Table S1 Geographic characteristics of the populations sampled and their respective voucher specimens. Pop, population. Pop Genus Species Country Major area Locality Coll. number Coll.date Collector Herba rium BRLU, LBV BRLU, LBV BRLU, LBV BRLU, LBV BRLU, LBV BRLU, LBV BRLU, LBV BRLU, LBV BRLU, LBV 1 Haumania danckelmaniana Gabon Estuaire Kingele 550 16.12.2008 Ley, A.C. 1 Haumania danckelmaniana Gabon Estuaire Lonmin 559 17.12.2008 Ley, A.C. 1 Haumania liebrechtsiana Gabon Estuaire Lonmin 560 17.12.2008 Ley, A.C. 1 Haumania liebrechtsiana Gabon Estuaire Lonmin 575 17.12.2008 Ley, A.C. 2 Haumania danckelmaniana Gabon Woleu-Ntem 439 19.11.2008 Ley, A.C. 2 Haumania Gabon Woleu-Ntem 438 19.11.2008 Ley, A.C. 3 Haumania danckelmaniana Gabon 484 04.12.2008 Ley, A.C. 3 Haumania Gabon 485 04.12.2008 Ley, A.C. 4 Haumania danckelmaniana Gabon Ivindo 477 27.11.2008 Ley, A.C. 4 Haumania Gabon Ivindo, parking ACL1203 27.11.2008 Ley, A.C. BRLU 5 Haumania danckelmaniana Gabon Ngounié Mandji ACL4182 13.11.2008 Ley, A.C. BRLU 5 Haumania Gabon Ngounié Mandji 429b 13.11.2008 Ley, A.C. 6 Haumania danckelmanniana Gabon Ngounié Doussala, mountains 406 04.11.2008 Ley, A.C. 6 Haumania Gabon Ngounié Doussala, along river 398 04.11.2008 Ley, A.C. 7 Haumania danckelmaniana Cameroun Littoral near Edea, on road to Yaounde 665 17.01.2009 Ley, A.C. 7 Haumania danckelmaniana Cameroun Littoral near Edea, on road to Douala 671 17.01.2009 Ley, A.C. liebrechtsiana liebrechtsiana liebrechtsiana liebrechtsiana liebrechtsiana OgoouéIvindo OgoouéIvindo OgoouéIvindo OgoouéIvindo East Mont de Cristal, Mikongo, chantier du Rougier Gabon East Mont de Cristal, Mikongo, chantier du Rougier Gabon Matote, road Makokou to Mekambo Matote, road Makokou to Mekambo BRLU, LBV BRLU, LBV BRLU, LBV BRLU, LBV BRLU, Lat/Long N0° 27.390‘ E10° 17.287 N0° 27.097‘ E10° 10.758 N0° 27.097‘ E10° 10.759 N0° 27.097‘ E10° 10.774 N0° 35.815‘ E11° 12.395 N0° 35.815‘ E11° 12.394 N0° 50.820‘ E13° 30.947 N0° 50.820‘ E13° 30.948 S0° 10.531‘ E12° 32.228 S0° 10.092’ E12° 29.988 S1° 40.842’ E10° 34.440 S1° 41.528‘ E10° 21.426 S2° 19.956‘ E10° 36.548 S2° 19.601‘ E10° 35.338 N3° 47.752‘ E10° 12.116´ N3° 55.860´ LBV BRLU, LBV BRLU, LBV BRLU, LBV BRLU, LBV BRLU, LBV BRLU, LBV BRLU, LBV 8 Haumania danckelmaniana Cameroun Centre road from Yaounde to Edea 649 16.01.2009 Ley, A.C. 9 Haumania danckelmaniana Cameroun Sud Bibondi Mountain; 15km from Lolodorf 755 06.02.2009 Ley, A.C. 9 Haumania danckelmaniana Cameroun Sud Ngovayang 777 07.02.2009 Ley, A.C. 10 Haumania danckelmaniana Cameroun Sud Mt. Elefant 688b 20.01.2009 Ley, A.C. 11 Haumania danckelmaniana Cameroun Est near Somalomo 617 08.01.2009 Ley, A.C. 12 Haumania danckelmaniana Gabon Woleu-Ntem Abang Medomou, road Oyem to Bitam 529 11.12.2008 Ley, A.C. 12 Haumania danckelmaniana Gabon Woleu-Ntem Bisok, road Oyem to Medouneu 543 12.12.2008 Ley, A.C. 13 Haumania danckelmaniana Sangha near Pokola 19.03.2009 Gillet, J.