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Figure 7 in Integrative taxonomy of crustacean y-larvae (Thecostraca: Facetotecta) using laboratory-rearing and molecular analyses of single specimens, with the description of a new vermiform species

Figure 7. Hansenocaris demodex sp. nov., holotype (A, B, D–I) and paratype (C), cyprids from Sesoko Island photographed before drying (A) and in SEM after drying and mounting (B–I). A, lateral view; B, lateral view; C, cephalic region, lateral view; D, cephalic region, ventral view; E, bifid appendix (frontal filaments?); F, labrum; G, pores and sensilla; H, close-up of hook of left first antenna; I, abdomen and telson, dorsal view. Abbreviations: a1, first antenna; a1 hk, first antenna hook; a2 rud, second antenna rudiment; ae, aesthetasc; en, endopod; ex, exopod; la, labrum; md rud, mandible rudiment; par occ pro, paraocular process. Roman numerals I–VI – thoracic segments. Large Arabic numerals 1–3 – abdominal segments. Small Arabic numerals, many annotated with l or r for left and right, respectively, refer to cuticular structures (see Table 5). Square with dotted outline: sample numbers, museum numbers and type status.

Figure 5 in Integrative taxonomy of crustacean y-larvae (Thecostraca: Facetotecta) using laboratory-rearing and molecular analyses of single specimens, with the description of a new vermiform species

Figure 5. Hansenocaris demodex sp. nov., paratype, last-stage nauplius (LSN) from Sesoko Island in SEM. A, lateral view; B, cephalic shield, anterior view; C–J, close-up views of pores and sensilla of cephalic shield and faciotrunk; K–M, labrum and naupliar limbs (a1, a2, md). Abbreviations: a1, first antenna; a2, second antenna; md, mandible; la, labrum; scl, sclerite of a1. Small Arabic numerals, many annotated with l or r for left and right, respectively, refer to cuticular structures (see Table 4). Yellow overlay, cephalic shield; blue overlay, faciotrunk; red overlay, anterior field of facets. Square with dotted outline: sample number, museum number and type status.

Figure 4 in Integrative taxonomy of crustacean y-larvae (Thecostraca: Facetotecta) using laboratory-rearing and molecular analyses of single specimens, with the description of a new vermiform species

Figure 4. Hansenocaris demodex sp. nov., paratype, last-stage nauplius (LSN) from Sesoko Island photographed live before fixation (A) and in SEM after fixation and mounting (B–H). A, ventral view; B, ventral view; C, dorsal view; D, pair of ventral pores situated in front of labrum; E, close-up views of pores and sensilla of cephalic shield; F, caudal end in dorsal view; G, caudal end in ventral view; H, caudal end viewed from behind. Abbreviations: a1, first antenna; a2, second antenna; arthro membr, arthrodial membrane; ce, compound eye; dc sp, dorsocaudal spine; en, endopod; ex, exopod; fur sp, furcal spine; la, labrum; md, mandible; ne, nauplius eye; rud, rudimentary. Small Arabic numerals, many annotated with l or r for left and right, respectively, refer to cuticular structures (see Table 4). Yellow overlay, cephalic shield; blue overlay, faciotrunk; red overlay, anterior field of facets. Square with dotted outline: sample number, museum number and type status.

Figure 3 in Integrative taxonomy of crustacean y-larvae (Thecostraca: Facetotecta) using laboratory-rearing and molecular analyses of single specimens, with the description of a new vermiform species

Figure 3. Overview of most specimens of Hansenocaris demodex sp. nov. collected at Sesoko Island during fieldwork in 2018 and 2019. A, 19 specimens, four of which reached the cyprid stage, collected in the plankton at the naupliar stage and reared individually, with length, dish number, sample number, and museum registration number indicated for each specimen as well as a colour code (red, blue, yellow) showing its ultimate treatment/fixation (respectively, molecular work, SEM or exuvium on slide); some larvae died before preservation and are only referred to by their dish number; B, overview of setup for individual rearing of larvae; top view of green tray containing 31 2.5-cm-wide dishes with tracking information written on lids, each containing one to five live larvae. Live video of H. demodex and other y-larvae can be seen here: https:// youtu.be/seo-63AK10E.

