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1 Introduction: Redfish Rocks Marine Reserve 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 Redfish Rocks began in 2010, two years before harvest restrictions began. Sampling is conducted in the marine reserve and one comparison area, Humbug (see methods Appendix for additional information about comparison area selection). We conducted five years of sampling at both sites, providing five years of data for our analysis and inclusion in the synthesis report.

• Table 1: Redfish Rocks Fish Monitoring Efforts. Sample sizes represent the number of transects per year at each site

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 Redfish Rocks Marine Reserve

Fig. 1: Map of SCUBA transect locations at Redfish Rocks Marine Reserve

1.1.2 Humbug Comparison Area

Fig. 1: Map of SCUBA transect locations at Humbug 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?

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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.

2.1 SCUBA Fish Results Summary

Fish species diversity was similar between the Redfish Rocks Marine Reserve and Humbug Comparison Area.

Fish species diversity was similar between the Redfish Rocks Marine Reserve and Humbug Comparison Area as evidenced by the results of multiple analyses in the diversity section of this report. They were similar numbers of observed species, and similar numbers of unique, common and rare species. The Hill Diversity indices, representing effective number of species that incorporate concepts of rarity and evenness, were also similar between the Redfish Rocks Marine Reserve and Humbug Comparison Area.

Fish community composition was similar between sites and years; variations were driven by trade-offs in densities of Black and Blue/Deacon Rockfish

There was no apparent structuring of fish community by sites or year at the Redfish Rocks Marine Reserve and the Humbug Comparison Area. The two most abundant species, Black and Blue/Deacon Rockfish drive the majority of variation in the fish community composition. There is also a trade-off observed in densities of these species - on transects with higher densities of Black Rockfish there are lower densities of Blue/Deacon Rockfish.

Lower densities of Black Rockfish, Blue/Deacon Rockfish contribute to lower aggregate fish density at the Redfish Rocks Marine Reserve than Humbug Comparison Area.

There were lower aggregate fish, Black and Blue/Deacon Rockfish densities at the marine reserve than the Humbug Comparison Area. The difference in aggregate fish density between the two sites is likely the result of the differences in the two most abundant species, Black Rockfish and Blue/Deacon Rockfish, where densities were lower in the reserve than comparison area.

• Table 2: Snapshot of Mean Abundance Results

Similar yearly trends in aggregate density and Black Rockfish density were detected at the Humbug Comparison Area, likely represent natural variability of a schooling species.

There were no yearly trends in aggregate or Black Rockfish density at the Redfish Rocks Marine Reserve. There were yearly trends in both aggregate and Black Rockfish densities at the Humbug Comparison Area with higher densities detected in the last year of sampling. Since the two most abundant species drove most of the variation in fish community composition data, likely this increase in aggregate density at Humbug represents an encounter with a school of Black Rockfish during the last year of sampling. The large variation surrounding both aggregate and Black Rockfish densities in 2019 at Humbug underscore that additional sampling is needed to determine if this is a true increase in the populations at this site.

• Table 3: Snapshot of Abundance Trend Results

Few observations and high variability of four focal species limited analysis for this report.

With the exception of Black Rockfish and Blue/Deacon Rockfish, all other focal species had too few observations to detect differences in density by site or trends by year, so statistical analyses were not conducted. Fewer than 10 individuals per species, per site were observed with (China and Yelloweye Rockfish, Cabezon and Lingcod) with five years of Scuba fish surveys.

2.2 Conclusions

Results of this report are consistent with the first Ecological Monitoring Report of 2010/2011.

In the first Ecological Monitoring Report of 2010-2011, the SCUBA summary concluded that the Redfish Rocks Marine Reserve is characterized by high numbers of Blue and Black Rockfish, followed by lower densities of Kelp Greenling. Those results are the same as this report which includes an additional three years of monitoring data. In the 2010/2011 report, it was determined that Humbug was a suitable comparison area because it had similar densities of those dominant species and similar species diversity as the marine reserve, and the results of this report support that conclusion.

Limited ability to detect changes and trends in nearshore fish populations with SCUBA Fish surveys.

