Phylogenetic Tree Shape Research Articles

Hierarchical graph maps for visualization of collaborative recommender systems

In this paper we provide a method that allows the visualization of similarity relationships present between items of collaborative filtering recommender systems, as well as the relative importance of each of these. The objective is to offer visual representations of the recommender system’s set of items and of their relationships; these graphs show us where the most representative information can be found and which items are rated in a more similar way by the recommender system’s community of users. The visual representations achieved take the shape of phylogenetic trees, displaying the numerical similarity and the reliability between each pair of items considered to be similar. As a case study we provide the results obtained using the public database Movielens 1M, which contains 3900 movies.

Recovering speciation and extinction dynamics based on phylogenies

Phylogenetic trees of only extant species contain information about the underlying speciation and extinction pattern. In this review, I provide an overview over the different methodologies that recover the speciation and extinction dynamics from phylogenetic trees. Broadly, the methods can be divided into two classes: (i) methods using the phylogenetic tree shapes (i.e. trees without branch length information) allowing us to test for speciation rate variation and (ii) methods using the phylogenetic trees with branch length information allowing us to quantify speciation and extinction rates. I end the article with an overview on limitations, open questions and challenges of the reviewed methodology.

Using phylogenetic trees to test for character displacement: a model and an example from a desert mammal community

The distribution of traits within communities is thought to provide information on the evolutionary and ecological forces that structure community composition. Ecological character displacement (evolutionary divergence among populations of interacting species within a community), as well as community‐wide character displacement (even dispersion of species traits within a community via species sorting), have been widely reported and are typically interpreted as evidence for interspecific competition. However, defining an appropriate null distribution with which to assess the observed distribution of traits within a community has proved controversial. Phylogenetic methods provide an alternative approach to evaluating community structure, but such methods also require an appropriate null and have typically overlooked the potential for evolutionary dynamics within communities. Here, we present a novel phylogenetic framework that uses evolutionary expectations to generate a simple null model of the expected distribution of traits among co‐occurring species. Using a stochastic Brownian motion model of trait change, we illustrate that the expected community‐wide dispersion of traits varies with phylogenetic tree shape. We then use data on body mass for mammals to evaluate the accuracy with which phylogeny can predict the empirical distribution of traits and find a strong correlation between predicted and observed trait distributions. We suggest that deviations from phylogenetic expectations may therefore provide a useful tool for evaluating the role of competition in shaping community structure. Finally, we demonstrate the utility of our approach using empirical data on body mass and a phylogeny for a small community of terrestrial mammals in Yotvata, Israel, and reveal evidence consistent with ecological and community‐wide character displacement. Our method unites ecological and evolutionary approaches, and it provides a novel framework for exploring community structure.

Spatial Predictions of Phylogenetic Diversity in Conservation Decision Making

Considering genetic relatedness among species has long been argued as an important step toward measuring biological diversity more accurately, rather than relying solely on species richness. Some researchers have correlated measures of phylogenetic diversity and species richness across a series of sites and suggest that values of phylogenetic diversity do not differ enough from those of species richness to justify their inclusion in conservation planning. We compared predictions of species richness and 10 measures of phylogenetic diversity by creating distribution models for 168 individual species of a species-rich plant family, the Cape Proteaceae. When we used average amounts of land set aside for conservation to compare areas selected on the basis of species richness with areas selected on the basis of phylogenetic diversity, correlations between species richness and different measures of phylogenetic diversity varied considerably. Correlations between species richness and measures that were based on the length of phylogenetic tree branches and tree shape were weaker than those that were based on tree shape alone. Elevation explained up to 31% of the segregation of species rich versus phylogenetically rich areas. Given these results, the increased availability of molecular data, and the known ecological effect of phylogenetically rich communities, consideration of phylogenetic diversity in conservation decision making may be feasible and informative.

