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Figure 2 in Three ways to distinguish species: using behavioural, ecological, and molecular data to tell apart two closely related ants, Camponotus renggeri and Camponotus rufipes (Hymenoptera: Formicidae)

Figure 2. Main vegetation physiognomies of the cerrado reserve at Mogi-Guaçu, Brazil. Cerrado sensu stricto consists of a dense scrub of shrubs and trees and a fair amount of herbaceous vegetation, whereas the cerradão is a closed woodland with a reduced ground layer. Nests of Camponotus renggeri (N = 46) were found in cerrado sensu stricto (22%) and cerradão (78%), whereas Camponotus rufipes (N = 40) occurred only in cerrado sensu stricto. Drawing by L. Mota.

Figure 1 in Three ways to distinguish species: using behavioural, ecological, and molecular data to tell apart two closely related ants, Camponotus renggeri and Camponotus rufipes (Hymenoptera: Formicidae)

Figure 1. Workers of (A) Camponotus renggeri and (B) Camponotus rufipes. The two species are usually differentiated in the field by nuances in the integument colour (C. renggeri is shiny; C. rufipes is matte), and colour of the legs (yellowish in C. renggeri; reddish in C. rufipes). Photographs courtesy of L. Mota.

Figure 6 in Three ways to distinguish species: using behavioural, ecological, and molecular data to tell apart two closely related ants, Camponotus renggeri and Camponotus rufipes (Hymenoptera: Formicidae)

Figure 6. Analyses of the cytochrome c oxidase subunit I haplotypes of Camponotus renggeri (yellow) and Camponotus rufipes (red). A, neighbour-joining tree constructed with Kimura two-parameter distances between C. renggeri and C. rufipes with bootstrap support values based on 10 000 replications indicated on each branch. B, median-joining network amongst the obtained haplotypes. Values on the branches represent the numbers of mutational steps distinguishing the haplotypes, represented as circles whose areas are proportional to the number of individuals with that haplotype.

Figure 3 in Three ways to distinguish species: using behavioural, ecological, and molecular data to tell apart two closely related ants, Camponotus renggeri and Camponotus rufipes (Hymenoptera: Formicidae)

Figure 3. Frequency distribution of nest categories in Camponotus renggeri and Camponotus rufipes in the cerrado reserve at Mogi-Guaçu, Brazil. The species differed in the structure and building materials used for nesting.

opencc-by-4.0Feb 2017View details →

TYPES: Male holotype from Panama: Panama: Parque Nacional Altos de Campana, 1 hectare PANCODING Inventory, 895 m, 8.68333°, -79.92972°, June 14–19, 2007, M. Arnedo, D. Dimitrov, G. Hormiga, F. Labarque, M. Ramírez, deposited in MIUP, PBI_OON 42313; same data, 1 male paratype deposited in MACN-Ar 29895, PBI_OON 42312. ETYMOLOGY: A noun in apposition; in Greek religion and mythology, Pan is the god of the wild natural world, of shepherds, flocks, and mountains, and of hunting and rustic music. He has hindquarters, legs, and horns of a goat, and the name is here employed to note the large mac- rosetae at the eye region of males that resemble the horns in some illustrations of this god. DIAGNOSIS: This is one of the most autapomor- phic species from the Americas; males have the labium fused with the sternum (fig. 34B), small chelicerae, shorter than the endite length, with anterior blunt projections, and directed backward in lateral view (fig. 34D, E); clypeus directed back- ward (fig. 34D); two light areas on the sternum just below the endites (fig. 34B), carapace almost flat in lateral view and two strong macrosetae at the eye region, pointing forward (fig. 34C–E). Other characters of the male palp, such as the presence of two apophyses, also distinguish this species from others (fig. 38D–F). MALE (PBI_OON 42312): Total length 1.00. Habitus as in figure 34A–C. CEPHALOTHO- RAX: Carapace orange, with brown stripe along in Taxonomic Revision Of The Jumping Goblin Spiders Of The Genus Orchestina Simon, 1882, In The Americas (Araneae: Oonopidae)

