1 Introduction: Redfish Rocks SCUBA Invertebrate Surveys

SCUBA invertebrate sampling targets the density of specific, conspicuous, solitary and mobile invertebrates. Organisms are chosen due to the large abundance, economic value, or ecological value. Only targeted invertebrates greater than 2.5 cm are counted along a 30 x 2 m belt transects across two target depths, 12.5 and 20 meters. No write-ins are allowed.

Our SCUBA invertebrate 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 SCUBA Invertebrate Monitoring Efforts. Sample sizes represent the number of transects per year at each site

Data from SCUBA invertebrate monitoring efforts can be used to explore questions about invertebrate 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 invertebrate 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

$Fig. 1: Map of SCUBA transect locations at Humbug Comparison Area$

Fig. 1: Map of SCUBA transect locations at Humbug Comparison Area

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?

2 Takeaways

Here we present a summary of our SCUBA invertebrate 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 Invertebrate Results Summary

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

The Redfish Rocks Marine Reserve and Humbug Comparison Areas had similar numbers of observed species, and similar numbers of unique, common and rare species. Both sites had similar diversity indices and a similar mean species richness for an average day of sampling.

Community composition was similar between the Redfish Rocks Marine and Humbug Comparison Area, but not among years.

There was no apparent structuring of the invertebrate community by site.There was a slight shift in community composition from early years (2010, 2011) to later years (2015, 2019) across both sites. Differences in community composition between years are largely driven by higher densities of Metridium farcimen (Giant Plumose Anemone) in 2010-2011 at the Redfish Rocks Marine Reserve and higher densities of Mesocentrotus franciscanus (Red Urchin), at both the marine reserve and Humbug Comparison Area in 2015 and 2019. Cucumaria miniata (Burrowing Sea Cucumber) also contributed to variation in community structure and had an inverse relationship with M. farcimen.

Aggregate invertebrate density was dominated by four broad taxonomic groups: barnacles, cucumbers, tunicates and sea urchins, with variable trends across groups and between sites.

Out of eleven invertebrate taxonomic groups, four dominated observations across sites: barnacles, cucumbers, tunicates and sea urchins. There were no clear trends in aggregate invertebrate densities among groups. Greater urchin densities were observed in the Humbug Comparison Area than the marine reserve, and there was an apparent increase in urchins in 2015 and 2019 at both sites, with a more pronounced trend at the comparison area than the marine reserve. A similar trend through time was evident with barnacles in 2019. Tunicates appeared to decrease through time at both sites.

Species densities differed for Red Urchins and Giant Plumose Anemones between the Redfish Rocks Marine and Humbug Comparison Area.

Of the seven focal species, two differed in densities between the marine reserve and comparison area. Densities of Mesocentrotus franciscanus (Red Urchin) were higher at Humbug Comparison Area than Redfish Rocks Marine Reserve. This trend was reversed for the Metridium farcimen (Giant Plumose Anemone) with higher densities at Redfish Rocks Marine Reserve than the comparison area. These two species were also identified in community composition analysis to drive some of variation in invertebrate community composition.

Table 2: Snapshots of Mean Abundance Results

Species densities displayed trends by year at the Redfish Rocks Marine Reserve, with similar trends between the reserve and Humbug Comparison Area for the Sunflower Sea Star, Purple Urchin, and Red Urchin.

We saw significant declines in densities of Pycnopodia helianthoides (Sunflower Sea Star) at both the marine reserve and Humbug Comparison Area; observations declined to zero in 2014 and 2019 sampling. Simultaneously we also saw increases in densities of both sea urchin species Strongylocentrotus purpuratus (Purple Urchin) and Mesocentrotus franciscanus (Red Urchin) at both the marine reserve and Humbug Comparison Area starting in 2015. There were greater increases in both sea urchin species at Humbug Comparison Area. At Redfish Rocks we observed a decline through time with Pisaster ochraceus (Ochre Sea Star) to zero observations in 2014, with a slight increase in observations in 2015 and 2019. At the marine reserve only there was also a decline in Metridium farcimen (Giant Plumose Anemone) after the first two years of sampling and Cucumaria miniata (Burrowing Sea Cucumber) density peaked in 2015 to a decline in 2019. For two focal species, Crassadoma gigantea (Rock Scallop) and Parastichopus californicus (CA Sea Cucumber) there were too few observations to detect differences in density by site or trends by year, so statistical analyses were not conducted.

