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Fig. 4 in Deep Instability in the Phylogenetic Backbone of Heteroptera is Only Partly Overcome by Transcriptome-Based Phylogenomics
Fig. 4. Subtree of Pentatomomorpha based on the ML analysis of concatenated nucleotides and subsequent quartet sampling. Clade support is depicted as: QC/QD/QI.
Fig. 2 in Phylogenomics and Fossil Data Inform the Systematics and Geographic Range Evolution of a Diverse Neotropical Ant Lineage
Fig. 2. MCMCTree time-scaled phylogeny (RAxML topology pruned to one tip per species) with historical biogeographic range inferences from the four-node fossil-constrained BioGeoBEARS analysis mapped onto nodes. An asterisk (*) indicates the location of a fossil node calibration.The light purple shading spans the proposed start and end dates (35–32 Mya) of the GAARlandia land bridge linking South America to the Antilles.The light gold shading spans the potential early start date and the complete closure date of the Panamanian land bridge (10–3.5 Mya).Transitions with boxes outlined in red denote differences from the historical geographic range inference without fossil constraints (Supp Fig. S7 [online only]). A, Antilles; C, Central America; S, South America.
Fig. 3. Phylorate plot from a in Phylogenomics and Fossil Data Inform the Systematics and Geographic Range Evolution of a Diverse Neotropical Ant Lineage
Fig. 3. Phylorate plot from a diversification rate-shift analysis in BAMM. A single rate regime is inferred without any rate shifts detected. Diversification rate gradient legend is in units of species/million years.
Fig. 16–18 in Species Paraphyly and Social Parasitism: Phylogenomics, Morphology, and Geography Clarify the Evolution of the Pseudomyrmex elongatulus Group (Hymenoptera:
Fig. 16–18. Pseudomyrmex elongatulus group, workers, full-face dorsal view of head (a) and lateral profile of body (b). 16, P. nimbus, holotype, Costa Rica (CASENT0863541); 17, P. salvini, syntype, Mexico (CASENT0902879); 18, P. veracruzensis, holotype, Mexico (CASENT0863542). Images from AntWeb (www. antweb.org); photographers Phil Ward (16, 18), Zach (Ziv) Lieberman (17).
Fig. 1 in Phylogenomics and Fossil Data Inform the Systematics and Geographic Range Evolution of a Diverse Neotropical Ant Lineage
Fig. 1. Cephalotes topology inferred with RAxML, with species groups inferred in this study annotated with reference to previous species group designations. Numbers along the phylogeny correspond to species groups listed in the inset. Black circles indicate nodes with bootstrap support <95%, with corresponding bootstrap values displayed. Species (and photo credit) imaged, from top: Cephalotes persimilis de Andrade, 1999 (Hymenoptera: Formicidae) (April Nobile), Cephalotes pellans de Andrade, 1999 (Hymenoptera: Formicidae) (April Nobile), Cephalotes pusillus (Klug, 1824) (Hymenoptera: Formicidae) (April Nobile), Cephalotes guayaki de Andrade, 1999 (Hymenoptera: Formicidae) (April Nobile), Cephalotes umbraculatus (Fabricius, 1804) (Hymenoptera: Formicidae) (Shannon Hartman), Cephalotes manni (Kempf, 1951) (Hymenoptera: Formicidae) (Will Ericson), Cephalotes depressus (Klug, 1824) (Hymenoptera: Formicidae) (Wade Lee), Cephalotes setulifer (Emery, 1894) (Hymenoptera: Formicidae) (Wade Lee),Cephalotes kukulcan (Ryan Perry),Cephalotes multispinosus (Norton, 1868) (Hymenoptera: Formicidae) (Wade Lee), Cephalotes rohweri (Wheeler, 1916) (Hymenoptera: Formicidae) (Wade Lee), Cephalotes complanatus (Guérin-Méneville, 1844) (Hymenoptera: Formicidae) (Wade Lee), Cephalotes clypeatus (Fabricius, 1804) (Hymenoptera: Formicidae) (April Nobile), Cephalotes unimaculatus (Smith, 1853) (Hymenoptera: Formicidae) (Wade Lee), Cephalotes opacus Santschi, 1920 (Hymenoptera: Formicidae) (Shannon Hartman). Images from antweb.org under a Creative Commons Attribution License. Accessed August 24, 2020.
Fig. 3 in Species Paraphyly and Social Parasitism: Phylogenomics, Morphology, and Geography Clarify the Evolution of the Pseudomyrmex elongatulus Group (Hymenoptera:
Fig. 3. Bivariate plots of measurements and indices concerned with eye size and petiole shape, in workers of P. apache (n = 17) and P. arcanus (n = 17). (a) PL/ LHT (petiole length/metatibia length) by HW (head width); (b) REL2 (eye length/head width) by PLI (petiole height/petiole length).
