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Phylogenetics in space: How continuous spatial structure impacts tree inference.

Zachary B Hancock1, Emma S Lehmberg2, Heath Blackmon2

  • 1Department of Biology at Texas A&M University, College Station, TX 77840, United States; Ecology & Evolutionary Biology IDP at Texas A&M University, College Station, TX 77840, United States; Department of Integrative Biology, Michigan State University, 293 Farm Ln., East Lansing, MI 48825, United States.

Molecular Phylogenetics and Evolution
|May 16, 2022
PubMed
Summary
This summary is machine-generated.

Biological models often simplify continuous populations into discrete groups. This study shows that continuous spatial structure significantly impacts phylogenetic inference, affecting gene trees, species delimitation, and more.

Keywords:
Gene treeHybridizationMultispecies coalescentSpecies delimitationSpecies tree

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Area of Science:

  • Evolutionary Biology
  • Phylogenetics
  • Population Genetics

Background:

  • Traditional biological models often oversimplify continuous population structures, assuming discrete units.
  • Existing phylogenetic models, like the multispecies coalescent, frequently ignore spatial independence, termed the 'missing z-axis'.
  • This simplification can lead to inaccuracies in understanding evolutionary processes.

Purpose of the Study:

  • To investigate the impact of continuous spatial structure on phylogenetic inference.
  • To demonstrate how spatial independence influences various aspects of evolutionary modeling.
  • To provide methods for identifying spatial structure in phylogenetic data.

Main Methods:

  • Reviewing existing evidence on spatial structure in phylogenetics.
  • Utilizing complex continuous-space demographic models with varied speciation modes.
  • Analyzing effects on gene tree stoichiometry, topological and branch-length variance, network estimation, and species delimitation.

Main Results:

  • Continuous spatial structure profoundly affects all facets of phylogenetic inference.
  • Specific impacts include alterations in gene tree properties and species delimitation accuracy.
  • The 'missing z-axis' in common models leads to significant inferential biases.

Conclusions:

  • Spatial structure is a critical, often overlooked, factor in phylogenetic analysis.
  • Researchers can identify spatial influences by examining specific phylogenetic metrics.
  • Incorporating spatial dynamics enhances the accuracy of evolutionary reconstructions.