Unraveling the evolutionary history of wild potatoes and...

Unraveling the evolutionary history ofUnraveling the evolutionary history of wild potatoes and tomatoeswild potatoes and tomatoes

FlorFlor RodriguezRodriguez

July 17July 17thth, 2009, 2009

OutlineOutline

Solanum subgenus Potatoe

Wild potato and wild tomato classifications

Previous phylogenetic studies

Materials and methods

Results and discussion

SolanumSolanum subgenus subgenus PotatoePotatoe

Family Family SolanaceaeSolanaceaeGenus Genus SolanumSolanum

Subgenus Subgenus PotatoePotatoeSection Section LycopersiconLycopersiconSection Section EtuberosumEtuberosumSection Section PetotaPetota

Wild potato and tomato distributionsWild potato and tomato distributions

Spooner and Hijmans, 2001 Peralta et al., 2008

potato tomato

Morphological variability in wild potatoMorphological variability in wild potato

Morphological variability in wild tomatoMorphological variability in wild tomato

Hawkes Hawkes phylogenetic/biogeographicphylogenetic/biogeographic hypothesis of hypothesis of genome evolution and migration in genome evolution and migration in SolanumSolanum sect. sect. PetotaPetota

Hawkes, 1990; Spooner and Hawkes, 1990; Spooner and SytsmaSytsma, 1992, 1992

““BB”” genome prototypegenome prototype

““BB”” genome migrationgenome migration

““AA”” genome evolvesgenome evolves““AA””, , ““AAAA””

““AA”” genomegenomemigrationmigration

““AA”” xx ““BB””allopolyploidsallopolyploids

evolveevolve

Previous molecular studiesPrevious molecular studies

HosakaHosaka et alet al., 1984; Spooner & ., 1984; Spooner & SytsmaSytsma, 1992;, 1992;Castillo & Spooner, 1997; Castillo & Spooner, 1997; RodrRodrííguezguez & Spooner, 1997& Spooner, 1997

Clade 2

Clade 3

Clade 4

Clade 1

Outgroup (S. palustre)

all ser. Piuranasome from ser. Megistacroloba & YungasensaDiploids ser. Conicibaccata & TuberosaRemaining SA speciesNA & CA polyploid speciesand S. verrucosum

Most US, Mexican & Central American diploids

S. bulbocastanumS. cardiophyllum subsp. cardiophyllumS. cardiophyllum subsp. ehrenbergii

plastid DNA restriction siteplastid DNA restriction site

Comparison of classifications of wild Comparison of classifications of wild tomatoestomatoes

Series Series LycopersiconLycopersicon

Series Series NeolycopersiconNeolycopersicon

Series Series EriopersiconEriopersicon

Muller,1940Muller,1940

Subgenus Subgenus EulycopersiconEulycopersiconL. L. esculentumesculentumL. L. pimpinellifoliumpimpinellifolium

Subgenus Subgenus EriopersiconEriopersiconL. L. peruvianumperuvianum

L. L. cheesmaniaecheesmaniaeL. L. hirsutumhirsutumL. L. glandulosumglandulosum

Rick, 1979Rick, 1979

EsculentumEsculentum complexcomplex

PeruvianumPeruvianum complexcomplex

L. L. pennelliipennellii

L. L. chmielewskiichmielewskiiL. L. parviflorumparviflorum

L. L. cheesmaniaecheesmaniae

L. L. hirsutumhirsutum

L. L. chilensechilenseL. L. peruvianumperuvianum

L. L. esculentumesculentumL. L. pimpinellifoliumpimpinellifolium

Child, 1990Child, 1990

S. S. pennelliipennellii

S. S. habrochaiteshabrochaitesS. S. chmielewskiichmielewskiiS. S. neorickiineorickii

S. S. lycopersicumlycopersicumS. S. pimpinellifoliumpimpinellifoliumS. S. cheesmaniaecheesmaniae

S. S. chilensechilenseS. S. peruvianumperuvianum

Peralta et al. 2008Peralta et al. 2008

LycopersiconLycopersicon groupgroupS. S. lycopersicumlycopersicumS. S. pimpinellifoliumpimpinellifoliumS. S. cheesmaniaecheesmaniaeS. S. galapagensegalapagense

