Supplementary material 1: List of species and number of watershed and sites the species was captured in.

Species name / Common Name / Number of Watersheds / Number of sites / Percent of sites
Ambloplites rupestris / Rock Bass / 5 / 19 / 11.9
Ameiurus nebulosus / Brown Bullhead / 2 / 5 / 3.1
Campostoma anomalum / Central stoneroller / 3 / 31 / 19.5
Carassius auratus / Goldfish / 4 / 8 / 5.03
Catostomidae1 / Sucker / 5 / 97 / 61.0
Chrosomus eos / Northern Redbelly Dace / 3 / 6 / 3.8
Clinostomus elongatus / Redside Dace / 2 / 14 / 8.8
Cottus bairdii / Mottled Sculpin / 3 / 13 / 8.2
Culaea inconstans / Brook Stickleback / 5 / 43 / 27.0
Cyprinus1 / Carps / 4 / 10 / 6.3
Etheostoma caeruleum / Rainbow Darter / 2 / 36 / 22.6
Etheostoma flabellare / Fantail Darter / 1 / 4 / 2.5
Etheostoma nigrum / Johnny Darter / 3 / 72 / 45.3
Gasterosteus aculeatus / Threespine Stickleback / 1 / 1 / 0.6
Lepomis cyanellus / Green Sunfish / 1 / 10 / 6.3
Lepomis gibbosus / Pumpkinseed / 4 / 28 / 17.6
Luxilus chrysocephalus / Striped Shiner / 1 / 1 / 0.6
Luxilus cornutus / Common Shiner / 4 / 48 / 30.2
Margariscus nachtriebi / Northern Pearl Dace / 1 / 2 / 1.3
Micropterus salmoides / Largemouth Bass / 2 / 8 / 5.0
Neogobius melanostomus / Round Goby / 3 / 4 / 2.5
Nocomis biguttatus / Hornyhead Chub / 1 / 6 / 3.8
Notemigonus crysoleucas / Golden Shiner / 1 / 2 / 1.3
Notropis atherinoides / Emerald Shiner / 2 / 2 / 1.3
Notropis bifrenatus / Bridle Shiner / 2 / 2 / 1.3
Notropis heterolepis / Blackchin Shiner / 1 / 1 / 0.6
Notropis stramineus / Sand Shiner / 2 / 2 / 1.3
Noturus flavus / Stonecat / 1 / 7 / 4.4
Oncorhynchus mykiss / Rainbow Trout / 3 / 29 / 18.2
Percina caprodes / Logperch / 1 / 1 / 0.6
Percopsis omiscomaycus / Trout-perch / 1 / 1 / 0.6
Petromyzontidae1 / Lampreys / 2 / 3 / 1.9
Pimephales notatus / Bluntnose Minnow / 4 / 31 / 19.5
Pimephales promelas / Fathead Minnow / 5 / 75 / 47.2
Pomoxis nigromaculatus / Black Crappie / 1 / 3 / 1.9
Pylodictis olivaris / Flathead Catfish / 1 / 1 / 0.6
Rhinichthys atratulus / Eastern Blacknose Dace / 4 / 117 / 73.6
Rhinichthys cataractae / Longnose Dace / 5 / 88 / 55.3
Salmo salar / Atlantic Salmon / 1 / 1 / 0.6
Salmo trutta / Brown Trout / 2 / 11 / 6.9
Salvelinus fontinalis fontinalis / Brook Trout / 1 / 4 / 2.5
Scardinius erythrophthalmus / Rudd / 1 / 1 / 0.6
Semotilus atromaculatus / Creek Chub / 5 / 121 / 76.1

1Species were identified to genus in some samples.

Supplementary material 2 - Analyses of individual watersheds

Methods

As the variation in land-cover among the watersheds was not represented in each of the watersheds (See Figs 3, 4, and 5 in main text) a complimentary analysis using the land-cover indices calculated for each watershed individually was conducted. By conducting a correspondence analysis on land-covers for each individual watershed separately, the full degree of variation in land-cover within each of the watersheds is considered given some watersheds may be much more heavily developed than others and therefore have less total variation across all land-cover types.

All analyses on species richness, Shannon’s diversity index, Pielou’s evenness index, the abundance of the most common species, total network species richness, βSOR, βSIM, and βSNE were conducted as described in the main text. The only difference in the analyses was how the correspondence analyses were conducted.

