uid=HFR,o=lter,dc=ecoinformatics,dc=org all public read doi:10.6073/pasta/1067adbb41ec6cccf4fb91d4055b184e Allyson Degrassi https://orcid.org/0000-0002-1634-1614 Steven Brantley Aaron Ellison https://orcid.org/0000-0003-4151-6081 Researcher Carrie Levine https://orcid.org/0000-0001-8083-6198 Researcher Robert Miller Researcher Jacqueline Mohan https://orcid.org/0000-0002-6697-6204 Researcher Sydne Record https://orcid.org/0000-0001-7293-2155 Researcher 2023 English

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.

invasive species microclimate species abundance LTER controlled vocabulary primary production populations LTER core area Harvard Forest HFR LTER USA HFR default

This dataset is released to the public under Creative Commons CC0 1.0 (No Rights Reserved). Please keep the dataset creators informed of any plans to use the dataset. Consultation with the original investigators is strongly encouraged. Publications and data products that make use of the dataset should include proper acknowledgement.

Creative Commons Zero v1.0 Universal https://spdx.org/licenses/CC0-1.0.html CC0-1.0 https://harvardforest.fas.harvard.edu/exist/apps/datasets/showData.html?id=hf259 Global. Coordinates based on WGS84 datum. -180 +180 +90 -90 2005 2014 complete Information Manager Harvard Forest

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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).

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.

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.

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.”

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.

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.

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.

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.”

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).

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(978) 724-3302 (978) 724-3595 https://harvardforest.fas.harvard.edu https://ror.org/059cpzx98 pointOfContact The Harvard Forest Long-Term Ecological Research (LTER) program examines ecological dynamics in the New England region resulting from natural disturbances, environmental change, and human impacts. National Science Foundation LTER grants: DEB-8811764, DEB-9411975, DEB-0080592, DEB-0620443, DEB-1237491, DEB-1832210. hf259-01-fs-research.csv foundation species research hf259-01-fs-research.csv 123375 dea72027c6f59ea65beb3323aef4b370 1 \r\n column , https://harvardforest.fas.harvard.edu/data/p25/hf259/hf259-01-fs-research.csv author.id name(s) of the contributing author(s) name(s) of the contributing author(s) NA missing value year.id year of publication YYYY 1 year NA missing value title.id title of documentation title of documentation NA missing value journal.id name of the journal where the article was published name of the journal where the article was published NA missing value 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 Free text (unrestricted) .* 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) Free text (unrestricted) .* 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 definition.cite citation of species concept if fs.defined was “Other” citation of species concept if fs.defined was “Other” NA missing value fs.other.defined how species concept was defined if fs.defined was “Other” how species concept was defined if fs.defined was “Other” NA missing value 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 country.id1 country where data was collected country where data was collected NA missing value country.id2 country where data was collected if data was collected in more than one country (in addition to Country.id1) country where data was collected if data was collected in more than one country (in addition to Country.id1) NA missing value 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 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 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 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 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 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 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 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 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 notes general notes regarding the study that would aid in the ability to clarify particular decisions on scoring methods general notes regarding the study that would aid in the ability to clarify particular decisions on scoring methods NA missing value 378 historical international long-term measurement