-F. ULB 13 Haumania Sangha near Pokola 23.03.2009 Gillet, J.-F. BRLU 14 Haumania danckelmaniana Gabon Estuaire Malibu 6 29.10.2004 Ley, A.C. 14 Haumania danckelmaniana Gabon Estuaire Sibang 27 30.10.2004 Ley, A.C. 15 Haumania danckelmaniana Gabon Makokou 162 08.01.2005 Ley, A.C. 16 Haumania danckelmaniana Gabon Belinga 495 07.12.2008 Ley, A.C. 17 Haumania danckelmaniana Gabon Bonzadie, 5km on road to Belinga 511 08.12.2008 Ley, A.C. 18 Haumania danckelmaniana Gabon 512 08.12.2008 Ley, A.C. 18 Haumania liebrechtsiana Gabon Ivindo 513 08.12.2008 Ley, A.C. 19 Haumania liebrechtsiana Rep. of the Congo CuvetteOuest 96/1124 (ACL4540) 1996 Lejoly, J. liebrechtsiana Rep. of the Congo Rep. of the Congo OgoouéIvindo OgoouéIvindo OgoouéIvindo OgoouéIvindo Bakwaka, road Makokou to Franceville Bakwaka, road Makokou to Franceville Odzala, Andzoyi JFG 62 (ACL0846) JFG99 (ACL1216) E10° 4.219´ N3° 46.534´ E11° 10.169´ N3° 18.181‘ E10° 38.969‘ N3° 13.694‘ E10° 36.409‘ N2° 48.251´ E10° 2.103´ N3° 22.528´ E12° 44.009´ N1° 45.697‘ E11° 37.171‘ N1° 13.103‘ E11° 35.319‘ N2° 09.024’ E16° 10.626’ N0° 12.30´ E16° 48.400´ WAG, N0° 20.340‘ E 9° LBV 12.900‘ WAG, N0° 15.000‘ E 9° LBV 17.640‘ WAG, N0° 18.410‘ LBV E12° 28.914‘ BRLU, N1° 05.312‘ LBV E13° 11.998‘ BRLU, N0 °46.673‘ LBV E13° 08.227‘ BRLU, N0° 06.093‘ LBV E13° 42.488‘ BRLU, N0° 06.093‘ LBV E13° 42.488‘ N1° 39.960’ BR E13° 28.998’ 20 Haumania danckelmaniana Gabon Ogooué-Lolo near Lastourville OHADN19 78 (ACL4435) 10.5.2009 Hardy, O.J. 21 Haumania danckelmaniana Cameroun Sud Campo 685 19.01.2009 Ley, A.C. 22 Haumania danckelmaniana Gabon Ogooué-Lolo Dibouka 67 20.11.2004 Ley, A.C. 23 Haumania danckelmaniana Gabon Ngounié Ndenga, road Mbigou to Lebamba 421 10.11.2008 Ley, A.C. 24 Haumania liebrechtsiana Gabon Estuaire Monts de Cristal, Lonmin 52 13.11.2004 Ley, A.C. 24 Haumania liebrechtsiana Gabon Estuaire Monts de Cristal, Lonmin 53 13.11.2004 Ley, A.C. 25 Haumania liebrechtsiana Gabon MoyenOgooué west of Ndjole, mountains on road towards Libreville 461 25.11.2008 Ley, A.C. 26 Haumania liebrechtsiana Gabon Lope 101 03.12.2004 Ley, A.C. 26 Haumania liebrechtsiana Gabon Lope 148 30.12.2004 Ley, A.C. 26 Haumania liebrechtsiana Gabon Lope 101 03.12.2004 Ley, A.C. 27 Haumania liebrechtsiana Gabon Mikongo 121 09.12.2004 Ley, A.C. 27 Haumania liebrechtsiana Gabon Mikongo 108 06.12.2004 Ley, A.C. 27 Haumania liebrechtsiana Gabon Mikongo 122 09.12.2004 Ley, A.C. 28 Haumania liebrechtsiana Gabon 370 30.10.2008 Ley, A.C. 28 Haumania liebrechtsiana Gabon 433 14.11.2008 Ley, A.C. 29 Haumania liebrechtsiana Gabon 