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1. Why is genetic diversity important?

All living organisms carry a genetic blueprint. This is so regardless of whether they are plants, animals, or fungi, whether they are short- or long-lived, and whether they reproduce sexually or clonally. Therefore, to the extent that restoration deals with living organisms, genetics are part of the picture. Although the basic principles underlying restoration genetics may be familiar, to date surprisingly little attention has been devoted to genetic considerations in restoration practice. The purpose of this Restoration Science and Policy Paper is to outline some considerations that restoration designers and managers should be aware of, and to identify more detailed resources that may be useful in practice.

1a. Genotypes partly determine organisms' physical form and function.

Biologists refer to two basic expressions of variation, the genotype and the phenotype. The genotype is the genetic code of an organism; in organisms with nucleated cells (most multi-cellular plants, animals, and fungi), the essential code is found in the nucleus of each cell. Additional genetic codes reside in other components of the cell, such as mitochondria (in animals) and chloroplasts (in plants). An organism's genotype consists of a large number of genes (50,000-100,000 in a typical vertebrate), which can be at multiple sites (loci) on chromosomes. Genes have a variety of functions, the most important of which is to code for the production of specific amino acids, which are ultimately used to synthesize proteins. In most higher plants and animals (but not fungi, bryophytes, and many marine invertebrates), the adult phase has two copies of each gene, one derived from each parent. When the two copies are the same, the individual is homozygous for that gene; if the two copies are different, the individual is heterozygous for that gene. The various forms of a gene are referred to as alleles; when these forms are identical across a population, the gene is considered monomorphic, and if more than one allele exists the gene is considered polymorphic.

Phenotype is the expression of these genes as a living organism in a particular environment, and is influenced by environmental context at every level from the cell to the whole organism. It is frequently very difficult to separate variation in an organism's traits with a genetic basis from traits that are phenotypically variable; mistakes are commonly made both ways (assuming a genetic basis when observed variation is really phenotypic plasticity; underestimating subtle genetic effects on traits that are assumed to be simply "phenotype"). For example, a plant growing in a poor environment might end up having a small and stunted phenotype, despite having "good" genes. This does not mean that genetic variation is not important to the fitness of individuals or populations. Both the environment and the genes will ultimately contribute to restoration success, but steps to ensure an optimal genetic makeup of a population are commonly overlooked.

Examples abound in the scientific literature illustrating how genetic composition affects the form and function of organisms (Hamrick, Linhart, and Mitton 1979; Hedrick 1985; Primack and Kang 1989; Rehfeldt 1990; Allen, Antos, and Hebda 1996; Hartl and Clark 1997). In fact, the recognition of genetic variation among individuals was a primary insight that led to the formulation of evolutionary theory as we know it today (Freeman and Herron 1998). Genes regulate body size, shape, physiological processes, behavioral traits, reproductive characteristics, tolerance of environmental extremes, dispersal and colonizing ability, the timing of seasonal and annual cycles (phenology), disease resistance, and many other traits (Raven, Evert, and Eichhorn 1986). Thus, to ignore genetic variation in ecology is to ignore one of the fundamental forces that shape the biology of living organisms. From a restoration perspective, organism and population genetics are fundamental considerations in the design, implementation, and expectations of any project, whether or not explicit consideration is given to the genetic dimension.

1b. Genetic diversity helps organisms cope with current environmental variability.

Organisms exist in environments that vary in time and over space. Such variation is often described in terms of the natural or historic range of variability (NRV, HRV) in environmental conditions such as weather, disturbance events, resource availability, population sizes of competitors, etc. (White and Walker 1997). If a group of organisms (say, a population of species X) were to live in a completely stable physical and biological environment, then a relatively narrow range of phenotypes might be optimally adapted to those conditions. Under these circumstances, Species X would benefit more by maintaining a narrow range of genotypes adapted to prevailing conditions, and allele frequencies might eventually attain equilibrium. By contrast, if the environment is patchy, unpredictable over time, or includes a wide and changing variety of diseases, predators, and parasites, then subtle differences among individuals increase the probability that some individuals and not others will survive to reproduce -- i.e., the traits are "exposed to selection." Since differences among individuals are determined at least partly by genotype, population genetic theory predicts (and empirical observation confirms) that in variable environments a broader range of genetic variation (higher heterozygosity) will persist (Cohen 1966; Chesson 1985; Tuljapurkar 1989; Tilman 1999).

Examples of traits with a genetic basis for tolerance of environmental variation important in restoration work include tolerance of freezing, drought or inundation, high or low light availability, salinity, heavy metals, soil nutrient deficiencies, and extreme soil pH values in plants; resilience to fluctuating temperature, dissolved oxygen, and nutrient availability in aquatic organisms; and resistance to novel diseases in all groups of organisms (Huenneke 1991). For example, if all individuals in a population are the same genotype with limited drought tolerance, then a single climatic event may destroy the entire population. Plant populations often include individuals with a range of flowering or emergence times. For instance, Great Basin shrub populations include individuals that leaf out and flower over a period of weeks, increasing the likelihood of persistence of the population through periods of unusually early or late growing conditions. Knapp et al. (2001) documented flowering periods in a population of individual blue oak trees and found that trees initiated flowering over a period of a month in the spring. Such variability could potentially be adaptive, since it is more likely that at least some trees in the population will flower during warm sunny periods when wind pollination is most successful.

