Diversification across biomes in a continental lizard radiation

SUPPORTING INFORMATION (Methods 1.1–1.3, Results 1.1–1.2, Figures S1–5,

Tables S1–12)

Methods 1.1 Bioinformatic workflow

The cleaned reads from Gehyra variegata group samples were assembled into contigs using a

pipeline described by Bragg et al. (2016). The pipeline performs a de novo assembly of each

target exon for each sample using Velvet v. 1.2.08 (Zerbino and Birney 2008), merges

contigs using CAP3 v. date 08/06/13 (Huang and Madan 1999), and truncates the contigs to

the exon boundaries using Exonerate v. 2.2.0 (Slater and Birney 2005). If multiple contigs

were assembled for a particular target, the putative ortholog was identified with a reciprocal

best BLAST criterion. The cleaned reads of each individual were then mapped onto the

corresponding contigs (to avoid reference bias) using Bowtie 2 v. 2.2.2 (Langmead and

Salzberg 2012), and heterozygous sites were identified using GATK release gb82c674

(McKenna et al. 2010). We inserted “N” bases where genotyping quality (GQ) was less than

20. Retained samples have a mean coverage of 36.42 bp with 1127 loci on average (Table

S1). For exons with multiple heterozygous sites, phase was determined from overlapping

reads (GATK), and one haplotype was retained from each exon and individual for

phylogenetic analyses.

The assembled haplotype sequences of each locus were aligned using MACSE v. 1.2

(Ranwez et al. 2011), which returns frame shift-corrected nucleotide and corresponding amino acid multiple sequence alignments. Terminal gap symbols and special characters referring to the occurrence of stop codons and frame shifts were replaced by "N" and "X" for nucleotide and amino acid alignments, respectively. In order to preserve the correct frame, we

used the amino acid alignments to remove all columns containing only gap symbols.

Subsequently, amino acid alignments were searched for randomly similar sequence sections

with ALISCORE v. 2.0 (Misof and Misof 2009; Kück et al. 2010) using the maximum

number of pairwise sequence comparisons and the default sliding window size. This

information was then applied to the nucleotide alignments to remove the corresponding

affected sections with ALICUT v. 2.3 (Kück 2009). Trailing ends were trimmed in each

nucleotide alignment by removing codon columns consisting of more than 50% gap symbols.

Methods 1.2 StarBEAST2 “divide and conquer” strategy

The basic procedure in a divide and conquer StarBEAST2 analysis is to identify diverse

subclades with many closely related species, and pull them out for smaller, subclade-specific

StarBEAST2 analyses. With the subclades removed, a “skeleton tree” is estimated with

StarBEAST2 (Ogilvie et al. 2017), and then the trees sampled from the posterior distribution of the dated skeleton tree are re-integrated with the trees sampled from the posterior of each subclade analysis.

Here, the skeleton tree consisted of 15 of the 44 Gehyra lineages (G. punctataA2, G. variegataC1, G. punctataB1, G. girloorloo, G. pseudopunctata, G. einasleighensis, G. lazelliLP, G. moritzi, G. variegataC2, G. punctataB4, G. pulingka, G. punctataA1, G. purpurascens, G. variegataA, and G. versicolor5), with two outgroup species (G. CYsp, G. dubia). These taxa were chosen either because (1) they represented a pair (or quartet) of lineages with a common ancestor that delimited a large monophyletic subclade, or (2) they were taxa with some ambiguity in phylogenetic position, so they were allowed to “float” and have their position be estimated (Fig. S3). We conducted StarBEAST2 analyses on four subtrees, with a tight age prior of

Normal (mean = 1, standard deviation = 0.001). Each subclade analysis also included an outgroup taxon to improve the likelihood that the rooting of the subclade would be consistent with the subclade’s position in the skeleton tree analysis. The four subclades were:

1. The “variegata+punctataA” subclade, with 16 lineages: G. punctataA2, G.

variegataB1, G. variegataB2, G. variegataB3, G. punctataA5, G. punctataA4, G.

punctataA3, G. minuta1, G. minuta2, G. montium, G. pilbara1, G. pilbara2, G.

punctataA1, G. variegataA, G. versicolor4, G. versicolor5. The outgroup was G.

variegataC1. In the skeleton tree, the common ancestor of this subclade was identified

as the common ancestor of G. punctataA2, G. punctataA1, G. variegataA, and G.

versicolor5.

2. The “punctataB” subclade, with 7 lineages: G. punctataB1, G. punctataB2, G.

punctataB3, G. punctataB4, G. punctataB5, and G. punctataB6. The outgroup was G.

variegataC1. In the skeleton tree, the common ancestor of this subclade was identified

as the common ancestor of G. punctataB1 and G. punctataB4.

3. The “lazelli” subclade, containing G. lazelli, G. lazelliLP, and G. pulingka. The

outgroup was G. moritzi. In the skeleton tree, the common ancestor of this subclade

was identified as the common ancestor of G. lazelliLP and G. pulingka.

4. The “nana group” subclade, containing 12 lineages: G. girloorloo, G. kimberleyi, G.

multiporosa, G. nana1, G. nana2, G. paranana, G. nana4, G. pseudopunctata, G.

granulum, G. nana7, G. pluraporosa, and G. occidentalis. The outgroup was G.

lazelliLP. In the skeleton tree, the common ancestor of this subclade was identified as

the common ancestor of G. pseudopunctata and G. girloorloo.

Methods 1.3 Morphological data collection

Ideally, 20 adults (preferably males) were measured per Gehyra variegata group lineage

(average = 13). The two lineages within each of G. pilbara and G. minuta were combined to

increase sample size, while two lineages known only from single specimens were excluded

from analyses (G. pluraporosa and G. punctataB4). One person (LGA) measured 11

ecologically relevant morphological traits, following Doughty et al. (2012) with some

additional variables (indicated with *): snout-vent length (SVL), trunk length (TrunkL; body

length between legs), trunk width* (TrunkW; width between ventral skin folds of forelegs),

foreleg length (ForelegL; elbow to base of wrist), hindleg length (HindlegL; knee to heel),

head length (HeadL; anterior edge of ear to tip of snout), head depth (HeadD; deepest part

posterior to eyes), head width (HeadW; widest part posterior to eyes), snout length* (SnoutL; anterior edge of eye to tip of snout), snout depth (SnoutD; deepest part anterior to eyes) and number of lamellae on fourth right toe pad (Lamellae; excluding distal wedge) (Table S3).

Tail length was not measured as tails were often missing or regenerated; precloacal pore count was recorded but not used for morphological analyses. Measurements were made on the right hand side of the body (dorsal view) to the nearest 0.1 mm using digital callipers.

Results 1.1 Lineage phylogeny comparison

Both the RAxML and ASTRAL analyses (Fig. 2) and the StarBEAST2 species tree (Fig. 3)

strongly infer paraphyly of G. punctata as currently described, with punctata A sister to a

diverse variegata clade rather than punctata B. Furthermore, G. variegata is polyphyletic, with one pair of lineages (G. variegata C1–2) being highly divergent from the remainder.

Within the variegata clade, “true” G. variegata (variegataA) is sister to G. pilbara and a closely related group of lineages including additional variants of G. variegata (variegataB1–

3), G. montium, G. minuta and G. versicolor. Some relationships within the main AAZ clade are not strongly supported, or are conflicting: variegataC1 and variegataC2 are in different

positions in each tree. Relationships among lineages within the punctata A clade are poorly resolved, but in all three trees relationships among the punctata B lineages are well resolved.

Results 1.2 Lineage diversity validation

Nearly all (28 of 30) of the candidate lineages across the Gehyra variegata group AAZ

species are found to be monophyletic in the RAxML concatenated tree (Fig. 2A). Using the

tr2 gene tree concordance approach for lineage discovery, and conditional on the topology of the RAxML tree used, all candidate lineages are supported and some are divided yet further

(e.g., G. lazelli, G. einasleighensis, G. punctataB6, G. montium, G. versicolor; Fig. S4).

All candidate lineages are also confirmed as evolutionarily independent using BPP (Table

S2); posterior support for each lineage is pp = 1.0, except some lineages within G. variegata

(variegataB1, B2, B3: pp = 0.88, also with uncertain species tree topologies).

Lineage diversity is especially high within G. variegata (six lineages) and G. punctata

(11 lineages). Populations of G. lazelli with clearly different body sizes collapse into a single

taxon, but only when each individual sample is treated as a separate species (Table S2; see

also Sistrom et al. 2012). The G. versicolor4 and the G. versicolor5 lineages are supported as

independent using BPP; however, we do not consider them genetically distinct as they group

by geography rather than lineage in the RAxML phylogenetic analysis. Consistent with

previous analyses (Sistrom et al. 2014), two sister lineages of G. minuta are nested within G.

versicolor, and are also supported as two separate lineages using BPP. The two samples

representing G. montium are paraphyletic with G. variegataB3, yet are still supported as

separate using BPP; we treat these two lineages as distinct based on Kealley et al. (in press).

Thus the 28 AAZ lineages, plus the 12 AMT nana group lineages (Moritz et al. 2018), gives

a total of 40 lineages in the variegata group. Supporting Information References

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Supplementary Figures S1–5

Figure S1 Summary of phylogenetic analyses, including sampling, sequencing, bioinformatics, and species delimitation.

Figure S2 Summary of ancestral state estimation, diversification rate, and morphological evolution analyses.

Figure S3 Gehyra phylogeny inferred using ASTRAL summary species tree method with

499 loci. Branch supports are maximum likelihood bootstrap values, and branch lengths are fixed. Lineages used in the “skeleton tree” for the StarBEAST2 analysis are coloured red, with red circles indicating the four subclades removed for separate StarBEAST2 analyses.

Figure S4 Gehyra phylogeny inferred using RAxML concatenation of 547 loci, showing tr2 species delimitations. Branch supports are maximum likelihood bootstrap values, and the

RAxML scale bar is nucleotide sequence change per My. Samples assigned to a single lineage by tr2 (i.e., nodes to collapse) are coloured red.

Figure S5 Gamma estimates showing slowdown of diversification rates in the StarBEAST2 species tree, from 100 posterior trees. The solid blue line indicates the mean (-2.85) and the dashed blue lines indicate the 95% highest posterior density (-3.80, -1.96).

