Microarray Analysis
... Linz, by way of genomics data processing algorithms developed by the
researchers and licensed by GNS.”
...
Typology now: Homology and developmental constraints explain
... the set of organisms’ morphological parts (the type) does change in phylogenetic lineages. The
presence of a type (set of particular homologues) is due to the morphological-developmental
make-up of organisms, and if the latter evolves in fundamental ways, the type can change.
However, the present di ...
A Single Eubacterial Origin of Eukaryotic
... eight PFO sequences, including those from the anaerobic eukaryotes Entamoeba histolytica, Giardia lamblia,
and Trichomonas vaginalis. They concluded that there
was little support for a common ancestry of eukaryote
PFO and that Entamoeba probably got its PFO independent of the other eukaryotes, and p ...
phylogenetic tree
... ● There are three such trees with (2n-3)=5 leaves
– they are distinct labelled branching patterns.
● There are then five ways of adding a further
branch labelled with a distinct label (‘5’),
giving in all 3x5=15 unrooted trees with five
leaves.
● The number of unrooted trees with n leaves is
equal ...
Seed plant phylogeny: Demise of the anthophyte
... angiosperms. Only a few analyses of ribosomal DNA
linked angiosperms and Gnetales, and this with low statistical support. Analyses of the chloroplast gene rbcL placed
Gnetales at the base of the seed plants, followed by
angiosperms (an arrangement supported by more recent
studies of photosystem gene ...
Random survival forests for highdimensional data
... different measures could yield different estimates of prediction error which ultimately could yield different selected
variables. Equally importantly, there are scenarios where it
may not even be clear how to measure prediction error.
For example, in competing risks where the outcome is time
Statist ...
PPTX - Tandy Warnow
... • MetaPhyler, MetaPhlAn, and mOTU are marker-based
techniques (but use different marker genes).
...
Title: Statistical Evidence for Common Ancestry
... under SA (see Materials and Methods). We also modified the tests to mask positions in which the exact
same codon was used in all taxa, since such invariant codon usage at a position might be due to some
unknown functional constraint (Figure 1, codon 2).
In addition to testing the hypothesis that cod ...
View Tutorial
... the appearance of the first complete bacterial genome, Haemophilus influenzae,
in 1995. Since then bacterial genomes have been sequenced at an exponential
rate with a doubling time of about 20 months, and archaeal genomes have been
sequenced with a doubling time of about 34 months [7]. With this rap ...
From Gene Trees with HGT to Species Trees
... A reconciliation map µ is TC if there is a gene-tree time map τT : V (T ) → R and species tree
time map τT : V (T ) → R such that
C0 u ≺T v =⇒ τT (u ) > τT (v )
C1 u ≺S v =⇒ τS (u ) > τS (v )
C2 If u speciation, then τT (u ) = τS (µ(u ))
C3 If u is no speciation, then τS (x ) < τT (u ) < τS (y ) whe ...
An rpoB signature sequence provides unique resolution for the
... NJ (Jukes–Cantor model) and MP trees were calculated by using
MEGA4 (Tamura et al., 2007). ML trees were computed with Phyml
v.2.4.1 (Guindon & Gascuel, 2003) and the HKY (Hasegawa–
Kishino–Yano) model of nucleotide substitution (Hasegawa et al.,
1985) using one category of substitution rate. For ea ...
Giant viruses, giant chimeras: The multiple evolutionary histories of
... incorporated these genes from its eukaryotic host, the
amoeba, into its own genome. While these studies were
based on only a handful of genes, we sought here to
understand how extensive was the role of HGT in shaping
the whole Mimivirus genome, and which were the sources
of the transferred genes. Th ...
canesbio
... • Cladistics groups organisms by common
descent.
• A clade is a group of species that includes an
ancestral species and all its descendants.
• Clades can be nested in larger clades, but not
all groupings of organisms qualify as clades.
...
Evolutionary history of the genus Capra
... The systematics of the genus Capra remain controversial in spite of studies conducted using morphology, mtDNA, and allozymes.
Here, we assess the evolutionary history of Capra (i) using phylogenetic analysis of two nuclear genes located on the Y-chromosome and
(ii) previously published and new cytoc ...
Learning Distance Functions in k-Nearest
... where wi is the weight for the i-th feature. Intuitively this can be understood
as defining that one feature is more important than others when comparing two
samples. The weights vector {w1 . . . wk } needs to be learned before classifying
unknown samples. In their approach [12] the weights are lear ...
species
... • A molecular clock uses constant rates of
evolution in some genes to estimate the
absolute time of evolutionary change
• In orthologous genes, nucleotide substitutions
are proportional to the time since they last
shared a common ancestor
• In paralogous genes, nucleotide substitutions
are proportio ...
Cophylogeny and disparate rates of evolution in sympatric lineages
... (‘‘missing the boat’’; Paterson and Gray, 1997) may disrupt
perfect correspondence among taxa. By comparing the
phylogenies (or the data upon which those phylogenies
are based) of hosts and their associates, it is possible to
determine if statistically significant cophylogeny is present
and discrimin ...
Module 8: Horizontal Gene Transfer
... 7. After clicking on the Image in PNG format (bitmap) in Figure 8.14 has been clicked, an unrooted
phylogenetic tree similar to the one shown in Figure 8.15 will appear. A concise review of the
interpretation of figure 8.14 can be found at: http://epidemic.bio.ed.ac.uk/how_to_read_a_phylogeny.
A sum ...
Introduction slides on BASE
... – How do I find interesting stuff? – learn
some analysis tools
– How do I trust the results? – statistics is
key
...
Langfelder-NetworkDay-clustering
... A single setting works well and produces comparable results in many
applications: Dynamic Tree Cut is suitable for automation
...
Maximum parsimony (phylogenetics)
In phylogenetics, maximum parsimony is an optimality criterion under which the phylogenetic tree that minimizes the total number of character-state changes is to be preferred. Under the maximum-parsimony criterion, the optimal tree will minimize the amount of homoplasy (i.e., convergent evolution, parallel evolution, and evolutionary reversals). In other words, under this criterion, the shortest possible tree that explains the data is considered best. The principle is akin to Occam's razor, which states that—all else being equal—the simplest hypothesis that explains the data should be selected. Some of the basic ideas behind maximum parsimony were presented by James S. Farris in 1970 and Walter M. Fitch in 1971.Maximum parsimony is an intuitive and simple criterion, and it is popular for this reason. However, although it is easy to score a phylogenetic tree (by counting the number of character-state changes), there is no algorithm to quickly generate the most-parsimonious tree. Instead, the most-parsimonious tree must be found in ""tree space"" (i.e., amongst all possible trees). For a small number of taxa (i.e., less than nine) it is possible to do an exhaustive search, in which every possible tree is scored, and the best one is selected. For nine to twenty taxa, it will generally be preferable to use branch-and-bound, which is also guaranteed to return the best tree. For greater numbers of taxa, a heuristic search must be performed.Because the most-parsimonious tree is always the shortest possible tree, this means that—in comparison to the ""true"" tree that actually describes the evolutionary history of the organisms under study—the ""best"" tree according to the maximum-parsimony criterion will often underestimate the actual evolutionary change that has occurred. In addition, maximum parsimony is not statistically consistent. That is, it is not guaranteed to produce the true tree with high probability, given sufficient data. As demonstrated in 1978 by Joe Felsenstein, maximum parsimony can be inconsistent under certain conditions, such as long-branch attraction.