Homoplastic versus xenoplastic evolution: exploring the emergence of key intrinsic and extrinsic traits in the montane genus Soldanella (Primulaceae).

Specific ecological conditions in the high mountain environment exert a selective pressure that often leads to convergent trait evolution. Reticulations induced by incomplete lineage sorting and introgression can lead to discordant trait patterns among gene and species trees (hemiplasy/xenoplasy), providing a false illusion that the traits under study are homoplastic. Using phylogenetic species networks, we explored the effect of gene exchange on trait evolution in Soldanella, a genus profoundly influenced by historical introgression. At least three features evolved independently multiple times: the single-flowered dwarf phenotype, dysploid cytotype, and ecological generalism. The present analyses also indicated that the recurring occurrence of stoloniferous growth might have been prompted by an introgression event between an ancestral lineage and a still extant species, although its emergence via convergent evolution cannot be completely ruled out. Phylogenetic regression suggested that the independent evolution of larger genomes in snowbells is most likely a result of the interplay between hybridization events of dysploid and euploid taxa and hostile environments at the range margins of the genus. The emergence of key intrinsic and extrinsic traits in snowbells has been significantly impacted not only by convergent evolution but also by historical and recent introgression events.

Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae).

Hybridization is a key mechanism involved in lineage diversification and speciation, especially in ecosystems that experienced repeated environmental oscillations. Recently radiated plant groups, which have evolved in mountain ecosystems impacted by historical climate change provide an excellent model system for studying the impact of gene flow on speciation. We combined organellar (whole-plastome) and nuclear genomic data (RAD-seq) with a cytogenetic approach (rDNA FISH) to investigate the effects of hybridization and introgression on evolution and speciation in the genus Soldanella (snowbells, Primulaceae). Pervasive introgression has already occurred among ancestral lineages of snowbells and has persisted throughout the entire evolutionary history of the genus, regardless of the ecology, cytotype, or distribution range size of the affected species. The highest extent of introgression has been detected in the Carpathian species, which is also reflected in their extensive karyotype variation. Introgression occurred even between species with dysploid and euploid cytotypes, which were considered to be reproductively isolated. The magnitude of introgression detected in snowbells is unprecedented in other mountain genera of the European Alpine System investigated hitherto. Our study stresses the prominent evolutionary role of hybridization in facilitating speciation and diversification on the one hand, but also enriching previously isolated genetic pools. [chloroplast capture; diversification; dysploidy; European Alpine system; introgression; nuclear-cytoplasmic discordance; ribosomal DNA.].

Spatio-temporal formation of the genetic diversity in the Mediterranean dwelling lichen during the Neogene and Quaternary epochs.

Genetic patterns of lichenized fungi often display a mosaic-like and difficult to interpret structure blurring their evolutionary history. The genetic diversity and phylogeographic pattern of a mycobiont of the predominantly Mediterranean dwelling lichen Solenopsora candicans were investigated on the base of extensive sampling (361 individuals, 77 populations) across its entire distribution range. We tested whether the genetic pattern of S. candicans mirrors paleoclimatic and paleogeological events in the Mediterranean and adjacent regions. The divergence time estimates indicated a Tertiary origin for S. candicans, with formation of intraspecific diversity initiated in the Late Miocene. The distribution of the most divergent haplotypes, mostly of a pre-Pleistocene origin, was restricted to the eastern or western extremities of the Mediterranean exhibiting Kiermack disjunction. The population genetic diversity analyses indicated multiple diversity centres and refugia for S. candicans across the entire Mediterranean Basin. While the south Mediterranean regions harboured both the Tertiary and Quaternary born diversity, conforming to the 'cumulative refugia' paradigm, the Apennine and Balkan Peninsulas in the north hosted mostly younger Pleistocene haplotypes and lineages. The recent population expansion of S. candicans might have occurred in the middle Pleistocene with a population burst in the Apennine and Balkan peninsulas. The presence of unique haplotypes in Central Europe indicates the existence of extra-Mediterranean microrefugia. This study presents the first comprehensive lichen phylogeography from the Mediterranean region and simultaneously reports for the first time the glacial survival of a warm-adapted lichen in the temperate zone.

