498: Statistical Physics, Biological Information and Complexity.

Homework 2 Essays: Phylogenetic trees

Author: Anoush Aghajani-Talesh
Title: Parsimony Analysis of Phylogenetic Trees (68kb)

Abstract:

This essay describes parsimony analysis, which is a common method to deduce evolutionary relationships between species from a given set of protein or nuclein acid sequences.

Author: Marco V. Bayas
Title: Rate of Molecular evolution (18kb)

Abstract:

The validity of the molecular clock hypothesis is discussed. Molecular clocks depend on both the particular protein considered and the group of species
being compared. This means that the neutral theory formulated by Kimura is not generally correct. Deviations from neutrality are explained in base of
different points of view such as selectivity.

Author : Swarbhanu Chatterjee.
Title  : The Relevance of Molecular Clocks (89 kb)

Abstract :

According to the neutral theory of evolution, mutations accumulate at a constant rate over time and therefore it is possible to time evolutionary events using a molecular clock. However, it has long been known that mutation rates vary over different species and for different climates. Researchers have recently discovered that the mutation rates in viruses depend on the transmission mode. This seriously brings into question the relevance of molecular clocks.

Author: Soon Yong Chang
Title:Are There Bugs in Our Genome?

Abstract:

It is known that the phylogenetic reconstruction of the "tree of life" suffers from weaknesses, among them the possibility of lateral gene transfer. One of the hypotheses of the lateral gene transfer is that it was characteristic of organisms at early stage of evolution and complexity (prokaryotes and unicellular eukaryotes) and took place among species very close each other.

Author:      Jordi Cohen
Title:       Learning to fly (75 kb)

Abstract:

I will examine recent scientific investigations that propose a plausible answer to the origin of flight in insects. The authors claim that flight in certain species of insect has evolved in a gradual manner from a different form of locomotion: water skimming. What is interesting about these results is that they hinge on phylogenetic methods, combined with a morphological and functional comparison of different species.

Author: Peter Fleck
Title: Studying the evolution of photosynthesis using phylogenetic trees (60 kb)

Abstract:

Phylogenetic trees are supposed to group species according to common 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 e ort has been invested to reduce the systematic errors of sequence alignment [1] and tree construction.

Author: Parag Ghosh
Title: Existence of Critical Phenomenon in Mutation Processes (96 kb)

Abstract:

In this essay the effect of phylogeny on correlations is studied. It is observed that the rate of mutation plays an important role in determining
the behavior of correlation functions. For mutation rates less than a critical value, all correlations are well described by the average and the tree
morphology does not play any role. Above the critical rate non-trivial phylogenies can give rise to strong correlation among species. The transition
is sharp and bear resemblance with the characteristics of second order transition. The studied behavior can also be generalized to stochastic tree
morphologies.

Author: Paul Grayson
Title: Human origins and genetic evolution (

Abstract:

Author: Matt Gordon
Title: Aminoacyl-tRNA Synthetases and the Evolution of the Genetic Code (260 kb)

Abstract:

Aminoacyl-tRNA synthetases catalyze the attachment of amino acids to transfer RNAs, and as such, form the fundamental bridge spanning genetic
information, in the form of DNA, with genetic products, in the form of proteins.  The evolution of the genetic code itself is discussed in
light of the evolution of the Aminoacyl-tRNA synthetases, both in terms of their structure and their phylogeny.

Author:Paul Grayson
Title: Human origins and genetic evolution (56 kb)

Abstract:

Recently, phylogenetic trees have begun to reveal informationabout the origin and spread of humans.  However, recent population explosions of certain groups of people make it difficult to accurately sample human genetic diversity.  This essay describes two recent studies that used language-group based sampling to create a human phylogenetic tree with the greatest possible diversity.
 

Author: Chalermpol Kanchanawarin
Title: The Root of the Tree of Life: The Universal Ancestor (10 kb)

Abstract:

A new model of the common ancestor of all life on earth was proposed by Dr. Carl Woese in 1998 [1,2] to support new experimental evidence which indicates
that the earliest life form was not a well defined entity in phylogenetic trees.

Author: David Larson
Title: Creating Phylogenetic Trees with the Metropolis Algorithm (117 kb)

Abstract:

This paper discusses the metropolis algorithm and how it can be used to create phylogenetic trees from pre-aligned DNA, RNA, or protein sequences.
This intuitive but computationally slow method came mainly from chapter 8 of _Biological Sequence Analysis_ by Durbin et. al.

