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opencc-by-4.0Jun 2018View details →

Videos of evolved robot swarms in a simulated collective construction scenario

The videos show robot swarms designed with population coding in an ARGoS simulation. In the videos 1 to 3 the swarm tries to shelter the pivot point in the middle by dragging cylinders in the gray target area. Viedeo 4 and 5 additionally try to collect or respectively avoid as much light as possible.

Fig. 9 in Quadrupedal dinosaurs did not evolve fully pronated forearms: New evidence from the ulna

Fig. 9. Comparison of variation in the semi-pronated distal antebrachial epiphyses of select facultatively bipedal ornithischian dinosaurs and those with obligatory quadrupedalism. A–C. Sauropelta edwardsorum Ostrom, 1970. A. AMNH 3035. B. AMNH 3035, reversed. C. YPM 5338. D. Texasetes pleurohalio Coombs, 1995 (USNM 337987), radius reversed. E. Panoplosaurus sp. (YPM PU-21178 or 16970), reversed. F, G. Centrosaurus sp. F. Juvenile TMP 94.12.798). G. TMP P81.19.292. H–J, M. Triceratops sp. H. Large ceratopsid (AMNH 5857), reversed. I. AMNH 5880. J. USNM 6530. M. FMNH 12003, reversed. K, L. Triceratops horridusMarsh, 1889. K. USNM 4842, reversed. L. USNM 4842. N, P, Q, T, U. Stegosaurus sp. N. USNM 4929. P. YPM 1854, reversed. Q. YPM 4835. T. YPM uncataloged, field number 9C-14-7J, reversed. U. USNM 7754. O, R, S. Stegosaurus sulcatus Marsh, 1887. O. YPM 4836, reversed. R. USNM 4937, reversed. S. YPM 4836, reversed. V. Gilmoreosaurus mongoliensis (Gilmore, 1933) (AMNH 6551). W. Hypacrosaurus altispinus Brown, 1913 (AMNH 5357), reversed. X–AA. Hadrosaurs. X. TMP 1981.29.2, reversed. Y. TMP 1981.41.13.7. Z. TMP 1980.29.101, reversed. AA. TMP 2005.09.84. AB. Tenontosaurus sp. (AMNH 3043). AC. Camptosaurus sp. (YPM 6794). In this and the following two figures radii and ulnae only touch if they are complementary; all others are oriented across from other elements in the standardized pose. Scale bars 30 mm.

Fig. 10. A in Quadrupedal dinosaurs did not evolve fully pronated forearms: New evidence from the ulna

Fig. 10. A comparison of the semi-pronated distal antebrachial epiphyses of select archosauromorphs and basal archosaurs. A. Archosauromorph, Trilophosaurus buettneri Case, 1928 (TMM 31025-140), reversed. B, F. Phytosaur, Machaeroprospus pristinus (Mehl, 1928) (B, UCMP 121989; F, UCMP 121982). C. Phytosaur, Heterodontosuchus ganei Lucas, 1898 (USNM 2159). D. Aetosaur, Typothorax coccinarum Cope, 1875 (NMMNH L-5806). E. Rauisuchid, Postosuchus alisonae Peyer, Carter, Sues, Novak, and Olsen, 2008 (cast of UNC 15575). G. Aetosaur, Typothorax antiquum Lucas, Heckert, and Hunt, 2002 (NMMNH P-36075). H. Aetosaur, Desmatosuchus haplocerus Cope, 1892 (UCMP 25838). I. Rauisuchid, Postosuchus kirkpatricki Chatterjee, 1985 (TTU P9000). Phytosaur elements oriented after M. pristinus (UCMP 27235), aetosaur elements oriented after T. coccinarum (NMMNH L-5806). Note that nearly all specimens possess torsion of the distal ulnar diaphysis that effectively supinated the distal ulnar articular surface, and that most (except A, B) also exhibit pre-axial elongation of the distal radial epiphysis. Note also, however, that specimen A possesses distorted radial and ulnar diaphyses, so the orientation of the distal ulnar epiphysis may not be vertical as shown. Not to scale.

