Coral reef benthic and fish monitoring data from Turneffe Atoll, Belize, 2010-2023

Boles, Jessica C.1 ; Martinez, Ninon1 ; Salazar, Jané1 ; Novelo, Kevin2 ; Alamina, Victor1 ; Galvez, Galento1 ; Young, Bonnie1 ; Romero, Allan1 ; Craig, Nicole1 ; Ugarte, Gabriela1 ; Bardalez, Stavros1 ; Borland, Joshua1 ; Blanco, Ivanna1 ; Gongora, Ronny1 ; Barona, Tanya1 ; Alamina, Elias1 ; Lizama, Anthony1 ; McLaughlin, Daniel2 ; Figueroa, Vanessa1 ; Maza, Fara2 ; Cho-Ricketts, Leandra1 ; Snaddon, Jake L.1

Published Mar 06, 2024 on Dryad. https://doi.org/10.5061/dryad.c866t1gcn

Data files

Mar 06, 2024 version files 97.49 MB

Master_Benthic_Inverts_2010-2023.csv

756.61 KB
Master_Benthic_PIM_2010-2023.csv

15.37 MB
Master_Coral_Community_2010-2021.csv

1.57 MB
Master_Fish_Survey_2010-2023.csv

79.74 MB
README.md

32.95 KB
Ref_Collectors_Turneffe.csv

775 B
Ref_Diseases_Coral.csv

590 B
Ref_Fish_Species.csv

8.43 KB
Ref_Organisms_Benthic.csv

19.38 KB
Ref_Sites_Turneffe.csv

1.93 KB

Abstract

Coral reefs are crucial centres of biodiversity, sustaining diverse marine species and providing ecosystem services to coastal communities. Monitoring coral reefs allows us to assess how the reefs are changing over time, discerning the potential impact of environmental changes, human activities, and climate events on their health and biodiversity. Here, we present a collection of data obtained through methodologies from the Mesoamerican Barrier Reef Systems Synoptic Monitoring Program (MBRS SMP) and Atlantic and Gulf Rapid Reef Assessment (AGRRA) protocols, including data of benthic point-intercept and invertebrate surveys, coral community characterizations, and reef fish surveys. The dataset encompasses observations spanning the years 2010 to 2023 within Turneffe Atoll Marine Reserve, Belize. By publishing this dataset, we aim to provide a resource for research endeavours related to coral reef dynamics and broader ecological trends. Use of this monitoring data supports the evolution of Turneffe Atoll Marine Reserve as a Marine Protected Area, contributing to informed decision-making and management strategies for the conservation of this vital ecosystem.

README: Coral Reef Benthic and Fish Monitoring Data from Turneffe Atoll, Belize, 2010-2023

Access this dataset on Dryad

Our dataset encompasses coral reef field data collected from Turneffe Atoll Marine Reserve, Belize, spanning the years 2010 to 2023. Using four distinct survey methods---benthic point intercept, benthic belt transect invertebrate, coral community characterization, and reef fish belt transect---the data were gathered along transects at various localities around the atoll, with individual sites targeting specific reef structures, including backreef, deep forereef, and shallow forereef. Data were validated with custom validation rules created in R Statistical Software.

Description of the data and file structure

Nine total data files are included in this dataset. Four files contain survey data, and five files contain supplementary information. Metadata for each file are provided below, including an explanation of each measured parameter, and in some cases, units of measurement and formatting rules. A tenth file, which contains an R script, provides the full code used to evaluate whether each measurement properly adheres to the rules of each column.

Within the dataset, MISSING values are used to represent unknown or unavailable values. Some parameters were only measured in certain years, and some data were lost or unreadable, resulting in these missing values. NA values are used when a parameter is not applicable in certain cases, such as algae height not being applicable to a coral organism.

File #1: Reef Benthic PIM Survey

DataFileName = 'Master_Benthic_PIM_2010-2023.csv'\
ProjectYears = 2010-2018, 2021, 2023\
CollectionProtocol = Point-intercept method from MBRS Manual, pg. 27^1^, and AGRRA benthic protocol^2,3^

Each row of this file represents a single point along a unique transect.

