* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download 8. Conservation genetics
Survey
Document related concepts
Quantitative trait locus wikipedia , lookup
Hybrid (biology) wikipedia , lookup
Genetic engineering wikipedia , lookup
Genome (book) wikipedia , lookup
Public health genomics wikipedia , lookup
Genetics and archaeogenetics of South Asia wikipedia , lookup
Behavioural genetics wikipedia , lookup
Medical genetics wikipedia , lookup
Genetic testing wikipedia , lookup
Hardy–Weinberg principle wikipedia , lookup
Polymorphism (biology) wikipedia , lookup
Heritability of IQ wikipedia , lookup
Koinophilia wikipedia , lookup
Genetic drift wikipedia , lookup
Human genetic variation wikipedia , lookup
Microevolution wikipedia , lookup
Population genetics wikipedia , lookup
Transcript
8. Conservation genetics 8.1. Extinctions 8.2. Molecular biology in conservation 8.3. Inbreeding 8.3.1. Genetic load 8.3.2. Genetic consequences of inbreeding 8.3.3. Genotype frequencies and breeding system 8.3.4. Estimation of F 8.3.5. Pedigrees and F 8.3.6. Inbreeding depression 8.3.7. Genetic basis of ID 8.4. Genetic diversity as a conservation issue 8.4.1. Genetic restoration 1 8.1. Extinctions • Commonplace – – – – 3-30 million species are thought to exist on earth today 5-50 billion species has existed at one time or another truly lousy survival record: 99.9% failure (Raup 1999) extinction rate not constant 2 Mass extinctions • Five – – – – – Ordovician Devonian Permian Triassic Cretacous (65 mya) • 38% marine animals went extinct; among land animals the percentage higher 3 Sixth mass extinction today? • World Conservation Union (IUCN) • founded 1948, assesses conservation status of species • Red List of Threatened Species http://www.iucnredlist.org/ – 20 219 species threatened by 2012 • • • • • • • EX = Extinct (hävinnyt) EW = Extinct in the wild (hävinnyt luonnosta) CR = Critically endangered (äärimmäisen uhanalainen) EN = Endangered (erittäin uhanalainen) VU = Vulnerable (vaaraantunut) NT = Near threatened (silmälläpidettävä) LC = Least consern (elinvoimainen) 4 5 501 mammals; 1 138 (25%)threatened 5 10 064 birds; 1 303 (13%) threatened EX EW CR EN VU NR LC bad data 6 Sixth mass extinction today? • • Many with small population sizes, for example island endemics Many with large populations has been progressively reduced to the point of endangerment – Last passenger pigeon (Ectopistes migratorious) died in Cincinnati zoo in 1914 – Less than 50 years earlier billions of individuals: – ’ John James Audubon watched a flock pass overhead for three days and estimated that at times more than 300 million pigeons flew by him each hour’ – Hunted for meat 7 8.2. Molecular biology in conservation • In early days destructive sampling • PCR-technology – non-destructive sampling – non-invasive sampling 8 • Conservation Genetics – understand the relationship between genetic variability and population viability • monitoring genetic diversity using both neutral and adaptive genetic markers • low level of genetic diversity may interact with other factors, such as demographic and environmental variation, to generate an "extinction vortex" – much of conservation genetics involves the estimation of effective population size, structure and gene flow among populations 9 • Example: Effective population size in Finnish wolf population 10 Jannson et al 2014 BMC Evolutionary Biology • Estimation using the temporal method § Is based on changes in allele frequencies that occur between two or more temporal samples taken from a small population § Larger changes in allele frequencies in smaller populations because of genetic drift § Effective population size could be estimated on the basis of the amount of change 11 • Estimates of Ne in Finnish wolf population using several temporal methods (Jansson et al. 2012 Mol Ecol) – – – – Number of breeding individuals in 2004 = 34 Migration and inbreeding avoidance increase Ne Ne/Nc = 0.16 – 1.17 Ne large enough for self sustaining population? 12 8.3. Inbreeding 8.3.1. Genetic load • • When parents of an individual share one or more common ancestors, the individual is inbred Inbreeding depression = Reduction of fitness due to breeding between close relatives • genetic load = The reduction in the mean fitness for a population compared to the theoretical maximum fitness – The magnitude depends on how many and how harmful recessive alleles are found in the population • Example: Great tit (van Nordwijk & Scharloo 1981) 13 Example: Swedish captive wolfs 14 Laikre & Ryman. 