The Search for Common Origin: Homology Revisited
This article is intended for readers with different research backgrounds. We challen ge their traditional approaches, inviting them to consider the proposed framework and offering them a new perspective for their own research. (Source: Systematic Biology)
Source: Systematic Biology - February 23, 2019 Category: Biology Source Type: research
Using Historical Biogeography Models to Study Color Pattern Evolution
AbstractColor is among the most striking features of organisms, varying not only in spectral properties like hue and brightness, but also in where and how it is produced on the body. Different combinations of colors on a bird ’s body are important in both environmental and social contexts. Previous comparative studies have treated plumage patches individually or derived plumage complexity scores from color measurements across a bird’s body. However, these approaches do not consider the multivariate nature of plumages (allowing for plumage to evolve as a whole) or account for interpatch distances. Here, we leverage a ri...
Source: Systematic Biology - February 20, 2019 Category: Biology Source Type: research
A Third Strike Against Perfect Phylogeny
AbstractPerfect phylogenies are fundamental in the study of evolutionary trees because they capture the situation when each evolutionary trait emerges only once in history; if such events are believed to be rare, then by Occam ’s Razor such parsimonious trees are preferable as a hypothesis of evolution. A classical result states that 2-state characters permit a perfect phylogeny precisely if each subset of 2 characters permits one. More recently, it was shown that for 3-state characters the same property holds but for s ize-3 subsets. A long-standing open problem asked whether such a constant exists for each number of st...
Source: Systematic Biology - February 14, 2019 Category: Biology Source Type: research
Fossils with Feathers and Philosophy of Science
AbstractThe last half century of paleornithological research has transformed the way that biologists perceive the evolutionary history of birds. This transformation has been driven, since 1969, by a series of exciting fossil discoveries combined with intense scientific debate over how best to interpret these discoveries. Ideally, as evidence accrues and results accumulate, interpretive scientific agreement forms. But this has not entirely happened in the debate over avian origins: the accumulation of scientific evidence and analyses has had some effect, but not a conclusive one, in terms of resolving the question of avian ...
Source: Systematic Biology - February 11, 2019 Category: Biology Source Type: research
Assessing Combinability of Phylogenomic Data Using Bayes Factors
AbstractWith the rapid reduction in sequencing costs of high-throughput genomic data, it has become commonplace to use hundreds of genes to infer phylogeny of any study system. While sampling a large number of genes has given us a tremendous opportunity to uncover previously unknown relationships and improve phylogenetic resolution, it also presents us with new challenges when the phylogenetic signal is confused by differences in the evolutionary histories of sampled genes. Given the incorporation of accurate marginal likelihood estimation methods into popular Bayesian software programs, it is natural to consider using the...
Source: Systematic Biology - February 6, 2019 Category: Biology Source Type: research
Robust Design for Coalescent Model Inference
AbstractThe coalescent process describes how changes in the size or structure of a population influence the genealogical patterns of sequences sampled from that population. The estimation of (effective) population size changes from genealogies that are reconstructed from these sampled sequences is an important problem in many biological fields. Often, population size is characterized by a piecewise-constant function, with each piece serving as a population size parameter to be estimated. Estimation quality depends on both the statistical coalescent inference method employed, and on the experimental protocol, which controls...
Source: Systematic Biology - February 6, 2019 Category: Biology Source Type: research
Strengthening the Interaction of the Virology Community with the International Committee on Taxonomy of Viruses (ICTV) by Linking Virus Names and Their Abbreviations to Virus Species
AbstractThe International Committee on Taxonomy of Viruses (ICTV) is tasked with classifying viruses into taxa (phyla to species) and devising taxon names. Virus names and virus name abbreviations are currently not within the ICTV ’s official remit and are not regulated by an official entity. Many scientists, medical/veterinary professionals, and regulatory agencies do not address evolutionary questions nor are they concerned with the hierarchical organization of the viral world, and therefore, have limited use for ICTV-dev ised taxa. Instead, these professionals look to the ICTV as an expert point source that provides t...
Source: Systematic Biology - January 28, 2019 Category: Biology Source Type: research
Marginal Likelihoods in Phylogenetics: A Review of Methods and Applications
AbstractBy providing a framework of accounting for the shared ancestry inherent to all life, phylogenetics is becoming the statistical foundation of biology. The importance of model choice continues to grow as phylogenetic models continue to increase in complexity to better capture micro- and macroevolutionary processes. In a Bayesian framework, the marginal likelihood is how data update our prior beliefs about models, which gives us an intuitive measure of comparing model fit that is grounded in probability theory. Given the rapid increase in the number and complexity of phylogenetic models, methods for approximating marg...
Source: Systematic Biology - January 22, 2019 Category: Biology Source Type: research
Integration of Anatomy Ontologies and Evo-Devo Using Structured Markov Models Suggests a New Framework for Modeling Discrete Phenotypic Traits
This article gives practical examples of using the new framework for phylogenetic inference and comparative analysis. (Source: Systematic Biology)
Source: Systematic Biology - January 22, 2019 Category: Biology Source Type: research
OSF-Builder: A New Tool for Constructing and Representing Evolutionary Histories Involving Introgression
AbstractIntrogression is an evolutionary process which provides an important source of innovation for evolution. Although various methods have been used to detect introgression, very few methods are currently available for constructing evolutionary histories involving introgression. In this article, we propose a new method for constructing such evolutionary histories whose starting point is a species forest (consisting of a collection of lineage trees, usually arising as a collection of clades or monophyletic groups in a species tree), and a gene tree for a specific allele of interest, or allele tree for short. Our method ...
Source: Systematic Biology - January 22, 2019 Category: Biology Source Type: research
Announcements
(Source: Systematic Biology)
Source: Systematic Biology - June 15, 2018 Category: Biology Source Type: research
Origins of Darwin ’s Evolution: Solving the Species Puzzle through Time and Place. By J. David Archibald
Origins of Darwin ’s Evolution: Solving the Species Puzzle through Time and Place. By ArchibaldJ. David. New York: Columbia University Press, 2017. 192 + xvi pp. ISBN 9780231776842, $65.00/£54.95 (hardcover); ISBN 9780231545297. $64.99/£54.95 (eBook). (Source: Systematic Biology)
Source: Systematic Biology - March 6, 2018 Category: Biology Source Type: research
Inferring Phylogenetic Networks Using PhyloNet
AbstractPhyloNet was released in 2008 as a software package for representing and analyzing phylogenetic networks. At the time of its release, the main functionalities in PhyloNet consisted of measures for comparing network topologies and a single heuristic for reconciling gene trees with a species tree. Since then, PhyloNet has grown significantly. The software package now includes a wide array of methods for inferring phylogenetic networks from data sets of unlinked loci while accounting for both reticulation (e.g., hybridization) and incomplete lineage sorting. In particular, PhyloNet now allows for maximum parsimony, ma...
Source: Systematic Biology - March 5, 2018 Category: Biology Source Type: research
Announcements
(Source: Systematic Biology)
Source: Systematic Biology - February 21, 2018 Category: Biology Source Type: research
