DOI: 10.5061/dryad.qrfj6q5mk
title: The relationship between genetic diversity, function, and stability in marine foundation species

description: Seagrasses, corals, marsh plants, kelps, and mangroves support valuable
 coastal ecosystems but are threatened by environmental stressors. The need
 to manage these foundation taxa has spurred more than a decade of study on
 the relationship between genetic diversity and function or stability. We
 synthesized this literature base (129 relevant publications) and found
 more reported instances of neutral to positive relationships between
 genetic diversity and function than negative. However, much of the
 scientific understanding is based on the response of three genera and from
 unreplicated observational studies that correlate genetic diversity to
 measured response variables. When a disturbance was present, the studies
 often lacked controls or baseline data. Only 5.5% of the studies robustly
 tested for stability. These shortcomings preclude a rigorous evaluation of
 whether more genetically diverse foundation populations increase stability
 and hinder the use of genetics-based conservation strategies. Future
 studies should be focused on diverse species and ecosystem-level impacts
 using manipulative designs.
description: To survey for literature on the topic of genetic diversity and
 resilience of the five coastal foundation taxa, we performed a Web of
 Science search in December 2021 using the following search
 string: <em>(((ALL=(Diversity or Variation) and
 (genet* or genotyp* or allel*) and (stability or resilience or function or
 epifauna or epibio* or epiphyte or productivity or production or trophic)
 and (seagrass* or mangrove* or submerged aquatic vegetation or coral* or
 saltmarsh or marsh* or kelp*)))))</em> The
 initial search returned 1,533 publications from peer-reviewed journals,
 which were each screened for relevance and inclusion by a team of
 researchers. To be included in the extraction process, publications could
 not be a review or a meta-analysis and had to (1) focus on one of the
 focal foundation species, (2) contain a metric of genetic diversity (e.g.,
 genotypic richness, allelic diversity), and (3) include a metric of
 function (e.g., survival, metabolism, production, or whole-ecosystem
 function) or the environment (e.g., temperature, salinity, irradiance).
 When a publication met the requirements of 1, 2, and 3, we noted whether
 the study design included replication at all levels (within and among
 diversity and disturbance treatments/observations). Furthermore, if these
 studies included any kind of disturbance, we noted whether the authors
 reported baseline information on function before the disturbance began and
 whether they included proper controls (i.e., plots/treatments that did not
 experience a disturbance). Finally, we also noted if these publications
 could be used to answer any of three predictions of the
 diversity-resilience relationship. The predictions are higher genetic
 diversity (1) is related to greater function, (2) helps maintain function
 under a disturbance, and (3) confers resilience to a disturbance. To test
 prediction 1, a study had to report both diversity and function. To test
 prediction 2, a study had to report genetic diversity and function under a
 disturbance; and to test prediction 3 a study had to follow a
 before-after-control-impact (BACI) design to truly assess
 resilience. To minimize personal bias among researchers
 in the selection process, the team held a workshop where we evaluated the
 relevancy and inclusion of five publications based on the criteria
 described above. Once we all agreed on the inclusion or exclusion of those
 five publications, the 1,533 publications returned by the search were
 broken up into three sets of 511 publications. A pair of researchers were
 assigned to each set. Both researchers in each pair independently
 evaluated at least 140 publications in their assigned set for the
 inclusion criteria and prediction(s) the publication could test. The two
 researchers then compared their evaluations and discussed and resolved
 discrepancies. Upon reaching full agreement, one or both researchers would
 move on to finish the remainder of the set. In the case when an agreement
 could not be reached between the two researchers, the publication was
 reviewed by a larger committee and was included or not based on a majority
 consensus. Reviews and meta-analyses (107 of the 1,533) were not included
 in our dataset, but the literature cited was cross-referenced to find 20
 additional relevant publications. We extracted metadata
 from the 129 publications that met our inclusion criteria. Metadata on the
 study design and results of each publication were extracted by one of four
 reviewers. Information on the focal organism (taxon and species), the
 study type (observational or manipulative), location (field or
 laboratory), region (including GPS coordinates when provided), and study
 duration were extracted from each publication. When researchers collected
 from or conducted experiments at multiple sites, GPS coordinates for all
 sites were recorded. Publications that included metrics of coral
 <em>Symbiodinium</em> diversity were included into the “coral”
 category. A single coral species can be functionally different as a result
 of the type of symbionts, so <em>Symbiodinium</em> types A-I
 were for this purpose considered genetically different entities of
 coral. We recorded the type of diversity metric used
 and the observed range of these values reported by each study. If the
 study manipulated levels of genetic diversity, we also noted the total
 number of levels in the study and the number of replicates used at each
 level. A list of all metrics used in each publication was compiled for
 each taxon (Table S1). When a paper reported multiple metrics, each metric
 was tallied separately to have a total &gt;129 instances of diversity
 metrics. Values are reported as the percentage of the total number of
 metrics tallied rather than the total number of publications.
