Genomics of Evolutionary Novelty in Hybrids and Polyploids

Abstract

It has long been recognized that hybridization and polyploidy are prominent processes in plant evolution. Although classically recognized as significant in speciation and adaptation, recognition of the importance of interspecific gene flow has dramatically increased during the genomics era, concomitant with an unending flood of empirical examples, with or without genome doubling. Interspecific gene flow is thus increasingly thought to lead to evolutionary innovation and diversification, via adaptive introgression, homoploid hybrid speciation and allopolyploid speciation. Less well understood, however, are the suite of genetic and genomic mechanisms set in motion by the merger of differentiated genomes, and the temporal scale over which recombinational complexity mediated by gene flow might be expressed and exposed to natural selection. We focus on these issues here, considering the types of molecular genetic and genomic processes that might be set in motion by the saltational event of genome merger between two diverged species, either with or without genome doubling, and how these various processes can contribute to novel phenotypes. Genetic mechanisms include the infusion of new alleles and the genesis of novel structural variation including translocations and inversions, homoeologous exchanges, transposable element mobilization and novel insertional effects, presence-absence variation and copy number variation. Polyploidy generates massive transcriptomic and regulatory alteration, presumably set in motion by disrupted stoichiometries of regulatory factors, small RNAs and other genome interactions that cascade from single-gene expression change up through entire networks of transformed regulatory modules. We highlight both these novel combinatorial possibilities and the range of temporal scales over which such complexity might be generated, and thus exposed to natural selection and drift.

Climate Vulnerability Assessment of the Espeletia Complex on Páramo Sky Islands in the Northern Andes

“…Besides range shifts (Chen et al, 2011;Feeley et al, 2011;Donoghue and Edwards, 2014;Kolar et al, 2016;Freeman et al, 2020) and adaptive responses (Hoffmann and Sgro, 2011;Franks and Hoffmann, 2012;Donoghue, 2019;Ørsted et al, 2019), introgression, hybridization (Lafon-Placette et al, 2016), and polyploidization (Han et al, 2019;Mason and Wendel, 2020;Nieto Feliner et al, 2020) which have not been explicitly explored in this study, may also provide innovative (Donoghue and Sanderson, 2015) adaptive sources in plants (Abbott et al, 2013;Marques et al, 2019). The Espeletia complex is known for a high incidence of natural hybrids as told by phenotypic and genetic markers (Rauscher, 2002;Pouchon et al, 2018).…”

Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

“…One potential explanation for this counterintuitive finding is that relaxed evolutionary constraint (reduced purifying selection) on the N subgenome may have allowed for accumulation of adaptive genetic variation through directional or diversifying selection. As such, the N subgenome has accumulated heritable variation 49 that future breeding regimes can target to shape natural switchgrass populations and improve biofuel yield.…”

A duplicated copy of the meiotic geneZIP4preserves up to 50% pollen viability and grain number in polyploid wheat

“…The Alexander and Feulgen staining methods provided further information revealing that the small pollen grains in the CRISPR Tazip4-B2 and ph1b mutants are a mixture of both immature (unfunctional) and unviable pollen grains. Discussion Most polyploid literature highlights the requirement for a new polyploid to ensure the production of balanced gametes and hence fertility, through both meiotic and genomic adaptations (Comai, 2005;Otto, 2007;Pelé et al, 2018;Feliner et al, 2020). However, few meiotic adaptions have been characterised, which is surprising given their suggested importance to the preservation of overall polyploid fertility.…”