Polyploidy, or whole genome duplication, is recognized as an important feature of eukaryotic genome evolution. Among eukaryotes, polyploidy has probably had the largest evolutionary impact on vascular plants where many contemporary species are of recent polyploid origin. Genomic analyses have uncovered evidence of at least one round of polyploidy in the ancestry of most plants, fueling speculation that genome duplications lead to increases in net diversity. In spite of the frequency of ancient polyploidy, recent analyses have found that recently formed polyploid species have higher extinction rates than their diploid relatives. These results suggest that despite leaving a substantial legacy in plant genomes, only rare polyploids survive over the long term and most are evolutionary dead-ends.Copyright © 2012 Elsevier Ltd. All rights reserved.

Polyploidy has extensive genetic, physiological, morphological, and ecological ramifications. While the patterns underlying the genetic and morphological consequences of polyploidy are being rapidly elucidated, the effects on ecological niche are still largely unknown. This study investigated 13 allopolyploid systems in North America (10 ferns and three angiosperms) using digitized natural history museum specimens. The abiotic niches of the allopolyploids were compared with those of their diploid progenitors using ecological niche modeling, niche analyses, and multivariate analyses. We identified four patterns of niche shifts through our analyses: niche expansion, niche contraction, niche intermediacy, and niche novelty. The classification of these shifts depended on the amount of niche overlap and breadth between the polyploid and progenitors. The most common niche shift was niche intermediacy in which the polyploid inhabited a geographic range between that of the progenitors and had a high degree of niche overlap. Each polyploid had at least partial geographic sympatry and abiotic niche overlap with one of its progenitors, suggesting that biotic and/or microclimate factors may play a larger role in polyploid establishment than previously hypothesized. This study provides a baseline for future comparisons of the diverse outcomes of genome merger and duplication on abiotic niche preference.© 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

The classical example of nonadditive contributions of the two parents to allopolyploids is nucleolar dominance, which entails silencing of one parental set of ribosomal RNA genes. This has been observed for many other loci. The prevailing explanation for this genome-wide expression disparity is that the two merged genomes differ in their transposable element (TE) complement and in their level of TE-mediated repression of gene expression. Alternatively, and not exclusively, gene expression dominance may arise from mismatches between trans effectors and their targets. Here, we explore quantitative models of regulatory mismatches leading to gene expression dominance. We also suggest that, when pairs of merged genomes are similar from one allopolyploidization event to another, gene-level and genome dominance patterns should also be similar.Copyright © 2018 Elsevier Ltd. All rights reserved.

Many large and economically important plant groups (e.g. Brassicaceae, Poaceae, Asteraceae, Fabaceae and Solanaceae) have had ancient whole genome duplications (WGDs) occurring near or at the time of their origins, suggesting that WGD contributed to the origin of novel key traits and drove species diversification. However, these large clades show phylogenetic asymmetries with a species-rich crown group and a species-poor sister clade, suggesting significant 'lag-times' between WGDs and radiations. The species-poor sister groups share many key traits, but are often restricted to the hypothesized center of origin for the larger clade. Thus, the ultimate success of the crown group does not only involve the WGD and novel key traits, but largely subsequent evolutionary phenomena including later migration events, changing environmental conditions and/or differential extinction rates.Copyright © 2012 Elsevier Ltd. All rights reserved.

Asparagaceae: Lomandroideae are a species-rich and economically important subfamily in the monocot order Asparagales, with a center of diversity in Australia. Lomandroideae are ecologically diverse, occupying mesic and arid biomes in Australia and possessing an array of key traits, including sexual dimorphism, storage organs and polyploidy that are potentially adaptive for survival in seasonally arid and fire-dependent habitats. The Lomandroideae phylogeny was reconstructed using maximum likelihood and Bayesian inference criteria, based on plastome data from genome-skimming to infer relationships. A fossil-calibrated chronogram provided a temporal framework for understanding trait transitions. Ancestral state reconstructions and phylogenetic comparative trait correlation analyses provided insights into the evolutionary and ecological drivers associated with Lomandroideae diversification. Lomandroideae diverged from the other Asparagaceae ca. 56.61 million years ago (95% highest posterior density values 70.31-45.34 million years) and the major lineages diversified since the Oligocene. The most recent common ancestor of the clade likely occupied the mesic biome, was hermaphroditic and geophytic. Biome occupancy transitions were correlated with polyploidy and the presence of storage roots. Polyploidy potentially serves as an "enabler" trait, generating novel phenotypes, which may confer tolerance to climatic ranges and soil conditions putatively required for expansion into and occupation of new arid biomes. Storage roots, as a key factor driving biome transitions, may have been associated with fire rather than with aridification events in the Australian flora. This study contributes significantly to our understanding of biome evolution by identifying polyploidy and storage organs as key factors associated with transitions in biome occupancy in this lineage.Copyright © 2020 Elsevier Inc. All rights reserved.

