1. Conservation Genetics and Phylogeny Dr Christopher L. Parkinson Parkinson Web Site cparkins@pegasus.cc.ucf.edu 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. This short course will serve as an introduction to the field of conservation genetics and phylogenetics. Conservation of genetic diversity. Conservation of genetic diversity. Genetic variation provides the raw material for adaptation, and is therefore critical to continued evolutionary change. 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. 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. This short course will serve as an introduction to the field of conservation genetics and phylogenetics. This short course will serve as an introduction to the field of conservation genetics and phylogenetics. Conservation of genetic diversity. Conservation of genetic diversity. Genetic variation provides the raw material for adaptation, and is therefore critical to continued evolutionary change. 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. 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 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. Apply insights gained from modern genetic techniques to improve the effectiveness of traditional approaches to conserve biological diversity. Modern tools of molecular genetics 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. Apply insights gained from modern genetic techniques to improve the effectiveness of traditional approaches to conserve biological diversity.

4. TIME AND PLACE: TIME AND PLACE: – Lecture: Web Site: http://biology.ucf.edu/~clp/Courses/colo mbia/powerpoints.php Web Site: http://biology.ucf.edu/~clp/Courses/colo mbia/powerpoints.php http://biology.ucf.edu/~clp/Courses/colo mbia/powerpoints.php http://biology.ucf.edu/~clp/Courses/colo mbia/powerpoints.php Username: congen Username: congen Password: evolve Password: evolve TIME AND PLACE: TIME AND PLACE: – Lecture: Web Site: http://biology.ucf.edu/~clp/Courses/colo mbia/powerpoints.php Web Site: http://biology.ucf.edu/~clp/Courses/colo mbia/powerpoints.php http://biology.ucf.edu/~clp/Courses/colo mbia/powerpoints.php http://biology.ucf.edu/~clp/Courses/colo mbia/powerpoints.php Username: congen Username: congen Password: evolve 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. The application of genetics to preserve species as dynamic entities capable of coping with environmental change. Encompasses: Encompasses: Genetic mgmt. of small populations Genetic mgmt. of small populations Resolution of taxonomic uncertainties Resolution of taxonomic uncertainties Defining mgmt. units w/in species Defining mgmt. units w/in species Use of molecular genetic analyses in forensics and understanding species biology Use of molecular genetic analyses in forensics and understanding species biology The application of genetics to preserve species as dynamic entities capable of coping with environmental change. The application of genetics to preserve species as dynamic entities capable of coping with environmental change. Encompasses: Encompasses: Genetic mgmt. of small populations Genetic mgmt. of small populations Resolution of taxonomic uncertainties Resolution of taxonomic uncertainties Defining mgmt. units w/in species Defining mgmt. units w/in species Use of molecular genetic analyses in forensics and understanding species biology Use of molecular genetic analyses in forensics and understanding species biology

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

8. Conservation genetics motivated by the need to reduce current rates of extinction and preserve biodiversity Conservation genetics motivated by the need to reduce current rates of extinction and preserve biodiversity Why conserve biodiversity? Why conserve biodiversity? – Bioresources Food, Pharmaceuticals, Raw materials Food, Pharmaceuticals, Raw materials – Ecosystem services E.g., O 2 production, nutrient cycling, pollination E.g., O 2 production, nutrient cycling, pollination – Aesthetics – Ethical reasons Conservation genetics motivated by the need to reduce current rates of extinction and preserve biodiversity Conservation genetics motivated by the need to reduce current rates of extinction and preserve biodiversity Why conserve biodiversity? Why conserve biodiversity? – Bioresources Food, Pharmaceuticals, Raw materials Food, Pharmaceuticals, Raw materials – Ecosystem services E.g., O 2 production, nutrient cycling, pollination E.g., O 2 production, nutrient cycling, pollination – Aesthetics – Ethical reasons

9. IUCN (World Conservation Union) recognizes 3 levels of biodiversity: 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 IUCN (1996) classified over 50% of vertebrate species and 12.5% of plant species as threatened IUCN (World Conservation Union) recognizes 3 levels of biodiversity: 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 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 Legal protection ESA and CITES ESA and CITES Legal protection Legal protection ESA and CITES ESA and CITES

16. What causes extinctions? Primarily humans, via direct or indirect impacts. Primarily humans, via direct or indirect impacts. Population growth 8.9 billion by 2050 Population growth 8.9 billion by 2050 Stochastic Stochastic – Naturally occurring catastrophic events Hurricanes for beach mice Hurricanes for beach mice – Small population pressures Primarily humans, via direct or indirect impacts. Primarily humans, via direct or indirect impacts. Population growth 8.9 billion by 2050 Population growth 8.9 billion by 2050 Stochastic Stochastic – Naturally occurring catastrophic events Hurricanes for beach mice 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 B. What is genetic diversity? Yellow-pine chipmunk

