this version to SSC

MAB_RiskAssess_2021update.Rmd

@@ -54,7 +54,7 @@ library(kableExtra)
 # Introduction
 The Council approved an EAFM Guidance Document in 2016 which outlined a path forward to more fully incorporate ecosystem considerations into marine fisheries management^[http://www.mafmc.org/s/EAFM_Guidance-Doc_2017-02-07.pdf], and revised the document in February 2019^[http://www.mafmc.org/s/EAFM-Doc-Revised-2019-02-08.pdf]. The Council’s stated goal for EAFM is "to manage for ecologically sustainable utilization of living marine resources while maintaining ecosystem productivity, structure, and function." Ecologically sustainable utilization is further defined as "utilization that accommodates the needs of present and future generations, while maintaining the integrity, health, and diversity of the marine ecosystem." Of particular interest to the Council was the development of tools to incorporate the effects of species, fleet, habitat and climate interactions into its management and science programs. To accomplish this, the Council agreed to adopt a structured framework to first prioritize ecosystem interactions, second to specify key questions regarding high priority interactions and third tailor appropriate analyses to address them [@gaichas_framework_2016]. Because there are so many possible ecosystem interactions to consider, a risk assessment was adopted as the first step to identify a subset of high priority interactions [@holsman_ecosystem-based_2017]. The risk elements included in the Council's initial assessment spanned biological, ecological, social and economic issues (Table \ref{riskel}) and risk criteria for the assessment were based on a range of indicators and expert knowledge (Table \ref{allcriteria}).
 
-This document updates the Mid-Atlantic Council’s initial EAFM risk assessment with indicators from the 2021 State of the Ecosystem report and with new analyses by Council Staff for the Management elements. The risk assessment was designed to help the Council decide where to focus limited resources to address ecosystem considerations by first clarifying priorities. Overall, the purpose of the EAFM risk assessment is to provide the Council with a proactive strategic planning tool for the sustainable management of marine resources under its jurisdiction, while taking interactions within the ecosystem into account. 
+This document updates the Mid-Atlantic Council’s initial EAFM risk assessment [@gaichas_implementing_2018] with indicators from the 2021 State of the Ecosystem report and with new analyses by Council Staff for the Management elements. The risk assessment was designed to help the Council decide where to focus limited resources to address ecosystem considerations by first clarifying priorities. Overall, the purpose of the EAFM risk assessment is to provide the Council with a proactive strategic planning tool for the sustainable management of marine resources under its jurisdiction, while taking interactions within the ecosystem into account. 
 
 Many risk rankings are unchanged based on the updated indicators for 2021 and the Council's risk criteria. Below, we highlight only the elements where updated information has changed the perception of risk. In addition, we present new indicators based on Council feedback on the original risk analysis that the Council may wish to include in future updates to the EAFM risk assessment.
 
@@ -136,11 +136,28 @@ A dissolved oxygen model operated by the Virginia Institute of Marine Science (V
 
 It is unclear how these annual updates in Chesapeake Bay temperature, salinity, dissolved oxygen, and SAV will affect the overall water quality indicator (which was not updated for the 2020 or 2021 report because it requires multiple years to update). The new information below suggests that high risk for estuarine-dependent species is still warranted. However, direct links between estuarine habitat conditions and population attributes for managed species (as reported for Chesapeake Bay striped bass and blue crabs) could be incorporated into future risk assessments as the science continues to develop.
 