The Brassicaceae include several major crop plants and numerous important model species in comparative evolutionary research such as Arabidopsis, Brassica, Boechera, Thellungiella, and Arabis species. As any evolutionary hypothesis needs to be placed in a temporal context, reliably dated major splits within the evolution of Brassicaceae are essential. We present a comprehensive time-calibrated framework with important divergence time estimates based on whole-chloroplast sequence data for 29 Brassicaceae species. Diversification of the Brassicaceae crown group started at the Eocene-to-Oligocene transition. Subsequent major evolutionary splits are dated to ∼20 million years ago, coinciding with the Oligocene-to-Miocene transition, with increasing drought and aridity and transient glaciation events. The age of the Arabidopsis thaliana crown group is 6 million years ago, at the Miocene and Pliocene border. The overall species richness of the family is well explained by high levels of neopolyploidy (43% in total), but this trend is neither directly associated with an increase in genome size nor is there a general lineage-specific constraint. Our results highlight polyploidization as an important source for generating new evolutionary lineages adapted to changing environments. We conclude that species radiation, paralleled by high levels of neopolyploidization, follows genome size decrease, stabilization, and genetic diploidization. © 2015 American Society of Plant Biologists. All rights reserved.

Due to wide hybridization and polyploidization, there are numerous species complexes with taxonomic challenges in the fern genus Asplenium. Integrative taxonomy using evidence of morphology, cytology and molecular phylogeny provides one of the best ways for the discovery and delimitation of species. The Asplenium coenobiale complex represents one of the spleenwort complexes, which are morphologically variable and difficult in species delimitation. Owing to the lack of comprehensive sampling and systematic study, the taxonomy of this complex remains unresolved. In this study, we selected representative individuals of this complex covering differences in morphology and geography. We conducted a palynological study to explore reproductive characteristics, and inferred the ploidy level through flow cytometry. Furthermore, based on the phylogenetic evidence from chloroplast and nuclear genomes, we discussed the evolutionary relationship and origin of this complex. Our results showed that: (1) The development of 64 spores within a single normal sporangium is indicative of the ability of sexual reproduction, although abortive sporangia are common in the Asplenium coenobiale complex. (2) Ploidy variation is found in this complex, i.e. A. cornutissimum is diploid, whereas other members are all tetraploid. (3) The maternally inherited chloroplast phylogeny supported four clades within this complex, and this was incongruent with the nuclear phylogeny; therefore, it was inferred that hybridization could be an important driving force during the formation of the complex. Based on our analyses, we conduct a revision to the A. coenobiale complex, i.e. one newly discovered autotetraploid species (A. maguanense sp. nov.), one diploid species (A. cornutissimum), and two allotetraploids with reciprocal origins (A. coenobiale and A. pulcherrimum).

