1 Introduction: Across Reserves SCUBA Invertebrate Report

In 2012, Oregon completed designation of five marine reserve sites with help from community groups working together with state officials. The five marine reserve sites are not considered a network, as they were selected individually, without consideration of any other proposed site. The result led to five unique areas, of different sizes, with different habitats, and historical fishing pressures. Even though the unique attributes of each reserve has led to the development of individual monitoring plans tailored to each reserve’s characteristics, some monitoring methods allow for across reserve comparisons to gain a better understanding of the similarities and differences across multiple reserve sites. SCUBA invertebrate swath sampling is one of those monitoring methods.

The purpose of SCUBA 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 m. 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 at the transect level.

Surveys occur in the fall and spring at each reserve. While the reserves are different ages, implementation was staggered, and not always sampled in the same years, we can explore the similarities and differences observed across the marine reserves with the same monitoring tool.

SCUBA invertebrate sampling occurs at four of the five marine reserves - Redfish Rocks, Otter Rock, Cascade Head and the Cape Falcon Marine Reserves. The rocky hard bottom habitat at the Cape Perpetua Marine Reserve is too deep to conduct SCUBA sampling, and is therefore not included in the analysis of this report. Sampling began at the Redfish Rocks and Otter Rock Marine Reserves in 2010, in 2013 for the Cascade Head Marine Reserves, and in 2016 for the Cape Falcon Marine Reserve. Due to limited ODFW staffing, not all sites were surveyed in all years.

Table 1: Marine Reserve 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 relative invertebrate abundance across nearshore reefs coastwide. We can also explore these data with questions about diversity and community composition to compare across reserves and validate trends at larger spatial or temporal scales. This can further help us understand how the invertebrate communities at these sites are similar or different. For all data our main focus is exploring trends spatially and temporally.

1.1 Research Questions

Diversity

Are there differences in species diversity across the marine reserves?

Community Composition

Are there differences in invertebrate composition across the marine reserves?
- If yes, what species drive this variation?
- If no, what other factors may explain structure in invertebrate composition?

Aggregate Abundance

Are there differences in aggregate invertebrate density across the marine reserves?
Are there similar trends in aggregate invertebrate density across the marine reserves through time?

Focal Species Abundance

Are there differences in focal species density across the marine reserves?
Are there similar trends in focal species density across the marine reserves through time?

2 Takeaways

Here we present a summary of our across reserves SCUBA invertebrate monitoring analysis and conclusions.

2.1 SCUBA Invertebrate Results Summary

Many aspects of invertebrate species diversity were similar among all four marine reserves monitored with SCUBA.

The four marine reserves monitored with SCUBA (Redfish Rocks, Otter Rock, Cascade Head and Cape Falcon Marine Reserves) had a similar species richness (observed and estimated) and similar diversity indices (effective number of species). Mean invertebrate species richness was similar among sites, and all the marine reserves had similar species identified as common species. The SCUBA surveys observed unique species at Redfish Rocks and Cascade Head Marine Reserves, while no unique species were observed at the Otter Rock and Cape Falcon Marine Reserves. The Cascade Head had more rare species than the other reserves.

Community composition had some structuring among reserves.

Redfish Rocks and Cape Falcon had distinct structuring of the invertebrate community that was both different from each other and different from the Cascade Head and Otter Rock Marine Reserves. The Otter Rock and Cascade Head Marine Reserves were the most similar to each other.

Aggregate density was dominated by six taxonomic groups: anemones, barnacles, cucumbers, gastropods, tunicates and sea urchins. There were variable trends across taxonomic groups and reserves

Six taxonomic groups dominated the relative abundance of aggregate invertebrate density. In each of these taxonomic groups there appear to be some differences among the marine reserve sites; all other taxonomic groupings show very low mean densities at all marine reserves. Many of the yearly trends by taxonomic groupings and reserves were variable. To note, sea urchin densities increased at the Redfish Rocks Marine Reserve through time to a degree not observed at any other reserve. Sea stars appear to show a decline at the Redfish Rocks Marine Reserve, but an increase at the Otter Rock Marine Reserve. Tunicates seem to have declined across most marine reserves.

