Changes
On March 5, 2024 at 8:00:11 AM UTC, Markus Schlegel:
-
Updated description of Supporting information for case study on the application of spore sampling for the monitoring of macrofungi from
Resources associated with the manuscript *A case study on the application of spore sampling for the monitoring of macrofungi* ([Schlegel et al. 2024](https://doi.org/10.1111/1755-0998.13941)). Airborne environmental DNA (eDNA) monitoring of fungi was evaluated on a species-rich grassland site. Extensive fruiting body surveys yielded 29 waxcap and clavarioid species, 19 of which were also detectable in air eDNA. The analysis indicates that spores of locally occurring fruiting bodies were detected, in addition to a large diversity of common fungal species, while rare and threatened species were under-represented in the air. The contents of the dataset (ZIP archive): * All analysis scripts in [R-Markdown](https://rmarkdown.rstudio.com) format, including the rendered PDF output with figures and tables (*analysis* directory) * eDNA sample metadata (*amplicon_meta*) and results of the amplicon clustering (*amplicon_data*) and the source code of the pipeline (*amplicon_pipeline*) * positions of all fruiting body groups found in the surveys (3838 GPS points) (*surveys*) * positions of the spore traps, taxonomy of studied grassland fungi and red-list species, and many more resources Version 1 was submitted during the review phase. Version 2 contains minor changes and clarifications, and was used to generate the currently published supplement of the study. Please refer to `README.pdf` inside the archive for a complete description of the file structure and information on how to reproduce the analyses.
toResources associated with the manuscript *A case study on the application of spore sampling for the monitoring of macrofungi* ([Schlegel et al. 2024](https://doi.org/10.1111/1755-0998.13941)). Airborne environmental DNA (eDNA) monitoring of fungi was evaluated on a species-rich grassland site. Extensive fruiting body surveys yielded 29 waxcap and clavarioid species, 19 of which were also detectable in air eDNA. The analysis indicates that spores of locally occurring fruiting bodies were detected, in addition to a large diversity of common fungal species, while rare and threatened species were under-represented in the air. The contents of the dataset (ZIP archive): * All analysis scripts in [R-Markdown](https://rmarkdown.rstudio.com) format, including the rendered PDF output with figures and tables (*analysis* directory) * eDNA sample metadata (*amplicon_meta*) and results of the amplicon clustering (*amplicon_data*) and the source code of the pipeline (*amplicon_pipeline*) * positions of all fruiting body groups found in the surveys (3838 GPS points) (*surveys*) * positions of the spore traps, taxonomy of studied grassland fungi and red-list species, and many more resources Version 1 was submitted during the review phase. *Version 2* contains minor changes and clarifications, and was used to generate the currently published supplement of the study. Please refer to `README.pdf` inside the archive for a complete description of the file structure and information on how to reproduce the analyses.
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17 | \"Deborah\", \"name\": \"Zani\", \"email\": \"deborah.zani@wsl.ch\", | 17 | \"Deborah\", \"name\": \"Zani\", \"email\": \"deborah.zani@wsl.ch\", | ||
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21 | \"jonas.braennhage@wsl.ch\", \"data_credit\": [\"collection\", | 21 | \"jonas.braennhage@wsl.ch\", \"data_credit\": [\"collection\", | ||
22 | \"validation\", \"publication\"], \"identifier\": \"\", | 22 | \"validation\", \"publication\"], \"identifier\": \"\", | ||
23 | \"affiliation\": \"WSL\"}, {\"given_name\": \"Andrin\", \"name\": | 23 | \"affiliation\": \"WSL\"}, {\"given_name\": \"Andrin\", \"name\": | ||