+## Update on Climate risks
+New information has been added to the SOE that could be used to update species-specific Climate risk rankings in the future. Risks to species productivity (and therefore to achieving OY) due to projected climate change in the Northeast US were evaluated in a comprehensive assessment [@hare_vulnerability_2016]. This assessment evaluated exposure of each species to multiple climate threats, including ocean and air temperature, ocean acidification, ocean salinity, ocean currents, precipitation, and sea level rise. The assessment also evaluated the sensitivity (*not extinction risk*) of each species based on habitat and prey specificity, sensitivity to temperature and ocean acidification, multiple life history factors, and number of non-climate stressors. 
+
+Mid-Atlantic species were all either highly or very highly exposed to climate risk in this region, and ranged from low to very high sensitivity to expected climate change in the Northeast US. The combination of exposure and sensitivity results in the overall vulnerability ranking. 
+
+The 2021 SOE includes multiple climate indicators including surface and bottom water temperature, marine heat waves, cold pool area, and new information on ocean acidification measurements. Combined with species sensitivity information from lab work, these indicators could be used to further clarify climate risks to managed species.
+
+For example, new glider-based observations revealed areas of low pH (7.8) during summer in Mid-Atlantic habitats occupied by Atlantic surfclams and sea scallops (Fig. \ref{fig:mab-oa}) [@wrightfairbanks_autonomous_2020]. This seasonal pH minimum is associated with cold-pool subsurface and bottom water, which is cut off from mixing with surface water by strong stratification. However, seawater pH in shelf waters increased during the fall mixing period due to the influence of a slope water mass characterized by warm, salty, highly alkaline seawater. Lower pH in nearshore waters is likely associated with freshwater input. 
+
+```{r mab-oa, fig.cap = " Seasonal glider-based pH observations on the Mid-Atlantic Bight shelf (New Jersey cross-shelf transect) in relation to Atlantic surfclam and Atlantic sea scallop habitats (modified from Wright-Fairbanks et al. 2020).", out.width='70%'}
+#knitr::include_url("https://github.com/NOAA-EDAB/ecodata/raw/master/docs/images/Seasonal%20pH%20on%20MAB%20shelf%20-%20Grace%20Saba.jpg")
+
+knitr::include_graphics("images/Seasonal pH on MAB shelf - Grace Saba.jpg")
+```
+
+Surclams were ranked high vulnerability in the Northeast Fish and Shellfish Climate Vulnerability Assessment (FCVA) completed in 2016 [@hare_vulnerability_2016], therefore they rank moderate-high risk for the Climate element of the MAFMC EAFM risk assessment. Surfclam climate vulnerability was based on both sensitivity and exposure to ocean acidificaiton, exposure to ocean warming, and low adult mobility.  Recent lab studies have found that surfclams exhibited  metabolic depression in a pH range of 7.46-7.28 [@pousse_energetic_2020]. At pH of 7.51, short term experiments indicated that surfclams were selecting particles differently, which may have long term implications for growth [@pousse_energetic_2020]. Computer models would help in determining the long term implications of growth on surfclam populations. Data from about one year of observations (2018-2019) show that seasonal ocean pH has not yet reached the metabolic depression threshold observed for surfclams in lab studies so far; however, thresholds at different life stages, specifically larval stages that are typically more vulnerable to ocean acidification, have not yet been determined. Monitoring pH in surfclam habitats could be used to assess Climate risk in the future.
+
 ## Potential new indicators
 
 ### Habitat Climate Vulnerability
 
-A Habitat Climate Vulnerability Assessment (HCVA) for habitat types in the Northeast US Large Marine Ecosystem was completed in 2020. To better understand which species depend on vulnerable habitats, the Atlantic Coastal Fish Habitat Partnership (ACFHP) [habitat-species matrix](https://www.atlanticfishhabitat.org/species-habitat-matrix/) (Kritzer et al. 2016) was used in conjunction with the results of the HCVA and the Northeast Fish and Shellfish Climate Vulnerability Assessment (FCVA) completed in 2016 [@hare_vulnerability_2016]. The ACFHP matrix identified the importance of nearshore benthic habitats to each life stage of select fish species, which helps elucidate species that may be highly dependent on highly vulnerable habitats that were identified in the HCVA.
+A Habitat Climate Vulnerability Assessment (HCVA; @johnson_vulnerability_nodate) for habitat types in the Northeast US Large Marine Ecosystem was completed in 2020. To better understand which species depend on vulnerable habitats, the Atlantic Coastal Fish Habitat Partnership (ACFHP) [habitat-species matrix](https://www.atlanticfishhabitat.org/species-habitat-matrix/) [@kritzer_importance_2016] was used in conjunction with the results of the HCVA and the Northeast Fish and Shellfish Climate Vulnerability Assessment (FCVA) completed in 2016 [@hare_vulnerability_2016]. The ACFHP matrix identified the importance of nearshore benthic habitats to each life stage of select fish species, which helps elucidate species that may be highly dependent on highly vulnerable habitats that were identified in the HCVA.
 
 Several MAFMC managed species, including black sea bass, scup, and summer flounder, are dependent on several highly vulnerable nearshore habitats from salt marsh through shallow estuarine and marine reefs. Details on highly vulnerable habitats with linkages to a variety of species, including which life stages have different levels of dependence on a particular habitat, are available in a detailed table.^[https://noaa-edab.github.io/ecodata/Hab_table]
 
@@ -154,7 +171,7 @@ Preliminary species narratives have been developed by Grace Roskar and Emily Far
 The habitats important to black sea bass, such as shellfish reefs, submerged aquatic vegetation, and subtidal rocky bottom habitats, are vulnerable to projected changes in sea surface temperature. Additionally, intertidal habitats such as shellfish reefs are also vulnerable to projected changes in air temperatures and sea level rise. Habitat condition and habitat fragmentation were also of concern for shellfish reefs and submerged aquatic vegetation. The species itself is also vulnerable to temperature changes, as mentioned above. The overlapping high importance of intertidal and subtidal shellfish reefs to black sea bass and the very high to high climate vulnerability of these habitats, respectively, show a potential critical nexus of climate vulnerability. 
 
