Conservation Genetics Image of DNA double helix from Wikipedia

Conservation of Genetic Diversity We are interested in conservation of genetic diversity spanning the Tree of Life. For example, we wish to conserve high levels of phylogenetic diversity. Even so, for this lecture we will focus on species-level genetic diversity and population genetics. Image from www.tolweb.org

Conservation of Genetic Diversity We are interested in conservation of genetic diversity spanning the Tree of Life. For example, we wish to conserve high levels of phylogenetic diversity. Even so, for this lecture we will focus on species-level genetic diversity and population genetics. Image from www.tolweb.org

Conservation of Genetic Diversity Some Mechanisms of Evolution Evolution – allele frequency change through time in a population Some Mechanisms of Evolution Mutation Genetic accommodation – adaptive evolution Random processes (e.g., genetic drift) Gene flow via emigration & immigration Artificial selection Natural selection (Thank you, Darwin [& Wallace]!) – adaptive evolution Sexual selection (Thank you, Darwin!) – adaptive evolution

Conservation of Genetic Diversity Mutations (substitutions, insertions, deletions, inversions) – ultimate sources of most genetic variation Generation 1 Generation 2 A mutation that arises in a germ-line cell can be passed on to offspring. Small populations provide few opportunities for positive mutations to arise

Conservation of Genetic Diversity Gene flow – exchange of genes between populations Pop. A Pop. B Genetic diversity erodes especially quickly in small, isolated populations

Conservation of Genetic Diversity Inbreeding – results from mating by closely related individuals Pop. A Generation 1 Pop. B Generation 2 In this case, assume that each set of parents produces one male and one female offspring. An individual has fewer opportunities for outbreeding in Generation 2 in the smaller population. Progeny from inbred parents have increased likelihood of inheriting alleles that are identical by descent, which increases the risk of expression of deleterious alleles. 33% chance of mating with sibling 50% chance of mating with sibling Genetic diversity erodes especially quickly in small, isolated populations

Conservation of Genetic Diversity Random processes (demographic bottlenecks, genetic drift, founder effects) Generation 1 Generation 2 Genetic diversity erodes especially quickly in small, isolated populations

Conservation of Genetic Diversity Not all phenotypic diversity results from genetic diversity Genetic diversity helps determine evolutionary potential R. A. Fisher (1890 – 1962) An architect of the Modern Synthesis From Ch. 2 in Groom et al. Fisher’s Fundamental Theorem: "The rate of increase in fitness [owing to selection] of any organism at any time is equal to its genetic variance in fitness at that time" Photo from Wikipedia

Conservation of Genetic Diversity Genetic diversity occurs at 3 levels in a species’ gene pool: Within individuals (e.g., heterozygosity – the proportion of gene loci in an individual that contains alternative forms of alleles) Among individuals in a population Among populations

Conservation of Genetic Diversity Genetic diversity helps determine evolutionary potential But, “gene pools are becoming diminished and fragmented into gene puddles” (Foose 1983) A gene pool for a population is analogous to a species pool for a metacommunity (as in mainland species pool in Island Biogeography Theory). Foose, T. J. 1983. The relevance of captive populations to the conservation of biotic diversity. In C. M. Schonewald-Cox, S. M. Chambers, B. MacBryde & L. Thomas, eds. Genetics and Conservation: A Reference for Managing Wild Animal and Plant Populations, pp. 374-401. Benjamin/Cummings, Menlo Park, CA. Image from www.brooklyn.cuny.edu

Conservation of Genetic Diversity Genetically effective population size (Ne) – the number of individuals that would result in the same level of inbreeding, or decrease in genetic diversity through time, if the population were an idealized, panmictic (randomly mating) population Typically  Ne < N (Because of variance in reproductive success and family sizes) Miller, Craig R. & Lisette P. Waits. 2003. The history of effective population size and genetic diversity in the Yellowstone grizzly (Ursus arctos): Implications for conservation. PNAS 100:4334-4339. Greater Yellowstone Ecosystem grizzlies: N ≈ 500 Ne ≈ 80 Image from www.time.com

Conservation of Genetic Diversity Genetically effective population size (Ne) – the number of individuals that would result in the same level of inbreeding, or decrease in genetic diversity through time, if the population were an idealized, panmictic (randomly mating) population Typically  Ne < N (Because of variance in reproductive success and family sizes) Generation 1: ♀ ♂ ♀ ♂ ♀ ♂ ♀ ♂ ♀ ♂ Generation 2: ♀ ♂ ♀ ♂ ♀ ♂ ♀ ♂ ♀ ♂

Extinction Vortex Small populations are at risk of extinction owing to the “one-two punch” from demographics and genetics Also see the classic original source: Gilpin, M. E. & M. E. Soulé. 1986. Minimum Viable Populations: Processes of Species Extinction. In M. E. Soulé. Conservation Biology: The Science of Scarcity and Diversity. Sinauer, Sunderland, Mass. pp. 19–34. Image from Campbell & Reece (2008) Biology 8th ed., Benjamin Cummings Pubs.

