Longline (LL) sampling targets demersal fishes living on rocky reef habitats using catch and release methods. All fish caught are identified to species level and measured for length. Fish are caught using standardized longline gear for a fixed amount of time, providing data on effort.
Our LL sampling at Redfish Rocks grew out of a pilot study comparing hook and line sampling to longline sampling. This pilot study was based on observations of our local fishing captain that there were several species targeted by commercial fisheries in the area that were not well represented in hook and line catch (Huntington and Watson 2017). Sampling is conducted in the marine reserve and two comparison areas, Humbug and Orford Reef (see methods Appendix for additional information about comparison area selection). The pilot study occurred in 2015 and 2016, sampling continued in 2017 and 2019, providing four years of data for our analysis and inclusion in the synthesis report.
Data from longline monitoring efforts can be used to explore questions about fish abundance and size from a method that is similar to local commercial nearshore longline fishing efforts. We can also explore these data with questions about diversity and catch composition to compare across monitoring tools to understand tool bias or to validate trends seen across tools. 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, biomass, and size have changed 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.
Diversity
Community Composition
Aggregate Abundance
Focal Species Abundance
Here we present a summary of our Longline monitoring results and our 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.
Species fish diversity sampled by longline was similar between the Redfish Rocks Marine Reserves and its associated comparison areas.
Species fish diversity was similar between the Redfish Rocks Marine Reserve and Humbug and Orford Reef Comparison Areas. Similar numbers of common, rare, and total species were observed among the survey sites. Diversity indices were also similar between sites, as was the mean species richness for an average day of sampling.
Catch composition was similar between the marine reserve and its comparison areas across sites and years; the majority of variation driven by catch of two species.
The CPUE of Lingcod and Cabezon drove most of the observed variation in catch composition rather than differences across sites and years. Season and habitat variables did not explain very much of variation in catch composition.
At an aggregated level and across species, there were very few differences detected between the marine reserve and its comparison areas.
Blue/Deacon Rockfish mean size was greater in Humbug Comparison Area compared to Redfish Rocks Marine Reserve. Across all other focal species, there were no significant differences in CPUE, BPUE, or mean size among survey sites. When data were aggregated across species, there were no statistical differences in either CPUE or BPUE among sample sites.
We were able to detect natural, interannual variability in CPUE, BPUE, and mean size for select species.
Across metrics of CPUE, BPUE, and mean size, there were species-specific, interannual patterns detected. These patterns were inconsistent across species and survey locations. For example, mean size declined through time for China Rockfish at Orford Reef Comparison Area, Lingcod at Redfish Rocks Marine Reserve, and for Yelloweye at the Humbug Comparison Area. For a number of species, there was an increase in CPUE or BPUE followed by a decrease in the later years of sampling. It was unclear what drove this pattern. Statistical changes detected at Redfish Rocks Marine Reserve were generally positive increases through time.
There were larger top quartile sizes of some focal species in the Redfish Rocks Marine Reserve.
The largest individuals for four of six focal species were found at Redfish Rocks Marine Reserve. These were: China and Yelloweye Rockfish, Cabezon, and Lingcod. The largest top quartile of sizes for Blue/Deacon Rockfish were observed at the Humbug Comparison Area. There were no differences detected among the top quartile of sizes for Black Rockfish.
Longline monitoring provides data for fisheries-targeted species, such as Canary, Copper, Quillback and Vermilion Rockfish.
The use of longline gear allowed us to collect sufficient sample sizes to analyze trends by site and year for solitary, demersal, fisheries-targeted species. This tool was specifically developed to mimic the local longline fishery out of Port Orford and to provide meaningful data on species important to this local fishing community. We found that for Canary and Vermilion Rockfish there was higher CPUE and BPUE in the Redfish Rocks Marine Reserve than Humbug Comparison Area. Copper Rockfish CPUE and BPUE increased through time at the Redfish Rocks Marine Reserve and Quillback Rockfish CPUE increased at Redfish Rocks Marine Reserve and Orford Reef Comparison Area. Quillback Rockfish BPUE increased at the marine reserve, but experienced a maximum in 2017 at the Humbug Comparison Area. Mean size did not vary by site, but there were slight interannual differences in size by year. We found larger top quartile sizes of Canary and Copper Rockfish in the marine reserve than in both comparison areas. With Vermilion Rockfish we found larger top quartile sizes in the marine reserve than the Orford Reef Comparison Area. Our ability to collect data on important fisheries species supports our decision to add this supplemental monitoring tool at Redfish Rocks to target these commercially important species with a tool that mimics local fishing efforts.
Monitoring with longline surveys will continue at current levels and intervals.
Current efforts are able to detect interannual trends for multiple species. It is unclear whether increasing effort across all sites would increase our ability to detect change for more species, given that this monitoring tool focuses on solitary demersal species. Without an increase to program budget or staff, longline survey efforts will likely continue at current levels and intervals and provide useful supplemental data to hook and line monitoring efforts.
Longline (LL) sampling is conducted in the Redfish Rocks Marine Reserve, Humbug Comparison Area and Orford Reef Comparison Area. Monitoring began in Redfish and Humbug in 2015 as a pilot study occurring simultaneously with hook and line sampling. In 2017 Orford Reef was added in as a comparison area, in part because it is a favorite fishing location of the nearshore longline fleet out of Port Orford. Sampling effort targeted 2 days in the reserve, 2 days at Orford Reef and 2 days at Humbug Reef for a total of 6 days, for both spring and fall monitoring. Each day between 5-6 cells (500m x 500 m grids) are targeted, with one longline set, approximately 2 hours in length, in each cell. The unit of replication for longline catch data is at the cell-day level, while all size data is at the individual fish level. All fish caught during each set are identified to species, measured and released. We calculate both a catch and biomass per unit effort (CPUE, BPUE) for each given cell-day and species. For additional details on data collection, please review documentation in the Methods Appendix.
