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Figure 6 from: Zaika MA, Kilian N, Jones K, Krinitsina AA, Nilova MV, Speranskaya AS, Sukhorukov AP (2020) Scorzonera sensu lato (Asteraceae, Cichorieae) – taxonomic reassessment in the light of new molecular phylogenetic and carpological analyses. PhytoKeys 137: 1-85. https://doi.org/10.3897/phytokeys.137.46544

Figure 6 Various arrangements of the parenchyma in the pericarp. Numbers correspond with the states of the character 8. Yellow area – parenchyma, red area – sclerenchyma, white area in the centre – seed hollow.

Figure 12 from: Zaika MA, Kilian N, Jones K, Krinitsina AA, Nilova MV, Speranskaya AS, Sukhorukov AP (2020) Scorzonera sensu lato (Asteraceae, Cichorieae) – taxonomic reassessment in the light of new molecular phylogenetic and carpological analyses. PhytoKeys 137: 1-85. https://doi.org/10.3897/phytokeys.137.46544

Figure 12 Schemes (A, C, E) and cross-sections of the achenes (B, D, F), Pseudopodospermum clade, A, BScorzonera brevicaulis (Brevicaulis type), B from Dubuis 12704 (B) C, DS. papposa (Calyculata type), D from Bornmüller 4131 (B) E, FS. hispanica (Pseudopodospermum type). F from Rechinger 1590 (B100047704). Designation of the colours: orange (A, E) – mechanical subepidermal parenchyma; yellow – thin-walled parenchyma, white small hollows in the pericarp – air cavities; grey – stout conglomerations (C); red – sclerenchyma (of parallel orientation); blue – seed coat; green – endosperm; violet dots in pericarp – tannins cells, violet dots in seed coat – vestiges of vascular bundles; central white area – seed hollow.

Figure 3 from: Zaika MA, Kilian N, Jones K, Krinitsina AA, Nilova MV, Speranskaya AS, Sukhorukov AP (2020) Scorzonera sensu lato (Asteraceae, Cichorieae) – taxonomic reassessment in the light of new molecular phylogenetic and carpological analyses. PhytoKeys 137: 1-85. https://doi.org/10.3897/phytokeys.137.46544

Figure 3 Cross-section of the middle achene part of Scorzonera stricta (from V. Prima 485 (LE)). Abbreviations in pericarp: oe – outer epidermis, ac – air cavity, p – parenchyma, scl – sclerenchyma, vb – vascular bundles, ie – inner epidermis; abbreviations in seed: sc – seed coat, en – endosperm, sh – seed hollow (embryo not shown).

Figure 7 from: Zaika MA, Kilian N, Jones K, Krinitsina AA, Nilova MV, Speranskaya AS, Sukhorukov AP (2020) Scorzonera sensu lato (Asteraceae, Cichorieae) – taxonomic reassessment in the light of new molecular phylogenetic and carpological analyses. PhytoKeys 137: 1-85. https://doi.org/10.3897/phytokeys.137.46544

Figure 7 Schemes (A, C) and cross-sections of the achenes (B, D). A, BTourneuxia variifolia (Tourneuxia clade), B from Bochantsev 862 (LE) C, DScorzonera villosa (Gelasia clade), D from Rechinger 23425 (B). Designation of the colours in A and C: yellow – thin-walled parenchyma, pink (A) – sclerenchyma obliquely orientated in the region of the wings; red – sclerenchyma (of parallel orientation); blue – seed coat; violet dots (C) – vestiges of vascular bundles in the seed coat; green – endosperm; white areas between pericarp and seed coat designate air cavities; central white area – seed hollow.

Figure 10 from: Zaika MA, Kilian N, Jones K, Krinitsina AA, Nilova MV, Speranskaya AS, Sukhorukov AP (2020) Scorzonera sensu lato (Asteraceae, Cichorieae) – taxonomic reassessment in the light of new molecular phylogenetic and carpological analyses. PhytoKeys 137: 1-85. https://doi.org/10.3897/phytokeys.137.46544

Figure 10 Schemes (A, C) and cross-sections of the achenes (B, D). A, BScorzonera longipapposa (Scorzonera polyclada clade), B from Rechinger 35489 (G181688) C, DKoelpinia macrantha (Koelpinia clade), D from Pimenov et al. 447 (MW0891267). Designation of the colours: yellow – thin-walled parenchyma (absent in C), hatched area – thick-walled parenchyma; pink (C) – sclerenchyma obliquely orientated in the region of the wings (present in C); red – sclerenchyma (of parallel orientation); blue – seed coat; violet dots (A, C) – vestiges of vascular bundles in the pericarp and seed coat (A) and in the seed coat (C); green – endosperm; central white area – seed hollow.

