# Natural neopolyploids: a stimulus for novel research

Patrick P. Edger, Douglas E Soltis, Shunsuke Yoshioka, Mario Vallejo-Marín, Rie Shimizu-Inatsugi, Kentaro Shimizu, Armel Salmon, Simon Hiscock, Malika Ainouche, Pamela S. Soltis

► To cite this version:

Patrick P. Edger, Douglas E Soltis, Shunsuke Yoshioka, Mario Vallejo-Marín, Rie Shimizu-Inatsugi, et al.. Natural neopolyploids: a stimulus for novel research. New Phytologist, 2025, 246 (1), pp.78-93.
10.1111/nph.20437 . hal-04975953

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Tansley review

Natural neopolyploids: a stimulus for novel
research

Authors for correspondence:

Patrick P. Edger

Email: edgerpat@msu.edu

Douglas E. Soltis

Email: dsoltis@ufl.edu

Pamela S. Soltis

Email: psoltis@flmnh.ufl.edu

Received: 10 September 2024

Accepted: 2 January 2025

Patrick P. Edger<fnref n="1" />,²* ID, Douglas E. Soltis³,⁴* ID, Shunsuke Yoshioka⁵,⁶, Mario Vallejo-Marin⁷ ID, Rie Shimizu-Inatsugi⁵, Kentaro K. Shimizu⁵,⁸ ID, Armel Salmon⁹ ID, Simon Hiscock¹⁰ ID, Malika Ainouche⁹ ID and Pamela S. Soltis⁴ ID

Contents

<table><tr><td>Summary</td><td>1</td><td>VIII. Changes through time – newly formed vs older polyploids</td><td>10</td></tr><tr><td>I. Introduction</td><td>2</td><td>IX. Every polyploid tells a story</td><td>11</td></tr><tr><td>II. Genetic and epigenetic changes following polyploidization</td><td>4</td><td>X. Factors of formation</td><td>11</td></tr><tr><td>III. Role of hybridization vs genome doubling</td><td>6</td><td>XI. Major gaps: other facets of evolution to be learned from new polyploids</td><td>11</td></tr><tr><td>IV. Genotypic and phenotypic diversity</td><td>7</td><td>XII. Conclusions</td><td>12</td></tr><tr><td>V. Reproduction</td><td>8</td><td>Acknowledgements</td><td>13</td></tr><tr><td>VI. Repeated evolutionary experiments</td><td>9</td><td>References</td><td>13</td></tr><tr><td>VII. New polyploids afford unique opportunities to distinguish inherited traits and rapid evolution</td><td>10</td><td></td><td></td></tr></table>

Summary

Recently formed allopolyploid species offer unprecedented insights into the early stages of polyploid evolution. This review examines seven well-studied neopolyploids (we use 'neopolyploid' to refer to very recently formed polyploids, i.e. during the past 300 years), spanning different angiosperm families, exploring commonalities and differences in their evolutionary trajectories. Each neopolyploid provides a unique case study, demonstrating both shared patterns, such as rapid genomic and phenotypic changes, and unique responses to hybridization and genome doubling. While previous studies of these neopolyploids have improved our understanding of polyploidy, significant knowledge gaps remain, highlighting the

New Phytologist (2025)

doi: 10.1111/nph.20437

**Key words:** allopolyploid, angiosperms, genetic and phenotypic variation, genome evolution, neopolyploidy, polyploidy, whole-genome duplication.

<footnote n="1">¹Department of Horticulture, Michigan State University, East Lansing, MI 48823, USA; ²Genetics and Genome Sciences, Michigan State University, East Lansing, MI 48824, USA; ³Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; ⁴Department of Biology, University of Florida, Gainesville, FL 32611, USA; ⁵Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, CH-8057, Switzerland; ⁶Graduate School of Agriculture, Kyoto University, Kyoto, 244-0813, Japan; ⁷Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, 752 36, Sweden; ⁸Kihara Institute for Biological Research, Yokohama City University, Yokohama, 641-12, Japan; ⁹UMR CNRS Ecobio, Rennes University, Rennes Cedex, 35042, France; ¹⁰Department of Biology, University of Oxford, Oxford, OX1 3RB, UK</footnote>

<footnote>*Co-first authors.</footnote>
need for further research into the varied impacts of whole-genome duplication on gene expression, epigenetic modifications, and ecological interactions. Notably, all of these neopolyploids have spontaneously arisen due to human activity in natural environments, underscoring the profound consequences of polyploidization in a rapidly changing world. Understanding the immediate effects of polyploidy is crucial not only for evolutionary biology but also for applied practices, as polyploidy can lead to novel traits, as well as stress tolerance and increased crop yields. Future research directions include investigating the genetic and epigenetic mechanisms underlying polyploid evolution, as well as exploring the potential of neopolyploids for crop improvement and environmental adaptation.

# I. Introduction

Polyploidy occurs frequently across the tree of life, not only in eukaryotes but also in Bacteria and Archaea (reviewed in Morris et al., 2024), and has played a particularly important role in the evolution of green life (Heslop-Harrison et al., 2023). Hence, long-standing research has attempted to identify the diverse consequences of polyploidy in plants at multiple levels (e.g. genetic, genomic, physiological, morphological, and ecological) and the role of polyploidy in evolutionary innovation (Levin, 1983; Soltis et al., 2015; Van de Peer et al., 2017, 2021). Most polyploid species and lineages studied to date formed thousands to millions of years ago, making it challenging to disentangle the immediate impact of genome doubling from longer-term evolutionary processes (Soltis et al., 2016; Free-ling, 2017). However, a few studies have focused on naturally occurring polyploids that formed more recently, in the past 300 years (i.e. neopolyploids as defined here): *Cardamine insueta* and *C. schulzii* (Brassicaceae), *Mimulus peregrinus* (Phrymaceae), *Spartina anglica* (Poaceae), *Senecio cambrensis* (Asteraceae), and *Tragopogon mirus* and *T. miscellus* (Asteraceae; Fig. 1). These species have served as model organisms, affording the novel opportunity to investigate the earliest stages of polyploid evolution in nature, something that can be simulated in other species only via the use of synthetic polyploids or via quickly reproducing plants in laboratory culture (Bafort et al., 2023).

Neopolyploids, due to their recent origin, provide a unique opportunity to study the immediate effects of polyploidization, allowing researchers to separate the impact of genome doubling from subsequent evolutionary changes. Unlike older polyploids, where extended periods of evolution have led to the divergence of the polyploid from its progenitor(s), neopolyploids offer a snapshot of the early stages of polyploid evolution. This allows identification of key genetic and epigenetic changes that happen immediately after polyploidization, such as gene loss, silencing, and transposon activation, which may be critical for polyploid establishment and adaptation.

Studying natural neopolyploids offers significant advantages over the study of older, established polyploids and synthetic lines. We can observe the immediate impact of interspecific hybridization and genome doubling on factors, such as epigenetic marks, gene expression, and meiotic chromosome pairing. These initial changes are often stabilized in older polyploids, hindering examination of the immediate changes occurring following polyploidy in natural

conditions. Neopolyploids allow direct comparison with the exact (or very close) parental genotypes from which they arose, an advantage not possible with older polyploids where both parents and polyploids have evolved and parental species might be extinct. In some polyploid systems, naturally established neoallopolyploids can be directly compared with not only their parents but also resynthesized hybrids and allopolyploids. This allows for deeper insights into the earliest epigenetic and genetic changes that occur in polyploid genomes (Edger et al., 2017). Neopolyploids also provide insights into early niche occupation and ecological interactions with parental species. Finally, the recurrent formation of the same polyploid allows researchers to assess parallel evolution and determine whether evolution repeats itself – that is, are some aspects of polyploid evolution actually hard-wired?

Despite these advantages, challenges remain. The evolutionary trajectories of neopolyploids are uncertain. The short evolutionary timescale limits the observable changes, hindering a full assessment of the long-term success of polyploid lineages. However, the benefits of studying neopolyploids outweigh these limitations. They offer invaluable insights into the initial stages of polyploid evolution, which are crucial for understanding the broader role of polyploidy in shaping biodiversity and driving agricultural innovation. Research on these species should be coordinated and continued by the next generation of plant scientists.

Here, we review what is collectively known about seven recently formed and well-studied naturally occurring neoallopolyploids (Fig. 1) and attempt synthesis and identification of broader implications and future research directions. We assess whether there are rules to the early stages of polyploidy. However, we acknowledge the inherent limitations in drawing unified conclusions across diverse model systems, given the variation in research objectives and methodologies. One goal of this review was to stimulate more coordinated/unified research on these systems in the future. The studies discussed herein were selected to represent a breadth of polyploid systems, with a focus on (epi)genetic and phenotypic changes that have been documented in neopolyploids. Specifically, this review focuses solely on recently established allopolyploids and does not cover neoautopolyploids. Our approach, while not exhaustive, aimed to highlight key trends and knowledge gaps in our understanding of allopolyploid evolution. Each section below reviews the current state of knowledge and concludes with questions for future study, with the goal of stimulating new research on recent polyploidy.
<figure><img src="image_5.png" /><figcaption>**Fig. 1** Evolutionary history of five polyploid complexes. (a) *Tragopogon* polyploid complex. The tetraploid species *T. miscellus* and *T. mirus* arose from hybridization and polyploidization of their respective diploid parental species: *T. pratensis* and *T. dubius* for *T. miscellus*, and *T. dubius* and *T. porrifolius* for *T. mirus*. (b) *Senecio* polyploid complex. The hybridization of the diploid species, *S. squalidus*, and tetraploid species, *S. vulgaris*, created the triploid intermediate species, *S. × baxteri*, and following a polyploidization event created the hexaploid species, *S. cambrensis*. The hybridization of *S. vulgaris* and *S. squalidus* produced an F₁ hybrid and following subsequent backcrossing of this F₁ hybrid with *S. vulgaris* led to the formation of *S. eboracensis*. (c) *Mimulus* polyploid complex. The hybridization of the diploid species, *M. guttatus*, and tetraploid species, *M. luteus*, created the triploid intermediate species, *M. × robertsii*, and following a polyploidization event created the hexaploid species, *M. peregrinus*. (d) *Cardamine* polyploid complex. The hybridization of the diploid species, *C. rivularis* and *C. amara*, created the triploid species, *C. insueta*, and following hybridization with the autotetraploid species, *C. pratensis*, created the mixed ploidy (5x and 6x) species, *C. schulzii*. The autotetraploid species *C. pratensis* arose from the polyploidization of a lineage close to *C. rivularis*. (e) *Spartina* polyploid complex. Two tetraploid species, *S. alterniflora* and *S. maritima*, hybridized to form two interspecific homoploid hybrids, *S. × townsendii* and *S. × neyrautii*. The octoploid species *S. anglica* arose following the polyploidization of the tetraploid *S. × townsendii*.</figcaption></figure>

Some of the polyploid systems reviewed here have reformed repeatedly, providing the opportunity to assess whether evolution repeats itself. Although commonalities are present across these polyploids, each new polyploid also represents a unique storyline and opportunity to investigate the impact of genome doubling. Although much has been learned about polyploid evolution from these newly formed species, major gaps in our understanding

remain. In many cases, differing aspects of polyploidy have been studied (Madlung, 2013; Soltis *et al.*, 2016). These new polyploids have all formed via human-mediated activity, suggesting major impacts of polyploidization for a planet undergoing rapid global change. Lastly, understanding the impacts of polyploidy on recent timescales has major implications not only for evolutionary biology but also for agricultural research.
## II. Genetic and epigenetic changes following polyploidization

### 1. The search for 'rules' via the study of young polyploids

Polyploid organisms arise through two main processes, which represent ends of a continuum: autopolyploidy, where duplicated chromosomes are derived from within the same species; and allopolyploidy, our focus here, where sets of chromosomes are derived from two or more species (Fig. 2). The process of polyploidization often leads to extensive genomic changes, including duplications, deletions, inversions, and translocations (Soltis *et al.*, 1993; Han *et al.*, 2003; Lim *et al.*, 2008; Mandáková *et al.*, 2010) and significant changes in gene expression, so-called ‘transcriptome shock’ (Hegarty *et al.*, 2006; Parisod *et al.*, 2009; Chelaifa *et al.*, 2010; Buggs *et al.*, 2011; Hegarty *et al.*, 2011), which can be accompanied by detectable epigenetic changes (Parisod *et al.*, 2009; Buggs *et al.*, 2011; Hegarty *et al.*, 2011).

