lecture_20_genomic_conflict_complexitySW

lecture_20_genomic_conflict_complexitySW -...

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Unformatted text preview: Phylogene)c
Approaches
to
Finding
 Genes
Under
Posi)ve
Selec)on
 M=mouse, C=chimpanzee, H=human -  pecific test for positive selection in humans s -  547 genes with significant evidence for positive selection 1 -  lfaction and nuclear transport genes show excess of positive o selection Evidence
for
Posi)ve
selec)on
 from
Ka/Ks>1
 e.g. Clark and Swanson, 2005 -seminal fluid proteins show high Ka/Ks ratios in primates -consistent with sperm competition/sexual conflict Evidence
for
Posi)ve
selec)on
 from
Ka/Ks>1
 e.g. T-cell receptor -genes involved in pathogen resistance often show high rates of protein evolution Tes)ng
for
Posi)ve
Selec)on
 •  Ka/Ks>1
quite
rare,
but
Ka/Ks<1
does
not
 mean
the
absence
of
selec)on
 •  need
other
means
to
detect
adap)ve
 evolu)on
 •  popula)on
gene)cs
approaches
can
help
 detect
adap)ve
evolu)on
 Effect
of
Posi)ve
Selec)on
on
 NEUTRAL
POLYMORPHISM
 Neutral variation is reduced with positive selection Effect
of
Posi)ve
Selec)on
on
 NEUTRAL
POLYMORPHISM
 Between-population differences are ELEVATED with positive selection •  Drosophila:
growing
evidence
for
high
rates
of
 adap)ve
evolu)on
in
protein
coding
DNA
AND
 noncoding
DNA
 •  other
organisms,
like
humans,
Arabidopsis
and
 yeast:
less
common?
 •  genes
involved
in
immune
system,
 gametogenesis,
muscle
development
and
 complex
diseases
show
evidence
for
posi)ve
 selec)on
in
humans
 How
common
is
adap)ve
 evolu)on?
 ANOTHER POSSIBILITY: THE NEARLY NEUTRAL MODEL OF MOLECULAR EVOLUTION T. Ohta Slightly
Deleterious
muta)ons
can
 get
fixed
in
popula)ons!
 •  utations that are under very weak selection can be fixed or M lost via genetic drift •  pecies with smaller population sizes will fix more slightly S deleterious mutations than those with larger population sizes •  f there are a lot of nearly-neutral mutations, slightly I deleterious mutations may play an important role in evolution, particularly in small populations •  lightly advantageous mutations can fix much more s effectively in larger populations Fig. 1. (A) Estimates of the composite parameter Neu for a phylogenetically diverse assemblage of species M. Lynch et al., Science 302, 1401 -1404 (2003) Published by AAAS Fig. 3. The relationship between average intron size (solid circles) in base pairs (bp) and intron number (open circles) and genome size M. Lynch et al., Science 302, 1401 -1404 (2003) Published by AAAS Evolution of Complexity: SOME lineages Have evolved greater complexity Major
Transi)ons
in
Evolu)on:
 Greater
Complexity
Arises
from
Greater
 ‘Coopera)on’
amongst
previously
 independent
replicators
 -  rigin of cells o -  rigin of chromosomes o -  rigin of genetic code o -  rigin of sexual reproduction o -  rigin of eukaryotes o -  rigin of multicellularity o -  rigin of colonies (e.g. nonreproductive castes) o Selec)on
on
Individual
Organisms
is
a
form
of
 group
selec)on!
 •  genomes
are
composed
of
unrelated
genes
 and
alleles
that
have
been
inherited
from
 different
places
 •  segrega)on,
recombina)on
and
random
 ma)ng
ensures
that
they
are
mostly
passed
on
 independently
 •  genes
typically
persist
by
improving
fitness
of
 the
group
(organism)
 Two
Basic
Problems
 1)
how
can
these
higher
levels
stay
coopera)ve?
 2)
to
what
extent
can
coopera)on
break
down?
 How
Do
Individual
Genomes
Stay
so
 Coopera)ve?

 -  any features of individual organisms prevent m competition and evolution WITHIN an individual -  nsures that many genes succeed by e enhancing the fitness of the organism (‘group’) How
Do
Individual
Genomes
Stay
so
 Coopera)ve?