Supplementary Tables S1–11

Table S1 List of 94 Gehyra specimens used for phylogenetic analyses (mapped in Fig. 1,

except for first two outgroup lineages). Latitude and longitude are reported up to 6 decimal

places; coverage is reported in base pairs (bp). Abbreviations: Australian Biological Tissue

Collection (ABTC); Craig Charles Moritz collection (CCM); National Museum of Victoria

(NMV); Museum (NTM); Queensland Museum (QM); South Australian

Museum (SAM); Western Australian Museum (WAM).

Mean Number of Lineage Catalogue no. Location Latitude Longitude coverage loci name (bp) recovered CYsp ABTC79193 Aquam Campt, Trans -9.09671 141.435 110.46 1543 Fly dubia Geck1 Wambiana stn, 40k S -20.54017 146.107916 48.43 1517 Charters Towers einasleighen- QM A013584 Lornevale -18.37555 143.52261 28.09 1170 sis einasleighen- QM J94587 Cobb Camp -18.79611 143.42386 20.18 1214 sis einasleighen- SAM R55786 31k N Einasleigh on Mt -18.289167 144.0775 38.42 1561 sis Surprise Road girloorloo WAM R113727 Cadjbut Mine 1 -18.75 126.15 105.08 1556 girloorloo WAM R175047 Gogo Station, Virgin -18.5149 125.9256 83.10 1437 Hills, 1 km from road near Bobs Bore Gogo11 granulum WAM R165439 Irvine Island -16.076944 123.550278 42.74 1559 granulum WAM R176205 Mitchell Plateau -14.6723 125.7319 81.13 799 Surveyors Pool kimberleyi WAM R175035 Meda Station tip -17.36813 124.0042 45.07 1546 kimberleyi WAM R176229 Potts camp -16.48927 125.35283 57.89 1566 lazelli SAM R38950 Tungkillo -34.816 139.1 36.96 1558 lazelli SAM R52012 4.7k NNE Warden Hill -30.40388 139.23527 22.48 1455 lazelliLP SAM R64428 Terrapinna Springs -29.915 139.666 28.55 1528 lazelliLP SAM R64431 8km E Terrapinna -29.90416 139.43777 62.28 1559 Springs minuta1 CCM1930 N Tennant Creek -18.77502 134.02632 44.71 1552 minuta1 NTM R13647 80k S Renner Springs -19 134.13 26.67 1155 minuta1 SAM R51087 Tennant Creek dump -19.65 134.183 32.31 1267 minuta2 CCM2774 Kurundie Station rocks -20.49926 134.67749 38.10 1558 minuta2 CCM2779 Whistleduck Camp, -20.63474 134.77609 37.87 1531 Davenport NP montium WAM R131737 Clutterbuck Hills -24.615833 126.223056 12.61 450 montium WAM R145513 69km S Port Hedland -20.91 118.68 14.20 473 moritzi CCM2772 Kurundie Station rocks -20.49926 134.67749 15.42 308 moritzi NTM R15356 6k SSW Claraville HS -23.42 134.73 12.85 706 moritzi NTM R20664 Finke Gorge NP -24.08 132.76 14.89 877 moritzi QM A007723 S-Bend Gorge, Cravens -23.063889 138.350833 25.87 925 Peak Reserve multiporosa CCM1217 Mitchell Plateau -14.8317 125.7192 47.48 659 Repeater Track multiporosa WAM R168579 Darcy Island -15.283333 124.383333 91.68 1559 nana1 NMV D77038 Ngumpan Cliff area -18.75114 126.08203 39.64 1540 nana1 WAM R175049 Vic River Region -15.61091 131.11597 46.33 927 Escarpment Walk nana2 CCM2174 Hartz Range camp -14.71124 134.28859 41.47 1554 Roper Hwy nana2 NTM R37066 50km SW Katherine -14.814117 131.918833 21.27 1335 nana2 NTM R37090 , approx 6 -13.285067 131.117433 104.81 1311 km from Stuart Hwy nana4 CCM0985 Mud Springs campsite, -14.88 126.35853 56.45 1563 20km SW Theda HS nana4 WAM R171085 Adolphus Island -15.078056 128.141389 140.77 1416 nana4 WAM R172134 Wargul Wargul -13.939167 126.174444 23.45 1525 nana4 WAM R173524 Drysdale River camp, -14.60824 126.93172 37.56 1531 50km SE Kalumburu nana7 CCM2213 Tomato Island 2k S -14.76098 134.68181 39.01 1536 occidentalis WAM R164773 Mt Nyulasy -16.745278 128.2825 168.19 1545 occidentalis WAM R172143 Kingfisher Island -16.081667 124.070556 129.99 1543 paranana NTM R37056 Dorat Road Robin Falls -13.35 131.138 64.88 396 Area paranana NTM R37831 Bullo River Boab -15.65862 129.65944 57.66 1554 pilbara1 NTM R22786 , W -22.72 136.58 31.61 516 Arthur Creek pilbara1 WAM R131070 CA 10km W -22.816667 127.65 19.94 935 Kiwirrkurra pilbara2 WAM R102167 5.8km NNW Mount -22.602222 118.520833 22.58 1091 Windell pilbara2 WAM R129336 1km SE Griffin Gas -21.783333 114.85 9.87 427 Plant, 30km WSW Onslow pluraporosa WAM R174024 Kind Edward River W -14.75373 126.2105 36.61 1409 pluraporosa WAM R174026 King Edward River W -14.75413 126.21037 38.87 1560 pseudopunc- WAM R176239 Sir John Gorge, -17.52933 126.21127 160.50 1532 tata Mornington pseudopunc- WAM R176288 Springvale Camp -17.67997 127.69066 23.97 1422 tata pulingka SAM R42069 29k SW Illintjitja -26.33762 130.16094 38.50 1281 pulingka SAM R54751 Mt Howe -26.25888 133.43749 18.68 882 punctataA1 WAM R110146 2km E Ti Tree Pool -21.833333 117.610833 12.26 150 punctataA1 WAM R114571 Poonthune Pool, East -20.783333 118.716667 13.01 876 Turner River punctataA2 WAM R132563 Burrup Peninsula -20.616111 116.785 21.37 1117 punctataA2 WAM R165508 West Intercourse Island -20.7 116.583333 10.21 554 punctataA3 WAM R110013 5km S Lake -21.036389 117.106111 29.32 914 Poongkaliyarra punctataA3 WAM R117027 15km NW Paraburdoo -23.133333 117.566667 16.02 243 punctataA3 WAM R141332 Cape Preston Area -20.905278 116.216944 24.83 1508 punctataA4 WAM R131008 Mount Herbert Area, -21.312778 117.233889 21.71 1450 Millstream-Chichester NP punctataA4 WAM R158267 47.5km W Roy Hill -22.633333 120.411111 15.72 1201 punctataA5 WAM R125472 30km E Newman -23.316667 120.033333 12.20 885 punctataB1 WAM R114335 35km SE Prairie Downs -23.716667 119.433333 23.49 1002 punctataB1 WAM R129925 West Angelas, 100km -23.25 118.666667 18.76 891 WNW Newman punctataB2 WAM R116893 25km ESE Kooline HS -22.789444 116.546111 13.68 892 punctataB2 WAM R129932 West Angelas, 100km -23.25 118.666667 22.82 1228 WNW Newman punctataB2 WAM R165601 Dampier Area -20.674444 116.715556 12.43 835 punctataB3 WAM R156587 Cundaline Gap -20.548889 120.168056 17.84 1307 punctataB3 WAM R160096 (NE Pilbara) Braeside -21.288889 121.096111 26.35 1543 punctataB3 WAM R162701 (NE Pilbara) Baldy -21.05 118.8 29.72 1533 Rock punctataB4 WAM R156168 Waldburg Station -24.778889 117.101111 17.67 1326 punctataB5 WAM R116898 22km S Mount Phillip -24.766667 116.216667 17.43 1396 Homestead punctataB6 WAM R123764 39km ESE Gascoyne -25.21 115.514167 32.02 1535 Junction punctataB6 WAM R139444 Cane River -22.135278 115.688889 29.31 1431 purpurascens CCM1919 Ellery Rock hole -23.78058 133.0724 12.72 854 purpurascens CCM2762 Barry Cave Barkly -20.0486 136.67242 20.95 735 Highway variegataA WAM R113685 5km E Dalwallinu -30.283333 116.716667 26.39 503 variegataA WAM R114039 Peron Station -25.833333 113.55 12.15 249 variegataA WAM R141460 Faure Island Homestead -25.896111 113.908889 15.43 847 variegataB1 WAM R123947 Cape Range, 10km S -22 114.083333 25.45 1190 Exmouth variegataB1 WAM R153818 Vlaming Head -21.8 114.1 19.93 610 variegataB2 WAM R165744 Barrow Island -20.766667 115.45 13.00 395 variegataB3 WAM R119017 63km E Sandston (road -28 120.5 19.39 551 to Leinster) variegataB3 WAM R170800 14.5km NNW Mount -21.710833 116.765833 11.93 864 Elvire variegataC1 WAM R156584 Cundaline Gap -20.557778 120.181944 29.77 947 variegataC1 WAM R161412 47.5km ESE -20.428056 119.969444 30.39 1531 Goldsworthy variegataC2 WAM R145555 18km S Port Hedland -20.47 118.59 17.54 1180 versicolor4 CCM0217 Thorntonia Stn tip -19.5015 138.94908 18.59 830 versicolor4 CCM0252 West Leichardt salvage -20.59802 139.70422 13.79 608 yard versicolor4 NTM R21507 Musselbrook Reservoir -18.59 138.13 21.74 1456 versicolor4 SAM R42789 Diamantina Station -23.75 141.133 15.62 1059 dump versicolor4 SAM R55694 13.4k NNE Hughenden -20.78499 144.30555 17.88 1293 on Kennedy Developmental Road versicolor5 CCM0214 West Leichardt salvage -20.59802 139.70422 18.61 894 yard versicolor5 SAM R38945 Lancoona HS -32.366 145.883 25.75 619 Table S2 Candidate Gehyra variegata group AAZ lineages and BPP species delimitation results. Average posterior probability across two BPP analyses are reported in parentheses after the lineage name.

