Research Article |
Corresponding author: Hong Yu ( hongyu@ynu.edu.cn ) Academic editor: Andrew Miller
© 2023 Yao Wang, Zhi-Qin Wang, Chinnapan Thanarut, Van-Minh Dao, Yuan-Bing Wang, Hong Yu.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Wang Y, Wang Z-Q, Thanarut C, Dao V-M, Wang Y-B, Yu H (2023) Phylogeny and species delimitations in the economically, medically, and ecologically important genus Samsoniella (Cordycipitaceae, Hypocreales). MycoKeys 99: 227-250. https://doi.org/10.3897/mycokeys.99.106474
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Samsoniella is a ubiquitous genus of cosmopolitan arthropod-pathogenic fungi in the family Cordycipitaceae. The fungi have economic, medicinal, and ecological importance. Prior taxonomic studies of these fungi relied predominantly on phylogenetic inferences from five loci, namely, the nuclear ribosomal small and large subunits (nr SSU and nr LSU), the 3’ portion of translation elongation factor 1 alpha (3P_TEF), and RNA polymerase II subunits 1 and 2 (RPB1 and RPB2). Despite many new species being described, not all of the recognized species inside this group formed well-supported clades. Thus, the search for new markers appropriate for molecular phylogenetic analysis of Samsoniella remains a challenging problem. In our study, we selected the internal transcribed spacer regions of the rDNA (ITS rDNA) and seven gene regions, namely, 3P_TEF, the 5’ portion of translation elongation factor 1 alpha (5P_TEF), RPB1, RPB2, γ-actin (ACT), β-tubulin (TUB), and a gene encoding a minichromosome maintenance protein (MCM7), as candidate markers for species identification. Genetic divergence comparisons showed that the ITS, RPB2, ACT, and TUB sequences provided little valuable information with which to separate Samsoniella spp. In contrast, sequence data for 3P_TEF, 5P_TEF, RPB1, and MCM7 provided good resolution of Samsoniella species. The phylogenetic tree inferred from combined data (5P_TEF + 3P_TEF + RPB1 + MCM7) showed well-supported clades for Samsoniella and allowed for the delimitation of 26 species in this genus. The other two species (S. formicae and S. lepidopterorum) were not evaluated, as they had abundant missing data.
Isaria-like fungi, multi-locus phylogeny, new species, species diversity
Samsoniella is a ubiquitous genus of cosmopolitan arthropod-pathogenic fungi containing several species with significant economic and medicinal value (
The genus Samsoniella was established on the basis of three species with orange cylindrical to clavate stromata, superficial perithecia, and orange conidiophores with Isaria-like phialides and white to cream conidia: the type species S. inthanonensis and two other species, S. alboaurantia and S. aurantia (
Phylogenetic relationships among the genus Samsoniella and its allies in Cordycipitaceae based on Bayesian inference (BI) and maximum likelihood (ML) analyses of a five-locus (nr SSU, nr LSU, 3P_TEF, RPB1, and RPB2) dataset. No significant differences in topology are observed between BI and ML (RAxML) phylogenies. Statistical support values (≥ 0.7/70%) are shown at the nodes for BI posterior probabilities/ML bootstrap support. Materials in bold type are those analyzed in this study.
In the current study, we analyzed species of the recently circumscribed genus Samsoniella, based on morphological observations and phylogenetic inference. Moreover, we selected the internal transcribed spacer regions of the rDNA (ITS rDNA) and six protein-coding genes (elongation factor EF-1α (3P_TEF and 5P_TEF, the 5’ portion of translation elongation factor 1 alpha), RNA polymerases (RPB1 and RPB2), γ-actin (ACT), β-tubulin (TUB), and a gene encoding a minichromosome maintenance protein (MCM7)) for evaluation as taxonomic candidate markers for phylogenetic inference; these have been commonly used in fungal species identification and in phylogenetic reconstructions of fungi (AFTOL, http://aftol.org/data.php). Finally, nucleotide sequences derived from four markers, namely, 3P_TEF, 5P_TEF, RPB1, and MCM7, were used to examine phylogenetic relationships and assess species boundaries within the genus.
