Supplementary Table 1 Collection localities for the northeast Queensland Petrogale used in this study: Cape York rock-wallaby (P. coenensis);
Godman’s rock-wallaby (P. godmani); Mareeba rock-wallaby (P. mareeba); Sharman’s rock-wallaby (P. sharmani); allied rock-wallaby (P.
assimilis) and the unadorned rock-wallaby (P. inornata). GenBank accession numbers are for mitochondrial control region sequences. Shared
mtDNA haplotypes are denoted by superscript integers (e.g. 1, 2, 3).
Species
Petrogale coenensis
Petrogale godmani
Sample ID
S100
S101
S102
S441
S865
S866
S868
S947
S097
S098
S104
S130
S410
S502
S504
S506
S511
S616
S617
S622
S657
Locality
Coen
Coen
Coen
Coen
Musgrave
Musgrave
Pascoe River
Musgrave
Byerstown Range
Byerstown Range
Dingo Hill
Byerstown Range
Dingo Hill
Dingo Hill
Mt. Elephant
Mt. Elephant
Laura
Dingo Hill
Dingo Hill
Mt. McDonald
Bathurst Heads
Latitude
-13.83
-13.83
-13.83
-13.91
-14.80
-14.80
-12.93
-14.80
-15.95
-15.95
-16.50
-15.95
-16.50
-16.50
-16.48
-16.48
-15.67
-16.50
-16.50
-15.70
-14.31
Longitude
143.13
143.13
143.13
143.11
143.43
143.43
143.03
143.43
144.92
144.92
145.03
144.92
145.03
145.02
144.92
144.92
144.53
145.03
145.03
145.02
144.21
GenBank Number
KT726258
KT7262591
1
KT726260
KT7262612
2
KT726262
KT726263
KT7262643
KT726265
KT726266
KT726267
KT7262684
4
KT726269
KT726270
3
KT7262715
5
KT726272
KT726273
Petrogale mareeba
Petrogale sharmani
S705
S924
S925
S929
S1210
S1211
S333
S346
S386
S401
S407
S408
S436
S492
S615
S703
S704
S876
S877
S928
S110
S114
S119
S423
S424
S427
S428
S432
Fairlight
Pinnacles
Pinnacles
Mt Mulgrave
Granite Gorge, Mareeba
Granite Gorge, Mareeba
Mt Aunt
Wolfram
Wallaroo Hills
Southedge
Lighthouse Mt.
Mt. Alto
Anthill Creek
-15.78
-15.73
-15.73
-16.44
-17.03
-17.03
-17.08
-17.08
-18.17
-16.82
-16.68
-16.57
-18.39
144.05
143.56
143.56
144.13
-145.34
145.34
145.38
145.38
145.30
145.22
145.25
145.10
145.14
Southedge
Walsh River Gorge
Walsh River Gorge
Mt. Garnet
Mt. Garnet
Bellevue
Mt. Claro
Mt. Claro
Mt. Claro
Poison Creek
Lincoln Springs
Taravale
Hidden Valley
Kangaroo Hills
-16.82
-16.88
-16.88
-17.70
-17.70
-16.50
-18.87
-18.87
-18.87
-18.75
-18.68
-19.13
-18.98
-18.95
145.22
143.95
143.95
145.18
145.18
144.17
145.73
145.73
145.73
145.67
145.50
146.15
146.07
145.67
KT726274
KT7262756
6
KT726277
KT7263077
7
KT726295
KT726296
KT726297
KT726298
KT726299
KT726300
KT726301
KT726302
KT726303
KT7263048
8
KT726305
KT726306
KT726276
KT7263089
9
KT726309
KT72631010
KT726311
KT726312
KT726313
KT72631411
Petrogale assimilis
S635
S855
S860
S126
S337
S421
S425
S468
S470
S471
S473
S477
S484
S522
S602
S603
S607
S611
S612
S625
S628
S631
S640
S650
S701
S721
S724
S732
Mt. Claro
Mt. Claro
Mt. Claro
Munday Bay, Palm Island
Mt. Elliot
Christmas Creek
Tabletop
Natal Downs
Charters Towers
Charters Towers
Mt Robbins
The Twins
Blue Range
Mt. Hope
Torver Valley
Spring Lawn Gorge
Porcupine Gorge
Hillsborough
Hillsborough
Croydon
Croydon
Valley of Lagoons
Mt. Stuart
Mt. Whickham
Routh Holding
Porcupine Gorge
Humpy Creek
Lolworth
-18.87
-19.03
-18.87
-18.76
-19.45
-19.08
-19.44
-21.07
-20.13
-20.26
-20.58
-20.54
-19.10
-21.43
-20.65
-20.38
-20.30
-20.11
-20.10
-18.22
-18.22
-18.58
-19.37
-20.49
-18.32
-20.35
-20.39
-20.18
145.73
145.72
145.73
146.62
146.95
145.30
146.41
146.27
146.25
146.01
146.98
146.98
145.57
146.73
144.12
144.34
144.50
147.06
147.04
142.36
142.36
145.13
146.79
147.46
143.68
144.45
144.67
145.01
10
11
KT726315
KT726229
KT726230
KT726232
KT726231
KT726233
KT726234
KT726235
KT726236
KT726237
KT72623812
KT726239
KT726240
KT726241
KT726242
KT726243
KT726244
KT726245
KT726246
KT726247
KT726248
KT726249
KT726250
KT726251
KT726252
KT726253
S851
S856
S874
S878
S914
S918
Petrogale inornata
S136
S137
S146
S155
S459
S462
S463
S467
S646
S648
S649A
S692
S735
S739
S740
S744
S871
S889
godmani x mareeba S416
S417
Petrogale penicillata S1776
Mt. Fullstop
Mt. Fullstop
Cape Ferguson
Croydon
Black Rock
Black Rock
Maiden Mountain
Seven Sisters
Blue Mountain
Apis Creek
Mt. Nicholson
Pine Mt.