330 13.10.2008 Ley, A.C. OgoouéIvindo OgoouéIvindo OgoouéIvindo OgoouéIvindo OgoouéIvindo OgoouéIvindo MoyenOgooué MoyenOgooué Lambarene, near Albert Schweitzer hospital Mitone, village north of Lambarene Ngounié Ikobey ULB S0° 49.074’ E13° 04.494’ BRLU, LBV WAG, LBV BRLU, LBV WAG, LBV WAG, LBV BRLU, LBV N2° 43.900´ E 9° 52.465´ S1° 11.316‘ E12° 07.728‘ S1° 56.609‘ E11° 46.964‘ N0° 11.718‘ E10° 33.300‘ N0° 11.718‘ E10° 33.300‘ S0° 09.191‘ E10° 44.393‘ WAG, LBV WAG, LBV WAG, LBV S0° 0.1287‘ E11° 21.018‘ S3° 14.778‘ E10° 24.666‘ S0° 07.722‘ E11° 21.018‘ WAG, LBV WAG, LBV WAG, LBV BRLU, LBV BRLU, LBV BRLU, LBV S0° 10.968‘ E11° 25.272‘ S0° 10.962‘ E11° 25.290‘ S0° 10.968‘ E11° 25.272‘ S0° 40.288‘ E10° 13.578‘ S0° 37.231‘ E10° 13.970‘ S1° 03.632‘ E10° 59.893‘ 29 Haumania liebrechtsiana Gabon Ngounié 29 Haumania liebrechtsiana Gabon Ngounié 30 Haumania liebrechtsiana Gabon Ngounié 31 Haumania liebrechtsiana Gabon 31 Haumania liebrechtsiana 32 Haumania liebrechtsiana 33 Haumania danckelmaniana 34 Haumania 35 36 Haumania Haumania WCS camp at the border to Waka National Park Makoko, pygmee village, on path to river BRLU, S1° 07.554‘ LBV E11° 08.109‘ BRLU, S1° 01.759‘ LBV E11° 17.109‘ BRLU, S1° 50.257‘ LBV E11° 02.951‘ BRLU, S2° 33.419‘ LBV E10° 43.957‘ BRLU, S2° 33.419‘ LBV E10° 43.957‘ LBV, S3° 41.05’ E10° WAG 68.51’ 339 13.10.2008 Ley, A.C. 362 23.10.2008 Ley, A.C. Mouila 379 31.10.2008 Ley, A.C. Nyanga Mourindi, along river 388 02.11.2008 Ley, A.C. Gabon Nyanga Mourindi, along river 388 02.11.2008 Ley, A.C. Gabon Nyanga Mayumba 148 30.12.2004 Ley, A.C. Gabon OgoouéIvindo Melondomiole ACL0702 08.12.2008 Ley, A.C. BRLU N0 °13.335’ E13° 30.061 liebrechtsiana Rep. of the Congo Sangha ACL0846/J FG 62 19.03.2009 Gillet, J.-F. BRLU N2° 9.028´ E16° 10.630´ liebrechtsiana Democratic Rep. of Congo 2005/06 G. Hohmann BRLU S2° 7.8´, E21° 55.2´ 07.05.2010 Boyekole Ebale Botany Team BR, YBI N0° 49.71´, E24° 19.58´ leonardiana Democratic Rep. of Congo Bandundu Orientale Salonga village Yafake near Yangambi ACL4659 BEB250 Table S2 Details on the 26 populations of Haumania danckelmaniana and H. liebrechtsiana collected for AFLP studies in tropical central Africa. ID Pop., population ID corresponds with IDs in Fig. 5 and Table S1 ; N, number; AFLP mark., AFLP markers; PPB, percentage of polymorphic markers; Nrare, number of rare markers per population and primer pair. H. danckelmaniana N (AFLP frag.) ID Pop. PPB (%) N(indiv.) H. liebrechtsiana N(rare) MseI(CAC) N (indiv.) N (AFLP frag.) PPB (%) MseI(CAG) N(rare) MseI(CAC) MseI(CAG) 1 5 26 26.92 1 2 4 21 16.67 1 0 2 8 36 35.9 4 3 19 39 44.87 4 2 3 12 39 44.87 5 4 16 36 35.9 4 4 1 25 na 3 2 5 8 36 38.46 2 8 6 34 32.05 3 3 6 5 23 19.23 0 4 7 32 24.36 4 4 8 7 34 37.18 3 0 0 8 0 37 39.74 4 2 9 7 41 46.15 1 9 0 10 7 30 24.36 4 0 0 11 8 36 43.59 5 4 0 12 7 26 21.79 2 2 0 13 5 31 32.05 3 2 0 14 10 53.85 6 9 0 15 1 49 10 (only MseI(CAG)) na 2 ? 