rosenberg lab - additional file 4...moupinensis_cfra1974_index21 gracilis_cfra1973_index20...

Analysis(ready,reads,aligned,to,the,reference,

GATK,(BaseRecalibrator,,PrintReads),

Base,quality,recalibra?on,

GATK,(UnifiedGenotyper,,RealignerTargetCreator,,IndelRealigner),

Realignment,of,reads,around,indels,

Samtools,(rmdup),

Removed,PCR,duplicates,

Samtools,(merge,,sort,,index),

Reads,mapped,to,a,reference,

BWA,(aln,,samse,,sampe);,Samtools,(view,,sort,,index),

Reads,mapped,to,a,reference,by,library,

Trimmoma?c,

Trimmed,and,filtered,reads,by,library,

Raw,sequencing,reads,by,library,

Consensus,sequence,for,every,gene,for,every,genome,and,posi?ons,with,low,coverage,

Samtools,,bcLools,(mpileup,,view),

Read,depth,for,every,posi?on,

GATK,(FastaAlternateReferenceMaker),

Consensus,sequence,

variant_filter.pl,

Filtered,set,of,variants,

GATK,(UnifiedGenotyper),

Raw,variants,

Analysis(ready,reads,aligned,to,the,reference,

Analysis(ready,variants,

variant_filter.pl,

Filtered,set,of,variants,

GATK,(UnifiedGenotyper),

Raw,variants,

GATK,(BaseRecalibrator,,PrintReads),

Base,quality,recalibra?on,

GATK,(UnifiedGenotyper,,RealignerTargetCreator,,IndelRealigner),

Realignment,of,reads,around,indels,

Samtools,(rmdup),

Removed,PCR,duplicates,

Samtools,(merge,,sort,,index),

Reads,mapped,to,new,reference,

BWA,(aln,,samse,,sampe);,Samtools,(view,,sort,,index),

Reads,mapped,to,new,references,by,library,

Trimmed,and,filtered,reads,by,library,and,new,references,

Haplotype,sequences,by,assembly,block,

get_halotypes.pl,

Haplotype,sequences,

HapCompas,

Variants,phased,using,assembly,

Analysis(ready,variants,and,reads,mapped,to,the,reference,

A. ## # # # # # # # # ##B.#

C. ## # # # # # # # # ##D.#

Figure S1. Haplotype assembly pipeline (Step 2 in Figure 1). Processing proceeds from step A to B to C to D, generating haplotype sequences by assembly blocks and consensus sequences for covered regions of the reference genome. These sequences are subsequently used in Step 3 in Figure 1.

A.!!!!!!!!!!!!!!B.!

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iturupensis_CFRA1841_index17 virginiana_0477−27−1_index14 virginiana_y33b2−12_index12 chiloensis_GP33−1_index10 chiloensis_SAL3−1_index09 moschata_CFRA117_index13 tibetica_CFRA1907_index18 orientalis_CFRA1801_index16 moupinensis_CFRA1974_index21 gracilis_CFRA1973_index20 corymbosa_CFRA1911_index19 viridis_CFRA1597_index36 viridis_CFRA1256_index02 vesca_CFRA438_index25 viridis_CFRA1812_index22 vesca_CFRA1967_index19x vesca_CFRA1922_index15x vesca_CFRA612_index04x pentaphylla_CFRA1198_index24 pentaphylla_CFRA1913_index11x nubicola_CFRA1797_index27 nubicola_CFRA1797_index08x nipponica_CFRA1863_index42 nipponica_CFRA1862_index38x nipponica_CFRA1009_index33 nipponica_CFRA1864_index07x nilgerrensis_CFRA1224_index45x nilgerrensis_CFRA1358_index32 nilgerrensis_CFRA1223_index28x nilgerrensis_CFRA1188_index20 mexicana_CFRA61_index05 mandshurica_CFRA1947_index07x iinumae_CFRA1849_index30 iinumae_CFRA1853_index35 iinumae_CFRA2025_index34x daltoniana_CFRA1685_index40 daltoniana_CFRA1685_index15 chinensis_CFRA1199_index16 chinensis_CFRA202_index33x californica_CFRA388_index43 californica_CFRA371_index21 bucharica_CFRA1906_index44 bucharica_CFRA522_index39 bucharica_CFRA520_index35 bracteata_CFRA456_index29x bracteata_CFRA174_index17 bracteata_CFRA107_index13 bracteata_CFRA1952_index12 bracteata_CFRA1334_index10 bracteata_CFRA106_index09x americana_CFRA554_index47 americana_CFRA988_index41 americana_CFRA989_index08 Drymocallis_glandulous_index40

