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262 results for “polyphyly”
FIGURE 6. Haymondia wallichii. A in Resolution of polyphyly in Pueraria (Leguminosae, Papilionoideae): The creation of two new genera, Haymondia and Toxicopueraria, the resurrection of Neustanthus, and a new combination in Teyleria
FIGURE 6. Haymondia wallichii. A. Terminal, branching inflorescence with newly-opened flowers. B. Fruits. C. Mature flowers. D. Habit and leaves. Photographs by Bo Pan.
FIGURE 5. Haymondia wallichii. A. Habit. B. Upper leaf surface. C. Stipule scar budding, axillary inflorescence. D. Calyx, inner view. E. Flower, lateral view. F. Flower, face view. G. Vexillum. H. Wing petal. I. Keel. J. Androecium. K. Fused stamens. L. Gynoecium. M. Fruits. N in Resolution of polyphyly in Pueraria (Leguminosae, Papilionoideae): The creation of two new genera, Haymondia and Toxicopueraria, the resurrection of Neustanthus, and a new combination in Teyleria
FIGURE 5. Haymondia wallichii. A. Habit. B. Upper leaf surface. C. Stipule scar budding, axillary inflorescence. D. Calyx, inner view. E. Flower, lateral view. F. Flower, face view. G. Vexillum. H. Wing petal. I. Keel. J. Androecium. K. Fused stamens. L. Gynoecium. M. Fruits. N. Seed. Voucher used for illustrations: A–C, E–L: A.N. Egan et al. 13-0750; D: J.D.A. Stainton 8462 (E); M–N: A. Henry 11568 (K). Illustrations by Alice R. Tangerini.
FIGURE 2. Neustanthus phaseoloides var. phaseoloides. A. Flowers. B. Leaves. C. Fruits. D in Resolution of polyphyly in Pueraria (Leguminosae, Papilionoideae): The creation of two new genera, Haymondia and Toxicopueraria, the resurrection of Neustanthus, and a new combination in Teyleria
FIGURE 2. Neustanthus phaseoloides var. phaseoloides. A. Flowers. B. Leaves. C. Fruits. D. Habit. Photographs by A.N. Egan of (A–C) A.N. Egan et al. 13-0715 (US) and (D) A.N. Egan et al. 13-0817 (US).
FIGURE 3. Teyleria stricta. A. Habit and inflorescence. B. Stipules. C. Stipels. D. Lower leaf surface. E in Resolution of polyphyly in Pueraria (Leguminosae, Papilionoideae): The creation of two new genera, Haymondia and Toxicopueraria, the resurrection of Neustanthus, and a new combination in Teyleria
FIGURE 3. Teyleria stricta. A. Habit and inflorescence. B. Stipules. C. Stipels. D. Lower leaf surface. E. Cross section of inflorescence rachis. F. Stem pubescence (detail). G. Close up of nodose inflorescence with buds and buds scars. H. Bracts. I. Calyx, inner view. J. Flower, lateral view. K. Flower, face view. L. Vexillum. M. Wing petal. N. Keel. O. Fused stamens. P. Gynoecium, ovary occasionally glabrous. Q. Fruits. R. Seed. Voucher used for illustrations: A: J.H. Lace 4903 & A. Rodger 615 (E); B–N: A.N Egan et al. 13-0749 (US); O: J.H. Lace 5938 (K); P: H.S. McKee 5891 (K). Illustrations by Alice R. Tangerini.
FIGURE 1. Neustanthus phaseoloides. A. Habit, Inflorescence. B in Resolution of polyphyly in Pueraria (Leguminosae, Papilionoideae): The creation of two new genera, Haymondia and Toxicopueraria, the resurrection of Neustanthus, and a new combination in Teyleria
FIGURE 1. Neustanthus phaseoloides. A. Habit, Inflorescence. B. Upper leaf surface (detail). C. Lower leaf surface (detail). D. Stipules. E. Stipels. F. Calyx, inner view. G. Flower, lateral view. H. Flower, face view. I. Vexillum. J. Wing petal. K. Keel. L. Androecium, lateral view, surrounding stigma and apex of style. M. Fused stamens and free stamen. N. Gynoecium. O. Fruit. P. Nodes (brachyblast) of pseudoraceme. Q. Seed, lateral view. R. Seed, dorsal view. Voucher used for illustrations: A–E: A.N. Egan & Xu Bo 13-0817 (US); F–N: A.N. Egan et al. 13-0715 (US); O–R: Shiu Ying Hu 5764 (US). Illustrations by Alice R. Tangerini.
