Transcript Evolutionary_biology_2014

Genetics and Evolutionary Biology
What are the major questions
How do we measure genetic variation in natural
populations?
What do we mean by a biological species.?
How can we use DNA to define species relationships.?
Why do proteins evolve at different rates?
Why does the mutation rate differ in different parts of the
the eukaryotic genome ?introns exons pseudogenes.
Modes of speciation
Allopatric separation
Sympatric separation
Genome Duplication events.
Segmental duplication of Chromosomes in the Arabidopsis genome
Comparative Genomic Highlights
Hedges, Nat Rev Genet 2003
Why Are Some Genomes So Large?
• There is no clear correlation between genome size and genetic
complexity.
• C-value – The total amount
of DNA in the genome (per
haploid set of chromosomes)
• C-value paradox – The
lack of relationship
between the DNA content
(C-value) of an organism
and its coding potential.
Haploid Genome Size (log scale)
The amount of TE correlate positively with genome size
Mb
Genomic DNA
3000
2500
TE DNA
2000
Protein-coding
DNA
1500
1000
500
0
Feschotte & Pritham 2006
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Transposable Elements
Gone Wild!
High Turnover in TEs
despite gene
conservation
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Transposable Elements…
• Variation in gene numbers cannot explain variation in genome size among
eukaryotes
• Most of variation in genome size is due to variation in the amount of repetitive
DNA (mostly derived from TEs)
• TEs accumulate in intergenic and intronic regions
•CONCLUSIONS…
•TEs have played an important role in genome evolution and
diversification
•Facilitate expansion and contraction of genomes AND gene
families
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Comparative Genomics – Synetny
Human Chrom.1 vs. Chimp
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Comparative Genomics – Synetny
Human Chrom.1 vs. Mouse
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Comparative Genomics – Synetny
Human Chrom.1 vs. Cow
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Comparative Genomics – Synetny
Human Chrom.1 vs. Opossum
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Comparative Genomics – Synetny
Human Chrom.1 vs. Platypus
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Comparative Genomics – Synetny
Human Chrom.1 vs. Chicken
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Synteny
• Large blocks of synteny exist even at
great phylogenetic distance
• Also substantial scrambling, even at
short distance…
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Whole Genome Alignments
• Functional sequences often evolve more slowly than
non-functional sequences, therefore sequences that
remain conserved may perform a biological function.
• Comparing genomic sequences from species at
different evolutionary distances allows us to identify:
– Coding genes
– Non-coding genes
– Non-coding regulatory sequences
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The Rate of Evolution Depends on
Constraints
Human vs. Rodent Comparison
Highest substitution rates:
pseudogenes
introns
3’ flanking (not transcribed
to mature mRNA)
4-fold degenerate sites
Intermediate substitution rates:
5’ flanking (contains promoter)
3’, 5’ untranslated (transcribed
to mRNA)
2-fold degenerate sites
Lowest substitution rates:
Nondegenerate sites
Selection of Species for DNA comparisons
Human vs..
Chimpanzee
Mouse
Opossum
Pufferfish
Size (Gbp)
3.0
2.5
4.2
0.4
Time since
divergence
~5 MYA
~ 65 MYA
~150 MYA
~450 MYA
Sequence
conservation (in
coding regions)
>99%
~80%
~70-75%
~65%
Aids identification
of…
Recently
changed
sequences and
genomic
rearrangements
Both
Both
Primarily
coding and coding and
coding
non-coding non-coding sequences
sequences sequences
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ENCODE Project
• Cross-reference existing with new data on human
genome function
• Identify the functional relevance of as many bases of
human genome as possible.
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