Appendix S1. Information of the specimens used in this study.
Appendix S2. GenBank accession numbers of the samples used in this study.
Appendix S3. The character coding of colour pattern in Pachyrhynchus sonani and outgroups.
Appendix S4. The character coding of colour pattern in Pachyrhynchus tobafolius and outgroups.
Appendix S5. Description of character states of colour traits in Pachyrhynchus sonani.
Appendix S6. Description of character states of colour traits in Pachyrhynchus tobafolius.
Appendix S7. Morphometric analyses of body shape between sexes based on 21 landmarks for (a–h) Pachyrhynchus sonani and (i–p) Pachyrhynchus tobafolius.
Appendix S8. Structure analyses of Pachyrhynchus sonani and Pachyrhynchus tobafolius.
Appendix S9. The gene trees of Pachyrhynchus sonani.
Appendix S10. The cox1 gene tree of Pachyrhynchus tobafolius.
Appendix S11. The posterior probability of parameters under four gamma prior distributions in iBPP analyses.
Appendix S12. The heritability of traits under four gamma prior distributions in iBPP analyses.
Appendix S13. The phylogeny of Pachyrhynchus sonani reconstructed from (a) Bayesian, (b) parsimony and (c) likelihood phylogenetic analyses based on combined four genes (cox1, nd2, EF1α and ITS).
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Appendix S1. Information of the specimens used in this study (GI: Green Island; OI: Orchid Island).
No. Specimen No. Taxon code Date Island Sitea Species Sex Host plantb
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59
60
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62 b Host plant numbers. 1: litsea, Litsea acutivens (Lauraceae); 2: beef wood, Casuarina equisetifolia (Casuarinaceae); 3:
Ceylon ardisia, Ardisia elliptica (Primulaceae); 4: sea poison tree, Barringtonia asiatica (Lecythidaceae); 5: Indian almond, Terminalia catappa (Combretaceae); 6: mulberry, Pipturus arborescens (Urticaceae); 7: copperleaf, Acalypha caturus (Euphorbiaceae).
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Appendix S2. GenBank accession numbers of the samples used in this study.
Species Island Taxon code GenBank Accession number
cox1 nd2 ef1-α ITS
P. sonani Green Island G01 KU953405 KU953501 KU953597 KU953693
P. sonani Green Island G02 KU953406 KU953502 KU953598 KU953694
P. sonani Green Island G03 KU953407 KU953503 KU953599 KU953695
P. sonani Green Island G05 KU953408 KU953504 KU953600 KU953696
P. sonani Green Island G06 KU953409 KU953505 KU953601 KU953697
P. sonani Green Island G07 KU953410 KU953506 KU953602 KU953698
P. sonani Green Island G08 KU953411 KU953507 KU953603 KU953699
P. sonani Green Island G09 KU953412 KU953508 KU953604 KU953700
P. sonani Green Island G10 KU953413 KU953509 KU953605 KU953701
P. sonani Green Island G11 KU953414 KU953510 KU953606 KU953702
P. sonani Green Island G12 KU953415 KU953511 KU953607 KU953703
P. sonani Green Island G19 KX263454 - - -
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P. sonani Orchid Island O01 KU953484 KU953580 KU953676 KU953759
P. sonani Orchid Island O02 KU953485 KU953581 KU953677 KU953760
P. sonani Orchid Island O03 KU953486 KU953582 KU953678 KU953761
P. sonani Orchid Island O04 KU953487 KU953583 KU953679 KU953762
P. sonani Orchid Island O06 KU953488 KU953584 KU953680 KU953763
P. sonani Orchid Island O07 KU953489 KU953585 KU953681 KU953764
P. sonani Orchid Island O08 KU953490 KU953586 KU953682 KU953765
P. sonani Orchid Island O09 KU953491 KU953587 KU953683 KU953766
P. sonani Orchid Island O10 KU953492 KU953588 KU953684 KU953767
P. sonani Orchid Island O12 KU953493 KU953589 KU953685 KU953768
P. sonani Orchid Island O14 KU953494 KU953590 KU953686 KU953769
P. sonani Orchid Island O15 KU953495 KU953591 KU953687 KU953770
P. sonani Orchid Island O16 KU953496 KU953592 KU953688 KU953771
P. sonani Orchid Island O21 KX263455 - - -
P. orbifer Babuyan Island outgroup KU953483 KU953579 KU953675 KU953776
P. orbifer Fuga Island outgroup KU953428 KU953524 KU953620 KU953715
P. infernalis Iriomote Island outgroup KU953476 KU953572 KU953668 KU953755
P. infernalis Ishigaki Island outgroup KU953433 KU953529 KU953625 KU953720
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P. tobafolius Green Island G01 KX358509 - - -
P. tobafolius Green Island G02 KX263463 - - -
P. tobafolius Green Island G03 KX263464 - - -
P. tobafolius Green Island G04 KX263469 - - -
P. tobafolius Orchid Island O01 KX358510 - - -
P. tobafolius Orchid Island O02 KU953499 - - -
P. tobafolius Orchid Island O03 KX263465 - - -
P. tobafolius Orchid Island O04 KX263466 - - -
P. tobafolius Orchid Island O05 KX263467 - - -
P. tobafolius Orchid Island O06 KX263468 - - -
P. tobafolius Orchid Island O08 KX263461 - - -
P. tobafolius Orchid Island O09 KX263462 - - -
P. sp. Batan Island outgroup KX358511 - - -
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Appendix S3. The character coding of colour pattern in Pachyrhynchus sonani and outgroups (GI: Green Island; OI: Orchid Island).
