jbi12697-sup-0001-AppendixS1-S2
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Journal of Biogeography SUPPORTING INFORMATION Comparison of phylogeographical structures of a lichen-forming fungus and its green algal photobiont in western North America Jin-Ming Chen, Silke Werth and Victoria L. Sork Appendix S1 Supplementary tables. Table S1 Localities, habitats, ecoregions and sample size (N) of each of the 73 localities of studied lichen R. menziesii. Localities Location Longitude Latitude Habitat Ecoregion N BA13 Baja California, Mexico -115.75 30.12 Coastal chaparral BC 2 BA14 Baja California, Mexico -115.74 30.11 Coastal chaparral BC 3 BA2 Baja California, Mexico -115.00 30.00 Desert BI 4 BA3 Baja California, Mexico -114.13 29.05 Desert BI 5 BA4 Baja California, Mexico -115.44 30.06 Desert BI 5 BA7 Baja California, Mexico -115.57 30.05 Desert BI 2 BA8 Baja California, Mexico -114.11 28.78 Desert BI 3 BA9 Baja California, Mexico -113.68 27.90 Desert BI 5 BA10 Baja California, Mexico -113.60 27.79 Desert BI 5 BA11 Baja California, Mexico -113.43 27.64 Desert BI 5 BA12 Baja California, Mexico -114.32 27.51 Desert BI 3 BA15 Baja California, Mexico -115.52 30.04 Desert BI 2 MA1 California, USA -122.89 38.16 Coastal woodland CC 2 MA2 California, USA -122.80 38.04 Coniferous forest CC 2 MA3 California, USA -122.70 37.93 Coastal woodland CC 3 MA4 California, USA -122.92 38.09 Coniferous forest CC 3 MA5 California, USA -122.90 38.10 Coastal woodland CC 3 MB4 California, USA -120.81 35.31 Coastal woodland CC 3 ME1 California, USA -123.77 39.66 Coniferous forest CC 3 ME2 California, USA -123.78 39.28 Coniferous forest CC 3 MO1 California, USA -121.89 36.57 Coastal woodland CC 2 1 MO3 California, USA -121.87 36.39 Coastal woodland CC 2 MO4 California, USA -121.95 36.52 Oak woodland CC 2 MO13 California, USA -121.60 36.08 Coniferous forest CC 3 SL9 California, USA -121.09 35.56 Coniferous forest CC 3 SL10 California, USA -121.19 35.64 Coniferous forest CC 3 SM California, USA -118.91 34.07 Coastal woodland CC 3 SN1 California, USA -122.39 37.36 Coastal woodland CC 3 SO1 California, USA -123.31 38.56 Coniferous forest CC 3 SRI5 California, USA -120.06 34.01 Coastal woodland CC 2 CA1 California, USA -120.50 38.27 Oak woodland CN 3 CA2 California, USA -120.63 38.05 Oak woodland CN 3 CL1 California, USA -121.71 37.13 Oak woodland CN 3 CL2 California, USA -121.75 37.36 Oak woodland CN 3 CL3 California, USA -121.67 37.32 Oak woodland CN 3 ME3 California, USA -123.01 38.83 Oak woodland CN 3 ME4 California, USA -123.22 39.08 Oak woodland CN 3 MO7 California, USA -121.55 36.39 Oak woodland CN 3 MO8 California, USA -121.44 36.27 Oak woodland CN 3 MO10 California, USA -121.61 36.42 Oak woodland CN 3 MR1 California, USA -121.20 37.06 Oak woodland CN 3 NA1 California, USA -122.28 38.78 Oak woodland CN 3 NA2 California, USA -122.15 38.49 Oak woodland CN 3 SO4 California, USA -122.50 38.44 Oak woodland CN 3 SB2 California, USA -121.46 36.79 Oak woodland CN 3 SB3 California, USA -121.14 36.50 Oak woodland CN 3 BR1 California, USA -120.28 34.73 Oak woodland CS 3 MO5 California, USA -121.08 36.04 Oak woodland CS 3 MO6 California, USA -121.31 36.06 Oak woodland