Understanding why some species have more genetic diversity than others is central to the study of ecology and evolution, and carries potentially important implications for conservation biology. Yet not only does this question remain unresolved, it has largely fallen into disregard. With the rapid decrease in sequencing costs, we argue that it is time to revive it.What evolutionary forces maintain genetic diversity in natural populations? How do diversity levels relate to
census population sizes (
Box 1)? Do low levels of diversity limit adaptation to novel selective pressures? Efforts to address such questions spurred the rise of modern population genetics and contributed to the development of the
neutral theory of molecular evolution—the null hypothesis for much of evolutionary genetics and comparative genomics
[1]–
[3]. Yet these questions remain wide open and, for close to two decades, have been neglected
[4]. Most notably, little progress has been made to resolve a riddle first pointed out 40 years ago on the basis of
allozyme data: the mysteriously narrow range of genetic diversity levels seen across taxa that vary markedly in their census population sizes
[5]. This gap in our understanding is glaring, and may hamper efforts at conservation (e.g.,
[6]).
Box 1. Glossary
Allozymes: Allelic variants of a protein, often detected by differences in gel electrophoresis.
Balancing selection: Natural selection that maintains variation longer than expected from genetic drift alone.
Census population size: The actual number of individuals in a population; methods to estimate this number vary depending on the species and may involve aerial, transect, or capture/recapture counts.
Diversity levels: The measure used here is the probability that a pair of randomly chosen haplotypes differ at a site.
Effective population size: The size of an idealized population with some of the same properties as the actual one, e.g., the same rate of genetic drift. Under simplifying assumptions, notably a constant population size and no population structure, this parameter can be estimated from observed diversity levels, given an independent estimate of the mutation rate.
Fluctuating selection: When the fitness of an allele changes over time or over space.
Genetic draft: A dramatic loss of genetic variation due to strong, frequent selection at nearby sites
[8].
Genetic drift: In a finite population, the loss of genetic variation due to the random sampling of gametes at each generation.
Local adaptation: Adaptation to a particular environment that is not shared by the entire species.
Nearly neutral theory of molecular evolution: A modification of the neutral theory, in which many mutations are slightly deleterious, rather than strictly neutral or strongly deleterious
[75].
Neutral theory of molecular evolution: The theory that most genetic variation seen within populations and between species is neutral, and most mutations are either neutral or strongly deleterious
[11].
Panmixia: Random mating among individuals, and hence no population structure.
Phylogenetically independent contrasts: A statistical method that allows one to compare properties of species controlling for their evolutionary relationship.
Purifying (negative) selection: Natural selection that favors the common, fitter allele against rare, deleterious alleles.
Selection at linked sites: Selection at sites linked to the locus under consideration, which can affect the population dynamics of alleles at that locus.
Silent sites: A general term for synonymous, intronic, and intergenic sites—all sites at which mutations do not change an amino acid.
Variation-reducing selection: Selection that leads to a decrease in diversity at linked sites.With the recent technological revolution in sequencing, the data needed to address questions about the determinants of genetic diversity levels are now within reach. As a first step towards reviving these questions, we compile existing estimates of nuclear sequence diversity. These data are highly preliminary, but they underscore how little is known about the narrow span of diversity levels across species or why some species maintain more genetic variation than others
[5],
[7],
[8], and they offer a glimpse of trends that may be worth pursuing.
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