NeolycopersiconNeolycopersicon groupgroupS. S. pennelliipennellii

EriopersiconEriopersicon groupgroupS. S. habrochaiteshabrochaitesS. S. huaylasensehuaylasenseS. S. corneliomullericorneliomulleriS. S. peruvianumperuvianumS. S. chilensechilense

Arcanum Arcanum groupgroupS. S. arcanumarcanumS. S. chmielewskiichmielewskiiS. S. neorickiineorickii

WaxyWaxyPeralta & Spooner, 2001

S.lycopersicumS.lycopersicumS.pimpinellifoliumS.pimpinellifoliumS.cheesmaniaeS.cheesmaniaeS.peruvianumS.peruvianum NNS.chmielewskiiS.chmielewskiiS.neorickiiS.neorickiiS.peruvianumS.peruvianum SSS.chilenseS.chilenseS.habrochaitesS.habrochaitesS.pennelliiS.pennelliiS.juglandifoliumS.juglandifoliumS.ochranthumS.ochranthumS.lycopersicoidesS.lycopersicoidesS.sitiensS.sitiensS.tuberosumS.tuberosumS.bulbocastanumS.bulbocastanumS.jamesiiS.jamesiiS.etuberosumS.etuberosumS.palustreS.palustreS.muricatumS.muricatum

24

70

100

100

100

64

86

97

100

100

ITSITSMarshall & all, 2001

S.pimpinellifoliumS.pimpinellifolium

S.lycopersicumS.lycopersicum


S.cheesmaniaeS.cheesmaniae

S.chmielewskiiS.chmielewskii

S.neorickiiS.neorickii

Cestrum, Cestrum, NicotianaNicotiana, Petunia, Petunia

S.habrochaitesS.habrochaites

S.pennelliiS.pennellii

S.lycopersicoidesS.lycopersicoides

S.nigrumS.nigrum

S.peruvianumS.peruvianum NNS.peruvianumS.peruvianum NN

S.peruvianumS.peruvianum SS

S.chilenseS.chilense

54

67

76

85

69

99

99

MorphologyMorphologyPeralta & Spooner, 2005


S.pimpinellifoliumS.pimpinellifolium

S.cheesmaniaeS.cheesmaniae

S.galapagenseS.galapagense

S.chmielewskiiS.chmielewskii

S.neorickiiS.neorickii

S.peruvianumS.peruvianum NN

S.peruvianumS.peruvianum SS

S.habrochaitesS.habrochaites

S.chilenseS.chilense

S.pennelliiS.pennellii

S.juglandifoliumS.juglandifolium

S.ochranthumS.ochranthum

S.lycopersicoidesS.lycopersicoides

S.sitiensS.sitiens

87

88

76

72

96

99

99

100

Previous studiesPrevious studies

Molecular phylogeny of potato genomes Molecular phylogeny of potato genomes with emphasis on origins of the with emphasis on origins of the polyploid speciespolyploid species

ObjectivesObjectives

Generate a nuclear molecular data set to reconstruct the phylogeny of wild potatoes

Evaluate previous circumscription of potato genomes

Infer the genomic contributors of potato polyploids

Materials and MethodsMaterials and Methods14 series, 45 ingroups and 3 outgroups

GenBank nitrate reductase tomato sequence (X14060)

Cloning

Exon 1 Exon 4E2 E3i1i1 i2i2 i3i3

1227 bp

NIA3F

NIA3R

74 bp74 bp 847 bp847 bp 436 bp436 bp

NIA 3

Data AnalysisData Analysis

Sequence editing and alignment

Phylogenetic analysis:ParsimonyMaximum LikelihoodBayesian

Hypothesis testing

Summary of sequence variation among Summary of sequence variation among 1) diploids and 1) diploids and 2) diploids and polyploids2) diploids and polyploids

