Conservation Genetics

1. Conservation Genetics • Why should we be concerned with genetic diversity when more severe threats threaten entire systems? • First, the rate of evolutionary change in a population is proportional to the amount of genetic diversity available • Fundamental Theorem of Natural Selection

2. Conservation Genetics • Second, diversity as measured at the level of genes or quantitative genetic traits represents the primary level of biodiversity • Every biochemical product, every growth pattern, every instinctive behavior, every color morph is encoded in the in the ‘genetic library’ of each species

3. Conservation Genetics • Third, there are many conservation challenges that benefit from the guidance and direction that genetic data, collected and interpreted with the constructs of sound population genetic theory, can furnish

4. Conservation Genetics • The basic link from genetics to conservation is that of small populations, which tend to lose genetic diversity over time • The power of conservation genetics comes in the form of tools which allow one to identify unique evolutionary lineages, monitor dispersal movements, estimate population size, or trace genetic changes through time

5. Conservation Genetics • In this chapter we will go over the principles of genetics and how they may aid in conservation • Next, we will provide a board overview of contemporary efforts and controversies in conservation genetics

6. Conservation Genetics

7. Genetic Variation • A species’ pool of genetic diversity exists on 3 levels: variation within an individual, differences among individuals w/in a pop(n), differences among popuations

8. Conservation Genetics

9. Conservation Geneticsvariation w/in the individual • Chromosomes consist of long sequences of nucleotides, some of which code for molecules that create the structure and the physiological functions of an organism • A gene represents a specific segment of DNA of a specific chromosome pair that (1) codes for the primary structure of proteins

10. Conservation Geneticsvariation w/in the individual • (2) codes for the formation of ribonucleic acid (RNA), or (3) regulates the location and time of gene expression • The majority of genetic material does not code for any product (thus not subject to NS, unless linked) • This is termed neutral genetic variation and is frequently analyzed when examining evolution change…problem?

11. Conservation Geneticsvariation w/in the individual • One such problem is you may be asking questions pertaining to adaptive variation (i.e. genes under selection) • So while we are very concerned with maintaining the adaptive variation, we usually don’t know where in the genome that exists (see Box 11.1)

12. Conservation Geneticsvariation w/in the individual • A physical or behavioral character (phenotype) can be expressed directly as a trait may be entirely due to genotype (e.g. eye color) or environment (nutritional regime), but more likely a combination of both (e.g. skin color) • Quantitative genetics are helpful in determining how much of the phenotype is attributable to genes (Box 11.1)

13. Conservation Geneticsvariation w/in the individual • The ultimate source of variation is mutation • Mutations range from a change in a single base, deletion or duplication of a group of nucleotides, to large-scale changes such as deletion, duplication, or translocation of large parts of the chromosome (or the entire chromosome) • Are they good, bad, or ugly?

14. Conservation Geneticsvariation w/in the individual • Recombination is another source of variation, requires sexual recombination • At the population level, a given locus is either monomorphic (both copies always found without variation) or polymorphic (two or more types of the alleles possible) • The overall level of heterozygosity (the proportion loci in an individual that contains alternative)

15. Conservation Geneticsvariation w/in the individual • What is the value of focusing on genetic variation within individuals? • First, heritable genetic variation is the basis for evolutionary change and the individual is where NS operates • Second, the individual is where problems associated with inbreeding occur

16. Conservation Geneticsvariation w/in the individual • Third, knowledge of individual genotypes may be important in some captive breeding programs • Finally, genetic variation is always measured in individuals and can only be estimated for collections (i.e. populations) through statistical summaries

17. Conservation Geneticsvariation among individuals • Variation among individuals, or pop-level variation, consists of the types of alleles present and their relative frequencies across all members of a population considered together (the gene pool)

18. Conservation Geneticsvariation among individuals • Which has the highest mean Hp? Why are other populations (e.g. Litchfield) so low?

19. Conservation Geneticsvariation among individuals • Are gene frequencies constant? • They frequently change over time due to mutation, NS, and random processes such as genetic drift, non-random mating, small pop size, and I & E (gene flow)

20. Conservation Geneticsvariation among individuals • There have been a number of attempts to link ecological characteristics ad levels of genetic variation • Not surprisingly, widespread organisms tend to have higher levels of genetic diversity while small range, small populations or large body size are correlated with low diversity (see Table 11.3)

21. Conservation Geneticsvariation among individuals

22. Conservation Geneticsvariation among populations • Species rarely exist as single, randomly interbreeding, or panmictic populations spread across large areas (or there is structure within and among populations)

23. Conservation Geneticsvariation among populations • Diversity is variable, but also higher than any individual site

24. Conservation Geneticsvariation among populations • Thus, genetic diversity among a set of populations consists of within-population diversity and among-population divergence • Thus a simple genetic diversity model is: where HT = total genetic variation, HP= average diversity within pop(n), and DPT= average divergence among pop(n) HT = HP + DPT

25. Conservation Geneticsvariation among populations • Divergence may result from a number of processes including random processes (e.g. founder effects, genetic drift, episodic population bottlenecks) and from local selection • Again, important to remember we can quantify within and among-population diversity components

26. Conservation Geneticsvariation among populations • RCWO has mean heterozygosity of 7.8% which is typical • Of total variation, 14% consists of among- and 86% consists of within pop(n) • The among is higher than most species, which tend to be more site-specific than many other sp

27. Conservation Geneticsvariation among populations • Ecological correlates can subsequently influence genetic structure by influencing movement • E.g. white-tail deer vs. Alpine Ibex

28. Conservation Geneticsvariation among populations • One frequent question is if current mortality rates are negatively impacting the health of the population (use previous approach) • The type of genetic marker has issues: molecular markers are usually neutral but are used as a proxy for adaptive variation…(because gene not known) • Adaptive divergence may not be the same as adaptive variation

29. Conservation Geneticsvariation at the metapopulation • We have utilized the metapopulation paradigm to describe populations on a fragmented landscape • By definition, metapopulations interact, thus influencing the genetic structure of the populations • Metapopulations lose genetic variation more rapidly than a single large pop(n)

30. Why is Genetic Diversity Important? • The amount of adaptive variation in a population should be related to the health of a population, or to its ability to withstand stresses and challenges • There have been a number of general correlates of genetic variation among populations (Table 11.5)

31. Why is Genetic Diversity Important?

32. Why is Genetic Diversity Important? • There is mixed results on the actual importance of adaptive genetic diversity • There is no absolute value of heterozygosity that indicates a population’s health, although it may be correlated with individual fitness (taxonomic comparisons see Table 11.4)

33. Why is Genetic Diversity Important? • However, while the absolute level of heterozygosity may not provide a clear level of risk, loss of it does indicate serious problems • E.g. low RS following inbreeding is usually accompanied by low HP • There is some evidence • E.g. Drosophila and inc. salinity & HP

34. Why is Genetic Diversity Important? • Among-population divergence may play a critical role in local fitness and population survival • First, pop(s) may be locally adapted (?) • Second, coadapted gene complexes may arise in local pop(s) (Essay 11.1)

35. Forces that Affect Genetic Variation w/in Pop(s) • When making predictions about likely changes in allele frequency, not the difference between N and Ne (effective populatiton size) • Ideal is large, panmictic, 1:1 sex ratio

36. Forces that Affect Genetic Variation w/in Pop(s) • Mutations are the ultimate source of new genetic variation with mutations being rare and most being neutral • This is generally not a problem until popo(s) become small…why? • The gradual accumulation of deleterious mutations results in the mutational meltdown (mean viability lowered, and pop(s) become smaller, with fixation)

37. Forces that Affect Genetic Variation w/in Pop(s) • Genetic drift is the random fluctuation of gene frequencies over time due to chance alone • Because of sexual mating (and only one copy being passed on) there is a high chance that not all alleles will not be passed on • Drift can occur very quickly in small pop(s)

38. Forces that Affect Genetic Variation w/in Pop(s) • Average % of genetic variance remains over 10 generation in a theoretical, idealized pop(n) at various genetically effective pop(n) size Ne

39. Forces that Affect Genetic Variation w/in Pop(s) • Ultimately, in any small pop(n) is genetic drift will result in the fixation of one allele at 100% • The likelihood of that occurring is equal to the initial allele frequency (e.g. 0.8)

40. Forces that Affect Genetic Variation w/in Pop(s) • When a demographic bottleneck occurs, the magnitude of the genetic loss depends not only on the size of the bottleneck but also on the growth rate of the population afterward

41. Forces that Affect Genetic Variation w/in Pop(s) • Recovery is quickest when pop(s) have a high growth rate (r) and when bottleneck is less severe

42. Forces that Affect Genetic Variation w/in Pop(s) • Rare alleles are lost from small, isolated populations

43. Forces that Affect Genetic Variation w/in Pop(s) • Gene flow is the movement of genes from one population to another • Measuring gene flow is problematic • Not all breed • Cannot account for historical dispersal • Similarity could be recent ancestor

44. Forces that Affect Genetic Variation w/in Pop(s) • Inbreeding can lead to decreased fitness (inbreeding depression) either by the expression of deleterious recessive alleles or the loss of heterozygosity

45. Forces that Affect Genetic Variation w/in Pop(s) • Data from domestic animals indicate a 10% increase in inbreeding coefficient will result in a 5-10% decline in ind RS

46. Forces that Affect Genetic Variation w/in Pop(s) • Lab studies of land snails and white-footed mice were inbred and outbred and released… • Results of WFM

47. Forces that Affect Genetic Variation w/in Pop(s) • Not all low levels of heterozygosity or even inbreeding should be alarming • Some natural populations have apparently experienced low levels of inbreeding for several generation with little to no harm

48. Forces that Affect Genetic Variation w/in Pop(s) • Outbreeding depression can

49. Forces that Affect Genetic Variation w/in Pop(s)

50. Forces that Affect Genetic Variation w/in Pop(s)