Evidence for Evolution

Comparative Genomics

Contributors

Ben Whitten

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What is genomics?
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Genomics is the study of the whole set of genes of a species and the interactions of the genes within a genome.


The genomes of many species have been fully sequenced, including humans, chimpanzees, koalas and bacteria. Some organisms share molecular and structural homologies.

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What is comparative genomics?
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Comparative genomics is a field of biological research in which researchers use a variety of tools to compare the genome sequences of different species. The more similar in sequence the genes and genomes of two species are, the more closely related those species are in their evolutionary history, as less time has passed in which mutation and other genetic changed have accumulated.

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Life and Diversity on Earth
Comparative Genomics
Comparative Biochemistry
Comparative Anatomy
The Fossil Record
Fossil Dating
Patterns of Evolution

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What is DNA-DNA hybridisation?

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In the past, DNA-DNA hybridisation methods have been widely used to analyse the relatedness of pairs of spcies, but can be unreliable when comparing closely related species.


  1. The DNA sequences to be compared are extracted, purified, amplified, and cut into short fragments (probes, restriction enzymes and PCR)

  2. The mixture is incubated (heated) to allow DNA strands to separate

  3. The single strands from different species are added together and cooled

  4. Sequences anneal with each other and form double stranded hybridised DNA

  5. Hybridised sequences with a high degree of similarity will bind more firmly (more hydrogen bonds)

  6. More related sequences require more heat to separate them: called “DNA melting”

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What is the role of bioinformatics in comparative genomics?
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Comparative genomics produces huge amounts of data that must be stored and analysed in a logical way. The scale of the computational; framework for this volume of biological analysis is massive, and only recently it has been possible thanks to bioinformatics.


Bioinformatics is the digital storage, retrieval, organisation and analysis of an enormous volume of bioloigcal data such as nucleotide and amino acid sequences from different species, and has dramatically increased the size, accuracy and scope of data sets.

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What are phylogenetic trees?
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Phylogenetic trees allow us to represent evolutionary relationships between groups in a diagrammatic form. A phylogenetic tree can be built using physical information like body shape, bone structure, or behaviour, or it can be built from molecular information such as mtDNA inheritance or genetic sequences.


The pattern of brnaching in a phylogenetic tree reflects how species or other groups evolved from a series of common ancestors. The more closely related species have a more recent common ancestor, while the more distantly related species have a distant common ancestor.

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Mutation rate in comparative genomics
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Outside of external influences, a basline rate of mutation occurs naturally in DNA. If mutations cause a change in the structure of function of proteins encoded in DNA, they may affect whether those proteins are passed to the next generation and will become more or less common in subsequent generations.


The frequency of new mutations in a single gene or organism over time is fairly constant within a species, being called the mutation rate. When comparing genomes of two species, the mutation rate can be used as a molecular clock to estimate at what point in time those species diverged from a common ancestor.


For humans, the mutation rate is estimated to be 10^-8 (changed nucleotides) per nucleotide base pair per generation.

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