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.

Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genus Sceloporus) in the southern Mexican highlands

Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genus Sceloporus) in the southern Mexican highlands

Jared A Grummer, Martha L. Calderón, Adrián Nieto Montes-de Oca, Eric N Smith, Fausto Méndez-de la Cruz, Adam Leaché
doi: http://dx.doi.org/10.1101/008623

Interspecific gene flow is pervasive throughout the tree of life. Although detecting gene flow between populations has been facilitated by new analytical approaches, determining the timing and geography of hybridization has remained difficult, particularly for historical gene flow. A geographically explicit phylogenetic approach is needed to determine the ancestral population overlap. In this study, we performed population genetic analyses, species delimitation, simulations, and a recently developed approach of species tree diffusion to infer the phylogeographic history, timing and geographic extent of gene flow in lizards of the Sceloporus spinosus group. The two species in this group, S. spinosus and S. horridus, are distributed in eastern and western portions of Mexico, respectively, but populations of these species are sympatric in the southern Mexican highlands. We generated data consisting of three mitochondrial genes and eight nuclear loci for 148 and 68 individuals, respectively. We delimited six lineages in this group, but found strong evidence of mito-nuclear discordance in sympatric populations of S. spinosus and S. horridus owing to mitochondrial introgression. We used coalescent simulations to differentiate ancestral gene flow from secondary contact, but found mixed support for these two models. Bayesian phylogeography indicated more than 60% range overlap between ancestral S. spinosus and S. horridus populations since the time of their divergence. Isolation-migration analyses, however, revealed near-zero levels of gene flow between these ancestral populations. Interpreting results from both simulations and empirical data indicate that despite a long history of sympatry among these two species, gene flow in this group has only recently occurred.

A Composite Genome Approach to Identify Phylogenetically Informative Data from Next-Generation Sequencing

A Composite Genome Approach to Identify Phylogenetically Informative Data from Next-Generation Sequencing
Rachel S. Schwartz, Kelly Harkins, Anne C. Stone, Reed A. Cartwright
(Submitted on 16 May 2013 (v1), last revised 12 Nov 2014 (this version, v3))

We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps of de novo whole genome assembly, genome-genome alignment, and annotation. For simulations SISRS is able to identify large numbers of loci containing variable sites with phylogenetic signal. For genomic data from apes, SISRS identified thousands of variable sites, from which we produced an accurate phylogeny. Finally, we used SISRS to identify phylogenetic markers that we used to estimate the phylogeny of placental mammals. We recovered phylogenies from multiple datasets that were consistent with previous conflicting estimates of the relationships among mammals. SISRS is open source and freely available at this https URL

Impacts of terraces on phylogenetic inference

Impacts of terraces on phylogenetic inference
Michael J Sanderson, Michelle M. McMahon, Alexandros Stamatakis, Derrick J. Zwickl, Mike Steel
Comments: 50 pages, 9 figures
Subjects: Populations and Evolution (q-bio.PE)

Terraces are potentially large sets of trees with precisely the same likelihood or parsimony score, which can be induced by missing sequences in partitioned multi-locus phylogenetic data matrices. The set of trees on a terrace can be characterized by enumeration algorithms or consensus methods that exploit the pattern of partial taxon coverage in the data, independent of the sequence data themselves. Terraces add ambiguity and complexity to phylogenetic inference particularly in settings where inference is already challenging: data sets with many taxa and relatively few loci. In this paper we present five new findings about terraces and their impacts on phylogenetic inference. First we clarify assumptions about model parameters that are necessary for the existence of terraces. Second, we explore the dependence of terrace size on partitioning scheme and indicate how to find the partitioning scheme associated with the largest terrace containing a given tree. Third, we highlight the impact of terraces on bootstrap estimates of confidence limits in clades, and characterize the surprising result that the bootstrap proportion for a clade can be entirely determined by the frequency of bipartitions on a terrace, with some bipartitions receiving high support even when incorrect. Fourth, we dissect some effects of prior distributions of edge lengths on the computed posterior probabilities of clades on terraces, to understand an example in which long edges “attract” each other in Bayesian inference. Fifth, we show that even if data are not partitioned, patterns of missing data studied in the terrace problem can lead to instances of apparent statistical inconsistency when even a small element of heterotachy is introduced to the model generating the sequence data. Finally, we discuss strategies for remediation of some of these problems.