Genomic changes eventually lead to alterations in base chromosome number and structure over deep evolutionary time (Murat *et al.*, 2015; Lysak *et al.*, 2016) but can sometimes be observed in the earliest generations in some polyploids (Xiong *et al.*, 2011; Chester *et al.*, 2012; Soltis *et al.*, 2016). This

restructuring can result in alterations in gene dosage, where the expression levels of genes may be altered due to changes in absolute copy number and the relative number of parental subgenome copies (Fig. 2). Consequently, genes involved in various cellular processes, such as growth, development, and reproduction, may exhibit altered expression patterns in polyploids compared with their diploid progenitors (Birchler & Veitia, 2012; Jeffrey Chen & Birchler, 2013). Changes in relative gene dosage of parental copies have been shown to contribute to rapid novel phenotypic variation. For example, variation in flowering time, beyond the extremes observed for either diploid progenitor, was observed across a newly formed allotetraploid rapeseed (*Brassica napus*) population and was correlated with relative dosage of parental alleles of *Flowering Locus C* genes (Pires *et al.*, 2004). Beyond changes in gene dosage, duplicated genes will accumulate mutations over time, leading to functional diversification and/or loss of function (Ohno, 1970; Force *et al.*, 1999; Maere *et al.*, 2005). The redundancy provided by multiple gene copies can facilitate the evolution of novel or diversified gene functions (Ohno, 1970). This can occur through neofunctionalization, where one duplicate acquires a new function, or subfunctionalization, where the ancestral gene's functions are partitioned between the duplicates. Both processes are driven by changes to regulatory and/or coding sequences (Lynch & Conery, 2000).

<figure><img src="image_6.png" /></figure>

**Fig. 2** Polyploidization and its impact on chromosomal evolution and polyploid formation. Polyploid organisms possess more than two complete sets of chromosomes. This phenomenon can arise through autopolyploidy, where the additional chromosomes are derived from the same species, typically due to errors during cell division. Alternatively, allopolyploidy involves the combination of chromosome sets from different species through hybridization and genome duplication. It is important to note that an allopolyploid could be formed by the hybridization of two autopolyploids (i.e. polyploidy preceding hybridization) or via an unreduced gamete and/or triploid bridge (Vallejo-Marin *et al.*, 2015). Homologous chromosomes are pairs of chromosomes that share the same genes in the same order, inherited from each parent in diploid organisms, while homoeologous chromosomes share a common ancestry and are similar but not identical to chromosomes derived from different ancestral species in allopolyploid organisms. Polyploidization sets the stage for dynamic chromosomal evolution. Newly formed polyploids can experience gain (a) or loss (b) of entire chromosomes or segments thereof, affecting gene dosage and expression. Partial chromosome deletions (c) may remove crucial genes or regulatory elements, while amplifications (d) create additional copies with potential functional consequences. Chromosomal rearrangements such as inversions (e) and translocations (f) shuffle gene order and create novel combinations, contributing to the genetic and phenotypic diversity seen in polyploids.
Gene expression changes in polyploids have been reported in multiple studies (Stupar *et al.*, 2007; Grover *et al.*, 2012; Fasano *et al.*, 2016; Visger *et al.*, 2019). In the recently formed allopolyploid *Senecio cambrensis*, massive changes in gene expression (termed ‘transcriptome shock’) were observed in first-generation synthetic hybrids (which are sterile) compared with their parents and with subsequent generations of allopolyploids (which are fertile) after colchicine-induced chromosome doubling (Hegarty *et al.*, 2005, 2006, 2008). Similarly, immediate changes in gene expression were observed in naturally occurring and synthetic *Tragopogon mirus* and *T. miscellus* (Buggs *et al.*, 2009, 2011, 2012). Significant transcriptome repatterning has occurred

following recent allopolyploidy in *Spartina*, where expression changes (consistent with epigenetic and regulatory alterations) that took place in 150–170-year-old hybrids and neoallopolyploid *S. anglica* far exceeded long-term divergent transcriptome evolution in the parents, which themselves are meso-polyploids (Giraud *et al.*, 2021).

In addition to genomic and transcriptomic changes, polyploidy can profoundly influence epigenetic regulation, the heritable modifications to DNA and chromatin that affect gene expression without altering the underlying DNA sequence (Fig. 3). Epigenetic mechanisms, including DNA methylation, histone modifications, and small RNA-mediated silencing, play crucial roles in shaping the

<figure><img src="image_7.png" /><figcaption>**Fig. 3** Polyploidy-induced epigenetic and transcriptome changes. Polyploidization may trigger substantial epigenetic changes, influencing gene expression and shaping the new polyploid's phenotype. (a) Chromatin, the complex of DNA and proteins that packages the genome, undergoes dynamic remodeling in response to polyploidization. (b) DNA methylation, a key epigenetic mark, can be altered, leading to hypermethylation (increased methylation) or (c) hypomethylation (decreased methylation) of specific genomic regions. These changes influence chromatin structure, with hypermethylation typically associated with condensed, closed chromatin and hypomethylation with open chromatin. In the promoter region of genes, DNA methylation changes directly impact the accessibility of transcription factors, thereby regulating gene expression levels. (d) Subgenome expression dominance is observed in some allopolyploids, where one of the parental subgenomes exhibits higher overall gene expression levels compared with the other subgenome, as seen in the left panel, compared with equal expression in the right panel. (e) Homoeolog expression ratio refers to the relative expression levels of homoeologous gene pairs, which originate from different parental subgenomes (A and B) in allopolyploids. In one polyploid (P1), the overall homoeolog expression ratio shows balanced expression, indicating that neither subgenome exhibits significant dominance. However, in the other polyploid (P2), gene expression levels are heavily biased toward subgenome A. Ac, acetylation; Me, methylation.</figcaption></figure>
transcriptome, and ultimately the phenotypic plasticity of
organisms (reviewed in Osborn *et al.*, 2003; Zhang *et al.*, 2018).
Hybridization, a key component of allopolyploid formation, can
lead to immediate genome-wide alterations in DNA methylation
patterns (Madlung *et al.*, 2002; Edger *et al.*, 2017), often associated
with the activation of transposons ('genomic shock' sensu;
McClintock, 1984; de Tomás & Vicient, 2023). Hypermethylation
and hypomethylation events can occur at specific genomic loci,
affecting gene expression and contributing to phenotypic variation
among polyploid individuals (Song & Chen, 2015; Mattei
et al., 2022). Furthermore, changes in histone modifications, such
as acetylation, methylation, and phosphorylation, can influence
chromatin structure and accessibility, thereby regulating gene
expression (Zhang *et al.*, 2018). In the recent allopolyploid
*T. miscellus*, methylation patterns were largely additive of the
parents, although some novel differentially methylated regions
were observed, again illustrating the ability of polyploidy to
generate novelty (Shan *et al.*, 2024).

Small RNAs, including microRNAs and small interfering RNAs, also contribute to the epigenetic regulation of gene expression (Holoch & Moazed, 2015; Cecere, 2021) and may be altered following allopolyploidy (Cavé-Radet et al., 2020, 2023). These small RNAs can target specific mRNAs for degradation or translational repression, thereby fine-tuning gene expression and buffering against potential dosage imbalances resulting from polyploidization (Birchler & Veitia, 2012; Conant et al., 2014). However, while the impact of polyploidy on mRNAs has been studied in various ways across multiple species, how other types of RNAs, including long noncoding RNAs (Palos et al., 2023), evolve following polyploid events remains poorly understood (Mohammadin et al., 2015; Chekanova, 2015). Similarly, beyond a few studies investigating DNA methylation changes in synthetic or naturally established polyploids, most other epigenetic markers, which may contribute to subgenome differences in accessible chromatin (Fang et al., 2024), have not been thoroughly studied nor in a holistic framework. Overall, the genetic and epigenetic changes that occur in polyploids are complex and multifaceted, reflecting the dynamic interplay between genomic and epigenomic processes. Understanding these changes is crucial for unraveling the evolutionary significance of polyploidy and its implications for biodiversity, adaptation, and speciation.

* There appear to be some ‘rules’ to polyploidy, including immediate regulatory/expression changes and instantaneously (or nearly so) inherited traits; these changes may affect the long-term evolutionary fate of polyploid genomes (i.e. subgenome dominance, fractionation – the loss of duplicate gene copies – and concomitant genome size reduction).

* Many questions remain:

* How does a newly formed cell in an allopolyploid control divergent (epi)genetic programs?

* Do parental subgenomes exhibit distinct spatial organization within the nucleus, occupying different nuclear domains?

* Which (epi)genetic changes contribute to specific observed phenotypic changes?

* What proportion of subfunctionalization among retained duplicated genes is attributable to changes in regulatory sequences vs changes in protein-coding sequences?

### III. Role of hybridization vs genome doubling

#### 1. Assessing the relative impacts of hybridization and genome duplication

Allopolyploid speciation involves two distinct processes: the merger of divergent genomes (resulting from hybridization); and genome duplication. These processes may have different consequences that may be detected at both the phenotypic and the genetic/genomic levels. Neopolyploids provide critical information for disentangling these impacts, in which a naturally formed homoploid hybrid may be compared with its derived allopolyploid. In the recently formed polyploids reviewed here, both hybridization and genome doubling *per se* have played important roles.

This twofold effect of hybridization and chromosome doubling was first observed through studies of gene expression in the neoallopolyploid *Senecio cambrensis* (6x), its immediate triploid progenitor, S. × *baxteri* (3x), and its parental species S. vulgaris (4x) and S. squalidus (2x) (Hegarty *et al.*, 2005, 2006, 2008). The greatest transcriptome shock was observed in the F₁ triploid hybrids. This hybridization effect was ameliorated following chromosome doubling, an effect seen in wild S. cambrensis and in the first and subsequent generations of synthetic 'S. cambrensis' (Hegarty *et al.*, 2005, 2006, 2008); after five generations, the synthetic allopolyploids displayed patterns of gene expression similar to wild S. cambrensis, indicating that chromosome doubling had a secondary ('calming') effect on changed patterns of gene expression that was detectable in the first synthetic (S₁) generation (Hegarty *et al.*, 2006, 2008). This two-fold effect on gene expression – transcriptome shock followed by a chromosome doubling effect – has subsequently been observed in other systems, including our other focal species (e.g. *Tragopogon* (Buggs *et al.*, 2011; Yoo *et al.*, 2024) and *Spartina* (Chelaifa *et al.*, 2010; Ferreira de Carvalho *et al.*, 2017; Giraud *et al.*, 2021), and *Mimulus* (Edger *et al.*, 2017)).