A diverse array of genotypes appears to be especially important in disease resistance (Schoen and Brown 1993; McArdle 1996). Genetically uniform populations (such as highly inbred crops) are famously vulnerable to diseases and pathogens, which can (and do) decimate populations in which all individuals are equally vulnerable. Such uniformity also predisposes a population to transmit disease from one individual to another: instead of having isolated diseased individuals, nearly every individual may be exposed to disease by direct contact or proximity. More diverse populations are more likely to include individuals resistant to specific diseases; moreover, infected individuals occur at lower density, and thus diseases or pathogens may move more slowly through the population.

Finally, genetic variation is a factor in competition among individuals in real ecological communities. Traits with a genetic basis such as flower size are key factors in competition among individuals. Among animals, behavioral traits may regulate interspecific competition. Since organisms make energetic or life history tradeoffs among traits (for example, allocating energy between growth and reproduction), genetic variability is an important factor in how populations function (Koyama and Kira 1956; Thompson and Plowright 1980; Fowler 1981; Gurevitch 1986; Goldberg 1987; Manning and Barbour 1988; Welden, Slauson, and Ward 1988; Grace and Tilman 1990; Tilman and Wedin 1991; Pantastico-Caldas and Venable 1993; Wilson and Tilman 1993; Delph, Weinig, and Sullivan 1998).

1c. Diversity within populations reduces potentially deleterious effects of breeding among close relatives.

In addition to its adaptive value at the population level, genetic variation (or its lack) within individuals can affect their survival and performance. When both copies of a gene (in a diploid organism) are identical (i.e., when an individual is homozygous at that gene or locus), the expression of that gene may include traits that are less beneficial to survival or reproduction in particular circumstances. This may lead to physiological or behavioral problems of genetic origin, such as malformed physical structure, poor biochemical balance, improper organ formation and function, altered social behavior, and susceptibility to disease (Chai 1976).

Homozygosity at key gene loci is a common result of inbreeding, which is sexual reproduction among closely related individuals. Small populations and species that do not disperse well (or are constrained by a fragmented landscape from exchanging genes with other populations) can be particularly susceptible to inbreeding depression, which is reduced overall survival and reproduction of organisms with low heterozygosity. Inbreeding depression arises from a variety of causes, including expression of unfavorable or deleterious alleles, and often leads to lower survival and birth or reproductive rates (Templeton 1991; Meffe and Carroll 1994; Husband and Schemske 1996).

Heterozygosity is not always beneficial, nor does inbreeding always have adverse effects. In some circumstances, a population may be so well adapted to its local circumstances that introducing alleles from other populations actually reduces its performance (outbreeding depression) (Templeton 1991). Paradoxically, organisms can experience outbreeding depression for some traits, while suffering the effects of inbreeding depression for other characters. Many organisms (particularly plants) have evolved breeding strategies, such as self-pollination, that allow successful persistence in small populations without apparent short-term effects of inbreeding depression.

1d. Genetic diversity is the primary basis for adaptation to future environmental uncertainty.

Finally, genetic variation holds the key to the ability of populations and species to persist over evolutionary time through changing environments (Freeman and Herron 1998). No organism can predict the future (and evolutionary theory does not require them to), nor can any organism be optimally adapted for all environmental conditions. Nonetheless, the current genetic composition of a species influences how well its members will adapt to future physical and biotic environments.

Consider, for example, the response of a population of plant Species A to a period of rapid climate change. Changes in climate are reflected locally in altered annual rainfall and its seasonal distribution, changes in annual mean maximum and minimum temperatures and their seasonality, changes in prevailing wind direction and speed, and many other factors. These changes cause the zone of suitable climate for Species A to shift geographically. Populations with a diverse array of optima for these climatic conditions (i.e., some individuals that are slightly more cold or heat tolerant, etc.) are more likely to persist, because some individuals will survive the new conditions and reproduce. If suitable climate zones shift across the landscape, seeds of some individuals may be dispersed into the new location and find good conditions for growing. In this manner, the population can "migrate" across the landscape over generations. By contrast, populations that have a narrower range of genotypes (and are more phenotypically uniform) may simply fail to survive and reproduce at all as conditions become less locally favorable. Such populations are more likely to become extirpated (locally extinct), and in extreme cases the entire species may end up at risk of extinction. For example, the Florida Yew (Torreya taxifolia) is currently one of the rarest conifer species in North America. But in the early Holocene (10,000 years ago), when conditions in southeastern North America were cooler and wetter than today, the species was probably widespread. For reasons that are not completely understood, T. taxifolia failed to migrate northward as climate changed during the Holocene. Today, it is restricted to a few locations in the Apalachicola River Basin in southern Georgia and the Florida panhandle.

As the T. taxifolia story illustrates, once species are pushed into marginal habitat at the limitations of their physiological tolerance, they may enter an "extinction vortex," a downward cycle of small populations, reduced genetic variability, reduced ability to adapt to novel conditions, leading to further reductions in population size, and so on (Shaffer and Samson 1985; Gilpin and Soulé 1986). Reduced genetic variability is a key step in the extinction vortex.

Next: How is genetic diversity distributed in natural populations?