1 Introduction: Cascade Head 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 Cascade Head began in 2013, one year before harvest restrictions began. Sampling is conducted in the marine reserve and two comparison areas, Cavalier and Schooner Creek (see methods Appendix for additional information about comparison area selection). We conducted four years of sampling that are included in our analysis and report. Note, sampling in Schooner Creek did not begin until 2014.

Table 1: Cascade Head 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 Cascade Head Marine Reserve

Fig. 1: Map of SCUBA transect locations at Cascade Head Marine Reserve

1.1.2 Schooner Creek Comparison Area

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

1.1.3 Cavalier Comparison Area

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

Fig. 1: Map of SCUBA transect locations at Cavalier 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 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 most similar between Cascade Head Marine Reserve and Schooner Creek Comparison Area

The Cascade Head and Schooner Creek Comparison Area had similar diversity indices (effective number of species) and species richness, with Cavalier Comparison Area having a the lowest diversity index and species richness. The marine reserve had the most unique and rare species compared to either comparison area. The common species were similar between the marine reserve and its comparison areas.

Community composition has some structuring between sites and years.

We detected some community structuring across all sites, with the early years (2013, 2014) differing from the later years (2017, 2018). The majority of community variation was driven by changing densities of barnacles, Mesocentrotus franciscanus (Red Sea Urchin), and Styela montereyensis (Stalked Tunicate). Specifically, the density of barnacles and M. franciscanus increased at the comparison areas while S. montereyensis was notably absent in the 2017-2019 sampling.

Aggregate density was dominated by three taxonomic groups: barnacles, tunicates and urchins. There were variable trends across taxonomic groups and sites.

As we looked across taxonomic groups, barnacles, tunicates and sea urchins dominate abundances across all sites. The most apparent difference by site was a higher mean density of barnacles at Schooner Creek and higher densities of sea urchins in the comparison areas compared to the Cascade Head Marine Reserve. Through time we saw variable trends across taxonomic groups at the reserve and comparison area. There was an evident increase in urchins at Schooner Creek Comparison Area, but not at the Cavalier Comparison Area. In contrast, there was a decline in tunicate densities across all sites.

Species densities that differed by site were mostly lower at the Cascade Head Marine Reserve relative to one or both of the comparison areas.

Densities of both sea urchin species, Strongylocentrotus purpuratus (Purple Sea Urchin) and M. franciscanus, were higher at the Schooner and Cavalier Comparison Areas than the Cascade Head Marine Reserve. Greater densities of Pisaster ochraceus (Ochre Sea Star) were observed at Cascade Head than Schooner Creek, but lower densities than Cavalier. Higher densities of Crassadoma gigantea (Rock Scallops) were found in Cavalier Comparison Area than in the Cascade Head Marine Reserve.

Table 2: Snapshot of Mean Abundance Results

Increasing yearly trends were detected in multiple species at the Cascade Head Marine Reserve and Schooner Creek Comparison Area, but not the Cavalier Comparison Area.

Four species had increasing yearly trends at the Cascade Head Marine Reserve and/or Schooner Creek Comparison Area, but no yearly trends in these species were detected at Cavalier Comparison Area. S.purpuratus had an increasing trend at Schooner Creek Comparison Area starting in 2018. M.franciscanus increased at Schooner Creek Comparison Area and at the Cascade Head Marine Reserve, both starting in 2017. This increase in M.franciscanus was greater at Schooner Creek than the marine reserve. We also detected increasing densities through time of C. gigantea at the Cascade Head Marine Reserve and Balanus nubilus (Giant Acorn Barnacle) at the marine reserve and Schooner Creek Comparison Area. The density of S. montereyensis declined through time at the marine reserve and comparison areas and was the only consistent species trend across sites.