The neoallopolyploid *Spartina anglica* is hardly distinguishable morphologically from its hybrid parent S. × *townsendii* (Huska *et al.*, 2016; Wong *et al.*, 2018; Granse *et al.*, 2021). Transcriptome shock was observed in *Spartina* with an impact on various stress-related genes (Chelaifa *et al.*, 2010). Genome doubling *per se* induces additional expression changes, with 33% differentially expressed genes between the *Spartina* hybrid and the allopolyploid (Giraud *et al.*, 2021). Notably, the number of genes mimicking the maternal (S. *alterniflora*) expression pattern and the number of *transgressively* expressed genes increased in S. anglica (Giraud *et al.*, 2021). Downregulation of transposable elements (TEs) was detected in hybrids, and this downregulation is accentuated following allopolyploidy (Giraud *et al.*, 2021). In *Spartina*, hybridization seems to have played a more important role in methylation changes than genome doubling (Salmon *et al.*, 2005). Small RNAs are also involved in this differential regulation between hybridization and polyploidy for both ra-siRNAs (targeting repetitive sequences) and miRNA targeting genes (Cavé-Radet *et al.*, 2019, 2020). Both hybridization and genome doubling have important transcriptomic effects, but these differ in nature and intensity. Morphological and genomic changes differed between
the two independently formed hybrids from the UK and France (Salmon *et al.*, 2005; Giraud *et al.*, 2021).

In *Tragopogon*, transcriptome shock occurs in F₁ hybrids; major expression changes were detected following both hybridization and genome doubling (Buggs *et al.*, 2011; reviewed in Soltis *et al.*, 2012). Genome doubling has a major impact and is accompanied by gene silencing and homoeolog loss as well as chromosomal changes (translocations, reciprocal, and nonreciprocal aneuploidy; Buggs *et al.*, 2009, 2011, 2012, 2014; Chester *et al.*, 2012, 2015). The differential effects of hybridization and polyploidy are also observed on the proteome in *Tragopogon* (Koh *et al.*, 2012).

Transcriptome changes were also observed in synthetic F₁ interspecific hybrids in *Mimulus*, with higher expression levels skewed toward one of the parental species (Edger *et al.*, 2017). The dominance of gene expression observed in the F₁ interspecific hybrid further amplified in the first-generation synthetic polyploid, reaching the greatest difference between subgenomes in the naturally occurring 140-year-old allopolyploid. Furthermore, the dominantly expressed subgenome has a significantly lower density of TEs near genes compared with the ‘submissive’ subgenome (Edger *et al.*, 2017). Methylated TEs may decrease the expression of adjacent genes, potentially through methylation ‘spill-over’ and/or accompanying chromatin alterations that restrict access to transcription factors (Hollister & Gaut, 2009; Woodhouse *et al.*, 2014). In *Mimulus*, the remodeled methylation patterns of TEs subsequent to the initial interspecific hybridization mirrored the expression levels of nearby genes, providing additional support for the association between methylated TEs and subgenome expression dominance (Alger & Edger, 2020). This observation prompts the question of whether subgenome dominance is inherently predetermined based on subgenome differences in methylated TE density in specific hybrids or polyploid species; this aspect appears to not have been thoroughly assessed. However, in six independent resynthesized lines of *Brassica napus*, the same parental species was repeatedly observed to be dominantly expressed, mirroring the results for the c. 7500-year-old naturally established *Brassica napus* (Bird *et al.*, 2021).

A recent study of synthetic *Brassica* allotetraploids challenged the expected negative association between methylated TE load and subgenome expression dominance, finding no evidence to support this relationship (Zhang *et al.*, 2023). However, follow-up studies are needed to verify the DNA methylation patterns for individual TEs using long-read sequencing technologies (or alternative methods), which can provide a more detailed and accurate assessment of epigenetic modifications across these highly repetitive genomic regions. Bisulfite conversion, a common technique used to assess DNA methylation, coupled with the short-read lengths generated by Illumina sequencing, can make it challenging to uniquely align reads to repetitive regions of the genome, hindering accurate methylation analysis in these regions. Importantly, other mechanisms, including *cis-trans* regulatory conflicts, have also been proposed, which are not mutually exclusive, to explain observed subgenome expression dominance patterns (Alger & Edger, 2020). Another major remaining question is whether environmental factors play a role in determining which subgenome attains dominance in certain hybrids and polyploids.

Previous studies have focused on surveying subgenome dominance in a single common environment.

* Both hybridization and genome duplication play major roles in altering gene expression, but these appear to differ in relative timing and intensity from one system to another.

* What is the impact of hybridization and subsequent genome doubling on the proteome, given that nearly all that we know about these events is based on the transcriptome?

* Is subgenome dominance inherently predetermined based on subgenome differences in TE density near genes and/or the methylation status of genes in interspecific hybrids, or is it established in the new polyploid species?

* Why is subgenome dominance not present in some new polyploids (e.g. *Tragopogon*)?

## IV. Genotypic and phenotypic diversity

### 1. Neopolyploids exhibit wide phenotypic variation intermediate between their progenitors

Many established polyploids exhibit wide variation in phenotypes intermediate between (and sometimes even transgressive to) their progenitors, and neopolyploids show a similar tendency. All neopolyploids noted here are known to have various intermediate phenotypes: floral and vegetative organs in *M. peregrinus*, *T. mirus*, *T. miscellus*, and *S. cambrensis*; and ecological niche in *Tragopogon* and *Cardamine*. Concomitantly, intraspecific phenotypic diversity may be extensive. Even though broadly intermediate in phenotype (Abbott & Lowe, 2004), the triploid hybrid, *S. × baxteri*, and the neoallopolyploid, *S. cambrensis*, tend to resemble their tetraploid parent (*S. vulgaris*) more closely in vegetative characters than they do their diploid parent (*S. squalidus*). However, the flower head (capitulum) of *S. cambrensis* is intermediate in size between *S. squalidus* (large) and *S. vulgaris* (small) (Ingram & Noltie, 1984; Abbott & Lowe, 2004; Hegarty *et al.*, 2011). The larger *S. squalidus* capitulum also bears petaloid (ray) flowers around the inner disk flowers. *Senecio × baxteri* and *S. cambrensis* both bear smaller (but variable) ray flowers (Ingram & Noltie, 1984), indicating they have inherited the *Cycloidea*-like genes that control ray flower development from *S. squalidus* (Kim *et al.*, 2008; Zhang *et al.*, 2017; Zhang & Elomaa, 2024). *Senecio squalidus* is outcrossing and strongly self-incompatible, with showy ray flowers attractive to pollinators, whereas tetraploid *S. vulgaris* is an obligate selfer and does not ‘need’ to attract pollinators (Hiscock, 2000; Abbott *et al.*, 2009). Studies of an introgressant hybrid form of *S. vulgaris* bearing ray flowers (*S. vulgaris* var. *hibernicus* (4x)) showed that it is more attractive to potential pollinators than its rayless counterpart (Marshall & Abbott, 1982, 1984a,b), and the same appears to be true for *S. cambrensis* (Hiscock and Abbott, unpublished). While triploid *S. × baxteri* is a sterile triploid, *S. cambrensis* is fully fertile and self-compatible; this fertility and self-compatibility appear in first-generation synthetic allohexaploid *S. cambrensis*, indicating that the self-incompatibility genes inherited from *S. squalidus* are not functional in wild and first-generation synthetic allohexaploids (Hegarty *et al.*, 2005, 2006; Brennan & Hiscock, 2010). This association between self-compatibility and polyploidy appears to
be widespread, with examples of self-incompatible auto- and allopolyploids both having been recorded (Mable, 2004; Brennan & Hiscock, 2010).

In *Mimulus peregrinus*, both natural and synthetic polyploids show a range of phenotypes overlapping the phenotypes of the parents (*M. guttatus* and *M. luteus*, Vallejo-Marín, 2012). Unlike most of the other recent allopolyploids, the sterile triploid intermediate is widespread and well established in the British Isles (Vallejo-Marín & Lye, 2013). This occurrence allows for the comparison of the phenotype and performance of both naturally occurring and synthetically produced triploids. Analyses of climate suitability models suggest that the ecological niche of the natural triploid hybrids coincides with the niche of the introduced populations of its parents, suggesting that it might directly compete with them in the introduced ecological settings (Da Re et al., 2020).

As in other systems, there is a strong asymmetry in the formation of these triploid hybrids. Crosses in which *M. guttatus* is the maternal parent and *M. luteus* the paternal one yield viable seeds, while the opposite cross direction mostly fails (Vallejo-Marín et al., 2016). This asymmetry is reflected in the parentage of naturally occurring triploids, with the vast majority having *M. guttatus* as the maternal parent (Vallejo-Marín et al., 2016). Comparisons of the triploid and allopolyploid lineages show clear evidence of the classic *gigas* effect of genome doubling. Synthetic lines recreating *M. peregrinus* show increased floral and leaf organ size, larger pollen grains, guard cell size, and slower flowering time compared with its triploid versions (Meeus et al., 2020). Importantly, genome doubling in *M. peregrinus* brings an instant increase in sexual fertility, rescuing the sterile triploid from evolutionary oblivion. As in other recent allopolyploids, *M. peregrinus* has originated more than once (Vallejo-Marín et al., 2015). However, these independent origins of *M. peregrinus* are partially interfertile (Vallejo-Marín et al., 2017), demonstrating the potential of parallel evolutionary lines to merge into a single species.

The reason for this phenotypic diversity is not yet clear, but the novel gene expression patterns generated by polyploidization could be a factor, although the causal factor of novel gene expression itself could be diverse, as discussed above. Transcriptomic patterns of polyploids differ from those of their progenitors in most studied cases, resulting in novel phenotypes (Zhao *et al.*, 2023), although the quantity and the pattern of change vary according to species. A spectrum of subgenome expression dominance has been reported for neoallopolyploid plants, ranging from nearly a complete lack (e.g. *Tragopogon*) to significant levels following hybridization (e.g. *Mimulus*).

At least two complementary models have been proposed to explain the spectrum of subgenome dominance observed in allopolyploids (see reviews Woodhouse et al., 2014; Bird et al., 2018; Alger & Edger, 2020). Both differences in methylated TEs near genes and genetic divergence (e.g. *cis*-regulatory and *trans*-regulatory mismatch conflicts) between subgenomes contributed by the diploid progenitors have been proposed as explanations that may contribute to the rapid emergence of subgenome dominance. Subgenome expression dominance in the earliest generations can ultimately lead to asymmetric evolutionary patterns between subgenomes over deeper time, including differences in fractionation (e.g. gene loss; Schnable

*et al.*, 2011), tandem duplication rates (Edger *et al.*, 2019), selective sweeps (Hardigan *et al.*, 2021), and ultimately phenotypic variation (Renny-Byfield *et al.*, 2017; Qi *et al.*, 2021). Nevertheless, the balanced expression at the subgenome level does not necessarily mean a simple intermediate phenotype. The alteration of the expression pattern of a few key regulatory gene(s) could lead to phenotypic diversity or novel phenotypes. Multiple causal factors, including *trans*-regulations between subgenomes and epigenetic regulation could contribute to phenotypic diversity, as well as spatial- and temporal-specific expression differences between or among homoeologs (Eckardt, 2014; Colle *et al.*, 2019; Zhao *et al.*, 2020).

