1 Introduction: Otter Rock SCUBA Invertebrate Surveys
SCUBA invertebrate sampling targets the density of specific, conspicuous, solitary and mobile invertebrates. Organisms are chosen due to the large abundance, economic value, or ecological value. Only targeted invertebrates greater than 2.5 cm are counted along a 30 x 2 m belt transects across two target depths, 5 and 12.5. No write-ins are allowed.
Our SCUBA invertebrate sampling at Otter Rock began in 2010, two years before harvest restrictions began. Sampling is conducted in the marine reserve and one comparison area, Cape Foulweather (see methods Appendix for additional information about comparison area selection). We conducted five years of sampling at the marine reserve and efforts resulted in three years of sampling at the comparison area. Data across all five years is included in our analysis and synthesis report.
Data from SCUBA invertebrate monitoring efforts can be used to explore questions about invertebrate diversity, community composition and density. Questions about diversity and community composition can be used to compare across monitoring tools to understand tool bias or to validate trends seen across tools. This can further help us understand how the invertebrate communities at these sites are similar or different. Data on density enable us to explore changes over time; and whether these changes are similar both inside the reserve and outside in comparison areas. For all data our main focus is exploring trends by site and year.
1.1 Survey Maps
1.1.1 Otter Rock Marine Reserve
Fig. 1: Map of SCUBA transect locations at Otter Rock Marine Reserve and Cape Foulweather Comparison Area
1.2 Research Questions
Diversity
- Does species diversity vary by site or year?
Community Composition
- Does community composition vary by site or year?
- If yes, what species drive this variation?
Aggregate Abundance
- Does aggregate density vary by site or year?
Focal Species Abundance
- Does focal species density vary by site or year?
2 Takeaways
Here we present a summary of our SCUBA invertebrate monitoring results and conclusions. Our conclusions are written with an evaluation of our sampling design, knowledge from prior marine reserves monitoring reports, and future directions of marine reserves monitoring in mind.
2.1 SCUBA Invertebrate Results Summary
Species diversity was mostly similar between the Otter Rock Marine Reserve and Cape Foulweather Comparison Area.
The Otter Rock Marine Reserve and Cape Foulweather Comparison Area had similar diversity indices and a similar mean species richness for an average day of sampling. The sites did differ in number of unique, rare, and common species, with the marine reserve having more unique and rare species, but less common species than the comparison area.
Community composition was mostly similar between sites and years.
There was minimal structuring of the invertebrate communities by site or year. There was slightly more transect variation at the marine reserve than Cape Foulweather Comparison Area with invertebrate community composition, and a slight shift in community composition from early years (2010, 2011) to later years (2015, 2017, 2019). Instead, species-specific differences drove the structuring of invertebrate communities with Pisaster ochraceus (Ochre Sea Star) and Mesocentrotus franciscanus (Red Sea Urchin) driving the majority of variation in communities, and slightly higher density of P. ochraceus in the marine reserve and slightly higher density of M. franciscanus in the comparison area. Higher densities of P. ochraceus and M. franciscanus were associated with later survey years (2015 - 2019).
Aggregate density was dominated by two taxonomic groups: tunicates and sea urchins. There were variable trends across taxonomic groups and sites.
Tunicates and sea urchins were the dominant taxonomic groups observed at both the Otter Rock Marine Reserve and Cape Foulweather Comparison Area. The most apparent difference by site was a higher density of sea urchins at the Cape Foulweather Comparison Area than at the the marine reserve. Through time we saw variable trends across taxonomic groups. There was a notable increase in sea urchins at Cape Foulweather Comparison Area in 2019, but this trend was not observed at the marine reserve. In contrast, there was an increase in sea stars at the reserve in 2019 not seen at the comparison area.
Species densities differed for Red Sea Urchins and Ochre Sea Stars between the Otter Rock Marine Reserve and Cape Foulweather Comparison Area.
Densities of Mesocentrotus franciscanus (Red Sea Urchin) were higher at Cape Foulweather Comparison Area than Otter Rock Marine Reserve. This trend was reversed for the Pisaster ochraceus (Ochre Sea Star) with higher densities at Otter Rock Marine Reserve than the comparison area. These two species were also identified in community composition analysis to drive the majority of variation in invertebrate community composition.
Sea Star focal species displayed opposite trends by year.
