1 Introduction: Across Reserves Hook and Line Report
In 2012, Oregon completed designation of five marine reserve sites with help from community groups working together with state officials. The five marine reserve sites are not considered a network, as they were selected individually, without consideration of the status of any other proposed site. The result led to five unique areas, of different sizes, with different habitats, and historical fishing pressures. Even though the unique attributes of each reserve has led to the development of individual monitoring plans tailored to each reserve’s characteristics, some monitoring methods allow for across reserve comparisons to gain a better understanding of the similarities and differences across multiple reserve sites. Hook and line sampling is one of those monitoring methods.
Hook and line (HnL) sampling targets demersal fishes living on rocky reef habitats using catch and release methods. At each marine reserve, 500 x 500 m sampling areas (called cells) were selected to represent varying hard bottom habitat and historical fishing pressure. At each reserve, sampling occurs in the spring and fall, using the same gear and methods. While the reserves are different ages, implementation was staggered, and sampling did not occur in the same years at all sites, we can explore the similarities and differences observed across the marine reserves with the same monitoring tool.
Hook and line sampling occurs at four of the five marine reserves - Redfish Rocks, Cape Perpetua, Cascade Head and the Cape Falcon Marine Reserves. The Otter Rock Marine Reserve is too shallow to conduct this sampling method, and is therefore not included in the analysis of this report. Sampling began at the Redfish Rocks Marine Reserve in 2011, in 2013 for the Cape Perpetua and Cascade Head Marine Reserves, and in 2014 for the Cape Falcon Marine Reserve. Due to limited ODFW staffing, not all sites were surveyed in all years.
Data from hook and line monitoring efforts can be used to explore questions about relative fish abundance and size from a method that is similar to local commercial nearshore hook and line fishing efforts across the coast. We can also explore these data with questions about diversity and community composition to compare across reserves and validate trends at larger spatial or temporal scales. This can further help us understand how the fish communities at these sites are similar or different. Data on abundance and size enable us to explore how fish catch, and size have changed over time; and whether these changes are similar across reserves. For all data our main focus is exploring trends spatially and temporally.
1.1 Research Questions
Diversity
- Are there differences in species diversity across the marine reserves?
Community Composition
- Are there differences in catch composition across the marine
reserves?
- If yes, what species drive this variation?
- If no, what other factors may explain structure in catch composition?
Aggregate Abundance
- Are there differences in aggregate catch across the marine reserves?
- Are there similar trends in aggregate catch across the marine reserves through time?
Focal Species Abundance & Size
Are there differences in focal species catch across the marine reserves?
Are there similar trends in focal species catch across the marine reserves through time?
Are there differences in the size of focal species caught across the marine reserves?
Are there similar trends in focal species size across the marine reserves through time?
2 Takeaways
Species diversity measures highlight differences across reserves, likely attributable to the site habitat characteristics.
Species diversity differences often reflected the habitat characteristics among marine reserve sites. Observed and estimated species richness was highest at the Redfish Rocks Reserve, one of the two reserves with the most rocky habitat, and lowest at the Cape Falcon Marine Reserve, a site with a small amount of protected rocky habitat. Unique species observed across the reserves often reflected the unique habitat and location of particular reserves. For example, Gopher Rockfish were only observed at Redfish Rocks Marine Reserve, near this species known northern range: Cape Blanco. At Cape Perpetua Marine Reserve, Bocaccio were unique and not surprisingly are a deeper water schooling species known to associate with deep rocky features. The two sites with the smallest distribution of rocky reef areas had the highest (Cape Perpetua) and lowest (Cape Falcon) number of commonly observed species. The deep isolated nature of rocky habitat at the Cape Perpetua Marine Reserve is thought to contribute to higher local densities and more common species at this site, whereas the minimal habitat at Cape Falcon is shallower with other hard bottom habitat nearby, contributing to no commonly observed species at this site.
The species catch composition of Cape Perpetua and Cape Falcon Marine Reserves are distinct from other reserves and from each other, likely attributable to site habitat characteristics.
Differences in species catch composition at Cape Perpetua are likely driven by greater relative abundances of Canary, Yellowtail, Copper, Quillback, and Yelloweye Rockfish, attributable to the deep isolated nature of the rocky habitat at this site. Cape Falcon Marine Reserve is also slightly different - likely due to the overall lower number of species observed at this marine reserve attributable to the small distribution of rocky habitat at this site and nearby location of other reefs. The catch composition at Redfish Rocks Marine Reserve and Cascade Head Marine Reserve are most similar to one another; these are the two sites with the most area of rocky reef protected.
Aggregate catch-per-unit-effort (CPUE) was lowest at the Cape Falcon Marine Reserve; yearly trends were detected at the Redfish Rocks and Cape Perpetua Marine Reserves.
Mean aggregate species CPUE was similar among Redfish Rocks, Cascade Head, and Cape Perpetua Marine Reserves, but significantly lower at Cape Falcon Marine Reserve. Non-linear yearly trends were detected at the Redfish Rocks and Cape Perpetua Marine Reserves for aggregate CPUE, but linear trends at the Cascade Head or Cape Falcon Marine Reserve were non-significant.
Differences in CPUE of focal species were detected among the marine reserves; Cape Falcon had the lowest CPUE for most species.
For our most commonly observed species, Black Rockfish and Lingcod, Cape Falcon had the lowest CPUE compared to the other marine reserves. For Blue/Deacon Rockfish, there was higher CPUE at the Redfish Rocks Marine Reserve than any other site. While some species had relatively low abundance across sites preventing formal statistical analysis due to model assumptions, summary plots reveal that China Rockfish were almost exclusively encountered at Redfish Rocks Marine Reserve, Yelloweye Rockfish primarily encountered at Redfish Rocks and Cape Perpetua Marine Reserves, and Cabezon were not encountered at the Cape Perpetua Marine Reserve.