TYPES: Male holotype from Panama: Panama: Parque Nacional Altos de Campana, 1 hectare PANCODING Inventory, 895 m, 8.68333°, -79.92972°, June 14–19, 2007, M. Arnedo, D. Dimitrov, G. Hormiga, F. Labarque, M. Ramírez, deposited in MIUP, PBI_OON 42313; same data, 1 male paratype deposited in MACN-Ar 29895, PBI_OON 42312. ETYMOLOGY: A noun in apposition; in Greek religion and mythology, Pan is the god of the wild natural world, of shepherds, flocks, and mountains, and of hunting and rustic music. He has hindquarters, legs, and horns of a goat, and the name is here employed to note the large mac- rosetae at the eye region of males that resemble the horns in some illustrations of this god. DIAGNOSIS: This is one of the most autapomor- phic species from the Americas; males have the labium fused with the sternum (fig. 34B), small chelicerae, shorter than the endite length, with anterior blunt projections, and directed backward in lateral view (fig. 34D, E); clypeus directed back- ward (fig. 34D); two light areas on the sternum just below the endites (fig. 34B), carapace almost flat in lateral view and two strong macrosetae at the eye region, pointing forward (fig. 34C–E). Other characters of the male palp, such as the presence of two apophyses, also distinguish this species from others (fig. 38D–F). MALE (PBI_OON 42312): Total length 1.00. Habitus as in figure 34A–C. CEPHALOTHO- RAX: Carapace orange, with brown stripe along

opencc-by-4.0Dec 2022View details →

Text-fig. 51. Number of specimens and number of species for the five categories of angiosperms distinguished from the Catefica mesofossil flora. in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 51. Number of specimens and number of species for the five categories of angiosperms distinguished from the Catefica mesofossil flora.

opencc-zeroJan 2023View details →

Data for: Distinguishing intrinsic photon correlations from external noise with frequency-resolved homodyne detection

Data for the publication C. Lüders, M. Aßmann, Distinguishing intrinsic photon correlations from external noise with frequency-resolved homodyne detection, Scientific Reports 10 (1), 1-11 (2020). In this work, we apply homodyne detection to investigate the frequency-resolved photon statistics of a cw light field emitted by a driven-dissipative semiconductor system in real time. We demonstrate that studying the frequency dependence of the photon number noise allows us to distinguish intrinsic noise properties of the emitter from external noise sources such as mechanical noise while maintaining a sub-picosecond temporal resolution. We further show that performing postselection on the recorded data opens up the possibility to study rare events in the dynamics of the emitter. By doing so, we demonstrate that in rare instances, additional external noise may actually result in reduced photon number noise in the emission. Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – SFB-Geschäftszeichen TRR142/3-2022 – Projektnummer 231447078, Project A04.

opencc-by-4.0Aug 2023View details →

Molecularly targetable cell types in mouse visual cortex have distinguishable prediction error responses

Raw data and code to reproduce figures in the manuscript "Molecularly targetable cell types in mouse visual cortex have distinguishable prediction error responses" # README ## Introduction This README provides essential information about the codebase for the manuscript titled "Molecularly targetable cell types in mouse visual cortex have distinguishable prediction error responses." The code in this repository is self-contained and is expected to run smoothly given the appropriate versions of the required libraries/packages. ## Directory structure and execution details ### R code - Main Figures 2A-2D, 3A-3C, and 4A-4E, as well as supplemental figures S2A-S2H, S3A-S3E, S4L, and S5A-S5I, were generated using R. Execute the `R_figs_master.r` script located in the `r_code` directory. - All figures will be saved within the `r_code/code_generated_figures` directory. - Note: Exact UMAP representations might vary across different hardware and operating systems, likely due to an issue with the UWOT package ([Reference Issue](https://github.com/satijalab/seurat/issues/5514)). If figures appear outside their designated plot ranges, set "FixAxes" to 'FALSE' in the `single_cell_variables.r` script. ### MATLAB code - Main figures 1B, 1D-1F, and 6A-6H, as well as supplemental figures S1A-S1J and S6A-S6I, were generated using MATLAB (version 9.11.0.1809720 (R2021b) Update 1). Execute the `get_the_figs_matlab.m` script located in the `matlab_code` directory. - All figures will be saved within the `matlab_code/code_generated_figures` directory. - Required: [fca_readfcs, version 2020.06.22](https://ch.mathworks.com/matlabcentral/fileexchange/9608-fca_readfcs). ### Python code - Figures 5B-5F panels were generated using Python (version 3.6.8). Run the `fig_5_analysis_code.py` script located in the `python_code` directory. - All figures will be saved within the `python_code/code_generated_figures` directory. - The preprocessed images located in `python_code/data_repository/Adamts2_processed`, `python_code/data_repository/Agmat_processed`, and `python_code/data_repository/Baz1a_processed` were generated using the ImageJ macro `python_code/cropped_to_processed_macro.ijm` from the raw images in `python_code/data_repository/Adamts2_cropped`, `python_code/data_repository/Agmat_cropped`, and `python_code/data_repository/Baz1a_cropped`. ## Supplementary code (for reference only as raw data is not included) ### Mapping code and genome construction code - Initial processing of Single-cell RNA-sequencing was performed with Cell Ranger, coordinated by the Python script:   `python_code/mapping_and_genome_construction/single_cell_mapping_pipeline.py`. Some components of this script are deprecated and were primarily used to pass .fastq files to Cell Ranger and organize the outputs. - A custom genome was constructed to account for the expression of CaMPARI2 in the single-cell RNA-sequencing dataset:   `python_code/mapping_and_genome_construction/campari2_genome_construction.py`. - Processing of Bulk RNA-sequencing, either single or paired-end, was executed through Python:   `python_code/mapping_and_genome_construction/bulk_single_end_mapping.py` and `python_code/mapping_and_genome_construction/bulk_paired_end_mapping.py`. - A custom genome was constructed to account for the expression of various artificial promoter viruses:   `python_code/mapping_and_genome_construction/bulk_seq_genome_construction.py`.

