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Fig. 2 in The roles of niche divergence, dispersal, and geology on the diversification of Neotropical true frogs from the Rana palmipes species group (Amphibia, Anura, Ranidae) during the Great American Biotic Interchange
Fig. 2 Best fit-model of ancestral area estimation for the Rana palmipes species group. a Geographical delimitation of the areas used to estimate ancestral areas and b ancestral areas estimated for the Rana palmipes species group (Ranidae). Arrows represent jump
Fig. 3 in The roles of niche divergence, dispersal, and geology on the diversification of Neotropical true frogs from the Rana palmipes species group (Amphibia, Anura, Ranidae) during the Great American Biotic Interchange
Fig. 3 Age-range correlation (ARC) between node age and D index. a Phylogenetic tree and nodes compared. b Correlation plot between node age and D index, each point corresponding to a specific node in the phylogenetic tree (r.2 = 0.035, P = 0.7, intercept = 0.097, slope = 0.002)
FIGURE 6. M in A revision of Mezoneuron (Leguminosae: Caesalpinioideae) in New Caledonia, with perspectives on vegetation, geology, and conservation
FIGURE 6. M. montrouzieri: 6a, c. leaves (Clark, R.P. 150, 160); 6b. young inflorescence (Clark, R.P. 160); 6d, e. inflorescences (Clark, R.P. 137, 150); 6f. fruit (Clark, R.P. 150)
FIGURE 11 in A revision of Mezoneuron (Leguminosae: Caesalpinioideae) in New Caledonia, with perspectives on vegetation, geology, and conservation
FIGURE 11. Phylogeny of the Mezoneuron containing clade of the informal Caesalpinia Group. Strict consensus of 100,000 equally parsimonious trees based on rps16 plastid sequences. Bootstrap support is shown in bold above branches, and posterior probability values are shown italicised, below the branch (Gagnon et al. 2013). The branches of the tree shown in yellow indicate species found in Australia, and the branch in red is a New Caledonian endemic species. Fruits of species within the New Caledonian species containing clade are shown (except C. nitens, the fruit of which are unknown), and contrasted with that of the winged fruit of Pterolobium within the sister clade. Fruit illustrations by R. Clark
FIGURE 2 in A revision of Mezoneuron (Leguminosae: Caesalpinioideae) in New Caledonia, with perspectives on vegetation, geology, and conservation
FIGURE 2. Illustration of M. montrouzieri, with leaf detail of all species. (a) M. montrouzieri habit, leaf and inflorescence, with detail showing idioblasts on leaf undersurface; flower, side view; flower opened out; petals, inner surface (median, 2 upper laterals, 2 lower laterals); ovary and style; fruit with detail of hairs—drawn from Clark, R.P. 160; (a)(i) M. montrouzieri glabrous ovary; (a)(ii) leaf pinna—drawn from Clark, R.P. 150 (specimen formerly identified as M. deverdiana); (b) pinna of M. baudouinii—drawn from Clark, R.P. 141; (c), (c)(i) pinnae of M. schlechteri (showing variation)–drawn from Clark, R.P., 132, 134; (d) pinna of M. rubiginosum—drawn from McPherson, G. 2089; (e) pinna of M. ouenensis—drawn from Balansa, B. 312. Illustration by Margaret Tebbs.
FIGURE 5 in Morphological variation of Jovibarba heuffelii (Crassulaceae) in the central Balkan Peninsula-The impact of geological, orographical and bioclimatic factors on the differentiation of populations
FIGURE 5. Cluster analysis of 11 populations of J. heuffelii from open grassland communities based on (A) 34 morphological characters, and (B) 19 bioclimatic parameters (C1 and C2 climate type, for details see Table 5.). The asterisk indicates the position of the morphologically most specific populations on both cluster diagrams, while the triangle indicates the position of the bioclimatically most specific populations on both cluster diagrams.
FIGURE 2 in Morphological variation of Jovibarba heuffelii (Crassulaceae) in the central Balkan Peninsula-The impact of geological, orographical and bioclimatic factors on the differentiation of populations
FIGURE 2. Results of the principal component analysis (PCA) for 34 quantitative morphological characters.
