why are color patterns in red- tailed hawks so polymorphic? ferruginous hawk
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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)
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