Yearly trends in species level CPUE and size were variable across marine reserves.
There was no consistent yearly trend across the species and marine reserves for species level CPUE or mean sizes. For example, there were significant, yet different trends in Black Rockfish CPUE detected at Redfish, Cape Perpetua, and Cascade Head Marine Reserve. Similarly, size data indicate natural variation was detected, but no compelling trends through time described.
The top quartile of fish size were generally greatest at Redfish Rocks and Cape Perpetua.
Black Rockfish had greatest top quartile of sizes at Cape Perpetua and the smallest at Cape Falcon. Blue/Deacon Rockfish had greatest top quartile of size at Cascade Head Marine Reserve. The top quartile of Lingcod size was greatest at Redfish Rocks and Cape Perpetua Marine Reserves compared with Cape Falcon.
2.1 Conclusions
This is the first report comparing a fishery-independent coast-wide dataset on subtidal rocky reef fish populations in Oregon.
The siting and design of Oregon’s marine reserve sites were community-led, and for many of the reserve proposals there was a lack of coast-wide spatially explicit data on subtidal fish communities to evaluate the proposed reserve sites. This report provides the first spatially explicit, fishery-independent evaluation of the subtidal rocky reef fish communities at four of the five marine reserves, and documents differences in the subtidal fish community associated with these sites.
We are protecting a range of different subtidal fish communities in our marine reserves, attributable to the different habitats in the marine reserves.
The Cape Falcon and Cape Perpetua Marine Reserves have distinct subtidal rocky reef fish communities that are different from each other and the fish communities of Redfish Rocks and Cascade Head Marine Reserves. The two marine reserves with the largest area of rocky habitat protection, Redfish Rocks and Cascade Head are the most similar. The deep, isolated nature of the patch reef at Cape Perpetua creates a distinct community, with a greater evenness of species, and greater relative abundances of Canary, Yellowtail, Copper, Quillback, and Yelloweye Rockfish. China Rockfish were almost exclusively encountered at the Redfish Rocks Marine Reserve. Black Rockfish was the most commonly abundant species at all marine reserve sites. Cape Falcon Marine Reserve, a site with a small area of rocky habitat protection and other reefs nearby, had the lowest aggregate CPUE of all sites, and relatively low species densities. The first data explorations into our coast-wide, fishery independent monitoring results indicate that we are protecting a range of different subtidal fish communities in our marine reserves.
3 Hook & Line Methods
Hook and Line (HnL) sampling is conducted at four of Oregon’s five marine reserves - the Redfish Rocks, Cape Perpetua, Cascade Head and Cape Falcon Marine Reserves. At each site, sampling efforts targeted 2-3 days in each reserve, for both spring and fall monitoring. Each day between 4-6 cells (500m x 500 m grids) are targeted, with 3 fifteen-minute fishing drifts occurring in each cell. All data collected from drifts are averaged for a single cell; the unit of replication for hook and line samples is at the cell-day level (except for size, which is at the individual fish level). All fish caught during each drift are identified to species, measured and released. During each drift we also determined the amount of time not spent fishing, such as when anglers hang up on the bottom, stop to rest, or take a photo with their fish caught, and the recorded total fishing effort is adjusted accordingly. We then calculate both a catch (CPUE) and biomass (BPUE) per unit effort (fish/angler-hour and weight(kg)/angler-hour) for each given cell-day and species. For additional details on data collection, please review documentation in the Methods Appendix.
3.1 Diversity
With hook and line gear, 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 each site (reserve or comparison area) likely has a species pool larger than can be sampled in any one year. We excluded unidentified species from the summaries as well as species not well targeted by hook and line gear (e.g. Wolf Eel).
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 hook and line gear 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. These tables exclude the unidentified individuals and species not well targeted by HnL gear. 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 caught in one out of every two cells sampled per day). 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 (effective number of species) across sites using the iNEXT diversity package in R (Hsieh et al 2016). Hill numbers are parameterized by a diversity order q, which determines the measures’ sensitivity to species relative abundances (Hsieh et al 2016). Hill numbers include the three most widely used species diversity measures; species richness (q = 0), Shannon diversity (q=1) and Simpson diversity (q=2) (Hsieh et al 2016). We used sampling based incidence data with the iNext package in R, to plot rarefaction and extrapolation curves for each Hill number, and compare results across sites. We also calculated 95% confidence intervals associated with these rarefaction & extrapolation curves.
3.1.4 Diversity Through Time
Finally we explored how diversity changed through time. First we plotted each species yearly rarefaction curve against the total cumulative rarefaction curve for all years combined to determine if we had sampled appropriately to compare species diversity from year to year. When our sampling effort was not adequate to compare across years, we pooled data from all years to compare average daily 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 around understanding if the variation in fish community structure was driven by marine reserve site. We did this through data visualization with non-multidimensional scaling (nMDS) plots and cluster analysis.
To explore variation by site, we used catch per unit effort (CPUE) data with a dispersion weighting transformation to downweight species that have high variability within each site. This allows us to better deal with highly aggregated schooling species without enhancing importance of rare species (Clarke et al. 2006). CPUE data are considered a rate (catch per angler hour) so a Euclidean distance 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 a nMDS plot using the centroids of all cells within each site, giving one estimate per marine reserve. We converted the Euclidean-distance based resemblance matrix to percent similarity for each marine reserve pairing using the equation Similarity = 1/(e^d), where d=distance function in matrix (akin to Generalized RBF Kernels). This equation was used as it more accurately represents similarities where distance values are >1.