0 16 7 30 23.08 4 4 0 17 6 30 26.92 3 2 0 18 6 28 24.36 1 1 1 6 (only MseI(CAG)) na 1 0 20 6 33 28.21 3 5 0 22 1 6 (only MseI(CAG)) na ? 3 0 23 3 28 21.79 4 0 0 25 0 22 23.08 0 0 5 0 7 4 25 0 29 1 7 31 28.21 2 2 15 46 51.28 6 9 30 0 4 28 21.79 3 1 31 0 4 28 17.95 4 1 32 0 1 18 na 0 0 33 4 25 24.36 0 3 0 34 7 31 25.64 4 2 0 147 14 na 0 1 80 Table S6 Statistics of AFLP peak selection: number of peaks eliminated among the 113,836 peaks detected in 363 samples by PeakScanner through tinyFLP (Arthofer 2010) given a specific setting of criteria applied to two primer pairs (EcoRI-MseI (CAC), EcoRI-MseI (CAG)) on a combined dataset of Haumania danckelmaniana and H. liebrechtsiana. Parameter settings: minimum peak height, 400; maximum peak width, 2; minimum size, 40bp; maximum size, 500bp; size tolerance range, 0.8; minimum peak-peak distance, 1; peak height difference, 0; minimum frequency, 0.1; maximum frequency, 99.9. n, number of deselected peaks; height, mean height(intensity) of peaks; width, mean width of peaks in base pairs. parameter setting n peak height below cutoff (<400) peak width above cutoff (>2bp) peak size too small (>40bp) peak size too big (> 500bp) no histogram match monomorphic markers excluded by tinyFLP EcoRI-MseI (CAC) height width (mean) (mean) EcoRI-MseI (CAG) height width (mean) (mean) n 31474 152.938 0.536 35086 152.258 0.522 64 3073.766 2.235 22 6644.5 2.134 3021 1718.067 0.675 4090 2391.54 0.578 253 1117.648 0.818 58 1092.603 0.837 64 6680.406 0.596 304 2307.658 0.502 1 (190.8bp) 2 (91bp, 164.8bp) Table S7 Quantitative characteristics of final peak selection from AFLP fingerprints in Haumania listed separately by species (H. danckelmaniana and H. liebrechtsiana) and primer pair (EcoRIMseI (CAC), EcoRI-MseI (CAG)). H. danckelmaniana H. liebrechtsiana 147 80 EcoRI-MseI (CAC) 119 66 EcoRI-MseI (CAG) 133 71 Number of markers present 79 78 EcoRI-MseI (CAC) 39 39 EcoRI-MseI (CAG) 40 39 Number of markers excluding markers private for one individual in replicate dataset 58 65 H² < 0.25 12 23 0.25 < H² < 0.5 17 16 0.5 < H² < 0.75 19 17 H² > 0.75 10 9 significant H² 44 42 Private markers per species 8 7 EcoRI-MseI (CAC) 5 5 EcoRI-MseI (CAG) 3 2 EcoRI-MseI (CAC) 0 0 EcoRI-MseI (CAG) 0 3 (108, 175, 292, bp) EcoRI-MseI (CAC) 22 (47.8%) 25 (54.3%) EcoRI-MseI (CAG) 24 (52.2%) 20 (43.5%) 12.28 ± 2.84 11.89 ± 2.45 Number of samples Number of markers present in > 70% of individuals Number of rare markers (< 10% of individuals) Average number of markers per individual EcoRI-MseI (CAC) 10.76 ± 3.30 11.87 ± 3.57 EcoRI-MseI (CAC) 1.35 ± 1.29 1.08 ±1.16 