Introduction
The Earth’s climate has experienced profound changes through geologic history (Zachos et al., 2001), between extreme hyperthermal periods and ice ages (Burke et al., 2018). As changing climate influences the distribution ranges of marine and terrestrial species (Shaviv et al., 2023), understanding their responses to past climatic or environmental changes is essential for predicting responses under future climate change scenarios (Araújo & Pearson, 2005).
Species distribution modelling (SDM) and Ecological niche modelling (ENM) offer new possibilities for estimating the environmental suitability and the past distributions of organisms (Svenning et al., 2011). Over the last few years, the number of studies using SDM and ENM to address paleobiological and paleoecological questions has increased considerably (Melo-Merino et al., 2020). SDM and ENM offer important opportunities for advances in these fields by providing a quantitative ecological perspective that contributes to the reconstruction of ancient ecosystems and conservation biology. For example, estimating the range shift of species due to past climate changes can give us clues about the modern climate change impacts and can be informative for ecological restoration (Beaugrand & Kirby, 2016; Svenning et al., 2011). Some studies complemented fossil and genetic evidence by providing projections of the past species distributions. Hereafter, we will use the term “paleo-SDM” to describe the application of SDM and/or ENM to paleobiology. In the marine realm, SDMs and ENMs have been used for some marine species of bivalves and gastropods, seaweed, molluscs, crustaceans, fish and mammals (Melo-Merino et al., 2020).
Here, we present a scoping review (ScR) protocol aiming at assessing the contribution of SDM and ENM in improving the description and the understanding of ancient marine species distribution, environmental suitability and ecology, and in determining how the past has shaped present-day biodiversity. Our scoping review will evaluate the latest developments at the cutting-edge of SDM and ENM application to paleobiology, in the marine realm, at a global scale. To our knowledge, the most recent review about the application of SDMs to paleobiology was published in 2011 and showed that they are mostly combined with genetically inferred patterns (49%), with palaeoecological records (22%), or both (6%) (Svenning et al., 2011).
The objectives of this ScR are as follows:
Identify the various objectives and outputs of paleo-SDMs for improving the knowledge of past species distribution and environmental suitability in the marine realm.
Map the extent of the current knowledge, and identify the geographic scope and the timeline of the studies.
Highlight the knowledge gaps by taxonomic group.
Identify and compare the methodologies used for addressing past marine species distribution and environmental suitability (e.g., models, types of variables, validation)
Explore and discuss key methodological issues, assumptions and uncertainties (regarding the data and the methods).
Review questions
The ScR will attempt to answer the following sub-questions:
1. What is the spatial and temporal coverage of the application of marine paleo-SDMs?
2. What are the marine taxonomic groups concerned with marine paleo-SDMs?
3. What are the criteria/methodologies/tools for implementing marine paleo-SDMs?
4. What are the challenges in the application of paleo-SDMs for the marine realm?
Methods
The Scoping Review (ScR) will adhere to the framework established by Arksey and O’Malley (2005), refined by Levac et al. (2010), and further advanced by the Joanna Briggs Institute (JBI). Specifically, the procedures outlined by Peters et al. (2020) for scoping reviews will be implemented. Moreover, PRISMA-Reporting guidelines will be used (Moher et al., 2015).
Inclusion/ exclusion criteria
(following the methodology of Peters et al., 2020 for scoping reviews)
The inclusion criteria of the ScR are presented in Table 1 and were discussed with participants of the ScR. The development of the inclusion criteria for the ScR determining which sources will be considered for inclusion, are aligned with the mnemonic “Participants, Concept, and Context (PCC)” (Peters et al., 2020) (Table 1).
Table 1. Inclusion and exclusion criteria for the scoping review.
| Inclusion criteria | Exclusion criteria |
|---|
| PARTICIPANTS | Studies applying SDM or ENM (to marine species) with clear
guidelines for Paleo-SDM
Studies informing Paleo-SDM approaches by providing
software, scripts, and algorithms | Studies that apply other types of modelling or
that mention ENM and SDM without details.
Studies that include geographic distribution or
environmental suitability without modelling
Studies applying SDM/ ENM to the present
Studies applying SDM/ENM to pseudo-species |
| CONCEPT | Systematic review about methods and tools used for SDM
or ENM: All studies applying paleo-SDM for marine species,
clearly describing the applied methods/tools and the used
databases. | Studies that do not provide sufficient
methodological details but simply mention the
use of ENM and SDM |
CONTEXT
Global, marine realm | Studies in:
- Marine realm
- Globally or regionally or locally
Studies that apply SDM and/ or ENM to ancient periods
from the Last Glacial Maximum (LGM) to the pre-
industrial Era (from approximately 22,000 yrs BP to
approximately 1850) | Studies where the marine component or
species will not be included.