With longline gear, we explored several concepts related to species diversity at a given site:
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.
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 longline 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.
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 longline 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 longline sets (cells) sampled per day). We also identified species that were unique to each marine reserve and comparison area.
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.
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. This would provide useful information about site diversity for an average sampling day of effort.
All analyses and graphs were created in R v4.0.2, using the iNEXT and Vegan packages.
We focused our community composition analysis on the question of whether variation in catch 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 other potential drivers of variation including species-specific differences, habitat and environmental factors.
To explore variation by site and year, we used catch per unit effort (CPUE) data with 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 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 nested mixed model with site and year as fixed effects factors, and cell, our sampling replicate for longline gear, as a random effect, nested under site. 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 significant factors identified by 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 several additional factors that could be driving the variation in fish community structure. We extended our data visualization, by performing a vector analysis of fish species in the community, selecting only the species with > 0.5 Pearson correlations (Hinkle et al. 2003). 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 euclidean distance resemblance matrix, which provides information on the percent of variation explained by each axis.
In addition to species specific drivers of variation, we also explored the relationship between community composition and environmental variable. We employed several models incorporating month, proportion of hard bottom (rock) within a sampling cell, and average drift depth (averaged among cell/day combinations) to test if these habitat or environmental variables explained significant variation across sites or years. Due to strict requirements of these variables needing to match with each specific biological sample, only samples that contained estimates of all the above variables were used for analysis. An initial histogram of data revealed non-normal distributions so an overall data transformation (Log(x+1)) was employed. CPUE data are considered a rate (catch per angler hour) so a distance based resemblance matrix was selected, using a euclidean distance with an addition of a dummy variable (=1). With these data a distance-based linear model (DistLM) and a distance-based redundancy analysis (dbRDA) were conducted to determine which variables may explain variation across sites or years (Legendre and Anderson 1999). DistLM is akin to a multivariate multiple regressions model where the relationship between a multivariate data cloud (resemblance matrix) and one or more predictor variables are analyzed and modeled. The dbRDA routine then visualizes the model and fits it into a multi-dimensional space. In the DistLM model AIC values were used as the selection criteria and a Best selection procedure was employed to find the best combination of variables with the lowest AIC value as the best model fit.
All analyses and graphs were made in PRIMERe version 7 with PERMANOVA extension.
We explored changes in aggregate and focal species catch rates (catch per unit effort, CPUE), biomass rates (biomass per unit effort, BPUE), and size (focal species only) by site and year with generalized additive mixed models (GAMM). We modeled raw catch and biomass data with an offset for fishing effort (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 and a gaussian distribution on log-transformed biomass for the BPUE 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 metrics 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 BPUE, and species-specific CPUE, BPUE and size for focal species. 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:
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)
BPUE = mgcv::gam(log(Biomass + 1) ~ Site + s(Year, by = Site, k = 3) + s(Cell_ID, bs = “re”), offset = log(Effort), family = gaussian)
Size = mgcv::gam(Length ~ site + s(Year, by = site, k = 3) + s(Cell_ID, bs = “re”), family = gaussian)
Longline sampling efforts at Redfish Rocks and its comparison areas resulted in four years of data collection, where varying sample sizes were collected per year (Fig. 2). The first two years of sampling (2015, 2016) were part of a pilot study comparing the video lander and longline gear at the Redfish Rocks Marine Reserve and Humbug Comparison Area. The results of that study informed future sampling (2017, 2019) where Orford Reef was included in sampling efforts.
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Species richness is similar across the Redfish Rocks Marine Reserve and its comparison areas
Over the four years of sampling with longline gear a total of 18 species (or species groups) were observed in the Redfish Rocks Marine Reserve (Table 5). The Humbug Comparison Area had slightly fewer species, 17, whereas Orford Reef had the fewest total species observed with 14 (Table 5). These observed numbers of species richness are similar to the estimated numbers of total species richness (Table 5)
library(kableExtra)
<- data.frame(Area = c("Redfish Rocks Marine Reserve",
pna "Humbug Comparison Area",
"Orford Reef Comparison Area"),
Observed_Richness = c("18","17","14"),
Estimated_Richness = c("19","19","16"),
LCL = c("18","17","14"),
UCL = c("28", "39","36"))
kbl(pna, caption = "Table 5: Observed and estimated species richness by site with lower (LCL) and upper (UCL) 95% confidence limits") %>%
::kable_classic() kableExtra
Area | Observed_Richness | Estimated_Richness | LCL | UCL |
---|---|---|---|---|
Redfish Rocks Marine Reserve | 18 | 19 | 18 | 28 |
Humbug Comparison Area | 17 | 19 | 17 | 39 |
Orford Reef Comparison Area | 14 | 16 | 14 | 36 |
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Species rarefaction curves highlight that at small samples sizes, such as those for any given year, the species richness is most similar between the Redfish Rocks Marine Reserve and Humbug Comparison Area (Fig. 3). As effort across sites increases, more rare species are observed at the Marine Reserve and Humbug Comparison Area than at Orford Reef, resulting in higher estimated species richness for these sites (Fig. 3, Table 5).
