TreeSimGM: Simulating phylogenetic trees under general Bellman-Harris models with lineage-specific shifts of speciation and extinction in R

The Limits of the Constant-rate Birth-Death Prior for Phylogenetic Tree Topology Inference

Birth-death models are stochastic processes describing speciation and extinction through time and across taxa and are widely used in biology for inference of evolutionary timescales. Previous research has highlighted how the expected trees under the constant-rate birth-death (crBD) model tend to differ from empirical trees, for example, with respect to the amount of phylogenetic imbalance. However, our understanding of how trees differ between the crBD model and the signal in empirical data remains incomplete. In this Point of View, we aim to expose the degree to which the crBD model differs from empirically inferred phylogenies and test the limits of the model in practice. Using a wide range of topology indices to compare crBD expectations against a comprehensive dataset of 1189 empirically estimated trees, we confirm that crBD model trees frequently differ topologically compared with empirical trees. To place this in the context of standard practice in the field, we conducted a meta-analysis for a subset of the empirical studies. When comparing studies that used Bayesian methods and crBD priors with those that used other non-crBD priors and non-Bayesian methods (i.e., maximum likelihood methods), we do not find any significant differences in tree topology inferences. To scrutinize this finding for the case of highly imbalanced trees, we selected the 100 trees with the greatest imbalance from our dataset, simulated sequence data for these tree topologies under various evolutionary rates, and re-inferred the trees under maximum likelihood and using the crBD model in a Bayesian setting. We find that when the substitution rate is low, the crBD prior results in overly balanced trees, but the tendency is negligible when substitution rates are sufficiently high. Overall, our findings demonstrate the general robustness of crBD priors across a broad range of phylogenetic inference scenarios but also highlight that empirically observed phylogenetic imbalance is highly improbable under the crBD model, leading to systematic bias in data sets with limited information content.

PhyloJunction: a computational framework for simulating, developing, and teaching evolutionary models

We introduce PhyloJunction, a computational framework designed to facilitate the prototyping, testing, and characterization of evolutionary models. PhyloJunction is distributed as an open-source Python library that can be used to implement a variety of models, through its flexible graphical modeling architecture and dedicated model specification language. Model design and use are exposed to users via command-line and graphical interfaces, which integrate the steps of simulating, summarizing, and visualizing data. This paper describes the features of PhyloJunction - which include, but are not limited to, a general implementation of a popular family of phylogenetic diversification models - and, moving forward, how it may be expanded to not only include new models, but to also become a platform for conducting and teaching statistical learning.

The Major Features of Macroevolution

Evolutionary dynamics operating across deep time leave footprints in the shapes of phylogenetic trees. For the last several decades, researchers have used increasingly large and robust phylogenies to study the evolutionary history of individual clades and to investigate the causes of the glaring disparities in diversity among groups. Whereas typically not the focal point of individual clade-level studies, many researchers have remarked on recurrent patterns that have been observed across many different groups and at many different time scales. Whereas previous studies have documented various such regularities in topology and branch length distributions, they have typically focused on a single pattern and used a disparate collection (oftentimes, of quite variable reliability) of trees to assess it. Here we take advantage of modern megaphylogenies and unify previous disparate observations about the shapes embedded in the Tree of Life to create a catalog of the "major features of macroevolution." By characterizing such a large swath of subtrees in a consistent way, we hope to provide a set of phenomena that process-based macroevolutionary models of diversification ought to seek to explain.

Inference of B cell clonal families using heavy/light chain pairing information

Next generation sequencing of B cell receptor (BCR) repertoires has become a ubiquitous tool for understanding the antibody-mediated immune response: it is now common to have large volumes of sequence data coding for both the heavy and light chain subunits of the BCR. However, until the recent development of high throughput methods of preserving heavy/light chain pairing information, these samples contained no explicit information on which heavy chain sequence pairs with which light chain sequence. One of the first steps in analyzing such BCR repertoire samples is grouping sequences into clonally related families, where each stems from a single rearrangement event. Many methods of accomplishing this have been developed, however, none so far has taken full advantage of the newly-available pairing information. This information can dramatically improve clustering performance, especially for the light chain. The light chain has traditionally been challenging for clonal family inference because of its low diversity and consequent abundance of non-clonal families with indistinguishable naive rearrangements. Here we present a method of incorporating this pairing information into the clustering process in order to arrive at a more accurate partition of the data into clonally related families. We also demonstrate two methods of fixing imperfect pairing information, which may allow for simplified sample preparation and increased sequencing depth. Finally, we describe several other improvements to the partis software package.