Total characters Variable characters

bp bp

exon 816 95 35 (4%)intron 626 182 81 (13%)DNA 1442 277 116 (8%)gaps 78 78 35 (45%)DNA & gaps 1520 355 151(10%)exon 816 129 64 (8%)intron 629 211 110 (18%)DNA 1445 340 174 (12%)gaps 87 87 42 (48%)DNA & gaps 1532 427 216 (14%)

Diploids and polyploids

Data set Region Number and Percentage of Parsimony Informative characters

Diploids

104 MP treesL = 5112CI = 0.764RI = 0.779

Maximum Parsimony Maximum Parsimony diploidsdiploids

NA & CA diploidsB genome

A genomeRemaining SA diploids

Piurana cladeP, C, D genome

Clade 3

Clade 1+2

Clade 4

ConclusionsConclusions1. Wild potato species are divided into three well-

defined clades

2. The North and Central American B genome species are well distinguish from SA species

3. S. verrucosum clusters with all SA diploid species (A genome)

4. Hawkes’s series PIN and POL are monophyletic

5. S. brevicaule and S. sparsipilum appear to have hybrid origins

6. Species did not group based on Hawkes’s four superseries (flower shape)

NIA data suggests:Monophyly of North and Central American diploid species exclusive of S. verrucosum

Plastid DNA suggested:S. cardiophyllum and S. bulbocastanum cluster with SA diploid species

ries

abz PIU AR 2adr TUB PR 2

chm CON PR 2imt TUB PR 2

sph PIN PS 1blb BUL PS 1

cph PIN PS 1ehr1 PIN PS 1ehr2 PIN PS 1

jam PIN PS 1

pnt PIN PS 1trf PIN PS 1

clr BUL PS 1mrl MOR PS 1les POL PS 1pld POL PS 1ber TUB PR 2tar YNG AS 2ifd1 CUN PR 2blv MEG PR 2mga MEG PR 2chc YNG AS 2gnd TUB PR 2brc1 TUB PR 2ifd2 CUN PR 2spl1 TUB PR 2

buk TUB PR 2

lgl LIG PS 1

mcd TUB PR 2

rap1 MEG PR 2rap2 MEG PR 2vio CON PR 2

brc2 TUB PR 2lph TUB PR 2spl2 TUB PR 2ver TUB AR 2lycetb ETU 1pls ETU 1

92

77

61

92

59

100

100

50

92

98

57

52

56

92

88

6256

100

88

SpeciesSeries

Superseries

EBN

Piurana clade

NA & CA diploids B genome

Remaining SA diploids




Clade 3

Clade 1+2

Clade 4




Clade 3Piurana clade

P, C, D genomePiurana clade

P, C, D genome

Clade 3

Clade 1+2

Clade 4






jam PIN PS 1



buk TUB PR 2

lgl LIG PS 1

mcd TUB PR 2



92

77

61

92

59

100

100

50

92

98

57

52

56

92

88

6256

100

88

SpeciesSeries

Superseries

EBN

Piurana clade




Monophyly of NA and Central American diploid species


P, C, D genome

Clade 1+2NA & CA diploids

B genome

Clade 4Remaining SA diploidsA genome

ConclusionsConclusions

1. Wild potato species are divided into three clades well defined


3. S. verrucosum clusters with all SA diploid species (A genome)


5. S. brc and spl appear to have hybrid origins

6. Species did not group based on Hawkes’s four superseries based on flower shape





jam PIN PS 1



buk TUB PR 2

lgl LIG PS 1

mcd TUB PR 2



92

77

61

92

59

100

100

50

92

98

57

52

56

92

88

6256

100

88

SpeciesSeries

Superseries

EBN

Piurana clade




Monophyly of ser. TUB?

Monophyly of ser. CON ?


