| Literature DB >> 25343723 |
Rodrigo Beas-Luna1, Mark Novak2, Mark H Carr1, Martin T Tinker3, August Black4, Jennifer E Caselle4, Michael Hoban1, Dan Malone1, Alison Iles2.
Abstract
Ecological network models and analyses are recognized as valuable tools for understanding the dynamics and resiliency of ecosystems, and for informing ecosystem-based approaches to management. However, few databases exist that can provide the life history, demographic and species interaction information necessary to parameterize ecological network models. Faced with the difficulty of synthesizing the information required to construct models for kelp forest ecosystems along the West Coast of North America, we developed an online database (http://kelpforest.ucsc.edu/) to facilitate the collation and dissemination of such information. Many of the database's attributes are novel yet the structure is applicable and adaptable to other ecosystem modeling efforts. Information for each taxonomic unit includes stage-specific life history, demography, and body-size allometries. Species interactions include trophic, competitive, facilitative, and parasitic forms. Each data entry is temporally and spatially explicit. The online data entry interface allows researchers anywhere to contribute and access information. Quality control is facilitated by attributing each entry to unique contributor identities and source citations. The database has proven useful as an archive of species and ecosystem-specific information in the development of several ecological network models, for informing management actions, and for education purposes (e.g., undergraduate and graduate training). To facilitate adaptation of the database by other researches for other ecosystems, the code and technical details on how to customize this database and apply it to other ecosystems are freely available and located at the following link (https://github.com/kelpforest-cameo/databaseui).Entities:
Mesh:
Year: 2014 PMID: 25343723 PMCID: PMC4208745 DOI: 10.1371/journal.pone.0109356
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Comparison and examples of five categories of ecosystem models (modified from Plagany 2007).
| Model type & examples | No. of nodes or functional groups | Currency | Life stages | Size structure | Spatial structure | Topology | Diet | Non- trophic interactions | Env. Data |
| Qualitative models Loop Analysis | <10 | Biomass | A | A | Input | A | |||
| Minimum Realistic GADGET | 6 to 8 | Nutrients | A | Input | R | ||||
| Individual Based OSMOSE | 7 to 20 | Biomass | A | R | A | Input | R | A | |
| Biogeochemical ATLANTIS | 20 | Nutrients | A | A | A | Input, output | R | A | R |
| Aggregate system EwE | >40 | Biomass | A | A | Input, output | R | A | A |
Globally Applicable Area-Disaggregated General Ecosystem Toolbox,
Object-oriented simulator of marine ecosystem exploration,
Ecopath with Ecosim.
“A” and “R” indicate that the model accommodates or requires information of this form, respectively. “Env” = environmental.
List of some of the most relevant marine ecological databases and their attributes to inform ecosystem models.
| Database | Subject taxa | Data type | Data visualization | Data export | Integration capabilities |
|
| Algae | 1,2,5,6,7 | x | ||
|
| Birds | 1,4,5,6,7 | x | ||
|
| Multiple | 1,11 | x | x | |
|
| Multiple | 2 | x | x | |
|
| Multiple | 2,5,6,9,10 | x | x | |
|
| Multiple | 1,2,3,4,5,6,7 | x | x | |
|
| Plankton | 2,5,6,10 | x | x | |
|
| Fish | 1,2,3,4,5,6,7,8 | x | x | |
|
| Multiple | 2,8,9,10 | x | x | x |
|
| Multiple | 2 | x | x | x |
|
| Multiple | 1,2,3,4,5,6,7,8,9,10,11 | x | x | x |
|
| Multiple | 1,2,3,4,5,6,7 | x | x | |
|
| Multiple | 1,2,4,5,6,7 | x | ||
|
| Multiple | 1,2,3,4,5,6,7 | x | ||
|
| Multiple | 2 | x | x |
“X” indicates available function. “Integration capability” refers to ability to link with another database.
Data types: 1) Life history, 2) taxonomy, 3) biometrics, 4) behavior, 5) distribution, 6) habitats, 7) photos, 8) species interactions, 9) temporal explicit data, 10) spatial explicit data, 11) references.
