Branch Lengths on Birth–Death Trees and the Expected Loss of Phylogenetic Diversity

Mooers, Arne Ø.; Gascuel, Olivier; Stadler, Tanja; Li, Heyang; Steel, Mike

doi:10.1093/sysbio/syr090

Cited by 72 publications

(88 citation statements)

References 43 publications

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“…Unless stated otherwise, each set is composed of several test cases generated as follows: first draw a species tree at random using a Yule birth model with a rate λ =0.8; assign population sizes as explained in the Results section of [5], using an expansion factor 0.7 and standard deviation 0.4. Each divergence time is assigned its own migration interval; the interval length is drawn at random from a log-normal distribution with mean S / 2 λ and standard deviation 0.25 in log space, 1 / 2 λ being the expected length of the species tree branch in a Yule tree [31]. The time of complete separation for any clade is restricted to be earlier (when time flows forward) than any separation time of its descendants.…”

Section: Resultsmentioning

confidence: 99%

Simulating gene trees under the multispecies coalescent and time-dependent migration

2013

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BackgroundThe multispecies coalescent model has become popular in recent years as a framework to infer a species phylogeny from multilocus genetic data collected from multiple individuals. The model assumes that speciation occurs at a specific point in time, after which the two sub-species evolve in total isolation. However in reality speciation may occur over an extended period of time, during which sister lineages remain in partial contact. Inference of multispecies phylogenies under those conditions is difficult. Indeed even designing simulators which correctly sample gene histories under these conditions is non-trivial.ResultsIn this paper we present a method and software which simulates gene trees under both the multispecies coalescent and migration. Our approach allows for both population sizes and migration rates to change over the species lifetime. Also, migration rates are specified in units of fraction of emigrants per time unit, which makes them easier to interpret. Overall this setup covers a wide range of migration scenarios. The software can be used to investigate properties of gene trees under different migration settings and to generate test cases for programs which infer species trees and/or migration from sequence data. Using simulated data we investigate the effect of migrations between sister lineages on the inference of multispecies phylogenies and on post analysis detection.ConclusionsOur results indicate that while estimation of species tree topology can be quite robust to the presence of gene flow, the inference and detection of migration is problematic, even with methods based on full likelihood models.

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Section: Resultsmentioning

confidence: 99%

Simulating gene trees under the multispecies coalescent and time-dependent migration

2013

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“…1b, c for pure birth and birth-death tree). Mooers et al ( 2012 ) explore further how tree shape impacts the expected loss of phylogenetic diversity. The phylogenetic non-random distribution of extinction risk and the shape of empirical phylogenies might therefore suggest that we risk losing a disproportionate amount of evolutionary history from the tree-of-life.…”

Section: Quantifying the Loss Of Evolutionary Historymentioning

confidence: 99%

Reconsidering the Loss of Evolutionary History: How Does Non-random Extinction Prune the Tree-of-Life?

Yessoufou

Davies

2016

Topics in Biodiversity and Conservation

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Analysing extinction within a phylogenetic framework may seem counter-intuitive because extinction is a priori a non-heritable trait. However, extinction risk is correlated with other traits, such as body size, that show a strong phylogenetic signal. Further, there has been much effort in identifying key traits important for diversifi cation, and recent evidence has demonstrated that the processes of speciation and extinction may be inextricably linked. A phylogenetic approach also allows us to quantify the impact of extinction, for example, as the loss of branches from the tree-of-life. Early work suggested that extinctions might result in little loss of evolutionary history, but subsequent studies indicated that nonrandom extinctions might prune more of the evolutionary tree. Loss of phylogenetic diversity might have ecosystem consequences because functional differences between species tend to be correlated with the evolutionary distances between them. Here we explore how extinction prunes the tree-of-life. Our review indicates that the loss of evolutionary history under non-random extinction (the emerging pattern in extinction biology) might be less pronounced than some previous studies have suggested. However, the loss of functional diversity might still be large, depending on the evolutionary model of trait change. Under a punctuated model of evolution, in which trait differences accrue in bursts at speciation, the number of branches lost is more important than their summed lengths. We suggest that evolutionary models need to be incorporated more explicitly into measures of phylogenetic diversity if we are to use phylogeny as a proxy for functional diversity.

