Francisco B.-G. Moore
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Research Interests
At the intersection between microevolution and macroevolution lie many of the most elusive and
important evolutionary questions. While micro- evolutionary biology addresses the changing genetic
variation within populations, macro-evolutionary biology focuses on changing variation between clades
above the species level. To understand the intersection of these two fields we must determine how the
processes at each level influence the patterns seen in the other. If Gould (1990) is correct in asserting that
evolution is a process shaped by contingency, then the past must in some way constrain future evolutionary
patterns. If there is a signature of past evolution it is in present constraints on genotypic variation within
and between clades. When phylogenetic (macro-evolutionary) constraints exist micro-evolutionary response
should differ between clades. My research addresses the follow 2 questions that arise at this interface of
these two fields. First, under what conditions can constraints be circumvented? Second, when constraints
exist, are they qualitatively and/or quantitatively different across phylogenetic levels?
Under what conditions can constraints can be circumvented within a population?
Theoretical work
I have been investigating the viability of Sewall Wright's shifting balance process (SBP) as a
mechanism for circumventing evolutionary constraints. The SBP describes how a population might shift
between genotypic fitness optima that are separated by a fitness sub-optimum. This sub-optimum is
normally a constraint on further adaptation because a population’s mean fitness must be reduced before a
new fitness optimum can be found. Since natural selection acts to increase fitness, it tends to constrain the
population to one optimum. The SBP requires the action of three dynamic elements; genetic drift, natural
selection and group selection. Wright predicted that in a fragmented population all three of these processes
might work to circumvent constraints within a species.
A central question in my work is, ‘how common are constraints within and between populations?’ In
my models the SBP can occationally circumvent constraints within a population. In those cases the
constraints are only seen as ephemera. In a largely undivided population where the SBP does not apply,
selection efficiently eliminates unfit genotypes, and will prevent us from seeing the constraints at all. My
modeling therefore indicates that the more important constraints are in a population, the more undetectable
they are.
We need to be able to explore the viable genotypes surrounding multiple optima to study constraints
within populations. Unfortunately, these genotypes will only be seen in a population when migration
between demes is extremely rare so that demes will be likely to drift to divergent optima. While this doesn’t
pose a difficulty for the study of constraints across species or higher taxa, it is a major obstacle for the
study of constraints within a population. If we want to understand the microevolutionary interface with
macroevolution we need to understand the development and effects of constraints within a population.
Experimental work
Experimental studies of evolution in Escherichia coli allow the flexibility needed to study constraints
within and between clades. I am exploring the extent to which a highly adapted E. coli genotype is
constrained. In order to explore constraints when no variation is likely to exist I have relied on molecular
techniques to produce the requisite variation. In collaboration with Dr. Daniel Rozen I have answered the
following question: If a mutation dramatically reduces the fitness of a highly adapted genotype, can
mutations at other loci easily ameliorate the effect of that mutation?
To answer that question I began with a clone of E. coli that had evolved in a constant selective
environment for 10,000 generations. Random mutations in that genotype were then created using insertions
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Research Interests
of mini-Tn10 transposons. These mutations are effectively irreversible. I propagated a number of
deleterious single and double insertion mutants in the same environment in which they had adapted. I
propagated the lineage for just 200 generations. In this short period, compensatory adaptation allowed no
more than one novel mutation to sweep through a given population. Because E. coli clones can be stored
frozen, I was able to determine each lineage’s fitness relative to its unmutated ancestor by competing them
in their adaptive environment. I found that compensatory mutations that largely restored the original fitness
were pervasive. Not only could individual compensatory mutations largely repair catastrophic single
deleterious mutations, but they could also largely compensate for the effect of two simultaneously
deleterious mutations (Moore et al. 2000). This evidence of pervasive compensatory mutation hints that
certain constraints are easily side stepped.
Ongoing Research
There is however, an alternative interpretation of the story presented above. These compensatory
mutations may themselves create new constraints. While they restore fitness in a given environment they
may alter the direction of future adaptation. If we really wish to understand the evolutionary consequences
of deleterious mutations followed by compensatory mutations, we need more information. First we need to
profile how the original unmutated genotype would respond to novel environments it might encounter.
Second we need to know how the initial deleterious mutation alters that response profile. Third we need to
know whether any of these changes in the response profile have been eliminated or changed by the addition
of a compensatory mutation. Finally we need to know if that compensatory mutation on its own alters the
original response profile. If we know all four response profiles we can determine the extent to which a
given compensatory mutation truly sidestep genetic constraints.
In collaboration with Dr. Dominique Schneider I am determining each of these four response profiles
for a number of compensated lineages. From the previous project we have three of the four necessary
genotypes for each compensation lineage. We have begun by constructing the final necessary genotype for
numerous lineages. That genotype is constructed by removing the initial deleterious mutation after a
compensatory mutation has occurred. I am now using direct competitions in multiple environments to
determine the extent to which these mutations alter adaptive response profiles. In order to understand the
changes in response between genotypes in a more mechanistic fashion I will investigate gene expression
changes in the same four genotypes per compensated lineage. Using Sigma-Genesys gene expression arrays
I will look for differences among the genotypes of each compensated lineage in the expression of over 4000
genes. If compensatory mutations do not largely restore original gene expression patterns then
compensation may be creating new, rather than circumventing old constraints. I will begin using gene
expression analysis technology, which is already in use in our lab, in the immediate future.
The results of these two portions of my compensatory mutation study will complement each other well.
The results from this first portion of the study will explore a modest portion of a near infinite number of
novel environments, but it will directly measure the changes in fitness caused by the different gene
combinations in those environments. The second portion of the study will not directly measure fitness
changes but will give a more complete view of the putative restoration of function by compensatory
mutations.