FIGURE 3 in Morphological variation of Jovibarba heuffelii (Crassulaceae) in the central Balkan Peninsula-The impact of geological, orographical and bioclimatic factors on the differentiation of populations
FIGURE 3. Results of the canonical discriminant analysis (CDA) based on 34 quantitative morphological characters of 299 individuals of J. heuffelii analyzed: (A) Canonical scores for each individual on the first and second DA axis; (B) Cluster analysis (UPGMA) for populations of J. heuffelii based on Mahalanobis distances. Full triangle, 8-SR: Radan; full square, 2-SR: Gradac; full circle, 5-SR: Nebeske stolice; full rhombus, 3-SR: Suvaja; gray triangle, 4-SR: Studenica; gray square, 6- SR: Treska; black-white circle, 11-SR: Stara planina; gray rhombus, 13-MA: Treskavec; empty triangle, 14-MA: Mavrovo; empty square, 12-BU: Trojanski prolaz; empty rhombus, 7-SR: Basarski kamik; plus, 9-SR: Pljačkovica; star, 10-SR: Besna Kobila; empty circle, 1-RO: Domogled.
FIGURE 4 in Morphological variation of Jovibarba heuffelii (Crassulaceae) in the central Balkan Peninsula-The impact of geological, orographical and bioclimatic factors on the differentiation of populations
FIGURE 4. Results of multiple correspondence analysis (MCA) of qualitative characters based on Mahalanobis distance between the populations of J. heuffelii analyzed.
FIGURE 1 in Morphological variation of Jovibarba heuffelii (Crassulaceae) in the central Balkan Peninsula-The impact of geological, orographical and bioclimatic factors on the differentiation of populations
FIGURE 1. Distribution of the population of J. heuffelii in Serbia, Macedonia, Bulgaria and Romania studied here. (see Table 1 for details.).
FIGURE 6 in Morphological variation of Jovibarba heuffelii (Crassulaceae) in the central Balkan Peninsula-The impact of geological, orographical and bioclimatic factors on the differentiation of populations
FIGURE 6. Results of canonical discriminant analysis (CDA) based on 34 quantitative morphological characters where the type of substrate was used as a categorical variable.
Constraints on global mined geological resource production from limited regional water availability
<p>This depository provides the input dataset and codes/analytical procedures required to assess the sustainable capacity of mineral production considering local water resources as a constraint. The output dataset derived from the study are also provided.</p>
Data from: A passerine bird's evolution corroborates the geologic history of the island of New Guinea
New Guinea is a biologically diverse island, with a unique geologic history and topography that has likely played a role in the evolution of species. Few island-wide studies, however, have examined the phylogeographic history of lowland species. The objective of this study was to examine patterns of phylogeographic variation of a common and widespread New Guinean bird species (Colluricincla megarhyncha). Specifically, we test the mechanisms hypothesized to cause geographic and genetic variation (e.g., vicariance, isolation by distance and founder-effect with dispersal). To accomplish this, we surveyed three regions of the mitochondrial genome and a nuclear intron and assessed differences among 23 of the 30 described subspecies from throughout their range. We found support for eight highly divergent lineages within C. megarhyncha. Genetic lineages were found within continuous lowland habitat or on smaller islands, but all individuals within clades were not necessarily structured by predicted biogeographic barriers. There was some evidence of isolation by distance and potential founder-effects. Mitochondrial DNA sequence divergence among lineages was at a level often observed among different species or even genera of birds (5-11%), suggesting lineages within regions have been isolated for long periods of time. When topographical barriers were associated with divergence patterns, the estimated divergence date for the clade coincided with the estimated time of barrier formation. We also found that dispersal distance and range size are positively correlated across lineages. Evidence from this research suggests that different phylogeographic mechanisms concurrently structure lineages of C. megarhyncha and are not mutually exclusive. These lineages are a result of evolutionary forces acting at different temporal and spatial scales concordant with New Guinea's geological history.
