Journal of Biogeography

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Evolution of sympatric species: a case study of the coral reef fish genus Pomacanthus (Pomacanthidae)

Jennifer R. Hodge, Charmaine I. Read, David R. Bellwood and Lynne van Herwerden

Appendix S1 Collection localities and GenBank accession numbers for specimens used in this study. Analyses were preformed on consensus sequences; where individual specimens were sampled from different locations, each location is listed. (—) = location/sequence unavailable.

/ GenBank accession numbers /
Genus / Species / Collection locations / 12S / 16S / S7 /
Ingroup taxa
Pomacanthus / annularis / Sri Lanka/Indonesia / KC820895 / KC820905 / KC820915
Pomacanthus / arcuatus / Caribbean / KC820896 / KC820906 / KC820916
Pomacanthus / asfur / Red Sea / a AY530826 / a AY530854 / KC820917
Pomacanthus / chrysurus / — / KC820897 / KC820907 / KC820918
Pomacanthus / imperator / Sri Lanka / KC820898 / KC820908 / KC820919
Pomacanthus / maculosus / Red Sea / KC820899 / KC820909 / KC820920
Pomacanthus / navarchus / Indonesia / KC820900 / KC820910 / KC820921
Pomacanthus / paru / Belize / a AY530824 / a AY530852 / KC820922
Pomacanthus / rhomboides / South Africa / KC820901 / KC820911 / KC820923
Pomacanthus / semicirculatus / Indonesia/One Tree Island, GBR / b AF108574 / a AY530844 / KC820924
Pomacanthus / sexstriatus / Lizard Island, GBR / b AF108575 / a AY530858 / KC820925
Pomacanthus / xanthometopon / Philippines/Indonesia / KC820902 / KC820912 / KC820926
Pomacanthus / zonipectus / Sea of Cortez / a AY530840 / a AY530874 / KC820927
Outgroup taxa
Pygoplites / diacanthus / Moorea/Younge Reef, GBR / b AF108577 / a AY530873 / KC820928
Holacanthus / africanus / Cape Verde Islands/São Tomé / c KC845393 / c KC845330 / c KC845372
Holacanthus / tricolor / Ceará State, Brazil/Marathon Key, Florida / c KC845399 / c KC845336 / c KC845378
Holacanthus / limbaughi / Clipperton Atoll / c KC845391 / c KC845328 / c KC845370
Chaetodontoplus / duboulayi / Mackay, GBR / KC820903 / KC820913 / KC820929
Chaetodontoplus / mesoleucus / Philippines/Indonesia / KC820904 / KC820914 / KC820930
Acanthurus / nigricans / Hick’s Reef, GBR/Cocos (Keeling) Island / d AY057239 / d AY057286 / e EF648230
Naso / lituratus / —/West Australia / f AF055603 / f AF055624 / e EF648256
Zanclus / cornutus / — / g EF616898 / g EF616980 / —
Luvarus / imperialis / —/Australian Museum, Sydney / f AF055601 / h AY264587 / —
Platax / orbicularis / Philippines / f AF055597/h AY279562 / f AF055618/i AY279665 / j FJ167848

Publication source for sequences obtained from GenBank: aBellwood et al. (2004); bNelson et al. (unpublished), location unavailable; cAlva-Campbell et al. (2010); dClements et al. (2003); eMarie et al. (2007); fTang et al. (1999), location unavailable; gFessler & Westneat (2007); hKlanten et al. (2004); iWestneat & Alfaro (2005), location unavailable; jBellwood et al. (2010). GBR, Great Barrier Reef.

REFERENCES

Alva-Campbell, Y., Floeter, S.R., Robertson, D.R., Bellwood, D.R. & Bernardi, G. (2010) Molecular phylogenetics and evolution of Holacanthus angelfishes (Pomacanthidae). Molecular Phylogenetics and Evolution, 56, 456–461.

Bellwood, D.R., van Herwerden, L. & Konow, N. (2004) Evolution and biogeography of marine angelfishes (Pisces: Pomacanthidae). Molecular Phylogenetics and Evolution, 33, 140–155.