The novel phenotypes in allopolyploids typically appear where the progenitors have very distinct phenotypes. These phenotypes would have evolved by the distinct adaptations of the progenitors to different ecological niches, pollinators, or geographical distributions, or by genetic drift due to reduced population sizes during neopolyploid establishment. In this process, the relevant genes would have acquired different patterns of genetic and/or epigenetic regulations. At the merger of the genomes of the progenitors, these genes might be the most sensitive to the new *trans*-regulation from the counterpart subgenomes. Despite this speculation, few studies have directly connected a novel phenotype with gene expression patterns (Zhao *et al.*, 2023). As an example, in the transcriptome analysis of *Cardamine* allopolyploids that clearly differ in habitat from their progenitors, many functional genes that potentially contribute to environmental tolerance showed significant homoeolog-specific changes in expression ratio that correspond to differences in environmental conditions (Sun *et al.*, 2020; Akiyama *et al.*, 2021).

* Novelty, as well as intermediacy, in morphology, physiology, and gene expression are all features of new polyploids.

* What are the underlying (epi)genetic factors that determine the phenotypic diversity of new polyploids?

* What are the parental genome features that most likely contribute to the appearance of novel traits in a polyploid derivative?

V. Reproduction

1. The mating systems of new polyploids

Clonal propagation and self-compatibility are typical characteristics of polyploid species, both of which may facilitate reproduction and avoidance of minority cytotype exclusion (Levin, 1975; Comai, 2005; Shimizu, 2022). The triploid *Cardamine insueta* indeed propagates vegetatively as a form of clonal propagation, although sexual reproduction is possible despite low fertility (Urbanska *et al.*, 1997). Furthermore, one of its progenitor species, *C. rivularis*, can propagate vegetatively via ectopic meristem formation on leaves. A transcriptomic study showed that the expression of stem cell genes, including *SHOOT MERISTEM-LESS*, in leaf tissues was inherited from *C. rivularis* (Sun *et al.*, 2020). These data suggest that clonal propagation of *C. insueta* could have been instantaneously established at the polyploidization event through inheritance of the trait of a progenitor species, contributing to the survival of this species despite its odd ploidy.
The transition from outcrossing with self-incompatibility to self-fertilization is one of the most frequent evolutionary transitions in flowering plants, and it is a typical characteristic of polyploid species (Shimizu & Tsuchimatsu, 2015). Studies using synthetic and natural polyploid species, such as *Arabidopsis kamchatica* and *A. suecica* showed the dominant inheritance of self-compatibility through epigenetic small RNA regulation (Kolesnikova et al., 2023; Yew et al., 2023), suggesting that allopolyploid plants can obtain self-compatibility instantaneously. This is the case in the self-compatible allohexaploid *Senecio cambrensis*, but through the intermediate sterile triploid hybrid S. × baxteri, which is an annual and unable to propagate clonally. Treating the branch shoots of synthetic triploid hybrids with colchicine to induce chromosome doubling generates hexaploid branches that produce fertile flower heads that produce seeds that germinate to form fully fertile, self-compatible allohexaploids (Hegarty et al., 2005, 2006). However, in subsequent generations of some synthetic allohexaploid lines, a few individuals express self-incompatible phenotypes (Brennan & Hiscock, 2010), suggesting that the self-incompatibility haplotype inherited from the self-incompatible diploid parent, *S. squalidus*, was not completely (epi)genetically repressed. This may reflect the different mechanisms of sporophytic self-incompatibility operating in Asteraceae (*Senecio*) and Brassicaceae (*Cardamine*) (Allen et al., 2011). A summary of what is known about mating systems for each neopolyploid species highlighted in this review is provided in Supporting Information Table S1.

Lastly, the molecular basis underlying the variation in mating systems (selfing vs outcrossing) observed in the neopolyploids reviewed here remains poorly understood. However, studies in other species, such as *Arabidopsis kamchatica* and *A. suecica*, suggested that dominance regulation through small RNA can facilitate the evolution of self-compatibility (Kolesnikova et al., 2023; Yew et al., 2023). Furthermore, it is likely that selfing confers a greater probability of survival for neopolyploids, especially annuals lacking asexual reproduction, by circumventing the challenges of finding compatible mates. This advantage may be particularly crucial for annual neopolyploids with limited time for reproduction and dispersal.

* The transition from outcrossing to self-fertilization is a typical feature of polyploid evolution.

* What are the various mating system mechanisms operating in different polyploid systems, and are these features lineage-dependent (i.e. at the clade levels corresponding to family or order)?

* What is the timeframe for shifts in mating systems in polyploid lineages?

# VI. Repeated evolutionary experiments

## 1. Does evolution repeat itself?

Several of the recently formed polyploids have formed multiple times in nature: *Senecio cambrensis*, *Tragopogon mirus*, *T. miscellus*, *Cardamine insueta*, and *Mimulus peregrinus*. The parents of *Spartina anglica* have hybridized twice in Europe, forming two established F₁ hybrid populations, but only one

event was followed by genome doubling. *Mimulus peregrinus* has formed twice, once in mainland Scotland and a second time in the Orkney islands, with genetic analyses showing that each origin is derived from local, sterile triploid hybrids (Vallejo-Marin *et al.*, 2015). In the *Tragopogon* allopolyploids (which have each formed over 10 times independently; Soltis *et al.*, 1995; Cook & Soltis, 1999; Symonds *et al.*, 2010), evolution has clearly repeated itself across multiple independent formations of the polyploids in nature and across synthetic lines, resulting in repeated changes in patterns of gene silencing and loss, gene expression, reciprocal aneuploidy, and chromosomal translocations (Buggs *et al.*, 2009, 2011, 2012, 2014; Chester *et al.*, 2012, 2015; Soltis *et al.*, 2012).

There were two origins of allohexaploid *Senecio cambrensis* (Abbott *et al.*, 1983; Ashton & Abbott, 1992; Harris & Ingram, 1992). This recent allohexaploid species provides a good example of how the movement of plants by humans can facilitate the evolution of new species via hybridization because the diploid parent of *S. cambrensis*, *S. squalidus* (Oxford ragwort), is itself a recent homoploid hybrid species originating in two gardens in the UK through the introduction of two exotic *Senecio* species, *S. aethnensis* and *S. chrysanthemifolius*, from Sicily in the late 17th century (Nevado *et al.*, 2020). *Senecio squalidus* formed from a hybridization event in the garden of the Duchess of Beaufort at Badminton, Gloucestershire, where both parent plants were growing (Harris, 2002; Nevado *et al.*, 2020). At the start of the 18th century, hybrids were shared with the Oxford Botanic Garden, which was already cultivating *S. chrysanthemifolius* (Harris, 2002). Backcrossing between the hybrid and *S. chrysanthemifolius* over the following 100 years most likely gave rise to *S. squalidus*, which then escaped from the Botanic Garden and spread across the UK via the burgeoning railway lines of the Industrial Revolution (Abbott *et al.*, 2009). On its journey of rapid colonization, *S. squalidus* hybridized with the native weedy species *S. vulgaris* to create two neoallopolyploid species, *S. cambrensis* (6x) and *S. eboracensis* (4x), and a tetraploid introgressant *S. vulgaris* var. *hibernicus* (Abbott *et al.*, 2009). As in *Tragopogon*, repeated patterns of evolution were observed across the natural polyploids *S. cambrensis* and *S. vulgaris* var. *hibernicus*. *S. eboracensis* (now extinct in the wild) appears to have evolved just once, in York (Lowe & Abbott, 2003). These evolutionary events can be repeated in synthetic lines of *S. cambrensis*, where transcriptome shock in triploid hybrids is followed by secondary expression changes induced by chromosome doubling, resulting in gene expression patterns resembling those seen in natural *S. cambrensis* (Hegarty *et al.*, 2006, 2008). As in *Tragopogon*, these data suggest that some aspects of polyploidization at the genetic level are hard-wired and the direct result of the combination/interaction of the parental genomes.

The multiple origins of *Tragopogon* and *Senecio* polyploids also permit examination of the complex scenarios that may occur postrecurrent polyploidization and the subsequent migration of these lineages and possible gene flow between the new polyploid lineages. The complexity of these demographics can be further enhanced by recurrent hybridization between the neopolyploid and one or both diploid parents. In *Tragopogon*, the separate polyploid
formations are largely isolated geographically, but there is some
evidence for gene flow between populations of independent origin
and between allotetraploids and their diploid parents in several
locations (Soltis & Soltis, unpublished data).

In contrast to *Tragopogon* and *Senecio*, the parents of *Spartina anglica* have independently formed F₁ hybrids two times with the same maternal (*S. alterniflora*) and paternal (*S. maritima*) parents, but only one of these hybridizations was followed by genome doubling. In contrast to the examples above, the two hybrids display marked phenotypic differences despite their similar genetic background. Furthermore, the two F₁ hybrids displayed > 25% differentially expressed genes and exhibited different expression patterns (Giraud *et al.*, 2021).

Genetic data indicate there have been at least two independent
origins of the triploid *C. insueta* (Zozomová-Lihová *et al.*, 2014).
Furthermore, pentaploid and hexaploid *C. schulzii* must have
originated through additional hybridization events between
*C. insueta* and the autotetraploid *C. pratensis* (Mandáková
*et al.*, 2013). Interspecific hybridization events have thus been
common in a single small village in the Swiss Alps within just the
past 150 years.

* Some aspects of the evolutionary trajectory of polyploid genomes may be hardwired, repeated across multiple origins of a newly formed polyploid.

* What are the genomic and genetic factors that promote this 'repeatability'?

* Are the outcomes of polyploidization predictable based on features of the parents?

* What are the trajectories of separate polyploid formations through time? Will they diverge in response to selective pressures?

VII. New polyploids afford unique opportunities to distinguish inherited traits and rapid evolution

When studying established polyploid species, it is not easy to
distinguish whether a new trait in the polyploid evolved
instantaneously at the time of polyploidization, through rapid
evolution following polyploidization, or more gradually since
polyploid formation. Contemporary speciation provides a unique
opportunity to observe the exact environmental differences
between progenitor and polyploid species. For example, niche
differentiation and the origin of clonal propagation in *C. insueta*
were important key traits for the establishment of this allopolyploid
species and appear to have occurred instantaneously with its
formation. More generally, the traits of progenitor species can be
transmitted to newly formed allopolyploids unless the traits are
recessive. These observations highlight an important gap in our
current observations: we are observing only established contem-
porary species and current phenotypic variation, but those species
and traits that we observe, such as niche divergence and
reproductive shifts, must have been selected as advantageous traits
for the polyploid among many more unobserved polyploidization
events. Larger-scale field observations, including ‘unsuccessful’
polyploidization events, are essential for understanding both the
rate of formation and the adaptation of incipient polyploid species.
The studies of contemporary polyploidy provide direct support

for the importance of inherited and merged traits observed in
established polyploid species (Akiyama *et al.*, 2021; Shimizu,
2022).

* Some traits (morphological, mating system, and habitat) are instantaneously inherited.

* Most polyploidizations fail. What are the main causal factors leading to the successful vs unsuccessful survival of newly formed polyploids?

