DOI: 10.5061/dryad.3bk3j9kt3
title: Data from: Burrowing crab effects on the properties and functions of coastal soft sediments

description: Burrowing ecosystem engineers, such as termites, crabs, marmots, and
 foxes, can profoundly affect the biological structure and ecosystem
 functions of their environments. However, the relative importance of
 burrowing engineers on sediments are challenging to predict and are
 expected to be influenced by engineer density, engineer functional traits
 (e.g., burrow morphology), and environmental conditions (e.g.,
 geomorphology, vegetation presence). To develop robust hypotheses
 predicting the impacts of burrowing ecosystem engineers, we conducted a
 systematic meta-analysis evaluating the effects of burrowing crabs on
 sediment properties, nutrient stocks, and ecosystem functions in coastal
 soft-sediment habitats (e.g., salt marshes, mangrove forests, tidal
 flats). The data set includes 1422 effect size calculations for the
 effects of burrowing crabs on sediments collected from 59 total
 manuscripts. The data suggest that burrowing crabs rework and oxygenate
 sediments and accelerate rates of nutrient cycling (i.e., nitrification
 and CO2 flux). However, the magnitude and direction of burrowing crab
 effects depend on burrowing crab superfamily, the presence of vegetation,
 and their interaction. Crab burrow density does not consistently predict
 burrowing engineer effects on sediments. 
description: <strong><em>Search string development and literature
 survey.</em></strong> To develop our search
 string, we consulted the preferred reporting items for systematic reviews
 and meta-analyses (PRISMA; Moher et al. 2009, Page et al. 2021) and
 implemented a modified version of the Population, Intervention,
 Comparison, Outcome (PICO) approach (Foster and Jewell 2017). We defined
 our populations as burrowing crab communities located within soft-sediment
 tidal ecosystems. Our variable was broadly defined and included all known
 pathways by which burrowing crab communities may influence sediments and
 their functions (e.g., bioturbation, excavation, burrowing, particle
 reworking, herbivory, facilitation). The outcome was any change in edaphic
 conditions or sediment functions. The final search string is as follows
 (the string is presented in sections to specify the intent of each group
 of search terms, underlined headings were not included in the Boolean
 string): Crab Engineer Populations:
 ((burrowing NEAR/0 crab) OR crab OR (ecosystem NEAR/0 engineer)) OR (uca
 OR leptuca OR  minuca OR (fiddler NEAR/0 crab) OR ocypodid) OR (sesarm OR
 grapsid OR purple marsh crab) OR (neohelice OR chasmagnathus) OR
 (pachygrapsus OR ("lined shore" NEAR/0 crab))
 AND Crab Engineer Effect
 Pathways: ((bioturbation OR bio-irrigation OR bioengineering OR
 excavation OR burrow OR biomixing OR (particle NEAR/0 rework) OR ventiliat
 OR morphodynamic OR geomorphic) OR (sediment OR soil OR (intertidal NEAR/0
 sediment*)) OR (herbivory OR mutualism OR "top-down control" OR
 (ecosystem NEAR/0 engineer) OR consum OR graz OR facilitat))
 AND Crab Engineering Outcomes for
 Sediments: (carbon OR "organic matter" OR decompos OR
 decay OR respira OR efflux OR (methane OR (CH4)) OR ("carbon
 dioxide" OR (CO2)) OR fixation OR carbon NEAR/0 flux) OR (nitrogen OR
 denitrification OR nitrification OR anammox OR DNRA OR nitrate OR ammonium
 OR nitrite) OR ((sediment NEAR/0 biogeochemistry) OR biogeochemistry OR
 (sediment NEAR/0 chemistry) OR (soil NEAR/0 chemistry) OR redox OR
 reduction OR oxygenation OR oxidation OR iron OR sulfur OR sulfate OR
 manganese) OR (erosion OR erod* OR sediment* OR accret* OR deposit* OR
 accumulat* OR import* OR export*) OR (nutrient cycling OR
 nutrient*) AND Focal
 Burrowing Crab Habitats:<em> </em>((salt NEAR/0
 marsh) OR saltmarsh OR marsh OR (salt NEAR/0 panne) OR Spartina OR Juncus
 OR Phragmities OR Salicornia OR Sarcocornia) OR (mangrove OR (mangrove
 NEAR/0 tree) OR Avicennia OR Rhizphora) OR (mudflat OR (mud NEAR/0 flat))
 OR (tidal OR coastal) NOT
 Exclude:<em> </em>(dune OR
 freshwater) OR (metal OR pesticide OR pollut) OR (larva OR embryo) OR
 (seagrass OR eelgrass). We input our Boolean search
 string into Web of Science (WoS) Core Collection
 (http://isiknowledge.com/) on 03 September 2021 and restricted the search
 to journal articles only. This search yielded 1424 articles. To capture as