Metrics on Multilabeled Trees: Interrelationships and Diameter Bounds

Multilabeled trees or MUL-trees, for short, are trees whose leaves are labeled by elements of some nonempty finite set X such that more than one leaf may be labeled by the same element of X. This class of trees includes phylogenetic trees and tree shapes. MUL-trees arise naturally in, for example, biogeography and gene evolution studies and also in the area of phylogenetic network reconstruction. In this paper, we introduce novel metrics which may be used to compare MUL-trees, most of which generalize well-known metrics on phylogenetic trees and tree shapes. These metrics can be used, for example, to better understand the space of MUL-trees or to help visualize collections of MUL-trees. In addition, we describe some relationships between the MUL-tree metrics that we present and also give some novel diameter bounds for these metrics. We conclude by briefly discussing some open problems as well as pointing out how MUL-tree metrics may be used to define metrics on the space of phylogenetic networks.

Decomposing phylogenetic entropy into α , β and γ components

Measuring the phylogenetic diversity of communities has become a key issue for biogeography and conservation. However, most diversity indices that rely on interspecies phylogenetic distances may increase with species loss and thus violate the principle of weak monotonicity. Moreover, most published phylogenetic diversity indices ignore the abundance distribution along phylogenetic trees, even though lineage abundances are crucial components of biodiversity. The recently introduced concept of phylogenetic entropy overcomes these limitations, but has not been decomposed across scales, i.e. into α, β and γ components. A full understanding of mechanisms sustaining biological diversity within and between communities needs such decomposition. Here, we propose an additive decomposition framework for estimating α, β and γ components of phylogenetic entropy. Based on simulated trees, we demonstrate its robustness to phylogenetic tree shape and species richness. Our decomposition fulfils the requirements of both independence between components and weak monotonicity. Finally, our decomposition can also be adapted to the partitioning of functional diversity across different scales with the same desirable properties.

The Shape and Temporal Dynamics of Phylogenetic Trees Arising from Geographic Speciation

Phylogenetic trees often depart from the expectations of stochastic models, exhibiting imbalance in diversification among lineages and slowdowns in the rate of lineage accumulation through time. Such departures have led to a widespread perception that ecological differences among species or adaptation and subsequent niche filling are required to explain patterns of diversification. However, a key element missing from models of diversification is the geographical context of speciation and extinction. In this study, we develop a spatially explicit model of geographic range evolution and cladogenesis, where speciation arises via vicariance or peripatry, and explore the effects of these processes on patterns of diversification. We compare the results with those observed in 41 reconstructed avian trees. Our model shows that nonconstant rates of speciation and extinction are emergent properties of the apportioning of geographic ranges that accompanies speciation. The dynamics of diversification exhibit wide variation, depending on the mode of speciation, tendency for range expansion, and rate of range evolution. By varying these parameters, the model is able to capture many, but not all, of the features exhibited by birth-death trees and extant bird clades. Under scenarios with relatively stable geographic ranges, strong slowdowns in diversification rates are produced, with faster rates of range dynamics leading to constant or accelerating rates of apparent diversification. A peripatric model of speciation with stable ranges also generates highly unbalanced trees typical of bird phylogenies but fails to produce realistic range size distributions among the extant species. Results most similar to those of a birth-death process are reached under a peripatric speciation scenario with highly volatile range dynamics. Taken together, our results demonstrate that considering the geographical context of speciation and extinction provides a more conservative null model of diversification and offers a very different perspective on the phylogenetic patterns expected in the absence of ecology.

Do languages originate and become extinct at constant rates?

The shape of phylogenetic trees of language families is used to test the null hypothesis that languages throughout a family originate and go extinct at constant rates. Trees constructed either by hand or by computer prove to be more unbalanced than predicted, with many languages on some branches and few on others. The observed levels of imbalance are not explainable by errors in the trees or by the population sizes or geographic density of the languages. The results suggest changes in rates of origination or extinction on a time scale shorter than the time depth of currently recognized families.

EXTINCTION RATES SHOULD NOT BE ESTIMATED FROM MOLECULAR PHYLOGENIES

Molecular phylogenies contain information about the tempo and mode of species diversification through time. Because extinction leaves a characteristic signature in the shape of molecular phylogenetic trees, many studies have used data from extant taxa only to infer extinction rates. This is a promising approach for the large number of taxa for which extinction rates cannot be estimated from the fossil record. Here, I explore the consequences of violating a common assumption made by studies of extinction from phylogenetic data. I show that when diversification rates vary among lineages, simple estimators based on the birth-death process are unable to recover true extinction rates. This is problematic for phylogenetic trees with complete taxon sampling as well as for the simpler case of clades with known age and species richness. Given the ubiquity of variation in diversification rates among lineages and clades, these results suggest that extinction rates should not be estimated in the absence of fossil data.

