Network Reticulate Evolution: Biology, Models, and Algorithms

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Network (Reticulate) Evolution Biology, Models,
and Algorithms

• C. Randal Linder, Bernard M.E. Moret, Luay
  Nakhleh, and Tandy Warnow
• University of Texas at Austin University of New
  Mexico

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Purpose of Tutorial

• Familiarize you with the nature of reticulate
  evolution in biology
• Discuss the implications of reticulation for our
  understanding of evolution
• Introduce other evolutionary events that can
  mimic reticulate evolution
• Present currently available methods for
  simulating, detecting and reconstructing
  reticulation
• Consider the deficiencies of the current methods

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Breakdown of Time

• 1330 Presentation of the Biology (45 min), Dr.
  Linder
• 1415 Questions for Dr. Linder (Part I) (15 min)
• 1430 Break (20 min)
• 1450 Presentation of the Computer Science (50
  min), Drs. Moret and Warnow
• 1540 Questions for Drs. Moret and Warnow (Part
  II) (15 min)
• 1555 Demo by Nakhleh (15 min)
• 1610 Questions for all four lecturers (20 min)
• 1630 End of tutorial

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Idealized Nature

• Wouldnt it be nice if
• Sexual creatures would just behave themselves.
• Asexual lineages would keep their pseudopods to
  themselves
• Then we could stick with bifurcating graphs
  (trees) to properly describe the evolutionary
  history of organismal lineages

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Unruly Nature Whatever is not forbidden will
occur.

• -- Gerald Myers
• (ca 1980)

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Life Aint a Tree

• Molecular phylogeneticists will have failed to
  find the true tree, not because their methods
  are inadequate or because they have chosen the
  wrong genes, but because the history of life
  cannot properly be represented as a tree.
• --Ford Doolittle

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Overview of Reticulate Biology

• What happens at the genetic level?
• How does it relate to population genetic
  processes?
• How can we detect it?
• How can we reconstruct it?
• What biological tools need to be in place to
  generate the requisite data?

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Before Reticulation

• Paradoxically, Ill begin with non-reticulate
  evolution
• Bifurcating evolution (and sometimes hard
  polytomies)
• Evolutionary lineages split and evolve
  independently from one another

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Before Reticulation

• Key Evolutionary Insight Because all evolution
  is a product of change from one generation to the
  next, the information must initially change in
  some form of bifurcating process.

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What Is Reticulation?

• Violation of the independence of each
  evolutionary lineage
• Instead of bifurcation, lineages can mix and
  produce new lineages
• This leads to the production of networks instead
  of trees

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Levels of Reticulation

• Life is organized hierarchically and so
  reticulation can occur at different levels
• Chromosomal (meiotic recombination)
• Population (sexual recombination)
• Species (generally speaking hybridization)

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Levels of Reticulation

• Chromosomal (meiotic recombination)

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Levels of Reticulation

• Population (sexual recombination)

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Levels of Reticulation

• Species (hybridization and gene transfer)

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Levels Nested within Levels
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What Were Interested In Today

• Most of the work on reticulation has been done at
  the population genetic level
• A great deal of work on recombination, especially
  meiotic recombination
• Our focus is on the higher level reticulation
  processes of hybrid speciation and lateral gene
  transfer
• Intersects with the population genetic
  perspective
• Will talk about this when appropriate

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Levels of Reticulation

• Species (hybridization and gene transfer)

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Types of Hybrid Speciation

• Allopolyploidization each parent of the hybrid
  contributes its entire nuclear genome (usually
  uniparental inheritance of the organelles)
• Parents neednt have the same number of
  chromosomes

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Types of Hybrid Speciation

• Diploid (Homoploid) Hybridization each parent
  contributes half of its diploid chromosome set,
  as it would with normal sex.
• Parents almost always have the same number of
  chromosomes

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Types of Hybrid Speciation

• Autopolyploidization a doubling of the diploid
  chromosome number in a single species
• From a biological and topological perspective,
  could be considered a type of bifurcating
  speciation

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Horizontal Gene Transfer

• Hybridization between lineages, but an
  independent lineage is not produced
• Hybrids backcross to one or both parents allowing
  introgression of genes between species
• Genes are moved between lineages by a third party
  (vector), e.g., a virus

