You are here

Harvard Forest Data Archive

HF259

Foundation Species Revisited: Citation Analysis of Ellison et al. 2005

Related Publications

Data

Overview

  • Lead: Allyson Degrassi, Steven Brantley
  • Investigators: Aaron Ellison, Carrie Levine, Robert Miller, Jacqueline Mohan, Sydne Record
  • Contact: Allyson Degrassi
  • Start date: 2005
  • End date: 2014
  • Status: completed
  • Location: Global
  • Latitude: -90 to +90
  • Longitude: -180 to +180
  • Elevation:
  • Taxa:
  • Release date: 2015
  • Revisions:
  • EML file: knb-lter-hfr.259.2
  • DOI: digital object identifier
  • Related links:
  • Study type: long-term measurement
  • Research topic: historical and retrospective studies; international research projects
  • LTER core area: primary production, populations
  • Keywords: invasive species, microclimate, species abundance
  • Abstract:

    Ecologists and environmental scientists often prioritize research efforts with conservation importance. Dominant, widespread, or locally abundant species at low risk of extinction receive relatively little attention unless they are invasive. Native foundation species create habitats and environmental conditions that support many associated species and modulate local-scale ecosystem processes, but the generally high local or regional abundance of foundation species may lead to less research about them. We used citation analysis (2005-2014) to examine research following from a suggestion to identify and study foundation species while they were still common and not threatened. We explored the use and expanding definition of the foundation species concept, as well as the trajectory and ecological focus of research on foundation species throughout the world in 378 papers published in this nine-year span. Contemporary authors who cite key papers defining a foundation species pay little attention to its actual definition and species studied in this context rarely were identified as foundation species. Although functions and roles of foundation species, such as creating unique microclimates or supporting dependent species, are being studied, less research is focused on identifying them before they are threatened or lost from the ecosystem that they otherwise define. Invasive species were identified as the most common threat to foundation species. Our citation analysis and synthesis provides a new conceptual framework linking identification of and research about foundation species with their functional roles and our ability to manage emerging threats to them.

  • Methods:

    Introduction

    Data collection was restricted to a citation analysis of Ellison et al. (2005). Using several research platforms and article databases (Web of Science, JSTOR, Google Scholar, Pub Med), we found that Ellison et al. (2005) was cited in at least 446 papers through December 2014. Three hundred seventy-eight papers were reviewed to determine the main focus of the original research described and its relationship to the key questions proposed by Ellison et al. (2005). Review papers, book chapters, commentaries, and all other non-primary literature were excluded from the present study (n= 45).

    Questions for Data Collection

    We developed a set of six of questions to assess research on foundation species published since 2005 and used that information to compare cohesiveness between individual studies and the goals of Ellison et al.’s.

    Question 1: Was a foundation species precisely or accurately defined and what definition was used?

    It is important to know whether other studies recognized or differentiated foundation species from other similar, but distinct, species roles. The definition of a foundation species definition found in each paper was placed into one of five categories: 1) Ellison et al.’s (2005) definition; 2) Dayton’s (1972) definition; 3) Dayton and Ellison’s definitions combined; 4) neither Dayton or Ellison’s definition (i.e., “Other”); or 5) not defined. If categorized as “Other”, then the alternative definition was recorded. If other definitions included multiple terms, each term was counted, so that a definition could be classified with multiple terms.

    Question 2: Was a foundation species explicitly studied?

    We recorded as a single binary variable (yes/no) indicating whether or not any single focal study species in the study was considered a “foundation species.”

    Question 3: What was the main role of the foundation species that were studied?

    Two broad roles of foundation species were distinguished: direct support of other species (e.g., effects on associated species or assemblages); and modulation and stabilization of fundamental ecosystem processes (e.g., effects on abiotic or biogeochemical processes). We classified each paper as focusing on support (“Community”), modulation/stabilization (“Ecosystem”), both, or neither.

    Question 4: Were threats to foundation species identified?