Fig. 5. A in Quadrupedal dinosaurs did not evolve fully pronated forearms: New evidence from the ulna

Fig. 5. A demonstration of the effects that changes in pronation of the distal radial epiphysis would have on manual orientation in a fully pronated tetrapod (the Virginia opossum Didelphis virginiana Kerr, 1792) that is using parasagittal forelimb kinematics with elbows inturned to the body wall. A. An unpronated forearm and manus, which if possible would point the manual digits posteriorly. B. A semi-pronated forearm and manus, which would point the manual digits laterally, analogous to many semi-pronated archosaurs, such as dinosaurs, that utilized quadrupedalism. C. A normal (for D. virginiana) fully pronated forearm and manus, which points the manual digits anteriorly. This demonstration illustrates why it was traditionally assumed that amniotes that evolve posteriorly directed elbows (i.e., archosaurs, therians and chameleons) would require an additional 90° of forearm pronation past the plesiomorphic 90°, because 180° of pronation is required to keep the wrist and finger joints aligned posteriorly during flexion, and therefore to continue operating in a parasagittal plane. Bonnan's (2003) radial hypothesis states that the radii of quadrupedal dinosaurs pronated to condition C, but the findings of this study show that the ulnae in these dinosaurs experienced an opposing supination that would have kept the planes of the wrist and finger joints wholly in condition in B, albeit with a tubular manus (e.g., Fig. 2E); see text for further discussion. The D. virginiana forelimb elements are from an adult specimen (FMNH 166984).

Fig. 11. A in Quadrupedal dinosaurs did not evolve fully pronated forearms: New evidence from the ulna

Fig. 11. A comparison of semi-pronated forearm views and distal antebrachial epiphyses of select pareiasaurs and synapsids. A. Pareiasaur, Embrithosaurus schwarzi Watson, 1914 (AMNH 2451), reversed. B. Pelycosaur, Dimetrodon loomisi Romer, 1937 (AMNH 21293), reversed, in flexor (B1) and distal (B2) views. C. Dinocephalian, Moschops capensis Broom, 1911 (AMNH 23930), reversed. D. Large dicynodont (AMNH 24096), reversed. E. Dinocephalian, Jonkeria haughtoni Broom, 1929 (AMNH 5577). F. Small dicynodont (uncataloged USNM), reversed. G. Dicynodont, Kannemeyeria simocephalus Weithofer, 1888 (AMNH 5591-93). Note that all specimens examined of the clades above possessed similar amounts of post-axial torsion of the distal ulnar diaphysis. Specimen in A oriented after Bradysaurus baini Seeley, 1892 ([FMNH] UC 1533 and UC 1525); specimens in C, F, and G after small dicynodonts Diictodon cf. grimbeeki (Broom, 1935) (USNM 412381 and USNM 452057). Not to scale.

Fig. 7 in Quadrupedal dinosaurs did not evolve fully pronated forearms: New evidence from the ulna

Fig. 7. Comparison of true standardized views of semi-pronated forearms in a representative sample of extant, nontherian tetrapods, in flexor (A1–F1) and distal (A2–F2) views. A. An allogatorid crocodilian, Alligator mississippiensis (Daudin, 1802) (FMNH 284695). B. A ratite bird, Struthio camelus Linnaeus, 1758 (FMNH 489294). C. A monitor lizard, Varanus komodoensis Ouwens, 1912 (FMNH 22197). D. A salamander, Ambystoma tigrinum (Green, 1825) FMNH 22010). E. A semi-aquatic turtle Apalone spinifera (Lesueur, 1827) (HDW NIU 1086), reversed. F. A more terrestrial turtle, Chrysemys picta (Schnei- der, 1783) (INHS 23894). Reversed specimens in this and following figures refer to elements from the right sides that have been digitally flipped. Note that in E the radius and ulna are fused in the morphology shown, and that the humerus may not be rotated far enough to the left. Note also that, in vivo, articular cartilage and, in some cases wrist bones (e.g., intermedium), may separate the distal radial and ulnar epiphyses beyond what is pictured here for specimens C and F. Not to scale.

Fig. 4. A in Quadrupedal dinosaurs did not evolve fully pronated forearms: New evidence from the ulna