 -  eiosis: ensures that alleles don’t compete m within an individual -  evelopment and multicellularity: starting from d a single cell prevents initial competition among cell lineages -  niparental inheritance of organelles: prevents u competition within cells of different organelle genomes Darwinian
Natural
selec)on:
Alleles
spread
 through
popula)on
by
increasing
an
 individual’s
fitness
 frequency of A allele AA - 1 Aa - 0.9 aa - 0.6 1 0.9 0.8 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0 0 20 40 60 80 100 120 generation How
do
Genomes
Stay
Coopera)ve?
 1)
Fair
Meiosis
 1 50% A 50% A 0.9 50% a 50% a AA 50% A Aa aa 0.6 50% a -  eiosis provides a fair representation of alleles’ fitness m effects on individuals To
What
Extent
Does
Coopera)on
 Break
Down:
 Chea)ng
a
fair
meiosis
 1)  Meio)c
drive
 2)  Overreplica)on
 Meio)c
Drive:
 If
an
allele
can
enhance
its
own
 transmission
it
can
spread
even
while
 reducing
individual
fitness
 Aa 2% A 98% a But:
If
an
allele
can
enhance
its
own
 transmission
it
can
spread
even
while
 reducing
individual
fitness
 Aa 2% A 98% a AA excess Aa! But:
If
an
allele
can
enhance
its
own
 transmission
it
can
spread
even
while
 reducing
individual
fitness
 Aa 2% A 98% a Aa,aa excess aa! Meio)c
Drive
can
RAPIDLY
 ELIMINATE
alleles
that
have
 higher
individual
fitness
 1.2 1 f(A) 0.8 0.6 0.4 0.2 0 0 20 40 60 80 100 120 Number of generations 1)
‘true’
meio)c
drive:
one
allele
more
likely
to
 end
up
in
gamete
during
meiosis=female
drive
 Two
Ways
to
Achieve
‘Meio)c
 Drive’
 “True”
Meio)c
Drive:
 Maize
Chromosomal
Knobs
and
Centromere
 Drive
 •  in
female
meiosis,
 typically
only
one
 


of
four
meio)c
products
 ends
up
in
a
gamete
 (megaspore)
 •  stronger
centromeres
will
 ‘lead
the
way’
and
end
up
 in
the
megaspore
 “True”
Meio)c
Drive:
 Maize
Chromosomal
Knobs
and
Centromere
 Drive
 •  approx.
70%
transmission
 rates
 •  reduced
fitness
in
pollen
 •  mito)c
abnormali)es
 •  widespread
 polymorphism
in
natural
 and
domes)cated
maize
 1)  ‘true’
meio)c
drive:
one
allele
more
likely
to
 end
up
in
gamete
during
meiosis
 2)  interference:
e.g.
one
allele
produces
a
 ‘toxin’
that
kills
the
other
allele
 K Two
Ways
to
Achieve
‘Meio)c
 Drive’
 K Meio)c
Drive:
Chea)ng
Mendel’s
 Law
of
Segrega)on
 Drosophila Segregation distorter locus, SD ss female x Ss male Almost ALL Ss (95-99%)! •  allele prevents proper s sperm formation S •  male
meio)c
drive
on
sex
chromosomes
is
 very
common
in
insects
 •  leads
to
skewed
sex
ra)os‐
e.g.
driving
X
 chromosome
leads
to
mostly
female
progeny
 Meio)c
Drive
and
Sex
 Chromosomes
 Why
is
Meio)c
Drive
enhanced
in
 between‐popula)on
crosses?
 1)
strong
selec)on
on
restorers
or
 suppressors
of
meio)c
drive
in
other
parts
 of
the
genome‐>arms
race

 How
Do
Genomes
Stay
 Coopera)ve?
 1)  Fair
meiosis
 2)  When
drivers
spread,
strong
selec)on
on
rest
 of
genome
for
suppression
 To
What
Extent
Does
Coopera)on
 Break
Down:
 Chea)ng
a
fair
meiosis
 1)  Meio)c
drive
 2)  Overreplica)on
 Transposable
elements:
 Chea)ng
Mendel’s
Laws
Through
 Over‐Replica)on
 1/2 -  elf-replicating segments of DNA s -  nsure their own over-representation in offspring e The
most
common
DNA
in
the
 genome
is
ojen
selfish!
 How do Genomes not ‘explode’ through transposition? 1) Selection on rest of genome for silencing: methylation, RNAi may have evolved as host silencing mechanisms How do Genomes not ‘explode’ through transposition? 1)  Selection on rest of genome for silencing: methylation, RNAi may have evolved as host silencing mechanisms 2)  transposition-selection balance ...
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