Measuring biodiversity:
conservation genetics
Robin Allaby
Outline
Conservation genetics
why conserve genetic diversity?
how is diversity organized?
what do we measure?
Concepts:
heterozygosity
populations: structure, size effects, drift
phylogenetic and
phylogeographic inference
Case studies
bumble bees
killer whales
Why conserve genetic diversity?
• All species need a certain amount of genetic diversity to
survive
• Different types of species are associated with different levels
of diversity
Different species lifestyles are associated with different levels of diversity
What happens when diversity is
‘wrong’?
How is diversity organized?
What do we measure?
Lots of options:
DNA sequences –
genes
ATGGACTAGACT
GAGGAGGAGGAG
microsatellites
other non-genic DNA ATGGACTAGACT
DNA fragments (DNA that has been ‘chopped up’ by sequence specific processes)
RAPD, ALFPs, RFLPs
products of genes – proteins (e.g.allozymes)
visible phenotype (e.g. colour)
Heterozygosity
heterozygous locus – different alleles
homozygous locus – same alleles
Heterozygosity
Heterozygosity is the probability that you
would pick two different alleles from a
population
Homozygosity is the probability that you
would pick two alleles which are the same
from a population
Heterozygosity + homozygosity = 1
In this case:
Probability of picking same:
White Goat x WG = 1/3 x 1/3 = 1/9 or
Grey Goat x GG = 1/3 x 1/3 = 1/9 or
Black Goat x BG = 1/3 x 1/3 = 1/9
1/9 + 1/9 + 1/9 = 1/3
Heterozygosity = diversity
Homozygosity = 1/3, therefore heterozygosity = 2/3
What happens to heterozygosity in
sub populations?
differentiation
Measuring differentiation
HT
X
Y
HS
HS
HT = total heterozygosity (always larger than HS)
HS = subpopulation heterozygosity
FST = HT – HS
HT
FST = 0.498 – 0.31 = 0.38
0.498
There are lots of variations of FST,
such as RST and GST
In this case
HT:
red allele: 8, green allele: 7
p(same) = p (RR) + p (GG) = (8/15 x 8/15) +
(7/15 x 7/15) = 0.502
p(diff) = 1 – 0.502 = 0.498
Avergare of HS:
X: p(RR) + p(GG) = (6/7 x 6/7) + (1/7 x 1/7) = 0.755
p(diff) = 1 – 0.755 = 0.245
Y: p(RR) + p(GG) = (2/8 x 2/8) + (6/8 x 6/8) = 0.625
p(diff) = 1 – 0.625 = 0.375
Average = (0.245 + 0.375)/2 = 0.31
Heterozygosities in various taxa
Small populations have lower
diversity – why?
Another way to look at it is through random genetic drift
• Random genetic drift affects smaller populations more than
larger ones
• Random genetic drift is the process where allele frequencies
change from generation to generation
• Random genetic drift REMOVES variation from the population
Random genetic drift
The size diversity relationship in
populations
The amount of diversity a population can carry depends on its size.
Another measure of diversity is θ which approximates heterozygosity
θ = 4Neμ
‘effective’ population size
For normal ‘nuclear’ genes
mutation rate
More about θ
θ is a measure of diversity, which approximates heterozygosity.
θ ≈ π (nucleotide diversity)
Nucleotide diversity is the average number of differences between two
DNA sequences.
3
1
2
2
3
1
π = 2/7 = 0.286
Even MORE about θ
θ = 4Neμ
For normal ‘nuclear’ genes
BUT often animal studies use mitochondrial DNA which is only
inherited through the female line………..in which case
θ = 2Nefμ
Where Nef is the effective female population size
And finally about θ
• θ is a frequently used symbol, and is also used
to describe other statistics, which can be
confusing.
• Today you will see also θw, Weir and
Cockerham’s statistic which is a version of FST
in the bumblebee case study……
The size diversity relationship in
populations
The amount of diversity a population can carry depends on its size.
Another measure of diversity is θ which approximates heterozygosity
and π (nucleotide diversity), which also approximates heterozygosity.
θ = 4Neμ
For normal ‘nuclear’ genes
θ = 2Nefμ
For normal ‘mitochondrial’ genes
Rare alleles are lost from small
populations
Gene flow bolsters diversity
Gene flow counters the
effects of differentiation
acting to homogenize.
FST =
1
1 + 4Nm
Number of migrants
per generation
habitat corridor
So, for FST = 0.38 in example
on previous slide,
Nm = [(1/FST-1)/4] = 0.41
What separates populations?
• Could be space
• Could be time
• Could be another niche aspect
Do small populations evolve
faster?
• Drift acts more quickly, therefore they
differentiate more quickly….so do they evolve
faster?
BUT…….
