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FIGURE 7 in Early-diverging bumblebees from across the roof of the world: the high-mountain subgenus Mendacibombus revised from species' gene coalescents and morphology (Hymenoptera, Apidae)

FIGURE 7. Frequency of specimen collection by decade among specimens examined for species of the subgenus Mendacibombus excluding B. mendax and B. handlirschianus.

FIGURE 73 in Early-diverging bumblebees from across the roof of the world: the high-mountain subgenus Mendacibombus revised from species' gene coalescents and morphology (Hymenoptera, Apidae)

FIGURE 73. Plot of elevation (y-axis) against latitude (x-axis) for the 4413 records of all species of the subgenus Mendacibombus world-wide. A key to the symbols identifying species is shown at the upper left.

FIGURES 71‒72 in Early-diverging bumblebees from across the roof of the world: the high-mountain subgenus Mendacibombus revised from species' gene coalescents and morphology (Hymenoptera, Apidae)

FIGURES 71‒72. Maps of (71) specimen richness and (72) species richness for the subgenus Mendacibombus among equalarea grid cells recorded from geo-referenced specimens in the database. The grid is based on longitudinal intervals of 10°, which are used to calculate graduated latitudinal intervals to provide equal-area cells (each cell of area approximately 611,000 km²). Grey scale (right) with equal-frequency richness classes, maximum value in a separate class. Cylindrical orthomorphic equal-area projection (excluding Antarctica) with north at the top of the map.

FIGURE 13 in Early-diverging bumblebees from across the roof of the world: the high-mountain subgenus Mendacibombus revised from species' gene coalescents and morphology (Hymenoptera, Apidae)

FIGURE 13. Assigning names to species from an estimate of phylogeny for 130 COI sequences of the subgenus Mendacibombus. Based on a BEAST analysis of the 30 unique haplotypes (Fig. 11), with the remaining sequences interpolated back into the tree with 0 branch lengths from their matching samples (where a sequence matches more than one longer sequence within a species in the Collapse results, it is added after the first matching sequence, with the addition of the two short-sequence yellow unbanded specimens from Pakistan, MD#4058, 4059). The sequence labels follow the format used in Figs 11, 12. Lineages accepted as species from the GMYC models (Fig. 11) are shown as thick branches, the most recent common ancestors of each species are shown with a black spot, and branches within species are shown as thin branches. Asterisks mark samples used as informal proxies for the type specimens of each of the taxon names (Table 1). The proxy sample for the type specimen for the oldest available name (the valid name) for each species (from Fig. 11) is marked in bold. The interpretations of the species with their valid names are shown in grey to the right.

opencc-by-4.0Mar 2024View details →

Data set for Control of Ge island coalescence for the formation of nanowires on silicon

This document contains all the data and the analysis used in the manuscript titled " Control of Ge island coalescence for the formation of nanaowires on silicon" <a title="Link to landing page via DOI" href="https://doi.org/10.1039/D3NH00573A">https://doi.org/10.1039/D3NH00573A</a>

opencc-by-4.0Apr 2024View details →

Segregation of a thermochemical anomaly and coalescence with a large low-velocity province

# This is a supplement to the manuscript "Segregation of a thermochemical anomaly and coalescence with a large low-velocity province" currently accepted of Nature Geoscience.  The objective of this supplement is to offer the user access to our model outputs, which include reproducible map data files and 3-D images. Additionally, we provide the seismological data utilized in the manuscript. 1. The "map_files" folder contains the map data obtained at a depth of 2800 km from our model, as listed in Extended Data Table 1. 2. The "paraview_files" directory includes a state file named "Reference_Model_Visualisation.pvsm" that enables the reproduction of Figure 2 as presented in the main text. 3.  The "tomography" folder contains the map and slice data files of the tomography utilized in the manuscript. 4. "quantitative_comparison" folder contains quantitative comparisons of the model results with the S-wave and P-wave votemap. (0: True Negatives, 1: True Positives, 2: False Negatives, 3: False Positives) 5. The file "Modeled_Kamchatka_LIPs.xyz" contains the Kamchatka Large Igneous Provinces (LIPs) created by our models, as depicted in Extended Data Figure 7.

opennotspecifiedNov 2021View details →

FIGURE26. Palhinhaea steyermarkii—(Ecuador: Øllgaard et al. 35959, AAU). A. Growth habit. A1. Close-up of major branchlet. A2. Close-up of terminal branchlet. A3. Portion of strobilus. A4. Close-up of strobilus apex, showing coalescent sporophyll bases. Drawing by K. Tind in The Lycopodiaceae of Panamá

FIGURE26. Palhinhaea steyermarkii—(Ecuador: Øllgaard et al. 35959, AAU). A. Growth habit. A1. Close-up of major branchlet. A2. Close-up of terminal branchlet. A3. Portion of strobilus. A4. Close-up of strobilus apex, showing coalescent sporophyll bases. Drawing by K. Tind

