Optimizing Phylogenetic Supertrees Using Answer Set Programming

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Optimizing Phylogenetic Supertrees Using Answer Set Programming

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1 Online appendix for the paper Optimizing Phylogenetic Supertrees Using Answer Set Programming published in Theory and Practice of Logic Programming LAURA KOPONEN and EMILIA OIKARINEN and TOMI JANHUNEN HIIT and Department of Computer Science Aalto University P.O. Box 15400, FI-00076 AALTO, Finland (e-mail: {Laura.J.Koponen, Emilia.Oikarinen, Tomi.Janhunen}@aalto.fi) LAURA SÄILÄ Department of Geosciences and Geography University of Helsinki P.O. Box 64, FI-00014 University of Helsinki, Finland (e-mail: Laura.Saila@helsinki.fi) submitted 29 April 2015; revised 3 July 2015; accepted 14 July 2015

2 Appendix A The optimal genus-level supertree of the projection encoding, using Felinae-Machairodontinae backbone constraint and weight 4 for source trees from molecular studies. outgroup Proailurus Pseudaelurus Hyperailurictis Stenailurus Metailurus Dinofelis Adelphailurus Promegantereon Paramachaerodus Smilodon Megantereon Nimravides Machairodus Amphimachairodus Xenosmilus Homotherium Styriofelis Neofelis Panthera Pardoides Catopuma Pardofelis Leptailurus Profelis Caracal Leopardus Lynx Felis Otocolobus Prionailurus Miracinonyx Puma Acinonyx

3 Appendix B Best-resolution 50% majority consensus MRP genus-level supertree from (Säilä et al. 2011; Säilä et al. 2012) projected to the set of genera considered in this paper. In the computation extant Felinae genus-level backbone from molecular studies constraint is used. outgroup Proailurus Pseudaelurus Hyperailurictis Stenailurus Metailurus Dinofelis Adelphailurus Promegantereon Paramachaerodus Smilodon Megantereon Nimravides Machairodus Amphimachairodus Xenosmilus Homotherium Styriofelis Neofelis Panthera Pardoides Catopuma Pardofelis Leptailurus Profelis Caracal Leopardus Lynx Felis Otocolobus Prionailurus Miracinonyx Puma Acinonyx

4 Appendix C Best-support 50% majority consensus MRP genus-level supertree from (Säilä et al. 2011; Säilä et al. 2012) projected to the set of genera considered in this paper. In the computation Felinae-Machairodontinae backbone constraint and weight 4 for source trees from molecular studies are used and best support is computed according to (Wilkinson et al. 2005). outgroup Proailurus Pseudaelurus Hyperailurictis Stenailurus Dinofelis Metailurus Adelphailurus Promegantereon Paramachaerodus Smilodon Megantereon Nimravides Machairodus Amphimachairodus Xenosmilus Homotherium Styriofelis Pardoides Neofelis Panthera Profelis Leptailurus Caracal Pardofelis Catopuma Leopardus Lynx Felis Otocolobus Prionailurus Puma Miracinonyx Acinonyx

