Logo of gbeAboutAuthor GuidelinesEditorial BoardGenome Biology and Evolution
Genome Biol Evol. 2010; 2: 225–239.
Published online Mar 24, 2010. doi:  10.1093/gbe/evq012
PMCID: PMC2997538

Using Phylogenomic Patterns and Gene Ontology to Identify Proteins of Importance in Plant Evolution

Abstract

We use measures of congruence on a combined expressed sequenced tag genome phylogeny to identify proteins that have potential significance in the evolution of seed plants. Relevant proteins are identified based on the direction of partitioned branch and hidden support on the hypothesis obtained on a 16-species tree, constructed from 2,557 concatenated orthologous genes. We provide a general method for detecting genes or groups of genes that may be under selection in directions that are in agreement with the phylogenetic pattern. Gene partitioning methods and estimates of the degree and direction of support of individual gene partitions to the overall data set are used. Using this approach, we correlate positive branch support of specific genes for key branches in the seed plant phylogeny. In addition to basic metabolic functions, such as photosynthesis or hormones, genes involved in posttranscriptional regulation by small RNAs were significantly overrepresented in key nodes of the phylogeny of seed plants. Two genes in our matrix are of critical importance as they are involved in RNA-dependent regulation, essential during embryo and leaf development. These are Argonaute and the RNA-dependent RNA polymerase 6 found to be overrepresented in the angiosperm clade. We use these genes as examples of our phylogenomics approach and show that identifying partitions or genes in this way provides a platform to explain some of the more interesting organismal differences among species, and in particular, in the evolution of plants.

Keywords: phylogenomics, orthologs, partition metrics, gene ontology, micro-RNAs, small interfering RNAs

Introduction

The integration of evolution and genomics has been advocated for many years as a fruitful and convenient feedback relationship (Eisen 1998; Eisen and Wu 2002; Mitchell-Olds and Clauss 2002; DeSalle et al. 2003). Phylogenomics, originally defined as a combination of phylogenetic tree construction, integration of experimental data and differentiation between orthologs and paralogs, has been proposed to improve predictions of gene function (Eisen 1998; Eisen and Fraser 2003; Sjölander 2004; Brown and Sjolander 2006). This area of scientific endeavor has gradually evolved as a broader concept that encompasses all the key aspects that characterize the symbiosis between systematics and genomics. Such phylogenomic approaches include orthology determination through phylogeny (Chiu et al. 2006; Paramvir and Jeffrey 2006) and phylogenetic shadowing the use of character state reconstruction analysis of gene function (Thornton et al. 2003; Bridgham et al. 2007; Dean and Thornton 2007) and evolutionary analysis of rates and patterns of gene evolution (Eisen 1998; Eisen and Fraser 2003). Phylogenomic approaches can greatly enhance our understanding of difficult problems and improve the prediction of, for instance, terminal or small exons, microRNA (miRNA) precursors, and small peptide-encoding open reading frames or combine gene prediction with expression and/or homology information to identify conserved gene candidates between two or more genomes and/or identification of novel coding regions and splice variants (Windsor and Mitchell-Olds 2006).

To date, traditional phylogenomic studies concentrate on the search for orthology groups in gene family trees to infer the function of unknown proteins, yet the use of such phylogenies to ascertain the function of the encoded proteins is overlooked. In particular, the potential to uncover insights into gene function by simultaneous character analysis of large multigene (or genome-wide) phylogenies has been less explored. Characters from different data sets are traditionally used to produce a phylogeny by total evidence approaches (Kluge 1989), conditional combination of data sets (Bull et al. 1993), and taxonomic congruence (Nelson 1979). Gatesy et al. (1999) point out that there is little consensus on how conflict among data sets is quantified in traditional and even more recent methods (see references within) and propose a set of phylogenetic metrics that measure the congruence of gene partitions and individual characters in a phylogenetic analysis that focuses on variations of methods to assess support or conflict for a particular branch.

In the present study, we suggest that congruence measures of character evolution such as consistency, degree of support, and hidden support as described by Gatesy et al. (1999) are useful in mining genomes for patterns of protein function, and we demonstrate their use in plants. We are mostly concerned with partitioned branch support (PBS) (Baker and DeSalle 1997) and partitioned hidden branch support (PHBS) (Gatesy et al. 1999) and their use in the assessment of the overall contribution (positive, negative, or neutral) of a particular gene to the various branches or nodes in a phylogenetic hypothesis. The Gatesy et al. (1999) review came at a time when systematists were using at most 20 gene partitions and perhaps a single morphological partition in their analyses. With the onslaught of genome level sequencing and large expressed sequenced tag (EST) studies in the past years, the number of gene partitions and ways of partitioning phylogenetic information have expanded greatly. In this study, we use measures of branch support to identify proteins and characters that may have functional significance in the evolution of seed plants based on the direction of their support from the concatenated hypothesis obtained in a seed plant phylogenomic tree, constructed from 2,557 orthologous genes spanning 16 species.