At the Otter Rock Marine Reserve and the Cape Foulweather Comparison Area we observed an increase in P. ochraceus densities. This increase in P. ochraceus densities was greater at the marine reserve than comparison area and increased most dramatically between 2017 and 2019 sampling, with a fairly flat line trend prior to this uptick. We saw significant declines in densities of P. helianthoides at the Otter Rock Marine Reserve, where observations declined to zero after 2015. Even though trends through time were not detected at the Cape Foulweather Comparison Area, it is worth noting that no P. helianthoides were observed in 2017 or 2019 sampling (this site was not sampled in 2015).
2.2 Conclusions
Differences between the results of this report and the 2010-2011 ODFW Ecological Monitoring report support the need for long-term monitoring.
In contrast to the initial Ecological Monitoring Report of 2010-2011, we did not detect a difference in species richness or diversity between the marine reserve and the comparison area, where the baseline report detected higher richness and diversity in the marine reserve. The most abundant species at the Otter Rock Marine Reserve were previously documented as P. ochraceus, Cucumaria miniata (Burrowing Sea Cucumber), and Styela montereyensis (Stalked Tunicate), with Henricia spp. (Blood Star) abundant across both sites. At the marine reserve, these species are mostly still abundant, but other species (e.g. Dermasterias imbricata or Cryptochiton stelleri) have been documented as abundant with additional data collected after initial sampling. Henricia spp. is still the most abundant species at the comparison area, but M. franciscanus is starting to increase at this site and should be further monitored.
We detected an interesting increase in P. ochraceus density at the Otter Rock Marine Reserve.
We detected a large increase in P. ochraceus in the 2015 and 2019 sampling at the marine reserve. While we can’t identify the exact cause, it could be related to a response to sea star wasting disease that hit the Oregon Coast in 2014 or perhaps a large recruitment year. Further monitoring is necessary to understand trends in subtidal density of this species.
Also, to note in the context of potential response to sea star wasting, we did not detect an increasing trend in Mesocentrotus franciscanus (Red Sea Urchin) at the marine reserve. While not statistically analyzed, there doesn’t appear to be an increase in Strongylocentrotus purpuratus (Purple Sea Urchin) at the marine reserve either. Both sea urchin species had too much variability to conclude any trends and require further monitoring.
A move toward permanent sites or transects is needed to confidently detect future trends in invertebrates with SCUBA surveys
The 2010/2011 ODFW Monitoring Report suggested 10 transects per site are needed to characterize the invertebrate community, in most years we did not achieved that sample size at either site. Limited sample sizes were a result of challenging logistics related to a small boat based survey method in Oregon’s nearshore environment; reducing required sample sizes needed to detect change such as moving to permanent sites or transects, would be beneficial because of these challenges. While we were able to detect several species’ yearly trends at either one site or both despite limited sample sizes, the magnitude of these changes was quite large (6 fold changes). In order for our program to confidently detect future changes in invertebrate species at smaller magnitudes of change than those detected in this report, increased sampling effort or a move to re-establish permanent sites or transects is needed. Increased sampling effort would likely require an increase to the research budget. With a better understanding of the sea states, visibility and communities of nearshore reefs, we can now select the appropriate permanent locations to focus monitoring efforts, maximizing efficiency in data collection and power to detect change over time.
3 SCUBA Invertebrate Methods
SCUBA invertebrate sampling is conducted in the Otter Rock Marine Reserve and Cape Foulweather Comparison Area following PISCO protocols, modified for diving safety in Oregon. Monitoring began in the Otter Rock Marine Reserve in 2010, successful sampling of Cape Foulweather occurred in 2011; 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 2 days for both spring and fall monitoring, splitting effort between the marine reserve and Cape Foulweather Comparison Area based on ocean conditions.
The purpose of invertebrate sampling is to estimate density of specific, conspicuous, solitary and mobile invertebrates. Organisms are chosen due to the large abundance, economic value, or ecological value. Only targeted invertebrates greater than 2.5 cm are counted along a 30 x 2 m belt transects across two target depths, 5 and 12.5 meters. The Otter Rock Marine Reserve is the shallowest of all marine reserve, and there are no 20 m sites to survey here. Sub-sampling occurs within each 10 m segment of the transect for those target species with very high densities (more than 30 individuals per 10 m segment).
