Ecological Archives E096-088-A1

Eric M. Lind, John B. Vincent, George D. Weiblen, Jeannine Cavender-Bares, and Elizabeth T. Borer. 2015. Trophic phylogenetics: evolutionary influences on body size, feeding, and species associations in grassland arthropods. Ecology 96:9981009. http://dx.doi.org/10.1890/14-0784.1

Appendix A. Phylogenetic tree methods, topological relationships, and sources of estimated clade ages.

Community phylogeny estimation. Ideally, hypotheses of evolutionary relatedness are based on thorough sampling of extant taxa and phylogenetic analysis of numerous characters including genetic data. Two major obstacles prevent such an approach for arthropod communities. First, arthropods have not been well characterized taxonomically or genetically, even in the comparatively well-sampled temperate zone. For instance, we conducted a GenBank search for each of 503 genera in the Cedar Creek dataset and four commonly used gene regions, namely the mitochondrial genes cytochrome oxidase subunit I (COI) and cytochrome B (cytB), and the nuclear genes elongation factor 1-alpha (EF-1α) and 28S subunit ribosomal RNA (28S rRNA). We used the 'seqinr' package [Charif et al. 2005] in R 2.14 [R Core Team 2011] to identify the number of nucleotide sequence datasets available for each genus in our dataset. As shown in Table 1, there were insufficient data to infer phylogenetic relationships among 39% of the genera in our sample based on a single gene region. Furthermore, the most commonly available gene region was the "DNA barcode" (COI) which may be useful for species identification in some cases but is far from sufficient to resolve relationships among deep branches in the tree of life [Will and Rubinoff 2004].

Second, and more fundamentally, community samples such as ours are ecologically coherent but are not distributed across the tree of life in patterns that are conducive to molecular phylogenetic analyses [Smith et al. 2009]. An alternative approach is to synthesize information available in the systematics literature by 'grafting' phylogenies [Beaulieu et al. 2012]. We followed this approach to assemble a phylogenetic hypothesis for 905 arthropod taxa from Cedar Creek. Initially, taxa named in the Tree of Life Web Project (http://tolweb.org) were assumed to be monophyletic at each rank in the Linnean hierarchy (e.g. order, family, subfamily, genus) unless contradicted by recent evidence from the systematics literature; in this case an unresolved polytomy was retained at the rank immediately above. The backbone topology of relationships among major clades and orders followed Regier et al. [2010] for arthropods and Trautwein et al. [2012] for the class Insecta. Relationships within orders were based on recently published molecular phylogenetic hypotheses (Table A2). Particular taxa not sampled in the recent literature were placed in the tree as polytomies of higher taxa on the assumption of monophyly of families, subfamilies, and genera, etc. Incompletely identified taxa (e.g. "geometrid larva") were also assigned as polytomies of the nearest identifiable clade (e.g., Geometridae). Polytomies were retained in all analyses.

Hierarchical ancestor-descendant relationships were specified in a three-column table by taxon, clade, and reference columns. Beginning with the observed taxon names at the tips of the tree, we assigned each a containing clade, representing the most recent common ancestor with at least one other taxon in our community sample. In turn, each clade (node) was named as a taxon, and likewise assigned to an ancestral clade (node). In this table, all tips and nodes appear once in the taxon column, all nodes appear two or more times in the clade column, and, where appropriate, taxon-clade relationships are annotated with reference to the literature on which the placement was based. We then used a custom function in R v2.14 [R Core Team 2011] to transform the resulting text file into an object of class 'phylo' which can be manipulated, plotted, and exported using the package 'ape' [Paradis et al. 2004]. The source table and R code use to create the phylogeny are available in a Supplement.

Appendix Tables

Table A1. Availability of genetic data in the year 2013 for 503 genera of Cedar Creek arthropods representing 905 named species and morphospecies.

genera with matching sequence in Genbank

COI

cytB

EF-1α

28S rRNA

count

316

105

41

57

percent

61%

21%

8%

11%

 

Table A2. Numbers of taxa, % resolution of topology, age estimates as reported in Grimaldi and Engel 2006, and topology sources from the literature and online for recognized clades.