Materials and Methods

Phylogenetic Hypothesis and Orthology Determination

We used a combination of amino acid sequences from whole genomes and EST projects (table 1) to extend a previously published phylogeny of seed-free and seed plants (De la Torre-Bárcena et al. 2009). We assembled a matrix of all available genomic and EST data to date for 16 plant species that includes the following 11 seed plants: five angiosperms (Amborella, rice, Arabidopsis, poplar, and grape) and six gymnosperms (Cryptomeria, pine, two cycads, gingko, Gnetum, and Welwitschia) and four seed-free plants: Filicalian fern (Adiantum), a thalloid liverwort (Marchantia), a moss (Physcomitrella), and a Lycophyte (Selaginella).

Table 1
Species List and Corresponding Genomic Databases

To construct this matrix, we established orthology of genes using the OrthologID platform first (Chiu et al. 2006) http://nypg.bio.nyu.edu/orthologid, which uses an automated approach to sort query sequences into gene family membership and determines sets of orthologs from the gene trees. All ortholog groups reflecting coded genes were then assembled into a concatenated matrix of 1,062,841 amino acids representing 2,557 proteins (referred to as genes thereafter), with delineated data partitions for each gene in NEXUS format using the ASAP program (Sarkar et al. 2008). Because orthology is not necessarily a one-to-one relationship, a gene from one species can be orthologous to multiple genes from another species, which is often true in plants due to gene and genome duplications. In these cases, only one of the equally valid orthologs were selected for inclusion in the matrix (Box 1). Indeed, the phylogenetic method (OrthologID) we used to select sets of orthologs for analysis works the same regardless of the number of duplications and as a result should be unbiased with respect to the branches that have undergone genome duplication. We only included partitions with at least two gymnosperms to ensure even representation across angiosperms and gymnosperms.

Box 1.

Establishing Orthology

For equally orthologous genes from the same species, only one is picked (with equal probability) for inclusion in the SA matrix. For instance, in the following rooted gene tree:

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where A, B, and C represent different species, A1 is orthologous to B1, B2, C1, and C2; B1 is orthologous to A1, C1, and C2, etc. In this case, (A1, B1, C1) could be chosen to be included in the SA matrix. Other combinations, such as (A1, B2, C1), would be equally valid from a phylogenetic standpoint. In fact, this points to the strength of our tree-based analysis using OrthologID, as opposed to reciprocal-best-hit-based methods which may not identify the genes above as orthologous if, for instance, B1’s best hit is A1, whereas A1’s best hit is B2. It is certainly true that ESTs included in our analysis may include multiple alleles for a single gene. However, these multiple alleles will likely show up as orthologous to the same set of genes, in which case they would be indistinguishable from duplicated genes. They are therefore treated the same ways as “many-to-many” orthologs, where one of the equally orthologous genes from each species is chosen to be included in the SA matrix. In the example above, either B1 or B2 can be chosen to be included in the SA matrix whether they are duplicated genes or in fact multiple alleles of the same gene.

A maximum parsimony tree was generated using all concatenated genes in a simultaneous analysis (SA) and individually (partitioned data). Parsimony analysis was performed in PAUP* 4b10 using equal weights (Swofford 2003). Branch support was evaluated using the nonparametric bootstrap and jackknife methods in PAUP (Felsenstein 1985; Farris et al. 1996). This tree complements previously published likelihood and parsimony trees constructed with a matrix with fewer partitions (De la Torre-Bárcena et al. 2009).

By simultaneously incorporating multiple genes, we minimize the risk of retrieving a topology that reflects the history of a single gene or gene family. Furthermore, new genes and new taxa can be added to our pipeline, allowing the integration of rapidly generated genomic data from public databases. We use an SA approach (Nixon and Carpenter 1996) that is equivalent to a concatenated analysis at the genome level (Rokas et al. 2003). With this approach, we are finding the most parsimonious tree (MPT) through character congruence first and then using the partitions to say something about their function. The delineation of data partitions allows the contribution of a gene (partition) to a branch to be assessed using congruence measures of support. These measures are calculated per branch (see next section). As with all phylogenetic reconstructions, a tree represents a hypothesis of species relationships. However, we have the most robust solution (100% bootstrap at each branch) given the data available for plants; indeed, our results do not contradict any of the major phylogenies to date (see Discussion).

Evaluation of Character Evolution Using the Seed Plant Phylogenetic Hypotheses

We used ASAP and a customized Perl script to calculate individual tree statistics such as the total number of characters, the number of phylogenetically informative characters, the consistency index (CI), retention index (RI), rescaled consistency (RC) index, and the variations of traditional Bremer support. These values measure the stability of a group (clade) by quantifying the difference in character steps (tree length) between a tree containing a group of interest and a similar tree where this group is absent. High positive Bremer Support (BS) values reflect the stability or robustness of the group in question. Modified elaborations of Bremer support—PBS and PHBS (Baker and DeSalle 1997; Gatesy et al. 1999)—apply Bremer support metrics to trees constructed from combining data from various sources (e.g., morphological and DNA, mitochondrial and nuclear DNA, or genes/proteins from different functional categories), whereby the contribution of particular/individual data sets (partitions) can be evaluated to measure the stability of relationships in the context of the SA of concatenated data sets.

