DOI: 10.6078/d1x12r
title: Environmental correlates of fine-scale juvenile steelhead trout (Oncorhynchus mykiss) habitat use and movement patterns in an intermittent estuary during drought

description: We used acoustic telemetry and environmental monitoring to elucidate
 preferred microhabitats of juvenile steelhead trout (Oncorhynchus mykiss)
 in a Central California intermittent estuary (IE) during historic drought.
 We collected over half a million fish locations in the Pescadero IE (San
 Mateo County, CA) across 15 weeks during an extended sandbar-closed period
 which permitted quantification of fine scale habitat use and movement
 patterns. Tagged juvenile steelhead expressed strong site fidelity,
 especially at night when core habitat area - defined as the 50%
 probability of being present in an area - contracted by over one order of
 magnitude. The rate of movement was slow overall (~0.4 to 0.6 lengths·s−1)
 and remained at baseline levels at night (~40 mm∙s−1). The daytime rate of
 movement generally tracked solar radiation levels and appeared to be
 moderated by water temperatures. Spikes in the rate of movement occurred
 during crepuscular periods and the maximum hourly rate of movement (138
 mm∙s−1) was observed during the early study period from 10:00 to 11:00
 when water temperatures were physiologically optimal (17–18 °C). Water
 quality worsened upstream when water temperatures exceeded 18 °C and
 dissolved oxygen concentrations declined below 7.0 mg·L−1. Fish tag
 detections at stationary receivers in the upper estuary declined linearly
 with deteriorating water quality conditions. Qualitative analysis of
 juvenile steelhead habitat utilization indicated a strong preference for
 two microhabitat features in the estuary during the study; both were
 shallow (~1.5 m), wind-protected, and possessed cover and sandy substrates
 that occurred within the fresh or near fresh epilimnion where lagoon water
 quality was best and benthic prey was likely most abundant. Upstream
 movement occurred in late fall for over half of the tagged cohort, which
 likely enhances population resiliency by allowing these fish to escape
 lethal water quality conditions coincident with the transition from closed
 to open estuary in late fall. Climate projections for California’s Central
 Coast predict an increase in extreme dry events and the information
 presented here can help natural resource managers prepare for the future,
 such as the critical need to promote development of a sufficiently
 oxygenated epilimnion during extended sandbar-closed ecosystem states.
description: Telemetry data – Data sets
 1-4  Here we use acoustic telemetry to
 elucidate preferred microhabitats of juvenile steelhead trout
 (<em>Oncorhynchus mykiss</em>) in a Central California
 intermittent estuary (IE) during historic drought. We collected over half
 a million fish locations in the Pescadero IE (San Mateo County, CA) across
 15 weeks during an extended sandbar-closed period which permitted quantification
 of fine scale habitat use and movement patterns, including via a VEMCO
 Positioning System array (VPS positions, data set 1), mobile tracking
 surveys (active acoustic telemetry, data set 2), and two stationary
 receivers deployed at the upper extent of the estuary (passive acoustic
 telemetry, data set 3). Data set 4 includes the geographic locations of
 all the moored VPS equipment (receivers and synchronization transmitters)
 used in this study. 1_ALL VPS
 POSITIONS_DATA.csv The VEMCO Positioning System (VPS) was
 comprised of 12 strategically-placed omnidirectional acoustic receivers
 (VEMCO VR2W-180 kHz) with overlapping ranges capable of triangulating
 fine-scale fish positions according to preliminary range testing. Eight
 receiver time synchronization transmitters (VEMCO V6-180 kHz; nominal code
 transmission delay: 500-700 s range) were strategically deployed at
 stations with or without VPS receivers. Synchronization transmitters are
 needed by the VPS to improve positioning accuracy by correcting for clock
 drift between stationary receivers. Due to unexpected station movements,
 the VPS software was used to determine the calculate receivers and
 synchronization transmitter locations based on the observed arrival time
 differences between signals at the receivers. Determinations of the
 geographic latitude and longitude coordinates of fish positions from VPS
 receiver detections were post-processed and provided by VEMCO (Bedford,
 Nova Scotia). 2_ALL MOBILE POSITIONS_Fig
 4a_DATA.csv To supplement the information from the VPS
 array, fish positions throughout the lower, middle, and upper estuary were
 determined by mobile tracking surveys conducted during the afternoon hours
 on October 1, November 7 and 21, and December 14 in 2013 throughout all
 navigable waters using a kayak-mounted acoustic receiver (VEMCO VR100) and
 omnidirectional hydrophone (VEMCO VH165). During the September 25 (both
 pre-noon and post-noon hours) and November 21 (afternoon hours only) fish
 surveys, lagoon water temperatures, salinity, pH, and DO were measured
 every 4 s using a compact water quality sonde (YSI 600XLM, YSI Inc.) that
 was slowly bobbed up and down throughout the water column in front of a
 foot pedal-powered kayak. Geographic coordinates were recorded during
 water quality cruises using a handheld GPS device (Garmin GPSMAP 78,
 Garmin Ltd., Olathe, KS). 3_ALL ST13 AND ST14
 DETECTIONS_DATA.csv Two stationary receivers were positioned
 upstream of the VPS in the Pescadero (station 13) and Butano (station 14)
 creek arms of the estuary (Fig. 1). Detections from these receivers
 allowed us to determine presence of acoustically tagged fish outside of
 our main array in the upper estuary, but did not allow us to triangulate
 positions. Rather, we used data from these two stationary receivers to
 infer upstream movement. 4_STATION LOCATIONS_Fig
 1_DATA.csv Locations (latitude and longitude) of the
 receivers and synchronization transmitters used in this study.
