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Misconceptions on Missing Data in RAD-seq Phylogenetics with a Deep-scale Example from Flowering Plants.

Deren A R Eaton¹, Elizabeth L Spriggs¹, Brian Park¹

¹Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, New Haven, CT, 06520, USA.

Systematic Biology

|November 1, 2016

Summary

This summary is machine-generated.

Restriction-site associated DNA sequencing (RAD-seq) can provide phylogenetic information, but missing data due to mutations or low coverage can impact results. Optimizing sequencing effort is crucial for resolving deeper evolutionary relationships.

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Area of Science:

Evolutionary Biology
Genomics
Bioinformatics

Background:

Restriction-site associated DNA (RAD) sequencing methods rely on conserved enzyme recognition sites, leading to missing data when mutations disrupt these sites.
Missing data in RAD-seq is often assumed to limit phylogenetic resolution, particularly for deep evolutionary timescales.
The distribution of missing data can be influenced by both biological factors (mutation-disruption) and technical factors (sequencing coverage).

Purpose of the Study:

To investigate the relationship between missing data at the tips of a phylogenetic tree and phylogenetic information at deeper evolutionary levels.
To differentiate between patterns of missing data caused by mutation-disruption versus low sequencing coverage.
To provide practical recommendations for maximizing phylogenetic informativeness in RAD-seq studies.

Main Methods:

Re-analysis of ten existing RAD-seq datasets to examine missing data distribution.
Phylogenetic simulations to model expected patterns of missing data under different scenarios.
Empirical study on the angiosperm clade Viburnum (Adoxaceae) with varying sequencing effort.

Main Results:

Missing data patterns from mutation-disruption can be distinguished from stochastic patterns caused by low sequencing coverage.
Insufficient or uneven sequencing coverage contributed significantly to missing data, comparable to mutation-disruption.
In Viburnum, increased sequencing coverage substantially enhanced the number of parsimony-informative sites and shared loci across taxa.

Conclusions:

RAD-seq data can be phylogenetically informative, even at deeper evolutionary scales, when data quality and coverage are optimized.
Distinguishing sources of missing data is critical for accurate phylogenetic inference.
Recommendations are provided to improve RAD-seq data utility for robust phylogenetic reconstruction.