The Behavior of Metropolis-Coupled Markov Chains When Sampling Rugged Phylogenetic Distributions
AbstractBayesian phylogenetic inference relies on the use of Markov chain Monte Carlo (MCMC) to provide numerical approximations of high-dimensional integrals and estimate posterior probabilities. However, MCMC performs poorly when posteriors are very rugged (i.e., regions of high posterior density are separated by regions of low posterior density). One technique that has become popular for improving numerical estimates from MCMC when distributions are rugged is Metropolis coupling (MC$^3$). In MC$^3$, additional chains are employed to sample flattened transformations of the posterior and improve mixing. Here, we highlight...
Source: Systematic Biology - February 15, 2018 Category: Biology Source Type: research
Modeling the Growth and Decline of Pathogen Effective Population Size Provides Insight into Epidemic Dynamics and Drivers of Antimicrobial Resistance
AbstractNonparametric population genetic modeling provides a simple and flexible approach for studying demographic history and epidemic dynamics using pathogen sequence data. Existing Bayesian approaches are premised on stochastic processes with stationary increments which may provide an unrealistic prior for epidemic histories which feature extended period of exponential growth or decline. We show that nonparametric models defined in terms of the growth rate of the effective population size can provide a more realistic prior for epidemic history. We propose a nonparametric autoregressive model on the growth rate as a prio...
Source: Systematic Biology - February 7, 2018 Category: Biology Source Type: research
Phenotypic and Genetic Structure Support Gene Flow Generating Gene Tree Discordances in an Amazonian Floodplain Endemic Species
In this study, we used an integrative approach, including sequence capture of ultra-conserved elements (UCEs), mtDNA Sanger sequencing and morphological data to investigate species limits and phylogenetic relationships in face of gene flow in an Amazonian endemic species (Myrmoborus lugubris: Aves). We used commonly implemented species tree and model-based approaches to understand the potential effects of gene flow in phylogenetic reconstructions. The genetic structure observed was congruent with the four recognized subspecies ofM. lugubris. Morphological and UCEs data supported the presence of a wide hybrid zone betweenM....
Source: Systematic Biology - January 29, 2018 Category: Biology Source Type: research
Bayesian Divergence-Time Estimation with Genome-Wide Single-Nucleotide Polymorphism Data of Sea Catfishes (Ariidae) Supports Miocene Closure of the Panamanian Isthmus
AbstractThe closure of the Isthmus of Panama has long been considered to be one of the best defined biogeographic calibration points for molecular divergence-time estimation. However, geological and biological evidence has recently cast doubt on the presumed timing of the initial isthmus closure around 3 Ma but has instead suggested the existence of temporary land bridges as early as the Middle or Late Miocene. The biological evidence supporting these earlier land bridges was based either on only few molecular markers or on concatenation of genome-wide sequence data, an approach that is known to result in potentially misle...
Source: Systematic Biology - January 27, 2018 Category: Biology Source Type: research
Inference of Adaptive Shifts for Multivariate Correlated Traits
We describe an Expectation–Maximization (EM) algorithm that allows for a maximum likelihood estimation of the shift positions, associated with a new model selection criterion, accounting for the identifiability issues for the shift localization on the tree. The method, freely available as an R-package (PhylogeneticEM) is fast, and can deal with missing values. We demonstrate its efficiency and accuracy compared to another state-of-the-art method ($\ell$1ou) on a wide range of simulated scenarios and use this new framework to reanalyze recently g athered data sets on New World Monkeys andAnolis lizards. (Source: Systematic Biology)
Source: Systematic Biology - January 27, 2018 Category: Biology Source Type: research
Accounting for Calibration Uncertainty: Bayesian Molecular Dating as a “Doubly Intractable” Problem
This study introduces a new Bayesian technique for molecular dating that explicitly accommodates for uncertainty in the phylogenetic position of calibrated nodes derived from the analysis of fossil data. The proposed approach thus defines an adequate framework for incorporating expert knowledge and/or prior information about the way fossils were collected in the inference of node ages. Although it belongs to the class of “node-dating” approaches, this method shares interesting properties with “tip-dating” techniques. Yet, it alleviates some of the computational and modeling difficulties that hamper tip-dating appro...
Source: Systematic Biology - January 27, 2018 Category: Biology Source Type: research
Information Criteria for Comparing Partition Schemes
AbstractWhen inferring phylogenies, one important decision is whether and how nucleotide substitution parameters should be shared across different subsets or partitions of the data. One sort of partitioning error occurs when heterogeneous subsets are mistakenly lumped together and treated as if they share parameter values. The opposite kind of error is mistakenly treating homogeneous subsets as if they result from distinct sets of parameters. Lumping and splitting errors are not equally bad. Lumping errors can yield parameter estimates that do not accurately reflect any of the subsets that were combined whereas splitting e...