Bellwood, D.R., Klanten, S., Cowman, P.F., Pratchett, M.S., Konow, N. & van Herwerden, L. (2010) Evolutionary history of the butterflyfishes (f: Chaetodontidae) and the rise of coral feeding fishes. Journal of Evolutionary Biology, 23, 335–349.

Clements, K.D., Gray, R.D. & Choat, J.H. (2003) Rapid evolutionary divergences in reef fishes of the family Acanthuridae (Perciformes: Teleostei). Molecular Phylogenetics and Evolution, 26, 190–201.

Fessler, J.L. & Westneat, M.W. (2007) Molecular phylogenetics of the butterflyfishes (Chaetodontidae): taxonomy and biogeography of a global coral reef fish family. Molecular Phylogenetics and Evolution, 45, 50–68.

Klanten, S.O., van Herwerden, L., Choat, J.H. & Blair, D. (2004) Patterns of lineage diversification in the genus Naso (Acanthuridae). Molecular Phylogenetics and Evolution, 32, 221–235.

Marie, A.D., van Herwerden, L., Choat, J.H. & Hobbs, J.-P.A. (2007) Hybridization of reef fishes at the Indo-Pacific biogeographic barrier: a case study. Coral Reefs, 26, 841–850.

Nelson, J.S., Hoddell, R.J., Ch’ng, L.M., Chou, L.M., Kara, A.U., Lim, T.M., Ng, P., Phang, V.P.E., Chan, W.K. & Lam, T.J. (Unpublished) Phylogeny of the Indo-Pacific Chaetodontidae and Pomacanthidae based on mitochondrial cytochrome b and 12S rDNA sequences.

Tang, K.L., Berendzen, P.B., Wiley, E.O., Morrissey, J.F., Winterbottom, R. & Johnson, G.D. (1999) The phylogenetic relationships of the Suborder Acanthuroidei (Teleostei: Perciformes) based on molecular and morphological evidence. Molecular Phylogenetics and Evolution, 11, 415–425.

Westneat, M.W. & Alfaro, M.E. (2005) Phylogenetic relationships and evolutionary history of the reef fish family Labridae. Molecular Phylogenetics and Evolution, 36, 370–390.

Appendix S2 Supplementary methods: details of phylogenetic analyses.

paup* v4.0b10 (Swofford, 2003) was used to perform maximum parsimony (MP) analyses for which five independent heuristic searches were executed using a tree bisection–reconnection (TBR) branch-swapping algorithm with 100 random sequence addition replicates. Analyses were run with and without weights assigned to transversions relative to transitions (5:1). The weighted stepmatrix was calculated based on estimates of substitution rates obtained from jModelTest (Posada, 2008). Nonparametric bootstrapping was also implemented, with 1000 bootstrap pseudo-replicates using heuristic searches and TBR branch-swapping with two random sequence additions per pseudo-replicate, to determine the level of support for each clade. A majority-rule consensus tree was produced from all topologies recovered from the bootstrap analyses. The final weighted MP tree was chosen based on consistency with other phylogenetic analyses.

Maximum likelihood (ML) analysis, implemented in Garli v1.0 (Zwickl, 2006), was used to search for the tree topology, branch lengths and substitution model parameters with the highest log-likelihood (–lnL) score based on the maximum likelihood criterion. Ten independent iterations of the analysis were performed using default settings for algorithm parameters. Of the ten best trees obtained, the tree with the best –lnL score was considered the best overall topology. Since the program simultaneously estimates substitution model parameters, the analysis was run with and without the substitution model specified (as per AICc). This served to further ensure the analyses were converging on similar solutions and not arriving in a suboptimal area of tree space. The final tree for use in further analyses was chosen based on the best overall –lnL score. A bootstrap analysis was also performed with 100 bootstrap replicates and the best ML tree specified as the starting tree. A majority-rule consensus tree was constructed in paup* to determine the level of support for the clades recovered.

