Investigating the evolution of the genome: phylogenetically controlled analyses

Overview

• Introduction

• Genomic character evolution

• Gene family evolution

• Summary

What do I do?

• Classic evolutionary methods

• Specific questions• Flood of genomic data• Lots of genomes being

released• Analysis very descriptive• Large scale approach

What have I done so far?

• Implementation of a genome informatics pipeline (GCAT)

• Comparative evolutionary genomic analyses of intron sequences in five teleost fish

• Identified a difference in the intron size frequency distribution in the zebrafish, Danio rerio

• Repetitive elements account for a large proportion of the difference in zebrafish

• Remainder due to ancient “degraded” repetitive elements

What did I learn from my previous research?

• Test of feasibility and robustness

• Pipeline development• Summary statistics• Improvements?• More characters• Phylogenetic

comparative method

Why use phylogenetic comparative methods?

• Unclear what is the interesting signal

• Assume no species relatedness

• Tell which differences are biologically informative

• Great deal of research into methods

• Number of high quality tools• Gives us statistical/ML

values

Why do all this?

• Robust pipeline• Output in various

formats• Description of the

genome• Formulate and test

specific hypotheses• Publication

Genomic character evolution

What characters can I investigate?

• What characters will I study?– Gene bio types– Genome size– Coding genome size– Introns– Exons– UTRs– Repetitive elements

• Why use these characters?• What can these characters

tell us?

What data do I have so far?

Gene family evolution

Why gene families?

• Important in human disease• Domestication of plants and animals• Adaptive radiations• Adaptation to differing environments• Duplications are frequent

What can we learn from gene families?

• Expansions and contractions across the tree

• Phylogenetic controls• Pipeline• Reproductive and

immunological loci• Expansions in humans• What do they tell us of

stuff of adaptive importance?

Can we use extinct species genomes?

• Include extinct/ancient human genomes in gene family analyses– What problems could I

encounter?• Genome annotation

quality?

– What questions could this address?

What can ants tell us about gene family evolution?

Summary

• Pipeline efficient and robust• Easily characterizing genome data• Output in various useful ways• Moving on to different types of analyses

What’s next?

• Gene characteristics• Can I get gene family data?• Hypotheses• General descriptive• Gene family size changes• Get gene family data• Implement

Thank you! Any questions?