In 2010/2011, scientific divers from Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO) selected survey locations with the intent that these sites would be permanent. Selected locations were representative of available rocky reef habitat with kelp, within targeted depth ranges. As monitoring continued, the challenges and safety constraints of diving in Oregon’s nearshore (see Methods Appendix for more details) led to the inevitable need to select alternate locations. Due to unpredictable weather and visibility conditions, sites were selected from randomly generated points based on available rocky reef habitat within targeted depth ranges. These changes resulted in greater spatial coverage of the reef and is more reflective of a stratified random sampling design, rather than one with permanent sites.
The unit of replication is at the transect level. Only fully completed, independent transects were included in analysis. Targeted 5 meter transects from early years of sampling (2010-2011) were included in analysis because of the shallow nature of this site, and several transects from later years occurred at similar depths. For additional details on data collection, please review documentation in the Methods Appendix.
3.1 Diversity
With SCUBA fish surveys, we explored several concepts related to species diversity at a given site:
- species richness
- unique, common & rare species
- diversity indices
- diversity through time
3.1.1 Species Richness
To explore species richness at a given site, we reported total observed species richness and also calculated total estimated species richness.
To report total observed species richness at a given site we used incidence data across all sampling years because species turnover at each site (reserve or comparison area) likely occurs on timescales greater than one year.
To calculate estimated species richness, we used a rarefaction and extrapolation technique as described in Hsieh et al 2016, to calculate the effective number of species at each given site. This is the equivalent of calculating Hill diversity = 0. Hill numbers represent a unified standardization method for quantifying and comparing species diversity across multiple sites (Hill 1973), and they represent an intuitive and statistically rigorous alternative to other diversity indices (Chao et al 2014).
We used the same sampling based incidence data as used to document total observed species richness, using the iNext package in R to estimate the asymptote of the species accumulation curve, or the estimated total number of species observable by SCUBA invertebrate surveys at a given site. We also calculated confidence intervals associated with these rarefaction and extrapolation curves and can therefore compare across sites to explore similarity of total estimated species richness for a given sampling effort.
3.1.2 Unique, Common, and Rare Species
Richness alone does not sufficiently describe species biodiversity; additionally uniqueness, rarity and common species also shape and define concepts of biodiversity.
As a first step to exploring unique, rare and common species we generated species count tables. The species count tables include a total count for each species summed for all years by site, and for each year-site combination, as well as mean frequency of occurrence across all samples. This information can tell us both about how frequently the species is observed, as well as its relative abundance.
From the species count tables we identified rare species, as those with a frequency of occurrence of 10% or less (Green and Young 1993), and common species as those with a frequency of occurrence greater than 50% (in other words, the species is observed on one of every two transects). We also identified species that were unique to each marine reserve and comparison area.
3.1.3 Diversity Indices
To gain additional insight into species diversity, we explored several diversity indices by comparing Hill diversity numbers across sites using the iNEXT diversity package in R (Hsieh et al 2016). Hill numbers are parameterized by a diversity order q, which determines the measures’ sensitivity to species relative abundances (Hsieh et al 2016). Hill numbers include the three most widely used species diversity measures; species richness (q = 0), Shannon diversity (q=1) and Simpson diversity (q=2) (Hsieh et al 2016). We used sampling based incidence data with the iNext package in R, to plot rarefaction and extrapolation curves for each Hill number, and compare results across sites. We also calculated 95% confidence intervals associated with these rarefaction & extrapolation curves.
3.1.4 Diversity Through Time
Finally we explored how diversity changed through time. First we plotted each species yearly rarefaction curve against the total cumulative rarefaction curve for all years combined to determine if we had sampled appropriately to compare species diversity from year to year. When our sampling effort was not adequate to compare across years, we pooled data from all years to compare average transect diversity using an anova.
All analyses and graphs were created in R v4.0.2, using the iNEXT and Vegan packages.
3.2 Community Composition
We focused our community composition analysis on the question of whether variation in invertebrate community composition was driven by spatial (site) or temporal (year) factors. We did this through both data visualizations with non-multidimensional scaling (nMDS) plots and with statistical tests such as principal coordinates analyses (PCO),multivariate ANOVA tests (PERMANOVA), and dispersion tests (PERMDISP). In addition to site and year, we also explored several species-specific drivers of variation.
To explore variation by site and year, we used invertebrate density data collected on SCUBA invert transects with a log transformation to downweight dominant species without overly enhancing importance of rare species (Clarke et al. 2006).Densities were calculated from SCUBA invertebrate count data (# inverts/ area) so a similarity-based resemblance matrix was selected. A dummy variable (=1) was added prior to creating the resemblance matrix due to the high prevalence of zeros in the dataset. To visualize the data, we ran a cluster analysis and generated nMDS plots by site and year.