Focal species differences among marine reserves were found with Ochre Sea Stars and Purple and Red Sea Urchins.

There was a higher density of Pisaster ochraceus (Ochre Sea Star) at the Otter Rock and Cascade Head Marine Reserves compared to Redfish Rocks. Both species of sea urchins Strongylocentrotus purpuratus (Purple Urchin) and Mesocentrotus franciscanus (Red Urchin) had higher densities at the Redfish Rocks Marine Reserve compared to all other marine reserves. There was no difference in Pycnopodia helianthoides (Sunflower Sea Star) densities among reserves due to the low densities and high variability observed at each site.

Table 2: Snapshot of Mean Abundance Results

Species with significant yearly patterns varied across reserves.

P. helianthoides yearly trends decreased across all reserves except for Cape Falcon. While there was not a statistically detectable trend at Cape Falcon, no P. helianthoides were observed at the site in 2017. Both sea urchin species had increasing trends, with S. purpuratus increasing at Redfish Rocks and Otter Rock Marine Reserves and M. franciscanus increasing at Redfish Rocks and Cascade Head Marine Reserves. The one species with differing yearly trends among reserves was P. ochraceus (Ochre Sea Star), with a decreasing trend found at Redfish Rocks, but an increasing trend at Otter Rock Marine Reserve. For Crassadoma gigantea, Parastichopus californicus, and Medtridium farcimen there were too few observations across all sites to conduct statistical analysis.

Table 3: Snapshot of Abundance Trend Results

2.2 Conclusions

The Sunflower Sea Star has not been observed at any site since 2016 sampling at Cape Falcon.

Zero P. helianthoides were observed at the Redfish Rocks, Otter Rock or Cascade Head Marine Reserve after 2015, but eight individuals were observed at Cape Falcon in the first year of sampling in 2016. There have been zero observations across 2017-2019 sampling in the marine reserves. This absence of P. helianthoides coincides with the aftermath of sea star wasting disease hitting the Oregon Coast in 2014.

A relationship between declining sea star densities and increasing sea urchin densities is found at the Redfish Rocks Marine Reserve, but is not apparent at the other marine reserves. Two sea star species are still considered common across all marine reserve sites.

Declines in both P.ochraceus and P.helianthoides were observed only at the Redfish Rocks Marine Reserve. At Otter Rock Marine Reserve, while observations of P.helianthoides declined, P.ochraceus densities increased in the final years of sampling. P.ochraceus densities did not have significant yearly trends at the Cascade Head or Cape Falcon Marine Reserves. Of note beyond the P.ochraceus and P.helianthoides, Henricia spp (Blood Star) and Dermasterias imbricata (Leather Star) were both observed with high frequencies of occurrence across all four marine reserves. Both Sea Urchin Species (S.purpuratus, M.franciscanus) had increasing densities at the Redfish Rocks Marine Reserve, but not at any other marine reserve site. This may suggest that either 1) the sea urchin recruitment observed on the south coast has not occurred at sites north of Cape Blanco with the same success or 2) the impact of sea star wasting disease did not impact all marine reserve sites equally.

We are protecting a range of different subtidal invertebrate communities in our marine reserves.

The Cape Falcon and Redfish Rocks Marine Reserves have distinct invertebrate communities that are different from each other and the invertebrate communities of Otter Rock and Cascade Head Marine Reserves. The two marine reserves of the central coast, Otter Rock and Cascade Head, are more similar to each other than the other marine reserves. The siting and design of Oregon’s marine reserve sites were community-led, and for many of the reserve proposals there was a lack of coast-wide spatially explicit data on subtidal invertebrate communities to evaluate the proposed reserve sites. This report provides the first spatially explicit evaluation of the subtidal invertebrate communities at four of the five marine reserves, and documents differences in the subtidal invertebrate community associated with these sites.

