Supporting InformationBurns and Strauss 10.1073/pnas.1013003108

SI Results and DiscussionPhylogeny Estimation. As in previous studies (1, 2), the methodof phylogenetic estimation had minimal influence on qualita-tive results for this study. The estimates of phylogenetic dis-tance from phylomatic and maximum likelihood phylogenybased on four genes (Fig. S1) were highly significantly positivecorrelated (Pearson product moment correlation = 0.84,P < 0.0001; model includes species as a covariate, slope =0.001, adjusted R2 = 0.74, F value = 7,910.3, P < 0.0001). Wepresent results using phylogenetic distance estimated from themaximum likelihood (ML) phylogeny with branch lengthsscaled using fossil calibration, because it was more resolvedthan the phylomatic phylogeny (Fig. S1). The results formodels using phylogenetic distance estimated from phylomaticwere very similar to the results for models using phylogeneticdistance estimated from our time-calibrated ML phylogeny,

patristic distances from the ML phylogeny, or taxonomy(Tables S4 and S5).

Germination Niche. A negative relationship between germinationsuccess and phylogenetic distance using taxonomic rankswas drivenby performance at the most distant relatives’ sites (Fig. S2) (P <0.01). If we did not consider distant relatives, then there was norelationship between germination and phylogenetic distance (P >0.10). This result suggests that germination and early survival wereconserved across phylogenetic distances up to family rank (mean=81 ± 0.75 Mya SE) (Fig. S2) (3).There was only one species that germinated significantly better

at an away site than at a conspecific site, Trifolium gracilentum(z value = 2.69; P < 0.01), although survival for this species, aftergermination, was not higher at away sites (z value = 0.0001; P >0.95). There were no species that performed significantly betterat away sites than conspecific sites for their first 3 mo of life.

1. Cadotte MW, Cardinale BJ, Oakley TH (2008) Evolutionary history and the effect ofbiodiversity on plant productivity. Proc Natl Acad Sci USA 105:17012–17017.

2. Cadotte MW, Cavender-Bares J, Tilman D, Oakley TH (2009) Using phylogenetic,functional and trait diversity to understand patterns of plant community productivity.PLoS ONE 4:e5695.

3. R Development Core Team (2008) R: A language and environment for statisticalcomputing, reference index version 2.8.1. R Foundation for Statistical Computing,Vienna, Austria, ISBN 3-900051-07-0. Available at http://www.R-project.org.

Burns and Strauss www.pnas.org/cgi/content/short/1013003108 1 of 10

Supporting Information Corrected June 21, 2012

Fig. S1. Maximum likelihood (ML) phylogeny based on four DNA regions (rbcL, matK, ITS, and trnL) (Table S1) generated in Garli (version 0.951) (1). Bootstrapvalues >50% from an ML bootstrap analysis with 100 replicates are shown above the branches. Additional runs of Garli with different random seeds resulted inidentical typology and nearly identical branch lengths. Rooted using Amborella trichopoda and archived in TreeBASE (SN4955). This phylogeny was used in thecalculation of phylogenetic distance for both the germination experiment and the species interaction experiment. Habitats are shown as coastal prairie, dunes,beach, marsh, rocky slopes, seeps, and wetland.

1. Zwickl DJ (2006) Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. PhD dissertation (Univ ofTexas, Austin, TX).

Burns and Strauss www.pnas.org/cgi/content/short/1013003108 2 of 10

0.0

0.1

0.2

0.3

0.4

Ger

min

atio

n (a

vera

ge p

ropo

rtion

)

Conspecific Congener Confamilial Distant 0.0

0.1

0.2

Last

cen

sus

Conspecific Congener Confamilial Distant

A B

Fig. S2. Mean proportion germination and mean survival to last census. Taxonomic ranks indicate conservation of the germination niche. (A) The germinationniche exhibited taxonomic signal (P < 0.01). The average proportion total germination across species for different ranks (conspecific, congener, confamilial, anddistant relatives’ sites). (B) The germination and survival niches exhibited taxonomic signal (P < 0.01). The total seedlings that germinated and survived to thelast census are shown on the y axis. Note that phylogenetic distance (measured on the ML phylogeny) (Fig. S1) scaled with taxonomic rank (Conspecific = 0,Congener = 30 ± 0.62, Confamilial = 81 ± 0.75, Distant = 264 ± 1.36 mean ± SE).

Fig. S3. Experimental design for the species interaction experiment to determine whether species interact more strongly with closer than with more distantrelatives. Each of 12 focal species (asterisks) was subjected to the interactor × soil experiment. Confamilial and congeneric taxa for this experiment wererandomly selected from the species list for Bodega Bay Marine Reserve.

