Old questions, new tools

Giant sequoia photo by Sally Aitken

As a tree enthusiast, I have always been curious about how long-lived and evolutionarily ancient conifers have been able to adapt to their spatially and temporally variable environments. When I was a grad student at UC Berkeley in the 80’s, I wanted to study the genetic basis of adaptation of Bolander pine (a subspecies of lodgepole pine) to the ancient acidic and nutrient poor soils of the Mendocino pygmy forest in California. At that time I could either a) use genotypes for a small number of presumably neutral genetic markers (i.e., not affected by natural selection) to learn about population history and evolutionary divergence, but not adaptation, or b) study relationships between phenotypes in common garden experiments and population environments, and learn about adaptive variation in a crude quantitative genetics manner. However, for the most part we couldn’t link specific differences in DNA sequence with differences in phenotypes and fitness any more than Darwin could.  Even as new genetic tools were developed, the long generation length and enormous genome size (~20Gb; 7x human) of most conifers made many genetic approaches intractable.

Fast forward to 2012.  As we kick off this blog, the first conifer whole genome sequences have been produced by labs in Canada, the US and Sweden. We now have sequence capture tools to reduce genomic DNA to the portions we are most interested in – the exome. Massively parallel next-generation sequencing generates mountains of data faster than bioinformaticians can analyze it, and it now costs less to sequence a base pair of DNA than to digitally store that datapoint. Finally, DNA sequencing is no longer the domain of hard-core molecular biologists – the technology has become accessible to non-molecular, organismal biologists like me (although funding remains a barrier for many scientists focused on natural populations rather than model organisms). As I had dreamed doing 25 years before, scientists at UC Davis and Cal State Sacramento recently sequenced a small number of candidate genes in lodgepole pine from in or near the pygmy forest and found variation in two of those genes putatively involved in phosphate and aluminum transport associated with pygmy forest soils.

So what does this have to do with forests and climate change? We now have the genetic and analytical tools to unravel the genetic basis of complex traits that are controlled by tens, hundreds or even thousands of genes (e.g., cold hardiness and phenology in Sitka spruce); to study the distribution of genetic variation for those traits across landscapes (e.g., Bayenv); and to better understand the relationships among phenotype, genotype and environment.  With these tools, we hope to answer the following questions:

  • Can tree populations adapt to rapid climate change?
  • What can the genetic history of populations tell us about adaptation over evolutionary time scales? (interesting example here)
  •  Does gene flow between populations assist or slow adaptation to new conditions?
  • What should forest managers and conservationists do to mitigate the impact of global warming on our forests?

On this blog, we hope to explore these questions in the context of progress in our AdapTree Project and other efforts.  I am fortunate to work with an amazing group of young scientists, and I learn more from them than they ever learn from me.  As we all share ideas, perspectives and experiences, I hope that our readers will benefit as much as I do.


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