Data on Larval Fish from Chicago River and Associated Water Quality Measurements

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 &amp; NCP), cobble (RP &amp; RBN), inorganic silt (WMS &amp; COP), organic sludge (P571 &amp; BC), bedrock or hardpan (RD &amp; 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^-1threshold 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