FIG UR E 3 (a) Dated phylogeny of the genus Theodoxus constructed in BEAST based on COI, 16S and ATPα. Node labels denote divergence times in millions of years ago (Ma); node bars indicate the 95% credibility interval around these dates. Small squares at nodes indicate significant support of divergence events found with BEAST and other phylogenetic analyses (see Figures S2.1 and S2.2), as explained through the key. Where MOTUs (A–R) show conspecifics among a number of morphospecies, species names are given in order of their year of description. Morphospecies, incorporated from GenBank, where determination was potentially dubious are highlighted by an asterisk. Clades (C) and subclades (SC) are demarcated by dashed lines between MOTUs. (b) LTT plots indicating the build‐up of lineages in Theodoxus over geological time. Dashed lines surrounding the solid LTT lines indicate the 95% confidence intervals. Where intra‐ and interspecific diversity diverge, interspecific diversity is highlighted in blue and intraspecific diversity in red. Transitions in geological ages are highlighted by narrow grey lines, while the grey bar marks the period of pronounced glacial cycles (last 900 kyr) [Colour figure can be viewed at wileyonlinelibrary.com] in Contributions of biogeographical functions to species accumulation may change over time in refugial regions
FIG UR E 3 (a) Dated phylogeny of the genus Theodoxus constructed in BEAST based on COI, 16S and ATPα. Node labels denote divergence times in millions of years ago (Ma); node bars indicate the 95% credibility interval around these dates. Small squares at nodes indicate significant support of divergence events found with BEAST and other phylogenetic analyses (see Figures S2.1 and S2.2), as explained through the key. Where MOTUs (A–R) show conspecifics among a number of morphospecies, species names are given in order of their year of description. Morphospecies, incorporated from GenBank, where determination was potentially dubious are highlighted by an asterisk. Clades (C) and subclades (SC) are demarcated by dashed lines between MOTUs. (b) LTT plots indicating the build‐up of lineages in Theodoxus over geological time. Dashed lines surrounding the solid LTT lines indicate the 95% confidence intervals. Where intra‐ and interspecific diversity diverge, interspecific diversity is highlighted in blue and intraspecific diversity in red. Transitions in geological ages are highlighted by narrow grey lines, while the grey bar marks the period of pronounced glacial cycles (last 900 kyr) [Colour figure can be viewed at wileyonlinelibrary.com]
FIGURE 6 in Biogeography of Glandulocaudinae (Teleostei: Characiformes: Characidae) revisited: phylogenetic patterns, historical geology and genetic connectivity
FIGURE 6. Spermann correlation between average genetic distances (GTR) and geographic distances showing no statistical support among variables.
FIGURE 5 in Biogeography of Glandulocaudinae (Teleostei: Characiformes: Characidae) revisited: phylogenetic patterns, historical geology and genetic connectivity
FIGURE 5. Bayesian cladogram showing the phylogentic relationships among populations of Mimagoniates microlepis from SE and S Brazil. Orange branches represent samples from rio Iguaçu basin. Blue branches represent streams from the coastal area. Numbers in branches indicates the posterior probabilities of the clusterings for GTR distances, obtained by Monte Carlo Markov Chains. Sampled localities are the follow: PIR= rio Piraquara, Piraquara, state of Paraná; CAE= rio Caerana, Piraquara, state of Paraná; PEQ= rio Pequeno, São José dos Pinhais, state of Paraná; VAR= rio da Várzea, Lapa, state of Paraná; AGU= rio Água Verde, Canoinhas, state of Santa Catarina; MER= rio Mergulhão, Antonina, state of Paraná; RIB= rio Ribeirão, Paranaguá, state of Paraná; MON= rio Mongaguá, Mongaguá, state of São Paulo; ITA= rio Caixa d'Água, Itariri, state of São Paulo; ACA= tributary of rio Acaraí, São Francisco do Sul, state of Santa Catarina. For each locality, 10 specimens were sampled and are indicated by numbers 0-9.
