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Systematic Biology

Benedict King, Tuo Qiao, Michael S Y Lee, Min Zhu, John A Long
The phylogeny of early gnathostomes provides an important framework for understanding one of the most significant evolutionary events, the origin and diversification of jawed vertebrates. A series of recent cladistic analyses have suggested that the placoderms, an extinct group of armoured fish, form a paraphyletic group basal to all other jawed vertebrates. We revised and expanded this morphological data set, most notably by sampling autapomorphies in a similar way to parsimony-informative traits, thus ensuring this data (unlike most existing morphological data sets) satisfied an important assumption of Bayesian tip-dated morphological clock approaches...
December 5, 2016: Systematic Biology
Eric W Holman, Søren Wichmann
Since the early 1970s biologists have debated whether evolution is punctuated by speciation events with bursts of cladogenetic changes, or whether evolution tends to be of a more gradual, anagenetic nature. A similar discussion among linguists has barely begun, but the present results suggest that there is also room for controversy over this issue in linguistics. The only previous study correlated the number of nodes in linguistic phylogenies with branch lengths and found support for punctuated equilibrium...
November 10, 2016: Systematic Biology
Ariadna E Morales, Nathan D Jackson, Tanya A Dewey, Brian C O'Meara, Bryan C Carstens
Growing evidence supports the idea that species can diverge in the presence of gene flow. However, most methods of phylogeny estimation do not consider this process, despite the fact that ignoring gene flow is known to bias phylogenetic inference. Furthermore, studies that do consider divergence-with-gene-flow typically do so by estimating rates of gene flow using a isolation-with-migration model (IM), rather than evaluating scenarios of gene flow (such as divergence-with-gene flow or secondary contact) that represent very different types of diversification...
November 7, 2016: Systematic Biology
Pascal O Title, Daniel L Rabosky
Advances in the generation, retrieval and analysis of phylogenetic data have enabled researchers to create phylogenies that contain many thousands of taxa. These "macrophylogenies" - large trees that typically derive from megaphylogeny, supermatrix, or supertree approaches - provide researchers with an unprecedented ability to conduct evolutionary analyses across broad phylogenetic scales. Many studies have now used these phylogenies to explore the dynamics of speciation, extinction, and phenotypic evolution across large swaths of the tree of life...
November 7, 2016: Systematic Biology
Douglas Chesters
While comprehensive phylogenies have proven an invaluable tool in ecology and evolution, their construction is made increasingly challenging both by the scale and structure of publically available sequences. The distinct partition between gene-rich (genomic) and species-rich (DNA barcode) data is a feature of data that has been largely overlooked, yet presents a key obstacle to scaling supermatrix analysis.I present a phyloinformatics framework for draft construction of a species-level phylogeny of insects (Class Insecta)...
October 26, 2016: Systematic Biology
John V Freudenstein, Michael B Broe, Ryan A Folk, Brandon T Sinn
The nature and definition of species continue to be matters of debate. Current views of species often focus on their nature as lineages -- maximal reproductive communities through time. Whereas many authors point to the Evolutionary Species Concept as optimal, in its original form it stressed the ecological role of species as well as their history as lineages, but most recent authors have ignored the role aspect of the concept, making it difficult to apply unambiguously in a time-extended way. This trend has been exacerbated by the application of methods and concepts emphasizing the notion of monophyly, originally applied only at higher levels, to the level of individuals, as well as by the current emphasis on molecular data...
October 26, 2016: Systematic Biology
Andrew M Ritchie, Nathan Lo, Simon Y W Ho
In Bayesian phylogenetic analyses of genetic data, prior probability distributions need to be specified for the model parameters, including the tree. When Bayesian methods are used for molecular dating, available tree priors include those designed for species-level data, such as the pure-birth and birth-death priors, and coalescent-based priors designed for population-level data. However, molecular dating methods are frequently applied to data sets that include multiple individuals across multiple species. Such data sets violate the assumptions of both the speciation and coalescent-based tree priors, making it unclear which should be chosen and whether this choice can affect the estimation of node times...
October 26, 2016: Systematic Biology
Sha Zhu, James H Degnan
Recent work in estimating species relationships from gene trees has included inferring networks assuming that past hybridization has occurred between species. Probabilistic models using the multispecies coalescent can be used in this framework for likelihood-based inference of both network topologies and parameters, including branch lengths and hybridization parameters. A difficulty for such methods is that it is not always clear whether, or to what extent, networks are identifiable - i.e., whether there could be two distinct networks that lead to the same distribution of gene trees...
