Does reproductive assurance explain the incidence of polyploidy in plants and animals?

Species delimitation 4.0: integrative taxonomy meets artificial intelligence

Although species are central units for biological research, recent findings in genomics are raising awareness that what we call species can be ill-founded entities due to solely morphology-based, regional species descriptions. This particularly applies to groups characterized by intricate evolutionary processes such as hybridization, polyploidy, or asexuality. Here, challenges of current integrative taxonomy (genetics/genomics + morphology + ecology, etc.) become apparent: different favored species concepts, lack of universal characters/markers, missing appropriate analytical tools for intricate evolutionary processes, and highly subjective ranking and fusion of datasets. Now, integrative taxonomy combined with artificial intelligence under a unified species concept can enable automated feature learning and data integration, and thus reduce subjectivity in species delimitation. This approach will likely accelerate revising and unraveling eukaryotic biodiversity.

Genetic variation in the brooding brittle-star: a global hybrid polyploid complex?

The widespread and abundant brooding brittle-star (Amphipholis squamata) is a simultaneous hermaphrodite with a complex mitochondrial phylogeography of multiple divergent overlapping mtDNA lineages, high levels of inbreeding or clonality and unusual sperm morphology. We use exon-capture and transcriptome data to show that the nuclear genome comprises multiple (greater than 3) divergent (π > 6%) expressed components occurring across samples characterized by highly divergent (greater than 20%) mitochondrial lineages, and encompassing several other genera, including diploid dioecious species. We report a massive sperm genome size in A. squamata, an order of magnitude larger than that present in other brittle-stars, and consistent with our SNP-based measure of greatly elevated ploidy. Similarity of these genetic signatures to well-known animal systems suggests that A. squamata (and related taxa) is a hybrid polyploid asexual complex of variable subgenome origins, ploidy and reproductive mode. We discuss enigmatic aspects of A. squamata biology in this light. This putative allopolyploid complex would be the first to be reported from the phylum Echinodermata.

Local adaptation, recombination, and the fate of neopolyploids

Polyploidy is widely recognized as an important speciation mechanism because it isolates tetraploids from their diploid progenitors. Polyploidy also provides new genetic material that may facilitate adaptive evolution. However, new mutations are more likely to arise after a neopolyploid already has successfully invaded a population. Thus, the role of adaptive forces in establishing a polyploid remains unclear. One solution to this apparent paradox may lie in the capacity of polyploids to suppress recombination among preexisting locally adapted alleles. The local adaptation mechanism requires that spatially heterogeneous selection acts on multiple loci and that gene flow introduces maladapted alleles to the population where the polyploid forms. The mechanism requires neither strong genetic drift nor any intrinsic benefit of genome doubling and can accommodate any mode of gene action. A unique prediction of the mechanism is that adaptive alleles should predate polyploidization, a pattern consistent with observations from a few well-studied polyploids. The mechanism is also consistent with the coexistence of both diploid and tetraploid cytotypes, fitness heterogeneity among independently derived polyploids, and the prevalence of outcrossing among older polyploids. The local adaptation mechanism also makes novel predictions about circumstances favoring polyploid invasions that can be tested using molecular genetic or comparative approaches.

Interspecific transfer of genetic information through polyploid bridges

Hybridization blurs species boundaries and leads to intertwined lineages resulting in reticulate evolution. Polyploidy, the outcome of whole genome duplication (WGD), has more recently been implicated in promoting and facilitating hybridization between polyploid species, potentially leading to adaptive introgression. However, because polyploid lineages are usually ephemeral states in the evolutionary history of life it is unclear whether WGD-potentiated hybridization has any appreciable effect on their diploid counterparts. Here, we develop a model of cytotype dynamics within mixed-ploidy populations to demonstrate that polyploidy can in fact serve as a bridge for gene flow between diploid lineages, where introgression is fully or partially hampered by the species barrier. Polyploid bridges emerge in the presence of triploid organisms, which despite critically low levels of fitness, can still allow the transfer of alleles between diploid states of independently evolving mixed-ploidy species. Notably, while marked genetic divergence prevents polyploid-mediated interspecific gene flow, we show that increased recombination rates can offset these evolutionary constraints, allowing a more efficient sorting of alleles at higher-ploidy levels before introgression into diploid gene pools. Additionally, we derive an analytical approximation for the rate of gene flow at the tetraploid level necessary to supersede introgression between diploids with nonzero introgression rates, which is especially relevant for plant species complexes, where interspecific gene flow is ubiquitous. Altogether, our results illustrate the potential impact of polyploid bridges on the (re)distribution of genetic material across ecological communities during evolution, representing a potential force behind reticulation.

