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Experimental Results for the study "A Modular Hybridization of Particle Swarm Optimization and Differential Evolution"
<p>This repository contains the experiment results and R scripts to analyze the data for the study "A Modular Hybridization of Particle Swarm Optimization andDifferential Evolution", which is accepted in <em>The Genetic and Evolutionary Computation Conference</em> (GECCO) '20 conference: </p> <p>Rick Boks, Hao Wang, and Thomas Bäck. 2020. A Modular Hybridization of Particle Swarm Optimization and Differential Evolution. In <em>Genetic and Evolutionary Computation Conference Companion (GECCO ’20 Companion), July 8–12, 2020, Cancún, Mexico. </em>ACM, New York, NY, USA, 8 pages. <a href="http://https: //doi.org/10.1145/3377929.3398123">https: //doi.org/10.1145/3377929.3398123</a></p> <p>Bibtex:</p> <pre><code class="language-markdown">@inproceedings{BoksWB20, author = {Rick Boks and Hao Wang and Thomas B\"ack}, title = {{A Modular Hybridization of Particle Swarm Optimization and Differential Evolution}}, booktitle = {Proceedings of the Genetic and Evolutionary Computation Conference, {GECCO} 2020, Canc\'un, Mexico, July 8-12, 2020}, publisher = {{ACM}}, year = {2020}, url = {https://doi.org/10.1145/3321707.3321816}, doi = {doi.org/10.1145/3377929.3398123, }</code></pre> <p><strong>Data description:</strong> we benchmarked <strong>800 </strong>different<strong> </strong>hybridizations of the Particle Swarm Optimization (PSO) and Differential Evolution (DE) algorithms on a well-known continuous black-box problem set called <a href="https://coco.gforge.inria.fr/">COCO/BBOB</a>, which consists of 24 test functions. 30 independent runs are conducted for each algorithm on each problem.</p> <ul> <li>'ERT.csv': a data frame with columns DIM (5D or 20D), funcId (F1-24), algId (algorithm names), target (<span class="math-tex">\(10^{\{-8,-7, \ldots, 1\}}\)</span>), ERT (expected running time), and sd (standard deviation).</li> <li>'raw-data.csv': the running time recorded in each independent run. </li> <li>'analysis.R': the R script that generates ERT tables in the paper.</li> <li>'ecdf.R': the R script that renders the ECDF (empirical cumulative distribution function) plots in the paper.</li> </ul>
Hybrid evolution repeats itself across environmental contexts in Texas sunflowers (Helianthus)
<p>To what extent is evolution repeatable? Little is known about whether the evolution of hybrids is more (or less) repeatable than non-hybrids. We used field experimental evolution in annual sunflowers (<em>Helianthus</em>) in Texas to ask the extent to which hybrid evolution is repeatable across environments compared to non-hybrid controls. We created hybrids between <em>Helianthus annuus</em> (L.) and <em>H. debilis</em> (Nutt.) and grew plots of both hybrids and non-hybrid controls through eight generations at three sites in Texas. We collected seeds from each generation and grew each generation × treatment × home site combination at two final common gardens. We estimated the strength and direction of evolution in terms of fitness and 24 traits, tested for repeated versus non-repeated evolution, and assessed overall phenotypic evolution across lineages and in relation to a locally adapted phenotype. Hybrids consistently evolved higher fitness over time while controls did not, though trait evolution varied in strength across home sites. Repeated evolution was more evident in hybrids versus non-hybrid controls, and hybrid evolution was often in the direction of the locally adapted phenotype. Our findings have implications for both the nature of repeatability in evolution and the contribution of hybridization to evolution across environmental contexts.</p>
Swordtail fish hybrids reveal that genome evolution is surprisingly predictable after initial hybridization
<p>Over the past two decades, biologists have come to appreciate that hybridization, or genetic exchange between distinct lineages, is remarkably common – not just in particular lineages but in taxonomic groups across the tree of life. As a result, the genomes of many modern species harbor regions inherited from related species. This observation has raised fundamental questions about the degree to which the genomic outcomes of hybridization are repeatable and the degree to which natural selection drives such repeatability. However, a lack of appropriate systems to answer these questions has limited empirical progress in this area. Here, we leverage independently formed hybrid populations between the swordtail fish <em>Xiphophorus birchmanni </em>and <em>X. cortezi </em>to address this fundamental question. We find that local ancestry in one hybrid population is remarkably predictive of local ancestry in another, demographically independent hybrid population. Applying newly developed methods, we can attribute much of this repeatability to strong selection in the earliest generations after initial hybridization. We complement these analyses with time-series data that demonstrates that ancestry at regions under selection has remained stable over the past ~40 generations of evolution. Finally, we compare our results to the well-studied <em>X. birchmanni×X. malinche </em>hybrid populations and conclude that deeper evolutionary divergence has resulted in stronger selection and higher repeatability in patterns of local ancestry in hybrids between <em>X. birchmanni </em>and <em>X. cortezi</em>.</p>
