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Fig. 5 in Morphology and evolutionary significance of the atlas-axis complex in varanopid synapsids
Fig. 5. Atlas−axis complexes of varanopid outgroups used in recent phylogenetic analyses (Botha−Brink and Modesto 2009; Campione and Reisz 2010). A. Atlas−axis complex of Archaeovenator hamiltonensis Reisz and Dilkes, 2003, Virgilian Series, Upper Pennsylvanian, Hamilton Quarry, Greenwood County, Kansas (modified from Reisz and Dilkes 2003). B. Cotylorhynchus romeri Stovall, 1937, Hennessey Formation, Permian, Logan County, Oklahoma (after Stovall et al. 1966). C. Ophiacodon retroversus Romer and Price, 1940, Admiral Formation, Wichita Group, Lower Permian, Wichita County, Texas (after Romer and Price 1940).
Fig. 4 in Morphology and evolutionary significance of the atlas-axis complex in varanopid synapsids
Fig. 4. Axis of an indeterminate mycterosaurine from Richards Spur, Oklahoma, USA, Lower Permian, OMNH 53514, identical to the undescribed mycterosaurine skull, OMNH 73500. This specimen has an anteroposteriorly elongate spine and a flat dorsal margin in lateral view. Specimen in right lateral (A) anterior (B), dorsal (C), left lateral (D), posterior (E), and ventral (F) views.
Fig. 1 in Morphology and evolutionary significance of the atlas-axis complex in varanopid synapsids
Fig. 1. Outline reconstructions of the skull of varanopids. A. Mesenosaurus romeri Efremov, 1938 (modified from Reisz and Berman 2001). B. Varanodon agilis Olson, 1965 (modified from Reisz and Laurin 2004). These taxa show the characteristic differences in the occiput of varanopids. Not to scale.
Fig. 2 in Morphology and evolutionary significance of the atlas-axis complex in varanopid synapsids
Fig. 2. Atlas−axis complex of varanodontines. A. Aerosaurus wellesi Langston and Reisz, 1981, Abo/Cutler Formation, Cutler Group, Upper Pennsylvanian–Lower Permian; El Cobre Canyon, Rio Arriba County, New Mexico, UCMP 40096, in right lateral view, drawing (A1) and reconstruction (A2). B. Varanodon agilis Olson, 1965, Chickasha Formation, Permian, Blaine County, Oklahoma, FMNH UR 986 in left lateral view, drawing (B1) and reconstruction (B2). C. Varanops brevirostris (Williston, 1911), Arroyo Formation, Clear Fork Group, Lower Permian; Indian Creek, Baylor County, Texas, FMNH UR 2423, drawing in left lateral view (C1), reconstruction in ventral view (C2), and reconstruction in left lateral view (C3).
Data from: Phylogenetic sampling affects evolutionary patterns of morphological disparity
<p>Cladistic character matrices are routinely repurposed in analyses of morphological disparity. Unfortunately, the sampling of taxa and characters within such datasets reflects their intended application - to resolve phylogeny, rather than distinguish between phenotypes - resulting in tree shapes that often misrepresent broader taxonomic and morphological diversity. Here we use tree shape as a proxy to explore how sampling can affect perceptions of evolving morphological disparity. Through analyses of simulated and empirical data, we demonstrate that sampling can introduce biases in trait space occupation between clades that are predicted by differences in tree symmetry and branch length distribution. Symmetrical trees with relatively long internal branches predict more expansive patterns of trait space occupation. Conversely, asymmetrical trees with relatively short internal branches predict more compact distributions. Additionally, we find that long external branches predict greater phenotypic divergence by peripheral morphotypes. Taken together, our results caution against the uncritical repurposing of cladistic datasets in disparity analyses. However, they also demonstrate that when morphological diversity is proportionately sampled, differences in tree shape between clades can speak to genuine differences in morphospace occupation. While cladistic datasets may serve as a useful starting point, disparity datasets must attempt to achieve uniformity of lineage sampling across time and topology. Only when all potential sources of bias are accounted for can genuine evolutionary phenomena be distinguished from artefactual signals. It must be accepted that the non-uniformity of the fossil record may preclude representative sampling and, therefore, a faithful characterization of the evolution of morphological disparity.</p>
Novel integrative modeling of molecules and morphology across evolutionary timescales
<p>Evolutionary models account for either population or species-level processes, but usually not both. We introduce a new model, the FBD-MSC, which makes it possible for the first time to integrate both the genealogical and fossilization phenomena, by means of the multispecies coalescent (MSC) and the fossilized birth-death (FBD) processes. Using this model, we reconstruct the phylogeny representing all extant and many fossil Caninae, recovering both the relative and absolute time of speciation events. We quantify known inaccuracy issues with divergence time estimates using the popular strategy of concatenating molecular alignments, and show that the FBD-MSC solves them. Our new integrative method and empirical results advance the paradigm and practice of probabilistic total evidence analyses in evolutionary biology.</p>
Figure 7 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record
Figure 7. Cartoon to depict consensus relationships among Charadriiformes ('shorebirds') along with the holotype specimen of Morsoravis sedile, a new and exceptionally well-preserved fossil from Palaeocene–Lower Eocene deposits in Jutland, Denmark (1–2; G. J. Dyke, M. van Tuinen & D. M. Waterhouse, unpubl. data). The tree is based on various sources; see text for details. Scale bar = 10 mm.
