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pmid:31988713

Population genomic structure of the gelatinous zooplankton species Mnemiopsis leidyi in its nonindigenous range in the North Sea.

Christophe Verwimp · Lies Vansteenbrugge · Sofie Derycke · Thomas Kerkhove · Hilde Muylle · Olivier Honnay · Tom Ruttink · Isabel Roldán-Ruiz · Kris Hostens

Ecology and evolution · 2020 doi:10.1002/ece3.5468

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
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1.2
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pmid:31988713
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science-record
revision
6
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https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:40:55Z
updated_at
2026-11-01T21:22:50Z
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paper object · 10 fields
state
complete
title
Population genomic structure of the gelatinous zooplankton species Mnemiopsis leidyi in its nonindigenous range in the North Sea.
doi
10.1002/ece3.5468
pmid
31988713
authors array · 9 items
[0]
Christophe Verwimp
[1]
Lies Vansteenbrugge
[2]
Sofie Derycke
[3]
Thomas Kerkhove
[4]
Hilde Muylle
[5]
Olivier Honnay
[6]
Tom Ruttink
[7]
Isabel Roldán-Ruiz
[8]
Kris Hostens
journal
Ecology and evolution
year
2020
abstract
Nonindigenous species pose a major threat for coastal and estuarine ecosystems. Risk management requires genetic information to establish appropriate management units and infer introduction and dispersal routes. We investigated one of the most successful marine invaders, the ctenophore Mnemiopsis leidyi, and used genotyping-by-sequencing (GBS) to explore the spatial population structure in its nonindigenous range in the North Sea. We analyzed 140 specimens collected in different environments, including coastal and estuarine areas, and ports along the coast. Single nucleotide polymorphisms (SNPs) were called in approximately 40 k GBS loci. Population structure based on the neutral SNP panel was significant (F ST .02; p < .01), and a distinct genetic cluster was identified in a port along the Belgian coast (Ostend port; pairwise F ST .02-.04; p < .01). Remarkably, no population structure was detected between geographically distant regions in the North Sea (the Southern part of the North Sea vs. the Kattegat/Skagerrak region), which indicates substantial gene flow at this geographical scale and recent population expansion of nonindigenous M. leidyi. Additionally, seven specimens collected at one location in the indigenous range (Chesapeake Bay, USA) were highly differentiated from the North Sea populations (pairwise F ST .36-.39; p < .01). This study demonstrates the utility of GBS to investigate fine-scale population structure of gelatinous zooplankton species and shows high population connectivity among nonindigenous populations of this recently introduced species in the North Sea. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at: The DNA sequences generated for this study are deposited in the NCBI sequence read archive under SRA accession numbers SRR6950721-SRR6950884, and will be made publically available upon publication of this manuscript.
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We performed the PCA‐based outlier test implemented in PCAdapt 4.0.1 (Luu, Bazin, & Blum, 2017) and the F ST outlier test implemented in OutFLANK 0.1 (Whitlock & Lotterhos, 2015).
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sections[7] "Outlier detection" paragraph 2
quote
We performed the PCA‐based outlier test implemented in PCAdapt 4.0.1 (Luu, Bazin, & Blum, 2017) and the F ST outlier test implemented in OutFLANK 0.1 (Whitlock & Lotterhos, 2015).
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complete
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The DNA sequences generated for this study are available at the NCBI sequence read archive under SRA accession numbers SRR6950721–SRR6950884.
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methodological
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sections[24] "DATA ACCESSIBILITY" paragraph 2
quote
The DNA sequences generated for this study are available at the NCBI sequence read archive under SRA accession numbers SRR6950721–SRR6950884.
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the published estimate and its evidence
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Apply the paper's statistical method to the resolved series and compare the result with the published target.
