##Supplemental Data 3: Intraspecific DNA polymorphism across M. rubra cp genomes.

 DnaSP  Ver. 6.12.03                        09 - May - 2024  10:05:07 AM
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 DNA Polymorphism
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 Input Data File: Z:\...\rubra_only_aligned.nex
 Number of sequences: 35    Number of sequences used: 35
 Selected region: 1-159451   Number of sites: 159451
 Total number of sites (excluding sites with gaps / missing data): 159297

 Number of polymorphic (segregating) sites, S: 36
 Total number of mutations, Eta: 36

 Number of Haplotypes, h: 12
 Haplotype (gene) diversity, Hd: 0.812
    Variance of Haplotype diversity: 0.00202
       Standard Deviation of Haplotype diversity: 0.045

 Nucleotide diversity, Pi: 0.00002
 Theta (per site) from Eta: 0.00005

 Theta (per site) from S, Theta-W: 0.00005
    Variance of theta (no recombination): 0.0000000
       Standard deviation of theta (no recombination): 0.00002
    Variance of theta (free recombination): 0.0000000
       Standard deviation of theta (free recombination): 0.00001

 Finite Sites Model 
    Theta (per site) from Pi: 0.00002
    Theta (per site) from S: 0.00005
    Theta (per site) from Eta: 0.00005

 Average number of nucleotide differences, k: 3.486
    Stochastic variance of k (no recombination), Vst(k): 3.125
    Sampling variance of k (no recombination), Vs(k): 0.189
       Total variance of k (no recombination), V(k): 3.314
    Stochastic variance of k (free recombination), Vst(k): 1.162
    Sampling variance of k (free recombination), Vs(k): 0.068
       Total variance of k (free recombination), V(k): 1.230

 Theta (per sequence) from S, Theta-W: 8.742
    Variance of theta (no recombination): 8.586
    Variance of theta (free recombination): 2.123

 Sliding Window Option
 Sites with alignment gaps were not counted in the window length (and slide)
   Window length: 500     Step size: 250




 DnaSP  Ver. 6.12.03                        09 - May - 2024  10:30:32 AM
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 Polymorphic Sites
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 Input Data File: Z:\...\rubra_only_aligned.nex
 Number of sequences: 35    Number of sequences used: 35
 Selected region: 1-159451   Number of sites: 159451
 Total number of sites (excluding sites with gaps / missing data): 159297

   Sites with alignment gaps or missing data: 154
   Invariable (monomorphic) sites: 159261
   Variable (polymorphic) sites: 36   (Total number of mutations: 36)
      Singleton variable sites: 29
      Parsimony informative sites: 7

      Singleton variable sites (two variants): 29
         Site positions:  496 3538 6677 8011 9347 19149 36227 38579 38598 38614 38632 38645 38685
           38793 49643 49664 49807 49848 49866 49917 49921 50001 50002 50003 76408 78680 114325
           128191 129965
      Parsimony informative sites (two variants): 7
         Site positions:  2731 17790 32822 38677 80244 118175 129209
      Variable sites (three variants): 0
      Variable sites (four variants): 0

 Protein Coding Region assignation:  No


