Fig 1.
Map of the Philippines showing the limits to Pleistocene Aggregates Island Complexes PAIC (outline) and emerged land (shaded) based on Heaney (1985), study areas are in dark grey.
Dotted circles represent sampling localities (See S1 Table for details). Maps show distribution for each taxa, and the subspecies described (Dickinson et al. 1991). Dashed lines represent putative borders for currently accepted subspecies in Luzon.
Fig 2.
The set of hierarchical hypothesis tested in this study, with their geographic representation and phylogenetic expec.
Blue: Greater Luzon, Red: Greater Negros-Panay; green: Bicol Peninsula. Areas in light grey were not considered.
Fig 3.
Maximum Likelihood tree and median-joining haplotype network of the mtDNA dataset for R. cyaniceps.
Numbers in the branches refer to bootstrap support for the ML (before slash) and posterior probabilities from the BI (after slash). In the Median-joining haplotype network each ellipse represents a unique haplotype; different sizes and shading (a black shaded portion represents an individual sharing that haplotype) according to the frequency of occurrence. Each line connecting haplotypes represent a single mutational step. Numbers along lines indicate two or more steps separating haplotypes. Small open circles represent missing (unsampled) haplotypes.
Fig 4.
mtDNA phylogram of C. luzoniensis.
Numbers in the branches refer to bootstrap support for the ML (before slash) and posterior probabilities from the BI (after slash). Median-joining haplotype network for the mtDNA dataset. Arrows signal haplotypes found in the Mingan Mountains, eastern Luzon. See Fig 3 for details.
Fig 5.
mtDNA phylogram of P. cebuensis.
Numbers in the branches refer to bootstrap support for the ML (before slash) and posterior probabilities from the BI (after slash). Median-joining haplotype network for the mtDNA dataset. See Fig 3 for details.
Table 1.
Gene flow parameters estimated for the three lowland Passerines under study.
Above the diagonal in each species, are Fst (Nm); below the diagonal, values of Dxy (Da), where Dx indicates the average number of nucleotide substitutions per site between populations (percentage), and Da indicates the average number of net nucleotide substitutions per site between populations (Nei 1987).
Table 2.
Molecular diversity and tests of neutral evolution for the three species in this study, grouped by region and clade.
Fig 6.
Mismatch distributions for each focal taxon.
Dots represent the observed mismatch distributions, the continuous line represent the expected mismatch distributions. Due to sample size, no mismatch graph was calculated for P. cebuensis from the Zambales region in Greater Luzon PAIC. * N Luzon + Zambales for R. cyaniceps and P. cebuensis; Bicol Peninsula + Zambales in C. luzoniensis.
Table 3.
AMOVA values estimated for the lowland passerines under study.
Table 4.
Estimated population expansion dates for the three taxa in Luzon Island.
Values are given for subpopulations in either NC Luzon (R. cyaniceps and P. cebuensis) or Bicol Peninsula (C. luzoniensis) that showed evidence of population expansion (see text). Columns indicate values of τ and three age estimates along with their 95% confidence intervals. Rates based on: 1Weir and Schluter 2008, 2Arbogast et al. 2006, and 3Lim et al. 2011. Mutation rates in Myr-1.