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Fig. 5 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

Fig. 5. Clevelandella hastula (Kidder, 1937). Vietnamese specimens isolated from Panesthia angustipennis cognata Bey-Bienko, 1969 from life (A, F–H) and after protargol impregnation (B–E). A–E. Ventral view of specimens with well-preserved body shape. Arrows mark the proximal end of the peristomial opening, black arrowheads mark the proximal end of the adoral zone of membranelles. F. Ventral view, showing general organization of body. G–H. Ciliary pattern of ventral and dorsal sides. Conspicuous cilia of adoral membranelles emerge out of the peristomial opening in (G). Asterisks indicate the position of the ciliary whorl (posterior suture), arrow marks the proximal end of the peristomial opening. Scale bars = 30 μm.

Fig. 10 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

Fig. 10. Clevelandella parapanesthiae (Kidder, 1937). Vietnamese specimens isolated from Panesthia angustipennis cognata Bey-Bienko, 1969 after protargol impregnation. A–J. Variability of body shape and size as well as of the nuclear (shaded grey) and oral (shaded yellow) apparatus. Scale bar = 30 μm.

Fig. 1 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

Fig. 1. Clevelandella constricta (Kidder, 1937). Vietnamese specimens isolated from Panesthia angustipennis cognata Bey-Bienko, 1969 from life (A) and after protargol impregnation (B–N). A. Ventral view of a representative specimen, length 120 μm. B–K. Variability of body shape and size as well as of the nuclear (shaded grey) and oral (shaded yellow) apparatus. L. Semi-schematic diagram, showing the general body organization. Black double arrowhead marks densely packed, oval, refractile bodies (probably paraglycogen platelets). M–N. Ciliary pattern of ventral and dorsal sides. Arrow marks the right suture, black arrowheads indicate the position of the ciliary whorl (posterior suture). O. Prokaryotes freely scattered throughout the cytoplasm posterior to the macronucleus. P. Detail of oval, refractile bodies (probably paraglycogen platelets) anterior to the macronucleus. Scale bars = 50 μm.

Fig. 3 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

Fig. 3. Clevelandella constricta (Kidder, 1937). Vietnamese (A, E–G) and Cambodian (D) specimens isolated from Panesthia angustipennis cognata Bey-Bienko, 1969, as well as Thai I specimens (B– C) isolated from Panesthia angustipennis angustipennis (Illiger, 1801) from life (A, D–G) and after protargol impregnation (B–C). A–C. Ventral view of specimens with well-preserved body shape. D–E. Ventral view, showing the general body organization. Arrows mark oval, refractile bodies anterior to the macronucleus, black arrowheads mark the proximal end of the adoral zone of membranelles, white arrowheads denote the karyophore attached to the right and left body margins and black double arrowhead marks the canal leading from the contractile vacuole to the cytopyge. F–G. Ciliary pattern of ventral and dorsal sides. Asterisks mark the position of the ciliary whorl (posterior suture), white double arrowhead denotes the right suture. Scale bars: A–C, E–G = 50 μm; D = 20 μm.

Fig. 11 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

Fig. 11. Clevelandella parapanesthiae (Kidder, 1937). Vietnamese specimens (A–B, E–G) isolated from Panesthia angustipennis cognata Bey-Bienko, 1969 and Thai I specimens (C–D) isolated from Panesthia angustipennis angustipennis (Illiger, 1801) from life (A, E–G) and after protargol impregnation (B–D). A–D. Ventral views of specimens with well-preserved body shape. Black arrowheads mark the proximal end of the adoral zone of membranelles. E–G. A strongly squeezed specimen by pressure of the cover slip, causing the body to become markedly wider and the notch at the base of the peristomial projection to be lost. The general body organization is shown in (E), the ciliary pattern of ventral and dorsal sides is shown in (F) and (G). Asterisks mark the position of the ciliary whorl (posterior suture), white arrowhead denotes the karyophore attaching to right body margin, white double arrowhead denotes the right suture. Scale bars = 30 μm.

opencc-by-4.0Oct 2020View details →

Molecular species delimitation of larks (Aves: Alaudidae), and integrative taxonomy of the genus Calandrella, with the description of a range-restricted African relic taxon

