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Fig. 1 in A revision of the Asian tree toad complex Rentapia hosii (Anura: Bufonidae) with the description of a new species from Peninsular Malaysia
Fig. 1. Distribution of samples used in this study. Inset photographs depict the distinct phenotypes present within the Rentapia hosii complex [Photo credit: Alexander Haas (Sarawak); Robert F. Inger (Sabah) ©Field Museum of Natural History]. FMNH 248199. Created by Field Museum of Natural History, Amphibian and Reptile Collection and licensed under CC-BY-SA 4.0.
Fig. 44. Tree topology taken from figure 43 in Freshwater Stingrays Of The Green River Formation Of Wyoming (Early Eocene), With The Description Of A New Genus And Species And An Analysis Of Its Phylogenetic Relationships (Chondrichthyes: Myliobatiformes)
Fig. 44. Tree topology taken from figure 43 (strict consensus tree) with ambiguous characters mapped (numbered as in text and matrix in table 5, unambiguous characters in fig. 43). Some of the characters are ambiguous because they are scored as uncertain in Hexatrygon (characters 4 and 21) and in Myliobatis (character 16); these are displayed conservatively on the tree (i.e., it is not simply assumed that they will be found in these taxa). Other characters have more than one equally parsimonious optimization (characters 3, 20, 32, 43), whereas others are scored as uncertain in the Green River stingrays (characters 12, 22, and 44). The optimization chosen in both of these cases is accelerated transformation, favoring reversals over independent gains. Characters denoted with an asterisk (*) are part of multistate transformation series that have unambiguous character states in figure 43.
Fig. 7. Neighbour-joining tree for 422 in A new species of Tritetrabdella (Hirudinida: Hirudiniformes: Haemadipsidae) from northern Indochina
Fig. 7. Neighbour-joining tree for 422 amino acid alignment positions of mitochondrial cytochrome c oxidase subunit I corresponding peptide sequences. Numbers on nodes indicate bootstrap values.
Fig. 6. Bayesian inference tree for 5,179 in A new species of Tritetrabdella (Hirudinida: Hirudiniformes: Haemadipsidae) from northern Indochina
Fig. 6. Bayesian inference tree for 5,179 bp alignment positions of nuclear 18S rRNA and 28S rRNA and mitochondrial cytochrome c oxidase subunit I markers. Numbers on nodes indicate bootstrap values for maximum likelihood and Bayesian posterior probabilities.
FIG. 6 in Three New Species of Musseromys (Muridae, Rodentia), the Endemic Philippine Tree Mouse from Luzon Island
FIG. 6. Cranium (in dorsal, ventral, and lateral views) and mandible of A, Musseromys gulantang, adult male (FMNH 178405, holotype); B, M. inopinatus, adult female (FMNH 193839, holotype); C, M. beneficus, adult female (FMNH 198714, holotype); and D, M. anacuao, adult female (FMNH 209522, holotype).
FIG. 2 in Three New Species of Musseromys (Muridae, Rodentia), the Endemic Philippine Tree Mouse from Luzon Island
FIG. 2. Projection of specimen scores onto the first two axes (A) and the second and third axes (B) of a principal components analysis (table 1) of 18 craniodental variables (log-10 transformed) from seven specimens representing four putative species of Musseromys.
FIG. 1 in Three New Species of Musseromys (Muridae, Rodentia), the Endemic Philippine Tree Mouse from Luzon Island
FIG. 1. Map of Luzon Island, Philippines, showing documented distributions of species and geographic features mentioned in the text, including the type localities of the four species of Musseromys.
FIG, 1. John William Daly (1933–2008) on the upper Río San Juan. This paper is dedicated to John Daly, our late friend and colleague, who helped collect three of the new species here described. In addition to his globally acclaimed discoveries in chemistry and pharmacology, John was an accomplished field herpetologist who contributed importantly to the systematics and natural history of dendrobatoid frogs (see Grant et al., 2006; Myers, 2009). This photograph shows John at age 37, with the upper Río San Juan behind him and branches overhead of a madroño tree (probably Garcinia magnifolia, syn. Rheedia chocoensis, Clusiaceae). When in South America, John was never far from a dendrobatid frog—this time, in the tree above his head, a tiny, undescribed semiarboreal species (also collected and later named "Dendrobates fuguritus" by our colleague Philip Silverstone). Other dendrobatids found nearby included Phyllobates aurotaenia (Boulenger, 1913), which was then being used for poisoning blowgun darts, and also the nontoxic species that we name Silverstoneia dalyi herein. (Photograph by C. W. Myers, 2 km above Playa de Oro, Chocó, February 16, 1971.) in Review of the Frog Genus Silverstoneia, with Descriptions of Five New Species from the Colombian Chocó (Dendrobatidae: Colostethinae)
FIG, 1. John William Daly (1933–2008) on the upper Río San Juan. This paper is dedicated to John Daly, our late friend and colleague, who helped collect three of the new species here described. In addition to his globally acclaimed discoveries in chemistry and pharmacology, John was an accomplished field herpetologist who contributed importantly to the systematics and natural history of dendrobatoid frogs (see Grant et al., 2006; Myers, 2009). This photograph shows John at age 37, with the upper Río San Juan behind him and branches overhead of a madroño tree (probably Garcinia magnifolia, syn. Rheedia chocoensis, Clusiaceae). When in South America, John was never far from a dendrobatid frog—this time, in the tree above his head, a tiny, undescribed semiarboreal species (also collected and later named "Dendrobates fuguritus" by our colleague Philip Silverstone). Other dendrobatids found nearby included Phyllobates aurotaenia (Boulenger, 1913), which was then being used for poisoning blowgun darts, and also the nontoxic species that we name Silverstoneia dalyi herein. (Photograph by C. W. Myers, 2 km above Playa de Oro, Chocó, February 16, 1971.)