 much of the literature as possible, we also input our Boolean search
 string into the WoS BIOSIS Previews, WoS Biological Abstracts, and
 Zoological Record databases on 03 September 2021. The four database
 searches were merged, and duplicates removed using Endnote
 (https://endnote.com/). This yielded a merged RIS file containing 1424
 unique articles. <strong><em>Literature
 screening.</em></strong> We input our
 merged RIS files into Rayyan (https://rayyan.ai/; Ouzzani et al. 2016). In
 Rayyan, each article (n = 1424) was randomly allocated to two blind
 reviewers. Reviewers evaluated the title and abstract of each article to
 determine if it should be included, excluded, or reconsidered (i.e.,
 “maybe” in Rayyan software). Included articles needed to evaluate the
 relationship between burrowing crab density (relative or absolute) on
 edaphic conditions and sediment functions in a soft-sediment tidal
 ecosystem. Articles were excluded if they did not include burrowing crabs,
 quantify sediment properties and functions, or perform the study in a
 soft-sediment tidal habitat. We also excluded articles that were 1)
 qualitative with no primary data, 2) modeling or meta-analyses with no
 primary data, or 3) a graduate thesis where the data was also in a
 published article. Reviewers could also mark the article for
 reconsideration if they felt the title and abstract did not provide enough
 information to include or exclude the article. Our
 first review of articles yielded 102 included articles, 112 ‘maybe’
 articles, and 1210 excluded articles. We did a secondary review of all
 included and ‘maybe’ articles (n = 214). This secondary review involved a
 single reviewer reading the article in its entirety and determining if the
 article was eligible for inclusion based on the same criteria used during
 the first review in Rayyan. Our second review resulted in 87 articles that
 we considered for data collection. After reviewing these 87 articles, we
 decided to focus on articles that used comparative methodologies to assess
 edaphic conditions and sediment functions in habitats with high vs. low
 relative burrowing crab density. We chose to focus on articles that used
 comparative approaches, rather than articles that took a strictly
 correlative approach, because studies used a variety of burrowing crab
 density proxies (e.g., individual crab vs. burrow counts) and
 standardizing measurements of edaphic conditions and sediment functions
 across studies limited our sample sizes. Ultimately, we had 56 articles
 that we used for data collection. We also added three additional articles
 (Walker et al. 2021, Rinehart et al. 2023, Rinehart et al. <em>in
 prep</em>) that were close to publication at the time of the search.
 This resulted in our data set containing 59 total articles.
 <strong><em>Data
 collection.</em></strong> From each
 article, we collected data on sediment physical conditions, nutrient
 stocks, and ecosystem functions in habitats with relatively high vs.
 relatively low burrowing crab activity. We extracted data from tables,
 text, and figures (using Web Plot Digitizer; Rohatgi 2022). For each
 relevant study, we extracted the sample size, mean, and variance (standard
 error or standard deviation). Because the mean was not reported for all
 data in five articles (Martinetto et al. 2011, Escapa et al. 2015, Alvarez
 et al. 2018, Giorgini et al. 2019, Wang et al. 2020), we extracted the
 sample size, minimum, first quartile, median, third quartile, and maximum
 values of sediment characteristics and functions for these studies. We
 used this information to estimate the means and standard deviations for
 these studies (n = 50; Wan et al. 2014). If articles included multiple
 relevant independent studies, we extracted each individual study. This
 process resulted in 1422 total studies evaluating the relative effect of
 burrowing crabs on coastal soft-sediments and their functions. For each
 extracted study, we also recorded the following potential covariates: (1)
 ecosystem type (categorical: tidal flats, tidal marsh, mangrove forest),
 (2) Crab burrow density (continuous: density per
 m<sup>2</sup>), (3) vegetation (categorical: vegetated,
 unvegetated), (4) burrowing crab superfamily (categorical: Grapsoidea,
 Ocypodoidea, mixed community), and (5) methodology (categorical:
 manipulative, observational). 