Table 3: Snapshots of Abundance Trend Results

2.2 Conclusions

Differences between the results of this report and the initial 2010-2011 ODFW Ecological Monitoring report support the need for long-term monitoring.

Continued monitoring efforts at the Redfish Rocks Marine Reserve and Humbug Comparison Area have documented similarities and changes of the invertebrate community first described in the 2010-2011 Ecological Monitoring Report. We detected similar species richness between Redfish Rocks Marine Reserve and the Humbug Comparison Area as found in the 2010/2011 report (ODFW 2014). In some cases, we have greater confidence in our results, such as with Styela montereyensis (Stalked Tunicate) and Henricia spp. (Blood Star), that were initially documented as common at the comparison area in 2010-2011, and are still considered common in our report. Baseline monitoring documented the marine reserve was dominated by Metridium farcimen (Giant Plumose Anemone) which were rare at the Humbug Comparison Area, our analysis shows densities became more similar through time. With additional years of sampling, initial increases in abundance documented with the 2010/2011 report, such as with Cucumaria miniata (Burrowing Sea Cucumber) at the Humbug Comparison Area, have turned out to be part of natural, interannual variability.

We were able to detect changes in trends associated sea star wasting disease across the Redfish Rocks Marine Reserve and Humbug Comparison Area.

The decline in Pycnopodia helianthoides (Sunflower Sea Star) and Pisaster ochraceus (Ochre Sea Star) densities and corresponding rise in Strongylocentrotus purpuratus (Purple Sea Urchin) and Mesocentrotus franciscanus (Red Sea Urchin) densities suggests our sampling detected a large shift related to sea star wasting impacting the Oregon Coast. While both species of sea stars reached their lowest densities in 2014/2015, both species of sea urchins started increasing in density in 2015 and 2019 sampling. With sea star wasting disease hitting Oregon in 2014, this indicates our sampling detected a shift that requires continued monitoring.

A move towards permanent sites or transects is needed to confidently detect future trends in invertebrates with SCUBA surveys

The initial 2010/2011 Ecological Monitoring Report suggested 10 transects per site are needed to characterize the invertebrate 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. Limited sample sizes were a result of challenging logistics related to a small boat based survey method in Oregon’s nearshore environment; reducing required sample sizes needed to detect change such as moving to permanent sites or transects would be beneficial because of these challenges.

While we were able to detect several species’ yearly trends at either one site or both despite limited sample sizes, the magnitude of these changes, such as those documented for sea star wasting disease, was quite large (2-10 fold changes). In order for our program to confidently detect future changes in invertebrate species at smaller magnitudes of change than those detected in this report, increased sampling effort or a move towards permanent sites or transects is needed. Increased sampling effort would likely require an increase to the research budget. With a better understanding of the sea states, visibility and communities of nearshore reefs, we can now select the appropriate permanent locations to focus monitoring efforts, maximizing efficiency in data collection and power to detect change over time.

3 SCUBA Invertebrate Methods

SCUBA invertebrate 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 with unequal sampling effort; in the initial years 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.

The purpose of invertebrate sampling is to estimate density of specific, conspicuous, solitary and mobile invertebrates. Organisms are chosen due to the large abundance, economic value, or ecological value. Only targeted invertebrates greater than 2.5 cm are counted along a 30 x 2 m belt transects across two target depths, 12.5 and 20 meters. Sub-sampling occurs within each 10 m segment of the transect for those target species with very high densities (more than 30 individuals per 10 m segment).