Studies applying SDM before the LGM or after
the pre-industrial Era. |
EVIDENCE TYPES &
SOURCES | - peer-review literature
- grey literature if any
- all years of publications | Conference papers
Strictly methodological papers |
Participants
The ScR will consider all studies applying paleo-SDMs (documenting spatial distributions studies / environmental suitability through SDM or ENM or including guidelines for paleo-SDM or informing them by providing software, scripts, and algorithms). Studies applying other correlative statistical modelling approaches such as trophic niche modelling will not be taken into account. Moreover, studies that apply other types of modelling or that mention ENM and SDM without methodological details, or that apply SDM to pseudo-species will not be considered for this ScR objectives.
Concept
The concept adopted by the ScR will be the assessment of how SDMs and/or ENMs were applied to paleobiological data to assess past species distribution and species environmental suitability and how the niche conservatism hypothesis was addressed, so far in the scientific literature. Studies that do not provide sufficient methodological details but simply mention the use of a specific paleo-SDM tool will not be taken into account.
Context
In our ScR, we will consider spatially explicit case studies of marine species, globally, regionally and at a national or a local level. Studies without a marine component (primarily terrestrial or freshwater) will not be included. In terms of past time frame, studies that apply SDM to past periods ranging from the Last Glacial Maximum (LMG) to the pre-industrial Era (from approximately 20,000 yrs BP to 1850) will be included in the scope of our review.
Types of sources
This Scoping Review (ScR) will include a range of peer-reviewed literature, such as research articles, reviews, book chapters, letters, editorials, and books. There will be no limitations on publication year, publication status (whether final or in press), subject area, or source type. Only peer-reviewed sources will be included. Language restrictions will be applied based on the authors' language proficiency, encompassing studies published in English, French, and Spanish.
Search strategy
The bibliographic search will be conducted using two databases: (a) Scopus (https://www.scopus.com/home.uri) and (b) Web of Science (https://clarivate.com/products/scientific-and-academic-research/research-discovery-and-workflow-solutions/webofscience-platform/). Our search will utilize a combination of keywords applied to the document title, abstract, and keywords fields (see Table 2).
Table 2. Details of Scoping Review databases.
| Language | English | Spanish | French |
Date of
search: | 30 April 2024 | 02 May 2024 | 02 May 2024 |
| Database | Scopus | Scopus | Scopus |
| Query: | TITLE-ABS-KEY "ecological niche
model*" OR “species distribution
model*”
AND
"paleo*" OR “palaeo*” OR “past” OR
“Holocene” OR “Pleistocene” OR
“Quaternary” OR “Pre-industrial”
OR “Preindustrial” OR ”Last glacial
maximum” OR “interglacial” OR
“ancient” OR “historical” OR “roman”
OR “antiquity” OR “medieval”
AND
“marine” OR “ocean*” OR “sea*”
Refine search “marine” | "modelo* de nicho ecológico"
OR “modelo* de distribución de
especies”
AND
“paleo*” OR “pasado” OR “Holoceno”
OR “Pleistoceno” OR “Cuaternario”
OR “Pre-industrial” OR “Preindustrial”
OR ”Último máximo glacial”
OR “interglacial” OR “antiguo”
OR “histórico” OR “romano” OR
“antigüedad” OR “medieval”
AND
“marino” OR “océano*” OR “mar*”
Refine search “marino” | “modèle de niche écologique*” OR “modèle
de distribution des espèces*”
AND
“paléo*” OR “palaeo*” OR “passé”
OR “Holocène” OR “Pléistocène” OR
“Quaternaire” OR “Pré-industriel” OR
“Préindustriel” OR “Dernier maximum
glaciaire” OR “interglaciaire” OR “ancien” OR
“historique” OR “romain” OR “antiquité” OR
“médiéval”
AND
“marin” OR “océan*” OR “mer*”
Refine search “marine” |
| Results: | 306 | 0 | 0 |
| Database | Web of Science Academy | Web of Science Academy | Web of Science Academy |
| Query: | Same as previous | Same as previous | Same as previous |
| Results: | 347 | 0 | 0 |
Data extraction
The data extraction tool will be embedded in the Covidence systematic review management software (Table 3) to facilitate the import, screening, uploading and export of selected literature (Table 3), as well as the cooperation and interaction between reviewers. Covidence is a web-based collaboration software platform that streamlines the production of systematic and other literature reviews (https://www.covidence.org/reviewers/). At least two co-authors should perform the same documents through ScR.