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iturupensis_CFRA1841_index17virginiana_0477−27−1_index14virginiana_y33b2−12_index12chiloensis_GP33−1_index10chiloensis_SAL3−1_index09moschata_CFRA117_index13tibetica_CFRA1907_index18orientalis_CFRA1801_index16moupinensis_CFRA1974_index21gracilis_CFRA1973_index20corymbosa_CFRA1911_index19viridis_CFRA1597_index36viridis_CFRA1256_index02vesca_CFRA438_index25viridis_CFRA1812_index22vesca_CFRA1967_index19pentaphylla_CFRA1913_index11nubicola_CFRA1797_index08nipponica_CFRA1862_index38nipponica_CFRA1864_index07nilgerrensis_CFRA1223_index28mexicana_CFRA61_index05mandshurica_CFRA1947_index07iinumae_CFRA1853_index35iinumae_CFRA2025_index34daltoniana_CFRA1685_index15chinensis_CFRA1199_index16chinensis_CFRA202_index33californica_CFRA371_index21bucharica_CFRA1906_index44bucharica_CFRA522_index39bucharica_CFRA520_index35bracteata_CFRA456_index29bracteata_CFRA107_index13bracteata_CFRA1952_index12bracteata_CFRA1334_index10bracteata_CFRA106_index09americana_CFRA988_index41americana_CFRA989_index08Drymocallis_glandulous_index40

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iturupensis_CFRA1841_index17virginiana_0477-27-1_index14virginiana_y33b2-12_index12chiloensis_GP33-1_index10chiloensis_SAL3-1_index09moschata_CFRA117_index13tibetica_CFRA1907_index18orientalis_CFRA1801_index16moupinensis_CFRA1974_index21gracilis_CFRA1973_index20corymbosa_CFRA1911_index19viridis_CFRA1597_index36viridis_CFRA1256_index02vesca_CFRA438_index25viridis_CFRA1812_index22vesca_CFRA1967_index19pentaphylla_CFRA1913_index11nubicola_CFRA1797_index08nipponica_CFRA1862_index38nipponica_CFRA1864_index07nilgerrensis_CFRA1223_index28mexicana_CFRA61_index05mandshurica_CFRA1947_index07iinumae_CFRA1853_index35iinumae_CFRA2025_index34daltoniana_CFRA1685_index15chinensis_CFRA1199_index16chinensis_CFRA202_index33californica_CFRA371_index21bucharica_CFRA1906_index44bucharica_CFRA522_index39bucharica_CFRA520_index35bracteata_CFRA456_index29bracteata_CFRA107_index13bracteata_CFRA1952_index12bracteata_CFRA1334_index10bracteata_CFRA106_index09americana_CFRA988_index41americana_CFRA989_index08Drymocallis_glandulous_index40

iturupensis_CFRA1841_index17 virginiana_0477-27-1_index14 virginiana_y33b2-12_index12 chiloensis_GP33-1_index10 chiloensis_SAL3-1_index09 moschata_CFRA117_index13 tibetica_CFRA1907_index18 orientalis_CFRA1801_index16 moupinensis_CFRA1974_index21 gracilis_CFRA1973_index20 corymbosa_CFRA1911_index19 viridis_CFRA1597_index36 viridis_CFRA1256_index02 vesca_CFRA438_index25 viridis_CFRA1812_index22 vesca_CFRA1967_index19x vesca_CFRA1922_index15x vesca_CFRA612_index04x pentaphylla_CFRA1198_index24 pentaphylla_CFRA1913_index11x nubicola_CFRA1797_index27 nubicola_CFRA1797_index08x nipponica_CFRA1863_index42 nipponica_CFRA1862_index38x nipponica_CFRA1009_index33 nipponica_CFRA1864_index07x nilgerrensis_CFRA1224_index45x nilgerrensis_CFRA1358_index32 nilgerrensis_CFRA1223_index28x nilgerrensis_CFRA1188_index20 mexicana_CFRA61_index05 mandshurica_CFRA1947_index07x iinumae_CFRA1849_index30 iinumae_CFRA1853_index35 iinumae_CFRA2025_index34x daltoniana_CFRA1685_index40 daltoniana_CFRA1685_index15 chinensis_CFRA1199_index16 chinensis_CFRA202_index33x californica_CFRA388_index43 californica_CFRA371_index21 bucharica_CFRA1906_index44 bucharica_CFRA522_index39 bucharica_CFRA520_index35 bracteata_CFRA456_index29x bracteata_CFRA174_index17 bracteata_CFRA107_index13 bracteata_CFRA1952_index12 bracteata_CFRA1334_index10 bracteata_CFRA106_index09x americana_CFRA554_index47 americana_CFRA988_index41 americana_CFRA989_index08 Drymocallis_glandulous_index40