 Measured diversity metrics were divided into eight different
 categories. “Genotypic Information” consisted of measurements such as
 calculated genotypic richness, number of genotypes, and evenness. The
 “Allelic Information” category included measurements such as the number of
 alleles, and calculations of allelic richness and allelic diversity.
 “Haplotype/Clade Metrics” included the number of clades, the number of
 ITS-2 (ribosomal internal transcribed spacer 2) types, and haplotype
 diversity. Other categories included “Observed Heterozygosity”, “Expected
 Heterozygosity”, “Inbreeding Coefficients” (F<sub>IS</sub> and
 F<sub>ST</sub>), “Nucleotide Specific Metrics”, and “Diversity
 Indices” (Simpson’s index, Shannon Wiener index, etc.).
 We recorded any metrics of the environment reported in the study
 and observed ranges. Based on the results, we tallied publications that
 found a correlation between genetic diversity and one or more
 environmental metrics. The type and duration (in days) of any manipulated
 or natural disturbances that occurred during the study were recorded. In
 studies that conducted a manipulative disturbance, the number of levels of
 each stress treatment was recorded. In studies that experienced a natural
 or accidental disturbance, it was noted whether the stressor was
 continuous and ongoing after the study ended.  We
 recorded the functional metric(s) used in the experiment and noted how
 many times throughout the experiment it was measured. We also noted
 whether there was a correlation (positive, neutral, or negative) between
 each diversity and function metric. In some cases, authors reported
 multiple function and diversity metrics in one paper and the correlation
 was dependent on the function or diversity metric reported. When positive
 and neutral outcomes were included in the same publication it was tallied
 as an overall “positive” outcome, because if one function metric is
 positive, the outcome for the population would also be positive. In
 publications that reported both positive and negative results, the
 responses were tallied in their own category. If all metrics reported in a
 publication were neutral, the outcome was reported as “neutral”. For
 example, in a study where genotypic richness is positively correlated with
 biomass but not correlated with leaf length, the publication would be
 tallied as positive. However, if genotypic richness was positively
 correlated with biomass, but negatively correlated with leaf length, the
 paper was tallied as “positive and negative”. Extracted
 metrics of function were categorized into five categories: “Abundance”,
 “Physiology”, “Morphometric”, “Reproduction”, and “Community”. Abundance
 metrics consisted of measurements such as density and biomass. Physiology
 included metrics related to metabolism, growth rates, and productivity.
 Morphometric measurements included height, length, width, and surface
 area. Reproduction consisted of measurements such as flower and fruit
 production and seed count. Community metrics were those that related to
 any other organism beyond the focal species. For example, macrofauna
 abundance, levels of herbivory, and grazer and epiphyte biomass/diversity
 were all counted as community metrics. We also looked for metrics that
 measured overall ecosystem function such as nitrogen cycling or
 decomposition, but ultimately did not find any within the 129 relevant
 publications. The number of metrics in each category was tallied for each
 taxon. Results are reported as a percentage of instances in each category
 out of the total number reported for each taxon.  We
 were also interested in the mechanism(s) behind the relationship between
 genetic diversity and function, which can be determined through some
 manipulative studies. These studies must have replication of genetic
 diversity treatments and genotypes within each treatment. Manipulative
 studies with proper replication were further investigated for any
 conclusions made about mechanisms behind the diversity-function
 relationship (functional redundancy, niche complementarity,
 etc.).