FIGURE 3. A in Biogeography of Glandulocaudinae (Teleostei: Characiformes: Characidae) revisited: phylogenetic patterns, historical geology and genetic connectivity
FIGURE 3. A) Distribution of the Glandulocaudinae and the topographic and tectonic features of SE South America. Double lines corresponds to the main axes of Quaternary tectonics in the area (according to Saadi, 1993; Saadi et al., 2002 and Riccomini et al. 2001) B) The same area showed within the contest of major tectonic provinces of South American Platform. I – South American Platform; II – Patagonian massif; III – Andean orogenic belt; IV – foreland basins; AM = Amazon craton; SL = São Luis craton; SF = São Francisco craton; LA = Luiz Alves craton; RP = Rio de la Plata craton; B = Borborema province; T = Tocantins province; M = Mantiqueira province; DF = Dom Feliciano belt. (Modified from Cordani et al., 2000).
FIGURE 1 in Biogeography of Glandulocaudinae (Teleostei: Characiformes: Characidae) revisited: phylogenetic patterns, historical geology and genetic connectivity
FIGURE 1. Representatives of the Glandulocaudinae and their caudal organs. A) Lophiobrycon weitzmani; paratype, LIRP 4338, photo by R.M.C. Castro; B) Glandulocauda melanogenys, uncatalogued specimens, collected at Estação Biológica de Boracéia, Rio Guaratuba basin, photo by J.C. Nolasco C) Mimagoniates microlepis, photo by R.L. Corte. Arrows indicate the caudal-fin rays 11 and 12. (modified from Menezes & Weitzman, 1990 and Castro et al. 2003).
Comparative genetics of Scyphozoan species reveals the geological history and contemporary processes of the Mediterranean Sea
<p>Jellyfish are attractive biological indicators of shifts in the marine environment, as they have limited mobility and they are highly exposed to the physics and chemistry of the water column. For this study, we focused on three Mediterranean macro-jellyfish - Rhizostoma pulmo, Aurelia sp. and Phyllorhiza punctata. We used comparative genomics and molecular clock (timetree) approaches to estimate occurrences of past geological events and contemporary anthropogenic effects in the Mediterranean Sea. Our results proved that these events have left their mark on the genomes of marine jellyfish. Genomic data of R. pulmo revealed a divergence point between the East and West MS populations that occurred 4.59 Ma, after the Zanclean flood, suggesting that at this time these regions had formed the two distinct ecological environments we know today. We propose that before that time (4.59 Ma), the highly mixed Atlantic and Mediterranean waters led to the wide dispersal of different species in the MS, including the ancestral R. pulmo. At 4.59 Ma, a marine barrier between the Western and Eastern MS formed, indicating the possibility of a dramatic environmental event. The Central and Western MS showed signs of separation processes only at much later stages and at much slower rates. Using comparative genomics of the Aurelia species, we examined contemporary anthropogenic impacts with a focus on migration of scyphozoa across the Suez Canal (Lessepsian migration). Aurelia sp. is among the few scyphozoa we find in both seas. DNA analysis revealed that the Red Sea Aurelia sp. is more related to the Pacific Ocean Aurelia sp. than to the Eastern MS Aurelia species, while the latter is closer to populations from Croatia and Slovenia. Therefore, we conclude that there was no Lessepsian migration of the Aurelia species. Data from P. punctata showed that this species was only recently introduced to the MS, as samples from the MS were closer to Australian populations while they were distant from Mexico and Thailand populations. The recent introduction of P. punctata, apparently, results from anthropogenic transportation activity, such as ballast water discharge, with a known migration vector from Australia to the MS. Our findings demonstrate that jellyfish genomes can be used as a phylogeographic molecular tool to trace back past events across large temporal scales and reveal invasive species introduction due to human activity.</p>
Figure 1. Shells.A–J in Tracking parallel adaptation of shell morphology through geological times in the land snail genus Pupilla (Gastropoda: Stylommatophora: Pupillidae)
Figure 1. Shells.A–J, Pupilla alpicola (A–E, lowland populations"P.pratensis"; F–J, typical mountain populations).K–P, P.loessica. Q–T, P. muscorum. A, M_6001_3_1, Lake Galenbeck (Mecklenburg-Western Pomerania, Germany). B, SMNS-ZI0138340, type locality Dinkelscherben near Augsburg (Bavaria, Germany). C, M_846_1_2, Burgtonna (Thuringia, Germany), fossil from Early
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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.