The genetics of adaptive evolution and speciation in...
Transcript of The genetics of adaptive evolution and speciation in...
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The genetics of adaptive evolution and speciation in monkeyflowers
Toby BradshawDept. of BiologyUniversity of Washington
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Why are there species?“… the living world is not a
formless mass of randomly combining genes and traits, but a great array of … gene combinations, which are clustered on a large but finite number of adaptive peaks.” – Theodosius Dobzhansky
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MimulusMimulus
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Mimulus as a model for ecological and evolutionary genetics
• ~160 species worldwide, with major radiations in western North America and Australia
• well-resolved phylogeny (except for the M. guttatus species complex)
• occupy habitats from sea level to alpine, desert to riparian to aquatic
• life history/habit/mating system diversity –annual, perennial, herbaceous, woody shrub, selfing, outcrossing, mixed, obligately asexual
• phenomenal floral diversity associated with pollination syndromes
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SpeciationBiological species concept
“Groups of actually or potentially interbreeding populations reproductively isolated from all other such groups.” – Ernst Mayr
“When we understand the origin of reproductive isolation, we understand the origin of species.” – Jerry Coyne
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Reproductive isolationPre-mating barriers to gene flow• Geographic• Ecological• Phenological• Behavioral• Mechanical
Post-mating barriers to gene flow• Gamete incompatibility• Sperm competition• Hybrid inviability• Hybrid sterility• Hybrid breakdown
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Jordan’s law“Given any species in any region, the nearest related species is not likely to be found in the same region nor in a remote region, but in a neighboring district separated from the first by a barrier of some sort.” -- David Starr Jordan (1905) Science 22: 545-562.
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“By far the commonest type of isolation in both the plant and the animal kingdom is that resulting from the existence of related types in different geographical regionswhich differ in climatic andedaphic conditions.” –G. Ledyard Stebbins (1950) Variation and Evolution in Plants
The origin of reproductive isolation by ecogeography
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The origin of reproductive isolation by ecogeography
“... not a single geographic race is known that is not also an ecological race; nor is there an ecological race that is not at the same time at least a microgeographic race.” -- Ernst Mayr (1963) Animal Species and Evolution
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The Jordan/Stebbins/Mayr pie diagram for mechanisms producing reproductive isolation
Ecogeographic
Premating barriers in sympatry
Post-mating barriers in sympatry
The speciation engine is powered primarily by divergent adaptive evolution
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Why use non-model plant systems?
Good genomics is faster than good ecology
• The whole Mimulus genome can be sequenced in less than one greenhouse generation, and in about 10% the length of a field season.
Genetic model systems are usually chosen for the same reasons that ecologists avoid them
• Small size, adapted as human commensals or to human-disturbed habitats
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Mimulus as a model for ecological and evolutionary genetics
>70 years of work on ecology, evolution, and genetics, starting with Clausen, Keck, and
Hiesey in 1929
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Bumblebee-pollinated Hummingbird-pollinatedPink RedWide corolla opening Narrow, tubular corolla
1-2μl nectar 40-100μl nectarMid-high elevation Low-mid elevation
Inserted stigma/anther Exserted stigma/anther
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Components of reproductive isolation between M. lewisii and M. cardinalis
Geography and ecology58.8%
Pollinator40.3%
Post-mating0.9%
Ramsey, J., Bradshaw, H.D., Jr., & Schemske, D.W. (2003) Evolution 57: 1520-1534.
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Components of reproductive isolation between M. lewisii and M. cardinalis
Geography and ecology58.8%
Pollinator40.3%
Post-mating0.9%
Ramsey, J., Bradshaw, H.D., Jr., & Schemske, D.W. (2003) Evolution 57: 1520-1534.
