding of its phylo- genetic context. Previous studies showed large mismatch between mtDNA phylogeny and morphological taxonomy in Chiastocheta. By using a large set of RAD-sequencing loci, we delineate the species limits that are congruent with morphology, and show that the discordance is best explained by the scenario of mitochondrial capture among fly species. Finally, we examine this system from a phylogeographic perspective, and identify the lack of congruence in spatial genetic structures of the plant and associated insects across their whole geographic range. The flies show lower numbers of spatial genetic groups than the plant, indicating that not all of the plant réfugia were shared by all the fly species or that the migration dynamics homogenized some of the groups. The incongruence in spatial genetic patterns indicates that fly migrations were largely independent from the genetic background of the plant, following rather a scenario of resource tracking, without the signature of coevolutionary process at this scale. Indeed, while the flies require the plant to survive climatic oscillations, the opposite is not true. Eventually, we show that there is no phylogenetic signal of spatial genetic structures, meaning that neither histories nor life- history traits are shared among closely related species and that species are characterized by unique trajectories of their genes. -- Cette étude vise à comprendre les processus évolutifs à l'oeuvre au sein d'interactions en¬tre espèces spécialisées. Du point de vue macroévolutif, la coévolution entre les taxons spécialisée a été considérée comme l'un des principaux processus générateur de biodiversité. Nous contestons cette idée du point de vue théorique et pratique à travers une revue de la littérature. Nous montrons que les hypothèses majeures reliant les processus coévolutifs avec les patterns de diversité au niveau macroévolutif ne prédisent pas nécessairement la co- diversification des lignées et leur spéciation parallèle, ce qui limite l'utilité de l'approche de phylogénie comparative pour étudier les processus coévolutifs . Nous rappelons également le peu d'exemples de dynamique coévolutive à long terme et proposons que la coévolution se produit plutôt dans des intervalles courts, suivis d'ajustements écologiques. Du point empirique, nous nous concentrons sur l'interaction de pollinisation entre le Trolle d'Europe Trollius europaeus (Ranunculaceae) et ses pollinisateurs associés, du genre Chiastocheta (Anthomyiidae; Diptera) en tant que système-modèle pour étudier l'évolution et le maintien des interactions spécialisées. Les mouches sont des parasites obligatoires des semences, mais pollinisent également la plante. Il a donc été proposé que les deux espèces soient mutuellement dépendantes. Contrastant avec le paradigme utilisé pendant deux décennies de recherche sur ce système, nous montrons, que la composante de fitness femelle de la plante est similaire dans les populations avec et sans Chiastocheta. La plante ne dépend donc pas exclusivement de son interaction avec les mouches pour la reproduction. Nous discutons de ce résultat dans le contexte des facteurs responsables de l'évolution des systèmes mutualistes. Comprendre l'évolution d'un système biologique nécessite la compréhension de son con- texte phylogénétique. Des études antérieures ont montré, chez Chiastocheta, de grandes disparités entre les phylogénies obtenues à partir d'ADN mitochondrial et la taxonomie basée sur les critères morphologiques. En utilisant un grand nombre de loci obtenus par RAD-sequencing, nous traçons les limites des espèces, qui concordent avec les car¬actéristiques morphologies, et montrons que la discordance s'explique en fait par un scénario de capture mitochondriale entre espèces de mouches. Enfin, nous examinons le système d'un point de vue phylogéographique, et identi¬fions les incohérences entre structurations génétiques spatiales de la plante et des insectes associés dans toute leur aire de distribution géographique. Les mouches présentent un nombre de groupes génétiques inférieur à la plante, indiquant que tous les refuges de la plante n'étaient pas partagés par toutes les espèces de mouches ou que les dynamiques migratoires ont homogénéisés certains des groupes chez les mouches. Les différences ob¬servées dans les patrons de structuration génétique spatiale indique que les migrations et dispersions des mouches ont été indépendantes du contexte génétique de la plante, et ces dernières ont été uniquement tributaires de la disponibilité des ressources, sans qu'il n'y ait de signature du processus de coévolution à cette échelle. En effet, tandis que les mouches ont besoin de la plante pour survivre aux oscillations climatiques, le contraire n'est pas exact. Finalement, nous montrons qu'il n'y a pas de signal phylogénétique des structurations génétiques spatiales chez les mouches, ce qui signifie que ni l'histoire, ni les traits d'histoire de vie ne sont partagés entre les espèces phylogénétiquement proches et que les espèces sont caractérisées par des trajectoires uniques de leurs gènes.

Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions.

BACKGROUND: Recent methodological advances allow better examination of speciation and extinction processes and patterns. A major open question is the origin of large discrepancies in species number between groups of the same age. Existing frameworks to model this diversity either focus on changes between lineages, neglecting global effects such as mass extinctions, or focus on changes over time which would affect all lineages. Yet it seems probable that both lineages differences and mass extinctions affect the same groups. RESULTS: Here we used simulations to test the performance of two widely used methods under complex scenarios of diversification. We report good performances, although with a tendency to over-predict events with increasing complexity of the scenario. CONCLUSION: Overall, we find that lineage shifts are better detected than mass extinctions. This work has significance to assess the methods currently used to estimate changes in diversification using phylogenetic trees. Our results also point toward the need to develop new models of diversification to expand our capabilities to analyse realistic and complex evolutionary scenarios.

Continental faunal exchange and the asymmetrical radiation of carnivores.

Lineages arriving on islands may undergo explosive evolutionary radiations owing to the wealth of ecological opportunities. Although studies on insular taxa have improved our understanding of macroevolutionary phenomena, we know little about the macroevolutionary dynamics of continental exchanges. Here we study the evolution of eight Carnivora families that have migrated across the Northern Hemisphere to investigate if continental invasions also result in explosive diversification dynamics. We used a Bayesian approach to estimate speciation and extinction rates from a substantial dataset of fossil occurrences while accounting for the incompleteness of the fossil record. Our analyses revealed a strongly asymmetrical pattern in which North American lineages invading Eurasia underwent explosive radiations, whereas lineages invading North America maintained uniform diversification dynamics. These invasions into Eurasia were characterized by high rates of speciation and extinction. The radiation of the arriving lineages in Eurasia coincide with the decline of established lineages or phases of climate change, suggesting differences in the ecological settings between the continents may be responsible for the disparity in diversification dynamics. These results reveal long-term outcomes of biological invasions and show that the importance of explosive radiations in shaping diversity extends beyond insular systems and have significant impact at continental scales.

Study of selenocompounds from selenium-enriched culture of edible sprouts

Selenium is recognised as an essential micronutrient for humans and animals. One of the main sources of selenocompounds in the human diet is vegetables. Therefore, this study deals with the Se species present in different edible sprouts grown in Se-enriched media. We grew alfalfa, lentil and soy in a hydroponic system amended with soluble salts, containing the same proportion of Se, in the form of Se(VI) and Se(IV). Total Se in the sprouts was determined by acidic digestion in a microwave system and by ICP/MS. Se speciation was carried out by enzymatic extraction (Protease XIV) and measured by LC-ICP/MS. The study shows that the Se content of plants depends on the content in the growth culture, and that part of the inorganic Se was biotransformed mainly into SeMet. These results contribute to our understanding of the uptake of inorganic Se and its biotransformation by edible plants.

Migration of antimony from polyethylene terephthalate used in mineral water bottles.

The influence of storage time and temperature on Sb migration from PET bottles into mineral water was studied in short-term tests lasting up to 15 days and long-term studies lasting up to 220 days. Samples purchased were stored in three different coloured bottles: clear (CL), light blue (LB) and dark blue (DB). Sb migration was assayed by HG-AFS for total determination and HPLC-ICP-MS for speciation analysis. Migration studies showed that waters stored at 4 and 20 oC were not subject to Sb migration. At 40 oC there was a significant increase in Sb concentration, although the maximum limit established by the European Union (5.0 ug/L) was not exceeded, whereas at 60 oC samples were subject to considerable Sb migration after 30 days of storage. In this case, the maximum limit established by the European Union was exceeded and both Sb (V) and Sb (III) were detected.

