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22 Oct 2001

Chapter 3: GENETIC ANALYSIS OF FITNESS

Bill Sherwin and Craig Moritz

SUMMARY:

  • One important aspect of conservation genetics is to retain genetic variants that assist in continued evolution of species in their changing environment and ecological roles. This should direct choice of appropriate genes or traits for management and monitoring. The most appropriate traits are of course, those whose genetic variation will affect lifetime fitness in the short-or long-term future, in a changing environment. Although it is difficult to specify exactly which loci are appropriate, some generalizations can be made. First, fitness traits tend to be multi-factorial – affected by multiple loci and the environment.




  • Genetic architecture is the way in which multifactorial traits are controlled. This includes the number of underlying loci, their physical arrangement (ploidy, linkages), their biochemical interactions (regulatory, protein-protein, and environment-gene), and the resulting pattern of additive and non-additive interactions such as dominance and epistasis. The genetic architecture is far from static, since it can alter in response to mutation at any of the contributing loci, recombination, environmental changes, and random genetic changes. Each of these can have substantial effects on multifactorial traits, especially under conditions that threatened species are likely to experience, such as periods of environmental stress or small population size.




  • Natural selection can appear to act at different levels from the individual locus through to complex traits such as disease resistance and reproductive output. The apparent type and direction of selection may differ at these levels, even in the same system of interacting loci. There can also be selection for traits to be more or less sensitive to variation at other loci or in the environment. Limited studies suggest that there is poor correlation between variation of different types, so the choice of appropriate suites of surrogates at different levels is an important direction for conservation genetics research.




  • Ideally, conservation managers would monitor and manage the genetic variance of lifetime fitness, but this strikes three problems: first, it is difficult to analyze multifactorial genetic variation in wild populations; second, it is difficult to analyze total fitness, and finally the analysis would be restricted to the current population. The first problem may be alleviated somewhat by use of molecular techniques, although the current methods are restricted to populations with an extremely wide range of relatedness values; better methods may come from molecular reconstruction of wild pedigrees




  • In the absence of a generally applicable way of measuring fitness and its genetic variation, there is a need for judicious choice of a suite of traits and loci to monitor, as representatives of the types of selection-related variation to be managed. There have been various suggestions about how to identify specific traits or loci for monitoring, but none have been validated. Maybe traits under strong selection could be identified by their insensitivity to environmental variation. It would also be possible to monitor variation in suites of single loci chosen for reasons such as their known selective importance or significance in metabolic networks



  • Heritability is important for short-term response to selection, but may be very low for fitness related traits. Additive genetic variance or the related measure called evolvability is what conservation genetics strives to maintain, and is often high for fitness related traits, so monitoring and maintenance is a worthwhile exercise. These measures do not generally show good correlation with molecular measures of variation.




3.1 Natural selection and conservation


Sticklebacks (Gasterosteus spp) are small fish that live in lakes in North America. Two closely related, hybridizing taxa prefer benthic and open habitat respectively ({Schluter, 1996 #457}). When individual fish were forced to live benthically or in open water, the growth rate reflected their origin (Figure 3.1a, {Schluter, 1996 #785}). While this is not surprising from a short-term point of view, it raises the question: “Since these taxa can hybridize, why don’t we see the emergence of a species with genes for high growth rate in BOTH habitats?”. It is likely that such a species would out-compete both of the other taxa. Or to put the question more generally: What are the limits to adaptation, and what role does genetic variation play in this? A full answer to that question would tell us everything that we need to know as conservation geneticists. This chapter will review some of the knowledge that we already have, and its implications for conservation.

Figure 3.1 (a) Mean growth rate (+ SE) of fish from open water (limnetics) and fish from the benthos, and their hybrids, in enclosures in open water or in the littoral zone. {Schluter, 1996 #785}




Figure 3.1 (b) This is the same data as Figure 3.1 (a) re-drawn to emphasise differences between benthic and limnetic (dashed line) genotypes in the same habitat


Surprisingly, a great deal of conservation genetics work focuses on genes that appear unrelated to adaptation. Conservation genetics is sometimes accused of being schizophrenic in its treatment of genetic variation {Hedrick, 1996 #25}. On the one hand, the field is built upon the assertion that higher levels of genetic variation allows adaptation to prevailing environment(s) and therefore reducing the chance of extinction of populations (Chapters 9&10). Genetic variants that affect fitness in a particular environment are said to be subject to natural selection (Box 3.1). Essentially, genetic diversity matters for conservation because of selection.


