Population Biology Primer PDF

1 Population biology: a primer Tania Gilbert, BSc, MSc, PhD Conservation Biologist, Marwell Wildlife Learning outcomes 2 At the end of this lecture you will be able to: 1. Demonstrate knowledge & understanding of the challenges faced by small populations 2. Evaluate the genetic factors that cau...

1 Population biology: a primer Tania Gilbert, BSc, MSc, PhD Conservation Biologist, Marwell Wildlife Learning outcomes 2 At the end of this lecture you will be able to: 1. Demonstrate knowledge & understanding of the challenges faced by small populations 2. Evaluate the genetic factors that cause population extinction & propose management interventions to counter these 3 Introduction • Many species threatened with extinction • Human related activities reduce population sizes (deterministic threats) where they then become susceptible to additional environmental, catastrophic, demographic and genetic factors (stochasticity) 4 The extinction process The extinction process • Declining population paradigm – The cause of ‘smallness’ (deterministic threats) • Habitat destruction • Habitat degradation • Habitat fragmentation • Over-hunting & live capture • Pollution • Invasive species • Major disease outbreaks 5 The extinction process • Small population paradigm – The effects of ‘smallness’ – Factors causing extinction under the small-population paradigm • Environmental stochasticity • Catastrophes • Demographic stochasticity • Genetic deterioration 6 • Environmental stochasticity: random unpredictable variation in environmental factors such as temperature and rainfall 7 • Demographic stochasticity: random unpredictable variation in sex ratios, and birth and death rates • Catastrophes: extreme environmental events such as disease epidemics or hurricanes • Genetic stochasticity: inbreeding depression, loss of genetic diversity and the accumulation of deleterious mutations • Small populations tend to be more inbred, lose genetic diversity more rapidly, and have a reduced ability to adapt to environmental change than large populations The extinction process • Small population paradigm – The effects of ‘smallness’ – Factors causing extinction under the small-population paradigm • Environmental stochasticity • Catastrophes • Demographic stochasticity • Genetic deterioration • Even if the cause of the original population decline is removed, the problems associated with small populations will persist • Threatened species have small and/or declining populations 8 9 Demography: the numbers game • Population growth rates • Mortality, reproductive rates and life tables • Demographic stability • Demographic stochasticity Stable age distributions • An age pyramid graphically demonstrates the sex and age structure of a population Scimitar-horned oryx EEP 11 Demographic stochasticity • If we genuinely want to understand how a population is likely to behave, we need to understand how stochasticity impacts it • Fluctuation in annual life-history events due to chance alone – Births – Deaths – Sex ratio at birth • Demographic stochasticity has a larger impact in smaller populations 12 600 Population size 500 400 λ = 1.053 300 200 100 0 1 2 3 4 5 6 7 8 9 10 Year 11 12 13 14 15 16 17 18 19 20 21 13 Including stochasticity 600 500 400 N λ = 1.053 300 200 100 0 1 2 3 4 5 6 7 8 9 10 Year 11 12 13 14 15 16 17 18 19 20 21 The effect of environmental & demographic stochasticity: 1 iteration 14 The effect of environmental & demographic stochasticity: 1 iteration 15 The effect of environmental & demographic stochasticity: 1 iteration 16 The effect of environmental & demographic stochasticity: 1 iteration 17 The effect of environmental & demographic stochasticity: 10 iterations 18 The effect of environmental & demographic stochasticity: 100 iterations 19 The effect of environmental & demographic stochasticity: 500 iterations 20 21 Population genetics 22 Population genetics • The long-term survival of a population depends on the retention of genetic diversity • Genetic variation enables populations to retain evolutionary potential for adaptation to both short- & long-term changing environmental conditions • New infectious pests, parasites & diseases, food sources, competitors, predators, pollution, global climate change • “Inbreeding & loss of genetic diversity are unavoidable in small populations of threatened species. They reduce reproduction and survival in the short term, diminish the capacity of populations to evolve in response to environmental change in the long term, and thereby increase extinction risk” - Frankham et al., 2010 23 What is genetic diversity? • Genetic diversity is the variety of alleles & genotypes present in the group (species, population, group) under study • All genetic diversity is originally generated by mutations that change the nucleotide sequence in the DNA • Polymorphism • Allelic diversity • Average heterozygosity – Expected heterozygosity – Observed heterozygosity 24 What is genetic diversity? E.g. African lions • 23% of coding loci were polymorphic • 7.1% of loci were heterozygous in an average individual • There were an average of 1.27 alleles per locus (allelic diversity) • Typical levels of genetic diversity for a non-threatened mammal species 25 Allelic diversity • Different forms of an allele for a particular trait (e.g. eccentricity) • Alleles present: A, b, c & d • Allelic diversity = 4 • Allelic diversity important for evolutionary adaptation to environmental change Ab Ac cc cd Ad 26 Heterozygosity How alleles are combined AA Ab Homozygote: same alleles (AA) Heterozygote: different alleles (Ab) 27 Observed heterozygosity (Ho) • Proportion of individuals in the population that are heterozygous • e.g. 23 heterozygotes & 42 homozygotes • Ho = 23/65 = 0.35 Expected heterozygosity (He) otherwise known as Gene Diversity (GD) 28 • Proportion of animals in the population expected to be heterozygous if random breeding takes place • It is defined as the probability that two homologous genes randomly drawn from the population are distinct alleles • It is the mean heterozygosity that would exist in a population if it were in Hardy-Weinberg equilibrium • The rate at which a population responds to selection is related to expected heterozygosity pp.69 – 86 Frankham et al. 2010. Introduction to Conservation Genetics 29 Small populations & the effective population size 30 Small populations & genetics • Evolutionary processes in small populations differ from those in large populations • In large populations selection is the predominant force for genetic change • In small populations, the role of chance predominates & the effects of selection are greatly reduced or removed • Chance introduces a stochastic element into the evolution of small populations • Small population have lower levels of genetic diversity & become inbred at a faster rate than large populations, and so are more likely to go extinct 31 Effective population size Ne • Genetically, it is not the actual size of the population that is important, rather the portion of the population that passes its genes onto the next generation i.e. the effective population size (Ne) N Ne 32 Effective population size Ne definition • The Ne is the number of individuals that would result in the same loss of genetic diversity, inbreeding or genetic drift if they behaved in the manner of an idealized population • Idealized population: a conceptual random mating population with equal numbers of hermaphrodite individuals breeding in each generation, and Poisson variation in family sizes Effective population size Ne Assumptions of an idealized population – – – – – – No fluctuations in population size from generation to generation Discrete (non-overlapping) generations Equal family sizes Hermaphrodite individuals Random mating N = 394; Ne = 74; Ne/N ratio = 0.20 33 34 Effective population size Ne • In reality the Ne is often much smaller than N • It is often expressed as Ne/N ratio • The rate that genetic diversity is lost is dependent on Ne not N • 50/500 rule • Ne > 50 short-term – to avoid the immediate deleterious effects of inbreeding • Ne > 500 long-term – to allow new mutations to restore heterozygosity and additive genetic variation as rapidly as it is lost by genetic drift • Now thought that Ne should be at least Ne = 1000, or even Ne= 5000 to avoid loss of genetic diversity through drift 35 Drift & selection in small populations 36 Genetic Drift & Selection in small populations • Consequences of random sampling in small populations as parents pass their genes onto the next generation: 1. Alleles (both adaptive & maladaptive) are lost due to genetic drift • Rare alleles are lost by chance • Potential increase in deleterious alleles 2. Loss of genetic diversity & fixation of alleles within populations (with the reduction in the ability to evolve) 3. Diversification of allele frequencies between replicate populations from the same original source • Loss is inversely proportional to Ne • Sampling occurs in every generation & the effects are cumulative • It is the primary process affecting genetic variation • Overrides the effects of selection & mutation 37 Genetic Drift N = 30 1.0 0.9 Allele frequency 0.8 0.7 A B C 0.6 D E 0.5 F G 0.4 H I 0.3 J 0.2 0.1 0.0 0 10 20 Year 30 40 50 38 Genetic Drift N = 300 1.0 0.9 Allele frequency 0.8 0.7 A B 0.6 C D E 0.5 F G 0.4 H I 0.3 J 0.2 0.1 0.0 0 10 20 Year 30 40 50 39 Genetic Drift N = 3000 1.0 0.9 Allele frequency 0.8 0.7 A B 0.6 C D 0.5 E F G 0.4 H I 0.3 J 0.2 0.1 0.0 0 10 20 Year 30 40 50 40 Population bottlenecks Population bottlenecks • Caused when populations undergo a substantial contraction – Catastrophes – Habitat loss – Population fragmentation • Created when individuals in the wild migrate to form new populations • When individuals from the wild are