0.0

0.1

0.2

0.3

0.4

0.5

Tota

l bio

mas

s (g

)

Alone Conspecific Congener Confamilial

Conspecific Congener Confamilial Potting soil

NA 0 30 ± 0.62 81 ± 0.75 phylogenetic distance (Mya)

Fig. S4. Total biomass was a function of soil type (zero inflation model count component: χ2 = 421.94, P < 0.001; zero inflation component: χ2 = 6.35, P = 0.10)and phylogenetic distance to the interacting species (zero inflation model count component: χ2 = 77.34, P < 0.001; zero inflation component: χ2 = 29.88, P <0.01). Squares are conspecific soil, triangles are congener soil, diamonds are confamilial soil, and circles are potting soil (means ± SE).

Burns and Strauss www.pnas.org/cgi/content/short/1013003108 3 of 10

Table

S1.

Sequen

cesusedto

estimatetheMLtree

(Fig.S1

)to

estimatephylogen

etic

distances

Species

SpeciesusedforrbcL

rbcL

SpeciesusedformatK

matK

SpeciesusedforITS

ITS

SpeciesusedfortrnL

trnL

Ach

illea

millefoliu

mAch

illea

millefoliu

mEU

3849

38Ach

illea

millefoliu

mEU

3853

15Ach

illea

millefoliu

mEU

7968

91Ach

illea

millefoliu

mGQ24

4530

Agoserisap

argioides

NA

NA

NA

NA

Agoserisheterophylla

AY21

8965

Agoserisretrorsa

AF2

0836

4Agropyron

Agropyroncristatum

AY83

6156

NA

NA

Agropyroncristatum

AY74

0891

Agropyroncristatum

AY74

0792

Agrostis

Agrostiscapillaris

AY39

5527

Agrostiscapillaris

FJ39

5420

Agrostiscapillaris

FM17

9384

Agrostisscab

raGQ24

4542

Amborella

trichopoda

Amborella

trichopoda

L126

28Amborella

trichopoda

AF4

6528

4NA

NA

Amborella

trichopoda

AY14

5324

Ambrosiach

amissonis

Ambrosiatrifida

GQ24

8548

Ambrosiatrifida

GQ24

8078

NA

NA

NA

NA

Amorphafrutico

saAmorphafrutico

saU74

212

Amorphafrutico

saAF2

7086

1Amorphafrutico

saGQ28

1030

Amorphafrutico

saAF2

0889

9Anap

halismargaritacea

NA

NA

NA

NA

Anap

halismargaritacea

AF0

4693

7Anap

halismargaritacea

AF1

4173

2Andropogon

Andropogongerardii

AJ784

818

Andropogongerardii

AF1

4457

7NA

NA

Andropogonfastigiatus

DQ00

4977

Artem

isia

pycnocephala

Artem

isia

annua

DQ00

6057

Artem

isia

triden

tata

AF4

5677

6NA

NA

Artem

isia

tilesii

GQ24

4617

Asclepias

Asclepiastuberosa

EF59

0504

Asclepiastuberosa

GQ24

8084

Asclepiascrispa

AM39

6882

Asclepiassyriaca

EF45

6111

Bouteloua

Boutelouagracilis

AJ784

829

Boutelouacu

rtipen

dula

AF1

4457

8Boutelouacu

rtipen

dula

EF06

0133

Boutelouatrifida

EF15

6676

Chen

opodium

Chen

opodium

botrys

AY27

0080

Chen

opodium

botrys

AY51

4835

Chen

opodium

murale

GQ47

0546

Chen

opodium

glaucu

mGQ24

4790

Chlorogalum

pomeridianum

Chlorogalum

pomeridianum

Z692

28NA

NA

NA

NA

Chlorogalum

pomeridianum

AJ232

449

Cirsium

occiden

tale

NA

NA

NA

NA

Cirsium

occiden

tale

AF4

4370

3NA

NA

Cirsium

quercetorum

NA

NA

NA

NA

Cirsium

quercetorum

AF4

4370

6NA

NA

Coreopsis

Coreopsisgrandiflora

L136

42Coreopsisgrandiflora

AY55

1493

Coreopsisve

rticillata

EU05

3653

