1 Introduction: Cape Falcon SCUBA Fish Surveys
SCUBA fish sampling monitors the density of select benthic fish species, following PISCO modified protocols, at depths between 10-20m. Midwater and canopy fishes are not included in Oregon Marine Reserves monitoring. Fish are counted along a 30 x 2 m belt transects across three target depths, 10, 15 and 20 meters. Species write-ins are allowed for species not specifically identified on PISCO datasheets.
Our SCUBA Fish sampling at Cape Falcon began in 2016, the year harvest restrictions began. Sampling attempts were made in 2015 but did not result in data collection due to poor visibility and challenging weather conditions. Sampling is conducted in the marine reserve and three comparison areas that represent varying levels of fishing pressure (see methods Appendix for additional information about comparison area selection). We conducted two years of sampling that are included in our analysis and report. Note, we were not able to successfully collect data in the comparison areas, and only one at that, until 2017.
Data from SCUBA fish monitoring efforts can be used to explore questions about fish diversity, community composition and density. Questions about diversity and community composition can be used to compare across monitoring tools to understand tool bias or to validate trends seen across tools. This can further help us understand how the fish communities at these sites are similar or different. Data on density enable us to explore changes over time; and whether these changes are similar both inside the reserve and outside in comparison areas. For all data our main focus is exploring trends by site and year.
1.1 Survey Maps
1.1.1 Cape Falcon Marine Reserve
Fig. 14: Map of SCUBA transect locations at Cape Falcon Marine Reserve
1.1.2 Moderate Fishing Pressure Comparison Area
Fig. 14: Map of SCUBA transect locations at Moderate Fishing Pressure Comparison Area
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1.2 Research Questions
Diversity
- Does species diversity vary by site or year?
Community Composition
- Does community composition vary by site or year?
- If yes, what species drive this variation?
Aggregate Abundance
- Does aggregate density vary by site or year?
Focal Species Abundance
- Does focal species density vary by site or year?
- Does focal species size vary by site or year?
2 Takeaways
Here we present a summary of our SCUBA fish monitoring results and our conclusions. Our conclusions are written with an evaluation of our sampling design, knowledge from prior marine reserves monitoring reports, and future directions of marine reserves monitoring in mind.
More effort needed on SCUBA fish surveys to determine differences by site and year for all analyses.
Additional SCUBA fish surveys are needed to determine differences by site and year for species diversity, community composition and abundance at the Cape Falcon Marine Reserve and its associated comparison areas. No successful fish surveys occurred at the Low or High Fishing Pressure Comparison Areas over the three years of attempted surveys. The Low Fishing Pressure Comparison Area is the appropriate comparison area for the Cape Falcon Marine Reserve based on similar rocky hard bottom habitat and historical fishing pressure. Without any successful SCUBA fish surveys in this area, it is hard to characterize the fish community at this site and evaluate if it is an appropriate reference site for the Cape Falcon Marine Reserve to assess change over time. Furthermore, the limited transects that were completed at the marine reserve and Moderate Fishing Pressure Comparison Area require additional surveys to appropriately characterize the fish communities at these sites (only 3 fish species were observed at each site) and successfully detect future changes at these sites. Limited sample sizes were a result of poor visibility and few survey opportunities at this site. Access to all four sites was challenging because of logistics related to a small boat based survey method in Oregon’s nearshore environment and the challenge to implement monitoring across all marine reserve sites with limited staff.
3 SCUBA Fish Methods
SCUBA fish sampling is conducted in the Cape Falcon Marine Reserve and its three associated comparison areas (Low, Moderate, High Fishing Pressure Areas) following PISCO protocols, modified for diving safety in Oregon. Monitoring attempts began in Cape Falcon Marine Reserve and its comparison areas in 2016, but only resulted in data from the marine reserve and Moderate Fishing Pressure Area due to poor visibility on sampling days. Attempts in 2017 resulted in data collection only in the Moderate Fishing Pressure Comparison Area, again due to poor visibility during surveys days. Sampling effort targeted 2 days for both spring and fall monitoring, splitting effort between the marine reserve and its comparison areas based on ocean conditions. Survey dives began at least one hour after sunrise and conclude one hour before sunset to avoid the crepuscular period. Two to three replicate transects were completed during a given dive,spaced 2m apart, at similar depths, depending on bottom time. All fish are identified to species and total length (cm), except small sculpins and gobies < 8 cm.
