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Genetic Aspects of Rarity and Endangerment Covered many aspects in discussion of vortices and readings dealing with viable populations I’ll fill in a few more details – Genetic diversity – Reduction in Ne – Unique applications of genetics to conservation Second Writing Assignment 50pts. Due Week From MONDAY Consider an Endangered or Threatened species (listed on US ESA) that occupies the borderlands between the USA and Mexico – Is this species naturally rare? What biological aspects constrain it to be rare? – What factors have and continue to endanger the species? – How would a physical barrier along the border affect this species? – Considering all factors causing the species’ decline and their feedbacks and interactions, describe the species’ place in an extinction vortex. Inbreeding Depression (Keller and Waller 2002) ‘Inbreeding’ is used to describe various related phenomena that all refer to situations in which matings occur among individuals that have variously similar genotypes (relatives). As conservation biologists we are concerned where this reduces genetic variability or otherwise reduces fitness (inbreeding depression). How to Measure Inbreeding? Keller and Waller 2002 Endangered Species Have Lower Genetic Diversity than Non-endangered Species Haig and Avise 1996 DNA band sharing inferred from fingerprinting All data from birds Inbreeding and Endangerment-Cause and Effect? Typical early studies suggested that endangered species are genetically impoverished Sonoran topminnow (Vrijenhoek et al. 1985) – isolated populations in desert southwest are genetically much less diverse than widespread Mexican populations – Recommend restocking from most diverse populations – But no direct link to suggest genetic impoverishment caused endangerment--rather it likely resulted from it! Effects of Inbreeding in the Wild Deer Mice (Jimenez et al. 1994) – captured in wild and inbred or not in lab – n=367 inbred and n=419 noninbred released – -inbred survived at rate only equal to 56% of noninbred – inbred lost weight after release, noninbred maintained weight Demonstrated effects of inbreeding in wild populations (Caro 2000) Species History of Low Heterozygosity Current inbreeding? Effects European Adder Recent Yes Small litters, deformed young Song sparrow Occasional Some Differential loss in cold weather Sonoran Topminnow Recent Yes High mortality, slow growth Florida Panther Recent Yes Testicular dysfunction Ngorongoro lion Very recent Yes Reduced yearling production White-footed mouse Recent Some (experimental) Lower survival, male weight loss Cheetah Long No Sperm abnormalities Glanville fritillary butterfly Recent Yes Low survival, reduce egg hatching Wide survey of inbreeding effects (Keller and Waller 2002) Genetic Rescue of Greater Prairie Chickens (Westemeier et al. 1998) 2000 chickens in 1962---only <50 in 1994 Genetic diversity was low and fitness poor Translocated chickens from large, diverse population (MN, KS, NE) in 1994 Fecundity rises after translocation Inbreeding Effects in Cheetah?? Low genetic variation (near clones) was associated with poor reproduction in captivity (O’Brien et al. 1985) – low sperm count, low fecundity, low conception, high infant mortality Classic signs of inbreeding – seems not the case! • Reproduction in wild is fine, but cubs are lost through predation to lions and hyenas (Caro and Laurenson 1994) • poor husbandry was likely source of poor reproduction in captivity Reasons for Cheetah declines Human population increase Direct killing by pastoralists Direct killing by farmers Overhunting of ungulate prey (Caro 2000) Black Robins Defy Genetic Bottlenecks (Ardern and Lambert 1997) Individuals (columns) nearly identical! Current population of 200 birds was derived from a SINGLE breeding pair – bottleneck down to n=5 in 1980, persistence as a small population for 100 years Minisatellite DNA Black Robin Bush Robin Recent bottleneck, but not historical small population variation non-existent But, reproduction and survival is normal Mauritius Kestrel Population was reduced to 2 pairs due to pesticides Increasing now with restoration efforts Nichols et al. 2001 Low Genetic Heterogeneity Typically low for island species Subdivision of population may allow heterogeneity to remain relatively high despite very low population size Nichols et al. 2001 Does Genetic Variation Matter? For commonly measured variation (multilocus heterozygosity) it does not appear to matter – DNA fingerprinting, mtDNA, etc. – Britten (1996) • meta-analysis of 22 correlations between heterozygosity and fitness surrogates (growth rate, developmental stability – no significant relationship – loci measured with molecular techniques are typically neutral in the eye of evolution – only a small sample of actual loci are measured Could Inbreeding be Good? Purging (Keller and Waller 2002) – Simple population genetics models predict that the increased homozygosity resulting from