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f
1
{
f
1
{
            
2
  "author": "[{\"given_name\": \"Romane\", \"name\": \"Rozanski\", 
2
  "author": "[{\"given_name\": \"Romane\", \"name\": \"Rozanski\", 
            
3
\"email\": \"romane.rozanski@usys.ethz.ch\", \"data_credit\": [], 
3
\"email\": \"romane.rozanski@usys.ethz.ch\", \"data_credit\": [], 
            
4
\"identifier\": \"\", \"affiliation\": \"Unit of Land Change Science, 
4
\"identifier\": \"\", \"affiliation\": \"Unit of Land Change Science, 
            
5
7u Federal Research Institute WSL, Birmensdorf, Switzerland\"}, 
5
7u Federal Research Institute WSL, Birmensdorf, Switzerland\"}, 
            
6
{\"given_name\": \"David\", \"name\": \"Eme\", \"email\": 
6
{\"given_name\": \"David\", \"name\": \"Eme\", \"email\": 
            
7
\"david.eme@inrae.fr\", \"data_credit\": [], \"identifier\": \"\", 
7
\"david.eme@inrae.fr\", \"data_credit\": [], \"identifier\": \"\", 
            
8
\"affiliation\": \"RiverLy Research Unit, National Research Institute 
8
\"affiliation\": \"RiverLy Research Unit, National Research Institute 
            
9
for Agriculture Food and Environment (INRAE), Villeurbanne, 
9
for Agriculture Food and Environment (INRAE), Villeurbanne, 
            
10
France.\"}, {\"given_name\": \"Eilish\", \"name\": \"Richards\", 
10
France.\"}, {\"given_name\": \"Eilish\", \"name\": \"Richards\", 
            
11
\"email\": \"eilishrichards@gmail.com\", \"data_credit\": [], 
11
\"email\": \"eilishrichards@gmail.com\", \"data_credit\": [], 
            
12
\"identifier\": \"\", \"affiliation\": \"WSL, ETH\"}, {\"given_name\": 
12
\"identifier\": \"\", \"affiliation\": \"WSL, ETH\"}, {\"given_name\": 
            
13
\"Marie emilie\", \"name\": \"Deschez\", \"email\": 
13
\"Marie emilie\", \"name\": \"Deschez\", \"email\": 
            
14
\"me.deschez@gmail.com\", \"data_credit\": [], \"identifier\": \"\", 
14
\"me.deschez@gmail.com\", \"data_credit\": [], \"identifier\": \"\", 
            
15
\"affiliation\": \"DECOD (Ecosystem Dynamics and Sustainability), 
15
\"affiliation\": \"DECOD (Ecosystem Dynamics and Sustainability), 
            
16
IFREMER, INRAE, Inst. Agro \\u2013 Agrocampus Ouest, Nantes, 
16
IFREMER, INRAE, Inst. Agro \\u2013 Agrocampus Ouest, Nantes, 
            
17
France\"}, {\"given_name\": \"Marta\", \"name\": \"Rufino\", 
17
France\"}, {\"given_name\": \"Marta\", \"name\": \"Rufino\", 
            
18
\"email\": \"marta.rufino@ipma.pt\", \"data_credit\": [], 
18
\"email\": \"marta.rufino@ipma.pt\", \"data_credit\": [], 
            
19
\"identifier\": \"\", \"affiliation\": \" IPMA- Portuguese Institute 
19
\"identifier\": \"\", \"affiliation\": \" IPMA- Portuguese Institute 
            
20
for the Sea and the Atmosphere, Division of Modeling and Management of 
20
for the Sea and the Atmosphere, Division of Modeling and Management of 
            
21
Fisheries Resources, Av. Dr. Alfredo Magalh\\u00e3es Ramalho, 6, 
21
Fisheries Resources, Av. Dr. Alfredo Magalh\\u00e3es Ramalho, 6, 
            
