Martin P. Schilling, Zach Gompert, Fay-Wei Li, Michael D Windham, Paul G. Wolf ... admixture prop. (q) interâlineage ancestry (Q. 12. ) q q q q qqq qqq qq qqqq q.
1 Admixture, evolutionary relationships, and variation in reproductive isolation in the Boechera puberula clade
Additional tables & figures Martin P. Schilling, Zach Gompert, Fay-Wei Li, Michael D Windham, Paul G. Wolf
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variance explained
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Figure S1: Percentage of variance explained and standard error of treemix runs with m = 0-11
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70
60
50
40
30
20
10
total
lasiocarpa
serpenticola
subpinnatifida
puberulaari
pubpub
exilis
retroXbucket
retroXilis
retrofracta
retroXstricta
stricta
0
Figure S2: Mean species-specific mapping rates and standard deviation for individuals represented in this study, with groups corresponding to groups used in treemix analyses (with sample ids 25, 26, 33, 34 in ’retroXbucket’).
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logit % admixed
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mapping percentage Figure S3: Scatterplot of individual mapping rates and logit percent admixed (i.e. 1 - maximum admixture proportion) for each individual (the best fit line from a linear model is included). We find no evidence that low mapping rates are associated with increased evidence of admixture, but rather a non-significant trend in the oppossite direction (β = 0.083, P = 0.256).
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Figure S4: Admixture proportions based on 14,815 common variants. Each bar represents Bayesian point estimates of admixture proportions for each respective individual, and thus the proportion of inheritance of each genome to the respective species. Results of 2 through 16 presumed source species are shown here, with k = 8 being the best model based on DIC. Given the higher number of putative source taxa, we chose a color palette that differs from the colors used in the figures which were included in the paper.
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stricta x retrofracta subpinnatifida x retro. retrofracta x exilis stricta retrofracta exilis p. puberula p. arida subpinnatifida serpenticaloa lasiocarpa
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inter−lineage ancestry (Q12)
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admixture prop. (q) Figure S5: The plot shows the relationship between the admixture proportion q1 (with k = 2) and inter-lineage ancestry (Q12 ; i.e., the proportion of the genome where an individual is heterozygous for ancestry). Colored dots denote individuals. Lines indicate the maximum possible inter-source population ancestry given global genetic ancestry (individuals on these line have at least one non-admixed parent)
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stricta
stricta
(1-20)
stricta x retrofracta
stricta
(1-20)
stricta x retrofracta
(11-14)
retrofracta
retrofracta
(15-24)
retrofracta x exilis
retrofracta x exilis exilis
exilis
(35-38)
lasiocarpa
lasiocarpa
(63-79)
(39-46,48,49)
puberula arida
subpinnatifidda
serpenticola (53-58)
stricta
retrofracta
stricta stricta x retrofracta retrofracta
(15-24)
(1-20)
stricta x retrofracta
(11-14)
retrofracta
(15-24)
(25,26,33,34)
retrofracta x exilis exilis
exilis
lasiocarpa
puberula puberula puberula arida
puberula arida
(50-52)
stricta
retrofracta
retrofracta
(1-20)
stricta x retrofracta