Box 3.1 Natural selection


Natural selection occurs when there are genetic variants that result in phenotypic differences between individuals, and these differences result in differences in survival or reproduction in the particular environment({Hartl, 1997 #762; Hedrick, 2000 #761}). (Survival and reproduction are sometimes combined together and called “fitness”). A natural consequence of the higher fitness of individuals carrying certain genetic variant is that these variants will increase in number relative to others. This process is called natural selection, and it generally results in improved adaptation to the current local environment.


Natural selection can only occur if the variants have some genetic basis. For example, the figure below shows a population in which short individuals have short offspring, because they carry certain alleles. If the short individuals are less able to escape predators, then the frequency of short individuals will go down each generation, as short individuals are eaten before they can pass on the allele for shortness. In the illustration below there are initially an equal number of tall and short individuals, but 2/3 of the short individuals die before they reproduce, compared to only 1/3 of the tall individuals. As a result, after each survivor reproduces twice, there are more tall individuals than short. The same result would occur if the “doomed” individuals stayed alive but did not reproduce.





As a result of the selection, the population is now better adapted to the predator-filled environment, being composed mostly of tall individuals who escape well.

Note that the effectiveness of the selection depends entirely on the presence of genetic variation for the trait concerned: if there were no alleles for shortness and tallness, then the selective predation would not affect the number of short and tall individuals next generation.




Thus little response to selection would occur, and the population would not show adaptation to the selective predation by gradually becoming taller. This is because the height of the prey is non-genetic and so the selected tall parents are no more likely to produce tall offspring than the short parents.


We say that individuals which have greater survival or reproduction have higher fitness. Fitness is often expressed as total reproductive output over some time period, such as an individual’s lifetime. Often we can only measure components of fitness, such as survival per year, or reproduction per year. Where fitness is genetically determined, there can be natural selection. Fitness can also be determined non-genetically, in which case natural selection cannot occur, despite selective death or reproductive failure. In the case above, non-genetic variation in fitness could derive from environmental variation, such as greater growth in individuals that find more food, or by chance during development.


There are many types of natural selection known and detected ({Endler, 1986 #77;), and an even greater a wealth of names for different types. In some cases these names reflect different processes which the conservation manager might strive to maintain, but in other cases, they do not. The typeshown in the first diagram above, which favours one allele at the expense of another, is called directional selection, so-called because of the gradual loss of one allele (eg, for shortness). Some authors grace directional selection with other names such as positive (referring to the favoured allele) or negative or purifying (referring to the disadvantageous allele); these are simply names for different aspects of the same directional selection process, since selection can only occur relative to other genotypes. Rather confusingly, ”positive selection” is also sometimes used to refer to balancing selection.


In a single-locus case, selection can be expressed as the relative fitness (eg, proportions of individuals that survive) of the different genotypes. The table below shows fitnesses for directional selection on a diploid locus. The selection coefficient “s” shows the additional deaths, relative to the fittest genotype (Z1 Z1); “h” expresses any dominance – if h is zero, then Z2 is only a disadvantage in the homozygote, not in the heterozygote.





GENOTYPEZ1 Z1Z1 Z2Z2 Z2Directional selection11-hs1-s

Balancing selection is qualitatively different from directional selection, in that it acts to maintain variation; there are several possible processes that can do this, and they each have a separate name. Three well-known sub-types of balancing selection are overdominance in which heteroygotes are at a selective advantage to homozygotes, frequency-dependent selection in which rare alleles are at an advantage, and patchy selection which varies spatially or temporally (whether the latter is classified as balancing selection depends upon the scale of observation) .


