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Figure 3 in Harbor seal use of glacier ice and terrestrial haul-outs in the Kenai Fjords, Alaska

Figure 3. Population trends of harbor seals on the southeastern Kenai Peninsula during pupping (Panel A) and the molt (Panel B) based on aerial surveys conducted from 2004 to 2013.

Figure 6 in Harbor seal use of glacier ice and terrestrial haul-outs in the Kenai Fjords, Alaska

Figure 6. Proportion of harbor seal pups counted during pupping relative to total seals (including pups) during pupping (Panel A) and during the subsequent molt (Panel B) at glacial ice (blue) and terrestrial (brown) haul-outs among different locations and time periods. The box (bounded by 13%–23%) represents range of the percent of pups to total seals counted at terrestrial haul-outs outside of Alaska (Venables and Venables 1955, Boulva 1975, Boulva and McLaren 1979, Brown and Mate 1983, Calambokidis et al. 1987). The vertical bar within the box represents the proportion of pups born into an increasing population in British Columbia (Bigg 1969). * designates proportions derived from mean values adjusted for standardized environmental conditions. Sources include (Hoover 1983; Calambokidis et al. 1987; Pitcher 1990; Mathews 1995; Jemison et al. 2006, 2016; Mathews and Pendleton 2006; Womble et al. 2010; Mathews et al. 2016; Kenai Fjords National Park, unpublished).

Figure 7 in Harbor seal pup dispersal and individual morphology, hematology, and contaminant factors affecting survival

Figure 7. Association between the survival probability estimate and mass (kg) at the time of release from rehabilitation from the best supported TMMC model: {Φ(mass)}.

Figure 3 in Harbor seal pup dispersal and individual morphology, hematology, and contaminant factors affecting survival

Figure 3. Map of the tracks taken by seals that traveled the greatest distance from their capture or release location for each of the three groups of seals. SF = San Francisco Bay, TB = Tomales Bay, and TMMC = The Marine Mammal Center. The TMMC seal that traveled the furthest was released from Cypress Point, Monterey.

Figure 5 in Harbor seal use of glacier ice and terrestrial haul-outs in the Kenai Fjords, Alaska

Figure 5. Comparison of numbers of mother-pup harbor seal pairs (MP) counted in Aialik Bay and Northwestern Fjord from 2004 to 2013 using multiple survey methods. Area charts indicate maximum annual counts of MP in Aialik Bay and Northwestern Fjord (light blue) and in Aialik Bay (darker blue). Maximum annual MP counts in Northwestern Fjord are indicated by the blue green line. White dots with 95% CI error bars show generalized linear model (GLM) mean estimate MP based on remote video observations in Aialik Bay during standardized favorable haul-out conditions.

Figure 6. Association between survival probability estimates with circulating T4 in Harbor seal pup dispersal and individual morphology, hematology, and contaminant factors affecting survival

Figure 6. Association between survival probability estimates with circulating T4 (nmol/L) at the time of capture/release from the best supported model: {Φ(g + T4)}.

Figure 5 in Harbor seal pup dispersal and individual morphology, hematology, and contaminant factors affecting survival

Figure 5. The last day of satellite tag transmission for each seal (circles) modeled by two exponential curves (solid lines) with 95% confidence intervals (dotted lines). Data and estimates are in black for the wild (SF and TB) seals and blue for the rehabilitated (TMMC) seals. The gray line represents tag survival based on a normal distribution. The dashed lines display the effect of tag loss on the two survival curves.

Figure 1 in Harbor seal pup dispersal and individual morphology, hematology, and contaminant factors affecting survival

Figure 1. Relationship between standard length and summed organohalogen contaminants (OH) for the three groups: San Francisco Bay [logOH = (length) × (−0.05) + 13.76, F = 6.117, df = 17, R2 = 0.2646, P = 0.024], Tomales Bay [logOH = (length) × (−0.05) + 24.45, F = 10.3, df = 5, R2 = 0.6733, P = 0.023], and The Marine Mammal Center (not significant).