Figure 1 in DNA barcoding and coalescent-based delimitation of endosymbiotic clevelandellid ciliates (Ciliophora: Clevelandellida): a shift to molecular taxonomy in the inventory of ciliate diversity in panesthiine cockroaches

Figure 1. Phylogenetic tree based on the 18S rRNA gene, ITS1-5.8S-ITS2 region and 28S rRNA gene, showing relationships among ciliates isolated from the digestive tract of panesthiine cockroaches. All tree-building methods resulted in very similar topologies. The single exception is the Anteclevelandella constricta cluster, where the IQTree topology differs from that of both Bayesian trees (shown in the box). Bootstrap values for the maximum likelihood conducted in IQTrees and posterior probabilities for Bayesian inferences conducted in MrBayes and Phycas are listed at corresponding nodes of the best scoring IQTree. Specimen codes and further details are listed in Table 1. The scale bar denotes two substitutions per one hundred nucleotide positions.

Figure 4 in DNA barcoding and coalescent-based delimitation of endosymbiotic clevelandellid ciliates (Ciliophora: Clevelandellida): a shift to molecular taxonomy in the inventory of ciliate diversity in panesthiine cockroaches

Figure 4. Consensus secondary structure of the ITS2 molecule of 54 members of the order Clevelandellida isolated from the digestive tract of cockroaches. Note that the central loop radiates four highly conserved helices. The structure logo of helices is shown on the right side. The height of a base is proportional to its frequency in the multiple sequence alignment.

Figure 3 in DNA barcoding and coalescent-based delimitation of endosymbiotic clevelandellid ciliates (Ciliophora: Clevelandellida): a shift to molecular taxonomy in the inventory of ciliate diversity in panesthiine cockroaches

Figure 3. MDS diagrams (A, C, E) and TCS networks (B, D, F) based on 18S rRNA gene (A, B), ITS1-5.8S-ITS2 region (C, D) and 28S rRNA gene (E, F) sequences of the family Clevelandellidae. The MDS diagrams show the distribution of specimens in the genotype space. Species belonging to the same genus form a cluster distinctly isolated from other such clusters. The TCS networks reflect the most parsimonious relationships among species given the individual markers. Numbers along edges indicate mutational steps between adjacent nodes. Species belonging to the same genus are marked by the same colour code.

Figure 7 in DNA barcoding and coalescent-based delimitation of endosymbiotic clevelandellid ciliates (Ciliophora: Clevelandellida): a shift to molecular taxonomy in the inventory of ciliate diversity in panesthiine cockroaches

Figure 7. Putative secondary structure models of the highly divergent helix c3-1 in the D2 domain of the 28S rRNA molecule of 17 species of the order Clevelandellida isolated from the digestive tract of cockroaches. Arrowheads denote the molecular diagnostic characters.

Figure 2. Coalescent species trees with 13 in DNA barcoding and coalescent-based delimitation of endosymbiotic clevelandellid ciliates (Ciliophora: Clevelandellida): a shift to molecular taxonomy in the inventory of ciliate diversity in panesthiine cockroaches

Figure 2. Coalescent species trees with 13 (A) and 14 (B) assumed species based on 18S rRNA gene, ITS1-5.8S-ITS2 region and 28S rRNA gene sequences. Posterior probabilities of clades are provided along internal branches and posterior probabilities for the presence of individual species are provided behind the terminal branches. Scale bars denote the fraction of substitutions per site.

Figure 9 in DNA barcoding and coalescent-based delimitation of endosymbiotic clevelandellid ciliates (Ciliophora: Clevelandellida): a shift to molecular taxonomy in the inventory of ciliate diversity in panesthiine cockroaches

Figure 9. MDS diagram (A) and TCS network (B) based on concatenated 18S rRNA gene, ITS1-5.8S-ITS2 region and 28S rRNA gene sequences of the family Clevelandellidae. The MDS diagram shows the distribution of specimens in the genotype space. Species belonging to the same genus form a cluster distinctly isolated from other such clusters. The TCS network reflects the most parsimonious relationships among species given the concatenated dataset. Numbers along edges indicate mutational steps between adjacent nodes. Species belonging to the same genus are marked by the same colour code.

Figure 6 in DNA barcoding and coalescent-based delimitation of endosymbiotic clevelandellid ciliates (Ciliophora: Clevelandellida): a shift to molecular taxonomy in the inventory of ciliate diversity in panesthiine cockroaches

Figure 6. Putative secondary structure models of helices 39‒44 in the V7 region of the 18S rRNA molecule of four Nyctotherus species isolated from the digestive tract of cockroaches. Arrowheads denote the molecular diagnostic characters. CBC, compensatory base change; hemi-CBC, hemi-compensatory base change.

