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FIGURE. 2. Most parsimonious tree obtained from the analysis using implied weights, K in A phylogenetic study of the relationships within Mirinae subfamily (Insecta: Heteroptera: Miridae) based on specimens from Northern Iran: Insight into analyses of genera complexes
FIGURE. 2. Most parsimonious tree obtained from the analysis using implied weights, K= 8. Node numbers correspond to nodes in the results section. Filled circles represent non-homoplasious characters, and open circles represent homoplasious characters.
Figure 4 in Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life
Figure 4. Consensus trees of individual gene trees. Left: extended majority-rule consensus (MRE) tree based on bootstrap replicates of individual gene analyses for all genes with no missing taxa (N = 175). Numbers above branches are internode certainty (IC) and internode certainty all (ICA) values for all individual bootstrap trees compared to the MRE tree. Numbers in bold represent nodes that are not present in the ASTRAL tree (right). Right: coalescentbased consensus tree recovered by ASTRAL using 208 single gene maximum likelihood trees from RAXML analysis. Numbers in bold above branches are IC, ICA values for all individual bootstrap trees that are not present in the MRE tree (left). Numbers below branches are bootstrap supports based on single gene bootstrap analysis (100 replicates each).
Figure 3 in Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life
Figure 3. Phylogenetic analysis of the order Agaricales based on a 208 single copy loci combined dataset. Chronogram is based on a partitioned analysis using RAXML with branch lengths transformed to reflect time using correlated penalized likelihood. Numbers next to branches indicate percent support from 50 nonparametric bootstraps.
Figure 6. Best maximum likelihood phylogeny using a in Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life
Figure 6. Best maximum likelihood phylogeny using a concatenated dataset of the 27 genes composing the best combination of top-ranked loci using five ranking criteria identified using measures of Tree Certainty (Salichos & Rokas, 2013). Numbers above branches (red) are bootstrap percentages based on the combined bootstrap replicates. Numbers below branches and adjacent to nodes indicate internode certainty (IC) and internode certainty all (ICA) values of the individual gene bootstrap trees compared with the best maximum likelihood tree depicted. Family/clade designations (fide Matheny et al., 2006 except 1 fide Henkel, Smith & Aime, 2010 and 2 fide Nakasone, Hibbett & Goranova, 2009) are indicated to the right of terminal labels and suborders are named with capital letters at the far right.
Figure 2 in Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life
Figure 2. Summary of data quality. A, distribution of alignment lengths for 208 loci after GBlocks processing. B, correlation of assembly quality (N50) and percent alignment coverage.
Data from: Moorean and Tahitian Partula tree snail survival after a mass extinction: new genomic insights using museum specimens
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According to this the mutual affinities of the species of the simpleX group might be expressed as follows t (the Ethiopian species are marked with an asterisk):— each other at base; in 4 p2 is half in row. To this latter I find no parallel in any specimen of ferrum-equinum (all races) I have seen, and in 4 skulls only, out of 33, there is a more or less distinct remnant of the interspace between the canine and p4. Of _R7z. deckeni I have seen one skull only; the dentition is as in many specimens of Ph. augur: c and p4 separated, p2 external. f I give the diagram the form of a genealogical tree, only because it is convenient to in On some Bats of the Genus Rhinolophus, with Remarks on their Mutual Affinities, and Descriptions of Twenty-six new Forms.
According to this the mutual affinities of the species of the simpleX group might be expressed as follows t (the Ethiopian species are marked with an asterisk):— each other at base; in 4 p2 is half in row. To this latter I find no parallel in any specimen of ferrum-equinum (all races) I have seen, and in 4 skulls only, out of 33, there is a more or less distinct remnant of the interspace between the canine and p4. Of _R7z. deckeni I have seen one skull only; the dentition is as in many specimens of Ph. augur: c and p4 separated, p2 external. f I give the diagram the form of a genealogical tree, only because it is convenient to
Figure 1c from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Figure 1c - Phylogenetic tree of cytochrome-b sequences of Odocoileini (continuation). This is a strict consensus topology resulting from the Bayesian inference analysis. Nodal support is indicated at each node, except where the relationship received negligible support. Posterior probabilities (from the Bayesian inference analysis) and bootstrap values (from the maximum-likelihood analysis) are indicated before and after the slashes ("/") at branches of interest (i.e., nodal support for fairly shallow relationships within intraspecific haplogroups are omitted). The scale represents substitutions per site. For each terminal, country of origin and next-largest administrative unit (state, department, province, etc.) are provided (when reported by the team that generated them; see detailed voucher and locality information in supplementary file 1 for sequences that we generated). GenBank accession numbers are indicated for each terminal.
