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Molecular Ecology (2003) 12, 1109 –1112
PREFACE TO THE SPECIAL ISSUE
Blackwell Publishing Ltd.
Merging Ecology, Molecular Evolution, and Functional
Genetics
M I C H A E L P U R U G G A N A N and G R E G G I B S O N
Department of Genetics, North Carolina State University, Gardner Hall, Raleigh, NC 27695–7614, USA
‘This structure has novel features which are of considerable
biological interest.’ This has to be one of the boldest
understatements in all of biology, written 50 years ago in
Nature by Francis Crick and Jim Watson in describing their
model for the DNA double helix (Watson & Crick 1953).
The unveiling of the structure of the molecule that carries
the hereditary information of living organisms is rightly
hailed as a landmark in the history of science, and we
rightly celebrate the golden anniversary of this discovery
this year.
Understanding the molecular basis of genes has transformed biological research since 1953, and ecologists have
participated in the fruits of this revolution. The use of
molecular markers, beginning with restriction fragment
length polymorphisms (RFLPs) to today’s single nucleotide polymorphisms (SNPs), has had a significant impact
on our ability to trace parentage and kinship, to measure
gene flow and migration patterns and to reconstruct the
demographic histories of populations and species. Few
will argue that the advent of modern genetic technology
has provided an unparalleled ability to examine evolutionary and ecological forces in nature.
Yet the full impact of molecular genetics (and today,
genomics) has yet to be felt by the discipline of ecology.
While the use of molecular markers by ecologists has been
fruitful, there is more to the molecules than their current
dominant role in ecological research as mere genetic
barcodes. We have yet to understand ecological processes
at a fundamentally molecular level, and our inability to
make this connection from the ecological gene to the
ecological organism hampers any dreams we may harbour
of creating a unified picture of life. We do not know, to a
large extent, the interplay between genes and the ecological processes that dominate life at and above the organismal level.
We stand today at a crossroads that provide unprecedented opportunity to make these connections. Molecular
biologists have proved adept at unravelling the molecular
mechanisms behind many of the physiological, developmental and at times behavioural processes that characterize organismal lives. It is time that ecologists make use
Correspondence: G. Gibson. Fax: (919) 515-3355; E-mail:
[email protected]
© 2003 Blackwell Publishing Ltd
of this information in meaningful ways to gain further
insights into the nature of organismal ecologies.
How do we go about doing this? There is no one single
answer to this question. There remains no single coherent
program of molecular ecology. But it is the diversity of
approaches that make this an interesting enterprise, and in
this issue we try to highlight some distinct ways in which
research into the nature of genes and ecology can be tackled.
The papers brought together in this issue represent three
complementary approaches to the molecular genetic dissection of microevolution: i) ecological genetics; ii) molecular evolutionary genetics; and iii) association studies.
Ecological genetics refers to experimental manipulation of
the environment for a series of genotypes representing
both natural variation and carefully chosen mutations that
interfere with the biological process of interest. It brings
the long tradition of developmental and biochemical genetics into the realm of ecology, illustrating important ways
that these all to disparate disciplines can reinforce one
another. Molecular evolutionary genetics has also been in
the ascendant, but there is a new push to interpret patterns
of nucleotide changes (either within or between species)
in the context of ecological and genomic variables, from
geography to polyploidy, and to relate these patterns to
diverse gene ontologies. The term ‘association study’ is
used here as a catch-all phrase for the attempt to map genotype onto phenotype. It includes quantitative trait locus
(QTL) mapping with and without regard to the nature of
any candidate genes in QTL intervals, as well as the morenarrowly defined approach of associating segregating variation in specific genes with morphological variation within
and between populations of a species. The latter is now the
centrepiece of human disease genetics, but has yet to see
broad application in microevolutionary analysis.
If we place the three approaches on the vertices of a triangle as suggested in Fig. 1, it becomes apparent that the
intellectual overlap between them is mediated by another
triad of common links. Biogeographical variables such as
altitude and salt stress provoke the physiological and
behavioural adaptations that geneticists seek to explain,
while their presence is presumed to leave a hidden signature in patterns of nucleotide variation. Genetic dissection
and QTL mapping suggest candidate genes, whose identification — oftentimes borrowing from other systems — in
1110 M I C H A E L P U R U G G A N A N and G R E G G I B S O N
Fig. 1 A schematic overview of the three approaches to genes
and ecology described in the text, and the types of data that link
them. In the coming years, various ‘omics’ (genomics, proteomics,
metabolomics, for example) will feed into the approaches in a
wide variety of ways.
turn provides new insight into regulation and physiology.
