Key drivers of change in Arctic fjord ecosystems
Robert Schlegel
01 December 2021
Last updated: 2021-12-01
Checks: 7 0
Knit directory: WP1/
This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20210216) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version 6e445e5. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Ignored files:
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: data/sst_trom.RData
Ignored: metadata/pangaea_parameters.tab
Ignored: poster/SSC_2021_landscape_files/paged-0.15/
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were made to the R Markdown (analysis/key_drivers.Rmd) and HTML (docs/key_drivers.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 6e445e5 | robwschlegel | 2021-12-01 | Re-built site. |
| html | 1e379a2 | robwschlegel | 2021-11-25 | Build site. |
| html | 79b2932 | Robert | 2021-11-10 | Build site. |
| html | 7caf87b | Robert | 2021-11-09 | Build site. |
| html | 49b83b1 | robwschlegel | 2021-11-01 | Build site. |
| Rmd | bd13b44 | Robert | 2021-10-21 | Finished adding D3.1 datasets to database and expanded on Kongsfjorden ship arrival data by ship type |
| html | ca5002a | robwschlegel | 2021-10-04 | Build site. |
| html | 3e117d4 | Robert | 2021-09-30 | Build site. |
| html | ad77318 | Robert | 2021-09-30 | Build site. |
| html | 3ad492f | Robert | 2021-09-28 | Build site. |
| html | 9615efe | Robert | 2021-09-28 | Build site. |
| html | e2b642e | Robert | 2021-09-28 | Build site. |
| html | 0f93d06 | Robert | 2021-09-28 | Build site. |
| html | 6f949b1 | Robert | 2021-09-28 | Build site. |
| html | 5786d9e | Robert | 2021-09-28 | Build site. |
| html | 72675ee | Robert | 2021-09-28 | Build site. |
| Rmd | 87df84a | Robert | 2021-09-28 | Rough draft of analysis talk |
| html | dc676c1 | Robert | 2021-09-23 | Build site. |
| html | d42750a | Robert | 2021-09-21 | Re-run |
| html | 2f621ee | Robert | 2021-09-21 | Build site. |
| html | 1caac63 | Robert | 2021-09-15 | Updates to WP1 website |
| html | 36454cc | Robert | 2021-08-17 | Build site. |
| html | 3d5b2ba | Robert | 2021-05-20 | Build site. |
| Rmd | 9e73062 | Robert | 2021-04-29 | Rethinking PANGAEA pipeline approach |
| html | 05db53f | robwschlegel | 2021-04-23 | Build site. |
| Rmd | 0f6c09a | robwschlegel | 2021-04-16 | Final update to D1.1 before submission |
| html | 0f6c09a | robwschlegel | 2021-04-16 | Final update to D1.1 before submission |
| Rmd | 3a43b49 | robwschlegel | 2021-04-13 | Fix a few internal links |
| html | 3a43b49 | robwschlegel | 2021-04-13 | Fix a few internal links |
| html | 30c05cf | robwschlegel | 2021-04-13 | More troubleshooting |
| Rmd | 80c27b6 | robwschlegel | 2021-04-13 | Rearranged the key drivers table |
| html | 80c27b6 | robwschlegel | 2021-04-13 | Rearranged the key drivers table |
| html | 82c5970 | robwschlegel | 2021-04-13 | Troubleshooting GitHub pages |
| html | 90f6ec9 | robwschlegel | 2021-04-13 | Build site. |
| html | 7e3f348 | robwschlegel | 2021-04-13 | Build site. |
| Rmd | 19eac79 | robwschlegel | 2021-04-13 | Re-built site. |
| html | 0b7ee0f | robwschlegel | 2021-04-13 | Build site. |
| Rmd | 9c8c647 | robwschlegel | 2021-03-31 | Tweak to header levels |
| html | 9c8c647 | robwschlegel | 2021-03-31 | Tweak to header levels |
| Rmd | 2dde048 | robwschlegel | 2021-03-31 | Added formatted summary sentences |
| html | 2dde048 | robwschlegel | 2021-03-31 | Added formatted summary sentences |
| Rmd | d24d7f2 | robwschlegel | 2021-03-31 | Removed the code for the tables in favour of simple summary sentences |
| html | 7582d79 | robwschlegel | 2021-03-26 | Build site. |
| Rmd | c43778d | robwschlegel | 2021-03-26 | Re-built site. |
Overview
This document is designed to satisfy D1.1 for the Horizon2020 project FACE-IT.