Genetic Tools for Conservation Pedigree analysis – especially useful for captive populations Estimation of relatedness (in the absence of pedigrees) Analysis of parentage and mating systems Forensics Species or population identification Estimation of population size Image of elephant ivory from www.guardian.co.uk

Case Study: Eurasian wolf Vilà et al. (2003) Rescue of a severely bottlenecked wolf (Canis lupus) population by a single immigrant “We show here that the genetic diversity of the severely bottlenecked and geographically isolated Scandinavian population of grey wolves (Canis lupus), founded by only two individuals [in 1983, after centuries of persecution that extirpated them from the Scandinavian peninsula by 1960s], was recovered by the arrival of a single immigrant.” As in North America, wolves have long been persecuted in Europe. Vilà et al. 2003. Rescue of a severely bottlenecked wolf (Canis lupus) population by a single immigrant. Proc. R. Soc. Lond. B 270:91-97. Abstract “The fragmentation of populations is an increasingly important problem in the conservation of endangered species. Under these conditions, rare migration events may have important effects for the rescue of small and inbred populations. However, the relevance of such migration events to genetically depauperate natural populations is not supported by empirical data. We show here that the genetic diversity of the severely bottlenecked and geographically isolated Scandinavian population of grey wolves (Canis lupus), founded by only two individuals, was recovered by the arrival of a single immigrant. Before the arrival of this immigrant, for several generations the population comprised only a single breeding pack, necessarily involving matings between close relatives and resulting in a subsequent decline in individual heterozygosity. With the arrival of just a single immigrant, there is evidence of increased heterozygosity, signi. cant outbreeding (inbreeding avoidance), a rapid spread of new alleles and exponential population growth. Our results imply that even rare interpopulation migration can lead to the rescue and recovery of isolated and endangered natural populations.” Quote from Vilà et al. (2003) Proc. R. Soc. Lond. B.; photo & map of Europe from Wikipedia

Case Study: Eurasian wolf Vilà et al. (2003) Rescue of a severely bottlenecked wolf (Canis lupus) population by a single immigrant A single immigrant arrived onto the Scandinavian peninsula in 1991 100 12 Estimated population size 50 Number of breeding packs Vilà et al. 2003. Rescue of a severely bottlenecked wolf (Canis lupus) population by a single immigrant. Proc. R. Soc. Lond. B 270:91-97. 8 4 1983 1991 2001 Figure from Vilà et al. (2003) Proc. R. Soc. Lond. B.

Case Study: Eurasian wolf Vilà et al. (2003) Rescue of a severely bottlenecked wolf (Canis lupus) population by a single immigrant A single immigrant arrived onto the Scandinavian peninsula in 1991 Each circle = 1 wolf 1.0 Founding female (est. date of birth = 1978) Pups with d.o.b. < 1991 (only 1 bottlenecked, inbred pack) (19 autosomal microsatellite loci) Individual heterozygosity 0.5 Vilà et al. 2003. Rescue of a severely bottlenecked wolf (Canis lupus) population by a single immigrant. Proc. R. Soc. Lond. B 270:91-97. Offspring of immigrant male Other pups with d.o.b.  1991 1978 1983 1991 2001 Figure from Vilà et al. (2003) Proc. R. Soc. Lond. B.

