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Figure 1 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures
Figure 1. Mitochondrial genome synteny in Cubaris murina and closely related species. A dash (-) before the gene name means that the gene is encoded on the light strand. NCR means a non-coding region that is longer than 100 bp. Cubaris murina is marked in bold black and shades of grey.
Figure 2 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures
Figure 2. Secondary structure of each transfer RNA (tRNA) visualised in Forna (http://rna.tbi.univie.ac. at/forna).
Table 3 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures
<p><b>Table 3.</b> Characteristic (AT content, repeat, number of predicted secondary structure, range of <i>ΔG</i> value (kcal/mol)) of control region of <i>Cubaris murina</i> by RNAstructure.</p><table><tbody><tr><th></th><th></th><th></th><th></th><th>Length</th><th></th><th></th><th></th><th>Number of predicted</th><th></th></tr></tbody><tbody><tr><th>Species [reference]</th><td>Name</td><td>Start</td><td>Stop</td><td>(bp)</td><td>Location</td><td>%AT</td><td>Repeat</td><td>secondary structures</td><td><i>ΔG</i> value (kcal/mol)</td></tr><tr><th><i>Cubaris murina</i></th><td>NCR1</td><td>5219</td><td>5360</td><td>142</td><td>Between <i>nad1</i> and <i>trnN</i></td><td>52.80%</td><td></td><td>7</td><td>−16.9 to −15.4</td></tr><tr><th>[present study]</th><td>NCR2</td><td>6297</td><td>6666</td><td>370</td><td>Between <i>trnS1</i> and <i>trnL1</i></td><td>59.70%</td><td>CT-rich & AT-loop</td><td>20</td><td>−103.7 to −101.0</td></tr><tr><th></th><td>NCR3</td><td>12,550</td><td>12,753</td><td>204</td><td>Between <i>rrnL</i> and <i>trnE</i></td><td>71.10%</td><td>poly-A</td><td>7</td><td>−17.5 to −17.1</td></tr><tr><th></th><td>NCR4</td><td>12,813</td><td>12,950</td><td>138</td><td>Between <i>trnE</i> and <i>trnV</i></td><td>71.70%</td><td>AG-rich</td><td>5</td><td>−13.4 to −12.3</td></tr><tr><th><i>Panulirus argus</i> [Baeza, 2018]</th><td>NCR</td><td>13,525</td><td>14,326</td><td>801</td><td>Between <i>rrnS</i> and <i>trnI</i></td><td>69.60%</td><td>AT-rich</td><td>7</td><td>−99.20 to −94.52</td></tr><tr><th><i>Synalpheus microneptunus</i> [Chak <i>et al.</i>, 2020]</th><td>NCR</td><td>13,365</td><td>14,198</td><td>834</td><td>Between <i>rrnS</i> and <i>trnI</i></td><td>79.50%</td><td>AT-rich</td><td>20</td><td>− 104 (lowest)</td></tr></tbody></table>
FIGURE 5 in Specific limits and emerging diversity patterns in East African populations of laminate-toothed rats, genus Otomys (Muridae: Murinae: Otomyini): Revision of the Otomys typus complex 3024
FIGURE 5. Principal components analysis (PCA) based on nine craniometric variables indicating scatter of individuals on PC1 and PC2 (a) and PC2 and PC3 (b) from six pre-defined taxon-groups of Ethiopian Otomys in relation to existing type specimens of fortior and degeni and new holotypes designated for new species (see Taxonomic Summary). Open squares = O. typus s.s., open triangles = O. fortior; open diamonds = O. yaldeni sp. nov. (= Sp. A); closed squares = O. helleri (= Sp. B); open circles = O. cheesmani sp. nov. (= Sp.C); closed diamonds = O. simiensis sp. nov. (= Sp. D); cross = degeni. Type specimens indicated; normal font indicates existing holotypes; bold font represents newly designated holotypes (see Taxonomic Summary).