Thinking in continua: beyond the “adaptive radiation” metaphor

"Adaptive radiation" is an evocative metaphor for explosive evolutionary divergence, which for over 100 years has given a powerful heuristic to countless scientists working on all types of organisms at all phylogenetic levels. However, success has come at the price of making "adaptive radiation" so vague that it can no longer reflect the detailed results yielded by powerful new phylogeny-based techniques that quantify continuous adaptive radiation variables such as speciation rate, phylogenetic tree shape, and morphological diversity. Attempts to shoehorn the results of these techniques into categorical "adaptive radiation: yes/no" schemes lead to reification, in which arbitrary quantitative thresholds are regarded as real. Our account of the life cycle of metaphors in science suggests that it is time to exchange the spent metaphor for new concepts that better represent the full range of diversity, disparity, and speciation rate across all of life.

Topological properties of phylogenetic trees in evolutionary models

The extent to which evolutionary processes affect the shape of phylogenetic trees is an important open question. Analyses of small trees seem to detect non-trivial asymmetries which are usually ascribed to the presence of correlations in speciation rates. Many models used to construct phylogenetic trees have an algorithmic nature and are rarely biologically grounded. In this article, we analyze the topological properties of phylogenetic trees generated by different evolutionary models (populations of RNA sequences and a simple model with inheritance and mutation) and compare them with the trees produced by known uncorrelated models as the backward coalescent, paying special attention to large trees. Our results demonstrate that evolutionary parameters as mutation rate or selection pressure have a weak influence on the scaling behavior of the trees, while the size of phylogenies strongly affects measured scaling exponents. Within statistical errors, the topological properties of phylogenies generated by evolutionary models are compatible with those measured in balanced, uncorrelated trees.

Limit theorems for patterns in phylogenetic trees

Studying the shape of phylogenetic trees under different random models is an important issue in evolutionary biology. In this paper, we propose a general framework for deriving detailed statistical results for patterns in phylogenetic trees under the Yule-Harding model and the uniform model, two of the most fundamental random models considered in phylogenetics. Our framework will unify several recent studies which were mainly concerned with the mean value and the variance. Moreover, refined statistical results such as central limit theorems, Berry-Esseen bounds, local limit theorems, etc., are obtainable with our approach as well. A key contribution of the current study is that our results are applicable to the whole range of possible sizes of the pattern.

Evolutionarily distinctive species often capture more phylogenetic diversity than expected

Evolutionary distinctiveness measures of how evolutionarily isolated a species is relative to other members of its clade. Recently, distinctiveness metrics that explicitly incorporate time have been proposed for conservation prioritization. However, we found that such measures differ qualitatively in how well they capture the total amount of evolution (termed phylogenetic diversity, or PD) represented by a set of species. We used simulation and simple graph theory to explore this relationship with reference to phylogenetic tree shape. Overall, the distinctiveness measures capture more PD on more unbalanced trees and on trees with many splits near the present. The rank order of performance was robust across tree shapes, with apportioning measures performing best and node-based measures performing worst. A sample of 50 ultrametric trees from the literature showed the same patterns. Taken together, this suggests that distinctiveness metrics may be a useful addition to other measures of value for conservation prioritization of species. The simplest measure, the age of a species, performed surprisingly well, suggesting that new measures that focus on tree shape near the tips may provide a transparent alternative to more complicated full-tree approaches.

The Shapes of Phylogenetic Trees of Clades, Faunas, and Local Assemblages: Exploring Spatial Pattern in Differential Diversification

Life on Earth is characterized by strong diversity skewness: related lineages typically show pronounced variation in diversification success, and clades contain hyperdiverse and depauperate subclades. Previous studies have documented diversity skewness only for entire (global) clades. We demonstrate methods for measurement and significance testing of diversity skewness of local assemblages and regional biotas; we illustrate this with an analysis of geographic structure in diversity skewness of primate assemblages. For primates, continental faunas differ in diversity skewness from expectations based on the global phylogeny: South American faunas have significantly low skewness and African faunas have significantly high skewness. However, no local assemblage has diversity skewness different from that expected based on sampling the continental fauna. We also document a latitudinal gradient in diversity skewness for the African assemblages and test for (but do not find) associations of skewness with longitude, local species richness, and net primary productivity. Our data suggest that continental-scale biogeographic events rather than local-scale processes have shaped diversity skewness in modern primate faunas.

