DOI: 10.5061/dryad.h44j0zpzv
title: Fish community survey data from 23 inland lakes of Isle Royale National Park (1929–2024)

description: Fish communities are shaped by environmental filters operating across
 different spatiotemporal scales. While many recent studies focus on
 anthropogenic gradients, few can isolate the role of natural drivers in
 community assembly. Isle Royale’s inland lakes offer a rare opportunity to
 explore long-term fish biodiversity dynamics with minimal confounding
 influences. We analyzed fish communities in 23 lakes surveyed in the
 1920s, 1990s, and 2020s to 1) assess temporal changes in richness and
 composition 2) identify lakes and species experiencing the greatest
 change, and 3) evaluate environmental drivers of community structure. We
 analyzed historical and contemporary fish survey data using species-area
 curves, PERMANOVA, and multivariate dispersion tests to quantify changes
 in richness and composition, temporal beta biodiversity indices and
 similarity percentage (SIMPER) to identify lakes and species changing
 most, and non-metric multidimensional scaling (NMDS) to examine
 relationships with environmental factors. Mean richness and species-area
 curve slopes declined slightly but non-significantly over time. Community
 composition remained largely stable with no homogenization, although
 subtle shifts from cold-water to cool-water species were observed in
 larger lakes. Species gains and losses were associated with isostatic
 rebound rate. Fast-rebounding lakes tended to gain species, while
 slower-rebounding lakes tended to lose species. Richness and predator
 presence were structured along lake area and elevation gradients,
 respectively. Fish biodiversity of Isle Royale’s lakes has remained
 remarkably stable over the past century, reflecting minimal anthropogenic
 influence. Subtle shifts suggest continuous filtering by geological and
 environmental processes, however, and spatial gradients in composition
 highlight interactions between large- and small-scale filters. This study
 provides a valuable baseline reference for understanding the processes of
 community assembly and environmental change in more impacted ecosystems.
description: # Isle Royale fish biodiversity trends Dataset DOI:
 [10.5061/dryad.h44j0zpzv](10.5061/dryad.h44j0zpzv) ## Description of the
 data and file structure These files contain the data and code for analyses
 in Gallagher et al. (in preparation), who address 1) how fish species
 richness and composition have changed in the inland lakes of Isle Royale
 National Park between the 1920s, 1990s, and 2020s, 2) which fish species
 and lakes have changed most, and 3) which environmental drivers most
 strongly influence current community structure. Historical data from the
 1920s (Koelz 1929) and 1990s (Kallemeyn 2000) were combined with recent
 data from a 2020s survey for analyses. Conventional survey methods
 included gillnets, minnow traps, beach seines, angling, and stomach
 content analysis. Species richness data include the total number of
 species found in each lake during each survey, as well as lake surface
 areas. Species composition data include presence-absence data for each
 lake during each survey. Lake characteristic data include physiochemical
 variables measured at the deepest point of each lake between late-July and
 early August once during 2022-2024, as well as morphometry and geological
 data taken from Kallemeyn (2000) and Gorman et al. (2014). ### Files and
 variables #### File: ISRO_FishTrends_Composition_AllSurveys.csv
 **Description:** Fish species composition (presence-absence data) of 23
 inland lakes sampled in the 1920s, 1990s, and 2020s on Isle Royale
 National Park. ##### Variables * Lake: Full name of each inland lake *
 LakeCode: Three letter lake name abbreviation * Year: Survey year in which
 each lake was sampled. Note "1995" lakes were sampled from
 1995-1997, and "2023" lakes were sampled from 2023-2024 *
 CodeYear: Combination of LakeCode and Year * BCS: Blackchin shiner
 (*Notropis heterodon*) * BNS: Blacknose shiner (*Notropis heterolepis*) *
 BST: Brook stickleback (*Culaea inconstans*) * BKT: Brook trout
 (*Salvelinus fontinalis*) * BUB: Burbot (*Lota lota*) * TLC: Cisco
 (*Coregonus artedi*) * CRC: Creek chub *(Semotilus atromaculatus*) * EMS:
 Emerald shiner (*Notropis atherinoides*) * FHM: Fathead minnow
 (*Pimephales promelas*) * FND: Finescale dace (*Chrosomus neogaeus*) *
 GSH: Golden shiner (*Notemigonus crysoleucas*) * IWD: Iowa darter
 (*Etheostoma exile*) * LKC: Lake chub (*Couesius plumbeus*) * LAT: Lake
 trout (*Salvelinus namaycush*) * LKW: Lake whitefish (*Coregonus
 clupeaformis*) * LGP: Logperch (*Percina caprodes*) * MMS: Mimic shiner
 (*Notropis volucellus*) * MTS: Mottled sculpin (*Cottus bairdii*) * NST:
 Ninespine stickleback (*Pungitius pungitius*) * NOP: Northern pike (*Esox
 lucius*) * NRD: Northern redbelly dace (*Chrosomus eos*) * PRD: Pearl dace
 (*Margariscus nachtriebi*) * PMK: Pumpkinseed (*Lepomis gibbosus*) * SMS:
 Slimy sculpin (*Cottus cognatus*) * SHS: Spoonhead sculpin *(Cottus
 ricei*) * SPO: Spottail shiner (*Notropis hudsonius*) * TRP: Trout-perch
 (*Percopsis omiscomaycus*) * WAE: Walleye (*Sander vitreus*) * WTS: White
 sucker (*Catostomus commersonii*) * YEP: Yellow perch (*Perca flavescens*)
 #### File: ISRO_FishTrends_LakeFactors_2020sSurvey.csv
 **Description:** Characteristics of 23 inland lakes on Isle Royale
 National Park. Lake morphometry data are from Kallemeyn (2000). Isostatic
 rebound rates, lake ages, and thermal scores are from Gorman et al.