24 | \"Gross\", \"email\": \"andrin.gross@wsl.ch\", \"data_credit\": | 24 | \"Gross\", \"email\": \"andrin.gross@wsl.ch\", \"data_credit\": | ||
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29 | "date": "[{\"date\": \"2018-10-05\", \"date_type\": \"created\", | 29 | "date": "[{\"date\": \"2018-10-05\", \"date_type\": \"created\", | ||
30 | \"end_date\": \"2019-11-12\"}, {\"date\": \"2018-10-05\", | 30 | \"end_date\": \"2019-11-12\"}, {\"date\": \"2018-10-05\", | ||
31 | \"date_type\": \"collected\", \"end_date\": \"2019-11-12\"}]", | 31 | \"date_type\": \"collected\", \"end_date\": \"2019-11-12\"}]", | ||
32 | "doi": "10.16904/envidat.434", | 32 | "doi": "10.16904/envidat.434", | ||
33 | "funding": "[{\"grant_number\": \"16.0100.PJ / R203-0209\", | 33 | "funding": "[{\"grant_number\": \"16.0100.PJ / R203-0209\", | ||
34 | \"institution\": \"Swiss Federal Office for the Environment\", | 34 | \"institution\": \"Swiss Federal Office for the Environment\", | ||
35 | \"institution_url\": \"https://www.bafu.admin.ch\"}]", | 35 | \"institution_url\": \"https://www.bafu.admin.ch\"}]", | ||
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40 | "license_id": "cc-by-sa", | 40 | "license_id": "cc-by-sa", | ||
41 | "license_title": "Creative Commons Attribution Share-Alike | 41 | "license_title": "Creative Commons Attribution Share-Alike | ||
42 | (CC-BY-SA)", | 42 | (CC-BY-SA)", | ||
43 | "license_url": "https://creativecommons.org/licenses/by-sa/4.0/", | 43 | "license_url": "https://creativecommons.org/licenses/by-sa/4.0/", | ||
44 | "maintainer": | 44 | "maintainer": | ||
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47 | "metadata_created": "2023-10-02T16:33:37.182679", | 47 | "metadata_created": "2023-10-02T16:33:37.182679", | ||
n | 48 | "metadata_modified": "2024-03-05T07:59:55.070350", | n | 48 | "metadata_modified": "2024-03-05T08:00:11.137698", |
49 | "name": | 49 | "name": | ||
50 | nformation-for-case-study-on-the-application-of-spore-sampling-for-t", | 50 | nformation-for-case-study-on-the-application-of-spore-sampling-for-t", | ||
51 | "notes": "Resources associated with the manuscript *A case study on | 51 | "notes": "Resources associated with the manuscript *A case study on | ||
52 | the application of spore sampling for the monitoring of macrofungi* | 52 | the application of spore sampling for the monitoring of macrofungi* | ||
53 | ([Schlegel et al. | 53 | ([Schlegel et al. | ||
54 | 2024](https://doi.org/10.1111/1755-0998.13941)).\n\nAirborne | 54 | 2024](https://doi.org/10.1111/1755-0998.13941)).\n\nAirborne | ||
55 | environmental DNA (eDNA) monitoring of fungi was evaluated on a | 55 | environmental DNA (eDNA) monitoring of fungi was evaluated on a | ||
56 | species-rich grassland site. Extensive fruiting body surveys yielded | 56 | species-rich grassland site. Extensive fruiting body surveys yielded | ||
57 | 29 waxcap and clavarioid species, 19 of which were also detectable in | 57 | 29 waxcap and clavarioid species, 19 of which were also detectable in | ||
58 | air eDNA. The analysis indicates that spores of locally occurring | 58 | air eDNA. The analysis indicates that spores of locally occurring | ||
59 | fruiting bodies were detected, in addition to a large diversity of | 59 | fruiting bodies were detected, in addition to a large diversity of | ||
60 | common fungal species, while rare and threatened species were | 60 | common fungal species, while rare and threatened species were | ||
61 | under-represented in the air.\n\nThe contents of the dataset (ZIP | 61 | under-represented in the air.\n\nThe contents of the dataset (ZIP | ||
62 | archive):\n\n* All analysis scripts in | 62 | archive):\n\n* All analysis scripts in | ||
63 | [R-Markdown](https://rmarkdown.rstudio.com) format, including the | 63 | [R-Markdown](https://rmarkdown.rstudio.com) format, including the | ||
64 | rendered PDF output with figures and tables (*analysis* directory)\n* | 64 | rendered PDF output with figures and tables (*analysis* directory)\n* | ||
