Why are color patterns in red-tailed hawks so polymorphic?

Ferruginous Hawk

Heterozygous advantage in European buzzards (Example 8.2)

Paper Outline

Today

Chapter 9: Population subdivision

Estimating gene flow

Questions???

Chapter 10 Multiple loci: Gametic disequilibrium

Concept

CausesLinkageSmall population sizeHybridization

Describing gene flow in natural populations

(1) Indirect:

Measure FST and estimate mN withisland model.

2. Direct:

Assign individuals into populations based on their genotype . “Assignment tests” approach.

(1) Indirect: Long-toed salamander

Tallmon et al. 2000. Genetic differentiation among long-toed salamander (Ambystoma macrodactylum) populations. Copeia 27-35.

Overall

FST

mN ≈ 1

Ne = 123 ± 79

mN ≈ 1 m ≈ 1%

mN ≈ 1 m ≈ 1%

Under- or over-estimate?

(2) Direct approach

Genotypes can be used as “genetic tags” to identify the population of origin of individuals and to detect migrants.

Waters, J. M., L. H. Dijkstra, and G. P. Wallis. 2000. Molec. Ecol. 9:1815-1821.

Adult

100 – 150 mm

(matures at 1- 3 years; spawns in estuaries)

Inanga (Galaxias maculatus)

Whitebait

50 mm

(21-23 weeks)

mtDNA sequence divergence

1%

Migrant haplotype found in NZ

Genetic marking

Genotypes can be used as “genetic tags” to identify the population of origin of individuals and to detect migrants.

“Assignment tests” approach. Assign individuals into populations based on their genotype at many nuclear loci. (See Sections 9.8.4 & 16.4.2).

See Section 16.4.2

The multiple locus genotype of an individual can be used to “assign” the individual to its most likely population of origin.

The multiple locus genotype of an individual can be used to “assign” the individual to its most likely population of origin.

Potential source populations

A B C D E Indiv

Which source population is Indiv most likely from? A, B, C, D, E

Potential source populations

A B C D E Indiv

Northwest Science 83:154-162

Genotyped at 16 microsatellite loci to determine if a native or migrant genotype.

Northwest Science 83:154-162

Genotyped at 16 microsatellite loci to determine if a native or migrant genotype.

Mountain lion killed by car in ConnecticutGenotyped at 18 microsatellite loci

Use of assignment tests in analysis of mixed stock harvest

Chulitna Lodge Beach 99

Idavain Ck 00

Nuyakuk L. 00

Koktuli R. 00

Lower Talarik 00

Margo Ck 01

American Ck 01

Nick-N-Ck 00

Dennis Ck 00

Fuel Island 00

Gibraltar L. 00

Brooks L. 00

Kijik L. 00

HaplotypesTC

Chinkelyes Ck 00

Triangle Island 00

Headwaters Ck. 01

Finger Beach 00

Tommy R 00

Iliamna R 99

Copper R 00

Southeast Ck 00

Tazimina R 01

American Ck 00

Knutsen Bay 00

Cytochrome b SNP

Bristol Bay

Port Moller test fishery (7 day advance warning)

Contract vessel used to test fish Port Moller transect

Bristol Bay

Port Moller test fishery (7 day advance warning)

Day 1

Fin clips taken from fish at each station

Bristol Bay

Port Moller test fishery (7 day advance warning)

Day 3 – Samples to Anchorage

Day 4 – Samples analyzed in Anchorage

0

0.05

0.1

0.15

0.2

0.25

0.3

0.35

0.4

6,000,000 fish surplus

Day 5 – Analyses reported

Day 6-7 – Directed Harvest

Chapter 9 Subdivision: Questions???

Which population structure is most likely to lead to long-term persistence?

Summary of Chapter 9

(1) Gene flow decreases divergence among populations and increases genetic variation within populations.

(2) In the absence of selection, divergence is a function of the number of migrants:

(3) Natural selection can ‘swamp’ the effects of gene flow in large populations (e.g., outlier loci).

r = 0.5 for unlinked loci on different chromosomes. Loci are linked if r < 0.5

r = recombination rate

Gametic (linkage) disequilibrium

D will be zero if genotypes at the two loci are randomly associated (multiplication rule)

A locus: p1 = 0.4; q1 = 0.6

B locus: p2 = 0.7; q2 = 0.3

D = (0.40) – (0.4)(0.7) = 0.12

NOTE: Each locus is in H-W proportions.

D=0[D=0.12]

When should we be concerned about possible gametic disequilibrium?

(1) Closely linked markers.

(2) Small effective population size

(3) Hybridization

When should we be concerned about possible gametic disequilibrium?

(1) Closely linked markers.

A neutral marker (e.g., microsatellite locus) can appear to be under selection because it is in gametic disequilibrium with a selected locus.

Hitchhiking during a selective sweep of advantageous mutatiion

Selected locus

0.033

CPA112

11 allozyme loci

8 microsatellite loci Outlier Locus

Expected distributions in absence of selection

When should we be concerned about possible gametic disequilibrium?

(1) Closely linked markers.

(2) Small effective population size

(3) Hybridization

N = 5

N = 2 AB/ab Ab/aB p1=0.5 p2=0.5 D=0

AB

ab

Ab

aB

aBaB

aB

ab

ab

ab

Ab

Ab

Ab

ABAB

AB

Random sample of 4 gametes from the gamete pool

N = 2 p1= p2= D=

Example 10.5Siberian jay103 microsatellite loci

83% loci on different chromosomes show significant gametic disequilibrium.

Even distant loci on the same chromosome are in gametic disequilibrium

Guest Box 10: Phillip Island foxes

When should we be concerned about possible gametic disequilibrium?

(1) Closely linked markers.

(2) Small effective population size

(3) Hybridization

Gryllus firmus (F) G. pennsylvanicus (P)

Example 10.3: Hybrid zone of field crickets

Yellowstone cutthroat trout

(YCT)

O. c. bouvieri

Rainbow trout

(RT)

O. mykiss

(Illustrations by Joseph R. Tomelleri)

Westslope cutthroat trout

(WCT)

Oncorhynchus clarki lewisi

D = coefficient of gametic disequilibrium (measure of nonrandom association of two loci)

Genotypes at eight diagnostic allozyme loci and mtDNA from Forest Lake, Montana.

W = homozygous WCT

WY = heterozygous

Y = homozygous YCT

Hybrid swarm: a population of individuals that all are hybrids by varying numbers of generations of backcrossing with parental types and mating among hybrids.

Decay of gametic disequilibrium

Which of these two hybrid swarms is older?

Note: A, B, and C are linked pairs of loci.

Bull trout = BL (L= homozygous)

Brook trout = BR (R = homozygous)