P, C, D genome


B genome


Species in clade 3





jam PIN PS 1



buk TUB PR 2

lgl LIG PS 1

mcd TUB PR 2



92

77

61

92

59

100

100

50

92

98

57

52

56

92

88

6256

100

88

SpeciesSeries

Superseries

EBN

Piurana clade




Monophyly of series Monophyly of series MEGMEG and and YNG ?YNG ?


P, C, D genome


B genome






jam PIN PS 1



buk TUB PR 2

lgl LIG PS 1

mcd TUB PR 2



92

77

61

92

59

100

100

50

92

98

57

52

56

92

88

6256

100

88

SpeciesSeries

Superseries

EBN

Piurana clade




ser. PIN is supported as monophyletic with the exclusion of S. bulbocastanum


P, C, D genome


B genome






jam PIN PS 1



buk TUB PR 2

lgl LIG PS 1

mcd TUB PR 2



92

77

61

92

59

100

100

50

92

98

57

52

56

92

88

6256

100

88

SpeciesSeries

Superseries

EBN

Piurana clade




Monophyly of ser. BUL ?


P, C, D genome


B genome





3. S. verrucosum cluster with all SA diploid species (A genome)








jam PIN PS 1



buk TUB PR 2

lgl LIG PS 1

mcd TUB PR 2



92

77

61

92

59

100

100

50

92

98

57

52

56

92

88

6256

100

88

SpeciesSeries

Superseries

EBN

Piurana clade




Monophyly of two distinct alleles from the same species ?

Clade 4a

Clade 4b


P, C, D genome


B genome


ConclusionsConclusions1. Wild potato species are divided into three clades

well defined




5. S. brevicaule and S. sparsipilum appear to have hybrid origins






jam PIN PS 1



buk TUB PR 2

lgl LIG PS 1

mcd TUB PR 2



92

77

61

92

59

100

100

50

92

98

57

52

56

92

88

6256

100

88

SpeciesSeries

Superseries

EBN

Piurana clade








P, C, D genome

Clade 1+2NA & CAdiploids

B genome


EBN

Hawkes’s four superseriesbased on flower shape



2. The North and Central American B genome species are well distinguish from SA species (B genome)





BayesianInference tree with the complete database

Diploid speciesPolyploid species ser. LongipedicellataPolyploid species ser. ConnicibaccataPolyploid species Acaulia GroupPolyploid species Iopetalum GroupPolyploid species ser. PiuranaPolyploid species ser. Tuberosa

