1 Introduction: Cascade Head Marine Reserve SCUBA Habitat Survey Report

SCUBA habitat sampling characterizes benthic habitat cover and associated reef attributes (substrate type, relief) following PISCO protocols for uniform point count (UPC) surveys. These surveys provide insight into the structure and function of nearshore rocky reef communities in Oregon’s state waters. Divers record three types of information every meter along a 30m transect: substrate type, physical relief and identity of the organism attached to the reef. The percent-cover of space-occupying organisms is estimated for species that are directly attached to the primary substrate and includes non-motile benthic invertebrates and algae. Two depths are targeted for these surveys 12.5 and 20 meters. Write-ins are allowed, for species not included on PISCO data-sheets.

Our SCUBA benthic habitat 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 Benthic Habitat Monitoring Efforts. Sample sizes represent the number of transects per year at each site

Data from SCUBA benthic habitat monitoring efforts can be used to explore questions about benthic habitat diversity, community composition and percent cover of various species groups. Questions about diversity and community composition can be used to help us understand how the benthic communities at these sites are similar or different. Data on percent cover can 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

Substrate

Does substrate surveyed vary by site or year?

Relief

Does relief surveyed vary by site or year?

Benthic Cover

*Does the diversity of benthic cover vary by site or year?

Does community composition of benthic cover vary by site or year? If yes, what species drive this variation?

Does aggregate benthic cover vary by site or year?

Focal Species Benthic Cover

Does focal species benthic cover vary by site or year?

2 Takeaways

Here we present a summary of our SCUBA Habitat and Cover 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 Benthic Habitat Habitat and Cover Results Summary

Relief and substrate types sampled were similar among sites.

Substrate types encountered in transects at the Cascade Head Marine Reserve and its associated comparison areas were mostly similar. There were a few distinct transects at Cascade Head from surveys in 2017 and 2018 which encountered small boulder habitat. Means across the different relief categories did not differ more than 10% between sites.

Benthic habitat and cover diversity is similar between Cascade Head Marine Reserve and its comparison areas

The diversity of cover categories was similar across survey sites for comparable levels of survey effort. There were 6 unique cover categories at Cascade Head Marine Reserve compared to only one at Schooner Creek Comparison Area and no unique cover categories at Cavalier Comparison Area. All unique cover categories were observed at low percent-cover and demonstrate that the additional survey effort at Cascade Head Marine Reserves likely corresponded with the detection of these additional rare categories. The marine reserve had similar effective number of cover categories to its two comparison areas.

Composition of benthic habitat and cover categories was similar among sites but had slight structuring by year.

The composition of benthic habitat categories across transects was similar among sites but had slight structuring by year. The benthic habitat composition during the first years of sampling (2013/2014) was slightly different from the later two years (2017/2018) of sampling across sites. There were two benthic cover groups driving the majority of the variation: Crustose Coralline Algae and Bare Bedrock / Boulder.

Four taxonomic groups dominate aggregate percent cover analyses: Barnacles, Bryozoans, Crustose Coralline Algae and Sponges.

There were four dominant taxonomic groups for aggregate percent cover - Barnacles, Bryozoans, Crustose Coralline Algae and Sponges. As we look across taxonomic groups through time we see variable trends at the reserve and comparison area, and there are no apparent differences in taxonomic groups by site.

We detected trends by year in Crustose Coralline Algae at the Cascade Head Marine Reserve and its two comparison areas.

As part of our focal species analysis, we explored trends in two morphological groupings of coralline algae: ‘crustose’ and ‘articulated’. There were no differences Crustose Coralline Algae percent cover among sites. Similar yearly trends were detected at all sites. Increases in Crustose Coralline Algae were detected at the Cascade Head Marine Reserve and its two comparison areas at Schooner Creek and Cavalier. There were too few observations of Articulated Coralline Algae to conduct separate statistical analyses.

2.2 Conclusions

This is the first report summarizing SCUBA habitat and cover 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 SCUBA monitoring efforts began at this site in 2013. Analysis of substrate and relief categories indicates that the references sites are comparable in available habitat and appropriately chosen for the Cascade Head Marine Reserve. Similarities in diversity, community composition and abundance estimates among sites further support the conclusion that both comparison areas are appropriate for this marine reserve. Crustose Coralline Algae is the most commonly observed benthic habitat cover category for all sites. Five of the seven most commonly observed habitat categories at the Cascade Head Marine Reserve are also considered common at one or both of the comparison areas.