Figure 5 in DNA barcoding and coalescent-based delimitation of endosymbiotic clevelandellid ciliates (Ciliophora: Clevelandellida): a shift to molecular taxonomy in the inventory of ciliate diversity in panesthiine cockroaches

Figure 5. Putative secondary structure models of the highly divergent helix 23e1 in the V4 region of the 18S rRNA molecule of 17 species of the order Clevelandellida isolated from the digestive tract of cockroaches. Arrowheads denote the molecular diagnostic characters.

opencc-zeroMay 2022View details →

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StarBeast3: Adaptive parallelised Bayesian inference under the multispecies coalescent

As genomic sequence data becomes increasingly available, inferring the phylogeny of the species as that of concatenated genomic data can be enticing. However, this approach makes for a biased estimator of branch lengths and substitution rates and an inconsistent estimator of tree topology. Bayesian multispecies coalescent methods address these issues. This is achieved by constraining a set of gene trees within a species tree and jointly inferring both under a Bayesian framework. However, this approach comes at the cost of increased computational demand. Here, we introduce StarBeast3 -- a software package for efficient. Bayesian inference under the multispecies coalescent model via Markov chain Monte Carlo. We gain efficiency by introducing cutting-edge proposal kernels and adaptive operators, and StarBeast3 is particularly efficient when a relaxed clock model is applied. Furthermore, gene tree inference is parallelised, allowing the software to scale with the size of the problem. We validated our software and benchmarked its performance using three real and two synthetic datasets. Our results indicate that StarBeast3 is up to one-and-a-half orders of magnitude faster than StarBeast2, and therefore more than two orders faster than *BEAST, depending on the dataset and on the parameter, and can achieve convergence on large datasets with hundreds of genes. StarBeast3 is open-source and is easy to set up with a friendly graphical user interface.

FIGURES 152‒153 in The arctic and alpine bumblebees of the subgenus Alpinobombus revised from integrative assessment of species' gene coalescents and morphology (Hymenoptera, Apidae, Bombus)

FIGURES 152‒153. Reconstruction of ancestral states by parsimony in Mesquite for two colour-pattern characters each with two states among species based on the estimate of phylogeny in Fig. 138, several of which are polymorphic and show both states for both characters (re-drawn from Williams et al. 2015): (152) banding colour pattern, with yellow spots showing yellow-banded (B) populations (minimally with yellow hair clearly visible anteriorly on the thoracic dorsum), black spots showing unbanded (U) populations, mixed yellow/black spots showing polymorphic populations, mixed yellow/grey spots showing uncertain polymorphic/monomorphic populations (*for B. alpinus, males from the Alps often have a yellow-banded pattern although this is rare among females); (153) tail colour pattern, with orange spots showing populations with pale (P: orange or white) hair on the tail (minimally with orange, yellow, or while hair clearly visible on metasomal tergum 5), black spots showing populations with dark (D: black) hair on the tail, mixed orange/black spots showing polymorphic populations.

FIGURES 148‒149 in The arctic and alpine bumblebees of the subgenus Alpinobombus revised from integrative assessment of species' gene coalescents and morphology (Hymenoptera, Apidae, Bombus)

FIGURES 148‒149. Anterior / left lateral aspect of the lower part of the clypeus, the labrum, and the mandibles of males of: (148) B. neoboreus (#4867), showing the small orange hair patches at the base of the mandibles and the long dense posterior fringing black beard; (149) B. kluanensis (#4876), showing the large dense orange hair pads on the mandibles and the sparse orange hairs in the posterior fringing beard.

FIGURES 150‒151 in The arctic and alpine bumblebees of the subgenus Alpinobombus revised from integrative assessment of species' gene coalescents and morphology (Hymenoptera, Apidae, Bombus)

FIGURES 150‒151. Maps of (150) specimen richness and (151) species richness for the subgenus Alpinobombus among equalarea grid cells recorded from 4450 geo-referenced specimens in the database. The grid is based on longitudinal intervals of 10°, which are used to calculate graduated latitudinal intervals to provide equal-area cells (each cell of area approximately 611,000 km²). Grey scale (right) with equal-frequency richness classes, maximum value in a separate class. Cylindrical orthomorphic equal-area projection (excluding Antarctica) with north at the top of the map.

FIGURES 144‒147 in The arctic and alpine bumblebees of the subgenus Alpinobombus revised from integrative assessment of species' gene coalescents and morphology (Hymenoptera, Apidae, Bombus)

FIGURES 144‒147. Morphology of males. Dorsal aspect of the penis valves of: 144, B. natvigi; 145, B. neoboreus (white lines indicate location of the subapical outer tooth of the left penis valve). Dorsal aspect of left gonostylus: 146 B. kirbiellus; 147, B. polaris (white lines indicate anterior, midpoint, and posterior median projections of left gonostylus).