1 Introduction: Cape Falcon Marine Reserve SCUBA Habitat and Cover 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 30 m 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 habitat and cover sampling at Cape Falcon began in 2016, the year harvest restrictions began. Sampling attempts were made in 2015 but did not result in data collection due to poor visibility and challenging weather conditions. Sampling is conducted in the marine reserve and three comparison areas that represent varying levels of fishing pressure (see methods Appendix for additional information about comparison area selection). We conducted two years of sampling that are included in our analysis and report. Note, we were not able to successfully collect data in the comparison areas until 2017.

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. Since limited sampling was conducted at Cape Falcon, our main focus is exploring trends by site.

1.1 Survey Maps

1.1.1 Cape Falcon Marine Reserve

Fig. 14: Map of SCUBA transect locations at Cape Falcon Marine Reserve

Fig. 14: Map of SCUBA transect locations at Cape Falcon Marine Reserve

1.1.2 Low Fishing Pressure Comparison Area

Fig. 14: Map of SCUBA transect locations at Low Fishing Pressure Comparison Area

Fig. 14: Map of SCUBA transect locations at Low Fishing Pressure Comparison Area

1.1.3 Moderate Fishing Pressure Comparison Area

Fig. 14: Map of SCUBA transect locations at Moderate Fishing Pressure Comparison Area

Fig. 14: Map of SCUBA transect locations at Moderate Fishing Pressure Comparison Area

1.1.4 High Fishing Pressure Comparison Area

Fig. 14: Map of SCUBA transect locations at High Fishing Pressure Comparison Area

Fig. 14: Map of SCUBA transect locations at High Fishing Pressure 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 benthic habitat and cover 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 Benthic Habitat and Cover Results Summary

Substrate and relief types sampled were similar between the Cape Falcon Marine Reserve and its associated comparison area.

Substrate types were most similar between Cape Falcon Marine Reserve and the Low and High Fishing Pressure Comparison Areas. Subtle differences in mean percent substrate type were driven by more cobble and small boulder substrate in the Moderate Fishing Pressure Comparison Area. There were minimal differences in relief categories across sites. Relief at the Moderate Fishing Pressure Comparison Area was dominated by the ‘10cm<1m’ category - corresponding with the higher proportion of cobble and small boulder.

Greater sampling effort at Cape Falcon Marine Reserve yielded greater species diversity.

Survey effort at Cape Falcon Marine Reserve was 3-4 times greater during these preliminary two years of effort. This likely corresponded with the greater observed and estimated species richness at the marine reserve compared to any of its comparison areas. There were also more rare and unique species at the Cape Falcon Marine Reserve. These results offer a preliminary comparison across survey sites at Cape Falcon, but more sampling is needed to better characterize benthic cover species diversity among sites.

Despite limited data, benthic cover community composition is similar among sites.

Benthic transects were similar between the Cape Falcon Marine Reserve and its associated comparison areas. There was no structuring by depth despite significance identified in a multivariate analysis; likely a result of limited and unequal sampling effort among depths and sites. There were five species groups driving the majority of the variation in benthic cover community composition - anemones, barnacles, bryozoans, crustose coralline algae, and encrusting red algae.

Four taxonomic groups dominate aggregate percent cover summaries: barnacles, bryozoans, coralline algae, and sponges.

There were four dominant taxonomic groups for aggregate percent cover - barnacles, bryozoans, coralline algae, and sponges. There were minimal apparent differences in mean percent cover of taxonomic groups by site, however there appear to be more Barnacles in the Cape Falcon Marine Reserve than the Low fishing Pressure Comparison Area.

There were not enough data to statistically evaluate percent cover for spatial or temporal trends.

Across all species, there were not enough surveys to conduct statistical analysis of focal species percent cover.

2.2 Conclusions

More sampling is needed to fully characterize the Cape Falcon Marine Reserve and its associated comparison areas, but current species lists provide a valuable foundation for these sites.

