Quizes are on Wednesdays

Week! ! Topic! Workshop! Notes1! 06-Jan !Species ! None Heard Chapter 1, reviews, papers2! 13-Jan! Taxonomy! Research Choose your papers3! 20-Jan! Phylogenetics! Lemurs! QUIZ on Wednesday4! 27-Jan! Extinction! Lemurs! Steadman on Wednesday5! 03-Feb!Diversification Lemurs finish lab6! 10-Feb!Reading Break------------------------- read your article7! 17-Feb! Extinction Economist lab due; QUIZ on Wednesday8! 24-Feb!Measurement/SAC Economist work on Economist9! 03-Mar!SAC Critique QUIZ on Wednesday10! 10-Mar!Species energy! Parks ! Economist due Monday11! 17-Mar!Species function Critique ! QUIZ on Wednesday12! 24-Mar!GCC! ! Critique! first draft due Friday13! 31-Mar!Extra ! Extra papers back Wednesday14! 07-Apr!Presentations! Presentations! final paper due Monday 14th

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Quiz 2

1. The Jukes-Cantor model for the observed percent substitutions (p) as a function of the actual genetic distance (µt) is below. What is the maximum that p can take under this model? Why?

2. How is the coalescent process relevant to taxonomy?

3. How is it relevant to studies of diversification dynamics?

4. Draw and label a Lineages-through-time plot for a Yule model of diversification.

5. Consider extinction risk correlates in mammals (from Cardillo et al., Science, 2005)

Draw separate curves for small and large-bodied mammals if lower range species are at higher risk generally and there is a positive interaction with body size (i.e. the effect is greater in large-bodied species)

risk level

geographic range size

low

high

low high

Flip side of tree creation: EXTINCTION Extinction is an extreme population bottleneck

--the final blow (whatever it is) happens tosmall populations (with notable exceptions)

1. Patterns of extinction2. Correlates of extinction (-risk)3. The final blow

"Evil Quartet" leading to small populations (J. Diamond)

1. Habitat loss (e.g. Spotted owl, Passenger pigeon, Florida panther)

2. Overexploitation (Passenger Pigeon, Dodo, large mammals etc...)

3. Introduced species (Brown snake on Guam, rats in NZ)

4. Chains of extinction (knock-on effects: end of lecture)

Threats to small populations: Ecological Genetic

A. Ecological and Genetic:

1. Demographic stochasticity: last 5 dusky seaside sparrows (Ammodramus maritimus nigrecens) were all male (Pall one sex =21-N). Only 2/9 baby Kakapos (N=62) were female in 1999N=122 Kakapos (2008) sex ratio still highly male-biased)

Great evolutionary conservation story attached to this:http://evolution.berkeley.edu/evolibrary/news/060401_kakapo

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2. Environmental stochasticity:If Var[growth rate] > growth rate, populations are doomed.

This suggests that larger bodied species are at higher risk, since their growth rates are so low?

Pop 1

Pop 2

Demographic stochasticity plus behavioural ecology can lead to the Allee effect (Allee, 1949):

Growth rate of the population falls as the population size falls.At the limit, can become negative, making extinction inevitable

Marmota vancouverensis

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Brashares et al., JAE, 2010

Social ʻmeltdownʼ in the demise of an island endemic:Allee effects and the Vancouver Island marmot

Marmota vancouverensis

...+Atlantic cod and other fishes?

B. Genetic

Depression of Ne (effective population size)leads to:

(i) inbreeding depression

(ii) mutational meltdown

(iii) loss of genetic variance

What is this?

Ne: size of female population if it were ideal - that means, if it has a:

- stable population size (so expect 2 offspring per pair)

- all individuals mate same number of times

- number of offspring is distributed across parents randomly(roughly, x = var(x) = 2 [this is a “Poisson” distribution])

However, we usually only measure N (census size)

What could lead to Ne<N? Ne>N?

Things that depress Ne - make population genetically smaller than it “looks”

Variation in-

population size:

sex ratio:

family size:

Ne is harmonic mean across generations t

Ne goes down with fewer males (m) than females (f) or vice versa

V_f is variation in family size.Ideal = 2, i.e. under Poisson

m

What is ratio of N/Ne in wild populations?

(Frankham, 95)

However, survey of 102 species: mean Ne/N ~ 0.1

(range 10-6 for pacific oysters to 0.994 for humans!)

from multiple regression, following factors influence Ne/N:

var(population size) Biggest factor by farvar(family size)taxonomic group sex ratio

Old rule of thumb says Ne/N ~ 0.33

‘Lab’: lots of evidence of detrimental effect

Lower Ne can lead to: (i) inbreeding depression

inbreeding: increase in homozygosity due to increased matingamong relatives. Always relative to some baseline...inbreedingdecreases performance

Human height 1.6 (% drop per 10% inbreeding) IQ 4.4

Cattle milk yield 3.2

Pig litter size 3.1 weight 4.3 Maize height ~2.2 yield ~6.2 (Falconer and Mackay, 1996)