Results

Alpha Diversity

For local land cover the first axis of the correspondence analyses explained between 35.2 and 44.8 % of the variation and the second axis explained between 26.2 and 29.9 % of the variation in local land cover so the first two axis were retained as an index of disturbance (S2 Fig. 1). For regional land-cover the first axis of the correspondence analyses explained between 69.4 and 93.2 % and the second axis explained between 5.7 and 20.3 % of the variation in land-cover so only the first axis was retained as an index of regional disturbance (S2 Fig. 2).

See S2 Table 1 for model coefficients and confidence intervals. None of the fixed factors were significant in single term deletions for Creek Chub (Semotilus atromaculatus) or Longnose Dace (Rhinichthys cataractae), therefore models were not fit. Differences between the results here and those in the main text are discussed in the main text.

Beta Diversity

The first axis of the correspondence analyses explained between 86.2 and 99.5 % and the second axis explained between 0.5 and 13.8 %of the variation in land-cover within drainage basins of habitat networks in each of the five watersheds (S2 Fig. 3). Only the first axis of the correspondence analyses was retained as an index of land-cover within drainage basins.

See S2 Table 1 for model coefficients and confidence intervals. Differences between the results here and those in the main text are discussed in the main text.

S2 Table 1 Model coefficient and confidence intervals for variables included in general linear mixed effect models for each of the response variables. Models were fit with land-cover indices calculated for each watershed individually. n = 159 sites; n = 46 habitat networks; R2GLMM(M) is the amount of variation explained by the complete model; R2GLMM(C) is the amount of variation explained by the random watershed factor.

Response / Variable / Estimate / Lower CI / Upper CI
Alpha Diversity
Species Richness / LocCA1 / -0.55 / -0.973 / -0.134
n = 159 / RegCA1 / 0.44 / 0.0248 / 0.858
R2GLMM(M) = 0.524 / Strahl1 / -0.84 / -6.270 / -3.237
R2GLMM(C) = 0.284 / Strahl2 / -3.077 / -4.187 / -1.948
Strahl3 / -3.36 / -4.430 / -2.333
Shannon’s Diversity Index / LocCA1 / -0.13 / -0.0205 / -0.0493
n = 159 / RegCA1 / 0.083 / 0.000767 / 0.164
R2GLMM(M) = 0.323 / Strahl1 / -0.48 / -7.409 / -0.221
R2GLMM(C) = 0.101
Pielou’s Evenness Index / Strahl4 / 0.043 / -0.0327 / 0.123
n = 159
R2GLMM(M) = 0.0229
R2GLMM(C) = 0.00808
Individual species
Brook Stickleback / Loc1 / -0.63 / -1.129 / -0.184
(Culaea inconstans) / RegCA1 / 0.73 / 0.0.285 / 1.213
n = 159 / Strahl2 / 1.71 / 0.698 / 2.833
R2GLMM(M) = 0.715
R2GLMM(C) = 0.342
Fathead Minnow / Strahl1 / -1.12 / -2.446 / 0.0232
(Pimephales promelas) / Strahl5 / -0.65 / -1.507 / 0.232
n = 159
R2GLMM(M) = 0.128
R2GLMM(C) = 0.128
Beta Diversity
Total Species Richness / Length / 4.19 / 2.762 / 5.567
n = 46 / DCIp / -2.14 / -3.525 / -0.773
R2GLMM(M) = 0.771
R2GLMM(C) = 0.406
βSOR / Length / 0.057 / 0.0155 / 0.101
n = 46 / DCIp / -0.13 / -0.176 / -0.0952
R2GLMM(M) = 0.761
R2GLMM(C) = 0.455
βSIM / Length / 0.091 / 0.0377 / .153
n = 46 / DCIp / -0.12 / -0.174 / -0.0627
R2GLMM(M) = 0.684
R2GLMM(C) = 0.385
βSNE / Length / -0.028 / -0.0540 / -0.00372
n = 46
R2GLMM(M) = 0.451
R2GLMM(C) = 0.338

S2 Fig. 1 Biplots for correspondence analyses conducted on local land-cover for each watershed individually.

S2 Fig. 2 Biplots for correspondence analyses conducted on regional land-cover for each watershed individually.

S2 Fig. 3 Biplots for correspondence analyses conducted on land-cover within drainage basins for each habitat network for analyses of beta diversity.