To test the statistical significance in our data of variation by site and year we ran a permutational analysis of variance (PERMANOVA), using a mixed model with site and year as fixed effects factors. Initial explorations of the first two years of data resulted in no apparent trends by depth between the two target depths, therefore depth was considered a random effect in the model. To account for uneven sample design (lack of comparison area sampled in early years) we employed a Type II sums of squares to account for missing data. To explore if any significant results of the PERMANOVA were related to true differences in location or differences in dispersion of samples (either by site or year to year), we ran a PERMDISP, a distance based test for homogeneity of multivariate dispersions for any factors that were significant in the PERMANOVA (Anderson and Walsh 2013). If a factor was significant in the PERMANOVA but not the PERMDISP, then it can be inferred that the significance is related to a location effect, but not a dispersion effect. If the factor is also significant in the PERMDISP, then significance in the PERMANOVA is related to dispersion, but there may also be a location effect.
Beyond site and year, we explored species-specific drivers in the variation of invertebrate community structure. We extended our data visualization, by performing a vector analysis of invertebrate species in the community, selecting only the species with > 0.5 Pearson correlations (Hinkle et al. 2003). If more than four species were identified, we only reported on species with a high ( > 0.7) Pearson correlations. We then generated density plots of the identified species to visualize their relationship to site or year. To better understand how these species contributed to variation in the data, we ran a principal coordinates (PCO) analysis, using a Bray-Curtis resemblance matrix, which provides information on the percent of variation explained by each axis.
All analyses and graphs were made in PRIMERe version 7 with PERMANOVA extension.
3.3 Abundance
We explored changes in aggregate and focal species densities by site and year. For aggregate density we summarized data across invertebrate taxonomic groups (similar to Lester et al. 2009) to identify broad scale differences in target invertebrates by site and year. Based on the target list of invertebrates, we had 11 broad taxonomic groupings (Table 4). A list of which species are included in each taxonomic groupings is provided in Table 5.
Table 4: Otter Rock SCUBA Invertebrate Aggregate Density Broad Taxonomic Groupings
Table 5: Otter Rock SCUBA Invertebrate Target Species List and Their Broad Taxonomic Groupings
To determine which taxonomic groups were the most dominant, we summarized means and 95% confidence intervals grouped by site and as a timeseries.
For focal species, we explored changes in aggregate and focal species densities by site and year with generalized additive mixed models (GAMMs). We modeled densities using raw count data with the offset of transect area (Maunder and Punt 2004, Zuur 2012) and a negative binomial distribution. GAMMs were chosen to account for non-linear trends in density by year detected in preliminary data exploration (Veneables and Dichmont 2004, Zuur et al. 2009). GAMMs were fitted using the mgcv package in R. Site was treated as a fixed categorical variable, while Year was continuous and smoothed with the thin-plate smoother ‘s()’ (Zuur et al 2009; Zuur 2012), grouped by Site, and k was restricted to 3 knots to prevent over-fitting. Depth-Bin was included as a random effect in the model to account for the sampling design targeting three fixed depths. We limited our modeling exercise to focus on Site and Year as these are two of the primary questions of interest. For species with very low densities across most sites and years, no statistical analyses were conducted as the data violated assumptions of the model framework.
There are eight focal invertebrate species for the OR Marine Reserves Ecological Monitoring Program; seven of which can be found in the shallow water habitats targeted by SCUBA surveys. They include the following:
- Ochre Sea Star; Pisaster ochraceus
- Sunflower Star; Pycnopodia halianthoides
- Purple Sea Urchin; Strongylocentrotus purpuratus
- Red Sea Urchin; Mesocentrotus franciscanus
- Rock Scallop; Crassadoma gigantea
- California Sea Cucumber; Parastichopus californicus
- Giant Plumose Anemone; Metridium farcimen
These species were chosen based on their ecological, economic or management importance. For more information please refer to the methods Appendix detailing focal species selection. Additional species beyond focal species were included for analysis when they were identified in community analysis as being an important driver of variation.