All analyses and graphs were made in PRIMERe version 7 with PERMANOVA extension.
3.3 Abundance
We explored changes in aggregate and focal species catch rates (catch per unit effort, CPUE), and size (focal species only) by site and year with generalized additive models (GAMM). We modeled raw catch data with an offset for fishing effort (per angler hour) (Maunder and Punt 2004, Zuur 2012); size data were modeled without an offset. A negative binomial distribution was used for the CPUE model. After exploration of spatial-temporal auto correlation of residuals with focal species data, a gaussian distribution for the size model. GAMMs were chosen to account for non-linear trends in CPUE (or size) 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. Cell was included as a random effect in the model to account for the nested nature of the sampling design and for random differences in depth and habitat among cells. 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 CPUE across most sites and years, no statistical analyses were conducted as the data violated assumptions of the model framework.
Specifically we analyzed aggregate CPUE, and species-specific CPUE and size for focal species across the four marine reserves. We used Redfish Rocks as the intercept site, since it had the longest timeseries of data collection. Additionally for focal species, we complemented the GAMM modeling results for size with an analysis of variance (ANOVA) exploring changes in the mean top quartile size of fish by site. The mean top quartile size of fish is a measure of how the mean size of the largest quartile of fish changes through time, a technique borrowed from fish longevity studies (Choat and Robertson 2002), whereas the GAMM modeling results evaluate change in mean size of all individuals of a species. The mean size of fish may obscure gains in the larger size classes through time if there has been a strong recruitment of juvenile fishes. When results were significant, a Tukey test was run to determine significant differences among sites.
There are six focal fish species for the OR Marine Reserves Ecological Monitoring Program:
- Black Rockfish; Sebastes melanops
- Blue/Deacon Rockfish; Sebastes mystinus / S. diaconus
- China Rockfish; Sebastes nebulosus
- Yelloweye Rockfish; Sebastes ruberrimus
- Cabezon; Scorpaenichthys marmoratus
- Lingcod; Ophiodon elongatus
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:
CPUE = mgcv::gam(Catch ~ Site + s(Year, by = Site, k = 3) + s(Cell_ID, bs = “re”), offset = log(Effort), family = nb)
Size = mgcv::gam(Length ~ site + s(Year, by = site, k = 3) + s(Cell_ID, bs = “re”), family = gaussian)
4 Across Reserves Hook and Line Results
Hook and line sampling efforts varied across the four marine reserve sites (Fig. 1). The most sampling (8 years) occurred at the oldest marine reserve site - Redfish Rocks. Five years of sampling occurred at the Cascade Head Marine Reserve and four years of sampling occurred at both the Cape Perpetua and Cape Falcon Marine Reserves.
Fig. 1: Hook and line monitoring efforts across marine reserve sites resulted in varied sample sizes over the eight years of data collection. Sample size is represented in cell-days.
\(~\) \(~\)
4.1 Diversity
4.1.1 Species richness
Species richness is lowest at the Cape Falcon Marine Reserve.
Observed species richness was lowest at the Cape Falcon Marine. Redfish Rocks had the highest observed species richness (n = 17), followed by Cascade Head (n = 15) and Cape Perpetua (n = 13). These observed numbers of species richness are similar to the estimated numbers of total species richness (Table 3).
library(kableExtra)
pna <- data.frame(Area = c("Redfish Rocks Marine Reserve",
"Cape Perpetua Marine Reserve",
"Cascade Head Marine Reserve",
"Cape Falcon Marine Reserve"),
Observed_Richness = c("17","13","15","10"),
Estimated_Richness = c("18","14","17", "14"),
LCL = c("17","13","15", "10"),
UCL = c("28", "27","37","50"))
kbl(pna, caption = "Table 3: Observed and estimated species richness by site with lower (LCL) and upper (UCL) 95% confidence limits") %>%
kableExtra::kable_classic()| Area | Observed_Richness | Estimated_Richness | LCL | UCL |
|---|---|---|---|---|
| Redfish Rocks Marine Reserve | 17 | 18 | 17 | 28 |
| Cape Perpetua Marine Reserve | 13 | 14 | 13 | 27 |
| Cascade Head Marine Reserve | 15 | 17 | 15 | 37 |
| Cape Falcon Marine Reserve | 10 | 14 | 10 | 50 |
\(~\) \(~\)
Species rarefaction curves highlight that across all samples sizes, the species richness at Cape Falcon is the lowest. Species richness is greatest at Redfish Rocks Marine Reserve and very similar to both Cape Perpetua Marine Reserve and Cascade Head Marine Reserve (Fig. 2). The higher species richness achieved at Redfish Rocks and Cascade Head Marine Reserves is driven by the number of rare species observed at these survey sites (Fig. 2, Table 2). The Redfish Rocks, Cape Perpetua and Cascade Head rarefaction curves appear to level off, suggesting saturation in species richness with this tool at these sites.
Fig. 2: Species rarefaction curves across marine reserve sites. Data are pooled across all years of sampling for each site.
\(~\) \(~\) \(~\) \(~\)
4.1.2 Unique, common and rare species
Although the number of unique and rare species are similar across the marine reserves, the Cape Perpetua Marine Reserve has the most common species.
The Redfish Rocks Marine Reserve had two unique species - the Brown Irish Lord (Hemilepidotus spinosus) and the Gopher Rockfish (S.carnatus). The Cape Perpetua Marine Reserve also had two unique species - the Brown Rockfish (S. auriculatus) and Bocaccio (S. paucispinis).The Shiner Perch (Cymatogaster aggregata) was unique to the Cape Falcon Marine Reserve. No unique species were found at the Cascade Head Marine Reserve. The northern range for Gopher Rockfish is Cape Blanco, Oregon, Bocaccio are a deeper water, schooling species.