The first Ecological Monitoring Report of 2010-2011, suggested 20 transects per site are needed to characterize the fish community, in most years we achieved that sample size at the Redfish Rocks Marine Reserve, but did not achieve that sample size at the Humbug Comparison Area. At the species level, we only had the ability to explore change between sites or trends by year with our two most abundant species - Black and Blue/Deacon Rockfish. We were able to detect some inter-annual and site differences with these two schooling species, but identifying future temporal changes may be challenging because of the high spatial variability of schooling species relative to the size of our sampling unit (i.e. 60m^2 transect). The first Ecological Monitoring Report of 2010-2011 suggests that for more residential homogeneously distributed fish like Kelp Greenling, we would have greater power to detect temporal change. Although Kelp Greenling was an abundant species in our results, we did not report on this species because it was not a focal species, and was not identified in community composition analyses as an important community driver of variation. For other benthic solitary demersal species, such as China Rockfish or Cabezon, low densities and high variability prevented us from statistically analyzing the data because it did not meet the assumptions of our modeling approach. It is unlikely that future survey efforts, would have the power to detect changes over time for these species as their populations are slow growing in our temperate ecosystem.

A move toward permanent sites or transects at the marine reserve and Humbug Comparison Area is needed for future SCUBA surveys to be effective.

Focusing dive survey efforts on permanent transects at each site would reduce spatial variability, and increase the ability to detect temporal variability, with a focus on comparing rates of change over time inside and outside the marine reserve. With a better understanding of the sea states, visibility and communities of nearshore reefs, we can now select the appropriate locations to re-focus monitoring efforts, maximizing efficiency in data collection and power to detect change over time. Future effort should focus on the Redfish Rocks Marine Reserve and Humbug Comparison Area only. Over the years there was intent to survey at Orford Reef, but variable sea states on survey days at this exposed site typically prevented access and therefore limited survey efforts.

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3 SCUBA Fish Methods

SCUBA fish sampling is conducted in the Redfish Rocks Marine Reserve and Humbug Comparison Area following PISCO protocols, modified for diving safety in Oregon. Monitoring began in Redfish and Humbug in 2010; in the initial years (2010/ 2011) there was a strong focus to place more sampling effort in the reserve to ensure adequate characterization of baseline conditions prior to closure. Since then, sampling effort targeted 6 days for both spring and fall monitoring, splitting effort between the marine reserve and Humbug Comparison Area based on ocean conditions. Surveys typically occur during spring and fall due to visibility constraints associated with upwelling. Survey dives begin at least one hour after sunrise and conclude one hour before sunset to avoid the crepuscular period. Two to three replicate transects are 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.

In 2010/2011, scientific divers from Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO) selected survey locations with the intent that these sites would be permanent. Selected locations were representative of available rocky reef habitat with kelp, within targeted depth ranges. As monitoring continued, the challenges and safety constraints of diving in Oregon’s nearshore (see Methods Appendix for more details) led to the inevitable need to select alternate locations. Due to unpredictable weather and visibility conditions, sites were selected from randomly generated points based on available rocky reef habitat within targeted depth ranges. These changes resulted in greater spatial coverage of the reef and is more reflective of a stratified random sampling design, rather than one with permanent sites.

The unit of replication is at the transect level. Only fully completed, independent transects were included in analysis. Targeted 5 meter transects from early years of sampling (2010-2011) were not included because evolving OR dive safety protocols prevented continued access to these sites. For additional details on the evoluation of data collection, please review documentation in the Methods Appendix.

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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
• diversity through time

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.

3.1.4 Diversity Through Time

Finally we explored how diversity changed through time. First we plotted each species yearly rarefaction curve against the total cumulative rarefaction curve for all years combined to determine if we had sampled appropriately to compare species diversity from year to year. When our sampling effort was not adequate to compare across years, we pooled data from all years to compare average transect diversity using an ANOVA

All analyses and graphs were created in R v4.0.2, using the iNEXT and Vegan packages.

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3.2 Community Composition

We focused our community composition analysis on the question of whether variation in fish density was driven by spatial (site) or temporal (year) factors. We did this through both data visualizations with non-multidimensional scaling (nMDS) plots and with statistical tests such as principal coordinates analyses (PCO),multivariate ANOVA tests (PERMANOVA), and dispersion tests (PERMDISP). In addition to site and year, we also explored several species-specific drivers of variation.

