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EPBC listed taxon - the northern quoll
Genetic analysis and spatial use of northern quolls from the Pilbara
Peter Spencer
School of Veterinary and Life Sciences
Ric How
Linc Schmitt
Annette Cook
Keith Morris
Mia Hillyer
Jonathan Webb
Consultant community
Why use genetic methodology ?
• Identical to genetic profiling used in human forensics
• The technology is very powerful
• We used 11 different microsatellite markers for genotyping quolls
• The probability that 2 quolls will have the same genotype is >>1 in 100 million
• Genes are a measure of the individual
• The genes carry ‘historical’ information also
• Can look at different time scales & evolutionary questions
PID = 1.63 x 1015 individuals
Important questions that population genetics can contribute to our collective knowledge of
quolls in the Pilbara
Measuring genetic diversity
Prioritising which populations are more genetically ‘important’
How are the quolls structured ? (small discrete, or large populations?)
Are the population being impacted (e.g. decreasing/increasing demographic trend, bottlenecked?)
How are quolls using the landscape (dispersal etc.)
Study aims
The aims of this genetic study were to determine the;
1. diversity and ‘genetic importance’ of the quolls in the Pilbara region;
2. population structure, or regional management units;
3. population trajectory (decreasing/increasing demographic trend)
4. Relationship between genetic relatedness and spatial distribution, to infer how quolls use the landscape in different regions of the Pilbara.
Schmitt, How et al. 2009
From WA Museum samples
47% (n=7)
73% (n=10)
64% (n=2)
What did the genetic data show?
Population No.Heterozygosity
(%) No. of alleles
Pilbara 19 Robe River 10 73 5.4 Woodstock 2 64 1.6
Dolphin Island 7 47 2.8
Kimberley 47 80 12
Big
ge I
sl.
Boon
gari
e I
sl.
Kimberleymainland
Koola
n I
sl.
Pil
bara
We now have a lot more sampling sites !!
BHPB Rail sites
(n = 33)
Rail Quarry 1 6
Rail Control 1 4
Rail Quarry 2 17
Rail Control 2 5
Rail Quarry 3 1Poondano sites
(n = 63)
Poondano Central 1 20
Poondano West 7
Granite Outcrop 2
Granite Range 1 12
Granite Range 2 3
Table Top Hill 14
Poondano East 5Yarrie sites(n = 33)
Nimingarra Mine 14
Callawa 19Pannawonica(n = 42)
Pannawonica 23
Red Hill Station 19 Abydos Station 39 Turner River* 23 McPhee Creek 11 Robe River 10 Dolphin Island 7 Headland (100km SE) 3 Mt Dove 2 Woodstock 2 Hamersley 1 Mars Rd 1 Nullagine 1 Wheatstone/Onslow 1
Increased sampling
32 sampling locations
13 sites with >10 samples collected
12 sites with <5 samples
4 sites with multiple locations
234 samples analysed (previously 19)
Study aims
1. diversity and ‘genetic importance’ of the quolls in the Pilbara region;
2. population structure, or regional management units;
3. population trajectory (decreasing/increasing demographic trend)
4. relationship between genetic relatedness and spatial distribution, to infer how quolls use the landscape in different regions of the Pilbara.
How does sampling low numbers of quolls influence our diversity indices ?
0 5 10 15 20 25 30 35 40 45 500.0
0.2
0.4
0.6
0.8
1.0
No. of quolls (per sampling site)
Me
an
he
tero
zyg
os
ity
(H
o)
Kimberley sample
Koolan Island
0 5 10 15 20 25 30 35 40 45 50
-1.0
-0.8
-0.6
-0.4
-0.2
0.0
0.2
0.4
0.6
0.8
1.0
Fix
ati
on
ind
ex
(F
)
Koolan Island
Kimberley sample
Koolan Island
Totally inbred
Random mating
Outcrossing
Does sample size effect diversity ?
0 5 10 15 20 25 30 35 40 45 500
2
4
6
8
10
12
14
R² = 0.808823753160164
Me
an
nu
mb
er
of
alle
les
(N
A)
Kimberley sample
Koolan Island
• Most measures are useful for samples of 5 (or more) quolls
• The number of alleles is sensitive to sampling effects
• More than 5 quolls in a population capture 80% of the information
• Single individuals are useful for assignment testing!
Big, scary table coming!.......
Sampling location n NA HE HO F
BHPB Rail sites
Rail Quarry 1 6 4.0 0.751 0.727 -0.112Rail Control 1 4 3.8 0.708 0.727 -0.187Rail Quarry 2 17 5.6 0.750 0.702 0.026Rail Control 2 5 4.4 0.786 0.782 -0.176
Yarrie sites
Nimingarra Mine 8 4.8 0.731 0.716 -0.039Callawa 19 5.6 0.736 0.706 -0.006
Abydos Station 39 4.9 0.726 0.656 0.078Turner River 23 6.2 0.705 0.664 0.028McPhee Creek 11 5.2 0.757 0.660 0.070Pannawonica
Pannawonica 23 5.5 0.690 0.691 -0.029Red Hill Station 19 5.5 0.701 0.629 0.076
Poondano site
Poondano Central 1 13 5.8 0.764 0.643 0.123Poondano Central 3 5 3.9 0.691 0.609 0.003Poondano West 7 4.7 0.730 0.697 -0.040Granite Range 1 12 5.6 0.784 0.738 0.017Table Top Hill 14 6.3 0.753 0.689 0.046Poondano East 5 3.7 0.664 0.589 -0.029
Robe River 10 5.5 0.726 0.736 Dolphin Island 7 2.8 0.474 0.390
What does the additional genetic data show?