The purpose of fish sampling is to generate densities of select species at depths between 10-20m. Multiple transects are completed across three target depths 10, 15 and 20 m. Fish surveys target benthic fishes only - midwater and canopy fishes are not included in Oregon Marine Reserves monitoring. Fish surveys are conducted on separate dives from algae and invertebrate surveys at each site due to time limitations of data collection and to reduce sampling artifacts from diver attraction / repulsion of fishes. No kelp habitat is located in the Cape Falcon Marine Reserve and its associated comparison areas, so dive site locations were randomly generated from available habitat within the targeted depth ranges.
The unit of replication is at the transect level. Only fully completed, independent transects were included in analysis. For additional details on data collection, please review documentation in the Methods Appendix.
3.1 Diversity
With SCUBA fish surveys, we explored several concepts related to species diversity at a given site:
- species richness
- unique, common & rare species
- diversity indices
3.1.1 Species Richness
To explore species richness at a given site, we reported total observed species richness and also calculated total estimated species richness.
To report total observed species richness at a given site we used incidence data across all sampling years because each site (reserve or comparison area) likely has a species pool larger than can be sampled in any one year. We excluded unidentified species from the summaries.
To calculate estimated species richness, we used a rarefaction and extrapolation technique as described in Hsieh et al 2016, to calculate the effective number of species at each given site. This is the equivalent of calculating Hill diversity = 0. Hill numbers represent a unified standardization method for quantifying and comparing species diversity across multiple sites (Hill 1973), and they represent an intuitive and statistically rigorous alternative to other diversity indices (Chao et al 2014).
We used the same sampling based incidence data as used to document total observed species richness, using the iNext package in R to estimate the asymptote of the species accumulation curve, or the estimated total number of species observable by SCUBA surveys at a given site. We also calculated confidence intervals associated with these rarefaction and extrapolation curves and can therefore compare across sites to explore similarity of total estimated species richness for a given sampling effort.
3.1.2 Unique, Common, and Rare Species
Richness alone does not sufficiently describe species biodiversity; additionally uniqueness, rarity and common species also shape and define concepts of biodiversity.
As a first step to exploring unique, rare and common species we generated species count tables. These tables exclude the unidentified individuals. The species count tables include a total count for each species summed for all years by site, and for each year-site combination, as well as mean frequency of occurrence across all samples. This information can tell us both about how frequently the species is observed, as well as its relative abundance.
From the species count tables we identified rare species, as those with a frequency of occurrence of 10% or less (Green and Young 1993), and common species as those with a frequency of occurrence greater than 50% (in other words, the species is observed on one out of every two transects). We also identified species that were unique to each marine reserve and comparison area.
3.1.3 Diversity Indices
To gain additional insight into species diversity, we explored several diversity indices by comparing Hill diversity numbers across sites using the iNEXT diversity package in R (Hsieh et al 2016). Hill numbers are parameterized by a diversity order q, which determines the measures’ sensitivity to species relative abundances (Hsieh et al 2016). Hill numbers include the three most widely used species diversity measures; species richness (q = 0), Shannon diversity (q=1) and Simpson diversity (q=2) (Hsieh et al 2016). We used sampling based incidence data with the iNext package in R, to plot rarefaction and extrapolation curves for each Hill number, and compare results across sites. We also calculated 95% confidence intervals associated with these rarefaction & extrapolation curves.
All analyses and graphs were created in R v4.0.2, using the iNEXT and Vegan packages.
3.2 Community Composition
We focused our community composition analysis on the question of whether variation in fish density was driven by spatial (site) factors. We did this through both data visualizations with non-multidimensional scaling (nMDS) plots and with vector analysis of fish species in the community, selecting only the species with > 0.5 Pearson correlations (Hinkle et al. 2003). Due to low sample sizes obtained at Cape Falcon Marine Reserve and its associated comparison areas, we did not perform statistical analyses.
To explore variation by site, we used fish density data collected on SCUBA fish transects with a square root transformation to downweight dominant species without overly enhancing importance of rare species (Clarke et al. 2006). Densities were calculated from SCUBA fish count data (# fish / area) so a similarity-based resemblance matrix was selected. A dummy variable (=1) was added prior to creating the resemblance matrix due to the high prevalence of zeros in the dataset. To visualize the data, we ran a cluster analysis and generated nMDS plots by site and year.
