Can microsatellite data allow identification of oleaster Plio-Pleistocene refuge zones in the Mediterranean Basin?

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Phylogenomics indicates the “living fossil” Isoetes diversified in the Cenozoic

The fossil record provides an invaluable insight into the temporal origins of extant lineages of organisms. However, establishing the relationships between fossils and extant lineages can be difficult in groups with low rates of morphological change over time. Molecular dating can potentially circumvent this issue by allowing distant fossils to act as calibration points, but rate variation across large evolutionary scales can bias such analyses. In this study, we apply multiple dating methods to genome-wide datasets to infer the origin of extant species of Isoetes, a group of mostly aquatic and semi-aquatic isoetalean lycopsids, which closely resemble fossil forms dating back to the Triassic. Rate variation observed in chloroplast genomes hampers accurate dating, but genome-wide nuclear markers place the origin of extant diversity within this group in the mid-Paleogene, 45–60 million years ago. Our genomic analyses coupled with a careful evaluation of the fossil record indicate that despite resembling forms from the Triassic, extant Isoetes species do not represent the remnants of an ancient and widespread group, but instead have spread around the globe in the relatively recent past

Finite Element Modelling and Experimental Validation of the Enamel Demineralisation Process at the Rod Level

In the past years, a significant amount of effort has been directed at the observation and characterisation of caries using experimental techniques. Nevertheless, relatively little progress has been made in numerical modelling of the underlying demineralisation process. The present study is the first attempt to provide a simplified calculation framework for the numerical simulation of the demineralisation process at the length scale of enamel rods and its validation by comparing the data with statistical analysis of experimental results. FEM model was employed to simulate a time-dependent reaction-diffusion equation process in which H ions diffuse and cause demineralisation of the enamel. The local orientation of the hydroxyapatite crystals was taken into account. Experimental analysis of the demineralising front was performed using advanced high-resolution synchrotron X-ray micro-Computed Tomography. Further experimental investigations were conducted by means of SEM and STEM imaging techniques. Besides establishing and validating the new modelling framework, insights into the role of the etchant solution pH level were obtained. Additionally, some light was shed on the origin of different types of etching patterns by simulating the demineralisation process at different etching angles of attack. The implications of this study pave the way for simulations of enamel demineralisation within different complex scenarios and across the range of length scales. Indeed, the framework proposed can incorporate the presence of chemical species other than H ions and their diffusion and reaction leading to dissolution and re-precipitation of hydroxyapatite. It is the authors\u2019 hope and aspiration that ultimately this work will help identify new ways of controlling and preventing caries

Polyploidy in the Olive Complex (Olea europaea): Evidence from Flow Cytometry and Nuclear Microsatellite Analyses

Background Phylogenetic and phylogeographic investigations have been previously performed to study the evolution of the olive tree complex (Olea europaea). A particularly high genomic diversity has been found in north-west Africa. However, to date no exhaustive study has been addressed to infer putative polyploidization events and their evolutionary significance in the diversification of the olive tree and its relatives. Methods Representatives of the six olive subspecies were investigated using (a) flow cytometry to estimate genome content, and (b) six highly variable nuclear microsatellites to assess the presence of multiple alleles at co-dominant loci. In addition, nine individuals from a controlled cross between two individuals of O. europaea subsp. maroccana were characterized with microsatellites to check for chromosome inheritance. Key Results Based on flow cytometry and genetic analyses, strong evidence for polyploidy was obtained in subspp. cerasiformis (tetraploid) and maroccana (hexaploid), whereas the other subspecies appeared to be diploids. Agreement between flow cytometry and genetic analyses gives an alternative approach to chromosome counting to determine ploidy level of trees. Lastly, abnormalities in chromosomes inheritance leading to aneuploid formation were revealed using microsatellite analyses in the offspring from the controlled cross in subsp. maroccana. Conclusions This study constitutes the first report for multiple polyploidy in olive tree relatives. Formation of tetraploids and hexaploids may have played a major role in the diversification of the olive complex in north-west Africa. The fact that polyploidy is found in narrow endemic subspecies from Madeira (subsp. cerasiformis) and the Agadir Mountains (subsp. maroccana) suggests that polyploidization has been favoured to overcome inbreeding depression. Lastly, based on previous phylogenetic analyses, we hypothesize that subsp. cerasiformis resulted from hybridization between ancestors of subspp. guanchica and europae