Clade
Name

# taxa

% Resolution

Clade age (Ma)*

Source of clade topology†

Arthropoda

905

43.4%

530

Regier et al. 2010

Arachnida

40

30.8%

420

Shultz 1990

Acari

4

66.7%

415

Grimaldi & Engel 2006

Acarina

3

50.0%

 

 

Araneae

35

23.5%

300

Grimaldi & Engel 2006

Araneus

9

25.0%

 

 

Thomisidae

10

22.2%

 

 

Hexapoda

865

43.9%

415

Grimaldi & Engel 2006

Insecta

862

43.8%

410

Trautwein et al. 2010

Pterygota

850

43.3%

390

Grimaldi & Engel 2006

Neoptera

818

42.8%

340

Grimaldi & Engel 2006

Parametabola

176

47.4%

 

 

Hemiptera

164

48.5%

290

Cryan & Urban 2012

Sternorrhynca

12

27.3%

220

 

HigherHemiptera

151

50.0%

 

 

Auchenorrhyncha

78

62.3%

275

 

Fulgoroidea

20

52.6%

180

Urban & Cryan 2007

Cicadomorpha

58

64.9%

270

 

Membracoidea

55

63.0%

180

Dietrich et al. 2001

Heteroptera

73

36.1%

275

tolweb.org

Trichophora

43

33.3%

 

 

Pentatomoidea

17

25.0%

200

 

Coreoidea

10

44.4%

140

 

Lygaeoidea

16

26.7%

100

 

Cicicomorpha

27

38.5%

200

 

Thysanoptera

6

20.0%

275

tolweb.org

Psocoptera

6

20.0%

160

tolweb.org

Holometabola

642

41.5%

310

Grimaldi & Engel 2006

Neuropteroidea

132

40.5%

290

Grimaldi & Engel 2006

Coleoptera

124

39.0%

250

tolweb.org

Polyphaga

115

37.7%

240

 

HigherPolyphaga

104

35.9%

 

 

Chrysomeloidea

36

25.7%

180

 

Cerambycidae

2

100.0%

160

 

Chrysomelidae

33

21.9%

160

 

Cucujiformia

50

32.7%

175

 

Tenebrionoidea

9

50.0%

160

 

Curculionoidea

20

21.1%

175

 

Curcilionidae

19

16.7%

155

 

Cucujoidea

20

36.8%

 

 

Coccinellidae

13

33.3%

100

 

Elateriformia

12

63.6%

210

 

Staphyliniformia

11

50.0%

220

 

Scarabaeiformia

4

33.3%

155

 

Staphylinoidea

7

50.0%

230

 

Adephaga

7

66.7%

240

 

Neuroptera

8

57.1%

280

tolweb.org

Mecopterida

286

38.6%

290

tolweb.org

Diptera

204

41.9%

260

tolweb.org

Brachycera

176

41.1%

210

 

Eremoneura

153

38.8%

165

 

Empidoidea

13

25.0%

147

 

Dolichopodidae

9

12.5%

133

 

Empididae

4

33.3%

140

 

Cyclorrhapha

140

39.6%

155

 

Schizophora

119

39.0%

65

 

Calyptratae

22

42.9%

62

 

Muscoidea

12

45.5%

61

 

Anthomyiidae

4

66.7%

60

 

Muscidae

8

28.6%

60

 

Oestroidea

10

33.3%

58

 

Tachinidae

7

16.7%

54

 

Sarcophagidae

3

50.0%

54

 

Acalyptratae

97

37.5%

65

 

Lauxanioidea

6

60.0%

 

 

Sciomyzoidea

7

33.3%

 

 

Ephydroidea

13

41.7%

 

 

Sphaeroceroidea

7

66.7%

 

 

Sphaeroceridae

4

66.7%

 

 

Heleomyzidae

3

50.0%

 

 

Carnoidea

30

24.1%

 

 

Chloropidae

27

19.2%

 

 

Milichiidae

3

50.0%

 

 

Opomyzoidea

13

41.7%

 

 

Agromyzidae

10

22.2%

 

 

Conopidae

3

50.0%

 

 

Tephrititoidea

18

29.4%

 

