CONSERVATION BIOLOGY BISC 309 Lec 2 - SFU.caConsGen1).pdf · CONSERVATION BIOLOGY BISC 309 Lec 2 . REMINDER Course info Where is it? Go to biology homepage Click courses Click Conservation

CONSERVATION BIOLOGY BISC 309 Lec 2

REMINDER

Course info Where is it?

Go to biology homepage

Click courses

Click Conservation Biology

Course information

Tutorial material -readings

Lecture outlines

Today Introduction to conservation genetics

Genetics (basics) – alleles, heterozygosity, genetic drift, inbreeding, quantitative traits Evolutionary Analysis

Conservation Genetics Ch 11. Principles of Conservation Biology 3e

Papers on Conservation Genetics Week 2 readings------ on course webpage Week 3 readings ----- coming

IUCN (the World Conservation Union)

recognizes the need to conserve biodiversity at three levels

genetic diversity

species diversity

ecosystem diversity

What causes extinction?

habitat loss introduced species overexploitation

So Why focus on genetics?

Genetic variation may reduce extinction risk allow future adaptive evolutionary change

Genetic data can be a tool to help monitor populations

Why focus on genetics?

“Wild species must have available a pool of genetic diversity if they are to survive environmental pressures exceeding the limits of developmental plasticity. If this is not the case extinction would appear inevitable”

OH Frankel 1983

“Gene pools are becoming diminished and fragmented into gene puddles” Thomas Foose 1983

ROADMAP for next 2-3 lectures

Genetic Variation What is it?

How do we describe it?

What influences genetic variation? Ne, genetic drift, inbreeding

How important is inbreeding and the loss of genetic variation?

- fitness and extinction risk - ability to adapt

Genetic material

1.! Coding (genes under selection) -! adaptive variation -! markers (allozymes, MHC, other genes)

2. Non-coding (not subject to selection) -! Neutral markers

variable number tandem repeat loci AFLP’s, RAPD’s, SNP’s

mini and microsatellites

Q. What are the limitations of microsatellite data?

A species’ pool of genetic diversity exists at three fundamental levels

Loci - monomorphic no variation - polymorphic variable

Genetic variation: individuals

A A A a

homozygous heterozygous

Heterozygosity - proportion of loci that are heterozygous

Allelic diversity - number of alleles per loci

Average heterozygosity (H) – proportion of heterozygous loci in an average individual

H= 1 1

L ! total heterozygotes L total individuals

Genetic variation: within populations

Genetic diversity in African lions

Allele Enzyme locus 1 2 3 Heterozygosity ADA 0.56 0.33 0.11 0.564 DIAB 0.61 0.39 0.476 ESI 0.88 0.12 0.211 GPI 0.85 0.15 0.255 GPT 0.92 0.11 0.196 MPI 0.92 0.08 0.147 20 other loci 1.00 0

Q. Calculate mean heterozygosity (H) and mean allelic diversity (A)

Genetic variation: among populations

H2

H1

H3

D12 D13

D23

Ht=Hp + Dpt Total genetic variation =

average diversity within pop’ns + average divergence among pop’ns

Red cockaded woodpecker

Overall mean heterozygosity = 0.078

Among population Dpt 14%

Within population Hp 86%

Q.!Are more vagile taxa (birds, insects) likely to have higher or lower Dpt

Q. How is variation likely to be partitioned in ibex (alpine) and white-tailed deer?

FST = HT-HS /HT

= degree of genetic differentiation among pop’ns

Genetic variation: calculating F-statistics

Individual HI Subpopulation - random mating HS Total population - random mating HT

FST = 0, indicate pop’ns are same FST =1, indicates pop’ns have unique gene for each locus

Mutation

Genetic drift

Inbreeding

All a function of EFFECTIVE population size

Ne

What influences genetic variation?