22
1495-165 Lisboa\"}, {\"given_name\": \"Verena\", \"name\": 
22
1495-165 Lisboa\"}, {\"given_name\": \"Verena\", \"name\": 
            
23
\"Trenkel\", \"email\": \"Verena.Trenkel@ifremer.fr\", 
23
\"Trenkel\", \"email\": \"Verena.Trenkel@ifremer.fr\", 
            
24
\"data_credit\": [], \"identifier\": \"\", \"affiliation\": \"DECOD 
24
\"data_credit\": [], \"identifier\": \"\", \"affiliation\": \"DECOD 
            
25
(Ecosystem Dynamics and Sustainability), IFREMER, INRAE, Inst. Agro 
25
(Ecosystem Dynamics and Sustainability), IFREMER, INRAE, Inst. Agro 
            
26
\\u2013 Agrocampus Ouest, Nantes, France\"}, {\"given_name\": 
26
\\u2013 Agrocampus Ouest, Nantes, France\"}, {\"given_name\": 
            
27
\"Pascal\", \"name\": \"Lorance\", \"email\": 
27
\"Pascal\", \"name\": \"Lorance\", \"email\": 
            
28
\"pascal.lorance@ifremer.fr\", \"data_credit\": [], \"identifier\": 
28
\"pascal.lorance@ifremer.fr\", \"data_credit\": [], \"identifier\": 
            
29
\"\", \"affiliation\": \"DECOD (Ecosystem Dynamics and 
29
\"\", \"affiliation\": \"DECOD (Ecosystem Dynamics and 
            
30
Sustainability), IFREMER, INRAE, Inst. Agro \\u2013 Agrocampus Ouest, 
30
Sustainability), IFREMER, INRAE, Inst. Agro \\u2013 Agrocampus Ouest, 
            
31
Nantes, France\"}, {\"given_name\": \"Virginie\", \"name\": 
31
Nantes, France\"}, {\"given_name\": \"Virginie\", \"name\": 
            
32
\"Marques\", \"email\": \"virginie.marques@wsl.ch\", \"data_credit\": 
32
\"Marques\", \"email\": \"virginie.marques@wsl.ch\", \"data_credit\": 
            
33
[], \"identifier\": \"\", \"affiliation\": \"Unit of Land Change 
33
[], \"identifier\": \"\", \"affiliation\": \"Unit of Land Change 
            
34
Science, Swiss Federal Research Institute WSL, Birmensdorf, 
34
Science, Swiss Federal Research Institute WSL, Birmensdorf, 
            
35
Switzerland\"}, {\"given_name\": \"Jer\\u00f4me\", \"name\": 
35
Switzerland\"}, {\"given_name\": \"Jer\\u00f4me\", \"name\": 
            
36
\"Spitz\", \"email\": \"jspitz@univ-lr.fr\", \"data_credit\": [], 
36
\"Spitz\", \"email\": \"jspitz@univ-lr.fr\", \"data_credit\": [], 
            
37
\"identifier\": \"\", \"affiliation\": \"Observatoire Pelagis, UAR 
37
\"identifier\": \"\", \"affiliation\": \"Observatoire Pelagis, UAR 
            
38
3462 La Rochelle Universit\\u00e9/CNRS, La Rochelle, France\"}, 
38
3462 La Rochelle Universit\\u00e9/CNRS, La Rochelle, France\"}, 
            
39
{\"given_name\": \"Florence\", \"name\": \"Cornette\", \"email\": 
39
{\"given_name\": \"Florence\", \"name\": \"Cornette\", \"email\": 
            
40
\"florence.cornette@ifremer.fr\", \"data_credit\": [], \"identifier\": 
40
\"florence.cornette@ifremer.fr\", \"data_credit\": [], \"identifier\": 
            
41
\"\", \"affiliation\": \"MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, 
41
\"\", \"affiliation\": \"MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, 
            
42
Montpellier, France \"}, {\"given_name\": \"Severine\", \"name\": 
42
Montpellier, France \"}, {\"given_name\": \"Severine\", \"name\": 
            