Coreopsisgigan

tea

EU04

7872

Cyp

erus

Cyp

erustenellus

AF4

4951

4Cyp

erusalternifoliu

sDQ40

1373

NA

NA

NA

NA

Elym

us

Elym

usfarctus

AM84

9350

Elym

usrepeX

FJ39

5421

Elym

usburchan

-buddae

AY74

0875

Elym

ustrachycau

lus

GQ24

4905

Epilo

bium

cilia

tum

NA

NA

NA

NA

Epilo

bium

cilia

tum

L280

15Ep

ilobium

cilia

tum

EF41

6726

Erigeronfolio

sus

NA

NA

NA

NA

Erigeronfolio

sus

AF1

1853

2NA

NA

Erigeronglaucu

sNA

NA

NA

NA

Erigeronglaucu

sAF1

1849

9NA

NA

Eriogonum

Eriogonum

tomen

tosum

AF2

9713

4Eriogonum

lemmonii

EF43

8007

Eriogonum

alatum

FJ15

4472

Eriogonum

flav

um

AJ312

250

Eriophyllum

NA

NA

Eriophyllum

congdonii

AF3

9169

1Eriophyllum

stae

chad

ifoliu

mAF2

2928

4NA

NA

Euphorbia

Euphorbia

humifusa

AB23

3884

Euphorbia

humifusa

AB23

3780

Euphorbia

spinosa

EU65

0625

Euphorbia

disco

lor

GQ24

4963

Frag

aria

chilo

ensis

NA

NA

NA

NA

Frag

aria

chilo

ensis

FJ35

6164

NA

NA

Frag

aria

vesca

NA

NA

Frag

aria

vesca

AF2

8810

2Frag

aria

vesca

AJ511

771

Frag

aria

vesca

EF01

0971

Fran

kenia

Fran

kenia

jamesii

AY09

9918

Fran

kenia

corymbosa

AY04

2587

NA

NA

NA

NA

Galium

Galium

mullu

go

FJ39

5593

Galium

mullu

go

FJ39

5417

NA

NA

Galium

trifidum

GQ24

4992

Gnap

halium

purpureum

NA

NA

NA

NA

Gnap

halium

purpureum

AY94

7411

NA

NA

Gnap

halium

ramosissim

um*

NA

NA

NA

NA

NA

NA

NA

NA

Helen

ium

NA

NA

NA

NA

Helen

ium

autumnale

AH01

4025

Helen

ium

bigelovii

DQ39

5175

Juncu

sbreweri*

NA

NA

NA

NA

NA

NA

NA

NA

Juncu

seffuses

Juncu

seffusus

L126

81Juncu

seffusus

AB08

8803

Juncu

seffusus

AY97

3509

Juncu

seffusus

AY43

7976

Juncu

slesueu

rii*

NA

NA

NA

NA

NA

NA

NA

NA

Koeleria

Koeleria

pyram

idata

AJ784

825

Koeleria

capen

sis

AM23

4558

Koeleria

capen

sis

FM17

9413

Koeleria

asiatica

GQ24

5059

Lactuca

Lactuca

sativa

L140

73La

ctuca

sativa

EU04

6561

Lactuca

sativa

L139

57La

ctuca

sibirica

GQ24

5063

Lesped

eza

Lesped

ezacu

nea

taU74

215

Lesped

ezacu

nea

taEU

7174

16Le

sped

ezaleptostachya

FJ40

9475

Lesped

ezacu

nea

taEU

7173

02Le

ymusmollis

NA

NA

NA

NA

Leym

usmollis

EF60

1996

Leym

usmollis

GQ24

5078

Liatris

Liatriscylin

dracea

AY81

6235

NA

NA

Liatrisolig

ocephala

AY80

4147

NA

NA

Limonium

Limonium

thinieXe

GQ24

8629

Limonium

thinieXe

GQ24

8145

Limonium

arboresceX

EU41

0356

Limonium

spectabile

AJ391

330

Linaria

canad

eXis

Linaria

vulgaris

GQ24

8631

Linaria

vulgaris

GQ24

8146

NA

NA

Linaria

canad

eXis

AF0

3486

7Lo

tushee

rman

nii*

NA

NA

NA

NA

NA

NA

NA

NA

Lotuswrangelianus

NA

NA

NA

NA

Lotuswrangelianus

AF4

5017

4NA

NA

Lupinusperen

nis

Lupinusperen

nis

Z700

58NA

NA

Lupinusperen

nis

Z721

62/Z72

163

Lupinusperen

nis

DQ41

7058

Burns and Strauss www.pnas.org/cgi/content/short/1013003108 4 of 10

Table

S1.Cont.