Figure 4 in Harbor seal use of glacier ice and terrestrial haul-outs in the Kenai Fjords, Alaska

Figure 4. Comparison of regional changes in numbers of harbor seal pups (Panel A), seals without pups present during pupping (Panel C), and molting seals (Panel D) in four regions of the coastline extending from McCarty Fjord through Johnstone Bay. Pup counts at individual fjords summarized as RB-JB are compared in Panel B. Bars represent maximum counts obtained during aerial surveys. Total counts for all regions (black dots) are measured on the secondary axis. Histogram bars of molt counts represent maximum counts for each year obtained from aerial surveys; triangles indicate counts in Northwestern Fjord based on KFT vessel surveys.

Figure 1 in Harbor seal use of glacier ice and terrestrial haul-outs in the Kenai Fjords, Alaska

Figure 1. Maps showing locations of the study area (Panel A) and of study area place names (Panel B). Red shading along the coastline, in the Panel A inset, illustrates the geographic extent of surveys (portions of flights flown at altitudes <335 m).

Figure 6 in Natural and human effects on harbor seal abundance and spatial distribution in an Alaskan glacial fjord

Figure 6. Estimated area of Disenchantment Bay (km2) containing three different ice cover types: scattered (1–3 tenths), intermediate (4–6 tenths), and dense (7–10 tenths), and all types combined (i.e., ice-covered area [ICA]) from 3 May to 4 August 2002. Estimates of ice cover were averaged within grid cells (when n> 1) and the areas of cells with each type of ice cover were summed (Jansen et al. 2006)) and then scaled upward (proportionately) based on the percent of the study area that was sampled on a given day.

Figure 7 in Natural and human effects on harbor seal abundance and spatial distribution in an Alaskan glacial fjord

Figure 7. Patterns of ship movement and visitation time in Disenchantment Bay, Alaska, in 2002 (n = 56 cruise ships of 105 total during study). Shading of cells represents the cumulative time that visiting ships spent within that cell for each of three months: May, June, and July (including early August). Four distinct shades, from gray to black, reflect increasing residence: <5 min, 5–10 min, 10–20 min,>20 min, respectively. Refer to Figure 1 for geographical points and scale.

Figure 5 in Natural and human effects on harbor seal abundance and spatial distribution in an Alaskan glacial fjord

Figure 5. Standardized resource selection coefficient by harbor seals for ice cover class in Disenchantment Bay, Alaska, 3 May to 4 August 2002, for the Bernoulli part of the P1B model (i.e., for the cell-based abundance of seals). The solid circles and lines are for all seals, and the open circles and dashed lines are for mother-pup pairs. Confidence intervals (95%) are shown by the vertical bars. The thin horizontal line represents equal selection for all ice cover classes.

Figure 4 in Natural and human effects on harbor seal abundance and spatial distribution in an Alaskan glacial fjord

Figure 4. Standardized resource selection coefficient by harbor seals for ice cover class in Disenchantment Bay, Alaska, 3 May to 4 August 2002, for the Bernoulli part of the P1B model (i.e., for the cell-based spatial distribution of seals). The solid circles and lines are for all seals, and the open circles and dashed lines are for mother-pup pairs. Confidence intervals (95%) are shown by the vertical bars. The thin horizontal line represents equal selection for all ice cover classes.

Figure 3 in Natural and human effects on harbor seal abundance and spatial distribution in an Alaskan glacial fjord

Figure 3. Spatial distribution of harbor seals, ice cover zones, and maximum penetration of cruise ships on the day of surveys () and the previous day () in Disenchantment Bay, Alaska, on (A) 6 May, (B) 16 May, (C) 31 May, (D) 20 June, (E) 18 July, and (F) 4 August 2002 (figures for all 18 survey dates are available as supplemental material online). The time of day that ships reached their maximum penetration appears near the location symbol. The range of seal counts summed per grid cell is shown in three levels: small dot (<5 seals), medium dot (5–20 seals), and large dot (>20 seals). A small, overlying white dot indicates the presence of at least one mother-pup pair within that grid cell. Ice cover is represented by a gradient in cell-color shading: light gray (scattered), medium gray (intermediate), dark gray (dense). For this graphic, if cells with no ice data were bounded on three sides by cells with ice measures, the average of neighboring cells was used as an estimate. Refer to Figure 1 for geographical points and scale.

