First cousins: A new assessment of robust Australopithecines in hominid phylogeny reconstruction

1985 ◽  
Vol 12 (2) ◽  
pp. 133-139
Author(s):  
Steven C. Ward
Keyword(s):  
Phylogeny Reconstruction

Exploring Modern FPGA Platforms for Faster Phylogeny Reconstruction with RAxML

2020 ◽  
Author(s):  
Pavlos Malakonakis ◽  
Andreas Brokalakis ◽  
Nikolaos Alachiotis ◽  
Evripides Sotiriades ◽  
Apostolos Dollas
Keyword(s):  
Phylogeny Reconstruction

scholarly journals Population genetic analysis and phylogeny reconstruction in Eucalyptus (Myrtaceae) using high-throughput, genome-wide genotyping

2011 ◽  
Vol 59 (1) ◽  
pp. 206-224 ◽  
Author(s):  
Dorothy A. Steane ◽  
Dean Nicolle ◽  
Carolina P. Sansaloni ◽  
César D. Petroli ◽  
Jason Carling ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
High Throughput ◽  
Population Genetic ◽  
Phylogeny Reconstruction ◽  
Population Genetic Analysis ◽  
Genome Wide

scholarly journals Mosaic Genomes of the Six Major Primate Lentivirus Lineages Revealed by Phylogenetic Analyses

2003 ◽  
Vol 77 (13) ◽  
pp. 7202-7213 ◽  
Author(s):  
Marco Salemi ◽  
Tulio De Oliveira ◽  
Valerie Courgnaud ◽  
Vincent Moulton ◽  
Barbara Holland ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Statistical Tests ◽  
Phylogenetic Analyses ◽  
Decomposition Analysis ◽  
Phylogeny Reconstruction ◽  
Origin And Evolution ◽  
Immunodeficiency Virus ◽  
Primate Lentiviruses ◽  
Recombinant Fragments ◽  
Clustering Patterns

ABSTRACT To clarify the origin and evolution of the primate lentiviruses (PLVs), which include human immunodeficiency virus types 1 and 2 as well as their simian relatives, simian immunodeficiency viruses (SIVs), isolated from several host species, we investigated the phylogenetic relationships among the six supposedly nonrecombinant PLV lineages for which the full genome sequences are available. Employing bootscanning as an exploratory tool, we located several regions in the PLV genome that seem to have uncertain or conflicting phylogenetic histories. Phylogeny reconstruction based on distance and maximum-likelihood algorithms followed by a number of statistical tests confirms the existence of at least five putative recombinant fragments in the PLV genome with different clustering patterns. Split decomposition analysis also shows that phylogenetic relationships among PLVs may be better represented by network-based graphs, such as the ones produced by SplitsTree. Our findings not only imply that the six so-called pure PLV lineages have in fact mosaic genomes but also make more unlikely the hypothesis of cospeciation of SIVs and their simian hosts.

scholarly journals Phylogenetic analysis of Na+/H+ (NuoL/MrpA) antiporters

2019 ◽  
pp. 8-15
Author(s):  
Lenin Sánchez-Calderón ◽  
Mauricio Nahuam Chávez-Avilés ◽  
Alma Laura Díaz-Pérez ◽  
Blanca Estela Gómez-Luna ◽  
Juan Carlos Ramírez-Granados ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Atp Synthesis ◽  
Domain Analysis ◽  
Phylogeny Reconstruction ◽  
Monovalent Cations ◽  
Minimum Evolution ◽  
Homologous Proteins ◽  
Conserved Domain ◽  
Low Concentrations ◽  
Eukaryotic Proteins

Objectives: Sodium/proton (Na+/H+) antiporters NuoL/MrpA-like proteins are important in monovalent cations homeostasis, ATP synthesis, are involved in growth using low concentrations of acetate, and in management of protons during methane production. To learn more about the evolutive origin and biological relevance of this protein, in this work a phylogenetic analysis of the NuoL/MrpA superfamily of proteins was done. Methodology: Phylogeny reconstruction was done with 596 NuoL/MrpA proteins and 39 MrpD-NuoM/N proteins. The algorithms used were minimum evolution and maximum likelihood, using MEGA program. Additionally, a conserved domain analysis was done. Contribution: NuoL/MrpA superfamily and their homologous proteins, MrpD-NuoM/N, form two paralogous groups. The NuoL/MrpA superfamily consists of two families. Family NuoL consist of arqueal, bacterial and eukaryotic proteins of around 600 aa in size. Family MrpA are formed by proteins from bacteria and archaea, with a 600 to 850 aa in size. Using the phylogenetic analysis and conserved domain analysis, a superfamily NuoL/MrpA evolution model was proposed.

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