Laz group Purp group PuncB group PuncA group Mainvar group Vers group lazelli (1.0) einasleighensis punctataB1 punctataA1 minuta1 (1.0) minuta1 (1.0) (1.0) (1.0) (1.0) lazelliLP moritzi (1.0) punctataB2 punctataA2 montium (1.0) minuta2 (1.0) (1.0) (1.0) (1.0) pulingka (1.0) purpurascens punctataB3 punctataA3 pilbara1 (1.0) montium (1.0) (1.0) (1.0) (1.0) variegataC1 punctataB4 punctataA4 pilbara2 (1.0) versicolor4 (1.0) (1.0) (1.0) (1.0) lazelli_1 variegataC2 punctataB5 punctataA5 variegataA (1.0) versicolor5 (1.0)† (1.0) (1.0) (1.0) (1.0) lazelli_2- punctataB6 variegataB1 lazelliLP (1.0) (0.88) (0.81)† pulingka_1 variegataB2 (1.0)† (0.88) pulingka_2 variegataB3 (1.0)† (0.88) †Additional analyses with individual samples (two per candidate lineage) treated as separate species Table S3 Summary of morphological traits measured for 40 Gehyra variegata group lineages. N is the number of specimens measured per

lineage (for catalogue numbers, see Table S4). All measurements are in mm and reported as means ± standard deviation.

Trunk Trunk Foreleg Hindleg Head Head Head Snout Snout Lineage name N SVL length width length length length depth width length depth Lamellae einasleighensis 7 37.1±1.5 14.9±0.9 7.6±0.2 4.5±0.5 5.2±0.2 8.7±0.2 4.0±0.2 7.6±0.1 3.4±0.1 3.0±0.1 4.9±0.4 girloorloo 4 43.4±3.1 18.9±2.1 7.8±0.6 5.2±0.4 6.2±0.2 10.0±0.5 4.9±0.3 8.1±0.3 3.9±0.2 3.6±0.2 6.3±0.5 granulum 10 39.6±2.3 15.6±1.1 7.8±0.6 4.8±0.2 5.3±0.3 10.0±0.6 4.4±0.3 8.1±0.5 4.0±0.2 3.2±0.2 6.0±0 kimberleyi 6 50.1±2.2 21.1±1.0 9.2±0.7 6.0±0.2 7.1±0.5 12.2±0.9 6.1±0.4 9.5±0.7 4.7±0.4 4.4±0.4 7.2±0.4 lazelli 22 46.2±2.2 18.8±1.8 9.7±0.7 5.3±0.6 6.1±0.7 11.8±0.6 5.0±0.3 10.2±0.5 4.8±0.3 3.9±0.3 6.3±0.6 lazelliLP 19 62.3±5.1 26.0±2.7 12.3±1.0 7.3±0.7 8.0±0.7 15.5±1.2 5.9±0.5 12.5±0.8 6.1±0.6 4.8±0.4 7.5±0.5 minuta 16 37.6±3.0 15.8±0.9 6.9±0.8 4.5±0.4 4.9±0.4 9.2±0.7 4.7±0.5 7.6±0.7 3.5±0.3 3.3±0.4 6.3±0.5 montium 26 44.2±4.5 18.2±2.0 7.8±0.8 5.2±0.4 5.5±0.5 10.5±0.9 4.7±0.8 8.4±1.0 3.9±0.3 3.4±0.5 6.5±0.5 moritzi 21 40.6±3.3 16.8±1.8 7.9±0.7 4.8±0.5 5.1±0.5 9.7±1.0 3.9±0.3 8.1±0.5 3.8±0.4 3.0±0.3 6.2±0.4 multiporosa 9 50.5±3.1 20.4±1.6 9.6±0.6 5.6±0.5 6.6±0.5 12.1±0.6 5.7±0.4 10.1±0.5 4.9±0.3 4.1±0.2 6.9±0.3 nana1 10 40.6±3.0 16.2±1.4 7.9±0.6 5.2±0.4 5.5±0.5 10.3±0.6 4.4±0.2 8.2±0.5 4.0±0.2 3.2±0.2 6.2±0.4 nana2 10 44.8±3.0 18.2±1.0 8.7±0.7 5.4±0.5 5.7±0.5 11.2±0.8 4.9±0.3 9.4±0.8 4.5±0.3 3.5±0.3 6.7±0.5 nana4 8 47.8±2.4 19.5±1.5 9.6±0.3 5.3±0.4 6.5±0.4 11.6±0.6 4.9±0.5 9.5±0.2 4.8±0.2 3.6±0.3 6.5±0.5 nana7 5 40.9±4.2 16.6±1.9 7.8±1.0 4.9±0.3 5.8±0.5 10.0±1.0 4.5±0.5 8.1±0.8 4.1±0.4 3.3±0.2 7.0±0 occidentalis 13 59.3±7.2 24.8±3.7 11.1±1.4 7.8±1.1 8.6±1.2 14.6±1.4 7.1±0.9 12.2±1.4 6.0±0.7 5.1±0.6 8.3±0.8 paranana 10 50.3±4.2 20.9±2.2 9.4±0.9 6.1±0.4 6.8±0.4 12.5±0.7 5.3±0.5 9.8±0.8 5.1±0.3 3.8±0.4 7.1±0.3 pilbara 10 45.4±2.3 19.3±1.5 7.8±0.7 5.5±0.5 5.8±0.4 9.6±0.5 5.5±0.5 8.6±0.6 3.5±0.2 4.0±0.4 7.0±0 pluraporosa 1 43.2±0 17.5±0 7.4±0 4.5±0 5.6±0 10.0±0 4.4±0 8.0±0 3.9±0 3.0±0 6.0±0 pseudopunctata 10 53.6±4.4 22.7±2.1 10.0±0.8 6.8±0.7 7.7±0.7 12.5±0.8 5.3±0.4 10.0±0.9 5.2±0.4 3.9±0.2 7.3±0.7 pulingka 16 41.6±4.4 18.1±2.4 7.4±0.7 4.9±0.4 5.2±0.4 9.9±0.7 4.3±0.6 8.0±0.7 3.8±0.3 3.1±0.3 6.4±0.5 punctataA1 21 43.6±6.8 17.6±3.1 8.5±1.5 5.5±0.8 6.1±0.8 10.7±1.4 4.8±0.7 9.0±1.5 4.1±0.5 3.5±0.6 6.6±0.7 punctataA2 10 42.3±4.4 17.2±2.0 7.7±0.9 5.2±0.7 5.8±0.7 10.1±1.5 4.7±0.6 8.1±1.0 4.0±0.6 3.3±0.4 7.0±0.5 punctataA3 16 37.5±3.1 15.4±1.7 7.3±0.5 4.7±0.4 5.1±0.5 8.9±0.6 4.3±0.5 7.2±0.5 3.5±0.3 3.0±0.4 6.6±0.5 punctataA4 4 35.1±2.0 14.3±1.1 6.4±0.7 4.5±0.2 4.9±0.3 8.7±0.4 4.0±0.5 7.0±0.6 3.4±0.2 2.9±0.4 6.0±0 punctataA5 3 43.7±2.0 18.2±0.9 7.4±0.7 5.3±0.3 6.0±0.5 10.6±0.6 5.2±0.7 8.3±0.4 4.3±0.0 3.6±0.3 7.0±0 punctataB1 8 41.0±4.0 16.4±1.8 8.0±0.7 5.2±0.3 5.8±0.2 10.7±0.9 4.8±0.6 8.5±0.6 4.2±0.5 3.3±0.4 7.0±0 punctataB2 21 57.5±3.2 23.2±1.7 11.6±1.2 6.8±0.3 7.4±0.5 14.5±0.8 6.1±0.6 11.6±0.9 5.6±0.3 4.5±0.4 7.7±0.5 punctataB3 15 64.7±5.0 27.0±3.0 12.3±1.1 8.1±0.7 8.7±0.8 15.7±0.9 7.0±0.8 13.2±1.2 6.2±0.5 4.9±0.5 9.2±0.7 punctataB4 1 44.1±0 17.1±0 8.1±0 5.2±0 5.9±0 11.7±0 4.7±0 8.7±0 4.6±0 3.8±0 6.0±0 punctataB5 19 50.6±5.2 20.4±2.3 9.5±1.5 6.1±0.5 6.6±0.6 12.0±1.2 5.4±0.7 10.2±1.2 4.6±0.5 3.9±0.5 7.4±0.5 punctataB6 9 48.7±4.8 19.5±2.0 9.1±1.1 5.9±0.5 6.6±0.5 11.8±1.1 5.3±0.5 9.7±1.1 4.4±0.4 3.8±0.4 7.4±0.5 purpurascens 21 55.1±3.5 24.1±2.2 10.6±1.0 6.5±0.6 7.1±0.7 13.7±1.0 6.5±0.8 11.8±1.1 5.5±0.5 5.0±0.6 7.1±0.3 variegataA 21 42.6±4.1 17.3±2.3 7.9±0.8 5.2±0.4 5.7±0.4 10.3±0.9 5.0±0.6 8.5±0.9 3.8±0.4 3.5±0.4 6.5±0.6 variegataB1 20 40.5±3.2 16.3±1.7 7.5±0.6 5.1±0.3 5.4±0.3 10.2±0.6 5.1±0.4 8.4±0.5 3.8±0.4 3.8±0.4 6.2±0.4 variegataB2 7 39.7±5.2 15.9±2.8 7.6±1.5 5.3±0.6 5.5±0.7 9.6±1.0 5.1±0.7 8.1±1.1 3.5±0.3 3.6±0.5 6.3±0.5 variegataB3 20 43.8±3.6 18.1±2.0 7.8±0.7 5.1±0.5 5.6±0.4 10.3±0.6 4.7±0.5 8.5±0.7 3.7±0.3 3.5±0.3 6.7±0.6 variegataC1 11 38.1±1.1 16.0±0.7 6.8±0.4 4.7±0.3 5.2±0.3 9.1±0.3 3.9±0.3 7.4±0.3 3.5±0.2 2.9±0.2 6.3±0.5 variegataC2 10 44.7±2.5 18.3±1.6 8.0±0.3 5.5±0.3 6.4±0.3 11.2±0.8 5.4±0.5 8.8±0.5 4.3±0.2 3.8±0.3 6.5±0.5 versicolor4 9 42.1±3.4 18.1±0.8 8.3±0.2 4.9±0.3 5.1±0.3 10.1±0.4 4.6±0.4 8.4±0.4 3.9±0.2 3.7±0.4 6.3±0.5 versicolor5 25 46.3±2.6 19.1±1.6 8.8±0.8 5.7±0.5 6.5±0.6 11.1±0.6 5.1±0.4 9.5±0.8 4.4±0.4 3.9±0.3 6.8±0.4

Table S4 List of Gehyra variegata group specimens measured for morphological analyses.

