Table S1. Summary of information of historical woylie (Bettongia penicillata ogilbyi) samples, including DNA preservation, age, and their use for statistical
analyses.
Sample
ID
153
173
187
191
190
794
808
802
803
810
804
805
811
812
813
814
815
816
806
817
818
807
820
821
C14 lab
codes
Wk
Wk
Wk
Wk
Wk
Wk
Wk
Wk
Wk
Wk
Wk
Wk
Wk
Wk
4517
5474
4516
3625
6706,
6707
4517
3626
3626,
4516
4517
3626
3954,
3955
Wk 3954
Wk
Wk
Wk
Wk
3954,
3955
3954,
3955
Wk 3954
Location
Uncalibrate Age
(C14 error)
Ct
value
Age (year*)
Sample
Bone
Bone
Skin
Bone
Skin
Skin
Bone
Bone
Bone
Bone
Bone
29.38
26.65
25.79
34.43
20.97
23.9
30.43
34.3
28.18
35.74
-
Largest
Amplicon
Faure Island
Tunnel Cave
Beaufort
Pingelly
Jerramungup
Jerramungup
Faure Island
Tunnel Cave
Tunnel Cave
Tunnel Cave
Tunnel Cave
12840 (90)
12890 (250)
4280 (60)
8270 (80)
n/a
15300 (14990-15570)
108
102
41
41
n/a
15300 (14990-15570)
15600 (14981-16262)
4800 (4739-4939)
9300 (9139-9384)
Tunnel Cave
9860 (95)
11400 (11107-11666)
Bone
-
Tunnel Cave
Tunnel Cave
12840 (90)
1370 (40)
15300 (14990-15570)
1300 (1278-1322)
Bone
Bone
23.48
Tunnel Cave
1370-4280 (40-60)†
3100 (1278-4939)
Bone
-
Tunnel Cave
Tunnel Cave
12840 (90)
1370 (40)
15300 (14990-15570)
1300 (1278-1322)
Bone
Bone
29.61
23.09
253
293
400-680 (50-90)†
500 (352-706)
Bone
36.39
293
400 (50)
400 (352-499)
Bone
27.86
293
400-680 (50-90)†
500 (352-706)
Bone
-
400-680 (50-90)†
500 (352-706)
Bone
23.86
400 (50)
400 (352-499)
Bone
-
108
44
Skin
Skin
33.22
28.25
Witchcliffe
Rock Shelter
Witchcliffe
Rock Shelter
Witchcliffe
Rock Shelter
Witchcliffe
Rock Shelter
Witchcliffe
Rock Shelter
Cranbrook
Contine
12840 (90)
293
253
253
253
293
293
293
253
253
253
-
Msat
typed
BEAST
BSP
Migrate-n
BSP
(mtDNA)
Migrate-n
BSP
(msats)
√
10
4
√
253
293
4
√
6
√
-
√
8
√
3
√
7
√
293
141
293
√
√
Sample
ID
822
823
824
825
826
827
828
829
830
832
833
834
835
836
837
838
840
841
842
843
844
845
846
848
849
850
851
852
853
C14 lab
codes
Location
Pingelly
Dwarladine
Pool
Beaufort
Dwarladine
Pool
Gracefield
Jerramungup
Beverley
Mammoth
Cave
Mammoth
Cave
Capel/Uralla
Chorkerup
Beverley
Pingelly/
Woyerling
Pingelly
Contine
Mooterdine
Mooterdine
Karridale
Karridale
Karridale
Unknown
location
Contine
Cuballing
Manjimup
Boyup Brook
Dryandra
Bernier Is.,
uncertain
Faure Island
Manjimup
Uncalibrate Age
(C14 error)
Ct
value
Largest
Amplicon
Msat
typed
BEAST
BSP
Migrate-n
BSP
(mtDNA)
Migrate-n
BSP
(msats)
8
√
√
√
Age (year*)
Sample
102
Skin
-
102
Skin
29.2
293
108
Skin
25.14
253
102
Skin
34.38
141
108
41
77
Skin
Skin
Skin
26.41
19.26
-
253
293
-
7
96
Skin
24.2
293
10
√
96
Skin
29.15
293
4
√
79
72
77
Skin
Skin
Skin
32.57
-
141
293
49
Skin
32.32
293
78
44
44
44
78
80
80
Skin
Skin
Skin
Skin
Skin
Skin
Skin
14.83
17.69
22.87
32.29
293
293
293
253
66
Skin
28.78
141
44
47
32
41
37
Skin
Skin
Bone
Bone
Bone
18.59
16.84
17.33
29.4
25.26
293
293
293
253
293
96
Bone
31.57
253
n/a
32
Bone
Bone
29.58
27.25
123
293
-
√
√
√
√
√
10
10
10
√
√
√
√
√
√
√
√
9
10
8
8
7
√
√
√
√
√
√
√
√
√
√
√
√
√
10
√
√
√
Sample
ID
854
855
1003
1004
1005
1006
1007
1008
1009
1010
1011
C14 lab
codes
Location
Uncalibrate Age
(C14 error)
Perup River
Manjimup
Peron
Peninsula
Faure Island
Faure Island
Faure Island
Nullarbor
(cave)
Nail Tail
Cave
Nullarbor
(cave)
Nullarbor
(cave)
Peak Charles
N.P.
Largest
Amplicon
Msat
typed
BEAST
BSP
28.88
23
293
293
10
√
√
Bone
-
293
n/a
n/a
n/a
Bone
Bone
Bone
40.33
29.8
253
293
n/a
Bone
-
-
n/a
Bone
35.37
-
n/a
Bone
-
-
n/a
Bone
42.95
n/a
Bone
-
Age (year*)
Sample
30
32
Bone
Bone
n/a
Ct
value
Migrate-n
BSP
(mtDNA)
√
√
Migrate-n
BSP
(msats)
√
253
-
* Years prior to 2008. Archaeological dates (i.e. more than 150 years) are based on calibrated radiocarbon age estimates of years before 1950. Between brackets range with ± s.e.