SNPs are single nucleotide or other simple polymorphisms,
most of which have no functional consequence, yet nevertheless report the myriad evolutionary processes that
shape the distribution of molecular variation. A major
challenge for the coming decades lies in the mapping of
SNP onto QTL effects, and while this seems feasible
where a single change accounts for 10% of the phenotypic
variation, there is still debate as to whether more subtle
contributions can be detected. Missing from this collection
of papers is any explicit effort to use ‘omics’ in ecological
genetics. Nevertheless, it is clear that genome, transcriptome, proteome, and metabolome profiling will play an
increasingly central role in feeding each of the research
strategies represented here.
Animals, plants, and microbes are all represented in this
volume, and each of the research strategies finds application in each of the kingdoms. Perhaps the strongest demonstration of the potential for ecological genetic strategies
to illuminate fundamental physiological processes comes
from the plant side. Coberly & Rausher (2003) show how
greenhouse studies can be used to demonstrate a novel
pleiotropic function for a central biochemical pathway,
namely a contribution of flavonoids to the protection of
gametogenesis against heat stress. In doing so the authors
provide a plausible explanation for the failure of the a floral
pigmentation locus to attain high frequencies in natural
populations of Ipomoea, while a similar mutation in the w
locus is a common variant. Similarly, Traw et al. (2003) use
genetic crosses to investigate the crosstalk between salicylate and jasmonate-mediated defense pathways in response
to herbivore and bacterial pathogen exposure. Notions of
antagonistic pleiotropy and trade-offs can now be studied
at the level of gene expression and function, but only if genetic
background and environment are controlled carefully.
McKay et al. (2003) continue this theme in their comparison of mutational and segregating variance for drought
resistance through physiological avoidance of dehydration
and escape from drought by early flowering. They demonstrate how genotype–by–environment interactions are
likely to affect the maintenance and spread of variation
in field populations, and this point is taken up by Weinig
et al.′s (2003) mapping of QTL for resistance to and tolerance of herbivory in Arabidopsis. They highlight significant
seasonal effects on the detection of QTL, implying that
ecologists should be willing to move back and forth
between laboratory and field, recognizing that quantitative genetic analyses in these settings can have different
power and advantages in relation to a range of research
questions. On the animal side, Williams et al. (2003) describe
some laboratory experiments designed to mimic the effect
of rapid temperature fluctuation in the wild on wing
abnormalities in fruitflies, and show that rather than being
protective, HSP70 may under some circumstances sensitize the organism to stress-induced damage. Presumably
organisms must balance steady-state signalling intensity
against the possible benefits of protection upon induction
of chaperone proteins. Even such an apparently stark
physiological system as the heat shock response holds
surprises when ecology is integrated with genetics. Dixon
et al. (2003) take a more traditional, experimental approach
in surveying phenotypic variation for sperm precedence
among allopatric populations in two different species of
Drosophila. While studies of a variety of animal species
have demonstrated that sperm precedence often evolves
more rapidly than premating isolation between species,
this study of conspecifics demonstrates that this need not
be the case between races.
Genetic association studies have the goal of confirming
that the genes that are thought to matter, really do matter.
These candidate genes can arise from a variety of approaches:
fine scale recombination mapping; microarray analyses;
knowledge of development and physiology; and comparative genomics spring readily to mind. The conceptually
most direct association strategy is to ask whether a particular allele or haplotype is significantly more prevalent in
one phenotypic class than another. This is clearly the case
for a haplotype of the melanocortin receptor Mcr1 that
distinguishes two melanic classes of rock pocket mice in
Arizona studied by Hoekstra and Nachman (2003). They
show though, that similar cases of adaptive colouration
in New Mexico populations must involve different loci,
providing one of the first instances of genetic heterogeneity
for convergent evolution. Not all candidate loci, however,
show an association as predicted by both molecular
genetic and ecological studies. Garcia-Gil et al. (2003), in a
study of nucleotide polymorphism in the phytochrome
© 2003 Blackwell Publishing Ltd, Molecular Ecology, 12, 1109 –1112
M E R G I N G E C O L O G Y , M O L E C U L A R E V O L U T I O N , A N D F U N C T I O N A L G E N E T I C S 1111
genes in Pinus sylvestris, show very low levels of variation
that are not correlated with timing of budset in this
forest conifer. What is surprising is the very low level of
nucleotide variation in this species for these and other
genes.
The associations that are observed need not necessarily be direct, but may hint at population structuring
that underlies phenotypic differences. Along these lines,
McGovern and Hellberg (2003) report a very interesting
association in northern vs. southern populations of the
bryozoan Bugula neritina. In this species, larvae from
southern populations produce chemical deterrents to fish
predators that northern populations lack. Using COII mitochondrial markers, they show population differentiation
between northern and southern B. neritina populations.
Moreover, RNA markers indicate that only the southern
populations have an association with the γ-proteobacteria
E. sertula, which produces bryostatins that may act as the
fish deterrents. This study nicely illustrates the use of molecular markers to identify bacterial associations that confer
phenotypic advantages to host species.
