... • Can only work for pairs of sequences that are similar
enough to be aligned
• All base changes are considered equal
• Insertion/deletions are generally given a larger weight than
replacements (gap penalties).
• Possible to correct for multiple substitutions at a single
site, which is common in dist ...
... • when and how were complex eyes evolved?
in what species are they lost? are the genes
required to develop eyes still there? can
they be expressed in different ways?
Chapter 20 Questions
... Suppose that species 1 and species 3 have similar appearances but very divergent gene
sequences. Species 2 and species 3 have very different appearances but similar gene sequences.
Which pair of species is more likely to be closely related: 1 and 2, or 2 and 3? Explain.
... 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 ...
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
Introduction to Phylogenetics - Lectures For UG-5
... Making trees using character-based
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.
... 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
... 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.
... 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
Using HIV Data Sets for Inquiry
... • Minimizes distance between nearest neighbors
• Minimizes total evolutionary change
• Maximizes likelihood of observed data
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 ...
... 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
The raw data
... • Breakthrough: Optimal logarithmic sequence length tree reconstruction
(Daskalakis, Mossel, Roch 05). Simpliﬁed version (Mihaescu et al. 06).
Preliminary Implementation [Adkins et al.].
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 ...
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
... 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.
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 ...
... of different nucleotides minus one.
... Genes for 11 tRNAs
1023 more likely than
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
... 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!
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
- often summarized in a branching diagram called a
Since we can’t travel back in time to identify common ancestors,
relationships of existing spec ...
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.