Species

SpeciesusedforrbcL

rbcL

SpeciesusedformatK

matK

SpeciesusedforITS

ITS

SpeciesusedfortrnL

trnL

Lupinusarboreus

Lupinusarboreus

Z700

54NA

NA

Lupinusarboreus

DQ52

4196

Lupinusarboreus

DQ41

7083

Lupinusch

amissonis

NA

NA

NA

NA

Lupinusch

amissonis

DQ52

4219

Lupinusch

amissonis

DQ41

7084

Lupinusnan

us

Lupinusnan

us

Z700

56NA

NA

Lupinusnan

us

AH00

6084

Lupinusnan

us

DQ41

7078

Lupinusva

riicolor*

NA

NA

NA

NA

NA

NA

NA

NA

Luzu

laco

mosa

NA

NA

NA

NA

Luzu

laco

mosa

AY72

7776

Luzu

laco

mosa

DQ09

9457

Mag

nolia

grandiflora

Mag

nolia

grandiflora

EF59

0545

Mag

nolia

grandiflora

GQ24

8151

Mag

nolia

grandiflora

EU59

3550

Mag

nolia

grandiflora

FJ49

0796

Monardafistulosa

Monardafistulosa

Z374

19Monardafistulosa

AY94

3528

Monardafistulosa

DQ66

7318

Monardafistulosa

DQ66

7506

Monardella

NA

NA

NA

NA

Monardella

hyp

oleuca

AY50

6637

Monardella

hyp

oleuca

AY50

6600

Nan

dinadomestica

Nan

dinadomestica

FJ44

9859

Nan

dinadomestica

AB06

9830

Nan

dinadomestica

EU92

6493

Nan

dinadomestica

AY36

2453

Nem

ophila

men

ziesii

NA

NA

NA

NA

Nem

ophila

meX

iezii

AF0

9118

3NA

NA

Panicum

Panicum

virgatum

AY63

2368

Panicum

virgatum

EU43

4294

Panicum

virgatum

DQ00

5062

Panicum

virgatum

AY28

9592

Potentilla

anserina

NA

NA

Potentilla

anserina

AF2

8811

3Po

tentilla

anserina

AJ511

773

Potentilla

anserina

GQ24

5311

Quercu

sQuercu

sserrata

AB06

0576

Quercu

sserrata

AB06

0067

Quercu

spetraea

EU62

8558

Quercu

sserrata

AB06

3538

Ran

uncu

lus

californicus

NA

NA

Ran

uncu

luscalifornicus

FM24

2782

Ran

uncu

luscalifornicus

FM24

2846

NA

NA

Rumex

occiden

talis

Rumex

occiden

talis

AF3

7254

6NA

NA

NA

NA

NA

NA

Rumex

salicifoliu

s*NA

NA

NA

NA

NA

NA

NA

NA

Saginamax

ima

NA

NA

Saginapilifera

AY93

6291

NA

NA

Saginasaginoides

GQ24

5423

Salvia

Salvia

offi

cinalis

AY57

0431

Salvia

coccinea

AY84

0147

Salvia

miltiorrhiza

FJ43

3876

Salvia

przew

alskii

EF05

3402

Schizachne

NA

NA

Schizachnepurpurascen

sFM

2531

26Schizachnepurpurascen

sFM

1794

32NA

NA

Scirpusmicrocarpus

NA

NA

NA

NA

Scirpusmicrocarpus

AF2

8496

1Scirpusmicrocarpus

AF1

6495

2Silene

Silenearmeria

AB51

6354

Silenelatifolia

EF64

7048

Sileneviscaria

FJ38

4058

Sileneviolascen

sGQ24

5546

Sisyrinch

ium

Sisyrinch

ium

montanum

AY14

9369

Sisyrinch

ium

micranthum

AJ579

982

Sisyrinch

ium

striatum

AF1

3083

8Sisyrinch

ium

montanum

AY14

7486

Solid

ago

Solid

agorugosa

EU67

7031

NA

NA

NA

NA

Solid

agovirgau

rea

GQ24

5553

Sorghastrum

nutans

Sorghastrum

nutans

EF12

5121

NA

NA

Sorghastrum

nutans

DQ00

5080

Sorghastrum

nutans

DQ00

5102

Trifoliu

mbarbigerum

NA

NA

NA

NA

Trifoliu

mbarbigerum

DQ31

2010

Trifoliu

mbarbigerum

DQ31

1743

Trifoliu

mfucatum

NA

NA

NA

NA

Trifoliu

mfucatum

DQ31

2054

Trifoliu

mfucatum

DQ31

1792

Trifoliu

mgracilentum

NA

NA

Trifoliu

mgracilentum

AF5

2212

3Trifoliu

mgracilentum

DQ31

2060

Trifoliu

mgracilentum

DQ31

1798

Trifoliu

mmacraei

NA

NA

NA

NA

Trifoliu

mmacraei

DQ31

2085

Trifoliu

mmacraei

DQ31

1829

Trifoliu

mmicrocephalum

NA

NA

Trifoliu

mmicrocephalum

AF5

2212

8Trifoliu

mmicrocephalum

DQ31

2092

Trifoliu

mmicrocephalum

DQ31

1837

Trifoliu

mmicrodon

NA

NA

NA

NA

Trifoliu

mmicrodon

DQ31

2093

Trifoliu

mmicrodon

DQ31

1838

Trifoliu

mva

rieg

atum

NA

NA

NA

NA

Trifoliu

mva

rieg

atum

DQ31

2185

Trifoliu

mva

rieg

atum

DQ31

1941

Trifoliu

mworm

skioldii

NA

NA

Trifoliu

mworm

skioldii

AF5

2213

8Trifoliu

mworm

skioldii

DQ31

2195

Trifoliu

mworm

skioldii

DQ31

1951

Triphysaria

eriantha

NA

NA

NA

NA

Triphysaria

eriantha

EF10

3735

Triphysaria

eriantha

EF10

3891

Dataarch

ived

inTree

BASE

(SN49

55).Se

quen

cesusedto

estimateaphylogen

yforspeciesat

BMRan

destimatethephylogen

eticdistancesam

ongspecies.Gen

Ban

kaccessionnumbersareshownforsequen

ces

weused.

*Speciesforwhichnosequen

ceswereav

ailable.