5 Appendix D Below is a listing of the 38 source trees included in the Felidae supertree computation and used in (Säilä et al. 2011; Säilä et al. 2012). Trees marked with an asterisk * have been obtained from molecular studies. *S1 = (Outgroup, (Homotherium serum, (Puma yagouaroundi, ((Acinonyx jubatus, (Miracinonyx trumani, Puma concolor)), (((Leopardus colocolo, (Leopardus tigrina, (Leopardus geoffroyi, Leopardus guigna))), ((Neofelis nebulosa, Neofelis diardi), (Panthera tigris, (Panthera leo, (Panthera pardus, (Panthera onca, Panthera uncia)))))), ((Lynx pardina, (Lynx lynx, Lynx canadensis)), (((Leopardus wiedii, Leopardus pardalis), (Prionailurus planiceps, (Prionailurus bengalensis, Prionailurus viverrina))), (Otocolobus manul, (Lynx rufus, ((Catopuma temmincki, Pardofelis marmorata), ((Felis magrita, (Felis catus, Felis silvestris, Felis lybica)), (Felis chaus, Felis nigripes)))))))))))); *S2 = (Outgroup, ((Felis bieti, (Felis silvestris, Felis catus, Felis lybica)), (Neofelis nebulosa, (Panthera leo, Panthera uncia, Panthera tigris)))); S3 = (Outgroup, (Panthera leo, (Panthera spelaea, Panthera atrox))); *S4 = (Outgroup, ((Homotherium serum, Smilodon populator), ((Leopardus pardalis, (Felis silvestris, (Acinonyx jubatus, (Puma yagouaroundi, (Miracinonyx trumani, Puma concolor))))), (Panthera leo, Panthera tigris)))); S5 = (Outgroup, (Hyperailurictis intreepidus, (Nimravides pediomus, Nimravides galiani, Nimravides catacopsis))); S6 = (Outgroup, (Nimravides catacopsis, Miomachairodus pseudailuroides, Machairodus aphanistus, (Dinobastis ischyrys, (Homotherium crenatidens, Homotherium johnsoni, Homotherium crusafonti, Homotherium idahoensis))), (Adelphailurus kansensis, Stenailurus teilhardi, Metailurus parvalus, (Dinofelis barlowi, Dinofelis christata), (Paramachaerodus orientalis, Promegantereon ogygia)), ((Smilodon fatalis, Smilodon populator, Smilodon gracilis), (Megantereon hesperus, (Megantereon whitei, Megantereon cultridens, Megantereon falconeri)))); *S7 = (Outgroup, (((((Leopardus geoffroyi, Leopardus pardalis), (Otocolobus manul, Felis magrita)), (Prionailurus bengalensis, Leptailurus serval)), (Catopuma temmincki, (Caracal caracal, Lynx rufus))), ((Acinonyx jubatus, (Puma concolor, (Panthera tigris, Panthera uncia))), (Panthera onca, (Panthera leo, Panthera pardus))))); *S8 = (Outgroup, (Felis catus, ((Neofelis nebulosa, Neofelis diardi), (Panthera leo, (Panthera uncia, (Panthera pardus, (Panthera onca, Panthera tigris))))))); *S9 = (Outgroup, (Felis catus, (Neofelis nebulosa, (Panthera tigris, (Panthera pardus, (Panthera leo, Panthera spelaea)))))); S10 = (Outgroup, (Leopardus pardalis, (Puma pardoides, (Puma concolor, (Miracinonyx inexpectatus, (Miracinonyx trumani, (Acinonyx pardinensis, Acinonyx jubatus))))))); *S11 = (Outgroup, (Neofelis nebulosa, ((Panthera onca, (Panthera leo, Panthera pardus)), (Panthera tigris, Panthera uncia)))); *S12 = (Outgroup, (Felis magrita, (Felis silvestris, (Felis bieti, (Felis catus, Felis lybica))))); *S13 = (Outgroup, (Panthera onca, (Lynx lynx, (Leopardus pardalis, (Felis catus, Acinonyx jubatus))))); *S14 = (Outgroup, ((((Puma concolor, (Felis catus, Felis silvestris)), Lynx rufus),