VIII. Changes through time – newly formed vs older polyploids

1. Assessing whether changes in new polyploids reflect patterns in older established polyploids

The extent to which changes observed in young polyploids reflect
patterns seen in more established, older polyploid systems is
unknown and understudied. Are phenomena that characterize older
polyploids already present in the early generations following
polyploid formation, and at what rates do such phenomena change
as polyploids age? For example, if there are initial changes in cell size
associated with genome doubling and possible resulting changes in
organ size, how do these properties change through time?
Experimental studies with natural and resynthesized polyploids have
established that cell size (pollen size, guard cell size) often increases
with genome doubling (Stebbins, 1971; Doyle & Coate, 2019).
Changes in cell size also translate in immediate gains in organ size and
in slower developmental times (Levin, 1983; Soltis *et al.*, 2014). For
example, in both auto- and allopolyploid *Mimulus*, genome
doubling in natural and synthetic lineages results in polyploids with
larger flowers, leaves, and stems but which take longer to flower and
produce fewer flowers (Simón-Porcar *et al.*, 2017; Meeus
*et al.*, 2020). Whether the gigas effect is persistent over evolutionary
time or how it might contribute to differences in the performance of
polyploids (Maherali *et al.*, 2009) is not well understood. Variation
in fertility among newly formed polyploids has also long been of
interest, with recent insights emerging from analyses of synthetic
Arabidopsis autopolyploids (Westermann *et al.*, 2024).

Efforts to approach morphological and genetic/genomic
change through time have involved analysis of related natural
polyploids in the same genus of greater age (Mavrodiev
et al., 2015; Boatwright et al., 2021) or synthetic generations
through time (e.g. Gaeta et al., 2007; Spoelhof et al., 2017;
Jordon-Thaden et al., 2023), but more work is needed. Polyploid
genomes undergo evolutionary changes, including gene loss,
leading to divergence from the initial polyploid state. Genome
fractionation (loss) is evident even at the very early stages of
polyploid evolution. For example, in *Tragopogon* and *Senecio*,
gene loss and silencing as well as chromosomal change are present
in both naturally occurring populations and the first few
generations of synthetic polyploids (Hegarty et al., 2005, 2006,
2008; Buggs et al., 2009, 2012). Furthermore, these changes
continue through time, as observed via analysis of older polyploids
and their diploid parents (Mavrodiev et al., 2015; Boatwright
et al., 2021). The rapid loss of DNA content in young polyploids
signals the dynamic nature of genome evolution in young
*Tragopogon* allotetraploids. Moreover, these changes through time have been reported more broadly in other plants, as well as in animals and yeast (Mayfield-Jones *et al.*, 2013).

* What is the extent to which changes in old polyploids reflect patterns in young polyploids?

* What general patterns govern the retention and loss of genetic content, as well as the role of the environment in driving patterns of genome evolution?

* Is there evidence of selection for the retention of one parental copy over the other?

* Are there biases on which parental gene copy is lost? Can these biases be predicted?

## IX. Every polyploid tells a story

### 1. Each new polyploid species has unique characteristics

Although we have stressed commonalities among the newly formed polyploids, there are many differences among each of these young species. Each new polyploid is an individual story in the early stages of evolution and therefore merits more investigation. In some of the new polyploids, there is a parental genome bias, whereas in others this is not the case (as described in the previous section). In some cases, hybridization seems to play a more significant role than genome doubling, but the relative roles differ from one recent polyploid to the next. In some cases, gene loss seems to predominate, whereas in other recent polyploids, gene silencing is more prevalent. Some new polyploids exhibit immediate chromosomal changes (e.g. structural rearrangements and chromosome content), while others show no evidence that this occurs immediately. However, there are gaps in our understanding of these properties because these neopolyploids have not been investigated in a concerted fashion. Different investigators have focused on different aspects of the polyploidy process (Table S1).

* New polyploids should be compared for the same processes using the same methods, with similar quality reference genomes, to address a consistent suite of questions, providing a foundational model study.

* What features of the parental genomes are the major drivers of change in newly formed polyploid genomes?

* Are there lineage (phylogenetic) effects, that is, do some clades have different drivers than others?

* What aspects of polyploidization are hard-wired and determined by features in the parental genomes?

## X. Factors of formation

### 1. New polyploids often form as a result of human activities

A consistent theme in the formation of these recently formed allopolyploid species is that all have formed as a result of human intervention and disturbance (Vallejo-Marín & Hiscock, 2016). *Spartina anglica* formed following the introduction of one parent from its native range in eastern North America to marshes in Europe (Ainouche *et al.*, 2004). The story is similar, but more complex, in the formation of *Senecio cambrensis*, with one parent

being a recent homoploid hybrid species that arose through hybridization between two *Senecio* species introduced to the UK from Sicily, and the other being a native tetraploid species (Abbott *et al.*, 2009; Nevado *et al.*, 2020).

In both allopolyploid *Mimulus peregrinus* and the two neotetraploid Tragopogons, all of the diploid parents are examples of intercontinental movement of plants by humans. In *Mimulus*, diploid parents were transported from North America to the UK as ornamentals (Vallejo-Marín, 2012). Both *Tragopogon mirus* and *T. miscellus* formed in the western United States following the introduction of the three diploid parents from Eurasia. One diploid parent, *T. porrifolius*, was likely deliberately introduced as a food plant, and the other two (*T. dubius* and *T. pratensis*) were likely accidentally introduced, perhaps with contaminated grain (Soltis *et al.*, 2023).

Most of these systems present an ethical dilemma in that the allopolyploids are native (and sometimes rare) species in their area of formation, but one or both parents are exotic: thus, do the polyploids merit protection or eradication? In contrast to the other recently formed polyploids, *Cardamine insueta* formed from species native to Switzerland, but nonetheless, because of human disturbance. The new polyploids formed in the Swiss Alps following deforestation and land use change to grazing, bringing into contact diploid progenitors with different ecological niches (Urbanska-Worytkiewicz & Landolt, 1972; Urbanska-Worytkiewicz & Landolt, 1974).

Given the increased tempo of human movement and migration, how many more similar scenarios will we observe in the coming decades? Indeed, how many other new polyploids have already formed via human-mediated transport to new ranges, disturbances and land use changes but have not been detected (Vallejo-Marín & Hiscock, 2016)? It is easy to imagine many new polyploids going undetected, and we emphasize that all the recently formed polyploids addressed in this paper were detected and described by highly observant systematists, cytogeneticists, and naturalists.

* Human disturbance creates opportunities for new polyploids to form.

* How many other new polyploids have formed that we (the botanical community) have missed?

* What are the implications of global change and increased human-mediated disturbance - will there be more opportunities for new polyploidizations?

## XI. Major gaps: other facets of evolution to be learned from new polyploids

### 1. Current work sets the stage for future studies

Despite the intensive efforts to understand the ecological and evolutionary advantages of polyploids, there remain gaps in our knowledge. First is the measurement of key traits and environments *in natura*, or in naturally fluctuating environments (Shimizu *et al.*, 2011; Kudoh, 2016). Our knowledge of the ecology and ecophysiology of the young polyploids considered here and their parents is limited. Contemporary speciation provides a unique
opportunity to measure key traits and environments relevant to the
speciation between progenitors and the polyploid species at the
place and time of birth. For example, habitat differences
accompanying the speciation of *C. insueta* support an interpreta-
tion of instantaneous niche differentiation. In addition to visible
phenotypes, for example morphology and preference for a specific
ecological factor, less visible factors that could contribute to the
speciation of polyploids also likely exist. These factors may include
the phenotypic traits affecting interactions with other species, such
as pollinators, pathogens, or herbivores. In *Cardamine*, two origins
of the triploid *C. insueta* and the subsequent cross with *C. pratensis*
to form *C. schulzii* were reported (Mandáková *et al.*, 2013;
Zozomová-Lihová *et al.*, 2014). Three allopolyploidization events
in the past 150 years suggest that pollination of different species is
not specific, an inference that can be tested by *in situ* observation.
Another critical gap is the lack of knowledge connecting the
genome, epigenome, transcriptome, and phenome. We have many
examples in which this connection is clear via intensive studies
using model species, but for most traits, there is a lack of
understanding of the genetic mechanism(s) controlling those traits,
particularly in nonmodels, such as the new polyploids emphasized
here. We propose that a study focusing on a phenotypic difference
between a new polyploid and its progenitors could provide a good
opportunity to reveal such mechanisms.

* We have learned a lot in the study of newly formed polyploids, but major gaps remain.

* What are the ecophysiological consequences of polyploidy? Such data are lacking for most new polyploids.

* Do the transcriptomic changes observed reflect the proteome? We know very little about changes at the protein level.

* What are the interactions between new polyploids and other species, such as pollinators, herbivores, fungi, and bacteria?

* Which (epi)genetic changes have contributed to the observed phenotypic changes of specific traits in neopolyploids?

XII. Conclusions

To facilitate a comparative analysis across the species discussed, we
have included Table S1, which summarizes the current state of
knowledge for each species regarding the key topics covered in this
review. However, we acknowledge the inherent limitations of
drawing unified conclusions across such diverse model systems,
given the variation in research objectives and methodologies.
Nonetheless, this table provides a concise overview of key findings
and highlights areas where further research is needed to address
knowledge gaps and move toward a more generalized under-
standing of polyploid evolution.

Polyploidy has played a significant role in the evolution of life.
While most polyploid species studied to date are ancient, a few
model neopolyploid plant species have emerged, offering unique
opportunities to study the immediate impacts of genome doubling
in nature. Previous studies on diverse neopolyploids have revealed
complex genetic and epigenetic changes, including altered gene
dosage and expression, DNA methylation patterns, and transposon
activity. Both hybridization and genome doubling contribute to
these changes, but their relative impact varies among different

allopolyploid species. Interspecific hybridization can induce
significant transcriptome shock, while genome doubling may lead
to further alterations in gene expression and epigenetic modifica-
tions. Interestingly, some polyploids exhibit subgenome expression
dominance, where one parental subgenome is more highly
expressed than the other subgenome(s). This dominance may be
influenced by the density of certain TEs and potentially by
environmental factors.

Despite significant advances in understanding polyploid evolu-
tion, many knowledge gaps remain. These include the extent of
epigenetic changes in influencing subgenome expression dom-
inance, stabilizing the newly formed nucleus following transcrip-
tome shock, and ultimately shaping the proteome. Addressing these
gaps will enhance our understanding of polyploid evolution, and its
impact on observed phenotypic variation, adaptation, and
speciation.

Newly formed polyploids may exhibit diverse phenotypic
variation, often intermediate to their progenitors' phenotypes.
This diversity can be observed in morphology, physiology, and
gene expression, with some polyploids displaying novel traits.
The underlying mechanisms driving this diversity are still
unclear, but novel gene expression patterns and epigenetic
modifications may play a role. While some polyploids (e.g.
*Spartina anglica*, *Tragopogon mirus*, and *T. miscellus*) have
successfully expanded their ranges and outcompeted parental
species, others (e.g. *Senecio cambrensis*) face challenges in
establishing and maintaining populations due to competition
and extensive niche overlap with their parents. Niche differentia-
tion is crucial for polyploid establishment and persistence.
Previous studies on neopolyploids, such as *T. mirus*, *T. miscellus*,
and *Cardamine insueta*, highlight the importance of both abiotic
and biotic factors in shaping their ecological niches. Future
studies to gain an improved understanding of the complex
interplay between genotype, phenotype, and environment in
neopolyploids are crucial for predicting their evolutionary
trajectories and ecological impacts.