The emerging importance of cross-ploidy hybridisation and introgression

Natural hybridisation is now recognised as pervasive in its occurrence across the Tree of Life. Resurgent interest in natural hybridisation fuelled by developments in genomics has led to an improved understanding of the genetic factors that promote or prevent species cross-mating. Despite this body of work overturning many widely held assumptions about the genetic barriers to hybridisation, it is still widely thought that ploidy differences between species will be an absolute barrier to hybridisation and introgression. Here, we revisit this assumption, reviewing findings from surveys of polyploidy and hybridisation in the wild. In a case study in the British flora, 203 hybrids representing 35% of hybrids with suitable data have formed via cross-ploidy matings, while a wider literature search revealed 59 studies (56 in plants and 3 in animals) in which cross-ploidy hybridisation has been confirmed with genetic data. These results show cross-ploidy hybridisation is readily overlooked, and potentially common in some groups. General findings from these studies include strong directionality of hybridisation, with introgression usually towards the higher ploidy parent, and cross-ploidy hybridisation being more likely to involve allopolyploids than autopolyploids. Evidence for adaptive introgression across a ploidy barrier and cases of cross-ploidy hybrid speciation shows the potential for important evolutionary outcomes.

Polyploidy impacts population growth and competition with diploids: multigenerational experiments reveal key life-history trade-offs

Ecological theory predicts that early generation polyploids ('neopolyploids') should quickly go extinct owing to the disadvantages of rarity and competition with their diploid progenitors. However, polyploids persist in natural habitats globally. This paradox has been addressed theoretically by recognizing that reproductive assurance of neopolyploids and niche differentiation can promote establishment. Despite this, the direct effects of polyploidy at the population level remain largely untested despite establishment being an intrinsically population-level process. We conducted population-level experiments where life-history investment in current and future growth was tracked in four lineage pairs of diploids and synthetic autotetraploids of the aquatic plant Spirodela polyrhiza. Population growth was evaluated with and without competition between diploids and neopolyploids across a range of nutrient treatments. Although neopolyploid populations produce more biomass, they reach lower population sizes and have reduced carrying capacities when growing alone or in competition across all nutrient treatments. Thus, contrary to individual-level studies, our population-level data suggest that neopolyploids are competitively inferior to diploids. Conversely, neopolyploid populations have greater investment in dormant propagule production than diploids. Our results show that neopolyploid populations should not persist based on current growth dynamics, but high potential future growth may allow polyploids to establish in subsequent seasons.

Adaptive responses drive the success of polyploid yellowcresses (Rorippa, Brassicaceae) in the Hengduan Mountains, a temperate biodiversity hotspot

Polyploids contribute substantially to plant evolution and biodiversity; however, the mechanisms by which they succeed are still unclear. According to the polyploid adaptation hypothesis, successful polyploids spread by repeated adaptive responses to new environments. Here, we tested this hypothesis using two tetraploid yellowcresses (Rorippa), the endemic Rorippa elata and the widespread Rorippa palustris, in the temperate biodiversity hotspot of the Hengduan Mountains. Speciation modes were resolved by phylogenetic modeling using 12 low-copy nuclear loci. Phylogeographical patterns were then examined using haplotypes phased from four plastid and ITS markers, coupled with historical niche reconstruction by ecological niche modeling. We inferred the time of hybrid origins for both species as the mid-Pleistocene, with shared glacial refugia within the southern Hengduan Mountains. Phylogeographic and ecological niche reconstruction indicated recurrent northward colonization by both species after speciation, possibly tracking denuded habitats created by glacial retreat during interglacial periods. Common garden experiment involving perennial R. elata conducted over two years revealed significant changes in fitness-related traits across source latitudes or altitudes, including latitudinal increases in survival rate and compactness of plant architecture, suggesting gradual adaptation during range expansion. These findings support the polyploid adaptation hypothesis and suggest that the spread of polyploids was aided by adaptive responses to environmental changes during the Pleistocene. Our results thus provide insight into the evolutionary success of polyploids in high-altitude environments.