† Sample is positioned in an undated layer between two dated layers
Calibrations were carried out using CalPal2007_HULU calibration curve of the Cologne Radiocarbon Calibration & Paleoclimate Research Package, available at http://www.calpal-online.de/
Table S2. Mitochondrial cytochrome b and control region primer information used to genetically
characterise Bettongia. All primers were newly designed for the purpose of this study and are typical for
Bettongia DNA.
Primer name
Primer sequence 5' → 3'
Annealing
Amplicon
temperature (°C)
size (bp)
53
220
This study
55
250
This study
54
205
This study
55
145
This study
55
140
This study
58
250
This study
Source
Cytochrome b primer sets
Woylie_cytb_32F
ATGAAAAACCATTGTTGTACTTC
Woylie_cytb_249R
AGGGTGTCAGATGTATAGTGTAT
Woylie_cytb_139F
ACCTTCCAACATTTGAGCCTGATG
Woylie_cytb_388R
TGAGCCGTAGTAGATTCCTC
Woylie_cytb_290F
AACTACGGCTGGTTAATCC
Woylie_cytb_493R
TCAGAATGATATTTGTCCTCATGGCA
Control region primer sets
Woylie_cr_98F
GGTTTATGGRTTTAGATTCGTGAATC
Woylie_cr_240R
CAAACCTATACCCATAGCATATCTCC
Woylie_cr_156F
GCTTTGGATGTAATGTTTAAGGTAGAT
Woylie_cr_296R
GCAAGYACAAATCAACCAAACTA
Woylie_cr_1448F
TTGTACTTGCTTATATGCTTGGGGTGA
Woylie_cr_1699R
GTGACTCGACCTTTTTCTACA
Table S3. Details of the microsatellite loci amplified in the woylie (Bettongia penicillata ogilbyi)
including the species where these were first developed.
Source species
Locus
Reference
Primer
name
Primer sequence 5 3
Bettongia tropica
Bt64
(Pope et al. 2000)
Bettongia tropica
Bt76
(Pope et al. 2000)
Bettongia tropica
Bt80
(Pope et al. 2000)
Petrogale
assimilis
Petrogale
xanthopus
Petrogale
xanthopus
Petrogale
xanthopus
Petrogale
xanthopus
Petrogale
xanthopus
Pa593
(Spencer et al.
1995)
Y105
(Zenger et al. 2002)
Y112
(Zenger et al. 2002)
Y151
(Pope et al. 1996)
Y170
(Pope et al. 1996)
Y175
(Zenger et al. 2002)
Bt64F
Bt64R
Bt76F
Bt76R*
Bt80F
Bt80R
Pa593F
Pa593R
Y105F
Y105R
Y112F
Y112R
Y151F
Y151R
Y170F
Y170R
Y175F
Y175R*
AATAGGAATCCATATGCTGATCC
ATAGCCAACTGGGTAATTTAGTG
CGATGGTAGGCAACAACGAATAG
AATCCTGTGTTTCATCT
CACTTTTACCAGGCTACCTAACC
CCCCTGATGAGATTATACTAAAC
TAGGGCACGTCATAAGGATGCAG
GCTTTCCAGTTTCTGACTTTTCATG
GGTAATGAGTCAGTGTGATGAGG
GGTAGGAGGAAAGGGAGAAAAG
CATGTACTGCTGAGAATAGGCAC
CCTGGAGAAGTCTATCTCCCAAC
ATATTACCTGCAAACTGGAAC
AGCCATTGCAGTAACTCCAAC
GGACTCAAACCCAACACTAGC
TGCATGCCTTTGTCATACACG
TGGGACATTTCCTGACCTAC
TCCTGGGCTAGAACTCTGGT
Potorous
longipes
Potorous
longipes
Macropus eugenii
Pl2
(Luikart et al. 1997)
Pl26
(Luikart et al. 1997)
T17-2
(Zenger & Cooper
2001)
PI2F
PI2R
PI26F
PI26R
T17-2F
T17-2R
CACTACATTTCACCC
TTGTCAGTCTGTGTCAGTGCC
TTGTGAAATAGTGCATTTTCTGC
GGCTTCTGAGCAGTCAGTTCTG
TGTAAAACGACGGCCAGTAGCTCAGAGTTCCA
GAAACTTATCCCAAGTGTTTCTGG
*Reverse primer modified from original publication
Fig. S1. The success rate of positive genotyping associated with the corresponding sample CT value, obtained
from the qPCR 302/425 assay
Fig. S2. Bayesian phylogeny of Bettoniga penicillata ogilbyi, showing the maximum a posteriori (MAP)
tree generated using BEAST. A GTR+G+I substitution model (assuming strict molecular clock) was
imposed on an alignment containing the 13 historical cytochrome b sequences (370 bp) and 15 modern
sequences (1000 bp, identified with an *). Posterior probabilities are shown on the selected outer nodes. The
scale represents the number of nucleotide substitutions per site.
Fig. S3. Comparison between reconstruction of the woylie (B. penicillata) demographic history based on
control region of mtDNA using a Bayesian Skyline Plot analysis implemented in BEAST v1.8 (Drummond
et al. 2012) - black - and Migrate-n (Beerli 2006) - purple. Historical data (n=13) for these analyses were
limited to samples that were geographically close to the extent populations. Shaded areas represent 95%
Highest Probability Density (HPD) and 1.96 standard deviation from parameter values, respectively.
Population size is expressed as population mutation parameter (Ө) and time as mutations per site per
generation time.