1991. Conservation Biology 5 8.3.2. Genetic consequences of inbreeding Genotype frequencies in self-fertilization: e.g. p = q = 0.5 Genotype Frequency AA 0.25 Aa 0.5 aa 0.25 Let’s assume individuals of each genotype has an offspring Parent genotypes Offspring genotypes Frequency AA Aa aa AA 0.5 Aa + 0.25 AA +0.25 aa aa 0.25x1 + 0.5x0.25 = 0.375 0.5x0.5 = 0.25 0.25x1 + 0.5x0.25 = 0.37515 • the frequency of heterozygotes is halved • no changes in allele frequencies 16 Inbreeding reveals diseases caused by rare resessive alleles; examples from human population: 17 8.3.3. Genotype frequencies and breeding system Genotypes Population F A/A A/a a/a Random mating 0 p2 2pq q2 Fully inbred 1 p 0 q Partially inbred F p2(1-F)+Fp =p2 + Fpq 2pq(1-F)+Fx0 =2pq(1-F) q2 (1-F)+Fq =q2 +Fpq • The ratio of heterozygosity in an inbred population relative to that in an outbred population is : HI/H0 = 2pq(1-F)/2pq = 1- F F = 1 – (HI/H0) (F is the inbreeding coefficient) 18 8.3.4. Estimation of F • Deficiency of heterozygotes at a locus controlling black vs. grey lemma colour in oats (kaleen väri kauralla) Genotype BB Bb bb Observed 0.548 0.071 0.281 Expected (HW) 0.340 0.486 0.173 F = 1 – (HI/H0) = 1-(0.071/0.486) = 0.85 19 • Loss of heterozygosity and F – Estimate of inbreeding coefficient for a population can be obtained from the loss of genetic diversity over time: Ht /H0 = (1- ½ Ne)t (1-F0)= 1 – F F = 1-(1- ½ Ne)t (1-F0) Where t = number of generations and F0 = initial inbreeding Or simplified, when heterozygosity of the original population is compared to inbred: F = 1 – (Ht/H0) 20 21 • Example: Grey wolf, Isle Royale 22 • Grey wolves – in the endangered Isle Royal population allozyme heterozygosity was 3.9% – In a nearby mainland population heterozygosity was 8.7% F = (1- Ht /H0 ) = (1- 0.039/0.087) = 0.55 23 8.3.5. Pedigrees and F • Calculation of F-coefficient A1A2 Probability that A1 is passed from A to D is ½ and D to X is ½ A D E Probability that A1 is passed from A to E is ½ and E to X = = ½ Probability that A2 is passed from A to D is ½ and D to X is ½ X ? Probability that A2 is passed from A to E is ½ and E to X = = ½ F = (½)4 + (½)4 = 1/8= 0.125 24 • More complicated pedigrees: – Chain counting method • Find all possible chains through different ancestors • Count number of individuals (n) in chains (except individual I, for which you are calculating F). • In each chain inbreeding coefficient is F = (1/2)n • Add the contributions of different counts: • F = Σ(½)n(1 + Fca), Where n is # of individuals in path to common ancestor and back and Fca is inbreeding coefficient of common ancestor 25 Example: The common ancestors, their chains, inbreeding coefficents and contribution to inbreeding coefficient of Z All other CAs have an inbreeding coefficient of 0 except H: FH (CAD) = 1+(1/2)3=1.125 CA Path n Effect to F A XKGCADHLY 9 (½)9 0.00195 B XKHDBEJMY 8 (½)8 0.00391 B XKHDBEALY 8 (½)8 0.00391 C XKGCHLY 7 (½)7 0.00781 H XKHLY 5 (½)5 (1.125) 0.03516 Fx = 0.05273 26 8.3.6. Inbreeding depression • Production of calves in muskox (Laikre, Ryman & Lundh 1997; Cons. Biol. 79: 197-204 27 • Production of cubs in Swedish wolves (Liberg et al. 2006; Biol Letters) 28 29 • Quantitative characters closely related to fitness show more inbreeding depression than those that are less closely related to fitness • DeRose & Roff 1999. Evolution: – At inbreeding coefficient of 0.25 (=full-sib mating): – In morphological traits inbreeding depression reduced fitness by 2.2 % – In life-history traits fitness reduced by 11.8% 30 Measuring inbreeding depression • • ID = inbreeding depression = 1(compare with F = 1 − ) Lethal equivalents - group of detrimental alleles that would cause on average one death if homozygous - Probability of survival (S) can be expressed as - S = e –(A+BF) => ln S = -A-BF • where e-A is the fitness in outbred population (A is a measure of death due largely to environmental factors but also to other factors not included in B) • B is a measure of the hidden genetic damage that would be expressed fully in a complete homozygote (F = l) • F is the coefficient of inbreeding 31 • Lethal equivalents in Okapi (de Bois et al. 1990) – slope of the regression line is –1.8 suggesting that population contains 1.8 haploid and 3.6 diploid lethal equivalents 32 • The number of lethal equivalents may be also estimated as Morton et al. (1956) and Sorensen (1969) 2B = - 4 ln R where R is the relative survivorship of offspring from selfpollination in relation to offspring from cross-pollination (=F) and 2B is the average number of lethal equivalents per zygote • In bilberry (Vacinium myrtillus) in the experimental field (Nuortila, Tuomi, Aspi & Laine, 2006): – mean inbreeding depression at the embryonic stage R = 0.8 (± 0.04) – Lead to a mean of 2B = 7.8 (± 0.8; N = 