Figure 6 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record
Figure 6. Cartoon to depict consensus relationships among Galliformes ('landfowl') along with some selected fossil material (based on Dyke, 2003b and Dyke et al., 2003): A, hypothesis for the phylogenetic positions of the Lower Eocene (c. 55 Mya) taxa Gallinuloides and Paraortygoides; B, fossil elements of Paraortygoides from the Lower Eocene London Clay Formation of England (see Dyke & Gulas, 2002); C, holotype specimen of Gallinuloides wyomingensis from the Lower Eocene Green River Formation of Wyoming (North America) (Dyke, 2003b). Scale bar = 10 mm.
Figure 5 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record
Figure 5. Cartoon depicting consensus phylogenetic relationships among Anseriformes ('waterfowl') (based on Livezey, 1997) (Presbyornithidae includes the taxa Presbyornis and Teviornis; see text for details) along with a selection of wellpreserved fossil taxa: A, holotype skull of Anatalavis oxfordi in lateral view from the Lower Eocene London Clay Formation (The Natural History Museum, London, Palaeontology Department Collections, BMNH PAL 5922) (see Dyke, 2001b); B, holotype coracoid of BMNH PAL 5922 in dorsal and medial views) (scale bars = 10 mm); C, holotype carpometacarpus of Teviornis gobiensis from the Late Cretaceous Nemegt Formation of Mongolia (Palaeontological Institute of the Russian Academy of Sciences, PIN 4499–1) in dorsal and ventral views (see Kurochkin et al., 2002). Scale bar = 10 mm.
Figure 4 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record
Figure 4. Phylogenetic relationships within Palaeognathae including the well-represented fossil taxa Palaeotis and Lithornis (see text for details): A, new specimen of Lithornis from the Palaeocene-Lower Eocene Fur Formation of Denmark (Dankrae Collections of the Geologisk Museum, Copenhagen, DK 330) encased in cement stone nodule; B, skull of DK 330 acid prepared in oblique lateral view; C, palate of Lithornis in ventral view (ba, basitemporal plate; de, dentary; pa, palatine; pt, pterygoid; vo, vomer); D, the phylogenetic placement of Lithornis and Palaeotis inferred from cladistic analysis of osteological characters (see G. J. Dyke & M. van Tuinen, unpubl. data for details of analysis and matrices).
Figure 3 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record
Figure 3. Seven possible definitions for the 'radiation of birds'. The true radiation of morphology observed in today's birds may have taken place as recently as points 6 or 7. Archaic ornithurines have not been found after the K–T boundary (black arrow). Although predicted from molecular clock analyses (dotted line; see text), little convincing evidence exists for neornithine fossils preceding the K–T boundary. The variation in number of species among traditional neornithine orders indicates that the 'radiation' was not equal across every major clade. Numbers refer to the following major evolutionary bird divergences: 1, diversification of Aves; 2, origin of Neornithes; 3, diversification of Neornithes; 4, origin of Neoaves; 5, origin of most orders (including 'Neoavian comb'); 6, diversification of most orders; 7, diversification of most families.
Figure 1 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record
Figure 1. Summary cladogram to show the phylogenetic relationships at the base of Neornithes (based on Cracraft et al., 2004). Despite advances in the use of genetic data to resolve the phylogenetic relationships of birds, differences between data sets remain and have led to conflict with regard to the interrelationships of clades within Neoaves. The part of this tree to the right-hand side (relationships within Neoaves) has often been referred to as the 'neoavian comb' (Cracraft et al., 2004).
Figure 1 in Evolutionary systematics of the Indian mouse Mus famulus Bonhote, 1898: molecular (DNA/DNA hybridization and 12S rRNA sequences) and morphological evidence
Figure 1. Phylogenetic trees derived from the DNA/DNA hybridization analysis. A and B: Consensus trees resulting from the bootstrap analysis of delta-Tm (A) and delta-mode (B) 12*12 matrices. BP values are indicated when different from 100%. The lengths of the branches correspond to one tree arbitrarily selected among those of the consensus. C and D: Average consensus trees resulting from the weighted jacknife procedure for delta-Tm (C) and delta-mode (D) 13*13 matrices. The thin lines represent nodes that were not present in maximum and minimum consensus trees or that are not supported for all combinations of single deletion analysis. uUnlabelled taxa. The names in bold indicate the differences that can be observed between the two distance estimators (Tm, Mode).