In 2010/2011, scientific divers from the 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 concerns 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. The reality of 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. Two replicate transects were completed at each dive location. 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 data collection, please review documentation in the Methods Appendix.

3.1 Diversity

With SCUBA invertebrate 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 species turnover at each site (reserve or comparison area) likely occurs on timescales greater than one year.

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 invertebrate 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. 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 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, also known as the effective number of species, 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 analysis of variance (ANOVA).

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 invertebrate community composition 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 invertebrate density data collected on SCUBA invert 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 invertebrate count data (# inverts/ 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, between the two target depths, therefore depth was considered a random effect, and nested under site. 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 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 invertebrate community structure. We extended our data visualization, by performing a vector analysis of invertebrate species in the community, selecting only the species with > 0.5 Pearson correlations (Hinkle et al. 2003). If more than four species were identified, we only reported on species with a high ( > 0.7) Pearson correlations. 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.

3.3 Abundance

We explored changes in aggregate and focal species densities by site and year. For aggregate density we summarized data across invertebrate taxonomic groups (similar to Lester et al. 2009) to identify broad scale differences in target invertebrates by site and year. Based on the target list of invertebrates, we had 11 broad taxonomic groupings (Table 4). A list of which species are included in each taxonomic groupings is provided in Table 5.

To determine which taxonomic groups were the most dominant, we summarized means and 95% confidence intervals grouped by site and as a timeseries..

For focal species, 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. GAMMs were chosen to account for non-linear trends in density 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.

There are eight focal invertebrate species for the OR Marine Reserves Ecological Monitoring Program; seven of which can be found in the shallow water habitats targeted by SCUBA surveys. They include the following:

Ochre Sea Star; Pisaster ochraceus
Sunflower Star; Pycnopodia halianthoides
Purple Sea Urchin; Strongylocentrotus purpuratus
Red Sea Urchin; Mesocentrotus franciscanus
Rock Scallop; Crassadoma gigantea
California Sea Cucumber; Parastichopus californicus
Giant Plumose Anemone; Metridium farcimen

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 Redfish Rocks Results

SCUBA invertebrate 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 2014, sampling efforts resulted in more transects completed in the marine reserve than in the Humbug Comparison Area.

Fig. 2: SCUBA invertebrate 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 6: Redfish Rocks SCUBA Invertebrate Monitoring Efforts

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4.1 Diversity

4.1.1 Species richness

Invertebrate 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 33 species (or species groups) were observed in the Redfish Rocks Marine Reserve (Table 7). The Humbug Comparison Area had similar total number of observed species (n=33). These observed numbers of species richness are similar to the estimated numbers of total species richness (Table 7).

library(kableExtra)
pna <- data.frame(Area = c("Redfish Rocks Marine Reserve", 
                           "Humbug Comparison Area"), 
                  Observed_Richness = c("33","33"),
                  Estimated_Richness = c("34","42"),
                  LCL = c("33","34"),
                  UCL = c("45", "85"))


  kbl(pna, caption = "Table 7: Observed and estimated invertebrate species richness by site with lower (LCL) and upper (UCL) 95% confidence limits") %>% 
  kableExtra::kable_classic()

Table 7: 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	33	34	33	45
Humbug Comparison Area	33	42	34	85

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Species rarefaction curves highlight that for any samples size, including those for any given year, the species richness among sites is very similar (Fig. 3). The Redfish Rocks Marine Reserve rarefaction curve appears to level off, suggesting saturation in species richness with this tool at this sit. The rarefaction curve has not reached an asymptote at Humbug Comparison Area suggesting that additional sampling is needed.

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 invertebrate species at the Redfish Rocks Marine Reserve and Humbug Comparison Area.

The Redfish Rocks Marine Reserve had one unique species - the Velcro Star, Stylasterias forreri which was observed a single instance. The Humbug Comparison Area also had one unique species - the Bat Star, Patiria miniata. The Redfish Rocks Marine Reserve (n = 8) had similar numbers of common species to the Humbug Comparison Area (n = 7). All seven common species at the Humbug Comparison Area were also common species at the marine reserve. The Redfish Rocks Marine Reserve and Humbug Comparison Area had similar numbers of rare species (n = 6, n = 8).