Figure S2. Heatmap depicting the fraction of gene length not covered by sequencing. The threshold for depth of coverage was set at 3 reads per position. The fraction depicted is normalized and standardized across all the genomes by gene. Colors represent individual values as described in the color key. Histogram in the color key indicates the distribution of the colors in the heatmap. A. All 54 genomes. Excluded genomes that had average normalized, standardized fractions of genes uncovered over 0.25 when averaged across all the genes, are marked by “x” before their names. B. The 40 retained genomes only.

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F .virginianaF .iturupensisF .chiloensisF .moschataF .tibeticaF .orientalisF .moupinensisF .gracilisF .corymbosaF .viridisF. pentaphyllaF. nubicolaF. nipponicaF. nilgerrensisF. mandshuricaF. iinumaeF. daltonianaF. chinensisF. bucharicaF. vescaDrymocallis

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F .virginianaF .iturupensisF .chiloensisF .moschataF .tibeticaF .orientalisF .moupinensisF .gracilisF .corymbosaF .viridisF. pentaphyllaF. nubicolaF. nipponicaF. nilgerrensisF. mandshuricaF. iinumaeF. daltonianaF. chinensisF. bucharicaF. vescaDrymocallis

Figure S3. Distance between haplotypes calculated under the Kimura (1980) substitution model and averaged across all the comparisons for a given fragment and species. Fragments are in columns and are marked with gene number and fragment number; species are in rows. Colors represent individual values as described in the color key. The histogram in the color key indicates the distribution of the colors in the heatmap.

Input: map = matrix, mapping positions of consensus sequences from different organisms onto each other, generated from the multiple sequence alignment blocks = for each individual it is a set of blocks where haplotypes were assembled, positions correspond to position in consensus reference sequence Output: haplotype_fragmets = regions with continuous haplotype assembly across all of the genomes blocks_new_borders = obtain new positions of haplotype assembly blocks by individual using map total_positions = number of columns in the map haplotype_fragmets = empty list set position to 1 while position <= total_positions

haplotypes_list_by_individual = obtain list of haplotype assembly blocks covering position by individuals using blocks_new_borders right_borders = empty list for each individual in map right_border = find haplotype from corresponding unit of haplotypes_list_by_individual which has largest end position

append right_border to right_borders remove haplotype blocks which have end before right_border from corresponding unit of haplotypes_list_by_individual

right_border = minimum of right_borders left_borders = empty list for each individual in map left_border = first position of haplotype assembly block from corresponding unit of haplotypes_list_by_individual

append left_border to left_borders

left_border = maximum of left_borders append right_border, left_border pair to haplotype_fragmets set position to right_border+1

set position to 1 while position <= total_positions

haplotypes_list_by_individual = obtain list of haplotype assembly blocks covering position by individuals using blocks_new_borders left_borders = empty list for each individual in map left_border = find haplotype from corresponding unit of haplotypes_list_by_individual which has smallest end position

append left_border to left_borders remove haplotype blocks which have start after left_border from corresponding unit of haplotypes_list_by_individual

left_border = maximum of left_borders

right_borders = empty list for each individual in map right_border = of haplotype assembly block from corresponding unit of haplotypes_list_by_individual

append right_border to right_borders right_border = minimum of right_borders append right_border, left_border pair to haplotype_fragmets set position to right_border+1

Figure S4. Outline of a procedure for cutting out sequence fragments for phylogenetic analysis. The procedure was applied in Step 3 in Figure 1.