Case Study: North American wolf Adams et al. (2011) Genomic sweep and potential genetic rescue during limiting environmental conditions in an isolated wolf population “…a male wolf (Canis lupus)… immigrated [in 1997]… across Lake Superior ice to the small, inbred wolf population in Isle Royale National Park. The immigrant’s fitness so exceeded that of native wolves that within 2.5 generations he was related to every individual in the population… resulting in a selective sweep of the total genome.” Adams, Jennifer R. et al. 2011. Genomic sweep and potential genetic rescue during limiting environmental conditions in an isolated wolf population. Proc. Roy. Soc. B Abstract “Genetic rescue, in which the introduction of one or more unrelated individuals into an inbred population results in the reduction of detrimental genetic effects and an increase in one or more vital rates, is a potentially important management tool for mitigating adverse effects of inbreeding. We used molecular techniques to document the consequences of a male wolf (Canis lupus) that immigrated, on its own, across Lake Superior ice to the small, inbred wolf population in Isle Royale National Park. The immigrant’s fitness so exceeded that of native wolves that within 2.5 generations, he was related to every individual in the population and his ancestry constituted 56 per cent of the population, resulting in a selective sweep of the total genome. In other words, all the male ancestry (50% of the total ancestry) descended from this immigrant, plus 6 per cent owing to the success of some of his inbred offspring. The immigration event occurred in an environment where space was limiting (i.e. packs occupied all available territories) and during a time when environmental conditions had deteriorated (i.e. wolves’ prey declined). These conditions probably explain why the immigration event did not obviously improve the population’s demography (e.g. increased population numbers or growth rate). Our results show that the beneficial effects of gene flow may be substantial and quickly manifest, short-lived under some circumstances, and how the demographic benefits of genetic rescue might be masked by environmental conditions.” Quote & photo from Adams et al. (2011) Proc. R. Soc. Lond. B.; map of North America from Wikipedia

Case Study: North American wolf Adams et al. (2011) Genomic sweep and potential genetic rescue during limiting environmental conditions in an isolated wolf population “The population inbreeding coefficient (f) averaged over each individual present in the population from 1950 to 2009... Our results show that the beneficial effects of gene flow may be substantial and quickly manifest…” f Adams, Jennifer R. et al. 2011. Genomic sweep and potential genetic rescue during limiting environmental conditions in an isolated wolf population. Proc. Roy. Soc. B Abstract “Genetic rescue, in which the introduction of one or more unrelated individuals into an inbred population results in the reduction of detrimental genetic effects and an increase in one or more vital rates, is a potentially important management tool for mitigating adverse effects of inbreeding. We used molecular techniques to document the consequences of a male wolf (Canis lupus) that immigrated, on its own, across Lake Superior ice to the small, inbred wolf population in Isle Royale National Park. The immigrant’s fitness so exceeded that of native wolves that within 2.5 generations, he was related to every individual in the population and his ancestry constituted 56 per cent of the population, resulting in a selective sweep of the total genome. In other words, all the male ancestry (50% of the total ancestry) descended from this immigrant, plus 6 per cent owing to the success of some of his inbred offspring. The immigration event occurred in an environment where space was limiting (i.e. packs occupied all available territories) and during a time when environmental conditions had deteriorated (i.e. wolves’ prey declined). These conditions probably explain why the immigration event did not obviously improve the population’s demography (e.g. increased population numbers or growth rate). Our results show that the beneficial effects of gene flow may be substantial and quickly manifest, short-lived under some circumstances, and how the demographic benefits of genetic rescue might be masked by environmental conditions.” 1950 1960 1970 1980 1990 2000 2010 Figure from Adams et al. (2011) Proc. R. Soc. Lond. B.

Case Study: Florida panther Johnson et al. (2010) Genetic restoration of the Florida panther (Puma concolor coryi) Eight females were translocated from Texas to Florida in 1995; “panther numbers increased threefold, genetic heterozygosity doubled, survival and fitness measures improved, and inbreeding correlates declined significantly” Johnson, Warren E. et al. 2010. Genetic restoration of the Florida panther. Science 329:1641-1645. “Fig. 1. (A and B) Southern Florida (1995, left; 2007, right) with locations of breeding-age Florida panthers (>1.5 years old), geographic features, number (N) alive, and effective population size (Ne). Labeled colored areas in (A) demarcate public land (23): Fakahatchee Strand Preserve State Park (FSPSP), Picayune Strand State Forest (PSSF), Florida Panther National Wildlife Refuge (FPNWR), BCNP, Big Cypress Seminole Indian Reservation (SEM), Okaloacoochee Slough State Forest (OSSF), and Everglades National Park (EVER) and in (B) show panther habitat. Circles are coded by ancestry: CFP [canonical Florida panthers], TX females (with a B if a successful breeder), EVG [Everglades Florida panthers], AdmFP [admixed Florida panthers], and SEM. Pie charts illustrate the genetic heritage of the population (fig. S1 and table S2) (13).” Figure from Johnson et al. (2010) Science

Torres del Paine, Chile – not only where I developed my stylish fashion sense (see photos), but was the defining experience that set me on my career path…