3 SCUBA Invertebrate Methods

SCUBA invertebrate sampling is conducted at four marine reserves - Redfish Rocks, Otter Rock, Cascade Head and Cape Falcon - following PISCO protocols, modified for diving safety in Oregon. Monitoring began at Redfish Rocks and Otter Rock in 2010, with staggered implementation of monitoring at the other two sites. Depending on site, sampling effort targeted 2-4 days for both spring and fall monitoring in each marine reserve.

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. The target depths at the Otter Rock Marine Reserve are at 5 m and 12.5 m due to the shallow nature of hard bottom habitat at this site. 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 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, 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 SCUBA 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 marine reserve site. We did this through data visualizations with non-multidimensional scaling (nMDS) plots and cluster analysis.

To explore variation by site, we used invertebrate density data collected on SCUBA invertebrate 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.

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 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 Across Reserves SCUBA Invertebrate Results

SCUBA invertebrate sampling efforts varied across the four marine reserve sites (Fig. 1). The most sampling (5 years) occurred at the oldest marine reserve sites - Redfish Rocks Marine Reserve and Otter Rock Marine Reserve. Four years of sampling occurred at the Cascade Head Marine Reserve and two years of sampling occurred at the Cape Falcon Marine Reserve.

Fig. 1: SCUBA invertebrate monitoring efforts across marine reserve sites resulted in varied sample sizes. Sample size is represented in number of transects.

Table 6: Marine Reserve SCUBA Invertebrate Monitoring Efforts

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4.1 Diversity

4.1.1 Species richness

Species richness is lowest at the Cape Falcon Marine Reserve.

Observed species richness was lowest at the Cape Falcon Marine (n = 29). Cascade Head had the highest observed species richness (n = 35), followed by Redfish Rocks (n = 33) and Otter Rock (n = 33). These observed numbers of species richness are similar to the estimated numbers of total species richness (Table 7). Estimated total species richness was also very similar across sites (n = 34-36).

library(kableExtra)
pna <- data.frame(Area = c("Redfish Rocks Marine Reserve", 
                           "Otter Rock Marine Reserve",
                           "Cascade Head Marine Reserve",
                           "Cape Falcon Marine Reserve"), 
                  Observed_Richness = c("33","33","35","29"), 
                  Estimated_Richness = c("34","35","35", "37"),
                  LCL = c("33","33","35", "30"), 
                  UCL = c("45", "52","38","90"))


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

Table 7: Observed and estimated 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
Otter Rock Marine Reserve	33	35	33	52
Cascade Head Marine Reserve	35	35	35	38
Cape Falcon Marine Reserve	29	37	30	90

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Species rarefaction curves highlight that across all samples sizes, the species richness is similar among reserves (Fig. 2). As effort across sites increases, more rare species are observed resulting in higher estimated species richness (Fig. 2, Table 7). The Redfish Rocks, Otter Rock and Cascade Head rarefaction curves appear to level off, suggesting saturation in species richness with this tool at these sites.

Fig. 2: Species rarefaction curves across marine reserve sites. Data are pooled across all years of sampling for each site.

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4.1.2 Unique, common and rare species

Although the number of unique and common species are similar across the marine reserves, the Cascade Head Marine Reserve has the most rare species.

The Redfish Rocks Marine Reserve had one unique species - the Velcro Star, Stylasterias forreri - and the Cascade Head Marine Reserve also had one unique species - the crab Loxorhynchus sp. No unique species were observed at the Otter Rock or Cape Falcon Marine Reserves.

The Cascade Head Marine Reserve had the highest common species observed (n = 10), but the other reserves had similar numbers of common species (Table 8-10). Nine of the ten common species observed at the Cascade Head Marine Reserve were also observed as common at one or more of the other reserves. Only Balanus sp. was common only at the Cascade Head Marine Reserve. Two species were common only at the Otter Rock Marine Reserve, Cryptochiton stelleri and Anthopleura xanthogrammica. Two species were common only at the Redfish Rocks Marine Reserve, Metridium farcimen and Strongylocentrotus purpuratus. One species was considered common only at the Cape Falcon Marine Reserve, Urticina coriacea.