43
\"Albouy-Boyer\", \"email\": \"boyerseverine6@gmail.com\", 
43
\"Albouy-Boyer\", \"email\": \"boyerseverine6@gmail.com\", 
            
44
\"data_credit\": [], \"identifier\": \"\", \"affiliation\": 
44
\"data_credit\": [], \"identifier\": \"\", \"affiliation\": 
            
45
\"Freelance, Wallisellen, Switzerland\"}, {\"given_name\": \"Andrea\", 
45
\"Freelance, Wallisellen, Switzerland\"}, {\"given_name\": \"Andrea\", 
            
46
\"name\": \"Polanco\", \"email\": \"andrea.polanco@gmail.com\", 
46
\"name\": \"Polanco\", \"email\": \"andrea.polanco@gmail.com\", 
            
47
\"data_credit\": [], \"identifier\": \"\", \"affiliation\": 
47
\"data_credit\": [], \"identifier\": \"\", \"affiliation\": 
            
48
\"Biodiversa Colombia Foundation, Colombia\"}, {\"given_name\": 
48
\"Biodiversa Colombia Foundation, Colombia\"}, {\"given_name\": 
            
49
\"Bruno\", \"name\": \"Ernande\", \"email\": 
49
\"Bruno\", \"name\": \"Ernande\", \"email\": 
            
50
\"bruno.Ernande@ifremer.fr\", \"data_credit\": [], \"identifier\": 
50
\"bruno.Ernande@ifremer.fr\", \"data_credit\": [], \"identifier\": 
            
51
\"\", \"affiliation\": \"bruno.Ernande@ifremer.fr\"}, {\"given_name\": 
51
\"\", \"affiliation\": \"bruno.Ernande@ifremer.fr\"}, {\"given_name\": 
            
52
\"Loic\", \"name\": \"Pellissier\", \"email\": 
52
\"Loic\", \"name\": \"Pellissier\", \"email\": 
            
53
\"loic.pellissier@wsl.ch\", \"data_credit\": [], \"identifier\": 
53
\"loic.pellissier@wsl.ch\", \"data_credit\": [], \"identifier\": 
            
54
\"0000-0002-2289-8259\", \"affiliation\": \"Landscape Ecology, 
54
\"0000-0002-2289-8259\", \"affiliation\": \"Landscape Ecology, 
            
55
Institute of Terrestrial Ecosystems, ETH Z\\u00fcrich, 8049 
55
Institute of Terrestrial Ecosystems, ETH Z\\u00fcrich, 8049 
            
56
Z\\u00fcrich, Switzerland\"}, {\"given_name\": \"Camille\", \"name\": 
56
Z\\u00fcrich, Switzerland\"}, {\"given_name\": \"Camille\", \"name\": 
            
57
\"Albouy\", \"email\": \"camille.albouy@wsl.ch\", \"data_credit\": [], 
57
\"Albouy\", \"email\": \"camille.albouy@wsl.ch\", \"data_credit\": [], 
            
58
\"identifier\": \"\", \"affiliation\": \"Unit of Land Change Science, 
58
\"identifier\": \"\", \"affiliation\": \"Unit of Land Change Science, 
            
59
7u Federal Research Institute WSL, Birmensdorf, Switzerland\"}]",
59
7u Federal Research Institute WSL, Birmensdorf, Switzerland\"}]",
            
60
  "author_email": null,
60
  "author_email": null,
            
61
  "creator_user_id": "13a3a263-24b9-4fdd-b63c-6f931f20a3b2",
61
  "creator_user_id": "13a3a263-24b9-4fdd-b63c-6f931f20a3b2",
            
62
  "date": "[{\"date\": \"2017-10-01\", \"date_type\": \"collected\", 
62
  "date": "[{\"date\": \"2017-10-01\", \"date_type\": \"collected\", 
            
63
\"end_date\": \"2020-10-31\"}, {\"date\": \"2024-03-12\", 
63
\"end_date\": \"2020-10-31\"}, {\"date\": \"2024-03-12\", 
            