(11-14)
retrofracta
(15-24)
retrofracta x exilis
(27-32)
exilis
(35-38)
lasiocarpa
(63-79)
stricta
(59-62)
stricta
retrofracta
(25,26,33,34) (27-32)
lasiocarpa
(39-46,48,49)
retrofracta x exilis
(27-32)
(11-14)
(15-24)
retrofracta x exilis exilis
(35-38)
lasiocarpa
(63-79)
(27-32)
(35-38) (63-79)
puberula puberula
puberula puberula
(39-46,48,49)
(39-46,48,49)
puberula arida
(50-52)
puberula arida
(50-52)
subpinnatifidda
(59-62)
subpinnatifidda
(59-62)
serpenticola (53-58)
(1-20)
(25,26,33,34)
lasiocarpa
(63-79)
puberula puberula
(59-62)
retrofracta
(15-24)
exilis
(35-38)
(50-52)
subpinnatifidda
stricta x retrofracta
(11-14)
(25,26,33,34)
retrofracta x exilis
puberula arida
serpenticola (53-58)
(1-20)
stricta x retrofracta
(11-14)
(15-24)
exilis
(39-46,48,49)
serpenticola (53-58)
(1-20)
(63-79)
puberula puberula
(50-52)
subpinnatifidda
(59-62)
(27-32)
(35-38)
lasiocarpa
(39-46,48,49)
puberula arida
(50-52)
serpenticola (53-58)
stricta x retrofracta
exilis (63-79)
puberula puberula
(39-46,48,49)
subpinnatifidda
retrofracta x exilis
(27-32)
(35-38)
lasiocarpa
puberula puberula puberula arida
(11-14)
(15-24)
(25,26,33,34)
(25,26,33,34)
retrofracta x exilis
(50-52) (59-62)
serpenticola (53-58)
stricta stricta x retrofracta
(25,26,33,34)
retrofracta
puberula arida subpinnatifidda
(59-62)
(1-20)
(11-14)
(15-24)
exilis
(39-46,48,49)
serpenticola (53-58)
(1-20)
(63-79)
puberula puberula
(50-52)
subpinnatifidda
(59-62)
(27-32)
(35-38)
lasiocarpa
(63-79)
(39-46,48,49)
serpenticola (53-58)
stricta x retrofracta
exilis
puberula puberula
(39-46,48,49)
subpinnatifidda
retrofracta x exilis
(27-32)
(35-38)
lasiocarpa
(63-79)
(11-14)
(15-24)
(25,26,33,34)
retrofracta x exilis
(27-32)
(35-38)
(50-52) (59-62)
serpenticola (53-58)
(1-20)
(11-14)
(25,26,33,34)
stricta
(39-46,48,49)
subpinnatifidda
(59-62)
serpenticola (53-58)
(1-20)
stricta x retrofracta
puberula puberula puberula arida
(50-52)
subpinnatifidda
(59-62)
(63-79)
(25,26,33,34)
(63-79)
puberula puberula
(39-46,48,49) (50-52)
(27-32)
(35-38)
lasiocarpa
(35-38)
puberula puberula puberula arida
stricta
(15-24)
(27-32)
(25,26,33,34)
(27-32)
exilis
stricta
(11-14)
retrofracta
(15-24)
retrofracta x exilis
(25,26,33,34)
(1-20)
stricta x retrofracta
(11-14)
serpenticola (53-58)
puberula arida subpinnatifidda
(50-52) (59-62)
serpenticola (53-58)
Figure S6: Population graphs inferred by treemix for diploid Boechera taxa included in this study, allowing 0-11 migration or admixture events. Branch lengths are proportional to genetic drift.
Table S1: Locality information, locality id (locID) sample numbers (id) for Fig. 2, internal id (iID) as well as ploidy and nominal taxa which were both determined from microsatellite data. Here, we use only the species epithet, omitting the genus name. arida = B. puberula arida, puberula = B. puberula puberula. The 23 samples not denoted with ”MS” came from air-dried herbarium specimens locID 1 1 1 2 3 4 5 1 6 7 8 9 8 8 10 11 12 10 10
id 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
iID MS556 MS557 MS558 CR1181 JB186 JB377 JB1255 MS554 CR1091 JB1258 MS465 MS328 MS469 MS471 MS169 MS280 JB867 MS163 MS165
locality Grizzly Peak, UT Grizzly Peak, UT Grizzly Peak, UT La Plata, CO Weber, UT Nye, NV Custer, ID Grizzly Peak, UT Teton, WY Madison, MO Steep Canyon, UT Deadfall Lake, CA Steep Canyon, UT Steep Canyon, UT Little Volcano, CA Hat Creek, CA Park, WY Little Volcano, CA Little Volcano, CA
latitude 41.41 41.41 41.41 37.44 41.41 38.95 43.86 41.41 43.85 45.56 41.97 41.33 41.97 41.97 39.86 40.7 44.41 39.86 39.86 next page