All analyses and graphs were made in PRIMERe version 7 with PERMANOVA extension.
3.3 Abundance
We explored changes in aggregate and focal species densities by site and year with generalized additive mixed models (GAMMs). We modeled densities using raw count data with the offset of transect area (Maunder and Punt 2004, Zuur 2012) and a negative binomial distribution. Focal species size data were modeled without an offset and after exploration of spatial-temporal auto-correlation of residuals, a gaussian distribution. GAMMs were chosen to account for non-linear trends in density (or size) by year detected in preliminary data exploration (Veneables and Dichmont 2004, Zuur et al. 2009). GAMMs were fitted using the mgcv package in R. Site was treated as a fixed categorical variable, while Year was continuous and smoothed with the thin-plate smoother ‘s()’ (Zuur et al 2009; Zuur 2012), grouped by Site, and k was restricted to 3 knots to prevent over-fitting. Depth-Bin was included as a random effect in the model to account for the sampling design targeting three fixed depths. We limited our modeling exercise to focus on Site and Year as these are two of the primary questions of interest. For species with very low densities across most sites and years, no statistical analyses were conducted as the data violated assumptions of the model framework.
Specifically we analyzed aggregate density and species-specific density for focal species.
There are six focal fish species for the OR Marine Reserves Ecological Monitoring Program:
- Black Rockfish; Sebastes melanops
- Blue/Deacon Rockfish; Sebastes mystinus / S. diaconus
- China Rockfish; Sebastes nebulosus
- Yelloweye Rockfish; Sebastes ruberrimus
- Cabezon; Scorpaenichthys marmoratus
- Lingcod; Ophiodon elongatus
These species were chosen based on their ecological, economic or management importance. For more information please refer to the methods Appendix detailing focal species selection. Additional species beyond focal species were included for analysis when they were identified in community analysis as being an important driver of variation.
All analyses and data plots were created in R v4.0.2, using the mgcv (version 1.8-36), mgcViz and gratia packages. Models were structured in R as follows:
Density = mgcv::gam(Counts ~ Site + s(Year, by = Site, k = 3) + s(Depth-Bin, bs = “re”), offset = log(Transect Area), family = nb)
4 Cape Falcon Results
SCUBA fish sampling efforts at the Cape Falcon Marine Reserve and its comparison areas resulted in limited data collection due to challenges with visibility on sampling days. The Cape Falcon Marine Reserve was only sampled in 2016. Out of all three comparison areas, only the Moderate Fishing Pressure Comparison Area was sampled; successful sampling occurred in both 2016 and 2017.
Fig. 2: SCUBA fish monitoring efforts at the Cape Falcon Marine Reserve and the Moderate Fishing Pressure Comparison Area resulted in limited sample sizes over the two years of data collection. Sample size is represented in number of transects.
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4.1 Diversity
4.1.1 Species richness
More SCUBA fish surveys needed to determine differences in species richness between the Cape Falcon Marine Reserve and its associated Comparison Areas.
Sampling efforts in the Cape Falcon Marine Reserve resulted in the observation of three species, Red Irish Lord (Hemilepidotus hemilopidotus), Kelp Greenling (Hexagrammos decagrammus) and Cabezon. The Moderate Fishing Comparison Area sampling efforts also resulted in the observation of three species, Black Rockfish, Kelp Greenling, and Buffalo Sculpin (Enophrys bison).
4.1.2 Unique, common and rare species
More SCUBA fish surveys needed to determine differences in unique, common and rare species between the Cape Falcon Marine Reserve and its comparison Areas.
Of the three fish species observed at the Cape Falcon Marine Reserve on SCUBA, two were unique to the marine reserve - Red Irish Lord and Cabezon. Of the three species observed in the Moderate Fishing Pressure Comparison Area, two were only observed there - Black Rockfish and Buffalo Sculpin. The Red Irish Lord was considered common in the Cape Falcon Marine Reserve; but no species were considered common in the Moderate Fishing Comparison Area. No species were considered rare in either location due to low sample sizes.
Not all species were observed each year, for a summary of species counts over the years by site please see tables below.
Poled species counts across all years and species counts by individual sampling year are included in the following tables:
Table 5: Moderate Fishing Pressure Comparison Area Pooled Species Counts
Table 6: Moderate Fishing Pressure Comparison Area Species Counts by Year
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4.1.3 Diversity Indices
Not enough fish species observations to run diversity indices.