Are constraints qualitatively and/or quantitatively different across phylogenetic levels?
The pattern of evolutionary change since the origin of life involves both divergence and convergence. If
variation within populations was unconstrained, predictions of evolutionary response in a given
environment would be relatively straightforward: Given the same environment all populations would
converge on the same solution. However that this is not the way evolution occurs. Instead, we know that the
response to selection is constrained by the variation that can be generated within a population. As described
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Research Interests
above, these constraints may be created by a population’s evolutionary history. I wish to answer the
following three questions: Are patterns of convergence and divergence of lineages related to phylogenetic
hierarchy? If so at what levels of relatedness will populations tend to diverge or converge? At what level
does relatedness just no longer matter?
Ongoing Research
I am currently conducting a long-term evolutionary experiment that will directly measure the patterns of
convergence and divergence across multiple phylogenetic scales. In this experiment I selected 12 wild
clonal isolates of putative E. coli to provide ancestral stocks. These wild bacteria were isolated from a wide
diversity of tetrapods and from 2 different continents in the hopes of representing a large portion of the
breadth of diversity within E. coli. I added a very fine scale of differentiation within each isolate by
developing 2 sister clones, that are separated by only one mutation from each parent isolate. This provided
me with 12 pairs of sister clones or 24 total ancestors. I have evolved 2 replicated lines from each of these
clones in a minimal glucose environment for 2000 generations saving frozen stocks from each lineage every
100 generations.
As a basis for hierarchical analysis an independent cladistic analysis of the genotypes is first needed. In
collaboration with Hanna Jaworski, an undergraduate under my supervision, I have nearly completed such
an analysis. We have been amplifying and sequencing three different genes in all twelve of the ancestral
genotypes. From this sequence data I am developing a molecular phylogeny of the 12 parent strains. This
portion of the project is essentially complete with 33 of the 36 total genes sequenced. When the cladistic
analysis is complete it will provide the hierarchical framework upon which I will base my analyses of
evolutionary patterns in the laboratory adapted lines. Given my present data I expect to be able to look at
convergence and divergence patterns across approximately 4 nested clades.
I am measuring a number of phenotypic traits in the ancestral and evolved strains in order to maximize
my ability to detect patterns of convergence and divergence. I am presently looking at two different types of
traits. The first are individual traits such as size, shape, and ability to grow on 96 different carbon sources.
The other traits are measured at the population level, and are likely to be directly related to fitness in the
selective environment. These traits include growth rate, lag time before first division, and carrying capacity.
Both sets of measures will be used in hierarchical analyses of divergence and convergence. Traits that are
closely related to fitness will always have strong and consistant selection acting on them. Unless strong
constraints exist they should converge. In traits that are more distantly related to fitness initial differences
in genotype are more likely to give a mixed pattern of convergence and divergence. These two sets of traits
may therefore provide fundamentally different insights into how the signature of past evolution influences
adaptive evolution. The comparative analysis of the evolvability of these diverse traits will also provide
insight into the underlying genetic mechanisms of quantitative traits and the inter-relationship of
biochemical pathways.
Long Term Research Goals
I have three major long term research goals. Each of these projects represents my interest in the
interplay of genetic and ecological factors that determine patterns of adaptation. Each of these goals has
prompted me to design an experiment that will shed light on a fundamental question in ecological genetics.
I plan to seek external funding for each of these projects as I develop my own research lab.
My first long-range goal is to expand my long-term study of phylogenetic constraints to include
multiple environments. I wish to determine if the types of patterns of convergence and divergence that are
found in one environment are particular to that evolutionary environment alone. In addition, I will
investigate whether lineages that are prone to converge in one environment are prone to converge in most
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Research Interests
environments. I believe that a project of this type will answer many new questions about the context
dependence of phylogenetic constraints.
My second goal is to examine the way in which biochemical pathways respond to long term selection
pressures. I would like to answer the following questions: When evolved in a single resource environment,
do lineages founded by different ancestors consistently simplify their biochemistry by down regulating
certain pathways? If so, are they consistently the same pathways or do different lineage down regulate
different pathways? In a multiple resource environment how would answers to these questions change?
My third long-range goal is to examine the evolution of competitive ability. I wish to examine how the
history of past competition affects the ability of a lineage to respond to new competitors. I am also
interested in determining whether processes like character displacement can alter the response of a lineage
when it is exposed to a new environment. This project will determine the extent to which realized niches
become fundamental niches over long term evolutionary time. I will study 3 replicate lineages of E. coli
each evolved in the presence of 14 different sets of competitors for over 2000 generations. In the past two
years many of the protocols for this study developed through a series of pilot studies that I designed in
conjunction with Dr. Sharon Strauss.
My greatest interest is in understanding the way in which the evolutionary past influences future
adaptation and diversification. My current and future goals reflect those interests. In the past ten years I
have pursued these interests in terrestrial and marine systems, and with organisms from three separate
kingdoms. I feel that one of my biggest assets is that I am not driven by the system that I work on. I hope to
always look for the most appropriate system to answer important questions as they arise.
Gould, S. J., 1990. Wonderful Life. Norton & Co.
Moore, Francisco B.-G., D. E. Rozen, and R. E. Lenski. 2000 Pervasive compensation for deleterious mutations in
experimental populations of E. coli. Proceedings of the Royal Society London B., 267: 515-522.
Moore, Francisco B.-G., and S. J. Tonsor. 1994 A simulation of Wright's shifting-balance process: migration and the
three phases. Evolution, 48: 69-80