To explore variation by site and year, we used fish density data collected on SCUBA fish transects with a log 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.

To test the statistical significance in our data of variation by site and year we ran a permutational analysis of variance (PERMANOVA), using a mixed model with site and year as fixed effects factors. Initial explorations of the first two years of data resulted in no apparent trends by depth among the three target survey depths, therefore depth was considered a random effect in the model. To explore if any significant results of the PERMANOVA were related to true differences in location or differences in dispersion of samples (either by site or year to year), we ran a PERMDISP, a distance based test for homogeneity of multivariate dispersions for any factors (site, year, depth) that were significant in the PERMANOVA (Anderson and Walsh 2013). If a factor was significant in the PERMANOVA but not the PERMDISP, then it can be inferred that the significance is related to a location effect, but not a dispersion effect. If the factor is also significant in the PERMDISP, then significance in the PERMANOVA is related to dispersion, but there may also be a location effect.

Beyond site and year, we explored species-specific drivers in the variation of fish community structure. We extended our data visualization, by performing a vector analysis of fish species in the community, selecting only the species with > 0.5 Pearson correlations (Hinkle et al. 2003). We then generated density plots of the identified species to visualize their relationship to site or year. To better understand how these species contributed to variation in the data, we ran a principal coordinates (PCO) analysis, using a Bray-Curtis resemblance matrix, which provides information on the percent of variation explained by each axis.

All analyses and graphs were made in PRIMERe version 7 with PERMANOVA extension.

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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
• Yellow-eye 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)

Size = mgcv::gam(Length ~ Site + s(Year, by = Site, k = 3) + s(Depth-Bin, bs = “re”), family = gaussian)

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4 Redfish Rocks Results

SCUBA habitat sampling efforts at Redfish Rocks and its comparison area resulted in five years of data collection, where varying sample sizes were collected per year (Fig. 2). With the exception of 2015, sampling efforts resulted in more transects completed in the marine reserve than in the Humbug Comparison Area.

Fig. 2: SCUBA habitat monitoring efforts at the Redfish Rocks Marine Reserve and surrounding comparison area resulted in varied sample sizes over the five years of data collection. Sample size is represented in number of transects.

• Table 4: Redfish Rocks SCUBA Fish Monitoring Efforts

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4.1 Diversity

4.1.1 Species richness

Fish species richness is similar across the Redfish Rocks Marine Reserve and Humbug Comparison Area.

Over the five years of sampling with SCUBA invertebrate surveys, a total of 15 species (or species groups) were observed in the Redfish Rocks Marine Reserve (Table 5). The Humbug Comparison Area had similar total number of observed species (n=13). These observed numbers of species richness are similar to the estimated numbers of total species richness.

library(kableExtra)
pna <- data.frame(Area = c("Redfish Rocks Marine Reserve", 
                           "Humbug Comparison Area"),
                  Observed_Richness = c("15","13"), 
                  Estimated_Richness = c("16","14"), 
                  LCL = c("15","13"), 
                  UCL = c("25", "21"))


  kbl(pna, caption = "Table 5: Observed and estimated invertebrate species richness by site with lower (LCL) and upper (UCL) 95% confidence limits") %>% 
  kableExtra::kable_classic()

Table 5: Observed and estimated invertebrate species richness by site with lower (LCL) and upper (UCL) 95% confidence limits

Area	Observed_Richness	Estimated_Richness	LCL	UCL
Redfish Rocks Marine Reserve	15	16	15	25
Humbug Comparison Area	13	14	13	21

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Species rarefaction curves highlight that for moderate samples size, including those for any given year, Humbug Comparison Area has similar species richness compared to Redfish Rocks Marine Reserve (Fig. 3). Both rarefaction curves begin to level off, suggesting saturation in species richness with this tool at these sites.

Fig. 3: Species rarefaction curves for the Redfish Rocks Marine Reserve and Humbug Comparison Area. Data are pooled across all years of sampling for each site.

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4.1.2 Unique, common and rare species

Similar numbers of unique, common and rare fish species at the Redfish Rocks Marine Reserve and Humbug Comparison Area.

