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Figure. Phylogram showing phylogenetic relationships estimated using maximum likelihood analysis of 16S rRNA and COXI gene revealed the grouping of Orthochirus iranus, O. farzanpay, O. stockwelli, O. zagrosensis, O. innesi (JQ514244.1 Morocco), and O. bicolor (KT716038.1 India), with the outgroup species Androctonus crassicauda (FJ217732). in A study of genetic diversity among different population of Orthochirus sp. based on cytochrome C oxidase subunit I and 16srRNA sequencing

Figure. Phylogram showing phylogenetic relationships estimated using maximum likelihood analysis of 16S rRNA and COXI gene revealed the grouping of Orthochirus iranus, O. farzanpay, O. stockwelli, O. zagrosensis, O. innesi (JQ514244.1 Morocco), and O. bicolor (KT716038.1 India), with the outgroup species Androctonus crassicauda (FJ217732).

Figure S2 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities

Figure S2. ABGD results of COXI gene. The histogram shows distribution of genetic distances among M. arvalis samples; yellow columns show mean intralineage distances and red columns show interlineage distances. The diagram implies the lineages according to initial partitions = Group 1 (n: 21): Anatolia, China, Asian and European parts of Russia; Group 2 (n: 16): Serbia, Hungary.

Figure S1 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities

Figure S1. ABGD results of CYTB gene region. The histogram shows distribution of genetic distances among M. arvalis samples; yellow columns show mean intralineage distances and red columns show interlineage distances. The diagram implies the lineages according to initial partitions = Group 1 (n: 56): Anatolia, Georgia, Armenia, Iran, Siberia, China, Asian parts of Russia and one sample from Ukraine; Group 2 (n: 31): European parts of Russia, three samples from Ukraine, Western, Central and Eastern Europe.

Figure 7 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities

Figure 7. Bayesian tree obtained from IRBP sequences based on HKY + G parameter (Hasegawa et al., 1985). Numbers on branches show posterior probability (pb) values above 50%.

Figure 6 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities

Figure 6. Median-joining network obtained from IRBP haplotypes of Anatolian, Asian and European populations of M. arvalis. Number of mutations are shown by black lines on the branches.

Figure 5 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities

Figure 5. Bayesian tree obtained from COXI sequences based on HKY + I parameter (Hasegawa et al., 1985). Numbers on branches show posterior probability (pb) values above 50%.

Figure 4 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities

Figure 4. Median-joining network obtained from COXI haplotypes of Anatolian, Asian and European populations of M. arvalis. Number of mutations are shown by black lines on the branches.

Figure S3 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities

Figure S3. ABGD results of IRBP gene region. The histogram shows distribution of genetic distances among M. arvalis samples; yellow columns show mean intralineage distances and red columns show interlineage distances. The diagram implies the lineages according to initial partitions = Group 1 (n: 28): Anatolia, Serbia, Hungary, Iberian Peninsula; Group 2 (n: 1): one sample from Anatolia.

Figure 3 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities

Figure 3. Bayesian tree obtained from CYTB sequences based on HKY+I+G parameter (Hasegawa et al., 1985). Numbers on branches show posterior probability (pb) values above 50%.

Figure 1. Figure 1 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities

Figure 1. Figure 1. Location map of AUMAC samples and GenBank Sequences (modified from Yiğit et al. 20161). Black line is the border of arvalis and obscurus forms; dotted lines show possible hybridization zone of the two forms. Western Europe (1: Orkney Island, 2: Spain, 3: France, 4: Belgium), Central Europe (5: Germany, 6: Switzerland, 7: Czech Republic), Eastern Europe (8: Austria, 9: Slovenia, 10: Bosnia, 11: Montenegro, 12: Serbia, 13: Hungary, 14: Poland, 15: Ukraine, 16: European Russia/Vladimir, 17: European Russia/ Arkhangelsk Oblast) groups are 'arvalis' form. Anatolia and its surroundings (18: Anatolia/Ardahan, Kars and Erzurum provinces, 19: Iran, 20: Armenia) and Asia (21: Russia/Orenburg Oblast, 22: Russia/ Chelyabinsk Oblast, 23: China/Xinjiang, 24: Siberia) belong to 'obscurus' form.

