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Lectures 21, 22, and 23: Phylogenic Trees and Evolution Steven
Lectures 21, 22, and 23: Phylogenic Trees and Evolution Steven

... • Each internal node is labeled by a number. • Each internal node has at least two children • Along any root to leaf path the labels strictly decrease. Note that if the labels mean “time units ago”, this is true of any evolutionary tree. ...
Chapter 26 Presentation-Phylogeny and the Tree of Life
Chapter 26 Presentation-Phylogeny and the Tree of Life

... For example, let’s look at hinged jaws. These are absent in lampreys, but are found in other members of the ingroup-this represents a branch point. The cladogram we’ve developed isn’t a phylogenetic tree, we need more information from fossils, etc. to indicate when the groups first appeared. ...
Lecture #1: Phylogeny & the “Tree of Life”
Lecture #1: Phylogeny & the “Tree of Life”

... “twigs” to phylogenetic trees • keep in mind - different genes evolve at different rates – the evolution of ribosomal genes are slow – allows us to investigate further back in time – the evolution of mitochondrial genes are fast – investigation of more recent ...
Ch_25 Phylogeny and Systematics
Ch_25 Phylogeny and Systematics

... apply principle of parsimony  simplest explanation  fewest evolutionary events that explain data ...
Bio 1B, Spring, 2007, Evolution section 1 of 4 Updated 3/21/07 7:49
Bio 1B, Spring, 2007, Evolution section 1 of 4 Updated 3/21/07 7:49

... • In a phylogenetic classification, species in the same genus had a most recent common ancestor more recently than species in different genera in the same family, and so on. • Phylogenetic systematics is based on the cladogram, not on the phylogenetic tree.  Finding the right cladogram The problem ...
introduction to molecular phylogeny
introduction to molecular phylogeny

... ATGCATCCGCCACCATGACCAGCAGGAGGTAGCactCAAAACAGCACCaacGTGCAAATG ATGCATCCGCCACCATGACCAGCGGGAGGTAGCtctCAAAACAGCACCaacGTGCAAATG ...
Diapositiva 1 - Universidad Autonoma de Madrid
Diapositiva 1 - Universidad Autonoma de Madrid

... Homoplasy in molecular data • Incongruence and therefore homoplasy can be common in molecular sequence data • One reason is that characters have a limited number of alternative character states ( e.g. A, G, C and T) • In addition, these states are chemically identical so that homology and homoplas ...
In the article entitled ‘Search for a Tree of Life... evolution, at least as far as bacteria and archaea are
In the article entitled ‘Search for a Tree of Life... evolution, at least as far as bacteria and archaea are

... and edges reflecting gene exchange [18]. The stakes here are high because replacement of the TOL with a network graph would change our entire perception of the process of evolution and invalidate all evolutionary recon­struc­ tion based on a species tree. However, the tree repre­ sentation is by no ...
PPTX - Tandy Warnow
PPTX - Tandy Warnow

... alignments and trees using treelength criteria (however – note that the developers of POY say to ignore the alignment and only use the tree). • BeeTLe (Better Tree Length) is a heuristic that is guaranteed to always be as least as accurate as POY for the treelength criterion. • The accuracy of the f ...
Talk in Powerpoint Format
Talk in Powerpoint Format

... • Objective: determine probability estimates that a given sample belongs to a class Probability(x Class | attribute values) • Baysian network: – One node for each attribute – Nodes connected in an acyclic graph – Conditional independance ...
Chapter 2 - FacStaff Home Page for CBU
Chapter 2 - FacStaff Home Page for CBU

... 'parallel' evolution is a false dichotomy, at best representing ends of a continuum. We can simplify our vocabulary; all instances of the independent evolution of a given phenotype can be described with a single term - convergent." "If the use of the terms 'parallelism' and 'convergence' cannot be a ...
ap® biology 2015 scoring guidelines
ap® biology 2015 scoring guidelines