1.00

0.98

0.98

0.97

1.00

0.78

0.59

0.991.000.740.77

0.78

10.69

0.71

0.95

0.960.98

0.981.00

1.000.85

1.001.00

1

0.830.96

110.94

0.52

1.000.96

1

0.98

0.99

0.96

0.91

0.760.69

0.98

1.000.99

0.97

0.93

0.751.00

0.740.68

1.001.00

1.00

0.79

1.0072

0.68

10.56

1

0.59

0.950.95

0.66

0.96

10.97

0.57

0.57

S. lycopersicumS. acaule 1

S. acaule 2S. demisum 1

S. demisum 2

S. raphanifolium 1S. raphanifolium 2

S. agrimonifolium 1S. colombianum 1

S longiconicum 1S. violaceimarmoratum

S. microdontumS. lignicauleS. berthaultii

S. tarijenseS. infundibuliforme 1

S. sparsipilum 1

S. bolivienseS. megistacrolobum

S. chacoenseS. gandarillasii

S. brevicaule 1S. infundibuliforme 2

S. brachycarpum 1S. verrucosum

S. hjertingii 1S. stoloniferum 1

S. demisum 3S. demisum 4S. fendleri 1S. schenkii 1S. demisum 5

S. demisum 6S. fendleri 2

S. schenkii 2S. oplosence A1S. oplosence A2

S. oplosence A3

S. oplosence A5S. oplosence A6S. oplosence B3S. oplosence B4

S. oplocense B1S. oplosence B2

S. sparsipilum 2

S. brevicaule 2

S. oplosence A4

S. leptophyes

S. agrimonifolium 2S. agrimonifolium 3S. agrimonifolium 4

S. brachycarpum 2S. colombianum 2S. colombianum 3

S longiconicum 2S. tuquerrense 1S. tuquerrense 2

S. andreanumS. paucijugum 1

S. paucijugum 2S. schenkii 5

S. schenkii 6S. albornozii

S. immite

S. paucijugum 4S. tuquerrense 3S. tuquerrense 4

S. paucijugum 3

S. stenophyllidium

S. cardiophyllum subsp.ehrenbergii 2S. cardiophyllum subsp.ehrenbergii 1

S. fendleri 3

S. stoloniferum 3

S. fendleri 4

S. stoloniferum 2S. hjertingii 2

S. stoloniferum 4

S. bulbocastanumS cardiophyllum

S.trifidum

S. jamesiiS. pinnatisectum

S. schenkii 3S. schenkii 4

S. clarumS. morelliformeS. lesteri

S. polyadenium

S. bukasovii

S. chomatophilum

S. palustreS. etuberosum

Clade 1+2Genome B

Clade 4Genome A

Clade 3Piurana CladeGenome C or D or P

BayesianInference tree for the complete database

Diploid speciesPolyploid species ser. LongipedicellataPolyploid species ser. ConnicibaccataPolyploid species Acaulia GroupPolyploid species Iopetalum GroupPolyploid species ser. PiuranaPolyploid species ser. Tuberosa

1.00

0.98

0.98

0.97

1.00

0.78

0.59

0.991.000.740.77

0.78

10.69

0.71

0.95

0.960.98

0.981.00

1.000.85

1.001.00

1

0.830.96

110.94

0.52

1.000.96

1

0.98

0.99

0.96

0.91

0.760.69

0.98

1.000.99

0.97

0.93

0.751.00

0.740.68

1.001.00

1.00

0.79

1.0072

0.68

10.56

1

0.59

0.950.95

0.66

0.96

10.97

0.57

0.57

S. lycopersicumS. acaule 1

S. acaule 2S. demisum 1

S. demisum 2

S. raphanifolium 1S. raphanifolium 2

S. agrimonifolium 1S. colombianum 1

S longiconicum 1S. violaceimarmoratum

S. microdontumS. lignicauleS. berthaultii

S. tarijenseS. infundibuliforme 1

S. sparsipilum 1

S. bolivienseS. megistacrolobum

S. chacoenseS. gandarillasii

S. brevicaule 1S. infundibuliforme 2

S. brachycarpum 1S. verrucosum

S. hjertingii 1S. stoloniferum 1

S. demisum 3S. demisum 4S. fendleri 1S. schenkii 1S. demisum 5

S. demisum 6S. fendleri 2

S. schenkii 2S. oplosence A1S. oplosence A2

S. oplosence A3

S. oplosence A5S. oplosence A6S. oplosence B3S. oplosence B4

S. oplocense B1S. oplosence B2

S. sparsipilum 2

S. brevicaule 2

S. oplosence A4

S. leptophyes

S. agrimonifolium 2S. agrimonifolium 3S. agrimonifolium 4

S. brachycarpum 2S. colombianum 2S. colombianum 3

S longiconicum 2S. tuquerrense 1S. tuquerrense 2

S. andreanumS. paucijugum 1

S. paucijugum 2S. schenkii 5

S. schenkii 6S. albornozii

S. immite

S. paucijugum 4S. tuquerrense 3S. tuquerrense 4

S. paucijugum 3

S. stenophyllidium

S. cardiophyllum subsp.ehrenbergii 2S. cardiophyllum subsp.ehrenbergii 1

S. fendleri 3

S. stoloniferum 3

S. fendleri 4

S. stoloniferum 2S. hjertingii 2

S. stoloniferum 4

S. bulbocastanumS cardiophyllum

S.trifidum

S. jamesiiS. pinnatisectum

S. schenkii 3S. schenkii 4

S. clarumS. morelliformeS. lesteri

S. polyadenium

S. bukasovii

S. chomatophilum

S. palustreS. etuberosum

Clade 1+2Genome B

Clade 4Genome A

Clade 3Piurana CladeGenome C or D or P


Species in the polyploid series Conicibaccata, Longipedicellata, and the Iopetalum group are derived from allopolyploidization