The Shape of Phylogenies Under Phase-Type Distributed Times to Speciation and Extinction

Phylogenetic trees describe relationships between extant species, but beyond that their shape and their relative branch lengths can provide information on broader evolutionary processes of speciation and extinction. However, currently many of the most widely used macro-evolutionary models make predictions about the shapes of phylogenetic trees that differ considerably from what is observed in empirical phylogenies. Here, we propose a flexible and biologically plausible macroevolutionary model for phylogenetic trees where times to speciation or extinction events are drawn from a Coxian phase-type (PH) distribution. First, we show that different choices of parameters in our model lead to a range of tree balances as measured by Aldous’ \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\beta $$\end{document}β statistic. In particular, we demonstrate that it is possible to find parameters that correspond well to empirical tree balance. Next, we provide a natural extension of the \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\beta $$\end{document}β statistic to sets of trees. This extension produces less biased estimates of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\beta $$\end{document}β compared to using the median \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\beta $$\end{document}β values from individual trees. Furthermore, we derive a likelihood expression for the probability of observing an edge-weighted tree under a model with speciation but no extinction. Finally, we illustrate the application of our model by performing both absolute and relative goodness-of-fit tests for two large empirical phylogenies (squamates and angiosperms) that compare models with Coxian PH distributed times to speciation with models that assume exponential or Weibull distributed waiting times. In our numerical analysis, we found that, in most cases, models assuming a Coxian PH distribution provided the best fit.

Accounting for errors in data improves divergence time estimates in single-cell cancer evolution

Single-cell sequencing provides a new way to explore the evolutionary history of cells. Compared to traditional bulk sequencing, where a population of heterogeneous cells is pooled to form a single observation, single-cell sequencing isolates and amplifies genetic material from individual cells, thereby preserving the information about the origin of the sequences. However, single-cell data is more error-prone than bulk sequencing data due to the limited genomic material available per cell. Here, we present error and mutation models for evolutionary inference of single-cell data within a mature and extensible Bayesian framework, BEAST2. Our framework enables integration with biologically informative models such as relaxed molecular clocks and population dynamic models. Our simulations show that modeling errors increase the accuracy of relative divergence times and substitution parameters. We reconstruct the phylogenetic history of a colorectal cancer patient and a healthy patient from single-cell DNA sequencing data. We find that the estimated times of terminal splitting events are shifted forward in time compared to models which ignore errors. We observed that not accounting for errors can overestimate the phylogenetic diversity in single-cell DNA sequencing data. We estimate that 30-50% of the apparent diversity can be attributed to error. Our work enables a full Bayesian approach capable of accounting for errors in the data within the integrative Bayesian software framework BEAST2.

A vectorial tree distance measure

A vectorial distance measure for trees is presented. Given two trees, we define a Tree-Alignment (T-Alignment). We T-align the trees from their centers outwards, starting from the root-branches, to make the next level as similar as possible. The algorithm is recursive; condition on the T-alignment of the root-branches we T-align the sub-branches, thereafter each T-alignment is conditioned on the previous one. We define a minimal T-alignment under a lexicographic order which follows the intuition that the differences between the two trees constitutes a vector. Given such a minimal T-alignment, the difference in the number of branches calculated at any level defines the entry of the distance vector at that level. We compare our algorithm to other well-known tree distance measures in the task of clustering sets of phylogenetic trees. We use the TreeSimGM simulator for generating stochastic phylogenetic trees. The vectorial tree distance (VTD) can successfully separate symmetric from asymmetric trees, and hierarchical from non-hierarchical trees. We also test the algorithm as a classifier of phylogenetic trees extracted from two members of the fungi kingdom, mushrooms and mildews, thus showimg that the algorithm can separate real world phylogenetic trees. The Matlab code can be accessed via: https://gitlab.com/avner.priel/vectorial-tree-distance .

Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs

Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always false positives in the reciprocal best match graph. We consider duplication/loss scenarios and characterize unambiguous false-positive (u-fp) orthology assignments, that is, edges in the best match graphs (BMGs) that cannot correspond to orthologs for any gene tree that explains the BMG. Moreover, we provide a polynomial-time algorithm to identify all u-fp orthology assignments in a BMG. Simulations show that at least [Formula: see text] of all incorrect orthology assignments can be detected in this manner. All results rely only on the structure of the BMGs and not on any a priori knowledge about underlying gene or species trees.

From pairs of most similar sequences to phylogenetic best matches

BACKGROUND

Many of the commonly used methods for orthology detection start from mutually most similar pairs of genes (reciprocal best hits) as an approximation for evolutionary most closely related pairs of genes (reciprocal best matches). This approximation of best matches by best hits becomes exact for ultrametric dissimilarities, i.e., under the Molecular Clock Hypothesis. It fails, however, whenever there are large lineage specific rate variations among paralogous genes. In practice, this introduces a high level of noise into the input data for best-hit-based orthology detection methods.

RESULTS

If additive distances between genes are known, then evolutionary most closely related pairs can be identified by considering certain quartets of genes provided that in each quartet the outgroup relative to the remaining three genes is known. A priori knowledge of underlying species phylogeny greatly facilitates the identification of the required outgroup. Although the workflow remains a heuristic since the correct outgroup cannot be determined reliably in all cases, simulations with lineage specific biases and rate asymmetries show that nearly perfect results can be achieved. In a realistic setting, where distances data have to be estimated from sequence data and hence are noisy, it is still possible to obtain highly accurate sets of best matches.

CONCLUSION

Improvements of tree-free orthology assessment methods can be expected from a combination of the accurate inference of best matches reported here and recent mathematical advances in the understanding of (reciprocal) best match graphs and orthology relations.

AVAILABILITY

Accompanying software is available at https://github.com/david-schaller/AsymmeTree.