Transcript EPBC listed taxon - the northern quoll Genetic analysis and spatial use of northern quolls from the Pilbara Peter Spencer School of Veterinary and.

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?
No. of alleles
19
10
2
7
73
64
47
5.4
1.6
2.8
Kimberley
47
80
12
Kimberley
mainland
Pilbara
(%)
Koolan Isl.
Pilbara
Robe River
Woodstock
Dolphin Island
Boongarie Isl.
No.
Bigge Isl.
Population
Heterozygosity
We now have a lot more sampling sites !!
BHPB Rail sites
(n = 33)
Poondano sites
(n = 63)
Yarrie sites
(n = 33)
Pannawonica
(n = 42)
Rail Quarry 1
Rail Control 1
Rail Quarry 2
Rail Control 2
Rail Quarry 3
Poondano Central 1
Poondano West
Granite Outcrop
Granite Range 1
Granite Range 2
Table Top Hill
Poondano East
Nimingarra Mine
Callawa
Pannawonica
Red Hill Station
Abydos Station
Turner River*
McPhee Creek
Robe River
Dolphin Island
Headland (100km SE)
Mt Dove
Woodstock
Hamersley
Mars Rd
Nullagine
Wheatstone/Onslow
6
4
17
5
1
20
7
2
12
3
14
5
14
19
23
19
39
23
11
10
7
3
2
2
1
1
1
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.
Mean heterozygosity (Ho)
How does sampling low numbers of quolls
influence our diversity indices ?
1.0
Kimberley sample
0.8
0.6
Koolan Island
0.4
0.2
0.0
Fixation index (F)
0
1.0
0.8
0.6
0.4
0.2
0.0
-0.2 0
-0.4
-0.6
-0.8
-1.0
10
20
30
No. of quolls (per sampling site)
40
50
Totally inbred
Kimberley sample
Random mating
10
Outcrossing
Koolan Island
20
30
40
50
Does sample size effect diversity ?
Mean number of alleles (NA)
14
Kimberley sample
12
10
R² = 0.8088
8
6
Koolan Island
4
2
0
0
10
20
30
40
50
• 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
BHPB Rail sites
Rail Quarry 1
Rail Control 1
Rail Quarry 2
Rail Control 2
Yarrie sites
Nimingarra Mine
Callawa
Abydos Station
Turner River
McPhee Creek
Pannawonica
Pannawonica
Red Hill Station
Poondano site
Poondano Central 1
Poondano Central 3
Poondano West
Granite Range 1
Table Top Hill
Poondano East
Robe River
Dolphin Island
n
NA
HE
HO
F
6
4.0
3.8
5.6
4.4
0.751
0.708
0.750
0.786
0.727
0.727
0.702
0.782
-0.112
-0.187
0.026
-0.176
4.8
5.6
4.9
6.2
5.2
0.731
0.736
0.726
0.705
0.757
0.716
0.706
0.656
0.664
0.660
-0.039
-0.006
0.078
0.028
0.070
5.5
5.5
0.690
0.701
0.691
0.629
-0.029
0.076
5.8
3.9
4.7
5.6
6.3
3.7
5.5
2.8
0.764
0.691
0.730
0.784
0.753
0.664
0.726
0.474
0.643
0.609
0.697
0.738
0.689
0.589
0.736
0.390
0.123
0.003
-0.040
0.017
0.046
-0.029
4
17
5
8
19
39
23
11
23
19
13
5
7
12
14
5
10
7
What does the additional genetic data show?
Population
No.
Heterozygosity (%)
No. of
alleles
Pilbara
234
77 (70)
10.3 (5.5)
7
47
2.8
32
84
11.1
600
40
4.1
54
73
7.9
Dolphin Island
Kimberley
Kimberley Islands
Kakadu, N.T.
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?
Kimberley
Pilbara samples
Mainland/ Islands
Kakadu, 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
Bayesian posterior probabilities, requiring supercomputer for calculations
Expanding
Declining
In the past
Now
Population expansion / decline
No quoll population shows a genetic signatures of decline (or expansion!)
0.5
Frequency
0.4
In ‘normal’ populations, there are lots of rare alleles
Expect an L-shaped distribution.
0.3
0.2
0.1
0
0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9
Alle le fre que ncy class
0.5
0.5
0.4
0.4
0.3
0.3
0.2
0.2
0.1
0.1
0
0
0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9
Alle le fre que ncy class
0.1
0.2
0.3 0.4
0.5 0.6
0.7
0.8 0.9
In populations that
have been through a
genetic bottlenecks,
there is loss of those
rare alleles
Allele frequency class
No evidence of any genetic bottlenecks in the northern quoll
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
+ve
0.6
0.5
A quoll is more related to another quoll
0.4
0.3
relatedness
0.2
0.1
0
-0.1
-0.2
-ve
-0.3
-0.4
-0.5
-0.6
Distance (km)
Can we infer how male and female quolls use space ?
(sex-biased dispersal)
0.16
0.12
0.08
r
0.04
0.00
-0.04
-0.08
-0.12
5
10
15
20
25
30
35
Distance class (km)
40
45
50
Yarrie site(s)
Yarrie site(s)
5 sites
33 samples
10 km
How quolls use space at different
sampling locations
Genetic relatedness
0.2
0.1
0.1
0.0
-0.1
-0.1
-0.2
0
5
10
15
20
25
30
Distance (km)
35
40
45
50
Poondano site(s)
Poondano site(s)
~ 5 km
10 site(s), 9 had DNA sampling
63 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
0.12
0.10
Poondano
Genetic relatedness
0.08
0.06
0.04
0.02
0.00
5
10
15
20
25
30
35
40
45
50
-0.02
-0.04
-0.06
Distance class (km)
De-clutter
How quolls use space at different
sampling locations
0.12
Abydos
Yarrie
Poondano
Pannawonica
0.10
Genetic relatedness
0.08
0.06
0.04
0.02
0.00
5
10
15
20
25
30
35
40
45
50
-0.02
-0.04
-0.06
Distance class (km)
De-clutter
How quolls use space at different
sampling locations
0.12
Poondano
Genetic relatedness
Pannawonica
0.06
0.00
5
-0.06
10
15
20
25
30
Distance class (km)
35
40
45
50
Poondano site(s)
Series of mesas and granite outcrops
Dispersal ability in quolls
20
Outcrop index
15
10
5
0
-5
-5
0
5
10
15
Neighbourhood size (km)
20
25
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 !!