inbreeding will expose recessive deleterious alleles to natural selection, thereby purging the genetic load – Further inbreeding would then cause little or no reduction in fitness. – Studies of purging are inconclusive in demonstrating consistent, positive effects – Purging may only work under limited conditions • Strong deleterious effect, isolation precludes reintroduction of deleterious alleles by immigration, inbreeding is gradual Do Molecular Techniques Measure the Right Genes? Mitton (1994) points out that variation detected by molecular techniques (DNA) does not correlate with fitness like variation measured at polymorphic protein loci (protein electrophoresis) – metabolism, growth rate, and viability are correlated with protein variation Fleischer (1998) points out that quantitative genetics measures variability in traits under multilocus control by measuring heritability – measure variability in potentially important traits like body size or clutch size Lynch (1996) details the potential importance of quantitative genetics to conservation biology Quantitative Genetics Measures and develops theory about heritability (in addition to other concepts) – how genotype influences phenotype and how genotypes change through time (evolution) Molecular genetics measures variation in loci, most of which are neutral with respect to evolution (do not affect fitness or even phenotype) What is Heritability? Heritability (Lynch 1996) – fraction of phenotypic variance that has an additive genetic basis • how much you can expect a trait to change in the next generation when selection acts on it in the present generation – the ability to respond to novel selective challenges is proportional to the heritability of a trait Do Heritable Traits Correlate with Fitness? Perhaps not in a simple way – body size in Pinyon Jays is heritable (parent and offspring mass is correlated), but not directly related to survival or reproduction (Marzluff and Balda 1988) But it is a fundamental LAW that heritability determines the ability of a population to evolve – change in mean phenotype=h2S • h=heritability; S = selection differential • evolution is determined by selection and inheritance Species Can have Low Heterozygosity but High Evolutionary Potential heterozygosity (variation at molecular level, or average heterozygotes per loci averaged across all loci) is produced by mutation (rate of 10-8 - 10-5 per year) heritability (variation in quantitative traits) is introduced at rate of 10-3-10-2 per generation – If population goes through a bottleneck and looses both sources of variation, heritability recovers more quickly. • Species can have low molecular variation, but high heritability (hence high ability to evolve) – Cheetahs are an example of this. – Lack of heterozygosity does not mean lack of evolutionary potential General Principles Relevant to Conservation (Lynch 1996) Genetic variance is determined by interplay of selection, drift, and mutation – when population size is constant and selection is constant then mutation balances drift which sets up an equilibrium level of variation – drift reduces variation at rate of 1/(2Ne) per generation as discussed earlier • 2Ne is the number of gametes that were “chosen” from all gametes to produce the genotype of current generation (assumes diploid adults). 1/2Ne is the probability of getting 2 alleles of same type in an individual if gametes are selected at random – mutation adds variation at 2m per generation Relationship of Population Size to Evolutionary Potential When Ne < few hundred, selection is unimportant – selection effects are spread over many loci that control a single character so effect on any 1 locus is swamped by drift – genetic variation in heritable characters is determined by equilibrium between drift and mutation, or • V=2m-(1/(2Ne)) = 2Ne 2m-1, or 2Ne 2m according to Lynch • Each incremental increase in population size is doubled with respect to heritable variation thereby doubling the evolutionary potential of the population When Ne > 1000, then drift is inconsequential – balance between mutation and selection drives variation (evolutionary potential) – Extreme selection can wipe out genetic variation (lead to fixation of “presently optimal” alleles – variation is independent of population size How Many Individuals do We Need to Get Ne > 1000? 