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Figure 2 from: Mar-Silva AF, Arroyave J, Díaz-Jaimes P (2022) The complete mitochondrial genome of the Mexican-endemic cavefish Ophisternon infernale (Synbranchiformes, Synbranchidae): insights on patterns of selection and implications for synbranchiform phylogenetics. ZooKeys 1089: 1-23. https://doi.org/10.3897/zookeys.1089.78182

Figure 2 Results from analysis of Relative Synonymous Codon Usage (RSCU) of the mitochondrial genome of O. infernale. Codon families are plotted on the x-axis. The label for the 2, 4, or 6 codons that compose each family is shown in the boxes below the x-axis, and the colors correspond to those in the stacked columns. RSCU values are shown on the y-axis.

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Figure 1 from: Mar-Silva AF, Arroyave J, Díaz-Jaimes P (2022) The complete mitochondrial genome of the Mexican-endemic cavefish Ophisternon infernale (Synbranchiformes, Synbranchidae): insights on patterns of selection and implications for synbranchiform phylogenetics. ZooKeys 1089: 1-23. https://doi.org/10.3897/zookeys.1089.78182

Figure 1 Annotated map of the mitochondrial circular genome of O. infernale. The outer ring corresponds to the H- (outermost) and L-strands, and depicts the location of PCGs (in black, except for ND6 which is encoded in the L-strand and is portrayed in red), the non-coding control region (in dark brown), tRNAs (in red), and rRNAs (in light brown). The inner ring (black sliding window) denotes GC content along the genome. Live specimen photograph taken in the Cenote Kancabchen (Homún, Yucatán), courtesy of cave diver Erick Sosa.

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Supplementary material 2 from: Dooley KE, Niemiller KDK, Sturm N, Niemiller ML (2022) Rediscovery and phylogenetic analysis of the Shelta Cave Crayfish (Orconectes sheltae Cooper & Cooper, 1997), a decapod (Decapoda, Cambaridae) endemic to Shelta Cave in northern Alabama, USA. Subterranean Biology 43: 11-31. https://doi.org/10.3897/subtbiol.43.79993

Table S2

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Supplementary material 1 from: Dooley KE, Niemiller KDK, Sturm N, Niemiller ML (2022) Rediscovery and phylogenetic analysis of the Shelta Cave Crayfish (Orconectes sheltae Cooper & Cooper, 1997), a decapod (Decapoda, Cambaridae) endemic to Shelta Cave in northern Alabama, USA. Subterranean Biology 43: 11-31. https://doi.org/10.3897/subtbiol.43.79993

Table S1

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Figure 1 in Tracking the trends of karyotype differentiation in the phylogenetic context of Gint, a scorpion genus endemic to the Horn of Africa (Scorpiones: Buthidae)

Figure 1. Map showing distribution of the sampled Gint species. Bottom right – G. amoudensis.

Supplementary material 3 from: Kanda K, Gomez AR, Van Driesche R, Miller KB, Maddison DR (2016) Phylogenetic placement of the Pacific Northwest subterranean endemic diving beetle Stygoporus oregonensis Larson & LaBonte (Dytiscidae, Hydroporinae). ZooKeys 632: 75-91. https://doi.org/10.3897/zookeys.632.9866

Table 1 : Explanation note: Collection and specimen data for material examined in this study.

Supplementary material 4 from: Kanda K, Gomez AR, Van Driesche R, Miller KB, Maddison DR (2016) Phylogenetic placement of the Pacific Northwest subterranean endemic diving beetle Stygoporus oregonensis Larson & LaBonte (Dytiscidae, Hydroporinae). ZooKeys 632: 75-91. https://doi.org/10.3897/zookeys.632.9866

Table 2 : Explanation note: PCR primers and amplification conditions for sampled gene fragments.