All analyses and data plots were created in R v4.0.2, using the mgcv (version 1.8-36), mgcViz and gratia packages. Models were structured in R as follows:
Density = mgcv::gam(Counts ~ Site + s(Year, by = Site, k = 3) + s(Depth-Bin, bs = “re”), offset = log(Transect Area), family = nb)
4 Otter Rock Results
SCUBA invertebrate sampling efforts at Otter Rock and its comparison area resulted in five years of data collection, where varying sample sizes were collected per year (Fig. 2). With the exception of 2019, sampling efforts resulted in more transects completed in the marine reserve than in the Cape Foulweather Comparison Area. Sampling did not result in data from Cape Foulweather Comparison Area in 2010 or 2015.
Fig. 2: SCUBA invertebrate monitoring efforts at the Otter Rock Marine Reserve and Cape Foulweather Comparison Area 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 Diversity
4.1.1 Species richness
Invertebrate species richness is similar across the Otter Rock Marine Reserve and Cape Foulweather Comparison Area.
Over the five years of sampling with SCUBA invertebrate surveys, a total of 33 species (or species groups) were observed in the Otter Rock Marine Reserve (Table 7). The Cape Foulweather Comparison Area had similar total number of observed species (n=28). These observed numbers of species richness are similar to the estimated numbers of total species richness (Table 7).
library(kableExtra)
pna <- data.frame(Area = c("Otter Rock Marine Reserve",
"Cape Foulweather Comparison Area"),
Observed_Richness = c("33","28"),
Estimated_Richness = c("35","29"),
LCL = c("33","28"),
UCL = c("51", "34"))
kbl(pna, caption = "Table 7: Observed and estimated invertebrate species richness by site with lower (LCL) and upper (UCL) 95% confidence limits") %>%
kableExtra::kable_classic()| Area | Observed_Richness | Estimated_Richness | LCL | UCL |
|---|---|---|---|---|
| Otter Rock Marine Reserve | 33 | 35 | 33 | 51 |
| Cape Foulweather Comparison Area | 28 | 29 | 28 | 34 |
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Species rarefaction curves highlight that for any samples size, including those for any given year, the species richness among sites is very similar (Fig. 3). Both rarefaction curves appear to level off, suggesting saturation in species richness with this tool at these sites.
Fig. 3: Species rarefaction curves for the Otter Rock Marine Reserve and Cape Foulweather Comparison Area. Data are pooled across all years of sampling for each site.
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4.1.2 Unique, common and rare species
Differences in unique, common and rare species between the Otter Rock Marine Reserve and Cape Foulweather Comparison Area.
The Otter Rock Marine Reserve had more unique species (n=6) than the Cape Foulweather Comparison Area (n=1) (Table 8, 11). The Otter Rock Marine Reserve (n= 7) had fewer common species than the Cape Foulweather Comparison Area (n=12). Six of the seven common species in the marine reserve were also found to be common in the Cape Foulweather Comparison Area (Table 9, 12). The Otter Rock Marine Reserve had more rare species (n=8) than its comparison area (n=3).
Many of the other target invertebrate species were not caught frequently resulting in low pooled counts. Not all species were observed each year, for a summary of species counts over the years by site please see tables below.
Unique species, pooled species counts across all years and species counts by individual sampling year are included in the following tables:
Table 12: Cape Foulweather Comparison Area Pooled Species Counts
Table 13: Cape Foulweather Comparison Area Species Counts by Year
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4.1.2.1 Otter Rock Marine Reserve
Fig. 4: Relative frequency of occurrence of invertebrate species observed at the Otter Rock Marine Reserve and Cape Foulweather Comparison Area from SCUBA transects. See separate tabs for each site.
4.1.2.2 Cape Foulweather Comparison Area
Fig. 4: Relative frequency of invertebrate species observed at the Otter Rock Marine Reserve and Cape Foulweather Comparison Area from SCUBA transects. See separate tabs for each site.
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4.1.3 Diversity Indices
The Otter Rock Marine Reserve and Cape Foulweather Comparison Area have similar diversity indices for target invertebrates.
The effective number of species is similar across all three diversity indices for the SCUBA invertebrate community at the marine reserve and Cape Foulweather Comparison Area (Fig. 5).
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Fig. 5: Comparing effective number of species (Hill diversity numbers) between the Otter Rock Marine Reserve and Cape Foulweather Comparison Area from SCUBA invertebrate transects. Hill numbers include the three most widely used species diversity measures; species richness (q = 0), Shannon diversity (q=1) and Simpson diversity (q=2) (Hsieh et al 2016).