Two duplicated gsdf homeologs cooperatively regulate male differentiation by inhibiting cyp19a1a transcription in a hexaploid fish

Although evolutionary fates and expression patterns of duplicated genes have been extensively investigated, how duplicated genes co-regulate a biological process in polyploids remains largely unknown. Here, we identified two gsdf (gonadal somatic cell-derived factor) homeologous genes (gsdf-A and gsdf-B) in hexaploid gibel carp (Carassius gibelio), wherein each homeolog contained three highly conserved alleles. Interestingly, gsdf-A and gsdf-B transcription were mainly activated by dmrt1-A (dsx- and mab-3-related transcription factor 1) and dmrt1-B, respectively. Loss of either gsdf-A or gsdf-B alone resulted in partial male-to-female sex reversal and loss of both caused complete sex reversal, which could be rescued by a nonsteroidal aromatase inhibitor. Compensatory expression of gsdf-A and gsdf-B was observed in gsdf-B and gsdf-A mutants, respectively. Subsequently, we determined that in tissue culture cells, Gsdf-A and Gsdf-B both interacted with Ncoa5 (nuclear receptor coactivator 5) and blocked Ncoa5 interaction with Rora (retinoic acid-related orphan receptor-alpha) to repress Rora/Ncoa5-induced activation of cyp19a1a (cytochrome P450, family 19, subfamily A, polypeptide 1a). These findings illustrate that Gsdf-A and Gsdf-B can regulate male differentiation by inhibiting cyp19a1a transcription in hexaploid gibel carp and also reveal that Gsdf-A and Gsdf-B can interact with Ncoa5 to suppress cyp19a1a transcription in vitro. This study provides a typical case of cooperative mechanism of duplicated genes in polyploids and also sheds light on the conserved evolution of sex differentiation.

Some sexual consequences of being a plant

Plants have characteristic features that affect the expression of sexual function, notably the existence of a haploid organism in the life cycle, and in their development, which is modular, iterative and environmentally reactive. For instance, primary selection (the first filtering of the products of meiosis) is via gametes in diplontic animals, but via gametophyte organisms in plants. Intragametophytic selfing produces double haploid sporophytes which is in effect a form of clonal reproduction mediated by sexual mechanisms. In homosporous plants, the diploid sporophyte is sexless, sex being only expressed in the haploid gametophyte. However, in seed plants, the timing and location of gamete production is determined by the sporophyte, which therefore has a sexual role, and in dioecious plants has genetic sex, while the seed plant gametophyte has lost genetic sex. This evolutionary transition is one that E.J.H. Corner called 'the transference of sexuality'. The iterative development characteristic of plants can lead to a wide variety of patterns in the distribution of sexual function, and in dioecious plants poor canalization of reproductive development can lead to intrasexual mating and the production of YY supermales or WW superfemales. Finally, plant modes of asexual reproduction (agamospermy/apogamy) are also distinctive by subverting gametophytic processes. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.

Retention of duplicated genes in evolution

Gene duplication is a prevalent phenomenon across the tree of life. The processes that lead to the retention of duplicated genes are not well understood. Functional genomics approaches in model organisms, such as yeast, provide useful tools to test the mechanisms underlying retention with functional redundancy and divergence of duplicated genes, including fates associated with neofunctionalization, subfunctionalization, back-up compensation, and dosage amplification. Duplicated genes may also be retained as a consequence of structural and functional entanglement. Advances in human gene editing have enabled the interrogation of duplicated genes in the human genome, providing new tools to evaluate the relative contributions of each of these factors to duplicate gene retention and the evolution of genome structure.