Parameter	Units	Description	Rules
Year	None	Year data were collected	Valid year (2010-2018, 2021 or 2023) in format YYYY
Date	None	Date data were collected	Format YYYY-MM-DD with the same year as Year
Site	None	Site where data were collected	From list of valid sites in Sites Turneffe data
Transect	None	Transect at which data were collected at that Site during that Year	Integer from 1-6
Uniq_Transect	None	Unique transect at which the data were collected	Format year.B.site.transect, where year is Year, site Site, and transect Transect
Protocol	None	Protocol data were collected under	MBRS for Year 2010-2018, or AGRRA for Year 2021-2023
Start_Time	None	Time at which data collection begins at that Site during that Year	Format must be 24 hour HH:MM
Start_Depth	m	Depth at start of the Transect	Integer from 1-60
End_Depth	m	Depth at end of the Transect	Integer from 1-60
Temp	°C	Bottom temperature at Site during that Year	Integer from 25-35
Point	m	Point along the transect at which data were collected	Point must be a multiple of 0.25 for 2010-2018, multiple of 0.1 for 2021-2023
Organism	None	Organism found directly below transect tape at that specific Point	Must be a an Organism from Organisms Benthic data
Algae_Height	cm	Height of algae Organism	Integer from 0-300 if the Organism of that row has Height = Yes in Organisms Benthic data
Bleaching	None	Bleaching status of coral Organism; P for pale, BL for bleached, UB for unbleached	P, BL, or UB if the Organism of that row has Bleaching = Yes in Organisms Benthic data
ND_A	None	Whether an Organism is alive or newly dead; A for alive, ND for newly dead	ND or A if the Organism of that row has ND_A = Yes in Organisms Benthic data
Cloud_Cover	None	Cloud cover at time of sampling	Integer from 0-8, where 0 is least cover and 8 is most
Collector	None	Collector code that corresponds to field data collector of Observations	From list of valid collector codes in Collectors Turneffe data
Notes	None	Any additional notes	Any string of text

File #2: Reef Benthic Invertebrates Survey

DataFileName = 'Master_Benthic_Inverts_2021-2023.csv'\
ProjectYears = 2010-2015, 2017, 2018, 2021, 2023\
CollectionProtocol = Fish method including Diadema urchin counts from MBRS Manual, pg. 30^1^, and AGRRA benthic protocol^3^

This file is structured so that each unique transect is allocated a row for each of the six surveyed benthic invertebrate types. If a specific invertebrate is absent on a given transect, it is assigned an observation number, Num, of 0. If the invertebrate type was not being observed during a particular year, it is denoted with a Num of MISSING.

Parameter	Units	Description	Rules
Year	None	Year data were collected	Valid year (2010-2015, 2017, 2018, 2021 or 2023) in format YYYY
Date	None	Date data were collected	Format YYYY-MM-DD with the same year as Year
Site	None	Site where data were collected	From list of valid sites in Sites Turneffe data
Transect	None	Transect at which data were collected at that Site during that Year	Integer from 1-8
Uniq_Transect	None	Unique transect at which the data were collected, matching either the fish (F) transect or benthic PIM (B) transect	Format year.B.site.transect or year.F.site.transect, where year is Year, site Site, and transect Transect
Protocol	None	Protocol data were collected under	MBRS for Year 2010-2018, or AGRRA for Year 2021-2023
Start_Time	None	Time at which data collection begins at that Site during that Year	Format must be 24 hour HH:MM
Temp	°C	Bottom temperature at Site during that Year	Integer from 25-35
Species	None	Species of invertebrate that may be found on the transect	DiademaJuv, Diadema (adult D. antillarum ), OtherUrchins, Lobster, Conch, or Cucumbers
Num	None	Number of that Species found on the transect	Integer from 0-100
Collector	None	Collector code that corresponds to field data collector of Observations	From list of valid collector codes in Collectors Turneffe data
Notes	None	Any additional notes	Any string of text

File #3: Coral Community Characterization

DataFileName = 'Master_Coral_Community_2010-2021.csv'\
ProjectYears = 2010-2018, 2021\
CollectionProtocol = Coral method from MBRS Manual, pg. 27^1^, and AGRRA coral protocol^4^

This file is organized so that each row represents a single observed coral organism.