Fig. 4. A demonstration of the effects that changes in pronation of the distal radial epiphysis would have on manual orientation in a semi-pronated tetrapod (Alligator mississippiensis [Daudin, 1802]) that is using sprawling forelimb posture and kinematics. A. A forearm and manus forcibly unpronated (0°) to demonstrate the erroneous starting point of dinosaurian pronation according to Bonnan's (2003) radial hypothesis; this dislocation would orient the manual digits laterally in a sprawling forelimb. B. A naturally (for A. mississippiensis) semi-pronated (90°) forearm and manus, which orients the manual digits anteriorly in a sprawling forelimb. C. A forcibly fully pronated (180°) forearm and manus; this dislocation would orient the manual digits medially in a sprawling forelimb. In this and the following figure the upper row of boxes shows the radius and ulna in proximal view, while the lower row of boxes shows their positions in distal view. The orientations represented serve to demonstrate why stem tetrapods with laterally-directed forelimbs are assumed to have evolved semi-pronated forearm morphology from an unpronated morphology, in order to pre-axially rotate the wrist and finger joints 90° so that these joints could participate in locomotion via posteriorly directed flexion (Hutson 2010). Note also that, as a consequence of being a semi-pronated tetrapod, if an A. mississippiensis inturns its elbows to the body wall, then the manual digits will then point laterally (Vialleton 1924). Bonnan's (2003) radial hypothesis assumes that condition A was the starting point of quadrupedal dinosaur evolution instead of condition B; see text for further discussion. This and all subsequently figured A. mississippiensis forelimb elements are from the left forelimb of a juvenile specimen (FMNH 284695).

Fig. 3 in Quadrupedal dinosaurs did not evolve fully pronated forearms: New evidence from the ulna

Fig. 3. The grades of forearm pronation, the incidence of tubular manual cross sections, and the prevalence of proximal radial migration overlaid onto a cladogram of major tetrapod clades. Note the isolated convergence upon tubular manual cross sections in non-avian saurischian and ornithischian dinosaurs. See Vialleton (1924) for reports of proximal radial migration in tetrapods. See text for a discussion of the reasoning that dinosaurs retained semi-pronation. Cladogram after Gauthier (1986).

Fig. 1 in Quadrupedal dinosaurs did not evolve fully pronated forearms: New evidence from the ulna

Fig. 1. An example of the stylized tetrapod skeleton and terminologies that are traditionally used to demonstrate the grades of forearm pronation. A. The three anatomical planes. B. Simplified tetrapod limbs with uniplanar joint alignments in the transverse plane, showing general limb terminology, including the directions required to pronate/supinate the limb segments, and thereby joint planes of action distal to these segments. Note that, like the hindlimb in this traditional characterization, the three major tetrapod forelimb bones are assumed to plesiomorphically lack any diaphyseal torsion or oblique planes of joint flexion/extension.

Fig. 8 in Quadrupedal dinosaurs did not evolve fully pronated forearms: New evidence from the ulna

Fig. 8. Comparison of standardized views of semi-pronated forearms in ornithischian dinosaurs that utilized quadrupedalism. A. A tracing of a representative neosauropod sauropodomorph, Apatosaurus excelsus (Marsh, 1879) (YPM 1980), in distal view. B. A hadrosaur, Edmontosaurus annectens (Marsh, 1892) (USNM 3814), reversed, in distal view. C. A stegosaur, Stegosaurus sp. (USNM 11659), reversed, in flexor (C1), distal (C2), and pre-axial (C3) views. D. A ceratopsid, Torosaurus cf. latus Marsh, 1891 (high fidelity YPM 57489 cast of MPM VP6841), reversed, in flexor (D1), distal (D2), and pre-axial (D3) views. E. An ankylosaur, Sauropelta edwardsorum Ostrom, 1970 (AMNH 3032), in flexor (E1), distal (E2), and pre-axial (E3) views. Pre-axial views are in full extension and scaled to equal radial length. Distal views not to scale.

Fig. 6 in Quadrupedal dinosaurs did not evolve fully pronated forearms: New evidence from the ulna

Fig. 6. Comparison of true standardized views of forearm pronation in tetrapods that have evolved a fully pronated manus, in flexor (A1–C1) and distal (A2–C2) views. A. A representative metatherian mammal (marsupial), Virginia opossum Didelphis virginiana Kerr, 1792 (FMNH 166984), oriented in a fully pronated orientation. B. A representative chameleon, Furcifer pardalis (Cuvier, 1829) (FMNH 250433). C. A representative anuran (toad), Bufo blombergi Myers and Funkhouser, 1951 (FMNH 210096). Flexor views are scaled to equal radial length; distal views are not to scale. The reader should note that the distal radial epiphyses of small therians and chameleons are often not located at exactly 180° of pronation relative to their ulnae, as it may not be necessary due to a crouching forelimb posture with moderately abducted elbows (Hutson 2010). Note also that, when present, the full pronation of an anuran manus is accomplished via carpal, not radial torsion (see Schwarz 1935: fig. 10), while the distal radial epiphysis remains in full contact with the plesiomorphically semi-pronated articulation (Ecker and Wiedersheim 1896).

