False Albacore Genetics Research

*Last Updated January 5th, 2023*

Albie genetic data have been collected and analyzed for Year 1 of The Albie Project. Samples were collected from New York, Massachusetts and North Carolina this past fall. Initial results indicate that we are likely looking at one coastwide stock. To gain more clarity, we are initiating a broader DNA study in Year 2 of The Albie Project in 2023.

A note from Steven Bogdanowicz:

“Briefly, I constructed a DNA library enriched for microsatellite loci from a single fish we caught with Vinny in Montauk last October. PCR primers to 4-base repeats were designed and ordered, and DNAs from fin clips were extracted with a simple Sodium Hydroxide/Tris protocol. Primer pairs were pooled in groups of 23 loci, DNA samples were amplified, barcoded, and sequenced, and the resulting diploid genotypes were called with a python script. Final data matrix has 77 individuals and 68 unique microsatellites.

Two different softwares (Structure and adegenet) were used to analyze the data. Important to remember here that we didn’t set out to determine whether fish from NY/MA/NC were different from each other; rather we’re asking “If we take a sample of albies from a pretty broad area at about the same time, how many genetic groups do we see?” Both softwares agree that the answer to that is “one.” The attached Probability by K graph (Figure 1 – screenshot below) is from Structure, and shows most likely number of groups (k) is 1. The attached Rplot_BIC pdf is from adegenet, and shows the same (lowest BIC value represents the most likely number of groups).”

Figure 1. “This Probability by K graph is from Structure, and shows most likely number of groups (k) is 1. “

3 Responses

  1. Please can you provide more info on the data? I’ve done tons of microsat work (I’m a popgen prof) but old school fragment analysis where each locus was genotyped separately and there were many alleles per locus. Is that what you get from Illumina data? Your comment about primers annealing to the repeats is confusing. But what I’d love to see is the basic data of # alleles per locus, He on average across loci, F averaged across loci, and what the structure plot looks like with K=2 . . ..

    This is very exciting!!!!!!!!!!!!!!!!!!

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