64
\"date_type\": \"created\", \"end_date\": \"2024-03-13\"}]",
64
\"date_type\": \"created\", \"end_date\": \"2024-03-13\"}]",
            
65
  "doi": "10.16904/envidat.495",
65
  "doi": "10.16904/envidat.495",
            
66
  "funding": "[{\"grant_number\": \"\", \"institution\": \"Region Pays 
66
  "funding": "[{\"grant_number\": \"\", \"institution\": \"Region Pays 
            
67
de la Loire\", \"institution_url\": 
67
de la Loire\", \"institution_url\": 
            
68
paysdelaloire.fr/les-aides/etoiles-montantes-en-pays-de-la-loire\"}]",
68
paysdelaloire.fr/les-aides/etoiles-montantes-en-pays-de-la-loire\"}]",
            
69
  "groups": [],
69
  "groups": [],
            
70
  "id": "1d2d5111-0c08-4549-b238-1345c550d580",
70
  "id": "1d2d5111-0c08-4549-b238-1345c550d580",
            
71
  "isopen": true,
71
  "isopen": true,
            
72
  "language": "en",
72
  "language": "en",
            
73
  "license_id": "cc-by-sa",
73
  "license_id": "cc-by-sa",
            
74
  "license_title": "Creative Commons Attribution Share-Alike 
74
  "license_title": "Creative Commons Attribution Share-Alike 
            
75
(CC-BY-SA)",
75
(CC-BY-SA)",
            
76
  "license_url": "https://creativecommons.org/licenses/by-sa/4.0/",
76
  "license_url": "https://creativecommons.org/licenses/by-sa/4.0/",
            
77
  "maintainer": "{\"affiliation\": \"\", \"email\": 
77
  "maintainer": "{\"affiliation\": \"\", \"email\": 
            
78
\"camille.albouy@wsl.ch\", \"given_name\": \"Camille\", 
78
\"camille.albouy@wsl.ch\", \"given_name\": \"Camille\", 
            
79
\"identifier\": \"\", \"name\": \"Albouy\"}",
79
\"identifier\": \"\", \"name\": \"Albouy\"}",
            
80
  "maintainer_email": null,
80
  "maintainer_email": null,
            
81
  "metadata_created": "2024-03-13T15:39:01.797881",
81
  "metadata_created": "2024-03-13T15:39:01.797881",
            
n
82
  "metadata_modified": "2024-11-22T18:32:21.408496",
n
82
  "metadata_modified": "2024-11-26T17:12:09.186754",
            
83
  "name": 
83
  "name": 
            
84
-12s-mitochondrial-reference-dataset-for-metabarcoding-atlantic-fish",
84
-12s-mitochondrial-reference-dataset-for-metabarcoding-atlantic-fish",
            
85
  "notes": "The global biodiversity crisis driven by anthropogenic 
85
  "notes": "The global biodiversity crisis driven by anthropogenic 
            
86
pressures significantly threatens marine ecosystems functioning. The 
86
pressures significantly threatens marine ecosystems functioning. The 
            
87
rate of climate change and the impacts of anthropogenic pressures 
87
rate of climate change and the impacts of anthropogenic pressures 
            
88
outpacing the capabilities of our observation tools, stresses the need 
88
outpacing the capabilities of our observation tools, stresses the need 
            
89
to develop new methods to assess these rapid modifications. 
89
to develop new methods to assess these rapid modifications. 
            