Many of the other target invertebrate 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:

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4.1.2.1 Redfish Rocks Marine Reserve

Fig. 4: Relative frequency of occurrence of invertebrate 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 invertebrate 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 target invertebrates.

The effective number of species for the SCUBA invertebrate 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 invertebrate 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 its comparison areas.

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). When plotting mean species richness by year with 95% confidence intervals, the confidence intervals overlap suggesting more sampling is needed to detect any meaningful differences in annual species rarefaction.

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For an average SCUBA transect, invertebrate species diversity does not differ between the Redfish Rocks Marine Reserve and Humbug Comparison Area.

When comparing mean species richness for an average SCUBA transect of sampling, there was no difference between the marine reserve and Humbug Comparison Area (F.0.485, p>0.05) (Fig. 8).

Fig. 8: Mean species richness by area with 95% confidence intervals at the Redfish Rocks Marine Reserve and Humbug Comparison Area from SCUBA invertebrate transects.

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4.2 Community Composition

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4.2.1 Variation by Site and Year

Invertebrate community composition was similar at the Redfish Rocks Marine Reserve and Humbug Comparison Area with SCUBA invertebrate data.

There was no structuring of invertebrate community composition data by site at the Redfish Rocks Marine Reserve and Humbug Comparison Area. (Fig. 9).

Invertebrate community composition differed between years at the Redfish Rocks Marine Reserve and its comparison area.

There was some apparent structuring of invertebrate community composition data by year at the Redfish Rocks Marine Reserve and Humbug Comparison Area, with differences largely lying between 2010-2011 data at Redfish Rocks Marine Reserve and 2015-2019 data at both the reserve and comparison area (Fig. 9).

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

PERMANOVA results indicate that year and year by site by depth interaction were significant factors for invertebrate community composition with SCUBA density data (p < 0.05, Table 12). Year by site by depth interaction described the largest variation in the data out of all factors (~28%), with year accounting for an additional 27% of variability in the model. Combined, year and the interaction between year, site and depth accounted for nearly equal variability (55%) as the residual variation (57%).

Table 12: PERMANOVA results

PERMDISP results indicate significant differences in dispersion by year (p = 0.002). The dispersion of 2014 was much smaller than all other years,and the only significant pairwise comparisons are between 2014 and all other years (Table 13-14).This suggests the significance identified in the PERMANOVA is likely a combination of differences in dispersion between years as well as differences in location among years.

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4.2.1.1 Site

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

4.2.1.2 Year

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

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4.2.2 Species specific drivers of variation

Three invertebrate species drive the majority of variation in community composition data regardless of site.

We explored species-specific drivers of variation, and found that M. franciscanus, C.miniata, and M. farcimen were driving the majority of variation in the invertebrate community (Fig. 10). Principal coordinate analysis revealed that ~33% of the variation is explained by the trade-off in density of M. franciscanus and 21% of variation is described by trade-offs between C.miniata and M. farcimen densities (Fig. 10). Together the abundance of these three species accounts for over 54% of model variability. Differences in community composition between years and year by site by depth interactions are largely driven by higher densities of M.farcimen in 2010-2011 at Redfish Rocks Marine Reserve, and higher densities of M.franciscanus at both the marine reserve and Humbug Comparison Area in 2015-2019.

4.2.2.1 PCO Vector Plot

Fig. 10: Results from species correlations and principal coordinate analysis demonstrating that M. franciscanus, C.miniata and M. farcimen drive variation in community structure regardless of site at the Redfish Rocks Marine Reserve (RR) and its surrounding comparison area (RRH). 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 M. franciscanus, C.miniata and M. farcimen drive variation in community structure regardless of site at the Redfish Rocks Marine Reserve and its surrounding comparison area. 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 Abundance

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4.3.1 Aggregate Density

Four dominate taxonomic groups at both the Redfish Rocks Marine Reserve and Humbug Comparison Area.