caught to form captive populations • When wild-to-wild conservation translocations take place • When reintroductions take place 41 42 Population bottlenecks • Threatened populations have lower genetic diversity than nonthreatened populations • Populations that have gone through bottlenecks have lower genetic diversity than those that have not Disease Habitat loss Subsequent bottlenecks in a wild population Time 43 Population bottlenecks • Threatened populations have lower genetic diversity than nonthreatened populations • Populations that have gone through bottlenecks have lower genetic diversity than those that have not Catch-up Wild Captive Release Reintroduced 44 Population bottlenecks • Many threatened species have been bottlenecked – – – – – – – – – – – Amur tiger Arabian oryx Black-footed ferrets California condor Chatham Island black robin European bison Guam rail Mauritius kestrel Père David’s deer Red-ruffed lemur Scimitar-horned oryx 25 10 7 14 5 13 12 2 ~5 7 45 45 Inbreeding & outbreeding 46 Inbreeding • Mating between relatives • Causes an increase in homozygosity & decrease in heterozygosity • Measured by an inbreeding coefficient (F) which is the probability that two alleles are identical by descent • Increases the chance of expression of recessive deleterious alleles in the phenotype • Can lead to inbreeding depression – – – – Increased juvenile mortality Reduced longevity Reduced reproduction Increased susceptibility to disease 47 • Inbreeding depression is found in almost all naturally outbreeding species (90%), but varies depending on the species, population & environment • Inbreeding increases the risk of extinction (80-90% of deliberately inbred populations went extinct) • Applicable to a wide range of species • It has caused population declines & extinctions in the wild in… – Bighorn sheep, Florida panthers, heath hens, greater prairie chickens, adders, wolf spiders, middle spotted woodpeckers & many plants species 48 Inbreeding coefficient (F): a measure of the relatedness of an individual’s parents ♂ ♀ Ab cd 0.5 c ♂ 0.5 A 0.5 A Ac 0.5 A AA 49 Inbreeding coefficient (F): a measure of the relatedness of an individual’s parents ♀ Ab ♂ 0.5 A 0.5 A Ac 0.5 A AA • A = 0.5 x 0.5 x 0.5 = 0.125 50 Inbreeding coefficient (F): a measure of the relatedness of an individual’s parents ♀ Ab ♂ 0.5 b 0.5 b bc 0.5 b bb • b = 0.5 x 0.5 x 0.5 = 0.125 51 Inbreeding coefficient (F): a measure of the relatedness of an individual’s parents ♀ Ab ♂ 0.5 A 0.5 A Ac 0.5 A AA • F = probability of AA or bb = 0.125 (AA) + 0.125 (bb) = 0.25 • 12.5% chance ‘AA’ + 12.5% chance ‘bb’ (homozygous) • 75% chance A or b with c or d (heterozygous) 52 Inbreeding coefficient (F) • Father/daughter • Brother/sister F = 0.2500 • Half brother/sister • Uncle/niece • Grandfather/granddaughter F = 0.1250 • First cousins F = 0.0625 • Unrelated male & female F = 0.0000 Outbreeding depression 53 • Deleterious effects (e.g. reduced reproductive fitness such as reduced offspring survival) that sometimes occur as a result of outcrossing genetically differentiated populations • Expected in crosses between different sub-species or species e.g. crosses between Bengal & Amur tigers would produce offspring maladapted to both environments • Ibex in the Tatra Mountains, Slovakia – Introduction of desert-adapted sub-species from Turkey & Sinai – Hybridised with local population – Maladapted hybrids mated in early autumn & gave birth in February at the height of winter. Offspring did not survive – The population went extinct Outbreeding depression • Inbreeding and outbreeding depression can occur simultaneously (Arabian oryx) • Heterosis (hybrid vigor) – improved fitness of hybrids 54 Population structure & fragmentation 55 56 Population structure & fragmentation • Population fragmentation results in a number of small populations. At risk of factors that impact all small populations EU BT 0 EU LRZ 8 EU BT 1 & 8 EU BT 8 Non-EU Ne = 10 Ne = 16 Ne = 33 Ne = 17 Ne = 0 Population structure & fragmentation 57 58 The extinction vortex Habitat loss Epidemic disease Overhunting 59 Invasive species Small fragmented isolated population Demographic stochasticity Catastrophes Reduced N Extinction vortex Environmental variation Reduced adaptability, survival and reproduction Loss of genetic diversity and inbreeding The extinction vortex • The adverse interaction between human impacts, inbreeding & demographic fluctuation that results in a feedback loop that spirals towards extinction • Small populations become more inbred & less demographically stable, further reducing N & increasing inbreeding • The complicated interactions between genetic, demographic and environmental factors can make it extremely difficult to identify the immediate cause of any extinction event • Small populations are more susceptible to extinction than larger ones for demographic, genetic and ecological reasons 60 61