65 | eDNA sample metadata (*amplicon_meta*) and results of the amplicon | 65 | eDNA sample metadata (*amplicon_meta*) and results of the amplicon | ||
66 | clustering (*amplicon_data*) and the source code of the pipeline | 66 | clustering (*amplicon_data*) and the source code of the pipeline | ||
67 | (*amplicon_pipeline*)\n* positions of all fruiting body groups found | 67 | (*amplicon_pipeline*)\n* positions of all fruiting body groups found | ||
68 | in the surveys (3838 GPS points) (*surveys*)\n* positions of the spore | 68 | in the surveys (3838 GPS points) (*surveys*)\n* positions of the spore | ||
69 | traps, taxonomy of studied grassland fungi and red-list species, and | 69 | traps, taxonomy of studied grassland fungi and red-list species, and | ||
t | 70 | many more resources\n\n\nVersion 1 was submitted during the review | t | 70 | many more resources\n\nVersion 1 was submitted during the review |
71 | phase. Version 2 contains minor changes and clarifications, and was | 71 | phase. *Version 2* contains minor changes and clarifications, and was | ||
72 | used to generate the currently published supplement of the | 72 | used to generate the currently published supplement of the | ||
73 | study.\n\nPlease refer to `README.pdf` inside the archive for a | 73 | study.\n\nPlease refer to `README.pdf` inside the archive for a | ||
74 | complete description of the file structure and information on how to | 74 | complete description of the file structure and information on how to | ||
75 | reproduce the analyses.", | 75 | reproduce the analyses.", | ||
76 | "num_resources": 2, | 76 | "num_resources": 2, | ||
77 | "num_tags": 5, | 77 | "num_tags": 5, | ||
78 | "organization": { | 78 | "organization": { | ||
79 | "approval_status": "approved", | 79 | "approval_status": "approved", | ||
80 | "created": "2018-05-18T09:12:30.577470", | 80 | "created": "2018-05-18T09:12:30.577470", | ||
81 | "description": "We study the relationship between threatened | 81 | "description": "We study the relationship between threatened | ||
82 | species and their habitat with the objective to develop evidence-based | 82 | species and their habitat with the objective to develop evidence-based | ||
83 | instruments for conservation. The viability of populations of habitat | 83 | instruments for conservation. The viability of populations of habitat | ||
84 | specialists is often limited due to restricted availability of | 84 | specialists is often limited due to restricted availability of | ||
85 | suitable habitat or discontinuous distribution. We focus on selected | 85 | suitable habitat or discontinuous distribution. We focus on selected | ||
86 | animal species of conservation concern (forest birds, bats, forest | 86 | animal species of conservation concern (forest birds, bats, forest | ||
87 | insects) and analyse species-habitat relationships at a scale ranging | 87 | insects) and analyse species-habitat relationships at a scale ranging | ||
88 | from single subpopulations to entire metapopulations. We strive | 88 | from single subpopulations to entire metapopulations. We strive | ||
89 | towards standardised recording of elusive species with novel | 89 | towards standardised recording of elusive species with novel | ||
90 | techniques, assessing environmental variables and combining these | 90 | techniques, assessing environmental variables and combining these | ||
91 | field data with data from remote sensing. We determine limiting | 91 | field data with data from remote sensing. We determine limiting | ||
92 | factors (habitat, climate, resources) and predict species occurrence | 92 | factors (habitat, climate, resources) and predict species occurrence | ||
93 | and habitat suitability with modelling techniques.\r\n\r\nThese models | 93 | and habitat suitability with modelling techniques.\r\n\r\nThese models | ||