By definition, for a particular combined data set, a particular node (branch) and a particular data partition, PBS is the minimum number of character steps for that partition on the shortest topologies for the combined data set that do not contain that node minus the minimum number of character steps for that partition on the shortest topologies for the combined data set that do contain that node (Baker and DeSalle 1997). PHBS is the difference between PBS for that data partition and the Bremer support value (Bremer 1988, 1994) for that node for that data partition (Gatesy et al. 1999). Values for these metrics can be positive, zero, or negative, and the value indicates the direction of support for the overall concatenated hypothesis: positive lends support, zero is neutral, and negative gives conflicting support (Gatesy et al. 1999) (Summarized in Box 2).

Box 2.

Congruence Measures of Support

Partitioned Bremer support localizes nodes at which data partitions disagree, by indicating the contribution of a particular data partition to the SA support at every node. Once the MPT using all data partitions is calculated, PBS equals the length of a partition of interest on the MPT minus the length of that partition on the MPT where the supported clade is absent. A positive PBS value indicates that the partition provides support for the node. Negative PBS means that the length of partition is shorter on an alternative tree (i.e., that partition provides contradictory evidence). The sum of PBS values for each data partition always equals BS for combined data.

Hidden Bremer support (HBS) measures increased support for a node in a combined analysis relative to combined support in individual analyses of separate partitions (1. 2, 3…).

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Partitioned HBS (PHBS) is the contribution of each data partition to HBS.

Distribution of GO Categories with Phylogenetic Relevance

We established a Gene Ontology (GO) term based on orthology with an Arabidopsis chromosome/AIG number using the current TAIR v8 database (http://www.arabidopsis.org, accessed 1 February, 2009). To compare the extent of sampling in our matrix with the Arabidopsis genome, we mapped the distribution of our genes with all of their counts onto the annotated Arabidopsis genes and then compared the distribution of each main GO category in the Arabidopsis genome to our GO distribution.

As mentioned, an SA of a particular matrix, in this case of seed and seed-free plants, reveals relationships that may not be supported by any of the separate analyses (individual genes). In this context, we were particularly interested in determining if the branches contain an enrichment, or overrepresentation, of a certain molecular or biological function allowing us to associate a molecular phenotype to the branches. We searched for statistically overrepresented GO categories to each of our partitions compared with the distribution of that GO term in the Arabidopsis genome (null distribution). Because each branch is comprised of partitions which represent genes that provide positive, negative, or neutral support, we first grouped genes into four sets: 1) genes that had a positive value for PBS (apparent), 2) genes that had a positive value for PHBS (hidden) support, 3) genes with neutral PBS, and 4) genes with neutral (zero) PHBS. We then compared these sets to set of genes under that category in the Arabidopsis genome (this is our null distribution) to identify which category contained overrepresented GO terms. After culling to eliminate partitions with too few taxa to provide phylogenetic resolution, remaining neutral scores belong to partitions that presumably have no impact on the phylogeny and have a minimal evolutionary signature for each branch; thus, providing a null hypothesis of GO term overrepresentation and contribution to a particular branch.

We used Sungear (Poultney et al. 2007), one of the tools available in VirtualPlant (http://www.virtualplant.org), to compare different sets of gene lists. Sungear allows for the visual and statistical analysis of overlapping relationships among different lists of data and Boolean combinations. Sungear can also be used to determine if there is a GO term that is overrepresented in a given intersect, compared with the distribution of that GO term in the Arabidopsis genome, again as a null distribution. GO term overrepresentation is measured by a z score (also known as standard or normal score) representing the number of standard deviations (SDs) a particular observation (i.e., number of genes) is above or below the mean (Dudoit et al. 2004). Generally, a score of ±7 is considered to be a threshold of significance although when dealing with limited random subsets (such as orthologous partitions derived from EST libraries), the information given by a negative score (underrepresentation) is practically null. Sungear creates a polygon with vertices, or anchors, which in this case correspond to a particular branch in the phylogeny. The circles with arrows within the polygon are called vessels, which represent genes with a positive z score. The size of the vessel is proportional to the number of genes contained within that subset. Vessels can be either shared across branches or can be unique to a branch, and this is easily visualized in the polygon.

We further investigated partitions with overrepresented GO terms and positive PBS within the angiosperms, nodes 4–7, using the Biomaps tool (Wang et al. 2004) as implemented in VirtualPlant. We compared the observed distribution of genes at each branch with the distribution of those GOs terms associated to Arabidopsis genes found in the matrix, using a hypergeometric distribution and a P < 0.05 as the limit for statistically significant terms.