Table 3: Snapshot of Abundance Trend Results

2.2 Conclusions

This is the first report summarizing SCUBA invertebrate monitoring efforts at the Cascade Head Marine Reserve

The Ecological Monitoring Report 2012-2013 (ODFW 2015) did not include any analysis or summary of SCUBA monitoring efforts at the Cascade Head Marine Reserve because the first successful SCUBA invertebrate transects did not take place until 2013, and only at two sites - the marine reserve and Cavalier Comparison Area. Schooner Creek Comparison Area was not surveyed until 2014. This report documents that species diversity is most similar between the marine reserve and Schooner Creek Comparison Area. The invertebrate community composition shows some structuring by sites and years with increased densities of the barnacle (B.nubilus) and the Red Sea Urchin (M.Franciscanus) predominantly found at the two comparison areas, and likely the result of differences between sites. Many of the common species found at the marine reserve are also common at its comparison areas: two sea stars, Henricia spp, and *Dermasterias imbricata** are the most commonly observed species at all sites.

There were no observations of the Pycnopodia helianthoides (Sunflower Sea Star) after sea star wasting disease hit the Oregon Coast in 2014.

We detected low densities of P. helianthoides in early years of sampling across all sites, but have no observation recorded in 2017 and 2018 sampling across all sites. There were no obvious trends in densities of P.ochraceus related to sea star wasting detected at the Cascade Head Marine Reserve or its two comparison area sites.

We also detected an increasing trend of M. franciscanus (Red Sea Urchin) or S. purpuratus (Purple Sea Urchin), but not consistently at all sites. Increasing trends in the Red Sea Urchin were detected at the marine reserve and Schooner Creek Comparison Area , and an increasing trend in Purple Sea Urchins was only detected at the Schooner Creek Comparison Area.

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

The ODFW Monitoring Report of 2010-2011 (ODFW 2014) suggested 10 transects per site are needed to characterize Oregon’s invertebrate communities, in most years we achieved that sample size at the marine reserve and Schooner Creek Comparison Area but not at the Cavalier Comparison Area. Limited sample sizes were a result of challenging 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. Reducing required sample sizes needed to detect change such as moving to permanent 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 was quite large (2-14 fold differences in density, most significant differences detected greater than 3-fold). 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 toward 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 Cascade Head Marine Reserve, Schooner Creek and Cavalier Comparison Areas following PISCO protocols, modified for diving safety in Oregon. Monitoring began in the Cascade Head Marine Reserve and Cavalier Comparison Area in 2013, successful sampling of Schooner Creek occurred in 2014. 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 comparison areas 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.Replicate transects are completed within a site, which are selected to encompass rocky reef habitats that range from 10-20 m depth. Minimal kelp habitat is located in the Cascade Head Marine Reserve and its associated comparison areas, so dive site locations were randomly generated from available habitat within the targeted depth ranges.

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). 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 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 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 daily diversity using an anova. This would provide useful information about site diversity for an average sampling day of effort.

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. We used raw data because there were no apparent dominant species and transformations all overly increased the distributions of less common 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. 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 may also be a location effect.

Beyond site and year, we explored species-specific drivers in the variation of invert 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 Oregon 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 Cascade Head Results

SCUBA invertebrate sampling efforts at Cascade Head and its comparison areas resulted in four years of data collection, where varying sample sizes were collected per year (Fig. 2). Sampling efforts resulted in more transects completed in the marine reserve than in the comparison areas. Schooner Creek Comparison Area was not sampled in 2013, and the Cavalier Comparison Area was not sampled in 2014.

Fig. 2: SCUBA invertebrate monitoring efforts at the Cascade Head Marine Reserve and its comparison areas resulted in varied sample sizes over the four years of data collection. Sample size is represented in number of transects.

Table 6: Cascade Head SCUBA Invertebrate Monitoring Efforts

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4.1 Diversity

4.1.1 Species richness

Invertebrate species richness is most similar between the Cascade Head Marine Reserve and Schooner Creek Comparison Area.

