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 96:998–1009. 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.

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.

* 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).

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