Diversification and independent polyploid origins in the disjunct species Alyssum repens from the Southeastern Alps and the Carpathians.

PREMISE: Disjunct distributions have been commonly observed in mountain plant species and have stimulated phylogeographic and phylogenetic research. Here we studied Alyssum repens, a member of the polyploid species complex A. montanum-A. repens, which exhibits SE Alpine-Carpathian disjunctions with a large elevational span and consists of diploid and tetraploid populations. We aimed to investigate the species' genetic and cytotype structure in the context of its distribution patterns, to elucidate the polyploid origins and to propose an appropriate taxonomic treatment. METHODS: We combined AFLP fingerprinting markers, sequence variation of the highly repetitive ITS region of rDNA and the low-copy DET1 nuclear gene, genome size, and morphometric data. RESULTS: We identified four geographically structured genetic lineages. One consisted of diploid populations from the foothills of the Southeastern Alps and neighboring regions, and the three others were allopatric montane to alpine groups comprising diploids and tetraploids growing in the Southeastern Carpathians and the Apuseni Mts. in Romania. CONCLUSIONS: We inferred a vicariance scenario associated with Quaternary climatic oscillations, accompanied by one auto- and two allopolyploidization events most likely involving a northern Balkan relative. Whereas genetic differentiation and allopatric distribution would favor the taxonomic splitting of this species, the genetic lineages largely lack morphological distinguishability, and their ecological, cytotype and genome size divergence is only partial. Even though we probably face here a case of incipient speciation, we propose to maintain the current taxonomic treatment of Alyssum repens as a single, albeit variable, species.

Diversification dynamics and transoceanic Eurasian-Australian disjunction in the genus Picris (Compositae) induced by the interplay of shifts in intrinsic/extrinsic traits and paleoclimatic oscillations.

Understanding transcontinental biogeographic patterns has been one of the main foci of the field of biogeography. While multiple explanations for transcontinental disjunctions have been proposed, little is still known about the relative importance of intrinsic and extrinsic traits for the diversification dynamics of disjunct taxa. Here, we study the evolutionary history of the genus Picris L. (Compositae), a great model for investigating the diversification dynamics of transoceanic bipolar disjunct organisms. Ancestral state reconstructions indicate that the most recent common ancestor (MRCA) of Picris was a semelparous and heterocarpic herb that lived in unpredictable environments of North Africa and West Asia. Diversification analyses suggest a significant shift in speciation ca. 1 million years ago, likely associated with the onset of the mid-Pleistocene revolution. Longevity characters are correlated with the evolution of particular fruit types and with environmental conditions. Heterocarpic species are mostly semelparous herbs strongly linked with unpredictable habitats, while homocarpic taxa are mostly iteroparous plants occurring in predictable environments. Binary-state speciation and extinction analyses suggest that homocarpy, iteroparity, and habitats predictability accelerate diversification. Although the combination of homocarpy and iteroparity evolved in several lineages, only members of the P. hieracioides group were able to colonise Eurasia and expand to Australia by transoceanic dispersal. Those findings indicate that large-scale colonisation events depend on a complex interplay of intrinsic and extrinsic factors.

A low-residue breakfast improves patient tolerance without impacting quality of low-volume colon cleansing prior to colonoscopy: a randomized trial.

OBJECTIVES: We compared the efficacy and patient tolerance of two dietary regimens used as an adjunct to standard bowel cleansing in preparation for elective colonoscopy. METHODS: Our prospective, randomized, single-blind, controlled, noninferiority trial compared two dietary regimens administered the day before colonoscopy. Subjects received low-volume bowel preparation. The primary outcome was efficacy of colon cleansing, rated by the Ottawa bowel preparation scale (OBPS). Patient acceptance of the assigned dietary regimen was assessed as a secondary outcome. RESULTS: The mean OBPS score for the standard clear-fluid diet group was 4.47, compared with 4.62 for the low-residue breakfast group, meeting criteria for noninferiority. The groups reported similar mean intensity of hunger on a visual analog hunger scale. However, overall satisfaction was higher with the low-residue diet than with the clear-fluid diet. CONCLUSIONS: A low-residue breakfast on the day before elective colonoscopy does not compromise the overall quality of bowel preparation as compared with a standard clear-fluid diet and is likely to be preferred by patients.