This is the first report attempting to analyze SCUBA benthic habitat and cover data at Cape Falcon and its associated comparison areas. A total of 22 benthic cover categories were recorded at the Cape Falcon Marine Reserve, and 11 at the Low Fishing Pressure Comparison Area. The comparison areas with higher fishing pressure (Moderate and High) had fewer documented cover categories (13 and 16 respectively) than the Cape Falcon Marine Reserve. This is likely due to the comparatively low sample sizes at comparison area sites. The most abundant benthic cover categories at the Cape Falcon Marine Reserve were crustose coralline algae, encrusting red algae and barnacles. Both crustose coralline algae and encrusting eed algae were the top two most abundant benthic cover categories at all comparison area sites as well. Limited sampling hindered our ability to appropriately characterize these four sites to 1) determine the appropriate nature of the Low Fishing Pressure Comparison Area as a reference site to the marine reserve and 2) document benthic cover at all sites. Still, these data provide a first snapshot of the expected list of benthic cover groups available at Cape Falcon Marine Reserve.

SCUBA 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 all sites. This is not surprising given the depths targeted by SCUBA surveys at the Cape Falcon 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 cover data provides useful information about the relative cover and change over time of red algae, not gathered in other monitoring tools. Encrusting red algae was identified as an important driver of variation in species community composition, with the limited data available. 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 these surveys will be useful in evaluating community stability through time.

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

The initial Ecological Monitoring Report of 2010/2011 suggested 10 transects per site are needed to characterize Oregon’s benthic habitat community, in one year (of two) at the Cape Falcon Marine Reserve we did achieve that sample size, but we did not achieve that sample size at any of the comparison area sites. 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 sites or transects, would be beneficial because of these challenges. In order for our program to confidently detect future changes in benthic habitat cover, 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.

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

The SCUBA habitat and cover surveys at Cape Falcon 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. SCUBA 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 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 and cover (uniform point count, UPC) sampling is conducted in the Cape Falcon Marine Reserve and its associated comparison areas (Low, Moderate, High Fishing Pressure) following PISCO protocols, modified for diving safety in Oregon. Monitoring attempts with SCUBA at Cape Falcon Marine Reserve and comparison areas began in 2016, but resulted in successful data collection only at cape Falcon. Successful data collection of comparison area sites occurred in 2017. Sampling effort targeted 4 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. Substrate type is recorded as sand/gravel (<2cm), cobble (2-10cm diameter), small boulder (10cm-1m diameter), large boulder (1-4m), or bedrock (> 4m diameter). Physical relief is measured as the greatest vertical relief that exists within a 1m x 0.5m rectangle. Two depths are targeted for these surveys 12.5 and 20 meters.

No kelp habitat is located in the Cape Falcon Marine Reserve and its associated comparison areas, so dive site locations were randomly generated from available habitat within the targeted depth ranges. Two replicate transects are conducted at each site (see methods Appendix for more details). 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

We focused our analysis on the question of whether variation in substrate surveyed was driven by site. 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, 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 ran a cluster analysis and generated nMDS plots by site.

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

We focused our analysis on the question of whether variation in relief surveyed was driven by site. 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, 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.

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:

  • 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.

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 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 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.

3.3.4 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 site. 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 we also explored several species-specific drivers of variation.

To explore variation by site, 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.

To test the statistical significance in our data of variation by site we ran a permutational analysis of variance (PERMANOVA), using a mixed model with site and year as fixed effects factors. We considered depth a random effect, since two depths were targeted but there was unequal sampling effort by depth. To explore if any significant results of the PERMANOVA were related to true differences in location or differences in dispersion of samples (by site), 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, we explored species-specific drivers in the variation of benthic community structure. We extended our data visualization, by performing a vector analysis of benthic 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.

3.3.7 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 X). A list of which species are included in each taxonomic groupings is provided in Table X.

To determine which taxonomic groups (aggregate) were the most dominant, we summarized means and 95% confidence intervals grouped by site. 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.

