Supplementary Material

Table S1. NC Division of Marine Fisheries river herring spawning habitat survey sampling history. Sampling was conducted within the tributaries and drainage areas of the listed rivers, creeks, or bays. AR = Alligator R., CH = Cashie R., CR = Chowan R., CS = Tull B., EB = Edenton B., LR = Little R., MC = Mackeys C., MR = Meherrin R., NR = North R., PK = Pasquotank R., PR = Perquimans R., RR = Roanoke R., SR = Scuppernong R., YR = Yeopim R.

Decade Years River Systems

AR CH CRCS EB

LR MC MR NR PK

PR RR

SR YR

1970 X X X X X X X X X X X1973 X X X X X X X1974 X X X X X X X1975 X X X1976 X X1977 X1978 X X1979 X

1980 X X X X X X1980 X X1982 X1983 X1987 X X X1988 X X X

2000 X X X X X X X2001 X X X2007 X2008 X X X2009 X X X X

2010 X X X X X X X X X X X X X2010 X X X X2011 X X X2012 X X X X2013 X X X X2014 X X X2015 X X X2016 X X X X

1

2

7

8

9

2

Table S2. Model selection for the generalized additive models for alewife (Alosa pseudoharengus) and blueback herring (Alosa aestivalis) in the Albemarle Sound, North Carolina watershed, 1973 – 2016. Models were assessed using Akaike Information Criterion (AIC), weighted AIC (AICw), and Receiver Operating Characteristic Area Under the Curve (AUC). The most parsimonious model is highlighted.

Model AIC ΔAIC AICw AUC % Dev ExpAlewifeFulla 9876.90 0.00 1 0.78 17.35-o*d 10078.23 201.33 0.00 0.77 15.59-dp 10191.59 314.69 0.00 0.75 14.59-d-o*d 10378.99 502.09 0.00 0.74 13.01-o-o*d 11255.85 1378.95 0.00 0.66 5.51Null 11891.48 11891.48 0.00 0.5 <0.001

Blueback HerringFulla 6285.50 0.00 1.00 0.86 25.56-o*d 6487.33 201.86 0.00 0.84 23.06-d-o*d 6514.21 228.73 0.00 0.84 22.68-dp 6772.35 483.88 0.00 0.82 19.61-o-o*d 7839.43 1553.95 0.00 0.70 6.89Null 8398.15 2112.68 0.00 0.5 <0.001

aFull is xo,d,(dp) = i + g1(d) + g2(o) + g3(o*d) + g4(dp) + eo,d(dp) where x = river herring presence probability, i = intercept, g = nonparametric smoothing function, d = decade, o = ordinal day, o*d = ordinal day and decade interaction, dp = distance proportion

101112131415

161718

Table S3. Model selection for the generalized additive models for alewife (Alosa pseudoharengus) and blueback herring (Alosa aestivalis) in the Chowan River and Edenton Bay tributaries, 2008 – 2016. Models were assessed using Akaike Information Criterion (AIC), weighted AIC (AICw), and Receiver Operating Characteristic Area Under the Curve (AUC). The most parsimonious model is highlighted.

Model AIC ΔAIC AICw AUC % Dev ExpAlewifeFulla 4449.33 0.00 1 0.84 26.12-o*y 4600.73 151.40 0.00 0.82 22.75-dp 4602.62 153.29 0.00 0.82 23.27-y-o*y 4688.78 239.45 0.00 0.80 21.03-o-o*y 5593.22 1143.89 0.00 0.67 5.47Null 5894.61 1445.28 0.00 0.5 <0.001

Blueback HerringFulla 2645.73 0.00 1.00 0.93 43.49-o*y 2794.44 148.71 0.00 0.91 39.21-y-o*y 2849.30 203.57 0.00 0.91 37.81-dp 3345.29 699.56 0.00 0.86 27.79-o-o*y 3862.55 1216.82 0.00 0.78 15.36Null 4532.28 1886.55 0.00 0.5 <0.001

aFull is xo,y,(dp) = i + g1(y) + g2(o) + g3(o*y) + g4(dp) + eo,y(dp) where x = river herring presence probability, i = intercept, g = nonparametric smoothing function, y = year, o = ordinal day, o*y = ordinal day and year interaction, dp = distance proportion.