Genomic anatomy of male-specific microchromosomes in a gynogenetic fish

Unisexual taxa are commonly considered short-lived as the absence of meiotic recombination is supposed to accumulate deleterious mutations and hinder the creation of genetic diversity. However, the gynogenetic gibel carp (Carassius gibelio) with high genetic diversity and wide ecological distribution has outlived its predicted extinction time of a strict unisexual reproduction population. Unlike other unisexual vertebrates, males associated with supernumerary microchromosomes have been observed in gibel carp, which provides a unique system to explore the rationales underlying male occurrence in unisexual lineage and evolution of unisexual reproduction. Here, we identified a massively expanded satellite DNA cluster on microchromosomes of hexaploid gibel carp via comparing with the ancestral tetraploid crucian carp (Carassius auratus). Based on the satellite cluster, we developed a method for single chromosomal fluorescence microdissection and isolated three male-specific microchromosomes in a male metaphase cell. Genomic anatomy revealed that these male-specific microchromosomes contained homologous sequences of autosomes and abundant repetitive elements. Significantly, several potential male-specific genes with transcriptional activity were identified, among which four and five genes displayed male-specific and male-biased expression in gonads, respectively, during the developmental period of sex determination. Therefore, the male-specific microchromosomes resembling common features of sex chromosomes may be the main driving force for male occurrence in gynogenetic gibel carp, which sheds new light on the evolution of unisexual reproduction.

Pleistocene dynamics of the Eurasian steppe as a driving force of evolution: Phylogenetic history of the genus Capsella (Brassicaceae)

Capsella is a model plant genus of the Brassicaceae closely related to Arabidopsis. To disentangle its biogeographical history and intrageneric phylogenetic relationships, 282 individuals of all five currently recognized Capsella species were genotyped using a restriction digest-based next-generation sequencing method. Our analysis retrieved two main lineages within Capsella that split c. one million years ago, with western C. grandiflora and C. rubella forming a sister lineage to the eastern lineage consisting of C. orientalis. The split was attributed to continuous latitudinal displacements of the Eurasian steppe belt to the south during Early Pleistocene glacial cycles. During the interglacial cycles of the Late Pleistocene, hybridization of the two lineages took place in the southwestern East European Plain, leading to the allotetraploid C. bursa-pastoris. Extant genetic variation within C. orientalis postdated any extensive glacial events. Ecological niche modeling showed that suitable habitat for C. orientalis existed during the Last Glacial Maximum around the north coast of the Black Sea and in southern Kazakhstan. Such a scenario is also supported by population genomic data that uncovered the highest genetic diversity in the south Kazakhstan cluster, suggesting that C. orientalis originated in continental Asia and migrated north- and possibly eastwards after the last ice age. Post-glacial hybridization events between C. bursa-pastoris and C. grandiflora/rubella in the southwestern East European Plain and the Mediterranean gave rise to C. thracica. Introgression of C. grandiflora/rubella into C. bursa-pastoris resulted in a new Mediterranean cluster within the already existing Eurasian C. bursa-pastoris cluster. This study shows that the continuous displacement and disruption of the Eurasian steppe belt during the Pleistocene was the driving force in the evolution of Capsella.

