Bayesian priors for tree calibration: Evaluating two new approaches based on fossil intervals

Bayesian priors for tree calibration: Evaluating two new approaches based on fossil intervals
Ryan W Norris, Cory L Strope, David M McCandlish, Arlin Stoltzfus
doi: http://dx.doi.org/10.1101/014340

Background: Studies of diversification and trait evolution increasingly rely on combining molecular sequences and fossil dates to infer time-calibrated phylogenetic trees. Available calibration software provides many options for the shape of the prior probability distribution of ages at a node to be calibrated, but the question of how to assign a Bayesian prior from limited fossil data remains open. Results: We introduce two new methods for generating priors based upon (1) the interval between the two oldest fossils in a clade, i.e., the penultimate gap (PenG), and (2) the ghost lineage length (GLin), defined as the difference between the oldest fossils for each of two sister lineages. We show that PenG and GLin/2 are point estimates of the interval between the oldest fossil and the true age for the node. Furthermore, given either of these quantities, we derive a principled prior distribution for the true age. This prior is log-logistic, and can be implemented approximately in existing software. Using simulated data, we test these new methods against some other approaches. Conclusions: When implemented as approaches for assigning Bayesian priors, the PenG and GLin methods increase the accuracy of inferred divergence times, showing considerably more precision than the other methods tested, without significantly greater bias. When implemented as approaches to post-hoc scaling of a tree by linear regression, the PenG and GLin methods exhibit less bias than other methods tested. The new methods are simple to use and can be applied to a variety of studies that call for calibrated trees.

Estimating phylogenetic trees from genome-scale data

Estimating phylogenetic trees from genome-scale data
Liang Liu, Zhenxiang Xi, Shaoyuan Wu, Charles Davis, Scott V. Edwards
Comments: 39 pages, 3 figures
Subjects: Populations and Evolution (q-bio.PE)

As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic methods known as “species tree methods” have been proposed to directly address one important source of gene tree heterogeneity, namely the incomplete lineage sorting or deep coalescence that occurs when evolving lineages radiate rapidly, resulting in a diversity of gene trees from a single underlying species tree. Although such methods are gaining in popularity, they are being adopted with caution in some quarters, in part because of an increasing number of examples of strong phylogenetic conflict between concatenation or supermatrix methods and species tree methods. Here we review theory and empirical examples that help clarify these conflicts. Thinking of concatenation as a special case of the more general model provided by the multispecies coalescent can help explain a number of differences in the behavior of the two methods on phylogenomic data sets. Recent work suggests that species tree methods are more robust than concatenation approaches to some of the classic challenges of phylogenetic analysis, including rapidly evolving sites in DNA sequences, base compositional heterogeneity and long branch attraction. We show that approaches such as binning, designed to augment the signal in species tree analyses, can distort the distribution of gene trees and are inconsistent. Computationally efficient species tree methods that incorporate biological realism are a key to phylogenetic analysis of whole genome data.

Geographic range size is predicted by plant mating system

Geographic range size is predicted by plant mating system
Dena Grossenbacher, Ryan Briscoe Runquist, Emma Goldberg, Yaniv Brandvain
doi: http://dx.doi.org/10.1101/013417

Species ranges vary enormously, and even closest relatives may differ in range size by several orders of magnitude. With data from hundreds of species spanning 20 genera and generic sections, we show that plant species that autonomously reproduce via self-pollination consistently have larger geographic ranges than their close relatives that generally require two parents for reproduction. Further analyses strongly implicate autonomous fertilization in causing this relationship, as it is not driven by traits such as polyploidy or annual life history whose evolution is sometimes correlated with the transition to autonomous self-fertilization. Furthermore, we find that selfers occur at higher maximum latitudes and that disparity in range size between selfers and outcrossers increases with time since their separation. Together, these results show that autonomous reproduction – a critical biological trait that eliminates mate limitation and thus potentially increases the probability of establishment – increases range size.

DensiTree 2: Seeing Trees Through the Forest

DensiTree 2: Seeing Trees Through the Forest

Remco Bouckaert, Joseph Heled
doi: http://dx.doi.org/10.1101/012401

Motivation: Phylogenetic analysis like Bayesian MCMC or bootstrapping result in a collection of trees. Trees are discrete objects and it is generally difficult to get a mental grip on a distributions over trees. Visualisation tools like DensiTree can give good intuition on tree distributions. It works by drawing all trees in the set transparently thus highlighting areas where the tree in the set agrees. In this way, both uncertainty in clade heights and uncertainty in topology can be visualised. In our experience, a vanilla DensiTree can turn out to be misleading in that it shows too much uncertainty due to wrongly ordering taxa or due to unlucky placement of internal nodes. Results: DensiTree is extended to allow visualisation of meta-data associated with branches such as population size and evolutionary rates. Furthermore, geographic locations of taxa can be shown on a map, making it easy to visually check there is some geographic pattern in a phylogeny. Taxa orderings have a large impact on the layout of the tree set, and advances have been made in finding better orderings resulting in significantly more informative visualisations. We also explored various methods for positioning internal nodes, which can improve the quality of the image. Together, these advances make it easier to comprehend distributions over trees. Availability: DensiTree is freely available from http://compevol. auckland.ac.nz/software/.

