Table 1. Target capture efficiency for the 76 herbarium samples of the Tamus clade of Dioscorea and four outgroup taxa studied. *DNA extracted from fresh material. ‘Paired-end reads’ is the number of reads obtained after quality trimming with Trimmomatic. ‘Length %’ is the recovery length percentage calculated based on the nucleotides retrieved per sample relative to the full length of the reference target gene set. ‘Enrich. eff.’ is the proportion of reads on target; ‘bp nDNA’ corresponds to the total number of bp retrieved for nuclear genes; ‘bp pDNA’ is the total number of bp retrieved for the plastome; ‘P(%)’ is the percentage of polymorphic sites (P) calculated as the coefficient between the SNPs and the total bp recovered for each sample; AR, allelic ratio; ‘%>2’ the percentage of SNPs with an allelic ratio <2.
Species Clade Sample Year collected Paired-end reads Enrich. eff. Assembled target genes Genes at 50% Length % bp nDNA bp pDNA SNPs P(%) Mean AR Median AR %<2
D. orientalis D. orientalis S23 1909 2980360 0.526 260 252 34.5 146415 146223 1652 1.13 2.79 2.96 18.71
R34 1958 43612 0.516 208 34 34.1 144729 76269 1474 1.02 2.28 2.00 45.9
S85 2008 1020080 0.448 260 134 50.3 213231 66768 835 0.39 2.71 2.80 31.9
S84 1957 2068305 0.528 260 244 82.1 348456 149412 779 0.22 2.42 2.05 47.0
S86 1957 795799 0.513 260 245 77.9 330582 110763 697 0.21 2.57 2.40 34.7
D. communis Clade DC1 (Macaronesia) S92 1960 299677 0.311 255 0 10.6 45171 34242 427 0.95 2.73 2.67 22.0
S91 1960 1637342 0.455 260 239 79.2 335889 141522 388 0.12 2.13 2.01 41.8
S40 2008 10339082 0.525 260 256 93.1 394977 145812 991 0.25 2.16 2.05 41.9
W33 2003 1370314 0.429 260 253 91.1 386241 145767 1025 0.27 2.83 3.05 19.5
S37 2008 10212202 0.502 260 257 92.6 392901 145089 1299 0.33 2.07 2.04 44.8
S41 2008 16196619 0.492 260 256 92.6 392970 141618 1459 0.37 2.04 2.02 46.8
R171 1788 5772951 0.381 260 240 80.4 341028 133494 1129 0.33 2.80 2.75 14.3
S95 1975 663825 0.454 260 142 51.1 216750 143307 705 0.33 2.49 2.27 34.9
S93 1867 2521444 0.460 260 230 72.5 308190 50046 1327 0.43 2.87 2.81 17.8
Clade DC2 (Trilobed leaves, Eastern Mediterranean) R32 1956 1238692 0.426 260 252 88.7 376359 144702 2304 0.61 2.62 2.74 22.6
S69 1905 782006 0.114 257 169 56.9 241176 119904 833 0.35 2.63 2.50 27.6
R15 1979 2481398 0.248 260 254 90.9 385665 141975 1466 0.38 1.46 1.22 85.3
R22 1955 1206365 0.297 260 255 91.1 386331 141084 0606 0.16 1.63 1.36 78.5
R95 1951 1483426 0.382 260 251 89.4 379077 143058 803 0.21 2.45 2.18 47.4
R14 1967 3918262 0.334 260 253 91.3 387393 141879 2230 0.58 1.86 1.62 67.9
S68 2007 782006 0.114 257 169 90.8 385149 77787 1404 0.36 1.64 1.29 81.5
W79 2010 1637458 0.485 260 254 91.5 387951 140592 1065 0.27 1.48 1.21 77.56
R18 1942 578726 0.604 260 246 84.3 357756 59802 1186 0.33 3.03 3.28 15.1
R16 1943 164691 0.330 256 172 76.6 324924 70617 3367 1.04 2.56 2.50 30.7
R17 1943 281364 0.595 260 231 58.3 247470 136824 3805 1.54 2.95 3.00 8.86
R20 2004 1925906 0.265 260 253 90.5 383769 141294 871 0.23 1.63 1.25 74.3
S78 1955 2705587 0.233 260 249 85.4 362205 144948 525 0.14 1.94 1.34 61.7
R96 1970 1514421 0.410 260 246 86.1 365292 143595 772 0.21 2.83 3.18 30.3
S71 1963 3234283 0.220 260 251 87.1 369312 145470 808 0.22 1.94 1.53 65.6
S70 1971 120618 0.245 243 34 29.4 124917 144003 259 0.21 2.59 2.50 39.0
Clade DC3 (Eastern Mediterranean) S67 1962 1879003 0.587 260 247 83.9 355812 145620 1064 0.30 1.47 1.27 83.7
R12 1957 2716763 0.355 260 251 89.6 380058 145545 1411 0.37 1.65 1.29 81.7
R21 1937 1624504 0.226 260 250 86.9 368490 146073 472 0.13 2.25 2.29 40.5