Results

Our analysis of the phylogenomic matrix of amino acid sequences for 2,557 genes/partitions across 16 seed plant species provided insights into the function of genes supporting key branches. The concatenated matrix (1,062,841 amino acid sites) with delineated data partitions for each gene in NEXUS format is included in supplementary table 1 (Supplementary Material online). A phylogenetic hypothesis on the relationships among seed and nonseed plants was generated with this matrix in a maximum parsimony framework. We obtained a single MPT (fig. 1). The various support parameters for each individual partition present in our data set are shown in supplementary table 2 (Supplementary Material online). The maximum parsimony (MP) tree shown in figure 1 is identical in topology to that described in De la Torre-Bárcena et al. (2009), which resulted from both MP and maximum likelihood (ML) analyses using fewer partitions (1,200) and various combinations of ingroup and outgroup taxa. A series of searches, with different combinations of ingroup and outgroup taxa, were tested until further addition of taxa and sequences had no effect on topology. These manipulations (as well as other details regarding phylogenetic analyses) are summarized in De la Torre-Bárcena et al. (2009). In this communication, we focus only on the MP tree given that measures of congruence apply only to a parsimony framework and that the recovered trees were identical with consistently high level of support across optimality criteria (MP and ML).

FIG. 1.
Phylogenetic relationships of seed plants using 2,557 proteins inferred using maximum parsimony (single tree; length 932,201). All nodes showed Bootstrap and Jackknife values above 99%. Bootstrap consensus (2,000 replicates) and Jackknife (with 50% removal ...

There is always risk of homoplasy, resulting in an “incorrect” phylogeny, which could bias the distribution of overrepresented genes that are at each node. However, this is the case with any phylogenetic reconstruction, a phylogeny is an informed hypothesis of species’ evolutionary history. A robust phylogeny that reflects the true organismal relationships is always desired, but regardless of the tree, our analyses will identify genes that are contributing disproportionately to a clade and that is the main goal of our approach. These sets of genes themselves are a hypothesis, and their relevance to that node can be tested further based on measures of selection (see last section of our Discussion). We obtained a single tree with high measures of branch support, with bootstrap and jackknife values all or nearly all at 100% (fig. 1, congruent with De la Torre-Bárcena et al. 2009) and our manipulations consistently retrieved the same basic topology. Thus, we are confident of our phylogenetic reconstruction.

Most of our genes, 1,706 and 66.7% of all 2,557 partitions, had an identifiable Arabidopsis ortholog. A subset of 1,503 (58.7%) had at least one functional GO category. Because some genes had more than one functional GO category, the total number of GO categories matched is 1,872. A list of all 2,557 of these genes and their associated GO categories are included in supplementary table 3 (Supplementary Material online). Genes from our matrix are distributed throughout all five Arabidopsis chromosomes (supplementary fig. 1, Supplementary Material online) and with the exception of genes in the “Other Molecular Function,” their distribution into functional categories is similar to those in Arabidopsis (table 2, fig. 2). This should minimize biases in patterns of overrepresentation when comparing our matrix with the Arabidopsis genome (vs. a particular node with our matrix as background).

Table 2
Counts Per Functional Categories Based on GO
FIG. 2.
Distribution of GO molecular function categories.

Correlating Function with Partition Metrics Across a Seed Plant Phylogeny (Sungear Analysis)

Except for all GO categories having a high CI, there was no discernible correlation observed for any GO categories within nodes in relation to other tree statistics, including the average of bootstrap proportions, RI, and RC. We examined groups of genes providing positive and neutral branch support for both PBS and PHBS to determine if there was a particular functional category that was significantly overrepresented in any of these gene sets compared with the observed distribution of GO terms in the Arabidopsis genome. We found a number of genes belonging to GO categories with very low probabilities of occurring by chance at the observed frequencies (based on high z scores, comparable with extremely low P values) for both positive PBS and PHBS.

Figure 3 illustrates the distribution of sets of overrepresented genes (represented by the circles or vessels) across nodes as depicted by Sungear (Poultney et al. 2007). As we expected, neutral PHBS and PBS scores did not show any significant outliers. The size of the vessel in this figure is proportional to the number of genes in the vessel, whereas the z score reflects the significance of the overrepresentation (with a +7 threshold). Vessels near the perimeter are composed of genes found only in those nodes or in nodes that are pointed to with an arrow. Node 6 (Arabidopsis, Populus, Vitis) and node 7 (Populus, Vitis) have the largest outlier vessels for both PBS and PHBS. A list of all overrepresented GO categories, the z score values associated with PBS and PHBS, and the list of genes they comprise is reported in supplementary table 4 (Supplementary Material online). We were interested in overrepresented genes that had positive PHBS support in all vessels as well as those that were found in outlier vessels only (fig. 4). Positive PHBS genes provided additional support at a particular node in the SA of all data partitions and, thus, provided a complement to genes with positive PBS, which showed support for a node in a separate analysis of each partition.

FIG. 3.
Distribution of genes across nodes. The Sungear figure has a shape of a polygon where the vertices, also referred to as anchors, represent the different gene lists. The circles with arrows within the polygon (vessels) represent genes. The position and ...
FIG. 4.
Distribution of relevant genes with positive PHBS that are also overrepresented across our phylogeny. Circle size is shown at the node and corresponds to z scores (>7; see key). Red circles and red labels correspond to categories that were only ...