Over the four years of sampling with SCUBA invertebrate surveys, a total of 35 species (or species groups) were observed in the Cascade Head Marine Reserve (Table 7). The Schooner Creek Comparison Area had similar total number of observed species (n=31), and the Cavalier Comparison Area had fewer total observed species (n=28). 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("Cascade Head Marine Reserve",
                           "Schooner Creek Comparison Area",
                           "Cavalier Comparison Area"), 
                  Observed_Richness = c("35","31", "28"),
                  Estimated_Richness = c("35","31", "30"),
                  LCL = c("35","31", "28"), 
                  UCL = c("38", "36", "46"))


  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
Cascade Head Marine Reserve	35	35	35	38
Schooner Creek Comparison Area	31	31	31	36
Cavalier Comparison Area	28	30	28	46

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Species rarefaction curves highlight that for small samples sizes, including those for any given year, the species richness between Cascade Head and Schooner Creek is very similar, and fewer species are observed at Cavalier (Fig. 3). All rarefaction curves appear to level off, suggesting saturation in species richness with this tool at these sites.

Fig. 3: Species rarefaction curves for the Cascade Head Marine Reserve and its associated comparison areas. Data are pooled across all years of sampling for each site.

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4.1.2 Unique, common and rare species

Similarities in common species but differences in unique and rare species between the Cascade Head Marine Reserve and its associated comparison areas.

The Cascade Head Marine Reserve had more unique species (n=3) than its comparison Areas (Table 8). Similar numbers of common species were observed between the marine reserve and its comparison areas; nine out of ten common species in the marine reserve were also common species in both comparison areas. The only exception was P.ochraceus which was a common species in the Cascade Head Marine Reserve but not at any other site. The marine reserve (n = 11) had more rare species than its comparison areas (Table 9).

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.

Unique species, 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 Cascade Head Marine Reserve

Fig. 4: Relative frequency of occurrence of invertebrate species observed at the Cascade Head Marine Reserve and its associated comparison areas from SCUBA transects. See separate tabs for each site.

4.1.2.2 Schooner Creek Comparison Area

Fig. 4: Relative frequency of invertebrate species observed at the Cascade Head Marine Reserve and its associated comparison areas from SCUBA transects. See separate tabs for each site.

4.1.2.3 Cavalier Comparison Area

$Fig. 4: Relative frequency of invertebrate species observed at the Cascade Head Marine Reserve and its associated comparison areas from SCUBA transects. See separate tabs for each site.$

Fig. 4: Relative frequency of invertebrate species observed at the Cascade Head Marine Reserve and its associated comparison areas from SCUBA transects. See separate tabs for each site.

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4.1.3 Diversity Indices

The Cascade Head Marine Reserve has similar diversity indices to the Schooner Creek Comparison Area, but has higher effective numbers of species than the Cavalier Comparison Area for target invertebrates.

Across diversity indices, the effective number of species is similar for the Cascade Head Marine Reserve and the Schooner Creek Comparison Area. However the effective number of species for the Cavalier Comparison Area is lower across all indices than the Cascade Head Marine Reserve (Fig. 5). These results indicate that the marine reserve has more rare species and also a greater evenness of species than the Cavalier Comparison Area.

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Fig. 5: Comparing effective number of species (Hill diversity numbers) across the Cascade Head Marine Reserve and its associated comparison areas fom 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 Cascade Head Marine Reserve and its associated 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. 6-8).

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For an average day of sampling, invertebrate species diversity does not differ between the Cascade Head Marine Reserve and either of its associated comparison areas.

When comparing mean species richness for an average day of sampling, there was no difference between the marine reserve and either of its associated comparison areas (F.1.301, p > 0.05) (Fig. 9).

Fig. 9: Mean species richness by site with 95% confidence intervals at the Cascade Head Marine Reserve and its associated comparison areas from SCUBA invertebrate transects.

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4.2 Community Composition

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4.2.1 Variation by Site and Year

There was some structuring of invertebrate community composition by site between the Cascade Head Marine Reserve and its comparison areas.

There was some structuring of invertebrate community composition data at the Cascade Head Marine Reserve and its comparison areas, with some clustering of samples at both Schooner Creek and Cavalier. (Fig. 10).

Invertebrate community composition appears different in the later years of sampling (2017, 2018), than in the early years (2013/2014) at the Cascade Head Marine Reserve and its surrounding comparison areas.

The early years of sampling (2013/2014) appear different from the later years of sampling (2017/2018) at the Cascade Head Marine Reserve and its surrounding comparison areas (Fig. 10).