Figure 4 in Evolutionary systematics of the Indian mouse Mus famulus Bonhote, 1898: molecular (DNA/DNA hybridization and 12S rRNA sequences) and morphological evidence
Figure 4. Fifty per cent majority rule consensus of 52 trees derived from the morphological analysis. Each mostparsimonious tree is 54 steps long, and has a Consistency Index of 0.52, a Retention Index of 0.72, and a Rescaled Consistency Index of 0.37. Values given below the branches represent the percentage of trees containing the specified clades.
Figure 3. Synthetic tree derived from the 12S in Evolutionary systematics of the Indian mouse Mus famulus Bonhote, 1898: molecular (DNA/DNA hybridization and 12S rRNA sequences) and morphological evidence
Figure 3. Synthetic tree derived from the 12S rRNA datasets with the inclusion of all substitutions (TV + TI). The thin lines indicate nodes that are not robustly supported by all kinds of analysis. The robustness of the different nodes are indicated as follows: [BP(BPweighted analysis)/BSI (Parsimony)]/[BP(NJ)/Reliability Percentage (ML)].
Figure 3 in Evolutionary relationships of euthyneuran gastropods (Mollusca): a cladistic re-evaluation of morphological characters
Figure 3. Proposition of a phylogeny of Heterobranchia. Here well supported nodes according to present results and character discussions are shown only. Interrupted lines indicate possible phylogenetic relationships. Unambiguous synapomorphies supporting the phylogenetic relationships of euthyneuran taxa are shown by character numbers such as listed in the text. The character numbers in italics are potentially important but require further analysis and discussion (see phylogenetic and taxonomic results).
Figure 1 in Evolutionary relationships of euthyneuran gastropods (Mollusca): a cladistic re-evaluation of morphological characters
Figure 1. Phylogeny of Euthyneura proposed by Salvini-Plawen & Steiner (1996) according to anatomical characters.
Figure 11 in Evolutionary morphology of the coelurosaurian arctometatarsus: descriptive, morphometric and phylogenetic approaches
Figure 11. Bayesian inference-derived phylogeny after matrix of Holtz (2000), showing distribution of the arctometatarsus and observed ligament correlates on theropod metatarsals. Posterior probabilities (in percent) are shown at each node. 'Arcto.' designates a complete arctometatarsus, while '(Arcto.)' indicates a variant of the morphology. Taxa with proximal intermetatarsal striations are highlighted in grey, and double asterisks signify distal ligament correlates. Phylogenetic bracketing (Witmer, 1995) indicates the presence of proximal intermetatarsal ligaments in taxa between Torvosaurus and Tyrannosauridae. This condition is interpreted as preceding the evolution of distal ligaments in the arctometatarsus. Outgroup comparison indicates broader distribution of proximal metatarsus ligaments in the Dinosauria (see text).
Figure 8 in Evolutionary morphology of the coelurosaurian arctometatarsus: descriptive, morphometric and phylogenetic approaches
Figure 8. Morphological features of nonarctometatarsalian MT III. Scale bars = 10 cm. Deinonychus antirrhopus MT III in (A) anterior and (B) proximal views. Carcharodontosaurid MT III in (C) anterior and (D) medial views. For description of features see text.
Figure 9 in Evolutionary morphology of the coelurosaurian arctometatarsus: descriptive, morphometric and phylogenetic approaches
Figure 9. Results of PCA of theropod MT III. Scale bars = 10 cm. A, PCI represents size variation, and PCII indicates proximal gracility. MT III with PCII scores above 0.14 (in bevelled square) are considered arctometatarsalian. Specimens of Albertosaurus sarcophagus (A.s.), Allosaurus fragilis (A.f.), Ingenia yanshini (I.y.), and Rinchenia mongoliensis (R.m.) are figured; note differences in proximal gracility of MT III. B, results of PCA with influence of isometry removed. PCI indicates variation in proximal gracility. Arctometatarsalian forms (bevelled square) group separately from proximally robust MT III, regardless of size. MT III of an ornithomimid (Om.), Deinonychus antirrhopus (D.a.), and Torvosaurus tanneri (T.t.) are depicted to emphasize shape variation. Abbreviations: bt, basal tetanuran Torvosaurus tanneri; c, Carnosauria; ca, Caenagnathidae; co, Coelophysis bauri; dr, Dromaeosauridae; e, Elaphrosaurus bambergi; f, Fukuiraptor kitadaniensis (Carnosauria); h, Herrerasaurus ischigualastensis; nc, NAMAL coelurosaur; om, Ornithomimidae; or, Ornitholestes hermani; ov, Oviraptoridae; se, Segnosaurus ghalbinensis; sn, Sinosauropteryx prima; t, Tyrannosauridae; tr, Troodon formosus.
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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.