california_estuaries — California estuary food webs with parasites (2011)

Description

Food webs of three estuaries of the Pacific coast of California and Baja California, including parasites (infectious agents), life stages, body sizes and biomasses, compiled by R. F. Hechinger and colleagues: Carpinteria Salt Marsh, California, USA (CSM, 61 ha, data from 2003 to 2008), Estero de Punta Banda, Baja California, Mexico (EPB, 707 ha, 1992 to 2005), and Bahía Falsa in Bahía San Quintín, Baja California, Mexico (BSQ, 144 ha, 1994 to 2005). Most nodes and their body sizes and biomasses come from a stratified random sampling of the intertidal zone of each estuary (including birds, fishes and plankton), which quantified the plants and animals larger than about 1 mm and many infectious agents (mostly metazoan parasites, such as trematodes, cestodes, nematodes and acanthocephalans, but also some microbes); this was complemented with published sources and additional sampling of unrepresented groups. Nodes are species, or life stages of species with complex life cycles (e.g. the parthenitae, cercariae, metacercariae and adults of trematodes, or the larvae and adults of polychaetes and bivalves, each of which is a separate node), as well as some aggregated assemblages (e.g. phytoplankton, benthic diatoms, meiofauna) and non-living resources (detritus, carrion). A directed edge goes from a consumer to its resource (prey or host). The links include 21 possible types of interaction (13 of which occur in the data), covering four general kinds of interaction: predators consuming prey, parasites consuming hosts, predators consuming parasites, and parasites consuming parasites. Note that some link types do not represent resource dependencies (e.g. "concurrent predation on symbionts", i.e. a predator consuming the parasites of its prey, "trophic transmission", "commensalism"), and may need to be excluded from some analyses. Free-living links were constructed by extending the earlier Carpinteria Salt Marsh web of Lafferty et al. (2006), which this one supplants (the earlier web is the network food_web_lafferty of the entry iwdb, and is also included in gateway_foodwebs): links were assumed to occur in the other estuaries when the nodes co-occur, and links of new nodes were modelled after similar nodes of the earlier web, and then modified based on the literature and observations; most parasite links were directly observed. Some groups are missing or under-represented, such as plant parasites, bird and fish ectoparasites, flying insects, protists, viruses, fungi and bacteria.

The entry contains four networks:

metaweb: the "metaweb" compiled from the nodes of all three estuaries (500 nodes, belonging to 314 species), with all 11,270 links projected to occur given the co-occurrence of the nodes. Of these, 9,247 are present in at least one of the estuaries, and the remaining 2,023 are hypothetical links between nodes that do not co-occur in any of the estuaries.
carpinteria: the web of Carpinteria Salt Marsh.
punta_banda: the web of Estero de Punta Banda.
bahia_falsa: the web of Bahía Falsa in Bahía San Quintín.

The estuary webs are the subsets of the metaweb present in each estuary. Versions of the three estuary webs aggregated by species (with the life stages of each parasite merged into a single node, and fewer node attributes) are in the entry coastal_parasite_webs. The node "roots" (belowground biomass of the terrestrial plants) has no links, but is included because of its biomass. There are two self-loops (cannibalism) in the metaweb.

Node properties (all networks):

node_id: the node identifier in the source, consistent across all four networks.
species_id: the species identifier, shared by the nodes corresponding to different life stages of the same species; stage_id: the life stage within the species, where 1 is the adult, and higher numbers are younger stages (with a meaning that depends on the group, e.g. for trematodes 2 = parthenitae); stage: the name of the life stage ("adult", "larva", "pupa", "cercaria", "metacercaria", "parthenitae", "procercoid", "plerocercoid", or empty for non-living nodes).
name: the working name of the node (common name, scientific name or descriptive name).
organismal_group: a broad group of organisms (e.g. "trematode", "bird", "fish", "snail", "plant", "detritus").
node_type: what the node represents ("taxon", "life stage" or "detritus").
resolution: the lowest taxonomic level that the node represents (e.g. "Species", "Genus", "Family", "assemblage"); resolution_notes: notes on the resolution.
feeding: whether the node is "feeding", "nonfeeding" (e.g. detritus and non-feeding life stages, such as cercariae) or an "autotroph".
lifestyle_stage and lifestyle_species: whether the life stage, or the species as a whole, is "free-living", "infectious", "commensal" or "non-living".
consumer_strategy: the consumer strategy of the life stage ("predator", "micropredator", "macroparasite", "parasitic castrator", "pathogen", "parasitoid", "trophically transmitted parasite", "detritivore", "autotroph", "nonfeeding", or empty for non-living nodes).
mobility: the short-term mobility of the free-living nodes ("low", "intermediate" or "high"; empty if not given).
kingdom, phylum, subphylum, class, subclass, order, suborder, family, genus, specific_epithet: the taxonomy of the node (empty if not given).
notes: notes on the node.

Node properties (metaweb only):

in_csm, in_epb, in_bsq: whether the node is present in the respective estuary.