6 Acinonyx jubatus), (Leopardus pardalis, (Panthera tigris, (Panthera uncia, Panthera leo))))); *S15 = (Outgroup, (Felis catus, ((Lynx lynx, Lynx rufus), (Puma concolor, (Panthera tigris, Panthera leo))))); *S16 = (Outgroup, ((((((((Felis chaus, (Felis nigripes, (Felis magrita, ((Felis catus, Felis silvestris), (Felis lybica, Felis bieti))))), (Otocolobus manul, (Prionailurus rubiginosa, (Prionailurus bengalensis, (Prionailurus viverrina, Prionailurus planiceps))))), (Acinonyx jubatus, (Puma yagouaroundi, Puma concolor))), (Lynx rufus, (Lynx canadensis, (Lynx lynx, Lynx pardina)))), ((Leopardus wiedii, Leopardus pardalis), ((Leopardus jacobitus, Leopardus colocolo), (Leopardus tigrina, (Leopardus geoffroyi, Leopardus guigna))))), (Caracal caracal, (Leptailurus serval, Profelis aurata))), (Pardofelis marmorata, (Catopuma temmincki, Catopuma badia))), (Neofelis nebulosa, ((Panthera pardus, (Panthera leo, Panthera onca)), (Panthera tigris, Panthera uncia))))); *S17 = (Outgroup, (Neofelis nebulosa, (Pardofelis marmorata, (Lynx rufus, (Lynx canadensis, (Lynx lynx, Lynx pardina)))))); *S18 = (Outgroup, (Panthera tigris, Panthera uncia, ((Neofelis nebulosa, ((((((Felis chaus, (Felis nigripes, (Felis magrita, (Felis catus, Felis bieti, (Felis lybica, Felis silvestris))))), (Otocolobus manul, (Prionailurus rubiginosa, (Prionailurus viverrina, (Prionailurus planiceps, Prionailurus bengalensis))))), (Puma yagouaroundi, Puma concolor, Acinonyx jubatus)), (Lynx rufus, (Lynx lynx, Lynx pardina, Lynx canadensis))), ((Leopardus wiedii, Leopardus pardalis), (Leopardus colocolo, (Leopardus tigrina, (Leopardus geoffroyi, Leopardus guigna)))), (Leptailurus serval, (Caracal caracal, Profelis aurata))), (Catopuma temmincki, Pardofelis marmorata))), (Panthera pardus, (Panthera leo, Panthera onca))))); S19 = (Outgroup, ((Pratifelis martini, (Pseudaelurus quadridentatus, Hyperailurictis intreepidus, Hyperailurictis marshi, Hyperailurictis stouti)), ((Nimravides galiani, (Nimravides catacopsis, Nimravides pediomus)), (((Felis proterolyncis, (Lynx lynx, Felis rexroadensis)), (Miracinonyx trumani, (Puma concolor, Felis lacustris))), (Adelphailurus kansensis, ((Dinofelis christata, Dinofelis palaeoonca), (((Machairodus aphanistus, Machairodus coloradensis), (Homotherium crenatidens, Dinobastis ischyrys, Homotherium johnsoni, Homotherium crusafonti, Homotherium idahoensis)), (Megantereon cultridens, Megantereon hesperus)))))))); S20 = (Outgroup, (Megantereon cultridens, (Megantereon whitei, Megantereon falconeri))); S21 = (Outgroup, ((((Pardofelis marmorata, (((Leptailurus serval, (Profelis aurata, Caracal caracal)), (Prionailurus viverrina, (Prionailurus bengalensis, Prionailurus planiceps))), ((Felis nigripes, (Felis chaus, ((Felis catus, Felis lybica), (Felis magrita, Felis silvestris)))), (Otocolobus manul, Prionailurus rubiginosa))), (Catopuma badia, Catopuma temmincki)), ((Lynx rufus, (Lynx canadensis, Lynx lynx)), (Acinonyx jubatus, (Puma concolor, Puma yagouaroundi)))), (((Leopardus colocolo, Leopardus tigrina), (Leopardus geoffroyi, Leopardus guigna)), (Leopardus pardalis, Leopardus wiedii))), (Neofelis nebulosa, (Panthera uncia, (Panthera pardus, (Panthera leo, (Panthera onca, Panthera tigris))))))); S22 = (Outgroup, (Panthera uncia, (Neofelis nebulosa, (Panthera onca, ((Panthera pardus, Panthera palaeosinensis), (Panthera tigris, (Panthera leo, Panthera spelaea))))))); S23 = (Outgroup, (Leopardus pardalis, (Puma concolor, (Neofelis nebulosa, (Panthera uncia, (Panthera palaeosinensis, ((Panthera tigris, Panthera zdanskyi),

