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727 results for “Molecular taxonomy”
Figure 4 from: Tan K, Lu T, Ren M-X (2020) Gesneriaceae in China and Vietnam: Perfection of taxonomy based on comprehensive morphological and molecular evidence. In: Shui Y-M, Chen W-H, Ren M-X, Wen F, Hong X, Qiu Z-J, Wei Y-G, Kang M (Eds) Taxonomy of Gesneriaceae in China and Vietnam. PhytoKeys 157: 7-26. https://doi.org/10.3897/phytokeys.157.34032
Figure 4 Genera phylogeny with geographical distribution pattern of the Asian Gesneriaceae. The number in the brackets is the species diversity of the genus. Phylogeny tree was redrawn based on Möller and Clark (2013), Middleton et al. (2015), Puglisi et al. (2016), Möller et al. (2016a), Middleton et al. (2018).
Data from: Nomenclature for the nameless: a proposal for an integrative molecular taxonomy of cryptic diversity exemplified by planktonic foraminifera
Investigations of biodiversity, biogeography and ecological processes rely on the identification of "species" as biologically significant, natural units of evolution. In this context, morpho-taxonomy only provides an adequate level of resolution if reproductive isolation matches morphological divergence. In many groups of organisms, morphologically defined species often disguise considerable genetic diversity, which may be indicative of the existence of cryptic species. The diversity hidden by morphological species can be disentangled through genetic surveys, which also provide access to data on the ecological distribution of genetically circumscribed units. These units can be identified by unique DNA sequence motifs and allow studies of evolutionary and ecological processes at different levels of divergence. However, the nomenclature of genetically circumscribed units within morphological species is not regulated and lacks stability. This represents a major obstacle to efforts to synthesize and communicate data on genetic diversity for multiple stakeholders. We have been confronted with such an obstacle in our work on planktonic foraminifera, where the stakeholder community is particularly diverse, involving geochemists, paleoceanographers, paleontologists and biologists, and the lack of stable nomenclature beyond the level of formal morphospecies prevents effective transfer of knowledge. To circumvent this problem, we have designed a stable, reproducible and flexible nomenclature system for genetically circumscribed units, analogous to the principles of a formal nomenclature system. Our system is based on the definition of unique DNA sequence motifs collocated within an individual, their typification (in analogy with holotypes), utilization of their hierarchical phylogenetic structure to define levels of divergence below that of the morphospecies, and a set of nomenclature rules assuring stability. The resulting molecular operational taxonomic units (MOTUs) remain outside the domain of current nomenclature codes, but are linked to formal morphospecies as regulated by the codes. Subsequently we show how this system can be applied to classify genetically defined units using the SSU rDNA marker in planktonic foraminifera and we highlight its potential use for other groups of organisms where similarly high levels of connectivity between molecular and formal taxonomies can be achieved.
FIGURE 38 in Revision of the genus Dinotoperla Tillyard, 1921 (Plecoptera: Gripopterygidae) using morphological characters and molecular data: Establishes two new genera, three new species and updates the larval taxonomy
FIGURE 38. General overview of leg showing terms for areas referred to in key and descriptions.
Supplementary material 1 from: Yahara T, Hirota SK, Fujii S, Kokami Y, Fuse K, Sato H, Tagane S, Suyama Y (2023) Molecular phylogeny and taxonomy of Hosta (Asparagaceae) on Shikoku Island, Japan, including five new species, one new subspecies, and two new status assignments. PhytoKeys 235: 137-187. https://doi.org/10.3897/phytokeys.235.99140
20 DNA samples and voucher specimens from 70 localities for 30 taxa of Hosta in Japan
Supplementary material 2 from: Yahara T, Hirota SK, Fujii S, Kokami Y, Fuse K, Sato H, Tagane S, Suyama Y (2023) Molecular phylogeny and taxonomy of Hosta (Asparagaceae) on Shikoku Island, Japan, including five new species, one new subspecies, and two new status assignments. PhytoKeys 235: 137-187. https://doi.org/10.3897/phytokeys.235.99140
Sample sets
Figure 6 from: Hirota SK, Yahara T, Fuse K, Sato H, Tagane S, Fujii S, Minamitani T, Suyama Y (2022) Molecular phylogeny and taxonomy of the Hydrangea serrata complex (Hydrangeaceae) in western Japan, including a new subspecies of H. acuminata from Yakushima. PhytoKeys 188: 49-71. https://doi.org/10.3897/phytokeys.188.64259
Figure 6 Fruits of Hydrangea acuminata subsp. yakushimensis Yahara & Tagane A and subsp. acuminataB Specimen: JPN1799 (holotype) AJPN2063B. Scale bars: 3 mm.