The Cascade Head Marine Reserve had the most rare species (n = 14), followed by the Otter Rock Marine Reserve (n = 8). The Redfish Rocks (n = 6) and Cape Falcon (n = 4) Marine Reserves had the fewest number of rare species.

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. (Tables 8-11).

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4.1.2.1 Redfish Rocks Marine Reserve

Fig. 3: Relative frequency of occurrence of species observed across marine reserve sites with SCUBA invertebrate surveys. See separate tabs for each site.

4.1.2.2 Otter Rock Marine Reserve

Fig. 3: Relative frequency of occurrence of species observed across marine reserve sites with SCUBA invertebrate surveys. See separate tabs for each site.

4.1.2.3 Cascade Head Marine Reserve

Fig. 3: Relative frequency of occurrence of species observed across marine reserve sites with SCUBA invertebrate surveys. See separate tabs for each site

4.1.2.4 Cape Falcon Marine Reserve

Fig. 3: Relative frequency of occurrence of species observed across marine reserve sites with SCUBA invertebrate surveys. See separate tabs for each site

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4.1.3 Diversity Indices

Similar effective number of species at the four marine reserve sites across the three diversity indices.

MInimal differences in the number of effective species across diversity indices and the marine reserve sites (Fig. 4).

Fig. 4: Comparing effective number of species (Hill diversity numbers) across the marine reserves 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 any of the marine reserve sites with SCUBA invertebrate data.

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. 5-8).

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Mean SCUBA transect richness is similar across all sites.

When comparing mean species richness for an average SCUBA transect, all sites were not statistically different from one another (p>0.05) (Fig. 9).

Fig. 9: Mean species richness by site with 95% confidence intervals across marine reserves from SCUBA data.

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4.2 Community Composition

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4.2.1 Variation by Site

The Redfish Rocks and Cape Falcon Marine Reserves have distinct invertebrate community compositions.

Results from nMDS plots highlight that both the Cape Perpetua and Cape Falcon Marine Reserves have distinct invertebrate community compositions - both from each other and from the other two marine reserve sites (Fig. 10). The invertebrate community composition from the Otter Rock Marine Reserve and Cascade Head Marine Reserve are the most similar.

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4.2.1.1 Site

Fig. 10: Results from nMDS plots with SCUBA invertebrate data across marine reserves, highlighting that the Redfish Rocks and Cape Falcon Marine Reserves are distinct in their respective invertebrate communities.

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4.3 Aggregate Abundance

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4.3.1 Aggregate Density

Six main taxonomic groups dominate the relative abundance across the marine reserves.

Six main taxonomic groups dominate the relative abundance among taxonomic groups - Anemones, Barnacles, Cucumbers, Gastropods, Tunicates and Sea Urchins (Fig. 11).

Higher site densities of Sea Urchins at Redfish Rocks.

There were variable site differences in densities across broad taxonomic categories (Fig. 11). For example, the Redfish Rocks Marine Reserve had the highest density of Sea Urchins and Cape Falcon Marine Reserve had the lowest densities of Tunicates (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 we see an increase through time, such as Sea Urchins at Redfish Rocks Marine Reserve and Seas Stars at Otter Rock Marine Reserve. With other groups, there are declines through time at one or both sites, such as with Anemones or Tunicates across most sites and Sea Stars at Redfish Rocks Marine Reserves (Fig. 11).

4.3.1.1 Mean Aggregate Density by Site

Fig. 11: Aggregate density timeseries of SCUBA targeted invertebrates across marine reserves. 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 across marine reserves. 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

Significantly lower P. ochraceus density at the Redfish Rocks Marine Reserve than the Otter Rock Marine Reserve.

There was significantly lower P. ochraceus density at the Redfish Rocks Marine Reserve than the Otter Rock Marine Reserve (p < 0.05; Table 12). There was no significant difference in P .ochraceus density between the Redfish Rocks Marine Reserve and Cape Falcon or Cascade Head Marine Reserves (p > 0.05; Table 12).