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The number of unique and common species among all sites is similar; however, Orford Reef Comparison Area had the fewest rare species
The Redfish Rocks Marine Reserve had three unique species the Brown Irish Lord (Hemilepidotus spinosus), the Red Irish Lord (H.hemilepidotus) and the Spiny Dogfish (Squalus acanthias). Two unique species were observed at the Humbug Comparison Area, the Rosy Rockfish (S.rosaceus) and the Spotted Ratfish (Hydrolagus colliei). No unique species were found at the Orford Reef Comparison Area. The number of common species was similar for Redfish Rocks Marine Reserve (n = 5), Humbug Comparison Area (n=3), and the Orford Reef Comparison Area (n = 4) had fewer. Cabezon and Lingcod had the highest frequency of occurrence at both the marine reserve and Orford Reef Comparison Area. China Rockfish were considered common species at both the marine reserve and Orford Reef Comparison Area. The Redfish Rocks Marine Reserve and Humbug Comparison Area had more rare species (both sites n = 7) than the Orford Reef Comparison Area (n = 3). This suggests that observations were more evenly distributed across the smaller species list at Orford Reef Comparison Area.
Many of the other species of fisheries interest - Quillback, Yelloweye, Copper and Vermillion Rockfish - were not considered common or rare, and were caught in a moderate amount. Not all species were observed each year, for a summary of species counts over the years by site please see tables below.
Pooled species counts across all years and species counts by individual sampling year are included in the following tables:
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Similarity in diversity indices between the Redfish Rocks Marine Reserve and its surrounding comparison areas.
Minimal differences in the effective number of species between the marine reserve and its comparison Areas (Humbug and Orford Reef) across the three diversity indices (Fig. 5).
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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. 6-8).
Fig. 6: Redfish Rocks Marine Reserves species rarefaction curves by year from longline data.
Fig. 7: Humbug Comparison Area species rarefaction curves by year from longline data.
Fig 8: Orford Reef Comparison Area species rarefaction curves by year from longline data.
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For an average day of sampling, there is similar average species diversity across all sites
When comparing mean species richness for an average day of sampling, there is no difference between the Redfish Rocks Marine Reserve or either of its comparison areas (F.2.063, p> 0.05; Fig. 9).
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There was no clear structuring of fish catch composition by site or year at the Redfish Rocks Marine Reserve and its comparison areas with longline data.
There was no structuring of fish catch composition data by site or year at the Redfish Rocks Marine Reserve and its comparison areas. (Fig. 10).
Multivariate statistics indicate some differences by year and cell, but explain little total variation in longline catch composition.
PERMANOVA results indicate that year and cell, but none of the interactions are significant (p< 0.05) for fish catch composition with longline data at Redfish Rocks Marine Reserve and its comparison areas (Table 12). Estimated variation described by each of the variables and variable interactions was very small. Cell accounted for the highest variability of all the variables/interactions but only accounted for 9% of total variation, (year = 5%), whereas the residuals describe over 87% of the variation in the results. Therefore, while these factors were significant they are likely not biologically relevant because they describe such a small portion of the variation in the data.
PERMDISP results indicate significant differences in dispersion by year and cell (p>0.05, Table 13). This suggests the significance identified in the PERMANOVA is likely because of differences in dispersion or dispersion and spatial location among both sampling cells and years. 2019 was the year with the largest dispersion, and was significantly different than the years with the smallest dispersions (2015,2016). There was no distinct patterns in dispersion between cells, indicating that significant differences in dispersion are more likely to be the result of randomized sampling and lower sample sizes within cells than cohesive patterns in cells within certain sites.
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Lingcod and Cabezon catch drive the majority of variation in fish catch composition regardless of site or year
We explored species-specific drivers of variation, and found that Lingcod and Cabezon were driving the majority of variation in the data (Fig. 11). Principal coordinate analysis revealed that ~20% of the variation is explained by CPUE of Lingcod (x-axis) and ~16% of variation is described by Cabezon.
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While models including season and habitat variables were statistically significant, they account for little of the total variation in the data
DISTLM results indicated four environmental variables (year, month, proportion rock and average set depth), were significant and the best model included all of these variables (Table 15). Year roughly correlated with the x axis and explained 64% of model variation, but only explained 3.5% of the total variation. Depth roughly correlated with the y axis and explained 26% of the model variation but only explained 2% of the overall variation. Proportion rock and month surveyed did not correlate strongly with either axis. While these variables were significant, the low amount of variance described in the model indicates that they likely do not play a discernible role in structuring fish communities.
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No significant difference in aggregate CPUE between the Redfish Rocks Marine Reserve and its associated comparison areas.
There was no significant difference in aggregate CPUE between the Redfish Rocks Marine Reserve and the Humbug Comparison Area or Orford Reef Comparison Area (all p > 0.05; Table 16).
No significant yearly trends in aggregate CPUE at the Redfish Rocks Marine Reserve and its associated comparison areas.
There were no significant trends by year in aggregate CPUE at the Redfish Rocks Marine Reserve, Humbug Comparison Area, or Orford Reef Comparison Area (all p > 0.05; Fig. 12, Table 17).
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:
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No significant difference in aggregate BPUE between the Redfish Rocks Marine Reserve and its associated comparison areas.
There was no significant difference in aggregate BPUE between the Redfish Rocks Marine Reserve and the Humbug Comparison Area or Orford Reef Comparison Area (all p > 0.05; Table 18).
No significant yearly trends in aggregate BPUE at the Redfish Rocks Marine Reserve and its associated comparison areas.
