Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

PREMISE OF THE STUDY

Phylogenetic support has been difficult to evaluate within the green plant tree of life partly due to a lack of specificity between conflicted versus poorly informed branches. As data sets continue to expand in both breadth and depth, new support measures are needed that are more efficient and informative.

METHODS

We describe the Quartet Sampling (QS) method, a quartet-based evaluation system that synthesizes several phylogenetic and genomic analytical approaches. QS characterizes discordance in large-sparse and genome-wide data sets, overcoming issues of alignment sparsity and distinguishing strong conflict from weak support. We tested QS with simulations and recent plant phylogenies inferred from variously sized data sets.

KEY RESULTS

QS scores demonstrated convergence with increasing replicates and were not strongly affected by branch depth. Patterns of QS support from different phylogenies led to a coherent understanding of ancestral branches defining key disagreements, including the relationships of Ginkgo to cycads, magnoliids to monocots and eudicots, and mosses to liverworts. The relationships of ANA-grade angiosperms (Amborella, Nymphaeales, Austrobaileyales), major monocot groups, bryophytes, and fern families are likely highly discordant in their evolutionary histories, rather than poorly informed. QS can also detect discordance due to introgression in phylogenomic data.

CONCLUSIONS

Quartet Sampling is an efficient synthesis of phylogenetic tests that offers more comprehensive and specific information on branch support than conventional measures. The QS method corroborates growing evidence that phylogenomic investigations that incorporate discordance testing are warranted when reconstructing complex evolutionary histories, in particular those surrounding ANA-grade, monocots, and nonvascular plants.

Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

PREMISE OF THE STUDY

Phylogenetic support has been difficult to evaluate within the green plant tree of life partly due to a lack of specificity between conflicted versus poorly informed branches. As data sets continue to expand in both breadth and depth, new support measures are needed that are more efficient and informative.

METHODS

We describe the Quartet Sampling (QS) method, a quartet-based evaluation system that synthesizes several phylogenetic and genomic analytical approaches. QS characterizes discordance in large-sparse and genome-wide data sets, overcoming issues of alignment sparsity and distinguishing strong conflict from weak support. We tested QS with simulations and recent plant phylogenies inferred from variously sized data sets.

KEY RESULTS

QS scores demonstrated convergence with increasing replicates and were not strongly affected by branch depth. Patterns of QS support from different phylogenies led to a coherent understanding of ancestral branches defining key disagreements, including the relationships of Ginkgo to cycads, magnoliids to monocots and eudicots, and mosses to liverworts. The relationships of ANA-grade angiosperms (Amborella, Nymphaeales, Austrobaileyales), major monocot groups, bryophytes, and fern families are likely highly discordant in their evolutionary histories, rather than poorly informed. QS can also detect discordance due to introgression in phylogenomic data.

CONCLUSIONS

Quartet Sampling is an efficient synthesis of phylogenetic tests that offers more comprehensive and specific information on branch support than conventional measures. The QS method corroborates growing evidence that phylogenomic investigations that incorporate discordance testing are warranted when reconstructing complex evolutionary histories, in particular those surrounding ANA-grade, monocots, and nonvascular plants.

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips-the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics.

Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications

Our growing understanding of the plant tree of life provides a novel opportunity to uncover the major drivers of angiosperm diversity. Using a time-calibrated phylogeny, we characterized hot and cold spots of lineage diversification across the angiosperm tree of life by modeling evolutionary diversification using stepwise AIC (MEDUSA). We also tested the whole-genome duplication (WGD) radiation lag-time model, which postulates that increases in diversification tend to lag behind established WGD events. Diversification rates have been incredibly heterogeneous throughout the evolutionary history of angiosperms and reveal a pattern of 'nested radiations' - increases in net diversification nested within other radiations. This pattern in turn generates a negative relationship between clade age and diversity across both families and orders. We suggest that stochastically changing diversification rates across the phylogeny explain these patterns. Finally, we demonstrate significant statistical support for the WGD radiation lag-time model. Across angiosperms, nested shifts in diversification led to an overall increasing rate of net diversification and declining relative extinction rates through time. These diversification shifts are only rarely perfectly associated with WGD events, but commonly follow them after a lag period.

Phylesystem: a git-based data store for community-curated phylogenetic estimates

MOTIVATION

Phylogenetic estimates from published studies can be archived using general platforms like Dryad (Vision, 2010) or TreeBASE (Sanderson et al., 1994). Such services fulfill a crucial role in ensuring transparency and reproducibility in phylogenetic research. However, digital tree data files often require some editing (e.g. rerooting) to improve the accuracy and reusability of the phylogenetic statements. Furthermore, establishing the mapping between tip labels used in a tree and taxa in a single common taxonomy dramatically improves the ability of other researchers to reuse phylogenetic estimates. As the process of curating a published phylogenetic estimate is not error-free, retaining a full record of the provenance of edits to a tree is crucial for openness, allowing editors to receive credit for their work and making errors introduced during curation easier to correct.