ploidy 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
nominal taxon B. stricta B. stricta B. stricta B. stricta B. stricta B. stricta B. stricta B. stricta B. stricta B. stricta B. retrofracta x stricta B. retrofracta x subpinnatifida B. retrofracta x stricta B. retrofracta x stricta B. retrofracta B. retrofracta B. retrofracta retrofracta (sexual) B. retrofracta B. retrofracta 7
longitude -111.97 -111.97 -111.97 -108.02 -111.59 -117.35 -114.65 -111.97 -110.52 -111.96 -111.6 -122.52 -111.6 -111.6 -120.89 -121.41 -110.57 -120.89 -120.89 Continued on
locID id 13 20 11 21 14 22 15 23 9 24 8 25 9 26 16 27 17 28 17 29 17 30 16 31 17 32 16 33 16 34 18 35 19 36 20 37 21 38 22 39 23 40 23 41 24 42 25 43 26 44 25 45 25 46
iID JB176 MS282 JB659 CR1043 MS313 MS473 MS327 MS413 MS9 MS7 MS18 MS425 MS11 MS426 MS422 FW241 CR1164 FW73 FW76 JB1275 MS79 MS80 JB382 MS93 JB381 MS102 MS94
nominal taxon B. retrofracta retrofracta (sexual) B. retrofracta B. retrofracta retrofracta (sexual) B. retrofracta retrofracta (sexual) B. retrofracta B. retrofracta x stricta B. retrofracta x subpinnatifida B. exilis x retrofracta B. exilis x retrofracta B. exilis x retrofracta B. exilis x retrofracta B. exilis x retrofracta B. exilis x retrofracta B. exilis x retrofracta B. exilis x retrofracta B. exilis B. exilis B. exilis B. exilis B. puberula puberula B. puberula B. puberula B. puberula puberula B. puberula B. puberula puberula B. puberula B. puberula 8
Table S1 – Continued from previous page locality longitude latitude ploidy Mineral, MO -115.7 47.45 2 Hat Creek, CA -121.41 40.7 2 Deschutes, OR -121.56 43.67 2 Humboldt, CA -123.65 40.48 2 Deadfall Lake, CA -122.51 41.33 2 Steep Canyon, UT -111.6 41.97 2 Deadfall Lake, CA -122.52 41.33 2 Bear Lake Summit, UT -111.47 41.93 2 Wells, NV -114.57 41.08 2 Wells, NV -114.57 41.08 2 Wells, NV -114.57 41.08 2 Bear Lake Summit, UT -111.47 41.93 2 Wells, NV -114.57 41.08 2 Bear Lake Summit, UT -111.47 41.93 2 Bear Lake Summit, UT -111.47 41.93 2 Elko, NV -115.08 40.68 2 Summit, UT -111.4078 40.7753 2 Nye, NV -117.54 38.97 2 Millard, UT -112.27 38.95 2 Baker, OR -117.11 44.7 2 Water Canyon, NV -116.71 40.64 2 Water Canyon, NV -116.71 40.64 2 Box Elder, UT -113.94 41.77 2 Lye Creek, NV -117.54 41.69 2 Humboldt, NV -117.55 41.67 2 Lye Creek, NV -117.54 41.69 2 Lye Creek, NV -117.54 41.69 2 Continued on next page
locID 11 23 23 27 28 29 30 30 30 30 30 30 31 31 31 31 32 33 33 34 34 34 34 34 34 35 35
id 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73
iID MS283 MS69 MS72 JB1611 JB1610 FW237 MS286 MS305 MS302 MS294 MS298 MS297 MS367 MS392 MS402 MS403 FW516 CR1308 CR1309 MS458 MS444 MS446 MS455 MS453 MS447 MS485 MS496
nominal taxon B. retrofracta B. puberula B. puberula B. puberula arida B. puberula arida B. puberula arida B. serpenticola B. serpenticola B. serpenticola B. serpenticola B. serpenticola B. serpenticola B. subpinnatifida B. subpinnatifida B. subpinnatifida B. subpinnatifida B. lasiocarpa (holotype) B. lasiocarpa B. lasiocarpa B. lasiocarpa B. lasiocarpa B. lasiocarpa B. lasiocarpa B. lasiocarpa B. lasiocarpa B. lasiocarpa B. lasiocarpa 9