SCUBA habitat and cover data provides valuable information about Red Algae not gathered in other monitoring tools.

We documented higher cover of Red Algae relative to Brown and Green Algae at both sites. This is not surprising given the depths targeted by SCUBA habitat and cover surveys at the Cascade Head Marine Reserve and its comparison areas. Red algae are the most diverse group of seaweeds in the Northeast Pacific, and many are used by humans for a variety of purposes including food, medical research or in cosmetics. The SCUBA benthic habitat data provides useful information about the relative cover and change over time of Red Algae, not gathered in other monitoring tools. Algal-dominated communities, when examined at the functional group level, can be more temporally stable and predictable than when examined at the species level (Steneck and Dethier 1994), suggesting the algal functional group data of the SCUBA habitat and cover surveys will be useful in evaluating community stability through time. -

A move toward permanent sites or transects needed to confidently detect future trends in benthic habitat cover with SCUBA surveys

The ODFW Ecological Monitoring Report of 2010-2011 suggested 10 transects per site are needed to characterize Oregon’s benthic habitat community (ODFW 2014). In most years we did achieve that sample size at the Cascade Head 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 all sites, despite limited sample sizes, the magnitude of these changes was quite large (typically a 2-6 fold difference in percent cover). In order for our program to confidently detect future changes in benthic habiat cover species at smaller magnitudes of change than those detected in this report, increased sampling effort or moving to permanent transects or sites 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.

SCUBA benthic habitat and cover surveys provide valuable context to ecological patterns detected in other SCUBA surveys

The SCUBA habitat and cover surveys at Cascade Head Marine Reserve and its comparison areas allowed us to collect valuable information on benthic cover species and cover groups. This tool collects reliable, fine-scale data on habitat cover that provides important context to ecological patterns detected, such as with changes to Coralline Algae, Sea Urchin, and Sea Star populations. SUCBA habitat and cover surveys are conducted simultaneously with SCUBA invertebrate surveys, and when water clarity allows, SCUBA fish transects are subsequently conducted along the same transect. While beyond the current capacity for inclusion in this report, conducting community analyses that explore change through time and by site with multiple components of the ecosystem is feasible with the suite of SCUBA surveys conducted at this site.

3 SCUBA UPC Methods

SCUBA benthic habitat sampling is conducted in the Cascade Head Marine Reserve, Schooner Creek and Cavalier Comparison Areas following PISCO uniform point count (UPC) 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 UPC sampling is to characterize benthic cover and associated reef attributes (substrate type, relief). Divers record three types of information beneath 30 points (one per meter mark), along a 30 meter transect: substrate type, physical relief and identity of the organism attached to the reef. The percent-cover of space-occupying organisms is estimated for species that are directly attached to the primary substrate and includes non-motile benthic invertebrates and algae. Two depths are targeted for these surveys 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.

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 Substrate

Substrate type is recorded as one of four categories: sand/gravel (<2cm), cobble (2-10cm diameter), small boulder (10cm-1m diameter), large boulder (1-4m), or bedrock (> 4m diameter).

3.1.1 Variation by Site and Year

We focused our analysis on the question of whether variation in substrate surveyed was driven by spatial (site) or temporal (year) factors. We did this through data visualizations with non-multidimensional scaling (nMDS) and an anova of mean percent cover of substrate class by site.

To explore variation by site and year, we used substrate data collected on SCUBA habitat and cover transects; data were not exceedingly skewed so no transformation was used (Clarke et al. 2006).Percent cover of substrate types were calculated from SCUBA count data (# points/ transect) 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 generated nMDS plots by site and year.

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

3.1.2 Variation in Substrate Category By Site

To explore variation in substrate type category by site we ran a Kruskal-Wallis comparison, and plotted mean substrate category by site with 95% confidence intervals.

3.2 Relief

Relief is recorded as one of four categories: 0 < 10 cm, 10 cm < 1m, 1 <2 m, and > 2m.

3.2.1 Variation by Site and Year

We focused our analysis on the question of whether variation in relief surveyed was driven by spatial (site) or temporal (year) factors. We did this through data visualizations with non-multidimensional scaling (nMDS) and an anova of mean percent cover of relief category by site.