Most complex traits are likely to be influenced by many
genes, and given the expense of genotyping the hundreds
of individuals required for statistical power, a first analytical step will often be the establishment of linkage in controlled crosses between morphologically divergent parents.
Voss et al. (2003) achieve this for one of two thyroid hormone receptors that they sampled in Ambystomatid salamanders in relation to metamorphic timing. They also find
strong genetic background effects, suggesting that both the
magnitude and direction of effects will be particular to
divergent lineages. Lexer et al. (2003) provide a more complicated application of QTL mapping technology in simultaneously detecting quantitative determinants of mineral
ion uptake and survivorship in a salt-tolerant species of
hybrid sunflowers, Helianthus paradoxus. They argue that
transgressive segregation facilitated rapid exploration of a
new ecological niche, namely a salt marsh, as a result of
selection for recombinant lines with favourable patterns
of complementary alleles affecting calcium uptake and
sodium exclusion. A very different type of candidate gene
study is presented by Miller (2003), who used maximum
likelihood methods to identify amino acid variants in the
rbcL gene of a clade of hot spring cyanobacteria that may
have been selected for thermotolerance. The author then
located the residues on the tertiary structure of the protein,
suggesting specific hypotheses for the molecular basis
of thermotolerance that can now be addressed in the
laboratory.
The sequence surveys presented in this special issue also
cover numerous topics with varying linkage to proximate
ecological causes. In a study comparing genes from the
selfing A. thaliana to the outcrossing A. lyrata, Wright et al.
(2003) explores the effect of mating system on levels of
© 2003 Blackwell Publishing Ltd, Molecular Ecology, 12, 1109–1112
molecular variation, which can have implications for the
dynamics of selection as well as strategies for candidate
association studies in these species. A more explicit discussion of the effect of environmental agents on the distribution of allelic variation comes from Watt et al.′s (2003)
ongoing study of Pgi polymorphism in Colias species. They
contrast the uniformity of allozyme frequencies in lowland
butterflies throughout Western North America with a
sharp discontinuity associated with altitude (but not geographical distance) in the alpine species, C. meadii. Duvernell
et al. (2003) also consider geography in their survey of clinal
variation associated with the methuselah locus in D. melanogaster, but with the twist that they are able to demonstrate
that two tandem duplicate paralogs experience different
selection pressures: only the more variable gene shows
the clinal distribution. They also argue that between 2%
and 10% of all fly genes may be subject to geographically structured selection, challenging the notion of panmixia in this cosmopolitan species. In another study of
tandem duplicates, the defense-related trypsin inhibitor
ATTI loci of Arabidopsis, Clauss and Mitchell-Olds (2003)
show how life history can strongly impact molecular
evolution, in so far as evidence for differential selection
pressure is only seen in the outcrossing species A. lyrata
and not in the heavily inbreeding A. thaliana. They also
make a case for subfunctionalization of trypsin inhibitor
protein domains on the basis of complementary patterns of
amino acid divergence.
Lawton-Rauh et al. (2003) add a further level of complexity in their consideration of the effect of allopolyploidy
on divergence of doubly paralogous copies of two floral
homeotic gene families in the Hawaiian silversword alliance. Their conclusion is that duplicate copies do experience different evolutionary trajectories, but that single
genes must be considered in the genomic context of levels
of duplication. By contrast, Riley et al. (2003) focus on a cassette of single-copy genes involved in Ras-mediated signal
transduction in Drosophila. They show that constraint is
highest for genes at the top of the biochemical pathway
and suggest that the molecular ecology of these genes
should be understood in light of biophysical models of
intracellular signalling — much as metabolic control theory
has been invoked to explain patterns of balancing selection
in enzyme pathways. Jovelin et al. (2003) add behavioural
ecology to the picture by developing chemosensation in
the soil nematode Caenorhabditis as a model quantitative
genetic study system. Much like the Wright et al. study in
Arabidopsis species, mating system is seen to be a major factor here as well; the outbreeding species C. remanei shows
more variation in the odr3 gene than does self-fertilizing
C. elegans.
One point that is clear from all of these surveys is that
different classes of gene experience very different selection
pressures. This is perhaps not surprising, but the point is
1112 M I C H A E L P U R U G G A N A N and G R E G G I B S O N
that despite two decades of molecular population genetics,
we are little closer to a general theory of the relationship
between genetic variation and phenotypic variation than
were the architects of the modern synthesis. As genomics
opens up, more and more opportunities for testing, not
just single genes, but whole complexes of genes, data will
accumulate with the potential for quite profound shifts
in understanding. However, knowledge will only accrue
when data is analysed and generated with increasingly
sophisticated experimental designs that incorporate
physiology and ecology into evolutionary genetics along
the lines hinted at in this issue.
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© 2003 Blackwell Publishing Ltd, Molecular Ecology, 12, 1109 –1112