Table S1 – Continued from previous page locality longitude latitude ploidy Hat Creek, CA -121.41 40.7 2 Water Canyon, NV -116.71 40.64 2 Water Canyon, NV -116.71 40.64 2 Box Elder, UT -113.69 41.53 2 Mono, CA -119.13 38.36 2 Lander, NV -117.37 39.24 2 Bully Choop Mtn, CA -122.94 40.65 2 Bully Choop Mtn, CA -122.94 40.65 2 Bully Choop Mtn, CA -122.94 40.65 2 Bully Choop Mtn, CA -122.94 40.65 2 Bully Choop Mtn, CA -122.94 40.65 2 Bully Choop Mtn, CA -122.94 40.65 2 Rogue River, OR -123.53 42.55 2 Rogue River, OR -123.53 42.55 2 Rogue River, OR -123.53 42.55 2 Rogue River, OR -123.53 42.55 2 Rich, UT -111.46 41.92 2 Cache, UT -111.71 41.8 2 Cache, UT -111.66 41.91 2 Logan Canyon Sinks, UT -111.48 41.93 2 Logan Canyon Sinks, UT -111.48 41.93 2 Logan Canyon Sinks, UT -111.48 41.93 2 Logan Canyon Sinks, UT -111.48 41.93 2 Logan Canyon Sinks, UT -111.48 41.93 2 Logan Canyon Sinks, UT -111.48 41.93 2 Steam Mill Peak, UT -111.61 41.95 2 Steam Mill Peak, UT -111.61 41.95 2 Continued on next page
locID 35 11 36 37 38 39 40 40 40 41 41 41 42 42 42 42 43 43 43 43 44 44 44 45 45 45 46
id 74 75 76 77 78 79 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
nominal taxon B. lasiocarpa B. retrofracta B. lasiocarpa B. lasiocarpa B. lasiocarpa B. lasiocarpa B. exilis x puberula x retrofracta B. exilis x puberula x retrofracta B. exilis x puberula x retrofracta B. p. arida x puberula x subpinnatifida B. retrofracta x sparsiflora (2:1) B. retrofracta x sparsiflora (2:1) B. exilis x retrofracta x sparsiflora B. exilis x retrofracta x sparsiflora B. exilis x retrofracta x sparsiflora B. exilis x retrofracta x sparsiflora B. retrofracta x lasiocarpa (2:1) B. retrofracta x lasiocarpa (2:1) B. retrofracta x lasiocarpa (2:1) B. retrofracta x lasiocarpa (2:1) B. p. arida x subpinnatifida (2:1) B. p. arida x subpinnatifida (2:1) B. p. arida x subpinnatifida (2:1) B. exilis x puberula x retrofracta B. exilis x puberula x retrofracta B. exilis x puberula x retrofracta B. lasiocarpa x retrofracta x stricta 10
Table S1 – Continued from previous page iID locality longitude latitude ploidy MS488 Steam Mill Peak, UT -111.61 41.95 2 MS275 Hat Creek, CA -121.41 40.7 2 JB419 Box Elder, UT -111.98 41.39 2 MS513 James Peak, UT -111.78 41.38 2 JB1587 Salt Lake, UT -111.72 40.63 2 FW1630 Tooele, UT -112.62 40.48 2 MS39 Angel Lake, NV -115.07 41.02 3 MS40 Angel Lake, NV -115.07 41.02 3 MS41 Angel Lake, NV -115.07 41.02 3 MS215 Frenchman Lake, CA -120.19 39.88 3 MS221 Frenchman Lake, CA -120.18 39.87 3 MS228 Frenchman Lake, CA -120.18 39.87 3 MS125 Indian Creek, NV -117.55 41.65 3 MS128 Indian Creek, NV -117.55 41.65 3 MS134 Indian Creek, NV -117.55 41.65 3 MS135 Indian Creek, NV -117.55 41.65 3 MS501 James Peak, UT -111.78 41.38 3 MS511 James Peak, UT -111.78 41.38 3 MS512 James Peak, UT -111.78 41.38 3 MS525 James Peak, UT -111.78 41.38 3 MS145 Peavine Peak, NV -119.93 39.59 3 MS150 Peavine Peak, NV -119.93 39.59 3 MS162 Peavine Peak, NV -119.93 39.59 3 MS47 Shoshone Mtns, NV -116.86 40.42 3 MS49 Shoshone Mtns, NV -116.86 40.42 3 MS54 Shoshone Mtns, NV -116.86 40.42 3 MS482 Steam Mill Peak, UT -111.61 41.95 3 Continued on next page
locID 46 47 47 47 47 47 47
id NA NA NA NA NA NA NA
iID MS499 MS536 MS538 MS539 MS543 MS550 MS552
Table S1 – Continued locality longitude Steam Mill Peak, UT -111.61 Willard Peak, UT -111.97 Willard Peak, UT -111.97 Willard Peak, UT -111.97 Willard Peak, UT -111.97 Willard Peak, UT -111.97 Willard Peak, UT -111.97
from previous page latitude ploidy 41.95 3 41.39 3 41.39 3 41.39 3 41.39 3 41.39 3 41.39 3
nominal taxon B. lasiocarpa x B. lasiocarpa x B. lasiocarpa x B. lasiocarpa x B. lasiocarpa x B. lasiocarpa x B. lasiocarpa x
retrofracta x stricta lemmonii x stricta lemmonii x stricta lemmonii x stricta lemmonii x stricta lemmonii x stricta lemmonii x stricta
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