Multivariate statistics indicate some differences by year and depth but they explain little total variation in the data.

PERMANOVA results indicate that year, depth, and the interaction between year and depth (p < 0.05) are significant for invertebrate community composition with SCUBA density data (Table 17). Site was barely non-significant (p = 0.055). Estimated variation described by each of the variables and variable interactions was fairlysmall. Year accounted for the highest variability of all the variables/interactions but only accounted for 15% of total variation (site = 12%, depth = 8%, year by depth = 5%), where as the residuals describe over 54% of the variation in the results. Therefore, while these factors and their interactions were significant they are likely not biologically relevant because they describe such a small portion of the variation in the data.

Table 17: PERMANOVA results

PERMDISP results indicates differences in dispersion by year (p = 0.002) and depth (p = 0.034), but not by site. The largest mean dispersion was from 2014 data, and indeed the only significant pairwise comparisons are between 2014 and all other years (Table 18-19).This suggests the significance of year and year by depth interactions identified in the PERMANOVA is likely because of differences in dispersion between years rather than of differences in spatial location among years. The 12.5 m depth had larger dispersion and was significantly different (p < 0.05) than the 20 m depth. Differences among depths and years are likely due to randomized sampling design and variable sampling effort among depths and years. Lack of significant differences in dispersions betrween sites indicate that there are some community differences between sites.

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4.2.1.1 Site

Fig. 10: Results from nMDS plots with SCUBA invertebrate data, demonstrating similarity in invertebrate community composition by site, but differences by year at the Cascade Head Marine Reserve and its comparison areas. See separate tabs for site and year.

4.2.1.2 Year

Fig 10: Results from nMDS plots for SCUBA invertebrate data, demonstrating similairity in invertebrate community composition by site, but differences by year at the Cascade Head Marine Reserve and its surrounding comparison areas. 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.

We explored species-specific drivers of variation, and found that B. nubilus, M. franciscanus and S. montereyensis were driving the majority of variation in the data (Fig. 11). Principal coordinate analysis revealed that ~28% of the variation along the x-axis is explained by B. nubilus and M. franciscanus and 15% of variation is explained along the y-axis from S. montereyensis. (Fig. 11). Together the abundance of these three species accounts for ~ 43% of model variability. The increased densities of B. nubilus and M. franciscanus occur predominantly at the two comparison areas, and are likely the result of differences between sites found in statistical models. Higher densities of B.nubilus and M.franciscanus were observed in the later two years of sampling (2017/2018), and higher densities of S.montereyensis were observed in the earlier years of sampling (2013/2014).

4.2.2.1 PCO Vector Overlay by Site

Fig. 11: Results from species correlations and principal coordinate analysis demonstrating that B. nubilus, M. franciscanus and S. montereyensis drive variaiton in community structure at the Cascade Head Marine Reserve and its comparison areas. Bubble color/size represents species-specific densities in each sample (species density range indicated in legend). See separate tabs for site, year and species bubble plots.

4.2.2.2 PCO by Year

4.2.2.3 PCO Bubble Plot

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4.3 Aggregate Abundance

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4.3.1 Aggregate Density

Three dominate groups at the Cascade Head Marine Reserve and its associated comparison areas.

Barnacles, tunicates, and urchins dominate the relative abundance at the Cascade Head Marine Reserve and its comparison areas (Fig. 12).

Variable trends through time across broad taxonomic groups.

There were variable trends through time across broad taxonomic invertebrate groups (Fig. 12). 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 densities of barnacles and urchins in the comparison areas compared to the Cascade Head Marine Reserve.

Out of all taxonomic groups, only barnacles and urchins had clear differences in 95% confidence intervals between the marine reserve and its comparison areas (Fig. 12). Higher densities of barnacles were observed in the Schooner Creek Comparison Area than the Cascade Head Marine Reserve, and higher densities of urchins were observed in both comparison areas than the marine reserve.

4.3.1.1 Mean Aggregate Density by Site

Fig. 12: Aggregate density timeseries of SCUBA targeted invertebrates at the Cascade Head Marine Reserve and its associated comparison areas. See separate tabs for density by site and timeseries plots.