There are two focal algae morphological species groups for the Marine Reserves Ecological Monitoring Program recorded on benthic habitat surveys:

  • Articulated Coralline Algae
  • Crustose Coralline Algae (CCA)

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:

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

4 Cape Falcon Results

SCUBA benthic habitat sampling efforts at the Cape Falcon Marine Reserve and its comparison areas resulted in two 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; with only one year of sampling effort in the comparison areas.

Fig. 2: SCUBA benthic habitat monitoring efforts at the Cape Falcon 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.

Fig. 2: SCUBA benthic habitat monitoring efforts at the Cape Falcon 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.

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4.1 Substrate

4.1.1 Variation by Site

Overall substrate types sampled by site were similar, with differences driven mostly by cobble and small boulder substrates.

There was no apparent structuring of substrate type sampled by site; however, slight differences in relative proportion of substrate type by survey site were detected (Fig. 4). These differences were mostly driven by differences in mean percent cover of cobble and small boulder substrates in the Moderate Fishing Pressure Comparison Area compared with any other survey site (Fig. 3, Table 5).

Fig. 4: Results from nMDS plots with SCUBA UPC data, demonstrating similarity in substrate at the Cape Falcon Marine Reserve and its associated comparison areas.

Fig. 4: Results from nMDS plots with SCUBA UPC data, demonstrating similarity in substrate at the Cape Falcon Marine Reserve and its associated comparison areas.

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4.2 Relief

4.2.1 Variation by Site

No apparent differences in relief by site at the Cape Falcon Marine Reserve and its associated comparison areas.

There was no structuring of relief by site at the Cape Falcon Marine Reserve and its comparison areas. (Fig. 6). The Medium Fishing Pressure comparison area was unique in that relief was dominated by the 10cm-1m category.

No differences in mean percent cover of relief categories by site between Cape Falcon Marine Reserve and its associated comparison areas.

The Medium Fishing Pressure Comparison Area was significantly different in mean percent cover across all relief categories (Fig. 5, Table 6). The mean percent cover of relief categories at Cape Falcon Marine Reserves were not significantly different from the Low or High Fishing Pressure Comparison Areas.

Fig. 6: Results from nMDS plots with SCUBA UPC data, demonstrating similarity in relief at the Cape Falcon Marine Reserve and its comparison areas.

Fig. 6: Results from nMDS plots with SCUBA UPC data, demonstrating similarity in relief at the Cape Falcon Marine Reserve and its comparison areas.

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4.3 Benthic Cover

4.3.1 Diversity

4.3.1.1 Species richness

Benthic habitat species richness is higher in the Cape Falcon Marine Reserve than any of its associated comparison areas

Over the two initial years of sampling with SCUBA UPC surveys, a total of 22 species (or species groups) were observed in the Cape Falcon Marine Reserve (Table 7). The Low Fishing Pressure Comparison Area had 11 species, Moderate Fishing Pressure Comparison Area had 13 species and High Fishing Pressure Comparison Area had 16 species. These observed numbers of species richness are similar to the estimated numbers of total species richness.

library(kableExtra)
pna <- data.frame(Area = c("Cape Falcon Marine Reserve",
                           "Low Fishing Pressure Comparison Area",
                           "Moderate Fishing Pressure Comparison Area",
                           "High Fishing Pressure Comparison Area"),
                  Observed_Richness = c("22","11", "13","16"), 
                  Estimated_Richness = c("26","12", "18", "18"), 
                  LCL = c("23","11", "14", "16"),
                  UCL = c("46", "19", "48", "32"))


  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
Cape Falcon Marine Reserve 22 26 23 46
Low Fishing Pressure Comparison Area 11 12 11 19
Moderate Fishing Pressure Comparison Area 13 18 14 48
High Fishing Pressure Comparison Area 16 18 16 32

With the limited data available, species rarefaction curves highlight that for any samples size, including those for any given year, the species richness among sites is different (Fig. 7). Sample sizes are low across all sites, suggesting more sampling is needed to understand saturation in species richness with this tool at these sites.