Burns and Strauss www.pnas.org/cgi/content/short/1013003108 5 of 10

Table S2. Germination analyses model selection

Species BPhylogenetic

distance S X B S x PD B x PDGeographicdistance Habitat

AICc – originalpaper (bold is model

with lowest)

AICc – with correctedtransformation

(bold is model with lowest)

Total Germination (SqrtPropG)X X X -1201.67 69.95X -1153.56 59.01X X -1151.25 67.57X X -1141.68 70.51X X X X -1139.18 78.56X X X -1139.18 79.20X X X X -1136.87 97.44

X -1130.41 96.75X -1124.40 96.06

X -1123.56 101.89X -1110.28 88.25

X X -1108.74 90.30X X X X -1098.38 77.71X X X X X -1095.31 97.01X X X X X -1061.21 96.81X X X X X -996.87 78.61X X X X X X X -994.25 99.04X X X X X X -992.74 96.91X X X X X X X -989.75 97.60X X X X X X X X -987.28 99.69Last Census (SqrtPropLC)X X X -926.00 -23.56

X -890.88 -29.74X -890.75 -37.44

X -889.84 -30.20X -880.48 -37.34X X -879.26 -29.57

X -869.60 -38.00X X -869.06 -36.74

X X -868.87 -23.93X X X -867.35 -15.87X X X X -864.70 2.26X X X X -823.74 -15.47X X X X X -820.24 2.71X X X X X X X NA* 0.25X X X X X X X NA -2.30X X X X X X NA -4.43X X X X X NA -0.008X X X X X NA -1.019X X X X NA -18.93X X X X X X X X NA 6.34

*Owing to incorrect transformation, not all models could be run on the first summary for last census.

Burns and Strauss www.pnas.org/cgi/content/short/1013003108 6 of 10

Table S3. Tests for generality of patterns of total germination and survival to the last censuswith respect to sign and habitat

Conspecific site and relative’s planting site

Coastal prairie

Coastal prairie Dunes Marsh Beach

Total germination− 13 8 1 2+ 7 7 4 0χ2 1.80 0.07 NA NAP value 0.18 0.80 NA NALast census− 14 7 1 2+ 2 6 3 0χ2 9.00 0.08 NA NAP value 0.00 0.78 NA NA

Tests for generality of patterns of total germination with respect to sign and gross habitat type. For example,species from coastal prairie populations might be expected to do worse in dunes or marsh habitat, potentiallydriving the negative relationship between phylogenetic distance and germination. In such a case, we wouldexpect species whose conspecific site is coastal prairie to do equally well in coastal prairie away sites (e.g., haveno pattern with respect to − or + signs describing the relationship between phylogenetic distance and germi-nation) but less well in dune, marsh, or beach sites (have a greater ratio of − to + signs). We see no evidence thatthe negative relationship between germination success and phylogenetic distance was driven by differences inperformance across habitat types. In fact, we see the strongest evidence for that relationship in coastal prairiespecies planted into coastal prairie away sites, contrary to the hypothesis that gross habitat differences drive thepattern. The majority of species were planted into coastal prairie, such that these tests could only be conductedfor coastal prairie conspecific sites.

Burns and Strauss www.pnas.org/cgi/content/short/1013003108 7 of 10

Table

S4.

Summaryofgerminationdata,

withav

erag

etotalgermination/ave

ragegerminationan

dsu

rvival

tothelast

censu

sacross

plantingsitesofrelative

sat

Bodeg

aMarine

Reserve

.Slopes

from

Fig.1remove

dan

dtyposco

rrected

Species

Conspecific1

Conspecific2

Close

1Close

2Close

3(only

plantedforCirsium)