QTL5
QTL7
QTL6QTL4
QTL3
QTL2 QTL1
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Mather1400m
Jamestown450m
White Wolf2200m
Timberline3050m
lewisii1200-3100m
cardinalis30-1400m
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Jamestown(lo = cardinalis habitat)
White Wolf(hi = lewisii habitat)
1.0
0.8
0.6
0.4
0.2
0.0
1.0
0.8
0.6
0.4
0.2
0.0cardinalis lewisiiF3 cardinalis lewisiiF3
Rel
ativ
e fit
ness
Relative Fitness of Parents and F1 Hybrids
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fates dead survive to flower
deadsurvive to flower
survive to flower
genotype random sample with
genome-wide markerslow elevation
survivorsgreenhouse
survivorshigh elevation
survivors
calculate the change in allele frequency at each locus
across the genomeΔp low
elevationΔp high
elevation
greenhouseN = 500
seedlings
M. lewisii1200m-3100mF1
F2
F3
Experimental evolution in nature: the “Δp” Experiment
M. cardinalis30m-1400m
X
low elevation(Jamestown,
450m)
high elevation(White Wolf,
2200m)
field transplantN = 8,032 seedlings
field transplantN = 4,755 seedlings
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****ns
ns
****ns
****
****
ns
***
ns
****
***
*
I II III IV V VI VII VIII
**
ns
****
ns nsns
****
ns
****
**** ****M. cardinalis alleles at Jamestown 2003
M. lewisii alleles at White Wolf 2003
GH
GH
P>0.05 nsP<0.05 *P<0.01 **P<0.001 ***P<0.0001 ****
****
****
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Relative fitness of F3 genotypes at MgSTS46 (LG III)
1.0
0.8
0.6
0.4
0.2
0.0
1.0
0.8
0.6
0.4
0.2
0.0CC CL LL
Rel
ativ
e fit
ness
CC CL LLGenotypeGenotype
Jamestown(lo = cardinalis habitat)
White Wolf(hi = lewisii habitat)
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Conclusions• Differential adaptation is responsible
for most of the reproductive isolation between M. lewisii and M. cardinalis (and, according to Jordan’s law, most other pairs of sister taxa).
• QTLs distributed throughout the genome affect local adaptation, with some showing fitness tradeoffs between environments.
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Components of reproductive isolation between M. lewisii and M. cardinalis
Geography and ecology58.8%
Pollinator40.3%
Post-mating0.9%
Ramsey, J., Bradshaw, H.D., Jr., & Schemske, D.W. (2003) Evolution 57: 1520-1534.
QTL5
QTL7
QTL6QTL4
QTL3
QTL2
QTL1
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Near-isogenic lines (NILs)
lewisii
cardinalis
F1 F2
xL xL xL
NIL1
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yupYUP
Bumblebees
N=1090
yupYUP
Hummingbirds
N=201
Bradshaw & Schemske (2003) Nature 426: 176-178.
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Components of reproductive isolation between M. lewisii and M. cardinalis
Geography and ecology58.8%
Pollinator40.3%
Post-mating0.9%
Ramsey, J., Bradshaw, H.D., Jr., & Schemske, D.W. (2003) Evolution 57: 1520-1534.
QTL5 = YUP
QTL7
QTL6QTL4
QTL3
QTL2
QTL1
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ConclusionsMajor QTLs control all aspects of reproductive isolation in Mimulus, from ecogeographic (allopatric) to pollinator preference (sympatric).
The tempo of speciation depends on the genetic details – are these major QTLs single genes, or clusters of linked genes?
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From QTLs to genes?For the traits producing the greatest
reproductive isolation in allopatry (adaptation to elevation) and sympatry (carotenoid pigment deposition) there are no obvious candidate genes. Until there are ...
Two options:• Positional cloning of major QTLs• Mutagenesis (at least when one QTL allele
is recessive)
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Mimulus as a model for ecological and evolutionary genomics
• NSF FIBR project (2004-2009)• develop genomics tools and apply them to cloning genes
involved in speciation• attract investigators from “traditional” genetic model
systems• recombinant inbred lines (RILs) for mapping• near-isogenic lines (NILs) for major QTLs• sub-cM genetic maps based on EST-derived markers• physical maps from BAC libraries (2006) • Mimulus guttatus genome sequence from JGI in 2007!• transgenesis• mutagenesis
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19.5
12.0
1.8
wt M. lewisii
LIGHT AREAS
LG VII
REFLEX1
ROSE INTENSITY
YELLOW UPPER
plus:FLOWERING TIME1PISTIL LENGTH1~100 new markers from JGI
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19.5
12.0
1.8
?
100kbp~0.3cM
}3600 F2 plants900 red-flowered1800 meioses
33 recombinants0.06cM resolution~10-20kbp resolution
BAC contig
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EMS mutagenesis of M. lewisii• Christina Pince• 1776 M1 lines• 31,968 M2 plants
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M. lewisii mutants
M. parishii
M. douglasii
M. bifidus
M. inconspicuus
M. cardinalis
wt M. lewisii
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ConclusionsMany phenotypes that characterize the radiation of floral form across the genus Mimulus seem to be controlled by single loci
There is an opportunity to describe a large-scale adaptive radiation at the level of individual genes
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