Polyploidy has not only played a significant role in the
evolution of plants, contributing to the splendid diversity in
nature, but has also been leveraged for agriculture over the past
several thousand years. Allopolyploidization can lead to hybrid
vigor, which may be expressed as larger plant or organ sizes,
extended blooming periods, increased yield, and improved crop
quality. Neopolyploids often exhibit enhanced tolerance to
diverse environmental conditions, making them adaptable to
different climates and soils. This adaptability is crucial in the face
of climate change and can contribute to climate-resilient
agriculture, agricultural productivity, and sustainability. The
study of naturally occurring polyploids provides a valuable
template for understanding how polyploidy can be further
leveraged in agriculture. However, current breeding practices
often select against diversity, limiting the potential benefits of
polyploidy. By adopting a more holistic approach, informed by
the study of naturally formed neopolyploids, breeders can
 harness the full potential of polyploidy to develop resilient, high-
performing crops and ornamental plants that meet the diverse
needs of industry, consumers, and the environment.
## Acknowledgements

This review is dedicated to the life and work of our colleague and friend Richard Abbott, who was a pioneer in the field of hybrid speciation. Many of his insights stemmed from his research on the recent origins of new allopolyploid species of *Senecio*, for which he will be most remembered. Richard was an inspiration to researchers in this field, making this review a fitting way to pay tribute to his life's work. This work was supported, in part, by an OPUS grant from the US National Science Foundation, DEB-2043478, to DES and PSS. This work was also supported by the US National Science Foundation grant IOS-2029959 and IOS-1929982 to PPE, Swiss National Science Foundation 310030_212674 to RS-I, CNRS-Rennes University funding to MA and AS, IRN-POLYDIV (polyploidy and biodiversity) project funding to MA and AS, 310030_212551 to KKS, UZH Global Strategy and Partnerships Funding Scheme of the University of Zurich to KKS, Japan Society for the Promotion of Science 22H05179 and 23K23582 and Global Affairs of the University of Zurich to KKS.

## Competing interests

None declared.

## Author contributions

PPE, DES, SY, MV-M, RS-I, KKS, AS, SH, MA and PSS contributed to the planning and writing of the manuscript.

## ORCID

Malika Ainouche ID https://orcid.org/0009-0004-6979-3405

Patrick P. Edger ID https://orcid.org/0000-0001-6836-3041

Simon Hiscock ID https://orcid.org/0000-0003-0954-0540

Armel Salmon ID https://orcid.org/0000-0003-4479-0801

Kentaro K. Shimizu ID https://orcid.org/0000-0002-6483-1781

Douglas E. Soltis ID https://orcid.org/0000-0001-8638-4137

Pamela S. Soltis ID https://orcid.org/0000-0001-9310-8659

Mario Vallejo-Marin ID https://orcid.org/0000-0002-5663-8025

## References

Abbott RJ, Brennan AC, James JK, Forbes DG, Hegarty MJ, Hiscock SJ. 2009. Recent hybrid origin and invasion of the British Isles by a self-incompatible species, Oxford ragwort (*Senecio squalidus* L., Asteraceae). *Biological Invasions* 11: 1145–1158.

Abbott RJ, Ingram R, Noltie HJ. 1983. Discovery of *Senecio cambrensis* Rosser in Edinburgh. *Watsonia* 14: 407–408.

Abbott RJ, Lowe AJ. 2004. Origins, establishment and evolution of new polyploid species: *Senecio cambrensis* and S. eboracensis in the British Isles. *Biological Journal of the Linnean Society. Linnean Society of London* 82: 467–474.

Ainouche ML, Baumel A, Salmon A, Yannic G. 2004. Hybridization, polyploidy and speciation in *Spartina* (Poaceae). *New Phytologist* 161: 165–172.

Akiyama R, Sun J, Hatakeyama M, Lischer HEL, Briskine RV, Hay A, Gan X, Tsiantis M, Kudoh H, Kanaoka MM et al. 2021. Fine-scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species. *New Phytologist* 229: 3587–3601.

Alger EI, Edger PP. 2020. One subgenome to rule them all: underlying mechanisms of subgenome dominance. *Current Opinion in Plant Biology* 54: 108–113.

Allen AM, Thorogood CJ, Hegarty MJ, Lawyer C, Hiscock SJ. 2011. Pollen-pistil interactions and self-incompatibility in the Asteraceae: new insights from studies of *Senecio squalidus* (Oxford ragwort). *Annals of Botany* 108: 687–698.

Ashton PA, Abbott RJ. 1992. Multiple origins and genetic diversity in the newly arisen allopolyploid species, *Senecio cambrensis* Rosser (Compositae). *Heredity* 68: 25–32.

Bafort Q, Wu T, Natran A, De Clerck O, Van de Peer Y. 2023. The immediate effects of polyploidization of *Spirodela polyrhiza* change in a strain-specific way along environmental gradients. *Evolution Letters* 7: 37–47.

Birchler JA, Veitia RA. 2012. Gene balance hypothesis: connecting issues of dosage sensitivity across biological disciplines. *Proceedings of the National Academy of Sciences, USA* 109: 14746–14753.

Bird KA, Niederhuth CE, Ou S, Gehan M, Pires JC, Xiong Z, VanBuren R, Edger PP. 2021. Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid *Brassica napus*. *New Phytologist* 230: 354–371.

Bird KA, VanBuren R, Puzey JR, Edger PP. 2018. The causes and consequences of subgenome dominance in hybrids and recent polyploids. *New Phytologist* 220: 87–93.

Boatwright JL, Yeh C-T, Hu H-C, Susanna A, Soltis DE, Soltis PS, Schnable PS, Barbazuk WB. 2021. Trajectories of homoeolog-specific expression in allotetraploid *Tragopogon castellanus* populations of independent origins. *Frontiers in Plant Science* 12: 679047.

Brennan AC, Hiscock SJ. 2010. Expression and inheritance of sporophytic self-incompatibility in synthetic allohexaploid *Senecio cambrensis* (Asteraceae). *New Phytologist* 186: 251–261.

Buggs RJA, Chamala S, Wu W, Tate JA, Schnable PS, Soltis DE, Soltis PS, Barbazuk WB. 2012. Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent origin. *Current Biology* 22: 248–252.

Buggs RJA, Doust AN, Tate JA, Koh J, Soltis K, Feltus FA, Paterson AH, Soltis PS, Soltis DE. 2009. Gene loss and silencing in *Tragopogon miscellus* (Asteraceae): comparison of natural and synthetic allotetraploids. *Heredity* 103: 73–81.

Buggs RJA, Wendel JF, Doyle JJ, Soltis DE, Soltis PS, Coate JE. 2014. The legacy of diploid progenitors in allopolyploid gene expression patterns. *Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences* 5: 369.

Buggs RJA, Zhang L, Miles N, Tate JA, Gao L, Wei W, Schnable PS, Barbazuk WB, Soltis PS, Soltis DE. 2011. Transcriptomic shock generates evolutionary novelty in a newly formed, natural allopolyploid plant. *Current Biology* 21: 551–556.

Cavé-Radet A, Giraud D, Lima O, El Amrani A, Ainouche M, Salmon A. 2020. Evolution of small RNA expression following hybridization and allopolyploidization: insights from *Spartina* species (Poaceae, Chloridoideae). *Plant Molecular Biology* 102: 55–72.

Cavé-Radet A, Salmon A, Lima O, Ainouche ML, El Amrani A. 2019. Increased tolerance to organic xenobiotics following recent allopolyploidy in *Spartina* (Poaceae). *Plant Science* 280: 143–154.

Cavé-Radet A, Salmon A, Tran Van Canh L, Moyle RL, Pretorius L-S, Lima O, Ainouche ML, El Amrani A. 2023. Recent allopolyploidy alters *Spartina* microRNA expression in response to xenobiotic-induced stress. *Plant Molecular Biology* 111: 309–328.

Cecere G. 2021. Small RNAs in epigenetic inheritance: from mechanisms to trait transmission. *FEBS Letters* 595: 2953–2977.

Chekanova JA. 2015. Long non-coding RNAs and their functions in plants. *Current Opinion in Plant Biology* 27: 207–216.

Chelaifa H, Monnier A, Ainouche M. 2010. Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species *Spartina × townsendii* and *Spartina anglica* (Poaceae). *New Phytologist* 186: 161–174.

Chester M, Gallagher JP, Symonds VV, da Silva AVC, Mavrodiev EV, Leitch AR, Soltis PS, Soltis DE. 2012. Extensive chromosomal variation in a recently formed natural allopolyploid species, *Tragopogon miscellus* (Asteraceae). *Proceedings of the National Academy of Sciences, USA* 109: 1176–1181.

Chester M, Riley RK, Soltis PS, Soltis DE. 2015. Patterns of chromosomal variation in natural populations of the neoallotetraploid *Tragopogon mirus* (Asteraceae). *Heredity* 114: 309–317.
Colle M, Leisner CP, Wai CM, Ou S, Bird KA, Wang J, Wisecaver JH, Yocca AE, Alger EI, Tang H *et al*. 2019. Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry. *GigaScience* 8: giz012.

Comai L. 2005. The advantages and disadvantages of being polyploid. *Nature Reviews. Genetics* 6: 836–846.

Conant GC, Birchler JA, Pires JC. 2014. Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time. *Current Opinion in Plant Biology* 19: 91–98.

Cook LM, Soltis PS. 1999. Mating systems of diploid and allotetraploid populations of trapogon (Asteraceae). I. Natural populations. *Heredity* 82(Pt 3): 237–244.

Da Re D, Olivares AP, Smith W, Vallejo-Marín M. 2020. Global analysis of ecological niche conservation and niche shift in exotic populations of monkeyflowers (*Mimulus guttatus*, *M. luteus*) and their hybrid (*M. × robertsii*). *Plant Ecology and Diversity* 13: 133–146.

Doyle JJ, Coate JE. 2019. Polyploidy, the nucleotype, and novelty: the impact of genome doubling on the biology of the cell. *International Journal of Plant Sciences* 180: 1–52.

Eckardt NA. 2014. Genome dominance and interaction at the gene expression level in allohexaploid wheat. *Plant Cell* 26: 1834.

Edger PP, Poorten TJ, VanBuren R, Hardigan MA, Colle M, McKain MR, Smith RD, Teresi SJ, Nelson ADL, Wai CM *et al*. 2019. Origin and evolution of the octoploid strawberry genome. *Nature Genetics* 51: 541–547.

Edger PP, Smith R, McKain MR, Cooley AM, Vallejo-Marín M, Yuan Y, Bewick AJ, Ji L, Platts AE, Bowman MJ *et al*. 2017. Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140-year-old naturally established neo-allopolyploid monkeyflower. *Plant Cell* 29: 2150–2167.

Fang C, Jiang N, Teresi SJ, Platts AE, Agarwal G, Niederhuth C, Edger PP, Jiang J. 2024. Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry. *Nature Communications* 15: 2491.

Fasano C, Direto G, Aversano R, D'Agostino N, Di Matteo A, Frusciante L, Giuliano G, Carputo D. 2016. Transcriptome and metabolome of synthetic Solanum autotetraploids reveal key genomic stress events following polyploidization. *New Phytologist* 210: 1382–1394.

Ferreira de Carvalho J, Boutte J, Bourdaud P, Chelaifa H, Ainouche K, Salmon A, Ainouche M. 2017. Gene expression variation in natural populations of hexaploid and allododecaploid Spartina species (Poaceae). *Plant Systematics and Evolution = Entwicklungsgeschichte und Systematik der Pflanzen* 303: 1061–1079.

Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J. 1999. Preservation of duplicate genes by complementary, degenerative mutations. *Genetics* 151: 1531–1545.

Freeling M. 2017. Picking up the ball at the K/pg boundary: the distribution of ancient polyploids in the plant phylogenetic tree as a spandrel of asexuality with occasional sex. *Plant Cell* 29: 202–206.

Gaeta RT, Pires JC, Iniguez-Luy F, Leon E, Osborn TC. 2007. Genomic changes in resynthesized *Brassica napus* and their effect on gene expression and phenotype. *Plant Cell* 19: 3403–3417.

