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A Practical Guide to Phylogenetics for Nonexperts
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Multi-locus phylogenetics, lineage sorting, and reticulation in Pinus subsection Australes.

David S Gernandt1, Xitlali Aguirre Dugua1, Alejandra Vázquez-Lobo2

  • 1Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico.

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|April 24, 2018
PubMed
Summary

Phylogenetic incongruence in New World pines (Pinus subsection Australes) is driven by gene flow and introgression, not just incomplete lineage sorting. Nuclear and plastid DNA trees show significant discordance, revealing complex evolutionary histories.

Keywords:
Pinaceaechloroplast capturecoalescencehybridincomplete lineage sortinglow-copy nuclear lociphylogenetic incongruencepineplastome

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Area of Science:

  • Botany
  • Evolutionary Biology
  • Genomics

Background:

  • Phylogenetic incongruence, arising from incomplete lineage sorting and reticulation, complicates evolutionary studies, especially in long-lived plants like pines.
  • Disentangling these evolutionary processes is crucial for understanding species divergence and relationships.

Purpose of the Study:

  • To investigate the causes of phylogenetic incongruence in Pinus subsection Australes, a group of ecologically and economically important New World pines.
  • To differentiate between incomplete lineage sorting and reticulation (gene flow/hybridization) as drivers of discordance between nuclear and plastid phylogenies.

Main Methods:

  • Employed Hyb-Seq (solution hybridization for targeted enrichment and massive parallel sequencing) to analyze low-copy nuclear genes and high-copy plastomes.
  • Inferred phylogenetic relationships using concatenation and coalescent-based methods, incorporating gene flow models.
  • Analyzed 74 individuals from ~30 species within Pinus subsection Australes.

Main Results:

  • Nuclear gene trees (concatenation and coalescent) largely agreed but conflicted with the plastid DNA tree regarding the monophyly of pine clades (Attenuatae, Oocarpae) and paraphyly of Australes.
  • The plastid tree showed discordance with morphological and geographic data.
  • Coalescent analyses improved data fit when gene flow was incorporated, though direct evidence for hybridization explaining specific non-monophyly was equivocal.

Conclusions:

  • Cytonuclear discordance is evident in Pinus subsection Australes, attributed to ancient and recent introgression.
  • A phylogenetic hypothesis is presented where hierarchical relationships are influenced by superimposed gene flow, highlighting the role of introgression in pine evolution.