Fig. 5 in Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation

Fig. 5. Phylogenetic tree based on analysis of mitochondrial COI sequences of the Sarcocystidae including the new Sarcocystis sp. examined in this study (black symbols). Other taxa of the Apicomplexa served as root. Evolutionary history was inferred by the Maximum Likelihood (ML) method based on the TamuraNei model, whereby 619 positions were included in the final data set. All positions with less than 95% site coverage were eliminated; that is, fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. Bootstrap percentages (1000 iterations) are shown next to branches. COI sequences E357-13 and E120-13 (not shown in the tree) are available at GenBank (MN732561 and MN732562, respectively).

Fig. 2 in Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation

Fig. 2. Ultrastructure of S. scandentiborneensis sp. nov. Note, due to ethanol-fixation some ultrastructural details are poorly resolved (e.g. membranes). A) Longitudinal section through the same sample as in Fig. 1C, showing a gross view of the sarcocyst and its villous protrusions (VP) that are sectioned in different orientations. The inset shows a cross section through various VP that reveals the arrangement of microtubules in their inner core; while in this case 16 microtubules are visible (asterisks), sections through more apical portions of the VP showed lower numbers. B) Longitudinal section through the fingerlike VPs that appear to be anchored in the ground substance (arrow) by microtubules (asterisks) that extend into each protrusion; note the electron-dense, U-shaped structure at each tip of the protrusions (arrowheads) and the apparently serrated surface of the VP (flat arrowheads). The inset shows a higher magnification of the apical part of a single VP with the typical U-shaped apex (asterisk), which appears to be connected with the host cell through an electronlucent contact zone (white arrowheads); interestingly, the protrusion appears fenestrated (also visible in the main image) possessing thorn-like structures (black arrows; the white arrow indicates a crosssectional view) that could be responsible for the serration visible at lower magnification. CZ, cystozoites; HC, host cell; VP, villous protrusion.

Fig. 1 in Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation

Fig. 1. Light microscopy of Sarcocystis scandentiborneensis sp. nov. A and B, Haematoxylin & Eosinstained histological sections of striated musculature; C and D, Richardson's dye-stained 1.0 μm thin sections of sarcocysts. A) Tissue section of laryngeal muscle with various sarcocysts in cross section (asterisks), indicating a relatively high density of cysts in this part of musculature. B) Longitudinal section through a sarcocyst, showing a cigar-shaped appearance; however, isolated native sarcocysts, which were not available, may look different. C) Part of a longitudinal section through the tip of a sarcocyst, note the very thin ground substance (arrows) and the fine septae extending into the interior of the cyst (arrowheads); cystozoites (CZ) were loosely scattered within chambers while metrocytes were rarely seen, indicating maturity of the cyst; bars indicate the variable thickness of the cyst wall: the wall was thinner in regions where the villous protrusions were bent (right bar); note that the intense staining at the interface between host cell (HC) and parasite is part of the host cell. D) Cross-section through a sarcocyst showing cystozoites and the cyst wall (bar) including its thin ground substance (arrows).