192021222324

252627

2

Table S4. Logistic GAM-derived migration metrics for alewife and blueback herring spawning in the Albemarle Sound, NC watershed. Metrics are ordinal date of ingress (5% probability of presence on left hand side of the distribution), egress (5% probability on right hand side), peak (maximum presence probability in a unimodal curve or mean day of maximum presence probabilities in bimodal/plateaued curve), and season length estimations (difference between ordinal dates of ingress and egress). The 95% confidence intervals for ingress, egress and peak are given in parentheses. Some estimates of ingress and egress are extrapolated predictions and are denoted with an asterisk (*). For migration metrics estimated by extrapolation, we also provide estimates of ingress and egress based upon first presence and last presence in brackets.

Alewife

Year Ingress Egress Peak Season Length

2008 24 [≤43]* 108 (104-111) 54 84 [≥65]2009 29 [≤34]* 105 (101-109) 71 (68-76) 76 [≥67]2010 34 [≤39]* 101 (96-103) 70 (66-74) 67 [≥62]2011 29 [≤39]* 101 (92-104) 54 72 [≥62]2012 28 [≤38] 98 (79-102) 62 70 [≥61]2013 30 [≤37] 103 (96-108) 70 (66-74) 73 [≥67]2014 29 [≤49] 105 (103-108) 70 (65-74) 76 [≥57]2015 26 [≤34] 101 (98-103) 72 (68-76) 75 [≥68]2016 24 (21-28) 94 (84-97) 69 69

Blueback HerringDecade Ingress Egress Peak Season Length2008 68 (67-70) 116 (106-119) 85 472009 71 (69-81) 109 (105-112) 95 (91-100) 382010 71 (70-80) 106 (102-109) 94 (86-99) 342011 78 (74-83) 105 (103-106) 93 (89-97) 262012 71 (70-73) 109 (82-113) 77 382013 84 (83-87) 108 (105-112) 96 (91-100) 242014 79 (73-84) 120 (118-121) 98 (94-105) 412015 73 (72-77) 119 (114-120) 94 (88-100) 45

2829303132333435

36

3

2016 70 (69-71) 118 (112-120) 87 48

4

Figure S1. The timing and length of the North Carolina Division of Marine Fisheries river herring spawning habitat survey have fluctuated across decades. The span of the first and last detections for alewife and blueback are plotted to show the sampling coverage for the river herring run.

37

383940

5

Figure S2. Comparison of phenology model (PM) and temperature model (TM) predictions of ingress/egress with data over the same range of ordinal days (reduction of late time-series data). The rate of change for water temperatures in the late time-series was reduced 3.7%, and temperature predicted ingress/egress was altered -1 day for alewife egress, -2 days for blueback

4142434445

6

herring egress, and +1 day for blueback herring ingress. See Figure 4 for full dataset temperature model results and explanation of model comparisons.

4647

48

7

Figure S3. Logistic GAM-derived predictions of (a) alewife and (b) blueback herring presence probability in the Chowan River and Edenton Bay tributary system 2008 – 2016. Probabilities were modeled using ordinal day, decade, distance proportion, and ordinal day * decade for samples collected in the North Carolina Division of Marine Fisheries river herring spawning

4950515253

8

habitat survey throughout the Albemarle Sound, NC watershed. Solid curves are model predictions over dates sampled while dotted curves are extrapolated predictions; points represent the raw presence proportions for all nets set on each day of the decade. Predicted presence probabilities are shown as a function of ordinal day while holding other covariates at mean values. Black horizontal line at 5% for estimates of ingress and egress.

5455565758

9

Figure S4. Egress dates for alewife and blueback herring were estimated using GAMs and presence data from the Chowan River and Edenton Bay tributaries, 2008 – 2016. The relationships between egress dates (ordinal day) and mean temperature (a, b) and rate of temperature change (c, d) over the range of egress days were examined to assess thermal drivers of egress. SE bars are shown for mean temperatures and rate of temperature change parameter estimates.

59606162636465