Demographic history

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(No Transcript)
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Signature of adaptation/selection (SFS, patterns
of LD)
Demographic history spatial structure (multiple
neutral loci)
Bottom-up approach
Population genetics
Candidate genes
Phenotype
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Talk outline objectives
1) Background information on wild tomatoes
2) Multilocus sequence data patterns of
variation and the pooling effect
3) Coalescent simulations of expanding
subdivided populations contrasting three
sampling schemes
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Morphological diversity in Lycopersicon
S. chilense
S. pennellii
S. peruvianum
S. lycopersicum
S. neorickii
S. habrochaites
S. pimpinellifolium
S. cheesmaniae
Photo C M Rick
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Hypothetical phylogeny of clade Lycopersicon
S. lycopersicum
red fruits
S. pimpinellifolium
S. cheesmaniae
SC
S. neorickii
S. chmielewskii
S. arcanum
S. peruvianum
green fruits
S. chilense
SI
S. habrochaites
S. pennellii
Solanum sp.
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S. peruvianum habitat (Nazca, 2150 m)
S. peruvianum (p, purple)S. chilense (c,
yellow)
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S. peruvianum (Canta, 2100 m)
curved anther cone
mesic habitat
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S. chilense (Tacna, 1250 m)
quebrada habitat
flower morphology
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S. chilense habitat (Quicacha, 1530 m)
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S. chilense Moquegua, 2800 m S.
peruvianum
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Counts of site categories across 9
peruvianumchilense population comparisons (7
loci)
253
174
73
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1-3 Tarapaca
4-6 Nazca
Sx1
Sx2
7-9 Canta
Ss
Sf
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Weighted nucleotide diversity (?) across 7 loci
Species/population bp SNPs
? () ?w /?betw DTajima
S. peruvianum TAR 9,314
322 1.181 0.877 0.22 ARE
9,286 186 0.795 0.590
0.41 NAZ 9,304 318 1.112
0.826 0.14 CAN 9,309 400
1.298 0.964 0.55 S.
chilense ANT 9,344 125
0.607 0.518 1.53 TAC 9,353
260 0.944 0.805 0.03 MOQ
9,347 276 1.055 0.900
0.05 QUI 9,317 257 0.977
0.833 0.13
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The site frequency spectrum summary of
genealogical information about the sample
Example CT179Tarapaca (S. peruvianum) 10
sequences, 29 segregating sites in 958 bp
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Site frequency spectrum of pooled S. peruvianum
sample
D 0.88
Example CT179, 43 sequences, S 99 in 899 bp
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The pooling effect means of within-deme
estimates vs. estimates from pooled samples (4
demes, 78 loci)
S. peruvianum
S. chilense
Similar patterns have been observed widely
humans, Drosophila, several studies on plants
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D 0.55
Ray, Currat Excoffier (MBE 2003) Intra-deme
molecular diversity in spatially expanding
populations
D 1.90
Simulated a range expansion under stepping-stone
spatial structure (50 x 50 grid) parameters
chosen with humans in mind
Samples (30 sequences) are taken from single
demes and evaluated by summary statistics
D 2.48
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Putting it all together Interpretations/qualita
tive predictions in Arunyawat, Stephan Städler
(MBE 2007)

• Pooling effect reflects the changed
  genealogical structure of combined samples,
  akin to adding (unrelated) migrants
• Site-frequency spectra should be ?intermediate
  between those of single-deme and species-wide
  (scattered) samples
• (Strongly) negative Tajimas D values reflect
  species-wide expansion and are conservative
  indicators of demography

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Population subdivision evaluating sampling
schemes
20 sequences from 1 (local), 4 (pooled), and 20
demes (scattered)equilibrium subdivided
population (stepping-stone model, 100 demes)
(level of gene flow, 4 N0m)
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Simulating a range expansion with population
subdivision
20 sequences from 1 (local), 4 (pooled), and 20
demes (scattered) Stepping-stone 100 demes
splitting from ancestral population at time ?,
with up to 100-fold expansion
expansion factor ?
level of gene flow, 4 N0m
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Simulating a range expansion with population
subdivision
20 sequences from 1 (local), 4 (pooled), and 20
demes (scattered) 100 demes splitting from
ancestral population at time ? (in 4 N0m gen.)
?
island model
stepping-stone model
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Contour plots showing average DT values in
simulations designed to mimic our wild tomato
data local 11 sequences, pooled 4 x 11
sequences 4 N0m 5 400 demeshere island
model
expansion factor ?
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Some implications and challenges

• (Consideration of) sampling scheme of utmost
  importance in drawing robust inferences
• Almost no species should be regarded as truly
  panmictic (FST is not measuring
  differentiation ? vs. S) ? of demes and ?
  as determinants of differentiation?
• Inferring selection using an appropriate
  demographic model?

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Acknowledgments
Gertraud Feldmaier-Fuchs Hildegard Lainer Uraiwan
Arunyawat Tobias Marczewski Carlos
Merino Kerstin Roselius Aurelien Tellier (LMU
Munich) Gabriel Clostre Asunción Cano
(Peru) DFG SPP 1127 Radiations Origins of
Biological Diversity
1a technical support
past and present Ph.D./M.S. students(LMU Munich)