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

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No. of quolls (per sampling site)

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an

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o)

Kimberley sample

Koolan Island

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Koolan Island

Kimberley sample

Koolan Island

Totally inbred

Random mating

Outcrossing

Does sample size effect diversity ?

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R² = 0.808823753160164

Me

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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

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Allele frequency class

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Alle le frequency class

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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

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Distance (km)

-ve

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+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

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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

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Poondano

Distance class (km)

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De-clutter

How quolls use space at different sampling locations

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0.12AbydosYarriePoondanoPannawonica

Distance class (km)

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De-clutter

How quolls use space at different sampling locations

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Poondano

Pannawonica

Distance class (km)

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Poondano site(s)

Series of mesas and granite outcrops

Dispersal ability in quolls

-5 0 5 10 15 20 25-5

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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 !!