To explore variation by site and year, we used substrate data collected on SCUBA UPC transects; data were not exceedingly skewed so no transformation was used (Clarke et al. 2006). Percent cover of substrate types were calculated from SCUBA UPC count data (# points/ transect) 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 generated nMDS plots by site and year.

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

3.2.2 Variation in Relief Category By Site

To explore variation in Relief category by site we ran a Kruskal-Wallis comparison, and plotted mean substrate category by site with 95% confidence intervals.

3.3 Benthic Cover

We explored three concepts related to benthic cover - diversity, community composition and changes in abundance (percent cover).

3.3.1 Diversity

With SCUBA benthic surveys, we explored several concepts related to species diversity at a given site:

Note: SCUBA UPC transects survey both biotic and abiotic habitat cover categories. We’ve used the term ‘species’ below to mean the combination of these cover categories.

species richness
unique, common & rare species
diversity indices
diversity through time

3.3.2 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.

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 rarefaction curve, or the estimated total number of cover categories observable by SCUBA UPC 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.

3.3.3 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 benthic cover category 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 cover category is observed, as well as its relative abundance.

From the ‘species count’ tables we identified rare cover categories, as those with a frequency of occurrence of 10% or less (Green and Young 1993), and common cover categories as those with a frequency of occurrence greater than 50% (in other words, the cover category is observed on one of every two transects). We also identified cover categories that were unique to each marine reserve and comparison area.

3.3.4 Diversity Indices

To gain additional insight into species diversity, we explored several diversity indices by comparing Hill diversity numbers, also known as 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.

3.3.5 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 analysis of variance (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.

3.3.6 Community Composition

We focused our community composition analysis on the question of whether variation in benthic cover 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 cover-category-specific drivers of variation.

To explore variation by site and year, we used percent cover data collected on SCUBA UPC transects with no transformation (Clarke et al. 2006). Percent cover was calculated from SCUBA UPC count data (# points/ transect) 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, even though SCUBA invert surveys target two 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 there may also be a location effect.

Beyond site and year, we explored cover-category-specific drivers in the variation of benthic community structure. We extended our data visualization, by performing a vector analysis of benthic cover categories in the community, selecting only the cover categories with > 0.5 Pearson correlations (Hinkle et al. 2003). If more than four cover categories were identified, we only reported on cover categories with high ( > 0.7) Pearson correlations. We then generated percent cover plots of the identified cover categories to visualize their relationship to site or year. To better understand how these cover categories 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.

3.3.7 Abundance

We explored changes in aggregate and focal species percent cover by site and year. For aggregate percent cover we summarized data across benthic habitat taxonomic groups (similar to Lester et al. 2009) to identify broad scale differences in benthic habitat by site and year. Based on the species observed, we had 16 broad taxonomic groupings (Table 3). A list of which species are included in each taxonomic groupings is provided in Table 4.

To determine which taxonomic groups (aggregate) were the most dominant, we summarized means and 95% confidence intervals grouped by site and as a timeseries. For focal species, we analyzed changes in percent cover by site and time with generalized additive mixed models (GAMMs). We modeled percent cover by using percent cover data with a quasi-binomial distribution to account for the metric (counts with an upper limit) and overdispersion (Zuur et al 2009). GAMMs were chosen to account for non-linear trends in percent cover 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 percent cover across most sites and years, no statistical analyses were conducted as the data violated assumptions of the model framework.

The Oregon Marine Reserves Ecological Monitoring Program recorded two focal algae species groups during SCUBA UPC surveys.

Crustose Coralline Algae
Articulated Coralline Algae

Focal 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:

PCT_Cover = mgcv::gam(Percent_Cover ~ Site + s(Year, by = Site, k = 3) + s(Depth_bin, bs = “re”), family = quasibinomial)

3.4 Focal Species Benthic Cover

4 Cascade Head Results

SCUBA habitat and cover 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 habitat and cover monitoring efforts at the Cascade Head Marine Reserve and its comparison areas resulted in varied sample sizes over the five years of data collection. Sample size is represented in number of transects.

Table 4: Cascade Head SCUBA Habitat and Cover Monitoring Efforts

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4.1 Substrate

4.1.0.1 Variation by Site and Year

Overall substrate types sampled by site were similar, but there are a few transects from the Cascade Head Marine Reserve that are distinct.

There was no apparent structuring of substrate type sampled by site, however a few transects from the Cascade Head Marine Reserve are distinct (Fig. 4).