5,000 to 10,000 (Lynch 1996) – Ne usually is .1 to .3census N Ne 1 ; N m males, N f females 1 1 4N 4 N m f 4N 2 Ne ; variance in progeny 2 2 1 1 1 1 ; N population size per generation N e .... t N1 N 2 Nt Mutational Meltdown (Lynch et al. 1993) Same as f-vortex – drift becomes more important as population declines to very small size – drift begins to act synergistically with accumulation of deleterious mutations • for flies when Ne<few dozen, extinction occurs in 10-few hundred generations without stochasticity • extinction occurs an order of magnitude or more faster with demographic or environmental stochasticity Is Adding Individuals from Captive Propagation Beneficial? Increase in numbers, but also may upset genetic adaptation to local conditions – esp. likely if use non-native stock • hatchery fish, yellowstone wolves – accentuated by long periods of selection in captivity • develop deleterious behavior with genetic component Also relevant when considering inducing migration between isolates – human activity fragments habitat and sets up unique selective regime in different fragments Using Genetics to Guide Recovery Red Wolves in SE United States (Roy et al. 1996) Are they a basal canid or a recent hybrid? – Listed because they were believed to be a native species from Pleistocene that was ancestral to coyotes and gray wolves – Mitochondrial and nuclear DNA suggest red wolves are result of hybridization between gray wolves and coyotes--timing of this is uncertain – Reintroduction sites should be selected that are in areas with few coyotes to reduce future hybridizing Thoughts from Lande (1999) Evaluates Extinction Risk from stochastic, deterministic, and genetic factors – Deterministic declines in population due to human factors (habitat loss, invasive species, climate change, etc.) are more important than stochastic factors in causing species declines – Very large populations (>5000) may be needed to maintain rare alleles such as those needed to resist new diseases – Once populations are small: • Inbreeding depression is most severe when population declines have been rapid (little purging occurred), but it is easily reversed with minimal migration (1 unrelated individual joins each population every 1 or 2 generations) • Small populations with low fitness may go extinct from fixation of new deleterious mutations. But even very small populations with high fitness rarely suffer from fixation of deleterious mutations. References Haig, SM and JC Avise. 1996. Avian conservation genetics. PP160-189 In. JC Avise and JL Hamrick (ed.) Conservation genetics. Chapman & Hall. New York. Lynch, M. 1996. A quantitative-genetic perspective on conservation issues. PP 471-501 In. JC Avise and JL Hamrick (ed.) Conservation genetics. Chapman & Hall. New York. Britten, HB. Meta-analyses of the association between multilocus heterozygosity and fitness. Evolution 50:2158-2164. Fleischer, RC. 1998. Genetics and avian conservation. PP 29-47 In. JM Marzluff and R Sallabanks (eds.) Avian Conservation. Island Press. Covelo, CA. Mitton, JB. 1994. Molecular approaches to population biology. Ann. Rev. Ecol. Syst. 25:45-69 Lynch, M. R. Burger, D. Butcher, and W. Gabriel. 1993. The mutational meltdown in asexual populations. J. Heredity 84:339-344. Westemeier, R. L., Brawn, J. D., Simpson, S. A., Esker, T. L., Jansen, R. W., Walk, J. W., Kershner, E. L., Bouzat, J. L., and K. N. Paige. 1998. Tracking the long-term decline and recovery of an isolated population. Science 282:1695-1698. More References Ardern, S. L. and D. M. Lambert. 1997. Is the black robin in genetic peril? Molecular Ecology 6:21-28 Caro, T. M. and M. K. Laurenson. 1994. Ecological and genetic factors in conservation: a cautionary tale. Science 263:485-486. Jimenez, J. A., K. A. Hughes, G. Alaks, L. Graham, and R. C. Lacy. 1994. An experimental study of inbreeding depression in a natural habitat. Science 266:271-273. O’Brien, S.J., Roelke, M. E., Marker, L., Newman, A., Winkler, C. A., Meltzer, D., Colly, L., Evermann, J. F., Bush, M., and D. E. Wildt. 1985. Genetic basis for species vulnerability in the Cheetah. Science 227:14281434. Roy, M. S., E. Geffen, D. Smith, and R. K. Wayne. 1996. Molecular genetics of pre-1940 red wolves. Conservation Biology 10:1413-1424. Vrijenhoek, R. C., M. E. Douglas, and G. K. Meffe. 1985. Conservation genetics of endangered fish populations in Arizona. Science 229:400-402. Still More Refs Hale, ML, Lurz, PWW, Shirley, MDF, Rushton, S., Fuller, RM, and K. Wolff. 2001. Impact of landscape management on the genetic structure of red squirrel populations. Science 293:2246-2248. Caro, T. 2000. Controversy over behavior and genetics in Cheetah conservation. In. LM Gosling and WJ Sutherland, eds. Behavior and Conservation. Keller, LF and DM Waller. 2002. Inbreeding effects in wild populations. Trends in Ecology and Evolution 17:230-241. Lande, R. 1999. Extinction risks from anthropogenic, ecological, and genetic factors. Pp 1-22. In Genetics and the Extinction of Species (Landweber, LF and AP Dobson, eds.). Princeton University Press Nicholl, M.A.C. Jones, C.G., and K. Norris. 2003. Declining survival rates in a reintroduced population of the Mauritius kestrel: evidence for non-linear density dependence and environmental stochasticity. J. Anim. Ecol. 72:917-926. Nichols, R. A., Bruford, M. W., and J. J. Groombridge. 2001. Sustaining genetic variation in a small population: evidence from the Mauritius kestrel. Molecular Ecology 10:593-602. Mandel, J. T., Donlan,C. J., and J. Armstrong. 2010. A derivative approach to endangered species conservation. Frontiers in Ecology and the Environment. 8:44-49.