Parameter	Units	Description	Rules
Year	None	Year data were collected	Valid year (2010-2018, or 2021) in format YYYY
Date	None	Date data were collected	Format YYYY-MM-DD with the same year as Year
Site	None	Site where data were collected	From list of valid sites in Sites Turneffe data
Transect	None	Transect at which data were collected at that Site during that Year	Integer from 1-5
Uniq_Transect	None	Unique transect at which the data were collected	Format year.C.site.transect, where year is Year, site Site, and transect Transect
Protocol	None	Protocol data were collected under	MBRS for Year 2010-2018, or AGRRA for Year 2021
Start_Time	None	Time at which data collection begins at that Site during that Year	Format must be 24 hour HH:MM
Start_Depth	m	Depth at start of the Transect	Integer from 1-60
End_Depth	m	Depth at end of the Transect	Integer from 1-60
Temp	°C	Bottom temperature at Site during that Year	Integer from 25-35
Organism	None	Organism found directly below transect tape at that specific Point	Must be an Organism from Organisms Benthic data
Isolates	None	FR for fragment, CL for clump, or number soft tissue isolates if colony/solitary	Must be FR, CL, or integer from 0-20
Depth_Top	m	Water depth at the highest point of the coral	Numeric from 0.1-50
Max_Diam	cm	Maximum projected diameter (live and dead areas) in plan view of the coral	Integer from 1-500
Max_Length	cm	Maximum length perpendicular to the axis of growth of the coral	Integer from 1-500
Max_Width	cm	Maximum width at right angles to the maximum length of the coral	Integer from 1-500
Max_Height	cm	Maximum height parallel to the axis of growth of the coral	Numeric from 0.1-1, or integer from 1-500
OD	Percent	Percent of the coral that has old mortality	Integer from 0-100
TD	Percent	Percent of the coral that has transitional mortality	Integer from 0-100
RD	Percent	Percent of the coral that has recent mortality	Integer from 0-100
Disease	None	Code for a disease observed on the coral	Must be a Disease code from Disease Coral data
Percent_Pale	Percent	Percent of the coral that is pale	Integer from 0-100
Percent_Bleach	Percent	Percent of the coral that is bleaching	Integer from 0-100
Bleaching	None	Discoloration; P for pale, PB for partly bleached, BL for bleached, UB for unbleached	Must be P, BL, PB, or UB
Collector	None	Collector code that corresponds to field data collector of Observations	From list of valid collector codes in Collectors Turneffe data
Notes	None	Any additional notes	Any string of text

File #4: Reef Fish Survey

DataFileName = 'Master_Fish_Survey_2010-2023.csv'\
ProjectYears = 2010-2015, 2017, 2018, 2021, 2023\
CollectionProtocol = Fish belt transect method from MBRS Manual, pg. 30^1^, and AGRRA fish belt transect protocol^5^

The data in this file is systematically arranged, wherein each unique transect is allocated a designated row for every combination of fish species and size class under investigation that year. To illustrate, if a specific transect is targeted that year for the observation of lionfish in the 0-5cm size range, and none are identified during the survey, the corresponding row is retained with the observation count denoted as '0.' Detailed listings of the targeted fish species and associated years can be referenced in the Fish Species reference sheet.

Parameter	Units	Description	Rules
Year	None	Year data were collected	Valid year (2010-2015, 2017, 2018, 2021 or 2023) in format YYYY
Date	None	Date data were collected	Format YYYY-MM-DD with the same year as Year
Site	None	Site where data were collected	From list of valid sites in Sites Turneffe data
Transect	None	Transect at which data were collected at that Site during that Year	Integer from 1-12
Uniq_Transect	None	Unique transect at which the data were collected	Format year.F.site.transect, where year is Year, site Site, and transect Transect
Protocol	None	Protocol data were collected under	MBRS for Year 2010-2018, or AGRRA for Year 2021-2023
Start_Time	None	Time at which data collection begins at that Site during that Year	Format must be 24 hour HH:MM
Start_Depth	m	Depth at start of the Transect	Integer from 1-60
End_Depth	m	Depth at end of the Transect	Integer from 1-60
Max_Relief	cm	Terrain height variation in 1m radius circles at 5m intervals along Transect	Integer series, each integer a multiple of 5cm, integers separated by periods
Temp	°C	Bottom temperature at Site during that Year	Integer from 25-35
Fish	None	Common name of fish	Must be a fish surveyed that Year, according to Fish Species data
Fish_Scientific	None	Scientific name of fish	Must be latin binomial for that Fish, according to Fish Species data
Size_Class	cm	Fish size grouping	Either 0_05, 05_10, 10_20, 20_30, 30_40, or 40
Observations	None	Number Fish observed of that Size_Class at that Uniq_Transect	Integer from 0-500
Cloud_Cover	None	Cloud cover at time of sampling	Integer from 0-8, where 0 is least cover and 8 is most
Sea_Conditions	None	Sea conditions at time of sampling, either Calm, Moderate, or Choppy	Either Calm, Moderate, or Choppy
Collector	None	Collector code that corresponds to field data collector of Observations	From list of valid collector codes in Collectors Turneffe data
Notes	None	Any additional notes	Any string of text

File #5: Collectors

DataFileName = 'Ref_Collectors_Turneffe.csv'\
ProjectYears = 2010-2018, 2021, 2023