opencc-by-nc-4.0Mar 2022View details →

Supplementary data files for Manzano-Marín et. al. 2022 "Co-obligate symbioses have repeatedly evolved across aphids, but partner identity and nutritional contributions vary across lineages"

The data set consists of four parts: 1) "FISH_data":TIF-formatted files or unmerged and merged fluorescent channels of FISH microscopies of Anoecia corni and Sipha maydis embryos. 2) "genome_data": GenBank- and FASTA-formatted files of genome assemblies and annotations for Buchnera and co-obligate symbionts. 3) "pathway_data": Presence/absence tables of genes/pseudogenes coding for enzymes involved in the biosynthesis of essential amino acids and B vitamins in ODS spreadsheets and tab-separated value formats. Also, list of genes and pseudogenes of Buchnera genomes. 4) "phylogeny_data": FASTA-formatted nucleotide alignment files, NEXUS-formatted files used for Bayesian phylogenetic reconstruction, and resulting trees. For Buchnera, manually-curated orthologous groups of proteins are also included as flat text files. In addition, the files to infer gene losses by maximum parsimony in Count are included in the "Buchnera_count" folder.

opencc-by-4.0Nov 2022View details →

Surfactant Transport on Evolving Surfaces - Solutions of Space-Time Trace Finite Element Methods visualized.

Videos of numerical experiments in the article "An accurate and robust Eulerian finite element method for partial differential equations on evolving surfaces" by H. Sass and A. Reusken. Surfactant transport on evolving surfaces with high curvatures and topological singularities is illustrated.

opencc-zeroJan 2023View details →

Aphid male wing polymorphisms are transient and have evolved repeatedly

Polymorphic phenotypes have long been used to examine the maintenance of genetic variation within and between species. Most studies have focused on persistent polymorphisms, which are retained across species boundaries, and their positive effects on speciation rates. Far less is known about the macroevolutionary impacts of more transient polymorphisms, which are also common. Here we investigated male wing polymorphisms in aphids. We estimated the phylogenetic history of wing states across species, along with several other traits that could affect wing evolution. We found that male wing polymorphisms are transient: they are found in only ~4% of extant species but have likely evolved repeatedly across the phylogeny. We reason that the repeated evolution of transient polymorphisms might be facilitated by the existence of the asexual female wing plasticity, which is common across aphids, and would maintain the wing development program even in species with wingless males. We also discovered that male winged morphs and wing polymorphisms are associated with higher speciation rates, and male wingedness correlates positively with host plant alternation and host plant breadth, and that winged morphs and wing polymorphisms may be associated with higher speciation rates. Our results provide new evolutionary insights into this well-studied group and suggest that even transient polymorphisms may impact species diversification rates.

opencc-zeroFeb 2023View details →

Data for: Induction of C4 genes during de-etiolation of Gynandropsis gynandra evolved through changes in cis allowing integration into ancestral C3 gene regulatory networks

C4 photosynthesis has evolved repeatedly and in doing so repurposed existing enzymes to drive a carbon pump that limits the oxygenation reaction of RuBisCO. C4 proteins accumulate to levels matching those of the photosynthetic apparatus, and to allow this gene expression must be modified over evolutionary time. To better understand this rewiring of gene expression we undertook RNA-SEQ and DNaseI-SEQ on de-etiolating seedlings of C4 Gynandropsis gynandra which is evolutionarily proximate to C3 A. thaliana. Changes in chloroplast ultrastructure and C4 gene expression in G. gynandra were coordinated and rapid. C3 and C4 photosynthesis genes showed similar induction patterns, but C4 genes from G. gynandra were more strongly induced than orthologs from A. thaliana. The cistrome of G. gynandra was enriched in TGA, TCP and homeodomain binding sites. Furthermore, in vivo binding data in G. gynandra highlighted TGA and homeodomain as well as light responsive elements such as G- and I-box motifs as being associated with the rapid increase in transcripts derived from C4 genes. Although promoters of PPDK and ASP1 from G. gynandra contained distinct light responsive elements, promoters from both A. thaliana and G. gynandra allowed high expression. Deletion analysis of the Ppa6 gene from G. gynandra showed that regions containing G- and I-boxes were necessary for high expression. The data support a model in which accumulation of transcripts derived from C4 genes in leaves of G. gynandra is enhanced compared with homologs in A. thaliana because a variety of modifications in cis allowed integration into ancestral transcriptional networks.

opencc-zeroMar 2023View details →

Data for: Female foraging strategy co-evolve with sexual harassment intensity in the Trinidadian guppy