There were no significant trends by year in aggregate BPUE at the Redfish Rocks Marine Reserve, Humbug Comparison Area, or Orford Reef Comparison Area (all p > 0.05; Table 19).
The random effect of cell was identified as a significant component of variation (Table 19).
GAMM model results can be found in the links below:
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No significant difference in Black Rockfish CPUE between the Redfish Rocks Marine Reserve and its associated comparison areas.
There was no significant difference in Black Rockfish CPUE between between the Redfish Rocks Marine Reserve and the Humbug Comparison Area or Orford Reef Comparison Area (p < 0.05; Table 20).
No significant yearly trends in Black Rockfish CPUE at the Redfish Rocks Marine Reserve or its associated comparison areas.
There were no significant trends in Black Rockfish CPUE by year at the Redfish Rocks Marine Reserve, Humbug Comparison Area, or Orford Reef Comparison Area (p < 0.05; Table 21).
The random effect of cell was identified as a significant component of variation (Table 21).
GAMM model results can be found in the links below:
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No difference in Black Rockfish mean size between the Redfish Rocks Marine Reserve and its comparison areas.
There were no statistically significant differences in mean size of Black Rockfish among sites (all p > 0.05, Table 22).
Significant yearly trends in Black Rockfish mean size at the Redfish Rocks Marine Reserve.
There were significant yearly trends in mean size at the Redfish Rocks Marine Reserve (p<0.05; Table 23). At the Redfish Rocks Marine Reserve, mean size increased to a peak in 2015/2016 and then declined gradually through 2019. Even though the model results reveal statistically significant yearly trends, the mean size 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 (Fig. 15).
The random effect of cell was identified as a significant component of variation (Table 23).
GAMM model results can be found in the links below:
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There was no significant difference between top quartile sizes of Black Rockfish at the marine reserve compared to either comparison area.
There were no differences by site in the top quartile of sizes of Black Rockfish between the marine reserve and either of its comparison areas (adj. p > 0.05).
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No significant difference in Black Rockfish BPUE between the Redfish Rocks Marine Reserve and its associated comparison areas.
There was no significant difference in Black Rockfish BPUE between the Redfish Rocks Marine Reserve and the Humbug Comparison Area or Orford Reef Comparison Area ( p> 0.05; Table 24).
No significant yearly trends in Black Rockfish BPUE at the Redfish Rocks Marine Reserve or its associated comparison areas.
There were no significant yearly trends at the Redfish Rocks Marine Reserve, Humbug Comparison Area, or Orford Reef Comparison Area with Black Rockfish BPUE (p > 0.05; Table 25).
The random effect of cell was identified as a significant component of variation (Table 25).
GAMM model results can be found in the links below:
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No significant difference in Blue/Deacon Rockfish CPUE between the Redfish Rocks Marine Reserve and its associated comparison areas.
There was no significant difference in Blue/Deacon Rockfish CPUE between the Redfish Rocks Marine Reserve and the Humbug Comparison Area or Orford Reef Comparison Area (p < 0.05; Table 26).
Significant yearly trends in Blue/Deacon Rockfish CPUE at the Orford Reef Comparison Area only.
There was a significant yearly trend in Blue/Deacon CPUE at the Orford Reef Comparison Area (p < 0.05; Table 27), with a decline across the two years of sampling. There were no significant trends at the Redfish Rocks Marine Reserve or the Humbug Comparison Area (p > 0.05; Table 27).
The random effect of cell was identified as a significant component of variation (Table 27).
GAMM model results can be found in the links below:
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Smaller mean size of Blue/Deacon Rockfish at the Redfish Rocks Marine Reserve than the Humbug Comparison Area.
Smaller mean size Blue/Deacon Rockfish were observed at the marine reserve than the HUmbug Comparison Area (p<0.05, Table 28). There were no significant differences in mean size of Blue/Deacon Rockfish between the marine reserve and Orford Reef Comparison ARea (p> 0.05).
No significant yearly trend in Blue/Deacon Rockfish mean size at the Redfish Rocks Marine Reserve or its surrounding comparison areas.
There were no significant yearly trends in mean size of Blue/Deacon Rockfish at the Redfish Rocks Marine Reserve or its surrounding comparison areas (all p> 0.05, Table 29, Fig. 18).
The random effect of cell was not identified as a significant component of variation (Table 29).
GAMM model results can be found in the links below:
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The top quartile of Blue/Deacon Rockfish sizes at Redfish Rocks Marine Reserve and Orford Reef Comparison Area were smaller than at Humbug Comparison Area.
There were differences by site in the top quartile of sizes of Blue/Deacon Rockfish (F. 17.16, p. <0.05). The Humbug Comparison Area had larger top quartile sizes of Blue/Deacon Rockfish than the marine reserve (adj. p < 0.05). There was no difference in top quartile sizes between the marine reserve and Orford Reef Comparison Area (adj. p > 0.05).
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No significant difference in Blue/Deacon Rockfish BPUE between the Redfish Rocks Marine Reserve and its associated comparison areas.
There was no significant difference in Blue/Deacon Rockfish BPUE between the Redfish Rocks Marine Reserve and the Humbug Comparison Area or Orford Reef Comparison Area (p < 0.05; Table 30).
Significant yearly trends in Blue/Deacon Rockfish BPUE at the Humbug and Orford Reef Comparison Areas.
There were significant yearly trends in Blue/Deacon Rockfish BPUE detected at Humbug and Orford Reef Comparison Areas (p < 0.05, Table 31). Humbug had an increasing trend between 2015-2018 followed by a leveling-off in 2019, while Orford Reef had with a decline across the two years of sampling. There was no significant yearly trend at the Redfish Rocks Marine Reserve (p > 0.05; Table 31).