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1 0.842 0.895 0 0.053 0 0 0.211 0.158 0.632 0.632 0 0 0.842 0.842 0 0.053 0.316 1 1 0.526
2 - - - 0.053 - - - - 0.211 0.211 0.105 0.105 - - - - - - - -
3 - - - - - - - - - 0.579 0.579 - - - - - - - -
4 - - - - - - - - - - 0.263 0.263 - - - - - - - -
P. orbifer Itbayat 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
P. orbifer Fuga 0 1 0 0 0 0 0 0 0 0 3 3 0 0 0 0 0 0 0 0
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Appendix S4. The character coding of colour pattern in Pachyrhynchus tobafolius and outgroups (GI: Green Island; OI:
Orchid Island).
Specimen Islands Colour traits
1 2 3 4
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222 OI 0 0 0 0
224 OI 0 0 0 1
Frequency 0 0.389 0.444 0.889 0.833 1 0.611 0.556 0.111 0.167
P. sp Batan 0 0 0 1
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Appendix S5. Description of character states of colour traits in Pachyrhynchus sonani.
Trait 1: The shape of the scale stripe at frontal thorax edge.
0. The scale stripe without posterior extension near middle body axis.
1. The scale stripe with posterior extension near middle body axis.
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Trait 2: The shape of crossing colour stripe at the middle of thorax 0. The crossing colour stripe without middle anterior extension.
1. The crossing colour stripe with middle anterior extension.
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Trait 3: The shape of crossing colour stripe at the middle of thorax.
0. Continuous colour stripe.
1. Discontinuous colour stripe.
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Trait 4: The shape of horizontal colour stripe at dorsal abdomen.
0. Continuous. 2. Discontinuous and broken into 3 parts.
1. Discontinuous and broken at midline.
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Trait 5 (anterior left), 6 (anterior right), 7 (posterior left), and 8 (posterior right): The longitudinal colour stripes.
0. The longitudinal colour stripe extended to horizontal crossing stripe.
1. The longitudinal colour stripe not extended to horizontal crossing stripe.
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Trait 9 (left) and 10 (right): The shape of colour stripe at L1 and R1, respectively.
0. Without extension. 2. With two extensions.
1. With one extension.
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Trait 11 (left) and 12 (right): The shape of colour stripe at L3 and R3, respectively.
0. No colour spot. 2. Linear colour spot without connection to posterior colour stripe.
1. Round colour spot. 3. Linear colour spot with connection to posterior colour stripe.
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4. Linear colour spot merged with posterior colour stripe.
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Trait 13 (left) and 14 (right): The shape of colour spot at L3 and R3, respectively.
0. Without colour spot.
1. With colour spot.
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Trait 15: The shape of posterior colour stripe at L4 and R4.
0. Without interior extension toward the midline of the abdomen.
1. With interior extension toward the midline of the abdomen.
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Trait 16: The shape of colour stripe on left lateral abdomen.
0. With gap in between.
1. Continuous without break.
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Trait 17: The shape of posterior colour stripe on ventral abdomen III.
0. With a gap in between.
1. Continuous without break.
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Trait 18: The colour spot near posterior colour stripe on ventral abdomen IV.
0. Without colour spot.
1. With colour spot.
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Trait 19: The colour spot near posterior colour stripe on ventral abdomen V.
2. Without colour spot.
3. With colour spot.
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Trait 20: The colour spot near posterior colour stripe on ventral abdomen VI.
4. Without colour spot.
5. With colour spot.
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Appendix S6. Description of character states of colour traits in Pachyrhynchus tobafolius.
Trait 1 (left) and 2 (right): The shape of colour stripe at posterior-lateral abdomen.
0. No connection.
1. Connected.
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Trait 3: The shape of colour spot on posterior-dorsal left elytra.