18) lethal equivalents per zygote 33 8.3.7. Genetic basis of ID • Dominance hypothesis Alleles Fitness A1A1 1 A1A2 1 – hs A2A2 1 –s h=degree of dominance of A2 s=selection coefficient against A2A2 Þ maladaptive and lethal, caused by partially or mostly recessive alleles – mutation brings new, selection against (mutation- selection model) • Overdominance hypothesis Alleles Fitness A1A1 1-t A1A2 1 A2A2 1 –s t=selection coefficient against A1A1 s=selection coefficient against A2A2 Þheterozygosity itself ‘good’ – allele frequencies higher than in the mutation-selection model 34 • How to study? – If heterozygosity itself is good, then individual heterozygosity and fitness should correlate • However, this phenomenon could be caused for example by population structure or partial inbreeding • Enzyme gene heterozygosity: only rarely heterozygosity-fitness correlation, which could not be explained by the population structure • However several cases of correlations with DNAstudies – Biometrical evidence: only a little evidence of overdominance 35 • If continuous and fragmented populations of a same species are considered then (Whitlock 2003; Genetics): – According to the dominance theory: small fragmented population should have less inbreeding depression: deleterious alleles are purged in small inbred populations A1A1 A1A2 A2A2 1 1 – hs 1–s – According to the overdominance theory: there should not be large differences between fragmented and continuous populations A1A1 A1A2 A2A2 1–t 1 1–s 36 • Example: Inbreeding depression in Glanville fritillary in Finland and France (Haikola et al. 2001, Conservation Genetics 2: 325-335) 37 • Finland (Åland): fragmented small populations • France: continuous large populations Less inbreeding depression in Finnish populations - dominance model – purging 38 8.4. Genetic diversity as a conservation issue • ”Small populations are generally likely to go extinct because of demographical and environmental stochasticity and genetics is unlikely to make a substantial difference” (Lande 1989) 39 • Models in which non-genetic (environmental stochasticity and population demography) and genetic processes are included have shown that many populations will loose most or all of their neutral genetic diversity before non-genetic random events lead to extinction (Vuketich, J. A. & Waite. T. A. 1998. Erosion of heterozygosity in fluctuating populations. Conservation Biology 13: 860-868) 40 • Genetic diversity is important: island populations more prone to extinctions (Frankham 1998) – – Of animal extinctions since 1600, 75% have been of island species 90% of species driven to extinction in historic times have been island dwellers 41 • In island populations inbreeding coefficients are high 42 • Example: Black robin (Petroica traversi, Chathaminsieppo) – In 1980 the entire black robin species comprised only of 5 birds, and the current population of 287 mature individuals (2013) is known to be derived from a single breeding pair (S. L. Ardern & D. M. Lambert. 1997. Is the black robin in genetic peril? Mol Ecol 6 : 21– 28) 43 • Levels of minisatellite DNA variation in the black robin are among the lowest reported for any avian species in the wild. • Surprisingly, similarly bottlenecked control populations of a closely related species (P. australis australis) exhibit significantly higher levels of genetic variation. 44 45 • The observed pattern suggests that the black robin's persistence in a single small population for the last 100 years, rather than the recent bottleneck itself, accounts for the low genetic variation observed. • Despite genetic impoverishment, survival and reproductive performance indicate that the black robin is viable under existing conditions. • This illustrates that significant levels of genetic variation are not a necessary prerequisite for endangered species' survival. 46 • Example: Glanville fritillary (Saccheri et al. 1998) – Genetic diversity important: extinction risk and inbreeding • Seven loci studied (5 allozymes, 2 microsatellites) in populations with different numbers of individuals 47 • • • Level of heterozygosity made a significant contribution to the model explaining the observed extinctions Inbreeding affects several fitness components in Glanville fritillary populations Single generation of brother-sister inbreeding decreased egg hatching rate by ca 30% Black = extinct White = surviving sample model: isoclines for the extinction risk predicted by the model, including ecological factors and heterozygosity 48 • Adder population in Sweden (Madsen et al. 1999; Nature 102: 34-35) – adding a single new male increased significantly the number of adults and recruits 49