Fig. 7: Species rarefaction curves for the Cape Falcon Marine Reserve and its associated comparison areas. Data are pooled across all years of sampling for each site.

Fig. 7: Species rarefaction curves for the Cape Falcon 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 species

More unique and rare species observed at the Cape Falcon Marine Reserve, but also more sampling.

More unique species were observed at the Cape Falcon Marine Reserve than any of its associated comparison areas. There were four unique species at Cape Falcon Marine Reserve: Petaloconchus montereyensis, Diopatra/Chaetopterus spp., Lacy Red Algae, Mussel (Table 8). Low Fishing Pressure Comparison Area had one unique species: Dodecaceria fewkesi. Moderate and High Fishing Pressure Comparison Areas did not have unique species observed.

Similar numbers of common species were observed between the marine reserve (n = 5) and the Low (n = 8) and High (n = 9) Fishing Pressure Comparison Areas (Tables 8,11,14,17). The Moderate Fishing Pressure Comparison Area did not have many common species (n = 2). The top two common species across all survey sites were Crustose Coralline Algae and Encrusting Red Algae. All of the common species at the Cape Falcon Marine Reserve were also considered common at either the Low or High Fishing Pressure Comparison Areas. The Cape Falcon Marine Reserve had more rare species (n = 5) than its comparison areas (n = 0 across all three sites). Note that for comparison areas, these estimates of common and rare species are based on seven SCUBA transects or less.

Many of the other target benthic habitat (UPC) 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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4.3.1.2.1 Cape Falcon Marine Reserve
Fig. 8: Relative frequency of occurrence of benthic habitat species observed at the Cape Falcon Marine Reserve and its associated comparison areas from SCUBA transects. See separate tabs for each site.

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

4.3.1.2.2 Low Fishing Pressure Comparison Area
Fig. 8: Relative frequency of benthic habitat species observed at the Cape Falcon Marine Reserve and its associated comparison areas from SCUBA transects. See separate tabs for each site.

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

4.3.1.2.3 Medium Fishing Pressure Comparison Area
Fig. 8: Relative frequency of benthic habitat species observed at the Cape Falcon Marine Reserve and its associated comparison areas from SCUBA transects. See separate tabs for each site.

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

4.3.1.2.4 High Fishing Pressure Comparison Area
Fig. 8: Relative frequency of benthic habitat species observed at the Cape Falcon Marine Reserve and its associated comparison areas from SCUBA transects. See separate tabs for each site.

Fig. 8: Relative frequency of benthic habitat species observed at the Cape Falcon 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

Similar effective number of species observed at the Cape Falcon Marine Reserve and its associated comparison areas across all three diversity indices

Broad confidence intervals around diversity estimates indicate that the effective number of benthic cover species is similar between Cape Falcon Marine Reserve and its associated comparison areas. Total observed species richness was greatest at Cape Falcon Marine Reserve where the greatest sampling was completed (Fig. 9).

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Fig. 9: Comparing effective number of species (Hill diversity numbers) across the Cape Falcon Marine Reserve and its associated comparison areas fom SCUBA UPC 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).Fig. 9: Comparing effective number of species (Hill diversity numbers) across the Cape Falcon Marine Reserve and its associated comparison areas fom SCUBA UPC 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).

Fig. 9: Comparing effective number of species (Hill diversity numbers) across the Cape Falcon Marine Reserve and its associated comparison areas fom SCUBA UPC 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 Cape Falcon 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. 10-11).

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For an average transect, benthic habitat species diversity does not differ between the Cape Falcon Marine Reserve and its associated comparison areas.

When comparing mean species richness for an average transect, there was no difference between the marine reserve and its associated comparison areas (F.2.51, p>0.05) (Fig. 14).

Fig. 14: Mean species richness by site with 95% confidence intervals at the Cape Falcon Marine Reserve and its associated comparison areas from SCUBA UPC transects.

