High-level classification of the Fungi and a tool for evolutionary ecological analyses

High-throughput sequencing studies generate vast amounts of taxonomic data. Evolutionary ecological hypotheses of the recovered taxa and Species Hypotheses are difficult to test due to problems with alignments and the lack of a phylogenetic backbone. We propose an updated phylum-and class-level fungal classification accounting for monophyly and divergence time so that the main taxonomic ranks are more informative. Based on phylogenies and divergence time estimates, we adopt phylum rank to Aphelidiomycota, Basidiobolomycota, Calcarisporiellomycota, Glomeromycota, Entomophthoromycota, Entorrhizomycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota and Olpidiomycota. We accept nine subkingdoms to accommodate these 18 phyla. We consider the kingdom Nucleariae (phyla Nuclearida and Fonticulida) as a sister group to the Fungi. We also introduce a perl script and a newick-formatted classification backbone for assigning Species Hypotheses into a hierarchical taxonomic framework, using this or any other classification system. We provide an example of testing evolutionary ecological hypotheses based on a global soil fungal data set.Peer reviewe

Notes for genera: basal clades of Fungi (including Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota)

Compared to the higher fungi (Dikarya), taxonomic and evolutionary studies on the basal clades of fungi are fewer in number. Thus, the generic boundaries and higher ranks in the basal clades of fungi are poorly known. Recent DNA based taxonomic studies have provided reliable and accurate information. It is therefore necessary to compile all available information since basal clades genera lack updated checklists or outlines. Recently, Tedersoo et al. (MycoKeys 13:1--20, 2016) accepted Aphelidiomycota and Rozellomycota in Fungal clade. Thus, we regard both these phyla as members in Kingdom Fungi. We accept 16 phyla in basal clades viz. Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota. Thus, 611 genera in 153 families, 43 orders and 18 classes are provided with details of classification, synonyms, life modes, distribution, recent literature and genomic data. Moreover, Catenariaceae Couch is proposed to be conserved, Cladochytriales Mozl.-Standr. is emended and the family Nephridiophagaceae is introduced

How do persons with dementia participate in decision making related to health and daily care? A multi-case study

Background Many countries have passed laws giving patients the right to participate in decisions about health care. People with dementia cannot be assumed to be incapable of making decisions on their diagnosis alone as they may have retained cognitive abilities. The purpose of this study was to gain a better understanding of how persons with dementia participated in making decisions about health care and how their family carers and professional caregivers influenced decision making. Methods This Norwegian study had a qualitative multi-case design. The triad in each of the ten cases consisted of the person with dementia, the family carer and the professional caregiver, in all 30 participants. Inclusion criteria for the persons with dementia were: (1) 67 years or older (2) diagnosed with dementia (3) Clinical Dementia Rating score 2, moderate dementia; (3) able to communicate verbally. The family carers and professional caregivers were then asked to participate. A semi-structured interview guide was used in interviews with family carers and professional caregivers. Field notes were written after participant observation of interactions between persons with dementia and professional caregivers during morning care or activities at a day centre. How the professional caregivers facilitated decision making was the focus of the observations that varied in length from 30 to 90 minutes. The data were analyzed using framework analysis combined with a hermeneutical interpretive approach. Results Professional caregivers based their assessment of mental competence on experience and not on standardized tests. Persons with dementia demonstrated variability in how they participated in decision making. Pseudo-autonomous decision making and delegating decision making were new categories that emerged. Autonomous decision making did occur but shared decision making was the most typical pattern. Reduced mental capacity, lack of available choices or not being given the opportunity to participate led to non-involvement. Not all decisions were based on logic; personal values and relationships were also considered. Conclusions Persons with moderate dementia demonstrated variability in how they participated in decision making. Optimal involvement was facilitated by positioning them as capable of influencing decisions, assessing decision-specific competence, clarifying values and understanding the significance of relationships and context

Petrographic study and geochemical investigation of the evaporites associated with the Germik Formation (Siirt Basin, Turkey)

Evaporites of the Oligocene Germik Formation are represented by massive, laminated, laminated-banded, banded, nodular and/or brecciated nodular and nodular-banded lithofacies in the Siirt-Kurtalan area. Observations of massive and laminated-banded gypsums with undulated-shaped stromatolitic algal mats, corrugated folded structures and clay-carbonate and interlayered marl in laminated gypsum levels are very important in terms of their mechanisms of occurrences. Petrographic and mineralogic examinations of secondary gypsums in the Germik Formation generally display alabastrine and porphyroblastic textures with corroded anhydrite. Structures as satin-spar, chickenwire, enterolithic and minerals as dolomite, calcite and celestite are also observed. Geochemical evaluations of gypsum and anhydrite samples belong to the lithofacies have provided an approach of their original formation and understandings the environmental impacts (such as pH, paleotemperature, paleosalinity, surface-groundwater activity and bacterial activity). Therefore, a number of analyses were conducted on the different samples for major and trace elements and the gypsum-anhydrite samples were analyzed for isotope compositions. Trace elements of these evaporites were found to be in the range of the geochemical values of the depositional environment of shallow marine evaporites. These values show also occasional influx of terrestrial waters to the environment. Moreover, the differences in the isotopic values of the lithofacies identified by the stable isotopic studies indicate the effects of temperature, salinity, biogenic activity and diagenetic processes for the formation of evaporites, under the influence of climate. Geochemical evolution of gypsum and anhydrite lithofacies of the Germik Formation leads up to muddy evaporites indicating that they were deposited in the coastal sabkha or shallow marine environments within effectively developed paleoclimatic conditions, tectonic activities, diagenetic processes and depositional system