Sexual harassment is a widespread evolutionary outcome of sexual conflict over mating rates. Male harassment can impose costs on females, and females often change their behaviors to avoid unwanted attention. In Trinidadian guppies (Poecilia reticulata), females experience two potential sources of male harassment: coercive sneak mating behavior (more harmful, and common in high-predation populations) and courtship displays (less harmful, and common in low-predation populations). Here, we tested whether female foraging strategy co-evolves with decreasing levels of male harassment as guppies colonize low-predation environments. We set up outdoor stream mesocosms with ecologically naïve males and females from either a high- or a low-predation population in a 2x2 design and tested whether populations diverge in female response to male harassment. We found that low-predation males used more courtship and fewer sneak tactics than their natural high-predation ancestors. Male sneak behavior reduced female foraging efficiency, and this effect was stronger for high-predation females. We then tested whether a similar pattern evolved in a population where high-predation guppies were artificially introduced to a low-predation habitat 12 years ago. Unexpectedly, the introduced males had evolved decreased courtship and increased sneak tactics. Here, increased male courtship, but not increased sneak behavior, reduced female foraging efficiency, and this effect existed only in the introduced, low-predation population. Altogether, our results suggest that both male mating behaviors harass females to differing degrees; females evolve foraging behavior in response to divergence in male mating strategies, but populations may differ in strategies of enduring or ignoring unwanted attention.

opencc-by-4.0Jun 2023View details →

The evolving landscape of sea-level rise science from 1990 to 2021

This dataset contains the bibliometric information (e.g., list of authors, keywords, journals, references, etc) for 14,951 sea-level rise related articles published between 1990 and 2021, as retrieved from the Web of Science. This dataset was used to scrutinise the evolution of sea-level rise science: <ul> <li>Khojasteh D, Haghani M, Nicholls R, Moftakhari H, Sadat-Noori M, Mach K, Fagherazzi S, Vafeidis A, Barbier E, Shamsipour A, Glamore W. The evolving landscape of sea-level rise science from 1990 to 2021. Communications Earth & Environment. 2023.</li> </ul> The zip file contains 30 text files where the bibliometric information is stored (each text file comprises the bibliometric information of maximum 500 sea-level rise articles). This dataset also includes an Excel file with data required to reproduce the figures presented in the manuscript.

opencc-by-4.0Sep 2022View details →

Prevalent bee venom genes evolved before the stinger and eusociality

Background: Venoms, which have evolved numerous times in animals, are ideal models of convergent trait evolution. However, detailed genomic studies of toxin-encoding genes exist for only a few animal groups. The hyper-diverse hymenopteran insects are the most speciose venomous clade, but investigation of the origin of their venom genes has been largely neglected. Results: Utilising a combination of genomic and proteo-transcriptomic data, we investigated the origin of 11 toxin genes in 29 published and 3 new hymenopteran genomes and compiled an up-to-date list of prevalent bee venom proteins. Observed patterns indicate that bee venom genes predominantly originate through single gene co-option with gene duplication contributing to subsequent diversification. Conclusions: Most Hymenoptera venom genes are shared by all members of the clade and only melittin and the new venom protein family anthophilin1 appear unique to the bee lineage. Most venom proteins thus predate the mega-radiation of hymenopterans and the evolution of the aculeate stinger.

opencc-zeroJul 2023View details →

Evolving to stay the same: Life history evolution and trade-offs in response to high and low total food

Food drives ecology and evolution, but few studies have directly investigated the impacts of the total amount of food on life history evolution within-species. Among the limited number of available case studies that do directly test total food effects on life history evolution we still lack consensus, partially owing to incompletely described life histories. We explored life history trade-offs across the whole lifecycle, and the consequences for trait and population dynamics, in a marine copepod evolved under high and low total food using an integral projection model (IPM). Populations were subjected to high- and low-food regimes and a common garden experiment after 30 generations of evolution. We then sampled and measured individual vital rates (growth, reproduction, and survival) from hatching until death, which were used to parameterise IPMs. Food regime had a significant but slight effect on life histories, which appeared 'slow' and 'fast' in low-food and high-food lineages respectively. Low-food lineages grew bigger and produced larger offspring to genetically compensate for their environment, but this compensation came with costs; notably shorter lifespans and less chance of producing clutches of eggs. Despite these differences, population ecology and fitness were similar in high- and low-food lineages as anticipated by per-capita rather than total food effects. Consequently, though natural planktonic populations may genetically mitigate the effects of climate-induced food scarcity, there are limits to this compensation and likely unforeseen impacts effects for wider food webs.