Fungus-infected insect specimens were collected from seven locations in 2016 and 2020, including three different locations within Yunnan Province, China, two locations within Lao Cai Province, Vietnam, one location within Oudomxay Province, Laos, and one location in Chiang Mai, Thailand. Teleomorph specimens were collected by carefully unearthing their hosts with a scoop and placing the samples in sterile bags. Conidia developing on insect cadavers were transplanted onto plates of potato dextrose agar (PDA; potato 200 g/L, dextrose 20 g/L, agar 20 g/L) and cultured at 25 °C. Colonies of the isolated filamentous fungi appearing in the culture were transferred onto fresh PDA media. The purified fungal strain was transferred to PDA slants and cultured at 25 °C until hyphae spread across the entire slope. Emerging fungal spores were washed with sterile physiological saline and made into a spore suspension of 1 × 103 cells/mL. To obtain monospore cultures, a portion of the spore suspension was placed on PDA using a sterile micropipette, and then incubated at 25 °C. Teleomorph specimens were rinsed with tap water, washed with sterile distilled water, and then dried on sterile filter paper. A mass of ascospores and asci was removed from perithecia with a fine needle and placed in a drop of sterile water that was stirred with a different needle to distribute the elements on the slide. A portion of the drop containing ascospores was placed on PDA using a sterile micropipette, and then incubated at 25 °C. The purified fungal strains were maintained in a culture room at 25 °C or transferred to PDA slants and stored at 4 °C. Voucher specimens and the corresponding isolated strains were deposited in the Yunnan Herbal Herbarium (YHH) and the Yunnan Fungal Culture Collection (YFCC), respectively, of Yunnan University, Kunming, China.
Macro-morphological characteristics, including the host, geographical location, color and shape of the stromata, and perithecial orientation (superficial, immersed, or semi-immersed; ordinal or oblique) were examined under a dissecting microscope (SZ61, Olympus Corporation, Tokyo, Japan). For morphological evaluation, microscope slides were prepared by placing mycelia from the cultures on PDA blocks (5 mm in diameter) and then overlaid with a coverslip. Medan dye solution was used to stain asci and ascospores. Other structures were mounted in water. The sizes and shapes of the microcharacteristics (e.g., asci, ascospores, conidiogenous cells, and conidia) were determined using a light microscope (CX40, Olympus Corporation, Tokyo, Japan) and a scanning electron microscope (Quanta 200 FEG, FEI Company, Hillsboro, USA). Individual length and width measurements were taken for 30–100 replicates, including the absolute minima and maxima.
Specimens and live axenic cultures were prepared for DNA extraction. Genomic DNA was extracted using a Genomic DNA Purification Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer’s protocol. The phylogenetic positions of unknown Samsoniella isolates were evaluated with phylogenetic inferences based on five genes, namely, nr SSU, nr LSU, 3P_TEF, RPB1, and RPB2. The primer pair nrSSU-CoF and nrSSU-CoR (
Amplified fragments were sequenced in both directions using the same primer pairs used for amplification. All retrieved sequences from GenBank were combined with those generated in our study. The taxonomic information and GenBank accession numbers are provided in Suppl. material
Specimen information and GenBank accession numbers for sequences used in this study. Boldface: data generated in this study.
We applied a (phylo-) genetic distance matrix calculation for the candidate markers, namely, ITS, 3P_TEF, 5P_TEF, RPB1, RPB2, ACT, TUB, and MCM7, to assess species boundaries of 11 Samsoniella spp. (Suppl. material
The host insects of Samsoniella spp. were identified on the basis of morphological characteristics and further identified using molecular analyses based on the mitochondrial cytochrome oxidase I gene (COX1) and mitochondrial cytochrome b gene (CYTB). Genomic DNA was extracted from the head and leg areas of the cadavers of the host insects using the CTAB method (
The 11 DNA loci were readily amplified and sequenced, and there was a fairly high success rate in this study. Phylogenetic analyses based on the combined five-gene (nr SSU + nr LSU + 3P_TEF + RPB1 + RPB2) sequences from 120 fungal taxa confirmed the presence and positions of Samsoniella and related genera within Cordycipitaceae. The concatenated five-gene dataset consisted of 4994 bp (nr SSU, 1134 bp; nr LSU, 901 bp; 3P_TEF, 1044 bp; RPB1, 759 bp; RPB2, 1156 bp). Eleven well-supported clades were recognized based on both BI and ML analyses of the combined dataset from Cordycipitaceae and Trichoderma, corresponding to the genera Akanthomyces, Amphichorda, Ascopolyporus, Beauveria, Blackwellomyces, Cordyceps, Gibellula, Hevansia, Samsoniella, Simplicillium, and Trichoderma as the outgroup (Fig.