S. verrucosum is the maternal genome donor for the polyploid species in ser. Longipedicellata, in the Iopetalum group and of S. demissum

The North and Central American B genome species are well distinguish from species of South America

NIA is useful in wild potato phylogenetic analysis

Do potatoes and tomatoes have a Do potatoes and tomatoes have a single evolutionary history? What single evolutionary history? What proportion of the genome supports proportion of the genome supports this history?this history?

Identify COS appropriate for wild potato and wild tomato phylogenetic studies

Generate a molecular data set to reconstruct the phylogeny of diploid wild tomato and wild potato

Reconstruct the evolutionary history of representatives of 14 wild potato and all 13 wild tomato species

ObjectivesObjectives

Materials and methodsMaterials and methods

IngroupIngroup: 13 species of wild tomatoes (section Lycopersicon)14 species of wild potatoes (section Petota)

OutgroupOutgroup:2 species of Solanum section Juglandifolium2 species of Solanum section Lycopersicoides2 species Solanum section Etuberosum1 species Solanum section Dulcamara1 species of Datura

COS selection criteriaCOS selection criteria

Chromosome coverage

Single-copy at least in potato and tomato

Sequence amplification length

Intron and exon content

MethodsMethods

COS fragments were amplified using PCR and direct cycle sequencing and cloning when necessary

COS sequences were edited using STADEN software, and were aligned with CLUSTALX and further manually aligned in MacClade

The sequence analyses were performed using Maximum Parsimony, Maximum Likelihood, Bayesian, and Concordance Analyses

Analyzing data from different sourcesAnalyzing data from different sources

There are 3 different traditional approaches:

1. The total evidence approach

2. The consensus approach

3. The prior agreement approach

Potato Potato datasetdataset

Individual COS

At1g50020 1,100 82.8 IAt1g30580 1000 92.3 IIAt3g03100 850 82.0 IIIAt2g24270 800 86.0 VIIAt1g14000 750 80.7 VAt1g77470 700 83.1 VI

ChromosomeIntron%COS marker Total length

bp

COS selection criteriaCOS selection criteria

Summary of potato phylogenetic Summary of potato phylogenetic analyses by MPanalyses by MP

Locus Exon bp

Exon PI

Intron bp

Intron PI

DNA bp

DNA PI Gap Gap

PITotal

CharactersTotal

PINo.

trees

COS 003 246 1 207 12 453 13 1 0 454 13 2

COS 005 146 4 850 47 996 51 30 13 1026 64 3

COS 008 200 3 102 11 302 14 13 6 315 20 2

COS 009 53 1 1781 44 1834 45 23 9 1857 54 5

COS 07B 16 0 806 40 822 40 9 7 831 47 4

COS 09B 24 0 1157 54 1181 54 14 5 1195 59 5

COS 10B 84 1 576 33 660 34 8 4 668 38 18

COS 011 250 8 402 40 652 48 13 7 665 55 2

COS 01C 171 5 522 40 693 45 12 5 705 50 1

COS 03C 79 2 706 18 785 20 8 1 793 21 1

COS 05C 46 0 1224 52 1270 52 21 9 1291 61 3

COS 02C 217 5 864 28 1081 33 5 4 1086 37 2

Number of total characters and number of Parsimony Informative characters

Summary of potato phylogenetic Summary of potato phylogenetic analyses by MPanalyses by MP

