First generation microarray-system for identification of primate species subject to bushmeat trade

Transcription

1 The following supplement accompanies the article First generation microarray-system for identification of primate species subject to bushmeat trade A.-C. Rönn 1, O. Andrés 2, F. López-Giráldez 2, 3, C. Johnsson-Glans 1, E. J. Verschoor 4, X. Domingo-Roura 2,, M. W. Bruford 5, A.-C. Syvänen 1, M. Bosch 2, * 11 Molecular Medicine, Department of Medical Sciences, Uppsala University, University Hospital, Entr., 3rd floor, Res. Dep. 2, Uppsala, Sweden 2 Genètica de la Conservació Animal, Institut de Recerca i Tecnologia Agroalimentàries, Carretera de Cabrils Km2, Cabrils, Spain 3 Department of Ecology and Evolutionary Biology, Yale University, PO Box 20810, Prospect Street 15, New Haven, Connecticut 0520, USA 4 Department of Virology, Biomedical Primate Research Centre, Lange Kleiweg 139, 2288 GJ Rijswijk, The Netherlands 5 Cardiff School of Biosciences, Cardiff University, PO Box 5 Cathays Park, Cardiff CF10 3TL, UK *Corresponding author. montse.bosch.gallego@gmail.com Deceased Endang Species Res 9: Supplement 1. Table S1. Samples used for the applicability test of the microarray system Samples No. of samples Aotus trivirgatus 1 Ateles fusciceps 2 Ateles paniscus 1 Callimico goeldii 1 Callithrix jacchus 2 Cebus apella 2 Cercocebus agilis agilis 1 Cercocebus torquatus 3 Cercopithecus cephus 1 Cercopithecus mitis albogularis 1 Cercopithecus mitis kolbi 1 Cercopithecus mona 1 Chlorocebus aethiops 3 Chlorocebus aethiops pygerythrus 1 Colobus polykomos 1 Dermoptera 1 Eulemur fulvus magotteri 1 Galago sp. 1 Galagoides demidoff 2 Gorilla gorilla 1 Gorilla gorilla gorilla 2 Hylobates lar 2 Hylobates syndactylus 1 Lemur catta 1 Leontopithecus chrysomelas 1 Lophocebus albigena 1 Lophocebus aterrimus 1 Loris tardigradus 2 Macaca fascicularis 1 Macaca mulatta 1 Macaca sylvanus 1 Mandrillus sphinx 2 Microcebus murinus 4 Miopithecus talapoin 2 Nycticebus coucang 1

2 2 Supplement 1 (continued) Table S1 (continued) Samples No. of samples Ovis aries 2 Pan paniscus 2 Pan troglodytes 2 Pan troglodytes schweinfurthii 1 Pan troglodytes verus 1 Papio hamadryas 1 Papio hamadryas anubis 1 Papio hamadryas cynocephalus 1 Perodicticus potto 1 Pongo abelii 1 Pongo pygmaeus 2 Saguinus oedipus 1 Saimiri boliviensis 1 Scandentia 1 Semnopithecus entellus 1 Tarsius sp. 1 Trachipithecus auratus 1 Tupaia 1 Varecia sp. 1 Varecia v. rubra 1 Fig. S1. Scatter plots for genotype assignment. Two clusters corresponding to the detected variations are shown. A and B in the figure correspond to the nucleotide variations A and T, respectively, in the apolipoprotein B (ApoB) example and T and C, respectively, in the epsilonglobin gene example. Negative controls had signal intensities lower than The genotype assignments made in these 2 examples are indicated by circles around the clusters and the negative controls. Note that as all nucleotide positions were genotyped simultaneously for all samples in each experiment, samples that did not belong to the Catarrhini infraorder were also visible in the analysis of the ApoB gene positions, but would mostly fall into the cluster of negative controls