 <strong><em>Effect size
 calculations.</em></strong> We conducted
 our meta-analysis using OpenMEE software (Build date: 26 July 2016;
 Wallace et al. 2017). We calculated the Hedges’ <em>d</em>
 (hereafter, <em>d</em>) to evaluate the effects of burrowing
 crabs (present/absent) on coastal sediment characteristics and functions
 (Hedges 1981). The Hedges’ <em>d</em> represents the relative
 difference between ‘Crab Present’ treatments and ‘Crab Absent’ treatments
 divided by the pooled standard deviation (Hedges 1981). If manuscripts
 included multiple ‘Crab Present’ treatments (e.g., Moore 2019), an
 individual Hedges’ <em>d</em> calculation was performed for
 each ‘Crab Present’ treatment relative to the ‘Crab Absent’ treatment. We
 used <em>d</em> because it is less sensitive to small sample
 sizes than other effect size calculations (Osenberg et al. 1997,
 Lajeunesse and Forbes 2003). A positive effect size indicates that
 burrowing crabs increased the response variable, while a negative effect
 size indicates that burrowing crabs decreased the response
 variable. <strong><em>Variability and
 publication bias</em></strong> We tested
 for potential publication bias by calculating Kendall’s Rank Correlations
 (T<sub>b</sub>) between effect size and pooled variance within
 each dataset (Begg and Mazumdar 1994).
 <strong><em>References</em></strong> Alvarez, M. F., M. C. Bazterrica, E. Fanjul, M. S. Addino, M. S. Valiñas, O. O. Iribarne, and F. Botto. 2018. Effects of two estuarine intertidal polychaetes on infaunal assemblages and organic matter under contrasting crab bioturbation activity. Journal of Sea Research 139:33–40. Begg, C. B., and M. Mazumdar. 1994. Operating Characteristics of a Rank Correlation Test for Publication Bias. Biometrics 50:1088–1101. Escapa, M., G. M. E. Perillo, and O. Iribarne. 2015. Biogeomorphically driven salt pan formation in Sarcocornia-dominated salt-marshes. Geomorphology 228:147–157. Foster, M. J., and S. T. Jewell. 2017. Assembling the pieces of a systematic review: A guide for librarians. Page (M. J. Foster and S. T. Jewell, Eds.). Rowman & Littlefield Publishers, Washington, DC. Giorgini, M., A. Miguez, K. S. Esquius, C. D. De Astarloa, O. Iribarne, E. Fanjul, and M. Escapa. 2019. Regenerative bioturbation by intertidal burrowing crabs modifies microphytobenthic composition and enhances primary production in SW Atlantic mudflats. Marine Ecology Progress Series 632:43–57. Hedges, L. V. 1981. Distribution Theory for Glass ’ s Estimator of Effect Size and Related Estimators. Journal of Educational Statistics 6:107–128. Lajeunesse, M. J., and M. R. Forbes. 2003. Variable reporting and quantitative reviews: A comparison of three meta-analytical techniques. Ecology Letters 6:448–454. Martinetto, P., G. Palomo, M. Bruschetti, and O. Iribarne. 2011. Similar effects on sediment structure and infaunal community of two competitive intertidal soft-bottom burrowing crab species. Journal of the Marine Biological Association of the United Kingdom 91:1385–1393. Moher, D., A. Liberati, J. Tetzlaff, and D. G. Altman. 2009. Academia and Clinic Annals of Internal Medicine Preferred Reporting Items for Systematic Reviews and Meta-Analyses : Annals of Internal Medicine 151:264–269. Moore, A. 2019. What is the role of ecosystem engineers in New England salt marshes? A mesocosm study of the fiddler crab and the purple marsh crab. Wetlands 39:371-379. Osenberg, C. W., O. Sarnelle, and S. D. Cooper. 1997. Effect size in ecological experiments: The application of biological models in meta-analysis. American Naturalist 150:798–812. Ouzzani, M., H. Hammady, Z. Fedorowicz, and A. Elmagarmid. 2016. Rayyan-a web and mobile app for systematic reviews. Systematic Reviews 5:210. Page, M. J., J. E. McKenzie, P. M. Bossuyt, I. Boutron, T. C. Hoffmann, C. D. Mulrow, L. Shamseer, J. M. Tetzlaff, E. A. Akl, S. E. Brennan, R. Chou, J. Glanville, J. M. Grimshaw, A. Hróbjartsson, M. M. Lalu, T. Li, E. W. Loder, E. Mayo-Wilson, S. McDonald, L. A. McGuinness, L. A. Stewart, J. Thomas, A. C. Tricco, V. A. Welch, P. Whiting, and D. Moher. 