Posi%on'='1 '

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Figure S5. Cartoon representation of a procedure for cutting out sequence fragments for phylogenetic analysis. The procedure was applied in Step 3 in Figure 1. Here two individuals are represented by haplotypes (grey and black horizontal lines). For each of them given gene was assembled in two haplotype blocks between which phase could not be determined. Procedure would follow 3 steps and would reach the end of the gene in 2 iterations yielding 2 fragments of continuous haplotype assembly across two individuals.

Input: List trees = (T1, T2, ... Tl) of MUL-trees on taxa set M. r in [0, 1], minimal fraction of trees to support cluster for it to be included into final species relationship graph even if it is in conflict with other clusters and would produce reticulation node. t in [0, 1], minimal fraction of trees to contain cluster for it to be included into final species relationship graph only if it is not in conflict with other clusters and would produce a tree node. b in [0, 1], minimal bootstrap support of clade in gene tree in order for a clade to contribute towards clusters supported by gene tree. Output: Species network networkFromMULTrees(trees, r, t, b):

set clusters as empty list of elements for tree in trees: clusters_i = clustersFromMULTree(tree, b) unique_clusters_i = unique clusters_i

append unique_clusters_i to clusters unique_clusters = unique clusters set l to length of list trees set clusters_to_include to empty list of lists set counts to empty list of elements for cluster in unique_clusters: set count to number of times cluster appears in clusters

append count to counts if count is larger or equal to r*l: append cluster to clusters_to_include

set count_ordered_clusters to list of clusters ordered by descending order of counts for cluster in clusters: if cluster is not in clusters_to_include: if not isConflicting(cluster, clusters_to_include): append cluster to clusters_to_include append species names to clusters_to_include sorted_clusters_to_include = sort clusters_to_include by size of cluster in ascending order set network to empty 0,2 matrix that will contain edges as (parent, child) pairs set parents to empty list of lists that will contain parent information for every node of network set node_names to empty list that will contain names of network nodes arranged in the order of nodes set current_node to 0

append (1, 2) edge to network

append “root” and first cluster from clusters to node_names set current_node to 2 append empty list and first cluster from clusters to parents starting from the second cluster for every cluster in clusters

increment current_node by 1 append empty list to parents set cluster_parents to empty list set organisms_in_cluster to species in cluster check all node_name already in node_names, from last node up to second one as first one is root, track node number (n) if no cluster_parents are equal to node_name set organisms_in_node to to species in node_name if all organisms_in_cluster are in organisms_in_node append new edge (n, current_node) to network append node_name and parents of node_name to last element of parents set cluster_parents to all clusters in the last element of parents if current_node is not yet in node_names append cluster to node_names if is.hybridization(network, current_node) append new edge (current_node, current_node+1) to network set parents of current_node+1 to parents of current_node increment current_node by 1

append cluster to node_names return network and node_names clusters_from_MUL_tree(tree, b): set clusters to empty list of lists

for each internal node of tree if node_label is larger or equal to b set labels to list of tip names of clade descendant from node set sorted_unique_labels to list of sorted, unique labels append sorted_unique_labels to clusters

return clusters isConflicting(cluster_to_test, clusters_to_include): set result to FALSE

for each accepted_cluster in clusters_to_include if organisms in accepted_cluster and organisms in cluster_to_test overlap

if there are unique organisms in both organisms in accepted_cluster and organisms in cluster_to_test set result to TRUE

return result is.hybridization(network, node): set node_parents to the list of node parents

if length of node_parents equal to 1 return FALSE else return TRUE

Figure S6. Outline of a procedure for building consensus species networks from gene trees. The procedure was applied in Step 5 in Figure 1.

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Figure S7. Consensus cluster networks for every set of taxa, constructed using all the fragments passing the SH test against 100 random trees. The percent indicates the minimum support required for a cluster to be included in the procedure for identifying putative hybridizations. (a) 15%. (b) 20%. (c) 30%. (d) 40%. (e) 50%. The asterisks indicate potential hybridization events with diploid progenitors involved in homoploid speciation (dataset 2) or the origins of a polyploid species (datasets 6-14). The asterisks are placed at the highest level of support for that hybridization event and indicate only those cases that were tested in STEMhy and PhyloNet (Tables 1 and 2).