Specimens with a cross (†) did not have mitochondrial (ND2) genotypes available. Latitude

and longitude are reported up to 6 decimal places. Abbreviations: Craig Charles Moritz

collection (CCM); National Museum of Victoria (NMV); Northern Territory Museum

(NTM); Queensland Museum (QM); South Australian Museum (SAM); Western Australian

Museum (WAM).

Catalogue no. Lineage name Location Latitude Longitude QM J94586 einasleighensis Cobb camp -18.79611 143.42386 QM J94587 einasleighensis Cobb camp -18.79611 143.42386 QM J94588 einasleighensis UNDA21 whitewater station -18.14897 144.57213 QM J94589 einasleighensis 9km west of Georgetown -18.28926 143.46529 QM J94591 einasleighensis East of Croydon -18.23171 142.4129 QM J94597 einasleighensis N. Forsayth -18.5667 143.56871 QM J94598 einasleighensis 6.6km SE of Petford -17.37989 144.96419 NMV D77029 girloorloo Ngumpan Cliff area -18.75097 126.08003 NMV D77030 girloorloo Ngumpan Cliff area -18.75097 126.08003 NMV D77031 girloorloo Ngumpan Cliff area -18.75097 126.08003 NMV D77032 girloorloo Ngumpan Cliff area -18.75097 126.08003 NMV D75778 granulum Western end of Artesian Range -16.54834 124.9961 NMV D75784 granulum Western end of Artesian Range -16.54834 124.9961 WAM R176205 granulum Mitchell Plateau Surveyors Pool -14.6723 125.7319 WAM R176208 granulum Bell Gorge rocks -17.04067 125.2268 WAM R176212 granulum Bell Gorge Walk, water hole side -16.99333 125.20489 WAM R176213 granulum Bell Gorge Walk, water hole side -16.99333 125.20481 WAM R176224 granulum GRR roadside -17.1189 125.1329 WAM R176235 granulum Sir John Gorge -17.52945 126.20999 WAM R176245 granulum GRR turnout -17.16653 125.34761 WAM R176436 granulum El Questro dump -16.00877 127.97836 WAM R112946 kimberleyi E of Beagle Bay -17.073056 122.712222 WAM R139383 kimberleyi 50km N Nullagine -21.23 120.312778 WAM R154504 kimberleyi Erskine Range -17.8486 124.3425 WAM R172080 kimberleyi Windjana Gorge -17.415 124.9425 WAM R176314 kimberleyi Gogo Stn, Pillara Range, N Menyous Gap -18.391 125.84 WAM R176435 kimberleyi Gogo Station, south of Bob's Bore -18.523 125.9227 SAM R53201 lazelli† Off Mambray Creek trk, Mt Remarkable NP -32.833 138.06416 SAM R56404 lazelli† 5.5 km SSE Mt Zion -33.23944 138.23221 SAM R56411 lazelli† 5.9 km SSE Mt Zion -33.24416 138.23082 SAM R56414 lazelli† 5.9 km SSE Mt Zion -33.24416 138.23082 SAM R56421 lazelli† 2.1 km NNE Graves Hill -33.1736 138.17027 SAM R57346 lazelli† approx 30km ENE Burra at Tourilie Gorge -33.24499 139.055 SAM R57347 lazelli† approx 30km ENE Burra at Tourilie Gorge -33.24499 139.055 SAM R57455 lazelli† 4.2 km NW Kanmantoo Post Office -35.03388 139.00583 SAM R57513 lazelli† 0.2 km ENE Sheoak Hill Rockhole -33.39055 136.76638 SAM R57704 lazelli† 12.8 km NW Kimba -33.07749 136.31943 SAM R58232 lazelli† 0.7km ESE Apoinga -33.93444 138.95111 SAM R58255 lazelli† 7.8km ESE of Mount Bryan East -33.41166 139.11 SAM R60316 lazelli† 18.7km SSW -33.07471 136.76804 SAM R61361 lazelli† 13.6 km SSE -32.09333 133.21416 SAM R62494 lazelli† 1.9km SSW Kanmantoo -35.08666 139.00444 SAM R63940 lazelli† 10.2km NNE Weeroona Homestead -33.93471 139.01721 SAM R64548 lazelli† 1.3km WNW of Nantawarrina -30.81638 138.96583 SAM R65473 lazelli† 2.75km SSW Tourilie Hill -33.44138 139.08805 SAM R66628 lazelli† 18.2km N Cowell -33.52193 136.93944 SAM R66943 lazelli† 2km SE Wandallah Homestead -33.62721 138.99444 SAM R66944 lazelli† 1.4km ENE Wandallah Homestead -33.60861 138.99416 SAM R67098 lazelli† 20.8km WNW of Mount Tabby Tabby -31.37916 131.29027 SAM R20377 lazelliLP Terrapinna Springs -29.916 139.666 SAM R52959 lazelliLP Arkaroola -30.1186 139.44833 SAM R64103 lazelliLP Terrapinna Springs -29.91527 139.66638 SAM R64104 lazelliLP Terrapinna Springs -29.91527 139.66638 SAM R64105 lazelliLP Terrapinna Springs -29.91527 139.66638 SAM R64106 lazelliLP Terrapinna Springs -29.91527 139.66638 SAM R64427 lazelliLP Terrapinna Springs -29.915 139.666 SAM R64428 lazelliLP Terrapinna Springs -29.915 139.666 SAM R64429 lazelliLP Terrapinna Springs -29.915 139.666 SAM R64431 lazelliLP 8km E Terrapinna Springs -29.90416 139.43777 SAM R64432 lazelliLP 8km E Terrapinna Springs -29.90416 139.43777 SAM R64941 lazelliLP Arkaroola -30.08471 139.52193 SAM R64942 lazelliLP Arkaroola -30.08304 139.5211 SAM R64943 lazelliLP Arkaroola -30.08138 139.60194 SAM R64944 lazelliLP Arkaroola -30.08138 139.60194 SAM R64945 lazelliLP Arkaroola -30.08082 139.6025 SAM R64950 lazelliLP Arkaroola -30.08054 139.60444 SAM R64955 lazelliLP 12km NW Terrapinna Springs -29.83999 139.54694 SAM R64956 lazelliLP 12km NW Terrapinna Springs -29.83583 139.54888 CCM1930 minuta 106km N Tennant Creek -18.77502 134.02632 CCM1932 minuta 106km N Tennant Creek -18.77502 134.02632 CCM1944 minuta 4.2km E Tennant Creek -19.65703 134.22966 CCM2763 minuta Barry Cave, -20.0486 136.67242 CCM2774 minuta Kurundie Station rocks -20.49926 134.67749 WAM R24243 minuta† 12mi E Tennant Creek -19.583333 134.366667 WAM R24244 minuta† 12mi E Tennant Creek -19.583333 134.366667 WAM R24246 minuta† 12mi E Tennant Creek -19.583333 134.366667 WAM R24249 minuta† 12mi E Tennant Creek -19.583333 134.366667 WAM R24250 minuta† 12mi E Tennant Creek -19.583333 134.366667 WAM R24251 minuta† 12mi E Tennant Creek -19.583333 134.366667 WAM R24258 minuta† 12mi E Tennant Creek -19.583333 134.366667 WAM R24259 minuta† 12mi E Tennant Creek -19.583333 134.366667 WAM R24269 minuta† 29mi S Tennant Creek -20.05 134.2 WAM R24270 minuta† 29mi S Tennant Creek -20.05 134.2 WAM R24271 minuta† 29mi S Tennant Creek -20.05 134.2 SAM R44369 montium 14km ENE Mt Cooparinna -26.33527 130.10166 SAM R44407 montium 8.4km NW Mt Kintore -26.49916 130.43888 SAM R46107 montium† 21km ENE Pipalyatjara -26.118056 129.371389 SAM R46134 montium 16km E Pipalyatjara -26.15888 129.33221 SAM R46139 montium 14km NE Pipalyatjara -25.983 129.48249 SAM R48731 montium† Mt Lindsay -27.02499 129.87554 SAM R48732 montium Mt Lindsay -27.02499 129.87554 SAM R48733 montium Mt Lindsay -27.02499 129.87554 SAM R56451 montium† 5.6km W Mount Hoare -27.0575 129.64388 SAM R61922 montium† Morgan Range -25.93749 128.43221 SAM R61924 montium† Morgan Range -25.93749 128.43221 WAM R77994 montium 23km NE Warburton -26 126.75 WAM R90826 montium Woodstock HS -21.616667 118.95 WAM R104135 montium Woodstock Station -21.611667 118.955556 WAM R104220 montium Woodstock Station -21.526389 119.149167 WAM R104936 montium Woodstock Station -21.621944 118.953056 WAM R106273 montium Woodstock HS -21.622222 118.953333 WAM R106275 montium Woodstock HS -21.622222 118.953333 WAM R110763 montium Jimblebar East -23.4575 120.3225 WAM R114914 montium 40km S Capricorn Roadhouse -23.716667 119.716667 WAM R117145 montium Yamana Station -27.966667 123.766667 WAM R120730 montium Boodarie Hill -20.4 118.516667 WAM R131488 montium Mount Whaleback -23.3375 119.696667 WAM R135118 montium Bullabulling -30.8625 120.906667 WAM R154278 montium Fortescue Marsh -22.259167 119.026389 WAM R164289 montium Mina Mina Clutterbuck Hills, Gibson Desert -24.566944 126.254444 CCM2766 moritzi Whistleduck Creek, Irrmweng Waterhole -20.64628 134.77342 CCM2772 moritzi Kurundie Station rocks -20.49926 134.67749 CCM2787 moritzi Whistleduck camp, Davenport NP -20.63474 134.77609 SAM R65875 moritzi† 2km S Devils Marbles -20.58638 134.25972 SAM R65878 moritzi† 2km S Devils Marbles -20.58638 134.25972 SAM R65880 moritzi† 2km S Devils Marbles -20.58638 134.25972 SAM R65881 moritzi† 20km S Barrow Creek -21.64555 133.74166 SAM R65895 moritzi† Corroboree Rock -23.68138 134.21804 SAM R65896 moritzi† Emily Gap -23.73971 133.95083 SAM R65897 moritzi† Emily Gap -23.73971 133.95083 SAM R65899 moritzi† Emily Gap -23.73971 133.95083 SAM R65900 moritzi† Emily Gap -23.73971 133.95083 SAM R65935 moritzi Rainbow Valley -24.33416 133.63527 SAM R65936 moritzi† Rainbow Valley -24.33416 133.63527 SAM R65937 moritzi Emily Gap -23.73971 133.95083 SAM R65938 moritzi† Emily Gap -23.73971 133.95083 SAM R65939 moritzi† Emily Gap -23.73971 133.95083 SAM R65941 moritzi Corroboree Rock, East MacDonnell Ranges -23.68166 134.21527 SAM R65943 moritzi 2km S Devils Marbles -20.58638 134.25972 SAM R65944 moritzi† 2km S Devils Marbles -20.58638 134.25972 SAM R65945 moritzi 20km S Barrow Creek -21.64555 133.74166 WAM R46831 multiporosa† Prince Regent Nature Res, nr St Andrew Is -15.333333 124.933333 WAM R46832 multiporosa† Prince Regent Nature Res, nr St Andrew Is -15.333333 124.933333 WAM R46837 multiporosa† Prince Regent Nature Res, nr St Andrew Is -15.333333 124.933333 WAM R167890 multiporosa Mitchell Plateau -14.8202 125.7211 WAM R168177 multiporosa Boongaree Island -15.0763 125.1836 WAM R168577 multiporosa Augustus Island -15.3851 124.5964 WAM R168584 multiporosa Byam Martin Island -15.391111 124.361528 WAM R171491 multiporosa Prince Regent Nature Reserve -15.2947 125.495 WAM R171547 multiporosa Prince Regent Nature Reserve -15.7616 125.2561 NMV D76950 nana1 Sandstone ridge? West f Leopold Downs Rd -17.90913 125.28525 NMV D76999 nana1 King Leopold Ranges, on Gibb River Road -17.12977 125.24276 NMV D77036 nana1 Ngumpan Cliff area -18.75114 126.08203 NTM R37808 nana1 15.7km NE East Baines Crossing -15.87227 130.32527 WAM R175049 nana1 Vic River Region Escarpment Walk -15.61091 131.11597 WAM R175053 nana1 Argyle rocks site 1 -16.11707 128.73813 WAM R175055 nana1 East Baines Camp -16.45158 130.10257 WAM R175056 nana1 Calcite Flow Camp -16.05033 130.4021 WAM R175059 nana1 Saw Tooth Gorge -18.42522 127.81967 WAM R175061 nana1 Elephant rock, Purnululu NP -17.52655 128.36438 CCM0606 nana2 Vic River Downs Station Tip -16.40246 131.01967 CCM1838 nana2 Delamere tip -15.6236 131.6334 CCM1949 nana2 -12.72606 130.85414 CCM2174 nana2 Hartz Range, camp, Roper Hwy -14.71124 134.28859 NTM R16344 nana2 Top Springs, Tanami Desert -16.53 131.8 NTM R36586 nana2 Victoria River Downs Homestead -16.3965 131.031167 NTM R36766 nana2 Echo Gorge, Wongalara Sanctuary, Roper -14.132833 134.343 District NTM R36840 nana2 Umbrawarra Gorge Road, near Pine Creek -13.965567 131.695117 NTM R36841 nana2 Umbrawarra Gorge Road, near Pine Creek -13.965567 131.695117 NTM R37050 nana2 , near Wooliana Rd turnoff -13.719717 130.714233 WAM R176164 nana4 Spring Creek [Doongan] -15.1998 126.0874 WAM R176188 nana4 80k N Drysdale Station (Doongan) -15.1328 126.2002 WAM R176199 nana4 Monorromboora Hill, Theda -14.7699 126.5788 WAM R176200 nana4 Monorromboora Hill, Theda -14.7699 126.5788 WAM R176275 nana4 King Edward sandstone -14.8791 126.172 WAM R176333 nana4 150m SE Berkeley camp -14.349779 127.750982 WAM R176334 nana4 Chopper site 2 - Berkeley -14.79563 127.93694 WAM R176335 nana4 Chopper site 2 - Berkeley -14.79563 