 Environmental data – data
 sets 5-11 Water
 depth, temperature, salinity, pH, DO, and light were measured throughout
 the study area, including at fixed water depths at multiple locations and
 at multiple water depths at fixed locations in order to investigate
 potential water quality effects on fish microhabitat
 utilization. All
 geographic data are presented using the WGS84 datum for coordinates and
 all times are UTC-8 hours. Fixed environmental sensor data were
 automatically logged at 15 min intervals except those obtained from the
 station 08 sonde cluster (30 min pulse rate). Some data gaps exist because
 of instrument unavailability, technical difficulties, or sensor
 biofouling. 5_SONDE_MULT DEPTHS_FIXED LOC_Fig
 3_DATA.csv Water quality sondes (Hydrolab
 MS5, OTT Hydromet-Hach<sup>®</sup> Co., Loveland, CO) were
 also deployed throughout the water column at 0.60, 1.60, 2.10, and 2.35 m
 depths in the middle of the VPS zone at station
 08. 6_CTD_FIG
 S1-1_DATA.csv The conductivity-temperature-depth (CTD)
 sensor clusters (XR-420 CTD, RBR Ltd., Ottawa, Ontario) were secured to
 weighted moorings and positioned approximately 0.25 m above the bottom of
 the estuary throughout the VPS array (stations 01, 02, 06, 09, 11, and
 12). A CTD was also deployed 0.25 m below the water surface in the middle
 estuary at station 06. 7_SONDE_MOBILE_Fig
 S1-2_DATA.csv During the September 25, 2013
 (both pre-noon and post-noon hours) and November 21, 2013 (afternoon hours
 only) fish surveys, lagoon water temperatures, salinity, pH, and DO were
 measured every 4 s using a compact water quality sonde (YSI 600XLM, YSI
 Inc.) that was slowly bobbed up and down throughout the water column in
 front of a foot pedal-powered kayak. Geographic coordinates were recorded
 during water quality cruises using a handheld GPS device (Garmin GPSMAP
 78, Garmin Ltd., Olathe, KS). 8_WSE_FIG S1-3a
 _DATA.csv Periodic measurements of a land-surveyed
 stage gauge attached to the CA Hwy-1 bridge in the lower estuary were used
 as reference points to convert CTD depth data to water surface elevations
 (WSEs). Lagoon WSE data were converted to meters using the NAVD88 vertical
 datum (GEOID 2009 model). 9_LUX_FIG S1-3b_Table
 S1-1_DATA.csv Solar radiation [and temperature, see
 below] sensors (HOBO<sup>®</sup> Pendant Temperature/Light
 Data Loggers, Onset Computer Corp., Bourne, MA) were deployed aerially in
 the upper estuary (37.260807°N, 122.407951°W) and within the VPS and
 non-VPS zones of the stationary array at water depths of 0.75 m (stations
 02, 03, 06, 08, 12, 13), 1.25 m (stations 02, 06, 08, 12, 13, 14), 1.50 m
 (st01), and 1.75 m (stations 08, 12). 10_SONDE_FIXED DEPTH_MULT LOC_FIG
 S1-4_DATA.csv Temperature, salinity, pH, and DO
 concentrations were measured by multiparameter water quality sondes (YSI
 6600, YSI Inc., Yellow Springs, OH) moored to stations in the lower (st02)
 and upper (stations 13, 14) estuary at 1.25 m depth. 11_TEMP_FIG
 S1-5_DATA.csv Temperature [and solar radiation, see
 above] sensors (HOBO<sup>®</sup> Pendant Temperature/Light
 Data Loggers, Onset Computer Corp., Bourne, MA) were deployed aerially in
 the upper estuary (37.260807°N, 122.407951°W) and within the VPS and
 non-VPS zones of the stationary array at water depths of 0.75 m (stations
 02, 03, 06, 08, 12, 13), 1.25 m (stations 02, 06, 08, 12, 13, 14), 1.50 m
 (st01), and 1.75 m (stations 08, 12). Additional temperature sensors
 (HOBO<sup>®</sup> Pendant Temperature Data Loggers, Onset
 Computer Corp., Bourne, MA) were deployed within the VPS and non-VPS zones
 of the stationary array at water depths of 0.25 m (stations 01, 02, 03,
 05, 07, 08, 09, 10, 13, 14), 0.75 m (stations 04, 05, 10, 11), 1.25 m
 (stations 04, 05, 09, 10, 11), and 1.75 m (stations 08, 12) (Fig.
 1). Rate of Movement data (data set
 12) 12_ROM_FIGS
 6_8e-h_DATA.csv Methods: The Tracking Analyst extension in
 ArcGIS 10.5® was used to determine distances from successively ordered
 fish positions for individual fish to calculate distance traveled per unit
 time or the “rate of movement” (ROM). All ROM analyses were restricted to
 instances when the time interval between successive position measurements
 was less than or equal to the maximum fish tag delay (90 s) to minimize
 error due to deviations from straight path movements.  
description: We include usage notes within "readme" files for each
 data set.