2021. The PRISMA 2020 statement: An updated guideline for reporting systematic reviews. BMJ 372:n71. Rinehart, S., J. M. Dybiec, B. Mortazavi, and J. A. Cherry. 2023. Stratified vertical sediment profiles increase burrowing crab effects on salt marsh edaphic conditions. Ecosphere 14:e4431. Rinehart, S., and D. Hawlena. 2020. The effects of predation risk on prey stoichiometry: a meta-analysis. Ecology 101:e3037. Rohatgi, A. 2022. WebPlotDigitizer. Pacifica, California. Walker, J. B., S. A. Rinehart, W. K. White, E. D. Grosholz, and J. D. Long. 2021. Local and regional variation in effects of burrowing crabs on plant community structure. Ecology 102:e03244. Wallace, B. C., M. J. Lajeunesse, G. Dietz, I. J. Dahabreh, T. A. Trikalinos, C. H. Schmid, and J. Gurevitch. 2017. OpenMEE: Intuitive, open-source software for meta-analysis in ecology and evolutionary biology. Methods in Ecology and Evolution 8:941–947. Wan, X., W. Wang, J. Liu, and T. Tong. 2014. Estimating the sample mean and standard deviation from the sample size, median, range and/or interquartile range. BMC Medical Research Methodology 14:1–13. Wang, X., Y. Li, B. Guan, J. Yu, Z. Zhang, H. Wu, and K. Zhang. 2020. Beneficial effects of crab burrowing on the surface soil properties of newly formed mudflats in the Yellow River Delta. Ecohydrology and Hydrobiology 20:548–555.
description: # Data from: Burrowing crab effects on the properties and functions of
 coastal soft sediments
 [https://doi.org/10.5061/dryad.3bk3j9kt3](https://doi.org/10.5061/dryad.3bk3j9kt3) Effect size calculations (including means, sample sizes, and standard deviation) of crab burrowing effects (i.e., high density vs low density) on the properties, nutrient stocks, and functions of coastal sediments. Data comes from studies conducted across Africa, Asia, Australia, North America, and South America. ## Description of the data and file structure **File list:** 1. Rinehart_et_al.202X_Effectsizes CSV file containing the Hedges d effect size calculations (including the raw means, sample sizes, and standard deviations) for each extracted comparison/study from all 59 manuscripts. Additional extracted data (e.g., crab taxa, experimental conditions, habitat, burrow density) are also included for each comparison/study. 2. Rinehart_et_al.202X_Publicationbias CSV file containing the pooled standard deviation and the Hedges d effect size calculation for each comparison/study. This datafile was used to conduct analyses of publication bias for a resulting systematic meta-analysis. **Data-specific information for:** (1) Rinehart_et_al.202X_Effectsizes **Number of variables:** 47 **Number of cases/rows:** 1423 Variable List:  1. id: the unique code assigned to each data row. 2. reference: author, year, and journal for each data source. 3. pub_year: year of reference publication. One in preparation study was included in the dataset (Rinehart et al. 20XX), it's publication year is denoted as 20XX. 4. paper id: the unique code assigned to each manuscript included in the dataset. 5. continent: the continent where the data was collected. 6. country: the country where the data was collected. 7. state: the state (united states only) where the data was collected. 8. estuary: the name of the estuary where the data was collected. 9. latitude_dd: the latitude associated with the data collected in decimal degrees (dd). 10. longitude_dd: the longitude associated with the data collected in decimal degrees (dd). 11. ecosystem: the type of ecosystem (e.g., salt marsh, mangrove forest, tidal flat) associated with the collected data. 12. vegetation: categorical variable noting the presence (vegetated) or absence (not unvegetated) of any vegetation. 13. ecosystem_type: categorical variable noting if the ecosystem was restored, created, or natural. 14. relative_salinity: categorical variable noting the relative salinity in the ecosystem where the data was collected. 15. tidal_amplitude_m: the tidal amplitude (in meters) in the ecosystem where the data was collected. 16. tidal_cycle: categorical variable noting the type of tidal cycle (e.g., diurnal) in the ecosystem where the data was collected. 