(Panthera onca, (Panthera atrox, (Panthera spelaea, (Panthera leo, Panthera pardus))))))))))); S24 = (Outgroup, (Neofelis nebulosa, (Panthera uncia, (((((Panthera tigris, Panthera zdanskyi), Panthera onca), Panthera pardus), Panthera palaeosinensis), (Panthera spelaea, (Panthera atrox, Panthera leo)))))); *S25 = (Outgroup, (Panthera onca, Panthera uncia, (Panthera pardus, Panthera leo))); *S26 = (Outgroup, (((((Felis chaus, (Felis nigripes, (Felis magrita, ((Felis catus, Felis silvestris), (Felis lybica, Felis bieti))))), (Otocolobus manul, (Prionailurus rubiginosa, (Prionailurus viverrina, (Prionailurus planiceps, Prionailurus bengalensis))))), (Acinonyx jubatus, (Puma yagouaroundi, Puma concolor)), (Lynx rufus, (Lynx lynx, Lynx pardina, Lynx canadensis))), (Leopardus wiedii, Leopardus pardalis, (Leopardus colocolo, (Leopardus tigrina, Leopardus geoffroyi, Leopardus guigna))), (Leptailurus serval, (Caracal caracal, Profelis aurata))), ((Catopuma temmincki, Pardofelis marmorata), (Neofelis nebulosa, (Panthera tigris, (Panthera uncia, (Panthera leo, Panthera pardus, Panthera onca))))))); S27 = (Outgroup, (Proailurus lemanensis, (Hyperailurictis validus, (Hyperailurictis skinneri, (Hyperailurictis marshi, (Hyperailurictis intreepidus, Hyperailurictis stouti, (Puma concolor, Lynx canadensis))))))); S28 = (Outgroup, (Proailurus lemanensis, (Pseudaelurus quadridentatus, (Promegantereon ogygia, (Paramachaerodus orientalis, Paramachaerodus maximiliani))))); S29 = (((Styriofelis turnauensis, (Styriofelis vallesiensis, (Pristifelis attica, ((Felis magrita, (Profelis aurata, Felis chaus)), (Felis silvestris, (Felis lybica, ((Panthera pardus, Panthera leo), (Caracal caracal, Prionailurus bengalensis, Lynx pardina, Lynx rufus, Leptailurus serval)))))))), Proailurus lemanensis), Outgroup); S30 = (Outgroup, ((Prionailurus planiceps, Prionailurus viverrina), (Profelis aurata, (Leopardus geoffroyi, (Leopardus tigrina, Leopardus guigna, (Leopardus pardalis, Leopardus wiedii), (Prionailurus bengalensis, Leptailurus serval), (Leopardus colocolo, Leopardus jacobitus, Prionailurus rubiginosa), (Puma yagouaroundi, (Puma concolor, (Acinonyx jubatus, (Panthera uncia, (Neofelis nebulosa, (Panthera tigris, (Panthera onca, Panthera leo, Panthera pardus))))))), (Catopuma temmincki, (Catopuma badia, (Pardofelis marmorata, ((Caracal caracal, (Lynx rufus, (Lynx lynx, (Lynx canadensis, Lynx pardina)))), (Felis chaus, (Felis lybica, (Felis silvestris, (Felis bieti, (Felis nigripes, (Felis magrita, Otocolobus manul))))))))))))))); S31 = (Outgroup, (Proailurus lemanensis, (((Styriofelis turnauensis, Styriofelis lorteti), ((Puma pardoides, (Panthera gombaszoegensis, Panthera onca), (Panthera tigris, Panthera uncia, Panthera pardus, (Panthera atrox, Panthera leo, Panthera spelaea))), (Puma concolor, ((Miracinonyx trumani, Miracinonyx inexpectatus), (Acinonyx jubatus,acinonyx pardinensis))))), (Pseudaelurus quadridentatus, ((Adelphailurus kansensis, Stenailurus teilhardi, ((Metailurus parvalus, Metailurus major), (Dinofelis christata, Dinofelis diastema, Dinofelis piveteaui, Dinofelis barlowi, Dinofelis abeli, Dinofelis palaeoonca))), (((Nimravides galiani, (Nimravides catacopsis, Nimravides pediomus)), (Machairodus aphanistus, (Amphimachairodus giganteus, (Amphimachairodus kurteni, (Xenosmilus hodsonae, (Homotherium johnsoni, Homotherium crusafonti, Homotherium idahoensis, Homotherium hadarensis, Homotherium serum, (Homotherium crenatidens, Homotherium latidens, Homotherium ultimus))))))), ((Paramachaerodus orientalis, Promegantereon ogygia), ((Megantereon whitei, Megantereon cultridens, 7