Distant1

Distant2

Ach

illea

millefoliu

mAch

illea

millefoliu

mAch

illea

millefoliu

mAnap

halismargaritea

eGnap

halium

ramosissim

um

NA

Galium

trifidum

Eriogonum

latifoliu

m

0.15

/0.00

0.00

/NA

0.05

/0.00

0.30

/0.00

0.30

/0.10

0.15

/0.00

Ambrosia

cham

issonis

Ambrosia

cham

issonis

Ambrosia

cham

issonis

Erigeronfolio

sus

Erigeronglaucu

sNA

Trifoliu

mbarbigerum

Sisyrinch

ium

californicum

0.55

/0.58

0.35

/0.35

0.05

/0.10

0.05

/0.00

0.40

/0.11

0.05

/0.00

Anap

halis

margaritea

eAnap

halis

margaritea

eAnap

halis

margaritea

eGnap

halium

purpureum

Helen

ium

puberulum

NA

Saginamax

ima

Trifoliu

mmacraei

0.25

/0.20

0.10

/0.05

0.05

/0.00

0.25

/0.05

0.20

/0.00

0.20

/0.00

Artem

isia

pycnocephala

Artem

isia

pycnocephala

Artem

isia

pycnocephala

Ambrosiach

amissonis

Eriophyllum

stae

chad

ifoliu

mNA

Trifoliu

mmicrocephalum

Scirpusmicrocarpus

0.25

/0.15

0.35

/0.17

0.05

/0.06

0.00

/0.00

0.35

/0.05

0.08

/0.00

Cirsium

occiden

tialis

Cirsium

occiden

tialis

Cirsium

occiden

tialis

Cirsium

quercetorum

Artem

isia

pycnocephala

Gnap

halium

ramosissim

um

Leym

usmollis

Juncu

slesueu

rii

0.25

/0.00

0.08

/0.33

0.30

/0.10

0.21

/0.00

0.45

/0.30

0.15

/0.06

0.30

/0.20

Cirsium

quercetorum

Cirsium

quercetorum

Cirsium

quercetorum

Cirsium

occiden

talis

Anap

halis

margaritea

eAmbrosiach

amissonis

Trifoliu

mmacraei

Potentilla

anserina

0.20

/0.10

0.00

/0.00

0.15

/0.10

0.00

/0.00

0.00

/0.00

0.00

/0.00

0.10

/0.10

Erigeronfolio

sus

Erigeronfolio

sus

Erigeronfolio

sus

Erigeronglaucu

sHelen

ium

puberulum

NA

Monardella

villo

saRumex

occiden

tialis

0.15

/0.00

0.14

/0.00

0.50

/0.00

0.25

/0.05

0.00

/NA

0.15

/0.00

Erigeronglaucu

sErigeronglaucu

sErigeronglaucu

sErigeronfolio

sus

Gnap

halium

ramosissim

um

NA

Nem

ophila

men

ziesii

Juncu

sbreweri

0.00

/NA

0.45

/0.00

0.24

/0.00

0.35

/0.15

0.10

/0.00

0.35

/0.21

Eriogonum

latifoliu

mEriogonum

latifoliu

mEriogonum

latifoliu

mRumex

occiden

tialis

Rumex

salicifoliu

sNA

Pentagramma

triangularis

Eriophyllum

stae

chad

ifoliu

m0.00

/0.00

0.00

/0.00

0.80

/0.53

0.10

/0.00

0.15

/0.00

0.00

/0.00

Eriophyllum

stae

chad

ifoliu

mEriophyllum

stae

chad

ifoliu

mEriophyllum

stae

chad

ifoliu

mSo

lidag

ocalifornica

Gnap

halium

purpureum

NA

Rumex

salicifoliu

sTrifoliu

mworm

skioldii

0.15

/0.00

0.10

/0.05

0.20

/0.00

0.45

/0.00

0.10

/0.05

0.45

/0.05

Gnap

halium

purpureum

Gnap

halium

purpureum

Gnap

halium

purpureum

Gnap

halium

ramosissim

um

Eriophyllum

stae

chad

ifoliu

mNA

Trifoliu

mva

rieg

atum

Rumex

occiden

tialis

0.00

/NA

0.00

/0.00

0.25

/0.00

0.25

/0.00

0.00

/0.00

0.05

/0.00

Gnap

halium

ramosissim

um

Gnap

halium

ramosissim

um

Gnap

halium

ramosissim

um

Gnap

halium

purpureum

Erigeronglaucu

sNA

Cirsium

occiden

tale

Rumex

occiden

tialis

0.25

/0.00

0.05

/0.00

0.10

/0.00

0.00

/NA

0.30

/0.00

0.00

/0.00

Helen

ium

puberulum

Helen

ium

puberulum

Helen

ium

puberulum

Cirsium

quercetorum

Gnap

halium

ramosissim

um

NA

Epilo

bium

cilia

tum

Juncu

slesueu

rii

0.15

/0.10

0.20

/0.10

0.00

/NA

0.45

/0.30

0.00

/0.00

0.30

/0.30

Juncu

sbreweri

Juncu

sbreweri

Juncu

sbreweri

Juncu

slesueu

rii

Luzu

laco

mosa

NA

Chen

opodium

californicum

Lupinusva

riicolor

0.00

/0.00

0.10

/0.10

0.00

/0.00

0.05

/0.05

0.00

/0.00

0.05

/0.00

Juncu

slesueu

rii

Juncu

slesueu

rii

Juncu

slesueu

rii

Juncu

sbreweri

Luzu

laco

mosa

NA

Lupinusarboreus

Lupinusnan

us

0.00

/0.00

0.05

/0.00

0.00

/0.00

0.00

/0.00

0.00

/0.00

0.10

/0.00

Lotushee

rman

iiLo

tushee

rman

iiLo

tushee

rman

iiLu

pinusnan

us

Lotuswrangelianus

NA

Frag

aria

chilo

ensis

Linaria

canad

ensis

0.40

/0.20

0.00

/0.00

0.00

/0.00

0.00

/0.00

0.00

/0.00

0.00

/NA

Burns and Strauss www.pnas.org/cgi/content/short/1013003108 8 of 10

Table

S4.Cont.