The Redfish Rocks Marine Reserve (n = 4) had similar numbers of unique species to its comparison area (n = 2). Buffalo Sculpin (Enophrys bison), Black and Yellow Rockfish (S.chrysomelas), Pile Surfperch (Rhacochilus vacca) and Wolf Eel (Anarrhichthys ocellatus) were unique species to the marine reserve; Striped Surfperch (Embiotoca lateralis) and Copper Rockfish (S.caurinus) were unique to the comparison area. The marine reserve had one common species, Black Rockfish. Black Rockfish were also considered common at Humbug Comparison Area, as was Kelp Greenling, and Blue/Deacon Rockfish. The Redfish Rocks Marine Reserve and Humbug Comparison Area had similar numbers of rare species (n = 10, n = 7).

Many of the other benthic fish species were not caught frequently resulting in low pooled counts. Not all species were observed each year, for a summary of species counts over the years by site please see tables below.

Pooled species counts across all years and species counts by individual sampling year are included in the following tables:

• Table 6: Redfish Rocks Marine Reserve Pooled Species Counts

• Table 7: Redfish Rocks Marine Reserve Species Counts by Year

• Table 8: Humbug Comparison Area Pooled Species Counts

• Table 9: Humbug Comparison Area Species Counts by Year

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4.1.2.1 Redfish Rocks Marine Reserve

Fig 4: Relative frequency of occurrence of fish species observed at the Redfish Rocks Marine Reserve and Humbug Comparison Area from SCUBA transects. See separate tabs for each site.

4.1.2.2 Humbug Comparison Area

Fig 4: Relative frequency of fish species observed at the Redfish Rocks Marine Reserve and Humbug Comparison Area from SCUBA transects. See separate tabs for each site.

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4.1.3 Diversity Indices

The Redfish Rocks Marine Reserve and Humbug Comparison Area have similar diversity indices for fish species observed with SCUBA.

The effective number of species for the SCUBA fish community are very similar for the marine reserve and Humbug Comparison Area across all three diversity indices (Fig. 5).

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Fig. 5: Comparing effective number of species (Hill diversity numbers) between the Redfish Rocks Marine Reserve and Humbug Comparison Area from SCUBA fish transects. 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).

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4.1.4 Diversity through time

We did not get enough samples to evaluate change in species diversity through time at the Redfish Rocks Marine Reserve and Humbug Comparison Area.

Species rarefaction curves by year for each site indicated that we did not sample enough on a yearly basis to compare changes in mean species richness through time (Fig. 6-7).

• Fig. 6: Redfish Rocks Marine Reserves species rarefaction curves by year from SCUBA transects.

• Fig. 7: Humbug Comparison Area species rarefaction curves by year from SCUBA transects.

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For an average transect of sampling, the Humbug Comparison Area has higher species diversity than the Redfish Rocks Marine Reserve.

When comparing mean species richness for an average day of sampling, Humbug Comparison Area was the most diverse (F = 17.91, p < 0.05) (Fig. 8).

Fig. 8: Mean species richness by site with 95% confidence intervals at the Redfish Rocks Marine Reserve and associated comparison areas from hook and line data.

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4.2 Community Composition

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4.2.1 Variation by Site and Year

Fish community composition was similar at the Redfish Rocks Marine Reserve and Humbug Comparison Area, and was not influenced by sampling year.

There was no structuring of fish community composition data across sites and years with SCUBA fish data at the Redfish Rocks Marine Reserve and Humbug Comparison Area. (Fig. 9).

While multivariate statistics indicate some differences in year, they account for little of the total variation in community composition.

PERMANOVA results indicate that only the interactions between year by depth and site by year by depth were significant (p < 0.05) (Table 10). Depth was nearly significant at p = 0.05. Estimated variation described by each of the variables and variable interactions was very small. Depth accounted for 2% of the model variability, year by depth accounted for 5% and site by year by depth accounted for 7 % where as the residuals explained 52% of model variability.

PermDISP tests among depths indicate that there are significant differences in dispersions between 15 m and 20 m depths. The significance of depth and the two interactions is likely driven by differences in dispersion between depths, and less likely the result of biologically relevant differences in community structure.

