Download Workshop on - Evolution and Genomics

Workshop on
population
and speciation
genomics
Walter Salzburger
Zoological Institute
University of Basel, Switzerland
evolution
“The process by which different kinds of living organism are believed
to have developed from earlier forms during the history of the earth.”
The Oxford Advanced Learner’s Dictionary
evolution
heritable variation
selection
+
ADAPTATION
INNOVATION
SPECIATION
species
distribution map
‣ …are fundamental (real) natural units
Bombina bombina
Bombina variegata
species
frequency
‣ …are varied
trait
?
time
species
‣ …are not (always) easy to define
Two species appear to be present at one place,
but those two “species” are connected by a
series of forms that are geographically
arranged in a ring. No phenetic character could
be used, except arbitrarily, to divide the ring
into two species. A division would be
meaningless, as there really is a continuum, not
a number of clear-cut, separate species.
Stebbins (1994)
Ring Species:
species
species
‣ “Species are groups of interbreeding natural populations that are
reproductively isolated from other such groups” (Mayr 1963)
Salzburger et al. (2002)
P.
ca
Eu erul
rop eus
e
The evolution of part of the original species into a
new one renders the remaining populations
paraphyletic. For example, the Blue Tit (Parus
caeruleus) is a paraphyletic species. The North
African subspecies P. c. degener and P. c.
ultramarinus are the sister group to the European
Blue Tit (P. c. caeruleus) plus the Eurasian Azul
Tit (P. cyanus) with four subspecies (P. c. cyanus,
flavipectus, tianshanicus, and yaniseensis).
P.
c
Eu yanu
ras s
ia
Paraphyletic Species:
P.
ca
N- erul
Af eus
ric
a
‣ …are not (always) easy to define
speciation continuum
species A
no
partial
complete
reproductive
isolation
ancestral
species
species B
time
speciation continuum
divergence
locus under
selection
species A
chromosome
[position]
disruptive
selection
divergence
hitchhiking
genome
hitchhiking
post-speciation
divergence
reproductive
isolation
species B
time
••• JL Feder, SP Egan & P Nosil (2012) TREE
speciation continuum
!
phenotypic difference
RAD genome scans
Misty
Joes
Roberts
Boot
••• M Roesti, A Hendry, W Salzburger & D Berner (2012) Molecular Ecology
`
`
••• FC Jones et al. (2012) Nature
Barrett et al. (2008) Science
speciation continuum
speciation continuum
••• V Soria-Carrasco et al. (2014) Science
selection
Charles R. Darwin (1809-1882)
natural selection
images: www.idscaro.net, www.wikipedia.com
‣ ... “is the process by which the forms of organisms in a
population that are best adapted to the environment increase in
frequency relative to less well-adapted forms over a number of
generations” (Ridley 1996)
sexual selection
images: www.crbs.umd.edu, www.smh.com.au
‣ ...“is the selection on mating behavior, either through
competition among members of one sex (usually males) for access to
members of the other sex or through
choice by members of one sex (usually females) for certain
members of the other sex” (Ridley 1996)
selection
fitness
competitors
sexual selection
individual fitness
other members of
the same sex
natural selection
fitness of the
genotype
other individuals in
the same
population
selection
reproduction
heredity
trait variation
variation in fitness
organisms must reproduce to form new
generations
offspring resemble parents
(“like must produce like”)
individuals in natural populations vary in
(adaptive) traits
individuals in natural populations vary in the
number of their offspring that survive to
reproduce (‘lifetime reproductive success’)
(Ridley 2004; Stearns & Hoekstra 2005)
‣ ...operates if the following conditions are met:
natural variation
‣ Natural populations show variation at all levels, from gross
morphology to DNA sequences. Selection can only operate, if
heritable variation exists.
natural variation
‣ Natural populations show variation at all levels, from gross
morphology to DNA sequences. Selection can only operate, if
heritable variation exists.
‣ Natural variation is generated by two processes:
recombination
mutation
“reshuffling” of genetic material
by introducing or breaking up
physical linkage
generation of new genetic
variation by “mistakes” during
the copying of a DNA strand
natural variation
‣ New mutations are only transmitted to the next generation, if
they occur in germinal tissue!
natural variation
variation in:
phenome
morphology
ecology
behavior
genome
genome
structure
and/or
ATG AAC GTA TGG AGG...
Met Asn Val Trp Arg
coding
sequence
and/or
regulatory
regions
ATG AAC GCA TGG AGG...
Met Asn Ala Trp Arg
natural variation
`
100%
astbur
50%
100%
1-90001
Astbur.:
50%
100%
1
Alignment
neobri
Neobri. (-)
1-89776 70%, 100 bp
Criteria: 61
Regions:
2
Alignment
orenil
orenil. (+) 755
bp
13819-106
70%, 100
Criteria: 78
Regions:
3
Alignment
psenye
psenye (+) 32
bp
9404-1062
70%, 100
Criteria: 49
Regions:
r
bu
X-axis: astn: 31
Resolutiosize: 100 bp
Window
gene
n
exo
UTR
CNS
mRNA
12k
10k
8k
18k
16k
14k
50%
20k
••• The Heliconius Genome Consortium (2012) Nature
C7orf57
100%
6k
4k
2k
natural variation
0k
50%
100%
50%
100%
24k
22k
20k
34k
32k
30k
28k
26k
50%
40k
38k
36k
100%
Fhl2 (2of2)
50%
100%
C7orf57
50%
100%
40k
42k
44k
52k
g element
non-codin
e
divergenc
46k
48k
50k
54k
56k
58k
50%
60k
miRNAs
relaxed selection
gene duplica
tion
transposable elements
••• D Brawand et al. (2014) Nature