Correlating Function with Partition Metrics within Angiosperms (Biomaps Analysis)

The Sungear analysis ranks genes based on number of SDs that a gene is either above or below the mean, using a z score. The Biomaps tool on the other hand (Gutiérrez et al. 2007) provides a different measure of overrepresentation by employing a hypergeometric distribution and significance based on a P value (P < 0.05). We used Biomaps to complement the statistical approach in Sungear and to focus on genes that had positive support based on PBS values, but only within the angiosperms: nodes 4, 5, 6, and 7. Most genes were distributed within photosynthesis, development, and hormone-related functional categories (supplementary table 4, Supplementary Material online; full list in supplementary table 5, Supplementary Material online). A few were present only at a single node.

Using Phylogenomics as a Guide for Finding Functional Sites in Proteins

A functional group within the angiosperms was of exceptional interest: genes involved in posttranscriptional gene silencing, in particular Argonaute (AGO1) and RDR6 within the rosids (Arabidopsis, Populus, Vitis). We used these to identify known functional sites that may have evolutionary relevance (fig. 5). Character comparison for AGO1 (fig. 5A and B) and RDR6 (fig. 5C and D) revealed a number of amino acid substitutions at regions in proteins with known functional importance (Marchler-Bauer et al. 2007). For AGO1, we found mutations unique to rice in the PAZ nucleic acid binding interface and in regions that correspond to the PIWI 5′ guide strand to the anchoring site and the PIWI active site. For RDR6, the SHOOTLESS2 (shl2) gene is the rice ortholog of RDR6 in Arabidopsis. The shl210 allele, shl2 has a G614D mutation, responsible for that mutant phenotype (Nagasaki et al. 2007). This specific site is one of those supporting cladogenetic variation in our matrix, that is, providing positive branch support as apomorphic for monocots.

FIG. 5. FIG. 5.
Character comparison for AGO1 (A, B) and RDR6 (C, D) among angiosperms without Amborella, Arabidopsis (Arab), rice (Oryz), poplar (Popu), and grape (Viti), reveals a number of amino acid substitutions at regions in proteins with known functional importance. ...

A separate analysis isolating genes involved in RNA binding, or associated with small interfering RNA (siRNA) pathways, revealed no single pattern of support or conflict, either apparent (PBS) or hidden (PHBS), for these groups of genes (supplementary table 5, Supplementary Material online). This suggests diverse evolutionary histories and constrains for each gene. However, both AGO1 and RDR6 showed significant positive support values (PBS of 16 and 4, respectively) for the entire SA tree topology, which argued for their use as examples in subsequent analyses to determine areas of potential functional importance underlying support for specific regions (nodes) of the tree.

Discussion

Seed Plant Phylogeny and Partition Dynamics

Although recent progress has been made using plastid genome-based phylogenies (Qiu et al. 2006; Barkman et al. 2007; Jansen et al. 2007; Moore et al. 2007; Raubeson et al. 2007), most plant phylogenies to date rely on only a few nuclear and plastid markers to infer relationships (Chase et al. 1993; Bowe et al. 2000; Burleigh and Mathews 2004; Barkman et al. 2007; Zhu et al. 2007; Bouchenak-Khelladi et al. 2008; Smith and Donoghue 2008; Burleigh et al. 2009). Our topology recovers major groups of seed plants as all previous morphological analyses and most molecular analyses with monophyletic seed plants: the cycads, the conifers, the gnetophytes, and the angiosperms. Congruent with all molecular data sets (Bowe et al. 2000; Schmidt and Schneider-Poetsch 2002; Burleigh and Mathews 2004), except for rbcL (Chase et al. 1993; Albert et al. 1994), and contrary to morphological analyses (Chase et al. 1993; Nixon et al. 1994; Rothwell and Serbet 1994), the gymnosperms are clearly a monophyletic group. One interesting disparity in topologies derived from most previous molecular data sets involves the placement of the gnetophytes (Bowe et al. 2000; Schmidt and Schneider-Poetsch 2002; Burleigh and Mathews 2004). Our analyses support the gnetophytes as the sister group to all other gymnosperms, congruent with phylogenetic studies using phytochrome genes (Mathews and Donoghue 2000; Schmidt and Schneider-Poetsch 2002; Mathews 2009), AGAMOUS-like genes (Winter et al. 1999; Becker et al. 2003), and FLORICAULA/LEAFY (Frohlich and Parker 2000).

Within the angiosperms, our tree for the most part is congruent with the Angiosperm Phylogeny Group (APG III) (APGIII 2009). Not surprisingly, Amborella is sister to all the angiosperms (Lockhart and Penny 2005). The single Monocot in our tree (Oryza) is well supported as an early divergent group sister to the rosids Arabidopsis, Populus, and Vitis. Controversial relationships of monocots with other groups, such as the placement of monocots and eudicots clade sister to the Magnolids (Chase et al. 2006), or monocots sister to Magnolids (Duvall et al. 1993; Davis et al. 2006), remain to be tested. Three taxa relationships in our tree will be explored further with the inclusion of more species and more genes, in particular the placement of Vitis. The systematics of Vitaceae has been uncertain (reviewed in Soltis et al. 2005, 2007; Jansen et al. 2006). Our SA places Vitis with Populus (fig. 1), in contrast to its placement as sister to the clade including both Arabidopsis and Populus based mostly on plastid genomes and a couple nuclear genes (Wang et al. 2009). The generally low support for its placement in most phylogenies to date and its position in our phylogeny, however, suggest that the relation of Vitis to the rest of the rosids will be only resolved with the addition of more nuclear genes/genomes, other rosids as ingroup taxa and asterids as outgroups.