Figure 1 in Integrative taxonomy of crustacean y-larvae (Thecostraca: Facetotecta) using laboratory-rearing and molecular analyses of single specimens, with the description of a new vermiform species

Figure 1. Facetotecta sampling sites in East Asia, 2017–20 and distribution of Hansenocaris demodex sp. nov. A, East China Sea showing distance (780 km) between the two main sampling sites, Sesoko Island (Okinawa, Japan) and Green Island (Taiwan). In 2020, several additional specimens of H. demodex were collected from Xiaoliuqiu Island (MJG, unpublished). B, Sesoko Island (Japan, Okinawa) with indication of sampling site (Sesoko Station); C, Green Island (Taiwan) with indication of sampling site (Gonguan Fishing Harbour); D, pier at Sesoko Station; E, Gonguan Fishing Harbour.

Figure 2 in Integrative taxonomy of crustacean y-larvae (Thecostraca: Facetotecta) using laboratory-rearing and molecular analyses of single specimens, with the description of a new vermiform species

Figure 2. Example of newly collected sample of still living y-larvae collected on 19 October 2018 at Sesoko Island off the pier shown in Figure 1D, representing a variety of developmental stages. A, 25 y-larvae likely representing> 15 different species, including 18 early lecithotrophic nauplii (*), five planktotrophic nauplii (†) and two cyprids (§). None of the depicted specimens can be assigned to already described species, but three of the planktotrophic nauplii are similar to Itô's (1986a) Pacific type I and one is a cyprid of the type nicknamed 'Big brown', both types of which are sequenced as a part of this work and belong to the same clade as Hansenocaris demodex sp. nov. (see Fig. 15). B, close-up of selected y-larvae with same numbers assigned as in A. Live video of H. demodex and other y-larvae can be seen here: https://youtu.be/seo-63AK10E.

opennotspecifiedNov 2018View details →

Fig. 2 in Inferring Ancestry and Divergence Events in a Forest Pest Using Low-Density Single-Nucleotide Polymorphisms

Fig. 2. Population tree inferred by TreeMix using all 42 sampling sites across the mountain pine beetle range. Terminal branches are labeled using locality information (see Supp Fig. 1 [online only] for further detail) and migration arrows are colored according to migration weight.

opennotspecifiedNov 2018View details →

Fig. 3. Scenario 9 in Inferring Ancestry and Divergence Events in a Forest Pest Using Low-Density Single-Nucleotide Polymorphisms

Fig. 3. Scenario 9 was identified as the 'best' from 11 competing phylogeographic scenarios. This scenario represents an east-to-west colonization route with stable population sizes in which cluster 4 is derived from clusters 1 and 3 through admixture. Terminal branch labels are consistent with the five STRUCTURE clusters identified (Fig. 1). T = time expressed as number of generations assuming one generation per year; R = inferred migration rate.

opennotspecifiedNov 2018View details →

Fig. 1 in Inferring Ancestry and Divergence Events in a Forest Pest Using Low-Density Single-Nucleotide Polymorphisms

Fig. 1. Map of mountain pine beetle sites throughout western North America. Each site is represented by a pie chart depicting the average assignment (Q values) of individuals to one of five STRUCTURE clusters (K = 5).

Figure 8 in Integrative taxonomy using historical specimens provides evidence for a single species of bushbuck, Tragelaphus scriptus (Mammalia: Bovidae)

Figure 8. Distribution of bushbuck crania according to size (log centroid size; A) and along the first three principal components of shape (B–D). Differences in size are non-significant between subclades and when assessed separately for males and females, despite the attainment of a larger maximum size in sylvaticus males. Differences in shape between subclades are significant, but only for males, not females.

Figure 5. A in Integrative taxonomy using historical specimens provides evidence for a single species of bushbuck, Tragelaphus scriptus (Mammalia: Bovidae)

Figure 5. A, plot of all specimens along the first two principal components (PCs) of shape. B, cranial outlines transformed via thin-plate spline from the mean shape to the extremes of PCs 1 and 2. Note the separation of subclades along PC1, which largely reflects sexual dimorphism and size allometry (see Fig. 3). The key is the same as that shown in Figure 1; labels refer to specimens in Table 1.

Figure 7 in Integrative taxonomy using historical specimens provides evidence for a single species of bushbuck, Tragelaphus scriptus (Mammalia: Bovidae)

Figure 7. Median-joining network of 28 sequences from bushbuck specimens, with missing and ambiguous sites removed. [Three sequences with many gaps (ZMB Mam 32456, ZMB Mam 40389 and ZMB Mam 107683) were removed before the analysis.] Branches are labelled with mutation distances; unlabelled branches have a distance of one. Note the structure, the long branch separating clades and the Tanzania/Nigeria haplogroup. One reference sequence was included from both clades (Table 2).

