Catching a Hooligan

Spirinchus thaleicthys (also known as Longfin Smelt, “Hoolies”, and “Tiokowe”) are an anadromous forage fish. They enter the lower mainstream river of the Nooksack annually.

To determine spawning locations of smelt in the Nooksack River, this project has developed a species-specific eDNA assay to detect the extent of the upstream migration of the Hoolies.

At each sampling locality, the Smith-Root eDNA Sampler Backpack (Thomas et al., 2018) was used with the extension pole and trident (see image below). In the field, 250mL of water from the Nooksack was filtered using 5µm polyethersulfone (PES) filters.

Image 1. Rachael Mallon collecting eDNA using the Smith-Root backpack sampler in the Nooksack at Hovander Park (image from October 26, 2021)

The annual spawning event happens in November.

This year, the furthest downstream site is located at Fish Point (48.77, -122.6), followed upstream by Marine Drive Bridge (48.79, -122.59), Rayhorst Drive (48.81, -122.58), Slater Bridge (48.82, -122.58), Hovander (48.83, -122.60), and Ferndale (48.84, -122.59). The distance from Fish Point to Ferndale is 6.1 miles.

Map that shows sampling locations of in the bay and along the Nooksack.

In addition to the freshwater samples collected along the Nooksack River, 8 marine sites were sampled for Hoolie eDNA. These sites include Sandy Point (48.78, -122.70), Gooseberry point (48.73, -122.68), Lummi Shore Drive (48.73, -122.63), Smokehouse Road (48.75, -122.60), Locust Beach (48.75, -122.54), Whatcom Creek (48.75, -122.49), Bellingham Buoy (48.72, -122.58), and Fairhaven Dock (48.73, -122.51).

Fish Point and Marine Drive Bridge are the most popular locations for catching Hoolies. The distance from Fish Point to Marine Drive Bridge is 1.59 miles.

There is saline influence from tidal intrusion at the Fish Point and Marine Drive Bridge locations. Tidal range exceeds more than 3 m. During periods of large tidal changes, a wall of water up to 3 m high can occur in the study area on the incoming tide.

On 10/26/2021, the “Hoolie eDNA team” collected 250mL of water at 6 locations along the Nooksack as part of their “Pre-Hoolie Run” effort to determine the baseline signal that is captured using eDNA. This was done while the tide was going out. DNA was extracted and qPCR was conducted. No Hoolie DNA was detected.

On 11/02/2021, the “Hoolie eDNA team” filtered water samples when the tide was highest. Based on DNA extracted from samples collected at Fish Point, Hoolies were present when using the Hoolie Taqman assay. The Ct values are below the limit of quantification. LNR fisherman, Jeff Solomon, had not yet begun fishing for Hoolies.

Image 2. Jeff Solomon with his Hoolie dipnet at Fish Point.

On 11/03/2021 the first Hoolie was caught by LNR fisherman, Jeff Solomon. The tide was outgoing at the time of capture. This Hoolie was a male. No eDNA sampling was done on the Nooksack on this day, only marine sampling was done during the low tide. An egg survey was conducted and samples were collected at Hovander Park, Slater Bridge, Marine Drive Bridge. No eggs were detected.

Figure 1.Tidal heights at Bellingham Bay, WA on 10/26/2021. The yellow box indicates when samples were collected from the Nooksack at all 6 sites from 1600 to 1800.

Figure 2. Tidal heights at Bellingham Bay, WA on 11/02/2021. The yellow box indicates when samples were collected at the 6 sampling locations along the Nooksack from 1600-1800.

Figure 3. Tidal heights at Bellingham Bay, WA on 11/03/2021. The yellow box indicates when fish were caught. White box indicates when marine samples were collected at the 8 sampling locations in the Bay from 1000 to 1200.

On 11/10/2021 Jeff Solomon captured a bucketful of Hoolies within a half-hour period. This was during a peak tide. eDNA was collected at Marine Drive Bridge and Fish Point during the high tide. 20 fish were preserved from this capture event. Marine samples were also collected on this day. An egg survey was conducted and samples were collected at Hovander, Slater Bridge Marine Drive Bridge. No eggs were detected.

Figure 5. Tidal heights at Bellingham Bay, WA on 11/10/2021. The yellow box indicates when Fish Point and Marine Bridge Drive samples were collected. The blue box indicates when marine samples were collected. The white box is time period when Jeff Solomon went fishing. Image is of fish caught by Jeff Solomon.