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4.1.4 Diversity through time
We did not get enough samples to evaluate change in species diversity through time at the Otter Rock Marine Reserve and Cape Foulweather Comparison Area.
Species rarefaction curves by year for each site indicated that we did not sample enough on a yearly basis to compare changes in mean species richness through time (Fig. 6-7). When plotting mean species richness by year with 95% confidence intervals, the confidence intervals overlap suggesting more sampling is needed to detect any meaningful differences in annual species rarefaction.
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For an average transect, invertebrate species diversity does not differ between the Otter Rock Marine Reserve and Cape Foulweather Comparison Area.
When comparing mean species richness for an average SCUBA transect, there was no difference between the marine reserve and Cape Foulweather Comparison Area (F.0.007, p > 0.05) (Fig. 8).
Fig. 8: Mean species richness by site with 95% confidence intervals at the Otter Rock Marine Reserve and Cape Foulweather Comparison Area from SCUBA invertebrate transects.
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4.2 Community Composition
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4.2.1 Variation by Site and Year
Invertebrate community composition was similar at the Otter Rock Marine Reserve and Cape Foulweather Comparison Area with SCUBA invertebrate data, although slightly more variation in samples is seen at the marine reserve.
There was no distinct structuring of invertebrate community composition data at the Otter Rock Marine Reserve and Cape Foulweather Comparison Area. (Fig. 9).
Invertebrate community composition was somewhat similar across years at the Otter Rock Marine Reserve and its comparison area, although slightly more variation in samples is seen in later years.
There was some structuring of invertebrate community composition data by year at the Otter Rock Marine Reserve and Cape Foulweather Comparison Area (Fig. 9). Transects from 2015 and 2019 had higher variability than transects sampled in initial survey years, of 2010-2011 (Fig.9).
Multivariate statistics indicate differences by site, year, depth and the interaction of site by year, likely representing the shift in targeted sampling locations as the dive program evolved.
PERMANOVA results indicate that site, year, depth, and the interaction between site and year were significant factors for invertebrate community composition (p < 0.05) with SCUBA density data (Table 14). Year accounted for the highest variability (21%), while site accounted for 12%, depth accounted for 4%, and site by year interaction accounted for 15% of model variability. Combined, these variables and variable interactions accounted for 52% of model variability, indicating that these factors likely influence invertebrate community composition at Otter Rock Marine Reserve and its comparison area.
PERMDISP results indicate significant differences in dispersion by year and depth (p < 0.05), but no differences in dispersion between sites. For year, the smallest mean dispersions were in the first two years of data collection 2010 and 2011, and many of the significant pairwise interactions are between early years of data collection and all other years (Table 15-16). This suggests the significance identified in the PERMANOVA is likely because of differences in dispersion between years rather than of differences in spatial location among years.
Differences in dispersion between depths were significant but not between sites. These results suggest the significance between site and year identified in the PERMANOVA is likely because of changes to targeted sampling areas between 2010-11 and 2015-19. Due to safety concerns, we moved away from sampling in kelp beds starting in 2013 (see methods section for additional information). As a result, it is likely there are community-based shifts at Otter Rock particularly, as this site is known for its dense kelp beds located inshore.
Table 15: PERMDISP mean dispersions and standard errors by year
Table 17: PERMDISP mean dispersions and standard errors by site
Table 19: PERMDISP mean dispersions and standard errors by Depth
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4.2.1.1 Site
Fig. 9: Results from nMDS plots with SCUBA invert data, demonstrating similarity in invertebrate community composition at the Otter Rock Marine Reserve and the Cape Foulweather Comparison Area. See separate tabs for site and year.
4.2.1.2 Year
Fig 9: Results from nMDS plots for SCUBA invert data, demonstrating similairity in invertebrate community composition at the Otter Rock Marine Reserve and the Cape Foulweather Comparison Area. See separate tabs for site and year
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4.2.2 Species specific drivers of variation
Two invertebrate species drive the majority of variation in community composition data.
We explored species-specific drivers of variation, and found that M. franciscanus and P. ochraceous were driving the majority of variation in the data (Fig. 10). Principal coordinate analysis revealed that ~23% of the variation along the x-axis is explained by P. ochraceous and 21% of variation is explained along the y-axis from M. franciscanus. (Fig. 10). Together the abundance of these two species accounts for ~ 44% of model variability. Vector plots from principal coordinate analysis indicate there are likely differences between the marine reserve and Cape Foulweather Comparison Area, with Otter Rock having higher densities of P. ochraceous than the comparison area. Densities of both species were higher in later survey years (2015-2019), than initial survey years (2010-2011).