Source: Systematic Biology - January 23, 2018 Category: Biology Source Type: research
Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case
AbstractPrimates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the Cretaceous –Paleogene (K–Pg) boundary and the timing of diversification of the main crown groups remain controversial. Here, we analysed a data set of 372 taxa (367 Primates and 5 outgroups, 3.4 million aligned base pairs) that includes nine primate genomes. We systematically explore the effect of differen t interpretations of fossil calibrations and molecular clock models on primate divergence time...
Source: Systematic Biology - January 12, 2018 Category: Biology Source Type: research
Automated Integration of Trees and Traits: A Case Study Using Paired Fin Loss Across Teleost Fishes
AbstractData synthesis required for large-scale macroevolutionary studies is challenging with the current tools available for integration. Using a classic question regarding the frequency of paired fin loss in teleost fishes as a case study, we sought to create automated methods to facilitate the integration of broad-scale trait data with a sizable species-level phylogeny. Similar to the evolutionary pattern previously described for limbs, pelvic and pectoral fin reduction and loss are thought to have occurred independently multiple times in the evolution of fishes. We developed a bioinformatics pipeline to identify the pr...
Source: Systematic Biology - January 9, 2018 Category: Biology Source Type: research
An In Silico Comparison of Protocols for Dated Phylogenomics
AbstractIn the age of genome-scale DNA sequencing, choice of molecular marker arguably remains an important decision in planning a phylogenetic study. Using published genomes from 23 primate species, we make a standardized comparison of four of the most frequently used protocols in phylogenomics,viz., targeted sequence-enrichment using ultraconserved element and exon-capture probes, and restriction-site-associated DNA sequencing (RADseq and ddRADseq). Here, we present a procedure to performin silico extractions from genomes and create directly comparable data sets for each class of marker. We then compare these data sets i...
Source: Systematic Biology - January 8, 2018 Category: Biology Source Type: research
Improbable Destinies, Fate, Chance, and the Future of Evolution
. —By LososJonathan B., New York: Riverhead Books, 2017. ISBN-13: 978-0399184925 (eBook). (Source: Systematic Biology)
Source: Systematic Biology - December 27, 2017 Category: Biology Source Type: research
Detecting Environment-Dependent Diversification From Phylogenies: A Simulation Study and Some Empirical Illustrations
AbstractUnderstanding the relative influence of various abiotic and biotic variables on diversification dynamics is a major goal of macroevolutionary studies. Recently, phylogenetic approaches have been developed that make it possible to estimate the role of various environmental variables on diversification using time-calibrated species trees, paleoenvironmental data, and maximum-likelihood techniques. These approaches have been effectively employed to estimate how speciation and extinction rates vary with key abiotic variables, such as temperature and sea level, and we can anticipate that they will be increasingly used i...
Source: Systematic Biology - December 20, 2017 Category: Biology Source Type: research
Improved Maximum Parsimony Models for Phylogenetic Networks
AbstractPhylogenetic networks are well suited to represent evolutionary histories comprising reticulate evolution. Several methods aiming at reconstructing explicit phylogenetic networks have been developed in the last two decades. In this article, we propose a new definition of maximum parsimony for phylogenetic networks that permits to model biological scenarios that cannot be modeled by the definitions currently present in the literature (namely, the “hardwired” and “softwired” parsimony). Building on this new definition, we provide several algorithmic results that lay the foundations for new parsimony-based met...
Source: Systematic Biology - December 20, 2017 Category: Biology Source Type: research
Announcements
(Source: Systematic Biology)
Source: Systematic Biology - December 14, 2017 Category: Biology Source Type: research
Online Bayesian Phylogenetic Inference: Theoretical Foundations via Sequential Monte Carlo
AbstractPhylogenetics, the inference of evolutionary trees from molecular sequence data such as DNA, is an enterprise that yields valuable evolutionary understanding of many biological systems. Bayesian phylogenetic algorithms, which approximate a posterior distribution on trees, have become a popular if computationally expensive means of doing phylogenetics. Modern data collection technologies are quickly adding new sequences to already substantial databases. With all current techniques for Bayesian phylogenetics, computation must start anew each time a sequence becomes available, making it costly to maintain an up-to-dat...
Source: Systematic Biology - December 13, 2017 Category: Biology Source Type: research
