Seagrant: Understanding climate impacts on the Maine coastal fish and invertrbrate community through synthesis of the Maine-New Hampshire Inshore Trawl Survey

Project Description

From the proposal:

The overarching goal of this research is to synthesize data collected through the Maine-New Hampshire Inshore Trawl Survey to understand how climate change, fishing, and other environmental drivers are impacting key fish and invertebrate communities in coastal Maine waters.

Objective 1

• Analyze changes in biodiversity in space and time and evaluate associations with environmental factors and fishing
• To be rerun with updated Maine DMR data

Analysis

• biodiversity metrics/ maps
• GAMMs

Data

• Will double check that all necessary data is available in data folder

Scripts

• See Ashley's code folder for scripts
• pulled relevant scripts from original Seagrant directory

Objective 2

• Identify species groups and assess changes in habitat suitability if functional groups and communities in space and time

Analysis

• removed shrimp and other unimportant invertebrates from top 50 species analysis
• feeding guilds from NOAA IEA definitions
• stratified mean for NMDS convergence and simplified plotting using NOAA IEA procedure
• Bray-Curtis dissimilarity matrix for NMDS and anosim/adonis

Data

• raw data from Maine DMR portal (MaineDMR_Trawl_Survey_Catch_Data_2021-05-14.csv)
• old data (full-me-dmr-expcatch.csv)
• species with feeding guild designation (species_groups.csv)
• 4 community matrices for top 50 species and functional groups (biomass and abundance) - output from ME_trawl_NMDS_species_7.21.R and ME_trawl_NMDS_groups_7.21.R saved for future use in Rmarkdowns or NMDS so you don't have to run beginning cleaning code

Scripts

• set up with here function, so directory paths should work on any computer
• Scripts located in code subfolder of objective 2 folder
• Scripts that end in 7.21 are updated scripts from July 2021, the older versions are saved and have more versions of plots but are pretty messy
• basic plotting that is not for NMDS in ME_trawl_plots.R
• old script (ME_trawl_NMDS.R) went with the old data and trying out different NMDS plots
• Pretty self explanatory anosim_adonis_analysis_7.21.R
• NEFSC_NMDS_groups.R putting science center data into functional groups- not needed anymore
• All Rmarkdowns in subfolder

Objective 3

• Analyze joint distribution of key predator-prey species within the community, with a particular focus on lobster and cod
• contact Andrew Allyn ([email protected]) for questions or code

Objective 4

• Evaluate how ecosystem changes align with shifts in diversity and composition of fishery landings over time in ports along Maine's coastline

Analysis

• Biodiversity metrics for landings data (by county and grouped into year)
• calculated with catch weight not abundance
• richness, shannon-weiner diversity, simpson's evenness, average taxonomic distinctness
• compare to new trawl biodiversity metrics calculated as fall and spring combined and with weight for most relevant comparison to landings metrics
• Functional groups defined for landings and plots based on NOAA IEA feeding guilds
• want to look at trawl region definitions for landings comparison next

Data

• Landings data from DMR portal
• In data folder MaineDMR_Landings_Time_Series_Data_2021-07-09.csv
• County and species specific landings 2008-2020
• Rob Watts ([email protected]) supplied older data (2006-2007)

Scripts

• fishery_landings.Rmd for landings biodiversity and functional group plots
• biodiversity.Rmd for new trawl biodiversity metrics calculated for comparison

Contact

Jerelle Jesse ([email protected])