Parameter:	Description:
Collector	The code which references a specific collector, including the first 2 letters of given name and first 2 letters of surname
Name	The full name, if available, of the collector to which the code refers

File #6: Coral Diseases

DataFileName = 'Ref_Diseases_Coral.csv'\
ProjectYears = 2010-2018, 2021, 2023

Parameter:	Description:
Disease	A code representing a specific kind of disease for coral
Name	Name of the disease for that code
Notes	Any notes about the disease code or disease by the data collector(s), compiler, or analyst

File #7: Fish Species

DataFileName = 'Ref_Fish_Species.csv'\
ProjectYears = 2010-2018, 2021, 2023

Parameter:	Description:
Fish	The common English name of a fish species
Fish_Scientific	The scientific name of that fish species
Fish_Family	The taxonomic family within which the fish species belongs
Status_2023	The status of the fish taxonomic species as of 2023. Status collected from the WoRMS database, WoRMS. Whether it is Accepted or Unaccepted as a taxonomic name for the species.
Aphia_ID	The ID given to the fish species on the WoRMS database; used to tie species to specific literature and attributes, WoRMS
GBIF_ID	The ID given to the fish species on the GBIF database; used to tie species to occurrence/distribution datasets worldwide, GBIF
List_2010	Whether the fish species was included in the list during 2010 surveying
List_2011	Whether the fish species was included in the list during 2011 surveying
… (cont.)	… (cont.)
List_2023	Whether the fish species was included in the list during 2023 surveying
Notes	Any notes about the fish by the data collector(s), compiler, or analyst

File #8: Benthic Organism Codes

DataFileName = 'Ref_Organisms_Benthic.csv'\
ProjectYears = 2010-2018, 2021, 2023

Parameter:	Description:
Organism	The code corresponding to a particular organism or non-living substrate in the benthic zone, at the point directly below the transect
Bucket	A bucket category used to classify the organism codes so to standardize across years, collectors, and protocols
Bucket_Name	Description of organisms included in the bucket
Bucket2	An alternative bucket category used to classify the organism codes so to standardize across years, collectors, and protocols
Bucket2_Name	Description of organisms included in the alternative bucket
AGRRA_Bucket	Bucket category used by AGRRA to classify the organism codes so to standardize across years, collectors, and protocols
AGRRA_Code	The code typically used in AGRRA protocol for that organism. May be found in raw or unprocessed data sheets. Codes used may vary by collector and year, however.
MBRS_Code	The code typically used in MBRS protocol for that organism. May be found in raw or unprocessed data sheets. Codes used may vary by collector and year, however.
Org_Name	A description of the organism or non-living substrate
Aphia_ID	The AphiaID from the WoRMS database for that Organism, if applicable; used to tie taxonomic groups to specific literature and attributes, WoRMS
GBIF_ID	The ID given to the taxonomic group on the GBIF database; used to tie species to occurrence/distribution datasets worldwide, GBIF
IUCN_ID	The ID given to the taxonomic group on the IUCN database; used to tie species to redlist dataset , IUCN
Height?	Whether algae height should be recorded for this organism in benthic PIM methods
Bleaching	Whether bleaching should be recorded for this organism in benthic PIM methods
ND_A	Whether ND_A should be recorded for this organism in benthic PIM methods

File #9: Sites

DataFileName = 'Ref_Sites_Turneffe.csv'\
ProjectYears = 2010-2018, 2021, 2023

Parameter:	Description:
Site	The site at which the data were collected, in a unique code format
Locality	The locality to which the site belongs
Reef_Zone	The reef zone for that site, either Backreef, Deep_Forereef , or Shallow_Forereef. Backreef is leeward facing (<3m), Deep\_Forereef is windward (>10m), Shallow_Forereef is windward (3-10m)
Management_Zone	The management zone in which the site is found, either Atoll, SpecialManagement, or Conservation
Latitude	The latitude coordinate at which the site is found, in decimal format
Longitude	The longitude coordinate at which the site is found, in decimal format
Notes	Any additional notes by the data collector(s), compiler, or analyst

File #10: Validation Script

RScriptName = 'Validation.Rmd'

References

1. Almada-Villela, P. C., Sale, P. F., Gold-Bouchot, G. & Kjerfve, B. Manual of methods for the MBRS synoptic monitoring program: Selected methods for monitoring physical and biological parameters for use in the Mesoamerican region. Link to Document (2003).

2. Lang, J. C., Marks, K. W., Kramer, P. A., Kramer, P. R. & Ginsburg, R. N. AGRRA Benthos Protocol. Summary Instructions. Link to Document (2016).

