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FIG. 1 in The Amidella clade in Europe (Basidiomycota: Amanitaceae): clarification of the contentious Amanita valens (E.-J.Gilbert) Bertault and the importance of taxon-specific PCR primers for identification

FIG. 1. — Locations of the collections used in this study (see Table 1 for details). The letters designate Landscape Units: P, Alto Alentejo; R, Alentejo Central; S, Baixo Alentejo; U, Serras do Algarve e do Litoral Alentejano. The area is outlined on the inset with a yellow rectangle. Source: DGT, Carta de Unidades de Paisagem (CUP), https://www.dgterritorio.gov.pt/dados-abertos

FIG. 2 in The Amidella clade in Europe (Basidiomycota: Amanitaceae): clarification of the contentious Amanita valens (E.-J.Gilbert) Bertault and the importance of taxon-specific PCR primers for identification

FIG. 2. — Phylogenetic placement of the type nrDNA sequences, in relation to ITS + LSU sequences from european Amanita Pers. taxa belonging to the Amidella clade (only the terminal epithets are shown). Using a 70% coverage cutoff, a total of 1121 aligned positions were analysed with the Maximum Likelihood method and the Tamura-Nei (Tamura & Nei 1993) substitution model, with a discrete Gamma distribution to model evolutionary rate differences among sites (five categories [gamma parameter 0.7526]), allowing for some sites to be evolutionarily invariable (40.90% sites). The percentage bootstrap support for each node (1000 replicates) is shown next to the branches. The support for each species clade is 99% (Amanita pseudovalens comb. nov., stat. nov.), 100% (Amanita curtipes E.-J.Gilbert), 100% (Amanita lepiotoides Barla) and 100% (Amanita ponderosa Malençon & R.Heim). The scale indicates 0.02 substitutions per site.

FIG. 3 in The Amidella clade in Europe (Basidiomycota: Amanitaceae): clarification of the contentious Amanita valens (E.-J.Gilbert) Bertault and the importance of taxon-specific PCR primers for identification

FIG. 3. — Photographs of Amanita pseudovalens var. tartessiana var. nov. specimens from Odemira. Some images taken in the field are matched with corresponding ones taken in the laboratory: A, grouped basidiomes (Ode12) and their appearance upon arrival at the laboratory; B, outcropping away from the vegetation, showing the coarse soil texture in this case (Ode02); inset shows squamulose inner cuticle remains; C, another specimen with cuticle squamules (Ode11); D, specimen with cracked cuticle (Ode05); E, example with stipe squamules (Ode06); F, side view of an emerging basidiome (Ode03) and the same specimen showing the darkened squamules on the stipe; G, view of the hymenophore and the appendiculate pileus margin (Ode02, specimen different from B); H, details of an immature basidiome (Ode06, specimen different from E) showing the annulus and insertion of the lamellae (left), and longitudinal section (right).

FIG. 5 in The Amidella clade in Europe (Basidiomycota: Amanitaceae): clarification of the contentious Amanita valens (E.-J.Gilbert) Bertault and the importance of taxon-specific PCR primers for identification

FIG. 5. — Ground view of the Luzianes locations, showing the Cistus ladanifer L. dominance: A, Luzianes A; B, Luzianes B. Both photos were taken in spring 2015 by Ana C. Silva.

FIG. 4 in The Amidella clade in Europe (Basidiomycota: Amanitaceae): clarification of the contentious Amanita valens (E.-J.Gilbert) Bertault and the importance of taxon-specific PCR primers for identification

FIG. 4. — Plotting of the measurements summarised in Table 5 (dots), comparing with the limits of the sporographs, based on the descriptions in Neville & Poumarat (2004) for Amanita curtipes f. pseudovalens Neville & Poumarat (continuous line) and A. ponderosa f. ponderosa Malençon & R.Heim (dashed line).

FIGURE 2 in Harmonizing taxon names in biodiversity data: A review of tools, databases and best practices

FIGURE 2 Taxonomy as a unifying key for ecological datasets. The two sides represent two exemplary datasets, with a containing conservation status of taxa (here species) and B their traits (colours show different traits). The datasets are indexed by taxon names 'Sp1' to 'Sp6'. The rounded rectangle in the middle depicts the taxonomic harmonization process: (a) the names are extracted from each dataset, respectively in the orange and purple rectangles; (b) both lists are then compared to a taxonomic database which harmonizes all names. Here the names 'Sp1' and 'Sp6' refer to the same taxon in the taxonomic database (as indicated by the dashed lines). Without taxonomic harmonization, the exact match of names would have resulted in the loss of Sp5 and Sp6 when merging both datasets. LC, NT, VU, and CR are abbreviations of Red List statuses, meaning least concern, not threatened, vulnerable, and critically endangered, respectively

FIGURE 1 in Harmonizing taxon names in biodiversity data: A review of tools, databases and best practices

FIGURE 1 Typology of taxonomic databases according to their taxonomic breadth and their spatial scale. The x-axis represents increasing taxonomic breadth from a single taxonomic group to no clear taxonomic restriction (e.g. considering all biota or all Eukaryota). The y-axis represents spatial scale from regional to global. Each box represents a specific type of taxonomic database, with examples. LCVP, Leipzig Catalogue of Vascular Plants; WorldFlora, World Flora Online; POWO, Plants of the World Online; GermanSL, German Simple List; Vascan, Database of Vascular Plants of Canada; WoRMS, World Register of Marine Species; CASD, Chinese Animal Scientific Database; COL, Catalogue of Life; GBIF, Global Biodiversity Information Facility; TAXREF, French Taxonomic Referential; FinBIF, Finnish Biodiversity Information Facility

