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1 In the format provided by the authors and unedited. SUPPLEMENTARY INFORMATION VOLUME: 1 ARTICLE NUMBER: 188 Body size shifts and early warning signals precede the historic collapse of whale stocks Authors: Christopher F. Clements 1, Julia L. Blanchard 2,3, Kirsty L. Nash 2,3, Mark A. Hindell 2,4, Arpat Ozgul 1 Affiliations: 1 Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 857, Switzerland. 2 Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 129, Hobart TAS 71, Australia. 3 Centre for Marine Socioecology, Private Bag 129, Hobart TAS Antarctic Climate and Ecosystems Cooperative Research Centre Correspondence to: chrisclementsresearch@gmail.com NATURE ECOLOGY & EVOLUTION DOI: 1.138/s Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

2 Supplementary note 1: Results for mean body size In addition to the primary analysis, below we present the same results as are presented in the main manuscript but using mean body size rather than the 95 th percentile of body size. Early warning signals are present for all species when mean body size rather than 95 th percentile body size was used, with more size-only early warning signals generated (three when mean body size was used, two when 95 th percentile was used), and more size-count early warning signals (Supplementary Figure 2). As in the main analysis, early warning signals were detectable with less data when mean body size was used, although this result is less clear than when 95 th percentile body size was analyzed (Supplementary Figure 3). Concurrent early warning signals were also detectable far in advance of inflection points when mean body size was analyzed (Supplementary Figure 4). Supplementary note 2: Results for the Southern Hemisphere In addition to the global analysis presented in the main text, we performed a secondary analysis on data from Southern Hemisphere whaling catches only, a scale previously used for the assessment of whaling on whale stocks, and where the majority of whales were caught in the IWC data (12). The southern Hemisphere data comprised of records from whaling carried from South Georgia, South Shetland, the South Atlantic, the South Pacific, the Indian Ocean, and Southern Hemisphere pelagic fisheries. This secondary analysis ensured that there were no effects of scale on our primary analysis, and that early warning signals could predict collapses at both a regional and a global scale. All analyses were carried out as described above. The Southern Hemisphere results corroborate those presented in the main text. The time series of catches show inflection points at approximately the same time as the global data sets for all species (Supplementary Table 1, Supplementary Figure 5). Declines in body size and the standard deviation of body size are more pronounced in the Southern Hemisphere only data (Supplementary Figure 5), and when early warning metrics were tested on the data, these strong trends translated into strong early warning signals, with those using size-catch data performing particularly well (Supplementary Figures 6-8). NATURE ECOLOGY & EVOLUTION DOI: 1.138/s Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

3 Landings (number of whales) Year Blue Fin Sperm Humpback Sei Byrdes Gray Bowhead Right Bottlenose Killer Pilot 95th percentile of mean body size (cm) Year Blue Fin Sperm Humpback Sei Byrdes Gray Bowhead Right Bottlenose Killer Pilot Supplementary Figure 1 Global landings and 95 th percentile mean body size data for the 15 cetacean species included in the IWC database. Trends in body size data are highlighted using LOESS smoothing. NATURE ECOLOGY & EVOLUTION DOI: 1.138/s Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

4 Supplementary Figure 2 Metrics that include body size-only (orange), those that contain count-only data (green), and those that contain size and count data (blue) produced early warning signals in all populations prior to the decline of each fishery when data from the first recorded landing after 19 until the year prior to the inflection point were analyzed., coefficient of variation;, mean body size;, σ of body size. NATURE ECOLOGY & EVOLUTION DOI: 1.138/s Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

5 Supplementary Figure 3 Early warning signals were detectable with as little as 1 years data prior to a the inflection point. Increasing the window size typically increased the prevalence of early warning signals. Points show an early warning signal present using size-only data (orange), count-only data (green), or size-count data (blue). Blue shaded areas indicate the 1-year starting window. Arrows show the increasing size of the window analyzed. Grey shaded areas indicate no further data is present., coefficient of variation;, mean body size;, σ of body size Data analysed prior to collapse (years) 217 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. NATURE ECOLOGY & EVOLUTION DOI: 1.138/s SUPPLEMENTARY INFORMATION

6 Year Supplementary Figure 4 Consistent early warning signals were present up to 4 years prior to fisheries declines. Metrics that included trait dynamics tended to produce consistent early warning signals approximately concurrent with those metrics based on count only data. Black vertical lines show the inflection point for each species, blue shaded areas indicate the 2 year rolling window used to calculate early warning signals, points indicate the presence of an early warning signal using size-only data (orange), count-only data (green), or size-count data (blue)., coefficient of variation;, mean body size;, σ of body size. NATURE ECOLOGY & EVOLUTION DOI: 1.138/s Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