127.93694 CCM2213 nana7 Tomato Island 2k south -14.76098 134.68181 CCM2216 nana7 Tomato Island 2k south -14.76098 134.68181 CCM2411 nana7 Ngukurr site 1 -14.65498 134.7812 CCM2475 nana7 Lake Katherine rocks -14.27311 135.06345 NTM R36720 nana7 Wongalara Sanctuary, Roper District -14.178 134.364 WAM R44159 occidentalis† Kingfisher Island -16.1 124.083333 WAM R44163 occidentalis† Kingfisher Island -16.1 124.083333 WAM R58757 occidentalis† Napier Downs -17.25 124.866667 WAM R58758 occidentalis† Napier Downs -17.25 124.866667 WAM R58759 occidentalis† Napier Downs -17.25 124.866667 WAM R70553 occidentalis† Napier Downs -17.233333 124.9 WAM R70587 occidentalis† Napier Downs -17.7 124.983333 WAM R70664 occidentalis† Napier Downs -17.233333 124.9 WAM R83713 occidentalis† Napier Downs -17.15 125.05 WAM R172071 occidentalis Windjana Gorge -17.408611 124.945278 WAM R172094 occidentalis Wulalam Island -16.368056 124.230278 WAM R172732 occidentalis Napier Range -17.432222 124.980833 WAM R172796 occidentalis Napier Range -17.432222 124.980833 NTM R20246 paranana Butterfly Gorge, 6Km NE Daly R. Crossing -13.73 130.73 NTM R36578 paranana Bullo River, 37.5k N -15.657667 129.659333 NTM R36579 paranana Bullo River, 37.5k N Victoria Highway -15.657667 129.659333 NTM R37056 paranana Dorat rd, Robin Falls area -13.35 131.138 NTM R37057 paranana Dorat rd, Robin Falls area -13.35 131.138 NTM R37831 paranana Bullo River Boab -15.65862 129.65944 NTM R37832 paranana Bullo River Boab -15.65862 129.65944 NTM R37834 paranana Tolmer Falls turnoff -13.19654 130.71394 NTM R37835 paranana Tolmer Falls turnoff -13.19654 130.71394 NTM R37836 paranana Florence Falls turnoff -13.12641 130.80463 WAM R108603 pilbara 15km SW Pannawonica -21.8 116.233333 WAM R108635 pilbara 15km SW Pannawonica -21.8 116.233333 WAM R119934 pilbara 3.5km NE Mount Brockman -22.466667 117.3 WAM R127509 pilbara 10 km S Onslow -21.733333 115.083333 WAM R129336 pilbara 1km SE Griffin Gas Plant, 30km WSW -21.783333 114.85 Onslow WAM R129339 pilbara 1km SE Griffin Gas Plant, 30km WSW -21.783333 114.85 Onslow WAM R131070 pilbara CA 10km W Kiwirkurra -22.816667 127.65 WAM R158313 pilbara 9.2km N Giralia Homestead -22.603611 114.393056 WAM R158435 pilbara 11km N Giralia Homestead -22.586944 114.387222 WAM R158437 pilbara 11km N Giralia Homestead -22.586944 114.387222 WAM R176170 pluraporosa King Ed River Theda, campsite, 30km N of -14.51903 126.45811 Homestead NMV D77003 pseudopunctata King Leopold Ranges, on Gibb River Road -17.11638 125.13335 WAM R164777 pseudopunctata Mount Nyulasy -16.745278 128.2825 WAM R164778 pseudopunctata Mount Nyulasy -16.745278 128.2825 WAM R172099 pseudopunctata Windjana Gorge -17.227222 124.895833 WAM R176238 pseudopunctata Sir John Gorge -17.52933 126.21127 WAM R176239 pseudopunctata Sir John Gorge -17.52933 126.21127 WAM R176242 pseudopunctata Teronis Gorge -17.29564 127.25612 WAM R176288 pseudopunctata Springvale Camp 2 -17.67997 127.69066 WAM R176303 pseudopunctata Nyulasy -16.74565 128.28288 WAM R176304 pseudopunctata Nyulasy -16.74565 128.28288 SAM R7584 pulingka† Itari Rocks, Musgrave Ranges N/A N/A SAM R13232 pulingka† 3km S Amata -26.183 131.15 SAM R13979 pulingka† 35km ESE Amata -26.266 131.416 SAM R28265 pulingka Kulgera -25.833 133.3 SAM R28322 pulingka† Btwn Victory and Betty Well, Everard Rng -27.05 132.466 SAM R28323 pulingka† Btwn Victory and Betty Well, Everard Rng -27.05 132.466 SAM R28324 pulingka† Btwn Victory and Betty Well, Everard Rng -27.05 132.466 SAM R28325 pulingka† Btwn Victory and Betty Well, Everard Rng -27.05 132.466 SAM R38829 pulingka 30k NW Elkedra -20.95 135.216 SAM R41877 pulingka† 15km W Mimili -27.0186 132.56693 SAM R44892 pulingka 8km SE Mitchell Knob -26.18971 131.88221 SAM R51565 pulingka 35km ESE Amata -26.28721 131.49166 SAM R54751 pulingka Mt Howe -26.25888 133.43749 SAM R61926 pulingka† Kurtjurntari Rockhole -24.89138 128.76916 SAM R65248 pulingka† 1km ENE Umuwa, Musgrave Ranges -26.47916 132.0236 WAM R166314 pulingka Kurtjurntari Rockhole -24.891389 128.769167 WAM R80232 punctataA1† 17km NE Barradale Roadhouse -22.783333 115.083333 WAM R80601 punctataA1† Uaroo Homestead -22.783333 115.366667 WAM R80617 punctataA1† Uaroo Homestead -22.783333 115.366667 WAM R114291 punctataA1 Myaree Pool -20.85 116.6 WAM R114571 punctataA1 Poonthune Pool, East Turner River -20.783333 118.716667 WAM R114926 punctataA1 37km ENE Port Hedland -20.4 118.95 WAM R120703 punctataA1 Boodarie Stn -20.4 118.466667 WAM R127645 punctataA1 Nifty Mine (Woodie Woodie mine) -21.666667 121.583333 WAM R131758 punctataA1 Millstream-Chichester Range NP -21.323611 117.125278 WAM R139365 punctataA1 Meentheena -21.288889 120.471944 WAM R145587 punctataA1† Unknown (S of Port Hedland) N/A N/A WAM R158086 punctataA1 5km WSW Python Pool -21.341111 117.188333 WAM R160940 punctataA1 9km NW Lake Poongkaliyarra -20.939722 117.034722 WAM R161245 punctataA1† 53km NNE Whim Creek Hotel -20.43 118.063889 WAM R162686 punctataA1 Baldy Rock -21.05 118.8 WAM R162687 punctataA1 Baldy Rock -21.05 118.8 WAM R162704 punctataA1 Baldy Rock -21.05 118.8 WAM R163044 punctataA1† Cane River Homestead -22.088889 115.626111 WAM R165181 punctataA1 7km SE Marda Pool -21.069722 116.206667 WAM R170795 punctataA1 17.5km E Pannawonica -21.633056 116.491667 WAM R172380 punctataA1† Port Hedland -20.529167 118.649722 WAM R125740 punctataA2† Burrup Peninsula, near Karratha -20.55 116.833333 WAM R132562 punctataA2 Burrup Peninsula -20.616111 116.785 WAM R132563 punctataA2 Burrup Peninsula -20.616111 116.785 WAM R146581 punctataA2 Burrup Peninsula -20.616667 116.785 WAM R165237 punctataA2† Hearson Cove, Burrup Peninsula -20.635 116.798889 WAM R165240 punctataA2† 3.4km NE Dampier, Burrup Peninsula -20.658056 116.741111 WAM R165508 punctataA2 West Intercourse Island -20.7 116.583333 WAM R165534 punctataA2 West Intercourse Island -20.685833 116.630556 WAM R165748 punctataA2 Dampier Port -20.616667 116.75 WAM R165749 punctataA2 Dampier Port -20.616667 116.75 WAM R102506 punctataA3 Barlee Range Nature Reserve -23.105833 116.997778 WAM R110011 punctataA3† 6km NW Roebourne -20.736111 117.098889 WAM R110013 punctataA3 5km S Lake Poongkaliyarra -21.036389 117.106111 WAM R110045 punctataA3 13.5km W Wickham -20.688333 117.006667 WAM R110073 punctataA3 13.5km W Wickham -20.688333 117.006667 WAM R114290 punctataA3 Myaree Pool -20.85 116.6 WAM R114292 punctataA3 Myaree Pool -20.85 116.6 WAM R117011 punctataA3 21km WNW Ashburton Downs HS -23.266667 116.85 WAM R117027 punctataA3 15km NW Paraburdoo -23.133333 117.566667 WAM R125029 punctataA3 Yandicoogina -22.7125 119.067222 WAM R139203 punctataA3 25km W Mount Minnie Homestead -21.966667 115.183333 WAM R141332 punctataA3 Cape Preston area -20.905278 116.216944 WAM R141352 punctataA3 Cape Preston area -20.905278 116.216944 WAM R160879 punctataA3† 3.5km S Marda Pool -21.065278 116.150278 WAM R165158 punctataA3 3.5km N Karratha Station -20.853889 116.668611 WAM R170756 punctataA3 5.2km WSW Pannawonica -21.663056 116.279167 WAM R111956 punctataA4 25km NW Balfour Downs Homestead -22.611111 120.728889 WAM R131008 punctataA4 Mt Herbert Area, Millstream-Chichester NP -21.312778 117.233889 WAM R145755 punctataA4 Chichester Range -21.943889 118.962778 WAM R154311 punctataA4 Weeli Wolli Creek -22.957778 119.178889 WAM R125472 punctataA5 30km E Newman -23.316667 120.033333 WAM R129655 punctataA5 120km NW Newman -22.995833 119.091667 WAM R145708 punctataA5 Weeli Wolli Creek -22.877778 119.24 WAM R111769 punctataB1 34km E Wheelarra Hill -23.358611 120.459167 WAM R114337 punctataB1 35km SE Prairie Downs -23.716667 119.433333 WAM R125083 punctataB1 15km E Newman -23.366667 119.9 WAM R127475 punctataB1 32km S Newman -23.65 119.716667 WAM R129925 punctataB1 West Angelas, 100KM WNW Newman -23.25 118.666667 WAM R129926 punctataB1 West Angelas, 100KM WNW Newman -23.25 118.666667 WAM R135013 punctataB1 Mount Whaleback -23.403056 119.696111 WAM R135018 punctataB1 Mount Whaleback -23.334722 119.669444 WAM R160939 punctataB2† 5km N Lake Poongkaliyarra -20.934444 117.115 WAM R161800 punctataB2† Woodie Woodie Mine -21.575 121.200278 WAM R162392 punctataB2† 3.5km WNW Mount Gregory -20.8525 117.095833 WAM R163132 punctataB2† 19.5km SSW Mount Amy -22.419167 115.837778 WAM R163135 punctataB2† 4km W Mount Stuart -22.446667 116.001667 WAM R163610 punctataB2† Cape Preston -20.936667 116.199722 WAM R163611 punctataB2† Cape Preston -20.936667 116.199722 WAM R165026 punctataB2† 24.5km N Cowra Line Camp -22.134722 119.023889 WAM R165027 punctataB2† 24.5km N Cowra Line Camp -22.134444 119.024167 WAM R165122 punctataB2† Black Hill Pool -21.333889 117.253056 WAM R165191 punctataB2† 3km SW Harding Dam -20.993889 117.081944 WAM R165193 punctataB2† 3km SW Harding Dam -20.993889 117.081944 WAM R165235 punctataB2† Hearson Cove, Burrup Peninsula -20.635 116.798889 WAM R165250 punctataB2 14.9km E Karratha -20.758889 116.685278 WAM R165251 punctataB2† 14.9km E Karratha -20.758889 116.685278 WAM R165255 punctataB2† 14.9km E Karratha -20.758889 116.685278 WAM R165518 punctataB2† West Intercourse Island -20.7 116.583333 WAM R165738 punctataB2† Barrow Island -20.85 115.4 WAM R165740 punctataB2 Barrow Island -20.85 115.4 WAM R165750 punctataB2† Dampier Port -20.616667 116.75 WAM R170815 punctataB2 Old Pilga Homestead -21.48 119.413889 WAM R114277 punctataB3† Myaree Pool -20.85 116.6 WAM R154517 punctataB3 Yarri Mining Camp -20.547778 120.245278 WAM R156587 punctataB3 Cundaline Gap -20.548889 120.168056 WAM R160096 punctataB3 13km SE Braeside -21.288889 121.096111 WAM R160097 punctataB3 13km SE Braeside -21.288889 121.096111 WAM R160098 punctataB3 13km SE Braeside -21.288889 121.096111 WAM R162688 punctataB3† Baldy Rock -21.05 118.8 WAM R162701 punctataB3 Baldy Rock -21.05 118.8 WAM R162702 punctataB3† Baldy Rock -21.05 118.8 WAM R162703 punctataB3 Baldy Rock -21.05 118.8 WAM R173362 punctataB3† Roy Hill, 67km S South Hedland -20.9618 118.6846 WAM R173363 punctataB3† Roy Hill, 65km S South Hedland -20.9588 118.6844 WAM R173364 punctataB3† Roy Hill, 67km S South Hedland -20.9618 118.6846 WAM R173365 punctataB3† Roy Hill, 65km S South Hedland -20.9588 118.6844 WAM R173366 punctataB3† Roy Hill, 67km S South Hedland -20.9618 118.6846 WAM R156168 punctataB4 Waldburg Station -24.778889 117.101111 WAM R97171 punctataB5 Yalgoo Peak -26.8 117.183333 WAM R106088 punctataB5 Mt Welcome -27.066667 116.266667 WAM R106089 punctataB5 Woodstock Station -27.033333 116.3 WAM R106090 punctataB5 Woodstock Station -27.033333 116.3 WAM R106202 punctataB5 Woodstock Station -27.133333 116.333333 WAM R114251 punctataB5 NW end of Mount Fraser -25.583333 118.366667 WAM