Giraud D, Lima O, Rousseau-Gueutin M, Salmon A, Aïnouche M. 2021. Gene and transposable element expression evolution following recent and past polyploidy events in *Spartina* (Poaceae). *Frontiers in Genetics* 12: 589160.

Granse D, Suchrow S, Jensen K. 2021. Long-term invasion dynamics of *Spartina* increase vegetation diversity and geomorphological resistance of salt marshes against sea level rise. *Biological Invasions* 23: 871–883.

Grover CE, Gallagher JP, Szadkowski EP, Yoo MJ, Flagel LE, Wendel JF. 2012. Homoeolog expression bias and expression level dominance in allopolyploids. *New Phytologist* 196: 966–971.

Han FP, Fedak G, Ouellet T, Liu B. 2003. Rapid genomic changes in interspecific and intergenic hybrids and allopolyploids of Triticeae. *Genome/National Research Council Canada = Genome/Conseil National de Recherches Canada* 46: 716–723.

Hardigan MA, Lorant A, Pincot DDA, Feldmann MJ, Famula RA, Acharya CB, Lee S, Verma S, Whitaker VM, Bassil N *et al*. 2021. Unraveling the complex hybrid ancestry and domestication history of cultivated strawberry. *Molecular Biology and Evolution* 38: 2285–2305.

Harris S. 2002. Introduction of Oxford ragwort, *Senecio squalidus* L. (Asteraceae), to the United Kingdom.

Harris SA, Ingram R. 1992. Molecular systematics of the genus Senecio L. II: The origin of S. vulgaris L. *Heredity* 69: 112–121.

Hegarty MJ, Barker GL, Brennan AC, Edwards KJ, Abbott RJ, Hiscock SJ. 2008. Changes to gene expression associated with hybrid speciation in plants: further insights from transcriptomic studies in Senecio. *Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences* 363: 3055–3069.

Hegarty MJ, Barker GL, Wilson ID, Abbott RJ, Edwards KJ, Hiscock SJ. 2006. Transcriptome shock after interspecific hybridization in Senecio is ameliorated by genome duplication. *Current Biology* 16: 1652–1659.

Hegarty MJ, Batstone T, Barker GL, Edwards KJ, Abbott RJ, Hiscock SJ. 2011. Nonadditive changes to cytosine methylation as a consequence of hybridization and genome duplication in Senecio (Asteraceae). *Molecular Ecology* 20: 105–113.

Hegarty MJ, Jones JM, Wilson ID, Barker GL, Coghill JA, Sanchez-Baracaldo P, Liu G, Buggs RJA, Abbott RJ, Edwards KJ *et al*. 2005. Development of anonymous cDNA microarrays to study changes to the Senecio floral transcriptome during hybrid speciation. *Molecular Ecology* 14: 2493–2510.

Heslop-Harrison JSP, Schwarzacher T, Liu Q. 2023. Polyploidy: its consequences and enabling role in plant diversification and evolution. *Annals of Botany* 131: 1–10.

Hiscock SJ. 2000. Genetic control of self-incompatibility in *Senecio squalidus* L. (Asteraceae): a successful colonizing species. *Heredity* 85(Pt 1): 10–19.

Hollister JD, Gaut BS. 2009. Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. *Genome Research* 19: 1419–1428.

Holoch D, Moazed D. 2015. RNA-mediated epigenetic regulation of gene expression. *Nature Reviews. Genetics* 16: 71–84.

Huska D, Leitch IJ, de Carvalho JF, Leitch AR, Salmon A, Ainouche M, Kovarik A. 2016. Persistence, dispersal and genetic evolution of recently formed Spartina homoploid hybrids and allopolyploids in Southern England. *Biological Invasions* 18: 2137–2151.

Ingram R, Noltie HJ. 1984. Ray Floret Morphology and the origin of variability in *Senecio cambrensis* Rosser a recently established allopolyploid species. *New Phytologist* 96: 601–607.

Jeffrey Chen Z, Birchler JA. 2013. *Polyploid and hybrid genomics*. Hoboken, NJ, USA: John Wiley & Sons.

Jordon-Thaden IE, Spoelhof JP, Viccini LF, Combs J, Gomez F Jr, Walker I, Soltis DE, Soltis PS. 2023. Phenotypic trait variation in the North American Tragopogon allopolyploid complex. *American Journal of Botany* 110: e16189.

Kim M, Cui M-L, Cubas P, Gillies A, Lee K, Chapman MA, Abbott RJ, Coen E. 2008. Regulatory genes control a key morphological and ecological trait transferred between species. *Science* 322: 1116–1119.

Koh J, Chen S, Zhu N, Yu F, Soltis PS, Soltis DE. 2012. Comparative proteomics of the recently and recurrently formed natural allopolyploid *Tragopogon mirus* (Asteraceae) and its parents. *New Phytologist* 196: 292–305.

Kolesnikova UK, Scott AD, Van de Velde JD, Burns R, Tikhomirov NP, Pfordt U, Clarke AC, Yant L, Seregin AP, Vekemans X *et al*. 2023. Transition to self-compatibility associated with dominant S-allele in a diploid Siberian progenitor of allotetraploid *Arabidopsis kamchatica* revealed by Arabidopsis lyrata genomes. *Molecular Biology and Evolution* 40: msad122.

Kudoh H. 2016. Molecular phenology in plants: in natura systems biology for the comprehensive understanding of seasonal responses under natural environments. *New Phytologist* 210: 399–412.

Levin DA. 1975. Minority cytotype exclusion in local plant populations. *Taxon* 24: 35–43.

Levin DA. 1983. Polyploidy and novelty in flowering plants. *The American Naturalist* 122: 1–25.

Lim KY, Soltis DE, Soltis PS, Tate J, Matyasek R, Srubarova H, Kovarik A, Pires JC, Xiong Z, Leitch AR. 2008. Rapid chromosome evolution in recently formed polyploids in Tragopogon (Asteraceae). *PLoS ONE* 3: e3353.

Lowe A, Abbott R. 2003. A new British species, *Senecio eboracensis* (Asteraceae), another hybrid derivative of *S. vulgaris* L. and *S. squalidus* L. *Watsonia* 24: 375–388.

Lynch M, Conery JS. 2000. The evolutionary fate and consequences of duplicate genes. *Science* 290: 1151–1155.

Lysak MA, Mandáková T, Schranz ME. 2016. Comparative paleogenomics of crucifers: ancestral genomic blocks revisited. *Current Opinion in Plant Biology* 30: 108–115.

Mable BK. 2004. Polyploidy and self-compatibility: is there an association? *New Phytologist* 162: 803–811.
Madlung A. 2013. Polyploidy and its effect on evolutionary success: old questions revisited with new tools. *Heredity* 110: 99–104.

Madlung A, Masuelli RW, Watson B, Reynolds SH, Davison J, Comai L. 2002. Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. *Plant Physiology* 129: 733–746.

Maere S, De Bodt S, Raes J, Casneuf T, Van Montagu M, Kuiper M, Van de Peer Y. 2005. Modeling gene and genome duplications in eukaryotes. *Proceedings of the National Academy of Sciences, USA* 102: 5454–5459.

Maherali H, Walden AE, Husband BC. 2009. Genome duplication and the evolution of physiological responses to water stress. *New Phytologist* 184: 721–731.

Mandáková T, Joly S, Krzywinski M, Mummenhoff K, Lysak MA. 2010. Fast diploidization in close mesopolyploid relatives of Arabidopsis. *Plant Cell* 22: 2277–2290.

Mandáková T, Kovárik A, Zozomová-Líhová J, Shimizu-Inatsugi R, Shimizu KK, Mummenhoff K, Marhold K, Lysak MA. 2013. The more the merrier: recent hybridization and polyploidy in cardamine. *Plant Cell* 25: 3280–3295.

Marshall DF, Abbott RJ. 1982. Polymorphism for outcrossing frequency at the ray floret locus in *Senecio vulgaris*. L. *I*. Evidence. *Heredity* 48: 227–235.

Marshall DF, Abbott RJ. 1984a. Polymorphism for outcrossing frequency at the ray floret locus in *Senecio vulgaris*. L. *II*. Confirmation. *Heredity* 52: 331–336.

Marshall DF, Abbott RJ. 1984b. Polymorphism for outcrossing frequency at the ray floret locus in *Senecio vulgaris*. L. *III*. Causes. *Heredity* 53: 145–149.

Mattei AL, Bailly N, Meissner A. 2022. DNA methylation: a historical perspective. *Trends in Genetics* 38: 676–707.

Mavrodiev EV, Chester M, Suárez-Santiago VN, Visger CJ, Rodriguez R, Susanna A, Baldini RM, Soltis PS, Soltis DE. 2015. Multiple origins and chromosomal novelty in the allotetraploid *Tragopogon castellanus* (Asteraceae). *New Phytologist* 206: 1172–1183.

Mayfield-Jones D, Washburn JD, Arias T, Edger PP, Pires JC, Conant GC. 2013. Watching the grin fade: tracing the effects of polyploidy on different evolutionary time scales. *Seminars in Cell & Developmental Biology* 24: 320–331.

McClintock B. 1984. The significance of responses of the genome to challenge. *Science* 226: 792–801.

Meeus S, Semberová K, De Storme N, Geelen D, Vallejo-Marín M. 2020. Effect of whole-genome duplication on the evolutionary rescue of sterile hybrid monkeyflowers. *Plant Communications* 1: 100093.

Mohammadin S, Edger PP, Pires JC, Schranz ME. 2015. Positionally-conserved but sequence-diverged: identification of long non-coding RNAs in the Brassicaceae and Cleomaceae. *BMC Plant Biology* 15: 217.

Morris JP, Baslan T, Soltis DE, Soltis PS, Fox DT. 2024. Integrating the study of polyploidy across organisms, tissues, and disease. *Annual Review of Genetics* 58: 297–318.

Murat F, Zhang R, Guizard S, Gavranović H, Flores R, Steinbach D, Quesneville H, Tannier E, Salse J. 2015. Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops. *Genome Biology and Evolution* 7: 735–749.

Nevado B, Harris SA, Beaumont MA, Hiscock SJ. 2020. Rapid homoploid hybrid speciation in British gardens: the origin of Oxford ragwort (*Senecio squalidus*). *Molecular Ecology* 29: 4221–4233.

Ohno S. 1970. *Evolution by gene duplication*. Berlin, Heidelberg, Germany: Springer Berlin Heidelberg.

Osborn TC, Pires JC, Birchler JA, Auger DL, Chen ZJ, Lee H-S, Comai L, Madlung A, Doerge RW, Colot V *et al*. 2003. Understanding mechanisms of novel gene expression in polyploids. *Trends in Genetics* 19: 141–147.

Palos K, Yu L, Riley CE, Nelson Dittrich AC, Nelson ADL. 2023. Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs. *Plant Cell* 35: 1762–1786.

Parisod C, Salmon A, Zerjal T, Tenaillon M, Grandbastien M-A, Ainouche M. 2009. Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in *Spartina*. *New Phytologist* 184: 1003–1015.

Pires JC, Zhao J, Schranz ME, Leon EJ, Quijada PA, Lukens LN, Osborn TC. 2004. Flowering time divergence and genomic rearrangements in resynthesized Brassica polyploids (Brassicaceae). *Biological Journal of the Linnean Society. Linnean Society of London* 82: 675–688.

Qi X, An H, Hall TE, Di C, Blischak PD, McKibben MTW, Hao Y, Conant GC, Pires JC, Barker MS. 2021. Genes derived from ancient polyploidy have higher

genetic diversity and are associated with domestication in *Brassica rapa*. *New Phytologist* 230: 372–386.

