1 Supplementary Information Figure S1 Plots of K (DeltaK) versus K in STRUCTURE analyses. K calculated according to Evanno et al. (2005) and based on 10 replicates for each value of K. (a) All samples of Pseudopanax ferox (b) Samples from cluster 1 (northern North Island and northern South Island) (c) Samples from cluster 2 (southern North Island and eastern and southern South Island. 2 Fig. S2 Representative STRUCTURE results for Pseudopanax ferox. (a) All samples with K = 2, partitioning populations from the northern North Island and northern South Island (= Cluster 1) from those in the southern North Island and eastern and southern South Island (= Cluster 2). (b) Cluster 1 with K = 2, partitioning populations from the northern North Island (= Cluster 1a) from those in the northern South Island (= Cluster 1b). (c) Cluster 2 with K = 2, partitioning populations from the southern North Island (= Cluster 2a) from those in the eastern and southern South Island (= Cluster 2b). 3 Fig. S3 Representative STRUCTURE result for Pseudopanax ferox samples from cluster 1 (northern North Island plus northern South Island) with K = 5. Fig. S4 Representative STRUCTURE result for Pseudopanax ferox samples from cluster 2 (southern North Island plus eastern and southern South Island) with K = 5. 4 Table S1 Nuclear heterozygosities and FST estimates for other tree species. Updated from Muller et al. (2009). Species Metrosideros boninensis Santalum austrocaledonicum Pterocapus officinalis Pseudopanax ferox Santalum insulare Grevillea macleayana Symphonia globulifera Caryocar brasiliense Swietenia macrophylla Swietenia macrophylla Vouacapoua americana Fraxinus excelsior Melaleuca alternifolia Betula maximowicziana Vitellaria paradoxa Prunus africana Picea abies Eugenia uniflora Fagus japonica Reference n HE per locus FST Kaneko et al. 2008 105 0.17-0.53 0.41 Bottin et al. 2005 431 0.03-0.74 0.33 Muller et al. 2009 202 0.24-0.59 0.29 This study 109 0.20-0.87 0.27 Lhuillier et al. 2006 162 0.27-0.56 0.23 England et al. 2002 130 0.42-0.53 0.22 Dick & Heuertz 2008 380 0.68-0.89 0.14 Collevatti et al. 2001 314 0.58-0.85 0.11 Novick et al. 2003 284 0.59-0.80 0.11 Lemes et al. 2003 194 0.75-0.81 0.10 Dutech et al. 2004 408 0.34-0.52 0.08 Heuertz et al. 2004 1069 0.43-0.98 0.08 Rossetto et al. 1999 500 0.52-0.85 0.07 Tsuda & Ide 2005 1014 0.04-0.63 0.06 Sanou et al. 2005 169 0.23-0.35 0.05 Farwig et al. 2008 110 0.76-0.82 0.03 Tollefsrud et al. 2009 1715 0.49-0.69 0.03 Ferreira-Ramos et al. 2008 84 0.82-0.83 0.03 Hiraoka & Tomaru 2009 545 0.63-0.68 0.02 References for Table S1 Bottin L, Verhaegen D, Tassin J, Olivier I, Vaillant A, Bouvet JM (2005) Genetic diversity and population structure of an insular tree, Santalum austrocaledonicum in New Caledonian archipelago. 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