It is well known that the Arctic is undergoing rapid systemic changes, and that these changes are likely to increase in both rate and extent. The FACE-IT project is primarily interested in how these changes will be impacting the socio-ecological fjord and adjacent coastal systems at seven study sites in the Arctic. There is a steadily growing body of data from these sites that can be used to document and investigate the changes that would be of scientific and societal interest. It is therefore necessary, at the outset of the FACE-IT project, to identify the key drivers of change in Arctic biodiversity and to identify the availability of data relating to these drivers.
A Google Sheet was created to allow the experts at FACE-IT to fill-in which drivers were relevant for their work/study sites. The key drivers identified have been distributed into several clusters presented below.
Cryosphere
The FACE-IT project is focused on fjord and adjacent coastal socio-ecological systems, which means it is concerned primarily with marine data, but changes in the terrestrial cryosphere have a direct impact on coastal systems and so are key variables when considering drivers of change. These terrestrial variables include any measure of glaciers, such as mass balance and changes to their terminating edges. Also of interest are changes to permafrost and snow cover thickness. All of these terrestrial changes are important to fjords as they have direct impacts on the rates and composition of runoff and river discharge in the coastal zone, which have in turn very large impacts on water quality variables such as salinity, nutrients concentration and turbidity. The importance of changes to water quality are discussed again in the physical and chemistry section.
One of the aspects of the cryosphere that most directly impacts fjord and adjacent coastal systems is sea-ice. This is because the presence of ice can have a dramatic effect on what may be considered the three most fundamental important physical variables of sea water: temperature, salinity, and light. There are many ways of measuring sea-ice including: concentration, extent, thickness, and age. Whereas only one of these variables can be used when necessary, it is almost always preferable to have as many different measures of sea-ice as possible. It has been documented that there is a reliable correlation between fast-ice (ice attached to the coast) and local air and sea temperatures. This means that it may be possible to use air and sea temperatures as a proxy for sea-ice when there is a paucity of these data.
Key Cryosphere Drivers
Coastal ice: formation/break up date, thickness; Fast ice: extent, thickness; Glacier: land mass balance, terminating edge; Permafrost: temperature, thickness; Sea ice: concentration, extent, freeboard, thickness; Snow cover: thickness
Physical
One could consider the cryosphere drivers to be physical drivers, but they are considered separately due to their importance in the Arctic. The physical aspects of coastal systems adjacent to fjords are generally well documented as part of global gridded datasets. However, the resolution of gridded data is often too coarse to capture well the local scale variability inside fjords. It is therefore preferable to identify local sources of these key drivers wherever possible. Bathymetry being a primary example of this issue.
As mentioned in the cryosphere section, potentially the three most important variables are seawater temperature, salinity, and light. This is because these three variables have systemic effects on the biology of the foundational species and ecosystems from which the other socio-ecological functioning of the fjords and adjacent coastlines are based. There are a number of global products that provide these data as well as a host of locally collected in situ data. While these three variables alone would generally suffice for the physical characterisation of drivers of change, there are many other variables that are of interest to FACE-IT. For example, seawater temperatures do not change uninvited. They are acted on by air-sea heat flux and so it is also desirable to know what changes may be occurring in: net heat flux, long+shortwave radiation, latent+sensible heat flux. As part of the balance of flux across the air-sea border, one would also want to know about: the mixed layer depth, sea level pressure, precipitation, evaporation, and wind speed+direction. All of these are important variables in their own right as they tell a more specific part of the story of a changing climate. Additionally, the historic location, direction, and volume of ocean currents have been changing, which have had published impacts on fjord and coastal systems, so it is also important to measure this driver.