Fig. 14: Mean species richness by site with 95% confidence intervals at the Cape Falcon Marine Reserve and its associated comparison areas from SCUBA UPC transects.

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4.3.3 Community Composition

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4.3.3.1 Variation by Site

Benthic communities were similar at the Cape Falcon Marine Reserve and its associated comparison areas with SCUBA UPC data.

There was no structuring of benthic community data at the Cape Falcon Marine Reserve and its associated comparison areas. (Fig. 15).

While multivariate statistics indicate differences by depth, and the interaction between depth and site are likely influenced by low sample sizes across sites and depths.

PERMANOVA results indicate that depth and the interaction between depth and site (all p < 0.05) were significant factors/interactions for benthic community composition with SCUBA UPC data (Table 20). Depth described 10% of variation in the data, and the interaction between depth and site accounted for 23% of model variability. The residuals describe over 53% of the variation in the results. PERMDISP results do not indicates differences in dispersion depth (p > 0.05, Table 21).This suggests the significance identified in the PERMANOVA is likely because of differences in location between depths. Although depth and depth by site interactions are significant, and explain approximately 33% of the variability, this significance is more likely influenced by the low and unequal sample sizes between depths/sites (>3x samples at 12.5 vs. 20m) rather than a true biological shift.

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4.3.3.1.1 Site
Fig. 15: Results from nMDS plots with SCUBA UPC data, demonstrating similarity in benthic community composition at the Cape Falcon Marine Reserve and its associated comparison areas.See separate tabs for site and depth.

Fig. 15: Results from nMDS plots with SCUBA UPC data, demonstrating similarity in benthic community composition at the Cape Falcon Marine Reserve and its associated comparison areas.See separate tabs for site and depth.

4.3.3.1.2 Depth
Fig. 15: Results from nMDS plots with SCUBA UPC data, demonstrating similarity in benthic community composition at the Cape Falcon Marine Reserve and its associated comparison areas.See separate tabs for site and depth.

Fig. 15: Results from nMDS plots with SCUBA UPC data, demonstrating similarity in benthic community composition at the Cape Falcon Marine Reserve and its associated comparison areas.See separate tabs for site and depth.

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4.3.3.2 Other drivers of variation

Five benthic species/complexes drive the majority of variation in community composition data.

We explored species-specific drivers of variation, and found that Crustose Coralline Algae, Encrusting Red Algae, Barnacles, Anemones and Bryozoans were driving the majority of variation in the benthic cover data (Fig. 16). Principal coordinate analysis revealed that ~44% of the variation along the x axis is explained by the trade-offs between Crustose Coralline Algae (CCA) and Barnacle cover. The y-axis accounts for an additional ~15% of the variability and is explained by trade-offs between Encrusting Red Algae and Anemones/Bryozoan cover (Fig. 16). Together the percent cover of these five species/complexes accounts for 59% of model variability.

4.3.3.2.1 PCO Vector Plot
Fig. 16: Results from species correlations and principal coordinate analysis demonstrating that five species drive variation in community structure regardless of site at the Cape Falcon Marine Reserve and its surrounding comparison areas. See separate tabs for vector and bubble plots. Bubble color / size represents species-specific densities in each sample (species density range indicated in legend).

Fig. 16: Results from species correlations and principal coordinate analysis demonstrating that five species drive variation in community structure regardless of site at the Cape Falcon Marine Reserve and its surrounding comparison areas. See separate tabs for vector and bubble plots. Bubble color / size represents species-specific densities in each sample (species density range indicated in legend).

4.3.3.2.2 PCO Bubble Plot
Fig. 16: Results from species correlations and principal coordinate analysis demonstrating that five species drive variation in community structure regardless of site at the Cape Falcon Marine Reserve and its surrounding comparison areas. Bubble color / size represents species-specific densities in each sample (species density range indicated in legend).

Fig. 16: Results from species correlations and principal coordinate analysis demonstrating that five species drive variation in community structure regardless of site at the Cape Falcon Marine Reserve and its surrounding comparison areas. Bubble color / size represents species-specific densities in each sample (species density 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 among taxonomic groups at both the Cape Falcon Marine Reserve and its associated comparison areas.

