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opencc-by-4.0Jan 1990View details →

Fig. 2 in TWO NEW SPECIES OF MIMAGONIA TES (TELEOSTEI: CHARACIDAE: GLANDULOCAUDINAE), THEIR PHYLOGENY AND BIOGEOGRAPHY AND A KEY TO THE GLANDULOCAUDIN FISHES OF BRAZIL AND PARAGUAY

Fig. 2. Mimagoniates barberi. unstained central basal region of caudal fin adjacent to caudal peduncle of a preserved adult male, lateral view. left side, anterior at left. SL 32.7 mm. UMMZ 205420, Paraguay, rio Aguarymi, tributary to rio Paraguay, San Pedro. Illustrates external features of a caudal gland without complex pump chamber. Darkly pigmented glandular groove between principal rays ll and 12 indicated by arrow. Modified dorsal caudal-fin lobe scales, although present, are transparent and not visible.

opencc-by-4.0Jan 1990View details →

Fig. 1 in TWO NEW SPECIES OF MIMAGONIA TES (TELEOSTEI: CHARACIDAE: GLANDULOCAUDINAE), THEIR PHYLOGENY AND BIOGEOGRAPHY AND A KEY TO THE GLANDULOCAUDIN FISHES OF BRAZIL AND PARAGUAY

Fig. 1. Diagram of tentative phylogenetic relationships of the species of the Glandulocaudini based on an analysis of synapomorphies found in the caudal skeleton of males. Filled in squares = apomorphies and empty squares - plesiomorphies at the levels indicated.

opencc-by-4.0Apr 2024View details →

Naturalis barcode-constrained-phylogeny: pipeline output files used in internship graduate paper

Data used for thesis written by Naomi van Es, bioinformatics student at University of Applied Sciences Leiden. Pipeline was contributed to during internship at Naturalis Biodiversity Centre, supervised by Dr Rutger A. Vos. Include all content of '/data' directory after running the pipeline barcode-constrained-phylogeny, branch <a href="https://github.com/naturalis/barcode-constrained-phylogeny/tree/researchpaper_version">researchpaper_version</a>. Configuration file was set to only use data from taxonomic order Primates and DNA marker COI-5P. Output files include custom database, alignments, constraint trees and subtrees of BOLD barcode data. Example taxonomic family in thesis results is Lemuridae.

opencc-zeroApr 2024View details →

Phylogeny and divergence time estimation of Io moths and relatives (Lepidoptera: Saturniidae: Automeris)

The saturniid moth genus Automeris includes 145 described species. Their geographic distribution ranges from the eastern half of North America to as far south as Peru. Automeris moths are cryptically colored and their forewings resemble dead leaves, with conspicuously colored, elaborate eyespots hidden on their hindwings. Despite their charismatic nature, the evolutionary history and relationships within Automeris and between closely related genera, remain poorly understood. In this study, we present the most comprehensive phylogeny of Automeris to date, including 80 of the 145 described species. We also incorporate two morphologically similar hemileucine genera, Pseudautomeris and Leucanella, as well as a morphologically distinct genus, Molippa. We obtained DNA data from both dry-pinned and ethanol-stored museum specimens and conducted Anchored Hybrid Enrichment (AHE) sequencing to reconstruct a high-quality dataset for phylogenetic analysis. The resulting phylogeny supports Automeris as a paraphyletic genus, with Leucanella and Pseudautomeris nested within, with the most recent common ancestor dating back to 21 mya. This study lays the foundation for future research on various aspects of Automeris biology, including anti-predator defense mechanisms, ecological adaptations, geographical distribution patterns, and potential drivers of speciation.

FIGURE 14 in Phylogeny of iguanodontian dinosaurs and the evolution of quadrupedality

FIGURE 14. Time-calibrated Bayesian MCC tree, showing character state changes for osteological correlates of quadrupedality. Light red, femur longer than tibia; yellow, proximal ulnar flange present; green, tab-shaped fourth trochanter; blue, rounded manual unguals. Note that some posterior probabilities and labels for Ankylopollexia and Styracosterna have been removed for clarity; the groups are still indicated by closed circles at their respective nodes.