FIGURE 4. Teyleria stricta. A. Flower. B. Nodose inflorescence with flowers. C. Fruits. D in Resolution of polyphyly in Pueraria (Leguminosae, Papilionoideae): The creation of two new genera, Haymondia and Toxicopueraria, the resurrection of Neustanthus, and a new combination in Teyleria
FIGURE 4. Teyleria stricta. A. Flower. B. Nodose inflorescence with flowers. C. Fruits. D. Inflorescence and leaf. Photographs by A.N. Egan of (A, B, D) A.N. Egan et al. 13-0749 (US) and by Bo Pan (C), no voucher.
Table 1 in Confirmed polyphyly, generic recircumscription and typification of Dysoxylum (Meliaceae), with revised disposition of currently accepted species
<p><b>Table 1.</b> Informative sites of each partition before and after the treatment by Gblocks (Castresana, 2000), displayed in percentages, for all sites including gaps and excluding gaps in brackets.</p><table><tbody><tr><th>Partition</th><th>Informative sites</th><th>Informative sites after Gblocks</th></tr></tbody><tbody><tr><th>ETS</th><td>63% (58%)</td><td>62% (60%)</td></tr><tr><th>ITS</th><td>57% (50%)</td><td>52% (52%)</td></tr><tr><th><i>rps15-ycf1</i></th><td>14% (6%)</td><td>– (–)</td></tr><tr><th><i>trnL-F</i></th><td>15% (7%)</td><td>13% (7%)</td></tr><tr><th>All</th><td>35% (28%)</td><td>38% (35%)</td></tr></tbody></table>
Data from: Species-level para- and polyphyly in DNA barcode gene trees: strong operational bias in European Lepidoptera
The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service "Monophylizer" to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ∼23%, but with operational factors still being included. Within the operational factors, we separately assessed the frequency of taxonomic limitations (presence of overlooked cryptic and oversplit species) and identification uncertainties. We observed that operational factors are potentially present in more than half (58.6%) of the detected cases of non-monophyly. Furthermore, we observed that in about 20% of non-monophyletic species and entangled species, the lineages involved are either allopatric or parapatric—conditions where species delimitation is inherently subjective and particularly dependent on the species concept that has been adopted. These observations suggest that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors.
Supplementary material 1 from: Cumming RT, Tirant SL, Büscher TH (2021) Resolving a century-old case of generic mistaken identity: polyphyly of Chitoniscus sensu lato resolved with the description of the endemic New Caledonia Trolicaphyllium gen. nov. (Phasmatodea, Phylliidae). ZooKeys 1055: 1-41. https://doi.org/10.3897/zookeys.1055.66796
Table S1. Material examined (specimen data and deposition/ observational records) for localities used within the distribution map (Fig. 21) and to accompany the discussion of each species
FIGURE 44 in Cladistic analysis reveals polyphyly of Tomarus (Coleoptera: Scarabaeidae: Dynastinae): new classification and taxonomic revision
FIGURE 44. Distributional records of Tomarus laevicollis, T. laticaudus, T. maracaiboensis, and T. colombianus.
FIGURE 19 in Cladistic analysis reveals polyphyly of Tomarus (Coleoptera: Scarabaeidae: Dynastinae): new classification and taxonomic revision
FIGURE 19. Parameres in lateral view. A) Tomarus adoceteus, B) T. amazonicus, C) T. bituberculatus, D) T. colombianus, E) T. discrepans, F) T. gyas, G) T. laevicollis, H) T. laticaudus, I) T. maimon.
FIGURE 22. Internal sac. A in Cladistic analysis reveals polyphyly of Tomarus (Coleoptera: Scarabaeidae: Dynastinae): new classification and taxonomic revision
FIGURE 22. Internal sac. A) Tomarus pullus, B) T. rostratus, C) T. maternus. Abbreviations: AL: Accessory lamellae, CL: Copulatory lamella, LSB: Lamellar spiny belt, Ra: Raspula, SD: Sclerotized diverticulum.
FIGURE 15 in Cladistic analysis reveals polyphyly of Tomarus (Coleoptera: Scarabaeidae: Dynastinae): new classification and taxonomic revision
FIGURE 15. Parameres in frontal view. A) Euligyrus ebenus, B) E. similis, C) Proculigyrus cicatricosus, D) Ligyrus (Anagrylius) cuniculus, E) L. (Anagrylius) moroni, F) L. (Ligyrodes) peruvianus, G) L. (Ligyrodes) relictus, H) L. (Ligyrodes) sallaei, I) L. (Ligyrus) allonasutus, J) L. (Ligyrus) bidentulus, K) L. (Ligyrus) burmeisteri, L) Ligyrus (Ligyrus) fossor, M) L. (Ligyrus) gibbosus, N) L. (Ligyrus) nasutus, O) L. (Ligyrus) neglectus, P) L. (Ligyrus) paranaensis, Q) L. (Ligyrus) peninsularis, R) L. (Ligyrus) rubripes, S) L. (Ligyrus) ruginasus, T) L. (Ligyrus) villosus.