4.2.2.1 PCO Vector Overlay by Site
Fig. 10: Results from species correlations and principal coordinate analysis demonstrating that M. franciscanus and P. ochraceous drive variation in community structure at the Otter Rock Marine Reserve and Cape Foulweather Comparison Area, with higher densities of both species in later survey years (2015-2019). Bubble color/size represents species-specific densities in each sample (species density range indicated in legend). See separate tabs for by site, year and species bubble plots.
4.2.2.2 PCO by Year
Fig. 10: Results from species correlations and principal coordinate analysis demonstrating that M. franciscanus and P. ochraceous drive variation in community structure at the Otter Rock Marine Reserve and Cape Foulweather Comparison Area, with higher densities of both species in later survey years (2015-2019). Bubble color/size represents species-specific densities in each sample (species density range indicated in legend). See separate tabs for by site, year and species bubble plots.
4.2.2.3 PCO Bubble Plot
Fig. 10: Results from species correlations and principal coordinate analysis demonstrating that M. franciscanus and P. ochraceous drive variation in community structure at the Otter Rock Marine Reserve and Cape Foulweather Comparison Area, with higher densities of both species in later survey years (2015-2019). Bubble color/size represents species-specific densities in each sample (species density range indicated in legend). See separate tabs for by site, year and species bubble plots.
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4.3 Aggregate Abundance
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4.3.1 Aggregate Density
Two dominate taxonomic groups at the Otter Rock Marine Reserve and Cape Foulweather Comparison Area.
Urchins and Tunicates dominate the relative abundance at the Otter Rock Marine Reserve and its comparison area (Fig. 11).
Variable trends through time across broad taxonomic groups.
There were variable trends through time across broad taxonomic invertebrate groups (Fig. 11). The majority of taxonomic groups show no clear trends over time (e.g. bivalves, chitons). For a few groups we see an increase through time at one or both sites (e.g. urchins at Cape Foulweather Comparison Area and sea stars at Otter Rock Marine Reserve).
Higher mean density of urchins in the Cape Foulweather Comparison Area compared to the Otter Rock Marine Reserve.
Out of all taxonomic groups, only urchins had clear differences in 95% confidence intervals between the marine reserve and Cape Foulweather Comparison Area (Fig. 11), with higher densities at the comparison area.
4.3.1.1 Mean Aggregate Density by Site
Fig. 11: Aggregate density timeseries of SCUBA targeted invertebrates at the Otter Rock Marine Reserve and the Cape Foulweather Comparison Area. See separate tabs for density by site and timeseries plots.
4.3.1.2 Mean Aggregate Density Timeseries
Fig. 11: Aggregate density timeseries of SCUBA targeted invertebrates at the Otter Rock Marine Reserve and the Cape Foulweather Comparison Area. 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 higher P. ochraceus density in the Otter Rock Marine Reserve than Cape Foulweather Comparison Area.
P.ochraceus density was higher in the marine reserve than Cape Foulweather Comparison Area (p < 0.05; Table 21).
Significant yearly trends in P. ochraceus density at the Otter Rock Marine Reserve and the Cape Foulweather Comparison Area.
There were significant trends by year in P. ochraceus density at the Otter Rock Marine Reserve and the Cape Foulweather Comparison Area (p < 0.05; Table 22). At the marine reserve, density increased mainly in the 2017 and 201 sampling. At the Cape Foulweather Comparison Area, density also increased through time, but not to as great an extent as in the marine reserve.
The random effect of depth was not identified as a significant component of variation (Table 22).
GAMM model results can be found in the links below:
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4.4.1.1.1 P. ochraceus Density Timeseries
Fig. 12: P. ochraceous density timeseries and GAMM model results with 95% confidence intervals, at the Otter Rock Marine Reserve and Cape Foulweather Comparison Area. See separate tabs for timseries and GAMM results.
4.4.1.1.2 P. ochraceus Density Modeled GAMM Results
Fig. 12: P. ochraceous density timeseries and GAMM model results with 95% confidence intervals, at the Otter Rock Marine Reserve and Cape Foulweather Comparison Area. 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 difference in P. helianthoides density between the Otter Rock Marine Reserve and the Cape Foulweather Comparison Area.