The genetic divergence comparisons showed that: (1) the mean thresholds (p-distances) of ITS, RPB2, ACT, and TUB were lower than 0.01, indicating that neither were qualified as DNA markers; (2) the mean thresholds (p-distances) of 3P_TEF, 5P_TEF, RPB1, and MCM7 were > 0.01, and (3) the highest number of species was delimited in the genetic distance analysis for the 3P_TEF sequence data, followed by 5P_TEF, MCM7, and RPB1 sequences (Suppl. material
The analyzed data matrix used to construct the phylogeny of Samsoniella species included sequences from 56 fungal taxa (Table
Phylogenetic tree of Samsoniella based on Bayesian inference and Maximum Likelihood analyses of a 4-locus (5P_TEF, 3P_TEF, RPB1 and MCM7) dataset. No significant differences in topology are observed between BI and ML (IQ-TREE) phylogenies. Numbers at the branches indicate support values (BI-PP/RAxML-BS/IQ-TREE-BS) above 0.7/70%/70%. Isolates in bold type are those analyzed in this study.
The tree topologies for the individual loci (5P_TEF, 3P_TEF, RPB1, and MCM7) did not show congruence (Suppl. material
Based on the results of the phylogenetic analyses and the morphological data, we add two new descriptions to the record of two known species and propose to erect two new species of Samsoniella.
Named after Asia (China, Vietnam and Laos), where the species was originally collected.
Samsoniella asiatica A fungus-infected lepidopteran pupa B stipes producing a mass of conidia at the apex C synnemata of fungus arising from lepidopteran larva D colony as obversed on PDA medium E–M conidiophores, phialides and conidia on PDA N conidia on PDA. Scale bars: 10 mm (A, C); 5 mm (B); 20 mm (D); 15 μm (E); 10 μm (F, G, H); 5 μm (I, J, K, N); 3 μm (L, M).
China, Yunnan Province, Yuanyang County, Xinjie Town, Duoyishu Village (23°4′50″N, 102°48′34″E, 1866 m above sea level), on a pupa of Lepidoptera in a dead twig, 10 December 2021, Yao Wang (holotype: YHH 869; ex-type living culture: YFCC 869).
Teleomorph: Undetermined. Anamorph: Synnemata arising from lepidopteran insects. Synnemata erect, flexuous, white or pale orange, 4–26 × 0.4–1.5 mm. Stipes cylindrical, producing a mass of conidia at the branches of synnemata, powdery and floccose. Colonies on PDA moderately fast-growing, 41–45 mm diameter in 14 days at 25 °C, white, cottony, generating several concentric rings at the centrum, sporulating abundantly, reverse white to pale yellow. Hyphae smooth-walled, branched, septate, hyaline, 1.3–2.0 µm wide. Conidiophores smooth-walled, cylindrical, solitary or verticillate, 4.6–10.3 × 0.8–1.9 µm. Phialides on conidiophores verticillate, usually in whorls of two to four, or solitary on hyphae, 2.7–8.6 µm long, basal portion cylindrical to narrowly lageniform, tapering gradually or abruptly toward the apex, from 0.7–1.7 µm wide (base) to 0.6–1.1 µm wide (apex). Conidia smooth and hyaline, fusiform or oval, one-celled, 1.1–1.8 × 0.8–1.2 µm, often in chains. Size and shape of phialides and conidia similar in culture and on natural substratum.
Yunnan Province, China; Lao Cai Province, Vietnam; Oudomxay Province, Laos.
Vietnam, Lao Cai Province, Sa Pa District, Hoang Lien Mountains (22°21′4″N, 103°46′29″E, 1931 m above sea level), on a larva of Noctuidae buried in soil, 31 October 2016, collected by Hong Yu (YHH 871; living culture: YFCC 871); Laos, Oudomxay Province, Muang Xay County, Nagang Village (20°42′51″N, 102°5′44″E, 698 m above sea level), on a larva of Spilosoma, 29 July 2019, Yao Wang (YHH 870; living culture: YFCC 870).