The Cape Perpetua Marine Reserve had the highest common species observed (n=5), and included Black Rockfish, Lingcod, Canary Rockfish, Yellowtail Rockfish and Quillback Rockfish. The Redfish Rocks Marine Reserve and Cascade Head Marine Reserve (n= 3) had similar numbers of common species and both sites had Black Rockfish and Lingcod as common species. The Cape Falcon Marine Reserve had no common species observed with hook and line gear.
The Redfish Rocks and Cascade Head Marine Reserves had more rare species (both sites n = 6) than the Cape Falcon (n = 5) or Cape Perpetua (n = 4) Marine Reserves.
Many of species of fisheries interest - China, Quillback, Cabezon, Yelloweye, Copper and Vermillion Rockfish - were not caught frequently across all sites with this monitoring tool resulting in low pooled counts. Not all species were observed each year, for a summary of species counts over the years by site please see tables below (Tables 4-7).
Table 4: Redfish Rocks Marine Reserve Pooled Species Frequency of Occurrence
Table 5: Cape Perpetua Marine Reserve Pooled Species Frequency of Occurrence
Table 6: Cascade Head Marine Reserve Pooled Species Frequency of Occurrence
Table 7: Cape Falcon Marine Reserve Pooled Species Frequency of Occurrence
\(~\) \(~\)
4.1.2.1 Redfish Rocks Marine Reserve
Fig. 3: Relative frequency of occurrence of species observed across marine reserve sites with hook and line gear. See separate tabs for each site.
4.1.2.2 Cape Perpetua Marine Reserve
Fig. 3: Relative frequency of occurrence of species observed across marine reserve sites. See separate tabs for each site.
4.1.2.3 Cascade Head Marine Reserve
Fig. 3: Relative frequency of occurrence of species observed across marine reserve sites. See separate tabs for each site
4.1.2.4 Cape Falcon Marine Reserve
Fig. 3: Relative frequency of occurrence of species observed across marine reserve sites.See separate tabs for each site
\(~\) \(~\) \(~\) \(~\)
4.1.3 Diversity Indices
The Redfish Rocks Marine Reserve has the highest number of effective species and Cape Falcon the lowest across all three diversity indices.
There are differences in the number of effective species across diversity indices and the marine reserve sites (Fig. 4). Consistently across all three indices the Redfish Rocks Marine Reserve has the highest number of effective species and the Cape Falcon Marine Reserve has the lowest number of effective species (Fig. 4). The Cape Perpetua and Cascade Head Marine Reserves are very similar to each other in terms of effective number of species across all three diversity indices.
Fig. 4: Comparing effective number of species (Hill diversity numbers) across the marine reserves from hook and line samples. 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).
\(~\) \(~\) \(~\) \(~\)
4.1.4 Diversity through time
We did not get enough samples to evaluate change in species diversity through time at the Redfish Rocks Marine Reserve and its comparison areas.
Species rarefaction curves by year for each site indicated that we did not sample enough on a yearly basis to compare changes in mean species richness through time (Fig. 5-8).
Fig. 5: Redfish Rocks Marine Reserve species rarefaction curves by year from hook and line data.
Fig. 6: Cape Perpetua Marine Reserve species rarefaction curves by year from hook and line data.
Fig 7: Cascade Head Marine Reserve species rarefaction curves by year from hook and line data.
Fig 8: Cape Falcon Marine Reserve species rarefaction curves by year from hook and line data.
\(~\) \(~\)
For an average day of sampling, Cape Falcon Marine Reserve has the lowest species richness
When comparing mean species richness for an average day of sampling, Redfish Rocks, Cape Perpetua, and Cascade Head Marine Reserves were similar, while Cape Falcon Marine Reserve had significantly lower mean daily species richness (Fig. 9, p < 0.05).
Fig. 9: Mean species richness by site with 95% confidence intervals across marine reserves from hook and line data.
\(~\) \(~\)
\(~\) \(~\)
4.2 Community Composition
\(~\) \(~\)
4.2.1 Variation by Site
The Cape Perpetua and Cape Falcon Marine Reserves have a distinct catch composition from the other reserve sites.
Results from nMDS plots highlight that both the Cape Perpetua and Cape Falcon Marine Reserves are distinct in their catch composition from the Redfish Rocks and Cascade Head Marine Reserves (Fig. 10). The catch composition from the Redfish Rocks Marine Reserve and Cascade Head Marine Reserve are 57% similar, the greatest similarity among any reserve pair. Cape Falcon is approximately 38% similar in catch composition to either the Redfish Rocks Marine Reserve or Cascade Head Marine Reserves, both sites with larger reef habitat. The Cape Perpetua Marine Reserve was 22% similar to Cape Falcon and 36% similar to either the Redfish Rocks or Cascade Head Marine Reserves.
\(~\) \(~\)
4.2.1.1 Site
Fig. 10: Results from nMDS plots with CPUE data across marine reserves, highlighting that the Cape Perpetua Marine Reserve is distinct from other sites.
\(~\) \(~\)
\(~\) \(~\)
4.3 Aggregate Abundance
\(~\) \(~\)
4.3.1 Aggregate CPUE
Significantly higher aggregate CPUE in the Redfish Rocks Marine Reserve than the Cape Falcon Marine Reserve.
Redfish Rocks Marine Reserve had statistically higher aggregate CPUE than the Cape Falcon Marine Reserve (p < 0.05; Table 8). There was no difference in aggregate CPUE between the Redfish Rocks Marine Reserve and the Cape Perpetua or Cascade Head Marine Reserve (p > 0.05; Table 8).