With only six total fish species observed across two sites, there was not enough fish species observations to run diversity indices.
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4.1.4 Diversity Through Time
More SCUBA fish sampling needed to evaluate changes in species diversity through time.
The limited number of fish transects at the Cape Falcon Marine Reserve and its associated comparison areas prevented any analysis to determine changes in species diversity through time.
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4.2 Community Composition
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4.2.1 Variation by Site and Year
The limited fish data from Cape Falcon shows similar community composition across sites.
There was no distinct structuring of fish community composition data across sites with SCUBA fish data at the Cape Falcon Marine Reserve and its nearby comparison area. (Fig. 3). Due to low sample sizes, differences in fish community composition are largely the result of presence/absence of a few species – e.g. the presence of Black Rockfish result in the shift of two samples along the x-axis in the comparison area, whereas separation along the y-axis is driven by a sample containing either Red Irish Lords or Cabezon/Kelp Greenlings.
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4.2.1.1 Site
Fig. 3: Results from nMDS plots with SCUBA fish data, demonstrating similarity in fish community composition at the Cape Falcon Marine Reserve and its nearby comparison area. See separate tabs for site and species.
4.2.1.2 Species
Fig. 3: Results from nMDS plots for SCUBA fish data, demonstrating similairity in fish community composition at the Cape Falcon Marine Reserve and its nearby comparison area. See separate tabs for site and species
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4.3 Aggregate Abundance
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4.3.1 Aggregate Density
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Too few observations of aggregate fish to detect differences in density by site or year.
A total of six species/species-groups were observed across all sites, representing 49 total individuals. Of these individuals 36 were Black Rockfish, and most were observed at the Moderate Fishing Pressure Comparison Area.
4.3.1.0.1 Aggregate Density by Site
Fig. 4: Aggregate fish density at the Cape Falcon Marine Reserve and the Moderate Fishing Pressure Comparison Area.
4.4 Focal Species Abundance
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4.4.1 Black Rockfish, S. melanops
4.4.1.1 Density
Too few observations of Black Rockfish to detect differences in density by site.
Densities of Black Rockfish were very low across all sites (Fig. 5), so statistical analyses were not conducted.
4.4.1.1.1 Black Rockfish Density
Fig. 5: Black Rockfish density at the Cape Falcon Marine Reserve and the Moderate Fishing Pressure Comparison Area.
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4.4.2 Blue/Deacon Rockfish, S.mystinus / S.diaconus
4.4.2.1 Density
No observations of Blue/Deacon Rockfish in two years of sampling at the Cape Falcon Marine Reserve and Moderate Fishing Pressure Comparison Area.
No Blue/Deacon Rockfish were observed across all sites and years, so statistical analyses were not conducted.
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4.4.3 China Rockfish, S. nebulosus
4.4.3.1 Density
No observations of China Rockfish in two years of survey effort at the Cape Falcon Marine Reserve or Moderate Fishing Pressure Comparison Area.
No China Rockfish were observed across all sites and years, so statistical analyses were not conducted.
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4.4.4 Yelloweye Rockfish, S.ruberrimus
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4.4.4.1 Density
No observations of Yelloweye Rockfish in two years of survey effort at the Cape Falcon Marine Reserve or Moderate Fishing Pressure Comparison Area.
No Yelloweye Rockfish were observed across all sites and years, so statistical analyses were not conducted.
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4.4.5 Cabezon, Scorpaenichthys marmoratus
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4.4.5.1 Density
Too few observations of Cabezon to detect differences in density by site.
Densities of Cabezon were very low across all sites (Fig. 6), so statistical analyses were not conducted.
4.4.5.1.1 Cabezon Density
Fig. 6: Cabezon density at the Cape Falcon Marine Reserve and the Moderate Fishing Pressure Comparison Area.
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4.4.6 Lingcod, Ophiodon elongatus
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4.4.6.1 Density
No observations of Lingcod in two years of survey effort at the Cape Falcon Marine Reserve or Moderate Fishing Pressure Comparison Area.
No Lingcod were observed across all sites and years, so statistical analyses were not conducted.
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4.5 Additional Species Density
Both Kelp Greenling and Red Irish Lord were identified by the community analysis as important drivers of variation. However sample sizes of both species were too low to detect differences in density by site. See species count tables for counts by year (Tables 3-6).
5 References
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