Boomer Range
Camp Hill, Burton Dns
Mt Louisa
Gregory Range
Gregory Range
Cape Upstart
Lowestoff
Emu Plains
Havilah
Pelican Creek
Whitsunday Is.
Mt. Inkerman
Dingo Hill
Dingo Hill
Ingles Rd Watagans
-19.19
-19.05
-19.28
-18.22
-19.08
-19.08
-19.93
-19.95
-21.53
-23.02
-23.33
-23.20
-23.22
-21.65
-19.89
-19.93
-19.93
-19.77
-22.87
-20.78
-20.90
-20.60
-20.26
-19.75
-16.50
-16.50
-32.76
145.56
145.67
147.06
142.37
144.46
144.45
147.87
147.88
149.13
149.57
150.62
150.62
149.82
148.11
147.24
147.32
147.32
147.77
148.19
148.03
147.81
147.68
148.95
147.50
145.03
145.03
151.11
KT726254
12
KT726255
KT726256
KT72625713
13
KT726286
KT726287
KT726288
KT726289
KT726278
KT726281
KT726292
KT726293
KT72629414
KT726290
KT726291
KT726279
KT726282
KT726283
KT726284
KT726285
KT726280
14
KT726316
KT726317
JQ623024
Supplementary Table 2 Genetic diversity indices for mtDNA and microsatellite data from six northeast Queensland Petrogale species. N =
number of samples 1 (mtDNA)/2 (microsatellites). MtDNA - H = number of mitochondrial haplotypes; π = nucleotide diversity; P sites =
polymorphic sites; H diversity = haplotype diversity. Microsatellites - AD = average allele number; HE = expected heterozygosity; HO = observed
heterozygosity.
Species
N
H
π
P sites
H diversity
AD
HE
P. coenensis
P. godmani
P. mareeba
P. sharmani
P. assimilis
P. inornata
8/8
17/17
16/14
11/11
31/29
18/18
6
12
14
8
28
59
0.034±0.019
0.046±0.024
0.055±0.029
0.038±0.020
0.057±0.028
0.044±0.023
51
94
78
79
144
53
0.929±0.084
0.941±0.043
0.983±0.028
0.891±0.092
0.994±0.010
0.994±0.021
6.588±1.543
10.765±3.750
9.824±3.450
8.176±2.298
14.059±3.211
11.059±4.337
0.815±0.074
0.855±0.064
0.860±0.085
0.819±0.102
0.887±0.046
0.859±0.084
HO
0.640±0.197
0.716±0.144
0.668±0.214
0.727±0.170
0.702±0.130
0.621±0.210
Supplementary Table 3 Genetic differentiation amongst six northeast Queensland Petrogale species. ΦST below the diagonal and FST values
above the diagonal. * denotes significant differentiation (P<0.05) after permutations.
P. coenensis
P. coenensis
P. godmani
P. mareeba
P. sharmani
P. assimilis
P. inornata
0.124*
0.259*
0.412*
0.251*
0.373*
P. godmani
0.070*
0.220*
0.302*
0.196*
0.332*
P. mareeba
0.072*
0.065*
0.230*
0.161*
0.291*
P. sharmani
0.091*
0.082*
0.073*
0.068*
0.363*
P. assimilis
0.072*
0.043*
0.022*
0.045*
0.249*
P. inornata
0.105*
0.080*
0.046*
0.083*
0.043*
Supplementary Table 4 Mean historical migration rates and effective population sizes θ amongst six northeast Queensland Petrogale species.
Migration rates are from the species in column one into the species listed in row one.
