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Fig. 2 in Phylogenetic relationships of Eurema butterflies from Peninsular Malaysia inferred from CO1 and 28S gene sequences with emphasis on Eurema hecabe

Fig. 2. Phylogenetic tree of Maximum-Likelihood method showing the comparison of phylogram as inferred from partial sequences of mtDNA CO1 and 28S rDNA genes. The bootstrap scores obtained from 1,000 replicates for ML/MP analyses are shown at the branching point. The trees were rooted with the genus Graphium.

Figure S1 in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods

Figure S1. Map of the Gigantometra gigas mitogenome using Sanger method (GenBank accession number: MF177288). Genes in the outer circle indicate the direction of transcription of the majority strand (J-strand), and those in the inner circle indicate that of the minority strand (N-strand). The GC content, GC skew+, and GC skew- are separately shown in the circle.

Figure 6 in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods

Figure 6. Two examples of the heteroplasmic sites in Sanger sequencing which correspond to the differently sequenced sites. Panels A and B indicate the sites at which the second-peak is obviously higher than the third-peak and fourth-peak, and the base state of the second-peak can be obtained by at least one result of HTS. The different fluorescence densities of base situated at np 1923 in the cox1 are shown in the panel A, and the panel B shows the nucleotides with amino acids at np 1923 in the results of Sanger and HTS methods. The nucleotides are C in the results of HTS sequencing, while the corresponding nucleotides are T in the results of Sanger method in both positions, and the different nucleotides lead not to the amino acids changed. Panels C and D indicate the site at the unobvious second-peak, which is slightly higher than the third-peak and fourth-peak, and the base state of the second-peak can also be obtained by at least one result of HTS. Panel C shows the unobvious second-peak at np 7125, and the nucleotide and amino acid of the site in the results of Sanger and HTS methods are shown in panel D. The amino acids are listed using single-letter amino acid abbreviations.

Figure 4. Intraspecific pairwise K2P in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods

Figure 4. Intraspecific pairwise K2P distance of G. gigas based on barcode fragment size of cox1 (Sanger). The red boxplot shows the genetic distances of individuals in all three collecting sites, and the boxplots (blue, green, and yellow) separately show the distances of individuals within each place (HNYG, HNDL, and VIET). The pink boxplot shows the distances of the corresponding cox1 sequences obtained by the two sequencing methods. Abbreviation: HNYG—Yinggeling Nature Reserve, Hainan; HNDL— Diaoluoshan Nature Reserve, Hainan; VIET—northern Vietnam.

Figure S5 in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods

Figure S5. The coverage of short fragments at each position in the assembly results of HTS. The three results of HTS method were separately used as reference sequences to be mapped back onto the corresponding HTS scaffolds, and the mitochondrial genes were shown below the corresponding coverage. The scale bar had an indicator at the mean coverage level and the coverage for each nucleotide position was indicated by the height of the blue line.

Figure 3 in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods

Figure 3. The different nucleotides in the ITS-1 and ITS-2 regions are shown. The result shows the different nucleotides at nucleotide position np 1897 (G nucleotide and T nucleotide) and np 2790 (C nucleotide and T nucleotide) obtained by Sanger and HTS methods.

Figure 1. Gigantometra gigas. A. Female, dorsal view. B. Male, dorsal view. C in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods

Figure 1. Gigantometra gigas. A. Female, dorsal view. B. Male, dorsal view. C. The narrow distribution of G. gigas.

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Fig. 1 in Molecular Systematics of Mouse Opossums (Didelphidae: Marmosa): Assessing Species Limits using Mitochondrial DNA Sequences, with Comments on Phylogenetic Relationships and Biogeography

Fig. 1. Provenance of sequenced specimens of Marmosa (localities of sequenced outgroup specimens are not shown). Numbers refer to entries in the Gazetteer (appendix).

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Fig. 3 in Molecular Systematics of Mouse Opossums (Didelphidae: Marmosa): Assessing Species Limits using Mitochondrial DNA Sequences, with Comments on Phylogenetic Relationships and Biogeography

Fig. 3. The maximum-likelihood tree inferred from the best-fit model of nucleotide substitution (table 4). ML bootstrap support values and Bayesian posterior probabilities are indicated above and below branches, respectively. Branch and terminal labels follow the same conventions explained in the caption to figure 2.