90
Environmental DNA (eDNA; DNA traces released by organisms) 
90
Environmental DNA (eDNA; DNA traces released by organisms) 
            
91
metabarcoding has emerged as a non-invasive method that has been 
91
metabarcoding has emerged as a non-invasive method that has been 
            
92
widely developed over the last decade.  Thanks to a large 
92
widely developed over the last decade.  Thanks to a large 
            
93
spatio-temporal coverage,  high detection of rare species and its time 
93
spatio-temporal coverage,  high detection of rare species and its time 
            
94
and cost effectiveness, eDNA metabarcoding represents a promising 
94
and cost effectiveness, eDNA metabarcoding represents a promising 
            
95
biomonitoring tool. However, capturing fish diversity using eDNA 
95
biomonitoring tool. However, capturing fish diversity using eDNA 
            
96
requires a high-quality genetic reference database, which we are 
96
requires a high-quality genetic reference database, which we are 
            
97
currently still lacking. For the South European Atlantic shelf area, 
97
currently still lacking. For the South European Atlantic shelf area, 
            
98
we estimated that only 41% of the fish species present were recorded 
98
we estimated that only 41% of the fish species present were recorded 
            
99
in the available eDNA reference databases. Improving reference 
99
in the available eDNA reference databases. Improving reference 
            
100
databases can notably rely on opportunistic sampling enabling the 
100
databases can notably rely on opportunistic sampling enabling the 
            
101
reporting of sequences for new species. Therefore, the data provided 
101
reporting of sequences for new species. Therefore, the data provided 
            
102
here consists of barcoding 95 species of ray-finned and cartilaginous 
102
here consists of barcoding 95 species of ray-finned and cartilaginous 
            
103
fishes over the 12S mitochondrial DNA gene. We generated 168 12S 
103
fishes over the 12S mitochondrial DNA gene. We generated 168 12S 
            
104
barcodes from fishes that were sampled in the Bay of Biscay (Northeast 
104
barcodes from fishes that were sampled in the Bay of Biscay (Northeast 
            
105
Atlantic, France) between 2017 and 2019. We also provided the 
105
Atlantic, France) between 2017 and 2019. We also provided the 
            
106
\u201cTeleo\u201d barcode associated with a specific 12S region for 
106
\u201cTeleo\u201d barcode associated with a specific 12S region for 
            
107
each individual. In addition to the sequences, we provided for each 
107
each individual. In addition to the sequences, we provided for each 
            
108
individual the taxonomy, the details associated with the barcode 
108
individual the taxonomy, the details associated with the barcode 
            
109
(Genbank accession number, chromatograms), a photograph, as well as 5 
109
(Genbank accession number, chromatograms), a photograph, as well as 5 
            
110
ecomorphological measures and 11 life-history traits. These traits 
110
ecomorphological measures and 11 life-history traits. These traits 
            
111
document several functions such as dispersion, diet, habitat use, and 
111
document several functions such as dispersion, diet, habitat use, and 
            
112
position in the food web. Furthermore, we provided the metadata of 
112
position in the food web. Furthermore, we provided the metadata of 
            
113
each sampling site (date, station, sampling hour, gear, latitude, 
113
each sampling site (date, station, sampling hour, gear, latitude, 
            
114
longitude, depth) and environmental variables measured in situ 
114
longitude, depth) and environmental variables measured in situ 
            
115
(conductivity, salinity, water temperature, water density, air 
115
(conductivity, salinity, water temperature, water density, air 
            
116
temperature).\r\nThis data set is highly valuable to improve the 
116
temperature).\r\nThis data set is highly valuable to improve the 
            
117
Northeast Atlantic eDNA genetic database, thus helping to better 
117
Northeast Atlantic eDNA genetic database, thus helping to better 
            
118
understand the effects of environmental forcing in the Bay of Biscay, 
118
understand the effects of environmental forcing in the Bay of Biscay, 
            
119
a transition zone housing mixed assemblages of boreal, temperate and 
119
a transition zone housing mixed assemblages of boreal, temperate and 
            
120
subtropical fish species susceptible to display variability in 
120
subtropical fish species susceptible to display variability in 
            
121
functional traits to adapt to changing conditions.\r\n",
121
functional traits to adapt to changing conditions.\r\n",
            
