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Systematic Biology

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https://www.readbyqxmd.com/read/28204787/inference-of-evolutionary-jumps-in-large-phylogenies-using-levy-processes
#1
Pablo Duchen, Christoph Leuenberger, Sandor M Szilagyi, Luke Harmon, Jonathan Eastman, Manuel Schweizer, Daniel Wegmann
No abstract text is available yet for this article.
February 16, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28204784/a-poissonian-model-of-indel-rate-variation-for-phylogenetic-tree-inference
#2
Yongliang Zhai, Alexandre Bouchard-Côté
No abstract text is available yet for this article.
February 16, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28204782/phrapl-phylogeographic-inference-using-approximate-likelihoods
#3
Nathan D Jackson, Ariadna E Morales, Bryan C Carstens, Brian C O'Meara
No abstract text is available yet for this article.
February 16, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28204803/erratum
#4
(no author information available yet)
No abstract text is available yet for this article.
February 13, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28204758/erratum
#5
(no author information available yet)
No abstract text is available yet for this article.
February 13, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28177510/an-integrated-model-of-phenotypic-trait-changes-and-site-specific-sequence-evolution
#6
Eli Levy Karin, Susann Wicke, Tal Pupko, Itay Mayrose
No abstract text is available yet for this article.
February 8, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28177088/using-genomic-location-and-coalescent-simulation-to-investigate-gene-tree-discordance-in-medicago-l
#7
F Sousa, Y J K Bertrand, J J Doyle, B Oxelman, B E Pfeil
No abstract text is available yet for this article.
February 8, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28169404/age-dependent-and-lineage-dependent-speciation-and-extinction-in-the-imbalance-of-phylogenetic-trees
#8
Eric W Holman
No abstract text is available yet for this article.
February 7, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28169402/can-we-future-proof-consensus-trees
#9
David Bryant, Andrew Francis, Mike Steel
No abstract text is available yet for this article.
February 7, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28158802/species-concepts-in-biology-historical-development-theoretical-foundations-and-practical-relevance-frank-e-zachos
#10
David A Morrison
No abstract text is available yet for this article.
February 1, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28173597/new-evidence-from-linguistic-phylogenetics-identifies-limits-to-punctuational-change
#11
Eric W Holman, Søren Wichmann
No abstract text is available yet for this article.
January 31, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28123117/phylogenomics-from-whole-genome-sequences-using-atram
#12
Julie M Allen, Bret Boyd, Nam-Phuong Nguyen, Pranjal Vachaspati, Tandy Warnow, Daisie I Huang, Patrick G S Grady, Kayce C Bell, Quentin C B Cronk, Lawrence Mugisha, Barry R Pittendrigh, M Soledad Leonardi, David L Reed, Kevin P Johnson
Novel sequencing technologies are rapidly expanding the size of datasets that can be applied to phylogenetic studies. Currently the most commonly used phylogenomic approaches involve some form of genome reduction. While these approaches make assembling phylogenomic datasets more economical for organisms with large genomes, they reduce the genomic coverage and thereby the long-term utility of the data. Currently, for organisms with moderate to small genomes (<1000 Mbp) it is feasible to sequence the entire genome at modest coverage (10-30X)...
January 25, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28123116/the-first-organ-based-free-ontology-for-arthropods-ontology-of-arthropod-circulatory-systems-oarcs-and-its-integration-into-a-novel-formalization-scheme-for-morphological-descriptions
#13
Christian S Wirkner, Torben Göpel, Jens Runge, Jonas Keiler, Bastian-Jesper Klussmann-Fricke, Katarina Huckstorf, Stephan Scholz, Istvan Mikó, Matt Yoder, Stefan Richter
Morphology, the oldest discipline in the biosciences, is currently experiencing a renaissance in the field of comparative phenomics. However, morphological/phenotypic research still suffers on various levels from a lack of standards. This shortcoming, first highlighted as the "linguistic problem of morphology", concerns the usage of terminology but also the need for formalization of morphological descriptions themselves, something of paramount importance not only to the field of morphology but also when it comes to the use of phenotypic data in systematics and evolutionary biology...
January 25, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28123115/homology-aware-phylogenomics-at-gigabase-scales
#14
M J Sanderson, Marius Nicolae, M M McMahon
Obstacles to inferring species trees from whole genome data sets range from algorithmic and data management challenges to the wholesale discordance in evolutionary history found in different parts of a genome. Recent work that builds trees directly from genomes by parsing them into sets of small k-mer strings holds promise to streamline and simplify these efforts, but existing approaches do not account well for gene tree discordance. We describe a "seed and extend" protocol that finds nearly exact matching sets of orthologous k-mers and extends them to construct data sets that can properly account for genomic heterogeneity...
January 25, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28123113/erratum
#15
(no author information available yet)
No abstract text is available yet for this article.
January 25, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28123112/how-the-aridification-of-australia-structured-the-biogeography-and-influenced-the-diversification-of-a-large-lineage-of-australian-cicadas
#16
Christopher L Owen, David C Marshall, Kathy B R Hill, Chris Simon
Over the last 30 million years, Australia's landscape has undergone dramatic cooling and drying due to the establishment of the Antarctic Circumpolar Current and change in global CO[Formula: see text] levels. Studies have shown that many Australian organisms went extinct during these major cooling events, while others experienced adaptive radiations and increases in diversification rates as a result of exploiting new niches in the arid zone. Despite the many studies on diversification and biogeography in Australia, few have been continent-wide and none have focused on a group of organisms adapted to feeding on plants...
January 25, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28108601/phylogenomics-using-target-restricted-assembly-resolves-intra-generic-relationships-of-parasitic-lice-phthiraptera-columbicola
#17
Bret M Boyd, Julie M Allen, Nam Nguyen, Andrew D Sweet, Tandy Warnow, Michael D Shapiro, Scott M Villa, Sarah E Bush, Dale H Clayton, Kevin P Johnson
Parasitic "wing lice" (Phthiraptera: Columbicola) and their dove and pigeon hosts are a well-recognized model system for coevolutionary studies at the intersection of micro- and macroevolution. Selection on lice in microevolutionary time occurs as pigeons and doves defend themselves against lice by preening. In turn, behavioral and morphological adaptations of the lice improve their ability to evade host defense. Over macroevolutionary time wing lice tend to cospeciate with their hosts; yet, some species of Columbicola have switched to new host species...
January 19, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28175908/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
#18
https://www.readbyqxmd.com/read/28057858/protasr-an-evolutionary-framework-for-ancestral-protein-reconstruction-with-selection-on-folding-stability
#19
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
#20
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
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