Figure 3 from: Kanda K, Gomez AR, Van Driesche R, Miller KB, Maddison DR (2016) Phylogenetic placement of the Pacific Northwest subterranean endemic diving beetle Stygoporus oregonensis Larson & LaBonte (Dytiscidae, Hydroporinae). ZooKeys 632: 75-91. https://doi.org/10.3897/zookeys.632.9866

Figure 3 - Maximum likelihood tree from concatenated dataset. Scale bar = 0.2 expected substitutions per position as estimated by RAxML. Stygoporus oregonensis in orange; other stygobitic dytiscids in blue; the epigean genus Sanfilippodytes, hypothesized by Larson and LaBonte (1994) to be the closest relative to Stygoporus oregonensis, in green. Bootstrap support given at nodes for Siettitiina and Stygoporus oregonensis + Ereboporus naturaconservatus.

Figure 2 from: Kanda K, Gomez AR, Van Driesche R, Miller KB, Maddison DR (2016) Phylogenetic placement of the Pacific Northwest subterranean endemic diving beetle Stygoporus oregonensis Larson & LaBonte (Dytiscidae, Hydroporinae). ZooKeys 632: 75-91. https://doi.org/10.3897/zookeys.632.9866

Figure 2 - The two known collection localities of Stygoporus oregonensis. Oregon/Washington State boundary in black. County boundaries in brown. Blue shaded region outlined with a dotted line corresponds to Willamette Lowland basin-fill aquifers. Type locality indicated by red star with black border. New collection locality indicated by black star.

Figure 4 from: Kanda K, Gomez AR, Van Driesche R, Miller KB, Maddison DR (2016) Phylogenetic placement of the Pacific Northwest subterranean endemic diving beetle Stygoporus oregonensis Larson & LaBonte (Dytiscidae, Hydroporinae). ZooKeys 632: 75-91. https://doi.org/10.3897/zookeys.632.9866

Figure 4 - Majority rule consensus of 1,000 bootstrap replicates performed on concatenated dataset. Bootstrap percentages given for clades recovered with more than 50% support. Branches and taxa colored as in Figure 3.

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Figure 8. Phylogenetic tree for 12S in New insight into the systematic position of the endemic Madagascan genus Amberiana (Hemiptera: Heteroptera: Dinidoridae) using 12S rDNA sequences

Figure 8. Phylogenetic tree for 12S rDNA sequences of 28 species used in this study generated by using the neighbor-joining method. Bootstrap support is indicated at nodes; the frame shows the clade consisting of Amberiana montana and Sehirus luctuosus.

Fig. 58. Hoplopleura ileile, female. A in Systematic Review of Endemic Sulawesi Squirrels (Rodentia, Sciuridae), with Descriptions of New Species of Associated Sucking Lice (Insecta, Anoplura), and Phylogenetic and Zoogeographic Assessments of Sciurid Lice

Fig. 58. Hoplopleura ileile, female. A, dorsoventral view; B, thoracic sternal plate; C, paratergal plates; D, genitalia.

Fig. 57. Hoplopleura heinrichi, female. A in Systematic Review of Endemic Sulawesi Squirrels (Rodentia, Sciuridae), with Descriptions of New Species of Associated Sucking Lice (Insecta, Anoplura), and Phylogenetic and Zoogeographic Assessments of Sciurid Lice

Fig. 57. Hoplopleura heinrichi, female. A, dorsoventral view; B, thoracic sternal plate; C, paratergal plates; D, genitalia.

Fig. 60 in Systematic Review of Endemic Sulawesi Squirrels (Rodentia, Sciuridae), with Descriptions of New Species of Associated Sucking Lice (Insecta, Anoplura), and Phylogenetic and Zoogeographic Assessments of Sciurid Lice

Fig. 60. Valley of Danau Lindu, 1000 m, in the northern highlands of the western mountain block of Sulawesi's central core. Part of Tomado village is in the foreground on the shore of a small cove. Tropical lowland evergreen rain forest is at lake level and mantles hillsides of the closer ridges. Upper slopes and summits in the background are clothed in montane forest formations. The large, red tree squirrel Rubrisciurus rubriventer lives in intact forest near the lake and in forests on the ridges to about 1500 m. Montane forests on the upper slopes and summits of the higher ridges (Gunung Nokilalaki is the farthest ridge seen in the background), support one ground squirrel, Hyosciurus heinrichi, which abuts the range of the other ground squirrel H. ileile at 1400–1500 m, and that species, while uncommon, occurs throughout the region at lower altitudes. The tree squirrels Prosciurillus topapuensis and P. murinus inhabit all oldgrowth habitats, from lakeside to tops of the highest ridges. Photographed in 1976.