Urchins, cucumbers, barnacles, and tunicates dominate the relative abundance at the Redfish Rocks Marine Reserve and its comparison area (Fig. 11).

Variable trends through time across broad taxonomic groups.

There were variable trends through time across broad taxonomic invertebrate groups (Fig. 11). The majority of taxonomic groups show no clear trends over time (e.g. bivalves, chitons). For a few groups, such as Urchins, we see an increase through time at one or both sites. With other groups, there are declines through time at one or both sites, such as with anemones or tunicates.

Higher mean density of urchins in the Humbug Comparison Area compared to the Redfish Rocks Marine Reserve.

Out of all taxonomic groups, only urchins had clear differences in 95% confidence intervals between the marine reserve and Humbug Comparison Area (Fig. 11).

4.3.1.1 Mean Aggregate Density by Site

Fig. 11: Aggregate density timeseries of SCUBA targeted invertebrates at the Redfish Rocks Marine Reserve and the Humbug Comparison Area. See separate tabs for density by site and timeseries plots.

4.3.1.2 Mean Aggregate Density Timeseries

Fig. 11: Aggregate density timeseries of SCUBA targeted invertebrates at the Redfish Rocks Marine Reserve and the Humbug Comparison Area. See separate tabs for density by site and timeseries plots.

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4.4 Focal Species

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4.4.1 Ochre Sea Star, P. ochraceus

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4.4.1.1 Density

No significant difference in P. ochraceus density between the Redfish Rocks Marine Reserve and Humbug Comparison Area.

There was no difference in P. ochraceus density between the marine reserve and Humbug Comparison Area (p > 0.05; Table 15).

Significant yearly trends in P. ochraceus density at the Redfish Rocks Marine Reserve only.

There were significant trends by year in P. ochraceus at the Redfish Rocks Marine Reserve (p < 0.05; Table 16), with a decline to zero observations in 2014 and a slight increase in 2019. There was no trend at the Humbug Comparison Area (p > 0.05; Table 16).

The random effect of depth was not identified as a significant component of variation (Table 16).

GAMM model results can be found in the links below:

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4.4.1.1.1 **P. ochraceus* Density Timeseries

Fig. 12: P. ochraceous density timeseries and GAMM model results with 95% confidence intervals, at the Redfish Rocks Marine Reserve and Humbug Comparison Area. See separate tabs for timseries and GAMM results.

4.4.1.1.2 P. ochraceus Density Modeled GAMM Results

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4.4.2 Sunflower Star, P. helianthoides

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4.4.2.1 Density

No significant difference in P. helianthoides density between the Redfish Rocks Marine Reserve and Humbug Comparison Area.

There was no difference in P. helianthoides density between the marine reserve and Humbug Comparison Area (p > 0.05; Table 17).

Significant yearly trends in P. helianthoides density at the Redfish Rocks Marine Reserve and the Humbug Comparison Area.

There were significant trends by year in P. helianthoides density at the Redfish Rocks Marine Reserve and the Humbug Comparison Area (p < 0.05; Table 18), with similar declines to zero observations in 2019.

The random effect of depth was not identified as a significant component of variation (Table 18).

GAMM model results can be found in the links below:

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4.4.2.1.1 P. helianthoides Density Timeseries

Fig. 13: P. helianthoides density timeseries and GAMM model results with 95% confidence intervals, at the Redfish Rocks Marine Reserve and Humbug Comparison Area. See separate tabs for timseries and GAMM results.

4.4.2.1.2 P. helianthoides Density Modeled GAMM Results

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4.4.3 Purple Sea Urchin; Strongylocentrotus purpuratus

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4.4.3.1 Density

No significant difference in S. purpuratus density between the Redfish Rocks Marine Reserve and Humbug Comparison Area.

There was no difference in S. purpuratus density between the marine reserve and Humbug Comparison Area (p > 0.05; Table 19).

