Ecological Archives E096-018-A1

Jiajia Liu, Xinxin Zhang, Feifan Song, Shurong Zhou, Marc W. Cadotte, and Corey J. A. Bradshaw. 2015. Explaining maximum variation in productivity requires phylogenetic diversity and single functional traits. Ecology 96:176183. http://dx.doi.org/10.1890/14-1034.1

Appendix A. Species list (Table A1), measures of diversity (Table A2) and their correlations (Table A3, Fig. A3),full GLM results (Tables A4and A5), phylogenetic trees (Fig. A1), the removal treatment test (Fig. A2), and correlation between two PDs (Fig. A4).

Table A1. Species list categorized by taxonomic group (TG) and family.

TG

Family

Genus species

Asteraceae

Asteraceae

Ligularia virgaurea

Asteraceae

Asteraceae

Saussurea pulchra

Asteraceae

Asteraceae

Artemisia mongolica

Asteraceae

Asteraceae

Taraxacum mongolicum

Asteraceae

Asteraceae

Anaphalis lactea

Asteraceae

Asteraceae

Saussurea nigrescens

Asteraceae

Asteraceae

Saussurea leontodontoides

Asteraceae

Asteraceae

Ajania tenuifolia

Asteraceae

Asteraceae

Leontopodium haplophylloides

Asteraceae

Asteraceae

Saussurea stella

Asteraceae

Asteraceae

Aster diplostephioides

Fabaceae

Fabaceae

Astragalus polycladus

Fabaceae

Fabaceae

Oxytropis kansuensis

Fabaceae

Fabaceae

Tibetia himalaica

Fabaceae

Fabaceae

Thermopsis lanceolala

Fabaceae

Fabaceae

Medicago lupulina

others

Apiaceae

Chamaesium paradoxum

others

Caryophyllaceae

Cerastium fontanum

others

Scrophulariaceae

Euphrasia regelii

others

Rosaceae

Potentilla anserina

others

Rosaceae

Potentilla bifurca

others

Geraniaceae

Geranium pylzowianum

others

Lamiaceae

Scutellaria rehderiana

others

Alliaceae

Allium sikkimense

others

Ranunculaceae

Thalictrum alpinum

others

Ranunculaceae

Ranunculus tanguticus

others

Rosaceae

Potentilla potaninii

others

Orchidaceae

Herminium monorchis

others

Scrophulariaceae

Lancea tibetica

others

Gentianaceae

Lomatogonium carinthiacum

others

Scrophulariaceae

Veronica eriogyne

others

Plantaginaceae

Plantago depressa

others

Saxifragaceae

Parnassia trinervis

others

Caryophyllaceae

Stellaria uda

others

Gentianaceae

Gentianopsis paludosa

others

Ranunculaceae

Anemone obtusiloba

others

Scrophulariaceae

Pedicularis szetschuanica

others

Polygonaceae

Rumex acetosa

others

Ranunculaceae

Anemone trullifolia

others

Gentianaceae

Halenia elliptica

others

Gentianaceae

Gentiana farreri

others

Ranunculaceae

Anemone rivularis

others

Polygonaceae

Polygonum macrophyllum

others

Euphorbiaceae

Euphorbia helioscopia

others

Ranunculaceae

Delphinium kamaonense

Poaceae and Cyperaceae

Cyperaceae

Scirpus distigmaticus

Poaceae and Cyperaceae

Cyperaceae

Kobresia capillifolia

Poaceae and Cyperaceae

Cyperaceae

Kobresia myosuroides

Poaceae and Cyperaceae

Poaceae

Poa pratensis

Poaceae and Cyperaceae

Poaceae

Elymus nutans

Poaceae and Cyperaceae

Poaceae

Agrostis hugoniana

Poaceae and Cyperaceae

Poaceae

Koeleria litvinowii

Poaceae and Cyperaceae

Poaceae

Stipa aliena

Poaceae and Cyperaceae

Poaceae

Festuca sinensis

 

Table A2. Measures of diversity considered in the analysis. Variables selected for model construction in boldface.