122
  "num_resources": 7,
122
  "num_resources": 7,
            
123
  "num_tags": 7,
123
  "num_tags": 7,
            
124
  "organization": {
124
  "organization": {
            
125
    "approval_status": "approved",
125
    "approval_status": "approved",
            
126
    "created": "2018-12-01T11:59:01.791513",
126
    "created": "2018-12-01T11:59:01.791513",
            
127
    "description": "We are an international research team with diverse 
127
    "description": "We are an international research team with diverse 
            
128
scientific expertise and backgrounds, connected by the goal to 
128
scientific expertise and backgrounds, connected by the goal to 
            
129
understand biodiversity. We study the mechanisms that shape 
129
understand biodiversity. We study the mechanisms that shape 
            
130
biodiversity patterns across spatial and temporal scales - in both 
130
biodiversity patterns across spatial and temporal scales - in both 
            
131
terrestrial and aquatic ecosystems -\u200bsuch as mountain ranges and 
131
terrestrial and aquatic ecosystems -\u200bsuch as mountain ranges and 
            
132
tropical reefs. We use an interdisciplinary approach, whereby we 
132
tropical reefs. We use an interdisciplinary approach, whereby we 
            
133
bridge ecology, evolution, Earth history and global change.\r\nTo make 
133
bridge ecology, evolution, Earth history and global change.\r\nTo make 
            
134
these connections, we collect data through biological monitoring, 
134
these connections, we collect data through biological monitoring, 
            
135
environmental DNA methods, remote sensing, and field sampling, and use 
135
environmental DNA methods, remote sensing, and field sampling, and use 
            
136
these data to answer questions with statistical and 
136
these data to answer questions with statistical and 
            
137
process-\u200bbased models of biological diversity.\r\nOur group is 
137
process-\u200bbased models of biological diversity.\r\nOur group is 
            
138
affiliated with ETH and WSL, but is also associated with Agroscope, 
138
affiliated with ETH and WSL, but is also associated with Agroscope, 
            
139
EAWAG, the European Joint Research Centre and Vogelwarte.",
139
EAWAG, the European Joint Research Centre and Vogelwarte.",
            
140
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      "description": "Mitochondrial tree based on the 12s sequences 
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      "description": "Mitochondrial tree based on the 12s sequences 
            
308
obtained for altantic fish. \r\nThis data represent the maximum 
308
obtained for altantic fish. \r\nThis data represent the maximum 
            
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likelihood phylogenetic tree allowing to assess 1) the clustering of 
309
likelihood phylogenetic tree allowing to assess 1) the clustering of 
            
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the different sequences generated in\r\nthis study and their closest 
310
the different sequences generated in\r\nthis study and their closest 
            
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sequences recovered through a MegaBLAST on GenBank, 2) the robustness 
311
sequences recovered through a MegaBLAST on GenBank, 2) the robustness 
            
312
of the clades and 3) the\r\nphylogenetic dissimilarities through the 
312
of the clades and 3) the\r\nphylogenetic dissimilarities through the 
            
313
branch length of the tree among the different sequences. This tree was 
313
branch length of the tree among the different sequences. This tree was 
            
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built with IQtree2\r\nusing the best substitution model found by 
314
built with IQtree2\r\nusing the best substitution model found by 
            
315
modelFinder. The robustness of the node was evaluated using 1000 
315
modelFinder. The robustness of the node was evaluated using 1000 
            
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ultra-fast bootstrap\r\n(node information indicated on the right of 
316
ultra-fast bootstrap\r\n(node information indicated on the right of 
            
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the /) and SH-aLRT procedures (node information indicated on the left 
317
the /) and SH-aLRT procedures (node information indicated on the left 
            
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of the /), using a hillclimbing nearest neighbor interchange (NNI) 
318
of the /), using a hillclimbing nearest neighbor interchange (NNI) 
            
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search to reduce the risk of overestimating branch supports with 
319
search to reduce the risk of overestimating branch supports with 
            
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ultra-fast Bootstrap\r\ncaused by too severe model violations.",
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ultra-fast Bootstrap\r\ncaused by too severe model violations.",
            
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