R116896 punctataB5 22km S Mount Phillip Homestead -24.766667 116.216667 WAM R116897 punctataB5 22km S Mount Phillip Homestead -24.766667 116.216667 WAM R117036 punctataB5 20km SW Cobra Homestead -24.3 116.35 WAM R117070 punctataB5 38km N Yinnietharra Homestead -24.366667 116.316667 WAM R119278 punctataB5 20km WSW Mount Levra Station HSD -26.433333 117.15 WAM R119369 punctataB5 50km SW Yalgoo -28.65 116.3 WAM R119370 punctataB5† 50km SW Yalgoo -28.65 116.3 WAM R127414 punctataB5 10.3km S Yinnietharra Homestead -24.720278 116.119722 WAM R127415 punctataB5 10.3km S Yinnietharra Homestead -24.720278 116.119722 WAM R127543 punctataB5 Barnong Homestead -28.633333 116.283333 WAM R132290 punctataB5 6km NW Noondie Outstation -27.074444 117.078889 WAM R132291 punctataB5† 6km NW Noondie Outstation -27.074444 117.078889 WAM R132294 punctataB5 Marlandy Hill -28.121667 117.233056 WAM R114315 punctataB6 Callytharra Springs HS -25.816667 115.383333 WAM R114316 punctataB6 Callytharra Springs HS -25.816667 115.383333 WAM R120534 punctataB6 39KM ESE Gascoyne Junction -25.21 115.514167 WAM R123764 punctataB6 39KM ESE Gascoyne Junction -25.21 115.514167 WAM R123770 punctataB6 39KM ESE Gascoyne Junction -25.21 115.514167 WAM R131769 punctataB6 Muggon Station -26.616667 115.533333 WAM R136281 punctataB6 Muggon Station -26.816944 115.547778 WAM R139194 punctataB6 Mount Minnie -22.265 115.407222 WAM R139444 punctataB6 Cane River -22.135278 115.688889 CCM1946 purpurascens Ellery Rock Hole -23.78058 133.0724 SAM R52762 purpurascens† 9.8 km ENE of Hamilton H/S -26.69721 135.17138 SAM R52845 purpurascens† 26.8 km NE of Lambina H/S -26.74749 134.25611 SAM R54268 purpurascens† 45.5 km NW Clayton HS, Etadunna Stn, -28.97166 138.066 OPP SAM R55486 purpurascens† 17.9 km ESE Mulka Hill -28.416 138.81333 SAM R57974 purpurascens† 28.5 SSW Memory Bore -28.91 132.81777 SAM R57975 purpurascens† 37.5 km WSW Memory Bore -28.84333 132.56999 SAM R58122 purpurascens† 13.9km WNW of Ant Hill -28.46583 134.4211 SAM R59443 purpurascens† 56.6km NW Maralinga -29.80527 131.15583 SAM R59499 purpurascens† opportune site 66.5km NW Maralinga -29.70777 131.07304 SAM R60567 purpurascens† 9.2km S -27.18499 135.53721 SAM R61146 purpurascens† 8.7km ESE -30.88721 132.20083 SAM R61160 purpurascens† 14.9 km E -30.87138 132.26305 SAM R61708 purpurascens† 13.8 km NNW -28.5361 132.12471 SAM R62219 purpurascens† 177.2km SSW of Wartaru -28.5075 129.14333 SAM R62603 purpurascens† 7.9km WNW Jack Hill -30.18416 135.61693 SAM R65494 purpurascens† 50km ENE Amata -26 131.616 SAM R65789 purpurascens† 3.9km E Maralinga (village) -30.16194 136.17666 SAM R67460 purpurascens† 18.2km SSE Hiltaba Homestead -32.305 135.16166 SAM R67490 purpurascens† 9.23km SE Jacinth Ambrosia Minesite -30.96888 132.27416 SAM R68098 purpurascens† 57.45km SW Ooldea -30.78194 132.30111 WAM R104995 variegataA Old Rainy Rocks -29.732778 119.616944 WAM R112680 variegataA 10km SSW Onslow -21.730833 115.096944 WAM R113685 variegataA 5km E Dalwallinu -30.283333 116.716667 WAM R114344 variegataA 8-10km S Cleaverville -20.733333 117 WAM R117153 variegataA Dead Horse Rocks, 6.5 km N Menzies -29.366667 121.283333 WAM R120033 variegataA Barrow Island -20.8 115.4 WAM R120508 variegataA Kennedy Range NP -24.493056 115.030556 WAM R120626 variegataA 8km NW Mardathuna Homestead -24.428889 114.5 WAM R120894 variegataA Woodleigh Stn -26.191667 114.509167 WAM R121016 variegataA 11km NE Meedo Homestead -25.625278 114.704167 WAM R124930 variegataA Kennedy Range NP -24.500833 115.0175 WAM R127504 variegataA 10 km S Onslow -21.733333 115.083333 WAM R131377 variegataA 40km S Exmouth -22.3 114.116667 WAM R132812 variegataA Yorkrakine Hill -31.433333 117.516667 WAM R140926 variegataA 27km SSE Peak Eleanora -33.166667 121.266667 WAM R141460 variegataA Faure Island Homestead -25.896111 113.908889 WAM R144114 variegataA 2km E Ora Banda -30.368889 121.0675 WAM R152913 variegataA Koolyanobbing Area -30.240278 119.347222 WAM R156487 variegataA Marillana Crk, Goodiadarrie Hills, Newman -22.6725 118.936667 WAM R157235 variegataA Yanrey Stn -22.157778 114.528611 WAM R162450 variegataA Meekatharra -26.591111 118.496944 WAM R11518 variegataB1† Learmonth -22.25 114.083333 WAM R11520 variegataB1† Learmonth -22.25 114.083333 WAM R11522 variegataB1† Learmonth -22.25 114.083333 WAM R16107 variegataB1† Shothole canyon -22.05 114.016667 WAM R16110 variegataB1† Shothole canyon -22.05 114.016667 WAM R52926 variegataB1† Shothole canyon, Cape Range -22.05 114.033333 WAM R52927 variegataB1† Shothole canyon, Cape Range -22.05 114.033333 WAM R52995 variegataB1† Exmouth -21.933333 114.116667 WAM R61097 variegataB1† Yardie Creek the watercourse -22.333333 113.816667 WAM R61098 variegataB1† Yardie Creek the watercourse -22.333333 113.816667 WAM R61273 variegataB1† Shothole canyon -22.05 114.033333 WAM R61274 variegataB1† Shothole canyon -22.05 114.033333 WAM R61475 variegataB1† Yardie Creek Mouth -22.333333 113.8 WAM R117869 variegataB1† Vlaming Head -21.8 114.1 WAM R123947 variegataB1 Cape Range, 10km S Exmouth -22 114.083333 WAM R130921 variegataB1† Vlamingh Head Lighthouse -21.8077 114.1111 WAM R134628 variegataB1† 8km N Exmouth -21.87 114.116944 WAM R142264 variegataB1† Shothole canyon -22.065556 114.009444 WAM R153817 variegataB1 Vlaming Head -21.8 114.1 WAM R153818 variegataB1 Vlaming Head -21.8 114.1 WAM R112645 variegataB2 Barrow Island -20.798056 115.349167 WAM R125413 variegataB2 Barrow Island -20.766667 115.4 WAM R165741 variegataB2 Barrow Island -20.85 115.4 WAM R165743 variegataB2 Barrow Island -20.8 115.383333 WAM R165744 variegataB2 Barrow Island -20.766667 115.45 WAM R165747 variegataB2† Barrow Island -20.8 115.383333 WAM R165971 variegataB2 Trimouille Island -20.386667 115.551111 WAM R102143 variegataB3 10km NW Mount Windell -22.602778 118.459722 WAM R102225 variegataB3 Barlee Range Nature Reserve -23.389167 115.886667 WAM R102806 variegataB3 Burrup Peninsula -20.5275 116.821389 WAM R106014 variegataB3 Kennedy Range -24.5 115.083333 WAM R108849 variegataB3 Cherralta Homestead -21.033333 116.816667 WAM R119017 variegataB3 63km E Sandstone (road to Leinster) -28 120.5 WAM R119018 variegataB3 5km N Yuinmery -28.516667 119.016667 WAM R119019 variegataB3 Hope Downs, 95km NE Newman -22.9 119.083333 WAM R119938 variegataB3 3.5km NE Mount Brockman -22.466667 117.3 WAM R126067 variegataB3 5km N Mount Magnet -28 117.833333 WAM R129903 variegataB3 West Angelas, 100km WNW Newman -23.25 118.666667 WAM R132636 variegataB3 Burrup Peninsula -20.592778 116.799444 WAM R135257 variegataB3 Hope Downs -23.067222 118.885833 WAM R135377 variegataB3 Mount Brockman -22.414167 117.355 WAM R135464 variegataB3 Mount Brockman area -22.466667 117.3 WAM R140699 variegataB3 Hope Downs -22.673611 119.416111 WAM R145731 variegataB3 Weeli Wolli Creek -22.833889 119.177778 WAM R157121 variegataB3 West Angelas -23.199167 118.846944 WAM R157125 variegataB3 West Angelas -23.186111 118.873611 WAM R157714 variegataB3 Packsaddle Range, Newman -22.934167 118.8875 WAM R170800 variegataB3 14.5km NNW Mount Elvire -21.710833 116.765833 WAM R94778 variegataC1† CA 80km S Telfer -22.34 122.0725 WAM R94779 variegataC1† CA 80km S Telfer -22.34 122.0725 WAM R94780 variegataC1† CA 80km S Telfer -22.314722 122.051944 WAM R94782 variegataC1† CA 80km S Telfer -22.335833 122.068611 WAM R108368 variegataC1† Sunrise Hill, Goldsworthy -20.460833 120.048333 WAM R108420 variegataC1† Nimingarra, Goldsworthy -20.436389 120.010833 WAM R156584 variegataC1 Cundaline Gap, Yarrie Minesite -20.557778 120.181944 WAM R161459 variegataC1 47.5km ESE Goldsworthy -20.428056 119.969444 WAM R161460 variegataC1† 47.5km ESE Goldsworthy -20.428056 119.969444 WAM R161461 variegataC1† 47.5km ESE Goldsworthy -20.428056 119.969444 WAM R162082 variegataC1† 16km W Mount de Courcey -22.74 116.461111 WAM R100666 variegataC2 Woodstock Station -21.609167 118.974167 WAM R104062 variegataC2 Woodstock Station -21.609167 118.974167 WAM R104168 variegataC2 Woodstock Station -21.609167 118.974167 WAM R108615 variegataC2 Weld Springs (Well 9), Canning Stock -25.016667 121.583333 Route WAM R114923 variegataC2 12k SSW Great N Hwy, Marble Bar Road -20.45 118.9 WAM R120728 variegataC2 Boodarie Hill -20.4 118.516667 WAM R120729 variegataC2 Boodarie Hill -20.4 118.516667 WAM R135207 variegataC2 10km NW Norseman -32.160278 121.741667 WAM R145629 variegataC2 18km S Port Hedland -20.47 118.59 WAM R165149 variegataC2 5km NNE Python Pool -21.310278 117.276111 CCM0217 versicolor4 Thorntonia Stn tip -19.5015 138.94908 CCM0252 versicolor4 West Leichardt salvage yard -20.59802 139.70422 SAM R34248 versicolor4 17km E Mount Isa -20.716 139.716 SAM R42789 versicolor4 Diamantina Station dump -23.75 141.133 SAM R55694 versicolor4 13.4k NNE Hughendon, Kennedy Dev'ment -20.78499 144.30555 Rd SAM R55749 versicolor4 5km E Toorak -20.97499 141.89166 SAM R55750 versicolor4† 5km E Toorak -20.97499 141.89166 SAM R55751 versicolor4 Toorak -20.96 141.82832 SAM R55752 versicolor4 Toorak -20.96 141.82832 CCM1892 versicolor5 200M W Ross River Camp -23.59513 134.48395 CCM1940 versicolor5 Barrow Creek -21.53197 133.88919 SAM R49645 versicolor5† Cowarie Stn -27.33499 138.56166 SAM R51771 versicolor5† 6 km SW of Yudnamutana Bore -30.20972 139.2361 SAM R51789 versicolor5† 2.5 km WSW of Yudnamutana Bore -30.17416 139.25111 SAM R51813 versicolor5† 350m WSW of Mudlapena Spring -30.61055 138.80305 SAM R51881 versicolor5† 1.4 km SSW of Mt Fitton -29.97193 139.54138 SAM R51918 versicolor5† 6.8 km SSW of Barraranna Hill, OPP -30.35444 139.37138 SAM R51920 versicolor5† 1.6 km NE of Nudlamutana Well -30.36361 139.36361 SAM R53144 versicolor5† 2.5 km ESE of Callory Bore -31.80305 138.78805 SAM R54064 versicolor5† Kalamurina Stn -27.89249 138.01999 SAM R54165 versicolor5† 6.6 km SSE of Kalamurina H/S -27.77832 138.27582 SAM R56554 versicolor5† 5.2km E (91 deg) Paney shearers -32.655 135.69721 SAM R59803 versicolor5† 3.5km ESE New Residence -34.38221 140.43638 SAM R60489 versicolor5† 49.4 km W -26.27554 134.98193 SAM R60500 versicolor5† 57.6 km NW -26.29027 134.74027 SAM R60564 versicolor5† 43.9 km SSE -26.44666 135.3886 SAM R60587 versicolor5† 5 km N -31.92777 140.10944 SAM R60813 versicolor5† 16.6km SSW of Mount Robinson -27.95972 136.30111 SAM R62443 versicolor5† 10km NNE Paringa -34.08583 140.783 SAM R62470 versicolor5† 9.9km E of Cooltong -34.08527 140.78304 SAM R62524 versicolor5† 4.9km W of Mt Havelock, Chace Range -31.66527 138.68304 SAM R63184 versicolor5† New Year's Gift Bore -29.64416 137.30111 SAM R63186 versicolor5† New Year's Gift Bore -29.64416 137.30111 SAM R63193 versicolor5† Curdimurka Railway Siding -29.47666 137.08444

