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FIGURE 1 in Morphological and genetic variation in North Atlantic giant file clams, Acesta spp. (Bivalvia: Limidae), with description of a new cryptic species in the northwest Atlantic

FIGURE 1. Location of the sampling sites where giant file clams (Acesta) were collected and observed in the northwest Atlantic. Base map generated with GeoMapApp (http://www.geomapapp.org) (Ryan et al. 2009).

FIGURE 4. Palola Lizard Island clade 6. All material ethanol preserved. A in Six genetically distinct clades of Palola (Eunicidae, Annelida) from Lizard Island, Great Barrier Reef, Australia

FIGURE 4. Palola Lizard Island clade 6. All material ethanol preserved. A. AM W.43905, dorsal view; B AM W.44645, dorso-lateral view. C. AM W.44645, parapodium 10; D. AM W.44645, parapodium 10, detail of compound falciger. Abbreviations: a = aciculum, cc = capillary chaeta, cf = compound falciger, dc = dorsal cirrus of parapodium, vc = ventral cirrus of parapodium. Scale bars: A, B, C = 0.1 mm, D = 20 µm.

FIGURE 3. Palola Lizard Island clades 3 in Six genetically distinct clades of Palola (Eunicidae, Annelida) from Lizard Island, Great Barrier Reef, Australia

FIGURE 3. Palola Lizard Island clades 3 (A, B), 4 (C, D) and 5 (E, F). All material ethanol-preserved. A. Palola Lizard Island clade 3, AM W.44407, dorsal view; B. Palola Lizard Island clade 3, same specimen as in A, lateral view; C. Palola Lizard Island clade 4, AM W.44653, dorsal view; D. Palola Lizard Island clade 4, same specimen as in C, ventro-lateral view; E. Palola Lizard Island clade 5, AM W.44146, dorsal view; F. Palola Lizard Island clade 5, same specimen as in E, lateral view. Scale bars: 0.1 mm.

FIGURE 2. Palola Lizard Island clades 1 in Six genetically distinct clades of Palola (Eunicidae, Annelida) from Lizard Island, Great Barrier Reef, Australia

FIGURE 2. Palola Lizard Island clades 1 (A–C) and 2 (D–F). Specimens shown in A–C and F ethanol preserved; specimen shown in D and F fixed in formalin and later transferred to to 70% ethanol. Labels in A–C serve as a reference for all following figures. A. Palola Lizard Island clade 1, AM W.44034, dorsal view; B. Palola Lizard Island clade 1, AM W.44146, ventrolateral view, note serrated anterior margin of mandible and length ratio between first and second peristomial ring; C. Palola Lizard Island clade 1, AM W.44034, dorsal view of parapodia in posterior region of the fragment, arrows indicate the black pigment spots on the dorsal side of the parapodia; D. Palola Lizard Island clade 2, AM W.44914, dorsal view; E. Palola Lizard Island clade 2, W.44914, lateral view; F. Palola Lizard Island clade 2, AM W.44006, lateral view. Abbreviations: cc = capillary chaetae, cf = compound falcigers, dc = dorsal cirrus of parapodium, la = lateral antenna, m = mandible, ma = median antenna, mx = maxillae,p = palps, pc = peristomial cirrus, 1pr = first peristomial ring, 2pr = second peristomial ring, pro = prostomium. Scale bars: A, B, F = 0.1 mm; C = 0.05 mm; D, E = 0.5 mm.

FIGURE 1. 50 in Six genetically distinct clades of Palola (Eunicidae, Annelida) from Lizard Island, Great Barrier Reef, Australia

FIGURE 1. 50% majority rule consensus tree resulting from Bayesian analysis of 601 bp of COI. Branch support is given as Bayesian posterior probability. Double asterisks (**) indicate 100% posterior probability; single asterisks (*) indicate 95–99% posterior probability; branch support <95% posterior probability not shown. Samples sequenced for previous studies are listed with their genbank accession numbers and collecting locality. Samples sequenced for the present study are listed as "Lizard" with their AM voucher numbers.

FIGURE 15. Schematic maps showing interpopulational genetic divergences within P in Taxonomic revision of Phascogale tapoatafa (Meyer, 1793) (Dasyuridae; Marsupialia), including descriptions of two new subspecies and confirmation of P. pirata Thomas, 1904 as a ' Top End' endemic

FIGURE 15. Schematic maps showing interpopulational genetic divergences within P. tapoatafa (sensu lato) for cytochrome b (ranges of pairwise raw sequence divergences): a) divergences between the 'Top End' population and each other regional population; and b) divergences among all populations of P. tapoatafa, excluding the 'Top End' population.