Inbreeding depression, simple conservation example

Wild: Florida panther - Texas panthers introduced after 1990

before 1990 F1 & F2kinked 0.88 (48) 0.00 (15)tail

cowlick 0.93 (46) 0.14 (14)

proportion (N)

(Hedrick, 2001)

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Rarely is Ne>N.But it does happen

NZ Dept. of ConservationCephalorhychus hectori maui

Maui's Dolphin (subspecies of Hector's)

Census size ~ 80genetic-based Ne ~112-200 (based on genetic markers)

Huge drop in N from 1970 (N=2000) to 2006 (N=79)

Rebecca Hamner

(ii). Mutational meltdown (Lynch, 1995)

1. genetic drift in small populations allows the fixation of mildlydeleterious mutations (“Muller’s ratchet”)

2. population mean fitness drops, which can decrease population size (e.g. fecundity drops)

3. the smaller population is now at even greater risk of fixingdeleterious allele due to drift

and this ‘extinction vortex’ spins faster and faster...

Empirical evidence of (impending) meltdown?

--Natterjack toads in Great Britain (Bufo calamita)

GB is northwestern edge of range (so all populations are ‘peripheral isolates’)

Rowe and Beebee, 2003

compared one (isolated) population with N=50 (Saltfleetby), and one (well-connected) population with N~500 (Ainsdale)

previous genetic (microsatellite) work suggests both are in H-W equilibriumbut polymorphism lower in Saltfleetby

same study estimated Ne=0.1*N

--fitness experiments performed in one environment ("transplant")1. transplanted eggs from large pop to small pop environment,2. raised in cages with or without predators, competitors, desiccation stress

Rowe and Beebee, 2003

large population

small population

Grown in the small population's environment

explanation is that Saltfleetby population is suffering froma “genetic load” due to both-lower polymorphism generally (less variation, recessives expressed?)-fixation of mildly deleterious alleles due to drift.

small

large

(iii). Loss of genetic variation - adaptation may be slowed becauseboth less standing variation and less input of new mutations

Experimental evidence (e.g. Drosophila in cages)

-but v. hard to measure meaningful evolution in the wild,so hard to know its importance (though often talked about)

“Adaptive evolution is effectively over for large mammals.” NAS panel, ‘03

Was this a factor in the demise of large mammals during the Pleistocenemegafaunal extinctions?

What is the relative importance of these three geneticprocesses?

inbreeding is short term (and so interacts with demography)

meltdown is medium-term (?)

response to selection is (probably) long-term

Outstanding questions:

1. Are genetic problems important, given ecological ones? -i.e. for a given N, which is more important?

2. How do the two processes interact (probably badly)?

we'll return to extinction after we look at species-area curves,and again when we consider Endangered Species Legislation

Knock-on effects (Crooks & Soule, '99)

coyote

mesopredators

passerines

+, - refer todirection ofcorrelation: more cats, fewer birdsbigger fragments, more birds

bigger fragments have more birds because theyhave more coyotes (and so fewer cats).

Coyotes mediate the relationship between fragment size and bird numbers

Sexual Selection and Local Extinction - Doherty et al. PNAS 2003

BirdRoadrunnerGeococcyx californiaus

Birders

Question: do dimorphic species disappear...

from Breeding Bird Survey routes from one year to the next more often than...

monomorphic species

Data collection: For every route:

1. 5 groups of 10 stops (each 0.8 km apart) every year (1975-1996)(there are 4000+ routes in US and Canada)

2. For every stop, what species are recorded?

3. This is turned into 2 pieces of information:

-number of dimorphic and monomorphic species-actual list of dimorphic and monomorphic species

www.mbr-pwrc.usgs.gov/bbs/bbs.html

Because the 2 classes of bird might have different detection probabilities,have to make correction to avoid bias:

Use a ‘jackknife estimator’ (we may see this again later) =

Ns = S + (x-1)/x * (number of species seen only once)

actual number seen over all stops

number of samples

So “harder to see class” gets bumped up by more species(at the limit, there is a missing species for every one only seen once!)

estimate rare species

These numbers and names are then converted into two measuresper route (for both dimorphic and monomorphic species separately)

‘extinction’ !" =1- !’ = 1# (#spp that returned in year t+1)(#spp in year t)

‘turnover’ !$ =1- !”= 1# (# new spp in year t+1)(#spp in year t+1)

Then calculate a ‘statistic’ (y) for each route and for each year:

!" d - !"

m

Under the null hypothesis, this should be zero on average:sometimes extinction is higher for dimorphic, sometimes higher for monomorphic species

One can use maximum likelihood to estimate the most likelyvalue for your statistic, and then see if it is different from zero(in which case, null hypothesis fails to account for the data)

y"= !" d - !"

m

For extinction:But “spatial autocorrelation” means observations aren’t independent

Most likely value for a route is actually mean across all routes for all years + ƒ(mean of routes near yours)

eg. if routes near you had large differences in extinctions betweendimorphic and monomorphic species (even if µ = 0), then your route will too! (stands to reason if ecology is involved).

y = µ + %

yE = !Ed - !E

m over 21 years, per route