22. Preliminary and background knowledge B. What is genetic diversity? Think of genetic diversity as occurring at four levels: a) Among species – differences among species of various organisms b) 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. a) Within populations – Loss of genetic diversity is believed to have implications for population persistence over various temporal scales. b) 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 Deleterious effects of inbreeding Loss of genetic diversity and ability to evolve in response to environmental change. Loss of genetic diversity and ability to evolve in response to environmental change. Fragmentation of populations and restriction of gene flow Fragmentation of populations and restriction of gene flow Random processes overriding natural selection Random processes overriding natural selection Accumulation and loss of deleterious mutations Accumulation and loss of deleterious mutations Deleterious effects of inbreeding Deleterious effects of inbreeding Loss of genetic diversity and ability to evolve in response to environmental change. Loss of genetic diversity and ability to evolve in response to environmental change. Fragmentation of populations and restriction of gene flow Fragmentation of populations and restriction of gene flow Random processes overriding natural selection Random processes overriding natural selection Accumulation and loss of deleterious mutations Accumulation and loss of deleterious mutations

32. 11 major issues Genetic adaptation to captivity and its adverse effects of reintroduction success Genetic adaptation to captivity and its adverse effects of reintroduction success Resolving taxonomic uncertainties Resolving taxonomic uncertainties Defining management units within a species Defining management units within a species Molecular issues in forensics Molecular issues in forensics Molecular genetic aspects of species biology Molecular genetic aspects of species biology Deleterious effects on fitness as a result of outbreeding (Outbreeding depression) Deleterious effects on fitness as a result of outbreeding (Outbreeding depression) Genetic adaptation to captivity and its adverse effects of reintroduction success Genetic adaptation to captivity and its adverse effects of reintroduction success Resolving taxonomic uncertainties Resolving taxonomic uncertainties Defining management units within a species Defining management units within a species Molecular issues in forensics Molecular issues in forensics Molecular genetic aspects of species biology Molecular genetic aspects of species biology Deleterious effects on fitness as a result of outbreeding (Outbreeding depression) 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 Reducing extinction risk by minimizing inbreeding and loss of genetic diversity Identifying populations of concern Identifying populations of concern Resolving population structure Resolving population structure Resolving taxonomic uncertainties Resolving taxonomic uncertainties Defining management units within species Defining management units within species Detecting hybridization Detecting hybridization Reducing extinction risk by minimizing inbreeding and loss of genetic diversity Reducing extinction risk by minimizing inbreeding and loss of genetic diversity Identifying populations of concern Identifying populations of concern Resolving population structure Resolving population structure Resolving taxonomic uncertainties Resolving taxonomic uncertainties Defining management units within species Defining management units within species Detecting hybridization Detecting hybridization

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

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

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

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

39. Though still debated, now compelling theoretical and empirical evidence supporting the effects of genetic changes on the fate of small populations 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 extinctions in deliberately inbred captive populations – Computer projections indicate that inbreeding will cause elevated extinction risks in realistic situations faced by natural populations Though still debated, now compelling theoretical and empirical evidence supporting the effects of genetic changes on the fate of small populations 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 extinctions in deliberately inbred captive populations – Computer projections indicate that inbreeding will cause elevated extinction risks in realistic situations faced by natural populations

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

41. Evidence of inbreeding depression Ralls and Ballou (1983) 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) 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 Ralls and Ballou (1983) 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) 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: Mammals: – Golden lion tamarins, lions, native mice, shrews, – Birds: – Greater prairie chicken, Mexican jay, song sparrow, American kestrel, reed warbler Fish: Fish: – Atlantic salmon, desert topminnow, rainbow trout Many others (reptiles, inverts, plants, etc.) Many others (reptiles, inverts, plants, etc.) Mammals: Mammals: – Golden lion tamarins, lions, native mice, shrews, – Birds: – Greater prairie chicken, Mexican jay, song sparrow, American kestrel, reed warbler Fish: Fish: – Atlantic salmon, desert topminnow, rainbow trout Many others (reptiles, inverts, plants, etc.) Many others (reptiles, inverts, plants, etc.)