Fig. 4 in Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation

Fig. 4. Mapping (to the Toxoplasma gondii reference molecule M97703) of frequencies (%) of base pair changes observed in sequence comparisons of nu clear 18S rDNA within the new Sarcocystis sp. from treeshrews (intraspecific variation: isolates E364–13 versus E357–13) and between the new species and Sarcocystis zuoi and/or S. clethrionomyelaphis (interspecific variation: E364–13 versus S. zuoi/clethrionomyelaphis). Results were combined for the two latter species to simplify the graph. Here, 87.2% of 2118 alignment positions showed moderate to high levels of consistency, while sections of ambiguous alignment did not relate to the species under investigation. Due to gaps in the alignment, not all of the observed nt changes could be mapped to a homologous position of the reference molecule (i.e., 7 out of 24 bp changes in intraspecific comparison; 33 out of 74 bp changes in interspecific comparison), in which case the position of each nt relative to the helix was inferred from neighboring nt for which such position was known. Gaps were mainly due to insertions in helices V2, V4, and V9 rendering E357-13/E364-13 longer than the sequence of T. gondii. The percentage of parsimony-informative (pi) bp changes per helix is shown for helices V1, V2, V4, V7, and V9 above each column. Also shown is the ratio of transitions versus transversions (Ti/Tv) for selected helices.

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Fig. 5. Maximum likelihood phylogenetic tree inferred from nucleotide sequence data from mitochondrial 16S in A herpetological survey of western Zambia

Fig. 5. Maximum likelihood phylogenetic tree inferred from nucleotide sequence data from mitochondrial 16S rRNA of Phrynobatrachus natalensis. Numbers above branches are non-parametric bootstrap support values. Specimen vouchers or GenBank accession numbers are shown in parentheses. Colored polygons highlight the clades comprising specimens from this study. (*) Nearest sample from type locality of Phrynobatrachus natalensis; (**) Haplotype groups A and B in Zimkus and Schick (2010).

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Fig. 2. Statistical parsimony cladogram network representing relationships among the 45 haplotypes for a 615 in Genetic diversity of Halyomorpha halys (Hemiptera, Pentatomidae) in Korea and comparison with COI sequence datasets from East Asia, Europe, and North America

Fig. 2. Statistical parsimony cladogram network representing relationships among the 45 haplotypes for a 615 bp fragment of the COI gene of Halyomorpha halys. Each circle is labeled with haplotype number, and the size of each circle is proportional to the frequency of each haplotype [H3 (n = 353); H1 (n = 285); H22 (n = 43); H8 (n = 34); H33 (n = 23); H2 (n = 16); H32 (n = 8); H7, H9–H13, and H43 (n = 3); H6, H14, H34, H39, and H40 (n = 2); H4–H5, H12, H15–H21, H23, H30–H31, H35–H38, H41, H42, and H44–H51 (n = 1)]. Differing colors indicate countries in which samples were collected.

Fig. 10 in Micropathogen community identification in ticks (Acari: Ixodidae) using third-generation sequencing

Fig. 10. Phylogenetic analysis of the isolated bacteria/viruses. Reference oligonucleotide sequences were selected by BLAST searches of the NCBI nt database. (A) Subtrees of the experimental sequences from the Borrelia burgdorferi 16S rRNA gene. (B) Subtrees of the experimental sequences from the Coxiella burnetii 16S rRNA gene. (C) Subtrees of the experimental sequences from the Anaplasma phagocytophilum MSP4 gene. (D) Subtrees of the experimental sequences from the Simian foamy virus pathogen. (E) Subtrees of the experimental sequences from the Crimean-Congo haemorrhagic fever orthonairovirus segment-S gene.

Fig. 7 in Micropathogen community identification in ticks (Acari: Ixodidae) using third-generation sequencing

Fig. 7. Population distribution of micropathogens in different samples. Note: "%" represents the proportion of micropathogen in the total community from each sample.

Fig. 3 in Micropathogen community identification in ticks (Acari: Ixodidae) using third-generation sequencing

Fig. 3. Venn diagram based on the eggNOG database. Note: The corresponding functional categories and non-supervised orthologous group (NOG) numbers were obtained from the eggNOG database.

Fig. 5 in Micropathogen community identification in ticks (Acari: Ixodidae) using third-generation sequencing

Fig. 5. Heat maps of community composition based on genera. Note: X-axis, template name; Y-axis, genus. The darker the blue colour is, the higher the enrichment of the genus in the sample.