• Table 10: PERMANOVA results

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4.2.1.1 Site

Fig. 9: Results from nMDS plots with SCUBA fish data, demonstrating similarity in fish community composition at the Redfish Rocks Marine Reserve and the Humbug Comparison Area. See separate tabs for site, year, and depth.

4.2.1.2 Year

Fig. 9: Results from nMDS plots for SCUBA fish data, demonstrating similairity in fish community composition at the Redfish Rocks Marine Reserve and the Humbug Comparison Area. See separate tabs for site, year, and depth

4.2.1.3 Depth

Fig. 9: Results from nMDS plots for SCUBA fish data, demonstrating similairity in fish community composition at the Redfish Rocks Marine Reserve and the Humbug Comparison Area. See separate tabs for site, year, and depth

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4.2.2 Other drivers of variation

Two species drive the majority of variation in fish community composition data at both the Redfish Rocks Marine Reserve and its comparison area.

We explored species-specific drivers of variation, and found that Black Rockfish and Blue/Deacon Rockfish were driving the majority of the variation in fish community structure (Fig. 10).

Principal coordinate analysis revealed that ~62% of model variation is explained by densities of Blue/Deacon Rockfish and Black Rockfish. There is also a trade-off in species composition; at higher densities of Black Rockfish, there are lower densities of Blue/Deacon Rockfish; this trade-off accounts for an additional 20% of model variability (Fig. 10). Together the abundance of these two species accounts for over 82% of model variability.

4.2.2.1 PCO Vector Plot

Fig. 10: Results from species correlations and principal coordinate analysis demonstrating that Black Rockfish and Blue/Deacon Rockfish drive variation in community structure regardless of site at the Redfish Rocks Marine Reserve and its surrounding comparison areas. See separate tabs for vector and bubble plots. Bubble color / size represents species-specific densities in each sample (species density range indicated in legend).

4.2.2.2 PCO Bubble Plot

Fig. 10: Results from species correlations and principal coordinate analysis demonstrating that Black Rockfish and Blue/Deacon Rockfish drive variation in community structure regardless of site at the Redfish Rocks Marine Reserve and its surrounding comparison areas. See separate tabs for vector and bubble plots. Bubble color / size represents species-specific densities in each sample (species density range indicated in legend).

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4.3 Aggregate Abundance

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4.3.1 Aggregate Density

Significantly lower aggregate fish density observed in the Redfish Rocks Marine Reserve than the Humbug Comparison Area.

Aggregate density was significantly lower at the Redfish Rocks Marine Reserve than the Humbug Comparison Area (p < 0.05; Table 11).

Significant yearly trends in aggregate fish density only at the Humbug Comparison Area.

There were significant trends by year in aggregate density at the Humbug Comparison Area (p < 0.05; Fig. 11, Table 12), with an increasing trend from the beginning sampling years through 2019. There were no significant yearly trends at the Redfish Rocks Marine Reserve (p > 0.05; Table 12).

The random effect of depth-bin was not identified as a significant component of variation (Table 12).

GAMM model results can be found in the links below:

• Table 11: GAMM model results: parametric terms

• Table 12: GAMM model results: smoothed terms

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4.3.1.1 Aggregate Density Timeseries

Fig. 11: Aggregate density timeseries and modeled GAMM results with 95% confidence intervals, at the Redfish Rocks Marine Reserve and its associated comparison area. See separate tabs for timeseries and GAMM results.

4.3.1.2 Aggregate Density modeled GAMM results

Fig. 11: Aggregate density timeseries and modeled GAMM results with 95% confidence intervals, at the Redfish Rocks Marine Reserve and its associated comparison area. See separate tabs for timeseries and GAMM results.

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4.4 Focal Species Abundance

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4.4.1 Black Rockfish, S. melanops

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4.4.1.1 Density

Significantly lower Black Rockfish density at the Redfish Rocks Marine Reserve than the Humbug Comparison Area.

Black Rockfish density was significantly lower at the Redfish Rocks Marine Reserve than the Humbug Comparison Area (p < 0.05; Table 13).

Significant yearly trends in Black Rockfish density only at the Humbug Comparison Area.