description: # The relationship between genetic diversity, function, and stability in
 marine foundation species --- These datasets contain compiled and
 extracted information that was used for a review focusing on the
 relationship between genetic diversity and resilience for coastal
 foundation species. ## Description of the data and file structure **Search
 Information.xlsx** This file contains information (author, article title,
 source, year of publication, and DOI) of 1,533 publications that were
 returned from a Web of Science Search conducted in December 2021\. An
 additional twenty publications (article numbers 1534-1554) were added
 after cross referencing all of the reviews/meta-analyses that were
 returned in the original search. The variables are: Code: The place in the
 search in which the publication was listed in the search Authors: the
 listed authors on the publication Article Title: the title of the
 publication Source Title: the name of the journal in which the article was
 published Year: the year the article was published DOI: the digital object
 identifier for the publication Species: Yes/No - Does the publication
 study one of the five focal taxa (seagrasses, corals, marsh plants, kelps,
 or mangroves)? Diversity: Yes/No - Does the publication provide values for
 at least one measure of genetic diversity (number of genotypes, allelic
 richness, heterozygosity, etc)? Function: Yes/No - Does the publication
 provide values for at least one measure of function (any biological trait
 that affects performance or fitness)? Environment: Yes/No - Does the
 publication provide values of any environmental metrics or include an
 accidental/manipulative disturbance? Review: Yes/No - Is the publication a
 review or meta-analysis? Notes: Any notes the reviewer felt pertinent
 \**'Authors,' 'Article Title,' 'Source
 Title,' 'Year,' and 'DOI' were taken directly
 from the Web of Science search output file. **Extracted Information.xlsx**
 This file contains information extracted from 129 publications that met
 the inclusion criteria for the review (must study one of the five focal
 taxa, measure at least one metric of diversity, and measure at least one
 metric of function and/or the environment. The variables are: Predictions:
 lists which of the following three predictions the publication provides
 evidence for. (1) Higher genetic diversity is related to greater function,
 (2) higher genetic diversity helps maintain function under a disturbance,
 and (3) higher genetic diversity confers resilience to a disturbance.
 Replication: Yes/No - Does the study include replication of diversity
 levels in treatments? Control: Yes/No - If the study included a
 disturbance/stressor, did the study design include control treatments that
 did not experience the stressor? Baseline: Yes/No - If the study included
 a disturbance/stressor, did it provide baseline information about function
 before the disturbance occurred? BACI: Yes/No/Yes* - Does this study
 include a Before-After-Control-Impact (BACI) design? Cells with
 "Yes*" entered refer to studies with a BACI design, but either
 did not report the results in the publication or only included one
 sampling after the disturbance. Taxon: the focal taxon (seagrasses,
 corals, marsh plants, kelps, and mangroves) the publication studies
 Species: the specific species the publication studies. If two or more
 species were studied, each were listed in their own row Study Type:
 Observational/Manipulative: lists whether the study is observational,
 manipulative, or both Lab/Field: lists whether the study occurred in the
 laboratory, the field, or both Region: Region: the region(s) where the
 study occurred Location: the specific areas where the study occurred (as
 specific as the study provided) Lat/Long: the GPS coordinates for each
 study location (if provided) in the units provided by the publiation.
 Duration: One time: lists whether this study had a one time sampling
 event, or if it was a long term study Time of sampling: when the
 collection or experimental set up occurred (as specific as the study
 provided) Length of study: how long the study occurred in days. Some
 values are estimated based on the start and end dates provided by the
 study. Not applicable for one or two time studies Diversity Metrics: Type:
 the specific diversity metric measured. If the study measured more than
 one, a new row was added for each metric Lowest: the lowest recorded value
 of the diversity metric. If only one value was reported, it was recorded
 in the "Lowest" cell.\ Highest: the highest recorded value of
 the diversity metric Total number of levels: if the study was
 manipulative, the number of levels of genetic diversity tested. Listed
 once per study unless otherwise noted. Replication: descriptions of the
 study design as it pertains to genetic diversity metrics Function Metrics:
 Type: lists all of the function metrics that were measured in this study
 Measurements: how often each of the metrics were measured over the course
 of this study Disturbance: Type: lists the type of disturbance that was
 included or characterized during the study Levels: lists how many levels
 of the disturbance were included, if manipulative Ongoing: Yes/No if the
 disturbance is a chronic stressor that is still occurring Environmental
 Metrics: Included metrics: lists all environmental measures that were
 collected during the study Range: lists the range of each environmental
 metric measured Findings: detailed description of the outcomes of the
 study specifically related to the relationship between genetic diversity
 and function and/or the environment Notes: any additional notes the
 extractor thought pertinent to the review Finding abbreviated:
 Environment: lists the outcome for the relationship between genetic
 diversity and the environmental metrics measured in the publication
 Function: lists the outcome for the relationship between genetic diversity
 and the function metrics measured in the publication 'Code,'
 'Authors,' 'Article Title,' 'Source Title,'
 'Year,' 'DOI,' 'Species,'
 'Diversity,' 'Function,' 'Environment,' and
 'Review,' follow the same descriptions outlined above.