The random effect of cell was identified as a significant component of variation (Table 31).
GAMM model results can be found in the links below:
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No significant difference in China Rockfish CPUE between the Redfish Rocks Marine Reserve and its associated comparison areas.
There was no significant difference in China Rockfish CPUE between the Redfish Rocks Marine Reserve and the Humbug or Orford Reef Comparison Area (p > 0.05; Table 32).
Significant yearly trends in China Rockfish CPUE at the Redfish Rocks Marine Reserves only.
There was a significant trend by year at the Redfish Rocks Marine Reserve, with an increase in China Rockfish CPUE over time (p < 0.05; Table 33). There were no significant trends detected at either the Humbug or Orford Reef Comparison Areas (p > 0.05; Table 33).
The random effect of cell was identified as a significant component of variation (Table 33).
GAMM model results can be found in the links below:
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The Redfish Rocks Marine Reserve does not have larger China Rockfish than its comparison areas.
There were no differences in mean size of China Rockfish among sites (p>0.05; table 34).
A significant yearly trend in China Rockfish mean size at the Orford Reef Comparison Area only
There was a difference in China Rockfish mean size through time at the Orford Reef Comparison Area only, with sizes gradually declining between surveys in 2017 and 2019. No significant yearly trends detected at the Redfish Rocks Marine Reserve or Humbug Comparison Area (p>0.05, Table 35).
GAMM model results can be found in the links below:
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The Redfish Rocks Marine Reserve has significantly larger top quartile sizes of China Rockfish, than the Orford Reef Comparison Area
There were differences by site in the top quartile of sizes of Black Rockfish (F. 5.728, p. <0.05). The marine reserve had larger top quartile sizes than the Orford Reef Comparison Area (adj. p < 0.05), but differences with the Humbug Comparison Area were not significant (adj. p > 0.05). There was no difference in size between the Humbug and Orford Reef Comparison Areas.
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No significant difference in China Rockfish BPUE between the Redfish Rocks Marine Reserve and its associated comparison areas.
There was no significant difference in China Rockfish BPUE between the Redfish Rocks Marine Reserve and the Humbug or Orford Reef Comparison Area (p < 0.05; Table 36
Significant yearly trends in China Rockfish BPUE at the Redfish Rocks Marine Reserves.
There was a significant trend by year in China Rockfish BPUE at the Redfish Rocks Marine Reserve, with an increase between 2015-2017, followed by a leveling-off in 2019 (p < 0.05; Table 37). There were no significant trends detected at either the Humbug or Orford Reef Comparison Areas (p > 0.05; Table 37).
The random effect of cell was identified as a significant component of variation (Table 37).
GAMM model results can be found in the links below:
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No significant difference in Yelloweye Rockfish CPUE between the Redfish Rocks Marine Reserve and its associated comparison areas.
There was no significant difference in Yelloweye Rockfish CPUE between the Redfish Rocks Marine Reserve and the Humbug Comparison Area or Orford Reef Comparison Area (p < 0.05; Table 38).
No significant yearly trends in Yelloweye Rockfish CPUE at the Redfish Rocks Marine Reserve or its associated comparison areas.
There were no significant trends in Yelloweye Rockfish CPUE by year at the Redfish Rocks Marine Reserve, Humbug Comparison Area, or Orford Reef Comparison Area (p < 0.05; Table 39).
The random effect of cell was identified as a significant component of variation (Table 39).
GAMM model results can be found in the links below:
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No difference in Yelloweye Rockfish mean size between the Redfish Rocks Marine Reserve and its comparison areas.
Significant yearly trends in Yelloweye Rockfish mean size at the Humbug Comparison Area only.
There were no significant yearly trends in Yelloweye Rockfish mean size at the Redfish Rocks Marine Reserve (p > 0.05; Table 41). No yearly trends detected at the Orford Reef Comparison Area in two years of sampling (p > 0.05). Significant yearly trends were detected at the Humbug Comparison Area, where Yelloweye Rockfish mean size declined through time (p<0.05, Table 40, Fig 24). This pattern at Humbug Comparison Area appears driven by largest sizes being observed in the first year of sampling (2015) compared to the next three surveys years.
The random effect of cell was not identified as a significant component of variation (Table 41).
GAMM model results can be found in the links below:
The Redfish Rocks Marine Reserve had larger top quartile sizes of Yelloweye Rockfish than its comparison areas.
For the top quartile of Yelloweye Rockfish sizes, there were differences by area (F. 12.52, p.< 0.05).The Marine Reserve had larger top quartile sizes than the Humbug Comparison Area and Orford Reef Comparison Area (all adj. p < 0.05). There was no difference in top quartile sizes between comparison areas (adj. p > 0.05).
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No significant differences in Yelloweye Rockfish BPUE between the Redfish Rocks Marine Reserve and its associated comparison areas.
There was no significant difference in Yelloweye Rockfish BPUE between the Redfish Rocks Marine Reserve and the Humbug Comparison Area or Orford Reef Comparison Area (p < 0.05; Table 42).
Significant yearly trends in Yelloweye Rockfish BPUE at the Redfish Rocks Marine Reserve only.
There was a significant trend by year in Yelloweye Rockfish BPUE at the Redfish Rocks Marine Reserve (p < 0.05; Table 43), with an increasing trend through time. There were no significant trends at the Humbug Comparison Area or Orford Reef Comparison Area (p < 0.05; Table 43).
The random effect of cell was identified as a significant component of variation (Table 43).