The river has been in Flood Stage since the afternoon of 11/12/2021. Jeff hasn’t had a successful catch during this flood stage. The eDNA team has not conducted sampling since the start of the Flood Stage. The last Nooksack sampling effort was on 11/11/2021.

Figure 6. USGS gage height date from station managed by the Northwest Washington Field Office (Ferndale).

Questions left unanswered:

1. Are we sampling at the correct times during the day?

a. Should we collect in the morning and at night?

b. Should we collect when Jeff is fishing?

2. Are we sampling at the correct times during the rise and fall of the tide?

a. TEK indicates the Hoolies are present as the tide is outgoing

3. Can we detect Hoolies during the Flood Stage?

a. Field sampling is extremely dangerous in flood stage

b. No data has been collected at this time (neither TEK (fish capture) or eDNA)

4. Do Hoolies have holding patterns at certain locations on the Nooksack?

5. Are the Hoolies traveling all the way from Fish Point to Ferndale?

6. Have the Hoolies made it to Marine Drive Bridge?

Genetic population structure of the round whitefish

Citation: Thomas D. Morgan, Carly F. Graham, Andrew G. McArthur, Amogelang R. Raphenya, Douglas R. Boreham, Richard G. Manzon, Joanna Y. Wilson, Stacey L. Lance, Kimberly L. Howland, Paul H. Patrick, and Christopher M. Somers. Genetic population structure of the round whitefish (Prosopium cylindraceum) in North America: multiple markers reveal glacial refugia and regional subdivision. Canadian Journal of Fisheries and Aquatic Sciences. 75(6): 836-849. https://doi.org/10.1139/cjfas-2016-0528

Purpose of study: Round whitefish (Salmonidae; Coregoninae; Prosopium cylindraceum) is a widespread species that has become a conservation concern in several regions of North America. Morgan et al., 2018 performed genetic analyses of round whitefish from 17 sites across its range using nine microsatellites, two mitochondrial DNA (mtDNA) loci, and 4918 to 8835 single-nucleotide polymorphism (SNP) loci. Analyses identified deep phylogenetic division between eastern and western portions of the range, likely indicative of origins from at least two separate Pleistocene glacial refugia.

Methods: Tissue samples (pectoral fin clip, adipose fin clip, or muscle stored in 95% ethanol or lysis buffer) were obtained for round whitefish from various sites across North America and one site in eastern Russia. Genomic DNA was extracted from 414 samples of round whitefish

tissue following the manufacturer’s guidelines (Genomic DNA Isolation Kit, Norgen Biotek Corp., Ontario, Canada).

Key words:

• microsatellites - portions of the mitochondrial control region (D-loop) and cytochrome

• c oxidase subunit I (COI) barcode regions were amplified using polymerase chain reaction (PCR) for 124 round whitefish individuals representing 7–12 samples from each site, with the exceptions of Russia (n = 3) and the Rat River site in the Yukon (n =4).

• The mitochondrial cytochrome oxidase subunit 1 (COI) gene is one of the most popular markers used for molecular systematics. Fragments of this gene are often used to infer phylogenies, particularly the region near the 5'-end, which is used by the DNA Barcoding Consortium.

• The Consortium for the Barcode of Life (CBOL) is an international initiative devoted to developing DNA barcoding as a global standard for the identification of biological species. CBOL has more than 130 Member Organizations from more than 40 countries.

• The Displacement (D-loop) region contains the leading strand for the origin of replication and a number of major promoters for transcription of the mitochondrial genome.

• single-nucleotide polymorphism (SNP) - A single nucleotide polymorphism, or SNP (pronounced "snip"), is a variation at a single position in a DNA sequence among individuals. Mutation is any kind of variation in the genome, including addition, deletion, duplication, substitution and... .But SNPs are just single-nucleotide substitutions of one base for another that occur in more than one percent of the general population. And frequency of mutation is less than one percent.

Results:

Analyses identified levels of subdivision and gene flow consistent with the hydrological connectivity of the Great Lakes.

The major mechanisms driving genetic population structure are most likely (a) origins in at least two separate glacial refugia representing current eastern and western parts of the round whitefish range and (b) barriers to gene flow presented by the hydrologic connectivity of currently occupied aquatic systems.

Lake Ontario and Lake Huron are key populations for long-term management of genetic diversity and stock structure in the Great Lakes region.

https://en.wikipedia.org/wiki/Last_Glacial_Maximum

They propose that Lake Ontario round whitefish are differentiated from those in the upper Great Lakes, and Lake Huron may be an important feeder lake for others in the system.

Learning how to identify algae

Today is the first day of instruction for the Bigelow algae identification course.