Diversity measure

Description

References

S

Realized species richness of plot

Tilman, Wedin and Knops 1996

H'

Shannon's diversity index

Tilman, Wedin and Knops 1996

D

Simpson's diversity

Tilman, Wedin and Knops 1996

PD

Phylogenetic diversity (the sum of all hylogentic branch lengths connecting species together)

Cardinale et al. 2006

MNND

Mean nearest-neighbor distance (the mean of the shortest distances connecting each species to any other species in the assemblage)

Webb et al. 2002

MPD

Mean pairwise distance (the mean of all the distances connecting species in an assemblage)

Webb et al. 2002

MNNDab

Abundance-weighted MNND

Webb et al. 2002

MPDab

Abundance-weighted MPD

Webb et al. 2002

Hed

Entropic measure of the distribution of evolutionary distinctiveness in an assemblage

Gamfeldt, Hillebrand and Jonsson 2008

Haed

Abundance-weighted Hed

Gamfeldt, Hillebrand and Jonsson 2008

Heed

Equitability of Haed

Gamfeldt, Hillebrand and Jonsson 2008

PAE

Phylogenetic abundance evenness: measures the skew in abundances along terminal branches

Gamfeldt, Hillebrand and Jonsson 2008

IAC

Imbalance of abundances among clades: measures the deviation in abundance distribution among internal splits from a null

Gamfeldt, Hillebrand and Jonsson 2008

FD

Functional diversity: the sum of all branch lengths connecting species together in a hierarchical clustering dendrogram based on a multivariate distance matrix

Petchey and Gaston 2002

FAD

Functional attribute diversity: the sum of all pairwise species distances calculated as the Euclidean distance between species

Walker, Kinzig and Langridge 1999

 

 

 

FEve

Functional Evenness: abundance-weighted pairwise functional distances

Villéger, Mason and Mouillot 2008

FDis

Functional dispersion: weighted distances from a weighted centroid in multi trait space

Villéger, Mason and Mouillot 2008

FDiv

 

Functional divergence: mean abundance-weighted deviance from an absolute abundance-weighted deviance

Villéger, Mason and Mouillot 2008

FRic

Functional richness: convex hull volume of the trait space

Cornwell et al. 2006, Villéger et al. 2008

RaoQ

Quadratic entropy

Botta-Dukát 2005

 

Table A3. Spearman's r correlation matrix for raw input variables. Shown are species richness (S), Shannon's evenness (H'), phylogenetic diversity (PD), mean pairwise distance (MPD), distribution of evolutionary distinctiveness (Hed), functional diversity (FD), functional attribute diversity (FAD), maximum plant height (Hmax), leaf phosphorus (P) and nitrogen (N) content, mean seed mass (SM) and specific leaf area (SLA). ρ > 0.3 in boldface.

 

S

H

PD

Hed

MPD

FD

FAD

Hmax

SM

N

P

H

0.938

                   

PD

0.975

0.924

                 

Hed

0.997

0.937

0.971

               

MPD

0.858

0.864

0.908

0.857

             

FD

0.848

0.767

0.775

0.843

0.634

           

FAD

0.973

0.903

0.925

0.969

0.807

0.933

         

Hmax

0.143

0.152

0.099

0.133

0.140

0.473

0.278

       

SM

0.091

0.196

0.144

0.094

0.291

0.204

0.148

0.607

     

N

0.087

0.116

0.129

0.101

0.159

-0.043

0.039

-0.411

-0.005

   

P

0.207

0.190

0.154

0.197

0.066

0.451

0.284

0.449

0.000

-0.387

 

SLA

-0.224

-0.169

-0.268

-0.227

-0.208

-0.030

-0.158

0.319

0.182

-0.258

0.412

 

Table A4. Generalized linear model (GLM) results for biomass production as a function of number of species (S), Shannon's evenness (H'), phylogenetic diversity (PD = phylogenetic diversity, MPD = mean pairwise distance and Hed = evolutionary distinctiveness), and various community-level means of single functional traits (Hmax = maximum plant height, P = leaf phosphorus content, N = leaf nitrogen content, SM = mean seed mass and SLA = specific leaf area) or multivariate functional trait indices (FD = functional diversity, FAD = functional attribute diversity). Shown are the estimated number of model parameters (k), maximum log-likelihood (LL), the information-theoretic Akaike's information criterion corrected for small samples (AICc), change in AICc relative to the top-ranked model (ΔAICc), AICc weight (wAICc = model probability) and the percent deviance explained (%DE) as a measure of the model's goodness-of-fit.