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Karen A Cranston, Open Tree of Life
doi: http://dx.doi.org/10.1101/012260

Reconstructing the phylogenetic relationships that unite all biological lineages (the tree of life) is a grand challenge of biology. However, the paucity of readily available homologous character data across disparately related lineages renders direct phylogenetic inference currently untenable. Our best recourse towards realizing the tree of life is therefore the synthesis of existing collective phylogenetic knowledge available from the wealth of published primary phylogenetic hypotheses, together with taxonomic hierarchy information for unsampled taxa. We combined phylogenetic and taxonomic data to produce a draft tree of life—the Open Tree of Life—containing 2.3 million tips. Realization of this draft tree required the assembly of two resources that should prove valuable to the community: 1) a novel comprehensive global reference taxonomy, and 2) a database of published phylogenetic trees mapped to this common taxonomy. Our open source framework facilitates community comment and contribution, enabling a continuously updatable tree when new phylogenetic and taxonomic data become digitally available. While data coverage and phylogenetic conflict across the Open Tree of Life illuminates significant 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 from which we can continue to improve through community contributions. Having a comprehensive tree of life 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 studies, agriculture, and genomics.

A new hierarchy of phylogenetic models consistent with heterogeneous substitution rates

A new hierarchy of phylogenetic models consistent with heterogeneous substitution rates

Michael D. Woodhams, Jesús Fernández-Sánchez, Jeremy G. Sumner
(Submitted on 4 Dec 2014)

When the process underlying DNA substitutions varies across evolutionary history, the standard Markov models underlying standard phylogenetic methods are mathematically inconsistent. The most prominent example is the general time reversible model (GTR) together with some, but not all, of its submodels. To rectify this deficiency, Lie Markov models have been developed as the class of models that are consistent in the face of a changing process of DNA substitutions. Some well-known models in popular use are within this class, but are either overly simplistic (e.g. the Kimura two-parameter model) or overly complex (the general Markov model). On a diverse set of biological data sets, we test a hierarchy of Lie Markov models spanning the full range of parameter richness. Compared against the benchmark of the ever-popular GTR model, we find that as a whole the Lie Markov models perform remarkably well, with the best performing models having eight parameters and the ability to recognise the distinction between purines and pyrimidines.

Detecting the anomaly zone in species trees and evidence for a misleading signal in higher-level skink phylogeny (Squamata: Scincidae).

Detecting the anomaly zone in species trees and evidence for a misleading signal in higher-level skink phylogeny (Squamata: Scincidae).

Charles W Linkem, Vladimir N. Minin, Adam D Leache
doi: http://dx.doi.org/10.1101/012096

The anomaly zone presents a major challenge to the accurate resolution of many parts of the Tree of Life. The anomaly zone is defined by the presence of a gene tree topology that is more probable than the true species tree. This discrepancy can result from consecutive rapid speciation events in the species tree. Similar to the problem of long-branch attraction, including more data (loci) will only reinforce the support for the incorrect species tree. Empirical phylogenetic studies often implement coalescent based species tree methods to avoid the anomaly zone, but to this point these studies have not had a method for providing any direct evidence that the species tree is actually in the anomaly zone. In this study, we use 16 species of lizards in the family Scincidae to investigate whether nodes that are difficult to resolve are located within the anomaly zone. We analyze new phylogenomic data (429 loci), using both concatenation and coalescent based species tree estimation, to locate conflicting topological signal. We then use the unifying principle of the anomaly zone, together with estimates of ancestral population sizes and species persistence times, to determine whether the observed phylogenetic conflict is a result of the anomaly zone. We identify at least three regions of the Scindidae phylogeny that provide demographic signatures consistent with the anomaly zone, and this new information helps reconcile the phylogenetic conflict in previously published studies on these lizards. The anomaly zone presents a real problem in phylogenetics, and our new framework for identifying anomalous relationships will help empiricists leverage their resources appropriately for overcoming this challenge.