 

Aschiza

21

40.0%

 

 

Syrphoidea

17

31.3%

80

 

Pipunculidae

3

50.0%

75

 

Syrphidae

14

23.1%

75

 

Platypezoidea

4

66.7%

135

 

Phoridae

3

50.0%

120

 

Asilodea

16

53.3%

175

 

Asilidae

3

50.0%

170

 

Therevidae

4

66.7%

165

 

Bombyliidae

9

37.5%

185

 

Stratiomyidae

5

25.0%

175

 

Tabanidae

2

100.0%

155

 

Tipulomorpha

4

33.3%

225

 

Bibionomorpha

7

50.0%

225

 

Culicomorpha

15

35.7%

220

 

Chironomoidea

8

28.6%

215

 

Ceratopogonidae

6

20.0%

150

 

Amphiesmenoptera

82

29.6%

200

 

Lepidoptera

80

27.8%

190

Regier et al. 2013

Gelechiidae

4

33.3%

105

 

Torticidae

6

20.0%

70

 

Crambidae

4

33.3%

 

 

Pyralidae

3

50.0%

65

 

Macrolepidoptera

40

35.9%

65

 

Noctuoidea

22

19.0%

63

 

Geometroidea

6

20.0%

60

 

Papilionoidea

12

63.6%

60

 

Papilioniformes

11

60.0%

 

 

Papilionidae

3

100.0%

 

 

Lycaenidae

5

50.0%

 

 

Trichoptera

2

100.0%

185

 

Hymenoptera

224

45.3%

240

tolweb.org

Tenthredinidae

3

100.0%

150

 

Apocrita

220

44.3%

200

 

Ichneumonoidea

51

42.0%

150

Quicke et al. 2009

Ichneumonidae

24

43.5%

 

 

Barconidae

4

33.3%

 

 

Microgastrinae

4

66.7%

 

 

Aculeata

88

62.1%

160

 

Apoidea

51

48.0%

150

 

Apidae_sensu_lato

33

62.5%

 

 

Megachilidae

3

50.0%

90

 

Apinae

10

77.8%

80

 

Bombus

7

100.0%

60

Cameron et al. 2007

Halictidae

12

36.4%

105

 

Sphecidae

18

17.6%

145

 

Vespoidea

29

85.7%

152

 

UpperVespoid

21

90.0%

 

 

Pompilidae

2

100.0%

110

 

Vespidae

19

88.9%

140

 

Formicidae

16

86.7%

138

Moreau et al. 2006, Astruc et al. 2004

Mulltillidae

3

50.0%

65

 

Tiphiidae

5

75.0%

142

 

Chrysidoidea

8

57.1%

150

 

Platygasteroidea

16

20.0%

155

 

Platygasteridae

7

16.7%

 

 

Chalcidoidea

56

20.0%

140

 

Chalcididae

4

33.3%

 

 

Eurytomidae

2

100.0%

 

 

Pteromalidae

17

12.5%

 

 

Eucharitidae

2

100.0%

 

 

Euplemidae

3

50.0%

 

 

Encrytidae

11

10.0%

 

 

Eulophidae

13

8.3%

 

 

Mymaridae

2

100.0%

 

 

Torymidae

2

100.0%

 

 

Cynipoidea

4

33.3%

 

 

Orthoptera

32

54.8%

320

tolweb.org

Caelifera

21

50.0%

245

 

Ensifera

11

60.0%

250

 

Palaeoptera

12

72.7%

 

 

Odonata

10

66.7%

270

 

Libelluloidea

5

75.0%

160

 

Ephemeroptera

2

100.0%

200

tolweb.org

Collembola

3

50.0%

400

 

* maximum clade age based on fossil evidence as reported in Grimaldi and Engel 2006.

† where no source is listed for a clade, relationships were arranged following information for that group from the Tree of Life project (tolweb.org).

Literature cited

Astruc, C., I. Julien, C. Errard, and A. Lenoir. 2004. Phylogeny of ants (Formicidae) based on morphology and DNA sequence data. Molecular Phylogenetics and Evolution 31:880–893.