Node properties (estuary webs only, specific to the estuary; numeric values are NaN when not given):

residency: the long-term residency of the free-living nodes ("resident" or "migrant"; empty if not given).
body_size: the mean body mass of an individual, in grams of wet weight (including hard parts, such as shells); body_size_sd: its standard deviation; body_size_n: the number of individuals measured; body_size_estimation: the method used to estimate the body size ("population": from the individuals sampled in the estuary; "species": from the literature, voucher specimens or volumetric estimates; "approximation": approximated from the body size of other nodes); body_size_notes: notes on the estimate.
abundance: the mean density of individuals (number per hectare); abundance_cl: its 95% confidence limit, as given in the source; abundance_df: the degrees of freedom of the confidence limit (fractional, due to the stratified sampling).
biomass: the mean biomass density, in kg (wet weight) per hectare; biomass_cl: its 95% confidence limit; biomass_df: the degrees of freedom of the confidence limit; biomass_estimation: the method used to estimate the biomass (e.g. "quantification, estuary-wide sampling", "quantified apportionment", "approximation, ratio", "field experience"; see Table 2B of the metadata of the source); biomass_notes: notes on the estimate.

Edge properties (all networks):

link_type: the type of interaction, one of "predation", "micropredation", "parasitic castration", "pathogen infection", "macroparasitism", "parasitoid infection", "commensalism", "trophically transmitted parasitism", "concurrent predation on symbionts", "trophic transmission", "predation on free-living non-feeding stage", "detritivory" and "parasite intraguild antagonism" (see Table 3C of the metadata of the source for definitions); link_type_id: the corresponding numeric code of the source.
present_csm, present_epb, present_bsq: whether the link is present in the respective estuary (in the estuary webs, these indicate whether the link is also present in the other estuaries).

Edge properties (metaweb only):

present_any: whether the link is present in at least one of the estuaries.

Edge properties (estuary webs only):

evidence: the evidence for the link ("observed": directly observed in the field, in gut contents or in parasitological examinations; "inferred": observed at other localities or in experiments, or based on expert opinion; "modeled": modelled after the interactions of similar species; "speculated": inferred from general knowledge of the taxon; empty if not given); evidence_notes: notes on the evidence.

According to the source, the data are freely available for non-commercial scientific use, given the appropriate citation.

Tags

Biological Food web Unweighted Metadata

Citation

R. F. Hechinger, K. D. Lafferty, J. P. McLaughlin, B. L. Fredensborg, T. C. Huspeni, J. Lorda, P. K. Sandhu, J. C. Shaw, M. E. Torchin, K. L. Whitney, A. M. Kuris, "Food webs including parasites, biomass, body sizes, and life stages for three California/Baja California estuaries." Ecology 92(3), 791 (2011) 10.1890/10-1383.1 Sci-Hub

Upstream URL OK

https://esapubs.org/archive/ecol/E092/066/default.htm

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
metaweb	500	11,270	22.54	40.47	68.45	3.83	-0.46	0.10	4	1.00	Directed	Unipartite	node_id species_id stage_id stage name organismal_group node_type resolution resolution_notes feeding lifestyle_stage lifestyle_species consumer_strategy mobility kingdom phylum subphylum class subclass order suborder family genus specific_epithet notes in_csm in_epb in_bsq	link_type link_type_id present_csm present_epb present_bsq present_any	22 KiB	74 KiB	62 KiB	58 KiB
carpinteria	273	3,971	14.55	24.25	42.46	3.33	-0.41	0.17	4	1.00	Directed	Unipartite	node_id species_id stage_id stage name organismal_group node_type resolution resolution_notes feeding lifestyle_stage lifestyle_species consumer_strategy mobility kingdom phylum subphylum class subclass order suborder family genus specific_epithet notes residency body_size body_size_sd body_size_n body_size_estimation body_size_notes abundance abundance_cl abundance_df biomass biomass_cl biomass_df biomass_estimation biomass_notes	link_type link_type_id evidence evidence_notes present_csm present_epb present_bsq	24 KiB	43 KiB	38 KiB	37 KiB
punta_banda	356	5,998	16.85	30.23	50.94	3.88	-0.47	0.13	4	1.00	Directed	Unipartite	node_id species_id stage_id stage name organismal_group node_type resolution resolution_notes feeding lifestyle_stage lifestyle_species consumer_strategy mobility kingdom phylum subphylum class subclass order suborder family genus specific_epithet notes residency body_size body_size_sd body_size_n body_size_estimation body_size_notes abundance abundance_cl abundance_df biomass biomass_cl biomass_df biomass_estimation biomass_notes	link_type link_type_id evidence evidence_notes present_csm present_epb present_bsq	28 KiB	57 KiB	49 KiB	48 KiB
bahia_falsa	290	3,997	13.78	27.41	44.52	3.63	-0.46	0.13	4	1.00	Directed	Unipartite	node_id species_id stage_id stage name organismal_group node_type resolution resolution_notes feeding lifestyle_stage lifestyle_species consumer_strategy mobility kingdom phylum subphylum class subclass order suborder family genus specific_epithet notes residency body_size body_size_sd body_size_n body_size_estimation body_size_notes abundance abundance_cl abundance_df biomass biomass_cl biomass_df biomass_estimation biomass_notes	link_type link_type_id evidence evidence_notes present_csm present_epb present_bsq	24 KiB	43 KiB	38 KiB	37 KiB