FIGURE 23. Internal sac. A in Cladistic analysis reveals polyphyly of Tomarus (Coleoptera: Scarabaeidae: Dynastinae): new classification and taxonomic revision
FIGURE 23. Internal sac. A) Tomarus amazonicus, B) T. discrepans, C) T. laticaudus, D) T. maimon. Abbreviations: AL: Accessory lamellae, CL: Copulatory lamella, LSB: Lamellar spiny belt, Ra: Raspula, SD: Sclerotized diverticulum.
FIGURE 26 in Cladistic analysis reveals polyphyly of Tomarus (Coleoptera: Scarabaeidae: Dynastinae): new classification and taxonomic revision
FIGURE 26. Habitus of the species of Ligyrus. Subgenus Ligyrus: A) Ligyrus fossor, B) L. gibbosus, C) L. nasutus, D) L. neglectus, E) L. paranaensis, F) L. peninsularis, G) L. rubripes, H) L. ruginasus, I) L. villosus. Scale bar: 5 mm.
FIGURE 13. Female genital plates. A in Cladistic analysis reveals polyphyly of Tomarus (Coleoptera: Scarabaeidae: Dynastinae): new classification and taxonomic revision
FIGURE 13. Female genital plates. A) Euligyrus ebenus, B) Proculigyrus cicatricosus, C) Ligyrus (Anagrylius) moroni, D) L. (Ligyrodes) sallaei, E) L. (Ligyrus) allonasutus, F) L. (Ligyrus) bidentulus, G) L. (Ligyrus) neglectus, H) Tomarus laticaudus, I) T. maternus, J) T. rostratus, K) T. subtropicus. Abbreviations: SCx: Subcoxite, Cx: Coxite.
FIGURE 12 in Cladistic analysis reveals polyphyly of Tomarus (Coleoptera: Scarabaeidae: Dynastinae): new classification and taxonomic revision
FIGURE 12. Mesotibia (A–F). A) Euligyrus similis, B) Proculigyrus cicatricosus, C) Ligyrus (Anagrylius) moroni, D) L. (Ligyrodes) sallaei; E) L. (Ligyrus) allonasutus, F) L. (Ligyrus) villosus. Metatibia (G–L). G) Euligyrus similis, H) Proculigyrus cicatricosus, I) Ligyrus (Anagrylius) moroni, J) L. (Ligyrodes) sallaei, K) L. (Ligyrus) allonasutus, L) L. (Ligyrus) villosus.
FIGURE 9 in Cladistic analysis reveals polyphyly of Tomarus (Coleoptera: Scarabaeidae: Dynastinae): new classification and taxonomic revision
FIGURE 9. Pygidium of male. A) Euligyrus ebenus, B) Proculigyrus cicatricosus, C) Ligyrus (Anagrylius) cuniculus, D) L. (Ligyrus) fossor, E) L. (Ligyrus) paranaensis, F) Tomarus bituberculatus, G) T. colombianus, H) T. maracaiboensis, I) T. pilcopataensis, J) T. pullus, K) T. roigjunenti, L) T. rostratus.
FIGURE 8. Stridulatory apparatus. A, D in Cladistic analysis reveals polyphyly of Tomarus (Coleoptera: Scarabaeidae: Dynastinae): new classification and taxonomic revision
FIGURE 8. Stridulatory apparatus. A, D) Proculigyrus cicatricosus, B, E) Ligyrus (Ligyrus) burmeisteri, C, F) L. (Ligyrodes) relictus, G, K) Tomarus amazonicus, H, L) T. maimon, I, M) T. maternus, J, N) T. gyas.
FIGURE 18 in Cladistic analysis reveals polyphyly of Tomarus (Coleoptera: Scarabaeidae: Dynastinae): new classification and taxonomic revision
FIGURE 18. Parameres in lateral view. A) L. (Ligyrus.) allonasutus, B) L. (Ligyrus) bidentulus, C) L. (Ligyrus) burmeisteri, D) Ligyrus (Ligyrus) fossor, E) L. (Ligyrus) gibbosus, F) L. (Ligyrus) nasutus, G) L. (Ligyrus) neglectus, H) L. (Ligyrus) paranaensis, I) L. (Ligyrus) peninsularis, J) L. (Ligyrus) rubripes, K) L. (Ligyrus) ruginasus, L) L. (Ligyrus) villosus.
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