A framework phylogeny of the American oak clade based on sequenced RAD data

Area of Science:

• Botany
• Evolutionary Biology
• Genomics

Background:

• Phylogenetic studies in oaks (Quercus, Fagaceae) have historically struggled to resolve the genus's backbone topology with high confidence.
• Understanding oak evolutionary history is crucial for conservation and understanding plant diversification.

Purpose of the Study:

• To resolve the framework phylogeny of a predominantly American oak clade using next-generation sequencing.
• To assess the utility of Restriction-site Associated DNA (RAD-Seq) data for inferring phylogenies in recently diverged clades.

Main Methods:

• Employed RAD-Seq to generate a large dataset of aligned nucleotides (1.40 E06) from a predominantly American oak clade.
• Utilized a new analytical pipeline for RAD-Seq phylogenetics, combining data across runs and assessing locus coverage.
• Introduced a partitioned RAD visualization method (RADami) to test for alternative phylogenetic topologies.

Main Results:

• Successfully resolved the backbone topology of the American oak clade, estimated to be 23-33 million years old.
• RAD-Seq data proved robust, with technical replicates showing consistent phylogenetic placement despite partial locus overlap.
• No evidence for strongly supported alternative topologies was found, indicating a robust phylogenetic estimate.

Conclusions:

• RAD-Seq is a powerful tool for resolving phylogenies in recently diverged clades like American oaks.
• The study provides a robust phylogenetic framework for the American oak clade, advancing our understanding of their evolutionary history.
• The findings demonstrate the utility of RAD-Seq for inferring phylogenies in clades with crown ages of 23-33 million years.