Figure 2 in Natural and human effects on harbor seal abundance and spatial distribution in an Alaskan glacial fjord

Figure 2. Counts of all seals and pups along video sampling transects (relative abundance) in Disenchantment Bay, May to August 2002. Raw counts for all seals are shown as solid circles, and raw counts for pups are shown as open circles. The thick solid curve is the fitted GAM model for all seals, with the 95% prediction intervals shown by the thinner solid lines. The thick dashed curve is the fitted GAM model for pups, with the 95% prediction intervals shown by the thinner dashed lines.

Figure 1 in Natural and human effects on harbor seal abundance and spatial distribution in an Alaskan glacial fjord

Figure 1. Map of Disenchantment Bay study areas near Yakutat, Alaska. Major tidewater glaciers are labeled. The location of the terminus of Hubbard Glacier was mapped in early June 2002 as part of this study. The extent of snow and ice-covered terrain (stippled area) was derived from a NOAA Coastal Service satellite photo taken in 1993. Icy Bay, an adjacent tidewater glacial fjord with a seal population (see Discussion), is shown for reference.

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Washington harbor seal stable isotope data

Understanding the response of predators to ecological change at multiple temporal scales can elucidate critical predator-prey dynamics that would otherwise go unrecognized. We performed compound-specific nitrogen stable isotope analysis (CSIA) of amino acids on 153 harbor seal museum skull specimens to determine how trophic position of this marine predator has responded to ecosystem change over the past century. The relationships between harbor seal trophic position, ocean condition, and prey abundance, were analyzed using hierarchical modelling of a multi-amino acid framework and applying 1-, 2-, and 3- year temporal lags. We identified delayed responses of harbor seal trophic position to both physical ocean conditions (upwelling, sea surface temperature, freshwater discharge) and prey availability (Pacific hake, Pacific herring and Chinook salmon). However, the magnitude and direction of the trophic position response to ecological changes depended on the temporal delay. For example, harbor seal trophic position was negatively associated with summer upwelling, but had a 1- year delayed response to summer sea surface temperature, indicating some predator responses to ecosystem change are not immediately observable. These results highlight the importance of considering dynamic responses of predators to their environment as multiple ecological factors are often changing simultaneously and can take years to propagate up the food web.

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Table 5 in Harbor seal pup dispersal and individual morphology, hematology, and contaminant factors affecting survival

Table 5. Model selection of apparent survival probability (Phi) for model set 3: morphology and sex.<table><tbody><tr><th></th><th></th><th></th><th>QAICc</th><th>Model</th><th>No.</th><th></th></tr></tbody><tbody><tr><th>Model</th><td>QAICc ΔQAICc weights likelihood parameters Deviance</td></tr><tr><th>{Φ (g + length)} 219.90</th><td>0.000</td><td>0.191</td><td>1.000</td><td>4</td><td>211.810</td></tr><tr><th>{Φ (g + mass)}</th><td>220.44</td><td>0.544</td><td>0.145</td><td>0.762</td><td>4</td><td>212.354</td></tr><tr><th>{Φ (g + sex + length)}</th><td>220.46</td><td>0.567</td><td>0.144</td><td>0.753</td><td>5</td><td>210.334</td></tr><tr><th>{Φ (g)}</th><td>220.57</td><td>0.672</td><td>0.136</td><td>0.715</td><td>3</td><td>214.517</td></tr><tr><th>{Φ (g + sex)}</th><td>220.83</td><td>0.935</td><td>0.120</td><td>0.627</td><td>4</td><td>212.745</td></tr><tr><th>{Φ (g + sex + mass)}</th><td>221.16</td><td>1.267</td><td>0.101</td><td>0.531</td><td>5</td><td>211.034</td></tr><tr><th>{Φ (g + bd)}</th><td>222.23</td><td>2.330</td><td>0.060</td><td>0.312</td><td>4</td><td>214.140</td></tr><tr><th>{Φ (g + cond)}</th><td>222.45</td><td>2.557</td><td>0.053</td><td>0.278</td><td>4</td><td>214.368</td></tr><tr><th>{Φ (g + girth)}</th><td>222.56</td><td>2.662</td><td>0.050</td><td>0.264</td><td>4</td><td>214.472</td></tr></tbody></table>Note: g = group (SF, TB, and TMMC), bd = blubber depth, cond = the body condition index. c ͡ adjustment = 1.15. Highest ranked model highlighted in bold.