CS 3 MO9 California, USA -121.15 36.10 Oak woodland CS 3 MO11 California, USA -121.34 35.98 Oak woodland CS 3 MO12 California, USA -121.12 35.94 Oak woodland CS 3 SD California, USA -116.77 33.24 Coastal woodland CS 3 SL5 California, USA -120.86 35.53 Oak woodland CS 2 SL6 California, USA -120.92 35.79 Oak woodland CS 4 SL7 California, USA -120.93 35.67 Oak woodland CS 3 SL8 California, USA -120.55 35.66 Oak woodland CS 3 OR11 Oregon, USA -123.96 45.15 Coniferous forest PN 3 OR14 Oregon, USA -124.43 43.09 Coniferous forest PN 3 2 OR16 Oregon, USA -123.44 43.11 Broad-leaved forest PN 4 OR17 Oregon, USA -123.22 43.80 Broad-leaved forest PN 5 OR18 Oregon, USA -123.29 44.36 Broad-leaved forest PN 5 HU1 California, USA -124.16 41.13 Coniferous forest PN 3 MI1 California, USA -123.30 48.86 Oak woodland PN 3 QC2 British Columbia, Canada -131.99 54.03 Coniferous forest PN 3 QC3 British Columbia, Canada -131.93 53.56 Coniferous forest PN 3 QC5 British Columbia, Canada -131.70 53.13 Coniferous forest PN 3 VI1 British Columbia, Canada -125.76 49.07 Coniferous forest PN 3 VI3 British Columbia, Canada -123.51 48.70 Broad-leaved forest PN 3 VI4 British Columbia, Canada -124.09 48.43 Coniferous forest PN 3 WA1 Washington, USA -122.83 47.64 Broad-leaved forest PN 3 WA2 Washington, USA -123.03 48.05 Coniferous forest PN 3 WA5 Washington, USA -124.41 47.71 Coniferous forest PN 3 3 Table S2 Number and position of recombination events of each DNA region used in migration analyses. Taxon R. menziesii DNA region Number Position bet efa gpd uid 1 2 1 1 620-810 2-192; 297-486 389-586 1-343 ITS rbcL 2 1 1-240; 385-569 543-594 T. decolorans 4 Table S3 Haplotype distribution in each sampled localities of the lichen-forming fungus R. menziesii (RHap1-RHap151) and the green algae photobiont T. decolorans (THap1-THap58). Ecoregions Localities Photobionts Mycobionts BC BA13 THap1 RHap10, RHap11 BC BA14 THap1 RHap12, RHap13, RHap14 BI BA10 THap2 RHap1, RHap2, RHap3 BI BA12 THap5 RHap1, RHap8, RHap9 BI BA11 THap2, THap3, THap4 RHap1, RHap4, RHap5, RHap6, RHap7 BI BA15 THap6, THap7 RHap15 BI BA2 THap7 RHap16, RHap17, RHap18, RHap19 BI BA3 THap7, THap8, THap9 RHap1, RHap2, RHap20 BI BA4 THap7, THap10, THap11, THap12 RHap21, RHap22, RHap23, RHap24, RHap25 BI BA7 THap1, THap13 RHap8, RHap22 BI BA8 THap14, THap15, THap16 RHap1, RHap26, RHap27 BI BA9 THap2, THap4, THap17 RHap1, RHap5, RHap28 CC MA1 THap1 RHap47, RHap48 CC MA2 THap1, THap18 RHap49, RHap50 CC MA3 THap1 RHap51, RHap52 CC MA4 THap1 RHap53, RHap54, RHap55 CC MA5 THap1 RHap50, RHap56, RHap57 CC MB4 THap1, THap19 RHap58, RHap59, RHap60 CC ME1 THap1 RHap61, RHap62, RHap63 CC ME2 THap1 RHap64, RHap65, RHap66 CC MO1 THap1 RHap46, RHap76 CC MO13 THap1 RHap46, RHap83, RHap84 CC MO3 THap20, THap21 RHap85, RHap86 CC MO4 THap1 RHap87, RHap88 CC SL9 THap1, THap22 RHap135, RHap136, RHap137 CC SL10 THap1, THap23, THap24 RHap124, RHap125, RHap126 CC SM THap11, THap25 RHap42, RHap138 CC SN1 THap1, THap26 RHap139, RHap140, RHap141 CC SO1 THap1, THap19 RHap46, RHap49, RHap142 CC SRI5 THap1 RHap46, RHap144 CN CA1 THap27, THap28, THap29 RHap32, RHap33, RHap34 CN CA2 THap30 RHap35 CN CL1 THap30, THap31, THap32 RHap36, RHap37, RHap38 CN