Polyploid phylogenetics

Abstract

Summary Polyploidy is a dominant feature of extant plant diversity. However, major research questions, including whether polyploidy is important to long‐term evolution or is just ‘evolutionary noise’, remain unresolved due to difficulties associated with the generation and analysis of data from polyploid lineages. Many of these difficulties have been recently overcome, such that it is now often relatively straightforward to infer the full and often reticulate phylogenetic history of groups with recently formed polyploids. This nascent field of ‘polyploid phylogenetics’ allows researchers to tackle long‐standing questions of polyploid macroevolution, supplies the foundation for mechanistic models of ploidy change, and provides the opportunity to include a more complete and representative sample of plant taxa in our analyses in general.

Allele Sorting as a Novel Approach to Resolving the Origin of Allotetraploids Using Hyb-Seq Data: A Case Study of the Balkan Mountain Endemic Cardamine barbaraeoides

“…Nevertheless, as a significant step further, we proceeded to allele assembly and sorting. Some approaches or tools for assembling allele sequences and distinguishing among homeologs have recently been proposed for polyploids ( Page et al, 2013 ; Kamneva et al, 2017 ; Rothfels et al, 2017 ; Schrinner et al, 2020 ; Rothfels, 2021 ). Several previous studies used parallel amplicon sequencing to analyze polyploid species, but capturing only a low number of loci (up to 12 loci) and with manual homeolog identification and sorting ( Brassac and Blattner, 2015 ; Rothfels et al, 2017 ; Dauphin et al, 2018 ; see also Eriksson et al, 2018 , specifically for target enrichment data).…”

“…High-throughput DNA sequencing has brought excellent opportunities to improve phylogenetic inferences, particularly when facing difficult evolutionary cases, such as rapid radiations or recent speciation characterized by low genetic divergence and presence of incomplete lineage sorting (ILS) often complicated by hybridization and polyploidy ( Schmickl et al, 2016 ; Nikolov et al, 2019 ; Karbstein et al, 2020 ; Larridon et al, 2020 ). Disentangling reticulate and polyploid evolution, however, has been a difficult task, and phylogenomic studies on polyploids have lagged behind ( Oxelman et al, 2017 ; Rothfels, 2021 ). Recent advances in this respect (see, e.g., Kamneva et al, 2017 ; Morales-Briones et al, 2018 ; Carter et al, 2019 ; Brandrud et al, 2020 ) have opened up new perspectives on analyses of polyploid species complexes.…”

“…The outcome of such consensus assembly is a mix of sequences retrieved from different homeologs (parental subgenomes) and chimeric sequences. Therefore, the crucial steps to resolve in polyploid phylogenetics are to separate sequencing reads originating from different subgenomes, assemble haplotype (allele) sequences, assign them to the subgenomes, and trace the parental origin of these subgenomes by multilabeled species tree or network inference methods ( Rothfels, 2021 ). A few recent studies have explored different ways how to accomplish these steps, either via mapping and categorization of the sequence reads to the reference diploid genomes ( Page et al, 2013 ; Grover et al, 2015 ), developing bioinformatics pipelines for amplicon sequences of polyploids from long-read sequencing platforms ( Rothfels et al, 2017 ), or via the assembly of haplotype sequences by read-backed phasing ( Eriksson et al, 2018 ; Kates et al, 2018 ).…”

Exploring Angiosperms353: An open, community toolkit for collaborative phylogenomic research on flowering plants

“…The authors attempted to use available phasing programs to separate duplicated gene copies, but these proved inefficient, possibly because the programs were designed for diploid organisms. Overall, we expect development of new analytical tools will continue to improve our ability to use Angiosperms353 and related data types to reconstruct difficult reticulate evolutionary histories (e.g., Freyman et al, 2020 [Preprint]; Rothfels, 2021). New methods, such as ASTRAL‐Pro (Zhang et al, 2020), should allow improved handling of paralogs in phylogenomic analyses.…”

Unraveling Phylogenetic Relationships, Reticulate Evolution, and Genome Composition of Polyploid Plant Complexes by Rad-Seq and Hyb-Seq

“…Polyploidy, the presence of two or more full genomic complements (whole genome duplication), occurs across the tree of life (Otto and Whitton 2000;Van De Peer et al 2017;Rothfels 2021). Whole-genome duplications have been observed in seed plants, and in several lineages of animals (mainly fish and amphibians), fungi, and protists (Mable et al 2011;Van De Peer et al 2017;Blischak et al 2018).…”