FIGURE 16. Photographs a in Specific limits and emerging diversity patterns in East African populations of laminate-toothed rats, genus Otomys (Muridae: Murinae: Otomyini): Revision of the Otomys typus complex 3024
FIGURE 16. Photographs a) comparing pairs of study skins from three populations in the Aberdares: O. tropicalis (from midaltitudes, two skins on left, and summit, two skins in middle) and O. orestes (two skins on right); and (b) comparing O. thomasi (left) with series of O. orestes (right). Apparent differences in size are not due to over-stuffing of specimens but more or less indicative of real size difference as can be verified from inspection of means of head and body length of relevant taxa in Table 9
FIGURE 3a. Bayesian phylogeny inferred from cyt b in Specific limits and emerging diversity patterns in East African populations of laminate-toothed rats, genus Otomys (Muridae: Murinae: Otomyini): Revision of the Otomys typus complex 3024
FIGURE 3a. Bayesian phylogeny inferred from cyt b sequences partitioned by codon position for 34 East African specimens of O. typus s.l. and O. tropicalis s.l. in relation to representatives of seven Otomys species and Parotomys brantsii from eastern, western and southern Africa. Representatives of nine murine taxa served as outgroups (see Appendix 1). Nodal support indices for the main clades (annotated 1 to 8) and subclades (a, b, c, d and e), as well as supported deeper nodes (A, H, I, M, N, O) are given beside the phylogram in the following order: Bayesian posterior probabilities (BPP)/ bootstrap support from 1000 replicates for maximum likelihood (MLbs), under an unpartitioned GTR+I+G model/ unweighted parsimony (UwPbs), six-parameter-weighted parsimony partitioned by codon positions (6PPbs)/ neighbour-joining using uncorrected p-distances (Njpbs)/ neighbour-joining using GTR+I+G-corrected distances (Njcbs). Estimated divergence dates (Myr) for the major lineages identified in the cyt b phylogeny are indicated to the left of each node. Bayesian estimation of divergence times was conducted under a relaxed clock model using BEAST v.1.4. Four well established murine fossil calibration points were specified (Pocock 1987; Rowe et al. 2008, see text).
FIGURE 9 in Specific limits and emerging diversity patterns in East African populations of laminate-toothed rats, genus Otomys (Muridae: Murinae: Otomyini): Revision of the Otomys typus complex 3024
FIGURE 9. RWA of lateral landmarks showing variation in samples from the Aberdares Range of Kenya, between O. orestes (closed squares), O. tropicalis (closed triangles) and the population from the Aberdares summit having 5 laminae in m1 (closed circles). Topotypic specimens of thomasi from Molo in the Guas Ngishu Plateau indicated by open circles; RMCA specimens R28198 and R28205 representing divergent cyt b lineages indicated. Position of type specimen indicated by "T".
FIGURE 2 in Specific limits and emerging diversity patterns in East African populations of laminate-toothed rats, genus Otomys (Muridae: Murinae: Otomyini): Revision of the Otomys typus complex 3024
FIGURE 2. Giemsa stained karyotypes of (a) Otomys helleri (= "Sp. B"; n=6), O. fortior (n=6) and O.typus s.s. (n=1) (2n=58, NFa=58), (b) Otomys yaldeni sp. nov. (= "Sp. A"; n=1; 2n=56, NFa=54), and (c) Otomys simiensis sp. nov. (= "Sp. D"; n=4; 2n=54, NFa=54).
FIGURE 4 in Specific limits and emerging diversity patterns in East African populations of laminate-toothed rats, genus Otomys (Muridae: Murinae: Otomyini): Revision of the Otomys typus complex 3024
FIGURE 4. Principal component analysis (PCA) of nine linear craniometric variables (a) and relative warps analysis (RWA) of dorsal landmarks (b) showing dispersion of relative age classes in one population of O. tropicalis from Tora, Burundi.