Phylogenetic challenges in a recently diversified and polyploid-rich Alyssum (Brassicaceae) lineage: low divergence, reticulation, and parallel polyploid speciation.

Elucidating the evolution of recently diverged and polyploid-rich plant lineages may be challenging even with high-throughput sequencing, both for biological reasons and bioinformatic difficulties. Here, we apply target enrichment with genome skimming (Hyb-Seq) to unravel the evolutionary history of the Alyssum montanum-A. repens species complex. Reconstruction of phylogenetic relationships in diploids supported recent and rapid diversification accompanied by reticulation events. Of the 4 main clades identified among the diploids, 3 clades included species from the Alps, Apennine, and Balkan peninsulas, indicating close biogeographic links between these regions. We further focused on the clade distributed from the Western Alps to the Iberian Peninsula, which comprises numerous polyploids as opposed to a few diploids. Using a recently developed PhyloSD (phylogenomic subgenome detection) pipeline, we successfully tracked the ancestry of all polyploids. We inferred multiple polyploidization events that involved 2 closely related diploid progenitors, resulting into several sibling polyploids: 2 autopolyploids and 6 allopolyploids. The skewed proportions of major homeolog-types and the occurrence of some minor homeolog-types, both exhibiting geographic patterns, suggest introgression with the progenitors and other related diploids. Our study highlights a unique case of parallel polyploid speciation that was enhanced by ecological and geographic separation and provides an excellent resource for future studies of polyploid evolution.

Multiple Drivers of High Species Diversity and Endemism Among Alyssum Annuals in the Mediterranean: The Evolutionary Significance of the Aegean Hotspot.

The Mediterranean Basin is a significant hotspot of species diversity and endemism, with various distribution patterns and speciation mechanisms observed in its flora. High species diversity in the Mediterranean is also manifested in the monophyletic lineage of Alyssum annuals (Brassicaceae), but little is known about its origin. These species include both diploids and polyploids that grow mainly in open and disturbed sites across a wide elevational span and show contrasting distribution patterns, ranging from broadly distributed Eurasian species to narrow island endemics. Here, we investigated the evolution of European representatives of this lineage, and aimed to reconstruct their phylogeny, polyploid and genome size evolution using flow cytometric analyses, chloroplast and nuclear high- and low-copy DNA markers. The origin and early diversification of the studied Alyssum lineage could be dated back to the Late Miocene/Pliocene and were likely promoted by the onset of the Mediterranean climate, whereas most of the extant species originated during the Pleistocene. The Aegean region represents a significant diversity center, as it hosts 12 out of 16 recognized European species and comprises several (sub)endemics placed in distinct phylogenetic clades. Because several species, including the closest relatives, occur here sympatrically without apparent niche differences, we can reject simple allopatric speciation via vicariance as well as ecological speciation for most cases. Instead, we suggest scenarios of more complex speciation processes that involved repeated range shifts in response to sea-level changes and recurrent land connections and disconnections since the Pliocene. In addition, multiple polyploidization events significantly contributed to species diversity across the entire distribution range. All seven polyploids, representing both widespread species and endemics to the western or eastern Mediterranean, were inferred to be allopolyploids. Finally, the current distribution patterns have likely been affected also by the human factor (farming and grazing). This study illustrates the complexity of evolutionary and speciation processes in the Mediterranean flora.

Genetic Diversity, Ochratoxin A and Fumonisin Profiles of Strains of Aspergillus Section Nigri Isolated from Dried Vine Fruits.

We investigated ochratoxin A (OTA) contamination in raisin samples purchased from Slovak markets and determined the diversity of black-spored aspergilli as potential OTA and fumonisin (FB1 and FB2) producers. The taxonomic identification was performed using sequences of the nuclear ITS1-5.8s-ITS2 region, the calmodulin and beta-tubulin genes. We obtained 239 isolates from eight fungal genera, of which 197 belonged to Aspergillus (82%) and 42 strains (18%) to other fungal genera. OTA contamination was evidenced in 75% of the samples and its level ranged from 0.8 to 10.6 µg/kg. The combination of all three markers used enabled unambiguous identification of A. carbonarius, A. luchuensis, A. niger, A. tubingensis and A. welwitschiae. The dominant coloniser, simultaneously having the highest within-species diversity isolated from our raisin samples, was A. tubingensis. Out of all analysed strains, only A. carbonarius was found to produce OTA, but in relatively high quantity (2477-4382 µg/kg). The production of FB1 and FB2 was evidenced in A. niger strains only.