Morphologically, S. asiatica resembles the phylogenetically closely related sister species S. yunnanensis in producing orange to pink stipes, a mass of conidia toward the apex synnemata and Isaria-like asexual conidiogenous structure. Additionally, both of the fungal sexual morphs have not been determined yet. However, S. asiatica can be distinguished from S. yunnanensis by its shorter phialides (2.7–8.6 µm) and smaller conidia (1.1–1.8 × 0.8–1.2 µm). Ecologically, S. asiatica has been found to parasitize larvae and pupae of Lepidoptera, whereas S. yunnanensis is associated with pupae of Limacodidae in cocoons and Cordyceps spp. (
Thailand (holotype: BBH 33739; ex-type living culture: TBRC 7271).
Samsoniella aurantia A, B perithecial stromata as encountered in the field C, D fungus on the pupae of Limacodidae inhabiting cocoons E, F synnemata arising from lepidopteran larvae G, H Perithecia I–K asci L colony as obversed on PDA. Scale bars: 10 mm (C, D, F); 5 mm (E); 200 µm (G); 100 µm (H); 10 µm (I, J, K); 20 mm (L).
Teleomorph: Stromata arising from lepidopteran insects, gregarious, branched or unbranched, up to 8.8–63.8 mm long. Stipes fleshly, flexuous, yellowish to orange, cylindrical to clavate, 4.1–49.1 × 0.2–2.3 mm. Fertile parts reddish orange, clavate, lateral side usually have a longitudinal section without producing perithecia, 3.8–17.7 × 0.8–4.1 mm. Perithecia crowded, superficial, narrowly ovoid to fusiform, 302.7–449.7 × 105.3–164.9 µm. Asci hyaline, cylindrical, 8‐spored, 92–190 × 1.8–3.6 μm. Apical caps prominent, hemiglobose, 2.1–3.4 µm wide, 1.2–2.3 µm high. Ascospores not observed. Anamorph: See
Chiang Mai Province, Thailand; Guizhou and Yunnan Province, China; Lao Cai Province, Vietnam.
China, Yunnan Province, Zhaotong City, Shuifu County, Taiping Town, Tongluoba National Forest Park (28°24′36″N, 104°9′0″E, 1750 m above sea level), on larvae of Hepialidae living in Qiongzhuea tumidinoda forests, 20 June 2015, collected by Hong Yu (YHH 874, YHH 890–YHH 893; living culture: 874). Vietnam, Lao Cai Province, Sa Pa District, Hoang Lien Mountains (22°21′8″N, 103°46′29″E, 1900 m above sea level), on a pupa of Limacodidae in a cocoon buried in soil, 31 October 2016, Hong Yu (YHH 880, YHH 894; living culture: YFCC 880). Thailand, Chiang Mai Province, Chiang Mai City, Queen Sirikit Botanic Garden (536 m above sea level), on lepidopteran larvae in leaf litter, 26 August 2018, Yao Wang (YHH 895–YHH 896).
Numerous species of Samsoniella were described originally from asexual morphs, including S. aurantia from Thailand (
China (holotype: IMM 82-2 = CHICMM 82-2; ex-type living culture: ICMM 82-2).
Samsoniella hepiali A stromata of fungus arising from lepidopteran pupa B stromata and synnemata arising from lepidopteran pupa C, D perithecia E, F asci G colony as obversed on PDA medium H–L conidiophores, phialides and conidia on PDA. Scale bars: 10 mm (A, B); 300 µm (C); 100 µm (D); 20 µm (E, F); 20 mm (G); 10 µm (H, I); 5 µm (J, K).
Teleomorph: Stromata from the whole body of lepidopteran pupae, gregarious, generally unbranched, up to 5–23 mm long. Stipes fleshly, flexuous or erect, yellowish to orange, cylindrical to clavate, 2.5–15.5 × 0.9–4.6 mm. Fertile parts orange, clavate, lateral side usually have a longitudinal section without producing perithecia, 1.3–8.5 × 0.8–5.2 mm. Perithecia crowded, superficial, narrowly ovoid to fusiform, 277.9–355.3 × 116.3–199.6 µm. Asci hyaline, cylindrical, 8‐spored, 145–300 × 3.5–5 μm. Apical caps prominent, hemiglobose, 2.5–4 µm wide, 2.4–3.2 µm high. Ascospores hyaline, bola‐shaped, septate, 120–240 × 0.8–1.5 μm. Anamorph: See
Yunnan, Qinghai, Anhui and Guizhou Province, China; Lao Cai Province, Vietnam; Buenos Aires City, Argentina.