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Overview and details of the sampling locations, dates, and geographic regions
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PMC6972810
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3
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Sample collection
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Table 1
caption
Overview and details of the sampling locations, dates, and geographic regions
rows array · 27 items
[0] array · 6 items
[0]
Region
[1]
Individual samples (n)
[2]
Location
[3]
Latitude
[4]
Longitude
[5]
Sampling date and individual samples (n)
[1] array · 4 items
[0]
2012
[1]
2013
[2]
2014
[3]
2015
[2] array · 13 items
[0]
8
[1]
9
[2]
10
[3]
8
[4]
9
[5]
6
[6]
7
[7]
8
[8]
9
[9]
10
[10]
11
[11]
4
[12]
5
[3] array · 18 items
[0]
Chesapeake Bay (*)
[1]
6
[2]
Chesapeake Bay
[3]
37.5704
[4]
−76.1718
[5]
[6]
[7]
[8]
7
[9]
[10]
[11]
[12]
[13]
[14]
[15]
[16]
[17]
[4] array · 18 items
[0]
Kattegat/Skagerrak
[1]
16
[2]
Gullmar Fjord
[3]
58.2490
[4]
11.4000
[5]
[6]
[7]
[8]
[9]
[10]
[11]
[12]
[13]
[14]
[15]
4
[16]
[17]
[5] array · 16 items
[0]
Kattegat
[1]
57.4256
[2]
10.8143
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
[11]
4
[12]
[13]
[14]
[15]
[6] array · 16 items
[0]
Skagerrak
[1]
57.7163
[2]
9.9361
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
[11]
8
[12]
[13]
[14]
[15]
[7] array · 18 items
[0]
Scheldt estuary
[1]
27
[2]
OS5
[3]
51.5220
[4]
4.0826
[5]
2
[6]
[7]
[8]
[9]
[10]
[11]
[12]
[13]
[14]
[15]
[16]
[17]
[8] array · 16 items
[0]
OS6
[1]
51.4821
[2]
4.1762
[3]
3
[4]
[5]
[6]
[7]
[8]
[9]
[10]
[11]
[12]
[13]
[14]
[15]
[9] array · 16 items
[0]
OS9
[1]
51.6057
[2]
4.0310
[3]
1
[4]
[5]
[6]
[7]
[8]
[9]
[10]
[11]
[12]
[13]
[14]
[15]
[10] array · 16 items
[0]
Eastern Scheldt 1
[1]
51.6277
[2]
3.9240
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
[11]
2
[12]
[13]
[14]
[15]
[11] array · 16 items
[0]
Grevelingen 1
[1]
51.7402
[2]
3.8308
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
[11]
4
[12]
[13]
5
[14]
[15]
[12] array · 16 items
[0]
Grevelingen 2
[1]
51.7078
[2]
4.0013
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
1
[11]
[12]
[13]
1
[14]
[15]
[13] array · 16 items
[0]
Mastgat 1
[1]
51.6577
[2]
4.1052
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
[11]
2
[12]
[13]
[14]
[15]
[14] array · 16 items
[0]
Mastgat 2
[1]
51.5953
[2]
4.0041
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
[11]
[12]
[13]
2
[14]
[15]
[15] array · 16 items
[0]
Veerse Meer 1
[1]
51.5347
[2]
3.6801
[3]
[4]
[5]
[6]
[7]
[8]
4
[9]
[10]
[11]
[12]
[13]
[14]
[15]
[16] array · 18 items
[0]
Belgian coastal zone east
[1]
44
[2]
Diep1
[3]
51.4857
[4]
3.0700
[5]
[6]
[7]
[8]
[9]
[10]
[11]
[12]
2
[13]
5
[14]
[15]
[16]
[17]
[17] array · 16 items
[0]
Knok1
[1]
51.4548
[2]
3.2218
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
4
[11]
2
[12]
[13]
[14]
[15]
[18] array · 16 items
[0]
Zee1
[1]
51.3375
[2]
3.1086
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
4
[11]
6
[12]
16
[13]
[14]
[15]
[19] array · 16 items
[0]
Blankenberge
[1]
51.3150
[2]
3.1140
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
[11]
5
[12]
[13]
[14]
[15]
[20] array · 18 items
[0]
Ostend port
[1]
12
[2]
Ostend
[3]
51.2269
[4]
2.9449
[5]
[6]
[7]
[8]
[9]
[10]
2
[11]
2
[12]
[13]
[14]
[15]
[16]
4
[17]
4
[21] array · 18 items
[0]
Belgian coastal zone west
[1]
28
[2]
Oost1
[3]
51.2299
[4]
2.8777
[5]
[6]
[7]
[8]
[9]
[10]
[11]
[12]
[13]
2
[14]
6
[15]
[16]
[17]
[22] array · 16 items
[0]
Kwint
[1]
51.2833
[2]
2.6617
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
[11]
9
[12]
[13]
[14]
[15]
[23] array · 16 items
[0]
West1
[1]
51.1929
[2]
2.6869
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
[11]
5
[12]
[13]
[14]
[15]
[24] array · 16 items
[0]
West2
[1]
51.1740
[2]
2.5810
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
[11]
6
[12]
[13]
[14]
[15]
[25] array · 18 items
[0]
Dunkirk port
[1]
6
[2]
Dunkirk
[3]
51.0484
[4]
2.2962
[5]
[6]
[7]
3
[8]
[9]
3
[10]
[11]
[12]
[13]
[14]
[15]
[16]
[17]
[26] array · 18 items
[0]
Total
[1]
140
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
[11]
[12]
[13]
