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Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

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Exploring Tree-Like and Non-Tree-Like Patterns Using Genome Sequences: An Example Using the Inbreeding Plant Species

Noah W M Stenz¹, Bret Larget², David A Baum¹

¹Department of Botany, University of Wisconsin-Madison, WI, 53706, USA;

Systematic Biology

|June 29, 2015

Summary

Analyzing genome data from Arabidopsis thaliana reveals complex genealogical history. A new method shows partially resolved population trees best fit the data, indicating reticulation alongside tree-like structures.

Keywords:

Concordance TICR gene tree discordance quartet species concepts

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Area of Science:

Genomics
Population Genetics
Phylogenetics

Background:

Genome sequences offer rich genealogical insights, but interpretation methods are developing.
Understanding the evolutionary history of species like Arabidopsis thaliana requires advanced analytical tools.

Purpose of the Study:

To infer and evaluate the population tree of Arabidopsis thaliana using genome sequence data.
To develop and apply a novel statistical test for assessing phylogenetic model fit.

Main Methods:

Analysis of genome sequences from multiple Arabidopsis thaliana accessions.
Inference of population trees using a parallel computing pipeline focused on four-taxon trees.
Implementation of a nonparametric test for quartet frequency analysis to evaluate model assumptions.

Main Results:

Gene tree discordance was observed, consistent with incomplete lineage sorting.
A partially resolved population tree model provided the best fit to the data.
Deviations from the model identified introgression and reticulation events, including a case among UK ecotypes.

Conclusions:

Arabidopsis thaliana exhibits a reticulating evolutionary history, not strictly tree-like.
The developed methods can distinguish between tree-like evolution and reticulation using genomic data.
Phylogenetic analyses of closely related species can benefit from these approaches to uncover complex evolutionary patterns.