FIGURE 5. A–B in Cryptic within cryptic: genetics, morphometrics, and bioacoustics delimitate a new species of Eleutherodactylus (Anura: Eleutherodactylidae) from Eastern Cuba

FIGURE 5. A–B) Holotype of Eleutherodactylus cattus (CZACC14.14152) in dorsal and ventral views. C) Male (CZACC14.14153, paratype) calling in the trail to Pico El Gato, Sierra del Cobre, 844m a.s.l.. D) Habitat in the type locality, dominated by montane rainforest, Pico del Gato in the background.

FIGURE 3 in Cryptic within cryptic: genetics, morphometrics, and bioacoustics delimitate a new species of Eleutherodactylus (Anura: Eleutherodactylidae) from Eastern Cuba

FIGURE 3. Advertisement call differences between the two phylogroups of Eleutherodactylus glamyrus sensu lato. Oscillograms of a five seconds fragment from a call series of a male from the phylogroup TUR (A), recorded on June 22, 2005 at Pico Cuba, Santiago de Cuba, air temperature = 16.0 °C and that of a male from phylogroup GAT (B), recorded on 14 May, 2010 at Loma El Gato, Santiago de Cuba, air temperature = 19.2 °C. C) and D) spectrogram (top) and oscillogram (bottom) of a single call from an individual of phylogroup TUR and GAT respectively. Spectrogram parameters: FFT size = 512 points, overlap = 90%, window = Hanning.

FIGURE 4 in Cryptic within cryptic: genetics, morphometrics, and bioacoustics delimitate a new species of Eleutherodactylus (Anura: Eleutherodactylidae) from Eastern Cuba

FIGURE 4. Call features showing statistically significant differences between the two phylogroups (TUR, N=63) and (GAT, N=11). Box plots and original data points are shown for each acoustic feature abbreviated as: call duration (CD), call rise time (RT), dominant frequency (DF), and frequency modulation (FM).

FIGURE 2 in Cryptic within cryptic: genetics, morphometrics, and bioacoustics delimitate a new species of Eleutherodactylus (Anura: Eleutherodactylidae) from Eastern Cuba

FIGURE 2. Morphometric characters measured and descriptive multivariate ordination of data. A) Measuring landmarks, variable names and abbreviations used. For visual simplicity, only the measurements of a finger/toe length and a finger/toe pad width are displayed. B) Scores of the first two principal components derived from the non-transformed morphometric data (31 variables, 82 specimens) from the five localities (color key as in figure 1) corresponding to phylogroups TUR (triangles) and GAT (circles). Gray arrows represent variable loadings for both axes (overlapping names were excluded, see Appendix V for a full numerical description of components); the inset shows the variance explained by the first five PCs, highlighting in black those displayed in the plot.

FIGURE 1 in Cryptic within cryptic: genetics, morphometrics, and bioacoustics delimitate a new species of Eleutherodactylus (Anura: Eleutherodactylidae) from Eastern Cuba

FIGURE 1. Genetic diversity in Eleutherodactylus glamyrus sensu lato. A) Topographic map of Eastern Cuba indicating the sampled localities (CUB: Pico Cuba, Sierra Maestra, Municipio Guamá, Santiago de Cuba; AJO: Aguada del Joaquín, Sierra Maestra, Municipio Bartolomé Masó, Granma; BNV: Barrio Nuevo, Municipio Buey Arriba, Granma; NVE: La Nueve, Sierra Maestra, Municipio Buey Arriba, Granma; and GAT: trail to Pico El Gato, Sierra del Cobre, Municipio Santiago de Cuba, Santiago de Cuba). The dashed lines encircle the two phylogroups detected in molecular analyses. B) Bayesian phylogenetic tree of aligned mitochondrial sequences of 16S and cob genes (1158bp) highlighting the two phylogroups identified (TUR and GAT), black dots indicate nodes supported by posterior probabilities> 0.9. C) Haplotype network of aligned 579 bp DNA sequences of the nuclear Rag-1 gene from 36 individuals with colors indicating sampling localities and mtDNA phylogroups indicated by polygons.

