Constructing a multicellular organism from scratch is a staggeringly challenging task.
It seems even more miraculous when you consider that it's actually entirely orchestrated
by a few thousand genes and their protein products, acting (largely autonomously)
within each one of the rapidly dividing cells. The most crucial of these genes and
proteins regulate each other in intricately interconnected ways as part of a gene
regulatory network, setting up the structure and physiology of the critter's body.
10.1371/journal.pbio.1001690.g001
By shifting the distribution of phenotypic variation during development, a gene regulatory
network can buffer perturbations yet retain the ability to adapt when the environment
changes.
Image credit: Greg Wray and David A. Garfield.
Already complicated enough, the development of multicellular organisms is also stuck
on the horns of a particularly tricky dilemma. On one side, for the short-term perpetuation
of an organism, this process must be robust –whatever the challenge, be it genetic
mutation or environmental perturbation, the developmental programme has to be able
to reliably deliver a viable organism as an end product. On the other side, long-term
survival of a species in the face of changing environmental conditions requires that
such an organism is able to change, in a genetically determined way, to provide the
variability on which natural selection can act. How is it possible to strike this
balance between robustness and evolvability?
In a new study, David Garfield, Gregory Wray, and their colleagues examine just this
issue, in impressive detail and scale. Their model is the purple sea urchin, a workhorse
of developmental biology. Sea urchin embryos develop from single cells to free-swimming
larvae over 4 days, and the authors set out to examine how the struggle between robustness
and evolvability plays out over this timescale.
To provide the natural genetic variation that acts as a fuel for evolution and a challenge
to robustness, the authors collected six female and six male sea urchins from a wild
population in the Santa Barbara Channel. They then mated them in every combination
to get 36 genetically distinct nurseries of developing embryos. At seven points throughout
the ensuing transformation from blob to swimming animal, the authors abstracted hundreds
of embryos from each population and monitored the transcript levels of 74 genes from
a well-studied developmental network of more than 100 genes.
The design of the experiment meant that the workers could determine whether any effects
on gene expression in the embryos had a genetic (as opposed to environmental) cause,
by assessing correlations between siblings and attributing influences to either the
father (largely genetic) or the mother (both genetic and – via egg provisioning –
environmental). Looking at the effects on the expression of single genes, they found
that, gratifyingly, natural genetic variation had significant effects on the timing
and magnitude of expression of most of the genes examined throughout the course of
development. They were then able to scrutinise their data for correlations between
genes, enabling them to ask broad questions about regulatory principles.
When two genes are regulated by a common regulator, do they tend to increase or decrease
in expression at the same time? Yes, they do, and this correlation tends to increase
strikingly as development progresses. Do expression levels of a downstream gene show
dependence on levels of an upstream regulator? Yes and no; genes tended to differ
substantially in their sensitivity to amounts of the regulator, being either rheostat-like
or switch-like. Intriguingly, there seems to be a shift from early switch-like, relatively
insensitive regulation to more finely tuneable rheostat-like regulation at later stages
of development. The authors speculate that these two distinct regimes reflect a need
for robustness (insensitivity to variation) during early development.
The particular gene network examined contains more than 100 interlinked genes involved
in determining the axes and cell types of the embryo as well as the structure of the
larval skeleton. Sea urchins' skeletons, like ours, are complex, three-dimensional
calcified structures. At the end of the 4-day developmental process, the authors took
up to 30 larvae from each population, imaged them, and established the three-dimensional
relationship between eight skeletal landmarks. The skeleton is a direct product of
the gene network under study, and its size and shape have already been shown to influence
the fitness of the animal. So by examining the intermediate and ultimate phenotypes
of gene expression and skeletal morphology, the authors were able to functionally
interrogate the connection between the immediate and ultimate targets of evolutionary
selection – fitness and genotype, respectively.
The authors performed a principal component analysis of skeletal data, boiling the
large body of information down to three components that captured most of the variation
in their sea urchins. Using these parameters to search for significant correlations
between shape and the expression of individual genes, Garfield et al. identified eight
crucial genes, most of which were already known to play a role in the terminal part
of their gene network that's responsible for constructing the skeleton. Naturally
occurring variation in genes that play a later and cell-specific role in making the
skeleton therefore seems to be responsible for the bulk of the adaptive phenotypic
variation in this tissue. There's also a very early, and probably non-genetic, maternal
effect on the skeleton that acts independently of the later genes.
Overall, this study builds a comprehensive picture of a large gene network in real,
developing animals that are responding to a natural level of genetic variation. What
emerges is domination in the early stages of development of switch-like regulatory
behaviour that buffers appreciable upstream (cryptic) genetic variation, preventing
its manifestation in the phenotype and helping to confer robustness on the system.
By contrast, when rheostat-like genes kick in later in development, such as those
that determine skeletal variation, variation in gene expression is more tightly and
quantitatively coupled to downstream consequences, including skeletal phenotype, and
thereby fitness.
Thus, at least for sea urchin development, it seems that the compromise between robustness
and evolvability is achieved by separating the fulfilment of these two conflicting
requirements in time. The act of making the animal starts with a series of firm binary
decisions that lay down a solid developmental foundation, insulating this delicate
process from much of the underlying source of variation. What follows is a later creative
phase of more sensitive and quantitative regulation, where genetic variation is freer
to have its effects and to act as the raw material for evolution.
Garfield DA, Runcie DE, Babbitt CC, Haygood R, Nielsen WJ, et al. (2013) The Impact
of Gene Expression Variation on the Robustness and Evolvability of a Developmental
Gene Regulatory Network.
doi:10.1371/journal.pbio.1001696