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V42

V43

V44

V45

V46

V47

V48

V49

V50

V51

V52

V53

V54

V55

V56

V57

V58

V59

V60

V61

V62

V63

V64

V65

V66

V67

V68

V69

V70

V71

V72

V73

V74

V75

V76

V77

V78

V79

V80

V81

V82

V83

V84

V85

V86

V87

V88

V89

V90

V91

V92

V93

V94

V95

V96

V97

V98

V99

V100

V101

V102

V103

V104

V105

V106

V107

V108

V109

V110

V111

V112

V113

V114

V115

V116

V117

V118

V119

V120

V121

V122

V123

V124

V125

V126

V127

V128

V129

V130

V131

V132

V133

V134

V135

V136

V137

V138

V139

V140

V141

V142

V143

V144

V145

V146

V147

V148

V149

V150

V151

V152

V153

V154

V155

V156

V157

V158

V159

V160

V161

V162

V163

V164

V165

V166

V167

V168

V169

V170

V171

V172

V173

V174

V175

V176

V177

V178

V179

V180

V181

V182

V183

V184

V185

V186

V187

V188

V189

V190

V191

V192

V193

V194

V195

V196

V197

V198

V199

V200

V201

V202

V203

V204

V205

V206

V207

V208

V209

V210

V211

V212

V213

V214

V215

V216

V217

V218

V219

V220

V221

V222

V223

V224

V225

V226

V227

V228

V229

V230

V231

V232

V233

V234

V235

V236

V237

V238

V239

V240

V241

V242

V243

V244

V245

V246

V247

V248

V249

V250

V251

V252

V253

V254

V255

V256

V257

V258

virginiana_y33b2−12_index12iturupensis_CFRA1841_index17chiloensis_GP33−1_index10chiloensis_SAL3−1_index09moschata_CFRA117_index13tibetica_CFRA1907_index18orientalis_CFRA1801_index16moupinensis_CFRA1974_index21gracilis_CFRA1973_index20corymbosa_CFRA1911_index19viridis_CFRA1597_index36viridis_CFRA1256_index02vesca_CFRA438_index25viridis_CFRA1812_index22vesca_CFRA1967_index19pentaphylla_CFRA1913_index11nubicola_CFRA1797_index08nipponica_CFRA1862_index38nipponica_CFRA1864_index07nilgerrensis_CFRA1223_index28mexicana_CFRA61_index05mandshurica_CFRA1947_index07iinumae_CFRA1853_index35iinumae_CFRA2025_index34daltoniana_CFRA1685_index15chinensis_CFRA1199_index16chinensis_CFRA202_index33californica_CFRA371_index21bucharica_CFRA1906_index44bucharica_CFRA522_index39bucharica_CFRA520_index35bracteata_CFRA456_index29bracteata_CFRA107_index13bracteata_CFRA1952_index12bracteata_CFRA1334_index10bracteata_CFRA106_index09americana_CFRA988_index41americana_CFRA989_index08Drymocallis_glandulous_index40