This deposition contains the phylogenetic and species delimitation data for the manuscript "Molecular species delimitation of larks (Aves: Alaudidae), and integrative taxonomy of the genus Calandrella, with the description of a range-restricted African relic taxon" by Stervander et al.  For details of samples/sequences/leaves, please refer to Appendix A of the above manuscript.   Phylogenetic analyses <ol> <li>Fasta sequence alignment of cytochrome b for the lark family and outgroups: Alaudidae_cytb_extended_200316.fa</li> <li>BEAST v. 2.6.1 input file: Alaudidae_cytb_HKYGI_BDrelLN_modOp2003_20M1K.xml</li> <li>BEAST v. 2.6.1 output log file: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K.log</li> <li>BEAST v. 2.6.1 output (raw) trees file: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K.trees</li> <li>TreeAnnotator maximum credibility clade tree based on BEAST v. 2.6.1 output, newick format: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K_c40Mbi5.mccmed.nwk</li> </ol> Species delimitation <ol> <li>Input tree, manipulated to remove negative branch lengths (replaced by 0) and tips/leafs that are single representatives of a species, based on current taxonomy (IOC v. 10.2), newick format: Alaudidae_cytb_HKYGI_BDrelLN_c40Mbi5_mccmed_nonNeg_multiSeq_ingroup_remDuplicate.nwk</li> <li>mPTP text output of the multi-rate species delimitation, containing command for run and species delimitation results: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.1602073064.txt</li> <li>mPTP likelihood log of the multi-rate species delimitation: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.out.txt</li> <li>mPTP output tree in SVG format, with support values for species delimitation: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.1602073064.combined.svg</li> </ol>

Figure 3 in A review of molecular genetic markers and analytical approaches that have been used for delimiting marine mammal subspecies and species

Figure 3. Published values of percent divergence between cetacean subspecies (black bars), species (white bars), and taxa of uncertain taxonomic status (gray bars). Values are based on mtDNA control region sequence data. Not all values represent net sequence divergence. See Table 1 for list of papers corresponding to each value. Since completing this work, Sousa species have been supported ((Mendez et al. 2013) and Inia subspecies changed.

Figure 1 in A review of molecular genetic markers and analytical approaches that have been used for delimiting marine mammal subspecies and species

Figure 1. Sample sizes used in publications of molecular genetic studies of marine mammals at different taxonomic levels. Graphs present the proportion of studies at each taxonomic level that fall into each sample size category. (A) minimum total sample size per focal taxon; (B) maximum sample size per single sampling locality. Papers were categorized as examining taxonomic questions at: species = subspecies/species boundary; subspecies = population/subspecies boundary; uncertain = taxonomic boundary uncertain (see text).

Figure 2 in A review of molecular genetic markers and analytical approaches that have been used for delimiting marine mammal subspecies and species

Figure 2. Types of molecular genetic data used in published studies examining questions at the species-level, subspecies-level, or undefined taxonomic level for marine mammals. Note that studies may have used more than one data type. Mitochondrial DNA sequence data (MtDNASeq), nuclear DNA sequence data (NuSeq), microsatellites (Msats), morphological data (Morph).

Figure 3 in Guidelines and quantitative standards to improve consistency in cetacean subspecies and species delimitation relying on molecular genetic data

Figure 3. Flow diagram for subspecies delineation using combined quantitative and qualitative standards. The threshold values assume the user is evaluating a case relying on mtDNA control region data. Percent Diagnosable (PD) is the smallest strata-specific correct classification score in a given comparison (e.g., PD50 in two-strata comparisons in Archer et al. 2017). The second box in the second row (other evidence to meet subspecies definition) allows for subspecies delineation when both conditions are not met using mtDNA. This box could be used either for the case when one condition is met and one unmet or when both just barely miss meeting the standards. For example, consider the case with PD <95% and dA> 0.004. Diagnosability could be achieved with morphological data or nuclear data that are sufficient for subspecies but not for full species.

Figure 2. A in Guidelines and quantitative standards to improve consistency in cetacean subspecies and species delimitation relying on molecular genetic data

Figure 2. A comparison of the pairs of populations (red triangles), subspecies (green squares) and species (blue circles) estimated by Rosel et al. (2017a). Net nucleotide divergence (dA) is shown on a natural log scale to better illustrate differences between the pairwise comparisons at low levels of divergence. Bars show the central 95th-pecentile of the estimate distributions. The solid vertical line at dA = 0.020 delimits all but one species and correctly excludes all subspecies pairs. The vertical dashed line at dA = 0.004 delimits all populations from the higher taxonomic levels and correctly delimits seven of eleven subspecies. The horizontal dashed lines are two potential thresholds for percent diagnosable (80% and 95%) that are discussed in the text.

