Two New Lyophyllum Species from Yunnan, China
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsLi et al. report on the discovery of two novel species of Lyophyllum in Yunnan, China, based on a combination of classical (morphological) and molecular (phylogenetic) approaches. The authors also update the description of L. rhombisporum, a previously published Chinese species.
Plates and phylogeny are of acceptable quality, so that the novelty of the two species and their phylogenetic placement within sect. Lyophyllum is not questionable. However, the manuscript suffers from a number of weaknesses that make it unsuitable for publication in its present form, in any journal of fungal taxonomy.
The most problematic issues are 1) the lack of a proper Introduction and Discussion that miss most of the relevant literature about the genus, including its defining features (the basidia siderophily), 2) the weakness of 3.1 (Phylogenetic analysis) and 3.2 (Taxonomy) sections, 3) the treatment of the updated description of L. rhombisporum, and 4) the insufficient, inadequate and completely messy bibliography. The poor quality of English throughout the manuscript also makes it difficult to understand in several places.
More specifically :
11- « floccus » : change to « flakes », « scales » or any other classical terms for these pileal ornamentations
12- « with » : change to « at » ; based : change to « base »
12-13 and 15-16- « narrowly cylindrical or narrowly clavate pleurocystidia and cheilocystidia, very broadly fusiform to broadly fusiform basidiospores » : this description is repeated for the two species and very vague (what is the limit between « very broadly fusiform » and « broadly fusiform » ?). If not different, no need to mention, especially in the Abstract
24- « is categorized within » : change to « belongs to » ; « belonging to » : change to « within »
25- « Index Fungorum 2024 » : this is not a proper reference, cite the author(s) of this Systematic choice
25-30- to be entirely rephrased to include the defining features of the genus (incl. the basidia siderophily) and with proper references
32-33- To my knowledge, L. cinerascens = L. fumosum, not L. decastes. Double check and cite a proper reference
33- « an additional » : remove « an »
36- « study that went into » : change to « studies performed within »
37- « Ellen and Henrik » : change to « Larsson & Sundberg »
38- « , later, » : change to « . Later, »
39- check references, as n°8 corresponds to a New Zealand study
43- check and add references, as the one cited corresponds to a New Zealand study only
44-45- reformulate the sentence, that misses a verb and is of poor English
48-66- add something about siderophily tests
Table 1- double check all references, many are wrong/missing ; double check also country of origin, several collections are listed as Swiss but they were just sequenced in Switzerland by Hofstetter et al., from strains of unknown origin. L. loricatum 01.12.09 is the holotype of L. loricatum f. subxantha
112-113- double check numbers : 225 + 277 + 300 ≠577
114-117- these numbers are useless in the Result section
122- add facts about tree topology and phylogenetic distances (intra-clade variability, distance to closest clades, comparison with other species…)
Figure 1- country is missing for L. moncalvoanum and L. lixivium
124-125- « based on combined sequence data of ITS1-5.8S-ITS2 alignment of Lyophyllum. » Rephrase, poor English
127- add that bold refers to type material
129- « Figs. 2 » : change to « Fig. 2 »
133 & 188- what does mean the exclamation mark after « holotype » ?
136-144, 190-196 & 239-245- too many English issues, ask a native to rephrase with proper taxonomical terms
146, 169-170, 198, 220 & 247- what is the limit between « very broadly fusiform » and « broadly fusiform » ?
149 & 201- « granulation » : change to « granulations »
152, 160, 204, 212, 253 & 261- « connection » : change to « connections »
162, 213 & 262- « Distribution » : change to « distribution »
167- these two additional specimens comes from the same locality as the holotype, so 1) how come the elevation can differ by 48 m (1950 m vs 1902 m) ? and 2) this fact should be discussed to acknowledge that a single individual/genet/mycelium has been described
169- « point and line » : change to « points and lines » or other more adequate taxonomic terms ; « based stipe base » : change to « stipe base »
171- « cheilocystidia pleurocystidia » : change to « cheilocystidia and pleurocystidia », or just « cystidia »
173- « rhombus » : change to « rhomboidal »
177- « thus considered them as differ species. » : change to e.g. « thus we considered them as differ species. »
184- « Figs. 3 » : change to « Fig. 3 »
223- « was clustered » : change to « clusters »
224- IFO 30978 (L. sykosporum) certainly does not occur in Switzerland, cf. comment above for Table 1
224-227- Rephrase, poor English
237- « Figs. 4 » : change to « Fig. 4 »
249- « sometime » : change to « sometimes »
265- « Additional specimens examined » : change to « Specimens examined »
268- « China Yunnan » : change to « Yunnan, China »
269- « , in origin description, specimen L1763 have a larger basidiospores » : change to « . In the original description, specimen L1763 has larger basidiospores »
271-272- Rephrase, poor English
274- « L. infumatum original description from Italy » : change to « L. infumatum, originally described from Italy »
275-276- « , the ITS genetic distance between the holotype L. rhombisporum L1762 » : change to « .The ITS genetic distance between the holotype of L. rhombisporum (L1763) »
268-276- this is not possible to propose an update of this species without re-analyzing the original material (L1763), and with such a poor critical point of view. Considering the spore size values originally reported, roughly twice as those of L. infumatum, the most likely hypothesis was that Li & Zhao miscalibrated their microscope or measured them at a wrong magnification. The new measurements on the ITS identical L5010 and L5084 support this hypothesis or at least that something is very special with the holotype, further justifying its re-analysis. The authors should at least comment this ! They should also yield a better analysis of the phylogenetic distance separating L. rhombisporum from L. infumatum, considering the genetic polymorphism of the latter. From a personal analysis of a large ITS dataset, the sequence of L1763 differs from L. infumatum sequences by a single C-T SNP at the end of the ITS1 domain, which is less than the average intra-clade phylogenetic distance. This would leave only basidia size (with doubts as far as the original material is concerned) and stipe context as separating criteria between the two species. Anyone would conclude to conspecificity with such observations...