Fig. 14 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a
Fig. 14. Wadeura species, petiole lateral views. (A) W. guianensis (CASENT0640150). (B) W. pauli (CASENT0637806). (C) W. holmgreni (CASENT0373370). (D) W. holmgrenita (CASENT0637779). Scale bars are 0.2 mm.
Fig. 6 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a
Fig. 6. Biogeography of the Cryptopone gilva complex within Central America. Chronogram inferred using BEAST2, 300 UCE loci, and a fixed topology (all UCE samples and SWSC-EN partitioning). Only results for the C. gilva complex are shown (see Supp Fig. 6 [online only] for the full results). Numbers on nodes are mean ages in millions of years ago and node bars are 95% Highest Posterior Densities (HPD).The map inset shows the distribution of C. gilva-clade samples within Central America. Colored dots match tip labels of the chronogram. Sites where specimens were identified by morphology alone (no sequencing) are shown as x for C. gilvagrande and a small black dot for C. guatemalensis. Samples of true C. gilva from the United States are not shown in the map.
Fig. 7 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a
Fig. 7. Shape of third abdominal sternite, Cryptopone vs.Wadeura. Cryptopone gilvagrande (CASENT064143), lateral view (A), oblique ventral view (B). Wadeura guianensis (CASENT0640149), lateral view (C), oblique ventral view (D). Scale bars are 0.2 mm.
Fig. 19–26 in Species Paraphyly and Social Parasitism: Phylogenomics, Morphology, and Geography Clarify the Evolution of the Pseudomyrmex elongatulus Group (Hymenoptera:
Fig. 19–26. Pseudomyrmex elongatulus group: distribution maps. 19, P. apache; 20, P. arcanus (circles), P. fasciatus (triangles); 21, P. championi; 22, P. capillatus (triangles), P. cognatus (circles); 23, P. elongatulus (circles), probable introduced populations (stars); 24, P. comitator (square), P. ereptor (triangle), P. exoratus (circles); 25, P. salvini; 26, P. nimbus (circles), P. veracruzensis (triangle).
Fig. 1 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a
Fig. 1. Relationships among Cryptopone lineages based on analysis of 2,232 UCE loci and the SWSC-EN partitioning scheme. Among lineages, the South American clade is separate from the North/Central American clade of Cryptopone and they are not closely related.The constituent species of the South American clade are transferred to the resurrected genus Wadeura. All node support values are at maximum (UFB/SH-aLRT values of 100/100).The photo insets are of Wadeura holmgreni (CASENT0373370, Credit: Michelle Esposito) and C. gilva (CASENT0003325, Credit: April Nobile). The same tree with support values is available in Supp Fig. 1 (online only).
Fig. 5 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a
Fig. 5. Species tree and species delimitation in the Cryptopone gilva complex.The species tree was inferred using SNP data and the Bayesian program SNAPP, with the resulting tree set displayed using DensiTree.The SNAPP densitree shows at least four clearly differentiated species-level lineages. Species delimitation using the programs BPP, SODA, and bPTP, recovered between 4 and 17 species.The results for the UCE samples only are mapped onto the SNAPP densitree result. The connected red bars represent single species that were not monophyletic in the SNAPP phylogeny. The colored boxes and blue species names represent the final species delimitation and taxonomy.
Fig. 2 in First Phylogenomic Assessment of the Amphitropical New World Ant Genus <i>Dorymyrmex</i> (Hymenoptera: Formicidae), a Longstanding Taxonomic Puzzle
Fig. 2. Maximum likelihood (ML) phylogeny of Dorymyrmex inferred in IQ-TREE v2.1.2., with an identical topology to the Bayesian phylogeny (Supp Fig. S3 [online only]) inferred in ExaBayes v1.5.1. Clades are highlighted by color and main nodes and clades are numbered for easy reference in the text. All support values are at maximum (100% bootstrap, posterior probability of 1) except where indicated. For ML analysis, IQ-TREE included three independent runs, each with 1000 ultrafast bootstrap replicates, drawing on the data matrix of 904 partitions determined using the SWSC-EN method and using the best-fit models chosen by IQ-TREE ModelFinder. For Bayesian analysis, ExaBayes included 4 independent runs of 2 chains each, which continued for 1.5 million generations (first 100,000 generations discarded for diagnostics), under the same SWSC-EN partitioning scheme and a GTR+G model (full details in Methods).
Fig. 3. Relationships among samples within the C in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a
Fig. 3. Relationships among samples within the C. gilva complex based on analysis of 2,199 UCE loci and the SWSC-EN partitioning scheme. Four main clades were recovered and these were delimited as species using an integrative approach. Support values are UFB/SH-aLRT with maximum supports (100/100) not shown.The photo inset is of C. guatemalensis (CASENT0646802; Credit: John Longino).The same tree with support values is available in Supp Fig. 2 (online only).