October 24, 2016: Systematic Biology
Thomas S Postler, Anna N Clawson, Gaya K Amarasinghe, Christopher F Basler, Sina Bavari, Mária Benkő, Kim R Blasdell, Thomas Briese, Michael J Buchmeier, Alexander Bukreyev, Charles H Calisher, Kartik Chandran, Rémi Charrel, Christopher S Clegg, Peter L Collins, Juan Carlos de la Torre, Joseph L DeRisi, Ralf G Dietzgen, Olga Dolnik, Ralf Dürrwald, John M Dye, Andrew J Easton, Sébastian Emonet, Pierre Formenty, Ron A M Fouchier, Elodie Ghedin, Jean-Paul Gonzalez, Balázs Harrach, Roger Hewson, Masayuki Horie, Dàohóng Jiāng, Gary Kobinger, Hideki Kondo, Andrew M Kropinski, Mart Krupovic, Gael Kurath, Robert A Lamb, Eric M Leroy, Igor S Lukashevich, Andrea Maisner, Arcady R Mushegian, Sergey V Netesov, Norbert Nowotny, Jean L Patterson, Susan L Payne, Janusz T Paweska, Clarence J Peters, Sheli R Radoshitzky, Bertus K Rima, Victor Romanowski, Dennis Rubbenstroth, Sead Sabanadzovic, Hélène Sanfaçon, Maria S Salvato, Martin Schwemmle, Sophie J Smither, Mark D Stenglein, David M Stone, Ayato Takada, Robert B Tesh, Keizo Tomonaga, Noël Tordo, Jonathan S Towner, Nikos Vasilakis, Viktor E Volchkov, Victoria Wahl-Jensen, Peter J Walker, Lin-Fa Wang, Arvind Varsani, Anna E Whitfield, F Murilo Zerbini, Jens H Kuhn
Botanical, mycological, zoological, and prokaryotic species names follow the Linnaean format, consisting of an italicized Latinized binomen with a capitalized genus name and a lower-case species epithet (e.g., Homo sapiens). Virus species names, however, do not follow a uniform format, and even when binomial, are not Linnaean in style. In this thought exercise, we attempted to convert all currently official names of species included in the virus family Arenaviridae and the virus order Mononegavirales to Linnaean binomials, and to identify and address associated challenges and concerns...
October 22, 2016: Systematic Biology
David M Williams, Malte C Ebach
No abstract text is available yet for this article.
October 20, 2016: Systematic Biology
Jarno Lintusaari, Michael U Gutmann, Ritabrata Dutta, Samuel Kaski, Jukka Corander
Bayesian inference plays an important role in phylogenetics, evolutionary biology, and in many other branches of science. It provides a principled framework for dealing with uncertainty and quantifying how it changes in the light of new evidence. For many complex models and inference problems, however, only approximate quantitative answers are obtainable. Approximate Bayesian computation (ABC) refers to a family of algorithms for approximate inference that makes a minimal set of assumptions by only requiring that sampling from a model is possible...
October 19, 2016: Systematic Biology
Mandev S Gill, Lam Si Tung Ho, Guy Baele, Philippe Lemey, Marc A Suchard
Understanding the processes that give rise to quantitative measurements associated with molecular sequence data remains an important issue in statistical phylogenetics. Examples of such measurements include geographic coordinates in the context of phylogeography and phenotypic traits in the context of comparative studies. A popular approach is to model the evolution of continuously varying traits as a Brownian diffusion process acting on a phylogenetic tree. However, standard Brownian diffusion is quite restrictive and may not accurately characterize certain trait evolutionary processes...
October 18, 2016: Systematic Biology
Deren A R Eaton, Elizabeth L Spriggs, Brian Park, Michael J Donoghue
Restriction-site associated DNA (RAD) sequencing and related methods rely on the conservation of enzyme recognition sites to isolate homologous DNA fragments for sequencing, with the consequence that mutations disrupting these sites lead to missing information. There is thus a clear expectation for how missing data should be distributed, with fewer loci recovered between more distantly related samples. This observation has led to a related expectation: that RAD-seq data are insufficiently informative for resolving deeper scale phylogenetic relationships...