0. Without colour spot.
1. With a colour spot.
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Trait 4: The shape of colour spot on posterior-dorsal right elytra.
0. Without colour spot.
1. With a colour spot.
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Appendix S7. Morphometric analyses of body shape between sexes based on 21 landmarks for (a–h) Pachyrhynchus sonani and (i–p)
Pachyrhynchus tobafolius. Green Island populations of P. sonani: (a) dorsal and (c) lateral view. Orchid Island populations of P. sonani: (e) dorsal and (g) lateral view. Green Island populations of P. tobafolius: (i) dorsal and (k) lateral view. Orchid Island population of P. tobafolius: (m) dorsal and (o) lateral view. Deformation grid of body shape from female to male (3×): Green Island populations of P. sonani, (b) dorsal and (d) lateral view, Orchid Island populations of P. sonani, (f) dorsal and (h) lateral view, Green Island populations of P. tobafolius, (j) dorsal and (l) lateral view and Orchid Island populations of P. tobafolius (n) dorsal and (p) lateral view.
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Appendix S8. Structure analyses of Pachyrhynchus sonani and Pachyrhynchus tobafolius. The log probability of the data for all individuals of (a) Pachyrhynchus sonani and (b) Pachyrhynchus
tobafolius given a particular number of genetic clusters (K) from 1 to 10, calculated based on 2×106 MCMC runs in STRUCTURE. The delta K statistic for (c) Pachyrhynchus sonani and (d) Pachyrhynchus tobafolius.
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Appendix S9. The gene trees of Pachyrhynchus sonani. Bayesian phylogenetic analyses were based on (a) cox1, (b) nd2, (c) EF1α, and (d) ITS gene. Numbers near the nodes are branch support values of Bayesian posterior probability (BPP) / parsimony bootstrap (PB) / likelihood bootstrap (LB). Nodes without number are support values lower than 50%.
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Appendix S10. The cox1 gene tree of Pachyrhynchus tobafolius. Bayesian phylogenetic analyses were based on cox1 gene.
Numbers near the nodes are branch support values of Bayesian posterior probability (BPP) / parsimony bootstrap (PB) / likelihood bootstrap (LB). Nodes without number are support values lower than 50%.
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Appendix S11. The posterior probability of parameters under four gamma prior distributions in iBPP analyses.
Parameter
Gamma prior Posterior
(α,β) Mean (95% CI)
θG (1, 10) 0.001460 (0.000712-0.002626)
θO (1, 10) 0.002006 (0.000942-0.003706)
θGO (1, 10) 0.012211 (0.006943-0.021212)
τGO (1, 10) 0.000492 (0.000248- 0.000814)
θG (1, 10) 0.001465 (0.000723-0.002627)
θO (1, 10) 0.002012 (0.000965-0.003698)
θGO (1, 10) 0.012213 (0.006944-0.021221)
τGO (2, 2000) 0.000493 (0.000259-0.000799)
θG (2, 2000) 0.001171 (0.000585-0.002036) θO (2, 2000) 0.001571 (0.000772-0.002742) θGO (2, 2000) 0.006139 (0.004316-0.008484) τGO (1, 10) 0.000370 (0.000177-0.000631)
θG (2, 2000) 0.001189 (0.000604-0.002051) θO (2, 2000) 0.001595 (0.000801-0.002761) θGO (2, 2000) 0.006142 (0.004312-0.008490)
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τGO (2, 2000) 0.000381 (0.000191-0.000636)
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Appendix S12. The heritability of traits under four gamma prior distributions in iBPP analyses.
Trait
Heritability
θ (1, 10), τ (1, 10) θ (1, 10), τ (2, 2000) θ (2, 2000), τ (1, 10) θ (2, 2000), τ (2, 2000)
Mean (95% CI) Mean (95% CI) Mean (95% CI) Mean (95% CI)
Island of origin 0.346333 (0.025434-0.829577) PC of dorsal GM 0.382829
(0.040440-0.847891) PC of lateral GM 0.553293
(0.172824-0.912790) PC of colour spectrum 0.422740
(0.062499-0.865965) Number of scales 0.398120
(0.048023-0.855485) Morph of scales 0.311012
(0.016018-0.810516)
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98 PC of male genitalia 0.423213
(0.062223-0.866376) PC of female genitalia 0.595338 (0.219340-
0.925253)
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Appendix S13. The phylogeny of Pachyrhynchus sonani reconstructed from (a) Bayesian, (b) parsimony and (c) likelihood phylogenetic analyses based on combined four genes (cox1, nd2, EF1α and ITS).
Numbers near the nodes are branch support values of (a) Bayesian posterior probability (BPP), (b) parsimony bootstrap (PB), and (c) likelihood bootstrap (LB). Nodes without number are support values lower than 50%