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Fig. 2 in Molecular Systematics of Mouse Opossums (Didelphidae: Marmosa): Assessing Species Limits using Mitochondrial DNA Sequences, with Comments on Phylogenetic Relationships and Biogeography

Fig. 2. Strict consensus of 96 equally most-parsimonious trees (L 5 2198; CI 5 0.36; RI 5 0.80). Bootstrap support values are indicated above branches subtending species and conspecific haplogroups discussed in the text. For each terminal, country of origin, next-largest political unit (state, department, province, etc.), and an alphanumeric specimen identifier (from table 2) are provided. Numbers in parentheses refer to localities mapped in figure 1 and listed in the Gazetteer (appendix).

Fig. 5 in Total Evidence, Sequence Alignment, Evolution of Polychrotid Lizards, and a Reclassification of the Iguania (Squamata: Iguania)

Fig. 5. The same consensus as shown in figure 4, with stems and taxa identified for ready comparison with evolutionary changes presented in appendix 4 (change list). Stems 5, 6, 16, 20, 23, 24 represent alternative relationships not rejected by the data.

Fig. 3. Sensitivity analysis graphic. Y in Total Evidence, Sequence Alignment, Evolution of Polychrotid Lizards, and a Reclassification of the Iguania (Squamata: Iguania)

Fig. 3. Sensitivity analysis graphic. Yaxis represents the logarithm of the ratio of transversion: transition weights. The xaxis represents the logarithm of the ratio of the indel cost versus the maximal cost of a molecular change. The colors represent the zaxis, which is congruence between the molecular and morphological data partitions. Red is good, blue is bad.

Fig. 2 in Total Evidence, Sequence Alignment, Evolution of Polychrotid Lizards, and a Reclassification of the Iguania (Squamata: Iguania)

Fig. 2. Strict consensus of 192 equally parsimonious trees based on morphology alone (length = 276; CI = 0.443; RI = 0.74). Numbers on branches are Bremer values.

Fig. 6 in Total Evidence, Sequence Alignment, Evolution of Polychrotid Lizards, and a Reclassification of the Iguania (Squamata: Iguania)

Fig. 6. Phylogenetic hypotheses for the Polychrotidae of Etheridge and de Queiroz (1988), and Frost and Etheridge (1989). Circles represent hypothesized rooting points.

Fig. 1 in Total Evidence, Sequence Alignment, Evolution of Polychrotid Lizards, and a Reclassification of the Iguania (Squamata: Iguania)

Fig. 1. Single tree obtained on molecularonly data (length = 2332; CI = 0.23; RI = 0.68). Numbers on branches are Bremer values.

Fig. 2 in Some Unusual Small-Subunit Ribosomal RNA Sequences of Metazoans

Fig. 2. Phylogenetic tree of the centipedes based on the combined analysis of Edgecombe et al. (1999). The arrow indicates where the insertion of ca. 300 bp at region V7 occurred during the evolution of centipedes.

Fig. 5 in Some Unusual Small-Subunit Ribosomal RNA Sequences of Metazoans

Fig. 5. Phylogenetic analysis of the data from fig. 4 using the ''fixed character states'' method of Wheeler (1999) implemented in the computer program POY (Gladstein and Wheeler, 1997). Commands: poy fixedstates noleading norandomizeoutgroup gap 1 maxtrees 20 multibuild 10 seed‾1 slop 2 checkslop 5. The two circles illustrate the insertions of the Geophilomorpha (ca. 300 bp), and the Scolopendridae (ca. 25 bp).

Fig. 1 in Some Unusual Small-Subunit Ribosomal RNA Sequences of Metazoans

Fig. 1. Schematic representation of the 18S rRNA locus. The gray squares represent the variable regions V2, V4, V7, and V9 with insertions (V2: Onychophora, Geophilomorpha, Cephalopoda, Archaeogastropoda; V4: Hexapoda, Crustacea, Pauropoda, Holothuroidea, Chaetognatha, Platyhelminthes, Cephalopoda; V7: Onychophora, Hexapoda, Crustacea, Pauropoda, Chilopoda, Platyhelminthes, Hirudinea, Cephalopoda, Gastropoda; V9: Onychophora, Crustacea, Cephalopoda). The black arrowheads represent particular insertions (10: Pauropoda; 11: Onychophora; E23–7: Onychophora and Pauropoda; E23–8: Pauropoda; 29: Pauropoda; 46: Protura). The black bar represents the 500 bp deletion of the Symphyla.

Fig. 3 in Some Unusual Small-Subunit Ribosomal RNA Sequences of Metazoans

Fig. 3. Phylogenetic tree based on 18S rRNA sequence data indicating the position of two symphylans (box) with respect to other myriapods (underlined taxa) in a phylogenetic analysis of arthropods (from Giribet, 1997). The two symphylans appear related to other myriapods.