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Sampling of a few vertebrate mitochondrial genomes aligned and gapstripped.
No full text<p>Complete mitochondrial genomes of a small sampling of fish, amphibians, reptiles, birds and mammals were downloaded from GenBank and aligned with MAFFT. The alignment was then gap-stripped to remove columns where any one sequence was missing information, or the alignment was uncertain. Alignment prior to gap-stipping is available from Brian Foley.</p
Mammal Molecular Clock Tree
No full text<p>Lartillot et al put together a data set of close to 15,000 bases of protein coding DNA from nulear genes (as opposed to mitochondrial) of 78 species of mammals and a few marsupials. Their purpose was to correlate molecular evolution and the fossile record with body mass and lifespan. I have begun exploring this data set for other studies of evolution.</p
Saturation of silent sites
No full text<p>DAMBE was used to plot the observed tranistions and transversion vs the phylogenetic distance for each pair of sequences in the alignments in the 2 data sets. In the complete genomes data set, I included more sequences which were closely related to each other such as modern human and neanderthal, domestic dog and wolf, tiger and leopard.</p>
<p>The point is to illustrate that the distances between mammals, fish, reptiles and amphibians are large and the transversions outnumber transitions which indicates the sequences are far beyond saturation with mutations and phylogenetic distance calculations will grossly underestimate their true distances.</p>
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<p>More information about this topic, and free download of the data sets I used, is at FigShare in the attached link.</p
Genomes-vs-patialData trees
No full text<p>Comparing trees, both built with maximum likelihood. One using complete mitochoindrial genomes and more species, the other using just 1998 of the >16kb genomes and fewer species. The point being to show how using more data influences the tree in subtle ways.</p
Missing Data in Phylogenetics Analyses
No full text<p>There is a discussion in the PhyloBabble phylogenetic methods discsuion group about the effects of missing data in sets used for phylogenetic reconstuctions. I found this data set is rather typical of the problem, when researchers attempt to gather large data sets,some species have been extensively sequenced and others have not been.</p
Phlylogeny of Human respiratory syncytial virus genomes. PDF phylogenetic tree
No full textPhylogenetic tree built from complete genomes of Human respiratory syncytial viruses aligned and gap-stripped.</pre
Primate Immunodeficiency Viruses phylogenetic tree
No full textMaximum Likelihood Phylogenetic tree constructed with complete genomes of primate immunodeficiency viruses (HIVs and SIVs)
PhyloHandbook Chapter 5 alignment
No full text<p>Chapter 5 from the Phylogenetic Handbook, has a data set online www.thephylogenetichandbook.org containing 1998 bases of mitochondrial DNA aligned and gapstripped. The online format is NEXUS and I am providing the same data in FASTA format here.</p
Saturation with mutations by Transition/Transversion analysis
No full textTransition mutations (G - A, C - T) are more frequent than transversions ( C to A or G, G to C or T, T to A or G, etc) for several biochemical reasons. However there are 2X more possible transversions than transitions, so any two random DNA sequences will have 2X more apparent transversions than transitions. As organisms evolve from a common ancestor (100% sequence identity) to different lineages with less and less identity, the ratio of transisitons:transversions changes to give an indication of how much saturation of silent sites has occurred. This plot show data from complete genomes of Primate Immunodeficiency Viruses (HIVs and SIVs) in comparison to data from Vertebrate (fish, reptiles, mammals, amphibians, birds) complete mitochondrial genomes. Vertebrates shared a common ancestor some 500 million years ago. The primate immunodeficiency viruses are of unknown age, but perhaps as much as 10 million years has passed since their origin
Human respiratory syncytial virus genomes aligned
No full textHuman respiratory syncytial virus complete genomes plus a bovine virus for outgroup.</pre
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