FIGURE 10 in Phylogeny of iguanodontian dinosaurs and the evolution of quadrupedality

FIGURE 10. Strict consensus of 3,086 MPTs produced from a parsimony analysis excluding the 80 novel postcranial characters used in this analysis. Styracosterna is composed of a large polytomy, and smaller polytomies are found outside Rhabdodontoidea and Thescelosauridae.

FIGURE 11 in Phylogeny of iguanodontian dinosaurs and the evolution of quadrupedality

FIGURE 11. Silhouettes showing the radius, ulna and manus of A, Iguanodon (from RBINS 1534 and 1558) and B, Lurdusaurus (from MNHN.F.GDF 1700).

FIGURE 13 in Phylogeny of iguanodontian dinosaurs and the evolution of quadrupedality

FIGURE 13. Dentary teeth in labial view of A, Thescelosaurus infernalis (SDSM 7210); B, Rhabdodon (MC.CY.QR1); C, Tenontosaurus tilletti (AMNH 3034); and D, Owenodon (NHMUK R2998). Abbreviations: c, cingulum; pr, primary ridge; sr, secondary ridge. Scale bars equal 5 mm.

FIGURE 8 in Phylogeny of iguanodontian dinosaurs and the evolution of quadrupedality

FIGURE 8. Maximum Clade Credibility tree produced by Bayesian analysis. Posterior probabilities are shown to the left of their nodes. The geologic timescale is shown across the top. Tips represent the average age found for each OTU across all sampled trees.

FIGURE 7 in Phylogeny of iguanodontian dinosaurs and the evolution of quadrupedality

FIGURE 7. Time scaled parsimony tree, showing assigned age ranges and broad-scale geographic data. Jackknife values above 20 (with 10% chance of character removal) are shown above and to the left of their respective nodes. Bremer supports above one are shown below and to the left of their respective nodes, and bolded.

FIGURE 12 in Phylogeny of iguanodontian dinosaurs and the evolution of quadrupedality

FIGURE 12. Sternals of A, Tenontosaurus (YPM 5456); B, the Kirkwood taxon (AM 6067); C, Macrogryphosaurus (MUCPv 321); D, Hypselospinus (NHMUK R1885). A and B are right sternals in ventrolateral view, C and D are coosified left and right sternals, C in caudodorsal view and D in cranioventral view, including the midline intersternal ossification. Abbreviations: cl, caudolateral process; cm, caudomedial process; iso, intersternal ossification. Scale bar equals 10 cm in A, C, and D, and 1 cm in B.

FIGURE 9 in Phylogeny of iguanodontian dinosaurs and the evolution of quadrupedality

FIGURE 9. Ancestral Area Reconstruction on MCC tree from Bayesian analysis. Squares at tips show taxon ranges, pie charts at nodes show likelihoods of ancestral ranges. Key shows colors corresponding to modern continents; blended colors (e.g., the orange wedge in the node leading to Leaellynasaura and Gasparinisaura) indicate an ancestral range in both descendant ranges.

FIGURE 6 in Phylogeny of iguanodontian dinosaurs and the evolution of quadrupedality

FIGURE 6. Parsimony (left) and Bayesian (right) trees plotted together. Strict consensus of 84 MPTs after pruning Oryctodromeus, Atlascopscosaurus, Planicoxa, Cumnoria, Cedrorestes, and NHMUK R28860. Jackknife values above 20 (with 10% chance of character removal) are shown above and to the left of their respective nodes. Bremer supports above one are shown below and to the left of their respective nodes, and bolded. CI=0.272, RI=0.634. Maximum clade credibility tree produced by Bayesian analysis showing posterior probabilities below and to the right of their respective node.

FIGURE 5 in Phylogeny of iguanodontian dinosaurs and the evolution of quadrupedality

FIGURE 5. Phylogeny of Boyd (2012), cropped to relevant portion with collapsed clades. Note that Thescelosauridae, composed of many taxa previously regarded as basally branching ornithopods, lies outside of both Ornithopoda and Cerapoda. Strict consensus of 36 MPTs.

FIGURE 3 in Phylogeny of iguanodontian dinosaurs and the evolution of quadrupedality

FIGURE 3. Iguanodontian phylogeny as presented by McDonald (2012a). This is an Adam's consensus tree of 24,460 MPTs, with terminology for higher taxa following Sereno (2005).