FIGURE 1 in Specific limits and emerging diversity patterns in East African populations of laminate-toothed rats, genus Otomys (Muridae: Murinae: Otomyini): Revision of the Otomys typus complex 3024
FIGURE 1. Map of east African montane and alpine zones showing distribution of type localities (large, open labeled squares) of forms previously attributed to (a) Otomys typus s. l. and (b) O. tropicalis s. l. Closed squares represent Museum cranial material examined. Circles enclosed localities assigned to OTU's for this study (in Ethiopia these represent hypothesized taxa based on cytogenetic, molecular and morphological data); numbers indicate OTU numbers in Table 1. Arrows indicate localities from which cytochrome-b sequences were available for this study. The asterisk indicates material from a specimen of uncertain identity assigned to cf. sungae.
FIGURE 3b. Maximum likelihood phylogram constructed from combined cyt b and 12S rRNA sequences for 20 in Specific limits and emerging diversity patterns in East African populations of laminate-toothed rats, genus Otomys (Muridae: Murinae: Otomyini): Revision of the Otomys typus complex 3024
FIGURE 3b. Maximum likelihood phylogram constructed from combined cyt b and 12S rRNA sequences for 20 Otomys specimens, one representative of Parotomys brantsii and four murine outgroups under the best-fit GTR+I+G model. Support indices for each node (1 – 23) are given beside the phylogram (BPP/ MLbs/ UwPbs/ 6PPbs/ NJpbs/ Njcbs). For both phylogenies (Figure 3a and 3b), the relative branch thickness indicates significant nodal support from the phylogenetic reconstruction methods employed herein (four to six methods—thick lines; two methods—intermediate lines). Dashed lines show unsupported relationships; Abbreviations and symbols: NS - BPP <0.95; "-" indicates that the node was not present in the relevant analysis, or percentage bootstrap support below 50%.
FIGURE 7 in Specific limits and emerging diversity patterns in East African populations of laminate-toothed rats, genus Otomys (Muridae: Murinae: Otomyini): Revision of the Otomys typus complex 3024
FIGURE 7. Relative warps analysis (RW) of 14 dorsal landmarks from 12 Ethiopian individuals assigned to O. typus s.s. from Simien Mts ("t"), O. helleri (= Sp. B: "b"; Dinsho and Arussi Plateau) and O. fortior ("ft*"; type specimen from Charada Forest).
FIGURE 6 in Specific limits and emerging diversity patterns in East African populations of laminate-toothed rats, genus Otomys (Muridae: Murinae: Otomyini): Revision of the Otomys typus complex 3024
FIGURE 6. Canonical variates analysis (plot of first two canonical variates) of six defined taxon-groups of Ethiopian Otomys based on nine craniometric variables. Position of individuals form "unknown" sample from Oromiya, Jimma (asterisks) predicted a posteriori. Open squares = O. typus s.s. (Mt Guna); Closed squares = O. fortior; open circles = O. helleri (= "Sp. B"); closed circles = O. yaldeni sp. nov. (= "Sp. A"); open triangles = O. cheesmani sp. nov. (= "Sp. C"); closed triangles = O. simiensis sp. nov. (= "Sp. D").
FIGURE 12 in Specific limits and emerging diversity patterns in East African populations of laminate-toothed rats, genus Otomys (Muridae: Murinae: Otomyini): Revision of the Otomys typus complex 3024
FIGURE 12. CVA (a) of linear variables showing craniometric separation between regional groups of specimens assigned to typus s.l. and phenogram (b) based on Mahalanobis distances between OTUs. Numbers represent OTU numbers in Table 2.
