Genetics – Parentage Analysis

We are using unique genetic patterns in each rockfish we sample to match parents with their offspring. Because kelp rockfish adults don’t move very far after they settle in suitable rocky reef habitat, when we find a juvenile rockfish that is a genetic match to an adult, we know that the baby rockfish traveled from the location of that parent to the place where we caught and sampled it.

For this project, we genotyped 15,000 rockfish!

Every time we sampled an adult and juvenile rockfish, we took a GPS location or identified the location on a map of Carmel and Monterey bays. This location information allows us to draw a line between our parent-offspring genetic matches, which helps us understand how far the individual baby fish traveled.

To find these genetic matches, we use a type of paternity testing. Paternity testing in humans and animals often relies on single base DNA mutations called SNPs (single nucleotide polymorphisms). Each SNP is a variable site: for example, rockfish #1 has one allele (DNA base) – let’s say an “A” – at that location in the genome. In rockfish #2, we could find the same allele as rockfish #1 (an “A”), or a different allele (perhaps a “G”). We can’t use just one SNP for paternity testing though, because unrelated individuals will have the same allele at some SNP locations, just by chance. But when we analyze dozens or hundreds of SNPs, the probability that unrelated individual will share many SNP alleles decreases.

However, we developed a new, more efficient method of looking at multiple SNPs in a short (100-150 base) DNA sequence. These short DNA sequences are referred to as “microhaplotypes.” The number of combinations of SNPs in a microhaplotype is far greater than the actual number of SNPs.

For example, let’s say we have three SNPs on one of our DNA sequences: SNP1 = A/C, SNP2 = G/A, SNP3 = C/T. Then if we observe all possible combinations of the alleles at these SNPs, we would have eight different combinations (3 SNPs = 8 potential combinations).

When we look at all of the combinations of SNPs in 100 of these short sequences (microhaplotypes), these data provide far greater statistical power to identify genetic matches among our kelp rockfish adults and juveniles.

If you want to get into the weeds of our new genetic markers for rockfish, check out our microhaplotypes page.