Renny-Byfield S, Rodgers-Melnick E, Ross-Ibarra J. 2017. Gene fractionation and function in the ancient subgenomes of maize. *Molecular Biology and Evolution* 34: 1825–1832.

Salmon A, Ainouche ML, Wendel JF. 2005. Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). *Molecular Ecology* 14: 1163–1175.

Schnable JC, Springer NM, Freeling M. 2011. Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. *Proceedings of the National Academy of Sciences, USA* 108: 4069–4074.

Shan S, Gitzendanner MA, Boatwright JL, Spoelhof JP, Ethridge CL, Ji L, Liu X, Soltis PS, Schmitz RJ, Soltis DE. 2024. Genome-wide DNA methylation dynamics following recent polyploidy in the allotetraploid *Tragopogon miscellus* (Asteraceae). *New Phytologist* 242: 1363–1376.

Shimizu KK. 2022. Robustness and the generalist niche of polyploid species: genome shock or gradual evolution? *Current Opinion in Plant Biology* 69: 102292.

Shimizu KK, Kudoh H, Kobayashi MJ. 2011. Plant sexual reproduction during climate change: gene function in natura studied by ecological and evolutionary systems biology. *Annals of Botany* 108: 777–787.

Shimizu KK, Tsuchimatsu T. 2015. Evolution of selfing: recurrent patterns in molecular adaptation. *Annual Review of Ecology, Evolution, and Systematics* 46: 593–622.

Simón-Porcar VI, Silva JL, Meeus S, Higgins JD, Vallejo-Marín M. 2017. Recent autopolyploidization in a naturalized population of Mimulus guttatus (Phrymaceae). *Botanical Journal of the Linnean Society. Linnean Society of London* 185: 189–207.

Soltis DE, Buggs RJA, Barbazuk WB, Chamala S, Chester M, Gallagher JP, Schnable PS, Soltis PS. 2012. The early stages of polyploidy: rapid and repeated evolution in Tragopogon. In: Soltis PS, Soltis DE, eds. *Polyploidy and genome evolution*. Berlin, Heidelberg, Germany: Springer Berlin Heidelberg, 271–292.

Soltis DE, Soltis PS, Rieseberg LH. 1993. Molecular data and the dynamic nature of polyploidy. *Critical Reviews in Plant Sciences* 12: 243–273.

Soltis DE, Tate JA, Soltis PS, Symonds VV. 2023. Parental genomic compatibility model: only certain diploid genotype combinations form allopolyploids. *The Nucleus* 66: 371–378.

Soltis DE, Visger CJ, Marchant DB, Soltis PS. 2016. Polyploidy: pitfalls and paths to a paradigm. *American Journal of Botany* 103: 1146–1166.

Soltis PS, Liu X, Marchant DB, Visger CJ, Soltis DE. 2014. Polyploidy and novelty: Gottlieb's legacy. *Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences* 369: 20130351.

Soltis PS, Marchant DB, Van de Peer Y, Soltis DE. 2015. Polyploidy and genome evolution in plants. *Current Opinion in Genetics & Development* 35: 119–125.

Soltis PS, Plunkett GM, Novak SJ, Soltis DE. 1995. Genetic variation in Tragopogon species: additional origins of the allotetraploid in *T. mirus* and *T. miscellus* (compositae). *American Journal of Botany* 82: 1329–1341.

Song Q, Chen ZJ. 2015. Epigenetic and developmental regulation in plant polyploids. *Current Opinion in Plant Biology* 24: 101–109.

Spoelhof JP, Chester M, Rodriguez R, Geraci B, Heo K, Mavrodiev E, Soltis PS, Soltis DE. 2017. Karyotypic variation and pollen stainability in resynthesized allopolyploids *Tragopogon miscellus* and *T. mirus*. *American Journal of Botany* 104: 1484–1492.

Stebbins GL. 1971. *Chromosomal evolution in higher plants*. London, UK: Edward Arnold.

Stupar RM, Bhaskar PB, Yandell BS, Rensink WA, Hart AL, Ouyang S, Veilleux RE, Busse JS, Erhardt RJ, Buell CR *et al*. 2007. Phenotypic and transcriptomic changes associated with potato autopolyploidization. *Genetics* 176: 2055–2067.

Sun J, Shimizu-Inatsugi R, Hofhuis H, Shimizu K, Hay A, Shimizu KK, Sese J. 2020. A recently formed triploid *Cardamine insueta* inherits leaf vivipary and submergence tolerance traits of parents. *Frontiers in Genetics* 11: 567262.

Symonds VV, Soltis PS, Soltis DE. 2010. Dynamics of polyploid formation in Tragopogon (Asteraceae): recurrent formation, gene flow, and population structure. *Evolution: International Journal of Organic Evolution* 64: 1984–2003.

de Tomás C, Vicient CM. 2023. The genomic shock hypothesis: genetic and epigenetic alterations of transposable elements after interspecific hybridization in plants. *Epigenomes* 8: 2.
Urbanska KM, Hurka H, Landolt E, Neuffer B, Mummenhoff K. 1997. Hybridization and evolution in Cardamine (Brassicaceae) at Urnerboden, Central Switzerland: biosystematic and molecular evidence. *Plant Systematics and Evolution* 204:233–256.

Urbanska-Worytkiewicz K, Landolt E. 1972. Natürliche Bastarde zwischen *Cardamine amara* L. und *C. rivularis* Schur aus den Schweizer Alpen. *Berichte des Geobotanischen Institutes der Eidg. Techn. Hochschule Stiftung Rübel* 41: 88–101.

Urbanska-Worytkiewicz K, Landolt E. 1974. Hybridization naturelle entre *Cardamine rivularis* Schur et *C. amara* L., ses aspects cytologiques et écologiques. *Actes de la Societe Helvetique des Sciences Naturelles* 1974: 89–90.

Vallejo-Marín M. 2012. *Mimulus peregrinus* (Phrymaceae): a new British allopolyploid species. *PhytoKeys* 14: 1–14.

Vallejo-Marín M, Buggs RJA, Cooley AM, Puzey JR. 2015. Speciation by genome duplication: Repeated origins and genomic composition of the recently formed allopolyploid species *Mimulus peregrinus*. *Evolution* 69: 1487–1500.

Vallejo-Marín M, Cooley AM, Lee MY, Folmer M, McKain MR, Puzey JR. 2016. Strongly asymmetric hybridization barriers shape the origin of a new polyploid species and its hybrid ancestor. *American Journal of Botany* 103: 1272–1288.

Vallejo-Marín M, Hiscock SJ. 2016. Hybridization and hybrid speciation under global change. *New Phytologist* 211: 1170–1187.

Vallejo-Marín M, Lye GC. 2013. Hybridisation and genetic diversity in introduced *Mimulus* (Phrymaceae). *Heredity* 110: 111–122.

Vallejo-Marín M, Quenu M, Ritchie S, Meeus S. 2017. Partial infertility between independently originated populations of the neo-allopolyploid *Mimulus peregrinus*. *Plant Systematics and Evolution* = *Entwicklungsgeschichte und Systematik der Pflanzen* 303: 1081–1092.

Van de Peer Y, Ashman T-L, Soltis PS, Soltis DE. 2021. Erratum to: polyploidy: an evolutionary and ecological force in stressful times. *Plant Cell* 33: 2899.

Van de Peer Y, Mizrachi E, Marchal K. 2017. The evolutionary significance of polyploidy. *Nature Reviews. Genetics* 18: 411–424.

Visger CJ, Wong GK-S, Zhang Y, Soltis PS, Soltis DE. 2019. Divergent gene expression levels between diploid and autotetraploid Tolmiea relative to the total transcriptome, the cell, and biomass. *American Journal of Botany* 106: 280–291.

Westermann J, Srikant T, Gonzalo A, Tan HS, Bomblies K. 2024. Defective pollen tube tip growth induces neo-polyploid infertility. *Science* 383: eadh0755.

Wong JXW, Costantini F, Merloni N, Savelli L, Geelen D, Airoldi L. 2018. The widespread and overlooked replacement of *Spartina maritima* by non-indigenous *S. anglica* and *S. townsendii* in north-western Adriatic saltmarshes. *Biological Invasions* 20: 1687–1702.

Woodhouse MR, Cheng F, Pires JC, Lisch D, Freeling M, Wang X. 2014. Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids. *Proceedings of the National Academy of Sciences, USA* 111: 5283–5288.

Xiong Z, Gaeta RT, Pires JC. 2011. Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus. *Proceedings of the National Academy of Sciences, USA* 108: 7908–7913.

Yew C-L, Tsuchimatsu T, Shimizu-Inatsugi R, Yasuda S, Hatakeyama M, Kakui H, Ohta T, Suwabe K, Watanabe M, Takayama S et al. 2023. Dominance in self-compatibility between subgenomes of allopolyploid Arabidopsis kamchatica shown by transgenic restoration of self-incompatibility. *Nature Communications* 14: 7618.

Yoo M-J, Koh J, Boatwright JL, Soltis DE, Soltis PS, Barbazuk WB, Chen S. 2024. Investigation of regulatory divergence between homoeologs in the recently formed allopolyploids, Tragopogon mirus and T. miscellus (Asteraceae). *The Plant Journal: For Cell and Molecular Biology* 117: 1191–1205.

Zhang H, Lang Z, Zhu J-K. 2018. Dynamics and function of DNA methylation in plants. *Nature Reviews. Molecular Cell Biology* 19: 489–506.

Zhang K, Zhang L, Cui Y, Yang Y, Wu J, Liang J, Li X, Zhang X, Zhang Y, Guo Z et al. 2023. The lack of negative association between TE load and subgenome dominance in synthesized Brassica allotetraploids. *Proceedings of the National Academy of Sciences, USA* 120: e2305208120.

Zhang T, Elomaa P. 2024. Development and evolution of the Asteraceae capitulum. *New Phytologist* 242: 33–48.

Zhang T, Zhao Y, Juntheikki I, Mouhu K, Broholm SK, Rijpkema AS, Kins L, Lan T, Albert VA, Teeri TH et al. 2017. Dissecting functions of SEPALLATA-like MADS box genes in patterning of the pseudanthial inflorescence of Gerbera hybrida. *New Phytologist* 216: 939–954.

Zhao K, Dong J, Xu J, Bai Y, Yin Y, Long C, Wu L, Lin T, Fan L, Wang Y et al. 2023. Downregulation of the expression of subgenomic chromosome A7 genes promotes plant height in resynthesized allopolyploid *Brassica napus*. *Theoretical and Applied Genetics* 137: 11.

Zhao N, Dong Q, Nadon BD, Ding X, Wang X, Dong Y, Liu B, Jackson SA, Xu C. 2020. Evolution of homeologous gene expression in polyploid wheat. *Genes* 11: 1401.

Zozomová-Lihová J, Krak K, Mandáková T, Shimizu KK, Spaniel S, Vít P, Lysak MA. 2014. Multiple hybridization events in Cardamine (Brassicaceae) during the last 150 years: revisiting a textbook example of neoallopolyploidy. *Annals of Botany* 113: 817–830.

## Supporting Information

Additional Supporting Information may be found online in the Supporting Information section at the end of the article.

<caption>**Table S1** Detailed information on the seven neopolyploid systems featured in this review (*Cardamine*, *Mimulus*, *Spartina*, *Tragopogon*, and *Senecio*), including their genomic characteristics and phenotypic traits.</caption>

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