Genetics schmetics! What is the difference between all the different methods used in conservation genetics?

Genetics is a powerful tool in the field of conservation, but the topic of genetics is so large that it can sometimes be overwhelming to begin to even understand. So here is a quick cheat sheet on different methods and genetic markers that are used in the field of biology, ecology and conservation in general.


Using genetics can help us understand the evolution of an organism, assess the status of a population, and conserve a species.  The basis for all of the is DNA, which can be found in every single cell of all life on earth!

Photo credit: Alex Avila. Fin clip sample preserved in alcohol

Photo Credit: Alex Avila. This is a fin clip, this is all you need to extract DNA ( very tiny sample)

Photo Credit: Alex Avila, tools of the trade

DNA helps us in species identification (very useful when two different species have very similar physical characteristics), understanding taxonomic relationship ( this can be important when making natural resource management decisions and guiding conservation/restoration efforts), determination of hybrids, identifying individuals with in a population, determination of parentage, migration of populations, genetic variation and historical size of populations, and also has forensic applications (like tracking down poachers!). As you can see there are many applications for genetics in conservation, and since DNA can be found anywhere, even in poop, it makes it a great tool for scientists and managers in this field to use.


Ok, let’s say I have convinced you that genetics is awesome, but now what? There are so many different methods out there, how do I know which one I should use?

In genetics different methods are known as markers. Which marker you need depends on what you want to learn. Here is a quick reference to what markers to use depending on the questions being asked.

Illustration Credit: Kathleen O’Malley

  • Allozymes: nor really used that much today, but used to be used for population differentiation.
  • RFLPs: were used for population differentiation, DNA fingerprinting, genome mapping and paternity tests
  • AFLPs: used for population differentiation, and genetic mapping
  • mtDNA: also known as mitochondrial DNA is used for population differentiation, phylogeography, phylogenetics, and is only passed down via the mother
  • Y-chomosomes: phylogeography, phylogenetics, and is only found in males
  • Introns: used to study population differentiation, phylogeography, phylogenetics, and selective adaptations
  • Microsatellites: population differentiation, gene flow and migration rates, individual identification, parentage (who’s the daddy), and relatedness
  • SNPs: population differentiation, gene flow and migration, individual identification, parentage, relatedness


As you can see, there is some overlap in the markers. In my case I a m studying China rockfish, and looking at how ocean currents affect their dispersal. To do this I am looking at whether the China rockfish in Oregon are connected, via ocean currents to China rockfish in Washington. I had the option of using microsatellites or SNPs for this. Even though both can provide information on gene flow, parentage and relatedness, I chose to work with SNPs because I am interested in a greater level of detail that microsatellites does not produce.

Photo Credit: Alex Avila China rockfish

Photo Credit: Alex Avila

So there you have it, next time you are considering working in the field of conservation, maybe give genetics a try! You’ll find it to be a very powerful tool


Here are some really cool examples of real life uses of genetics in conservation:

Wolf conservation:

Whale conservation:



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About Alex Avila

Alexandra M. Avila recently earned her PhD in fisheries from Oregon State University. She is now working as Oregon Sea Grant Coastal Resilience and Adaptation Fellow part of the Research & Scholars Program. Alex has always loved anything and everything having to do with water, whether it’s the ocean, rivers or lakes. This has led her to work in many coastal areas in the United States and in Ecuador. She has studied genetic connectivity of Chinar Rockfish (S. nebulosus) in Oregon and Washington, the genetic diversity and conservation of the misty grouper (Hyporthodus mytacinus) in the Galapagos Islands, conducted environmental impact research in the Amazon, researched the oyster (Crassostera virginica) and blue crab (Callinectes sapidus) populations in the Chesapeake Bay with the Smithsonian Environmental Research Center (SERC), and helped in assessing the salmon habitat in Oregon with the U.S. Forest Service. She has also done wildland firefighting. Alex is really excited to be here for it has been a dream of hers for a long time and she is truly grateful for this unique opportunity to work with people who are as passionate about protecting our oceans as she is. Alex Avila graduated with a B.A. in Biology from Hood College in Maryland, with two minors: Coastal Studies and Environmental Science and Policy. She obtained her M.Sc. in Ecology at the Universidad San Francisco de Quito (USFQ) in Ecuador is 2012, and her PhD in fisheries from Oregon State University in 2023.

One thought on “Genetics schmetics! What is the difference between all the different methods used in conservation genetics?

  1. Hi Alex, thanks for this post! It was a nice, easy run down of the different types of genetic information used in conservation and management. Im definitely convinced on its power as a tool in this field! It was nice to see a couple of other examples too. Thanks!

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