4.3.1.2 Mean Aggregate Density Timeseries

Fig. 12: Aggregate density timeseries of SCUBA targeted invertebrates at the Cascade Head Marine Reserve and its associated comparison areas.See separate tabs for density by site and timeseries plots.

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4.4 Focal Species Abundance

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4.4.1 Ochre Sea Star, P. ochraceus

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4.4.1.1 Density

Significant higher P. ochraceus density in the Cascade Head Marine Reserve than Schooner Creek Comparison Area, but lower density than the Cavalier Comparison Area.

P. ochraceus density was higher in the marine reserve than the Schooner Creek Comparison Area, but lower than the Cavalier Comparison Area (p < 0.05; Table 20).

No significant yearly trends in P. ochraceus density at Cascade Head Marine Reserve or its comparison areas.

There were no significant trends by year in P. ochraceus density at the Cascade Head Marine Reserve or its comparison areas (Table 21).

The random effect of depth was identified as a significant component of variation (Table 21).

GAMM model results can be found in the links below:

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4.4.1.1.1 P. ochraceus Density Timeseries

Fig. 13: P. ochraceous density timeseries and GAMM model results with 95% confidence intervals, at the Cascade Head Marine Reserve and its associated comparison areas. 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

Few observations across all sites and no P. helianthoides observed at any site after 2014.

There were too few observations to detect differences by site. Across all sites, all observations of P. helianthoides occurred in 2013-2014. No observations of this species were observed in 2017 or 2018.

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4.4.2.1.1 P. helianthoides Density Timeseries

Fig. 14: P. helianthoides density timeseries at the Cascade Head Marine Reserve and its associated comparison areas.

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4.4.3 Purple Sea Urchin; Strongylocentrotus purpuratus

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4.4.3.1 Density

Significant lower S. purpuratus density in the Cascade Head Marine Reserve than its associated comparison areas.

There were lower densities of S. purpuratus in the marine reserve than in both the Schooner Creek and Cavalier Comparison Areas (p < 0.05; Table 22).

Significant yearly trends in S. purpuratus density at the Schooner Creek Comparison Area only.

There were significant yearly trends in S. purpuratus density at the Schooner Creek Comparison Area (p < 0.05; Table 18), with an increase in 2018 sampling. There were no significant trends by year in S. purpuratus at the Cascade Head Marine Reserve or Cavalier Comparison Area (p > 0.05; Table 23).

The random effect of depth was identified as a significant component of variation (Table 23).

GAMM model results can be found in the links below:

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4.4.3.1.1 S. purpuratus Density Timeseries

Fig. 15: S. purpuratus density timeseries and GAMM model results with 95% confidence intervals, at the Cascade Head Marine Reserve and its associated comparison areas. 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 Cascade Head Marine Reserve than both its comparison areas.

Lower density in M. franciscanus was found in the marine reserve compared to the Schooner Creek or Cavalier Comparison Areas (p<0.05, Table 24).

Significant yearly trends in M. franciscanus density observed at the Cascade Head Marine Reserve and Schooner Creek Comparison Area.

There were significant trends by year in M. franciscanus at the Cascade Head Marine Reserve where density increased slightly from 2013 through 2018 (p < 0.05; Table 25). A greater increase through time was observed at the Schooner Creek Comparison Area (p < 0.05; Table 25). No significant yearly trends through time were observed at the Cavalier Comparison Area (p > 0.05; Table 25).

The random effect of depth was identified as a significant component of variation (Table 25).

GAMM model results can be found in the links below:

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4.4.4.1.1 M. franciscanus Density Timeseries

Fig. 16: M. franciscanus density timeseries and GAMM model results with 95% confidence intervals, at the Cascade Head Marine Reserve and its associated comparison areas. 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

Significantly higher C. gigantea density in the Cavalier Comparison Area than the Cascade Head Marine Reserve.