    We identified six broad classes of threats to foundation species: “climate change” (e.g., changes in atmospheric composition, temperature, or hydrological flow): “invasive species” (i.e., nonnative or invasive species); “habitat degradation” (e.g., pollution, habitat loss, human disturbance,); “exploitation” (i.e., over-use by humans or increased herbivory or predation by non-human species); “disease or pathogen”; or “no threat”. Note that studies could be classified into more than one of the threat categories.

    Question 5: Where were experiments on foundation species done?

    We counted the number of studies on foundation species done in each country. We recognize that these data were biased toward journals printed in English and that national or regional resources will influence where foundation species are studied. However, as a first pass of the citation record, identifying geographic location of the studies allowed us to identify regions where the study of foundation species is focused.

    Question 6: To what extent did Ellison et al. (2005) influence research on foundation species?

    We inferred strength of influence from the results of three of the previous questions. Influence was based on 1) whether the definition of foundation species followed Ellison et al. (2005) (question 1); 2) if the foundation species was identified as the main study organism (question 2); and 3) identification of possible threats to foundation species loss (question 4). Studies that contained all three qualities were categorized as “Strongly Influenced.” Studies that contain two qualities in any combination were categorized as “Moderately Influenced.” Studies that contain one quality were categorized as “Marginally Influenced.”

    Data Analysis

    All data were analyzed using RStudio version 3.0.2 (R Core Team 2013). The packages “maps” (Brownrigg and Minka 2014), “plotrix” (Lemon et al. 2015), and “rworldmap” (South 2013) was used to display geographic locations of surveyed studies. The package “plyr” (Wickham 2014) was used for data frame manipulation. Because our sample size was large and no experiment was conducted (Gotelli and Ellison 2013), we coded the answers to our Questions as categorical data and analyzed them using Pearson’s chi-square statistic (Pearson 1900) in the R package “MASS” (Ripley et al. 2013).

  • Use:

    This dataset is released to the public under Creative Commons license CC BY (Attribution). Please keep the designated contact person informed of any plans to use the dataset. Consultation or collaboration with the original investigators is strongly encouraged. Publications and data products that make use of the dataset must include proper acknowledgement.

  • Citation:

    Degrassi A, Brantley S. 2015. Foundation Species Revisited: Citation Analysis of Ellison et al. 2005. Harvard Forest Data Archive: HF259.