8 Megantereon falconeri), (Smilodon gracilis, Smilodon populator, Smilodon fatalis))))))))); S32 = (Outgroup, (Leopardus pardalis, (Puma concolor, (Miracinonyx inexpectatus, (Miracinonyx trumani, (Acinonyx pardinensis, Acinonyx jubatus)))))); *S33 = (Outgroup, (Neofelis nebulosa, (Panthera tigris, (Panthera onca, (Panthera pardus, (Panthera leo, Panthera uncia))))), (Felis catus, (Lynx lynx, (Puma concolor, Acinonyx jubatus)))); S34 = (Outgroup, (Dinofelis christata, Dinofelis diastema, Dinofelis barlowi, Dinofelis palaeoonca, Dinofelis petteri, (Dinofelis piveteaui, Dinofelis aranoki))); S35 = (Outgroup, (Lynx issiodorensis, (Lynx pardina, Lynx rufus, (Lynx lynx, Lynx canadensis)))); *S36 = (Outgroup, (Felis catus, ((Neofelis diardi, Neofelis nebulosa), (Panthera pardus, ((Panthera uncia, Panthera leo), (Panthera onca, Panthera tigris)))))); *S37 = (Outgroup, (Lynx lynx, (Catopuma temmincki, Prionailurus bengalensis, Otocolobus manul, ((Panthera tigris, (Neofelis nebulosa, (Panthera leo, (Panthera pardus, Panthera uncia)))), (Felis bieti, (Felis silvestris, Felis catus)))))); *S38 = (Outgroup, (Lynx lynx, (((((Felis bieti, Otocolobus manul), (Felis chaus, Felis lybica)), (Prionailurus bengalensis, Prionailurus viverrina)), (Catopuma temmincki, Pardofelis marmorata)), (Panthera pardus, (Panthera tigris, (Panthera uncia, Neofelis nebulosa)))))); References Säilä, L. K., Fortelius, M., Oikarinen, E., Werdelin, L., and Corfe, I. 2012. Fossil mammals, phylogenies and climate: the effects of phylogenetic relatedness on range sizes and replacement patterns in changing environments. In Proceedings of 60th Annual Symposium of Vertebrate Palaeontology and Comparative anatomy, SVPCA 2012. Poster. Säilä, L. K., Fortelius, M., Oikarinen, E., Werdelin, L., Corfe, I., and Tuomola, A. 2011. Taxon replacement: Invasion or speciation? First results for a supertree of Neogene mammals. Journal of Vertebrate Paleontology 31, 3, suppl., 184A. Wilkinson, M., Pisani, D., Cotton, J. A., and Corfe, I. 2005. Measuring support and finding unsupported relationships in supertrees. Systematic Biology 54, 5, 823 831.

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