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Table 3 in Harbor seal pup dispersal and individual morphology, hematology, and contaminant factors affecting survival

Table 3. Model selection of apparent survival probability (Phi) for model set 1: group and time.<table><tbody><tr><th></th><th></th><th></th><th>QAICc</th><th>Model</th><th>No.</th><th></th></tr></tbody><tbody><tr><th>Model</th><td>QAICc</td><td>ΔQAICc</td><td>weights</td><td>likelihood</td><td>parameters</td><td>Deviance</td></tr><tr><th>{Φ (g)}</th><td>222.45</td><td>0.000</td><td>0.538</td><td>1.000</td><td>3</td><td>49.658</td></tr><tr><th>{Φ (SF and</th><td>222.95</td><td>0.501</td><td>0.419</td><td>0.779</td><td>2</td><td>52.184</td></tr><tr><th>TMMC v TB)}</th><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>{Φ (SF and</th><td>227.55</td><td>5.102</td><td>0.042</td><td>0.078</td><td>2</td><td>56.786</td></tr><tr><th>TB v TMMC)}</th><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>{Φ (.)}</th><td>233.43</td><td>10.983</td><td>0.002</td><td>0.004</td><td>1</td><td>64.684</td></tr><tr><th>{Φ (t)}</th><td>254.10</td><td>31.655</td><td>0.000</td><td>0.000</td><td>22</td><td>41.095</td></tr><tr><th>{Φ (g × t)}</th><td>320.74</td><td>98.291</td><td>0.000</td><td>0.000</td><td>66</td><td>0.000</td></tr><tr><th>Model</th><td>QAICc</td><td>ΔQAICc</td><td>weights</td><td>likelihood</td><td>parameters</td><td>Deviance</td></tr><tr><th>{Φ (mass)}</th><td>101.79</td><td>0.000</td><td>0.220</td><td>1.000</td><td>2</td><td>97.704</td></tr><tr><th>{Φ (T4)}</th><td>102.08</td><td>0.287</td><td>0.190</td><td>0.866</td><td>2</td><td>97.991</td></tr><tr><th>{Φ (.)}</th><td>102.42</td><td>0.625</td><td>0.161</td><td>0.732</td><td>1</td><td>100.387</td></tr><tr><th>{Φ (change in</th><td>102.80</td><td>1.013</td><td>0.133</td><td>0.603</td><td>2</td><td>98.717</td></tr><tr><th>mass)}</th><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>{Φ (days in rehab)}</th><td>103.47</td><td>1.679</td><td>0.095</td><td>0.432</td><td>2</td><td>99.383</td></tr><tr><th>{Φ (admit date)}</th><td>103.73</td><td>1.942</td><td>0.083</td><td>0.379</td><td>2</td><td>99.646</td></tr><tr><th>{Φ (logOH)}</th><td>104.38</td><td>2.593</td><td>0.060</td><td>0.273</td><td>2</td><td>100.297</td></tr><tr><th>{Φ (mass per day)}</th><td>104.46</td><td>2.666</td><td>0.058</td><td>0.264</td><td>2</td><td>100.370</td></tr></tbody></table>Note: t = time, g = group (SF = San Francisco, TB = Tomales Bay, and TMMC = The Marine Mammal Center). c ͡ adjustment = 1.15. Highest ranked model highlighted in bold.Note: T4 = total thryroxine, adjustment = 1.15.