Overall substrate type was not substantially different among years, however a few transects from the last two years of surveys are distinct.

Substrate type was not substantially different among years, with the exception of a few transects from the last two years of sampling where substrate sampled appears distinct.(Fig. 4)

More small boulder habitat surveyed in the Cascade Head Marine Reserve than its associated comparison areas.

The only significant difference in substrate type by site was in the small boulder (10 cm < 1 m), where the marine reserve had greater percent cover than its comparison areaa; for all other subtrate types there was no difference in mean percent cover of substrate type by site (Fig. 3, Table 5).

4.1.0.1.1 Site

Fig. 4: Results from nMDS plots with SCUBA habitat and cover data, demonstrating similarity in substrate at the Cascade Head Marine Reserve and its associated comparison areas. See separate tabs for site and year.

4.1.0.1.2 Year

Fig 4: Results from nMDS plots with SCUBA habitat and cover data, demonstrating similarity in substrate at the Cascade Head Marine Reserve and its associated comparison areas. See separate tabs for site and year

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4.2 Relief

4.2.0.1 Variation by Site and Year

No apparent differences in relief by site or year at the Cascade Head Marine Reserve and its associated comparison areas.

There was no structuring of relief by site or year at the Cascade Head Marine Reserve and its comparison areas. (Fig. 6).

Differences in mean percent cover of relief categories by site.

There were significant differences in mean percent cover of relief categories by site , though absolute difference in percent cover did not exceed 10% among the survey sites (Fig. 5, Table 6).

4.2.0.1.1 Site

Fig. 6: Results from nMDS plots with SCUBA habitat and cover data, demonstrating similarity in relief at the Cascade Head Marine Reserve and its comparison areas. See separate tabs for site and year.

4.2.0.1.2 Year

Fig. 6: Results from nMDS plots for SCUBA habitat and cover data, demonstrating similairity in relief at the Cascade Head Marine Reserve and its comparison areas. See separate tabs for site and year

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4.3 Benthic Cover

4.3.1 Diversity

4.3.1.1 Species richness

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

Over the four years of sampling with SCUBA benthic habitat surveys, a total of 30 habitat cover categories were observed in the Cascade Head Marine Reserve (Table 7). Both comparison areas had slightly fewer total observed cover categories (Schooner Creek Comparison Area n = 26, Cavalier Comparison Area n = 25). The marine reserve and Schooner Creek Comparison Area has similar estimated total species richness, the Cavalier Comparison Area had a lower estimate of total species richness.

library(kableExtra)


pna <- data.frame(Area = c("Cascade Head Marine Reserve",
                           "Schooner Creek Comparison Area",
                           "Cavalier Comparison Area"), 
                  Observed_Richness = c("30","26", "25"), 
                  Estimated_Richness = c("39","38", "29"),
                  LCL = c("31","28", "26"),
                  UCL = c("82", "92", "49"))


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

Table 7: Observed and estimated benthic habitat species richness by site with lower (LCL) and upper (UCL) 95% confidence limits
Area	Observed_Richness	Estimated_Richness	LCL	UCL
Cascade Head Marine Reserve	30	39	31	82
Schooner Creek Comparison Area	26	38	28	92
Cavalier Comparison Area	25	29	26	49

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Rarefaction curves highlight that across all samples sizes, including those for any given year, the species richness between Cascade Head Marine Reserve and its comparison areas is similar (Fig. 7). All rarefaction curves begin to level off, suggesting saturation in species richness with this tool at these sites.

Fig. 7: 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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4.3.1.2 Unique, common and rare cover categories

Slight differences in unique, common, and rare cover categories between the Cascade Head Marine Reserve and its associated comparison areas.

The Cascade Head Marine Reserve had more unique cover categories (n = 6) than its comparison Areas (Table 8). The marine reserve had slightly more common cover categories than its comparison areas; six out of seven common cover categories in the reserve were also considered common cover categories in one or more of the comparison areas. The only exception was branching red algae which was a common cover category in the Cascade Head Marine Reserve but not at any other site. The marine reserve (n = 14) had similar numbers of rare cover categories as its comparison areas (Table 9).

Many of the other benthic habitat cover categories were not observed frequently resulting in low percent cover. Not all cover categories were observed each year, for a summary of frequency of occurrence over the years by site please see tables below.