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“…Turning to Part (2), a key observation is that in any rooted binary tree at least half of the internal nodes are adjacent to at least one leaf, and the lengths of the pendant edges they are incident with have expected length of 1/2 on average (Mooers et al 2012). Thus, for at least half the internal nodes that are adjacent to a leaf, selecting the state of that leaf as an estimate leads to nontrivial predictive accuracy, regardless of the speciation and substitution rates, and n. Note that the assumption that the model is conservative is required only for the proof of Part (2); also the assumption in Part (2) of a Yule (pure-birth) process could be weakened to allow extinction also, since the expected average of the branch lengths across the extant pendant edges is still bounded, even for trees produced by a critical birth-death process .…”

Section: Proposition 4 Consider the Tree Shown Inmentioning

confidence: 99%

Predicting the Ancestral Character Changes in a Tree is Typically Easier than Predicting the Root State

Gascuel¹,

Steel²

2014

Systematic Biology

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Abstract.-Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed for this purpose. Theoretical results are available that show that when the substitution rates become too large, reconstructing the ancestral state at the tree root is no longer feasible. Here, we also study the reconstruction of the ancestral changes that occurred along the tree edges. We show that, depending on the tree and branch length distribution, reconstructing these changes (i.e., reconstructing the ancestral state of all internal nodes in the tree) may be easier or harder than reconstructing the ancestral root state. However, results from information theory indicate that for the standard Yule tree, the task of reconstructing internal node states remains feasible, even for very high substitution rates. Moreover, computer simulations demonstrate that for more complex trees and scenarios, this result still holds. For a large variety of counting, parsimony-and likelihood-based methods, the predictive accuracy of a randomly selected internal node in the tree is indeed much higher than the accuracy of the same method when applied to the tree root. Moreover, parsimony-and likelihood-based methods appear to be remarkably robust to sampling bias and model mis-specification. [Ancestral state prediction; character evolution; majority rule; Markov model; maximum likelihood; parsimony; phylogenetic tree.]A fundamental challenge in evolutionary biology is to understand how the traits we observe today in different species evolved from some common ancestral state. A phylogenetic tree linking the species in question provides the usual way to study this question (Liberles 2007). With a tree, one can attempt to reconstruct the evolution of the traits that we observe at the leaves of the tree by estimating the ancestral state at the root of the tree and at the other interior nodes. Typical questions of interest include: what the likely ancestral state was, whether a particular trait evolved just once in the tree or several times, and how reliable our estimates of ancestral states at internal nodes of the tree are. It is this last question that we are concerned with in this article. Using both mathematical and simulation-based analyses, we provide new results concerning the performance of various methods for predicting the ancestral states in a tree. Our work complements and builds on earlier work in this area (Maddison 1995;Zhang and Nei 1997;Mossel 2003;Li et al. 2008Li et al. , 2010Fischer and Thatte 2009;Gascuel and Steel 2010;Zhang et al. 2010) much of which has focused on the mathematical performance of maximum parsimony, with an emphasis on tree root prediction rather than on the global scenario of all changes along the tree. Two recent papers have further investigated the relative merits and limitations of various ancestral state reconstruction methods; RoyerCarenzi et al. (2013) show that the performance ranking of likelihood-ba...

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Branch Lengths on Birth–Death Trees and the Expected Loss of Phylogenetic Diversity

Cited by 72 publications

References 43 publications

Simulating gene trees under the multispecies coalescent and time-dependent migration

Simulating gene trees under the multispecies coalescent and time-dependent migration

Reconsidering the Loss of Evolutionary History: How Does Non-random Extinction Prune the Tree-of-Life?

Predicting the Ancestral Character Changes in a Tree is Typically Easier than Predicting the Root State

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