Abstract:

Code used in the publication: Girard, F., Shea, K., & Fisher, C. R. (2018). Projecting the recovery of a long-lived deep-sea coral species after the Deepwater Horizon oil spill using state-structured models. Journal of Applied Ecology. doi:10.1111/1365-2664.13141 to model the recovery of deep-sea corals impacted by the Deepwater Horizon oil spill. The data files used in the model are also included. An impact-dependent state-structured matrix model was used to project the level of total visible impact for each coral colony. In the model, three states were considered: branches could either be healthy, unhealthy or colonized by hydroids. The input data used in the model was obtained from high- resolution monitoring of individual coral colonies that were impacted by the Deepwater Horizon oil spill (April 2010).

Suggested Citation:

Charles Fisher, Fanny Girard. 2018. Dataset for: Projecting the recovery of a long-lived deep-sea coral species after the Deepwater Horizon oil spill using state-structured models. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7QF8RH8

Publications:

Girard, F., Shea, K., & Fisher, C. R. (2018). Projecting the recovery of a long-lived deep-sea coral species after the Deepwater Horizon oil spill using state-structured models. Journal of Applied Ecology. doi:10.1111/1365-2664.13141

Purpose:

To model coral recovery and estimate the time necessary for every colony to recover as well as branch loss.

Data Parameters and Units:

Transition values for healthy branches (2011-2015): nv_counts_size_novn_MC294_11-15.csv: coral (individual colony identifier), total (total number of branches), total nv (total number of healthy branches), nv_to_nv, nv_to_nh, nv_to_hy (number of healthy branches that transitioned to healthy, unhealthy or hydroid-colonized, respectively), impact (total visible impact proportion), size (total coral size, m), site name, year (imaging year) Transition values for unhealthy branches (2011-2015): nh_counts_size_novn_MC294_11-15.csv: coral (individual colony identifier), total (total number of branches), total nh (total number of unhealthy branches), nh_to_nv, nh_to_nh, nh_to_hy (number of unhealthy branches that transitioned to healthy, unhealthy or hydroid-colonized, respectively), impact (total visible impact proportion), size (total coral size, m), site name, year (imaging year) Transition values for branches colonized by hydroids (2011-2015): hy_counts_size_novn_MC294_11-15.csv: coral (individual colony identifier), total (total number of branches), total hy (total number of branches colonized by hydroids), hy_to_nv, hy_to_nh, hy_to_hy (number of hydroid-colonized branches that transitioned to healthy, unhealthy or hydroid-colonized, respectively), impact (total visible impact proportion), size (total coral size, m), site name, year (imaging year) Number of branches in each state in 2011: initial_impact_counts.csv: Number of branches in each state in 2011 (initial conditions) for every coral colony at MC 294, MC 297 and MC 344. Coral (individual colony identifier), no visible impact (nv), not healthy (nh), hydroids (hy) Coral size in 2011: impact_values.csv: Size (m) of every coral colony at MC 294, MC 297 and MC 344 Average coral size used for model simulations: initial_size_simulations_100_170br.csv: Average coral size (m) calculated based on coral colonies from MC 294, MC 297 and MC 344 Proportions of unhealthy and hydroid-colonized branches: impact_values.csv: Proportions of unhealthy (I) and hydroid-colonized (Hy) branches for every coral colony (Coral) at MC 294, MC 297 and MC 344 R script for the model: contains the structure-matrix model (R-code) to estimate how long it will take for the impacted corals to visibly recover from damage and hydroid colonization Impact-dependent state-structured matrix model (Caswell, 2001) Caswell, H. (2001). Matrix population models: Construction, analysis, and interpretation. Sunderland, MA: Sinauer Associates.

Methods:

High resolution still images of individual coral colonies were taken every year at three impacted sites (MC 294, MC 297 and MC 344) between 2011 and 2017. Images were then digitized to estimate the level of impact and size of each coral, as well as changes in the state of individual branches.

Instruments:

Digital still camera held by the manipulator arm of a Remotely Operated Vehicle (ROV). The camera model and ROV used differed from one year to another.

Provenance and Historical References:

Data were collected at three sites where corals were impacted by the Deepwater Horizon oil spill. MC 294 was the first impacted coral community discovered (in November 2010) while MC 297 and MC 344 were discovered a year later.

Individual Files: