Conservation Genetics and Phylogeny

1. Conservation Genetics and Phylogeny Dr Christopher L. Parkinson Parkinson Web Site cparkins@pegasus.cc.ucf.edu

2. This short course will serve as an introduction to the field of conservation genetics and phylogenetics. • Conservation of genetic diversity. • Genetic variation provides the raw material for adaptation, and is therefore critical to continued evolutionary change. • Many ongoing, human-associated changes to the environment erode genetic diversity at the population level. • founder effects, • genetic drift in small populations, • inbreeding, • altered patterns of gene flow.

3. Modern tools of molecular genetics • population structures • breeding systems • evolutionary relationships among taxa. • Apply insights gained from modern genetic techniques to improve the effectiveness of traditional approaches to conserve biological diversity.

4. TIME AND PLACE: • Lecture: • Web Site: http://biology.ucf.edu/~clp/Courses/colombia/powerpoints.php • Username: congen • Password: evolve

5. Assignments READINGS: Readings are very important; please have all papers/book chapters read prior to lecture.

6. Conservation Genetics • The application of genetics to preserve species as dynamic entities capable of coping with environmental change. • Encompasses: • Genetic mgmt. of small populations • Resolution of taxonomic uncertainties • Defining mgmt. units w/in species • Use of molecular genetic analyses in forensics and understanding species biology

7. Sixth Extinction • Mass extinctions vs background extinction • 5 mass extinctions based of paleontology • KT boundary most recent 65 mya • Dinosaurs • humans

8. Conservation genetics motivated by the need to reduce current rates of extinction and preserve biodiversity • Why conserve biodiversity? • Bioresources • Food, Pharmaceuticals, Raw materials • Ecosystem services • E.g., O2 production, nutrient cycling, pollination • Aesthetics • Ethical reasons

9. IUCN (World Conservation Union) recognizes 3 levels of biodiversity: • Genetic diversity • Species diversity • Ecosystem diversity • IUCN (1996) classified over 50% of vertebrate species and 12.5% of plant species as threatened

10. Endangered Vertebrates

13. What is an endangered species?

14. Why list? • Legal protection • ESA and CITES

16. What causes extinctions? • Primarily humans, via direct or indirect impacts. • Population growth 8.9 billion by 2050 • Stochastic • Naturally occurring catastrophic events • Hurricanes for beach mice • Small population pressures

18. Preliminary and background knowledge • A. What is a gene? • - A general term • - The physical entity transmitted from parent to offspring in reproduction that influences hereditary traits. • e.g. Genes influence human characteristics such as hair color and height, but also various aspects of behavior. However, a gene need not code for a protein.

19. Preliminary and background knowledge • A. What is a gene? • - A general term • - The physical entity transmitted from parent to offspring in reproduction that influences hereditary traits. • e.g. Genes influence human characteristics such as hair color and height, but also various aspects of behavior. However, a gene need not code for a protein. • Various forms of a gene are called alleles. An allele can be used as a synonym for gene.

20. Preliminary and background knowledge • A. What is a gene? • - A general term • - The physical entity transmitted from parent to offspring in reproduction that influences hereditary traits. • e.g. Genes influence human characteristics such as hair color and height, but also various aspects of behavior. However, a gene need not code for a protein. • Various forms of a gene are called alleles. An allele can be used as a synonym for gene. • A locus (plural is loci) is a physical location of a gene on a chromosome and is also a synonym for a gene.

21. Preliminary and background knowledge • What is genetic diversity? Yellow-pine chipmunk

22. Preliminary and background knowledge • What is genetic diversity? • Think of genetic diversity as occurring at four levels: • Among species – differences among species of various organisms • Among populations – Differentiation among populations may reflect historical impediments to movement and thus to relatively ancient population subdivisions. Differences among populations can also reflect natural, contemporary patterns of gene flow, provide insights into how natural populations maintain genetic variation and indicate the impact of anthropogenic fragmentation events on the movement of individuals. • Within populations – Loss of genetic diversity is believed to have implications for population persistence over various temporal scales. • Within individuals – In diploid organisms, within-individual genetic diversity is an important component of variability where any particular locus may be heterozygous (with two alleles distinct in DNA sequence) or homozygous (identical alleles on both homologous chromosomes).

23. Preliminary and background knowledge • C. How does genetic diversity arise? • MUTATIONS!

24. Preliminary and background knowledge • C. How does genetic diversity arise? • 1) Types of mutations • a. Point mutations • transitions vs. transversions Purine Pyrimidine

25. Preliminary and background knowledge • C. How does genetic diversity arise? • 1) Types of mutations • a. Point mutations • transitions vs. transversions • replacement vs. silent site

26. Preliminary and background knowledge • C. How does genetic diversity arise? • 1) Types of mutations • a. Point mutations • transitions vs. transversions • replacement vs. silent site • b. Frameshift mutations – “In-del’s”

27. Preliminary and background knowledge • C. How does genetic diversity arise? • 1) Types of mutations • a. Point mutations • transitions vs. transversions • replacement vs. silent site • b. Frameshift mutations – “In-del’s” • 2) Mutations only matter in genetics if they are germ-line mutations (as opposed to somatic mutations).

28. Preliminary and background knowledge D. Segregation, independent assortment and recombination 1) Segregation and Independent Assortment P1: AABB x aabb F1: AaBb => F1 cross = AaBb x AaBb F2: GenotypePhenotype AABB AaBB A_B_ AABb AaBb aaBB aaBb aaB_

29. Conservation genetics

31. 11 major genetic issues • Deleterious effects of inbreeding • Loss of genetic diversity and ability to evolve in response to environmental change. • Fragmentation of populations and restriction of gene flow • Random processes overriding natural selection • Accumulation and loss of deleterious mutations

32. 11 major issues • Genetic adaptation to captivity and its adverse effects of reintroduction success • Resolving taxonomic uncertainties • Defining management units within a species • Molecular issues in forensics • Molecular genetic aspects of species biology • Deleterious effects on fitness as a result of outbreeding (Outbreeding depression)

33. How is genetics used to minimize extinction? • Reducing extinction risk by minimizing inbreeding and loss of genetic diversity • Identifying populations of concern • Resolving population structure • Resolving taxonomic uncertainties • Defining management units within species • Detecting hybridization

34. How is genetics used to minimize extinction? • Non-intrusive sampling • Defining sites for reintroduction • Choosing the best populations for introduction • Forensics • Understanding species biology

36. Island themes • Many parallels between island populations and fragmented habitats

37. Genetics and Extinction • Inbreeding and loss of genetic diversity are inevitable in small populations • Short Term Consequences: • reduced reproduction and survival • Long Term Consequences: • diminished capacity of a population to evolve in response to environmental change

38. Genetics were previously considered inconsequential to the fate of endangered species • E.g., Lande (1988) ‘demographic and environmental catastrophes will cause extinction before genetic deterioration becomes a serious threat to wild populations’

39. Though still debated, now compelling theoretical and empirical evidence supporting the effects of genetic changes on the fate of small populations • Many surviving pops show reduced genetic diversity and evidence of inbreeding • Inbreeding causes extinctionsin deliberately inbred captive populations • Computer projections indicate that inbreeding will cause elevated extinction risks in realistic situations faced by natural populations

40. Inbreeding • Inbreeding: • The production of offspring by individuals related by descent (e.g., self-fertilization, brother-sister, parent-offspring matings) • Inbreeding Depression: • Reduced reproduction and survival (reproductive fitness) due to inbreeding

41. Evidence of inbreeding depression • Ralls and Ballou (1983) • In 41 of 44 captive mammal pops, inbred ind. showed higher juvenile mortality than outbred ind. • Brother-sister mating resulted in a 33% reduction in juvenile survival • Crnokrak & Roff (1999) • Reviewed 157 data sets including 34 species for inbreeding depression in natural situations • In 141 cases (90%), inbred individuals had poorer attributes than comparable outbred individuals

42. Documented cases of inbreeding depression • Mammals: • Golden lion tamarins, lions, native mice, shrews, • Birds: • Greater prairie chicken, Mexican jay, song sparrow, American kestrel, reed warbler • Fish: • Atlantic salmon, desert topminnow, rainbow trout • Many others (reptiles, inverts, plants, etc.)

43. How do we measure the extent of inbreeding? • The inbreeding coefficient (F) • For an individual, F refers to how closely related its parents are • When parents are unrelated, offspring F = 0 • When inbreeding is complete, F = 1

44. Inbreeding • Inbreeding accumulates in closed populations (those without immigration) • Complete inbreeding can be reached with repeated inbred matings • An F of 0.999 is reached after 10 generations of self-fertilization • An F of 0.986 is reached after 20 generations of brother-sister mating

45. Nigerian Giraffe • Giraffe X was born in Paris Zoo in 1992 • Highly inbred calf had an inbreeding coefficient of 0.52 • Calf died 3 weeks after birth

46. Average Inbreeding • The AVERAGE inbreeding coefficient of ALL individuals in a population • Small, closed populations: • Average F will rise as mates become increasingly related • Average F increases at a rate of 1/(2N) per generation in a randomly breeding population of size N

47. Average inbreeding coefficient • Increase in average inbreeding coefficient in populations of 10 and 20 randomly breeding individuals

48. Inbreeding Relative to Random Breeding • Comparison of the average relatedness of mates (parents) to what one would expect if the population is mating at random

49. Genetic Diversity • The extent of heritable variation in a population, or species, or across a group of species, e.g. heterozygosity, or number of alleles, or heritability.

50. Inbreeding and Extinction • Frankel & Soule‘ (1981) • 80-95% of deliberately inbred populations of laboratory and domestic plants and animals die out after eight generations of brother-sister mating or three generations of self-fertilization • E.g., Japanese quail • 383 populations inbred by continued brother-sister mating, all populations went extinct after four generations