So Closely Related and Yet So Different: Strong Contrasts Between the Evolutionary Histories of Species of the Cardamine pratensis Polyploid Complex in Central Europe.

Recurrent polyploid formation and weak reproductive barriers between independent polyploid lineages generate intricate species complexes with high diversity and reticulate evolutionary history. Uncovering the evolutionary processes that formed their present-day cytotypic and genetic structure is a challenging task. We studied the species complex of Cardamine pratensis, composed of diploid endemics in the European Mediterranean and diploid-polyploid lineages more widely distributed across Europe, focusing on the poorly understood variation in Central Europe. To elucidate the evolution of Central European populations we analyzed ploidy level and genome size variation, genetic patterns inferred from microsatellite markers and target enrichment of low-copy nuclear genes (Hyb-Seq), and environmental niche differentiation. We observed almost continuous variation in chromosome numbers and genome size in C. pratensis s.str., which is caused by the co-occurrence of euploid and dysploid cytotypes, along with aneuploids, and is likely accompanied by inter-cytotype mating. We inferred that the polyploid cytotypes of C. pratensis s.str. are both of single and multiple, spatially and temporally recurrent origins. The tetraploid Cardamine majovskyi evolved at least twice in different regions by autopolyploidy from diploid Cardamine matthioli. The extensive genome size and genetic variation of Cardamine rivularis reflects differentiation induced by the geographic isolation of disjunct populations, establishment of triploids of different origins, and hybridization with sympatric C. matthioli. Geographically structured genetic lineages identified in the species under study, which are also ecologically divergent, are interpreted as descendants from different source populations in multiple glacial refugia. The postglacial range expansion was accompanied by substantial genetic admixture between the lineages of C. pratensis s.str., which is reflected by diffuse borders in their contact zones. In conclusion, we identified an interplay of diverse processes that have driven the evolution of the species studied, including allopatric and ecological divergence, hybridization, multiple polyploid origins, and genetic reshuffling caused by Pleistocene climate-induced range dynamics.

Low-residue breakfast during the preparation for colonoscopy using a polyethylene glycol electrolyte solution: a randomised non-inferiority trial.

GOALS: To test the hypothesis that the use of a low-residue breakfast (LRB) the day prior to colonoscopy was not inferior to consuming clear fluids alone (CFD) in patients undergoing outpatient colonoscopy with a polyethylene glycol (PEG) bowel preparation. BACKGROUND: Optimal colon cleansing is essential for complete visualisation of the mucosa during colonoscopy. Few studies have examined the effect of diet on the quality of bowel cleansing or tolerance in patients using a PEG bowel preparation for colonoscopy. METHODS: Randomised, single-blinded non-inferiority trial. Adult patients scheduled for outpatient colonoscopy with PEG solution were randomised to an LRB followed by clear fluids or CFD using either a traditional or split-dose PEG solution for bowel preparation. The primary outcome was colon cleansing based on the Ottawa Bowel Preparation Score (OBPS). RESULTS: On an intention-to-treat (ITT) basis, a total of 109 and 105 patients were included in the CFD and LRB arms, respectively, with 116 and 98 patients, respectively, for the per-protocol (PP) analysis. Although there was no difference in the mean total OBPS between the CFD or LRB arms in either the ITT or PP analysis, the threshold for non-inferiority was not met. Patient acceptance of the regimens was higher in the LRB arm than in the CFD arm in the ITT and PP analyses. CONCLUSIONS: This study failed to show the non-inferiority of an LRB in patients receiving bowel preparation with a PEG-based solution. A CFD should be prescribed when using a PEG bowel preparation. TRIAL REGISTRATION NUMBER: This trial is registered at ClinicalTrials.gov (NCT01454388).