 (2014). Physiochemical variables were measured once between late-July and
 early August between 2022-2024. ##### Variables * Lake: Full name of each
 inland lake * LakeCode: Three letter lake name abbreviation * Area_ha:
 Surface area in hectares * ElevationALS_m: Elevation above Lake Superior
 in meters * ReboundRate_m100yr: Rate of isostatic rebound in meters per
 100 years * EstimateAge_y1: Estimated age of formation in years *
 Koelz_Richness: Species richness from the 1929 survey *
 Kallemeyn_Richness: Species richness from the 1995-1997 survey *
 Gallagher_Richness: Species richness from the 2023-2024 survey *
 ThermalScore: Average thermal classifications of each fish community, with
 &lt;1.00 = cold-water, 1.00-1.39 = cool-water, &gt;1.39 = cool-warm or
 warm water) * WshdArea_ha: Watershed area in hectares * AreaWshdRatio:
 Ratio of surface area to watershed area * ShorelineDev: Shoreline
 development index, calculated as the ratio of shoreline length to the
 circumference of a circle with the same surface area as the lake * Zmax_m:
 Maximum depth in meters * GR: Geometry ratio, calculated as fourth-root of
 surface area divided by maximum depth * Chla_ugL: Chlorophyll-*a*
 concentration in micrograms per liter * TP_ugL: Total phosphorus
 concentration in micrograms per liter * TN_ugL: Total nitrogen
 concentration in micrograms per liter * NOx_ugL: Nitrate/nitrite
 concentration in micrograms per liter * NHx_ugL: Ammonium/ammonia
 concentration in micrograms per liter * Ca_mgL: Calcium concentration in
 milligrams per liter * Mg_mgL: Magnesium concentration in milligrams per
 liter * Na_mgL: Sodium concentration in milligrams per liter * K_mgL:
 Potassium concentration in milligrams per liter * SO4_mgL: Sulfate
 concentration in milligrams per liter * Si_mgL: Silicate (SiO~2~)
 concentration in milligrams per liter * Cl_mgL: Chloride concentration in
 milligrams per liter * Alkalinity_mgL: Alkalinity concentration in
 milligrams per liter * DOC_mgL: Dissolved organic carbon concentration in
 milligrams per liter * Secchi_m: Secchi disk depth in meters *
 MeanEpiTemp_C: Average epilimnion water temperature in Celsius *
 MeanHypoTemp_C: Average hypolimnion water temperature in Celsius *
 MeanEpiDO_mgL: Average epilimnion dissolved oxygen in milligrams per liter
 * MeanHypoDO_mgL: Average hypolimnion dissolved oxygen in milligrams per
 liter * MeanpH: Average pH of the water column * MeanEC_uScm: Average
 conductivity of the water column in micro-Semiens per centimeter ####
 File: ISRO_FishTrends_SppRichness_AllSurveys.csv **Description:** Fish
 species richness of 23 inland lakes sampled in the 1920s, 1990s, and 2020s
 on Isle Royale National Park. ##### Variables * Lake: Full name of each
 inland lake * Area_ha: Surface area in hectares * SurveyYear: Survey year
 in which each lake was sampled. Note "1995" lakes were sampled
 from 1995-1997, and "2023" lakes were sampled from 2023-2024 *
 SppRichness: Species richness, total number of species detected during
 each survey ## Code/software ISRO_FishTrends_Gallagher_et_al_Script.R R
 version 4.4.2 was used for all analyses. The R script for these analyses
 is broken into sections representing the three main objectives of the
 manuscript. For objective 1, patterns of alpha diversity were assessed
 using generalized linear mixed models ('lme4') and species-area
 curves on the species richness data. Gamma diversity was assessed used
 total counts and species accumulation curves ('iNEXT') on the
 composition data. Changes in spatial beta diversity were assessed using
 NMDS, PERMANOVA, and betadisper ('vegan') on the composition
 data. For objective 2, patterns of lakes and species changing most were
 explored with a combination temporal beta diversity indices
 ('adespatial') and SIMPER ('vegan') using composition
 data. Regression tree analysis was also used to relate patterns of gains
 and losses to lake characteristics ('rpart') with the lake
 characteristic data. For objective 3, drivers of current community
 structure were assessed using composition and lake factor data vectors
 over NMDS plots ('vegan'). All code for creation of figures is
 also included ('ggplot2'). ## Access information Other publicly
 accessible locations of the data: * n/a Data was derived from the
 following sources: * n/a