Significant yearly trends in P.ochraceus density at the Redfish Rocks and Otter Rock Marine Reserves.

There were significant trends by year in P. ochraceus at the Redfish Rocks and Otter Rock Marine Reserves but they had opposite trends through time (p < 0.05; Table 13). At the Redfish Rocks Marine Reserve, P. ochraceus density dropped to nearly absent after the 2010-2011 sampling. At Otter Rock Marine Reserve P. ochraceus density increased in the final two years of sampling (2017 and 2019). No significant trends were observed at the Cascade Head or Cape Falcon Marine Reserves (p > 0.05; Table 13).

The random effect of depth was identified as a significant component of variation (Table 13).

GAMM model results can be found in the links below:

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4.4.1.1.1 P. ochraceus Density by Site

Fig. 12: P. ochraceous density by site, yearly timeseries and GAMM model results with 95% confidence intervals, across marine reserves. See separate tabs for timseries and GAMM results.

4.4.1.1.2 P. ochraceus Density Timeseries

Fig. 12: P. ochraceous density by site, yearly timeseries and GAMM model results with 95% confidence intervals, across marine reserves. See separate tabs for timseries and GAMM results.

4.4.1.1.3 P. ochraceus Density Modeled GAMM Results

Fig. 12: P. ochraceous density by site, yearly timeseries and GAMM model results with 95% confidence intervals, across marine reserves. See separate tabs for timseries and GAMM results.

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4.4.2 Sunflower Star, P. helianthoides

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4.4.2.1 Density

No significant differences in P. helianthoides density between the Redfish Rocks Marine Reserve and the other three marine reserves.

No significant differences in P. helianthoides density between the Redfish Rocks Marine Reserve and the Otter Rock, Cascade Head, or Cape Falcon Marine Reserves (p > 0.05; Table 14).

Significant yearly trends in P. helianthoides density at the Redfish Rocks, Otter Rock, and Cascade Head Marine Reserves.

There were significant trends by year in P. helianthoides at the Redfish Rocks, Otter Rock, Cascade Head Marine Reserves (p < 0.05; Table 15), all with declining trends to nearly absent after 2014/2015 sampling. No significant yearly trend was observed at the Cape Falcon Marine Reserves (p > 0.05; Table 15), but no P. helianthoides were observed in 2017.

The random effect of depth was not identified as a significant component of variation (Table 15).

GAMM model results can be found in the links below:

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4.4.2.1.1 P. helianthoides Density by Site

Fig. 13: P. helianthoides density by site, yearly timeseries and GAMM model results with 95% confidence intervals, across marine reserves. See separate tabs for timseries and GAMM results.

4.4.2.1.2 P. helianthoides Density Timeseries

Fig. 13: P. helianthoides density by site, yearly timeseries and GAMM model results with 95% confidence intervals, across marine reserves. See separate tabs for timseries and GAMM results.

4.4.2.1.3 P. helianthoides Density Modeled GAMM Results

Fig. 13: P. helianthoides density by site, yearly timeseries and GAMM model results with 95% confidence intervals, across marine reserves. See separate tabs for timseries and GAMM results.

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4.4.3 Purple Sea Urchin; Strongylocentrotus purpuratus

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4.4.3.1 Density

Significantly higher S. purpuratus density at the Redfish Rocks Marine Reserve than the other three marine reserve sites.

There were significantly higher S. purpuratus densities at the Redfish Rocks Marine Reserve than any the Otter Rock, Cascade Head, or Cape Falcon Marine Reserves (p < 0.05; Table 16).

Significant yearly trends in S. purpuratus at the Redfish Rocks and Otter Rock Marine Reserves.

There were significant trends by year in S. purpuratus at the Redfish Rocks and Otter Rock Marine Reserves (p < 0.05; Table 17), but not at Cascade Head or Cape Falcon Marine Reserves (p > 0.05; Table 17). At the Redfish Rocks Marine Reserve, density increased through time. At the Otter Rock Marine Reserve S. purpuratus density slightly increased in the later years of sampling (Fig X).