Population No. Heterozygosity (%) No. of alleles
Pilbara 234 77 (70) 10.3 (5.5)
Dolphin Island 7 47 2.8
Kimberley 32 84 11.1
Kimberley Islands 600 40 4.1
Kakadu, N.T. 54 73 7.9
Study aims
1. diversity and ‘genetic importance’ of the quolls in the Pilbara region;
2. population structure, or regional management units;
3. population trajectory (decreasing/increasing demographic trend)
4. relationship between genetic relatedness and spatial distribution, to infer how quolls use the landscape in different regions of the Pilbara.
How are northern quolls related at a landscape scale?
Pilbara samplesKimberley
Mainland/ IslandsKakadu, NT
Study aims
1. diversity and ‘genetic importance’ of the quolls in the Pilbara region;
2. population structure, or regional management units;
3. population trajectory (decreasing/increasing demographic trend);
4. relationship between genetic relatedness and spatial distribution, to infer how quolls use the landscape in different regions of the Pilbara.
Population expansion / decline
Declining Expanding
NowIn the past
Bayesian posterior probabilities, requiring supercomputer for calculations
Population expansion / decline
No quoll population shows a genetic signatures of decline (or expansion!)
No evidence of any genetic bottlenecks in the northern quoll
0
0.1
0.2
0.3
0.4
0.5
0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9
Allele frequency class
0
0.1
0.2
0.3
0.4
0.5
0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9
Allele frequency class
0
0.1
0.2
0.3
0.4
0.5
0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9
Alle le frequency class
Fre
quen
cy
In populations that have been through a genetic bottlenecks, there is loss of those rare alleles
In ‘normal’ populations, there are lots of rare allelesExpect an L-shaped distribution.
Study aims
1. diversity and ‘genetic importance’ of the quolls in the Pilbara region;
2. population structure, or regional management units;
3. population trajectory (decreasing/increasing demographic trend);
4. Relationship between genetic relatedness and spatial distribution, to infer how quolls use the landscape in different regions of the Pilbara.
Spatial autocorrelation
-0.6
-0.5
-0.4
-0.3
-0.2
-0.1
0
0.1
0.2
0.3
0.4
0.5
0.6
Distance (km)
-ve
rela
tedn
ess
+ve A quoll is more related to another quoll
Can we infer how male and female quolls use space ?(sex-biased dispersal)
5 10 15 20 25 30 35 40 45 50-0.120.721.562.403.244.084.925.766.607.448.289.129.96
Distance class (km)
r
Yarrie site(s)
Yarrie site(s)
10 km
5 sites33 samples
How quolls use space at different sampling locations
0 5 10 15 20 25 30 35 40 45 500.0
2.0
4.0
6.0
8.0
10.0
12.0
Distance (km)
Gen
etic
rela
tedn
ess
Poondano site(s)
Poondano site(s)
~ 5 km
10 site(s), 9 had DNA sampling63 samples, mostly sub-adult (between 2 - 14 samples/site)
Poondano site(s)
Series of mesas and granite outcrops
How quolls use space at different sampling locations
5 10 15 20 25 30 35 40 45 50
-0.06
-0.04
-0.02
0.00
0.02
0.04
0.06
0.08
0.10
0.12
Poondano
Distance class (km)
Gen
etic
rela
tedn
ess
De-clutter
How quolls use space at different sampling locations
5 10 15 20 25 30 35 40 45 50
-0.06
-0.04
-0.02
0.00
0.02
0.04
0.06
0.08
0.10
0.12AbydosYarriePoondanoPannawonica
Distance class (km)
Gen
etic
rela
tedn
ess
De-clutter
How quolls use space at different sampling locations
5 10 15 20 25 30 35 40 45 50
-0.06
0.00
0.06
0.12
Poondano
Pannawonica
Distance class (km)
Gen
etic
rela
tedn
ess
Poondano site(s)
Series of mesas and granite outcrops
Dispersal ability in quolls
-5 0 5 10 15 20 25-5
0
5
10
15
20
Neighbourhood size (km)
Out
crop
inde
x
Key findings from the genetic work
The northern quolls from the Pilbara region;
• Comprise a single (genetic) management unit• Sampling sites maintain high levels of diversity• No one population has more diversity than another• Contain lowest diversity of all northern quoll
populations (with the exception of some islands)• No signatures of decline or genetic bottlenecks• Show male-biased dispersal• Highly vagile• Remarkable adaptable
What are the key areas for future research
• Need a bigger, better population-focus
• Like the Kimberley, before/after toads – the Pilbara will play an important role in quantifying Extinction Debt in the Kimberley?
• Spatial use is intriguing – Interesting to look at radio-tracking information– More data is needed on ‘genetic space’
• Plug: please continue to collect tissue !!