Most of our overrepresented genes provide congruent support from the tips to the base of the node of interest, minimizing the risk that new, additional taxa cause a major shift the nodes at which those genes are overrepresented. More ESTs and full genomes could theoretically improve support (e.g., measures for support are highest within the angiosperms probably driven by the complete genomes in that group). A more detailed explanation of the importance of an SA, as well as of support dynamics, the role of outgroup choice, taxon sampling, and missing data for the same tree as figure 1 is discussed (De la Torre-Bárcena et al. 2009). Our main goal in this study is to exploit this large phylogenomic matrix to analyze the function of proteins and residues supporting the key nodes of seed plant evolution.

Using Branch Support Measures to Mine Genes of Interest

We suggest that a powerful way to tease apart the role of evolutionary change in protein function is to study the behavior of the genes used to reconstruct phylogeny through analysis of their effect on tree topology and branch support and their potential correlation(s) with functional processes of interest. This approach allows all character information to interact freely and reveal a more accurate description of species relationships and at the same time makes it possible to observe snapshots of how genes or groups of genes may have evolved in the context of the overall phylogeny. If one assumes that the tree obtained from concatenated analysis best represents the evolutionary history of the taxa involved, then partitions that are in agreement or in conflict with the overall evolutionary history of the groups in the analysis can be detected and used to explain some of the more interesting organismal differences among the taxa in an analysis. Phylogenetic incongruence between a partitioned functional class of genes (such as RNA silencing genes) and the organismal phylogeny would suggest that the partition has experienced a unique evolutionary history relative to the organisms. In this way, incongruence of a particular class of genes in a partitioned analysis allows us to establish hypotheses about the evolution and potential function of these gene classes. Detection of such sequences is given by character information, meaning that no previous knowledge about the gene or gene function is required. Apart from its blind, unbiased nature, this approach allows for the discovery of candidate proteins with potential evolutionary and functional relevance. Once these proteins are detected, additional experimental valida-tion may ascertain their specific functional role.

Seed Plant Divergence: Genes with Basic Metabolic Function

Overrepresented functional categories that are common throughout nodes are largely metabolic processes. One such category is photosynthesis and categories related to it (e.g., plastids or pigments). Their prevalence throughout our phylogeny is somewhat expected, as they are among the best-characterized and widely annotated plant genes (Leister 2003). Nonetheless, their distribution also echoes the importance of key biochemical pathways that plants have developed to deal with novel environments. In their transition from water to land, emerging plant lineages had to evolve an array of genetic mechanisms that would allow for rapid adaption to changes in light and stress from desiccation, whereas simultaneously being restricted by their sedentary life form. For instance, changes in photosynthetic chemical pathways are used not only to adapt to novel light conditions but also to reduce evaporative water loss (Bohnert et al. 1988).

The Gnetophyta (node 13) had the highest number of overrepresented photosynthetic genes (supplementary table 4, Supplementary Material online). Within this group, Welwitschia mirabilis is well known for its crassulacean acid metabolism photosynthetic pathway in which stomata are open at night, avoiding water diffusion during the day (von Willert et al. 2005). Ephedra is found in Mediterranean climates and in semi-to desert conditions on all continents except Australia. Thus, all species of Ephedra experience water stress during part of the year, although little is known about their physiology. Most Gnetum species are distributed in lowland tropical rainforests and are uniquely characterized by a relatively lower photosynthetic capacity as well as reduced capacity for stem water transport (Feild and Balun 2008). Interestingly, all gnetophytes have the smallest known chloroplast genomes in photosynthetic vascular plants, possibly as a result of selection to reduce costs in stressful or competitive environments (Wu et al. 2009). Welwitschia mirabilis, Ephedra equisetina, and the congener to our Gnetum gnemon, G. parvifolium, all have highly reduced chloroplast genomes, with high proportions of coding versus noncoding regions (Wu et al. 2009). Our approach sets the framework for exploring evolutionary mechanisms acting upon photosynthetic genes that are uniquely overrepresented in this group. For instance, it is possible to test for selective advantages specifically in the Gnetales, where some representatives are adapted to extreme environments (Welwitschia) and others have undergone drastic genome reductions (Gnetum). Estimates for Gnetum fossils could provide a timeline for specific genomic and gene changes. Genes such as NADP+ reduction, PSAO photosystem I subunit O, photosystem II subunit Q-2, and those genes may have been preferentially conserved during gnetophyte genome reduction would be key targets for measuring selection patterns. We come back to this in the last section of the Discussion.