The table below shows fitnesses for overdominant balancing selection on a diploid locus. The selection coefficients s1 and s2 express the reduced fitness of the two extreme genotype (homozygotes) relative to the heterozygote


GENOTYPEZ1 Z1Z1 Z2Z2 Z2Overdominant balancing selection1-s111-s2

One of the earliest examples of overdominance in a natural populations was human Sickle-cell anaemia in malarial areas. This disorder is caused by homozygosity for a variant beta-globin chain (HbBs/HbBs); in the absence of medical intervention, affected individuals have a shortened life-span because their haemoglobin has a tendency to form long crystals inside the red cells, which then assume a sickle shape and block capillaries. On the other hand, homozygotes for the common allele worldwide (HbBa/HbBa) not infrequently die from the effects of malaria. In malarial areas, heterozygotes (HbBs/HbBa) have the highest survival rate, only rarely suffering from malformed red cells, but having enhanced resistance to malarial infection, because any parasitised cells sickle and are broken down. There are few examples of overdominance at single loci, possibly because of the difficulty of measuring selection in natural populations ({Curtsinger, 1994 #842}), but many more examples in loci of small effect underlying quantitative traits ({Falconer, 1996 #91}).


The following figure shows single-locus selection coefficients from {Endler, 1986 #77}.






End Box 3.1


On the other hand, most models of loss of genetic variation in small or fragmented populations are based on what is called neutral variation {see Box 2.*} - genetic variants which do not affect reproduction or survival and are therefore not under selection ({Franklin, 1980 #68} {Falconer, 1996 #91}). Additionally, most experimental investigations in conservation genetics use marker genes that are likely to be neutral, and thus may be poor representatives of the selective variants that we aim to conserve. Unfortunately, during events such as population crashes, selective variation is likely to respond differently to neutral variants. This will be discussed further in Chapters 9 and 10, but the difference in response is for two reasons - firstly because of the action of selection during and after the crash, and secondly because of other differences between the loci. For example, relative to highly mutable markers such as microsatellites, other neutral loci with lower mutation rates are expected to have less alleles. As well as this, loci under balancing or directional selection may have more or less variants than neutral expectations, respectively. Finally, the markers are usually a set of independent loci, whereas traits such as tallness or reproductive success are often the outcome of complex interactions between many loci and environmental effects on development.


There are several ways out of this dilemma:


(1) We can recognise that some allelic variants may have very small differences in fitness, the selection coefficient, “s”. Genetic variants with small selective coefficients may be reasonably modelled by neutral methods. Ohta {Ohta, 1973 #739} suggested that selected variants may behave as if neutral when s < 1/(2Ne), where Ne is the effective population size (see Ch5). However, variants with higher selective coefficients would not be reasonably approximated by neutral models except in very small populations, and yet these are likely to include many of the most important variants to be conserved in a management program.


(2) We can suppose that markers may be neutral for much of the time and only of selective importance in particular environments (Thoday) {Thoday, 1962 #740}, in which case neutral models could be a reasonable description of their behaviour during a population crash. This explanation is probably true in some cases, but there may also be cases in which the sporadic selection is sufficient to prevent neutral behaviour of the variants, especially if harsh conditions which result in selection coincide with times of population crashes, as seemed to be the case in Keller’s (199*) work on sparrows, where selection against homozygous individuals was particularly intense after a fire.


(3) We can investigate the behaviour of selected traits and loci in large, declining, and small populations, and see in what ways this differs from neutral loci. This option seems so sensible that one wonders why it is not done more often, until one realises that selection does not act directly on alleles or loci - it acts on the phenotypes that they produce, such as the ability to withstand different temperatures. Each individual has its phenotype formed by the interaction of one or more loci and the environment; an individual whose phenotype is better matched to the current local environment will survive or reproduce better than those with alternative alleles. To work on selected loci we must make a connection between allelic variants, their phenotypic effects, and the consequences for survival and reproduction; this is usually time-consuming and impractical.


In this chapter, we will first review the evidence that some single loci may have a major effect on fitness, and survey methods for identifying these loci. We will then take the opposite view, and see how traits such as survival, or fitness itself, can be analysed genetically, to establish whether there is genetic variation for the trait, or even identify the loci responsible, called “quantitative trait loci”, or “QTLs”. With this background, we will then explore the ways that organisms can respond to environmental change. The environment has two avenues of influence, since it can both affect the way that a trait is expressed (“plasticity”), as well as affecting the fitness of individuals that express the trait. The major task for a conservation geneticist is to identify useful indicators of the ability to respond to environmental change, and the second half of the chapter will be devoted to this quest, first for single populations, and then for subdivided populations.

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