##Supplemental Data 4: The interspecific DNA polymorphism across M. rubra and M. alba cp genomes. DnaSP Ver. 6.12.03 09 - May - 2024 10:28:30 AM ======================================================================= DNA Polymorphism ---------------- Input Data File: Z:\...\alba_rubra_aligned.nex Number of sequences: 45 Number of sequences used: 45 Selected region: 1-160039 Number of sites: 160039 Total number of sites (excluding sites with gaps / missing data): 158608 Number of polymorphic (segregating) sites, S: 441 Total number of mutations, Eta: 441 Number of Haplotypes, h: 13 Haplotype (gene) diversity, Hd: 0.841 Variance of Haplotype diversity: 0.00084 Standard Deviation of Haplotype diversity: 0.029 Nucleotide diversity, Pi: 0.00093 Theta (per site) from Eta: 0.00064 Theta (per site) from S, Theta-W: 0.00064 Variance of theta (no recombination): 0.0000000 Standard deviation of theta (no recombination): 0.00018 Variance of theta (free recombination): 0.0000000 Standard deviation of theta (free recombination): 0.00003 Finite Sites Model Theta (per site) from Pi: 0.00093 Theta (per site) from S: 0.00064 Theta (per site) from Eta: 0.00064 Average number of nucleotide differences, k: 147.707 Stochastic variance of k (no recombination), Vst(k): 3973.163 Sampling variance of k (no recombination), Vs(k): 186.544 Total variance of k (no recombination), V(k): 4159.707 Stochastic variance of k (free recombination), Vst(k): 49.236 Sampling variance of k (free recombination), Vs(k): 2.238 Total variance of k (free recombination), V(k): 51.474 Theta (per sequence) from S, Theta-W: 100.852 Variance of theta (no recombination): 816.818 Variance of theta (free recombination): 23.064 Sliding Window Option Sites with alignment gaps were not counted in the window length (and slide) Window length: 500 Step size: 250 ------------------------------------------------------------------------------------ Window Midpoint Pi Theta S 1-509 257 0.00080 0.00091 2 258-759 509 0.00080 0.00091 2 510-1009 759 0.00071 0.00046 1 760-1259 1009 0.00071 0.00046 1 1010-1509 1259 0.00000 0.00000 0 1260-1766 1509 0.00212 0.00137 3 1510-2018 1766 0.00212 0.00137 3 1767-2270 2018 0.00212 0.00137 3 2019-2520 2270 0.00283 0.00183 4 2271-2770 2520 0.00243 0.00137 3 2521-3020 2770 0.00314 0.00183 4 2771-3270 3020 0.00141 0.00091 2 3021-3520 3270 0.00000 0.00000 0 3271-3770 3520 0.00009 0.00046 1 3521-4021 3770 0.00009 0.00046 1 3771-4271 4021 0.00000 0.00000 0 4022-4521 4271 0.00000 0.00000 0 4272-4777 4521 0.00354 0.00229 5 4522-5047 4777 0.00424 0.00274 6 4778-5302 5047 0.00354 0.00229 5 5048-5553 5302 0.00424 0.00274 6 5303-5804 5553 0.00212 0.00137 3 5554-6061 5804 0.00283 0.00183 4 5805-6311 6061 0.00283 0.00183 4 6062-6561 6311 0.00212 0.00137 3 6312-6811 6561 0.00150 0.00137 3 6562-7066 6811 0.00080 0.00091 2 6812-7317 7066 0.00071 0.00046 1 7067-7567 7317 0.00212 0.00137 3 7318-7825 7567 0.00212 0.00137 3 7568-8081 7825 0.00080 0.00091 2 7826-8331 8081 0.00150 0.00137 3 8082-8581 8331 0.00071 0.00046 1 8332-8838 8581 0.00212 0.00137 3 8583-9103 8838 0.00283 0.00183 4 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0.00071 0.00046 1 144900-145399 145149 0.00071 0.00046 1 145150-145664 145399 0.00566 0.00366 8 145400-145914 145664 0.00566 0.00366 8 145665-146164 145914 0.00000 0.00000 0 145915-146414 146164 0.00000 0.00000 0 146165-146664 146414 0.00000 0.00000 0 146415-146914 146664 0.00000 0.00000 0 146665-147164 146914 0.00000 0.00000 0 146915-147414 147164 0.00000 0.00000 0 147165-147664 147414 0.00000 0.00000 0 147415-147914 147664 0.00000 0.00000 0 147665-148164 147914 0.00000 0.00000 0 147915-148414 148164 0.00000 0.00000 0 148165-148664 148414 0.00000 0.00000 0 148415-148922 148664 0.00000 0.00000 0 148665-149172 148922 0.00000 0.00000 0 148923-149422 149172 0.00000 0.00000 0 149173-149672 149422 0.00000 0.00000 0 149423-149930 149672 0.00000 0.00000 0 149673-150180 149930 0.00000 0.00000 0 149931-150430 150180 0.00000 0.00000 0 150181-150680 150430 0.00000 0.00000 0 150431-150930 150680 0.00071 0.00046 1 150681-151180 150930 0.00071 0.00046 1 150931-151430 151180 0.00000 0.00000 0 151181-151680 151430 0.00000 0.00000 0 151431-151930 151680 0.00000 0.00000 0 151681-152180 151930 0.00000 0.00000 0 151931-152430 152180 0.00000 0.00000 0 152181-152680 152430 0.00000 0.00000 0 152431-152930 152680 0.00000 0.00000 0 152681-153180 152930 0.00000 0.00000 0 152931-153430 153180 0.00000 0.00000 0 153181-153680 153430 0.00000 0.00000 0 153431-153930 153680 0.00000 