Habitat Shape Affects Polyploid Establishment in a Spatial, Stochastic Model

Polyploidy contributes massively to the taxonomic and genomic diversity of angiosperms, but certain aspects of polyploid evolution are still enigmatic. The establishment of a new polyploid lineage following whole-genome duplication (WGD) is a critical step for all polyploid species, but this process is difficult to identify and observe in nature. Mathematical models offer an opportunity to study this process by varying parameters related to the populations, habitats, and organisms involved in the polyploid establishment process. While several models of polyploid establishment have been published previously, very few incorporate spatial factors, including spatial relationships between organisms, habitat shape, or population density. This study presents a stochastic, spatial model of polyploid establishment that shows how factors such as habitat shape and dispersal type can influence the fixation and persistence of nascent polyploids and modulate the effects of other factors. This model predicts that narrow, constrained habitats such as roadsides and coastlines may enhance polyploid establishment, particularly in combination with frequent clonal reproduction, limited dispersal, and high population density. The similarity between this scenario and the growth of many invasive or colonizing species along disturbed, narrow habitats such as roadsides may offer a partial explanation of the prevalence of polyploidy among invasive species.

Genomic mosaicism due to homoeologous exchange generates extensive phenotypic diversity in nascent allopolyploids

Allopolyploidy is an important process in plant speciation, yet newly formed allopolyploid species typically suffer from extreme genetic bottlenecks. One escape from this impasse might be homoeologous meiotic pairing, during which homoeologous exchanges (HEs) generate phenotypically variable progeny. However, the immediate genome-wide patterns and resulting phenotypic diversity generated by HEs remain largely unknown. Here, we analyzed the genome composition of 202 phenotyped euploid segmental allopolyploid individuals from the fourth selfed generation following chromosomal doubling of reciprocal F1 hybrids of crosses between rice subspecies, using whole-genome sequencing. We describe rampant occurrence of HEs that, by overcoming incompatibility or conferring superiority of hetero-cytonuclear interactions, generate extensive and individualized genomic mosaicism across the analyzed tetraploids. We show that the resulting homoeolog copy number alteration in tetraploids affects known-function genes and their complex genetic interactions, in the process creating extraordinary phenotypic diversity at the population level following a single initial hybridization. Our results illuminate the immediate genomic landscapes possible in a tetraploid genomic environment, and underscore HE as an important mechanism that fuels rapid phenotypic diversification accompanying the initial stages of allopolyploid evolution.

Balanced Genome Triplication in Wheat Causes Premature Growth Arrest and an Upheaval of Genome-Wide Gene Regulation

Polyploidy, or whole genome duplication (WGD), is a driving evolutionary force across the tree of life and has played a pervasive role in the evolution of the plant kingdom. It is generally believed that a major genetic attribute contributing to the success of polyploidy is increased gene and genome dosage. The evolution of polyploid wheat has lent support to this scenario. Wheat has evolved at three ploidal levels: diploidy, tetraploidy, and hexaploidy. Ample evidence testifies that the evolutionary success, be it with respect to evolvability, natural adaptability, or domestication has dramatically increased with each elevation of the ploidal levels. A long-standing question is what would be the outcome if a further elevation of ploidy is superimposed on hexaploid wheat? Here, we characterized a spontaneously occurring nonaploid wheat individual in selfed progenies of synthetic hexaploid wheat and compared it with its isogenic hexaploid siblings at the phenotypic, cytological, and genome-wide gene-expression levels. The nonaploid manifested severe defects in growth and development, albeit with a balanced triplication of the three wheat subgenomes. Transcriptomic profiling of the second leaf of nonaploid, taken at a stage when phenotypic abnormality was not yet discernible, already revealed significant dysregulation in global-scale gene expression with ca. 25.2% of the 49,436 expressed genes being differentially expressed genes (DEGs) at a twofold change cutoff relative to the hexaploid counterpart. Both up- and downregulated DEGs were identified in the nonaploid vs. hexaploid, including 457 genes showing qualitative alteration, i.e., silencing or activation. Impaired functionality at both cellular and organismal levels was inferred from gene ontology analysis of the DEGs. Homoeologous expression analysis of 9,574 sets of syntenic triads indicated that, compared with hexaploid, the proportions showing various homeologous expression patterns were highly conserved in the nonaploid although gene identity showed moderate reshuffling among some of the patterns in the nonaploid. Together, our results suggest hexaploidy is likely the upper limit of ploidy level in wheat; crossing this threshold incurs severe ploidy syndrome that is preceded by disruptive dysregulation of global gene expression.