Table S5 Estimated range sizes for Gehyra variegata group lineages, in increasing range size by region. Short-range endemics (range size <10,000 km2) are marked with a cross (†).

Lineage name Region Range size (km2) pluraporosa† AMT 314 girloorloo† AMT 315 paranana† AMT 8,585 nana7 AMT 12,611 pseudopunctata AMT 20,315 multiporosa AMT 24,691 nana4 AMT 46,567 einasleighensis AMT 66,410 occidentalis AMT 67,323 granulum AMT 71,012 kimberleyi AMT 115,954 nana2 AMT 144,310 nana1 AMT 176,268 minuta1† Central AAZ 268 minuta2† Central AAZ 413 lazelliLP† Central AAZ 477 moritzi Central AAZ 135,556 versicolor4 Central AAZ 282,687 pilbara1 Central AAZ 317,369 pulingka Central AAZ 467,270 lazelli Central AAZ 1,123,022 montium Central AAZ 1,479,804 variegataA Central AAZ 1,673,573 versicolor5 Central AAZ 2,208,588 purpurascens Central AAZ 3,481,785 variegataB2† Pilbara 146 punctataB4† Pilbara 314 variegataC1† Pilbara 315 variegataB1† Pilbara 1,039 punctataA5† Pilbara 1,442 punctataA2† Pilbara 2,771 punctataB1† Pilbara 4,447 punctataB3† Pilbara 8,995 punctataA4† Pilbara 9,691 punctataB5 Pilbara 16,129 variegataC2 Pilbara 21,352 punctataA3 Pilbara 40,847 pilbara2 Pilbara 47,888 punctataA1 Pilbara 55,212 punctataB6 Pilbara 110,067 punctataB2 Pilbara 152,900 variegataB3 Pilbara 509,829

