Silverside genomics

NCMA2022 experiment update: Phenotyping 1,147 fish

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Groton, 24 July 2022. A remarkable week ends with a sense of pride, accomplishment and a good dose of exhaustion. After more than two months of rearing, the silversides from our crosses in May have grown big, and at least for the warm, 26C treatment, they reached their final, intended size (~40 mm). Our rearing job came to a successful end, and now post-doctoral researcher Jessica Rick and PhD-student Maria Akopyan came back to the Rankin Lab equipped with hundreds of tubes and lots of RNAlater to finalize the sampling. This involved measuring the critical sustained swim speed of every individual fish, followed by meticulous measurements, photographs, and eventually an individual tube for preservation in RNAlater. Over the course of 9 days (and over 10h of work each day), the team measured 1,147 fish, which ranged in size between 15 and 50 mm. A big hat tip to the hard-working geneticists!

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On 16 July 2022, Maria (left) and Jessi (right) are working meticulously through their individual sampling protocol of silversides reared for two months at 26C. Every rearing container contains about 40 fish.

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On 21 July 2022, most of the rearing containers have been sampled and only 5 remain.

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Maria is tackling individual length and weight measurments, photographing, labeling and preserving of silversides.

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The old swim flume that has seen its fair share of experimental work, is being put to good use once again.

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To calibrate the dial of the swim flume to flow speeds, we use dye and video recording.

Now, our rearing job still continues until the crosses in the 20C treatment reach their final size, when the second session of phenotyping will need to happen. And of course, there iare so many more steps to follow. Stay tuned.

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On 16 July 2022, Maria looks concentrated while taking a picture of a reared silverside.

NCMA2022 experiment update: first genetic material sampled

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18 June 2022. We are happy to report that our genomic silverside experiment has progressed from "Can we really pull this off?" to "We think we just might" over the past weeks. The silverside larvae of these different crosses show stunning size variability, between populations and temperatures. We already obtained two early life mortality estimates and lots of genetic material, including a full set of crosses reared at 26C and ad libitum food, reaching 20 mm in roughly 4 weeks post hatch. Fingers crossed for the rest of the rearing time.

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9 dph larvae from the North Carolina Batch fertilization, waiting to be counted on 9 June 2022

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Visually stunning comparison of 9 dph silverside larvae reared at 20C from North Carolina batches vs. Massachusetts batches

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Digital length measurements of a small subsample of silverside larvae from the 26C treatment (crosses unknown)

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Silverside juveniles subsampled on 16JUN 2022 from bucket 3 of tank D (D#), housing the Massachusetts Batch (B4 of 7) in the 26C treatment, counted via ImageJ, preserved in RNAlater

Another crazy road trip for genetic silverside research

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15 May 2022. A full, blood red moon rises over Pine Island this Sunday evening. The sight makes not just humans swoon – its pull extents underwater to all kinds of critters that take it as cue for reproduction. Critters just like the Atlantic Silverside, which once again we pursue this season to extract more of its genomic 'secrets'.

Specifically, it is this weekend that we embark on yet another ambitious road trip to find and sample spawning-ripe silversides from two very far apart places: Morehead City, North Carolina and Beverly, Massachusetts. The goal: transport spawners live from each population to UConn's Rankin Seawater lab and produce calculated crosses that will allow studying the role of genomic inversions in local adaptation.

The crew this time are Maria Akopyan and Jessica Rick from Cornell University, along with Lucas Jones and Hannes Baumann from UConn. Big shout-out to Tara Duffy for her help with beach seining at Beverly, MA. During the spawning event on May 15th, Nina Therkildsen also joined the efforts. The design and experiment are part of Jessi's successful NSF post-doctoral fellowship proposal, which the whole UConn-Cornell silverside team supports.

Click through the pictures below to retrace the steps of an exhausting but so far successful effort. Fingers crossed that all goes well during the next weeks, when the fish need to hatch, survive and grow, so they can be assessed for their traits.

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The US east coast map illustrates our ambitious sampling plan.

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On 12th May, fog envelopes the Chesapeake Bridge on our drive south to Morehead City, NC.

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Maria, Hannes, Lucas, and Jessi getting ready to beach seine the Morehead City site

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Our 100ft beach seine is being laid out on the Morehead City site.

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On May 13th, Atlantic silversides caught in Morehead City swim in a bucket.

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Lucas checking whether the fish are properly prepared for transport.

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Ripe adult silversides are being transported in large coolers, with proper aeration and water changes underway.

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Maria driving through the night. The long trip back up north is especially taxing.

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On May 14th, Jessi and Tara pull our seine net up the beach on Obear Park, Beverly, MA.

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Maria bringing a new sampling bucket to Jessi and Tara (background) seining.

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Seining at low tide in Obear Park is made more difficult by ankle deep mud.

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On May 15th, at UConn's Rankin Seawater lab, Nina and Jessi strategize about designing crosses.

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On May 15th, Hannes, Jessi, and Nina spawn individual silversides.

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Jessi squeezing a silverside female for eggs in UConn's Rankin Lab.

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A 24 hours old silverside embryo developing at 26C.

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On May 15th, Jessi lays out individual crosses to be reared in the circle tanks in UConn's Rankin Lab.

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Nina and Maria extract DNA from male and female spawners to determine a specific regions homo- vs. heterozygosity.

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Screens with attached embryos are being suspended in buckets for development under two different temperatures.

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A specific capture probe (TARMS gel) allows the quick determination whether adult spawners were homo- or heterozygous for specific inversions on chromosomes 11, 18, or 24

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A silverside larva 6 days post hatch produced from NC spawners. The stomach is full of brine shrimp nauplii, pigmentation just started.