Unique cover categories, pooled cover category counts across all years and cover category percent cover by individual sampling year are included in the following tables:

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4.3.1.2.1 Cascade Head Marine Reserve

Fig. 8: Relative frequency of occurrence of benthic habitat cover categories observed at the Cascade Head Marine Reserve and its associated comparison areas from SCUBA transects. See separate tabs for each site.

4.3.1.2.2 Schooner Creek Comparison Area

Fig. 8: Relative frequency of benthic habitat cover categories observed at the Cascade Head Marine Reserve and its associated comparison areas from SCUBA transects. See separate tabs for each site.

4.3.1.2.3 Cavalier Comparison Area

Fig. 8: Relative frequency of benthic habitat cover categories 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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4.3.1.3 Diversity Indices

The Cascade Head Marine Reserve has similar benthic habitat species diversity indices to both of its comparison areas.

Across diversity indices and sample sizes, the effective number of species is similar for the Cascade Head Marine Reserve and its associated comparison areas (Fig. 9).

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Fig. 9: Comparing effective number of species (Hill diversity numbers) across the Cascade Head Marine Reserve and its associated comparison areas fom SCUBA benthic habitat 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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4.3.2 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 did not reach an asymptote and indicate that we did not sample enough on a yearly basis to compare changes in species richness through time (Fig. 10-12).

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For an average SCUBA transect, benthic habitat 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 transect, there was no difference between the marine reserve and either of its associated comparison areas (F.1.301, p>0.05) (Fig. 13).

Fig. 13: Mean species richness by area with 95% confidence intervals at the Cascade Head Marine Reserve and its associated comparison areas from SCUBA transects.

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4.3.3 Community Composition

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4.3.3.1 Variation by Site and Year

Benthic communities were similar at the Cascade Head Marine Reserve and its associated comparison areas with SCUBA data.

There was no structuring of benthic habitat composition data at the Cascade Head Marine Reserve and its associated comparison areas. (Fig. 14).

There was some structuring by year with benthic habitat composition data at the Cascade Head Marine Reserve and its comparison areas.

There was some apparent structuring by year with benthic habitat composition data at the Cascade Head Marine Reserve and its associated comparison areas. However, transects from the early survey years (2013-2014) appear to separate slightly from the later survey years (2017, 2018) (Fig. 14).

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

PERMANOVA results indicate that year and depth (p < 0.05) were significant factors for benthic cover community composition with SCUBA data (Table 17). Year described the largest variation in the data out of all factors (~26%) and depth accounted for 9% of the variation, whereas the residuals describe over 57% of the variation in the results. Non-multidimensional scaling plots confirm possible community shifts between both years sampled and depths, as there is some structuring between earlier and later years sampled, as well as some structuring between 12.5 m and 20 m depths.

Table 17: PERMANOVA results

PERMDISP results do not indicates differences in dispersion by year or depth (p > 0.05, Table **).This suggests the significance identified in the PERMANOVA is likely because of differences in location between years and or depths.

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4.3.3.1.1 Site

Fig. 14: Results from nMDS plots with SCUBA data, demonstrating similarity in benthic cover community composition at the Cascade Head Marine Reserve and its associated comparison areas. See separate tabs for site, year, and depth.

4.3.3.1.2 Year

Fig. 14: Results from nMDS plots for SCUBA data, demonstrating similairity in benthic cover community composition at the Cascade Head Marine Reserve and its associated comparison areas. See separate tabs for site, year, and depth.

4.3.3.1.3 Depth

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4.3.3.2 Other drivers of variation

Two benthic cover categories drive the majority of variation in community composition data regardless of site.

We explored category-specific drivers of variation, and found that Crustose Coralline Algae and Bare Bedrock/Boulder were driving the majority of variation in the benthic cover data (Fig. 15). Principal coordinate analysis revealed that ~33% of the variation along the x axis is explained by the percent cover of Crustose Coralline Algae (CCA), with higher percent cover in later sampling years. The y-axis accounts for ~14% of the variability and is likely associated with percent cover of Bare Bedrock / Boulder, with higher percent cover in later sampling years (Fig. 15). Together the abundance of these two habitat categories accounts for 47% of model variability.

4.3.3.2.1 PCO Vector Plot by Site

Fig. 15: Results from habitat cover correlations and principal coordinate analysis demonstrating that Crustose Coralline Algae (CCA) and Bare Bedrock/Boulder drive variation in community structure regardless of site at the Cascade Head Marine Reserve and its surrounding comparison areas. See separate tabs for site, year and cover group bubble plots. Bubble color / size represents species-specific percent cover in each sample .