S72 2004 198920 0.266 256 161 55.0 233424 143145 878 0.38 2.67 2.67 32.9
S21 2004 991796 0.301 260 181 61.4 260340 147450 641 0.25 2.64 2.83 32.8
S36 1957 298300 0.537 259 160 54.6 231513 93522 512 0.22 2.44 2.40 30.7
R11 1936 1955793 0.256 260 251 87.5 370965 146694 4029 1.09 2.30 2.27 41.1
R10 1931 1859291 0.187 260 251 86.8 368178 145881 1079 0.29 2.90 2.94 13.7
S22 1969 1300587 0.233 259 55 89.3 378783 112770 859 0.23 2.58 2.66 23.6
R26 1858 759663 0.095 258 173 60.4 256383 147990 2769 1.08 2.81 2.80 19.5
S33 1932 1895199 0.103 260 218 71.9 304818 150111 972 0.32 2.62 2.58 23.9
S63 1999 1742636 0.226 260 252 89.5 379584 143289 1452 0.38 2.59 2.74 24.4
S18 1900 1014934 0.181 256 2 11.2 47622 31500 332 0.70 2.33 2.00 38.0
S34 1959 1441193 0.191 260 250 83.8 355620 144501 775 0.22 2.84 2.90 12.1
Clade DC3 (Central Mediterranean) R23 1978 1319618 0.238 260 253 87.4 370599 143055 814 0.22 2.76 2.89 23.6
R06 1965 2526479 0.280 260 251 88.0 373401 148890 3306 0.89 2.35 2.42 35.8
S61 1990 1760430 0.090 259 233 73.6 312126 151014 812 0.26 2.32 2.19 36.1
R08 1931 1169102 0.192 260 242 79.4 337011 146019 2148 0.64 3.03 3.17 9.73
R24 1930 895451 0.121 259 214 71.1 301512 144822 1340 0.44 2.77 2.75 20.7
S79 2016 3929348 0.283 260 256 92.5 392268 151239 3010 0.77 2.48 2.67 27.3
R30 2016 1677314 0.256 260 253 91.3 387120 144900 2464 0.64 2.59 2.73 24.8
R28 2016 1999986 0.342 260 253 91.3 387408 142863 3335 0.86 2.51 2.67 26.7
S28 1967 2114903 0.288 260 250 85.6 363141 148317 1107 0.30 2.66 2.74 25.6
R07 1847 1912677 0.136 260 244 79.9 339057 104967 1365 0.40 2.81 3.00 21.5
R100 1906 1536342 0.114 260 202 66.0 279993 146673 903 0.32 2.51 2.43 30.6
S35 1929 1846641 0.125 260 226 73.7 312624 148557 902 0.29 2.57 2.67 33.0
S20 1929 776828 0.172 260 9 21.1 89439 144906 520 0.58 2.37 2.00 36.9
Clade DC3 (Western European) P06* 2018 793772 0.576 260 253 91.6 388401 142761 3371 0.87 2.51 2.72 25.8
R84* 2018 1525356 0.226 260 240 86.2 365586 148377 5476 1.50 2.89 2.90 12.9
R76 2004 1653906 0.448 260 239 86.3 365946 144525 2086 0.57 3.15 3.38 13.8
R27 2017 2060161 0.340 260 253 91.7 388935 143238 2810 0.72 2.46 2.66 33.0
S42 2017 1432342 0.336 260 254 92.3 391608 143334 2576 0.66 2.48 2.57 28.7
R04 1956 2921528 0.304 260 253 89.1 377823 149163 2165 0.57 2.60 2.73 23.2
R05 1948 2418558 0.322 260 251 87.4 370722 144150 3443 0.93 2.22 2.19 44.2
S64 2015 4389479 0.307 260 255 92.3 391437 142944 2165 0.55 2.34 2.54 37.7
R129 1932 1893572 0.262 260 243 78.7 333720 146958 1221 0.37 2.43 2.13 42.6
S54 1976 1744816 0.164 260 214 68.7 291213 112173 662 0.23 2.50 2.40 33.8
S55 1980 124177 0.576 254 26 28.6 121518 30666 294 0.24 2.37 2.00 42.2
S53 1971 1811439 0.130 260 221 72.3 306672 145788 714 0.23 2.38 2.30 33.5
R25 1934 1189706 0.151 260 251 83.5 354219 141843 758 0.21 2.49 2.46 31.5
S76 1972 1882846 0.589 260 247 85.2 361521 145740 1424 0.39 2.72 2.82 16.2
S62 2003 2401716 0.200 260 249 88.4 375072 150357 1452 0.39 2.24 2.18 43.6
R29 2016 2093906 0.341 260 252 91.5 388347 142563 2415 0.62 2.57 2.75 24.14
R01 2016 5236808 0.415 260 255 92.0 390150 142731 3043 0.78 2.41 2.68 32.3
R31 2016 8920132 0.566 260 255 92.1 390780 143364 2972 0.76 2.41 2.72 31.1
S25 2016 3546012 0.358 260 252 90.6 384462 147363 1004 0.26 2.43 2.55 42.5
S80 2016 1341416 0.231 260 252 88.6 375798 142617 764 0.20 2.46 2.50 34.0
D. elephantipes Outgroup W32 2001 1020073 0.467 260 254 95.2 403968 152598
D. sylvatica Outgroup S49* 2018 2658330 0.541 260 255 94.4 400443 150822
D. chouardii Borderea D66 2003 5285968 0.355 260 257 92.5 392553 146505
D. pyrenaica Borderea W34 1956 1648853 0.298 260 237 76.8 325572 146466