Results 31 to 40 of about 17,330 (247)

SimPhy : Phylogenomic Simulation of Gene, Locus and Species Trees [PDF]

Systematic Biology, 2015
Abstract We present here a fast and flexible software – SimPhy – for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer –all three potentially leading to the species tree/gene tree discordance– and ...
Mallo, D, De Oliveira Martins, L, Posada, D   +2 more
openaire   +3 more sources

Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes

Frontiers in Plant Science, 2022
We assess relationships among 192 species in all 12 monocot orders and 72 of 77 families, using 602 conserved single-copy (CSC) genes and 1375 benchmarking single-copy ortholog (BUSCO) genes extracted from genomic and transcriptomic datasets ...
Prakash Raj Timilsena, Eric K. Wafula, Craig F. Barrett, Saravanaraj Ayyampalayam, Saravanaraj Ayyampalayam, Joel R. McNeal, Jeremy D. Rentsch, Michael R. McKain, Karolina Heyduk, Alex Harkess, Matthieu Villegente, John G. Conran, Nicola Illing, Bruno Fogliani, Cécile Ané, Cécile Ané, J. Chris Pires, Jerrold I. Davis, Wendy B. Zomlefer, Dennis W. Stevenson, Sean W. Graham, Thomas J. Givnish, James Leebens-Mack, Claude W. dePamphilis   +23 more
doaj   +1 more source

Evidence of introgression amid phylogenetic conflict in Brachyotum, a plant radiation from the Tropical Andes. [PDF]

Am J Bot
Abstract Premise The species‐rich flora of Tropical Andes underwent multiple rapid and recent diversifications, yet resolving their evolutionary histories remains challenging despite increasing phylogenomic data. Here, we examined phylogenomic conflict in Brachyotum (Melastomataceae) to identify sources preventing its resolution.
Paredes-Burneo D, Bedoya AM, Michelangeli FA, Majure LC, Ulloa Ulloa C, Lagomarsino LP.   +5 more
europepmc   +2 more sources

The complete mitochondrial genome of an endangered mangrove plant: Scyphiphora hydrophyllacea

Mitochondrial DNA. Part B. Resources, 2020
The complete mitochondrial genome of an endangered mangrove plant: Scyphiphora hydrophyllacea was analyzed in this paper, which is the first for the genus within the family Rubiaceae. The mitogenome sequence is 354,155 bp in length containing 3 ribosomal
Yuechao Chen, Xianya Wei, Guangxuan Lin, Yiming Liu, Ying Zhang   +4 more
doaj   +1 more source

Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life

Systematic Biology, 2020
AbstractMolecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid ...
Hime, Paul M., Lemmon, Alan R., Lemmon, Emily C. Moriarty, Prendini, Elizabeth, Brown, Jeremy M., Thomson, Robert C., Kratovil, Justin D., Noonan, Brice P., Pyron, R. Alexander, Peloso, Pedro L. V., Kortyna, Michelle L., Keogh, J. Scott, Donnellan, Stephen C., Mueller, Rachel Lockridge, Raxworthy, Christopher J., Kunte, Krushnamegh, Ron, Santiago R., Das, Sandeep, Gaitonde, Nikhil, Green, David M., Labisko, Jim, Che, Jing, Weisrock, David W.   +22 more
openaire   +4 more sources

Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics

BMC Bioinformatics, 2008
Background The availability of sequences from whole genomes to reconstruct the tree of life has the potential to enable the development of phylogenomic hypotheses in ways that have not been before possible.
Lee Ernest K, Coruzzi Gloria, Egan Mary G, Sarkar Indra, DeSalle Rob   +4 more
doaj   +1 more source

Phylogenomic Analyses and Molecular Signatures Elucidating the Evolutionary Relationships amongst the Chlorobia and Ignavibacteria Species: Robust Demarcation of Two Family-Level Clades within the Order Chlorobiales and Proposal for the Family Chloroherpetonaceae fam. nov

Microorganisms, 2022
Evolutionary relationships amongst Chlorobia and Ignavibacteria species/strains were examined using phylogenomic and comparative analyses of genome sequences.
Sarah Bello, Mohammad Howard-Azzeh, Herb E. Schellhorn, Radhey S. Gupta   +3 more
doaj   +1 more source

Phylogenomic Models from Tree Symmetries

SIAM Journal on Applied Algebra and Geometry
A model of genomic sequence evolution on a species tree should include not only a sequence substitution process, but also a coalescent process, since different sites may evolve on different gene trees due to incomplete lineage sorting. Chifman and Kubatko initiated the study of such models, leading to the development of the SVDquartets methods of ...
Elizabeth S. Allman, Colby Long, John A. Rhodes   +2 more
openaire   +4 more sources

Phylogenetic and Phylogenomic Definition of Rhizopus Species

G3: Genes, Genomes, Genetics, 2018
Phylogenomic approaches have the potential to improve confidence about the inter-relationships of species in the order Mucorales within the fungal tree of life.
Andrii P. Gryganskyi, Jacob Golan, Somayeh Dolatabadi, Stephen Mondo, Sofia Robb, Alexander Idnurm, Anna Muszewska, Kamil Steczkiewicz, Sawyer Masonjones, Hui-Ling Liao, Michael T. Gajdeczka, Felicia Anike, Antonina Vuek, Iryna M. Anishchenko, Kerstin Voigt, G. Sybren de Hoog, Matthew E. Smith, Joseph Heitman, Rytas Vilgalys, Jason E. Stajich   +19 more
doaj   +1 more source

The complete mitochondrial genome of a mangrove associated plant: Sesuvium portulacastrum and its phylogenetic implications

Mitochondrial DNA. Part B. Resources, 2020
The complete mitochondrial genome of mangrove associated plant: Sesuvium portulacastrum was analyzed in this paper, which is the first for the genus within the family Aizoaceae. The mitogenome sequence is 392,221 bp in length containing six ribosomal RNA
Renmao Li, Xianya Wei, Yun Wang, Ying Zhang   +3 more
doaj   +1 more source