Bayesian inference (BI) methods were implemented in MrBayes v3.1.2 (Ronquist & Huelsenbeck, 2003), using a partition mix model. Partitions were assigned according to gene region and the general substitution model structure (as per AICc) was specified for each partition. Parameters were unlinked across partitions and each was allowed to evolve under different rates using a flat Dirichlet prior. Posterior probabilities of clades were calculated following two 10 million generation Markov chain Monte Carlo (MCMC) analyses, each with four chains sampling every 500 generations. Convergence was assessed using awty (Wilgenbusch et al., 2004) and Tracer 1.5 (Rambaut & Drummond, 2007). Upon examination of the trace files, a conservative burn-in of 10% (1 million generations or 2000 trees) was discarded from each run and a 50% majority-rule consensus tree was computed using the remaining sampled trees.

REFERENCES

Posada, D. (2008) jModelTest: phylogenetic model averaging. Molecular Biology and Evolution, 25, 1253–1256.

Rambaut, A. & Drummond, A.J. (2007) Tracer v1.4. Available at: http://beast.bio.ed.ac.uk/‌Tracer.

Ronquist, F. & Huelsenbeck, J.P. (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572–1574.

Swofford, D.L. (2003) PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4.0b10. Sinauer Associates, Sunderland, MA.

Wilgenbusch, J.C., Warren, D.L. & Swofford, D.L. (2004) AWTY: a system for graphical exploration of MCMC convergence in Bayesian inference. Available at: http://ceb.csit‌.fsu.edu/awty/.

Zwickl, D.J. (2006) Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under maximum likelihood criterion. PhD Thesis, University of Texas, Austin, TX.


Appendix S3 Supplementary figures. awty output for Bayesian inference analyses implemented in MrBayes (Figs S1 S2). Phylogeny of Pomacanthus (Fig. S3). awty output for Bayesian inference analyses implemented in beast (Figs S4 S5).


Figure S1 awty output from the phylogenetic analysis of Pomacanthus. The bivariate plot is a pairwise comparison of the posterior probabilities of nodes for each of two independent Bayesian inference analyses implemented in MrBayes. Low correlation among runs would diagnose lack of convergence; however, that was not detected here.

Figure S2 awty output from the phylogenetic analysis of Pomacanthus. Each plot shows the cumulative posterior probabilities of the 18 most variable nodes for trees searched by two independent Markov chain Monte Carlo analyses implemented in MrBayes: (a) analysis 1; and (b) analysis 2. A trend in the frequency of posterior probabilities for nodes diagnoses lack of convergence, but was not observed here.

Figure S3 Inferred phylogeny of Pomacanthus obtained by Bayesian inference (BI), maximum likelihood (ML) and maximum parsimony (MP) analyses of three loci (12S, 16S and S7). The topology shown is the best Bayesian tree with bootstrap support values (>50%) from MP and ML (1000 and 100 bootstrap replicates respectively) and posterior probabilities from BI (consensus of 36,002 trees). Asterisks denote 100% support for the node across all three analyses. Sister taxa include Chaetodontoplus mesoleucus, Chaetodontoplus duboulayi, Pygoplites diacanthus, Holacanthus tricolor, Holacanthus limbaughi and Holacanthus africanus. Platax orbicularis was used to root the phylogeny.

Figure S4 awty output from the phylogenetic analysis of Pomacanthus. Each bivariate plot is a pairwise comparison of the posterior probabilities of nodes for each of four independent Bayesian inference analyses implemented in beast. Low correlation among runs would diagnose lack of convergence; however, that was not detected here.

Figure S5 awty output from the phylogenetic analysis of Pomacanthus. Each plot shows the cumulative posterior probabilities of the 18 most variable nodes for trees searched by four independent Markov chain Monte Carlo analyses implemented in beast: (a) analysis 1; (b) analysis 2; (c) analysis 3; and (d) analysis 4. A trend in the frequency of posterior probabilities for nodes diagnoses lack of convergence, but was not observed here.