Appendix S4 Details on the shipping layer and implementation of the CM2.1 model A global map of commercial shipping traffic was obtained from Halpern et al. (2008). This layer was derived from 12 months (Oct 2004 – Sep 2005) of ship location data, which amounted to 1,189,127 data points from 3,374 commercial and research vessels. This data represents roughly 11% of the 30,851 merchant ships >1000 gross tonnage at sea in 2005. These points were then connected to create ship tracks, removing any tracks that crossed land. The remaining 799,853 line segments were buffered 1 km wide to account for the width of shipping lanes and converted to a raster of 1 km2 grid cells representing the density of shipping traffic. Halpern et al. (2008) note that an incomplete dataset was used to derive this layer, as not all ships reported locations. Therefore, it is possible that shipping traffic may be underestimated in some locations. This layer of shipping traffic was overlaid on prediction maps of southern right whale habitat suitability to identify potential areas of risk. We assume there is no seasonality to shipping traffic and a yearly composite is relevant to all seasonal maps of whale distribution. Overlap between shipping traffic density and predicted habitat suitability for southern right whales is variable (Fig. 1). Shipping traffic density in the Australasian region is generally lower than regions with large population centres such as Europe, the US east coast, and the coasts of China and Japan. Predicted ocean temperature data were derived from the CM2.1 coupled climate model, generated by the NOAA Geophysical Fluid Dynamics Laboratory (Delworth et al., 2006; Gnanadesikan et al., 2006; http://data1.gfdl.noaa.gov/CM2.X/). These CM2.1 model simulations contributed to the Intergovernmental Panel on Climate Change (IPCC) fourth assessment report (AR4). The CM2.1 model was determined to be among the two best models that contributed to AR4 (Russell et al., 2006). We used the 'business as usual' IPCC emissions scenario (A2) that generated outputs with 1° grid cell resolution. To describe seasonal variability, the mean temperature from each month for the 2090 -2100 decade was derived. Monthly vertical averages of projected temperatures for t0 (surface) and t0_200 were obtained because these variables contributed significantly to BRT models of southern right whale distribution. All averages were weighted by the volume of the vertical grid boxes in the CM2.1 model. These data were converted to in situ temperature (C°) from the potential temperature, and then used to calculate seasonal averages. Grids of these temperature layers were converted to 0.5° resolution to match the other environmental layers implemented in the boosted regression tree models. Predictions of southern right whale habitat suitability produced using these predicted ocean temperature layers describe how whale distribution patterns may shift in 90 years due to climate change. Ocean temperature change is not consistent across the study region, but rather is dynamic spatially and temporally. Seasonal plots of the predicted change in surface temperature (t0) between today and the 2090-2100 decade (future – present) illustrate that within our spatial extent some areas increase in temperature while others decrease, and these areas shift seasonally (Fig. 2). 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Journal of Climate, 19, 4560-4575. Figure 1. Spatial overlap of shipping traffic on current predictions of southern right whale distribution. Colour scale of habitat suitability and ship traffic density are standardized across all prediction maps. (a) Eastern region, spring; (b) Eastern region, summer; (c) Eastern region, autumn; (d) Western region, spring; (e) Western region, summer. Maps in Mercator projection, datum wgs1984. a c b d Figure 2. Seasonal change in surface temperature (t0) between today and the 2090-2100 decade (future - present). Colour ramp indicates positive or negative changes in degrees Celsius. (a) spring, (b) summer, (c) autumn, (d) winter.