FIG. 8. A, The tree resulting from a in Archboldomys (Muridae: Murinae) Reconsidered: A New Genus and Three New Species of Shrew Mice from Luzon Island, Philippines
FIG. 8. A, The tree resulting from a maximum-likelihood analysis of the IRBP data set under the best-fitting model (HKY + Γ4). Numbers at nodes indicate maximum-likelihood (above the line) or parsimony (below the line) bootstrap support. B, The tree resulting from a mixed-model maximum-likelihood analysis of the combined IRBP + cytochrome b data set. Numbers at nodes indicate maximum-likelihood bootstrap support (above the line) or posterior probabilities resulting from a mixed-model Bayesian analysis (below the line). Trees are rooted with Phloeomys cumingi and Batomys granti as outgroups (not shown).
Text-fig. 2. Species of Masillamys considered on the phylogenetic tree of theridomorphs (Vianey-Liaud and Marivaux 2017: fig. 7), within the basal Theridomorpha, before the polyphyletic genus Protadelomys. Position inferred from their dental features (see text). in A Reevaluation Of The Taxonomic Status Of The Rodent Masillamys Tobien, 1954 From Messel (Germany, Late Early To Early Middle Eocene, 48-47 M.Y.)
Text-fig. 2. Species of Masillamys considered on the phylogenetic tree of theridomorphs (Vianey-Liaud and Marivaux 2017: fig. 7), within the basal Theridomorpha, before the polyphyletic genus Protadelomys. Position inferred from their dental features (see text).
Fig. 4. Maximum Parsimony consensus tree for the mitochondrial gene Cytochrome Oxidase I in New species of Moenkhausia Eigenmann, 1903 (Characiformes: Characidae) with comments on the Moenkhausia oligolepis species complex
Fig. 4. Maximum Parsimony consensus tree for the mitochondrial gene Cytochrome Oxidase I. Numbers represent values of 1000 bootstrap replicates.
Figure 7. The strict consensus tree obtained from the parsimony analysis with 35 in Descriptions and phylogenetic relationships of two new genera and four new species of Oligo-Miocene waterfowl (Aves: Anatidae) from Australia
Figure 7. The strict consensus tree obtained from the parsimony analysis with 35 characters ordered. Support values above lines at each node show bootstrap> 50% and Bayesian credibility values> 70% (100% = *). Values below lines are numbers of unambiguous synapomorphies for each node. Clades A, B, and C are referred to in text and Table 4.
Figure 3. Likelihood trees generated from the X in Forest monkeys and Pleistocene refugia: a phylogeographic window onto the disjunct distribution of the Chlorocebus lhoesti species group
Figure 3. Likelihood trees generated from the X- and Y-chromosomal datasets. Bootstrap values of 50 and above (100 replicates, 'fast' stepwise addition) are included throughout the trees. The dashed ovals indicate the consistent recovery of a lhoesti group monophyly. One Chlorocebus solatus sample (CS026) is derived from a female (XX), and therefore is not represented in the Y-chromosomal tree.
Admixture may be extensive among hyperdominant Amazon rainforest tree species
<p><span><span><span><span><span><span><span><span><span><span><span>Admixture is a mechanism by which species of long-lived plants may acquire novel alleles. However, the potential role of admixture in the origin and maintenance of tropical plant diversity is unclear. We ask whether admixture occurs in an ecologically important clade of Eschweilera (Parvifolia clade, Lecythidaceae), which includes some of the most widespread and abundant tree species in Amazonian forests.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>Using target capture sequencing, we conducted a detailed phylogenomic investigation of 33 species in the Parvifolia clade and investigated specific hypotheses of admixture within a robust phylogenetic framework. We assembled target loci from raw sequence reads, conducted tree-based paralog trimming, and estimated species trees using maximum likelihood approaches. In addition, we called single nucleotide polymorphisms for members of the Parvifolia clade and used a Bayesian clustering approach to estimate the ancestry of individuals. We distinguished between population structure and evidence of admixture using a test based on rooted gene trees. We also investigated overlap in geographical range, phenology, and morphology of species, including those we found to admix.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>We found strong evidence of admixture among three ecologically dominant species, E. coriacea, E. wachenheimii and E. parviflora, but a lack of evidence for admixture among other lineages. Accepted species were largely distinguishable from one another, as was geographic structure within species.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>We show that hybridization may play a role in the evolution of the most widespread and ecologically variable Amazonian tree species. While admixture occurs among some species of Eschweilera, it has not led to widespread erosion of most species' genetic or morphological identities. Therefore, current morphological based species circumscriptions appear to provide a useful characterization of the clade's lineage diversity.</span></span></span></span></span></span></span></span></span></span></span></p>
Data for: Using spatial patterns of seeds and saplings to assess the prevalence of heterospecific replacements among cloud forest canopy tree species
<p><b>Questions:</b> To gain insights into the role of species-by-species replacements in cloud forest community structuring, we asked: (1) What are the effects of the spatial distribution of standing individuals on the seed rain, soil seed bank, and sapling density and survival in this cloud forest? and (2) What is the prevalence of conspecific vs<i>.</i> heterospecific replacements in the regeneration of this forest?</p> <p><b>Location:</b> Santo Tomás Teipan, Oaxaca State, southern Mexico.</p> <p><b>Methods:</b> In a 1-ha cloud forest plot we assessed seed rain, seed bank, and sapling density and survival of four canopy tree species (<i>Chiranthodendron pentadactylon</i>, <i>Cornus disciflora</i>,<i> Quercus laurina</i>, <i>Oreopanax</i> <i>xalapensis</i>). All standing individuals of these and other tree species (dbh ≥ 2.5 cm) were mapped. We used neighbourhood models to examine the spatial patterns of the three life cycle stages relative to the spatial distribution of adults. The neighbourhood effect was assessed through the Neighbourhood Index, which integrates information on size (dbh) and distance to adults. Data analysis was based on maximum likelihood and model selection procedures.</p> <p><b>Results:</b> We found large between-species differences regarding the spatial patterns of seeds and saplings. Three species showed evidence for the Janzen-Connell effect operating at the seed (<i>C. pentadactylon</i> and <i>Q. laurina</i>) or sapling (<i>O.</i> <i>xalapensis</i>) stage. We also found support for a critical role of specific microsite factors (i.e., niche differentiation) in the regeneration of two species (<i>C. pentadactylon</i> and <i>C. disciflora</i>).</p> <p><b>Conclusions:</b> Seed and sapling distribution patterns suggest the prevalence of heterospecific replacements, and that both Janzen-Connell and niche differentiation effects contribute to this pattern. Our results largely support the notion that the prevalence of heterospecific replacements among canopy species promotes species coexistence in cloud forest.</p>
Fig. 9. Neighbour-Joining tree using the 658 in A new species of the genus Milesia Latreille (Diptera: Syrphidae) from Crete
Fig. 9. Neighbour-Joining tree using the 658 bp COI sequences. Numbers at nodes indicate the bootstrap support values above 80. Each specimen name has the morphological identification, the country of origin and the GenBank Accession Number.
FIG. 60 in An annotated checklist of the tree species of French Guiana, including vernacular nomenclature
FIG. 60. — Vochysiaceae: A, Qualea amapaensis Balslev & S.A.Mori (M.-F. Prévost & D. Sabatier 2755); B, Qualea tricolor Benoist (D. Sabatier 6341); C, Qualea moriboomiorum Marc.-Berti; D, Vochysia densiflora Spruce ex Warm.; E, Vochysia sabatieri Marc.-Berti (D. Sabatier & M.-F. Prévost 4850). © D. Sabatier/IRD.
FIG. 59 in An annotated checklist of the tree species of French Guiana, including vernacular nomenclature
FIG. 59. — Verbenaceae:A, Citharexylum macrophyllum Poir. (M.-F. Prévost 1404). Violaceae: B, C, Leonia glycycarpa Ruiz & Pav. (D. Sabatier 3502); D, Paypayrola hulkiana Pulle (M.-F. Prévost et al. 4587); E, Rinorea falcata (Mart. ex Eichler) Kuntze (D. Sabatier 5573). A, C, © M.-F. Prévost/IRD; B, D, E, © D. Sabatier/IRD.
FIG. 58 in An annotated checklist of the tree species of French Guiana, including vernacular nomenclature
FIG. 58. — Urticaceae: A, Cecropia granvilleana C.C.Berg (D. Sabatier & J.-F. Molino 5016); B, Cecropia silvae C.C.Berg (D. Sabatier & J.-F. Molino 5137); C, Pourouma saulensis C.C.Berg & Kooy (D. Sabatier & M.-F. Prévost 4846); D, Pourouma tomentosa subsp. maroniensis (Benoist) C.C.Berg & Heusden. © D. Sabatier/IRD.
FIG. 57 in An annotated checklist of the tree species of French Guiana, including vernacular nomenclature
FIG. 57. — Styracaceae: A, Styrax pallidus A.DC. Symplocaceae: B, Symplocos martinicensis Jacq. Theaceae: C, Gordonia fruticosa (Schrad.) H.Keng. Ulmaceae: D, Ampelocera edentula Kuhlm. (D. Sabatier & J.-F. Molino 5641). A, B, D, © D. Sabatier/IRD; C, © C. Girod.
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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.