In addition to changes in the air-sea fluxes and currents, it is also of great importance to understand what changes to water quality may be occurring. Many of these drivers have been grouped into the chemistry section below, so in this section we focus on river discharge and the more physical aspects of water quality: sedimentation, suspended matter, suspended solids, suspended organics. These drivers are important because they may have a very large impact on light penetration at depth, which can change the competitiveness of different biological groups and have disruptive influences on local ecosystems. For example, changes in the timing and intensity of river runoff can unduly promote the early growth of phytoplankton blooms, which will then deplete nutrients earlier than expected, making it more difficult for kelp forests to grow, thereby limiting benthic primary production, which in turn may cascade up the trophic food-web.
Key Physical Drivers
Bathymetry; Current: direction, location, volume; Evaporation; Heatflux: net, latent/sensible, long/shortwave radiation; Light extinction coefficient (Kd); Mixed layer depth (MLD); Precipitation; River discharge; Salinity; Sea level pressure; Seawater temperature: surface, mid, bottom; Sedimentation rate; Suspended matter: organic, mineral; Wind: direction, speed
Chemistry
The first of the two primary areas of interest for the chemistry drivers is the changes to the nutrient load of seawater. The main nutrients of interest are: nitrate, nitrite, ammonium, phosphate, and silicate. These are important to monitor as dramatic short-term, or significant long-term changes to the nutrient profiles in fjord and adjacent coastal waters can cause bottom up forcing of ecological structures. Potentially fundamentally restructuring the species composition/biodiversity of a study site. Also of interest for water quality measurements are dissolved organic carbon (DOC), dissolved organic nitrogen (DON), and dissolved O2. These variables are important for similar reasons to the nutrients.
The other primary area of interest for this category is the amount of inorganic carbon and related minerals such as aragonite and calcite as changes to these minerals are related to shifts in the pH of seawater. This is of concern because the acidification of the ocean has a wide range of well documented effects on sea life. Primarily on calcifying organisms such as coralline algae, coccolithophores, molluscs and sea urchins, which are a foundational species in some pelagic and benthic ecosystems. Parameters of the carbonate system which are of interest are pCO2, pH, total alkalinity, and the concentration of dissolved inorganic carbon (DIC).
Key Chemistry Drivers
CaCO3 saturation state; Dissolved inorganic carbon (DIC); Dissolved organic carbon (DOC); Dissolved organic nitrogen (DON); Dissolved O2; Nutrients: nitrate (NO3), nitrite (NO2), ammonium (NH4), phosphate (PO4), silicate (SiO4); Partial pressure of CO2; pH; Total alkalinity
Biology
This category is comprised of individual species and the broader ecosystems that they populate. These variables are controlled by a lot of chemical, physical, and biological drivers and their change is itself a driver of changes, for example on upper trophic levels of relevance for humans, including emblematic and species of commercial interest. Foremost amongst the drivers for these categories is the very broad concept of biodiversity. One of the FACE-IT work packages (WP2) focuses on this driver primarily oriented around their target species (e.g. kelps and seabirds). To this end the biology category could contain a near limitless list of drivers if every aspect of biological change for the myriad of potential target species found within fjord and adjacent coastal systems were to be considered. As the FACE-IT researchers are experts in their field of study, the specifics of a given target species are left to them to track. In most cases this is of no concern as they will have been the one who generated the original data. Variables that have a broader interest across focal species and ecosystems are also considered as key drivers of change. These include biogeochemical variables such as photosynthesis, respiration, primary production, calcification and nitrogen fixation.