opencc-zeroDec 2010View details →

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Data from: Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional, and separate models for combined molecular phylogenetic analyses of multilocus sequence data

Proportional and separate models able to apply different combination of substitution rate matrix and among-site rate variation model to each locus are frequently used in phylogenetic studies of multilocus data. However, the selection from among nonpartitioned (i.e., a common combination of models is applied to all-loci concatenated sequences), proportional, and separate models is usually based on the researcher's preference rather than on any information criteria. The present study describes two programs, "Kakusan4" (for DNA sequences) and "Aminosan" (for amino-acid sequences), that allow the selection of evolutionary models based on several types of information criteria. The programs can handle both multilocus and single-locus data, in addition to providing an easy-to-use wizard interface and a non-interactive command line interface. In the case of multilocus data, substitution rate matrices and among-site rate variation models are compared at each locus and at all-loci concatenated sequences, after which nonpartitioned, proportional, and separate models are compared based on information criteria. The programs also provide model configuration files for MrBayes, PAUP*, PHYML, RAxML, and Treefinder to support further phylogenetic analysis using a selected model. The best-fit models were found to differ depending on the data set. Furthermore, differences in the information criteria among nonpartitioned, proportional, and separate models were much larger than those among the nonpartitioned models. These findings suggest that selecting from nonpartitioned, proportional, and separate models results in a better phylogenetic tree. Kakusan4 and Aminosan are available at http://www.fifthdimension.jp/. They are licensed under GNU GPL Ver.2, and are able to run on Windows, MacOS X, and Linux.

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Data from: Phylogenetic analyses reveal molecular signatures associated with functional divergence among Subtilisin like Serine Proteases are linked to lifestyle transitions in Hypocreales

Background: Subtilisin-like serine proteases or Subtilases in fungi are important for penetration and colonization of host. In Hypocreales, these proteins share several properties with other fungal, bacterial, plant and mammalian homologs. However, adoption of specific roles in entomopathogenesis may be governed by attainment of unique biochemical and structural features during the evolutionary course. Due to such functional shifts Subtilases coded by different family members of Hypocreales acquire distinct features according to respective hosts and lifestyle. We conducted phylogenetic and DIVERGE analyses and identified important protein residues that putatively assign functional specificity to Subtilases in fungal families/species under the order Hypocreales. Results: A total of 161 Subtilases coded by 10 species from five different families under the fungal order Hypocreales was included in the analysis. Based on the presence of conserved domains, the Subtilase genes were divided into three subfamilies, Subtilisin (S08.005), Proteinase K (S08.054) and Serine-carboxyl peptidases (S53.001). These subfamilies were investigated for phylogenetic associations, protein residues under positive selection and functional divergence among paralogous clades. The observations were co-related with the life-styles of the fungal families/species. Phylogenetic and Divergence analyses of Subtilisin (S08.005) and Proteinase K (S08.054) families of proteins revealed that the paralogous clades were clear-cut representation of familial origin of the protein sequences. We observed divergence between the paralogous clades of plant-pathogenic fungi (Nectriaceae), insect-pathogenic fungi (Cordycipitaceae/Clavicipitaceae) and nematophagous fungi (Ophiocordycipitaceae). In addition, Subtilase genes from the nematode-parasitic fungus Purpureocillium lilacinum made a unique cluster which putatively indicated that the fungus might have developed distinctive mechanisms for nematode-pathogenesis. Our evolutionary genetics analysis revealed evidence of positive selection on the Subtilisin (S08.005) and Proteinase K (S08.054) protein sequences of the entomopathogenic and nematophagous species belonging to Cordycipitaceae, Clavicipitaceae and Ophiocordycipitaceae families of Hypocreales. Conclusions: Our study provided new insights into the evolution of Subtilisin like serine proteases in Hypocreales, a fungal order largely consisting of biological control species. Subtilisin (S08.005) and Proteinase K (S08.054) proteins seemed to play important roles during life style modifications among different families and species of Hypocreales. Protein residues found significant in functional divergence analysis in the present study may provide support for protein engineering in future.

opencc-zeroDec 2015View details →

Figure 4 from: Mu T, Zhang Z, Liu R, Liu S, Li Z, Zhang X, Xia J (2021) Morphological and molecular phylogenetic analyses reveal three species of Colletotrichum in Shandong province, China. MycoKeys 85: 57-71. https://doi.org/10.3897/mycokeys.85.75944

Figure 4 Colletotrichum pandanicola (SAUCC201152) a lesion fruit of host plant b, c surface (b) and reverse (c) sides of colony after incubation for 7 days on PDA d conidiomata e, f conidiophores, conidiogenous cells and conidia g, h conidiophores, conidiogenous cells i–k conidia. Scale bars: 10 μm (e–k).

