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Systematic Biology

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https://www.readbyqxmd.com/read/28057859/evolutionary-theory-a-hierarchical-perspective-edited-by-niles-eldredge-telmo-pievani-emanuele-serrelli-and-ilya-t%C3%A3-mkin-2016-vii-385-pp-chicago-chicago-university-press-isbn-978-0-226-42605-1-us105-hardcover-isbn-978-0-226-42622-8-us35-paperback-isbn-978-0
#1
https://www.readbyqxmd.com/read/28057858/protasr-an-evolutionary-framework-for-ancestral-protein-reconstruction-with-selection-on-folding-stability
#2
Miguel Arenas, Claudia C Weber, David A Liberles, Ugo Bastolla
The computational reconstruction of ancestral proteins provides information on past biological events and has practical implications for biomedicine and biotechnology. Currently available tools for ancestral sequence reconstruction (ASR) are often based on empirical amino acid substitution models that assume that all sites evolve at the same rate and under the same process. However, this assumption is frequently violated because protein evolution is highly heterogeneous due to different selective constraints among sites...
January 5, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28053140/efficient-bayesian-species-tree-inference-under-the-multispecies-coalescent
#3
Bruce Rannala, Ziheng Yang
We develop a Bayesian method for inferring the species phylogeny under the multispecies coalescent (MSC) model. To improve the mixing properties of the Markov chain Monte Carlo (MCMC) algorithm that traverses the space of species trees, we implement two efficient MCMC proposals: the first is based on the Subtree Pruning and Regrafting (SPR) algorithm and the second is based on a node-slider algorithm. Like the Nearest-Neighbor Interchange (NNI) algorithm we implemented previously, both new algorithms propose changes to the species tree while simultaneously altering the gene trees at multiple genetic loci to automatically avoid conflicts with the newly proposed species tree...
January 4, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28003535/species-delimitation-with-gene-flow
#4
Nathan D Jackson, Bryan C Carstens, Ariadna E Morales, Brian C O'Meara
Species are commonly thought to be evolutionarily independent in a way that populations within a species are not. In recent years, studies that seek to identify evolutionarily independent lineages (i.e., to delimit species) using genetic data have typically adopted multispecies coalescent approaches that assume that evolutionary independence is formed by the differential sorting of ancestral alleles due to genetic drift. However, gene flow appears to be common among populations and nascent species, and while this process may inhibit lineage divergence (and thus independence), it is usually not explicitly considered when delimiting species...
December 20, 2016: Systematic Biology
https://www.readbyqxmd.com/read/28003534/dental-data-perform-relatively-poorly-in-reconstructing-mammal-phylogenies-morphological-partitions-evaluated-with-molecular-benchmarks
#5
Robert S Sansom, Matthew Albion Wills, Tamara Williams
Phylogenetic trees underpin reconstructions of evolutionary history and tests of evolutionary hypotheses. They are inferred from both molecular and morphological data, yet the relative value of morphology has been questioned in this context due to perceived homoplasy, developmental linkage, and non-independence of characters. Nevertheless, fossil data are limited to incomplete subsets of preserved morphology, and different regions are treated as equivalent. Through meta-analysis of 40 datasets, we show here that the dental and osteological characters of mammals convey significantly different phylogenetic signals, and that osteological characters are significantly more compatible with molecular trees...
December 20, 2016: Systematic Biology
https://www.readbyqxmd.com/read/28003533/a-unifying-comparative-phylogenetic-framework-including-traits-coevolving-across-interacting-lineages
#6
Marc Manceau, Amaury Lambert, Hélène Morlon
- Models of phenotypic evolution fit to phylogenetic comparative data are widely used to make inferences regarding the tempo and mode of trait evolution. A wide range of models is already available for this type of analysis, and the field is still under active development. One of the most needed developments concerns models that better account for the effect of within- and between-clade interspecific interactions on trait evolution, that can result from processes as diverse as competition, predation, parasitism, or mutualism...
December 20, 2016: Systematic Biology
https://www.readbyqxmd.com/read/28003531/bayes-factors-unmask-highly-variable-information-content-bias-and-extreme-influence-in-phylogenomic-analyses
#7
Jeremy M Brown, Robert C Thomson
As the application of genomic data in phylogenetics has become routine, a number of cases have arisen where alternative datasets strongly support conflicting conclusions. This sensitivity to analytical decisions has prevented firm resolution of some of the most recalcitrant nodes in the tree of life. To better understand the causes and nature of this sensitivity, we analyzed several phylogenomic datasets using an alternative measure of topological support (the Bayes factor) that both demonstrates and averts several limitations of more frequently employed support measures (such as Markov chain Monte Carlo estimates of posterior probabilities)...
December 20, 2016: Systematic Biology
https://www.readbyqxmd.com/read/27920231/bayesian-morphological-clock-methods-resurrect-placoderm-monophyly-and-reveal-rapid-early-evolution-in-jawed-vertebrates
#8
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
https://www.readbyqxmd.com/read/27837192/new-evidence-from-linguistic-phylogenetics-identifies-limits-to-punctuational-change
#9
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
https://www.readbyqxmd.com/read/27821704/speciation-with-gene-flow-in-north-american-myotis-bats
#10
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
https://www.readbyqxmd.com/read/27821703/do-macrophylogenies-yield-stable-macroevolutionary-inferences-an-example-from-squamate-reptiles
#11
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
https://www.readbyqxmd.com/read/27798407/construction-of-a-species-level-tree-of-life-for-the-insects-and-utility-in-taxonomic-profiling
#12
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
https://www.readbyqxmd.com/read/27798406/biodiversity-and-the-species-concept-lineages-are-not-enough
#13
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
https://www.readbyqxmd.com/read/27798404/the-impact-of-the-tree-prior-on-molecular-dating-of-data-sets-containing-a-mixture-of-inter-and-intraspecies-sampling
#14
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
https://www.readbyqxmd.com/read/27780899/displayed-trees-do-not-determine-distinguishability-under-the-network-multispecies-coalescent
#15
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-that is whether there could be two distinct networks that lead to the same distribution of gene trees...
October 24, 2016: Systematic Biology
https://www.readbyqxmd.com/read/27798405/possibility-and-challenges-of-conversion-of-current-virus-species-names-to-linnaean-binomials
#16
Thomas S Postler, Anna N Clawson, Gaya K Amarasinghe, Christopher F Basler, Sbina 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, De La Torre Juan Carlos, 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
https://www.readbyqxmd.com/read/27770056/what-is-intuitive-taxonomic-practise
#17
David M Williams, Malte C Ebach
No abstract text is available yet for this article.
October 20, 2016: Systematic Biology
https://www.readbyqxmd.com/read/27892430/systematic-biology-volume-65-number-6-november-2016-back-cover
#18
(no author information available yet)
No abstract text is available yet for this article.
November 2016: Systematic Biology
https://www.readbyqxmd.com/read/27892429/information-for-members-and-subscribers-subscriptions
#19
(no author information available yet)
No abstract text is available yet for this article.
November 2016: Systematic Biology
https://www.readbyqxmd.com/read/27892428/systematic-biology-editorial-board
#20
(no author information available yet)
No abstract text is available yet for this article.
November 2016: Systematic Biology
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