Model

LL

k

AICc

DAICc

wAICc

%DE

~Hed+Hmax

-271.463

3

551.497

0.000

0.574

77.7

~PD+Hmax

-271.856

3

552.283

0.786

0.388

77.5

~S+Hmax

-274.217

3

557.006

5.509

0.037

76.0

~MPD+Hmax

-277.387

3

563.345

11.848

0.002

74.0

~H'+Hmax

-280.501

3

569.574

18.077

<0.001

71.7

~Hed+N+SM

-285.986

4

582.841

31.344

<0.001

67.4

~S+N+SM

-286.326

4

583.521

32.024

<0.001

67.1

~Hed+N+SM+SLA

-285.980

5

585.195

33.698

<0.001

67.4

~S+N+SM+SLA

-286.273

5

585.782

34.285

<0.001

67.1

~H'+N+SM

-289.698

4

590.266

38.770

<0.001

64.0

~H'+N+SM+SLA

-289.467

5

592.169

40.672

<0.001

64.2

~MPD+N+SM

-291.528

4

593.927

42.430

<0.001

62.3

~PD+N+SM

-291.803

4

594.476

42.979

<0.001

62.0

~MPD+N+SM+SLA

-291.528

5

596.292

44.795

<0.001

62.3

~PD+N+SM+SLA

-291.791

5

596.818

45.321

<0.001

62.0

~Hed+P+SM

-293.852

4

598.574

47.078

<0.001

59.9

~Hed+N

-295.878

3

600.327

48.830

<0.001

57.7

~Hed+SM

-296.253

3

601.078

49.581

<0.001

57.3

~H'+N

-296.959

3

602.489

50.993

<0.001

56.5

~Hed+N+SLA

-295.832

4

602.534

51.037

<0.001

57.8

~Hed+SM+SLA

-295.835

4

602.540

51.044

<0.001

57.8

~S+P+SM

-296.104

4

603.077

51.581

<0.001

57.5

~H'+N+SLA

-296.940

4

604.750

53.253

<0.001

56.6

~H'+P+SM

-297.194

4

605.259

53.762

<0.001

56.3

~S+SM

-298.644

3

605.860

54.363

<0.001

54.6

~H'+SM

-298.702

3

605.975

54.478

<0.001

54.5

~MPD+N

-298.832

3

606.235

54.738

<0.001

54.4

~S+SM+SLA

-298.354

4

607.578

56.081

<0.001

54.9

~H'+SM+SLA

-298.664

4

608.198

56.701

<0.001

54.6

~MPD+N+SLA

-298.736

4

608.342

56.845

<0.001

54.5

~MPD+P+SM

-298.901

4

608.671

57.175

<0.001

54.3

~Hed+P

-300.239

3

609.049

57.552

<0.001

52.7

~FD

-302.065

2

610.467

58.971

<0.001

50.4

~S+N

-301.423

3

611.417

59.921

<0.001

51.2

~H'+P

-301.483

3

611.538

60.041

<0.001

51.1

~PD+P+SM

-300.715

4

612.299

60.802

<0.001

52.1

~Hed

-303.261

2

612.861

61.364

<0.001

48.8

~H'