Figure 2 from: Mu T, Zhang Z, Liu R, Liu S, Li Z, Zhang X, Xia J (2021) Morphological and molecular phylogenetic analyses reveal three species of Colletotrichum in Shandong province, China. MycoKeys 85: 57-71. https://doi.org/10.3897/mycokeys.85.75944

Figure 2 Colletotrichum gloeosporioides (SAUCC201001) a lesion fruit of host plant b, c surface (b) and reverse (c) sides of colony after incubation for 7 days on PDA d conidiomata e conidiophores, conidiogenous cells and conidia f–h conidia. Scale bars: 10 μm (e–h).

Figure 3 from: Mu T, Zhang Z, Liu R, Liu S, Li Z, Zhang X, Xia J (2021) Morphological and molecular phylogenetic analyses reveal three species of Colletotrichum in Shandong province, China. MycoKeys 85: 57-71. https://doi.org/10.3897/mycokeys.85.75944

Figure 3 Colletotrichum mengyinense (SAUCC200702) a branch with leaves of host plant b, c surface (b) and reverse (c) sides of colony after incubation for 7 days on PDA d conidiomata e-g conidiophores, conidiogenous cells and conidia h–j conidia. Scale bars: 10 μm (e–j).

Figure 1 from: Mu T, Zhang Z, Liu R, Liu S, Li Z, Zhang X, Xia J (2021) Morphological and molecular phylogenetic analyses reveal three species of Colletotrichum in Shandong province, China. MycoKeys 85: 57-71. https://doi.org/10.3897/mycokeys.85.75944

Figure 1 Phylogram of Colletotrichum gloeosporioides complex based on combined ITS, GAPDH, CHS-1, ACT, TUB2, CAL and GS genes. The ML and BI bootstrap support values above 50% and 0.90 BYPP are shown at the first and second position, respectively. Strains marked with "*" are ex-type or ex-epitype. Strains from this study are shown in red. Two branches were shortened to fit the page size-these are indicated by the symbol (//) with an indication number showing how many times they are shortened.

opennotspecifiedNov 2015View details →

FIGURE 1 in Molecular phylogenetic analyses of Cucurbitaceae tribe Benincaseae urge for merging of Pilogyne with Zehneria

FIGURE 1. Summary of taxonomic history of Zehneria, Neoachmandra and Pilogyne.

opennotspecifiedJan 2015View details →

FIGURE 8 in Molecular phylogenetic and morphological analyses of the traditional tribe Coriandreae (Umbelliferae-Apioideae)

FIGURE 8. Photo of the holotype of Schrenkia alaica Pimenov (Pimenov et al. 503, MW).

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Genome-wide molecular phylogenetic analyses and mating experiments which reveal the evolutionary history and an intermediate stage of speciation of a giant water bug

The intermediate stages of speciation are important for understanding the processes involved in the creation of biodiversity, and also comprise a number of interesting phenomena. However, difficulties are associated with dividing clear speciation stages because speciation is a continuous process. Therefore, the elucidation of speciation is an interesting and important task in evolutionary biology. We herein present an example of a species in an intermediate stage of speciation using the giant water bug Appasus japonicus (Heteroptera, Belostomatidae) that was investigated using mating experiments and phylogenetic analyses of the mtDNA COI (658 bp) and 16S rRNA (435 bp) regions, and nDNA SSR (13 loci) and its genome-wide SNPs (11,241 SNPs). The results of our phylogenetic analyses based on their mtDNA dataset and the genome-wide SNPs dataset strongly supported the paraphyly of the Japanese populations. Therefore, it is suggested that their ancestral lineage which being distributed in the Japanese Archipelago subsequently migrated to the Eurasian Continent (i.e., "back-dispersal" occurred). Furthermore, the results of the mating experiments suggested that among A. japonicus, even between closely related lineages, pre-mating reproductive isolation has been established by the differentiation of copulatory organ morphologies. In contrast, pre-mating reproductive isolation is not established in the absence of the differentiation of copulatory organ morphologies, even if genetic differentiation is prominent. These results suggested that their phylogenetic distance does not predict pre-mating reproductive isolation. Furthermore, in the present study, we present a clear example of pre-mating reproductive isolation driving speciation between closely related lineages.

