Mapping phylogenetic trees to reveal distinct patterns of evolution

Kendall, Michaela; Colijn, Caroline

doi:10.1101/026641

Cited by 4 publications

(1 citation statement)

References 28 publications

(27 reference statements)

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“…The phylogenetic landscape was investigated using the R package treespace (Jombart et al, 2017). The statistical distribution of the tree topologies was calculated using principal component analysis with the Kendall-Colijn (KC) distance for rooted trees (Kendall and Colijn, 2016). The trees were rooted using the function reroot of the package phytools v.0.6-99 (Revell, 2012) on Hypseocharis bilobata Killip (Geraniaceae).…”

Section: Model Violation and Tree Landscape Assessment-mentioning

confidence: 99%

A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set

Maurin

Anest

Bellot

et al. 2021

American J of Botany

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To further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents (except Antarctica), we tested the Angiosperms353 probe kit. METHODS:We combined high-throughput sequencing and target enrichment with the Angiosperms353 probe kit to evaluate a sample of 485 species across 305 genera (76% of all genera in the order). RESULTS:Results provide the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks, such as the relationship of the early-diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. Technical considerations for processing HTS data are also discussed.CONCLUSIONS: High-throughput sequencing and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to identify genes and gene trees that account for likely incomplete lineage sorting and/or hybridization events.

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Section: Model Violation and Tree Landscape Assessment-mentioning

confidence: 99%

A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set

Maurin

Anest

Bellot

et al. 2021

American J of Botany

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Properties for the Fréchet mean in Billera-Holmes-Vogtmann treespace

Anaya

Anipchenko-Ulaj

Ashfaq

et al. 2020

Advances in Applied Mathematics

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A metric on phylogenetic tree shapes

Colijn

Plazzotta

2016

Preprint

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Abstract.-The shapes of evolutionary trees are influenced by the nature of the evolutionary process but comparisons of trees from different processes are hindered by the challenge of completely describing tree shape. We present a full characterization of the shapes of rooted branching trees in a form that lends itself to natural tree comparisons. We use this characterization to define a metric, in the sense of a true distance function, on tree shapes. The metric distinguishes trees from random models known to produce different tree shapes. It separates trees derived from tropical versus USA influenza A sequences, which reflect the differing epidemiology of tropical and seasonal flu. We describe several metrics based on the same core characterization, and illustrate how to extend the metric to incorporate trees' branch lengths or other features such as overall imbalance. Our approach allows us to construct addition and multiplication on trees, and to create a convex metric on tree shapes which formally allows computation of average tree shapes. [tree metric; phylodynamics; tree shapes]

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Mapping phylogenetic trees to reveal distinct patterns of evolution

Cited by 4 publications

References 28 publications

A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set

A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set

Properties for the Fréchet mean in Billera-Holmes-Vogtmann treespace

A metric on phylogenetic tree shapes

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