Dispersal is a major driver of the latitudinal diversity gradient of Carnivora

AimUnderstanding the relative contribution of diversification rates (speciation and extinction) and dispersal in the formation of the latitudinal diversity gradient - the decrease in species richness with increasing latitude - is a main goal of biogeography. The mammalian order Carnivora, which comprises 286 species, displays the traditional latitudinal diversity gradient seen in almost all mammalian orders. Yet the processes driving high species richness in the tropics may be fundamentally different in this group from that in other mammalian groups. Indeed, a recent study suggested that in Carnivora, unlike in all other major mammalian orders, net diversification rates are not higher in the tropics than in temperate regions. Our goal was thus to understand the reasons why there are more species of Carnivora in the tropics. LocationWorld-wide. MethodsWe reconstructed the biogeographical history of Carnivora using a time-calibrated phylogeny of the clade comprising all terrestrial species and dispersal-extinction-cladogenesis models. We also analysed a fossil dataset of carnivoran genera to examine how the latitudinal distribution of Carnivora varied through time. ResultsOur biogeographical analyses suggest that Carnivora originated in the East Palaearctic (i.e. Central Asia, China) in the early Palaeogene. Multiple independent lineages dispersed to low latitudes following three main paths: toward Africa, toward India/Southeast Asia and toward South America via the Bering Strait. These dispersal events were probably associated with local extinctions at high latitudes. Fossil data corroborate a high-latitude origin of the group, followed by late dispersal events toward lower latitudes in the Neogene. Main conclusionsUnlike most other mammalian orders, which originated and diversified at low latitudes and dispersed out of the tropics', Carnivora originated at high latitudes, and subsequently dispersed southward. Our study provides an example of combining phylogenetic and fossil data to understand the generation and maintenance of global-scale geographical variations in species richness.

Method development for the simultaneous determination of methylmercury and inorganic mercury in seafood

This paper reports the method development for the simultaneous determination of methylmercury MeHgþ) and inorganic mercury (iHg) species in seafood samples. The study focused on the extraction and quantification of MeHgþ (the most toxic species) by liquid chromatography coupled to on-line UV irradiation and cold vapour atomic fluorescence spectroscopy (LC-UV-CV-AFS), using HCl 4 mol/L as the extractant agent. Accuracy of the method has been verified by analysing three certified reference materials and different spiked samples. The values found for total Hg and MeHgþ for the CRMs did not differ significantly from certified values at a 95% confidence level, and recoveries between 85% and 97% for MeHgþ, based on spikes, were achieved. The detection limits (LODs) obtained were 0.001 mg Hg/kg for total mercury, 0.0003 mg Hg/kg for MeHgþ and 0.0004 mg Hg/kg for iHg. The quantification limits (LOQs) established were 0.003 mg Hg/kg for total mercury, 0.0010 mg Hg/kg for MeHgþ and 0.0012 mg Hg/kg for iHg. Precision for each mercury species was established, being 12% in terms of RSD in all cases. Finally, the developed method was applied to 24 seafood samples from different origins and total mercury contents. The concentrations for Total Hg, MeHg and iHg ranged from 0.07 to 2.33, 0.003-2.23 and 0.006-0.085 mg Hg/kg, respectively. The established analytical method allows to obtain results for mercury speciation in less than 1 one hour including both, sample pretreatment and measuring step.

The genetic content of chromosomal inversions across a wide latitudinal gradient

There is increasing evidence regarding the role of chromosomal inversions in relevant biological processes such as local adaptation and speciation. A classic example of the adaptive role of chromosomal polymorphisms is given by the clines of inversion frequencies in Drosophila subobscura, repeatable across continents. Nevertheless, not much is known about the molecular variation associated with these polymorphisms. We characterized the genetic content of ca. 600 individuals from nine European populations following a latitudinal gradient by analysing 19 microsatellite loci from two autosomes (J and U) and the sex chromosome (A), taking into account their chromosomal inversions. Our results clearly demonstrate the molecular genetic uniformity within a given chromosomal inversion across a large latitudinal gradient, particularly from Groningen (Netherlands) in the north to Málaga (Spain) in the south, experiencing highly diverse environmental conditions. This low genetic differentiation within the same gene arrangement across the nine European populations is consistent with the local adaptation hypothesis for th evolutionof chromosomal polymorphisms. We also show the effective role of chromosomal inversions in maintaining different genetic pools within these inverted genomic regions even in the presence of high gene flow. Inversions represent thus an important barrier to gene flux and can help maintain specific allelic combinations with positive effects on fitness. Consistent patterns of microsatellite allele-inversion linkage disequilibrium particularly in loci within inversions were also observed. Finally, we identified areas within inversions presenting clinal variation that might be under selection.