Discussion- this section should be entirely and thoroughly revised, focussing on the unique features of the two spp. nov. compared to at least other species occurring in China. Lines 294-300 make no sense, as most cited species are not from China. Lines 301-309 are just meaningless. A thorough discussion of the status of L. rhombisporum (cf. above) would nicely fit there.
References- this section is absolutely a shame ! Essential references are missing, several are duplicated (n° 2 = n° 8 = n° 23 ; n° 5 = n° 24 = n° 26), some seems randomly cited in the text (e.g. n° 27) or Table 1. This sole issue may justify rejection of the manuscript in some journals !
Comments for author File: 
Comments.pdf
The English needs to be seriously improved, as in several places, it is just hard to understand what the authors mean.
Author Response
Dear reviewer
Thank you so much for your valuable comments which greatly improved our paper.
Author Response File: Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsThis study contributes to fungal biodiversity in China and bases on the integrative approach to new species descriptions in the genus Lyophyllum. This data were well documented by the authors.
The points below speak in favor of accepting the manuscript for the journal:
*The manuscript is clear, relevant for the field and well-structured.
*The abstract presented in the article characterizes the subject, reflects the purpose of the study, the main content and novelty of the article.
*The introduction contains historical and theoretical data according to modern literary sources.
I have only several minor comments. Please, see them below:
Lines 11 and 14 – Please indicate two latin names not bold (such style used in syntaxonomic works).
Keywords – Please add “integrative approach» once it was applied.
Line 30 – habits. [1-2]. > habits [1-2].
Lines 32-33 – L. decastes AUTHORITY.
Lines 40-41 – L. shimeji AUTHORITY, L. decastes, and L. fumosum AUTHORITY,
Lines 44-45 – L. bulborhizum AUTHORITY and L. nigrum AUTHORITY
Materials and methods – This part of the manuscript almost repetition of such part your recent paper https://doi.org/10.3390/d15091027, so I recommend make a citations in appropriate way to decrease the size.
Line 110-122 – This part of the manuscript almost repetition of such part your recent paper https://doi.org/10.3390/d15091027, so I recommend to rewrite it in appropriate way.
Fig.1 – Indicate in the caption what bold accessions mean.
Line 128 – 3.2 Taxonomy – not bold.
Line 129 – Figs. 2 > Figures 2A–H and next descriptions too. Please check through the text according instructions for authors.
Line 177 – You may add: Gene sequence: DNA sequences obtained from Lyophyllum bulborhizum were deposited in GenBank under accession no. XX000000. And next description too.
Line 175 – Please avoid incorrect L. sp > Lyophyllum sp. Check through the text.
Lines 176, 226 – Please add about ITS genetic distances calculation in the M&M chapter and mean inter- intraspecific percentage of ITS rRNA marker through your tree.
Thank you!
Author Response
Dear reviewer
Thank you so much for your comment which improved.
All the best
Tang
Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
Comments and Suggestions for AuthorsAlthough the authors somehow improved their manuscript, they addressed the easiest/fastest issues but left many problems unsolved. The Discussion needs to be entirely revised along lines already suggested in my previous review and checked by a native English.
