Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events in Alchemilla s.l. (Rosaceae)

Diego F. Morales-Briones, Berit Gehrke, Chien-Hsun Huang, Aaron Liston, Hong Ma, Hannah Marx, David Tank & Ya Yang
Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci, especially in groups experiencing whole-genome duplication (WGD) events. Common approaches for processing paralogs in target enrichment data sets include random selection, manual pruning, and mainly, the removal of entire genes that show any evidence of paralogy. These approaches are prone...
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2 downloads reported since publication in 2021.

These counts follow the COUNTER Code of Practice, meaning that Internet robots and repeats within a certain time frame are excluded.
What does this mean?