Polyploidy promotes species diversification of Allium through ecological shifts

Abstract

Summary Despite the role of polyploidy in multiple evolutionary processes, its impact on plant diversification remains controversial. An increased polyploid frequency may facilitate speciation through shifts in ecology, morphology or both. Here we used Allium to evaluate: (1) the relationship between intraspecific polyploid frequency and species diversification rate; and (2) whether this process is associated with habitat and/or trait shifts. Using eight plastid and nuclear ribosomal markers, we built a phylogeny of 448 Allium species, representing 46% of the total. We quantified intraspecific ploidy diversity, heterogeneity in diversification rates and their relationship along the phylogeny using trait‐dependent diversification models. Finally, we evaluated the association between polyploidisation and habitat or trait shifts. We detected high ploidy diversity in Allium and a polyploidy‐related diversification rate shift with a probability of 95% in East Asia. Allium lineages with high polyploid frequencies had higher species diversification rates than those of diploids or lineages with lower polyploid frequencies. Shifts in speciation rates were strongly correlated with habitat shifts linked to particular soil conditions; 81.7% of edaphic variation could be explained by polyploidisation. Our study emphasises the role of intraspecific polyploid frequency combined with ecological drivers on Allium diversification, which may explain plant radiations more generally.

Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication inBrassica rapa

“…Presently, our results provide a testable hypothesis to explain the observed correlation of polyploidy and crop domestication 10 .More broadly, our results suggest that paleopolyploidy may leave behind a legacy of elevated genetic diversity across the duplicated remnants of diploidized genomes. Although most models and studies of polyploid evolution compare diploids and polyploids11,12,14,16,17,19,[70][71][72] , our comparison of paleologs and non-paleologs within a diploidized paleopolyploid uncovered evidence for similar dynamics ongoing within plant genomes even millions of years after whole genome duplication. The extensive genome duplication history of plants may result in genomes with different levels of diversity based on the mechanisms of gene origin.…”

A deep dive into the ancestral chromosome number and genome size of flowering plants

“…Polyploidy is a common and ongoing phenomenon, especially in plants (Wood et al ., 2009), which has played an important role in many lineages, with evidence of several rounds of both ancient and recent polyploidization (Jiao et al ., 2011; Li et al ., 2015; Leebens‐Mack et al ., 2019), albeit its distribution over time remains contested (Ruprecht et al ., 2017). Indeed, although the crucial role of polyploidy in plant diversification on small timescales is widely accepted (Stebbins, 1971; Grant, 1981), the evolutionary significance of polyploidization for the long‐term diversity of angiosperms is still controversial (Mayrose et al ., 2011; Soltis et al ., 2014; Han et al ., 2020). On the other hand, while dysploidy is more frequent than polyploidy in angiosperms (Grant, 1981), its adaptive consequences have been mostly unexamined (Weiss‐Schneeweiss & Schneeweiss, 2013), until recent studies demonstrated its high evolutionary impact (Escudero et al ., 2014).…”

Substantially adaptive potential in polyploid cyprinid fishes: evidence from biogeographic, phylogenetic and genomic studies

“…Polyploids usually have a broader range of environmental tolerance, and often occur in newly created, disrupted or harsh environments compared with diploids [2,5,7,8]. Second, polyploidy is expected to contribute to species diversification, especially in unstable environments, although this process is usually slow due to the stabilization of environmental conditions after polyploidization [2,3,5,6]. Therefore, how polyploidy affects speciation and diversification rates remains controversial, largely because it is difficult to find a polyploid lineage that shows those abovementioned signs of adaptive potential (i.e.…”