• Small populations gain new mutations more slowly than large populations
• Those mutations are processed more quickly (through drift)
• The two processes cancel out so that mutation turnover is the same in large
and small populations (basis of the neutral theory of evolution).
prob mutation = 1/6
number of mutants in next generation
Rate of evolution and population
size
• Populations of different sizes change (evolve)
at the same rate
• But large populations have more diversity, and
are therefore more ‘adaptable’
• Speciation often does involve small
populations though
Population separation is the basis
of speciation
reproductively incompatible
cryptic species
lineage sorting
obvious species
Often we are looking for ‘structure’
in populations
•
•
•
As we have seen, structure is the term we use to describe the loss of heterozygosity in
sub-populations relative to what we would expect if they were all one large population.
Structure can tell us that populations have become isolated from each other. Relate this
to the bumblebee example later.
The program STRUCTURE is the ‘de rigeur’ way for looking at structure, when you
consider multiple loci. And it’s free! (http://pritch.bsd.uchicago.edu/structure.html)
Knowles & Richards 2005
Mol. Ecol. 14:4023-4032
phylogenetics and phylogeography
• Allow us to reconstruct evolutionary history of
genes
• And how they have moved over time (relating
the tree to geography)
Phylogenetic tree
time
fossil calibration point
outgroup
2
root
Taxon A
3
number of mutations
occuring along
branch
Taxon B
Taxon C
Taxon D
node
branch
leaf/tip
Phylogenetic trees are calculated
from alignments
Taxon A
Taxon B
Taxon C
Taxon D
Outgroup
AATGACA
AATAACA
GATGACA
AACGGCA
GATGTTA
There are numerous (free) programs
which will align sequences for you
e.g. clustalw (go to
http://www.ebi.ac.uk/FTP/ and look in
the software repositry)
outgroup
3
1
2
2
3
1
π = 2/7 = 0.286
GATGTTA
Phylogenetic methods
Taxon A
Taxon B
Taxon C
Taxon D
Outgroup
AATGACA
AATAACA
GATGACA
AACGGCA
GATGTTA
Tree building methods are either
character based or distance based
There are a huge number of methods out there…..some popular ones are:
Neighbor-joining – distance based method, very quick (clustalw, PHYLIP)
Maximum parsimony – character based, computationally intensive (Mesquite)
Maximum likelihood - character based, computationally intensive (PHYLIP)
Bayesian trees – a more recent development, fantastically intensive (BEAST, Mr Bayes)
There are lots of free programs (examples in brackets) that will do these methods.
Mesquite is a nice free package!
Maximum parsimony package
obtain from http://mesquiteproject.org
Phylogeography is interpreting
phylogenetics geographically
Hewitt (1999) Biol. J. Linn. Soc. 68:87-112
Sources of genetic material
• Sample organisms directly in the field
destructive
non destructive
• Dead remains – ancient DNA
bones in the field
museum specimens
• Sample scat – also ancient DNA
UK Pipistrellus genus is a result of
postglacial expansion
REVIEW
Brown bears in Europe
Brown bears in Europe
Pleistocene Iberian bears moved to Italy,
and Pleistocene Italian bears moved to
Iberia!
Complex movements revealed.
Valdiosera et al 2008 Proc. Natl. Acad. Sci.
USA 105:5123-5128
REVIEW
Case study 1: Flight of the
bumblebee….
What is different
about these
bees?
Bombus muscorum
Bombus jonellus
This bee is suffering from
This bee is more resilient,
habitat destruction, now
not in danger.
endangered. Needs to be
away from intensive
They are sympatric across the
agriculture.
Western Isles, so can be compared
directly.
Darvill et al (2010) Molecular Ecology 19:53-63.
Bees have big populations, right?
Only the queen and a drone
(often just one) reproduce, so
there are two individuals per hive
– Ne approximated by 1.5 x
number colonies.
Bees are prone to loss of genetic
diversity.
Western Isles bee samples
9 microsatellite loci surveyed
GAGGAGGAGGAG
Heterozygosity
B. muscorum has
markedly lower
diversity, despite being
the more frequenty
found bee on the
islands
FST equivalent values
B. muscorum
populations show a
higher level of
differentiation than B.
jonellus.
Structure analysis
What is different?
This bee’s populations are
more structured, meaning
that they have more
restricted gene flow – they
are not good dispersers
Conservation action: these
bees are more likely to need
relocating when habitat is
destroyed, or to bolster
diversity.
This bee’s populations
disperse over long
distances, and are therefore
robust to environmental
change.
Case study 2: Killer whales in North
Atlantic
Foote et al 2009 Molecular Ecology 18:5207-5217
Characteristics of Killer whales
• Low genetic diversity in species (recent
bottleneck)
• ‘behavioural’ groups:
Pacific marine-mammal eating and pisciverous types
Antarctic minke eating, seal eating and pisciverous types
North Atlantic Orcas
There appear to be two types, based on dental wear – different diets?
Recent divergence between type1
and type 2
Killer whale phylogeny
Type 1 & 2 have recently diverged
• Type 1 smaller with varied diet, fish
eaters
• Type 2 have a specialized diet –
baleen whale eaters
• Very recent divergence, based on
niche diversification
• same pattern confirmed from museum
samples spanning last 100 years
• independent origin of diet based
diversification to Antarctic and Pacific
killer whales
• environmental gradients driving the
phylogeny
• conservation has two ecotypes to
consider that are protospecies