[14]
[15]
[16]
[17]
row_count
27
column_count
18
numeric_cells
111
header_rows
3
locator
section[3]/table-wrap[1]#ece35468-tbl-0001
[2] object · 16 fields
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Analysis of molecular variance (AMOVA) of the datasets including and excluding the native region Chesapeake Bay, based on the SNP panels containing all 74 k SNPs or 35 k neutral SNPs separately
structure object · 5 fields
pmcid
PMC6972810
section_index
13
section_title
Genetic diversity, population structure, and population assignment of individuals
row_count
19
column_count
7
table object · 8 fields
label
Table 2
caption
Analysis of molecular variance (AMOVA) of the datasets including and excluding the native region Chesapeake Bay, based on the SNP panels containing all 74 k SNPs or 35 k neutral SNPs separately
rows array · 19 items
[0] array · 7 items
[0]
[1]
df
[2]
SS
[3]
MSS
[4]
Variance (%)
[5]
σ 2
[6]
p
[1] array · 1 item
[0]
Including Chesapeake Bay
[2] array · 1 item
[0]
All SNPs
[3] array · 7 items
[0]
Between regions
[1]
6
[2]
1.02
[3]
.170
[4]
34.3
[5]
.00835
[6]
.00
[4] array · 7 items
[0]
Within regions
[1]
133
[2]
1.96
[3]
.015
[4]
65.7
[5]
.01472
[6]
[5] array · 7 items
[0]
Total
[1]
139
[2]
2.98
[3]
.021
[4]
100.0
[5]
[6]
[6] array · 1 item
[0]
Neutral SNPs
[7] array · 7 items
[0]
Between regions
[1]
6
[2]
0.29
[3]
.048
[4]
9.3
[5]
.00145
[6]
.00
[8] array · 7 items
[0]
Within regions
[1]
133
[2]
2.84
[3]
.021
[4]
90.7
[5]
.02139
[6]
[9] array · 7 items
[0]
Total
[1]
139
[2]
3.14
[3]
.023
[4]
100.0
[5]
[6]
[10] array · 1 item
[0]
Excluding Chesapeake Bay
[11] array · 1 item
[0]
All SNPs
[12] array · 7 items
[0]
Between regions
[1]
5
[2]
0.16
[3]
.031
[4]
6.0
[5]
.00059
[6]
.00
[13] array · 7 items
[0]
Within regions
[1]
127
[2]
2.45
[3]
.019
[4]
94.0
[5]
.01929
[6]
[14] array · 7 items
[0]
Total
[1]
132
[2]
2.61
[3]
.020
[4]
100.0
[5]
[6]
[15] array · 1 item
[0]
Neutral SNPs
[16] array · 7 items
[0]
Between regions
[1]
5
[2]
0.14
[3]
.027
[4]
5.0
[5]
.00033
[6]
.00
[17] array · 7 items
[0]
Within regions
[1]
127
[2]
2.57
[3]
.020
[4]
95.0
[5]
.02024
[6]
[18] array · 7 items
[0]
Total
[1]
132
[2]
2.71
[3]
.021
[4]
100.0
[5]
[6]
row_count
19
column_count
7
numeric_cells
61
header_rows
1
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note
Pairwise F ST between regions and p‐values (between brackets) for all 74 k SNPs, and the neutral SNP panel of 35 k SNPs
structure object · 5 fields
pmcid
PMC6972810
section_index
13
section_title
Genetic diversity, population structure, and population assignment of individuals
row_count
17
column_count
7
table object · 8 fields
label
Table 3
caption
Pairwise F ST between regions and p‐values (between brackets) for all 74 k SNPs, and the neutral SNP panel of 35 k SNPs
rows array · 17 items
[0] array · 7 items
[0]
[1]
Chesapeake Bay
[2]
Kattegat/Skagerrak
[3]
Scheldt estuary
[4]
Belgian coastal zone east
[5]
Ostend port
[6]
Belgian coastal zone west
[1] array · 1 item
[0]
All SNPs
[2] array · 7 items
[0]
Chesapeake Bay
[1]
–
[2]
–
[3]
–
[4]
–
[5]
–
[6]
–
[3] array · 7 items
[0]
Kattegat/Skagerrak
[1]
0.38 (0.00)
[2]
–
[3]
–
[4]
–
[5]
–
[6]
–
[4] array · 7 items
[0]
Scheldt estuary
[1]
0.38 (0.00)
[2]
0.00 (1.00)
[3]
–
[4]
–
[5]
–
[6]
–
[5] array · 7 items
[0]
Belgian coastal zone east
[1]
0.38 (0.00)
[2]
0.00 (1.00)
[3]
0.00 (0.02)
[4]
–
[5]
–
[6]
–
[6] array · 7 items
[0]
Ostend port
[1]
0.36 (0.00)
[2]
0.04 (0.00)
[3]
0.04 (0.00)
[4]
0.03 (0.00)
[5]
–
[6]
–
[7] array · 7 items
[0]
Belgian coastal zone west
[1]
0.39 (0.00)
[2]
0.00 (0.33)
[3]
0.00 (0.00)
[4]
0.00 (0.37)
[5]
0.04 (0.00)
[6]
–
[8] array · 7 items
[0]
Dunkirk port
[1]
0.37 (0.00)
[2]
0.00 (1.00)
[3]
0.00 (1.00)
[4]
0.00 (1.00)
[5]
0.03 (0.00)
[6]
0.00 (1.00)
[9] array · 1 item
[0]
Neutral SNPs
[10] array · 7 items
[0]
Chesapeake Bay
[1]
–
[2]
–
[3]
–
[4]
–
[5]
–
[6]
–
[11] array · 7 items
[0]
Kattegat/ Skagerrak
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We performed the PCA‐based outlier test implemented in PCAdapt 4.0.1 (Luu, Bazin, & Blum, 2017) and the F ST outlier test implemented in OutFLANK 0.1 (Whitlock & Lotterhos, 2015).