Four main taxonomic groups dominate the relative abundance among taxonomic groups - barnacles, bryozoans, coraline algae, and sponges - at the Cape Falcon Marine Reserve and its comparison areas. (Fig. 17).

More percent cover of Barnacles in the Cape Falcon Marine Reserve than Low Fishing Pressure Comparison Area.

There was more percent cover of barnacles in the Cape falcon Marine Reserve than the Low Fishing Pressure Comparison Area (Fig. 17).

4.4.1.1 Mean Aggregate Percent Cover by Site

Fig. 17: Mean aggregate percent cover timeseries of SCUBA benthic habitat species at the Cascade Head Marine Reserve and its associated comparison areas.

Fig. 17: Mean aggregate percent cover timeseries of SCUBA benthic habitat species at the Cascade Head Marine Reserve and its associated comparison areas.

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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.

Too few observations of Articulated Coralline Algae to detect differences in percent cover by site or year at the Cape Falcon Marine Reserve and its associated comparison areas, so statistical analyses were not conducted.

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4.5.1.1.1 Articulated Coralline Algae Percent Cover by Site
Fig 18: Articulated Coralline Algae percent cover at the Cape Falcon Marine Reserve and its associated comparison areas.

Fig 18: Articulated Coralline Algae percent cover at the Cape Falcon 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

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

Too few observations of Crustose Coralline Algae to detect differences in percent cover by site or year at the Cape Falcon Marine Reserve and its associated comparison areas, so statistical analyses were not conducted.

4.5.2.1.1 Crustose Coralline Algae Percent Cover by Site
Fig. 19: Crustose Coralline Algae percent cover at the Cape Falcon Marine Reserve and its associated comparison areas.

Fig. 19: Crustose Coralline Algae percent cover at the Cape Falcon Marine Reserve and its associated comparison areas.

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4.6 Additional Species Percent Cover

4.6.1 Anemone

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4.6.1.1 Percent cover

Too few observations of Anemones 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 anemones was very low across sites and years (Fig. 20), so statistical analyses were not conducted.

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4.6.1.1.1 Anemone Percent Cover by Site
Fig 20: Anemone percent cover at the Cape Falcon Marine Reserve and its associated comparison areas.

Fig 20: Anemone percent cover at the Cape Falcon Marine Reserve and its associated comparison areas.

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4.6.2 Barnacle

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4.6.2.1 Percent cover

Too few observations of Barnacles 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 barnacles was very low across sites and years (Fig. 21), so statistical analyses were not conducted.

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4.6.2.1.1 Barnacle Percent Cover by Site
Fig. 21: Barnacle percent cover at the Cape Falcon Marine Reserve and its associated comparison areas.

Fig. 21: Barnacle percent cover at the Cape Falcon Marine Reserve and its associated comparison areas.

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4.6.3 Bryozoan

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4.6.3.1 Percent cover

Too few observations of Bryozoans 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 bryozoans was very low across sites and years (Fig. 22), so statistical analyses were not conducted.

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4.6.3.1.1 Bryozoan Percent Cover by Site
Fig. 22: Bryozoan percent cover at the Cape Falcon Marine Reserve and its associated comparison areas.

Fig. 22: Bryozoan percent cover at the Cape Falcon Marine Reserve and its associated comparison areas.

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4.6.4 Encrusting Red Algae

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4.6.4.1 Percent cover

Too few observations of Encrusting Red Algae 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 Encrusting Red Algae was very low across sites and years (Fig. 23), so statistical analyses were not conducted.

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4.6.4.1.1 Encrusting Red Algae Percent Cover by Site
Fig. 23: Encrusting Red Algae percent cover at the Cape Falcon Marine Reserve and its associated comparison areas.

Fig. 23: Encrusting Red Algae percent cover at the Cape Falcon Marine Reserve and its associated comparison areas.

5 References

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