3. Atlantic and Gulf Rapid Reef Assessment. AGGRA Benthos Protocol. Summary Instructions, April 2021 Updated. Link to Document (2021).

4. Lang, J. C., Marks, K. W., Kramer, P. A., Kramer, P. R. & Ginsburg, R. N. AGGRA Detailed Fish Protocol. Instructions for Use, June 2016. Link to Document (2016).

5. Atlantic and Gulf Rapid Reef Assessment. AGGRA Coral Protocol. Summary Instructions, April 2021. Link to Document (2021).

Methods

Our dataset consists of data collected for four surveys (benthic point-intercept-method (PIM), benthic invertebrates, coral community, and reef fish) carried out at the Turneffe Atoll Marine Reserve in Belize, annually between the years of 2010-2018, and biennially between 2021-2023. For our annual surveys from 2010-2018, we followed the Mesoamerican Barrier Reef System Synoptic Monitoring Program (MBRS SMP) protocol¹. For 2021 and 2023, our data collection followed the Atlantic and Gulf Rapid Reef Assessment (AGRRA) protocol^2-6. The change in protocol between 2018 and 2021 is due to the National adoption of the AGRRA protocol for coral reef monitoring in Belize⁷. The two protocols are very similar, as the MBRS SMP was based on AGRRA and Caribbean Coastal and Marine Productivity (CARICOMP) protocols¹.

Between 2010-2021, we archived our collected data in Excel sheets, stored locally at the UB-ERI. Under UB-ERI guidance, volunteers digitized the data, entering it into tabular data format from waterproof data collection sheets used in the field. In 2023, we transformed the data format according to tidy data principles⁸, and FAIR data principles⁹ using R Statistical Software¹⁰. We wrote custom validation rules in R, which allowed us to feed our data in and receive a report on any cell that violated a rule, such as a temperature measurement in Fahrenheit instead of Celcius. We then manually investigated each flagged cell to consider individually whether we should fix or exclude the measurement.

Citations:

Almada-Villela, P. C., Sale, P. F., Gold-Bouchot, G., & Kjerfve, B. (2003). Manual of methods for the MBRS synoptic monitoring program: Selected methods for monitoring physical and biological parameters for use in the Mesoamerican region (Protocol 4; p. 155). Mesoamerican Barrier Reef Systems Project. https://rris.biopama.org/sites/default/files/2021-03/MBRS%20synoptic%20monitoring.pdf
Lang, J., Marks, K., Kramer, P., Kramer, P., & Ginsburg, R. (2010). Agrra protocols version 5.4. ReVision A Journal of Consciousness and Transformation.
Lang, J. C., Marks, K. W., Kramer, P. A., Kramer, P. R., & Ginsburg, R. N. (2016a). AGRRA Benthos Protocol. Summary Instructions. (Protocol Revision 2016-09-12; p. 3). Atlantic and Gulf Rapid Reef Assessment. https://www.agrra.org/wp-content/uploads/2016/06/AGRRA-Benthos-Protocol.pdf
Lang, J. C., Marks, K. W., Kramer, P. A., Kramer, P. R., & Ginsburg, R. N. (2016b). AGGRA Detailed Fish Protocol. Instructions for Use, June 2016. (Revision 2016-09-12; p. 2). Atlantic and Gulf Rapid Reef Assessment. https://www.agrra.org/wp-content/uploads/2021/05/AGRRA-Fish-Protocol_June-2016.pdf
AGRRA. (2021a). AGGRA Benthos Protocol. Summary Instructions, April 2021 Updated. (Revision 2021-04-12; p. 4). Ocean Research & Education. https://agrra.org/wp-content/uploads/2021/05/AGRRA-Benthos-Protocol-April_13_2021.pdf
AGRRA. (2021b). AGGRA Coral Protocol. Summary Instructions, April 2021. (Revision 2021-04-12; p. 5). Ocean Research & Education. https://agrra.org/wp-content/uploads/2021/05/AGRRA-Coral-Protocol-April_13_2021.pdf
McField, M., & Craig, N. (2018, February 28). Healthy Reefs letter to Belize Fisheries Department
Wickham, H. (2014). Tidy Data. Journal of Statistical Software, 59(10). https://doi.org/10.18637/jss.v059.i10
Wilkinson, M. D., Dumontier, M., Aalbersberg, Ij. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., Da Silva Santos, L. B., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R., … Mons, B. (2016). The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data, 3(1), 160018. https://doi.org/10.1038/sdata.2016.18
R Core Team. (2023). R: A Language and Environment for Statistical Computing (version 4.3.1) [Computer software]. R Foundation for Statistical Computing. https://www.R-project.org