There were significant yearly trends in Black Rockfish density at the Humbug Comparison Area (p<0.05; Fig.12, Table 14), with density increasing from the beginning sampling years through 2019. There were no significant yearly trends at the Redfish Rocks Marine Reserve (p > 0.05; Table 14).

The random effect of depth-bin was not identified as a significant component of variation (Table 14).

GAMM model results can be found in the links below:

• Table 13: GAMM model results: parametric terms

• Table 14: GAMM model results: smoothed terms

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4.4.1.1.1 Black Rockfish Density Timeseries

Fig. 12: Black Rockfish density timeseries and GAMM model results with 95% confidence intervals, at the Redfish Rocks Marine Reserve and its associated comparison area. See separate tabs for timseries and GAMM results.

4.4.1.1.2 Black Rockfish Density Modeled GAMM Results

Fig. 12: Black Rockfish density timeseries and GAMM model results with 95% confidence intervals, at the Redfish Rocks Marine Reserve and its associated comparison area. See separate tabs for timseries and GAMM results.

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4.4.2 Blue/Deacon Rockfish, S.mystinus / S.diaconus

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4.4.2.1 Density

Significantly lower Blue/Deacon Rockfish density at the Redfish Rocks Marine Reserve than the Humbug Comparison Area.

Blue/Deacon Rockfish density was significantly lower at the Redfish Rocks Marine Reserve than the Humbug Comparison Area (p < 0.05; Table 15).

No significant yearly trends in Blue/Deacon Rockfish density detected at the Redfish Rocks Marine Reserve or the Humbug Comparison Area.

There were no significant yearly trends in Blue/Deacon Rockfish density at the marine reserve or Humbug Comparison Area (p > 0.05; Fig.13, Table 16).

The random effect of depth-bin was identified as a significant component of variation (Table 16).

GAMM model results can be found in the links below:

• Table 15: GAMM model results: parametric terms

• Table 16: GAMM model results: smoothed terms

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4.4.2.1.1 Blue/Deacon Rockfish Density Timeseries

Fig. 13: Blue/Deacon Rockfish density timeseries and GAMM model results with 95% confidence intervals, at the Redfish Rocks Marine Reserve and its associated comparison areas. See separate tabs for timseries and GAMM results.

4.4.2.1.2 Blue/Deacon Rockfish Density Modeled GAMM Results

Fig. 13: Blue/Deacon Rockfish density timeseries and GAMM model results with 95% confidence intervals, at the Redfish Rocks Marine Reserve and its associated comparison areas. See separate tabs for timseries and GAMM results.

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4.4.3 China Rockfish, S. nebulosus

4.4.3.1 Density

Too few observations of China Rockfish to detect differences in density by site or year.

Densities of China Rockfish were very low across all sites and years (Fig. 14), so statistical analyses were not conducted.

4.4.3.1.1 China Rockfish Density Timeseries

Fig. 14: China Rockfish density timeseries with 95% confidence intervals, at the Redfish Rocks Marine Reserve and its associated comparison area.

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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 detected in five years of SCUBA fish surveys.

No observations of Yelloweye Rockfish were observed at in any survey year at the Redfish Rocks Marine Reserve or Humbug Comparison Area so statistical analyses were not conducted.

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4.4.5 Cabezon, Scorpaenichthys marmoratus

\(~\)

4.4.5.1 Density

Too few observations of Cabezon to detect differences in density by site or year.

Densities of Cabezon were very low across all sites and years (Fig. 15), so statistical analyses were not conducted.

4.4.5.1.1 Cabezon Density Timeseries

Fig. 15: Cabezon density timeseries with 95% confidence intervals, at the Redfish Rocks Marine Reserve and its associated comparison area.

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4.4.6 Lingcod, Ophiodon elongatus

\(~\)

4.4.6.1 Density

Too few observations of Lingcod to detect differences in density by site or year.

Densities of Lingcod were very low across all sites and years (Fig. 16), so statistical analyses were not conducted.

4.4.6.1.1 Lingcod Density Timeseries

Fig. 16: Lingcod density timeseries with 95% confidence intervals, at the Redfish Rocks Marine Reserve and its associated comparison area.

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4.5 Additional Species Density

No other fish species were identified by the community analysis as important drivers of variation.

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5 References

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