Spectral evolution of hot hybrid white dwarfs I. Spectral analysis
<p>Hydrogen-rich white dwarfs (WDs) comprise the majority of the WD population, but are only rarely found at the very hot end of the WD cooling sequence. A small subgroup that exhibits both hydrogen and helium lines in their spectra, the so-called hybrid (or DAO) WDs, represents the majority of hydrogen-rich WDs at effective temperatures <em>T</em>eff<em> ≈ </em>100 kK. We aim to understand the spectral evolution of hot hybrid WDs. Although small in number, they represent an evolutionary phase for most (≈ 75 %) WDs. We conducted a nonlocal thermodynamic equilibrium (NLTE) analysis with fully metal line blanketed model atmospheres for the ultraviolet (UV) and optical spectra of a sample of 19 DA and 13 DAO WDs with <em>Teff </em>> 60 kK. The UV spectra allow us to precisely measure the temperature through model fits to metal lines in different ionization stages, which enables us to place the WDs accurately on the cooling sequence. Here we present model fits to the UV and optical spectra in our sample. Aditionally, the <em>T</em>eff, log <em>g</em>, and abundance values of our sample objectss are compared to previous studies. </p>
Figure 11 in Hybridization in the evolution of animal form and life-cycle
Figure 11. Four mid-Cambrian species from the Burgess Shale of British Columbia. A, Laggania cambria (= Anomalocaris nathorsti), ventral; B, Anomalocaris canadensis, ventral; C, Amiskwia sagittiformis; D, Nectocaris pteryx. Scale bar = ∼200 mm (A, B), ∼5 mm (C, D). [A, B reproduced with permission from S M Gonn III (from 'The Anomalocarid Bauplan' http://www.geocities.com/goniagnostus/background3.html); C, D, from Marianne Collins in Gould, 1989.]
Figure 9 in Hybridization in the evolution of animal form and life-cycle
Figure 9. Reticulate phylogeny of adults and larvae of extant hemichordates and echinoderms, showing probable sequence of events. Time (horizontal) not to scale. Ord/Sil, Ordovician/Silurian boundary; pres, present; thick black lines, adults; thin black lines, larvae; grey arrows, larval transfers.
Figure 7. Two Cambrian trilobites. A–D in Hybridization in the evolution of animal form and life-cycle
Figure 7. Two Cambrian trilobites. A–D, stages in the development of Sao hirsute: A, protaspis; B–D, early segmented stages. E, adult Agnostus pisiformis. Scale bar = ∼1 mm (A–D from Borradaile et al., 1935; E redrawn after Fortey, 2000.)
Figure 6 in Hybridization in the evolution of animal form and life-cycle
Figure 6. Stages in the development of the branchiopod crustacean Leptestheria syriaca, to different magnifications. (From Gurney, 1942; as Estheria.)
Figure 5. A in Hybridization in the evolution of animal form and life-cycle
Figure 5. A, nauplius of Penaeus sp. (recent Crustacea: Penaeidae). B, C, Martinssonia elongata (upper Cambrian): B, paranauplius II (left first appendage omitted); C, oldest known stage. Scale bar = ∼0.1 mm (A after Gurney, 1942; B, C adapted from Müller & Walossek, 1986b.)
Figure 4 in Hybridization in the evolution of animal form and life-cycle
Figure 4. Enteropneust and pterobranch hemichordates and a planctosphere. A–E, enteropneusta: A, adult Dolichoglossus, B, tornaria larva; C–E, stages in metamorphosis; F, G, Pterobranchia: F, adult Rhabdopleara; G, pterobranch larva. H, Planctosphaeromorpha: adult Planctoshaera pelagica. Scale bar = ∼10 mm (A), ∼1 mm (B–E, G), ∼5 mm (F, H). (Adapted from Borradaile et al., 1935; Hyman, 1959.)
Figure 3. Bryozoan larvae and adult. A in Hybridization in the evolution of animal form and life-cycle
Figure 3. Bryozoan larvae and adult. A, trochophore larva of Alcyonidium; B, cyphonautes larva of Membranipora; C, adult zooid of Electra. (After Williamson, 1992.)
Figure 2 in Hybridization in the evolution of animal form and life-cycle
Figure 2. Examples of overlapping metamorphosis. A, Luidia sarsi (Echinodermata): swimming bipinnaria larva and detached juvenile starfish; B, Polygordius sp. (Annelida): two stages showing segmented polychaete worm protruding from swimming trochophore larva; C, Cerebratulus sp. (Nemertea): juvenile nemertean worm within swimming pilidium larva; D, Doliolum mulleri (Urochordata): juvenile doliolid tunicate within cuticle of tadpole larva. Juvenile stippled in each case. (A, C adapted from Williamson, 1992; B, D adapted from Borradaile et al., 1935.)
Figure 1 in Hybridization in the evolution of animal form and life-cycle
Figure 1. Hydroid and medusae of Hebella (Hydrozoa: Thecata). A, gonophores of H. parasitica; B, male and female medusae of H. parasitica; C, medusa of H. furax. (A, B adapted from Boero, 1980; C adapted from Migotto & de Andrade, 2000.)