FIGURE 2 in Phylogeny of iguanodontian dinosaurs and the evolution of quadrupedality

FIGURE 2. Early cladistic analyses of ornithischian phylogeny found by (A) Norman, 1984, and (B) Sereno, 1984. H1 and H2 indicate alternate positions for Heterodontosauridae, and P1 and P2 indicate alternate positions for Pachycephalosauridae.

FIGURE 1 in Phylogeny of iguanodontian dinosaurs and the evolution of quadrupedality

FIGURE 1. Simplified phylogeny showing the current understanding of ornithischian relationships, based on Butler et al. (2008). Silhouettes from Phylopic.org. Daspletosaurus by Tasman Dixon, Brachiosaurus by Michael P. Taylor, Lambeosaurus by Craig Dylke (all public domain). Triceratops by Raven Amos, Heterodontosaurus by Jaime Headden, Stegosaurus by Andrew A. Farke, Hypsilophodon by Mathew Wedel (https://creativecommons.org/licenses/by/3.0/). Stegoceras by Caleb M. Brown (http://creativecommons.org/licenses/by-sa/3.0/).

opencc-zeroApr 2024View details →

Data from: defining the pyro-thermal niche: do seed traits, ecosystem type and phylogeny influence thermal thresholds in seeds with physical dormancy

Seeds are a key pathway for plant population recovery following disturbance. To prevent germination during unsuitable conditions, most species produce dormant seeds. In fire-prone regions, physical dormancy (PY) enables seeds to germinate after fire. The thermal niche, incorporating seed dormancy and mortality temperature responses, has not been characterised for PY seeds from fire prone environments. We aimed to assess variation in thermal thresholds between species with PY seeds and if the pyro-thermal niche is aligned with seed mass, ecosystem type or phylogenetic relatedness. We collected post heat-shock germination data for 58 Australian species that produce PY seeds. We applied species-specific thermal performance curves to define three critical thresholds (DRT50, dormancy release temperature; Topt, optimum dormancy release temperature and LT50, lethal temperature), defining the pyro-thermal niche. Each species was assigned a mean seed weight and ecosystem type. We constructed a phylogeny to account for species relatedness and calculated phylogenetic signal (h2) for LT50, Topt, and DRT50. Seeds of Pomaderris (Rhamnaceae) had the highest Topt and LT50, and Pomaderris bodalla having the highest DRT50 of 101.3°C. Seeds from species within this family exhibited higher temperature thresholds than those from Fabaceae. Seed mass was only influential in explaining LT50 variation.

opencc-zeroMay 2024View details →

First global phylogeny of whip spiders (Amblypygi)

Asymmetrical rates of cladogenesis and extinction abound in the Tree of Life, resulting in numerous minute clades that are dwarfed by larger sister groups. Such taxa are commonly regarded as phylogenetic relicts or "living fossils" when they exhibit an ancient first appearance in the fossil record and prolonged external morphological stasis, particularly in comparison to their more diversified sister groups. Due to their special status, various phylogenetic relicts tend to be well-studied and prioritized for conservation. A notable exception to this trend is found within Amblypygi ("whip spiders"), a visually striking order of functionally hexapodous arachnids that are notable for their antenniform first walking leg pair (the eponymous "whips"). Paleoamblypygi, the putative sister group to the remaining Amblypygi, is known from Late Carboniferous and Eocene deposits but is survived by a single living species, Paracharon caecus Hansen, 1921, that was last collected in 1899. Due to the absence of genomic sequence-grade tissue for this vital taxon, there is no global molecular phylogeny for Amblypygi to date, nor a fossil-calibrated estimation of divergences within the group. Here, we report several individuals of a previously unknown species of Paleoamblypygi from a cave site in Colombia. Capitalizing upon this discovery, we generated the first molecular phylogeny of Amblypygi, integrating ultraconserved element sequencing with legacy Sanger datasets and including described extant genera. To quantify the impact of sampling Paleoamblypygi on divergence time estimation, we performed in silico experiments with pruning of Paracharon. We demonstrate that the omission of relicts has a significant impact on the accuracy of node dating approaches that outweighs the impact of excluding ingroup fossils. Our results underscore the imperative for biodiversity discovery efforts in elucidating the phylogenetic relationships of "dark taxa", and especially phylogenetic relicts in tropical and subtropical habitats. The lack of reciprocal monophyly for Charontidae and Charinidae leads us to subsume them into one family, Charontidae (new synonymy).