investigating the evolution of the genome: phylogenetically controlled analyses
DESCRIPTION
My lab chat to members of the Evolutionary Biology Group in November 2011.TRANSCRIPT
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Investigating the evolution of the genome: phylogenetically controlled analyses
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Overview
• Introduction
• Genomic character evolution
• Gene family evolution
• Summary
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What do I do?
• Classic evolutionary methods
• Specific questions• Flood of genomic data• Lots of genomes being
released• Analysis very descriptive• Large scale approach
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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
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What did I learn from my previous research?
• Test of feasibility and robustness
• Pipeline development• Summary statistics• Improvements?• More characters• Phylogenetic
comparative method
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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
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Why do all this?
• Robust pipeline• Output in various
formats• Description of the
genome• Formulate and test
specific hypotheses• Publication
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Genomic character evolution
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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?
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What data do I have so far?
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Gene family evolution
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Why gene families?
• Important in human disease• Domestication of plants and animals• Adaptive radiations• Adaptation to differing environments• Duplications are frequent
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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?
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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?
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What can ants tell us about gene family evolution?
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Summary
• Pipeline efficient and robust• Easily characterizing genome data• Output in various useful ways• Moving on to different types of analyses
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What’s next?
• Gene characteristics• Can I get gene family data?• Hypotheses• General descriptive• Gene family size changes• Get gene family data• Implement
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Thank you! Any questions?