-303.488

2

613.314

61.817

<0.001

48.5

~MPD+P

-302.496

3

613.563

62.066

<0.001

49.8

~S+N+SLA

-301.415

4

613.700

62.203

<0.001

51.2

~Hed+SLA

-302.577

3

613.725

62.228

<0.001

49.7

~H'+SLA

-303.323

3

615.218

63.721

<0.001

48.7

~PD+N

-304.420

3

617.411

65.915

<0.001

47.2

~PD+SM

-304.707

3

617.985

66.488

<0.001

46.9

~PD+SM+SLA

-304.280

4

619.429

67.933

<0.001

47.4

~PD+N+SLA

-304.369

4

619.607

68.110

<0.001

47.3

~MPD+SM

-305.589

3

619.750

68.253

<0.001

45.6

~MPD+SM+SLA

-304.947

4

620.764

69.267

<0.001

46.5

~S+P

-306.727

3

622.026

70.530

<0.001

44.0

~S

-309.802

2

625.942

74.445

<0.001

39.4

~S+SLA

-309.248

3

627.068

75.572

<0.001

40.2

~PD+P

-309.484

3

627.539

76.042

<0.001

39.9

~MPD+SLA

-309.968

3

628.506

77.010

<0.001

39.1

~MPD

-311.139

2

628.617

77.120

<0.001

37.3

~FAD

-312.941

2

632.220

80.723

<0.001

34.3

~PD

-314.134

2

634.606

83.110

<0.001

32.2

~PD+SLA

-313.311

3

635.193

83.696

<0.001

33.6

~N+SM+SLA

-314.022

4

638.914

87.418

<0.001

32.4

~N+SM

-316.040

3

640.652

89.155

<0.001

28.8

~Hmax

-318.529

2

643.396

91.899

<0.001

24.2

~SM

-322.101

2

650.540

99.043

<0.001

16.9

~P+SM

-321.426

3

651.424

99.927

<0.001

18.3

~SM+SLA

-321.584

3

651.740

100.243

<0.001

18.0

~N+SLA

-323.393

3

655.357

103.860

<0.001

14.1

~N

-324.636

2

655.610

104.113

<0.001

11.4

~1

-329.409

1

662.985

111.488

<0.001

0.0

~P

-328.601

2

663.540

112.043

<0.001

2.0

~SLA

-329.159

2

664.656

113.159

<0.001

0.6

 

Table A5. After substituting the five original control quadrats with 10 quadrats where rare species were removed (see Methods), generalized linear model (GLM) results for biomass production as a function of number of species (S), Shannon's evenness (H') and phylogenetic diversity (PD = phylogenetic diversity, MPD = mean pairwise distance and Hed = evolutionary distinctiveness), and various community-level means of single functional traits (Hmax = maximum plant height, P = leaf phosphorus content, N = leaf nitrogen content, SM = mean seed mass and SLA = specific leaf area) or multivariate functional trait indices (FD = functional diversity, FAD = functional attribute diversity). Shown are the estimated number of model parameters (k), maximum log-likelihood (LL), the information-theoretic Akaike's information criterion corrected for small samples (AICc), change in AICc relative to the top-ranked model (ΔAICc), AICc weight (wAICc = model probability) and the percent deviance explained (%DE) as a measure of the model's goodness-of-fit.