opencc-by-4.0Jan 2015View details →

Fig. 3 in Molecular and cytogenetic analyses of cryptic species within the Synbranchus marmoratus Bloch, 1795 (Synbranchiformes: Synbranchidae) grouping: species delimitations, karyotypic evolution and intraspecific diversification

Fig. 3. Representative ideograms of the analyzed karyomorphs of Synbranchus marmoratus showing the heterochromatic blocks, as determined by C-banding, and hybridization patterns of ribosomal sites.

opencc-by-4.0Jan 2015View details →

Fig. 1. A in Molecular and cytogenetic analyses of cryptic species within the Synbranchus marmoratus Bloch, 1795 (Synbranchiformes: Synbranchidae) grouping: species delimitations, karyotypic evolution and intraspecific diversification

Fig. 1. A map showing the Synbranchus marmoratus specimen collection sites. Numbers indicate the sample locality, whereas symbols represent the karyomorphs found at each locality.

opencc-by-4.0Jan 2015View details →

Fig. 4. A in Molecular and cytogenetic analyses of cryptic species within the Synbranchus marmoratus Bloch, 1795 (Synbranchiformes: Synbranchidae) grouping: species delimitations, karyotypic evolution and intraspecific diversification

Fig. 4. A dendrogram representing the relationship between the sampled Synbranchus marmoratus specimens based on the mitochondrial 16S, COI and Cyt B genes. The colors represent each of the characterized karyomorphs, and the groups (IA, IB, IC, ID and II) used as references are shown on the right side. Bootstrap support (>50%) are given above the branches. Diploid numbers of the samples are given along the branches. 2n=46* Diploid number of Ophisternon aenigmaticum (Nirchio et al., 2011).

opencc-by-4.0Dec 2023View details →

Figure 1 in Molecular diversity and species delimitation in the genus Mideopsis Neuman, 1880 in Europe (Acari, Hydrachnidia, Mideopsidae)

Figure 1. Maximum Likelihood tree (GTR+I model) of the Mideopsis spp. obtained from 71 nucleotide COI sequences. The results of the three species delimitation methods are indicated by vertical bars (BIN number given). The outgroup was removed from the figure. Only a bootstrap that supported more than 50% is reported.

Fig.14 in Molecular and morphological approaches for species delimitation and hybridization investigations of two Cichla species

Fig.14. Cluster similarity based on the meristic data of Cichla Bloch & Schneider, 1801 specimens, indicating the relationship among Cichla kelberi Kullander & Ferreira, 2006, Cichla piquiti Kullander & Ferreira, 2006 and carijó samples.

Figs 9-12. Fig. 9 in Molecular and morphological approaches for species delimitation and hybridization investigations of two Cichla species

Figs 9-12. Fig. 9, patterns of PCR-multiplex for the COI mitochondrial gene. Fig. 10, PCR-RFLP patterns of the COI gene with NlaIV enzymes. Fig. 11, patterns of PCR-multiplex for the RAG nuclear gene. Fig. 12, PCR-RFLP patterns of the RAG gene with the BsrI enzyme. The species are indicated as: column 1, Cichla kelberi Kullander & Ferreira, 2006; column 2, Cichla piquiti Kullander & Ferreira, 2006; column 3 and 4, Cichla kelberi; column 5 and 6, Cichla piquiti; column 7 and 8, carijó; M, 1 kb molecular weight marker.

Fig. 8 in Molecular and morphological approaches for species delimitation and hybridization investigations of two Cichla species

Fig. 8. Restriction maps of the COI gene and RAG1 gene for the species Cichla kelberi Kullander & Ferreira, 2006 and Cichla piquiti Kullander & Ferreira, 2006.

Fig. 13 in Molecular and morphological approaches for species delimitation and hybridization investigations of two Cichla species

Fig. 13. Principal Component Analysis (PCA) for Cichla Bloch & Schneider, 1801 specimens using morphological data. Highlight: Cichla kelberi Kullander & Ferreira, 2006, Cichla piquiti Kullander & Ferreira, 2006 and carijó samples distribution.

Figs 4-6. Fig. 4 in Molecular and morphological approaches for species delimitation and hybridization investigations of two Cichla species

Figs 4-6. Fig. 4: Cichla kelberi Kullander & Ferreira, 2006; Fig. 5: Cichla piquiti Kullander & Ferreira, 2006; Fig. 6: carijó.