Seed Plant Divergence: Specialized Genes

Some of the overrepresented genes are directly associated to a single trait or phenotype, characteristic of that clade. For example, overrepresented amylopectin genes at the conifers (node 9) and mannose biosynthesis genes at the cycad node (node 11) have a direct association to their morphology. Amylopectic is fundamental to the manoxylic wood in cycads and differs from the pycnoxylic wood in conifers and the Gnetales, in which mannose is an important component (Greguss 1955). Another example is napthoate synthase genes involved in cleavage of carbon–carbon bonds. These are overrepresented in the node that includes the Japanese cypress (Cryptomeria) and pine. Soils in cypress and pine forests are acidic and have increased oxidized iron (i.e., are lateritic), which requires active degradation of hydrocarbons, one of the main functions of napthoate synthases (Ohashi and Gyokusen 2007; Sawata and Kato 2007).

Toward Epigenetic Regulation—Posttranscriptional Regulation by Small RNAs

We found that genes involved in posttranscriptional regulation by small RNAs are highly overrepresented functional categories at particular clades in our phylogeny (see fig. 2 and supplementary table 6, Supplementary Material online). Posttranscriptional gene silencing and mismatch repair received high z-values at several nodes, for PHBS and/or PBS in both gymnosperms and angiosperms. The functional role of highly conserved miRNAs and siRNAs is well known. Mutations in conserved small RNA pathways for instance are important for developmental phenotypes in different tissues (Willman and Poetig 2005; Sunkar and Zhu 2007; Wang et al. 2007). Therefore, overrepresented siRNAs and miRNAs that provide positive support for a particular node are interesting as they may have a novel or specific function. Among the highest significance values (also with Biomaps) for overrepresented genes are found in the node that defines the split between Amborella and the rest of the Angiosperms (node 4) and in the split between Monocots and the rest of the rosids (node 5).

Genes Correlated with Divergence within the Angiosperms (Biomaps Analysis)

With the highest proportion of annotated genes, two complete genomes (Oryza and Arabidopsis) and robust monophyly based on both molecular and morphological data (Loconte and Stevenson 1990; Chase et al. 1993; Schmidt and Schneider-Poetsch 2002; Doyle 2006; Mathews 2009), the angiosperms in our matrix provide an ideal platform for identifying genes of evolutionary interest node. Plant hormones and genes involved in circadian clock and photoperiodism were among the most interesting overrepresented partitions. Plant hormones are often part of complex networks with a common set of signaling components and common target genes (Nemhauser et al. 2006). Brassinosteroids were found to be uniquely overrepresented in the angiosperm clade (node 4). Carotenoid biosynthesis factors, involved in shoot-branching and long-range signaling (Mouchel and Leyser 2007), were identified in the same node. Although widely distributed across plants, brassinosteroid hormones differ in their signaling from other hormones, with a relatively longer pathway than either auxin or giberellin (Bajguz and Tretyn 2003). It would be interesting to test if the function of brassinosteroids and carotenoid-derived hormones differs across angiosperms.

Genes uniquely overrepresented in the angiosperms included genes overrepresented in the rosids (node 6) that are involved in the regulation of the circadian clock and photoperiodism, often part of quantitative trait loci (Balasubramanian et al. 2006). Of particular interest was csn1 (previously fus6), which provides support for the node separating monocots from the rest of the angiosperms (node 5) and which was not found to be overrepresented elsewhere in the phylogeny. This protein was originally discovered as a photomorphogenic mutant in Arabidopsis and is a member of to the multisubunit COP9 signalosome (CSN) complex (Staub et al. 1996), which is ubiquitous to all eukaryotes (Wei and Deng 1992). In plants, the COP9 signalosome has been shown to be involved a variety of cellular processes throughout development, including signaling, defense, and growth (Serino and Deng 2003). The CSN not only regulates multiple cullin-based E3 ubiquitin ligases (Gusmaroli et al. 2007) but also functions as a kinase and conversely can be targeted by kinases (for review, see Wang et al. 2003; Harari-Steinberg and Chamovitz 2004). Its specific function in the monocots and the rest of the angiosperms must be tested in future studies, but its relevance is highlighted with our approach.

Character Analyses Toward Revealing Function—AGO1 and RDR6

Two genes in our matrix are of utmost importance in RNA-dependent regulation during vital plant processes, such as embryo and leaf development. These are AGO1 and the RNA-dependent RNA polymerase 6 (RDR6). These genes have roles in various stages of embryo and leaf development, polarity, and shape through siRNA and miRNA pathways (Kidner and Martienssen 2004, 2005; Peragine et al. 2004). Our results show that AGO1 provides 11 steps of positive hidden support for our tree for the angiosperms (node 4), five steps for the split of Amborella and the rest of the angiosperms (node 5), and the dicots only (node 6). RDR6 provides five steps of positive hidden support for the dicots (node 6). Sequence variation at these important nodes may define relevant differences in leaf structure and overall development among the divergent groups defined by those nodes.

