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 |
|
|
|
|
|