Table 3. Data extraction tool of the Scoping Review (ScR) with examples.
| Field | Metadata | Data to be extracted (examples) | Remarks/guidance
to reviewers |
|---|
| 1 | Study ID | | free text |
| 2 | Title | | free text |
| 3 | Author(s) | | free text |
| 4 | Year of publication | | free text |
| 5 | Journal | | free text |
| 6 | Keywords | | free text |
| 7 | DOI | | free text |
| 8 | URL | | free text |
| 9 | Literature category | Journal article, Book chapter, Report (grey literature) | Single choices field |
| 10 | Language | English; Spanish; French | Single choices field |
| 11 | Marine realm (sensu
Spalding et al., 2007) | Arctic; Mediterranean; temperate northern Atlantic; temperate northern
Pacific; tropical Atlantic; western IndoPacific; central Indo-Pacific; eastern
Indo-Pacific; tropical eastern Pacific; temperate South America; temperate
southern Africa; temperate Australasia; southern Ocean; more than one
realm; global | Single or multiple choices field |
| 12 | Marine taxonomic
group | Bacillariophyta, Dinoflagellata, Chlorophyta, Rhodophyta, Haptophyta
(Coccolithophores), Ochrophyta (Brown algae (including kelp)), Porifera,
Cnidaria, Ctenophora, Annelida, Mollusca, Platyhelminthes, Sipuncula,
Arthropoda, Chaetognatha, Brachiopoda, Bryozoa, Phoronida,
Echinodermata, Ascidiacea, Thaliacea, Agnatha, Chondrichthyes,
Osteichthyes, Reptilia, Aves, Mammalia | Single or multiple
choices field |
| 13 | Does the study
concern one species
or more? | one species, more than one species | single choice field |
| 14 | If "more" is the
answer to the
previous question,
how many species are
considered? | | Free text |
| 15 | Taxon common name | | Free text |
| 16 | Taxon scientific name | | Free text |
| 17 | Spatial scale | Global, regional, National, local | Single or multiple
choices field |
| 18 | Spatial resolution of
the model | | Free text |
| 19 | Rationale | the objective of the study, of using SDM /ENM | Free text |
| 20 | Methodology 1 | ex: Ecological Niche modelling: Boosted Regression Trees (BRT) | Free text |
| 21 | Methodology 2 if any | | Free text |
| 22 | Methodology 3 if any | | Free text |
| 23 | Methodology 4 if any | | Free text |
| 24 | Environmental data
source | ex: Interdisciplinary Research on Climate (MIROC) and the Community
Climate System Model (CCSM) | Free text |
| 25 | Model Evaluation
method | ex: TSS | Free text |
| 26 | Highlighted
challenges and
criticism | Not discussed | Free text |
| 27 | Was Niche
conservatism
addressed? If yes,
how? | No | Free text |
| 28 | Validation dataset
DOI/URL | http://dx.doi.org/10.1016/j.marenvres.2015.11.005 | if the code is published |
| 29 | Time period | Last maximum Glacial (20,000 years ago), Mid-Holocene (6,000 years ago),
present (since 1990), and future (2050 and 2100) | Provide start and end |
| 30 | Temporal resolution | Temporal time lapse | Free text |
| 31 | Code used (and DOI) | if the code is published | Free text |
| 32 | Software/ algorithm
used | ex: parallel computing using the packages adehabitat, doParallel, gbm,
gdata, gstat, raster and SDMTools. | Free text |
Data analysis and presentation
The findings synthesized in this Scoping Review (ScR) will be aligned with the review's objectives and questions. Data will be showcased through a combination of graphical and tabular formats, utilizing various software tools. A narrative summary will supplement these tables and charts, elucidating how the results address the review's objectives and questions. The analysis of the extracted data will be confined to basic descriptive statistics. These descriptive findings will be illustrated using various visual representations.
We will organize data into two main sections: (1) the first outlining the results of the search strategy and selection process, including a PRISMA flow diagram, and (2) the second presenting the key information or findings pertinent to the scoping review's objectives and questions.
Ethics and consent
Ethical approval and consent were not required.
Data availability
No data associated with this article.
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