CL2 THap30, THap33, THap34 RHap29, RHap39, RHap40 5 CN CL3 THap27, THap30, THap33 RHap41, RHap42, RHap43 CN ME3 THap35, THap36, THap37 RHap67, RHap68, RHap69 CN ME4 THap35, THap38 RHap41, RHap70, RHap71 CN MO10 THap36, THap38 RHap38, RHap74, RHap75 CN MO7 THap30, THap33, THap38 RHap36, RHap68, RHap92 CN MO8 THap30, THap39, THap40 RHap93, RHap94, RHap95 CN MR1 THap34, THap41 RHap41, RHap43 CN NA1 THap27, THap38 RHap34, RHap98, RHap99, RHap100 CN NA2 THap35, THap38 RHap35, RHap41, RHap92 CN SO4 THap25, THap27, THap28 RHap41, RHap143 CN SB2 THap33, THap36, THap38 RHap92, 118, RHap119 CN SB3 THap26, THap42, THap43 RHap29, RHap43, RHap120 CS BR1 THap43, THap44, THap45 RHap29, RHap30, RHap31, RHap38 CS MO5 THap38, THap47, THap48 RHap33, RHap43, RHap89 CS MO6 THap30, THap35, THap46 RHap68, RHap90, RHap91 CS MO9 THap28, THap30, THap43 RHap41, RHap96, RHap97 CS MO11 THap38, THap46 RHap77, RHap78, RHap79 CS MO12 THap30, THap35, THap38 RHap80, RHap81, RHap82 CS SD THap30, THap49, THap50 RHap121, RHap122, RHap123 CS SL5 THap25 RHap127, RHap128 CS SL6 THap30, THap35, THap38, THap46 RHap77, RHap129, RHap130, RHap131 CS SL7 THap30, THap35, THap38 RHap33, RHap132, RHap133 CS SL8 THap26, THap38 RHap42, RHap43, RHap134 PN HU1 THap1, THap19 RHap44, RHap45, RHap46 PN MI1 THap31, THap53 RHap72, RHap73 PN OR11 THap19, THap51 RHap46, RHap53 PN OR14 THap1, THap19 RHap61, RHap101 PN OR16 THap38 RHap102, RHap103, RHap104 PN OR17 THap31, THap35, THap52 RHap56, RHap105, RHap106, RHap107 PN OR18 THap28, THap30, THap33, THap36 RHap108, RHap109, RHap110, RHap111 PN QC2 THap35, THap54 RHap112, RHap113, RHap114 PN QC3 THap54 RHap113, RHap115, RHap116 PN QC5 THap35 RHap114, RHap117 PN VI1 THap1 RHap145 PN VI3 THap26 RHap146, RHap147, RHap148 PN VI4 THap35, THap56 RHap46, RHap149 PN WA1 THap53 RHap72, RHap150 PN WA2 THap35, THap57, THap58 RHap56, RHap151 PN WA5 THap35 RHap53 6 Table S4 Co-divergence analyses of congruence between mycobionts and photobionts. Boldface entries show localities that contributed significantly to the overall congruence between mycobionts and photobionts at P< 0.01 level, based on both the F1 and F2 tests. Ecoregions BC BC BI BI BI BI BI BI BI BI BI BI BI CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CN CN CN CN Localities ParaFitLink1 ParaFitLink2 Fungi Algae F1 P1 F2 P2 RBA13 RBA14 RBA10 RBA11 RBA12 RBA15 RBA2 RBA3 RBA4 RBA7 RBA8 RBA9 RMA1 RMA2 RMA3 RMA4 RMA5 RMB4 RME1 RME2 RMO1 RMO13 RMO3 RMO4 RSL9 RSL10 RSM RSN1 RSO1 RSRI5 RCA1 RCA2 RCL1 RCL2 RCL3 TBA13 TBA14 TBA10 TBA11 TBA12 TBA15 TBA2 TBA3 TBA4 TBA7 TBA8 TBA9 TMA1 TMA2 TMA3 TMA4 TMA5 TMB4 TME1 TME2 TMO1 TMO13 TMO3 TMO4 TSL9 TSL10 TSM TSN1 TSO1 TSRI5 TCA1 TCA2 TCL1 TCL2 TCL3 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 >-0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 >-0.000005 <0.000005 <0.000005 >-0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 0.02100 0.03370 0.00010 0.00010 0.07431 0.00020 0.00010 0.00010 0.00850 0.98760 0.00010 0.00010 0.00860 0.00470 0.00630 0.00550 0.00560 0.00360 0.00530 0.00800 0.07241 0.00660 0.61466 0.00680 0.00390 0.98250 0.06821 0.00980 0.00580 0.00580 0.02610 0.02830 0.04170 0.02510 0.02610 0.00456 0.00396 0.04987 0.05446 0.00483 