Significant yearly trends in aggregate CPUE at both the Redfish Rocks Marine Reserve and Cape Perpetua Marine Reserves.
There were significant yearly trends in aggregate CPUE at both the Redfish Rocks Marine Reserve (p < 0.05; Table 9) and Cape Perpetua Marine Reserve. Both sites exhibited similar non-linear trends, where CPUE increased in the first few years until 2015/2106, and then declined in later sampling years. There was no significant yearly trend for aggregate CPUE at the Cascade Head or Cape Falcon Marine Reserves (p > 0.05; Table 9).
The random effect of cell was identified as a significant component of variation (Table 9).
GAMM model results can be found in the links below:
\(~\) \(~\)
4.3.1.1 Aggregate CPUE timeseries
Fig. 11: Aggregate catch per unit effort (CPUE) timeseries and modeled GAMM results with 95% confidence intervals, across marine reserve sites. See separate tabs for timeseries and GAMM results.
4.3.1.2 Aggregate CPUE modeled GAMM results
Fig. 11: Aggregate catch per unit effort (CPUE) timeseries and modeled GAMM results with 95% confidence intervals, across marine reserve sites. See separate tabs for timeseries and GAMM results.
\(~\) \(~\)
\(~\) \(~\)
4.4 Focal Species Abundance & Size
\(~\) \(~\)
4.4.1 Black Rockfish, S. melanops
\(~\)
4.4.1.1 CPUE
Significantly higher Black Rockfish CPUE at the Redfish Rocks Marine Reserve than at the Cape Falcon Marine Reserve.
Redfish Rocks Marine Reserve had higher CPUE of Black Rockfish than the Cape Falcon Marine Reserve (p < 0.05; Table 10). There were no differences in Black Rockfish CPUE between the Redfish Rocks Marine Reserve and the Cape Perpetua or Cascade Head Marine Reserves (p > 0.05; Table 10).
Significant yearly trends in Black Rockfish CPUE at the Redfish Rocks Marine Reserve only.
There were significant trends by year at the Redfish Rocks Marine Reserve in Black Rockfish CPUE (p < 0.05; Table 11). At this marine reserve, CPUE increased to a peak around 2015, then declined through 2019. There was not a significant yearly trend in Black Rockfish CPUE through time at any other marine reserve (p > 0.05; Table 11).
The random effect of cell was identified as a significant component of variation (Table 11).
GAMM model results can be found in the links below:
\(~\) \(~\)
4.4.1.1.1 Black Rockfish CPUE by Site
Fig. 12: Black Rockfish catch per unit effort (CPUE) by site, yearly timeseries and GAMM model results with 95% confidence intervals, across marine reserves.See separate tabs for timseries and GAMM results.
4.4.1.1.2 Black Rockfish CPUE Timeseries
Fig. 12: Black Rockfish catch per unit effort (CPUE) by site, yearly timeseries and GAMM model results with 95% confidence intervals, across marine reserves.See separate tabs for timseries and GAMM results.
4.4.1.1.3 Black Rockfish CPUE Modeled GAMM Results
Fig. 12: Black Rockfish catch per unit effort (CPUE) by site, yearly timeseries and GAMM model results with 95% confidence intervals, across marine reserves. See separate tabs for timseries and GAMM results.
\(~\) \(~\)
4.4.1.2 Size
Larger mean size Black Rockfish at the Redfish Rocks Marine Reserve than the Cascade Head or Cape Falcon Marine Reserves.
There were significant differences in mean size of Black Rockfish between the Redfish Rocks Marine Reserve and the Cascade Head and Cape Falcon Marine Reserves (p < 0.05, Table 12). Larger Black Rockfish were found at Redfish than at those two sites. There was no difference in mean size Black Rockfish between the Redfish Rocks Marine Reserve and Cape Perpetua marine Reserve.
Significant yearly trends in Black Rockfish mean size at the Redfish Rocks, Cape Perpetua and Cascade Head Marine Reserves.
There were significant yearly trends in mean size at three marine reserve sites (p < 0.05) but not at the Cape Falcon Marine Reserve (p > 0.05, Table 13). Weak non-linear trends are observed at Redfish and Cascade Head, whereas an increasing linear trend is detected at the Cape Perpetua Marine Reserve. Even though the model results reveal statistically significant yearly trends, the timeseries underscores that mean sizes do not fluctuate more than 1-2 cm per year, per site, and likely represents natural variation as opposed to biological significance through time.
The random effect of cell was identified as a significant component of variation (Table 13).
GAMM model results can be found in the links below:
\(~\)
Cape Perpetua Marine Reserve has the largest top quartile sizes of Black Rockfish and Cape Falcon Marine Reserve the smallest.
There were differences by site in the top quartile of sizes of Black Rockfish (F. 192.311, p. <0.05). Cape Perpetua had the largest fish, followed by the Redfish Rocks Marine Reserve, and then the Cascade Head Marine Reserve. Cape Falcon had the smallest top quartile of Black Rockfish sizes (all adj. p < 0.05).
\(~\) \(~\)
4.4.1.2.1 Black Rockfish Mean Size by Site
Fig. 13: Black Rockfish mean size by site, yearly timeseries and GAMM model results with 95% confidence intervals across the marine reserves. See separate tabs for timseries and GAMM results.
4.4.1.2.2 Black Rockfish Mean Size Timeseries
Fig. 13: Black Rockfish mean size by site, yearly timeseries and GAMM model results with 95% confidence intervals across the marine reserves. See separate tabs for timseries and GAMM results.
4.4.1.2.3 Black Rockfish Modeled GAMM Results
Fig. 13: Black Rockfish mean size by site, yearly timeseries and GAMM model results with 95% confidence intervals across the marine reserves. See separate tabs for timseries and GAMM results.