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Data from: A few essential genetic loci distinguish Penstemon species with flowers adapted to pollination by bees or hummingbirds

In the formation of species, adaptation by natural selection generates distinct combinations of traits that function well together. The maintenance of adaptive trait combinations in the face of gene flow depends on the strength and nature of selection acting on the underlying genetic loci. Floral pollination syndromes exemplify the evolution of trait combinations adaptive for particular pollinators. The North American wildflower genus Penstemon displays remarkable floral syndrome convergence, with at least 20 separate lineages that have evolved from ancestral bee pollination syndrome (wide blue-purple flowers that present a landing platform for bees and small amounts of nectar) to hummingbird pollination syndrome (bright red narrowly tubular flowers offering copious nectar). Related taxa that differ in floral syndrome offer an attractive opportunity to examine the genomic basis of complex trait divergence. In this study, we characterized genomic divergence among 229 individuals from a Penstemon species complex that includes both bee and hummingbird floral syndromes. Field plants are easily classified into species based on phenotypic differences and hybrids displaying intermediate floral syndromes are rare. Despite unambiguous phenotypic differences, genomewide differentiation between species is minimal. Hummingbird-adapted populations are more genetically similar to nearby bee-adapted populations than to geographically distant hummingbird-adapted populations, in terms of genomewide dXY. However, a small number of genetic loci are strongly differentiated between species. These ~ 20 "species-diagnostic loci", which appear to have nearly fixed differences between pollination syndromes, are sprinkled throughout the genome in high recombination regions. Several map closely to previously established floral trait QTLs. The striking difference between the diagnostic loci and the genome as whole suggests strong selection to maintain distinct combinations of traits, but with sufficient gene flow to homogenize the genomic background. A surprisingly small number of alleles confer phenotypic differences that form the basis of species identity in this species complex.

opencc-zeroAug 2023View details →

FIGURE 5 in Identification of past and present gobies: distinguishing Gobius and Pomatoschistus (Teleostei: Gobioidei) species using characters of otoliths, meristics and body morphometry

FIGURE 5 Otoliths (mesial view) of Gobius bucchichi (a–c: Selce, 3l, 1l, 4l), G. cruentatus (d–f: Selce, 2l, 3l, 8l), G. niger (g–i: Pilsey Island, 2l, 6l, 5l) and G. roulei (j–l: Selce, 2l, 1l, 3l). Numbers following the localities refer to the fish specimen from which the otolith was extracted; l, left otolith. SL denotes the standard length (in mm) of the corresponding fish specimen. Scale bars: 0.5 mm. All figured otoliths are kept in the Bavarian State Collection (collection number SNSB-BSPG 2020 LIV).

FIGURE 6 in Identification of past and present gobies: distinguishing Gobius and Pomatoschistus (Teleostei: Gobioidei) species using characters of otoliths, meristics and body morphometry

FIGURE 6 Otoliths (mesial view) of Pomatoschistus knerii (a–d: Krk, 1r, 2r, each mirrored, 9l, 4r mirrored), P. marmoratus (e–h: Selce, 1r, 2r, 3r, each mirrored, 4l), P. microps (i–l: Stralsund, 8l, 5l, 6l, 14l), P. minutus (m: Stralsund, 1l), P. montenegrensis (n–p: Skadar lake, 8l, 9l, 6l), P. pictus (m: Norway, 2r mirrored), and P. quagga (r–t: Krk, 2l, 8r mirrored, 4l). Numbers following the localities refer to the fish specimen from which the otolith was extracted; l, left otolith; r, right otolith, mirrored for better comparison. SL denotes the standard length (in mm) of the corresponding fish specimen. Scale bars: 0.5 mm. All figured otoliths are kept in the Bavarian State Collection (collection number SNSB-BSPG 2020 LIV). Downloaded from Brill.com10/07/2022 07:35:45PM via free access