Figure 4 from: Hirota SK, Yahara T, Fuse K, Sato H, Tagane S, Fujii S, Minamitani T, Suyama Y (2022) Molecular phylogeny and taxonomy of the Hydrangea serrata complex (Hydrangeaceae) in western Japan, including a new subspecies of H. acuminata from Yakushima. PhytoKeys 188: 49-71. https://doi.org/10.3897/phytokeys.188.64259
Figure 4 Molecular phylogenetic tree reconstructed using cpDNA sequences. Bootstrap values are shown on the nodes. Nodes supported by less than 60% bootstrap values are not shown.
Figure 2 from: Hirota SK, Yahara T, Fuse K, Sato H, Tagane S, Fujii S, Minamitani T, Suyama Y (2022) Molecular phylogeny and taxonomy of the Hydrangea serrata complex (Hydrangeaceae) in western Japan, including a new subspecies of H. acuminata from Yakushima. PhytoKeys 188: 49-71. https://doi.org/10.3897/phytokeys.188.64259
Figure 2 Molecular phylogenetic tree reconstructed using MIG-seq. Bootstrap values are shown on the nodes, and branch lengths are shown on the internodes. Branch length represents the average number of substitutions per SNP site.
Figure 5 from: Hirota SK, Yahara T, Fuse K, Sato H, Tagane S, Fujii S, Minamitani T, Suyama Y (2022) Molecular phylogeny and taxonomy of the Hydrangea serrata complex (Hydrangeaceae) in western Japan, including a new subspecies of H. acuminata from Yakushima. PhytoKeys 188: 49-71. https://doi.org/10.3897/phytokeys.188.64259
Figure 5 Hydrangea acuminata subsp. yakushimensis Yahara & Tagane A a tree growing on cliff along stream B a fruiting twig of the specimen JPN1799 (holotype) C lower leaf surface of the specimen JPN1799. Scale bars: 20 cm (A); 10 cm (B); 2 cm (C).
Figure 3 from: Hirota SK, Yahara T, Fuse K, Sato H, Tagane S, Fujii S, Minamitani T, Suyama Y (2022) Molecular phylogeny and taxonomy of the Hydrangea serrata complex (Hydrangeaceae) in western Japan, including a new subspecies of H. acuminata from Yakushima. PhytoKeys 188: 49-71. https://doi.org/10.3897/phytokeys.188.64259
Figure 3 Molecular phylogenetic tree reconstructed using ITS sequences. Bootstrap values are shown on the nodes. Nodes supported by less than 70% bootstrap values are not shown.
Figure 1 from: Hirota SK, Yahara T, Fuse K, Sato H, Tagane S, Fujii S, Minamitani T, Suyama Y (2022) Molecular phylogeny and taxonomy of the Hydrangea serrata complex (Hydrangeaceae) in western Japan, including a new subspecies of H. acuminata from Yakushima. PhytoKeys 188: 49-71. https://doi.org/10.3897/phytokeys.188.64259
Figure 1 Localities of Hydrangea acuminata subsp. acuminata (including Shikoku lineage), subsp. australis , and subsp. yakushimensis where DNA samples and voucher specimens were collected in this study. The map was produced from Chiriin Chizu Vector (https://maps.gsi.go.jp/vector/).
Supplementary material 4 from: Teruya S, Setiamarga DHE, Nakano T, Sasaki T (2022) Molecular phylogeny of Nipponacmea (Patellogastropoda, Lottiidae) from Japan: a re-evaluation of species taxonomy and morphological diagnosis. ZooKeys 1087: 163-198. https://doi.org/10.3897/zookeys.1087.78193
Figure S4
Supplementary material 3 from: Teruya S, Setiamarga DHE, Nakano T, Sasaki T (2022) Molecular phylogeny of Nipponacmea (Patellogastropoda, Lottiidae) from Japan: a re-evaluation of species taxonomy and morphological diagnosis. ZooKeys 1087: 163-198. https://doi.org/10.3897/zookeys.1087.78193
Figure S3
Supplementary material 2 from: Teruya S, Setiamarga DHE, Nakano T, Sasaki T (2022) Molecular phylogeny of Nipponacmea (Patellogastropoda, Lottiidae) from Japan: a re-evaluation of species taxonomy and morphological diagnosis. ZooKeys 1087: 163-198. https://doi.org/10.3897/zookeys.1087.78193
Figure S2
Supplementary material 1 from: Teruya S, Setiamarga DHE, Nakano T, Sasaki T (2022) Molecular phylogeny of Nipponacmea (Patellogastropoda, Lottiidae) from Japan: a re-evaluation of species taxonomy and morphological diagnosis. ZooKeys 1087: 163-198. https://doi.org/10.3897/zookeys.1087.78193
Figure S1
Figure 9 from: Teruya S, Setiamarga DHE, Nakano T, Sasaki T (2022) Molecular phylogeny of Nipponacmea (Patellogastropoda, Lottiidae) from Japan: a re-evaluation of species taxonomy and morphological diagnosis. ZooKeys 1087: 163-198. https://doi.org/10.3897/zookeys.1087.78193
Figure 9 Plot of the results of discriminant function analysis of shell length, width, and height for individuals of Nipponacmea species.