0 0.005 0.01 0.015 0.02Value

04000


Count

V2 V3 V4 V5 V6 V7 V8 V9 V10

V11

V12

V13

V14

V15

V16

V17

V18

V19

V20

V21

V22

V23

V24

V25

V26

V27

V28

V29

V30

V31

V32

V33

V34

V35

V36

V37

V38

V39

V40

V41

V42

V43

V44

V45

V46

V47

V48

V49

V50

V51

V52

V53

V54

V55

V56

V57

V58

V59

V60

V61

V62

V63

V64

V65

V66

V67

V68

V69

V70

V71

V72

V73

V74

V75

V76

V77

V78

V79

V80

V81

V82

V83

V84

V85

V86

V87

V88

V89

V90

V91

V92

V93

V94

V95

V96

V97

V98

V99

V100

V101

V102

V103

V104

V105

V106

V107

V108

V109

V110

V111

V112

V113

V114

V115

V116

V117

V118

V119

V120

V121

V122

V123

V124

V125

V126

V127

V128

V129

V130

V131

V132

V133

V134

V135

V136

V137

V138

V139

V140

V141

V142

V143

V144

V145

V146

V147

V148

V149

V150

V151

V152

V153

V154

V155

V156

V157

V158

V159

V160

V161

V162

V163

V164

V165

V166

V167

V168

V169

V170

V171

V172

V173

V174

V175

V176

V177

V178

V179

V180

V181

V182

V183

V184

V185

V186

V187

V188

V189

V190

V191

V192

V193

V194

V195

V196

V197

V198

V199

V200

V201

V202

V203

V204

V205

V206

V207

V208

V209

V210

V211

V212

V213

V214

V215

V216

V217

V218

V219

V220

V221

V222

V223

V224

V225

V226

V227

V228

V229

V230

V231

V232

V233

V234

V235

V236

V237

V238

V239

V240

V241

V242

V243

V244

V245

V246

V247

V248

V249

V250

V251

V252

V253

V254

V255

V256

V257

V258


Figure S8. The fraction of all sites that were variable within covered regions of the gene divided by ploidy level of the organism. Different genes are shown in columns and individuals are in rows. Colors represent individual values as described in the color key. The histogram in the color key indicates the distribution of the colors in the heatmap.

Dry

moc

allis

itu

rupe

nsis

8vi

rgin

iana

8ch

iloen

sis

8ni

ppon

ica

ch

inen

sis

nu

bico

la

pent

aphy

lla

tibet

ica

4m

oupi

nens

is 4

cory

mbo

sa 4

grac

ilis 4

iinum

ae

nilg

erre

nsis

da

ltoni

ana

m

osch

ata

6m

ands

huric

a

orie

ntal

is 4

virid

is

vesc

a

buch

aric

a

Drymocallis8 iturupensis8 virginiana8 chiloensis nipponica chinensis nubicola pentaphylla4 tibetica4 moupinensis corymbosa4 gracilis iinumae nilgerrensis daltoniana6 moschata mandshurica4 orientalis viridis vesca bucharica

0 0.02 0.04Value

040

8012

0


Cou

nt

Figure S9. Distances between consensus sequences calculated under the Kimura (1980) substitution model, averaged across all the individual comparisons across species pairs and genes. Ploidy level is given for non-diploid species next to species names. Colors represent individual values as described in the color key. The histogram in the color key indicates the distribution of the colors in the heatmap.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 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 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100

101

102

103

104

105

106

107

108

109

110

111

112

113

114

115

116

117

118

119

120

121

122

123

124

125

126

127

128

129

130

131

132

133

134

135

136

137

138

139

140

141

142

143

144

145

146

147

148

149

150

151

152

153

154

155

156

157

158

159

160

161

162

163

164

165

166

167

168

169

170

171

172

173

174

175

176

177

178

179

180

181

182

183

184

185

186

187

188

189

190

191

192

193

194

195

196

197

198

199

200

201

202

203

204

205

206

207

208

209

210

211

212

213

214

215

216

217

218

219

220

221

222

223

224

225

226

227

228

229

230

231

232

233

234

235

236

237

238

239

240

241

242

243

244

245

246

247

248

249

250

251

252

253

254

255

256

257

virginiana_0477−27−1_index14virginiana_y33b2−12_index12iturupensis_CFRA1841_index17chiloensis_GP33−1_index10chiloensis_SAL3−1_index09moschata_CFRA117_index13tibetica_CFRA1907_index18orientalis_CFRA1801_index16moupinensis_CFRA1974_index21gracilis_CFRA1973_index20corymbosa_CFRA1911_index19viridis_CFRA1597_index36viridis_CFRA1256_index02vesca_CFRA438_index25vesca_CFRA1812_index22vesca_CFRA1967_index19pentaphylla_CFRA1913_index11nubicola_CFRA1797_index08nipponica_CFRA1862_index38nipponica_CFRA1864_index07nilgerrensis_CFRA1223_index28mexicana_CFRA61_index05mandshurica_CFRA1947_index07iinumae_CFRA1853_index35iinumae_CFRA2025_index34daltoniana_CFRA1685_index15chinensis_CFRA1199_index16chinensis_CFRA202_index33californica_CFRA371_index21bucharica_CFRA1906_index44bucharica_CFRA522_index39bucharica_CFRA520_index35bracteata_CFRA456_index29bracteata_CFRA107_index13bracteata_CFRA1952_index12bracteata_CFRA1334_index10bracteata_CFRA106_index09americana_CFRA988_index41americana_CFRA989_index08Drymocallis_glandulous_index40