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The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pca.
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capability:computational_analysis
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The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here.
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The DNA sequences generated for this study are available at the NCBI sequence read archive under SRA accession numbers SRR6950721–SRR6950884.
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The paper names SRR6950721–SRR6950884, but the accession does not resolve in the repository (no reason recorded), so the data cannot be reached from here. No dataset was downloaded and no licence was read.
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Complete file 
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31988713", "kind": "science-record", "revision": 6, "content_hash": "sha256:eb3c11425640ba785aca997d48ab2ca275dd93b0298789788f97ab495f34d6fe", "created_at": "2026-11-01T15:40:55Z", "updated_at": "2026-11-01T21:22:50Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Population genomic structure of the gelatinous zooplankton species Mnemiopsis leidyi in its nonindigenous range in the North Sea.", "doi": "10.1002/ece3.5468", "pmid": "31988713", "authors": ["Christophe Verwimp", "Lies Vansteenbrugge", "Sofie Derycke", "Thomas Kerkhove", "Hilde Muylle", "Olivier Honnay", "Tom Ruttink", "Isabel Roldán-Ruiz", "Kris Hostens"], "journal": "Ecology and evolution", "year": 2020, "abstract": "Nonindigenous species pose a major threat for coastal and estuarine ecosystems. Risk management requires genetic information to establish appropriate management units and infer introduction and dispersal routes. We investigated one of the most successful marine invaders, the ctenophore Mnemiopsis leidyi, and used genotyping-by-sequencing (GBS) to explore the spatial population structure in its nonindigenous range in the North Sea. We analyzed 140 specimens collected in different environments, including coastal and estuarine areas, and ports along the coast. Single nucleotide polymorphisms (SNPs) were called in approximately 40 k GBS loci. Population structure based on the neutral SNP panel was significant (F ST .02; p < .01), and a distinct genetic cluster was identified in a port along the Belgian coast (Ostend port; pairwise F ST .02-.04; p < .01). Remarkably, no population structure was detected between geographically distant regions in the North Sea (the Southern part of the North Sea vs. the Kattegat/Skagerrak region), which indicates substantial gene flow at this geographical scale and recent population expansion of nonindigenous M. leidyi. Additionally, seven specimens collected at one location in the indigenous range (Chesapeake Bay, USA) were highly differentiated from the North Sea populations (pairwise F ST .36-.39; p < .01). This study demonstrates the utility of GBS to investigate fine-scale population structure of gelatinous zooplankton species and shows high population connectivity among nonindigenous populations of this recently introduced species in the North Sea.\nOPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at: The DNA sequences generated for this study are deposited in the NCBI sequence read archive under SRA accession numbers SRR6950721-SRR6950884, and will be made publically available upon publication of this manuscript.", "claims": [{"id": "claim-method", "statement": "We performed the PCA‐based outlier test implemented in PCAdapt 4.0.1 (Luu, Bazin, & Blum, 2017) and the F ST outlier test implemented in OutFLANK 0.1 (Whitlock & Lotterhos, 2015).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31988713", "locator": "sections[7] \"Outlier detection\" paragraph 2", "quote": "We performed the PCA‐based outlier test implemented in PCAdapt 4.0.1 (Luu, Bazin, & Blum, 2017) and the F ST outlier test implemented in OutFLANK 0.1 (Whitlock & Lotterhos, 2015)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The DNA sequences generated for this study are available at the NCBI sequence read archive under SRA accession numbers SRR6950721–SRR6950884.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31988713", "locator": "sections[24] \"DATA ACCESSIBILITY\" paragraph 2", "quote": "The DNA sequences generated for this study are available at the NCBI sequence read archive under SRA accession numbers SRR6950721–SRR6950884."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:31988713"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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