FIGURE 4 in A molecular phylogenetic study on South Korean Tettigonia species (Orthoptera: Tettigoniidae) using five genetic loci: The possibility of multiple allopatric speciation

FIGURE 4. Inter- (gray) and intraspecific (open) genetic differences in Tettigonia species for CO1 calculated using the pdistance method and treatment of pairwise deletion for gaps with the range of genetic difference within clusters. The box plot displays the median (internal transverse thick line) and interquartile range (box). Short lines indicate maximum and minimum genetic differences. Asterisk denotes a sequence from NCBI; T. viridissima, JN609414–JN609420; T. hispania, EF515121; T. chinensis, HQ609468–HQ609470. (JJ-TU = Jeju Island population of T. ussuriana; JS-TU = Jeongseon population of T. ussuriana; PC-TU = Pyeongchang population of T. ussuriana; MJ-TU = Muju population of T. ussuriana; MG-TU = Mungyeong population of T. ussuriana)

FIGURE 3 in A molecular phylogenetic study on South Korean Tettigonia species (Orthoptera: Tettigoniidae) using five genetic loci: The possibility of multiple allopatric speciation

FIGURE 3. Neighbor-joining tree inferred from the concatenated dataset of all five genetic loci: CO1, CO2, ND1, TA1, and ITS2. Neighbor-joining (left) and parsimony (right) bootstrap values are indicated above internodes; Bayesian posterior probabilities are shown below internodes.

FIGURE 2 in A molecular phylogenetic study on South Korean Tettigonia species (Orthoptera: Tettigoniidae) using five genetic loci: The possibility of multiple allopatric speciation

FIGURE 2. Neighbor-joining (A), parsimony (B), and Bayesian inference (C) trees inferred from the combined dataset of three mtDNA loci (CO1 + CO2 + ND1). Numbers next to nodes are bootstrap or posterior probability values.

FIGURE 1 in A molecular phylogenetic study on South Korean Tettigonia species (Orthoptera: Tettigoniidae) using five genetic loci: The possibility of multiple allopatric speciation

FIGURE 1. Neighbor-joining phylogenetic tree of each mtDNA gene analysis: (A) CO1, (B) CO2, (C) ND1. Numbers next to nodes are bootstrap values. Numbers on arrows are genetic differences between two clusters.

opencc-by-4.0Jan 2017View details →

Optimizing agents with genetic programming - An evaluation of hyper-heuristics in dynamic real-time logistics - datasets and results

This directory contains the data and results that we used and obtained during the realization of the following paper: <blockquote> Optimizing agents with genetic programming - An evaluation of hyper-heuristics in dynamic real-time logistics. Rinde R.S. van Lon, Juergen Branke, and Tom Holvoet. Genetic Programming and Evolvable Machines (2017). </blockquote> The code that has been used can be found on GitHub (https://github.com/rinde/vanLon17-GPEM-code), an archive is available at https://doi.org/10.5281/zenodo.260130. This repository contains the following files: <ul> <li>evo.zip (expands to 21.2 GB) A zip file containing all results of the training experiment and tuning experiment.</li> <li>JAAMAS.zip (expands to 227.6 MB) A zip file containing the main results of the JAAMAS experiment, also available at https://doi.org/10.5281/zenodo.209760</li> <li>realtime.zip (expands to 913.5 MB) A zip file containing the main results</li> <li>dataset10k.zip (expands to 4.9 GB) Contains the scenarios used for the training and tuning experiments.</li> <li>overview.zip (expands to 42 MB) Contains the following files: <ul> <li>overview/experiment-overview.csv - table containing basic overview of the 40 main evolutionary runs that were performed for this paper.</li> <li>overview/heuristics/ - folder with a tree visualization for every evolved heuristic.</li> <li>overview/makefile - executes the analysis scripts that were used in the paper (requires the R programming language, https://www.r-project.org/). All tables and figures will be placed in results/generated/.</li> <li>readme.txt - this file.</li> <li>overview/results/ - contains the scripts</li> <li>overview/results/data/ - empty directory in which evo.zip, JAAMAS.zip, and realtime.zip have to be unpacked for the analysis scripts to work.</li> </ul> </li> </ul>

FIGURE 3b in Morphometric and preliminary genetic characteristics of Branchinecta orientalis populations from Iran (Crustacea: Anostraca)

FIGURE 3b. Scatterplot of the discriminant analysis (DA) on female morphometric variables measured in Branchinecta orientalis populations. For abbreviations of sites see table 1.

FIGURE 2 in Morphometric and preliminary genetic characteristics of Branchinecta orientalis populations from Iran (Crustacea: Anostraca)

FIGURE 2. Definition of morphometric characteristics in Branchinecta orientalis (by author based on literature source: Amat, 1980; Timms, 2012).

FIGURE 4 in Morphometric and preliminary genetic characteristics of Branchinecta orientalis populations from Iran (Crustacea: Anostraca)

FIGURE 4. Maximum Likelihood inference tree based on the COI sequences of Branchinecta species. The first and the second numbers above nodes represent BI and ML supports respectively.

FIGURE 3a in Morphometric and preliminary genetic characteristics of Branchinecta orientalis populations from Iran (Crustacea: Anostraca)

FIGURE 3a. Scatterplot of the discriminant analysis (DA) on male morphometric variables measured in Branchinecta orientalis populations. For abbreviations of sites see table 1.