Specific points (that are not exclusive of what precedes !):
24- « with » : change to « within »
25- Index Fungorum is not a proper reference to introduce a taxon, this is just a data repository. Please cite here the author(s) of the genus Lyophyllum P. Karst., Acta Soc. Fauna Flora fenn. 2(no. 1): 29 (1881)
25-30- Siderophily of basidia is not especially weak and is not just one feature of Lyophyllum among others, it is the sole unifying criterion within Lyophyllaceae. You need to introduce it better and cite proper references, e.g. : Kühner R. (1938) Utilisation du carmin acétique dans la classification des Agarics leucosporés. Bulletin Mensuel de la Société Linnéenne de Lyon 7: 204–211 ; or Jülich W. (1982) Lyophyllaceae. Bibl. Mycol. 85: 378.
29-30- Remove one « and » (there are two).
32-33- To my knowledge, L. cinerascens = L. fumosum, not L. decastes. Double check and cite a proper reference. Your answer that « is L. decastes based on index Fungroum 302:1(2016) » is inapropriate because Gminder just published a new comb. of Agaricus fumosus in the genus Lyophyllum and chose the taxonomic rank of variety. This choice is purely personal and does not fit to the phylogenetic organization of the group that resolves several clades. If you want to follow this unfortunate taxonomy, fine but you have to replace « L. decates (Fr.) Singer » by « L. decastes var. fumosum (Pers.) Gminder », otherwise, your statement is not only misleading but wrong !
Line 40 and 41- replace « nrLSU » by « LSU ».
Line 41-42 and 133-134- remove the two examples, useless and incorrectly written (English), i.e. stop the sentence after the refs 9-12.
Line 135- correct « shemeji » by « shimeji »
Line 136- split the sentence in two, after « Orton ».
Line 142-144- reformulate (English)
Line 151-152- siderophily is revealed with acetate carmine, not cotton blue. The cited reference concerns Rhodocybe, which is not a Lyophyllaceae !!! Please read Kühner R. (1938) Utilisation du carmin acétique dans la classification des Agarics leucosporés. Bulletin Mensuel de la Société Linnéenne de Lyon 7: 204–211
207-209- reformulate (English)
Figure 1 legend- Add a coma after « specimen number » and change « original » by « country » (also in Table 1). Remove « black » after « bold » and change « before taxa » by « after specimen number ».
Table 1- L. atrofuscum sequences are not from ref. 29, only one sequence (that of L. turcicum) has been published in ref. 13, I did not check all but clearly, this column is full of wrong references. Please double (triple as I already requested this in my previous review) check and edit these references
270-272- These numbers don’t make sense, as I already pointed out : 300 conserved characters + 277 variable but parsimony-uninformative characters. If your alignment = 577, there is no parsimony-infomative character, which is highly unlikely…
272-275- As I already pointed out previously, these numbers are useless in the Results section. Please discard them, as they are really of limited interest to the readers, or transfer them in the Materials and methods.
279- change « significantly distinguished from » by « not conspecific with »
285- rephrase as « based on a partial ITS1-5.8S-ITS2 sequence alignment of Lyophyllum. »
295, 350- if you really want to keep the « ! » after the holotype mention, please indicate its meaning in the Materials and methods section.
298-305, 352-358 & 401-407- too many English issues, ask a native to rephrase with proper taxonomical terms (already requested before).
307, 360, 382, 410-411 & 454- what is the limit between « very broadly fusiform » and « broadly fusiform » ? Your answer is not satisfactory because 1) you do not cite any reference from Vellinga (1998) and 2) I could not fin dit either. Please provide the full reference for me to check what these authors define as broadly and very broadly fusiform and if this distinction is indeed well established by Vellinga, please add the relevant reference.
338- edit « differ » by « different »
381- change « soon change to grey dark when lamellae bruised » by « lamellae soon changing to dark grey when bruised »
385- remove « was »
386- remove « from Switzerland »
386-388- too many English errors, ask a native to rephrase
435-436- too many English errors, ask a native to rephrase
439-440- this last sentence (the holotype number is L1763) is incorrect and misleading, as you omit the infraspecific variability of L. infumatum in this comparison. Please refer to my previous comment on these distances, I did the work for you, use it !!!
Discussion- too many English errors, ask a native to rephrase. See my previous comments that still hold. The only added part about L. rhombisporum hardly reads, please ask a native to review the entire manuscript, it cannot be published in an international journal in the present form.
Comments on the Quality of English LanguageAs already requested, many parts need to be revised by a native English to edit vocabulary and grammar.In its present form, this manuscript does not meet the standards of an international journal of fungal taxonomy.
Author Response
Dear review
Thank you for your comments, please see my reply on the file.
Thank you again for your help
All the best
Tang
Author Response File: Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsLines 38-41 - Not bold
2.4 ITS genetic distances calculation - Ok, but next time use program calculation, e.g. MEGA 11 program.
Author Response
Dear review
Thank you for your comments.
All the best
Tang
Author Response File: Author Response.pdf