Species

Conspecific1

Conspecific2

Close

1Close

2Close

3(only

plantedforCirsium)

Distant1

Distant2

Lupinusarboreus

Lupinusarboreus

Lupinusarboreus

Trifoliu

mmacraei

Lupinusva

riicolor

NA

Frag

aria

chilo

ensis

Potentilla

anserina

0.10

/NA

0.10

/0.00

0.30

/0.30

0.15

/0.10

0.30

/0.10

0.40

/0.00

Lupinusnan

us

Lupinusnan

us

Lupinusnan

us

Lupiusch

amissonis

Trifoliu

mva

rieg

atum

NA

Cyp

eruserag

rostis

Luzu

laco

mosa

0.65

/0.65

0.00

/NA

0.05

/0.00

0.40

/0.20

0.44

/0.06

0.05

/0.00

Lupinusva

riicolor

Lupinusva

riicolor

Lupinusva

riicolor

Lupinus

cham

issonis

Lotushee

rman

iiNA

Agoserisap

argioides

Solid

agocalifornica

0.50

/0.20

0.10

/0.00

0.00

/0.00

0.20

/0.00

0.10

/0.10

0.00

/0.00

Lupinus

cham

issonis

Lupinus

cham

issonis

Lupinusch

amissonis

Trifoliu

mworm

skioldii

Lupinusnan

us

NA

Nem

ophila

men

ziesii

Helen

ium

puberulum

0.50

/0.00

0.50

/0.00

1.00

/0.50

0.50

/0.50

0.50

/0.00

0.50

/0.00

Luzu

laco

mosa

Luzu

laco

mosa

Luzu

laco

mosa

Juncu

sbreweri

Juncu

slesueu

rii

NA

Eriogonum

latifoliu

mTrifoliu

mbarbigerum

0.00

/0.00

0.00

/0.00

0.20

/0.00

0.00

/0.00

0.00

/0.00

0.00

/0.00

Potentilla

anserina

Potentilla

anserina

Potentilla

anserina

Frag

aria

vesca

Frag

aria

chilo

ensis

NA

Lupinusnan

us

Cirsium

quercetorum

0.20

/0.10

0.25

/0.33

0.00

/0.00

0.00

/0.00

0.05

/0.00

0.00

/0.00

Rumex

occiden

tialis

Rumex

occiden

tialis

Rumex

occiden

tialis

Rumex

salicifoliu

sEriogonum

latifoliu

mNA

Agrostisblasdalei

Trifoliu

mmicrocephalum

0.35

/0.00

0.10

/0.00

0.45

/0.40

0.00

/0.00

0.40

/0.30

0.65

/0.15

Solid

agocalifornica

Solid

ago

californica

Solid

agocalifornica

Gnap

halium

purpureum

Eriophyllum

stae

chad

ifoliu

mNA

Lotuswrangelianus

Lupinusva

riicolor

0.35

/0.10

0.60

/0.05

0.25

/0.05

0.15

/0.00

0.35

/0.00

0.00

/0.00

Trifoliu

mbarbigerum

Trifoliu

mbarbigerum

Trifoliu

mbarbigerum

Trifoliu

mmacraei

Lupiusch

amissonis

NA

Chlorogalum

pomeridianum

Eriophyllum

stae

chad

ifoliu

m0.50

/0.15

0.35

/0.20

0.35

/0.15

0.15

/0.00

0.00

/0.00

0.00

/0.00

Trifoliu

mfucatum

Trifoliu

mfucatum

Trifoliu

mfucatum

Lotushee

rman

iiTrifoliu

mmacraei

NA

Ran

uncu

luscalifornicus

Erigeronfolio

sus

0.30

/0.11

0.25

/0.10

0.15

/0.05

0.15

/NA

0.50

/0.21

0.25

/0.00

Trifoliu

mgracilentum

Trifoliu

mgracilentum

Trifoliu

mgracilentum

Trifoliu

mmacraei

Lupinusarboreus

NA

Cirsium

quercetorum

NA

0.22

/0.00

0.11

/0.00

0.25

/0.00

0.95

/0.00

NA/NA

NA

Trifoliu

mmacraei

Trifoliu

mmacraei

Trifoliu

mmacraei

Trifoliu

mworm

skioldii

Lotushee

rman

iiNA

Nem

ophila

men

ziesii

Gnap

halium

ramosissim

um

0.45

/0.30

0.45

/0.25

0.30

/0.00

0.10

/0.10

0.25

/0.11

0.35

/0.25

Trifoliu

mmicrocephalum

Trifoliu

mmicrocephalum

Trifoliu

mmicrocephalum

Trifoliu

mva

rieg

atum

Lupinusarboreus

NA

Leym

usmollis

Eriogonum

latifoliu

m0.45

/0.30

0.45

/0.20

0.40

/0.20

0.20

/0.00

0.55

/0.20

0.15

/0.00

Trifoliu

mmicrodon

Trifoliu

mmicrodon

Trifoliu

mmicrodon

Trifoliu

mgracilentum

NA

NA

Allium

dichlamyd

eum

Helen

ium

puberulum