17. soil_type: categorical variable noting the soil type (e.g., sand) in the ecosystem where the data was collected. 18. elevation_m: the elevation (in meters) of the ecosystem where the data was collected. 19. study_duration_d: the length of time (in days) that the study ran (applies mainly to manipulative studies). 20. study_timing: the seasons or months during which the study was run. 21. dominant_plant_genus: the genus of the dominant plant present in the ecosystem where the data was collected. 22. dominant_plant_species: the species of the dominant plant present in the ecosystem where the data was collected. 23. dominant_plant_functional_group: categorical variable noting the functional group (e.g., grass) of the dominant plant species in the ecosystem where the data was collected. 24. crab_genus: the genus of the dominant burrowing crab used in the study. Studies with mixed crab communities are denoted with by "mixed". 25. crab_species: the species of the dominant burrowing crab used in the study. Studies with mixed crab communities are denoted with by "mixed". 26. crab_diet: categorical variable noting the main feeding strategy (e.g., herbivore, detritivore) used by the dominant crab species. 27. crab_superfamily: the superfamily of the dominant burrowing crab used in the study. Studies with mixed crab communities are denoted with by "mixed". 28. mean_burrow_diameter_high_crab_treatment_mm: the mean burrow diameter in the study's high crab treatment in mm. 29. mean_burrow_diameter_low_crab_treatment_mm: the mean burrow diameter in the study's low crab treatment in mm. 30. mean_burrow_depth_cm: the mean burrow depth in cm reported by the study. 31. burrow_density_high_crab_m^2: the mean crab burrow density per meter-squared reported in the study's high crab treatment. 32. burrow_density_low_crab_m^2: the mean crab burrow density per meter-squared reported in the study's low crab treatment. 33. experiment_type: categorical variable noting if the study used observational or manipulative methodologies. 34. experiment_setting: categorical variable noting if the study was conducted in a laboratory or field setting. Laboratory studies also include outdoor mesocosm studies. 35. field_location: categorical variable noting where studies conducted in the field placed their study relative to the shoreline. Specifically, we noted if studied sampled in the ecosystem interior (far from shoreline) or at the ecosystem edge (adjacent to the shoreline). 36. soil_depth_cm: the depth, in cm, within the soil profile from which the sediment samples were collected. 37. soil_characteristic_measured: categorical variable identifying the specific sediment property, nutrient stock, or function that was quantified by the study. 38. soil_characteristic_units: the original units used to quantify the soil characteristic within the study. 39. mean_low_crab: the mean value of the soil characteristic measured in the low crab treatment within the study. 40. sd_low_crab: the standard deviation of the soil characteristic measured in the low crab treatment within the study. 41. n_low_crab: the sample size of the soil characteristic measured in the low crab treatment within the study. 42. mean_high_crab: the mean value of the soil characteristic measured in the high crab treatment within the study. 43. sd_high_crab: the standard deviation of the soil characteristic measured in the high crab treatment within the study. 44. n_high_crab: the sample size of the soil characteristic measured in the high crab treatment within the study. 45. crab_density: categorical variable noting if the study documented relative burrowing crab density within their study using burrow density (burrow) or counts of individuals (individuals). 46. hedges_d: the hedges d effect size calculated for the effects of burrowing crabs on the measured sediment characteristic. Hedges d values were calculated in OpenMee software (see code/software below). Positive effect sizes indicate that burrowing crabs increased the value of the sediment measurement, while negative effect sized indicate that burrowing crabs decreased the value of the sediment measurement. 