GAMM model results can be found in the links below:
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No significant difference in Cabezon CPUE between the Redfish Rocks Marine Reserve and its associated comparison areas.
There was no significant difference in Cabezon CPUE between the Redfish Rocks Marine Reserve and the Humbug Comparison Area or Orford Reef Comparison Area (p < 0.05; Table 44).
Significant yearly trends in Cabezon CPUE at the Redfish Rocks Reserve and Humbug Comparison Area.
There were significant yearly trends in Cabezon CPUE detected at the Redfish Rocks Marine Reserve and Humbug Comparison Area (p < 0.05, Table 45), with similar increasing trends through time at both sites. There was no significant trend detected at the Orford Reef Comparison Area (p > 0.05; Table 45).
The random effect of cell was identified as a significant component of variation (Table 45).
GAMM model results can be found in the links below:
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No significant difference in Cabezon mean size between the marine reserve and its associated comparison areas.
There were no significant differences in mean size of Cabezon among sites (all p > 0.05, Table 46).
No significant yearly trends in Cabezon mean size detected at the Redfish Rocks Marine Reserve or its comparison areas.
There were no significant yearly trends in mean size of Cabezon at the marine reserve or its associated comparison areas (p>0.05).
The random effect of cell was identified as a significant component of variation (Table 47).
GAMM model results can be found in the links below:
\(~\)
The Redfish Rocks Marine Reserve has significantly larger top quartile sizes of Cabezon than the Orford Reef Comparison Area.
There were significant differences by site in the top quartile sizes of Cabezon (F. 15.35, p.< 0.05). The marine reserve and Humbug Comparison Area had significantly larger top quartile sizes of Cabezon than the Orford Reef Comparison Area (adj. p <0.05). The top quartile of sizes at the marine reserve was not significantly different from Humbug Comparison Area (adj. p > 0.05).
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No significant difference in Cabezon BPUE between the Redfish Rocks Marine Reserve and its associated comparison areas.
There was no significant difference in Cabezon BPUE between the Redfish Rocks Marine Reserve and the Humbug Comparison Area or Orford Reef Comparison Area (p < 0.05; Table 48).
Significant yearly trends for Cabezon BPUE at the Redfish Rocks Marine Reserve only.
There was a significant trend by year for Cabezon BPUE at the Redfish Rocks Marine Reserve (p < 0.05; Table 49), with an increasing trend through time. There were no significant trends detected at the Humbug or Orford Reef Comparison Areas (p > 0.05; Table 49).
The random effect of cell was identified as a significant component of variation (Table 49).
\(~\) \(~\)
GAMM model results can be found in the links below:
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No significant difference in Lingcod CPUE between the Redfish Rocks Marine Reserve and its associated comparison areas.
There was no significant difference in Lingcod CPUE between the Redfish Rocks Marine Reserve and the Humbug Comparison Area or Orford Reef Comparison Area (all p > 0.05, Table 50).
A significant yearly trend in Lingcod CPUE at the Redfish Rocks Marine Reserve only.
The only site with a significant yearly trend in Lingcod CPUE was at the Redfish Rocks Marine Reserve (p < 0.05; Table 51), with an increase until a to peak in 2017, followed by a declined through 2019. There were no significant trends detected at the Humbug or Orford Reef Comparison Areas (p > 0.05; Table 51).
The random effect of cell was not identified as a significant source of variation. (Table 51).
GAMM model results can be found in the links below:
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No significant difference in mean size Lingcod between the marine reserve and its associated comparison areas.
The mean size of Lingcod did not differ between the Redfish Rocks Marine Reserve and its associated comparison areas (p>0.05, Table 52, Fig. 30).
Significant yearly trends in Lingcod size at the Redfish Rocks Marine Reserve.
There was a significant yearly trend in Lingcod mean size through time at the Redfish Rocks Marine Reserve (p=0.05, Table 53). At the Redfish Rocks Marine Reserve, there was a linear decrease in Lingcod mean size through time (Fig. 30).
The random effect of cell was identified as a significant component of variation for mean size of Lingcod (Table 53).
GAMM model results can be found in the links below:
\(~\)
The Redfish Rocks Marine Reserve has larger top quartile sizes of Lingcod than the Humbug Comparison Area.
There were differences by site in the top quartile of sizes of Lingcod (F.5.191, p.< 0.05). The Redfish Rocks Marine Reserve had larger top quartile sizes of Lingcod than the Humbug Comparison Area (adj p<0.05) but not the Orford Reef Comparison Area (adj. p > 0.05). Orford Reef had larger top quartile sizes of Lingcod than the Humbug Comparison Area (adj p<0.05).
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No significant differences in Lingcod BPUE between the Redfish Rocks Marine Reserve and its associated comparison areas.
There was no significant difference in Lingcod BPUE between the Redfish Rocks Marine Reserve and the Humbug Comparison Area or Orford Reef Comparison Area (all p > 0.05, Table 54).
A significant yearly trend in Lingcod BPUE at the Redfish Rocks Marine Reserve only.
The only site with a significant yearly trend in Lingcod BPUE was at the Redfish Rocks Marine Reserve (p < 0.05; Table 55), with an increase until 2017, followed by a declined through 2019. There were no significant trends detected at the Humbug or Orford Reef Comparison Areas (p > 0.05; Table 55).
The random effect of cell was not identified as a significant source of variation (Table 55).
GAMM model results can be found in the links below:
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Significantly higher Canary Rockfish CPUE at the Redfish Rocks Marine Reserve than Humbug Comparison Area.
