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coastal_parasite_webs — Coastal food webs with metazoan parasites (2013)

Description

Seven coastal marine or estuarine food webs that include metazoan parasites, in the species-level (aggregated) versions compiled by J. A. Dunne and colleagues for a comparative analysis of how parasites affect food web structure. Three webs are from the North American Pacific coast, compiled by R. F. Hechinger and colleagues: Carpinteria Salt Marsh (California, USA), Estero de Punta Banda and Bahía Falsa in Bahía San Quintín (both in Baja California, Mexico). Three are from Europe and New Zealand, compiled by a second research group: Flensburg Fjord (Baltic Sea, between Germany and Denmark), Sylt Tidal Basin (North Sea, between Germany and Denmark) and Otago Harbour (Dunedin, New Zealand). The seventh is the Ythan Estuary web (North Sea, near Aberdeen, Scotland) of M. Huxham, S. Beaney and D. Raffaelli (1996). The parasite data were mostly obtained by dissecting individuals of the free-living species sampled in each habitat, supplemented with the literature for the same or nearby sites and with inferences from host and parasite biology; some groups (e.g. protozoans and bacteriophages) are not, or only poorly, identified.

The original webs represent the life stages of parasites with complex life cycles (e.g. the cercariae, metacercariae and adults of trematodes) as separate nodes. In these versions, the life stages of each parasite species, and their links, were aggregated into a single node. Nodes are therefore species (or coarser taxa, functional groups and non-living resources, such as detritus and carrion), and a directed edge points from a consumer to its resource (prey or host). Self-loops represent cannibalism.

Each network contains the most complete version of the web (with parasites and concomitant links), and the edge property link_type identifies the nested subsets that correspond to the three versions of each web analysed in the source:

  • "free-living": links among free-living taxa only (the free-living web).
  • "parasitic": the additional links of the web with parasites but without concomitant links, i.e. parasites consuming their hosts, free-living taxa consuming parasites (targeted predation, e.g. on free-living parasite stages), and parasite–parasite links. The Ythan Estuary web only has parasite–host links here.
  • "concomitant": concomitant predation links, i.e. predators consuming the parasites of their prey, inferred by assuming that a predator eats all the parasites of infected prey. In the Ythan Estuary web, this set also contains all the links of free-living taxa to parasites and the parasite–parasite links, and in the three Californian webs it also contains a few (8 to 11) links among free-living taxa.

The networks are:

| Network | Location | Nodes (parasites) | free-living | parasitic | concomitant | |---|---|---|---|---|---| | bahia_falsa | Bahía Falsa, Baja California | 171 (52) | 1,077 | 1,157 | 1,486 | | carpinteria | Carpinteria Salt Marsh, California | 165 (58) | 970 | 1,217 | 1,521 | | punta_banda | Estero de Punta Banda, Baja California | 214 (76) | 1,657 | 1,677 | 2,319 | | flensburg | Flensburg Fjord, Germany/Denmark | 123 (46) | 579 | 389 | 438 | | otago | Otago Harbour, New Zealand | 142 (19) | 1,206 | 281 | 357 | | sylt | Sylt Tidal Basin, Germany/Denmark | 161 (35) | 1,052 | 898 | 1,055 | | ythan | Ythan Estuary, Scotland | 133 (42) | 420 | 177 | 794 |

The bahia_falsa, carpinteria and punta_banda networks are derived from the life-stage resolved webs in the entry california_estuaries, and flensburg from the one in the entry flensburg_fjord; the ones here differ by the aggregation of parasite life stages into species, and contain fewer node attributes. An earlier version of the Carpinteria Salt Marsh web (Lafferty et al. 2006) is the network food_web_lafferty of the entry iwdb, and is also included in gateway_foodwebs. In the Ythan Estuary web, the species 100 of the original data, an animal without resources, was removed together with its only link; the remaining nodes were not renumbered.

Node properties:

  • node_id: the identifier of the node in the source (in the Ythan web, 100 is missing).
  • name: the name of the taxon or resource.
  • is_parasite: whether the node is a parasite taxon (type 2 in the source) or a free-living taxon or non-living resource (type 1).

Edge properties:

  • link_type: the version of the web in which the link first appears ("free-living", "parasitic" or "concomitant", see above).
Tags
Biological Food web Unweighted Metadata
Citation
  • J. A. Dunne, K. D. Lafferty, A. P. Dobson, R. F. Hechinger, A. M. Kuris, N. D. Martinez, J. P. McLaughlin, K. N. Mouritsen, R. Poulin, K. Reise, D. B. Stouffer, D. W. Thieltges, R. J. Williams, C. D. Zander, "Parasites affect food web structure primarily through increased diversity and complexity." PLoS Biology 11(6), e1001579 (2013) 10.1371/journal.pbio.1001579 Sci-Hub
  • J. A. Dunne, K. D. Lafferty, A. P. Dobson, R. F. Hechinger, A. M. Kuris, N. D. Martinez, J. P. McLaughlin, K. N. Mouritsen, R. Poulin, K. Reise, D. B. Stouffer, D. W. Thieltges, R. J. Williams, C. D. Zander, "Data from: Parasites affect food web structure primarily through increased diversity and complexity." Dryad (2013) 10.5061/dryad.b8r5c Sci-Hub
Upstream URL OK
https://doi.org/10.5061/dryad.b8r5c
Upstream license
Creative Commons CC0 1.0 Universal, https://creativecommons.org/publicdomain/zero/1.0/
Networks
Tip: click on a column header to sort the list, or hover over it for a description.
Column legend
$\left<k\right>$
Mean degree
$\sigma_k$
Standard deviation of the degrees
$\lambda_h$
Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$
Random walk mixing time
$r$
Degree assortativity
$c$
Global clustering coefficient
$\oslash$
(Pseudo-) diameter
$S$
Relative size of the largest component
NPs
Node properties
EPs
Edge properties
Name Nodes Edges $\left<k\right>$ $\sigma_k$ $\lambda_h$ $\tau$ $r$ $c$ $\oslash$ $S$ Kind Mode NPs EPs gt GraphML GML csv
bahia_falsa 171 3,720 21.75 30.38 48.13 2.20 -0.12 0.28 4 1.00 Directed Unipartite node_id name is_parasite link_type 6 KiB 15 KiB 14 KiB 15 KiB
carpinteria 165 3,708 22.47 29.09 50.03 1.89 0.08 0.36 4 1.00 Directed Unipartite node_id name is_parasite link_type 6 KiB 14 KiB 14 KiB 15 KiB
punta_banda 214 5,653 26.42 34.12 61.82 1.83 -0.10 0.33 4 1.00 Directed Unipartite node_id name is_parasite link_type 7 KiB 20 KiB 19 KiB 21 KiB
flensburg 123 1,406 11.43 18.13 29.94 2.98 -0.30 0.30 4 1.00 Directed Unipartite node_id name is_parasite link_type 4 KiB 8 KiB 7 KiB 8 KiB
otago 142 1,844 12.99 18.90 31.82 2.67 -0.27 0.28 4 1.00 Directed Unipartite node_id name is_parasite link_type 5 KiB 9 KiB 9 KiB 9 KiB
sylt 161 3,005 18.66 27.32 44.11 1.43 -0.17 0.28 4 1.00 Directed Unipartite node_id name is_parasite link_type 6 KiB 13 KiB 12 KiB 13 KiB
ythan 133 1,391 10.46 15.49 27.59 2.42 -0.15 0.24 4 1.00 Directed Unipartite node_id name is_parasite link_type 5 KiB 9 KiB 8 KiB 8 KiB