\(~\) \(~\)
4.4.2 Blue/Deacon Rockfish, S.mystinus / S.diaconus
\(~\)
4.4.2.1 CPUE
Significantly higher Blue/Deacon Rockfish CPUE at the Redfish Rocks Marine Reserve than any other marine reserve.
Redfish Rocks Marine Reserve had higher CPUE than either the Cape Perpetua or Cascade Head Marine Reserves (p < 0.05; Table 14). No Blue/Deacon Rockfish were caught at the Cape Falcon Marine Reserve.
Significant yearly trends in Blue/Deacon Rockfish CPUE at the Redfish Rocks Marine Reserve and Cascade Head Marine Reserves.
There were significant yearly trends in CPUE at the Redfish Rocks Marine Reserve and Cascade Head Marine Reserve (p < 0.05; Table 15). Both sites showed a decline through time. No significant yearly trends were detected at the Cape Perpetua or Cape Falcon Marine Reserves.
The random effect of cell was identified as a significant component of variation (Table 15).
GAMM model results can be found in the links below:
\(~\) \(~\)
4.4.2.1.1 Blue/Deacon Rockfish CPUE by Site
Fig. 14: Blue/Deacon Rockfish catch per unit effort (CPUE) by site, yearly timeseries and modeled GAMM results with 95% confidence intervals, across marine reserves.See separate tabs for timseries and GAMM results.
4.4.2.1.2 Blue/Deacon Rockfish CPUE Timeseries
Fig. 14: Blue/Deacon Rockfish catch per unit effort (CPUE) by site, yearly timeseries and modeled GAMM results with 95% confidence intervals, across marine reserves.See separate tabs for timseries and GAMM results.
4.4.2.1.3 Blue/Deacon Rockfish CPUE Modeled GAMM Results
Fig. 14: Blue/Deacon Rockfish catch per unit effort (CPUE) by site, yearly timeseries and modeled GAMM results with 95% confidence intervals, across marine reserves. See separate tabs for timseries and GAMM results.
\(~\) \(~\)
4.4.2.2 Size
No difference in mean size of Blue/Deacon Rockfish between the Redfish Rocks Marine Reserve and Cascade Head or Cape Perpetua Marine Reserves.
There were no significant differences in mean size of Blue/Deacon Rockfish among sites (all p > 0.05, Table 16). No Blue/Deacon Rockfish were observed at the Cape Falcon Marine Reserve.
Significant yearly trend in Blue/Deacon Rockfish mean size at the Cascade Head Marine Reserve only.
Significant yearly trends in mean size of Blue/Deacon Rockfish at the Cascade Head Marine Reserve, where a decrease in size is observed over time (p < 0.05, Table 17). There were no significant yearly trends at the Redfish Rocks or Cape Perpetua Marine Reserves in Blue/Deacon mean size.
The random effect of cell was identified as a significant component of variation (Table 17).
GAMM model results can be found in the links below:
\(~\)
The Cascade Head Marine Reserve has larger top quartile sizes of Blue/Deacon Rockfish than the Redfish Rocks or Cape Perpetua Marine Reserves.
There were differences by site in the top quartile of sizes of Blue/Deacon Rockfish (F. 24.449, p. <0.05). The Cascade Head Marine Reserve had significantly larger top quartile sizes of Blue/Deacon Rockfish than the Redfish Rocks or Cape Perpetua Marine Reserves (adj p < 0.05). There was no significant difference in top quartile sizes between the Redfish Rocks and Cape Perpetua Marine Reserves (adj p > 0.05).
\(~\) \(~\)
4.4.2.2.1 Blue/Deacon Rockfish Mean Size by Site
Fig. 15: Blue/Deacon Rockfish mean size by site, yearly timeseries and GAMM model results with 95% confidence intervals across marine reserves.See separate tabs for timseries and GAMM results.
4.4.2.2.2 Blue/Deacon Rockfish Mean Size Timeseries
Fig. 15: Blue/Deacon Rockfish mean size by site, yearly timeseries and GAMM model results with 95% confidence intervals across marine reserves.See separate tabs for timseries and GAMM results.
4.4.2.2.3 Blue/Deacon Rockfish Modeled GAMM Results
Fig. 15: Blue/Deacon Rockfish mean size by site, yearly timeseries and GAMM model results with 95% confidence intervals across marine reserves.See separate tabs for timseries and GAMM results.
\(~\) \(~\)
4.4.3 China Rockfish, S. nebulosus
\(~\)
4.4.3.1 CPUE
China Rockfish only observed at the Redfish Rocks and Cascade Head Marine Reserves.
Catch rates of China Rockfish were very low across all sites and years (e.g. 1 fish caught per 25 angler hours fishing), so statistical analyses were not conducted (Fig. 16). China Rockfish were only observed at two marine reserves - the Redfish Rocks Marine Reserve and Cascade Head Marine Reserve. No China Rockfish were observed at the Cape Perpetua or Cape Falcon Marine Reserves.
4.4.3.1.1 China Rockfish CPUE by Site
Fig. 16: China Rockfish catch per unit effort (CPUE) by site and yearly timeseries with 95% confidence intervals, across marine reserves.
4.4.3.1.2 China Rockfish CPUE Timeseries
Fig. 16: China Rockfish catch per unit effort (CPUE) by site and yearly timeseries with 95% confidence intervals, across marine reserves.
\(~\) \(~\)
4.4.3.2 Size
Too few observations of China Rockfish to detect differences in size by site or year.