Figure 1b from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Figure 1b - Phylogenetic tree of cytochrome-b sequences of Odocoileini (continuation). This is a strict consensus topology resulting from the Bayesian inference analysis. Nodal support is indicated at each node, except where the relationship received negligible support. Posterior probabilities (from the Bayesian inference analysis) and bootstrap values (from the maximum-likelihood analysis) are indicated before and after the slashes ("/") at branches of interest (i.e., nodal support for fairly shallow relationships within intraspecific haplogroups are omitted). The scale represents substitutions per site. For each terminal, country of origin and next-largest administrative unit (state, department, province, etc.) are provided (when reported by the team that generated them; see detailed voucher and locality information in supplementary file 1 for sequences that we generated). GenBank accession numbers are indicated for each terminal.
Figure 3 from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Figure 3 - Hind foot bones of Mazama rufina (A) and Pudu puda (B) sensu Hershkovitz (1982). According to Hershkovitz (1982; see also Brooke 1874, 1878), the union of the cuboideonavicular and external and middle cuneiform tarsal bones into a single bone in Pudu is the only osteological characteristic shared by P. puda and P. mephistophiles that consistently separates them from all other living deer, with exception of the genera Elaphodus and Muntiacus.
Figure 2 from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Figure 2 - Overall morphological appearance of "M." pandora (panels A–C) and that of the genus Odocoileus (panels D–F). Notice the grayish pelage and divergent antlers larger than in other species currently classified in Mazama. "M." pandora, panels A and C individuals kept in captivity at the Parque Zoológico del Bicentenario Animaya, Mérida, Yucatán, Mexico (photographs by Luis A. Escobedo-Morales)—provenance unknown; panel B individual kept in captivity in Tekax, Yucatán, Mexico (photograph by Rosa María González Marín)—provenance unknown. Odocoileus virginianus (see proposals by Molina and Molinari 1999 and Molinari 2007); panels D and E Monteredondo, Parque Nacional Chingaza, ca. 47 km (by road) E Bogota, Cundinamarca, Colombia (photographs by Aideé Vargas-Espinoza and Irene Aconcha, respectively); panel F Laguna de Mucubají, Parque Nacional Sierra Nevada, Mérida, Venezuela (photograph by Rodrigo Díaz Lupanow).
Figure 1a from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Figure 1a - Phylogenetic tree of cytochrome-b sequences of Odocoileini. This is a strict consensus topology resulting from the Bayesian inference analysis. Nodal support is indicated at each node, except where the relationship received negligible support. Posterior probabilities (from the Bayesian inference analysis) and bootstrap values (from the maximum-likelihood analysis) are indicated before and after the slashes ("/") at branches of interest (i.e., nodal support for fairly shallow relationships within intraspecific haplogroups are omitted). The scale represents substitutions per site. For each terminal, country of origin and next-largest administrative unit (state, department, province, etc.) are provided (when reported by the team that generated them; see detailed voucher and locality information in supplementary file 1 for sequences that we generated). GenBank accession numbers are indicated for each terminal.
FIGURE. Phylogenetic tree derived from Bayesian analysis, based on nrITS1-5.8S-ITS2 region data. Posterior probability (PP> 0.95) values from the Bayesian analysis are added at the nodes. The scale bar represents the number of nucleotide changes per site. (T) indicates the type specimen for this species. The new species are in bold. in Four new species of Entoloma (Entolomataceae, Agaricomycetes) subgenera Cyanula and Claudopus from Vietnam and their phylogenetic position
FIGURE. Phylogenetic tree derived from Bayesian analysis, based on nrITS1-5.8S-ITS2 region data. Posterior probability (PP> 0.95) values from the Bayesian analysis are added at the nodes. The scale bar represents the number of nucleotide changes per site. (T) indicates the type specimen for this species. The new species are in bold.
Figure 5. A, topological similarities between gene trees. A in Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life
Figure 5. A, topological similarities between gene trees. A non-metric multidimensional ordination plot, based on the Robinson–Foulds (RF) distance between each pair of genes, is used to visualize the topological similarity among the 208 single gene trees. Pairs of gene trees with similar topologies are closer together in the two-dimensional space. Colours represent RF distances between individual gene trees and the extended majority-rule consensus (MRE) phylogeny. B, identifying optimal subsets of genes with the least topological incongruence. The graph shows the Tree Certainty (TC) values from Salichos & Rokas (2013). Information theory approach using the MRE phylogeny as a reference tree, where higher values represent greater congruency between the gene trees and the MRE tree. The x-axis represents the number of genes sampled, following an iterative procedure beginning with the first two genes in the respective ranking and progressively adding genes according to their order in the list. The five ranking criteria all outperformed random gene orders.
Figure 1 in Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life
Figure 1. Bioinformatic pipeline used for the identification and phylogenetic analysis of 210 single copy genes from Illumina short-read sequence data. The box with the dashed line indicates a pre-processing step that was necessary prior to assembly when sequence quality was low.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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