0.00000 0 153681-154180 153930 0.00000 0.00000 0 153931-154430 154180 0.00000 0.00000 0 154181-154680 154430 0.00000 0.00000 0 154431-154930 154680 0.00000 0.00000 0 154681-155180 154930 0.00071 0.00046 1 154931-155430 155180 0.00071 0.00046 1 155181-155680 155430 0.00000 0.00000 0 155431-155930 155680 0.00000 0.00000 0 155681-156180 155930 0.00000 0.00000 0 155931-156430 156180 0.00000 0.00000 0 156181-156680 156430 0.00000 0.00000 0 156431-156930 156680 0.00071 0.00046 1 156681-157180 156930 0.00071 0.00046 1 156931-157430 157180 0.00000 0.00000 0 157181-157680 157430 0.00000 0.00000 0 157431-157930 157680 0.00000 0.00000 0 157681-158180 157930 0.00000 0.00000 0 157931-158430 158180 0.00000 0.00000 0 158181-158680 158430 0.00000 0.00000 0 158431-158930 158680 0.00000 0.00000 0 158681-159180 158930 0.00071 0.00046 1 158931-159430 159180 0.00071 0.00046 1 159181-159680 159430 0.00000 0.00000 0 159431-159930 159680 0.00000 0.00000 0 159681-160039 159859 0.00099 0.00064 1 DnaSP Ver. 6.12.03 09 - May - 2024 10:18:16 AM ======================================================================= Polymorphic Sites ----------------- Input Data File: Z:\...\alba_rubra_aligned.nex Number of sequences: 45 Number of sequences used: 45 Selected region: 1-160039 Number of sites: 160039 Total number of sites (excluding sites with gaps / missing data): 158608 Sites with alignment gaps or missing data: 1431 Invariable (monomorphic) sites: 158167 Variable (polymorphic) sites: 441 (Total number of mutations: 441) Singleton variable sites: 26 Parsimony informative sites: 415 Singleton variable sites (two variants): 26 Site positions: 496 3545 6691 8039 9391 19241 36380 38769 38785 38803 38816 38861 49870 49891 50039 50080 50149 50153 50233 50234 50235 76767 79044 114750 128754 130530 Parsimony informative sites (two variants): 415 Site positions: 308 840 1722 1723 1728 2109 2119 2127 2481 2542 2738 2855 2991 4599 4639 4722 4742 4771 4959 5136 5156 5216 5229 5401 5411 5718 5815 5855 6022 6119 6512 6519 6868 7379 7493 7528 7868 8142 8595 8636 8739 8964 9215 9262 9268 9295 9303 9466 9490 9581 9878 10229 10230 10822 10892 11122 11162 11163 11164 11166 11167 11168 11443 11986 12146 12464 13338 13544 13591 14258 14535 14540 15040 15199 15791 16855 17875 17955 19118 19709 21392 21770 22627 22635 24114 24597 25161 25513 27009 28406 28621 28807 28812 28878 29251 29816 29844 30098 30368 30568 30868 31289 31442 31484 31641 31689 32337 32338 32350 32452 32485 32550 32712 32945 33466 33675 33837 33967 34167 34297 34964 35466 35468 37563 37660 37695 37696 37697 37698 37699 37700 37701 37742 38366 38370 38401 38750 38836 38841 38843 38853 38874 38901 39317 39326 39372 39695 40294 41146 42357 43193 44570 44575 45238 45413 45810 45885 45904 46139 46194 47013 47141 47293 47344 47610 47902 48517 49338 49468 49483 49485 49500 49696 49809 49821 50094 50097 50098 50285 50529 50607 50738 51225 51616 52027 52209 52212 52488 52496 52759 53181 53237 53333 54509 54700 54702 54712 54740 55270 55558 55601 55630 55825 55937 55940 56175 56630 57437 58041 58269 58849 59365 59448 59927 60022 60179 61374 62411 62779 62996 63081 63613 64417 64617 64692 65086 65124 65270 65521 66089 67824 68003 68939 68956 69047 69173 69274 69440 69533 69626 69627 69628 69631 69634 69804 69858 70405 70620 70704 70813 70872 71007 71374 71403 71640 71774 72040 72954 74145 74511 75567 75660 75927 76017 76020 76021 76056 76070 76325 76600 76842 78686 79617 79764 79885 80619 81461 82374 82654 82663 82807 83251 83690 83788 83835 83996 84190 84689 84697 85023 85040 85797 85859 86511 87086 87120 87845 88238 88291 88489 88664 89601 91774 93583 97830 103082 103083 103086 103087 103106 103108 103111 103114 103604 114358 114632 114757 114836 114911 115005 115095 115229 115346 115417 115777 116229 116837 117078 117149 117289 117316 117503 117654 117731 117856 117890 118146 118184 118265 118637 118711 119103 119111 119212 119259 119296 119451 119459 119736 119737 119740 120005 120273 120563 121251 121325 122223 122522 123362 123772 123851 124232 124695 124806 124858 125906 126053 126201 126286 126365 126611 126622 126636 127068 127513 129026 129596 129774 130160 130486 130628 130737 130929 131377 131942 131968 132092 132103 132132 132491 132502 132556 132871 133110 133305 133720 133743 134035 134057 134106 134338 145095 145585 145588 145591 145593 145612 145613 145616 145617 150869 155116 156925 159098 160035 Variable sites (three variants): 0 Variable sites (four variants): 0 Protein Coding Region assignation: No