EcoRI-MseI (CAG) 1.15 ± 1.51 0.80 ± 1.18 EcoRI-MseI (CAG) Average number of rare markers per individual Table S8 Statistics of the retrieval of significantly (p < 0.05) heritable markers from AFLP fingerprints depending on the number of replicates used; exemplified on randomly selected subsets of replicates (only one replicates per individual considered) from the Haumania dataset of this study using two primer pairs (EcoRI-MseI (CAC), EcoRI-MseI (CAG)). Grey, statistics based on entire data set used in this study (including various numbers of replicates per individual). number of replicates 72 60 50 40 30 25 20 number of markers with signif. H² 86 79 81 73 57 52 51 H² min signif. 0.20 0.29 0.34 0.42 0.42 0.42 0.49 H² max nonsignif. 0.30 0.48 0.48 0.48 0.66 0.66 0.66 Table S9 Comparison of the average slope (± standard errors by jackknifing over loci) of kinshipdistance curves (i.e. mean rate of decrease of kinship coefficients per ln(distance)) within and among species based on datasets including AFLP markers with different ranges of heritability (H2). Estimators of kinship coefficient corrected (F’(d)) or uncorrected (F(d)) for the limited heritability of markers were computed in SPAGeDi 1.4 (Hardy & Vekemans 2002). H. danckelmaniana: 147 individuals; H. liebrechtsiana: 80 individuals. N H. danckelmaniana (markers) Corrected estimators of kinship, F’(d) all markers 132 -0.0354 ± 0.0058 H2 < 0.25 35 -0.0433 ± 0.0154 0.25 < H2 < 0.5 33 -0.0408 ± 0.0108 2 0.5< H < 0.75 36 -0.0249 ± 0.0062 2 H > 0.75 19 -0.0490 ± 0.0162 H2 significant H² 86 -0.0352 significant H² excluding individuals 86 from southern populations Uncorrected estimators of kinship, F(d) all markers 132 -0.0177 2 H < 0.25 35 -0.0071 0.25 < H2 < 0.5 33 -0.0156 2 0.5< H < 0.75 36 -0.0155 2 H > 0.75 19 -0.0405 significant H² 86 -0.0201 ± 0.0061 ± 0.0031 ± 0.0017 ± 0.0044 ± 0.0039 ± 0.0133 ± 0.0038 H. liebrechtsiana among species -0.0266 -0.0128 -0.0128 -0.0351 -0.0277 ± 0.0057 ± 0.0340 ± 0.0074 ± 0.0101 ± 0.0105 -0.0150 0.0134 -0.0156 -0.0156 -0.0174 ± 0.0069 ± 0.0199 ± 0.0083 ± 0.0128 ± 0.0131 -0.0275 ± 0.0059 -0.0162 ± 0.0073 -0.0073 ± 0.0063 -0.0075 0.0003 -0.0058 -0.0096 -0.0145 -0.0092 ± 0.0035 ± 0.0025 ± 0.0032 ± 0.0080 ± 0.0108 ± 0.0042 -0.0132 -0.0015 -0.0049 -0.0217 -0.0232 -0.0158 ± 0.0030 ± 0.0038 ± 0.0028 ± 0.0064 ± 0.0084 ± 0.0035 Table S10 Number of NON-assigned individuals according to the minimal heritability (H²) of the AFLP markers included in the Bayesian clustering analysis applied on H. danckelmaniana and/or H. liebrechtsiana individuals for a number of clusters K ranging from 1 to 4. The software STRUCTURE was run under the admixture model with correlated allele frequencies and individuals were assigned to a cluster with an