Figure 3 in Integrative taxonomy using historical specimens provides evidence for a single species of bushbuck, Tragelaphus scriptus (Mammalia: Bovidae)

Figure 3. Plots of size allometry examined via ln-transformed centroid size and principal component 1 (PC1) (A); or regression of shape (B). Note the strong influence of size on shape. The key is the same as that shown in Figure 1; labels refer to specimens in Table 1.

Figure 2 in Integrative taxonomy using historical specimens provides evidence for a single species of bushbuck, Tragelaphus scriptus (Mammalia: Bovidae)

Figure 2. Surface model of Tragelaphus scriptus cranium in dorsal, lateral and ventral views, with points representing 53 digitized landmarks used to characterize cranial shape (22 blue landmarks mirrored on left and right sides; 9 orange medial landmarks). See the Supporting Information (Table S1) for anatomical descriptions of the locations of landmarks.

Figure 6 in Integrative taxonomy using historical specimens provides evidence for a single species of bushbuck, Tragelaphus scriptus (Mammalia: Bovidae)

Figure 6. Phylomorphospace shows poor correspondence between mitogenomic relationships and morphological differences. Axes refer to the first and second principal components (PC1 and PC2) of the geometric morphometric analysis. The key is the same as that shown in Figure 1; labels refer to specimens in Table 1. Note that this figure includes only specimens for which mitochondrial DNA was extracted.

Figure 1 in Integrative taxonomy using historical specimens provides evidence for a single species of bushbuck, Tragelaphus scriptus (Mammalia: Bovidae)

Figure 1. Map of specimens with location information used in this study (39 individuals; four additional specimens did not have location information and are not shown here). Mitochondrial subclade designations (scriptus and sylvaticus) are based on the molecular phylogeny, and are designated NA (grey) where this could not be determined. Location coordinates are based on locality information on historical specimens and were estimated as closely as possible. The modern range of the bushbuck is shown in grey (IUCN SSC Antelope Specialist Group 2016). See Supporting Information, Fig. S2 for a map labelled with specimen numbers and countries.

opencc-by-4.0Jul 2019View details →

Systematic assessment of burst impurity in confocal-based single-molecule fluorescence detection using Brownian motion simulations - raw figures of all quantities from all simulations

We performed many simulations in many conditions, calculated many quantities and reported them in the main paper. However, the journal manuscript did not place for so many figures. Nevertheless, the reported values of all simulations rely on the results that were also summarized in the figures. These figures were produced by the Jupyter notebooks analyzing the simulation results. Each figure file has the following nomenclature: TypeOfFigure_concentration_diffusionCoefficient_1or2pop_simulationDuration(long)_Type of PSF. For example: molecule_positions_pure_and_impure_bursts_varying_F_C62_D22_5_psfNumeric - report on the molecular position histograms of pure and impure bursts for varying F values, in the simulation with C=62pM, D=22.5 um^2/s, a NUmerical PSF model and 60s duration of simulation (if nothing appears, it was 60s; if the word long appears, it was 180s).

opennotspecifiedJul 2019View details →

FIGURE 3 in Using integrative taxonomy to establish the status of Alpheus peasei (Armstrong, 1940) (Decapoda: Alpheidae) as a single species throughout its distribution

FIGURE 3. Currently known distribution of Alpheus peasei (Armstrong, 1940), based on the material examined in this study and on literature records. Green point: type-locality; red points: occurrence reported previously; blue points: new records. Stars: localities of origin of the specimens used in the genetic analyses.

opennotspecifiedJul 2019View details →

FIGURE 2 in Using integrative taxonomy to establish the status of Alpheus peasei (Armstrong, 1940) (Decapoda: Alpheidae) as a single species throughout its distribution

FIGURE 2. Alpheus peasei (Armstrong, 1940), ovigerous female, Recife, Pernambuco, Brazil, MOUFPE 19428: (A) major cheliped, mesial view; (B) the same, lateral view; (C) minor cheliped, lateral view; (D) the same, mesial view; (E) second pereiopod, lateral view; (F) third pereiopod, lateral view; (G) fourth pereiopod, lateral view; (H) fifth pereiopod, lateral view; (I) detail of plunger of the major cheliped. Setae omitted. Scale bars = 1 mm.