94 | allow to predict species occurrence patterns and to delineate | 94 | allow to predict species occurrence patterns and to delineate | ||
95 | evidence-based priority areas for conservation. Our long-term | 95 | evidence-based priority areas for conservation. Our long-term | ||
96 | collaboration with federal and cantonal stakeholders of forest and | 96 | collaboration with federal and cantonal stakeholders of forest and | ||
97 | nature conservation enables the combination of research results with | 97 | nature conservation enables the combination of research results with | ||
98 | conservation requirements (e.g. species action plans, forest | 98 | conservation requirements (e.g. species action plans, forest | ||
99 | biodiversity expert panel, scientific counsel for bat protection). | 99 | biodiversity expert panel, scientific counsel for bat protection). | ||
100 | While we investigate complete distribution ranges in bats, we focus on | 100 | While we investigate complete distribution ranges in bats, we focus on | ||
101 | forest habitats in birds and insects given the large extent and high | 101 | forest habitats in birds and insects given the large extent and high | ||
102 | importance of forests for biodiversity conservation in Switzerland.", | 102 | importance of forests for biodiversity conservation in Switzerland.", | ||
103 | "id": "32672ec5-c180-471e-92f7-ef58e00eb1fb", | 103 | "id": "32672ec5-c180-471e-92f7-ef58e00eb1fb", | ||
104 | "image_url": "2018-07-10-090115.162284LogoWSL.svg", | 104 | "image_url": "2018-07-10-090115.162284LogoWSL.svg", | ||
105 | "is_organization": true, | 105 | "is_organization": true, | ||
106 | "name": "conservation-biology", | 106 | "name": "conservation-biology", | ||
107 | "state": "active", | 107 | "state": "active", | ||
108 | "title": "Conservation Biology", | 108 | "title": "Conservation Biology", | ||
109 | "type": "organization" | 109 | "type": "organization" | ||
110 | }, | 110 | }, | ||
111 | "owner_org": "32672ec5-c180-471e-92f7-ef58e00eb1fb", | 111 | "owner_org": "32672ec5-c180-471e-92f7-ef58e00eb1fb", | ||
112 | "private": false, | 112 | "private": false, | ||
113 | "publication": "{\"publication_year\": \"2023\", \"publisher\": | 113 | "publication": "{\"publication_year\": \"2023\", \"publisher\": | ||
114 | \"EnviDat\"}", | 114 | \"EnviDat\"}", | ||
115 | "publication_state": "published", | 115 | "publication_state": "published", | ||
116 | "related_datasets": "* [ITS barcode sequences of studied grassland | 116 | "related_datasets": "* [ITS barcode sequences of studied grassland | ||
117 | ps://www.ncbi.nlm.nih.gov/nuccore/?term=OP538697%3AOP538830%5Baccn%5D) | 117 | ps://www.ncbi.nlm.nih.gov/nuccore/?term=OP538697%3AOP538830%5Baccn%5D) | ||
118 | (GenBank accessions OP538697-OP538830)\r\n* [raw sequencing data for | 118 | (GenBank accessions OP538697-OP538830)\r\n* [raw sequencing data for | ||
119 | this study](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA994926) (NCBI | 119 | this study](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA994926) (NCBI | ||
120 | BioProject PRJNA994926)", | 120 | BioProject PRJNA994926)", | ||
121 | "related_publications": "", | 121 | "related_publications": "", | ||
122 | "relationships_as_object": [], | 122 | "relationships_as_object": [], | ||
123 | "relationships_as_subject": [], | 123 | "relationships_as_subject": [], | ||
124 | "resource_type": "dataset", | 124 | "resource_type": "dataset", | ||
125 | "resource_type_general": "dataset", | 125 | "resource_type_general": "dataset", | ||
126 | "resources": [ | 126 | "resources": [ | ||
127 | { | 127 | { | ||
128 | "cache_last_updated": null, | 128 | "cache_last_updated": null, | ||
129 | "cache_url": null, | 129 | "cache_url": null, | ||
130 | "created": "2023-10-03T09:33:24.248776", | 130 | "created": "2023-10-03T09:33:24.248776", | ||
131 | "description": "This ZIP archive contains the data and source | 131 | "description": "This ZIP archive contains the data and source | ||
