Repository List / ismb2007_collaboration / 01_Introduction.tex @ HEAD

\leftheader{Introduction to phylogenetics workflows}

\foilhead{Introduction}
\centering{\includegraphics{images/intro_overview.pdf}} \\

\foilhead[-0.5in]{Outline}
\thispagestyle{nohnof}
\begin{itemize}  \itemsep -10pt
 \item Research questions in Comparative Genomics
 \begin{itemize} \itemsep -4pt
   \item Automated Orthologous and Paralogous gene identification
   \item Sequence evolution: adaptive, constrained, and neutral 
   \item Gene family evolution: lineage-specific changes   
 \end{itemize} 
 \item Tools for comparative genomics
 \begin{itemize} \itemsep -4pt
   \item Sequence similarity \& Gene family clustering
   \item Multiple sequence alignment
   \item Phylogenetics
   \item Molecular evolution
 \end{itemize} 
 \item BioPerl for building Pipelines
 \begin{itemize} \itemsep -4pt
  \item Data conversion
  \item Running external applications
  \item Processing results
 \end{itemize}
\end{itemize}

\foilhead{Comparative Genomics}
\begin{itemize}
 \item Comparisons to study evolutionary history of genomes
 \item Identify commonalities and differences between genomes
 \item Orthologous and unique genes among species 
 \item Paralogous gene families
 \item Use similarity search and alignment tools to identify homologs
 \item Use phylogenetic approaches to reconstruct evolutionary history
\end{itemize}

\foilhead[-0.5in]{Principles of molecular evolution}
\begin{itemize}
 \item Sequences that share significant similarity are likely homologous
 \item Homologous sequences often have the same function
 \item Identification of sequence differences and similarities can suggest regions with new or conserved functions
 \item Models of sequence evolution allow inference of rates of evolution
 \item Comparison of multiple genes and genomes can identify sequences evolving at significantly different rates
 \item Sequences or regions with different rates may be under different selective constraint and can suggest innovation or relaxation of pressure.
\end{itemize}

\foilhead[-1in]{Detecting selection between species}
\thispagestyle{nohnof}
\begin{itemize} \itemsep -4pt
 \item For aligned orthologous genes 
 \item Using codon-based methods identify where rate of change is faster in Non-Synonymous ($K_{A}$) than in Synonymous ($K_{S}$).
\end{itemize}
\centering{\includegraphics[height=3.85in]{images/dnds_tree2.jpg}} \\

\foilhead{Gene family evolution}
\begin{itemize}
 \item Changes in family content can be powerful for understanding
 species differences
   \begin{itemize}
   \item 6\% different between Humans and Chimps (Demuth et al, PLoS
   One 2006).
   \item Hydrophobin expansion in basidiomycete mushrooms
   \item \textit{C. elegans} chemoreceptor family expansions (Chen et
   al, PNAS 2006)
   \item Purine salvage enzyme HPRT1 family in vertebrates (Keebaugh
   et al, Genomics 2007)
   \item Odorant receptor loss associated with gain of trichromatic
   vision in primates (Gilad et al, PLoS Biology 2004)
   \end{itemize}
\end{itemize}

\foilhead[-0.80in]{Local expansion of chemoreceptor genes in \textit{C. elegans}}

\centering{\includegraphics[height=4.80in]{images/chen_pnas_fig6.pdf}} \\
{\footnotesize Chen et al, PNAS 2006; 102(1):146-151.}

\foilhead[-0.5in]{Tree of Hydrophobins in 3 fungi}

\includegraphics[height=5in]{images/hydrophobins_tree.pdf}

\foilhead[-1.0in]{Hydrophobin expansion driven by local duplications}

\centering{\includegraphics[height=5.5in]{images/hydrophobins_local.pdf}}

\foilhead{Definitions for sequence relationships}
\begin{itemize}
\item Homology - Similar sequences that share a common ancestor.
\item Orthology - Similar sequences that descended from a common
  ancestor through speciation events.
\item Paralogy - Similar sequences which arose through a duplication
  event within a species lineage. 
\item Sequences are generally considered similar if they share at least 30\%
  identity at the amino acid level.
\end{itemize}

\foilhead[-0.75in]{Species Tree and Gene Tree}
\centering{\includegraphics[height=4.75in]{images/speciestree-genetree.jpg}} \\
{\small Li C, Orti G, Zhang G, Lu G. BMC Evol Biology 2007; 7:44.}

\foilhead{Gene tree/Species tree reconciliation}
\begin{itemize}
\item Parsimony
\begin{itemize}
\item For each node in the tree identify whether it arose via
  duplication or speciation minimizing the number of duplication
  events. 
\end{itemize}
\item Maximum Likelihood and Bayesian frameworks
\begin{itemize}
\item Maximize likelihood of data given gene tree and species tree,
  inserting branches on gene tree to represent losses and gains.
\end{itemize}
\end{itemize}

\foilhead[-0.75in]{Orthology and Paralogy types}
\centering{\includegraphics[height=5.25in]{images/homology_types1.pdf}} \\

\foilhead{Paralogous family creation through duplication}

\begin{itemize}
\item Duplication may be substrate for novel function (Ohno)
\item Mechanisms of duplications
 \begin{itemize}
 \item Unequal crossing-over during recombination
 \item Retrotransposition
 \item Translocations of large regions
 \end{itemize}
 \item Different mechanisms will create different patterns of duplication  
 \begin{itemize} 
  \item Members of a family are Local and physically clustered
  \item Family members are dispersed
  \item Duplicated blocks of genes
 \end{itemize}
\end{itemize}

\foilhead[-0.75in]{Paralogous gene relationship and inference}

\centering{\includegraphics[height=5.25in]{images/homology_types2.pdf}} \\