Phylogenetic analyses
An MJ haplotype network of COI was constructed using 108 sequences from the species’ range (Figure 2a). This network inferred three genetic groups, which were supported as distinct clades in the BI phylogenetic tree (Figure S1.2); the archipelagic, northern, and southern clades possibly reflected the three subspecies, L. c. superciliosus ,L. c. cristatus , and L. c. lucionensis , respectively (Figure 1c). In this network, a split between the southern and archipelagic clades was observed with nine mutational gaps. The northern clade was genetically most distant from the southern clade and its major haplotype (H1) was separated only by two mutational positions from one of the archipelagic major haplotypes. A similar structure was supported by the multi-locus network including both the mitochondrial and nuclear loci. Two individuals appeared to be intermediate between the southern and northern clusters (Figure 2b).
The southern clade was inferred as the basal lineage of the Brown Shrike by the BI tree (Figure S1.2). The first split occurred between the southern and the archipelagic/northern clades, around 0.80 [0.55, 1.10] million years ago (Mya), corresponding to the late Early to Middle Pleistocene while the northern and the archipelagic clade diverged around 0.32 [0.20, 0.47] Mya, during the Middle Pleistocene (numbers within square brackets indicate 95% highest posterior density).