Vietnam, Lao Cai Province, Sa Pa District, Hoang Lien Mountains (22°21′10″N, 103°46′29″E, 1989 m above sea level), on pupae of Hepialidae buried in soil, 30 October 2016, collected by Hong Yu (YHH 868, YHH 897–YHH 899; living culture: YFCC 868, YFCC 897–YFCC 899).
The strain (YFCC 868) isolated from the pupa of Hepialidae from Vietnam formed a well-supported clade with S. hepiali ex-type isolate (ICMM 82-2) (Fig.
In the current study, the sexual morph of S. hepiali was first reported. As for other teleomorph species of Samsoniella, S. hepiali has fleshy stromata, clavate fertile parts, superficial perithecia, and cylindrical asci with bola‐shaped ascospores. Among these species, only three, namely, S. cardinalis, S. hepiali, and S. kunmingensis, have short stromata (
Named after the location Sa Pa District where the species was collected.
Samsoniella sapaensis A stromata of fungus arising from lepidopteran larva B, C stromata and synnemata arising from lepidopteran insects D synnemata of fungus E, F perithecia G, H asci I, J colony as obversed and its backside on PDA K–M conidiophores, phialides and conidia on PDA N conidia on PDA. Scale bars: 10 mm (A, C); 5 mm (B); 20 mm (D); 100 µm (E, F, G); 50 µm (H); 20 mm (I); 30 mm (J); 5 µm (K, N); 10 µm (L, M).
Vietnam, Lao Cai Province, Sa Pa District, Hoang Lien National Park (22°19′30″N, 103°46′50″E, 2178 m above sea level), on a larva of Lepidoptera buried in soil, 26 October 2017, collected by Hong Yu (holotype: YHH 873; ex-type living culture: YFCC 873).
Teleomorph: Stromata arising from the whole body of lepidopteran pupae or larvae, gregarious, generally unbranched, up to 22–38 mm long. Stipes fleshly, flexuous, yellowish to orange, cylindrical to clavate, 7.5–14.5 × 0.7–4.6 mm. Fertile parts yellowish to reddish orange, clavate, lateral side usually have a longitudinal section without producing perithecia, 1.5–21.3 × 1.0–2.8 mm. Perithecia crowded, superficial, narrowly ovoid to fusiform, 383.2–412.1 × 125.4–156.9 µm. Asci cylindrical, hyaline, 282.5–444.5 × 2.6–3.9 µm, with a hemispheric apical cap of 1.8–2.2 × 2.6–3.0 µm. Ascospores not observed. Anamorph: Synnemata arising from lepidopteran insects. Synnemata flexuous, irregularly branched, white or pale orange, 9–58 × 0.2–1.6 mm, Isaria-like morph producing a mass of conidia at the branches of synnemata, powdery and floccose. Colonies on PDA moderately fast-growing, 36–40 mm diameter in 14 days at 25 °C, white to pale pink, cottony, sporulating abundantly, reverse yellow to orange. Hyphae smooth-walled, branched, septate, hyaline, 1.0–1.9 µm wide. Conidiophores smooth-walled, cylindrical, solitary or verticillate, 6.5–17.5 × 1.0–1.6 µm. Phialides verticillate, usually in whorls of two to three, or solitary on hyphae, 2.8–7.6 µm long, basal portion cylindrical to narrowly lageniform, tapering gradually or abruptly toward the apex, from 0.8–1.5 µm wide (base) to 0.6–0.9 µm wide (apex). Conidia smooth and hyaline, fusiform or oval, one-celled, 1.2–1.5 × 0.8–1.0 µm, often in chains. Size and shape of phialides and conidia similar in culture and on natural substratum.
At present, known only in Sa Pa District, Lao Cai Province, Vietnam.
