Phylogenetics of dispersal

BIOL33221: Bioinformatics

Dr Axel Barlow
email: axel.barlow@ntu.ac.uk, office: IBRC115

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Phylogenetics of dispersal

  • Population trees
  • The process of dispersal
  • Examples
  • Viral pandemics

Essential reading

We can calculate phylogenies of different things...

Species trees

  • These are phylogenies of species
  • Each tip is a different, reproductively isolated species
  • Can be inferred from a variety of data types

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Gene trees

  • These are phylogenies of individual loci (e.g. a gene)
  • Or related sets of loci (e.g. multigene families)
  • Each tip is a different allele (i.e. a gene variant)

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Population-level trees

  • Each tip is an individual
  • Each node is their most recent ancestor (coalescence event)
  • Shows the relationships of individuals and populations

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How does that work?

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Calculating population-level trees

We'll think about mitochondrial haplotypes (diploid loci 2x more complex)

  • Sequence variation provides phylogenetic information
  • Similar sequences are more closely related
  • Branch lengths are (loosely) proportional to sequence divergence
  • Coalescence times also depend on population size
  • Described by coalescent theory

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Human mitochondrial phylogeny

Rishishwar L, Jordan IK. BMC Genomics. 2017;18:140. CC BY 4.0

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PhyloTree.org visualisation

Geographic occurrence

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Rishishwar L, Jordan IK. BMC Genomics. 2017;18:140. CC BY 4.0

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PIECE TO CAMERA

The dispersal process

  • Imagine 2 Islands: A and B
  • B is colonised from A by a single individual
  • This transports one lineage from A to the new island B
  • Individuals from B are nested within the A clade

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Subsequent expansion

  • The newly introduced B population expands
  • All individuals are descendants of the founding lineage
  • The B clade is nested within A
  • A individuals are paraphyletic with respect to B

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Examples: Golden Lancehead

plot of chunk unnamed-chunk-14 Queimada Grande, Prefeitura Municipal de Itanhaém, CC BY 2.5

plot of chunk unnamed-chunk-15 Bothrops insularis, Nayeryouakim, CC BY 4.0

plot of chunk unnamed-chunk-16 Bothrops jararaca, Fernando Tatagiba, CC BY 3.0

Examples: Golden Lancehead

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Wüster et al. Journal of Zoology 266.1 (2005): 1-10

plot of chunk unnamed-chunk-18 Bothrops insularis, Nayeryouakim, CC BY 4.0

plot of chunk unnamed-chunk-19 Bothrops jararaca, Fernando Tatagiba, CC BY 3.0

Examples: Barbados anoles

plot of chunk unnamed-chunk-21 Anolis roquet, Adamhesim, CC BY 4.0

plot of chunk unnamed-chunk-22 Anolis extremus, Postdlf, CC BY SA-3.0

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Examples: Barbados anoles

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Thorpe et al. Mol phylogenet evol 127 (2018): 682-695.

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Complicating factors

  • So far we have considered a small and genetically similar founding population
  • What happens if the founding population is large and genetically diverse?
  • This can "look" like multiple colonisation events
  • And even make the direction of colonisation uncertain

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So what about viruses?

Racoon rabies in Ontario

Nadin-Davis et al. Virus Research 232 (2017): 123-133. CC BY 4.0

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Avian influenza H5N1 in Asia

Tian et al. Proceedings of the National Academy of Sciences 112.1 (2015): 172-177.

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Ebola virus in West Africa

Suchard, et al. Virus evolution 4.1 (2018): vey016.

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Phylogenetics of dispersal

  • Population trees
  • The process of dispersal
  • Examples
  • Viral pandemics

Next time

Bayesian phylogenetics