Significant yearly trends in S.purpuratus density at the Redfish Rocks Marine Reserve and the Humbug Comparison Area.

There were significant trends by year in S. purpuratus density at the Redfish Rocks Marine Reserve and the Humbug Comparison Area (p < 0.05; Table 20), with an increase at both sites in 2019; however this increase was more pronounced at the Humbug Comparison Area (Fig 14).

The random effect of depth was not identified as a significant component of variation (Table 20).

GAMM model results can be found in the links below:

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4.4.3.1.1 S. purpuratus Density Timeseries

Fig. 14: S. purpuratus density timeseries and GAMM model results with 95% confidence intervals, at the Redfish Rocks Marine Reserve and Humbug Comparison Area. See separate tabs for timseries and GAMM results.

4.4.3.1.2 S. purpuratus Density Modeled GAMM Results

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4.4.4 Red Sea Urchin; Mesocentrotus franciscanus

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4.4.4.1 Density

Significantly lower M. franciscanus density in the Redfish Rocks Marine Reserve than the Humbug Comparison Area.

M. franciscanus density was lower in the marine reserve compared to the Humbug Comparison Area (p < 0.05; Table 21).

Significant yearly trends in M.franciscanus density at the Redfish Rocks Marine Reserve and the Humbug Comparison Area.

There were significant trends by year in M. franciscanus density at the Redfish Rocks Marine Reserve and the Humbug Comparison Area (p < 0.05; Table 22), with an increase at both sites in 2019; however this increase was more pronounced at the Humbug Comparison Area (Fig 15).

The random effect of depth was not identified as a significant component of variation (Table 22).

GAMM model results can be found in the links below:

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4.4.4.1.1 M. franciscanus Density Timeseries

Fig. 15: M. franciscanus density timeseries and GAMM model results with 95% confidence intervals, at the Redfish Rocks Marine Reserve and Humbug Comparison Area. See separate tabs for timseries and GAMM results.

4.4.4.1.2 M. franciscanus Density Modeled GAMM Results

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4.4.5 Rock Scallop; Crassadoma gigantea

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4.4.5.1 Density

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

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

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4.4.5.1.1 C. gigantea Density Timeseries

Fig 16: C. gigantea density timeseries at the Redfish Rocks Marine Reserve and Humbug Comparison Area.

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4.4.6 California Sea Cucumber; Parastichopus californicus

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4.4.6.1 Density

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

Densities of P. californicus were very low across all sites and years (Fig. 17), so statistical analyses were not conducted.

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4.4.6.1.1 P. californicus Density Timeseries

Fig 17: P. californicus density timeseries at the Redfish Rocks Marine Reserve and Humbug Comparison Area.

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4.4.7 Giant Plumose Anemone; Metridium farcimen

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4.4.7.1 Density

Significantly higher density of M. farcimen in the the Redfish Rocks Marine Reserve than the Humbug Comparison Area.

M. farcimen density was higher in the marine reserve compared to the Humbug Comparison Area (p < 0.05; Table 23).

Significant yearly trends in M. farcimen density at the Redfish Rocks Marine Reserve only.

There were significant trends by year in M. farcimen density at the Redfish Rocks Marine Reserve (p < 0.05; Table 24), with a decline after the first two years of sampling. There was no trend at the Humbug Comparison Area (p > 0.05; Fig. 18, Table 24).

The random effect of depth was identified as a significant component of variation (Table 24).

GAMM model results can be found in the links below:

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4.4.7.1.1 M. farcimen Density Timeseries

Fig. 18: M. farcimen density timeseries and GAMM model results with 95% confidence intervals, at the Redfish Rocks Marine Reserve and Humbug Comparison Area. See separate tabs for timseries and GAMM results.

4.4.7.1.2 M. farcimen Density Modeled GAMM Results

Fig. 18: M.farcimen density timeseries and GAMM model results with 95% confidence intervals, at the Redfish Rocks Marine Reserve and Humbug Comparison Area. See separate tabs for timseries and GAMM results.

