How challenging RADseq data turned out to favor coalescent-based species tree inference. A case study in Aichryson (Crassulaceae)

Philipp Hühn,Markus S Dillenberger,Michael Gerschwitz-Eidt,Elvira Hörandl,Jessica A Los,Thibaud F E Messerschmid,Claudia Paetzold,Benjamin Rieger,Gudrun Kadereit

Molecular Phylogenetics and Evolution（2022）

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摘要

•Modified RADseq protocol yields strongly reduced number of length extended loci.•Evaluation of assembly metrics eases clustering threshold selection using ipyrad.•Locus filtering by length facilitates detection of biased data.•Dataset reduction improves overall data quality.•Informative RADseq loci support coalescent-based phylogenetic inference with ASTRAL.

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关键词

[clustering threshold selection,coalescent-based summary method,data bias,locus filtering,RADseq,species tree inference]

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