A Default Logic Patch for Default Logic

International audienceThis paper is about the fusion of multiple information sources represented using default logic. More precisely, the focus is on solving the problem that occurs when the standard-logic knowledge parts of the sources are contradictory, as default theories trivialize in this case. To overcome this problem, it is shown that replacing each formula belonging to Minimally Unsatisfiable Subformulas by a corresponding supernormal default allows appealing features. Moreover, it is investigated how these additional defaults interact with the initial defaults of the theory. Interestingly, this approach allows us to handle the problem of default theories containing inconsistent standard-logic knowledge, using the default logic framework itself

On the origin of the invasive olives (Olea europaea L., Oleaceae).

The olive tree (Olea europaea) has successfully invaded several regions in Australia and Pacific islands. Two olive subspecies (subspp. europaea and cuspidata) were first introduced in these areas during the nineteenth century. In the present study, we determine the origin of invasive olives and investigate the importance of historical effects on the genetic diversity of populations. Four invasive populations from Australia and Hawaii were characterized using eight nuclear DNA microsatellites, plastid DNA markers as well as ITS-1 sequences. Based on these data, their genetic similarity with native populations was investigated, and it was determined that East Australian and Hawaiian populations (subsp. cuspidata) have originated from southern Africa while South Australian populations (subsp. europaea) have mostly derived from western or central Mediterranean cultivars. Invasive populations of subsp. cuspidata showed significant loss of genetic diversity in comparison to a putative source population, and a recent bottleneck was evidenced in Hawaii. Conversely, invasive populations of subsp. europaea did not display significant loss of genetic diversity in comparison to a native Mediterranean population. Different histories of invasion were inferred for these two taxa with multiple cultivars introduced restoring gene diversity for europaea and a single successful founder event and sequential introductions to East Australia and then Hawaii for cuspidata. Furthermore, one hybrid (cuspidata x europaea) was identified in East Australia. The importance of hybridizations in the future evolution of the olive invasiveness remains to be investigated

A saturated consensus linkage map of Picea abies including AFLP, SSR, STS, 5S rDNA and morphological markers

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Phylogenomics using low-depth whole genome sequencing: a case study with the olive tribe

Species trees have traditionally been inferred from a few selected markers, and genome-wide investigations remain largely restricted to model organisms or small groups of species for which sampling of fresh material is available, leaving out most of the existing and historic species diversity. The genomes of an increasing number of species, including specimens extracted from natural history collections, are being sequenced at low depth. While these datasets are widely used to analyse organelle genomes, the nuclear fraction is generally ignored. Here we evaluate different reference-based methods to infer phylogenies of large taxonomic groups from such datasets. Using the example of the Oleeae tribe, a worldwide-distributed group, we build phylogenies based on single-nucleotide polymorphisms (SNPs) obtained using two reference genomes (the olive and ash trees). The inferred phylogenies are overall congruent, yet present differences that might reflect the effect of the distance to the reference on the amount of missing data. To limit this issue, the genome complexity was reduced by using pairs of orthologous coding sequences as the reference, thus allowing combining SNPs obtained using two distinct references. Concatenated and coalescence trees based on these combined SNPs suggest events of incomplete lineage sorting and/or hybridization during the diversification of this large phylogenetic group. Our results show that genome-wide phylogenetic trees can be inferred from low-depth sequence datasets for eukaryote groups with complex genomes, and histories of reticulate evolution. This opens new avenues for large-scale phylogenomics and biogeographic analyses covering both the extant and historic diversity stored in museum collections