opencc-zeroJul 2021View details →

opennotspecifiedNov 2022View details →

FIGURE 1 in Phylogenetic analyses and species delimitation of Aconurella Ribaut (Hemiptera Cicadellidae: Deltocephalinae: Chiasmini) in China based on molecular data

FIGURE 1. Distribution of sampled specimens of Aconurella in China.

opencc-by-4.0Feb 2020View details →

FIGURE 1 Maximum Parsimony phylogenetic analyses. A in Dating the origin and diversiFIcation of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches

FIGURE 1 Maximum Parsimony phylogenetic analyses. A: Morphological phylogeny. B: Molecular phylogeny. C: Total-evidence phylogeny. Bootstrap supports are coded in grayscale. Australasian species are shown in red; South American species are shown in green. Abbreviations: A, Acanthochelys; B, Bonapartemys; Ch, Chelodina; El, Elseya; H, Hydromedusa; L, Lomalatachelys; M, Mesoclemmys; Me, Mendozachelys; My, Myuchelys; Pa, Palaeophrynops; Ph, Phrynops; Pl, Platemys; Pr, Prochelidella; Ps, Pseudemydura; Ri, Rionegrochelys; Y, Yaminuechelys. †, extinct taxa.

Figure 8 from: Capa M, Nygren A, Parapar J, Bakken T, Meißner K, Moreira J (2019) Systematic re-structure and new species of Sphaerodoridae (Annelida) after morphological revision and molecular phylogenetic analyses of the North East Atlantic fauna. ZooKeys 845: 1-97. https://doi.org/10.3897/zookeys.845.32428

Figure 8 Photographs of live specimens (included in analyses shown in Fig. 1). AClavodorumkristiani comb. n., nom. n. (ZMBN 127258, SPH313) BGeminofilumdistichum comb. n. from Skagerrak (ZMBN 127263, SPH295) CGeminofilum sp. 1, from UK (SPH324) DSphaerephesiaphilippi comb. n., from Skagerrak (ZMBN 125432, SPH297) E Sphaerephesiaphilippi comb. n., from Finnmark (ZMBN 127311, SPH304).

Figure 5 from: Capa M, Nygren A, Parapar J, Bakken T, Meißner K, Moreira J (2019) Systematic re-structure and new species of Sphaerodoridae (Annelida) after morphological revision and molecular phylogenetic analyses of the North East Atlantic fauna. ZooKeys 845: 1-97. https://doi.org/10.3897/zookeys.845.32428

Figure 5 Stylized drawings of parapodia, showing the relative position and arrangement of parapodial lobes, cirri, and papillae, in mid-body chaetigers of all sphaerodorid species reported in the North East Atlantic waters.

Figure 3 from: Capa M, Nygren A, Parapar J, Bakken T, Meißner K, Moreira J (2019) Systematic re-structure and new species of Sphaerodoridae (Annelida) after morphological revision and molecular phylogenetic analyses of the North East Atlantic fauna. ZooKeys 845: 1-97. https://doi.org/10.3897/zookeys.845.32428

Figure 3 Clavodorumfauchaldi (IINH 38781: A–E, K–M; IINH 38782: F–J), scanning electron micrographs. A Complete specimen, lateral view B anterior end, dorsal view C anterior end, ventral view D mid-body chaetigers, arrangement of dorsal macrotubercles and papillae E dorsal macrotubercles and papillae, detail F complete specimen, ventral view G mid-body chaetigers, arrangement of ventral tubercles H, I mid-body chaetigers, parapodia and ventral tubercles J mid-body parapodium, anterior view K–M compound chaetae.

Figure 29 from: Capa M, Nygren A, Parapar J, Bakken T, Meißner K, Moreira J (2019) Systematic re-structure and new species of Sphaerodoridae (Annelida) after morphological revision and molecular phylogenetic analyses of the North East Atlantic fauna. ZooKeys 845: 1-97. https://doi.org/10.3897/zookeys.845.32428

Figure 29 Sphaerodoridiumgudmunduri (NTNU-VM 74199), scanning electron micrographs. A Complete specimen, dorsal view B anterior end, frontal view C detail of head, frontal view D complete specimen, ventral view E parapodium, chaetiger 1, anterior view F parapodium, anterior chaetiger, dorsal view G parapodium, mid-body chaetiger, side view H parapodia, mid-body chaetigers, anterior view I, J detail of chaetae, mid-body chaetigers.