Another requirement for biology data is to be able to perform species distribution modelling (SDM) in order to project where the target species may currently be present, and where they may be with future projections. In order to perform SDM a researcher needs access to as much data describing the focal species as possible. Traditionally this is species presence/absence and abundance/biomass for a given site or geographical location.
Key Biology Drivers
Calcification; Nitrogen fixation; Photosynthesis; Primary production; Respiration; Species: presence/absence, abundance/biomass
Data availability
The data for the drivers outlined above are available from multiple established data sources. Large gridded data sets for most physical drivers at the Arctic scale can be accessed via: Copernicus, EMODnet, and NOAA. Site specific datasets can be accessed via: NPDC, NSF, openpolar, PANGAEA, and SIOS. Data for drivers pertaining more to policy may be found at: INTAROS and SAON. The data portals for national statistics and other social drivers are: Grønlands statistik, kystverket, SSB, and statistikknett. The specific data of relevance to the key drivers that may be found within each of these sources are given in greater detail in D1.2: Meta-database.
Summary
| Category | Driver | Why | Sites | Reference |
|---|---|---|---|---|
| Cryosphere | Coastal ice: formation/break up date, thickness | |||
| Cryosphere | Fast ice: extent, thickness | Decreasing (fast) ice cover can have a range of ecological effect. | Muckenhuber et al. (2016) | |
| Cryosphere | Glacier: land mass balance, terminating edge | An indicator of the change to other drivers. | ||
| Cryosphere | Permafrost: temperature, thickness | |||
| Cryosphere | Sea ice: concentration, extent, freeboard, thickness | Affects pelagic and benthic production. | EU Arctic | Stroeve and Notz (2018) |
| Cryosphere | Snow cover: thickness | EU Arctic | ||
| Physical | Bathymetry | |||
| Physical | Current: direction, location, volume | |||
| Physical | Evaporation | |||
| Physical | Heatflux: net, latent/sensible, long/shortwave radiation | Responsible for the changing of seawater temperature in various important ways. | EU Arctic | |
| Physical | Light extinction coefficient | Indicates the amount of light to benthic producers. | EU Arctic | |
| Physical | Mixed layer depth | EU Arctic | Popova et al. (2014) | |
| Physical | Precipitation | Affects the amount of fresh water runoff into coasts. | EU Arctic | |
| Physical | River discharge | Delivers carbon and nutrient rich freshwater to coast. | EU Arctic | Delpech et al. (2021) |
| Physical | Salinity | EU Arctic | ||
| Physical | Sea level pressure | |||
| Physical | Seawater temperature: surface, mid, bottom | EU Arctic | Popova et al. (2014) | |
| Physical | Sedimentation rate | |||
| Physical | Suspended matter: organic, mineral | |||
| Physical | Wind: direction, speed | |||
| Chemistry | CaCO3 saturation state | EU Arctic | ||
| Chemistry | Dissolved inorganic carbon | EU Arctic | Popova et al. (2014) | |
| Chemistry | Dissolved organic carbon | |||
| Chemistry | Dissolved organic nitrogen | |||
| Chemistry | Dissolved 02 | |||
| Chemistry | Nutrient: nitrate, nitrite, ammonium, phosphate, silicate | |||
| Chemistry | Partial pressure of CO2 | EU Arctic | Popova et al. (2014) | |
| Chemistry | pH | EU Arctic | ||
| Chemistry | Total alkalinity | EU Arctic | ||
| Biology | Calcification | |||
| Biology | Nitrogen fixation | |||
| Biology | Photosynthesis | |||
| Biology | Primary production | |||
| Biology | Primary production | |||
| Biology | Respiration | |||
| Biology | Species: presence/absence, abundance/biomass | |||
| Social | Fish landings: commercial, recreational, quotas, seasonality | Porsangerfjorden + Isfjorden + Disko Bay | ||
| Social | Game landings: quotas, seasonality | Porsangerfjorden + Isfjorden + Disko Bay | ||
| Social | Local and national resource management | |||
| Social | National statistics: demography, income, unemployment | EU Arctic | ||
| Social | Tourist arrivals: per month, nationality | Isfjorden + Disko Bay | ||
| Social | Tourist vessels: count, mileage | Indicative of direct anthropogenic disturbance. | Isfjorden + Disko Bay |
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] kableExtra_1.3.4 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7
[5] purrr_0.3.4 readr_2.0.1 tidyr_1.1.3 tibble_3.1.4
[9] ggplot2_3.3.5 tidyverse_1.3.1 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 svglite_2.0.0 lubridate_1.7.10 assertthat_0.2.1
[5] rprojroot_2.0.2 digest_0.6.28 utf8_1.2.2 R6_2.5.1
[9] cellranger_1.1.0 backports_1.2.1 reprex_2.0.1 evaluate_0.14
[13] highr_0.9 httr_1.4.2 pillar_1.6.2 rlang_0.4.11
[17] readxl_1.3.1 rstudioapi_0.13 whisker_0.4 jquerylib_0.1.4
[21] rmarkdown_2.11 webshot_0.5.2 munsell_0.5.0 broom_0.7.9
[25] compiler_4.1.2 httpuv_1.6.3 modelr_0.1.8 xfun_0.26
[29] systemfonts_1.0.2 pkgconfig_2.0.3 htmltools_0.5.2 tidyselect_1.1.1
[33] viridisLite_0.4.0 fansi_0.5.0 crayon_1.4.1 tzdb_0.1.2
[37] dbplyr_2.1.1 withr_2.4.2 later_1.3.0 grid_4.1.2
[41] jsonlite_1.7.2 gtable_0.3.0 lifecycle_1.0.0 DBI_1.1.1
[45] git2r_0.28.0 magrittr_2.0.1 scales_1.1.1 cli_3.0.1
[49] stringi_1.7.4 fs_1.5.0 promises_1.2.0.1 xml2_1.3.2
[53] bslib_0.3.0 ellipsis_0.3.2 generics_0.1.0 vctrs_0.3.8
[57] tools_4.1.2 glue_1.4.2 hms_1.1.0 fastmap_1.1.0
[61] yaml_2.2.1 colorspace_2.0-2 rvest_1.0.1 knitr_1.34
[65] haven_2.4.3 sass_0.4.0
Social
Putting the ‘socio’ in socio-ecological fjord systems, the social category contains the most relevant drivers that involve or directly affect human activities in the fjords and adjacent coastlines. Of most direct impact on fjord systems for this category is fish landings, both commercial and recreational. This is because the biomass removed from the study sites has a significant impact on the ecosystem. Also, species migration could create opportunities. Hunting (i.e. game landings) is also of importance as the removal of larger terrestrial organisms can have a trickle down effect on the pressure between trophic levels. To this end, it is necessary to document the local and national management regulations strategies for these livelihood activities, and how these are linked to science and scientific advice. It is relevant to understand how and on what basis hunting and fish catch quotas are set. This will provide insights into how the extent to which fish and marine mammals are managed in a multispecies and ecosystems frame. Resource management is therefore another driver which will impact the species composition and abundance of commercially important fish and marine mammal species and their prey.
An indirect impact on the fjord and adjacent coastal systems comes from human activities and presence, such as the traffic from tourism and recreational vessels, and other activities in the fjords and along the coasts. Indirect impacts of human activities are harder to measure and estimate when compared to intentional direct impacts on the fjord ecosystems such as regulated fishing and hunting. Human activities create waste and pollution to such a degree that it can have disturbing effects in the natural state of the study sites. The drivers that may be tracked to determine changes to anthropogenic perturbations at a study site are: the tourist arrivals per month and their nationality, tourist vessel counts and mileage, seasonal patterns of activities and the national statistics of demography, income, coastal livelihoods, and unemployment.
Key Social Drivers