The shape of human gene family phylogenies.

BackgroundThe shape of phylogenetic trees has been used to make inferences about the evolutionary process by comparing the shapes of actual phylogenies with those expected under simple models of the speciation process. Previous studies have focused on speciation events, but gene duplication is another lineage splitting event, analogous to speciation, and gene loss or deletion is analogous to extinction. Measures of the shape of gene family phylogenies can thus be used to investigate the processes of gene duplication and loss. We make the first systematic attempt to use tree shape to study gene duplication using human gene phylogenies.ResultsWe find that gene duplication has produced gene family trees significantly less balanced than expected from a simple model of the process, and less balanced than species phylogenies: the opposite to what might be expected under the 2R hypothesis.ConclusionWhile other explanations are plausible, we suggest that the greater imbalance of gene family trees than species trees is due to the prevalence of tandem duplications over regional duplications during the evolution of the human genome.

Which Random Processes Describe the Tree of Life? A Large-Scale Study of Phylogenetic Tree Imbalance

The explosion of phylogenetic studies not only provides a clear snapshot of biodiversity, but also makes it possible to infer how the diversity has arisen (see for example, Purvis and Hector, 2000; Harvey et al., 1996; Nee et al., 1996; Mace et al., 2003). To this aim, variation in speciation and extinction rates have been investigated through their signatures in the shapes of phylogenetic trees (Mooers and Heard, 1997). This issue is of great importance, as fitting stochastic models to tree data would help to understand underlying macroevolutionary processes. Although the prevailing view is that it does not represent phylogenies so well, the most popular model of phylogenetic trees is a branching process introduced by Yule, in which lineages split at random (Yule, 1924). Here we report the study of one major database of published

ApTreeshape: statistical analysis of phylogenetic tree shape

apTreeshape is a R package dedicated to simulation and analysis of phylogenetic tree topologies using statistical imbalance measures. It is a companion library of the R package 'ape', which provides additional functions for reading, plotting, manipulating phylogenetic trees and for connecting to public phylogenetic tree databases. One strength of the package is to include appropriate corrections of classical shape statistics as well as new tests based on the statistical theory of likelihood ratios.

Tree Balance, Time Slices, and Evolutionary Turnover in Cretaceous Planktonic Foraminifera

Studies of phylogenetic tree shape often concentrate on the balance of phylogenies of extant taxa. Paleontological phylogenies (which include extinct taxa) can contain additional useful information and can directly document changes in tree shape through evolutionary time. Unfortunately, the inclusion of extinct taxa lowers the power of direct examinations of tree balance because it increases the range of tree shapes expected under null models of evolution (with equal rates of speciation and extinction across lineages). A promising approach for the analysis of tree shape in paleontological phylogenies is to break the phylogeny down into time slices, examining the shape of the phylogeny of taxa alive at each time slice and changes in that shape between successive time slices. This method was illustrated with 57 time slices through a stratophenetic phylogeny of the Cretaceous planktonic foraminiferal superfamily Globotruncanacea. At 3 of 56 intervals between time slices, 93–92.5 million years ago (MYA), 89–88.5 MYA, and 85.5–84 MYA, the group showed steep increases in imbalance. Although none of these increases were significant after Bonferroni correction, these points in the history of the Globotruncanacea were nevertheless identified as deserving of further macroevolutionary investigation. The 84 MYA time slice coincides with a peak in species turnover for the superfamily. Time slices through phylogenies may prove useful for identifying periods of time when evolution was proceeding in a nonstochastic manner.