Estimation of effective population size

Sex ratio Ne=(4 x Nm x Nf)/ (Nm + Nf)

Variation in RS Ne=k(Nk-1)/(Vk+k(k-1)) k, number surviving progeny Vk, variance in progeny number

Fluctuation in Population size 1/Ne= 1/t(1/N1+1/N2+…+1/Nt) Ne=t/!(1/Nei)

Estimating effective population size. 1

If a harem has 1 male and 100 females, the effective size is

Ne =(4 x Nm x Nf)/ (Nm + Nf)

=

Unequal sex ratios reduce effective size


When Vk/k >1 Ne is less than census size

Variance in LRS = 12.1 Mean family size, k=1.7

If captive population N=10

Ne=k(Nk-1)/(Vk+k(k-1))

Ne=


Effective size is much closer to minimum than mean

Hunting reduced Northern elephant seal pop’n to 20-30 individuals before they recovered to over 100,000. Assume Ne1= 100,000

Ne2= 20 Ne3=100,000

Calc Ne Ne=t/(1/ Ne1 + 1/ Ne2 + 1/ Ne3) Ne=

Effective population size

Ne can be estimated from demographic data on sex ratio, variance in family size, and pop’n fluctuations

Fluctuations in pop’n size have greatest impact on reducing Ne, followed by variance in population size

Estimates of Ne that incorporate all factors average only 11% of census sizes

What influences genetic variation? Genetic drift:

random change in gene freq over time due to chance

If population crashes to Ne of 20 After 5 generations Predict 88% of heterozygosity remains

Change in heterozygosity

Ht=H0*(1-1/2Ne)t

Q. What assumptions are made in this eq’n?


Heterozygosity is lost more quickly from small pop’ns


random loss of alleles over time due to chance

Rare alleles are lost more quickly from small pop’ns

Genetic drift

is the random change in gene frequency or random loss of alleles due to chance

the effects of chance are greater in small than large populations

population bottlenecks can lead to rapid loss of rare alleles and a reduction in heterozygosity

What influences genetic variation Inbreeding

What is it?

Inbreeding is the mating of individuals related by ancestry

Inbreeding is unavoidable in small populations


How is it measured?

The inbreeding coefficient of an individual (F)

- refers to how closely related its parents are

- is the probability that it carries alleles at a locus that are identical by descent

Unrelated F=0 Brother-sister F=0.25 First cousins F=0.0625 Self-fertilization F=0.5


How is it calculated?

pedigrees F=!(1/2)n (1+Fca)

Only 1 pathway link the two parents

n=7, FDBACEG

If A not inbred, Fca=0

Fx= (1/2)n = 1/128


How is it calculated?

pedigrees F=!(1/2)n (1+Fca)

Q.!Calculate Fx for this male dorca’s gazelle Hint - there are 5 paths and FE=1/4


Inbreeding accumulates over time

Inbreeding accumulates more rapidly in small pop’ns, "F= 1/2Ne

F

generation


How else is it calculated?

heterozygosity data

Ht/H0 = (1-1/2Ne)t = 1-F

Fe = 1-(Ht/H0)

Estimating population inbreeding coefficients

Fe = 1-(Ht/H0) Fe =

Isle Royale gray wolves Established in 1949 n = low 1980 n=50, 1990 n=14 Allozymes 25 loci

heterozygosity = 3.9% Mainland pop’n

heterozygosity = 8.7%

Q. Calculate inbreeding coefficient for the island


What does inbreeding do?

Reduces the frequency of heterozygotes Exposes deleterious recessive mutations

May therefore reduce fitness Does NOT change allele frequencies

Inbreeding

Is mating of individuals related by ancestry

Accumulates over time and does so more rapidly in small populations

the increment in inbreeding per generation is equal

to the loss of heterozygosity

Exposes any deleterious recessive mutations

May reduce fitness

Frankham 1996 summarized available data

Species with more diversity have larger pop’ns and occupy more area Does this mean greater diversity is beneficial?

TODAY You should be able to:

Calculate Ne,and F Understand how:

Ne affects drift and inbreeding Drift and inbreeding influence genetic

diversity

NEXT How do inbreeding and the loss of genetic variation influence

- fitness and extinction risk - ability to adapt

CONSERVATION BIOLOGY BISC 309 Lec 2 - SFU.caConsGen1).pdf · CONSERVATION BIOLOGY BISC 309 Lec 2 . REMINDER Course info Where is it? Go to biology homepage Click courses Click Conservation

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