Handfish DNA

September 23, 2019

Our Red Handfish IMAS/CSIRO PhD student, Tyson Bessell, is incorporating a genetic component into his research. Under the direction of expert geneticists, Dr Sharon Appleyard (CSIRO, Hobart) and Dr Carolyn Hogg (University of Sydney), he will be looking at several key areas, including:

  • Characterising gene regions in Red Handfish
  •  Assessing whether we can use non-harmful methods for collecting DNA (e.g. loose skin ‘tags’)
  •  Looking at whether we can collect genetic material from water samples (‘eDNA’ sampling), since all animals (including us) leave traces of DNA in their environment (via mucus, reproduction, dead skin, waste products, breathing etc.).

And if it’s successful, not only will it present an effective/reliable method for looking for new populations of red handfish… but it’ll also be incredibly useful for similar work with other cryptic/rare species.

More about DNA

Every living organism has the same four nucleotides (‘building blocks’)—A, C, G, and T— that make up its’ DNA sequence (and therefore encodes the genetic information specific to individuals and species). It’s just the order and how many building blocks that differ.

We first need to “screen the handfish DNA” for the most appropriate gene or DNA fragment. This just means figuring out the specific order that the nucleotides occur in specific regions of the DNA in Red Handfish. Sounds easy enough…. But for comparison, the human genome contains over 3.5 billion of these genetic letters…

How we sequence genes in Red Handfish:

  • Collect known handfish tissue samples (e.g. from deceased Red handfish that have been found in the field, and seeing if we can also use loose skin tags)
  • Create multiple copies of the DNA using a genetic procedure called PCR (Polymerase Chain Reaction; or ‘molecular photocopying’)
  • Separate and analyse the DNA
    • using a method called DNA sequencing, we determine the length and order of the nucleotides in the DNA sequence or gene of interest 
    • this includes sequencing other closely related fish (and handfish e.g. Spotted handfish) to determine how similar or dis-similar the DNA in Red Handfish is to other species
    • we then take the sequences from the genes or DNA fragments that we are interested in, and compare them to sequences in international repositories of DNA sequences (such as the BarCode of Life Database – ‘BOLD’)

More about eDNA

Environmental DNA (eDNA) is a complex mixture of DNA (from many organisms) that is found in a sample (e.g. water). Once we know the sequence of a gene region in a species – we can hopefully search for it using eDNA techniques (i.e. analysing water samples to look for handfish DNA).

Why it would be useful for handfish:

  • sampling can be undertaken by non-scientists, so we could involve the community in searching for new populations
  • sampling is non-destructive
  • it’s an emerging tool for biological surveys of organisms that are not required to be captured or when animals are difficult to observe in the environment (e.g. tracking rare & threatened species; monitoring invasive or threatening species)
    • we could help refine search areas before sending in dive teams to confirm

Tyson has spent a great deal of time learning genetic methods in both University of Sydney and CSIRO (Hobart) labs – pictured below. We’ll keep you updated on the findings from this research.

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