Vietnam, Lao Cai Province, Sa Pa District (22°21′4″N, 103°46′29″E, 1931 m above sea level), on a pupa of Limacodidae in a cocoon buried in soil, 31 October 2016, collected by Hong Yu (YHH 872; living culture: YFCC 872). Vietnam, Lao Cai Province, Sa Pa District, Hoang Lien National Park (22°19′30″N, 103°46′50″E, 2178 m above sea level), on larvae of Lepidoptera buried in soil, 26 October 2017, collected by Yuan-Bing Wang (YHH 900–YHH 906).
Samsoniella sapaensis was identified as belonging to Samsoniella based on the phylogenetic analyses and was shown to resolve closely to S. haniana (Fig.
DNA sequence data for nr SSU, nr LSU, 3P_TEF, RPB1, and RPB2 have been used extensively to explore phylogenetic relationships among Samsoniella species in recent years (
The ITS, RPB2, ACT, and TUB sequences provided limited valuable information to separate Samsoniella spp. In contrast, sequence data for the 3P_TEF, 5P_TEF, RPB1, and MCM7 loci provided good resolution of Samsoniella species (Suppl. material
In addition to identifying the most of the useful gene regions to accurately identify species of Samsoniella, an important goal of this study was to re-establish well-supported boundaries in this genus. Having determined that the 3P_TEF, 5P_TEF, MCM7 and RPB1 regions yielded the best resolution for distinguishing species of Samsoniella, a phylogenetic tree based on the combined data (5P_TEF + 3P_TEF + RPB1 + MCM7) for the genus was generated (Fig.
Our multilocus phylogeny demonstrated the cryptic nature of the genus. First, the species status of S. pseudogunii is doubtful. From a phylogenetic point of view, S. pseudogunii cannot be distinguished from S. coleopterorum, being inside the clade of the latter. Regarding the micro-morphology, the two species are also very similar (
Because
The authors have declared that no competing interests exist.
No ethical statement was reported.
This work was supported by the National Natural Science Foundation of China (grants 32200013, 31870017 and 32160005).
Conceptualization: YW. Formal analysis: YW. Funding acquisition: HY. Investigation: VMD, CT, YW, ZQW, HY, YBW. Methodology: YW. Software: ZQW. Writing - original draft: YW. Writing - review and editing: HY.
All of the data that support the findings of this study are available in the main text or Supplementary Information.
Specimen information and GenBank accession numbers
Data type: docx
Explanation note: table S1. Specimen information and GenBank accession numbers for sequences used in the analyses of a five-locus (nr SSU, nr LSU, 3P_TEF, RPB1, and RPB2) dataset.
Pairwise genetic distance matrix of Samsoniella species
Data type: docx
Explanation note: table S2. Pairwise genetic distance matrix of Samsoniella species for ITS sequences. table S3. Pairwise genetic distance matrix of Samsoniella species for 3P-TEF sequences. table S4. Pairwise genetic distance matrix of Samsoniella species for 5P-TEF sequences. table S5. Pairwise genetic distance matrix of Samsoniella species for RPB1 sequences. table S6. Pairwise genetic distance matrix of Samsoniella species for RPB2 sequences. table S7. Pairwise genetic distance matrix of Samsoniella species for ACT sequences. table S8. Pairwise genetic distance matrix of Samsoniella species for TUB sequences. table S9. Pairwise genetic distance matrix of Samsoniella species for MCM7 sequences.
Phylogenetic tree of Samsoniella
Data type: docx
Explanation note: figure S1. Phylogenetic tree of Samsoniella based on Maximum Likelihood (ML) analysis from the 5P-TEF sequences. Statistical support values (≥50%) are shown at the nodes for ML boostrap support. figure S2. Phylogenetic tree of Samsoniella based on Maximum Likelihood (ML) analysis from the 3P-TEF sequences. Statistical support values (≥50%) are shown at the nodes for ML boostrap support. figure S3. Phylogenetic tree of Samsoniella based on Maximum Likelihood (ML) analysis from the RPB1 sequences. Statistical support values (≥50%) are shown at the nodes for ML boostrap support. figure S4. Phylogenetic tree of Samsoniella based on Maximum Likelihood (ML) analysis from the MCM7 sequences. Statistical support values (≥50%) are shown at the nodes for ML boostrap support.
Highlights
Data type: docx