C. gigantea densities were higher in the Cavalier Comparison Area than the Cascade Head Marine Reserve (p < 0.05; Table 26). There was no difference in densities of C. gigantea between the marine reserve and Schooner Creek Comparison Area (p > 0.05; Table 26).

Significant yearly trends in C. gigantea density at the Cascade Head Marine Reserve only

Only the Cascade Head Marine Reserve had significant yearly trends in C. gigeantea (p < 0.05; Table 27), with an increase through time from 2013 through 2018.

The random effect of depth was not identified as a significant component of variation (Table 27).

GAMM model results can be found in the links below:

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4.4.5.1.1 C. gigantea Density Timeseries

Fig. 17: C. gigantea density timeseries and GAMM model results with 95% confidence intervals, at the Cascade Head Marine Reserve and its associated comparison areas. See separate tabs for timseries and GAMM results.

4.4.5.1.2 C. gigantea Density Modeled GAMM Results

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4.4.6 California Sea Cucumber; Parastichopus californicus

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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. 18), so statistical analyses were not conducted.

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4.4.6.0.1 P. californicus Density Timeseries

Fig. 18: P. californicus density timeseries at the Cascade Head Marine Reserve and its associated comparison areas.

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4.4.7 Giant Plumose Anemone; Metridium farcimen

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4.4.7.1 Density

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

Densities of M. farcimen were very low across all sites and years (Fig. 19), so statistical analyses were not conducted.

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4.4.7.1.1 M. farcimen Density Timeseries

Fig. 19: M. farcimen density timeseries at the Cascade Head Marine Reserve and its associated comparison areas.

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4.5 Additional Species Density

4.5.1 Giant Acorn Barnacle, Balanus nubilus

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4.5.1.1 Density

Significantly lower B. nubilus density in the Cascade Head Marine Reserve than the Schooner Creek Comparison Area.

B. nubilus density was lower in the the Cascade Head Marine Reserve than the Schooner Creek Comparison Area (p < 0.05; Table 28). There was no difference in densities of B. nubilus between the marine reserve and Cavalier Comparison Area (p > 0.05; Table 28).

Significant yearly trends in B. nubilus density at the Cascade Head Marine Reserve and Schooner Creek Comparison Area.

The Cascade Head Marine Reserve and Schooner Creek Comparison Area both had significant yearly trends in B. nubilus density (p < 0.05; Table 29). At the marine reserve, B. nubilus densities increased through time from 2013 through 2018 (Fig X). The Schooner Creek Comparison saw an steep increase through time in B. nubilus densities from 2014 through 2017, but then densities leveled off through 2018. No significant yearly trend was detected at the Cavalier Comparison Area (p > 0.05; Table 29).

The random effect of depth was not identified as a significant component of variation (Table 29).

GAMM model results can be found in the links below:

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4.5.1.1.1 B. nubilus Density Timeseries

Fig. 20: B. nubilus density timeseries and GAMM model results with 95% confidence intervals, at the Cascade Head Marine Reserve and its associated comparison areas. See separate tabs for timseries and GAMM results.

4.5.1.1.2 B.nubilus Density Modeled GAMM Results

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4.5.2 Stalked Tunicate, Styela montereyensis

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4.5.2.1 Density

No significant difference in S. montereyensis density between the Cascade Head Marine Reserve and its associated comparison areas.

No significant difference in density of S. montereyensis between the Cascade Head Marine Reserve and its comparison areas (p > 0.05; Table 30).

Significant yearly trends in S.montereyensis density detected at all sites

Significant yearly trends in S. montereyensis density detected at the Cascade Head Marine Reserve and its associated comparison areas (all p < 0.05; Table 31). At the marine reserve S. montereyensis densities declined significantly from 2013 through 2018. Similar trends were detected at both comparison areas.

The random effect of depth was identified as a significant component of variation (Table 31).

GAMM model results can be found in the links below:

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4.5.2.1.1 S. montereyensis Density Timeseries

Fig. 21: S. montereyensis density timeseries and GAMM model results with 95% confidence intervals, at the Cascade Head Marine Reserve and its associated comparison areas. See separate tabs for timseries and GAMM results.

4.5.2.1.2 S. montereyensis 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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