 ##### Mid-Atlantic  
-*Summary:* Shellfish reef habitats are highly important for both juveniles/young-of-the-year and adults. These life stages utilize both marine and estuarine shellfish reefs, in both intertidal and subtidal zones, which are very highly vulnerable and highly vulnerable, respectively. Other important habitats for black sea bass include submerged aquatic vegetation, which is highly vulnerable, and subtidal sand and rocky bottom habitats, which have low vulnerability. More information is needed on use of intertidal benthic habitats by black sea bass. Juvenile occurrence on sandy intertidal flats or beaches is rare, according to Drohan et al. (2007), but additional information on the use and importance of intertidal rocky bottom or intertidal benthic habitat use by adults is lacking. According to Drohan et al. (2007), black sea bass eggs have been collected in the water column over the continental shelf, as has larvae. As water column habitats were not included in ACFHP’s assessment of habitat importance, finer-scale information on the importance of specific pelagic habitats is needed for the species.
+*Summary:* Shellfish reef habitats are highly important for both juveniles/young-of-the-year and adults. These life stages utilize both marine and estuarine shellfish reefs, in both intertidal and subtidal zones, which are very highly vulnerable and highly vulnerable, respectively. Other important habitats for black sea bass include submerged aquatic vegetation, which is highly vulnerable, and subtidal sand and rocky bottom habitats, which have low vulnerability. More information is needed on use of intertidal benthic habitats by black sea bass. Juvenile occurrence on sandy intertidal flats or beaches is rare, according to @drohan_essential_2007, but additional information on the use and importance of intertidal rocky bottom or intertidal benthic habitat use by adults is lacking. According to @drohan_essential_2007, black sea bass eggs have been collected in the water column over the continental shelf, as has larvae. As water column habitats were not included in ACFHP’s assessment of habitat importance, finer-scale information on the importance of specific pelagic habitats is needed for the species.
 
 $\text{\underline{Habitat importance by life stage:}}$ 
 
@@ -173,7 +190,7 @@ $\text{\underline{Habitat importance by life stage:}}$
     + Marine (<200 m) and estuarine subtidal sand habitats, including sandy-shelly areas, which have a low vulnerability to climate change, are also of moderate importance.  
 
 ##### New England  
-*Summary:* All habitats in New England for black sea bass were ranked as moderately important, likely indicating that the species uses a diverse range of habitats rather than high dependence on a specific habitat type. Shellfish reef habitats are moderately important for both juveniles/young-of-the-year and adults. These life stages utilize both marine and estuarine shellfish reefs, in both intertidal and subtidal zones, which are very highly vulnerable and highly vulnerable, respectively. Juveniles/young-of-the-year are also moderately dependent on native salt marsh habitats, which are highly vulnerable to climate change. Other moderately important habitats for black sea bass include submerged aquatic vegetation, which is highly vulnerable, and subtidal sand and rocky bottom habitats, which have low vulnerability. More information is needed on use of intertidal benthic habitats by black sea bass. Juvenile occurrence on sandy intertidal flats or beaches is rare, according to Drohan et al. (2007), but additional information on the use and importance of intertidal rocky bottom or intertidal benthic habitat use by adults is lacking.
+*Summary:* All habitats in New England for black sea bass were ranked as moderately important, likely indicating that the species uses a diverse range of habitats rather than high dependence on a specific habitat type. Shellfish reef habitats are moderately important for both juveniles/young-of-the-year and adults. These life stages utilize both marine and estuarine shellfish reefs, in both intertidal and subtidal zones, which are very highly vulnerable and highly vulnerable, respectively. Juveniles/young-of-the-year are also moderately dependent on native salt marsh habitats, which are highly vulnerable to climate change. Other moderately important habitats for black sea bass include submerged aquatic vegetation, which is highly vulnerable, and subtidal sand and rocky bottom habitats, which have low vulnerability. More information is needed on use of intertidal benthic habitats by black sea bass. Juvenile occurrence on sandy intertidal flats or beaches is rare, according to @drohan_essential_2007, but additional information on the use and importance of intertidal rocky bottom or intertidal benthic habitat use by adults is lacking.
 
 $\text{\underline{Habitat importance by life stage:}}$  
 

latex/header.tex

@@ -47,7 +47,7 @@
 
 \AddEverypageHook{%
    \ifthenelse{\value{page}=1}%
-     {\rhead{\textsf{\emph{1 March 2021}}}
+     {\rhead{\textsf{\emph{2 March 2021}}}
       \lhead{\textsf{\LARGE Mid-Atlantic EAFM Risk Assessment: 2021 Update}}
       }%
      {\rhead{}