47. hedges_d_var: the variation of the hedges d effect size calculated for the effects of burrowing crabs on the measured sediment characteristic. Hedges d variation values were calculated in OpenMee software (see code/software below). **Missing data codes:** na Data-specific information for: (2) Rinehart_et_al.202X_Publicationbias ***Number of variables:*** 22 ***Number of cases/rows:*** 1423 Variable List:  1. id: the unique code assigned to each data row. 2. reference: author, year, and journal for each data source. 3. pub_year: year of reference publication. One in preparation study was included in the dataset (Rinehart et al. 20XX), it's publication year is denoted as 20XX. 4. paper id: the unique code assigned to each manuscript included in the dataset. 5. ecosystem: the type of ecosystem (e.g., salt marsh, mangrove forest, tidal flat) associated with the collected data. 6. vegetation: categorical variable noting the presence (vegetated) or absence (not unvegetated) of any vegetation. 7. crab_superfamily: the superfamily of the dominant burrowing crab used in the study. Studies with mixed crab communities are denoted with by "mixed". 8. burrow_density_high_crab_m^2: the mean crab burrow density per meter-squared reported in the study's high crab treatment. 9. experiment_type: categorical variable noting if the study used observational or manipulative methodologies. 10. experiment_setting: categorical variable noting if the study was conducted in a laboratory or field setting. Laboratory studies also include outdoor mesocosm studies. 11. soil_characteristic_measured: categorical variable identifying the specific sediment property, nutrient stock, or function that was quantified by the study. 12. soil_characteristic_units: the original units used to quantify the soil characteristic within the study. 13. mean_low_crab: the mean value of the soil characteristic measured in the low crab treatment within the study. 14. sd_low_crab: the standard deviation of the soil characteristic measured in the low crab treatment within the study. 15. n_low_crab: the sample size of the soil characteristic measured in the low crab treatment within the study. 16. mean_high_crab: the mean value of the soil characteristic measured in the high crab treatment within the study. 17. sd_high_crab: the standard deviation of the soil characteristic measured in the high crab treatment within the study. 18. n_high_crab: the sample size of the soil characteristic measured in the high crab treatment within the study. 19. pooled_sd: the pooled standard deviation of the high and low crab treatments for each study. 20. crab_density: categorical variable noting if the study documented relative burrowing crab density within their study using burrow density (burrow) or counts of individuals (individuals). 21. hedges_d: the hedges d effect size calculated for the effects of burrowing crabs on the measured sediment characteristic. Hedges d values were calculated in OpenMee software (see code/software below). Positive effect sizes indicate that burrowing crabs increased the value of the sediment measurement, while negative effect sized indicate that burrowing crabs decreased the value of the sediment measurement. 22. hedges_d_var: the variation of the hedges d effect size calculated for the effects of burrowing crabs on the measured sediment characteristic. Hedges d variation values were calculated in OpenMee software (see code/software below). **Missing data codes:** na ## Sharing/Access information All data are included in the provided datafiles. ## Code/Software Hedges’ *d* (hereafter, *d*) effect sizes were calculated using meta-analysis using OpenMEE software (Build date: 26 July 2016; Wallace et al. 2017). Wallace, B. C., M. J. Lajeunesse, G. Dietz, I. J. Dahabreh, T. A. Trikalinos, C. H. Schmid, and J. Gurevitch. 2017. OpenMEE: Intuitive, open-source software for meta-analysis in ecology and evolutionary biology. Methods in Ecology and Evolution 8:941–947.