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4.5 Additional Species Density

4.5.1 Embedded Sea Cucumber; Cucumaria miniata

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4.5.1.1 Density

No significant difference in C. miniata density between the the Redfish Rocks Marine Reserve and the Humbug Comparison Area.

There was no difference in density of C. miniata between the marine reserve then Humbug Comparison Area (p > 0.05; Table 25).

Significant yearly trends in C. miniata density at the Redfish Rocks Marine Reserve only.

There were significant trends by year in C. miniata density at the Redfish Rocks Marine Reserve (p < 0.05), with an increase through 2015 followed by a decline through 2019. There was no trend at the Humbug Comparison Area (p > 0.05; Table 26).

The random effect of depth was not identified as a significant component of variation (Table 26).

GAMM model results can be found in the links below:

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4.5.1.1.1 C. miniata Density Timeseries

Fig. 19: C. miniata density timeseries and GAMM model results with 95% confidence intervals, at the Redfish Rocks Marine Reserve and Humbug Comparison Area. See separate tabs for timseries and GAMM results.

4.5.1.1.2 C. miniata Density Modeled GAMM Results

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5 References

Anderson M.J., Walsh D.C.I. 2013. PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: What null hypothesis are you testing? Ecological Monographs 83(4): 557-574.

Chao A., Gotelli N.J., Hsieh T.C., Sander E.L., Ma K.H., Colwell R.K., Ellison A.M. (2014) Rarefaction and extrapolation with Hill numbers: A framework for sampling and estimation in species diversity studies. Ecol Monogr 84:45–67

Choat, J. H., & Robertson, D. R. (2002). Age-based studies. Coral reef fishes: Dynamics and diversity in a complex ecosystem, 57-80.

Clarke K.R., Chapman M.G., Somerfield P.J., Needham H.R. (2006). Dispersion-based weighting of species counts in assemblage analyses. Mar Ecol Prog Ser 320: 11-27.

Green, R. H., & Young, R. C. (1993). Sampling to detect rare species. Ecological Applications, 3(2), 351-356.

Hill M.O. (1973) Diversity and Evenness : A Unifying Notation and Its Consequences. Ecology 54:427–432.

Hinkle D.E., Wiersma W., Jurs S.G. Applied Statistics for the Behavioral Sciences. 5th ed. Boston: Houghton Mifflin; 2003

Hsieh, T. C., Ma, K. H., & Chao, A. (2016). iNEXT: an R package for rarefaction and extrapolation of species diversity (H ill numbers). Methods in Ecology and Evolution, 7(12), 1451-1456.

Legendre P. and Anderson M.J. 1999. Distance-based redundancy analysis: Testing multispecies responses in multifactorial ecological experiments. Ecological Monographs 69(1): 1-24.

Lester, S. E., Halpern, B. S., Grorud-Colvert, K., Lubchenco, J., Ruttenberg, B. I., Gaines, S. D., … & Warner, R. R. (2009). Biological effects within no-take marine reserves: a global synthesis. Marine Ecology Progress Series, 384, 33-46.

Love, M. S., & Yoklavich, M. M. (2006). Deep rock habitats. In The ecology of marine fishes (pp. 253-266). University of California Press.

ODFW (2014). Oregon Marine Reserve Ecological Monitoring Report 2010-2011. Oregon Department of Fish and Wildlife. Marine Resources Program. Newport Oregon. 1-131.

R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL: https://www.R-project.org/.

Venables, W. N., & Dichmont, C. M. (2004). GLMs, GAMMs and GLMMs: an overview of theory for applications in fisheries research. Fisheries research, 70(2-3), 319-337.

Zuur, A., Ieno, E. N., Walker, N., Saveliev, A. A., & Smith, G. M. (2009). Mixed effects models and extensions in ecology with R. Springer Science & Business Media.

Zuur, A. F. (2012). A beginner’s guide to generalized additive models with R (pp. 1-206). Newburgh, NY, USA: Highland Statistics Limited.

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