4.3.3.2.2 PCO Plot by Year

4.3.3.2.3 PCO Bubble Plot

Fig. 15: Results from habitat cover correlations and principal coordinate analysis demonstrating that Crustose Coralline Algae (CCA) and Bare Bedrock/Boulder drive variation in community structure regardless of site at the Cascade Head Marine Reserve and its surrounding comparison areas. See separate tabs for site, year and cover bubble plots. Bubble color / size represents species-specific percent cover in each sample (species percent cover range indicated in legend).

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4.4 Abundance

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4.4.1 Aggregate Percent Cover

Four main taxonomic groups dominate the relative abundance at both the Cascade Head Marine Reserve and its associated comparison areas.

Four main taxonomic groups dominate the relative abundance among taxonomic groups - barnacles, bryozoans, Coralline Algae (aggregate of both crustose and articulated groups), and Sponges - at the Cascade Head Marine Reserve, Schooner Creek Comparison Area, and Cavalier Comparison Area (Fig. 16).

No apparent differences by site in mean percent cover of benthic habitat species.

There were no apparent differences in mean percent cover of benthic habitat categories between the Cascade Head Marine Reserve and its associated comparison areas (Fig. 16).

Variable trends through time across broad taxonomic groups.

There were variable trends through time across broad taxonomic benthic habitat groups (Fig. 16). The majority of taxonomic groups show no clear trends over time (e.g. bryozoans, Red Algae). For a few groups, such as aggregate Coralline Algae, 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 sponges or tunicates.

4.4.1.1 Mean Aggregate Percent Cover by Site

Fig 16: Aggregate percent cover of SCUBA benthic habitat taxanomic groups at the Cascade Head Marine Reserve and its associated comparison areas. See separate tabs for percent cover by site and timeseries plots.

4.4.1.2 Mean Aggregate Percent Cover Timeseries

Fig 16: Aggregate percent cover timeseries of SCUBA benthic habitat taxanomic groups at the Cascade Head Marine Reserve and its associated comparison areas. See separate tabs for percent cover by site and timeseries plots.

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4.5 Focal Species

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4.5.1 Articulated Coralline Algae

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4.5.1.1 Percent cover

Too few observations of Articulated Coralline Algae to detect differences in percent cover by site or year.

Percent cover of Articulated Coralline Algae was very low across sites and years (Fig. 17), so statistical analyses were not conducted.

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4.5.1.1.1 Articulated Coralline Algae Percent Cover Timeseries

Fig. 17: Articulated Coralline Algae percent cover timeseries with 95% confidence intervals, at the Cascade Head Marine Reserve and its associated comparison areas.

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4.5.2 Crustose coralline algae

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4.5.2.1 Percent cover

No significant difference in Crustose Coralline Algae percent cover between the Cascade Head Marine Reserve and its associated comparison areas.

There was no difference in Crustose Coralline Algae percent cover between the marine reserve and the Schooner Creek or Cavalier Comparison Area (p > 0.05; Table 22).

Significant yearly trends in Crustose Coralline Algae at the Cascade Head Marine Reserve and its associated comparison areas.

There were significant trends by year in Crustose Coralline Algae at the Cascade Head Marine Reserve and the Schooner Creek and Cavalier Comparison Areas (p < 0.05; Table 23). At all sites, percent cover increased linearly through time (Fig. 18).

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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4.5.2.1.1 Crustose Coralline Algae Percent Cover Timeseries

Fig. 18: Crustose Coralline Algae percent cover 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 Crustose Coralline Algae Percent Cover Modeled GAMM Results

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4.6 Additional Habitat Category Percent Cover

4.6.1 Bare Bedrock / Boulder

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4.6.1.1 Percent Cover

Too few observations of Bare Bedrock / Boulder to detect differences in percent cover by site or year.

Despite identification in the community analysis as a significant driver of variation in the benthic community, percent cover of Bare Bedrock / Boulder was very low across sites and years (Fig. 19), so statistical analyses were not conducted.

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4.6.1.1.1 Bare Bedrock / Boulder Percent Cover Timeseries

Fig. 19: Bare Bedrock / Boulder percent cover timeseries with 95% confidence intervals, at the Cape Falcon Marine Reserve and its associated comparison areas.

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5 References

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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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