Table 1.
Sequences and locations of novel control region primers used in this study.
Table 2.
Summary of polymorphism data and population parameter estimates in populations of Agelaius phoeniceus and A. tricolor.
Figure 1.
Number of rate categories (k) affects model likelihoods and parameter estimates.
Discrete Γ model negative log-likelihoods for the control region data are shown on the left axis, and estimated α parameters on the right. The line at k = 12 indicates the point at which addition of a class of constant characters (piv>0) does not significantly improve the model fit.
Figure 2.
Sliding window analysis of model fit across Agelaius control region and ND2 regions.
Each point plots parameter values of either an HKY85+G12 (for CR, left), or HKY85+I (for ND2, right) model, for a 250 base pair window centered at that position, for each position sampled (step size = 1). The upper panels show values of the transition/transversion ratio (left axis and black line; some spurious values estimated due to the absence of transversions in given windows omitted), and the parameter of the discrete Γ approximation (CR; 12 categories) or proportion of invariant sites (ND2; right axes and gray lines). The lower panels show the nucleotide proportion parameters πi.
Figure 3.
Trees obtained in maximum likelihood analyses of CR and ND2 data.
Shown are: A) one of ≥270 maximum likelihood trees obtained via heuristic search under the HKY85+G12 model (−lnL = 2907.7, κ = 16.702, πA = 0.312, πC = 0.285, πG = 0.134, α = 0.1019) with a molecular clock, for the set of unique Agelaius CR haplotypes and a single outgroup Molothrus (see Appendix S1 for sample identification); and B) the single best tree obtained via heuristic search under the GTR+I model (−lnL = 2337.7, rAC = 5.122, rAG = 118.9, rAT = 3.560, rCG = 8.226e−4, rCT = 47.54, πA = 0.310, πC = 0.355, πG = 0.098, pinv = 0.723) with a molecular clock, for the unique ND2 haplotypes and the same outgroup. Numbers next to branches indicate support as estimated by the non-parametric bootstrap (200 replicates; molecular clock not enforced due to time constraints), and thickened branches indicate estimated Bayesian posterior probabilities ≥0.95.
Figure 4.
Rate heterogeneity in Agelaius control region and ND2.
Shown are the inferred number of changes per site (left axis and black line; based on marginal reconstruction of ancestral states on arbitrarily-chosen ML trees) in the alignment of Agelaius CR (above) and ND2 (below), and sliding window analysis (plotted at the center of each window, width = 100 bases, step = 1 base) of site-specific rate estimates (right axis and gray line; empirical Bayes estimates from PAML 4.4, correlation of true and estimated rates was 0.583 for CR and 0.545 for ND2). Asterisks mark five hotspots identified by polymorphism within both A. phoeniceus and A. tricolor, and plus symbols mark “hypervariable” CR sites (defined as sites in the 95th percentile or higher of site-specific rate estimates for variable sites). Horizontal lines on bars for individual site change reconstructions indicate the number of intraspecific mutations as opposed to fixed differences between species.
Table 3.
Tests of neutral equilibrium assumptions in Agelaius phoeniceus and A. tricolor.
Table 4.
Maximum likelihood and Bayesian estimates (approximate 95% confidence and credibility intervals in parentheses, parameter estimates for intervals exclusive of 0 are highlighted in bold) of the neutral parameter and population growth for Agelaius phoeniceus and A. tricolor, derived from analyses using LAMARC v2.1.3 [78] and BEAST v1.4.8 [79].