Locus Potato Mexican Clade1+2 blb-bst Piurana

Clade 3Clade

4aClade

4b Clade 4Clade3

with Clade4

Clade2 with

Clade4

Clade3 with

Clade2COS 003 61 56 87 100 no no 68 65 no no

COS 005 99 100 no <51 yes 100 no unres. no no

COS 008 95 66 no 55 yes 89 100 59 no no

COS 009 100 unres. 96 93 yes 98 95 81 no no

COS 07B 100 100 54 100 no no 100 no 90 no

COS 09B 100 60 88 100 yes 64 95 no no 60

COS 10B 100 unres. unres. unres. yes 97 100 no no 100

COS 011 100 100 76 62 unres. unres. 95 100 no no

COS 01C 100 98 76 100 yes 99 60 no <51 no

COS 03C 100 55 53 93 no no 93 no 69 no

COS 05C 100 no no no no no 95 no no no

COS 02C 100 unres. <51 no no <51 no no no no

Bootstrap clade values (%)

Clade 1&2

blb

bst

trf

pld

abz

adr

rap

brc

ver

Clade 3

Clade 4

Potato Potato datasetdataset

Combined COS

Results of ILD test in potatoesResults of ILD test in potatoes

At α= 0.0008 (0.05/66)

COS 3 5 8 9 7bR 09b 10b 11 1c 3c 5c 2c3 _ 0.22 0.12 1 0.48 0.68 0.11 1 0.54 0.72 0.047 0.005

5 0.27 _ 0.08 0.06 0.0001 0.06 0.0016 0.27 0.11 0.14 0.0001 0.09

8 0.17 0.06 _ 0.03 0.07 0.08 0.04 0.15 0.07 0.10 0.0046 0.0037

9 1.00 0.04 0.02 _ 0.0002 0.70 0.15 1.00 0.0065 0.15 0.02 0.03

7bR 0.39 0.0001 0.05 0.0003 _ 0.56 0.01 0.07 0.02 1.00 0.0001 0.0001

09b 0.66 0.04 0.10 0.70 0.48 _ 1.00 0.07 1.00 0.82 0.02 0.0061

10b 0.11 0.0017 0.10 0.12 0.0022 1.00 _ 0.0006 0.26 0.28 0.0009 0.0014

11 1.00 0.21 0.15 1.00 0.03 0.04 0.0006 _ 0.0064 0.63 0.0002 0.03

1c 0.60 0.14 0.14 0.02 0.02 1.00 0.36 0.0063 _ 0.48 0.0001 0.0002

3c 0.73 0.18 0.09 0.19 1.00 0.85 0.42 0.75 0.41 _ 0.19 0.02

5c 0.0421 0.0001 0.0043 0.0074 0.0004 0.0102 0.0018 0.0001 0.0001 0.1663 _ 0.0037

2c 0.0032 0.13 0.0047 0.0224 0.0001 0.0062 0.0014 0.0057 0.0001 0.0149 0.0028 _

Phylogenetic trees based on a combined Phylogenetic trees based on a combined analysisanalysis

12 COS 6 COS 3 COS

2 COS1 COS

Concordance analysesConcordance analyses

Tomato datasetTomato dataset

Combined COS

Phylogenetic Phylogenetic tree tree based on a combined analysisbased on a combined analysis

Concordance analysesConcordance analyses


Intron contents more than 60% are the best to investigate relationships among closely related species

The total evidence approach produce a completely resolved potato phylogeny

In potato, three COS are enough to obtain a resolved phylogeny

The “prior agreement” approach and “concordance analysis” identified two histories in potato, one of them is the same as that obtained by “total evidence”


COS data support the segregation of S. peruvianuminto at least three species

The total evidence approach completely resolved 19 of the 21 nodes in tomato

COS are useful for potato and tomato phylogenetic studies

Concordance analyses is useful to summarize discordance among genes

AcknowledgementsAcknowledgements

Dr. David Spooner

People in Spooner’s lab

Dr. David Baum and Cecile Ane

Alberto Salas

University of Wisconsin Plant Breeding and Plant Genetics Program

US Potato and Tomato genebanks

Unraveling the evolutionary history of wild potatoes and...

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