FIGURE 15 in Specific limits and emerging diversity patterns in East African populations of laminate-toothed rats, genus Otomys (Muridae: Murinae: Otomyini): Revision of the Otomys typus complex 3024
FIGURE 15. PCA summarizing variation in altitude and eight bioclimatic variables in localities of O. typus s.l. (48 localities). Asterisks denote type localities. Symbols of localities assigned to revised taxa given in lower case as follows: "ty" = typus s.s. (Ethiopia: Simien Mts, Mt Guna); "a" = yaldeni: Sp. A (Ethiopia: Bale Mts); "ft" = fortior (Ethiopia: Charada (type locality), Beletta and Sheka Forests); "b" = helleri: Sp B (Ethiopia: Bale Mts, Arussi Plateau); "c" = cheesmani: Sp. C (Ethiopia: Dangila – Debra Marcos); "d" = dartmouthi (Ruwenzori Range); "j" = jacksoni (Mt Elgon); "o" = orestes (Kenya: Aberdares and Mt Kenya); "th" = thomasi (Kenya: Uasin Gisho Plateau); "u" = uzungwensis (Malawi: Nyika Plateau and Tanzania: Southern Rift and Eastern Arc); "z" = zinki (Mt Kilimanjaro). Symbols of localities from Ethiopia, which could not be unambiguously assigned to revised taxa are labelled in upper case as follows: AN = Ankober; BK = Bongke; CH = Chenca; CL = Chilalo (type locality of helleri); H = Hirna; M = Malka (type locality of malkensis); JM = Oromiya, Jimma.
FIGURE 14 in Specific limits and emerging diversity patterns in East African populations of laminate-toothed rats, genus Otomys (Muridae: Murinae: Otomyini): Revision of the Otomys typus complex 3024
FIGURE 14. Relative warps analysis of lateral landmarks showing craniometric separation between regional groups of specimens from alpine habitats assigned to typus s.l. Closed squares = orestes; closed circles = Aberdare summit; closed triangles = dartmouthi, closed diamonds = typus s.1. (Ethiopia); open squares = jacksoni; open circles = thomasi; open triangles = uzungwensis; open diamonds = zinki.
FIGURE 13 in Specific limits and emerging diversity patterns in East African populations of laminate-toothed rats, genus Otomys (Muridae: Murinae: Otomyini): Revision of the Otomys typus complex 3024
FIGURE 13. Relative warps analysis of dorsal landmarks showing craniometric separation between regional groups of specimens from alpine habitats assigned to typus s.l. Closed squares = orestes; closed circles = Aberdare summit; closed triangles = dartmouthi, closed diamonds = typus s.1. (Ethiopia); open squares = jacksoni; open circles = thomasi; open triangles = uzungwensis; open diamonds = zinki.
FIGURE 17 in Specific limits and emerging diversity patterns in East African populations of laminate-toothed rats, genus Otomys (Muridae: Murinae: Otomyini): Revision of the Otomys typus complex 3024
FIGURE 17(d–f). Photographs comparing dorsal, ventral and lateral views of the skulls of holotype of O. simiensis (ZMMU 178757).
Figure 14 in Species limits within the Praomys delectorum group (Rodentia: Muridae: Murinae) of East Africa: a morphometric reassessment and biogeographical implications
Figure 14. Fifty-nine major collecting localities of Praomys reported herein, sequentially numbered from north to south. Numbers refer to the localities gazetted in Appendix 1 and to those used to define the 21 OTUs (see Material and Methods).
Figure 13 in Species limits within the Praomys delectorum group (Rodentia: Muridae: Murinae) of East Africa: a morphometric reassessment and biogeographical implications
Figure 13. Interpretations of area relationship among Tanzanian mountains, as derived from documented occurrences (Appendix 4) of terrestrial small mammals in all montane settings (A, C) or those restricted to montane forest (B, D) and based on two measures of faunal similarity, Sørensen's (A, B) and Raup-Crick's (C, D) indices. Mountain abbreviations: EUS, East Usambara Mts; MAL, Malundwe Mts; NGU, Nguu Mts; NGR, Nguru Mts; NHI, Northern Highlands (Mt Kilimanjaro, Mt Meru, Ngorongoro Crater Highlands); NPA, North Pare Mts; RUB, Rubeho Mts; SHI, Southern Highlands (Livingstone Mts, Poroto Mts, Mt Rungwe); SPA, South Pare Mts; TAI, Taita Hills; UDZ, Udzungwa Mts; UKA, Ukaguru Mts; ULU, Uluguru Mts; WUS, West Usambara Mts.
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