The random effect of depth was identified as a significant component of variation (Table 17).

GAMM model results can be found in the links below:

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4.4.3.1.1 S. purpuratus Density by Site

Fig. 14: S. purpuratus density by site, yearly timeseries and GAMM model results with 95% confidence intervals across marine reserves. See separate tabs for timseries and GAMM results.

4.4.3.1.2 S. purpuratus Density Timeseries

Fig. 14: S. purpuratus density by site, yearly timeseries and GAMM model results with 95% confidence intervals across marine reserves. See separate tabs for timseries and GAMM results.

4.4.3.1.3 S. purpuratus Modeled GAMM Results

Fig. 14: S. purpuratus density by site, yearly timeseries and GAMM model results with 95% confidence intervals, across marine reserves. See separate tabs for timseries and GAMM results.

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4.4.4 Red Sea Urchin; Mesocentrotus franciscanus

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4.4.4.1 Density

Significantly higher M. franciscanus density in the Redfish Rocks Marine Reserve compared to other marine reserve sites.

There were significantly higher M. franciscanus densities at the Redfish Rocks Marine Reserve than any the Otter Rock, Cascade Head, or Cape Falcon Marine Reserves (p < 0.05; Table 18).

Significant yearly trends in M. franciscanus at the Redfish Rocks and Cascade Head Marine Reserves.

Significant yearly trends in M. franciscanus was observed at the Redfish Rocks and Cascade Head Marine Reserves (p < 0.05; Table 19), at both sites density increased through time. There were no significant trends by year in M. franciscanus at the Otter Rock Marine Reserve or Cape Falcon Marine Reserves (p > 0 .05; Table 19).

The random effect of depth was not identified as a significant component of variation (Table 19).

GAMM model results can be found in the links below:

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4.4.4.1.1 M. franciscanus Density by Site

Fig. 15: M. franciscanus density by site, yearly timeseries and GAMM model results with 95% confidence intervals across marine reserves. See separate tabs for timseries and GAMM results.

4.4.4.1.2 M. franciscanus Density Timeseries

Fig. 15: M. franciscanus density by site, yearly timeseries and GAMM model results with 95% confidence intervals across marine reserves. See separate tabs for timseries and GAMM results.

4.4.4.1.3 M. franciscanus Density Modeled GAMM Results

Fig. 15: M. franciscanus density by site, yearly timeseries and GAMM model results with 95% confidence intervals across marine reserves. See separate tabs for timseries and GAMM results.

$~$ $~$

4.4.5 Rock Scallop; Crassadoma gigantea

$~$

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.

$~$ $~$

4.4.5.1.1 C. gigantea Density by Site

Fig. 16: C. gigantea density by site and yearly timeseries across marine reserves with 95% confidence intervals.

4.4.5.1.2 C. gigantea Density Timeseries

Fig. 16: C. gigantea density by site and yearly timeseries across marine reserves with 95% confidence intervals.

$~$ $~$

4.4.6 California Sea Cucumber; Parastichopus californicus

$~$

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. No observations of P. californicus found at the Otter Rock Marine Reserve.

$~$ $~$

4.4.6.1.1 P. californicus Density by Site

Fig. 17: P. californicus density by site and yearly timeseries across marine reserves with 95% confidence intervals.

4.4.6.1.2 P. californicus Density Timeseries

Fig. 17: P. californicus density by site and yearly timeseries across marine reserves with 95% confidence intervals.

$~$ $~$

4.4.7 Giant Plumose Anemone; Metridium farcimen

$~$

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. 18), so statistical analyses were not conducted.

$~$ $~$

4.4.7.1.1 M. farcimen Density by Site

$Fig. 18: *M. farcimen* density by site and yearly timeseries with 95% confidence intervals across marine reserves.$

Fig. 18: M. farcimen density by site and yearly timeseries with 95% confidence intervals across marine reserves.

4.4.7.1.2 M. farcimen Density Timeseries

Fig. 18: M. farcimen density by site and yearly timeseries with 95% confidence intervals across marine reserves.

$~$ $~$

5 References

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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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