Canary Rockfish CPUE was significantly higher in the Redfish Rocks Marine Reserve than Humbug Comparison Area (p < 0.05; Table 56). There was no significant difference in Canary Rockfish CPUE between the marine reserve and Orford Reef Comparison Area (p > 0.05; Table 56).
No significant yearly trends in Canary Rockfish CPUE detected at the Redfish Rocks Marine Reserve or its associated comparison areas.
There were no significant trends in Canary Rockfish CPUE by year at the Redfish Rocks Marine Reserve, Humbug Comparison Area, or Orford Reef Comparison Area (p < 0.05, Table 57).
The random effect of cell was identified as a significant source of variation. (Table 57).
GAMM model results can be found in the links below:
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No significant difference in mean size Canary Rockfish between the marine reserve and its associated comparison areas.
The mean size of Canary Rockfish did not differ between the Redfish Rocks Marine Reserve and its associated comparison areas (p>0.05, Table 58, Fig. 33).
Significant yearly trends in Canary Rockfish mean size at the Redfish Rocks Marine Reserve.
There was a significant yearly trend in Canary Rockfish mean size through time at the Redfish Rocks Marine Reserve (p<0.05, Table 59). At the Redfish Rocks Marine Reserve, Canary Rockfish mean sizes were at a minimum in 2017 (Fig. 33).
The random effect of cell was identified as a significant component of variation for mean size of Canary Rockfish (Table 59).
GAMM model results can be found in the links below:
\(~\)
The Redfish Rocks Marine Reserve has larger top quartile sizes of Canary Rockfish than both comparison areas.
There were differences by site in the top quartile of sizes of Canary Rockfish (F.45.809, p.< 0.05). The Redfish Rocks Marine Reserve had larger top quartile sizes of Canary Rockfish than the Humbug and Orford Reef Comparison Areas (adj p<0.05). Humbug Comparison Area had larger top quartile sizes of Canary Rockfish than the Orford Reef Comparison Area (adj p<0.05).
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Significantly higher Canary Rockfish BPUE at the Redfish Rocks Marine Reserve compared to the Humbug Comparison Area.
Canary Rockfish BPUE was significantly higher at the Redfish Rocks Marine Reserve than at the Humbug Comparison Area (p < 0.05; Table 60). There was no difference between the marine reserve and Orford Reef Comparison Area (p > 0.05; Table 60).
No significant yearly trends in Canary Rockfish BPUE at the Redfish Rocks Marine Reserve or its associated comparison areas.
There were no significant trends by year in Canary Rockfish BPUE at the Redfish Rocks Marine Reserve, Humbug Comparison Area, or Orford Reef Comparison Area (p > 0.05; Table 61).
The random effect of cell was identified as a significant source of variation (Table 61).
GAMM model results can be found in the links below:
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No significant difference in Copper Rockfish CPUE between the Redfish Rocks Marine Reserve and its associated comparison areas.
There was no significant difference in Copper Rockfish CPUE between the Redfish Rocks Marine Reserve and the Humbug Comparison Area or Orford Reef Comparison Area (p > 0.05; Table 62).
Significant yearly trends in Copper Rockfish CPUE detected at the Redfish Rocks Marine Reserve only.
There were significant yearly trends in Copper Rockfish CPUE detected at the marine reserve (p < 0.05; Table 63), with an increase through time. There were no significant trends detected at the Humbug or Orford Reef Comparison Areas (p > 0.05; Table 63).
The random effect of cell was identified as a significant source of variation (Table 63).
GAMM model results can be found in the links below:
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No significant difference in mean size Copper Rockfish between the marine reserve and its associated comparison areas.
The mean size of Copper Rockfish did not differ between the Redfish Rocks Marine Reserve and its associated comparison areas (p>0.05, Table 64, Fig. 36).
No significant yearly trends in Copper Rockfish mean size at the Redfish Rocks Marine Reserve or its associated comparison areas.
There were no significant yearly trends in Copper Rockfish mean size at any site (p>0.05, Table 65).
The random effect of cell was not identified as a significant component of variation for mean size of Copper Rockfish (Table 65).
GAMM model results can be found in the links below:
\(~\)
The Redfish Rocks Marine Reserve has larger top quartile sizes of Copper Rockfish than both comparison areas.
There were differences by site in the top quartile of sizes of Copper Rockfish (F.6.33, p.< 0.05). The Redfish Rocks Marine Reserve had larger top quartile sizes of Copper Rockfish than both comparison areas (both adj p<0.05). There was no difference in top quartile sizes of Copper Rockfish between the Orford Reef and Humbug Comparison Area (adj p<0.05).
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Significantly higher Copper Rockfish BPUE at the Redfish Rocks Marine Reserve compared to its associated Comparison Areas.
Higher Copper Rockfish BPUE at the Redfish Rocks Marine Reserve than at the Humbug or Orford Reef Comparison Area (p < 0.05; Table 66).
Significant yearly trends in Copper Rockfish BPUE at the Redfish Rocks Marine Reserve only.
There were significant trends by year in Copper Rockfish BPUE at the Redfish Rocks Marine Reserve (p < 0.05; Table 67), with an increase through time. There were no significant trends detected at the Humbug or Orford Reef Comparison Areas (p > 0.05; Table 67).
The random effect of cell was identified as a significant source of variation (Table 67).
GAMM model results can be found in the links below:
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No significant differences in Quillback Rockfish CPUE between the Redfish Rocks Marine Reserve and its associated comparison areas.