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Horizontal Gene TransferIntrogressive
Hybridization

• Genetic material is moved by hybridization and
  backcrossing

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Horizontal Gene TransferGenome Capture

• A complete organellar genome is transferred by
  hybridization

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Horizontal Gene TransferBacterial Sex

• Genetic material is moved by conjugation between
  compatible bacteria

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Bacteria Promiscuous DNA Sharers

• Lawrence, Ochman estimated that 755 of 4,288 ORFs
  in E. coli were from at least 234 lateral gene
  transfer events (Proc. Natl Acad. Sci. USA 95,
  9413-9417 (1998) )
• General evidence

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Horizontal Gene TransferExchange by a Vector

• Genetic material is moved by a third party such
  as a virus or a combination of organisms, e.g.,
  mosquito and protozoan.

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Neworks Have Incongruent Trees Within Them
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Reticulation Events Have Incongruent Trees Within
Them
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Reticulation Events Have Incongruent Trees Within
Them
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Fundamental Insight

• At the lowest possible level (individual DNA
  nucleotides on a single DNA strand) all evolution
  is ultimately tree-like.

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How Might We Detect Reticulation?

• Fundamentally, reticulation is a mixing of
  different evolutionary signals. Therefore
• The signal from a genome that has experienced
  reticulation will be an average of its parents
  (Median approach)
• Unrecombined stretches of DNA will have a signal
  that comes from one parent. (Incongruence
  approach)
• Will see both approaches in methods for detection
  and reconstruction

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Evolutionary Events that Mimic Species-Level
Reticulation

• Lineage Sorting (gene tree/species tree problem)
• Reticulation at lower levels, e.g., meiotic
  recombination

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Evolutionary Events that Mimic Species-Level
Reticulation

• Lineage Sorting (gene tree/species tree problem)
• When reconstructing a species-level phylogeny
  using DNA sequence information we are actually
  reconstructing a gene tree.
• Ancient alleles (alleles arising prior to some
  monophyletic group) may not be inherited by all
  species.
• In essence, it is either a sampling problem or an
  irretrievable information loss problem.

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Gene Tree/Species Tree
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Gene Tree/Species Tree

• All of the versions of a gene from a single
  common history (everything that is the same
  color) are referred to as orthologues.
• Versions of a gene from a duplication event or
  the production of a new allele are paralogues

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Gene Tree/Species Tree
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Gene Tree/Species Tree
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Gene Tree/Species Tree
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Gene Tree/Species Tree
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Gene Tree/Species Tree
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Gene Tree/Species Tree
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Gene Tree/Species Tree

• Under a molecular clock, it is possible to
  detect the difference between incongruence due to
  hybridization and to a gene tree/species tree
  sampling problem.
• GT/ST incongruences will occur at different
  depths.

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Evolutionary Events that Mimic Species-Level
Reticulation

• Reticulation at lower levels, e.g., meiotic
  recombination
• Recombination can lead to loss of an allele for a
  lineage in a particular region of DNA essentially
  giving rise to a lineage sorting problem.

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Recombination Example
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Second Key Insight

• Events that masquerade as species-level
  reticulate evolution are always the product of
  either true data loss or inadequate sampling.
• Here, we encounter the importance of a population
  genetic perspective in phylogenetics.

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Given the problem of misleading signals, how can
we distinguish true species-level reticulation
from reticulation at other levels, simple data
loss, and inadequate sampling?
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Possible Solution

• This one looks easy. Just increase the number of
  individuals sampled from a species/population and
  the number of markers.
• Therefore, must take a multiple marker approach
  to recovering the species-level relationships
• Data loss and lower level reticulation events
  should almost always act randomly with respect to
  which phylogeny is favored
• Species-level reticulation will be biased toward
  a particular interpretation

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Practical Concerns

• Practical problems (for biologists)
• Cost
• Time
• Lack of prior knowledge that all of the
  orthologues are there to be found

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Caveats

• Reticulation events that quickly follow
  speciation may not be detectable
• Ancient reticulation events may not be
  recoverable
• The computational requirements to detect and
  reconstruct reticulation may be considerable
• We may have to rethink our ideas of species
  (levels/units of speciation)

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Assembling the Network of Life ANOL