... This question focused on using evidence to support biological evolution. Students were asked to evaluate amino acid sequences from five related species to construct a phylogenetic tree reflecting the evolutionary relationships among them, and justify the placement on the tree of the species that is ...
TAXONOMY and EVOLUTION Test Review: Complete the following
TAXONOMY and EVOLUTION Test Review: Complete the following

... 3. What is the name of our scientific name system? 4. What are the levels of classification in order? 5. How are scientific names written? 6. Using a scientific name, how can you tell if two organisms are closely related? 7. What are the three domains and the 6 kingdoms that belong to them? 8. Defin ...
Branching Activity Instructions:
Branching Activity Instructions:

... In what ways does this activity model an actual evolutionary branching tree? Hint: In what ways is this activity similar to a real situation? ________________________________________________________________________ ________________________________________________________________________ In what ways ...
PHYOGENY & THE Tree of life
PHYOGENY & THE Tree of life

... search for trees that are parsimonious & have a high probability ...
Slide 1
Slide 1

... annotation of a genomic sequence • Determine ability to correlate genes to the particular phenotype • Determine ability to use BLAST to obtain orthologous sequences • Explain how genes diverge at the molecular level through the process of evolution • Determine students’ confidence in ability to cons ...
Proposal to change linear sequence of orders to place Galliformes
Proposal to change linear sequence of orders to place Galliformes

... al. (2001) found that Passeriformes were basal to all Neognaths or even all living birds. These studies can be faulted, as the authors themselves often pointed out, for combinations of limited taxon sampling, rooting the tree with distantly related alligator sequence, or assuming equal rates of mtDN ...
Studying the evolution of photosynthesis using phylogenetic trees
Studying the evolution of photosynthesis using phylogenetic trees

... ancestors [2]. Mapping the evolutionary relationships of all living beings have been undertaken by comparing highly conserved gene sequences present in all of the above [1] and considerable intellectual effort has been invested to reduce the systematic errors of sequence alignment [1] and tree const ...
Molecular evolution and phylogenetic implications in clinical research
Molecular evolution and phylogenetic implications in clinical research

... UPGMA is one of the simplest methods of phylogenetic trees construction. It has numerous limitations and wrong assumptions; therefore, this method is not readily used. The UPGMA algorithm assumes that the tree is additive (the distance between any two nodes is equal to the total length of the branch ...
Computational Biology
Computational Biology

... Maximum likelihood approach Method uses probability calculations to find a tree that best accounts for the variation in a set of sequences. Similar to maximum parsimony method in that analysis is performed on each column of a multiple sequence alignment. All trees are considered. Because the rate o ...
File
File

... The main idea of decision tree construction tree is to evaluate different attributes and different partitioning conditions, and pick the attributes and partitioning condition that results in the maximum information gain ratio. The same procedure works recursively on each of the sets resulting from t ...
CSCE590/822 Data Mining Principles and Applications
CSCE590/822 Data Mining Principles and Applications

... Rooting a tree, and definition of outgroup Neighbor-joining produces an unrooted tree How do we root a tree between N species using n-j? An outgroup is a species that we know to be more distantly related to all remaining species, than they are to one another Example: Human, mouse, rat, pig, dog, ch ...
Natural selection and phylogenetic analysis
Natural selection and phylogenetic analysis

... extent that phylogenetic analysis groups them together (6). However, long branch attraction is predicted to yield a pattern in which the sites with the highest evolutionary rate show the greatest signal favoring the wrong tree (7); this was not the case in their data. A careful process of eliminati ...
Analysis of Crop Plant Genomes
Analysis of Crop Plant Genomes

... represented as a tree of evolution (often called a phylogenetic tree). ...
Phylogenetic Trees - Elhanan Borenstein
Phylogenetic Trees - Elhanan Borenstein

... each sequence to a list of N tree nodes. 2) look through current list of nodes (initially these are all leaf nodes) for the pair with the smallest distance. 3) merge the closest pair, remove the pair of nodes from the list and add the merged node to the list. ...
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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.
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