The Power and Promise of Population Genomics
from genotyping to genome typing
Gordon Luikart, Phillip R. England, David Tallmon, Steve Jordan & Pierre Taberlet
Nature Reviews Genetics 4, 981-994 (2003)
articolo
completo
Conclusions
Does population genomics warrant recognition as a new discipline and
paradigm? On the one hand, population genomics is nothing new. Geneticists
have long realized that analysing only a few loci, or only one class of loci
(for example, allozymes), can provide an incomplete or biased view of the
genome and of population history or relationships. On the other hand, only
now is it becoming feasible to genotype vast numbers of marker loci (genome
typing) in many individuals and populations of non-model organisms. Many
statistical methods and computer programs have only recently become
available to test for outlier loci and to resolve locus-specific effects
versus genome-wide patterns in populations (for example, see Refs 34,37,39).
It is evident from the numerous publications that fail to test for outlier
loci before estimating population parameters - the interpretations of which
rest heavily on assumptions of neutrality - that the power and promise of
population genomics is not fully appreciated among population biologists and
geneticists. It can be argued that a conceptual shift that emphasizes a
genome-wide perspective is still needed. Embracing a genomic perspective
would improve population-genetic studies, including study design (for
example, strategic sampling across genomes, populations, phenotypes and
environments) and data analysis (testing for outlier loci). Recognition of
population genomics as a model could help promote genome-wide thinking,
which would improve evolutionary studies.
Molecular technologies are bridging the gap between genotyping and genome
typing, which promises to help unlock the secrets of adaptive evolution and
to refine inferences about population history. Population genomics will
advance our understanding of the genetic basis of fitness, adaptation and
speciation, in ways that were impossible only a few years ago. For example,
we will have genome-wide studies that estimate the number, map position and
relative contribution of the genes that are involved in inbreeding
depression, adaptation to extreme climates and the onset of reproductive
isolation. The population-genomic approach will speed the discovery,
conservation and use of economically important molecular variation in
agricultural species by identifying the genes that are important for drought
and disease resistance and for milk, meat and grain yield - but also by
improving estimates of population size and evolutionary relationships. By
providing candidate SNPs (as in Akey et al.35) population genomics will
contribute to the identification of disease-related genes in humans through
association studies.
The understanding of adaptive evolution is exciting and important, but
improved inference of population parameters and reconstruction of the
evolutionary history of populations will probably be the widest influence of
population genomics on population genetics. The population-genomic approach
will vastly improve the power and sensitivity of many molecular
investigations in conservation, ecology and population genetics by ensuring
that the assumption of selective neutrality is met by as many markers as
possible. Recent advances in molecular and statistical methodology have
bolstered the population-genomic approach; nonetheless, statistical methods
must mature before they can adequately and reliably deal with the molecular
genetic data explosion.
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