One important predictive aspect of the approach we outline is that once a gene or gene category has been identified, the specific amino acids that are contributing to the correlations can then be analyzed further (i.e., through mutation, overexpression, and in situ experiments) to determine if they have any functional implication. We analyzed the aminoacid sequences from both AGO1 and RDR6 and searched for correlations with known mutants. Figure 5 shows color-coded alignments of data partitions containing seed plant orthologs of the (A) AGO1 and (B) RDR6 proteins. Character analysis reveals a number of amino acid substitutions among species in the clades with high support, at regions in the proteins with known functional importance (e.g., the RDRp or “RNA-dependent RNA polymerase,” domain in RDR6; and the PIWI and PAZ domains in AGO1). Further mutagenesis or expression analysis using these sequence variants may confirm a role for these amino acid residues in determining significant phenotypic effects, similar to differences seen in nature among the species involved. A very interesting finding is that mutants in RDR6, which support the dicot clade, have much milder phenotypes in Arabidopsis than in the monocot rice (Adenot et al. 2006; Fahlgren et al. 2006; Nagasaki et al. 2007), in which asymmetry and shoot meristem organization in the monocotyledonous embryo are profoundly affected, whereas the symmetrical dicotyledonous embryo of Arabidopsis is left almost unchanged. Unique changes to rice are also sites of potentially important mutants. One of the fundamental splits of monocots and dicots is indeed the embryo morphology. Overall, our results implicate both AGO1 and RDR6 (and thence the processing or transport of trans-acting siRNA), in this defining feature of the angiosperm seed.

Establishing a Framework for Selection Studies

Natural selection is a critical process for plant morphology and phenology, but identifying genes involved in these patterns is often a difficult task, even in model species. By identifying subsets of genes that are overrepresented and provide positive support for a particular clade—without a priori knowledge of their role or function—, we establish independent hypotheses (e.g., different sets of genes) regarding the evolution of that plant group, which can be tested relative to selection studies. With our approach, it is feasible to test for directional, balancing, or positive selection on sets of overrepresented genes, using likelihood tests for positive selection (i.e., estimates of nonsynonymous substitution dN, rate as compared with synonymous substitution rates dS) (Yang and Nielsen 1998) or other commonly used tests (Yang and Bielawski 2000; Creevey and McInerney 2002; Huelsenbeck and Dyer 2004; Biswas and Akey 2006). These results can then be compared, validated, and complemented with genome-wide scans for selection signals (e.g., Zayed and Whitfield 2008; Pickrell et al. 2009). Although the main goal of our paper is to identify those genes providing positive support for a clade, genes with high negative support could also be tested for selection, as they may be reflecting other aspects of the species tree history, in addition to the history of the genes themselves. Given our phylogenetic framework, it is also possible to estimate the impact—and in some cases the timing of—major evolutionary processes occurred, such as major climatic events, large-scale changes in geographic distribution, genomic rearrangements or duplications, or major disease outbreaks, to name a few (Garrigan and Hedrick 2003; Franks et al. 2007; Hongyan et al. 2009). Presumably, these events leave evidence of selection pressure on the gene and/or protein sequences, which can be detected by comparing evolutionary rates among species and timed within our phylogenetic context (Palmé et al. 2009). Sets of overrepresented genes (and their measures of conflict or support) can be then correlated to these processes and their distribution patterns tested as hypothesis that could explain species’ adaptations. Ideally, it would also be possible to identify the actual amino acid change(s) that could account for the selective advantage and/or speciation event, as we discuss for AGO1 supporting node 4 and RDR6 in the monocots. Functional laboratory analyses targeting those genes could further verify the role of a candidate gene or gene family in specific morphological or biological changes that may allowed that species to adapt, persist, and/or diverge. Interestingly, this can be readily tested in model species or on groups with a large number of domesticated species (e.g., Vitis, Oryza) that are known to undergo intense selective pressure (Purugganan and Fuller 2009). We are currently testing this approach with various sets of genes throughout our phylogeny and given the rapid technological advances, we can expect to apply this approach to nonmodel species in the near future.

Conclusions

By studying the behavior of clade-specific variation of phylogenetic characters in a partitioned context, the effect of individual genes or groups of genes (i.e., GO categories) on support metrics and their statistical correlation with functional processes of interest (such as seed development and posttranscriptional gene silencing) can be determined. In this way, we demonstrate a novel method for using a phylogenomic perspective to postulate hypotheses of gene function distributions and evolutionary mechanisms that can be tested experimentally. Upon testing, functional hypotheses can be further coupled with expression and genetic data, to arrive at better gene annotations and functional analyses for genome level studies, and ultimately a better understanding of plant evolution.

Supplementary Material

Supplementary figure 1 and supplementary tables 16 are available at Genome Biology and Evolution online (http://www.oxfordjournals.org/our_journals/gbe/).

Acknowledgments

We thank the members of the New York Plant Genomics Consortium, Barbara Ambrose (NYBG), Sergios-Orestis Kolokotronis (AMNH), and Richard H. Baker (AMNH) for helpful comments on the manuscript, GO Sungear patterns, and measures of support. This work was supported by US National Science Foundation Plant Genome Grant (DBI-0421604) to G.M.C., R.D, D.W.S, and R.M., which provided support to E.K.L., M.S.K., R.D., and E.K.L. We thank the Lewis B. and Dorothy Cullman Program in Molecular Systematics, the Sackler Institute for Comparative Genomics, and the Korein Family Foundation, all at the AMNH, for continued support. A.C.J. thanks the Lewis B. and Dorothy Cullman Program in Molecular Systematics at both NYBG and AMNH.

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