RESULTS

Here, we report the development of software infrastructure to support the open curation of phylogenetic data by the community of biologists. The backend of the system provides an interface for the standard database operations of creating, reading, updating and deleting records by making commits to a git repository. The record of the history of edits to a tree is preserved by git's version control features. Hosting this data store on GitHub (http://github.com/) provides open access to the data store using tools familiar to many developers. We have deployed a server running the 'phylesystem-api', which wraps the interactions with git and GitHub. The Open Tree of Life project has also developed and deployed a JavaScript application that uses the phylesystem-api and other web services to enable input and curation of published phylogenetic statements.

AVAILABILITY AND IMPLEMENTATION

Source code for the web service layer is available at https://github.com/OpenTreeOfLife/phylesystem-api. The data store can be cloned from: https://github.com/OpenTreeOfLife/phylesystem. A web application that uses the phylesystem web services is deployed at http://tree.opentreeoflife.org/curator. Code for that tool is available from https://github.com/OpenTreeOfLife/opentree.

CONTACT

mtholder@gmail.com.

Some limitations of public sequence data for phylogenetic inference (in plants)

The GenBank database contains essentially all of the nucleotide sequence data generated for published molecular systematic studies, but for the majority of taxa these data remain sparse. GenBank has value for phylogenetic methods that leverage data–mining and rapidly improving computational methods, but the limits imposed by the sparse structure of the data are not well understood. Here we present a tree representing 13,093 land plant genera—an estimated 80% of extant plant diversity—to illustrate the potential of public sequence data for broad phylogenetic inference in plants, and we explore the limits to inference imposed by the structure of these data using theoretical foundations from phylogenetic data decisiveness. We find that despite very high levels of missing data (over 96%), the present data retain the potential to inform over 86.3% of all possible phylogenetic relationships. Most of these relationships, however, are informed by small amounts of data—approximately half are informed by fewer than four loci, and more than 99% are informed by fewer than fifteen. We also apply an information theoretic measure of branch support to assess the strength of phylogenetic signal in the data, revealing many poorly supported branches concentrated near the tips of the tree, where data are sparse and the limiting effects of this sparseness are stronger. We argue that limits to phylogenetic inference and signal imposed by low data coverage may pose significant challenges for comprehensive phylogenetic inference at the species level. Computational requirements provide additional limits for large reconstructions, but these may be overcome by methodological advances, whereas insufficient data coverage can only be remedied by additional sampling effort. We conclude that public databases have exceptional value for modern systematics and evolutionary biology, and that a continued emphasis on expanding taxonomic and genomic coverage will play a critical role in developing these resources to their full potential.

Analyzing and synthesizing phylogenies using tree alignment graphs

Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe.

Using supermatrices for phylogenetic inquiry: an example using the sedges

In this article, we use supermatrix data-mining methods to reconstruct a large, highly inclusive phylogeny of Cyperaceae from nucleotide data available on GenBank. We explore the properties of these trees and their utility for phylogenetic inference, and show that even the highly incomplete alignments characteristic of supermatrix approaches may yield very good estimates of phylogeny. We present a novel pipeline for filtering sparse alignments to improve their phylogenetic utility by maximizing the partial decisiveness of the matrices themselves through a technique we call "phylogenetic scaffolding," and we present a new method of scoring tip instability (i.e. "rogue taxa") based on the I statistic implemented in the software Mesquite. The modified statistic, which we call I(S), is somewhat more straightforward to interpret than similar statistics, and our implementation of it may be applied to large sets of large trees. The largest sedge trees presented here contain more than 1500 tips (about one quarter of all sedge species) and are based on multigene alignments with more than 20 000 sites and more than 90% missing data. These trees match well with previously supported phylogenetic hypotheses, but have lower overall support values and less resolution than more heavily filtered trees. Our best-resolved trees are characterized by stronger support values than any previously published sedge phylogenies, and show some relationships that are incongruous with previous studies. Overall, we show that supermatrix methods offer powerful means of pursuing phylogenetic study and these tools have high potential value for many systematic biologists.

Stem architecture in Eleocharis subgenus Limnochloa (Cyperaceae): Evidence of dynamic morphological evolution in a group of pantropical sedges

We examined phylogenetic relationships and patterns of stem structural evolution in Eleocharis subgenus Limnochloa, an ecologically and economically important group of tropical to temperate-growing sedges, whose stems serve as the primary photosynthetic organs. We used maximum parsimony, likelihood, and Bayesian inference to develop phylogenetic trees and stochastic mapping and a Markov one-rate model to develop character history reconstructions of stem architecture. A complex history of stem shape evolution characterized by a high degree of homoplasy and rapid rates of change (an average of 13 transitions per character history for about 25 species) was identified across subgenus Limnochloa. Character states transition much more frequently in some lineages than others, but tend to follow a consistent directional pattern of evolutionary change. Our data also suggest that changes in stem shape and anatomy may be associated with speciation events in the subgenus (Pagel's κ = 0.3503, P = 0.04579) and may have some adaptive significance. The potential adaptive roles of stem structural traits are unclear, but may be elucidated by further studies. This work serves as a starting point for future evolutionary studies of stem shape and structure in monocots and provides important background knowledge for further studies of ecological adaptations of Eleocharis.