FIGURE 4 in Harmonizing taxon names in biodiversity data: A review of tools, databases and best practices

FIGURE 4 Diagram of different taxonomic harmonization workflows. The workflows differ in the number of steps they consider and the databases they leverage on. Rounded rectangles are lists of taxon names while diamonds represent taxonomic databases against which the names are matched. The different colours used at step 2 represent different taxonomic groups

FIGURE 3 in Harmonizing taxon names in biodiversity data: A review of tools, databases and best practices

FIGURE 3 Screenshot showing the network view of taxharmonizexplorer. The left section shows a table of each of the nodes in the network to let the user select manually nodes of interest, the top part presents a summary of the information on the selected node in the network. The right section displays the relationships between packages (which depends on which other), between databases (how one populates another one) and between packages and databases (which packages access which databases)

opencc-by-4.0Jun 2019View details →

Figure 1. Taxon 1 in Descriptions of two interesting chironomid pupae collected in Yunnan Province, China (Chironomidae: Chironominae)

Figure 1. Taxon 1: a) frontal apotome; b) thoracic horn; c) thorax; d) abdoman dorsal view; e) posterolateral spines of segment VIII. Taxon 2: f) abdoman dorsal view; g) posterolateral spines of segment VIII. Scale bar = XX μm.

Abb. 6 in Neues vom Taxon Phengaris alcon rebeli (Hirschke, 1904) auf der Hochebene Obersand (GL)

Abb. 6. Ei des Enzianbläulings Phengaris alcon rebeli an einem Feldenzian Gentiana campestris. (Foto André Rey)

Abb. 5 in Neues vom Taxon Phengaris alcon rebeli (Hirschke, 1904) auf der Hochebene Obersand (GL)

Abb. 5. Feldenzian Gentiana campestris mit Ei () des Enzianbläulings Phengaris alcon rebeli (Hirschke, 1904) am 4.8.2017 auf Obersand (GL). (Foto Rainer Neumeyer)

Abb. 3 in Neues vom Taxon Phengaris alcon rebeli (Hirschke, 1904) auf der Hochebene Obersand (GL)

Abb. 3. Vier Puppen des Enzianbläulings Phengaris alcon rebeli (Hirschke, 1904) in einem Nest der Braunen Knotenameise Myrmica sulcinodis Nylander, 1846 auf Obersand (GL), am 19.6.2017. (Foto Rainer Neumeyer)

Abb. 2 in Neues vom Taxon Phengaris alcon rebeli (Hirschke, 1904) auf der Hochebene Obersand (GL)

Abb. 2. Fundort der Puppen des Enzianbläulings (Phengaris alcon rebeli) im Nest der Braunen Knotenameise (Myrmica sulcinodis) unter einem Stein () auf der Hochebene Obersand (GL) am 19.6.2017. (Foto Rainer Neumeyer)

Abb. 4 in Neues vom Taxon Phengaris alcon rebeli (Hirschke, 1904) auf der Hochebene Obersand (GL)

Abb. 4. Weibchen (a, b) und Männchen (c, d) des Enzianbläulings Phengaris alcon rebeli aus Obersand (GL) von oben (a, c) und unten (b, d). Abgebildet ist auch das männliche Genital (d). Beide Falter befinden sich in der Entomologischen Sammlung der ETH Zürich. (Fotos Jürg Sommerhalder)

Abb. 1 in Neues vom Taxon Phengaris alcon rebeli (Hirschke, 1904) auf der Hochebene Obersand (GL)

Abb. 1. Aspekte der Hochebene Obersand (GL, Glarus Süd) am 19.6. (a) und am 4.8.2017 (b). (Fotos Rainer Neumeyer)

opencc-zeroJun 2023View details →

Impacts of taxon-sampling schemes on Bayesian tip dating under the fossilized birth-death process

<p>Evolutionary timescales can be inferred by molecular-clock analyses of genetic data and fossil evidence. Bayesian phylogenetic methods such as tip dating provide a powerful framework for inferring evolutionary timescales, but the most widely used priors for tree topologies and node times often assume that present-day taxa have been sampled randomly or exhaustively. In practice, taxon sampling is often carried out so as to include representatives of major lineages, such as orders or families. We examined the impacts of different densities of diversified sampling on Bayesian tip dating on unresolved fossilized birth-death (FBD) trees, in which fossil taxa are topologically constrained but their exact placements are averaged out. We used synthetic data generated by simulations of nucleotide sequence evolution, fossil occurrences, and diversified taxon sampling. Our analyses under the diversified-sampling FBD process show that increasing taxon-sampling density does not necessarily improve divergence-time estimates. However, when informative priors were specified for the root age or when tree topologies were fixed to those used for simulation, the performance of tip dating on unresolved FBD trees maintains its accuracy and precision or improves with taxon-sampling density. By exploring three situations in which models are mismatched, we find that including all relevant fossils, without pruning off those that are incompatible with the diversified-sampling FBD process, can lead to underestimation of divergence times. Our reanalysis of a eutherian mammal data set confirms some of the findings from our simulation study, and reveals the complexity of diversified taxon sampling in phylogenomic data sets. In highlighting the interplay of taxon-sampling density and other factors, the results of our study have practical implications for using Bayesian tip dating to infer evolutionary timescales across the Tree of Life.</p>

publicMay 2020View details →

Reconciling supertramps, great speciators and relict species with the taxon cycle stages of a large island radiation (Aves: Campephagidae)

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publicOct 2019View details →

Data from: Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics

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