Beaulieu, J. M., R. H. Ree, J. Cavender-Bares, G. D. Weiblen, and M. J. Donoghue. 2012. Synthesizing phylogenetic knowledge for ecological research. Ecology 93:S4–S13.

Cameron, S. A., H. M. Hines, and P. H. Williams. 2007. A comprehensive phylogeny of the bumble bees (Bombus). Biological Journal of the Linnean Society 91:161–188.

Chapco, W., and G. Litzenberger. 2002. A molecular phylogenetic study of two relict species of melanopline grasshoppers. Genome 45:313–318.

Charif, D., J. Thioulouse, J. R. Lobry, and G. Perriere. 2005. Online synonymous codon usage analyses with the ade4 and seqinR packages. Bioinformatics 21:545–547.

Cryan, J. R., and J. M. Urban. 2012. Higher-level phylogeny of the insect order Hemiptera: is Auchenorrhyncha really paraphyletic? Systematic Entomology 37:7–21.

Cryan, J. R., B. M. Wiegmann, L. L. Deitz, C. H. Dietrich, and M. F. Whiting. 2004. Treehopper trees: phylogeny of Membracidae (Hemiptera : Cicadomorpha : Membracoidea) based on molecules and morphology. Systematic Entomology 29:441–454.

Dietrich, C. H., R. A. Rakitov, J. L. Holmes, and W. C. Black. 2001. Phylogeny of the major lineages of Membracoidea (Insecta : Hemiptera : Cicadomorpha) based on 28S rDNA sequences. Molecular Phylogenetics and Evolution 18:293–305.

Grimaldi, D., and M. S. Engel. 2006. The Evolution of the Insects. Cambridge University Press, New York, New York, USA.

Moreau, C. S., C. D. Bell, R. Vila, S. B. Archibald, and N. E. Pierce. 2006. Phylogeny of the ants: Diversification in the age of angiosperms. Science 312:101–104.

Paradis, E., J. Claude, and K. Strimmer. 2004. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 20:289–290.

Quicke, D. L. J., N. M. Laurenne, M. G. Fitton, and G. R. Broad. 2009. A thousand and one wasps: a 28S rDNA and morphological phylogeny of the Ichneumonidae (Insecta: Hymenoptera) with an investigation into alignment parameter space and elision. Journal of Natural History 43:1305–1421.

Regier, J. C., C. Mitter, A. Zwick, A. L. Bazinet, M. P. Cummings, A. Y. Kawahara, J.-C. Sohn, D. J. Zwickl, S. Cho, D. R. Davis, J. Baixeras, J. Brown, C. Parr, S. Weller, D. C. Lees, and K. T. Mitter. 2013. A large-scale, higher-level, molecular phylogenetic study of the insect iorder Lepidoptera (moths and butterflies). Plos One 8:e58568.

Regier, J. C., J. W. Shultz, A. Zwick, A. Hussey, B. Ball, R. Wetzer, J. W. Martin, and C. W. Cunningham. 2010. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 463:1079–1083.

Shultz, J. 1990. Evolutionary morphology and phylogeny of Arachnida. Cladistics-the International Journal of the Willi Hennig Society 6:1–38.

Smith, S. A., J. M. Beaulieu, and M. J. Donoghue. 2009. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. Bmc Evolutionary Biology 9.

Team, R. D. C. 2011. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.

Trautwein, M. D., B. M. Wiegmann, R. Beutel, K. M. Kjer, and D. K. Yeates. 2012. Advances in insect phylogeny at the dawn of the postgenomic era. Annual Review of Entomology 57:449–468.

Urban, J. M., and J. R. Cryan. 2007. Evolution of the planthoppers (Insecta : Hemiptera : Fulgoroidea). Molecular Phylogenetics and Evolution 42:556–572.

Will, K. W., and D. Rubinoff. 2004. Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification. Cladistics-the International Journal of the Willi Hennig Society 20:47–55.

Zahniser, J. N., and C. H. Dietrich. 2010. Phylogeny of the leafhopper subfamily Deltocephalinae (Hemiptera: Cicadellidae) based on molecular and morphological data with a revised family-group classification. Systematic Entomology 35:489–511.


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