0.2 0.4 0.6 0.8 1Value

03000


Count

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 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 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100

101

102

103

104

105

106

107

108

109

110

111

112

113

114

115

116

117

118

119

120

121

122

123

124

125

126

127

128

129

130

131

132

133

134

135

136

137

138

139

140

141

142

143

144

145

146

147

148

149

150

151

152

153

154

155

156

157

158

159

160

161

162

163

164

165

166

167

168

169

170

171

172

173

174

175

176

177

178

179

180

181

182

183

184

185

186

187

188

189

190

191

192

193

194

195

196

197

198

199

200

201

202

203

204

205

206

207

208

209

210

211

212

213

214

215

216

217

218

219

220

221

222

223

224

225

226

227

228

229

230

231

232

233

234

235

236

237

238

239

240

241

242

243

244

245

246

247

248

249

250

251

252

253

254

255

256

257


0.2 0.4 0.6 0.8 1Value

01500


Count

A.!!!!!!!!!!!!B.!

Percent'of'sequence'in'longest'haplotype'

Percent'of'heterozygous'posi5ons'in'longest'haplotype'

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 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 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100

101

102

103

104

105

106

107

108

109

110

111

112

113

114

115

116

117

118

119

120

121

122

123

124

125

126

127

128

129

130

131

132

133

134

135

136

137

138

139

140

141

142

143

144

145

146

147

148

149

150

151

152

153

154

155

156

157

158

159

160

161

162

163

164

165

166

167

168

169

170

171

172

173

174

175

176

177

178

179

180

181

182

183

184

185

186

187

188

189

190

191

192

193

194

195

196

197

198

199

200

201

202

203

204

205

206

207

208

209

210

211

212

213

214

215

216

217

218

219

220

221

222

223

224

225

226

227

228

229

230

231

232

233

234

235

236

237

238

239

240

241

242

243

244

245

246

247

248

249

250

251

252

253

254

255

256

257


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 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 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100

101

102

103

104

105

106

107

108

109

110

111

112

113

114

115

116

117

118

119

120

121

122

123

124

125

126

127

128

129

130

131

132

133

134

135

136

137

138

139

140

141

142

143

144

145

146

147

148

149

150

151

152

153

154

155

156

157

158

159

160

161

162

163

164

165

166

167

168

169

170

171

172

173

174

175

176

177

178

179

180

181

182

183

184

185

186

187

188

189

190

191

192

193

194

195

196

197

198

199

200

201

202

203

204

205

206

207

208

209

210

211

212

213

214

215

216

217

218

219

220

221

222

223

224

225

226

227

228

229

230

231

232

233

234

235

236

237

238

239

240

241

242

243

244

245

246

247

248

249

250

251

252

253

254

255

256

257


C.!!!!!!!!!!!!D.!

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 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 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100

101

102

103

104

105

106

107

108

109

110

111

112

113

114

115

116

117

118

119

120

121

122

123

124

125

126

127

128

129

130

131

132

133

134

135

136

137

138

139

140

141

142

143

144

145

146

147

148

149

150

151

152

153

154

155

156

157

158

159

160

161

162

163

164

165

166

167

168

169

170

171

172

173

174

175

176

177

178

179

180

181

182

183

184

185

186

187

188

189

190

191

192

193

194

195

196

197

198

199

200

201

202

203

204

205

206

207

208

209

210

211

212

213

214

215

216

217

218

219

220

221

222

223

224

225

226

227

228

229

230

231

232

233

234

235

236

237

238

239

240

241

242

243

244

245

246

247

248

249

250

251

252

253

254

255

256

257


0.2 0.4 0.6 0.8 1Value

03000


Count

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 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 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100