Figure 5 from: Teruya S, Setiamarga DHE, Nakano T, Sasaki T (2022) Molecular phylogeny of Nipponacmea (Patellogastropoda, Lottiidae) from Japan: a re-evaluation of species taxonomy and morphological diagnosis. ZooKeys 1087: 163-198. https://doi.org/10.3897/zookeys.1087.78193
Figure 5 Pigmentation of side of foot AN. gloriosa, RM31861, Manazuru, Kanagawa (14) BN. fuscoviridis, RM31847, Tateyama, Chiba (13) CN. boninensis, RM31816, Chichijima Is., Ogasawara (43) DN. schrenckii, RM31908, Kazamaura, Aomori (6) EN. concinna, RM31830, Omura, Nagasaki (34) FN. radula, RM31900, Nagato, Yamaguchi (31) GN. nigrans, RM32361, Kushimoto, Wakayama (20) HN. habei, RM31870, Otaru, Hokkaido (2) IN. teramachii, RM31917, Tateyama, Chiba (13). Scale bars: 5 mm.
Figure 1 from: Teruya S, Setiamarga DHE, Nakano T, Sasaki T (2022) Molecular phylogeny of Nipponacmea (Patellogastropoda, Lottiidae) from Japan: a re-evaluation of species taxonomy and morphological diagnosis. ZooKeys 1087: 163-198. https://doi.org/10.3897/zookeys.1087.78193
Figure 1 Collection localities of the specimens used in this study. The numbers are shown in Table 1.
Figure 7 from: Teruya S, Setiamarga DHE, Nakano T, Sasaki T (2022) Molecular phylogeny of Nipponacmea (Patellogastropoda, Lottiidae) from Japan: a re-evaluation of species taxonomy and morphological diagnosis. ZooKeys 1087: 163-198. https://doi.org/10.3897/zookeys.1087.78193
Figure 7 Scanning micrographs of radular teeth of of NipponacmeaAN. gloriosa, RM32355, Ibusuki, Kagoshima (41) BN. gloriosa, RM31860, Tateyama, Chiba (13) CN. fuscoviridis, RM31858, Kimotsukicho, Kagoshima (42) DN. fuscoviridis, RM32354, Akune, Kagoshima (39) EN. fuscoviridis, RM31834, Rumoi, Hokkaido (1) FN. boninensis, RM31817, Chichijima Is., Ogasawara (43) GN. boninensis, RM31815, Chichijima Is., Ogasawara (43) HN. schrenckii, RM31915, Suo-Oshima, Yamaguchi (30) IN. schrenckii, RM31906, Kazamaura, Aomori (6) JN. schrenckii, RM31916, Nagatamachi, Nagasaki (35) KN. concinna, RM31831, Omura, Nagasaki (34) LN. concinna, RM32353, Nagatamachi, Nagasaki (35) MN. concinna, RM31823, Tahara, Aichi (19) NN. radula, RM31898, Hamamatsu, Shizuoka (18) ON. radula, RM31904, Omura, Nagasaki (34) PN. radula, RM32363, Akune, Kagoshima (37) QN. nigrans, RM32360, Kushimoto, Wakayama (20) RN. nigrans, RM32359, Kushimoto, Wakayama (20) SN. nigrans, RM32358, Kushimoto, Wakayama (20) TN. habei, RM32364, Tateyama, Chiba (13) UN. habei, RM31872, Suttu, Hokkaido (3) VN. habei, RM31873, Usujiri, Hokkaido (5) WN. habei, RM32357, Usujiri, Hokkaido (5) XN. habei, RM32356, Tateyama, Chiba (13) YN. teramachii, RM31926, Sanuki, Kagawa (28) ZN. teramachii, RM31924, Ohira, Oita (25). Scale bars: 50 μm.
Figure 6 from: Teruya S, Setiamarga DHE, Nakano T, Sasaki T (2022) Molecular phylogeny of Nipponacmea (Patellogastropoda, Lottiidae) from Japan: a re-evaluation of species taxonomy and morphological diagnosis. ZooKeys 1087: 163-198. https://doi.org/10.3897/zookeys.1087.78193
Figure 6 Configuration of radula sac of nine species of NipponacmeaAN. gloriosa, RM32355, Ibusuki, Kagoshima (41) BN. fuscoviridis, RM32354, Akune, Kagoshima (39) CN. boninensis, RM31817, Chichijima Is., Ogasawara (43) DN. schrenckii, RM31906, Kazamaura, Aomori (6) EN. concinna, RM32353, Nagatamachi, Nagasaki (35) FN. radula, RM32363, Akune, Kagoshima (37) GN. nigrans, RM32362, Kushimoto, Wakayama (20) HN. habei, RM32356, Tateyama, Chiba (13) IN. teramachii, RM31928, Suo-Oshima, Yamaguchi (30). Scale bars: 5 mm.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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