Author: Yan Li
Title:  How to Build a Phylogenetic Tree (229 kb)

Abstract:

This article briefly reviewed different methods of tree building and compared their validity, reliability and efficiency. The calculation of genetic distance and methods of trees rooting are also discussed.

Author: Ian O'Dwyer
Title:  Using Mitochondrial DNA and Phylogenetic Trees to Trace Early Human Expansions (292 kb)

Abstract:

In the first part of the essay I review the use of mt-DNA to examine the movement of early humans on the Earth.  In the second part of the essay I
review an attempt to recreate a phylogenetic tree using complete mt-DNA sequences.  I also discuss various pieces of software used during this tree
building, the computational power and my results.  The resulting tree was disappointing, but perhaps not overly so for a first attempt .

Author:Kapil Rajaraman
Title: Coalescence time distributions for hypothesis testing (442 kb)

Abstract:

As we follow a history of genetic lineages  back in time, they join up into a common ancestral type called the coalescent, the age of which is
called the coalescent time. There has been considerable debate over the coalescent time for humans, and this essay discusses one method which has
been put forward to resolve this debate. From this study, it is concluded that the "out-of-Africa" model for hominoid evolution is more likely to be
true than the "multiregional hypothesis" model.

Author : Rahul Roy
Title : Molecular Phylogenetic Analysis (21 kb)

Abstract:

In this submission, we discuss the proposed theories of the eukaryotic cell evolution and test them with phylogenetic analysis tools.

Author: Prasanth Sankar
Title: History of human migration from genetic data (705 kb)

Abstract:

This essay describes recently used methods to infer prehistoric human migrations from the analysis of genetic data. Three of the methods use human genes and one uses the gene of a virus carried along by the humans. The analysis points out to human origin in Africa and possibly three seperate migration of humans out of Africa.

Author:    Martin Ph. Stehno
Title:        Discrete FT for phylogenetic trees (75 kb)

Abstract:

Discrete Fourier transformations (DFTs) provide a useful tool to assign a phylogenetic tree (PGT) to an observed frequency of nucleotide patterns in DNA
sequences of species.  The advantage of this sort of spectral analysis is that it allows global correction for multi-substitution processes.

Author: Kalin Vestigan
Title: Computational approaches for functional genomics (185 kb)

Abstract:

The rapidly increasing number of completely sequenced genomes have stimulated the development of new methods for  finding functional linkages between proteins.

Author: Qing-jun Wang
Title: Endosymbiosis Theory (735 kb)

Abstract:

This essay introduces what endosymbiosis theory is. The phylogenetic trees of cytochrome c, cytochrome c553 and ferredoxin are built. Together with
the phylogenetic tree of the small-subunit rRNA, they support the endosymbiosis theory.

Author: Paul Welander
TitleToward a More Reliable Morphological Data Set for Phylogenetic Reconstruction (121 kb)

The phylogenetic relationships among hominoids and papionins derived from quantitative craniodental data has been shown to vary significantly from
those created through molecular means.  However, recent evidence lends support for the use of soft tissues as a reliable method for morphological
phylogenetic reconstruction.

Author: Elizabeth Villa Rodriguez
Title: Scoring matrices: Yet another approach (102 kb)

Abstract:

This paper reviews an attempt to build new scoring matrices based on low resolution fields. I do not think the authors provide a new insight to the
area, but it is an interesting attempt.

Author: Jin Yu
Title: Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes (315 kb)

Abstract:

This essay introduces a research which studied frozen tissue from a chimpanzee, came from a sub-group known as Pan troglodytes troglodytes. It is claimed that all HIV-1 strains known to infect man are closely related to just one of the SIVcpz lineages that found in the chimpanzee. The resul indicated that Pan
troglodytes troglodytes may be the primary reservoir for HIV-1, and that the virus at some point crossed species from chimpanzees to human.

Author:  Jian Xu
Title:  Phylogenetic Analysis of the Origin of the HIV virus (823 kb)

Abstract:

This essay describes the use of phylogenetic tree and molecular clock to determine when did HIV enter human population.  The calculation base on an
outgroup which is constructed by the consensus sequences of each type.  Thus they get more accurate result and claim that the HIV-1M group entered human
population around 1931 (1915-1941, 95% confidence intervals).
 


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