There was no significant difference in Quillback Rockfish CPUE between the marine reserve and and the Humbug Comparison Area or Orford Reef Comparison Area (p > 0.05; Table 68).
Significant yearly trends in Quillback Rockfish CPUE detected at the Redfish Rocks Marine Reserve and Orford Reef Comparison Area.
There were significant trends in Copper Rockfish CPUE by year detected at the marine reserve and the Orford Reef Comparison Area (p < 0.05; Table 69). The Redfish Rocks Marine Reserve had an increasing linear trend over time The Orford Reef Comparison Area had a similar increasing trend across the two years of sampling. There were no significant yearly trends detected at the Humbug Comparison Area (p > 0.05; Table 69).
The random effect of cell was identified as a significant source of variation. (Table 69).
GAMM model results can be found in the links below:
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No significant difference in mean size Quillback Rockfish between the marine reserve and its associated comparison areas.
The mean size of Quillback Rockfish did not differ between the Redfish Rocks Marine Reserve and its associated comparison areas (p>0.05, Table 70, Fig. 39).
No significant yearly trends in Quillback Rockfish mean size at the Redfish Rocks Marine Reserve or its comparison areas.
There were no significant yearly trends in Quillback Rockfish mean size detected at any site (p>0.05, Table 71).
The random effect of cell was identified as a significant component of variation for mean size of Quillback Rockfish (Table 71).
GAMM model results can be found in the links below:
\(~\)
No significant difference in top quartile sizes of Quillback Rockfish between the Redfish Rocks Marine Reserve and its associated comparison areas.
There were no differences by site in the top quartile of sizes of Quillback Rockfish (F.2.151, p.> 0.05).
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No significant differences in Quillback Rockfish BPUE between the Redfish Rocks Marine Reserve and its associated comparison areas.
There was no significant difference detected between the marine reserve and either comparison area in Quillback Rockfish BPUE (p > 0.05; Table 72).
Significant yearly trends in Quillback Rockfish BPUE detected at the Redfish Rocks Marine Reserve and Humbug Comparison Area.
There were significant trends in Quillback Rockfish BPUE by year detected at the marine reserve and the Humbug Comparison Area (p < 0.05; Table 73), with an increasing trend over time at the reserve and a increasing trend until 2017 followed by a decreasing trend through 2019 at the Humbug Comparison Area. There were no significant yearly trends in BPUE detected at the Orford Reef Comparison Area (p > 0.05; Table 73).
The random effect of cell was identified as a significant source of variation (p > 0.05).
GAMM model results can be found in the links below:
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Significantly higher Vermilion Rockfish CPUE at the Redfish Rocks Marine Reserve than Humbug Comparison Area.
Vermilion Rockfish CPUE was significantly higher in the Redfish Rocks Marine Reserve than Humbug Comparison Area (p < 0.05; Table 74). There was no difference between the marine reserve and Orford Reef Comparison Area (p > 0.05; Table 74).
No significant yearly trends in Vermilion Rockfish CPUE detected at the Redfish Rocks Marine Reserve or its associated comparison areas.
There were no significant trends in Vermilion Rockfish CPUE by year at the Redfish Rocks Marine Reserve, Humbug Comparison Area, or Orford Reef Comparison Area (p > 0.05; Table 75).
The random effect of cell was identified as a significant source of variation. (Table 75).
GAMM model results can be found in the links below:
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No significant difference in mean size Vermilion Rockfish between the marine reserve and its associated comparison areas.
The mean size of Vermilion Rockfish did not differ between the Redfish Rocks Marine Reserve and its associated comparison areas (p>0.05, Table 76, Fig. 42).
No significant yearly trends in Vermilion Rockfish mean size at the Redfish Rocks Marine Reserve or its associated comparison areas.
There were no significant yearly trends in Vermilion Rockfish mean size detected at any site (p<0.05, Table 77).
The random effect of cell was identified as a significant component of variation for mean size of Vermilion Rockfish (Table 77).
GAMM model results can be found in the links below:
\(~\)
The Redfish Rocks Marine Reserve has larger top quartile sizes of Vermilion Rockfish than the Orford Reef Comparison Area.
There were differences by site in the top quartile of sizes of Vermilion Rockfish (F.5.323, p.< 0.05). The Redfish Rocks Marine Reserve had larger top quartile sizes of Vermilion Rockfish than the Orford Reef Comparison Area (adj p<0.05) but not the Humbug Comparison Area (adj. p > 0.05). Orford Reef Comparison Area was not significantly different from Humbug Comparison Area (p >0.05).
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Significantly higher Vermilion Rockfish BPUE at the Redfish Rocks Marine Reserve than Humbug Comparison Area.
Vermilion Rockfish BPUE was significantly higher in the Redfish Rocks Marine Reserve than Humbug Comparison Area (p < 0.05; Table 78). There was no difference between the marine reserve and Orford Reef Comparison Area (p > 0.05; Table 78).
No significant yearly trends in Vermilion Rockfish BPUE at the Redfish Rocks Marine Reserve or its associated comparison areas.
There were no significant trends in Vermilion Rockfish BPUE by year at the Redfish Rocks Marine Reserve, Humbug Comparison Area, or Orford Reef Comparison Area (p > 0.05; Table 79).
The random effect of cell was not identified as a significant source of variation (Table 79).
GAMM model results can be found in the links below:
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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
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Huntington, B.E. and Watson, J.L. (2017). Tailoring ecological monitoring to individual marine reserves: Comparing longline to hook-and-line gear to monitor fish species. Marine and Coastal Fisheries, 9(1): 432-440.
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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.
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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()