Detailed Metadata

hf259-01: foundation species research

  1. author.id: name(s) of the contributing author(s)
  2. year.id: year of publication
  3. title.id: title of documentation
  4. journal.id: name of the journal where the article was published
  5. literature.type: type of literature
    • Primary: literature that is original research papers. Includes peer reviewed scientific methods and model papers
    • Review: literature that includes peer reviewed research on original research papers that review specific scientific topics
    • Communication: literature that provides comments, explanations, or annotations without including scientific method
    • Letter: literature that does not research involving the scientific methods
    • Response: literature that is a correspondence, does not research involve the primary scientific methods, but usually is a comment on primary literature or previous commentary
    • Commentary: literature that is a correspondence, does not research involve the scientific methods
    • Not Published/Primary: literature that includes original research papers that includes scientific methods and model papers, but has not been peer reviewed or published in a scientific journal
  6. fs.role: main role of the foundation species
    • Community: when the research studied direct support of other species and/or community in any capacity. The effects on associated species or assemblages.
    • Ecosystem: when the research studied direct support of abiotic and/or biogeochemical processes
    • Ecosystem + Community: when the research studied both the support of community and biogeochemical processes
    • Not Identified: when the study did not specifically identify its purpose as researching community, ecosystem, or the combination of the two
    • NA: when the data was not available or identified as with non-primary literature (LiteratureType)
  7. fs.defined: citation of foundation species concept
    • Ellison et al.: foundation species concept was defined and contributed to Ellison et al. 2005
    • Dayton: foundation species concept was defined and contributed to Dayton 1972
    • Dayton & Ellison: foundation species concept was defined and contributed to both Dayton 1972 and Ellison et al. 2005
    • Other: foundation species concept was defined and not contributed to either Dayton 1972 or Ellison et al. 2005
    • Not Defined: foundation species concept was not defined in any identified/notable capacity
    • NA: the data was not available or not recorded as with non-primary literature
  8. definition.cite: citation of species concept if fs.defined was “Other”
  9. fs.other.defined: how species concept was defined if fs.defined was “Other”
  10. fs.claim: whether or not research identified if species was foundation species
    • Foundation Species: study identified the species of interest as a foundation species
    • Not Foundation Species: study did not identify the species of interest as a foundation species
    • NA: data was not available or not recorded as with non-primary literature
  11. country.id1: country where data was collected
  12. country.id2: country where data was collected if data was collected in more than one country (in addition to Country.id1)
  13. climate.change: threat to foundation species loss from climate change mentioned or researched in the study
    • 1: authors identified climate change as a threat to studied foundation species
    • 0: authors did not identified climate change as a threat to studied foundation species
    • NA: data was not available or not recorded as with non-primary literature
  14. invasive.spp: threat to foundation species loss from invasive, exotic, or non-native species mentioned or researched in the study
    • 1: authors identified invasive, exotic, or non-native species as a threat to studied foundation species
    • 0: authors did not identified invasive, exotic, or non-native species as a threat to studied foundation species
    • NA: data was not available or not recorded as with non-primary literature
  15. habitat.degradation: threat to foundation species loss from types of habitat degradation researched in the study
    • 1: authors identified habitat degradation as a threat to studied foundation species
    • 0: authors did not habitat degradation as a threat to studied foundation species
    • NA: data was not available or not recorded as with non-primary literature
  16. exploitation: threat to foundation species loss from types of exploitation researched in the study
    • 1: authors identified types of exploitation as a threat to studied foundation species
    • 0: authors did not identify types of exploitation as a threat to studied foundation species
    • NA: data was not available or not recorded as with non-primary literature
  17. disease.pathogen: threat to foundation species loss from types of diseases and/or pathogens researched in the study
    • 1: authors identified types diseases and/or pathogens as a threat to studied foundation species
    • 0: authors did not identify types diseases and/or pathogens as a threat to studied foundation species
    • NA: data was not available or not recorded as with non-primary literature
  18. no.threat: threat to foundation species loss was not identified in the study
    • 1: authors did not was not identified a particular threat to studied foundation species
    • 0: authors identified other types of threats to studied foundation species
    • NA: data was not available or not recorded as with non-primary literature
  19. strong: study was strongly influenced by Ellison et al. 2005
    • 1: research was strongly influenced by Ellison et al. 2005. Received “1” if the foundation species was identified as the main study organism, identification of possible threats to foundation species loss, and used Ellison et al. 2005 to define foundation species.
    • 0: authors identified other types of threats to studied foundation species
    • NA: data was not available or not recorded as with non-primary literature
  20. moderate: study was moderately influenced by Ellison et al. 2005
    • 1: research was moderately influenced by Ellison et al. 2005. Received “1” if only two in any combination occurred: the foundation species was identified as the main study organism, identification of possible threats to foundation species loss, and used Ellison et al. 2005 to define foundation species.
    • 0: authors identified other types of influence
    • NA: data was not available or not recorded as with non-primary literature
  21. marginal: study was marginally influenced by Ellison et al. 2005
    • 1: research was moderately influenced by Ellison et al. 2005. Received “1” if only one or none in any combination occurred: the foundation species was identified as the main study organism, identification of possible threats to foundation species loss, and used Ellison et al. 2005 to define foundation species.
    • 0: authors identified other types of influence
    • NA: data was not available or not recorded as with non-primary literature
  22. notes: general notes regarding the study that would aid in the ability to clarify particular decisions on scoring methods