Table S6 Results of BioGeoBEARS geographic range analysis (AMT, central AAZ, Pilbara) on the StarBEAST2 species tree of the Gehyra variegata group.

Log No. of AICc Model d e j a AICc Model support likelihood parameters weight DEC -27.51 2 7.50E-03 1.00E-12 0 0 59.33 5.20E-01 52.0% DEC+J -27.22 3 6.90E-03 1.00E-12 8.60E-03 0 61.08 0.22 22.0% DIVALIKE -30.17 2 1.50E-02 1.00E-12 0 0 64.64 3.60E-02 3.6% DIVALIKE+J -27.18 3 6.90E-03 1.00E-12 2.10E-02 0 60.99 0.23 23.0% BAYAREALIKE -44.64 2 1.40E-02 5.60E-02 0 0 93.59 1.90E-08 0.0% BAYAREALIKE+J -31.03 3 5.60E-03 1.00E-07 3.50E-02 0 68.70 4.80E-03 0.5%

Table S7 Results of BioGeoBEARS biome analysis (AMT vs. AAZ) on the StarBEAST2 species tree of the Gehyra variegata group.

AICc Relative AICc Log No. of Model Model d e j a AICc weight likelihood weight likelihood parameters support (6 models) (7 models) (7 models) DEC -8.89 2 1.90E-03 1.00E-12 0 0 22.08 0.08 0.09 0.04 4.3% DEC+J -6.94 3 3.80E-10 1.00E-12 1.40E-02 0 20.52 0.17 0.20 0.09 9.4% DIVALIKE -7.69 2 5.70E-03 1.00E-12 0 0 19.69 0.26 0.31 0.14 14.2% DIVALIKE+J -6.00 3 1.10E-09 1.00E-12 1.40E-02 0 18.63 0.45 0.52 0.24 24.2% BAYAREALIKE -16.63 2 1.00E-02 1.30E-02 0 0 37.58 3.50E-05 4.0E-05 1.9E-05 0.0% BAYAREALIKE+J -8.66 3 1.00E-07 1.00E-07 2.50E-02 0 23.95 0.03 0.04 0.02 1.7% Mk -7.62 1 0 0 0 0.01 17.33 1.00 0.46 46.2%

Table S8 Results of BioGeoBEARS habitat analysis (rock vs. generalist) on the StarBEAST2 species tree of the Gehyra variegata group.

AICc Relative AICc Log No. of Model Model d e j a AICc weight likelihood weight likelihood parameters support (6 models) (7 models) (7 models) DEC -32.87 2 2.50E-02 1.00E-12 0 0 70.05 8.50E-06 1.3E-05 5.2E-06 0.0% DEC+J -21.09 3 1.00E-12 1.00E-12 0.11 0 48.81 0.35 0.55 0.21 21.4% DIVALIKE -32.54 2 4.10E-02 1.00E-12 0 0 69.39 1.20E-05 1.9E-05 7.3E-06 0.0% DIVALIKE+J -21.14 3 1.00E-12 1.00E-12 0.11 0 48.92 0.33 0.52 0.20 20.2% BAYAREALIKE -48.84 2 2.50E-02 6.60E-02 0 0 102 9.90E-13 1.5E-12 6.0E-13 0.0% BAYAREALIKE+J -21.18 3 1.00E-07 1.00E-07 0.1 0 48.99 0.32 0.50 0.20 19.5% Mk -22.76 1 0 0 0 0.05 47.61 1.00 0.39 38.9%

Table S9 Loadings, variance, and percentage of data variance explained from the principal components (PC) analyses on all log-transformed morphological traits (“sPCA”) of the

Gehyra variegata group, and on the residuals of body shape traits against SVL (“rPCA”).

Important loadings (≥0.40) are shown in bold.

Trait sPC1 sPC2 sPC3 rPC1 rPC2 rPC3 SVL -0.31 -0.07 -0.06 N/A N/A N/A Trunk length -0.31 -0.03 -0.01 0.37 0.00 0.12 Trunk width -0.30 -0.40 -0.12 -0.36 -0.36 0.14 Foreleg length -0.31 0.11 -0.05 -0.20 0.43 -0.23 Hindleg length -0.31 0.05 -0.08 -0.22 0.37 -0.30 Head length -0.31 -0.16 -0.15 -0.49 0.00 -0.10 Head depth -0.29 0.28 0.58 -0.10 0.51 0.39 Head width -0.31 -0.24 0.01 -0.43 -0.13 0.33 Snout length -0.30 -0.24 -0.31 -0.44 0.00 -0.26 Snout depth -0.30 0.03 0.58 -0.13 0.37 0.58 Lamellae -0.27 0.77 -0.42 0.00 0.36 -0.39 Component variance 9.98 0.39 0.30 3.17 2.49 1.65 % data variance explained 91 4 3 32 25 16

Table S10 Results of phylogenetic signal analyses on rPCA axes and morphological traits of the Gehyra variegata group using the StarBEAST2 species tree. Significance is indicated with an asterisk (p=0.05–0.01*, p=0.01–0.001**).

Trait Blomberg's K p value rPC1 0.36 0.153 rPC2 0.54 0.043* rPC3 0.48 0.020* Trunk length 0.37 0.134 Trunk width 0.52 0.009** Foreleg length 0.36 0.155 Hindleg length 0.44 0.038* Head length 0.48 0.018* Head depth 0.53 0.009** Head width 0.49 0.007** Snout length 0.50 0.022* Snout depth 0.49 0.009** Lamellae 0.44 0.045*

Table S11 Results of PGLS analyses on important (PC loading) morphological traits of the

Gehyra variegata group using the StarBEAST2 species tree. Significance is indicated with an asterisk (p=0.01–0.001**, p<0.001***).

Region (AMT, central Habitat (rock vs. generalist) Biome (AAZ vs. AMT) AAZ, Pilbara) Trait T statistic p value T statistic p value F statistic p value Foreleg length 0.29 0.774 0.33 0.744 3.10 0.058 Head length 0.86 0.394 0.09 0.927 0.06 0.942 Head depth 2.89 0.007** 0.34 0.734 0.866 0.430 Head width 0.61 0.544 0.60 0.552 1.68 0.201 Snout length 0.05 0.959 -0.70 0.491 1.166 0.324 Snout depth 4.46 <0.001*** 0.51 0.617 0.335 0.718

Table S12 Results of mvMORPH model comparison and morphological evolution rates of the Gehyra variegata group using the StarBEAST2 species tree. Significance is indicated with an asterisk (multiple rate log likelihood ≥2 greater than single rate log likelihood).

Morphological Log likelihood Log likelihood Trait Analysis evolution rates (single rate) (multiple rate) (σ2/My) Snout depth Habitat 84.22 85.27 Rock: 1.17E-4 Generalist: 3.23E-4 Biome 83.98 84.13 AAZ: 1.64E-4 AMT: 1.24E-4 Region 84.22 84.72 AMT: 1.20E-4 Central: 2.23E-4 Pilbara: 1.37E-4 Body size Habitat 46.76 47.80 Rock: 1.23E-3 (SVL) Generalist: 3.35E-4 Biome 46.18 46.91 AAZ: 1.29E-3 AMT: 6.76E-4 Region 46.76 50.14* AMT: 6.71E-4 Central: 2.46E-3 Pilbara: 6.93E-4