0.02732 0.05348 0.05207 0.01540 -0.00518 0.05270 0.05123 0.00227 0.00265 0.00244 0.00202 0.00256 0.00219 0.00192 0.00232 0.00060 0.00174 -0.00007 0.00132 0.00223 -0.00106 0.00044 0.00158 0.00188 0.00132 0.00149 0.00103 0.00131 0.00128 0.00074 0.01160 0.01950 0.00010 0.00010 0.05201 0.00020 0.00010 0.00010 0.00460 0.99350 0.00010 0.00010 0.00430 0.00140 0.00220 0.00190 0.00240 0.00120 0.00250 0.00330 0.04840 0.00240 0.63206 0.00330 0.00170 0.98790 0.04690 0.00450 0.00180 0.00240 0.01550 0.01660 0.02810 0.01520 0.01710 7 CN CN CN CN CN CN CN CN CN CN CN CN CS CS CS CS CS CS CS CS CS CS RME3 RME4 RMO10 RMO7 RMO8 RMR1 RNA1 RNA2 RSO4 RSB2 RSB3 RBR1 RMO5 RMO6 RMO9 RMO11 RMO12 RSD RSL5 RSL6 RSL7 RSL8 TME3 TME4 TMO10 TMO7 TMO8 TMR1 TNA1 TNA2 TSO4 TSB2 TSB3 TBR1 TMO5 TMO6 TMO9 TMO11 TMO12 TSD TSL5 TSL6 TSL7 TSL8 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 >-0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 <0.000005 0.02910 0.01960 0.11751 0.02280 0.03140 0.95520 0.08661 0.02420 0.07831 0.04930 0.03980 0.09161 0.01210 0.02000 0.02140 0.11521 0.04480 0.04110 0.02150 0.02850 0.07631 0.02360 0.00149 0.00137 0.00061 0.00146 0.00208 -0.00068 0.00058 0.00151 0.00047 0.00175 0.00135 0.00086 0.00141 0.00147 0.00179 0.00069 0.00126 0.00134 0.00322 0.00168 0.00100 0.00103 0.01800 0.01170 0.08261 0.01410 0.01980 0.97090 0.05921 0.01460 0.05351 0.03090 0.02530 0.06441 0.00530 0.01190 0.01360 0.08141 0.03220 0.02760 0.01430 0.01760 0.05481 0.01470 CS RHU1 THU1 <0.000005 0.00350 0.00239 0.00110 PN RMI1 TMI1 <0.000005 0.22672 0.00040 0.18222 PN ROR11 TOR11 <0.000005 0.01800 0.00116 0.01170 PN ROR14 TOR14 <0.000005 0.00570 0.00235 0.00220 PN ROR16 TOR16 <0.000005 0.02430 0.00148 0.01390 PN ROR17 TOR17 <0.000005 0.06411 0.00100 0.04220 PN ROR18 TOR18 <0.000005 0.06561 0.00102 0.04310 PN RQC2 TQC2 <0.000005 0.02540 0.00130 0.01550 PN RQC3 TQC3 <0.000005 0.02700 0.00090 0.01650 PN RQC5 TQC5 <0.000005 0.03150 0.00132 0.02130 PN RVI1 TVI1 <0.000005 0.00640 0.00201 0.00290 PN RVI3 TVI3 <0.000005 0.09471 0.00090 0.06281 PN RVI4 TVI4 <0.000005 0.00760 0.00152 0.00290 PN RWA1 TWA1 <0.000005 0.05191 0.00120 0.03400 PN RWA2 TWA2 <0.000005 0.00410 0.00258 0.00150 PN RWA5 TWA5 <0.000005 0.07611 0.00067 0.05011 8 Appendix S2 Details of phylogenetic tree analyses and supplementary figures. Methods To test whether the symbionts showed parallel phylogenies, we first performed a Bayesian phylogenetic analysis of both mycobiont and photobiont sequence datasets. The best-fit models (photobiont: HKY + I + G; mycobiont: GTR + I + G) for Bayesian analyses were selected according to Akaike Information Criterion (AIC; Akaike, 1974) using MrModeltest 2.3 (Nylander, 2004) in conjunction with PAUP 4.0 (Swofford, 1998) to generate model scores. Bayesian Markov Chain Monte Carlo (BMCMC) estimates of phylogenies were inferred using MrBayes 3.1.2 (Huelsenbeck & Ronquist, 2005). Bayesian analysis was performed for 10,000,000 generations. Two simultaneous chains were run sampling every 1,000 generations. The first 10% of trees were discarded and > 50% posterior probability consensus trees were calculated from the remaining trees. Bayesian trees were annotated in TreeAnnotator 1.6.0 (Rambaut & Drummond, 2009) and edited in FigTree 1.3.1 (Rambaut & Drummond, 2010). We rooted the photobiont tree using T. jamesii as an outgroup (Werth & Sork, 2014), and we rooted the mycobiont tree using R. sonorensis (Sork & Werth, 2014). Results Bayesian analysis of the 58 two-locus haplotypes of T. decolorans using T. jamesii as outgroup resulted in three main haplotype groups (Group I-III; Fig. S1), with all the haplotypes from two coastal ecoregions of PN and CC occurring in the Group I cluster. Group I also included several haplotypes from two inland California ecoregions of CN and CS. Four haplotypes (THap6, 10-12) of BI formed a subgroup (PP = 1.0) in Group I. Only one haplotype (THap13) of BC was included in this group. The Bayesian posterior probability (PP) of Group I was high (PP = 1.0). Most of the haplotypes from two inland California ecoregions of CS and CN tended to group together and formed the Group II; the Group III consisted of haplotypes only from the ecoregion of BI. The Bayesian tree based on 151 four-locus haplotypes of fungus R. menziesii 9 showed six main haplotype groups (Group A-F) and all the groups were supported by a high posterior probability (PP > 90%; Fig. S2): Group A consisted of haplotypes from two inland ecoregions of CS and CN; Group B consisted of several haplotypes from ecoregion CS; the Group C consisted of all the haplotypes from two coastal ecoregions of CC and PN; Group D consisted of the other haplotypes from the two inland California ecoregions of CS and CN; the Group E consisted of all the haplotypes from ecoregion BC, and the Group F consisted of all the haplotypes from ecoregion BI. References Akaike, H. (1974) A new look at the statistical model identification. IEEE Transactions on Automatic Control 19,716-723. Huelsenbeck, J.P. & Ronquist, F. (2005) Bayesian analysis of molecular evolution using MrBayes. Statistical Methods in Molecular Evolution (ed. by R. Nielsen), pp.183-226. Springer, New York, USA. Nylander, J.A.A. (2004) MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University. Rambaut, A. & Drummond, A.J. (2009) TreeAnnotator v1.5.3: MCMC output analysis. Available from http://beast.bio.ed.ac.uk/TreeAnnotator. Rambaut, A. & Drummond, A.J. (2010)) FigTree v1.3.1. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK. Available from http://tree.bio.ed.ac.uk/software/figtree/. Swofford, D.L. (1998) PAUP*: phylogenetic analysis using parsimony (*and other methods), version 4. Sinauer, Sunderland, Massachusetts, USA. 10 Fig. S1 Phylogenetic tree of the green algal photobiont (T. decolorans) haplotypes (THap1-THap58) estimated using Bayesian approach. Numbers associated with each branch indicate Bayesian posterior probabilities (branch supports of over 0.50 posterior probability are shown). The tree was rooted using the outgroup species T. jamesii. 11 Fig. S2 Phylogenetic tree of the lichen-forming fungus R. menziesii haplotypes (RHap1-RHap151) estimated using Bayesian approach. Numbers associated with each branch indicate Bayesian posterior probabilities (branch supports of over 0.50 posterior probability are shown). Tree was rooted using the outgroup species R. sonorensis. 12
