Speciation II

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Drosophila chromosome bacterial gene
Widespread Lateral Gene Transfer from
Intracellular Bacteria to Multicellular
Eukaryotes, Published Online August 30,
2007Science DOI 10.1126/science.1142490
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Nikoh Nakabachi. 2009. BMC Biology 2009, 712.
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Reconstructing DWM

• Major, independent approaches
• Cladistics
• Statistical
• Similar goal
• Form best hypothesis of genetic lineages

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Challenges of phylogenies based on sequences

• Aligning sequences
• Finding the most parsimonious tree among
  thousands of possibilities
• Insufficient or excessive divergence
• Distinguishing genes that are paralogs vs.
  orthologs
• Gene duplication creates paralogs
• Speciation creates orthologs

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Relations between trees and DWM
monophyletic
paraphyletic
polyphyletic
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Applying Phylogenetic Analysis

• How can we reconcile alternative trees derived
  from different data?
• What are some difficulties in phylogenetic
  analysis?
• What promotes new clades in addition to
  bifurcation?
• Can phylogenies help us understand ecological
  processes?

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Phylogenetic histories and biogeography

• Biogeography the study of distributions
• How do similar organisms get separated?
  vicariance vs. dispersal
• Phylogenetic trees imply sequence as well as
  similarity
• Relative timing can be used to test hypotheses
  about the history of geological processes
• Understanding of geology helps to understand
  evolutionary relationships

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Hawaiian fruit fly phylogeny
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What data can be used to determine timing?

• Fossil evidence

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What data can be used to determine timing?

• Molecular clocks
• based on randomness of mutations
• applicable to selectively neutral DNA
• must account for variability in mutation process
  among
• coding vs. non-coding
• loci for different products
• variation in generation time of organisms

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Reconstructing the early evolution of life

• What is the relationship of Archea, Bacteria, and
  Eucarya?
• What characteristics should be most informative?
• What is the role of RNA in the early evolution of
  life?

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Phylogeny of life molecular evidence
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Phylogeny of life linear model
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Complexity of molecular evidence lateral gene
transfer model (gene evolution)
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Recombination through symbiosis model