assignment threshold of 0.7. Each analysis being repeated 10 times, the range of the number of unassigned individuals as well as the standard errors of the DIC values are given. both species H² > 0 average DIC H. danckelmaniana H. liebrechtsiana total K=1 -10600.3 +/- 1.2 0 0 0 K=2 -9921.8 +/- 5.3 21 4-6 25-27 K=3 -9777.9 +/- 8.23 28-31 15-17 43-48 K=4 -9683.6 +/- 22.9 35-36 20-22 55-58 total significant H² average DIC H. danckelmaniana H. liebrechtsiana total K=1 -8461.3 +/- 0.8 0 0 0 K=2 -7816.0 +/- 3.2 14-15 2-3 17-18 K=3 -7716.2 +/- 19.9 15-39 4-10 20-46 K=4 -7524.3 +/- 8.6 27-29 9-10 36-39 total H² > 0.5 average DIC H. danckelmaniana H. liebrechtsiana total K=1 -5356.5 +/- 0.4 0 0 0 K=2 -4814.6 +/- 2.5 9-10 0 9-10 K=3 -4689.2 +/- 5.4 27-36 1 28-37 K=4 -4684.9 +/- 15.5 51-60 6-7 58-67 total H² > 0.75 average DIC H. danckelmaniana H. liebrechtsiana K=1 -1680.1 +/- 0.1 0 0 K=2 -1533.0 +/- 1.9 28-30 17-18 K=3 -1530.92 +/- 3.8 55-59 25-28 K=4 -1554.3 +/- 8.3 84-87 46-50 total 12 146 81 227 146 81 227 146 81 227 146 81 only H.danckelmaniana only H. liebrechtsiana total 0 44-47 81-86 H² > 0 K=1 K=2 K=3 total average DIC H. danckelmaniana -6485.8 +/- 0.8 0 -6468.1 +/- 62.4 19-147 -6222.2 +/- 10.8 56-66 146 significant H² average DIC H. danckelmaniana K=1 -5090.7 +/- 0.8 0 K=2 -4999.4 +/- 19.2 17-22 K=3 -4862.0 +/- 28.4 26-32 total H² > 0.5 K=1 K=3 total average DIC -3137.02 +/- 0.329 -3025.79 +/- 8.865 H. danckelmaniana 0 K=2 -3057.02 +/24.620 25-26 68-72 146 H² > 0.75 average DIC H. danckelmaniana K=1 -1005.36 +/- 0.171 0 K=2 -974.8 +/- 3.0 36-37 K=3 -967.3 +/- 3.8 85-93 total significant H² K=1 K=2 K=3 total average DIC H. liebrechtsiana -2666.5 +/- 1.5 0 -2634.2 +/- 12.9 77 -2706.3 +/- 62.5 72-80 81 13 130-135 227 146 146 Table S11 Number of individuals per population of H. danckelmaniana and H. liebrechtsiana assigned to K = 2 and K = 3 homogenous genetic clusters after Bayesian clustering implemented in STRUCTURE version 2.3.3 (Pritchard et al. 2000). ua, unassigned. K=2 K=3 H. danckelmaniana Pop ID 1 2 3 4 5 6 8 9 10 11 12 13 14 15 16 17 18 20 22 23 25 Cl1 4 9 10 16 1 4 7 6 7 8 7 5 9 1 6 6 5 4 1 2 Cl2 1 ua 2 1 6 1 1 1 1 1 1 1 1 Total 5 9 12 16 8 5 7 7 7 8 7 5 10 1 7 6 6 6 1 3 H. liebrechtsiana Cl1 Cl2 3 18 1 6 7 1 ua 1 1 H. danckelmaniana Total 4 19 1 6 7 Cl1 Cl2 3 9 10 15 1 1 1 Cl3 1 2 1 7 4 7 6 7 8 6 5 7 1 6 6 4 3 1 4 1 1 1 3 1 2 2 1 4 ua 1 2 H. liebrechtsiana Total 5 9 12 16 8 5 7 7 7 8 7 5 10 1 7 6 6 6 1 3 Cl1 3 18 1 5 6 1 1 1 4 14 Cl3 ua Total 1 4 1 19 1 6 7 1 4 26 28 29 30 31 32 33 4 34 7 Total 129 4 14 [%] 87.76 2.721 9.524 7 7 15 4 4 1 4 7 147 100 7 7 15 4 4 1 1 77 2 80 0.68 52.38 1.361 54.42 7 7 14 4 4 1 2 1.361 15 4 7 115 78.23 13 8.844 17 11.56 4 7 147 100 1 74 2 4 92.5 2.5 5 7 7 15 4 4 1 80 100