Team members: Dr. Peter Lind, Dr. Gayle Ferguson, Dr. Sylke Nestmann, Andy Farr, Dr. Philippe Remigi
Collaborators: Dr. Jenna Gallie, Dr. Michael J McDonald
Key publications: Spiers et al 2002 Genetics, McDonald et al 2009 Genetics, Beaumont et al 2009 Nature, Refardt & Rainey 2010 Evolution, Bertels & Rainey 2011 PLOS Genetics, Ferguson et al 2013 Genetics, Gallie et al 2014 (under revision)
This general area underlies a good deal of our work -- motivated to a large extent by a wish to understand the mechanistic bases of evolutionary change. But equally, genetics holds so much fascination and there is so much that remains unknown. It is also one awful lot of fun doing genetics with organisms that are experimentally tractable and where it becomes possible to dissect phenotypes that have arisen during the course of real-time evolution (selection) experiments.
The evolution of phenotypic diversity
Natural selection shapes patterns of diversity, but its ability to do this is constrained by the supply of phenotypically useful variants. This interests us a great deal and is a motivating factor behind the many years spent painstakingly dissecting the phenotypic and gentics bases of wrinkly spreader fitness. This work was begun by Sophie Kahn, one of my first D. Phil. students (see Spiers et al 2002 Genetics 161, 33). She did a wonderful -- pioneering -- job, back in the days before we had a genome sequence and where identifying the genomic location of transposons required Southern blotting and cloning pieces of impossibly large genomic DNA using restriction enzymes whose positions were unknown. Things have progress: we now have a genome sequence of the ancestor (one day it will get published) and this has greatly facilitated our genetic analyses. Of course with such a reference sequence it becomes possible to take advantage of some of the latest genome re-sequencing technologies to wonderful effect.
Our approach has been phenotype back to genotype: it took many years to find the causal mutations, but once found, we understood why the mutations had the effects that they do. So far we have published only the wspF story (Bantinaki et al 2007 Genetics 176, 441), but we now know that there are three (and only three) simple genetic routes to WS. Genetic characterization has unravelled some emerging 'rules' governing the origins of these mutants. Mike McDonald -- in particular -- has extended this work to study the full spectrum of mutations (and fitness effects) generating WS in both the presence and absence of selection.
All-in-all, this part of our work is entering an exciting stage with understanding of the system beginning to coincide with the assays and tools to answer the kinds of quesitons that motivate us.
Evolution of a genetic switch
In addition to our work on the evolutionary genetics of thePseudomonas radiation we have a general interest in the evolution of gene regulation that manifests in various projects (see for example the histidine work). More recently, thanks to Dominik Refardt's interest in the evolution of virulence we got to deal with the genetic switch of phage lambda that determines lysogenic vs. lytic growth. This well-studied switch has been shown to be genetically robust (i.e. it keeps working even through peturbed), which leads to questions about the ecological significance of the swtich and the capacity of the switch to respond to selection.
Dominik performed an interesting selection experiment in which he tried to change the sensitivity of the lambda switch. To our surprise -- and contrary to expectation -- it proved relatively easy to select for either more sensitive or less sensitive switches. In fact in some lines we observed not only a change in switch sensitivity, but also a change in the response time of the switch. Some re-sequencing of derived genomes, along with analysis of candidate loci has provided some new insights into the workings of the lambda switch.
This project took a further interesting turn upon looking at variation in switch sensitivity among natural isolates of lambda phage. It turns out that the switch is very different in different isolates suggestion that natural selection in the wild does tune the switch to prevailing ecological conditions.
In 2004 Bertus Beaumont joined our lab on a Marsden-funded programme to explore the fitness and genetic consequences of repeated bouts of reverse evolution. This whole project has turned into a real gas thanks to Bertus' fine efforts. Sadly Bertus is back in the Netherlands (doing just fine and no longer needing to shade from the sun), but the project roars ahead thanks to the dedicated efforts of Jenna Gallie and Christian Kost.
In a nut shell: Bertus performed a large-scale selection experiment in which he favoured genotypes that changed their phenotype rapidly (a consequence of selection in two contrasting evnironments). The outcome of this experiment was surprising in several regards. Arguably the most exciting finding was a genotype (actually three genotypes from a total of 12 replicate lines) capable of rapid switching between two phenotypic states. Jenna, aided by careful genetics and genome re-sequencing, has been working hard to crack the mechanistic basis. James Sneyd has been helping us to apply some math to the problem of bistability. Gayle Ferguson is thinking about the subsequent evolution of the 'switcher' genotypes
Christian has been doing some very laborious strain reconstructions involving many mutations so that he can explore questions relating to epistasis, contingency and evolutionary history. He is nearly at the fun part. He is being aided in this by Gayle Ferguson, who figured there was no better way to get to understand wrinkly spreaders and their extraordinary capabilities than by the hands-on manipulation of their genomes.