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A Phase Transition in Molecular Evolution with Applications to the Assembly of the Tree of Life
A Phase Transition in Molecular Evolution with Applications to the Assembly of the Tree of Life

... Recent advances in DNA sequencing technology have led to new challenges in the analysis of the massive data sets produced in current evolutionary studies. In particular, the estimation of evolutionary trees on increasingly large scales has prompted the development of novel reconstruction methods. An ...
Document
Document

... • The 3/4 and 4/3 terms reflect that there are four types of nucleotides and three ways in which a second nucleotide may not match a first - with all types of change being equally likely (i.e. unrelated sequences should be 25% identical by chance alone) ...
CSCE590/822 Data Mining Principles and Applications
CSCE590/822 Data Mining Principles and Applications

... So what do the results mean? • 2 of 3 patients closer to dentist than to local controls. Statistical significance? More powerful analyses? • Do we have enough data to be confident in our conclusions? What additional data would help? • If we determine that the dentist’s virus is linked to those of p ...
Shared character
Shared character

... 1. choose organisms—they go in left column, and put the outgroup there too. Top, going right, characteristics they could share 2. score the organisms lacking certain characteristic 0, and if it has it, score 1 3. most commonly shared derived character (this case vascular tissues) goes at the base of ...
lecture 03 - phylogenetics - Cal State LA
lecture 03 - phylogenetics - Cal State LA

... - how were ancestral traits modified in different lineages? A hypothesis of the evolutionary history of a group is called its phylogeny - often summarized in a branching diagram called a phylogenetic tree Since we can’t travel back in time to identify common ancestors, relationships of existing spec ...
Lecture 7-POSTED-BISC441-2012
Lecture 7-POSTED-BISC441-2012

... for finding trees with the best value for the objective function. Can identify many equally optimal trees, if such exist. Warning: Finding an optimal tree is not necessarily the same as finding the "true” tree. Random data will give you an ‘optimal’ (best ) tree! ...
An Introduction to Phylogenetics
An Introduction to Phylogenetics

... more taxa that are known to have diverged prior to the group being studied • The node where the outgroup lineage joins the other taxa is the root ...
Evolution, 2e
Evolution, 2e

... Genes for 11 tRNAs 6 proteins Human-chimpanzee relationship 1023 more likely than Chimpanzee-gorilla relationship ...
生物計算
生物計算

... of different nucleotides minus one. ...
Phylogenetics Molecular Phylogenetics
Phylogenetics Molecular Phylogenetics

... a problem because of some change in behaviour? Or is there another explanation for their origin? Host species tree ...
Phylogeny of the Primates
Phylogeny of the Primates

... As promised, you are going to get your chance to create a phylogenetic tree from some molecular clock data. We are going to give you some mutation differences in DNA. This is just like the bird phylogeny we did. Below is a table of REAL data. This date represents difference in DNA. It is obtained by ...
Trees
Trees

... Amino-acid sites are partially ordered characters. An amino acid cannot change into all other amino acids in a singe step, as sometimes 2 or 3 steps are required. For example, a tyrosine may only change into a leucine through an intermediate state, i.e., phenylalanine or histidine. ...
Classification and phylogeny – Chapter 2
Classification and phylogeny – Chapter 2

... (Cercopithecidae) and Homo – Oldest fossils of Cercopithidae are dated at 25 mya • Average rate for Rhesus monkey lineage = 457/25 my = 1.83 x 10-3 per my • Average rate for Homo line is 310/25 my = 1.24 x 10-3 per my • Average rate is 1.54 x 10-3 per my ...
Diagrams Nov 8
Diagrams Nov 8

... Phenetic: classification of the organisms based on their similarities, trees obtained using a phenetic approach may not reflect evolutionary relationships. A tree based on this method is called a phenogram Cladistic (Hennig 1966): study of the different pathways of evolution, the most parsimonious p ...
CIPRES.2006.algorthms_sr
CIPRES.2006.algorthms_sr

... • Breakthrough: Optimal logarithmic sequence length tree reconstruction (Daskalakis, Mossel, Roch 05). Simplified version (Mihaescu et al. 06). Preliminary Implementation [Adkins et al.]. ...
Slajd 1
Slajd 1

... The construction of phylogenetic trees from numerical methods The principle of maximum parsimony (Occam’s razor) holds that we should accept that phylogenetic tree that can be constructed with the least number of morphological changes. The raw data Species A B C D E ...
Comparative Anatomy: Phylogenetics Assignment
Comparative Anatomy: Phylogenetics Assignment

... 4. Print out a distance matrix in which you include all characters in the calculations. From looking at the distances, answer the following questions: a. Is there any reason to think that the dataset you are using will not be useful in determining phylogenetic relationships among taxa? Write your an ...
Using HIV Data Sets for Inquiry
Using HIV Data Sets for Inquiry

... • Minimizes distance between nearest neighbors Maximum parsimony • Minimizes total evolutionary change Maximum likelihood • Maximizes likelihood of observed data ...
Lecture5
Lecture5

... Creates noise in the data  Some characters give conflicting information about relationships  Systematists try to minimize homoplasy in a data set  Choose characters that evolve slowly relative to age of taxa ...
Day6
Day6

... time, this process may repeat itself, so that at any time, each population can be said to be most closelyrelated to some other population with which it shares a direct common ancestor. ...
Diapositiva 1
Diapositiva 1

... GENE PHYLOGENIES • Parsimony (Fitch 1977), • Pairwise distances (Saitou and Nei 1987), • Maximum likelihood (Felsenstein 1981): Use of explicit models of sequence evolution (computationally very intensive) Divergence dates of genes and species can also be estimated from phylogenetic distances (Ramb ...
Introduction to Phylogenetics - Lectures For UG-5
Introduction to Phylogenetics - Lectures For UG-5

... Making trees using character-based methods The main idea of character based methods is to search for a tree that requires the smallest number of evolutionary changes to explain the differences among the OTUs under study. ...
Creating Phylogenetic Trees with MEGA
Creating Phylogenetic Trees with MEGA

... Kumar, S., Dudley, J., Nei, M., and Tamura, K., MEGA: A biologist‐centric software for evolutionary  analysis of DNA and protein sequences. Briefings in Bioinformatics 9: 299‐306  (2008) Hulsenbeck, J.P., and Ronquist, F., MyBayes: Bayesian inferences of phylogeny. Bioinformatics  ...
m12-comparative_genomics
m12-comparative_genomics

... the one that explains observed changes using the smallest number of point mutations o Maximum Likelihood: Analog of Maximum Parsimony that attempts to identify the most likely tree rather than the cheapest one; these are the most common methods used today  A single-gene tree does not always reflect ...
Phylogenetic - Nematode bioinformatics. Analysis tools and data
Phylogenetic - Nematode bioinformatics. Analysis tools and data

... divergence order of taxa, as well as the lengths of the branches that connect them. There are many phylogenetic methods available today, each having strengths and weaknesses. Most can be classified as follows: ...
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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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