We asked H. Bradley Shaffer, a distinguished professor of ecology and evolutionary biology at the University of California, Los Angeles, and the director of the La Kretz Center for California Conservation Science, about the future of nature.
Boom: What do we need to do now to preserve biodiversity in the future in California?
Brad Shaffer: One of the things I am really hoping we can accomplish is to collect baseline population genomics data, ideally for every species of plant and animal in California, and beyond for that matter, so that we know what kind of genetic diversity currently exists across the state. What we have now is a poor substitute for what we had, but it’s all we’ve got. And as we move forward, having that baseline is really useful in that it allows us evaluate how we’re doing in ten years or twenty years or whatever—how we’re doing in terms of retaining what we had and how we’re doing in terms of potentially improving on what we had or what we lost.
Boom: What is “conservation genomics” and why do we need it?
Shaffer: The relationship between conservation and genetics is a very old and very deep relationship, and it simply says that there is a lot of information in the genetics of wild populations of organisms that’s relevant to how we should conserve and protect them. Say you have a species that is in trouble and we want to try to come up with a conservation plan for it. One of the things we want to do is conserve the diversity within that species. If that species occurs in Central California and in Southern California, we would like to know if they are genetically very different on either side of the Tehachapi Mountains that separate those two parts of their range. If there are genetically different parts of a species’ range, we want to make sure we conserve populations in genetic region one, genetic region two, etc. You can also use genetics to learn about how plants and animals move across landscapes. You can do studies of migration and gene flow—the movement of individuals and their genes—by using genetics. When people use the term “conservation genomics,” what they mean is scaling up the genetics that we would have traditionally done in the past to much larger and more informative studies. So, traditionally we might have studied five or ten or fifteen genes, and now genomics means scaling that up by one or two or three orders of magnitude and studying a lot of genetic material from those individuals and populations in a species—going up to a thousand or ten thousand genes. In principle, it could mean studying the entire genome and analyzing all of the genetic variation found in a species, although that hasn’t been done except in few model systems to date.
Boom: Does conservation genomics mean that we can afford to be ecologically risky or reckless––as long as we are going to conserve these genomes, then it doesn’t matter about the effects we have on the environment?
Shaffer: Let’s say we had full genomic knowledge of population variation for every species of plant and animal. Would that allow us to be ecologically risky or reckless? Hopefully not. It would allow us to be ecologically and environmentally better informed in terms of what our actions will mean for those populations of plants and animals. What that might mean is that certain things that we thought we had to be careful about, in fact, with that greater depth of knowledge we now feel we don’t have to be as careful about. Other things we felt that we didn’t need to be careful about, perhaps we do. My way of looking at it is that it will allow us to better understand what it means to be reckless and avoid it because we’ll be better informed. Deeper knowledge does not provide carte blanche to do things that are going to destroy or scramble the environment even more. Hopefully, it gives us better insights into what the consequences of different actions, different environmental and ecological actions, will be.
Boom: How does conservation genomics change the way we think about traditional threats to conservation, like increasing land conversion, infrastructure, and agriculture? Does genomics show us that species might work around or adapt to these threats?
Shaffer: Genomics may in some cases either inform us or allow us to make more educated predictions about how organisms will deal with those threats. It can do that by informing us about specific ways that organisms adapt to the environment and change. It can also allow us to make better predictions about what they will do as they adapt to human mediated change. Climate change, and how organisms will and will not adapt to it, is a great example. If you learn about how organisms in the past—or currently—have been able to successfully adapt to some natural change, and humans are currently creating similar kinds of changes, that should help us better predict how organisms might adapt in the face of human disturbances and environmental challenges.
Boom: What would you put in a time capsule for 2050?
Shaffer: I’d put two things. One is a frozen sample of a native plant—say, an oak tree acorn—and a weed to look at changes in those species’ DNA over forty years as they adapt to climate and other human-mediated changes. The other is a sample of dirt from Pershing Square in downtown LA, from the Santa Monica Mountains, and from the beach in Santa Monica to be able to look at changes in soil bacteria and fungi over the same time period.
Image at top courtesy of Ed Schipul.