Fig 1.
Complete F. heteroclitus mitochondrial genome.
Fragments (amplicons) used to PCR amplify the mitochondrial sequence. The primers used for F. majalis were designed using F. heteroclitus as a template.
Table 1.
Primers utilized to amplify the complete mitochondrial genome.
Table 2.
Library Preparation Costs.
Fig 2.
Quality control measurements of raw reads for F. heteroclitus (A, C, E) and F. majalis (B, D, F).
A-B) Figure shows number of all available reads after trimming vs. read size. Nucleotide window analyses of F. heteroclitus aligned reads (C) and unaligned reads (E). Nucleotide window analyses of F. majalis aligned reads (D) and unaligned reads (F). The outer ribbon of low opacity represents the 10th and 90th quality percentiles. The inner opaque ribbon represents the upper and lower quality quartiles. Black lines represent averages.
Fig 3.
Quality control information for Fundulus heteroclitus samples.
A) Average coverage depth along the mtDNA genome. Amplification products (amplicons) are shown across the top. B) Amplified view of the average, F. heteroclitus mitochondrial genome, coverage depth. C) Percent of samples (out of 192) showing non-N nucleotides. D) Percent of samples showing different coverage depths. E) Percent of samples showing different mapping quality levels.
Fig 4.
Quality control information for Fundulus majalis samples.
A) Average coverage depth along the mtDNA genome. Amplification products (amplicons) are shown across the top. B) Amplified view of the average, F. majalis mitochondrial genome, coverage depth. C) Percent of samples (out of 191) showing non-N nucleotides. D) Percent of samples showing different coverage depths. E) Percent of samples showing different mapping quality levels.
Fig 5.
Base composition across all sequences.
Regular calls (A,C,T,G, or N) in A) F. heteroclitus, and C) F. majalis. Degenerate calls (W,S,M,K,Y) in B) F. heteroclitus, and D) F. majalis.
Fig 6.
Maximum likelihood phylogenetic reconstructions.
A) Global phylogenetic tree produced using 5,088 sites dispersed throughout the entire mtDNA of most samples sequenced in this study. B) Gene tree for the CytB gene. Sequences CG1 through CG192 (F. heteroclitus samples) clustered with the F. heteroclitus CytB NCBI sequence (blue cartoon). Similarly, samples CG193 through CG384 (F. majalis samples) clustered with the F. majalis CytB NCBI sequence (red cartoon). C) Just as for CytB, sequenced samples form clades with their respective reference COI sequence from NCBI in the case of F. heteroclitus and from BOLD system v3 in the case of F. majalis.