132 | code necessary to reproduce the analyses for the manuscript \"A case | 132 | code necessary to reproduce the analyses for the manuscript \"A case | ||
133 | study on the application of spore sampling for the monitoring of | 133 | study on the application of spore sampling for the monitoring of | ||
134 | fungi\". Please refer to README.pdf inside the archive for more | 134 | fungi\". Please refer to README.pdf inside the archive for more | ||
135 | information.", | 135 | information.", | ||
136 | "doi": "", | 136 | "doi": "", | ||
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162 | code necessary to reproduce the analyses for the manuscript \"A case | 162 | code necessary to reproduce the analyses for the manuscript \"A case | ||
163 | study on the application of spore sampling for the monitoring of | 163 | study on the application of spore sampling for the monitoring of | ||
164 | macrofungi\". Please refer to README.pdf inside the archive for more | 164 | macrofungi\". Please refer to README.pdf inside the archive for more | ||
165 | information.", | 165 | information.", | ||
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175 | changes)", | 175 | changes)", | ||
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189 | "spatial": | 189 | "spatial": | ||
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191 | "spatial_info": "Switzerland", | 191 | "spatial_info": "Switzerland", | ||
192 | "state": "active", | 192 | "state": "active", | ||
193 | "subtitle": "", | 193 | "subtitle": "", | ||
194 | "tags": [ | 194 | "tags": [ | ||
195 | { | 195 | { | ||
196 | "display_name": "AIR SAMPLING", | 196 | "display_name": "AIR SAMPLING", | ||
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199 | "state": "active", | 199 | "state": "active", | ||
200 | "vocabulary_id": null | 200 | "vocabulary_id": null | ||
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204 | "id": "dab1a17e-9bf9-4e0a-9a60-c3ca8f8a9154", | 204 | "id": "dab1a17e-9bf9-4e0a-9a60-c3ca8f8a9154", | ||
205 | "name": "EDNA", | 205 | "name": "EDNA", | ||
206 | "state": "active", | 206 | "state": "active", | ||
207 | "vocabulary_id": null | 207 | "vocabulary_id": null | ||
208 | }, | 208 | }, | ||
209 | { | 209 | { | ||
210 | "display_name": "METABARCODING", | 210 | "display_name": "METABARCODING", | ||
211 | "id": "00af76c6-a1b0-407c-a7f3-898398363cfc", | 211 | "id": "00af76c6-a1b0-407c-a7f3-898398363cfc", | ||
212 | "name": "METABARCODING", | 212 | "name": "METABARCODING", | ||
213 | "state": "active", | 213 | "state": "active", | ||
214 | "vocabulary_id": null | 214 | "vocabulary_id": null | ||
215 | }, | 215 | }, | ||
216 | { | 216 | { | ||
217 | "display_name": "MONITORING", | 217 | "display_name": "MONITORING", | ||
218 | "id": "c5b72e0c-e21f-4255-bfac-78d7688e0307", | 218 | "id": "c5b72e0c-e21f-4255-bfac-78d7688e0307", | ||
219 | "name": "MONITORING", | 219 | "name": "MONITORING", | ||
220 | "state": "active", | 220 | "state": "active", | ||
221 | "vocabulary_id": null | 221 | "vocabulary_id": null | ||
222 | }, | 222 | }, | ||
223 | { | 223 | { | ||
224 | "display_name": "SPORE DISPERSAL", | 224 | "display_name": "SPORE DISPERSAL", | ||
225 | "id": "eb753e9f-5df4-4c3a-ab60-778104acc9ae", | 225 | "id": "eb753e9f-5df4-4c3a-ab60-778104acc9ae", | ||
226 | "name": "SPORE DISPERSAL", | 226 | "name": "SPORE DISPERSAL", | ||
227 | "state": "active", | 227 | "state": "active", | ||
228 | "vocabulary_id": null | 228 | "vocabulary_id": null | ||
229 | } | 229 | } | ||
230 | ], | 230 | ], | ||
231 | "title": "Supporting information for case study on the application | 231 | "title": "Supporting information for case study on the application | ||
232 | of spore sampling for the monitoring of macrofungi", | 232 | of spore sampling for the monitoring of macrofungi", | ||
233 | "type": "dataset", | 233 | "type": "dataset", | ||
234 | "url": null, | 234 | "url": null, | ||
235 | "version": "1.0" | 235 | "version": "1.0" | ||
236 | } | 236 | } |