FIGURE 1 in Speciation and secondary contact in a fossorial island endemic, the São Tomé caecilian

FIGURE 1 Schistometopum sampling on São Tomé Island. (a) Map shows distribution of genomic samples with the size of circles proportional to the number of individuals at that site. Individuals with at least 90% ancestry assigned to Schistometopum thomense (S. thomense) are shown in purple, 90% ancestry assigned to Schistometopum ephele (S. ephele) in green, and admixed individuals in orange. Site abbreviations are as follows: AA, Anselmo Andrade; BO, Bombaim; BS, Bom Sucesso; CN, Contador Valley North; CS, Contador Valley South; CV, Canavial; JA, Java + Abade; LB, Lemba River; ML, Rio Maria Luisa; ON, Obo National Park; PA, Porto Alegre; QI, Quisinda; RD, Rio d'Ouro; SF, Santa Fe; SL, Santa Luzia. The type locality of S. ephele (Água Izé, 400–700 m) is probably between the coastal community of Água Izé (indicated by black star) and Java. (b) Plot of ancestry coefficients estimated with ADMIXTURE version 1.3.0 (Alexander et al. (2009) for K = 2. Circles above the plot show the haplotype of each individual from the mitochondrial ND4 locus, and morphological assignment (yellow, unflecked = yellow; brown, flecked = grey). (c) ND4 haplotype network for new samples and previously published data (Stoelting et al., 2014) estimated in PopART (Leigh & Bryant, 2015). Twenty-six mutations separate the haplotype groups. (d) Principal component analysis (PCA) of single nucleotide polymorphism (SNP) data with individuals coloured according to their ancestry assignment from (b). Photo credits: A. Stanbridge