43. How do we measure the extent of inbreeding? The inbreeding coefficient (F) 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 The inbreeding coefficient (F) 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 accumulates in closed populations (those without immigration) Inbreeding accumulates in closed populations (those without immigration) Complete inbreeding can be reached with repeated inbred matings 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 0.999 is reached after 10 generations of self-fertilization An F of 0.986 is reached after 20 generations of brother-sister mating An F of 0.986 is reached after 20 generations of brother-sister mating Inbreeding accumulates in closed populations (those without immigration) Inbreeding accumulates in closed populations (those without immigration) Complete inbreeding can be reached with repeated inbred matings 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 0.999 is reached after 10 generations of self-fertilization An F of 0.986 is reached after 20 generations of brother-sister mating An F of 0.986 is reached after 20 generations of brother-sister mating Inbreeding

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

46. Average Inbreeding The AVERAGE inbreeding coefficient of ALL individuals in a population The AVERAGE inbreeding coefficient of ALL individuals in a population Small, closed populations: 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 The AVERAGE inbreeding coefficient of ALL individuals in a population The AVERAGE inbreeding coefficient of ALL individuals in a population Small, closed populations: 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 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 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. 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) 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 E.g., Japanese quail – 383 populations inbred by continued brother-sister mating, all populations went extinct after four generations Frankel & Soule‘ (1981) 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 E.g., Japanese quail – 383 populations inbred by continued brother-sister mating, all populations went extinct after four generations

51. Relationship between inbreeding and extinction

52. Inbreeding cont. Even slow rates of inbreeding increase the risk of extinction Even slow rates of inbreeding increase the risk of extinction Taxonomic groups such as mammals, birds, and invertebrates show similar levels of susceptibility to inbreeding depression Taxonomic groups such as mammals, birds, and invertebrates show similar levels of susceptibility to inbreeding depression – In plants, inbreeding depression higher in gymnosperms than angiosperms polyploidy polyploidy Growing evidence shows that inbreeding elevates extinction risks in wild populations Growing evidence shows that inbreeding elevates extinction risks in wild populations Even slow rates of inbreeding increase the risk of extinction Even slow rates of inbreeding increase the risk of extinction Taxonomic groups such as mammals, birds, and invertebrates show similar levels of susceptibility to inbreeding depression Taxonomic groups such as mammals, birds, and invertebrates show similar levels of susceptibility to inbreeding depression – In plants, inbreeding depression higher in gymnosperms than angiosperms polyploidy polyploidy Growing evidence shows that inbreeding elevates extinction risks in wild populations Growing evidence shows that inbreeding elevates extinction risks in wild populations

53. Computer simulations

54. Butterfly extinction

55. Interactions Create

56. Island populations Majority of extinctions have been on islands Majority of extinctions have been on islands Human factors drive population size down. Human factors drive population size down. Island pops typically have less diversity and are more inbreed than mainland congeners Island pops typically have less diversity and are more inbreed than mainland congeners Majority of extinctions have been on islands Majority of extinctions have been on islands Human factors drive population size down. Human factors drive population size down. Island pops typically have less diversity and are more inbreed than mainland congeners Island pops typically have less diversity and are more inbreed than mainland congeners

57. Genetic diversity and extinction To evolve species require genetic diversity To evolve species require genetic diversity Genetic variations allows pops to tolerate a wide range of environmental extremes. Genetic variations allows pops to tolerate a wide range of environmental extremes. Low diversity on islands, less evolution? Low diversity on islands, less evolution? To evolve species require genetic diversity To evolve species require genetic diversity Genetic variations allows pops to tolerate a wide range of environmental extremes. Genetic variations allows pops to tolerate a wide range of environmental extremes. Low diversity on islands, less evolution? Low diversity on islands, less evolution?

58. Motivations for considering the genetic consequences of inbreeding Management of captive populations of rare or endangered species Management of captive populations of rare or endangered species – Breeding programs usually designed to minimize inbreeding and maximize outbreeding In situ management of rare species (small population sizes) In situ management of rare species (small population sizes) – Lack of unrelated mates Random genetic drift Random genetic drift – In small, finite populations, genetic drift can occur even if the population is randomly mating More generally, these issues apply to any species with artificially or naturally fragmented or naturally patchy spatial distributions More generally, these issues apply to any species with artificially or naturally fragmented or naturally patchy spatial distributions Management of captive populations of rare or endangered species Management of captive populations of rare or endangered species – Breeding programs usually designed to minimize inbreeding and maximize outbreeding In situ management of rare species (small population sizes) In situ management of rare species (small population sizes) – Lack of unrelated mates Random genetic drift Random genetic drift – In small, finite populations, genetic drift can occur even if the population is randomly mating More generally, these issues apply to any species with artificially or naturally fragmented or naturally patchy spatial distributions More generally, these issues apply to any species with artificially or naturally fragmented or naturally patchy spatial distributions