DOI: 10.6084/m9.figshare.28436717.v1
title: Data on Larval Fish from Chicago River and Associated Water Quality Measurements

description: Study SitesI chose 10 locations to represent the Chicago River system (Fig. 1), which were easily accessible from shore or had a pier. In the North, 2 locations to represent the North Shore Channel downstream of the O’Brien Water Reclamation Plant (Park 526 and Northside College Prep; P526 and NCP respectively), 1 location at the confluence with the upper North Branch of the Chicago River (River Park; RP), and 2 locations on the lower North Branch of the Chicago River (River Bank Neighbors and WMS Boathouse at Clark Park; RBN and WMS respectively). Although technically two of these locations are within the North Shore Channel, I used these locations to represent the North Branch and generally North of downtown Chicago. In the South, 1 location in Bubbly Creek (BC), its mouth with the South Branch of the Chicago River (Park 571; P571), a Barge Slip (Canal Origins Park; COP), and then a location both upstream (Lawrence Fish and Shrimp; LFS) and downstream (Richard Daley Boat Dock; RD) of these to represent main channel areas and together represent the South Branch of the Chicago River.Known dominate substrates around my study locations include sand (P526 & NCP), cobble (RP & RBN), inorganic silt (WMS & COP), organic sludge (P571 & BC), bedrock or hardpan (RD & LFS) (Gallagher and Wasik, 2018; LimnoTech, 2010). Macrophyte coverage at or near these study sites, when estimated in 2010, was low to non-existent(Gallagher and Wasik, 2018; LimnoTech, 2010). However, during sampling collection I noted dense stands of <i>Vallisneria</i> spp. were visible at the RBN site, and unidentified pond weeds (<i>Potemogeton spp.</i>) and <i>Ceratophyllum spp.</i> at the extreme southern end of the COP site.Field CollectionsI used quatrefoil light traps (30 cm diameter, 25 cm height, with 5 mm slits and 500 micron mesh) to capture phototaxic organisms (Doherty, 1987; Kelso et al., 2012). I placed two to three traps at each location 1 hr after civic twilight (~1.5 hr after sunset) for periods of approximately 1 hour, recording set and pull times. I equipped each trap with a battery powered green LED dive light as a light source (GLO-TOOB; Nextorch Industries Co., Guangdong, China). Light traps were tethered to the shore, but never exhibited flow induced tilting or dislodgement; more frequently traps were noted as floating with slack in their tethers. In general, the Chicago River’s flows rarely exceed the 30 cm sec<sup>-1 </sup>threshold found by Lindquist and Shaw (2005) to be detrimental to light trap efficiency. I gently lifted traps out of the water and stored all contents in 20 ml 90% ethanol until lab analysis. I recorded water temperature at each site upon collection of traps using a YSI ProDSS handheld unit. In 2021 and 2022, I collected a 250 ml sample water from each location for turbidity analysis, conducted within 24 hrs using a Hach 2100N Turbidimeter.Lab IdentificationI took photos of each larval fish prior to genetic analysis for visual confirmation of identifications. I excluded fish &gt; 25.0 mm in length from the dataset as it was determined that for a majority of species the juvenile stage was reached by this size (Auer, 1982; Kelso et al., 2012). Admittedly, some species are juveniles at much smaller sizes however I did not measure lengths for all captured individuals and continue to use the word “larvae” to describe my results.I extracted total DNA from individuals using cetyltrimethylammonium bromide (CTAB)-chloroform extraction followed by ethanol precipitation. I used universal primers of the 16S rRNA gene (16SAR 5′-CGCCTGTTTAACAAAAACAT-3′ and 16SBR 5′-CCGGTTTGAACTCAGATCACGT-3′,Palumbi, 1991) for polymerase chain reaction (PCR) amplification. I performed PCR reactions in 10 µL volumes, including 5 µL of GoTaq® G2 Master Mix (Promega Corp., Madison, WI, USA), 1 µL of primer, 1 µL of DNA, and 3 µL of water. I used the following PCR conditions: initial denaturing at 95°C for 2 min, followed by 35 cycles at 95°C for 40 s, annealing at 50°C for 60 s, extension at 72°C for 60 s, and final extension at 72°C for 10 min. I conducted sequencing on a 3730xl DNA Analyzer (ThermoFisher Scientific, Inc., Waltham, MA, USA) at the Field Museum (Chicago, IL, USA) using BigDye Terminators v. 3.1 Cycle Sequencing Kit (Applied Biosystems, Foster-City, CA, USA). I used Geneious Prime software and the NIST neocleotide library, as well as visual identification, to identify individuals to species. I veried the process using tissues from known species from the Field Museum Collections, including <i>Cyprinella spiloptera, Fundulus notatus, Labidesthes sicculus, Nortropus antherinoides, Notropus hudsonius, Notropus stramineus, Notropus volucellus, </i>and<i> Pimephales notatus. </i>Forward and reverse sequences can be found in GenBANK