0.40

/0.20

0.40

/0.00

0.40

/0.00

NA/NA

0.60

/0.20

0.60

/0.00

Trifoliu

mva

rieg

atum

Trifoliu

mva

rieg

atum

Trifoliu

mva

rieg

atum

Lupinusarboreus

Trifoliu

mmacraei

NA

Juncu

seffusus

Solid

agocalifornica

0.60

/0.05

0.60

/0.35

0.25

/0.00

0.40

/0.20

0.15

/0.00

0.50

/0.05

Trifoliu

mworm

skioldii

Trifoliu

mworm

skioldii

Trifoliu

mworm

skioldii

Trifoliu

mmicrocephalum

Lupinus

cham

issonis

NA

Triphysaria

eriantha

Cirsium

quercetorum

0.90

/0.18

0.40

/0.40

0.40

/0.15

0.55

/0.10

0.20

/0.05

0.05

/0.00

Additional

speciesdestinationsweread

ded

totheex

perim

entaldesignforthetw

oCirsium

species.

Burns and Strauss www.pnas.org/cgi/content/short/1013003108 9 of 10

Table

S5.

Relativeinteractionintensity

asafunctionoftrea

tmen

tsincludingsp

eciesinteractoran

dso

ilen

vironmen

t

Speciesinteractor

trea

tmen

t

Conspecificsoil

Congen

ersoil

Confamilial

soil

Pottingsoil

Slope

CS

CG

CF

Slope

CS

CG

CF

Slope

CS

CG

CF

Slope

CS

CG

CF

Erigeronfolio

sus

+−1.00

−1.00

−0.96

+−0.76

−0.81

−0.75

+−0.79

−0.95

−1.00

NA

−1.00

−1.00

−1.00

Erigeronglaucu

s+

0.74

0.74

0.92

+0.50

0.88

0.92

+0.68

0.79

0.76

—−0.16

−0.02

−0.20

Frag

aria

chilo

ensis

+0.55

0.94

0.95

+0.75

0.72

0.93

+0.50

0.92

0.87

—0.77

0.90

0.59

Frag

aria

vesca

+0.64

0.70

0.90

+0.78

0.88

0.87

+0.11

−0.05

−0.33

+0.59

0.84

0.89

Gnap

halium

purpureum

+0.69

0.88

0.72

—−0.16

−0.26

−1.00

+−0.60

−0.85

−0.73

—−0.72

−0.82

−1.00

Gnap

halium

ramosissim

um

+−1.00

−0.33

−0.06

—−0.69

−1.00

−1.00

+−0.61

−1.00

−0.65

—−1.00

−0.85

−1.00

Juncu

sbreweri

+−0.89

−1.00

−1.00

+−0.62

−0.60

0.05

+−1.00

−0.71

−1.00

+−0.19

0.04

0.35

Juncu

slesueu

rii

—0.03

−0.58

−0.25

+−0.89

−1.00

−0.15

+−0.30

−0.39

−0.15

+0.04

0.03

0.27

Rumex

occiden

talis

+0.66

0.60

0.67

+0.47

0.30

0.74

+0.79

0.31

0.96

—0.18

−0.03

−1.00

Rumex

salicifoliu

s+

−0.66

−0.68

−0.54

+−1.00

−0.73

−0.57

+−0.88

−0.66

−0.60

—−0.67

−1.00

−1.00

Trifoliu

mbarbigerum

+−0.63

−1.00

−0.39

—−0.06

0.16

−0.57

—−0.49

−0.18

0.00

—−0.71

−0.75

−0.95

Trifoliu

mmacraei

—0.60

0.52

0.45

+0.23

0.56

0.48

+0.37

0.58

0.34

—−0.64

−0.21

−0.88

Signtest

10/12;

P=0.04

9/12

;P=0.19

11/12;

P<

0.01

3/11

;P>

0.10

CF,

confamilial;C

G,congen

er;C

S,co

nspecific.Th

egreater

perform

ance

ofspecieswithmore

distantrelative

swas

only

gen

eralizab

leacross

speciesin

conspecific,co

ngen

ers,an

dco

nfamilial

fieldsoils

andnot

inpottingsoils

(Fig.S

4).S

ummaryofdataforrelative

interactionintensity

(RII)

forthelath

house

experim

ent.RIIva

lues

of−1indicateco

mpetitiveex

clusion,R

IIva

lues

of+1indicateoblig

atefacilitation,a

ndRII

values

of0indicatenointeraction.Ave

rageva

lues

areshown.Slopes

referto

therelationship

betwee

nRIIan

dthephylogen

etic

distance

totheinteractingspeciesin

amixed

model

withspeciesan

dspecies×

phylogen

etic

distance

asrandom

effects,an

dthey

could

notbecalculatedforallspeciesin

alltrea

tmen

tsbecau

seofsm

allsample

size

san

dhighmortality.

Burns and Strauss www.pnas.org/cgi/content/short/1013003108 10 of 10