Using Tree Shape

Although the primary purpose of phylogenies is to depict evolutionary relationships among taxa, they have other interesting properties. One of the most interesting is their shape, some quantifiable measure of how they look. Such measures come in two general flavors: diversity variation among contemporaneous clades (e.g., when averaged over the whole tree, this is tree balance) and distribution of splitting times (e.g., lineages-through-time plots). These measures represent variation in diversification rates among taxa at a given time and within a taxon through time, respectively. As such, tree shape is the signature of the forces that produce biodiversity, and its study informs one of the major areas in evolutionary biology. It has been over a decade since Craig Guyer and Joseph Slowinski (Slowinski and Guyer, 1989; Guyer and Slowinski, 1991, 1993) began the current era of tree shape work (for a history and general review, see Mooers and Heard, 1997). The concept was elegant: compare shapes of published trees with expectations from reasonable null models, deal with uninteresting technical confounds, and interpret what remains with an eye to explaining past and (perhaps) predicting future biodiversification (though we might not have called it that a decade ago). A decade on, it is well established that trees shapes contain interesting and important information about the evolutionary process (see, e.g., Gaston and Spicer, 1998; Schluter, 2000; Felsenstein, in press). For the 2001 joint SSB/SSE/ASN meeting, we were fortunate to be able to organize a symposium titled Developing uses for phylogenetic tree shape in the study of evolution, an opportunity to organize the decade's work and foster collaboration for the future. Collected here are papers representing many of the contributing authors and others who presented related material in other sessions of that 2001 meeting. We gratefully acknowledge the support of the Society of Systematic Biologists, which both sponsored the symposium and agreed to review these papers for publication. These papers are an excellent, if incomplete, update on the decade's work on tree shape. As expected, the descriptive aspect has become more sophisticated, with new software tools and ever better statistical power (contributions in this issue by Agapow and Purvis, and Chan and Moore; see also McKenzie and Steel, 2000; Stam, 2002). We are getting better at incorporating and analyzing branch length information (the latest update and extension is by Pybus et al., this issue). There are also some new observations: perhaps the most intriguing is the idea that species-level and higher level phylogenies might actually differ in shape (Purvis and Agapow, this issue). Along with these changes is a welcome expansion into new fields. Two sampled here are comparative methods (a potentially powerful way to summarize tree shapes is presented by Martins and Housworth, this issue) and community structure (Webb and Pitman, this issue). An important distinction between neontological and paleontological phylogenies has been recognized, and tools for dealing with the latter have been developed (Harcourt-Brown, this issue). Finally, Alan de Queiroz submits a provocative essay on the complexity of the question of why some taxonomic groups might diversify more than others. But we have still just begun. The patterns are certainly real and are becoming better documented (Purvis and Agapow, and Savolainen et al., this issue; Stam, 2002), and the evolutionary models are inching towards increased realism (Heard and Mooers, this issue). However, present explanations for nonrandom tree shapes are incomplete, and the application of tree-shape concepts in related disciplines is still in its infancy (see, e.g., Heard and Mooers, 2000; von Euler, 2001). We expect to see major advances made with

Tree balance, time slices, and evolutionary turnover in cretaceous planktonic foraminifera.

Studies of phylogenetic tree shape often concentrate on the balance of phylogenies of extant taxa. Paleontological phylogenies (which include extinct taxa) can contain additional useful information and can directly document changes in tree shape through evolutionary time. Unfortunately, the inclusion of extinct taxa lowers the power of direct examinations of tree balance because it increases the range of tree shapes expected under null models of evolution (with equal rates of speciation and extinction across lineages). A promising approach for the analysis of tree shape in paleontological phylogenies is to break the phylogeny down into time slices, examining the shape of the phylogeny of taxa alive at each time slice and changes in that shape between successive time slices. This method was illustrated with 57 time slices through a stratophenetic phylogeny of the Cretaceous planktonic foraminiferal superfamily Globotruncanacea. At 3 of 56 intervals between time slices, 93-92.5 million years ago (MYA), 89-88.5 MYA, and 85.5-84 MYA, the group showed steep increases in imbalance. Although none of these increases were significant after Bonferroni correction, these points in the history of the Globotruncanacea were nevertheless identified as deserving of further macroevolutionary investigation. The 84 MYA time slice coincides with a peak in species turnover for the superfamily. Time slices through phylogenies may prove useful for identifying periods of time when evolution was proceeding in a nonstochastic manner.