3 Supplement 1 (continued) 3 7 ColobusCTM20 2 TheropithecusgeladaT 3 Prmelalophos1974 Semnopithecusentellu CoguerezaCTM9 47 Trachypithecusfranco 13 CercopithecusmitisCM Papiohamadryas1300 Cercopithecusaethiop Cercopithecusaethiop 2 Erythrocebuspatas11 Catarrhini 5 Pongo PongopygmaeusCTM MandrillussphinxCTM2 MacacatonkeanaCTM33 MACAADMacacamulatta Macacafuscata37 HSU41Hylobatessyn HylobateslarHLA1 37 HomosapiensV GORAACGorilla CHPAAAPantroglodytes CHPAABPanpaniscus Pan 25 MNKEGLOBINAtelesbelz 21 LAYEGLOBINLagothrixl MNKEGLOBIMAtelesgeof 2 BCHEGLOBINBrachytele ALOEGLOBIN ALOEGLOBIMAlouattase CJAEGLOBINCacajaocal PIKEGLOBINPitheciair Platyrrhini CHWEGLOBIMChiropotes CCBEGLOBINCallicebus 80 CCBEGLOBIMCallicebus 20 SBU181Saimiriboliv SAIEGLOBIMSaimirisci SSU1818Saimirisciur COU1810Cebusolivace CKU1808Cebuskaapori 41 LNOEGLOBINLeontopith 19 SOEEGLOBINSaguinusmi 22 ATREGLOBINAotusazara 1 45 CALEGLOBIMCallithrix Callithrixargentatap 57 CGU929Callithrixge CITEGLOBIMCallimicog 98 Galagocrassicaudatus 94 Otolemurcrassicaudat PerodicticuspottoPPU Strepsirrhini NycticebuscoucangNCU 8 75 Loris Daubentoniamadagasca MicrocebusmurinusMMU CheirogaleusmediusCM 42 Propithecusverreauxi 33 LemurbrownLEMHBE Eulemur TarsiussyrichtaTARHB Tarsiiformes Fig. S2. Neighbour-joining (NJ) tree of epsilonglobin sequences displaying the unambiguous discrimination of different infraorders. Numbers represent bootstrap values from NJ (1000 replications)

4 4 Supplement 1 (continued) Macaca nemestrina AY Papio hamadryas CTM45Consensus Macaca sylvanus CTM55Consensus 55 Mandrillus leucophaeus CTM28Consensus Macaca mulatta AY Macaca mulatta MMUConsensus Mandrillus sphinx CTM37Consensus 95 Mandrillus sphinx CTM23Consensus Macaca thibetana CTM44Consensus Mandrillus leucophaeus CTM30Consensus Cercopithecinae Mandrillus sphinx CTM35Consensus 2 Mandrillus leucophaeus CTM31Consensus Mandrillus sphinx CTM41Consensus Erythrocebus patas CTM13Consensus 9 Erythrocebus patas CTM4Consensus Cercopithecus mitis CMIa1Consensus Colobus CTM20Consensus Colobus guereza CTM9Consensus 51 Pygathrix nemaeus PNE1Consensus Nasalis larvatus AY Colobiane 9 Semnopithecus entellus AY Trachypithecus francoisi CTM87Consensus 9 Semnopithecus entellus pcconsensus Semnopithecus entellus pc5consensus Hylobates lar AY Pongo pygmaeus AY Gorilla gorilla AY Hominidae 85 Pan troglodytes AY Pan paniscus AY Alouatta seniculus AY Saguinus labiatus AY Saimiri sciureus AY Callicebus moloch AY Platirrhini Fig. S3. Neighbour-joining (NJ) tree of apolipoprotein B (ApoB) sequences displaying the unambiguous discrimination of different Catarrhine subfamilies. Four Platirrhine sequences are included as outgroup. Numbers represent bootstrap values from NJ (1000 replications)

5 Supplement 1 (continued) 5 03Pbieti AY232 03Proxellana 2 AY Pbieti AY232 03Pbieti AY2328 Pygathrix 90 03Proxellana AY Proxellana 3 AY Pbrelichi AY232 04Pcristatus Sawa 04Pcristata Sawa 04Presbytis cristatu Presbytis 88 01Colobus 01Colobus 2 01Cguereza 01Cguereza 2 Colobus 8 01Cguereza 3 01Colobus guereza L3 01Cpolykomos G555 05Piliocolobus Piliocolobus 0Procolobus badius Procolobus 02Nlarvatis AF0 Nasalis 08Tjohnii Sentellus 2 07Sentellus 07Sentellus London 07Sentellus 3 Semnopithecus and Trachypithecus 07Sentellus London 2 08Tobscurus Q85 Fig. S4. Neighbour-joining (NJ) tree of 12S rrna Colobinae sequences displaying the unambiguous discrimination of different genera. Numbers represent bootstrap values from NJ (1000 replications)