Model

LL

k

AICc

ΔAICc

wAICc

%DE

~Hed+Hmax

-290.438

3

589.410

0.000

0.665

77.7

~PD+Hmax

-291.421

3

591.375

1.965

0.249

77.1

~S+Hmax

-292.509

3

593.552

4.143

0.084

76.5

~MPD+Hmax

-296.914

3

602.362

12.952

0.001

73.8

~H'+Hmax

-297.543

3

603.619

14.210

0.001

73.4

~Hed+N+SM

-303.915

4

618.642

29.232

<0.001

68.9

~S+N+SM

-304.273

4

619.357

29.948

<0.001

68.6

~Hed+N+SM+SLA

-303.904

5

620.959

31.549

<0.001

68.9

~S+N+SM+SLA

-304.258

5

621.666

32.257

<0.001

68.6

~H'+N+SM

-307.244

4

625.299

35.890

<0.001

66.2

~H'+N+SM+SLA

-307.170

5

627.490

38.081

<0.001

66.3

~PD+N+SM

-310.341

4

631.494

42.084

<0.001

63.6

~PD+N+SM+SLA

-310.335

5

633.820

44.410

<0.001

63.6

~Hed+P+SM

-313.346

4

637.503

48.093

<0.001

60.8

~Hed+SM

-315.403

3

639.340

49.931

<0.001

58.8

~Hed+SM+SLA

-314.760

4

640.331

50.921

<0.001

59.4

~Hed+N

-316.028

3

640.589

51.179

<0.001

58.1

~H'+N

-316.407

3

641.347

51.938

<0.001

57.8

~S+P+SM

-315.629

4

642.070

52.660

<0.001

58.5

~Hed+N+SLA

-315.845

4

642.501

53.091

<0.001

58.3

~H'+P+SM

-316.208

4

643.228

53.818

<0.001

58.0

~H'+SM

-317.529

3

643.592

54.182

<0.001

56.6

~H'+N+SLA

-316.395

4

643.600

54.191

<0.001

57.8

~S+SM

-317.840

3

644.212

54.803

<0.001

56.2

~H'+SM+SLA

-317.389

4

645.590

56.180

<0.001

56.7

~MPD+N

-318.585

3

645.704

56.294

<0.001

55.4

~S+SM+SLA

-317.448

4

645.708

56.298

<0.001

56.7

~MPD+N+SLA

-318.146

4

647.103

57.693

<0.001

55.9

~Hed+P

-321.392

3

651.318

61.908

<0.001

52.3

~H'+P

-321.822

3

652.178

62.769

<0.001

51.8

~S+N

-321.915

3

652.363

62.953

<0.001

51.7

~PD+P+SM

-320.845

4

652.502

63.092

<0.001

52.9

~H'

-323.513

2

653.342

63.932

<0.001

49.8

~FD

-323.729

2

653.774

64.364

<0.001

49.5

~Hed

-323.873

2

654.063

64.653

<0.001

49.3

~Hed+SLA

-322.886

3

654.305

64.895

<0.001

50.5

~S+N+SLA

-321.854

4

654.518

65.108

<0.001

51.7

~H'+SLA

-323.148

3

654.829

65.420

<0.001

50.2

~MPD+P

-323.869

3

656.271

66.862

<0.001

49.3

~PD+SM

-324.457

3

657.447

68.038

<0.001

48.6

~PD+SM+SLA

-323.775

4

658.361

68.952

<0.001

49.4

~PD+N

-325.344

3

659.222

69.812

<0.001

47.5

~PD+N+SLA

-325.117

4

661.045

71.635

<0.001

47.8

~S+P

-328.381

3

665.296

75.886

<0.001

43.5

~S

-330.864

2

668.044

78.635

<0.001

39.9

~MPD+SLA

-330.018

3

668.569

79.159

<0.001

41.2

~S+SLA

-330.114

3

668.761

79.351

<0.001

41.0

~MPD

-331.951

2

670.218

80.809

<0.001

38.3

~PD+P

-331.694

3

671.921

82.511

<0.001

38.7

~FAD

-334.467

2

675.249

85.840

<0.001

34.5

~N+SM

-334.052

3

676.637

87.228

<0.001

35.1

~N+SM+SLA

-332.952

4

676.714

87.305

<0.001

36.8

~PD+SLA

-334.443

3

677.419

88.010

<0.001

34.5

~PD

-335.723

2

677.762

88.353

<0.001

32.5

~Hmax

-341.253

2

688.821

99.411

<0.001

22.9

~SM

-342.079

2

690.473

101.064

<0.001

21.3

~P+SM

-341.582

3

691.698

102.288

<0.001

22.3

~SM+SLA

-341.944

3

692.421

103.012

<0.001

21.6

~N

-345.920

2

698.156

108.747

<0.001

13.7

~N+SLA

-345.507

3

699.548

110.138

<0.001

14.6

~1

-352.136

1

708.428

119.018

<0.001

0.0

~P

-351.718

2

709.752

120.342

<0.001

1.0

~SLA

-352.131

2

710.577

121.167

<0.001

0.0

 

FigA1

Fig. A1. (a) Maximum-likelihood and (b) Bayesian phylogenetic trees.


 

FigA2

Fig. A2. The effect of number of removed groups on the biomass of each taxonomic group.


 

FigA3

Fig. A3. Bivariate plots of the raw species (S and H'), phylogenetic (PD), evolutionary distinctiveness (Hed), mean pairwise distance (MPD) and multivariate functional diversity (FD, FAD) indices.


 

FigA4

Fig. A4. Correlation between phylogenetic diversity (PD) determined via maximum likelihood and Bayes theorem (Spearman's ρ = 0.999).


 

Literature cited

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