7 SUPPLEMENTARY INFORMATION Landings (# of whales) Total whales harvested: Total whales harvested: (a) Total whales harvested: Total whales harvested: th percentile of mean body length (cm) Southern Hemisphere (b) SD of body size (c) Supplementary Figure 5 Time series of (a) number of whales caught per year, (b) 95 th percentile of body size, and (c) σ of body size calculated from records of individual whales caught in the Southern Hemisphere between 19 and 1985 (the year of the moratorium on commercial whaling, vertical black lines). An inflection point was calculated when the number of individuals of a species caught per year declined significantly, quantified by fitting Generalized Additive models to the landings data (GAM fits plotted on top of landings data, red segments indicate periods of significant decline). s show the year at which fisheries were inferred to have begun to decline NATURE ECOLOGY & EVOLUTION DOI: 1.138/s Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

8 Southern Hemisphere Supplementary Figure 6 Metrics that include body size-only (orange), those that contain count-only data (green), and those that contain size and count data (blue) produced early warning signals in all populations prior to the inflection point of each fishery when data from the first recorded landing after 19 until the year prior to the inflection point using data from the Southern Hemisphere were analyzed., coefficient of variation;, 95 th percentile mean body size;, σ of body size. NATURE ECOLOGY & EVOLUTION DOI: 1.138/s Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

9 Supplementary Figure 7 Early warning signals were detectable with as little as 1 years data prior to the inflection point using data from the Southern Hemisphere. Increasing the window size typically increased the prevalence of early warning signals. Points show an early warning signal present using size-only data (orange), count-only data (green), or size-count data (blue). Blue shaded areas indicate the 1-year starting window. Arrows show the increasing size of the window analyzed. Grey shaded areas indicate no further data is present., coefficient of variation;, 95 th percentile mean body size;, σ of body size Data analysed prior to collapse (years) Southern Hemisphere 217 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. NATURE ECOLOGY & EVOLUTION DOI: 1.138/s SUPPLEMENTARY INFORMATION

10 Southern Hemisphere Year Supplementary Figure 8 Consistent early warning signals were present up to 4 years prior to population decline. Metrics that included trait dynamics tended to produce consistent early warning signals approximately concurrent with those metrics based on count only data. Black vertical lines show the inflection point for each species, blue shaded areas indicate the 2 year rolling window used to calculate early warning signals, points indicate the presence of an early warning signal using size-only data (orange), count-only data (green), or size-count data (blue)., coefficient of variation;, 95 th percentile mean body size;, σ of body size. NATURE ECOLOGY & EVOLUTION DOI: 1.138/s Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

11 Supplementary Table 1 Inferred time of global and Southern Hemisphere fisheries declines for each species, estimated by fitting Generalized Additive Models to the time series of landings data. Species Inflection point Southern hemisphere inflection point Blue whale Fin whale Sei whale Sperm whale NATURE ECOLOGY & EVOLUTION DOI: 1.138/s Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

12 References: 1. IWC, International Convention for the Regulation of Whaling, 1946 (214). 2. M. J. Rochet et al., Do changes in environmental and fishing pressures impact marine communities? An empirical assessment. J. Appl. Ecol. 47, (21). 3. S. J. Burthe et al., Do early warning indicators consistently predict nonlinear change in long-term ecological data? J. Appl. Ecol. (215), doi:1.1111/ S. N. Wood, mg: Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness estimation (213), p. R package version R Development Core Team, R: A language and environment for statistical computing (216), (available at 6. C. F. Clements, A. Ozgul, Including trait-based early warning signals helps predict population collapse. Nat. Commun. (216), doi:1.138/ncomms J. Drake, B. Griffen, Early warning signals of extinction in deteriorating environments. Nature. 467, (21). 8. V. Dakos et al., Methods for detecting early warnings of critical transitions in time series illustrated using simulated ecological data. PLoS One. 7, e411 (212). 9. C. a. Pfister, F. R. Stevens, The genesis of size variability in plants and animals. Ecology. 83, (22). 1. C. N. K. Anderson et al., Why fishing magnifies fluctuations in fish abundance. Nature. 452, (28). 11. S. R. Carpenter et al., Early Warnings of Regime Shifts: A Whole-Ecosystem Experiment. Science. 332, (211). 12. R. Hilborn et al., State of the world s fisheries. Annu. Rev. Environ. Resour. 28, (23). NATURE ECOLOGY & EVOLUTION DOI: 1.138/s Macmillan Publishers Limited, part of Springer Nature. All rights reserved.