Supplementary data for

Strong and lasting impacts of past global warming on baleen whales and their prey

Andrea A. Cabrera, Elena Schall, Martine Bérubé, Pia Anderwald, Lutz Bachmann, Simon Berrow, Peter B. Best, Phillip J. Clapham, Haydée A. Cunha, Luciano Dalla Rosa, Carolina Dias, Kenneth P. Findlay, Tore Haug, Mads Peter Heide-Jørgensen, Rus A. Hoelzel, Kit M. Kovacs, Scott Landry, Finn Larsen, Xênia Moreira Lopes, Christian Lydersen, David K. Mattila, Tom Oosting, Richard M. Pace III, Chiara Papetti, Angeliki Paspati, Luis A. Pastene, Rui Prieto, Christian Ramp, Jooke Robbins, Richard Sears, Eduardo R. Secchi, Mónica A. Silva, Malene Simon, Gísli Víkingsson, Øystein Wiig, Nils Øien and Per J. Palsbøll

Global Change Biology (in press)

Directory structure

1_mtDNA_sequence_information

A single Microsoft Excel^TM file (and corresponding individual, plain tab-separated, text files) with DNA sequence data set information

2_MIGRATE_analyses

In and output files necessary to replicate the MIGRATE skyline plots presented in the paper and supplementary materials.

2_1_MIGRATE_baleen_whales

Input data and parameter files for all MIGRATE analyses

2_1_1_MIGRATE_baleen_whales_input_files

MIGRATE input mtDNA sequence data and parameter files for all baleen whale species

2_1_2_MIGRATE_baleen_whales_output_files

MIGRATE main output file and abundance skyline plot files

2_2_MIGRATE_prey

2_2_1_\MIGRATE_prey_input_files

MIGRATE input mtDNA sequence data and parameter files for all prey species

2_2_2_MIGRATE_prey_output_files

MIGRATE main output file and abundance skyline plot files

2_3_MIGRATE_mtDNA_genes_comparison_input_files

MIGRATE input mtDNA sequence data and parameter files for the comparative analysis of different mtDNA loci in single species

3_CORRELATION_analyses

Scripts as well as in and outfiles for the correlation assessments undertaken in the paper

3_1_analyses

Files and scripts to estimate Pearson correlation coefficients over time intervals of either 1,000, 2,000, and 5,000 years.

3_1_1_scripts_and_input

Scripts to generate the input files with the pooled means and standard deviatiations in years (folder 3_1_2)

3_1_2_final_results_correlations

The final input files for the correlation estimation as well as the script to plot and estimate the Pearson correlation coefficient for time intervals at 1,000, 2,000, and 5,000 years.

3_2_species_combined

The MIGRATE skyline output data of the three replicates of whales and prey combined including the pool mean and pool standard deviation. These files were the raw data for the correlation analysis

3_3_temperature_infiles

The raw temperature data for the Actic and Antarctic used in the correlation analysis

4_RAD_based_STAIRWAY_plot_analyses

Please read the STAIRWAY_README file for a description of the analysis pipeline

4_1_STAIRWAY_scripts

The scripts used for the RAD based analyses.

4_2_RAD_ID_files

The list of RAD sample identification IDs.

4_3_STAIRWAY_blueprint_files

The blueprints used for generating the STAIRWAY (ver. 2.0 beta) plots presented in the paper.

4_4_RAD_data_information

The RAD data set information.

January 6th, 2022