Catch rates of China Rockfish were very low across all sites and years (e.g. 1 fish caught per 25 angler hours fishing), so statistical analyses were not conducted.(Fig. 16). China Rockfish were only observed at two marine reserves - the Redfish Rocks Marine Reserve and Cascade Head Marine Reserve, and data plots suggest mean sizes are similar between these sites. No China Rockfish were observed at the Cape Perpetua or Cape Falcon Marine Reserves.
Too few observations of China Rockfish to detect differences in top quartile sizes.
\(~\) \(~\)
4.4.3.2.1 China Rockfish Mean Size by Site
Fig. 17: China Rockfish mean size by site and yearly timeseries with 95% confidence intervals, across marine reserves.
4.4.3.2.2 China Rockfish Mean Size Timeseries
Fig. 17: China Rockfish mean size by site and yearly timeseries with 95% confidence intervals, across marine reserves.
\(~\) \(~\)
4.4.4 Yelloweye Rockfish, S.ruberrimus
\(~\)
4.4.4.1 CPUE
Too few observations of Yelloweye Rockfish to detect differences in CPUE by site or year.
Catch rates of Yelloweye Rockfish were very low across all sites and years (e.g. 1 fish caught per 25 angler hours fishing; Fig. 18), so statistical analyses were not conducted. Data plots suggest that Cape Perpetua and Redfish Rocks had the highest mean CPUE of Yelloweye Rockfish. No Yelloweye Rockfish were caught at the Cape Falcon Marine Reserve.
\(~\) \(~\)
4.4.4.1.1 Yelloweye Rockfish CPUE by Site
Fig. 18: Yelloweye Rockfish catch per unit effort (CPUE) by site and yearly timeseries with 95% confidence intervals,across marine reserves.
4.4.4.1.2 Yelloweye Rockfish CPUE Timeseries
Fig. 18: Yelloweye Rockfish catch per unit effort (CPUE) by site and yearly timeseries with 95% confidence intervals,across marine reserves.
4.4.4.2 Size
Too few observations of Yelloweye Rockfish to detect differences in size by site or year
Catch rates of Yelloweye Rockfish were very low across all sites and years (e.g. 1 fish caught per 25 angler hours fishing), so statistical analyses were not conducted.(Fig. 18). No Yelloweye Rockfish were observed at the Cape Falcon Marine Reserves. Data plots suggest mean sizes are similar among the three marine reserve with catches of Yelloweye Rockfish.
Too few observations of Yelloweye Rockfish to detect differences in top quartile sizes
\(~\) \(~\) \(~\) \(~\)
4.4.4.2.1 Yelloweye Rockfish Mean Size by Site
Fig. 19: Mean Yelloweye Rockfish sizes with 95% confidence intervals by site and year, across the marine reserves.
4.4.4.2.2 Yelloweye Rockfish Mean Size Timeseries
Fig. 19: Mean Yelloweye Rockfish sizes with 95% confidence intervals by site and year, across the marine reserves.
4.4.5 Cabezon, Scorpaenichthys marmoratus
\(~\)
4.4.5.1 CPUE
Too few observations of Cabezon to detect differences in CPUE by site or year.
Catch rates of Cabezon were low across all sites and years (e.g. 1 fish caught per 10 angler hours fishing; Fig. 20), so statistical analyses on CPUE data were not conducted. Data plots suggest the highest catch rates of Cabezon at the Cascade Head Marine Reserve. No Cabezon were caught at the Cape Perpetua Marine Reserve.
\(~\) \(~\)
4.4.5.1.1 Cabezon CPUE by Site
Fig. 20: Cabezon catch per unit effort (CPUE) by site and yearly timeseries with 95% confidence intervals,across marine reserves.
4.4.5.1.2 Cabezon CPUE Timeseries
Fig. 20: Cabezon catch per unit effort (CPUE) by site and yearly timeseries with 95% confidence intervals,across marine reserves.
4.4.5.2 Size
Too few observations of Cabezon to detect differences in size by site or year.
Catch rates of Cabezon were very low across all sites and years (e.g. 1 fish caught per 10 angler hours fishing), so statistical analyses were not conducted.(Fig. 20). No Cabezon were observed at the Cape Perpetua Marine Reserve. Data plots suggest that mean size of Cabezon is similar at the three marine reserve sites with positive catch rates.
Too few observations of Cabezon to detect differences in top quartile sizes.
\(~\) \(~\) \(~\) \(~\)
4.4.5.2.1 Cabezon Mean Size by Site
Fig. 21: Mean Cabezon sizes with 95% confidence intervals by site and year, across the marine reserves.
4.4.5.2.2 Cabezon Mean Size Timeseries
Fig. 21: Mean Cabezon sizes with 95% confidence intervals by site and year, across the marine reserves.
\(~\) \(~\)
4.4.6 Lingcod, Ophiodon elongatus
\(~\)
4.4.6.1 CPUE
Significantly higher Lingcod CPUE at the Redfish Rocks Marine Reserve than the Cape Falcon Marine Reserve.
There were significantly higher Lingcod CPUE at the Redfish Rocks Marine Reserve than the Cape Falcon Marine Reserve (p < 0.05; Table 18). No significant difference in Lingcod CPUE between the Redfish Rocks Marine Reserve and Cape Perpetua or Cascade Head Marine Reserves (p > 0.05; Table 18).
Significant yearly trends in Lingcod CPUE observed at Redfish Rocks, Cape Perpetua, and Cascade Head Marine Reserves, but not at the Cape Falcon Marine Reserve.
There were significant similar trends in Lingcod CPUE observed at the Redfish Rocks, Cape Perpetua and Cascade Head Marine Reserves (p < 0.05; Table 19), with a gradual increase until around 2014-2016, followed by a decrease through time. The only site without significant yearly trends was the Cape Falcon Marine Reserve (p > 0.05; Table 19).
The random effect of cell was identified as a significant source of variation (Table 19).
GAMM model results can be found in the links below:
\(~\) \(~\)
4.4.6.1.1 Lingcod CPUE by Site
Fig. 22: Lingcod catch per unit effort (CPUE) by site, yearly timeseries and GAMM model results with 95% confidence intervals across marine reserves. See separate tabs for timseries and GAMM results.
4.4.6.1.2 Lingcod CPUE Timeseries
Fig. 22: Lingcod catch per unit effort (CPUE) by site, yearly timeseries and GAMM model results with 95% confidence intervals across marine reserves. See separate tabs for timseries and GAMM results.
4.4.6.1.3 Lingcod Modeled GAMM Results
Fig. 22: Lingcod catch per unit effort (CPUE) by site, yearly timeseries and GAMM model results with 95% confidence intervals, across marine reserves.See separate tabs for timseries and GAMM results.
\(~\) \(~\)
4.4.6.2 Size
The Redfish Rocks Marine Reserve has significantly larger mean size Lingcod than Cascade Head and Cape Falcon Marine Reserves.
The Redfish Rocks Marine Reserve had larger mean size Lingcod than the Cascade Head and Cape Falcon Marine Reserves (p < 0.05, Table 20). There was no difference in Lingcod mean size between the Redfish Rocks and Cape Perpetua Marine Reserves (p > 0.05).
Significant yearly trends in Lingcod size at the Redfish Rocks Marine Reserve only.
There was a significant yearly trend in Lingcod mean size through time at both the Redfish Rocks Marine Reserve with an increase in size from 2011 to 2019 (p < 0.05, Table 21).
The random effect of cell was identified as a significant component of variation for mean size of Lingcod (Table 21).
GAMM model results can be found in the links below:
\(~\)
The Redfish Rocks and Cape Perpetua Marine Reserve have the largest top quartile sizes of Lingcod and Cape Falcon Marine Reserve has the smallest top quartile sizes of Lingcod
There were differences by site in the top quartile of sizes of Lingcod (F.69.1, p < 0.05). The Redfish Rocks and Cape Perpetua Marine Reserve had the largest top quartile sizes of Lingcod than the other two reserves (adj. p < 0.05), but were not significantly different from each other (adj p > 0.05). Cape Falcon had significantly smaller top quartile sizes of Lingcod than all other marine reserves (all adj. p < 0.05).
\(~\) \(~\)
4.4.6.2.1 Lingcod Mean Size by Site
Fig. 23: Lingcod mean size by site, yearly timeseries and GAMM model results with 95% confidence intervals across marine reserves.See separate tabs for timseries and GAMM results.
4.4.6.2.2 Lingcod Mean Size Timeseries
Fig. 23: Lingcod mean size by site, yearly timeseries and GAMM model results with 95% confidence intervals across marine reserves.See separate tabs for timseries and GAMM results.
4.4.6.2.3 Lingcod Modeled GAMM Results
Fig. 23: Lingcod mean size by site, yearly timeseries and GAMM model results with 95% confidence intervals across marine reserves. See separate tabs for timseries and GAMM results.
\(~\) \(~\)
5 References
Anderson M.J., Walsh D.C.I. 2013. PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: What null hypothesis are you testing? Ecological Monographs 83(4): 557-574.
Chao A., Gotelli N.J., Hsieh T.C., Sander E.L., Ma K.H., Colwell R.K., Ellison A.M. (2014) Rarefaction and extrapolation with Hill numbers: A framework for sampling and estimation in species diversity studies. Ecol Monogr 84:45–67
Choat, J. H., & Robertson, D. R. (2002). Age-based studies. Coral reef fishes: Dynamics and diversity in a complex ecosystem, 57-80.
Clarke K.R., Chapman M.G., Somerfield P.J., Needham H.R. (2006). Dispersion-based weighting of species counts in assemblage analyses. Mar Ecol Prog Ser 320: 11-27.
Green, R. H., & Young, R. C. (1993). Sampling to detect rare species. Ecological Applications, 3(2), 351-356.
Hill M.O. (1973) Diversity and Evenness : A Unifying Notation and Its Consequences. Ecology 54:427–432.
Hinkle D.E., Wiersma W., Jurs S.G. Applied Statistics for the Behavioral Sciences. 5th ed. Boston: Houghton Mifflin; 2003
Hsieh, T. C., Ma, K. H., & Chao, A. (2016). iNEXT: an R package for rarefaction and extrapolation of species diversity (H ill numbers). Methods in Ecology and Evolution, 7(12), 1451-1456.
Legendre P. and Anderson M.J. 1999. Distance-based redundancy analysis: Testing multispecies responses in multifactorial ecological experiments. Ecological Monographs 69(1): 1-24.
Lester, S. E., Halpern, B. S., Grorud-Colvert, K., Lubchenco, J., Ruttenberg, B. I., Gaines, S. D., … & Warner, R. R. (2009). Biological effects within no-take marine reserves: a global synthesis. Marine Ecology Progress Series, 384, 33-46.
Love, M. S., & Yoklavich, M. M. (2006). Deep rock habitats. In The ecology of marine fishes (pp. 253-266). University of California Press.
Maunder, M. N., & Punt, A. E. (2004). Standardizing catch and effort data: a review of recent approaches. Fisheries research, 70(2-3), 141-159.
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/.
Starr, R. M., Wendt, D. E., Barnes, C. L., Marks, C. I., Malone, D., Waltz, G., … & Yochum, N. (2015). Variation in responses of fishes across multiple reserves within a network of marine protected areas in temperate waters. PLoS One, 10(3), e0118502.
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.
### This can be a useful function to play a sound at the end of a long script
#beepr::beep()