FIGURE 4 in Identification of past and present gobies: distinguishing Gobius and Pomatoschistus (Teleostei: Gobioidei) species using characters of otoliths, meristics and body morphometry

FIGURE 4 Otoliths (mesial view) of Gobius cobitis (a–c: Montenegro, 7l, 4l, 1l), G. geniporus (d: Montenegro, 3l; e, f: Selce, 2l, 'medium'), G. incognitus (g–i: Pelješac Peninsula, J1914l, J1910r mirrored, J1906l), G. paganellus (j–l: Galicia, 1l, 6l, 8l) and G. vittatus (m, Selce, 2l; n, o, Krk, Krk, 1l; 2l; p: Selce 2l). Numbers following the localities refer to the fish specimen from which the otolith was extracted; l, left otolith; r, right otolith, mirrored for better comparison. SL denotes the standard length (in mm) of the corresponding fish specimen. Scale bars: 0.5 mm. All figured otoliths are kept in the Bavarian State Collection (collection number SNSB-BSPG 2020 LIV).

FIGURE 3 in Identification of past and present gobies: distinguishing Gobius and Pomatoschistus (Teleostei: Gobioidei) species using characters of otoliths, meristics and body morphometry

FIGURE 3 Otoliths (mesial view) of the species of the Gobius auratus complex, i.e. G. auratus (a: Selce, 6l; b: Selce, 5l; c: Krk, 2r mirrored), G. couchi (d–f: Krk, 2l, 3r mirrored, 1l), G. fallax (g, h: Unije Island, 2r mirrored, 1l), G. gasteveni (i, j: Galicia, 1l, 1r mirrored) and G. kolombatovici (k, l: Krk, 1l, 2l). Numbers following the localities refer to the fish specimen from which the otolith was extracted; l, left otolith; r, right otolith, mirrored for better comparison. SL denotes the standard length (in mm) of the corresponding fish specimen. Scale bars: 0.5 mm. All figured otoliths are kept in the Bavarian State Collection (collection number SNSB-BSPG 2020 LIV).

FIGURE 2 in Identification of past and present gobies: distinguishing Gobius and Pomatoschistus (Teleostei: Gobioidei) species using characters of otoliths, meristics and body morphometry

FIGURE 2 Plots of the discriminant function scores derived from the different arrays of variables (as indicated in the figure) of the studied species of Gobius (a–c) and Pomatoschistus (d–f). The reduced datasets for Gobius and Pomatoschistus were used for this analysis. LD1, 2, linear discriminant functions 1 and 2. See tables 3 and 5 for details and values.

FIGURE 1 a–b in Identification of past and present gobies: distinguishing Gobius and Pomatoschistus (Teleostei: Gobioidei) species using characters of otoliths, meristics and body morphometry

FIGURE 1 a–b, Schematic drawing of a goby skeleton depicting the standard morphometric (1a) and meristic (1b) characters used in this study; c–d, Schematic drawing (c) and SEM image (d) of a right goby otolith (based on G. bucchichi) showing the measured distances and areas (after Gierl et al., 2018) and the established otolith terminology. Colors in a: red, horizontal measurements; blue, measurements along fin bases; green vertical measurements. Abbreviations: (a) Ab, length of anal fin base; B, body depth at origin of first dorsal fin; CP, length of caudal peduncle; D2b, length of second dorsal fin base; D2C, distance between end of second dorsal fin and first dorsal (procurrent) ray of caudal fin; SL, standard length (from snout to begin of caudal fin); SN/A, distance from snout to origin of anal fin; SN/D1, distance from snout to origin of first dorsal fin; SN/D2, distance from snout to origin of second dorsal fin; TL, total length; (b) AbVert, abdominal vertebrae; AP, anal fin pterygiophores inserting in front of haemal spine of first caudal vertebra; Arays, rays of anal fin; CaudVert, caudal vertebrae; D2rays, rays of second dorsal fin; DProCur, dorsal procurrent rays; VProCur, ventral procurrent rays; (c) OA, otolith area; OH, otolith height; OL, otolith length; OP, otolith perimeter; SuA, sulcus area; SuH, sulcus height; SuL, sulcus length; SuP, sulcus perimeter; SuEndV, vertical distance from posterior end of sulcus to ventral margin of otolith; SuTipV, vertical distance from anterior end of sulcus to ventral margin of otolith.