Revealing Hidden Species Interactions Through the Building Blocks of Life By: Kristen Hasenstab-Lehman, Ph.D., Conservation Geneticist and Lab Manager
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ne of the most foundational properties of living organisms on our planet is DNA. And the underlying molecular structure of DNA is the double-stranded helix, an image you’ve likely seen countless times, in various styles and iterations. The double helix is used as a motif in jewelry, art, and more, evoking its connection shared by nearly all living things. But for scientists, it is the link to understanding how species interact. We at Santa Barbara Botanic Garden are excited to be using advances in DNA science as a new tool in our conservation tool belt. Let’s get into specifics for a moment. We know DNA, or deoxyribonucleic acid, codes the plans for cellular machinery necessary for life to function and replicate. Deoxyribonucleic acid is composed of repeating units of nucleotides often called the building blocks of life. Each nucleotide or building block (you can think of them like LEGO pieces) contains three parts: a phosphate group, a sugar group, and one of four types of nitrogen bases (A)denine, (T)hymine, (G)uanine, and (C)ytosine. The nitrogenous bases form the core of the nucleotide, with A only ever pairing with T, and G pairing with C. So, with these pairs plus phosphate and sugar as the backbone, you have one nucleotide block. The blocks then join together further to form two long, reverse-complement strands that we recognize as the double-stranded helix. Changes in the order of nucleotides over millions of years results in the dynamic and rich forms of biodiversity around us.
Leveraging Science To Protect Threatened Species Each creature has a unique combination of A T G and C bases, and that unique sequence presents scientists with a novel way, known as DNA metabarcoding, to identify what animals have been eating. In the Garden’s Plant Genetics Lab, we’re using DNA metabarcoding to better characterize species interactions and food webs for taxa native to the Channel Islands, from foxes to snails. With that information, we can better protect these important food webs for their survival. There is a rich body of literature describing the diet of imperiled animals, such as Channel Island foxes, based on the physical examination of their scat (or 14 Ironwood
feces). In these studies, researchers collected scat and identified various prey items in the samples. However, this approach requires expertise in recognizing the small body parts of invertebrates, or soft-bodied animals, that form a large part of the diets of these charismatic omnivores. Soft-bodied animals and plants are particularly difficult to identify, as they do not preserve as well passing through the digestive tract of a fox. This is where DNA-based methods come in. This cutting-edge metabarcoding technology improves our ability to examine predator-prey food webs in two ways. First, they can be applied to charismatic vertebrates like foxes to detect softtissued components of their diet. Second, the approach works for any kind of animal, including invertebrates, with equal success in food item detection and precise identification.
The DNA Process at a Glance To begin a diet study using DNA metabarcoding, scat of the focal species is collected either fresh or in the field. Back in the lab, we then grind up the scat and isolate any DNA present in the sample. We copy small, specific segments of DNA of the prey, often referred to as “barcodes,” that allow us to identify the DNA in the scat. We do this through a lab technique called Polymerase Chain Reaction (PCR) that can generate thousands of copies of these barcodes of prey items. Small identification tag molecules, which are also made out of A T G and C bases, are then added to each of these individual PCR samples. We then place all the identification-tagged PCR reactions into a single, small tube, which when full will appear as nondescript as water to the naked eye. However, once that clear liquid is put on a highthroughput DNA sequencer, it is turned into billions of A T G and Cs. Following an initial sorting of data by sample, we then compare those unknown sequences found in the scat samples to a large reference database of barcode sequences with known identities. Once we identify our unknown sample sequences using this reference database, a new understanding of the diet composition can emerge, one generated in a Opposite: San Clemente Island bird’s-foot trefoil (Acmispon argophyllus ssp. adsurgens) is eaten by San Clemente Island fox (Photo: Kristen Hasenstab-Lehman, Ph.D.)