Figure 10. A in Hybridization in the evolution of animal form and life-cycle
Figure 10. A phylogram of some metazoans, based on 18S rRNA. (From Williamson, 2002; after Michael Syvanen, unpubl. data)
Figure 8 in Hybridization in the evolution of animal form and life-cycle
Figure 8. Larvae of an enteropneust hemichordate and echinoderms. A, tornaria larva of an acorn-worm (Enteropneusta); B, auricularia larva of a sea-cucumber (Holothuromorpha); C, bipinnaria larva of a starfish (Asteromorpha); D, echinopluteus larva of a sea-urchin (Echinomorpha); E, ophiopluteus larva of a brittle-star (Ophiuromorpha); F, doliolaria larva of a sea-lily (Crinomorpha). Scale bar = ∼1 mm (Adapted from Williamson, 1992, 2003.)
Swordtail fish hybrids reveal that genome evolution is surprisingly predictable after initial hybridization
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Hybrid evolution repeats itself across environmental contexts in Texas sunflowers (Helianthus)
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Data from: Selfish evolution of cytonuclear hybrid incompatibility in Mimulus
Intraspecific coevolution between selfish elements and suppressors may promote interspecific hybrid incompatibility, but evidence of this process is rare. Here, we use genomic data to test alternative models for the evolution of cytonuclear hybrid male sterility in Mimulus. In hybrids between Iron Mountain (IM) Mimulus guttatus × Mimulus nasutus, two tightly linked M. guttatus alleles (Rf1/Rf2) each restore male fertility by suppressing a local mitochondrial male-sterility gene (IM-CMS). Unlike neutral models for the evolution of hybrid incompatibility loci, selfish evolution predicts that the Rf alleles experienced strong selection in the presence of IM-CMS. Using whole-genome sequences, we compared patterns of population-genetic variation in Rf at IM to a neighbouring population that lacks IM-CMS. Consistent with local selection in the presence of IM-CMS, the Rf region shows elevated FST, high local linkage disequilibrium and a distinct haplotype structure at IM, but not at Cone Peak (CP), suggesting a recent sweep in the presence of IM-CMS. In both populations, Rf2 exhibited lower polymorphism than other regions, but the low-diversity outliers were different between CP and IM. Our results confirm theoretical predictions of ubiquitous cytonuclear conflict in plants and provide a population-genetic mechanism for the evolution of a common form of hybrid incompatibility.
Something old, something new: evolution of Colombian weedy rice (Oryza spp.) through de novo de-domestication, exotic gene flow, and hybridization
<p>Weedy rice (<i>Oryza</i> spp.) is a worldwide weed of domesticated rice (<i>O. sativa</i>), considered particularly problematic due to its strong competition with the crop, which leads to reduction of yields and harvest quality. Several studies have established multiple independent origins for weedy rice populations in the U.S. and various parts of Asia; however, the origins of weedy rice in South America have not been examined in a global context. We evaluated the genetic variation of weedy rice populations in Colombia, as well as the contributions of local wild<i> Oryza </i>species, local cultivated varieties, and exotic <i>Oryza</i> groups to the weed, using polymorphism generated by genotyping by sequencing (GBS). We found no evidence for genomic contributions from local wild <i>Oryza </i>species<i> </i>(<i>O. glumaepatula</i>, <i>O. grandiglumis</i>, <i>O. latifolia </i>and <i>O. alta</i>) to Colombian weedy rice. Instead, Colombian weedy rice has evolved from local <i>indica</i> cultivars, and has also likely been inadvertently imported as an exotic pest from the US. Additionally, weeds comprising <i>de novo</i> admixture between these distinct weedy populations now represent a large proportion of genomic backgrounds in Colombian weedy rice. Our results underscore the impressive ability of weedy rice to evolve through multiple evolutionary pathways, including in situ de-domestication, range expansion, and hybridization.</p>
Data from: Convergent evolution of disordered lipidic structural color in the fruits of Lantana strigocamara (syn. L. camara hybrid cultivar)
<p><em>Research conducted:</em> The majority of plant colors are produced by anthocyanin and carotenoid pigments, but coloration obtained by nanostructured materials (i.e., structural colors) is increasingly reported in plants. Here, we identify a multilayer photonic structure in the fruits of <em>Lantana strigocamara</em> and compare it to a previously described origin in <em>Viburnum tinus</em>.</p> <p><em>Methods:</em> We used a combination of transmission electron microscopy, serial EM tomography, scanning force microscopy, and optical simulations to characterize the photonic structure in<em> L. strigocamara</em>. We also examine the development of the structure during maturation.</p> <p><em>Key results:</em> We find that the structural color derives from a disordered, multilayered reflector consisting of lipid droplets of ~105 nm that form a plate-like structure in 3D. This structure begins to form early in development and reflects blue wavelengths of light with increasing intensity over time as the structure develops. The lipids used are likely polymers of lipid monomers.</p> <p><em>Main conclusions:</em> <em>Lantana strigocamara</em> is the second origin of a lipid-based photonic structure, convergently evolved with the structure in <em>Viburnum tinus</em>. Chemical differences between the lipids in<em> L. strigocamara</em> and those of <em>V. tinus</em> suggest a distinct evolutionary trajectory with implications for the signaling function of structural colors in fruits.</p>
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