P. coenensis
P. godmani
P. mareeba
P. sharmani
P. assimilis
P. inornata
θ
P. coenensis
4.14
3.62
1.91
5.8
0.79
2.22
P. godmani
4.71
3.12
2.74
6.77
2.91
2.77
P. mareeba
2.51
2.75
1.47
7.73
1.85
3.59
P. sharmani
2.43
2.46
1.79
2.4
5.12
1.98
P. assimilis
4.37
5.46
5.83
3.17
6.62
3.27
P. inornata
0.83
2.33
2.21
2.04
6.03
4.51
Supplementary Table 5 Tests of nested models between three northeast Queensland Petrogale species (P. assimilis = A; P. mareeba = M; P.
sharmani = S) representing complex (A/M; A/S) and simple (M/S) rearrangements. Only models with m = 0 (representing no introgression) are
presented. The 2LLR value is the calculated chi-square test statistic between the null model and the nested models. Nested models with
P<0.05 are rejected and imply that the null model fit the data better. 1A/M, 2S/A, 3M/S.
Model
θ1, θ2, θA, m1, m2
θ1, θ2, θA, m1, m2=0
θ1, θ2, θA, m1=0, m2
θ1, θ2, θA, m1=0, m2=0
θ1=θ2, θA, m1=0, m2=0
θ1=θ2=θA, m1=0, m2=0
θ1=θA, θ2, m1=0, m2=0
θ1, θ2=θA, m1=0, m2=0
log(P)
-6.61511
-6.01632
-6.16373
-13.0416
-460.5170
-77.2184
-12.2145
-460.5170
-9.5975
-255.4984
-460.5170
-460.5170
-290.4285
-460.5170
-460.5170
-290.4285
-460.5170
-460.5170
-290.4285
-460.5170
-460.5170
-255.4981
-460.5170
-460.5170
2LLR
df
P-value
12.8530
909.0015
142.1094
11.1989
909.0015
6.8676
497.7667
909.0015
908.7067
567.6268
909.0015
908.7067
567.6268
909.0015
908.7067
567.6268
909.0015
908.7067
497.7661
909.0015
908.7067
1
1
1
1
1
1
2
2
2
3
3
3
4
4
4
3
3
3
3
3
3
<0.0011
<0.0012
<0.0013
<0.0011
<0.0012
0.0093
<0.0011
<0.0012
<0.0013
<0.0011
<0.0012
<0.0013
<0.0011
<0.0012
<0.0013
<0.0011
<0.0012
<0.0013
<0.0011
<0.0012
<0.0013
Supplementary Table 6 Summary of chromosome rearrangements detected by G-banding amongst the six Petrogale species from northeast
Queensland. * = plesiomorphic morphology [25, 26]. - = fused to another autosome. 3a = an apomorphic acrocentric chromosome 3a which is
derived from the submetacentric plesiomorphic 3 by a centromeric transposition [27-29]. 4a = an apomorphic acrocentric chromosome 4a
which is derived from the submetacentric plesiomorphic 4 by a centromeric transposition [27-29]. 5i = an apomorphic chromosome 5 which is
derived from the plesiomorphic 5 by a large centromeric transposition or pericentric inversion [27-29]. 5-10 = the centric (Robertsonian) fusion
of plesiomorphic acrocentric chromosomes 5 and 10 to form a submetacentric [28, 30]. 6-10 = the centric (Robertsonian) fusion of
plesiomorphic acrocentric chromosomes 6 and 10 to form a submetacentric [28, 30]. 6-10a = an apomorphic acrocentric chromosome derived
from the centric (Robertsonian) fusion of plesiomorphic acrocentric chromosomes 6 and 10, followed by a centromeric transposition [29, 30].
6-9a = an apomorphic acrocentric chromosome derived from the centric (Robertsonian) fusion of plesiomorphic acrocentric chromosomes 6
and 9, followed by a centromeric transposition [28, 30]. 7a = an apomorphic acrocentric chromosome 7a which is derived from the
metacentric plesiomorphic 7 by an unknown mechanism [25, 30]. xl = submetacentric X chromosome with NOR (nucleolar organizer region)
located towards the end of the short arm [25]. xp = acrocentric X chromosome with NOR located towards the end of the long arm [25]. xr =
acrocentric X chromosome with NOR located below the centromere [25].
N.B. X chromosome morphology is polymorphic within P. godmani, P. assimilis and P. inornata. Since fertile females heterozygous for different
X chromosome morphologies are regularly encountered in the field these differences are not thought to have a role reproductive isolation
[25]. ** References are in Supplementary Material.
Supplementary Table 6
Species
P. coenensis
P. godmani
P. mareeba
P. sharmani
P. assimilis
P. inornata
Chromosome number relative to 2n=22 plesiomorphic macropodid karyotype
1
2
3
4
5
6
7
8
9
10
X
*
* 3a
*
*
*
7a
*
*
*
xl
*
* 3a 4a
5i
6-10a
7a
*
*
xl, xp
*
* 3a 4a 5-10 6-9a
7a
*
xl
*
* 3a 4a 5-10
*
7a
*
*
xl
*
* 3a 4a
5i
6-10
7a
*
*
xl, xp, xr
*
*
*
*
5i
*
7a
*
*
*
xl, xp