101

102

103

104

105

106

107

108

109

110

111

112

113

114

115

116

117

118

119

120

121

122

123

124

125

126

127

128

129

130

131

132

133

134

135

136

137

138

139

140

141

142

143

144

145

146

147

148

149

150

151

152

153

154

155

156

157

158

159

160

161

162

163

164

165

166

167

168

169

170

171

172

173

174

175

176

177

178

179

180

181

182

183

184

185

186

187

188

189

190

191

192

193

194

195

196

197

198

199

200

201

202

203

204

205

206

207

208

209

210

211

212

213

214

215

216

217

218

219

220

221

222

223

224

225

226

227

228

229

230

231

232

233

234

235

236

237

238

239

240

241

242

243

244

245

246

247

248

249

250

251

252

253

254

255

256

257


0.2 0.4 0.6 0.8 1Value

01500


Count

Percent'of'sequence'in'haplotype'with'largest'number'of'heterozygous'posi8ons''

Percent'of'heterozygous'posi8ons'in'haplotype'with'largest'number'of'heterozygous'posi8ons''

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 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 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100

101

102

103

104

105

106

107

108

109

110

111

112

113

114

115

116

117

118

119

120

121

122

123

124

125

126

127

128

129

130

131

132

133

134

135

136

137

138

139

140

141

142

143

144

145

146

147

148

149

150

151

152

153

154

155

156

157

158

159

160

161

162

163

164

165

166

167

168

169

170

171

172

173

174

175

176

177

178

179

180

181

182

183

184

185

186

187

188

189

190

191

192

193

194

195

196

197

198

199

200

201

202

203

204

205

206

207

208

209

210

211

212

213

214

215

216

217

218

219

220

221

222

223

224

225

226

227

228

229

230

231

232

233

234

235

236

237

238

239

240

241

242

243

244

245

246

247

248

249

250

251

252

253

254

255

256

257


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 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 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100

101

102

103

104

105

106

107

108

109

110

111

112

113

114

115

116

117

118

119

120

121

122

123

124

125

126

127

128

129

130

131

132

133

134

135

136

137

138

139

140

141

142

143

144

145

146

147

148

149

150

151

152

153

154

155

156

157

158

159

160

161

162

163

164

165

166

167

168

169

170

171

172

173

174

175

176

177

178

179

180

181

182

183

184

185

186

187

188

189

190

191

192

193

194

195

196

197

198

199

200

201

202

203

204

205

206

207

208

209

210

211

212

213

214

215

216

217

218

219

220

221

222

223

224

225

226

227

228

229

230

231

232

233

234

235

236

237

238

239

240

241

242

243

244

245

246

247

248

249

250

251

252

253

254

255

256

257


E.!!!!!!!!!!!!F.!

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 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 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100

101

102

103

104

105

106

107

108

109

110

111

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Figure S10. Results of haplotype assembly. A. Percent of sequence in longest haplotype out of entire length of the gene covered by reads; B. Percent of heterozygous positions in longest haplotype out of all heterozygous positions; C. Percent of sequence in haplotype with largest number of variants out of entire length of the gene covered by reads; D. Percent of heterozygous positions in haplotype with largest number of variants out of all heterozygous positions; E. Average haplotype length for a given gene in a given individual; F. Average number of heterozygous positions per haplotype for the given gene in a given individual. Different genes are shown in columns and individuals are in rows. Colors represent individual values as described in the color key in every panel. The histogram in the color key indicates the distribution of the colors in the heatmap.

F. vesca F. mandshurica

F. bucharica

F. viridis

F. nilgerrensis

F. nipponica F. chinensis F. pentaphylla F. nubicola F. iinumae F. daltoniana

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Set 1

F vesca F bucharica

F viridis

F nilgerrensis F daltoniana F nipponica F chinensis F tibetica 4 F nubicola F moupinensis 4 F pentaphylla F gracilis 4 F corymbosa 4

F chiloensis 8 F virginiana 8 F iturupensis 10 F iinumae

F moschata 6 F orientalis 4 F mandshurica

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Set 5

Figure S11. Species trees reconstructed using ASTRAL for two datasets. Topologies were tested using bootstrap trees generated by PhyML. Clades observed in over 85% of bootstrap replicates are not labeled, clades observed in 70% to 85% of replicates are marked with small circles, and those observed in 70% of replicates or less are marked with large circles. Ploidy levels are shown for non-diploid species. Branch lengths are not to scale. This figure shows two datasets not included in Figure 3.

rosenberg lab - additional file 4...moupinensis_cfra1974_index21 gracilis_cfra1973_index20...

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