Score: Sum of number of attributes valuable for data accessibility for ecosystem modelers. These attributes provide basic information for the parameterization and validation of ecosystem models.
Figure 1Database schema to enter, query and retrieve data for parameterizing ecological network models.
The central element of the schema is the citation value table that links all entries and queries to the data source (red box). The ITIS identifier in the “nodes” table (red line) is used to link the kelpforest database to the ITIS database.
Figure 2Map interface with delimited regions in the northeast Pacific.
The interface allows users to identify location from which data were collected in the data entry process. Orange color represents regions, green sub regions and purple locations.
Figure 3Example of the database visualization tool illustrating a trophic interaction network for an assemblage of kelp forest seastars, color-coded by functional group after Graham et al. [25].
Example of a csv file exported from the database.
| Node 1 working name | Node 1 Stage | Node 2 working name | Node 1 Stage | Type | Citations |
| b&y rockfish | general | crabs | general | trophic | (Larson, 1972) |
| b&y rockfish | general | tubesnout | general | trophic | (Quast, 1968) |
| b&y rockfish | general | kelp perch | general | trophic | (Robbins, 2006) |
| b&y rockfish | general | spiral bryozoan | general | trophic | (Perez, 1981) |
| b&y rockfish | general | foliate kelp crab | general | trophic | (Hines, 1982) |
| b&y rockfish | general | moss crab | general | trophic | (Hines, 1982) |
| b&y rockfish | general | sharpnose crab | general | trophic | (Hines, 1982) |
| b&y rockfish | general | cryptic kelp crab | general | trophic | (Hines, 1982) |
| b&y rockfish | general | hairy chiton | general | trophic | (Love et al. 2002) |
| b&y rockfish | general | monkeyface prickleback | general | trophic | (Love et al. 2002) |
| b&y rockfish | general | rock prickleback | general | trophic | (Love et al. 2002) |
| b&y rockfish | general | giant kelpfish | general | trophic | (Love et al. 2002) |
| b&y rockfish | larval | copepods | general | trophic | (Love et al. 2002) |
| b&y rockfish | juvenile | zooplankton | general | trophic | (Love et al. 2002) |
| b&y rockfish | adult | monkeyface prickleback | general | trophic | (Love et al. 2002) |
| b&y rockfish | adult | rock prickleback | general | trophic | (Love et al. 2002) |
| b&y rockfish | adult | northern clingfish | general | trophic | (Love et al. 2002) |
| b&y rockfish | adult | rockweed gunnel | general | trophic | (Love et al. 2002) |
| b&y rockfish | adult | fluffy sculpin | general | trophic | (Love et al. 2002) |
| b&y rockfish | adult | smoothhead sculpin | general | trophic | (Love et al. 2002) |
| b&y rockfish | adult | striped kelpfish | general | trophic | (Love et al. 2002) |
| b&y rockfish | adult | octopus | general | trophic | (Love et al. 2002) |
| b&y rockfish | adult | amphipods | general | trophic | (Love et al. 2002) |
| b&y rockfish | adult | polycheate worm | general | trophic | (Love et al. 2002) |
| b&y rockfish | general | china rockfish | juvenile | trophic | (Love et al. 2002) |
| b&y rockfish | general | squid | general | trophic | (Love et al. 2002) |
| b&y rockfish | general | octopus | general | trophic | (Hallacher & Roberts, 1985) |
| b&y rockfish | general | blue rockfishes | juvenile | trophic | (Hallacher & Roberts, 1985) |
| b&y rockfish | general | euphausiids | general | trophic | (Hallacher & Roberts, 1985) |
| b&y rockfish | general | caprellid amphipod | general | trophic | (Hallacher & Roberts, 1985) |
| b&y rockfish | general | gammarid amphipod | general | trophic | (Love et al. 2002) |
| b&y rockfish | general | Idotea isopods | general | trophic | (Hallacher & Roberts, 1985) |
| b&y rockfish | general | polycheate worm | general | trophic | (Hallacher & Roberts, 1985) |
| b&y rockfish | general | hydroids | general | trophic | (Hallacher & Roberts, 1985) |
This table identifies some trophic interactions of the black and yellow (b&y) rockfish (Sebastes chrysomelas).