There was no difference in P. helianthoides density between the marine reserve and the Cape Foulweather Comparison Area (p > 0.05; Table 23).
Significant yearly trends in P. helianthoides density at the Otter Rock Marine Reserve only.
There were significant trends by year in P. helianthoides density at the Otter Rock Marine Reserve (p < 0.05; Table 24) with a decline from the initial sampling in 2010-11 and no observations of P. helianthoides after 2015. There was no trend at the Cape Foulweather Comparison Area (p > 0.05; Table 24).
The random effect of depth was not identified as a significant component of variation (Table 24).
GAMM model results can be found in the links below:
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4.4.2.1.1 P. helianthoides Density Timeseries
Fig. 13: P. helianthoides density timeseries and GAMM model results with 95% confidence intervals, at the Otter Rock Marine Reserve and Cape Foulweather Comparison Area. See separate tabs for timseries and GAMM results.
4.4.2.1.2 P. helianthoides Density Modeled GAMM Results
Fig. 13: P. helianthoides density timeseries and GAMM model results with 95% confidence intervals, at the Otter Rock Marine Reserve and Cape Foulweather Comparison Area. 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
Too few observations of S.purpuratus to detect differences in density by site or year.
Densities of S.purpuratus were very low across all sites and years (Fig. 14), so statistical analyses were not conducted.
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4.4.3.1.1 S.purpuratus Density Timeseries
Fig. 14: S.purpuratus density timeseries at the Otter Rock Marine Reserve and the Cape Foulweather Comparison Area.
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4.4.4 Red Sea Urchin; Mesocentrotus franciscanus
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4.4.4.1 Density
Significantly lower M. franciscanus density in the Otter Rock Marine Reserve than to the Cape Foulweather Comparison Area.
M. franciscanus density was lower in the marine reserve compared to the Cape Foulweather Comparison Area (p < 0.05; Table 25).
No significant yearly trends in M. franciscanus density at the Otter Rock Marine Reserve or the Cape Foulweather Comparison Area.
There were no significant trends by year in M. franciscanus density at the Otter Rock Marine Reserve or the Cape Foulweather Comparison Area (p > 0.05; Table 26).
The random effect of depth was not identified as a significant component of variation (Table 26).
GAMM model results can be found in the links below:
\(~\) \(~\)
4.4.4.1.1 M. franciscanus Density Timeseries
Fig. 15: M. franciscanusdensity timeseries and GAMM model results with 95% confidence intervals, at the Otter Rock Marine Reserve and Cape Foulweather Comparison Area. See separate tabs for timseries and GAMM results.
4.4.4.1.2 M. franciscanus Density Modeled GAMM Results
Fig. 15: M. franciscanus density timeseries and GAMM model results with 95% confidence intervals, at the Otter Rock Marine Reserve and Cape Foulweather Comparison Area. See separate tabs for timseries and GAMM results.
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4.4.5 Rock Scallop; Crassadoma gigantea
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4.4.5.1 Density
Too few observations of C. gigantea to detect differences in density by site or year.
Densities of C. gigantea were very low across all sites and years (Fig. 16), so statistical analyses were not conducted.
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4.4.5.1.1 C. gigantea Density Timeseries
Fig. 16: C. gigantea density timeseries at the Otter Rock Marine Reserve and the Cape Foulweather Comparison Area.
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4.4.6 California Sea Cucumber; Parastichopus californicus
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4.4.6.1 Density
Too few observations of P. californicus to detect differences in density by site or year.
Densities of P. californicus were very low across all sites and years (Fig. 17), so statistical analyses were not conducted. No observations of P. californicus were observed at the Otter Rock Marine Reserve.
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4.4.6.1.1 P. californicus Density Timeseries
Fig. 17: P. californicus density timeseries at the Otter Rock Marine Reserve and the Cape Foulweather Comparison Area.
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4.4.7 Giant Plumose Anemone; Metridium farcimen
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4.4.7.1 Density
Too few observations of M. farcimen to detect differences in density by site or year.
Densities of M. farcimen were very low across all sites and years (Fig. 18), so statistical analyses were not conducted.
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4.4.7.1.1 M. farcimen Density Timeseries
Fig. 18: M. farcimen density timeseries at the Otter Rock Marine Reserve and Cape Foulweather Comparison Area.
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4.5 Additional Species Density
No additional species were identified as significant drivers of variation in the community; so no additional species density analyses were conducted.
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.
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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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