Fig. 1 in First Phylogenomic Assessment of the Amphitropical New World Ant Genus <i>Dorymyrmex</i> (Hymenoptera: Formicidae), a Longstanding Taxonomic Puzzle
Fig. 1. Diagnostic characters of Dorymyrmex workers (Shattuck 1992; Bolton 1994). Angle of propodeum (ppd) with single medial dorsal spine/tooth; psammophore (ps) present; segment 3 of maxillary palp (mxp3) elongate; numerous elongate, curved clypeal setae (cs) extending from the anterior margin of the clypeus forward over the mandibles; apical tooth (at) of mandibles greatly elongate. Specimen: D. richteri, CASENT0249680, phot. Ryan Perry.
Fig. 3 in First Phylogenomic Assessment of the Amphitropical New World Ant Genus <i>Dorymyrmex</i> (Hymenoptera: Formicidae), a Longstanding Taxonomic Puzzle
Fig. 3. Divergence dates of Dorymyrmex and outgroups as estimated in MCMCTree (in PAML v4.9), with a map of specimen collection localities. Estimated node ages are displayed with 95% highest probability density (HPD) distributions.Two soft calibration points were used, indicated with grey HPD distributions: (i) The root node 'L(DF)', uniting Leptomyrmex + (Dorymyrmex + Forelius), was assigned a range of 59–42 Ma, and (ii) the divergence between D. planidens and D. bicolor (Node 1) was assigned a range of 33–13 Ma, both based on previous studies incorporating other dolichoderine genera and fossil calibrations (Ward et al. 2010; Boudinot et al. 2016). For full collection details, please see SuppTable 2 (online only); for all HPD distributions, Supp Fig. S4 (online only); for all node age estimations, Supp Fig. S5 (online only). Figure was created using the R packages MCMCTreeR and phytools (phylo.to.map function).
Fig. 1 in Phylogenomic Delimitation of Morphologically Cryptic Species in Globetrotting Nylanderia (Hymenoptera: Formicidae) Species Complexes
Fig. 1. Maps of sampling localities for all 165 samples used in UCE library preparation for this study. (A) (top) indicates sampling localities of all nonglobetrotting species (i.e., species in their native ranges; red points). |(B) (bottom) indicates sampling localities of all globetrotting species. See Supp Table S1 [online only] for detailed locality information for each sample.
Fig. 5 in Phylogenomic Delimitation of Morphologically Cryptic Species in Globetrotting Nylanderia (Hymenoptera: Formicidae) Species Complexes
Fig. 5. Species delimitation hypotheses of the bourbonica complex. (Left) Cloudogram based on the STACEY analysis using 565 SNPs extracted from the 'bourb27-phased_90p' dataset, with the 'root canal' (blue) summarizing the main features of the tree set. (Right) Summary of species delimitation schemes based on morphospecies sorting and for each analysis performed in this study, with each different colored bar (also labeled with different letters) representing a single species.
Fig. 4 in Phylogenomic Delimitation of Morphologically Cryptic Species in Globetrotting Nylanderia (Hymenoptera: Formicidae) Species Complexes
Fig. 4. Multi-species coalescent phylogenies of the guatemalensis and fulva complexes, generated in ASTRAL-III using 75% complete alignment matrices. (A) (left) represents the unphased MSC analysis and (B) (right) represents the phased MSC analysis. Values on the internal nodes represent local posterior probabilities (LPP), with ≥0.95 indicating strong support and ≤0.75 indicating weak support. Scale bars under phylogenetic trees indicate number of substitutions per site. Photos of N. guatemalensis (Ny097), N. steinheili (Ny101), and N. fulva (Ny191) workers in profile view are to scale and were taken by Brandon Mai.
Fig. 2 in Phylogenomic Delimitation of Morphologically Cryptic Species in Globetrotting Nylanderia (Hymenoptera: Formicidae) Species Complexes
Fig. 2. Circular maximum likelihood phylogeny of Nylanderia generated in IQ-TREE 2 from the 80% complete SWSC-partitioned UCE matrix. Biogeography of terminal taxa is based on inferred native ranges and may not indicate collecting locality for known non-native species. Samples indicated with red text are globetrotting species. Nodal support is provided in SH-aLRT (Shimodaira–Hasegawa approximate likelihood ratio test) values on the left side of the node, and UFBoot (ultrafast bootstrap) values on the right side of the node. For both support values, less than 80% is considered weak support, between 80 and 94.9% is considered moderate support, and greater than or equal to 95% is considered strong support.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.