Abstract Detail



Exploring the utility and limits of target enrichment methods to study polyploidy and reticulate evolution

Morales-Briones, Diego [1], Gehrke, Berit [2], Huang, Chien-Hsun [3], Liston, Aaron [4], Ma, Hong [5], Marx, Hannah [6], Tank, David [7], Yang, Ya [8].

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

Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci. Common approaches for processing paralogs in target enrichment datasets include removing entire loci that show evidence of paralogy, the random selection of paralogs, and manual pruning. These approaches can introduce errors in orthology inference, and sometimes significantly reduce the number of loci, especially in groups experiencing whole-genome duplication (WGD) events. As dataset size increases, manual processing becomes prohibitive. Here we apply two automated approaches for paralog processing in a target enrichment dataset of 68 species of Alchemilla s.l. (Rosaceae), a widely distributed clade of plants primarily from temperate climate regions. Previous molecular phylogenetic studies and chromosome numbers both suggested the allopolyploid origin of the group. However, putative parents of allopolyploidy events remain unknown. By taking paralogs into consideration, we identified four nodes in the backbone of Alchemilla s.l. with a high likelihood of multiple gene duplication events. Furthermore, we established that the detected WGDs are products of ancient allopolyploidy events, corresponding to the allopolyploid origin of the entire Alchemilla s.l. clade and subsequent allopolyploidy origin of several of the major clades of the group. Here we showed the utility of automated orthology methods, commonly used in genomic or transcriptomic datasets, to study complex scenarios of polyploidy and reticulate evolution from target enrichment data sets.


1 - University of Minnesota, Plant and Microbial Biology, 1445 Gortner Avenue, Saint Paul, MN, 55108, USA
2 - University of Bergen, University Gardens, University Museum, Bergen, Norway
3 - Fudan University, School of Life Sciences, Shanghai, China
4 - Oregon State University, Botany and Plant Pathology, Corvallis, OR, 97331, USA
5 - Pennsylvania State University, Department of Biology, the Huck Institute of the Life Sciences, University Park, PA, 16802, USA
6 - University of Michigan, Ecology and Evolutionary Biology, Ann Arbor, MI, 48109, USA
7 - University of Idaho, Biological Sciences, Moscow, ID, 83844, USA
8 - University Of Minnesota, Plant And Microbial Biology, 1445 Gortner Avenue, St. Paul, MN, 55108, United States

Keywords:
Alchemilla
allopolyploidy
Gene tree discordance
Hyb-Seq
hybridization
Orthology inference
Paralogs
Rosaceae
Target Enrichment
Whole-genome duplication.

Presentation Type: Colloquium Presentations
Number: COL04002
Abstract ID:309
Candidate for Awards:None


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