October 18, 2016: Systematic Biology
Daniel Edler, Thaís Guedes, Alexander Zizka, Martin Rosvall, Alexandre Antonelli
Biogeographical regions (bioregions) reveal how different sets of species are spatially grouped and therefore are important units for conservation, historical biogeography, ecology and evolution. Several methods have been developed to identify bioregions based on species distribution data rather than expert opinion. One approach successfully applies network theory to simplify and highlight the underlying structure in species distributions. However, this method lacks tools for simple and efficient analysis. Here we present Infomap Bioregions, an interactive web application that inputs species distribution data and generates bioregion maps...
October 1, 2016: Systematic Biology
Kevin M Kocot, Torsten H Struck, Julia Merkel, Damien S Waits, Christiane Todt, Pamela M Brannock, David A Weese, Johanna T Cannon, Leonid L Moroz, Bernhard Lieb, Kenneth M Halanych
Phylogenomic studies have improved understanding of deep metazoan phylogeny and show promise for resolving incongruences among analyses based on limited numbers of loci. One region of the animal tree that has been especially difficult to resolve, even with phylogenomic approaches, is relationships within Lophotrochozoa (the animal clade that includes molluscs, annelids, and flatworms among others). Lack of resolution in phylogenomic analyses could be due to insufficient phylogenetic signal, limitations in taxon and/or gene sampling, or systematic error...
September 23, 2016: Systematic Biology
Charles S P Foster, Hervé Sauquet, Marlien van der Merwe, Hannah McPherson, Maurizio Rossetto, Simon Y W Ho
The evolutionary timescale of angiosperms has long been a key question in biology. Molecular estimates of this timescale have shown considerable variation, being influenced by differences in taxon sampling, gene sampling, fossil calibrations, evolutionary models, and choices of priors. Here, we analyse a data set comprising 76 protein-coding genes from the chloroplast genomes of 195 taxa spanning 86 families, including novel genome sequences for 11 taxa, to evaluate the impact of models, priors, and gene sampling on Bayesian estimates of the angiosperm evolutionary timescale...
September 20, 2016: Systematic Biology
Ryan A Folk, Jennifer R Mandel, John V Freudenstein
While hybridization has recently received a resurgence of attention from systematists and evolutionary biologists, there remains a dearth of case studies on ancient, diversified hybrid lineages - clades of organisms that originated through reticulation. Studies on these groups are valuable in that they would speak to the long-term phylogenetic success of lineages following gene flow between species. We present a phylogenomic view of Heuchera, long known for frequent hybridization, incorporating all three independent genomes: targeted nuclear (~400,000 bp), plastid (~160,000 bp) and mitochondrial (~470,000 bp) data...
September 16, 2016: Systematic Biology
Nathan V Whelan, Kenneth M Halanych
As phylogenetic datasets have increased in size, site-heterogeneous substitution models such as CAT-F81 and CAT-GTR have been advocated in favor of other models because they purportedly suppress long-branch attraction (LBA). These models are two of the most commonly used models in phylogenomics, and they have been applied to a variety of taxa ranging from Drosophila to land plants. However, many arguments in favor of CAT models have been based on tenuous assumptions about the true phylogeny rather than rigorous testing with known trees via simulation...
September 14, 2016: Systematic Biology
Marcin Bogusz, Simon Whelan
Phylogenetic tree inference is a critical component of many systematic and evolutionary studies. The majority of these studies are based on the two-step process of multiple sequence alignment followed by tree inference, despite persistent evidence that the alignment step can lead to biased results. Here we present a two-part study that first presents PaHMM-Tree, a novel neighbor joining-based method that estimates pairwise distances without assuming a single alignment. We then use simulations to benchmark its performance against a wide-range of other phylogenetic tree inference methods, including the first comparison of alignment-free distance-based methods against more conventional tree estimation methods...
September 14, 2016: Systematic Biology
Alexandre Antonelli, Hannes Hettling, Fabien L Condamine, Karin Vos, R Henrik Nilsson, Michael J Sanderson, Hervé Sauquet, Ruud Scharn, Daniele Silvestro, Mats Töpel, Christine D Bacon, Bengt Oxelman, Rutger A Vos
Rapidly growing biological data-including molecular sequences and fossils-hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyze these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction...
September 10, 2016: Systematic Biology
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