Download Organellar Genomes and Genetic Markers

Organellar Genomes and
Genetic Markers
Level 3 Molecular Evolution and
Bioinformatics
Jim Provan
Organellar variation
Ploidy
Recombination
Inheritance
Nucleus
Chloroplast
Mitochondrion
Diploid
Haploid
Haploid



Biparental
Uniparental:
Angiosperms (M)
Gymnosperms (P)
Maternal
Variation at drift/mutation equilibrium
Nuclear (diploid)
1.0
0.8
4Nµ
(4Nµ + 1)
0.6
0.4
0.2
0.0
0.0001 0.001
0.01
0.1
1
Nµ
Diploid
Haploid
10
100
1000
Organellar (haploid)
2Nµ
(2Nµ + 1)
Selective sweeps
3
A

3
A
B
1
3


1

A
3

A
C
2


A
Plant organelle genomes implications for markers
Generally lower diversity due to:
Haploid genome
Lower mutation rates
Lack of recombination - selective sweeps
Lack of intraspecific variation  species specific markers
Detection of intraspecific variation  variable regions
Non-coding regions
Tandemly-duplicated genes
Mononucleotide microsatellites
Very little mitochondrial variation
Genetic change during fragmentation
In fragmented populations,
differentiaton due to drift
will be more marked in
haploid organellar genomes
Maternally inherited
markers travel via seed 
organellar gene flow less
substantial
Maternal markers useful for
recording historical events
Ratios of pollen:seed flow
Combined analysis of nuclear and organellar markers
can give information on relative importance of seed
and pollen flow
Important for:
Dynamics of natural populations
Transgene movement
Species
Dispersal
Pollen
Seed
Quercus
Argania
Pinus
Wind
Insect
Wind
Bird
Ruminant
Wind
Pollen:Seed
Ratio
196
2.5
18
Animal mitochondrial DNA in
population genetics
Maternal inheritance and relatively rapid rate of
evolution have led to widespread use in studies of
matrilineal gene flow
Sensitive indicator of:
Female-mediated gene flow (maternal inheritance)
Founder events (haploid genome)
Comparisons of spatial distribution of nuclear and
mitochondrial markers provides information on sexual
bias in dispersal
Geographical structuring with
sedentary females
Offspring from each
mother will have maternal
mtDNA genotype and half
paternal nuclear genotype
If mothers have different
mtDNA genotypes, groups
of offspring will be:
Completely different for
mitochondrial markers
At least 50% similar for
nuclear markers
The “Mitochondrial Eve” hypothesis
Studies suggested that
between 140,000 and
360,000 years ago, a single
mtDNA haplotype existed!
Theoretical studies dispute
this:
Rate of extinction of maternal
lineages is high
Even if several thousand
mtDNAs were present, high
probability that only one
would have survived
Chloroplast DNA phylogeography of
Alnus glutinosa (L.) Gaertn.
R. Andrew King and Colin Ferris
Molecular Ecology (1998) 7: 1151-1161
Introduction
Until recently, fossil pollen mapping was the only way
to study history of plant populations
Studies in various trees have shown that after the
last (Würrm) glaciation, Europe was recolonised from
at least three separate refugia:
Southern Spain
Southern Italy
Balkan peninsula
Use of chloroplast-specific markers should give new
insights into post-glacial histories of plant species
Chloroplast haplotype distribution in
alder (Alnus)
Post-glacial history of Alnus
Obvious high levels of genetic variation below the
southern limit of the ice during the last glaciation
Two dominant haplotypes found throughout northern
Europe
Majority of Europe colonised from single refugium in
the Balkans
Patterns of variation at a
mitochondrial sequence-tagged-site
locus provides new insights into the
postglacial history of European Pinus
sylvestris populations
Nicole Soranzo, Ricardo Alia, Jim Provan and
Wayne Powell
Molecular Ecology (2000) 9: 1205-1211
Maternal markers in conifers
In virtually all embryophytes (seed plants), the
mitochondrial genome is inherited maternally i.e. via
the seed
Chloroplast genome inherited in a different manner in
angiosperms and gymnosperms:
In angiosperms, chloroplast genome is also mostly inherited
maternally
In gymnosperms, chloroplast genome is inherited paternally
i.e. via both pollen and seed
In conifers, mitochondrial markers will be good
indicators of historical events
Mitochondrial variation in Scots pine
in Spain
Two haplotypes found in
mitochondrial nadI
region
General NE / SW split in
haplotype distribution
Only one (dark) haplotype
found in rest of Europe
Distribution of variation in Spanish
Pinus sylvestris
Within
populations
(40%)
Between
populations
(60%)
Mitochondrial variation in European
P. sylvestris
Levels of population differentiation revealed using
mitochondrial markers were 10- to 30-fold higher than
in previous studies using nuclear and chloroplast
markers
Low degree of variation in non-Spanish populations
probably due to post-glacial recolonisation from a
common refugium
Spanish populations below southern limit of glaciation:
Not subjected to glaciation - represent ancient gene pools
Physical isolation of populations on different mountain ranges
accounts for high levels of between-population differentiation
rbcL sequences reveal multiple
cryptic introductions of the Japanese
red alga Polysiphonia harveyii
Lynne McIvor, Christine Maggs, Jim Provan
and Michael Stanhope
Molecular Ecology (2001) 10: 911-919
Introductions of Polysiphonia harveyii
from Japan
Aim: to test whether global
populations of P. harveyii
had arisen from a single or
multiple introductions
Methodology:
Sequence rbcL gene
Align sequences
Construct phylogenetic tree
showing relationships
between observed genotypes
Compare with geographic
distribution
Minimum-spanning phylogenetic
network
E
Choshi
D
Shimoda
Oshoro
X
North Carolina
New Zealand
Monterey
F
Europe
Nova Scotia
Y
A
Z
C
HOKKAIDO
Akkeshi
B
Multiple introductions of P. harveyii
Multiple hypothetical ancestral genotypes present which
were not observed:
Consistent with Japan being the centre of diversity of P. harveyii
Most likely not observed due to limited sampling, rather than
extinction
Non-Japanese populations of P. harveyii represented by
two divergent genotypes:
One possibly linked to Honshu genotypes
One possibly linked to Hokkaido genotypes
Most likely represent at least two separate introductions
from original centre of diversity in Japan
Nuclear and mitochondrial variation
in Scots pine in Sweden
Scots pine believed to
have recolonised Sweden
from both North and
South after glaciation
Nuclear
Mitochondrial
Nuclear (monoterpene)
markers suggest clinal
variation but not definite
Mitochondrial markers
show definite boundary at
60°N, even after ~50
generations of contact