Fig. 53. Hoplopleura murinus, female. A in Systematic Review of Endemic Sulawesi Squirrels (Rodentia, Sciuridae), with Descriptions of New Species of Associated Sucking Lice (Insecta, Anoplura), and Phylogenetic and Zoogeographic Assessments of Sciurid Lice

Fig. 53. Hoplopleura murinus, female. A, dorsoventral view; B, thoracic sternal plate; C, paratergal plates; D, genitalia.

Fig. 44. A in Systematic Review of Endemic Sulawesi Squirrels (Rodentia, Sciuridae), with Descriptions of New Species of Associated Sucking Lice (Insecta, Anoplura), and Phylogenetic and Zoogeographic Assessments of Sciurid Lice

Fig. 44. A closer look at the squirrel shown in figure 43, just as it was fleeing the confines of the cage.

Fig. 42 in Systematic Review of Endemic Sulawesi Squirrels (Rodentia, Sciuridae), with Descriptions of New Species of Associated Sucking Lice (Insecta, Anoplura), and Phylogenetic and Zoogeographic Assessments of Sciurid Lice

Fig. 42. Habitat of Hyosciurus heinrichi in upper montane forest on Gunung Nokilalaki, 2256 m. Traps set on top and beneath the rotting log in foreground took examples of H. heinrichi, which is common on the summit and upper slopes in this mossy, wet and cold forest. Photographed in 1975.

Fig. 48. Hoplopleura leucomus, female. A in Systematic Review of Endemic Sulawesi Squirrels (Rodentia, Sciuridae), with Descriptions of New Species of Associated Sucking Lice (Insecta, Anoplura), and Phylogenetic and Zoogeographic Assessments of Sciurid Lice

Fig. 48. Hoplopleura leucomus, female. A, dorsoventral view; B, thoracic sternal plate; C, D, paratergal plates showing slight variation between specimens from two geographic regions (C is from the holotype louse from Labuan Sore in Central Sulawesi, D is from a louse specimen from Rurukan in north Sulawesi); E, genitalia.

Fig. 38 in Systematic Review of Endemic Sulawesi Squirrels (Rodentia, Sciuridae), with Descriptions of New Species of Associated Sucking Lice (Insecta, Anoplura), and Phylogenetic and Zoogeographic Assessments of Sciurid Lice

Fig. 38. Specimen scores representing population samples of Hyosciurus heinrichi (filled circle, Gunung Kanino and Gunung Nokilalaki; N 5 35) and H. ileile (filled triangle, Sungai Sadaunta, Gunung Kanino, and Sungai Tolewonu; N 5 11) projected onto the first and second principal components extracted from principal-components analysis. Each ellipse outlines 95% confidence limits for specimen scores of each cluster. Equations for the regression lines are: H. ileile, Y 5 20.121X+0.095 (F 5 3.20, P 5,0.10); H. heinrichi, Y 5 20.213X20.033 (F 5 18.96, P 5,0.001). The regression lines of the second principal component on the first are unambiguously distinct: their Y-intercepts are significantly different (+0.095 versus 20.033; F 5 15.38, P 5,0.001), but not their slopes (20.121 versus 20.213; F 5 1.16, P 5 0.288). The distribution of scores along the first axis is strongly influenced by length of tail, and the single point for H. ileile and the two for H. heinrichi situated far to the left of the main clouds of scores represent specimens with the shortest tails in the samples; the tails are naturally short, not damaged in traps or mangled by a predator and subsequently healed. Data were derived only from specimens captured and measured by Musser. See table 46 for correlations and percent variance.

Fig. 31 in Systematic Review of Endemic Sulawesi Squirrels (Rodentia, Sciuridae), with Descriptions of New Species of Associated Sucking Lice (Insecta, Anoplura), and Phylogenetic and Zoogeographic Assessments of Sciurid Lice

Fig. 31. Specimen scores representing Prosciurillus murinus (filled circle; N 5 57) and P. abstrusus (filled triangle; N 5 14) projected onto the first and second principal components extracted from principalcomponents analysis. Arrow identifies holotype of abstrusus. See table 39 for correlations and percent variance.