广泛的杂交和多倍化使得铁角蕨属(Asplenium)下存在着许多分类困难的物种复合体, 针对这些类群进行整合分类学的研究, 有助于我们更加全面和深入地理解物种的界限以及形成机制。线裂铁角蕨复合体(Asplenium coenobiale complex)是铁角蕨属下一个形态多样性较高的类群, 由于缺乏全面取样和系统研究, 该复合体的物种划分长期存在争议。本研究选取线裂铁角蕨复合体中形态变异和地理分布具有代表性的个体, 通过孢粉学研究确定该类群的生殖特性, 运用流式细胞分析获取倍性信息, 同时结合叶绿体和核基因组片段系统发生分析的证据, 对该类群的系统演化关系和起源方式进行了探讨。结果表明: (1)虽然部分孢子囊败育的情况在线裂铁角蕨复合体中十分普遍, 但正常孢子囊内形成的64个孢子说明该类群植物仍能进行正常的有性生殖; (2)该复合体中存在着倍性变异, 其中多角铁角蕨(A. cornutissimum)是二倍体, 而其他成员均为四倍体; (3)依据母系遗传的叶绿体序列所构建的系统发生关系将该类群划为4个分支, 与基于核基因序列构建的系统树存在冲突, 这暗示杂交可能在该复合体的形成过程中起到了重要的推动作用。综上所述, 我们建议将线裂铁角蕨复合体划分为4个物种, 即同源四倍体新种马关铁角蕨(A. maguanense sp. nov.), 二倍体多角铁角蕨, 以及两个由同一对亲本正反交产生的异源四倍体线裂铁角蕨(A. coenobiale)和叶基宽铁角蕨(A. pulcherrimum)。

Polyploidy, the doubling of genomic content, is a widespread feature, especially among plants, yet its macroevolutionary impacts are contentious. Traditionally, polyploidy has been considered an evolutionary dead end, whereas recent genomic studies suggest that polyploidy has been a key driver of macroevolutionary success. We examined the consequences of polyploidy on the time scale of genera across a diverse set of vascular plants, encompassing hundreds of inferred polyploidization events. Likelihood-based analyses indicate that polyploids generally exhibit lower speciation rates and higher extinction rates than diploids, providing the first quantitative corroboration of the dead-end hypothesis. The increased speciation rates of diploids can, in part, be ascribed to their capacity to speciate via polyploidy. Only particularly fit lineages of polyploids may persist to enjoy longer-term evolutionary success.

Much of the diversity of flowering plants is associated with genomic duplication through polyploidy. Little is known, however, about the evolutionary mechanisms responsible for the diversification of novel polyploid lineages. We evaluated the possibility that divergence is driven by natural selection by estimating the strength of phenotypic selection acting on three floral traits in sympatric populations of diploid and autotetraploid Heuchera grossulariifolia over three years. Our results demonstrate consistent directional selection for increasing scape length and floral display in both diploid and tetraploid populations. In contrast, selection acting on flowering phenology varied across year and ploidy. Specifically, selection was found to favor late-flowering diploids in 2001 and 2002 but early-flowering tetraploids in 2003. We investigated the mechanistic basis of divergent selection for flowering phenology in 2003 by estimating the relationship between plant flowering phenology and the probability of intercytotype pollinator movement. The results demonstrated that less divergent tetraploids were significantly more likely to experience intercytotype flights than were more divergent tetraploids. This result is consistent with the pattern of phenotypic selection observed. Taken together, our results suggest that divergence of polyploids and their diploid progenitors may be driven by a process analogous to reinforcement whereby selection favors phenotypes that reduce the probability of intercytotype matings with reduced fertility.

Gene duplications provide evolutionary potentials for generating novel functions, while polyploidization or whole genome duplication (WGD) doubles the chromosomes initially and results in hundreds to thousands of retained duplicates. WGDs are strongly supported by evidence commonly found in many species-rich lineages of eukaryotes, and thus are considered as a major driving force in species diversification. We performed comparative genomic and phylogenomic analyses of 59 public genomes/transcriptomes and 46 newly sequenced transcriptomes covering major lineages of angiosperms to detect large-scale gene duplication events by surveying tens of thousands of gene family trees. These analyses confirmed most of the previously reported WGDs and provided strong evidence for novel ones in many lineages. The detected WGDs supported a model of exponential gene loss during evolution with an estimated half-life of approximately 21.6 million years, and were correlated with both the emergence of lineages with high degrees of diversification and periods of global climate changes. The new datasets and analyses detected many novel WGDs widely spread during angiosperm evolution, uncovered preferential retention of gene functions in essential cellular metabolisms, and provided clues for the roles of WGD in promoting angiosperm radiation and enhancing their adaptation to environmental changes.Copyright © 2018 The Author. Published by Elsevier Inc. All rights reserved.

Like the formation of animal species, plant speciation is characterized by the evolution of barriers to genetic exchange between previously interbreeding populations. Prezygotic barriers, which impede mating or fertilization between species, typically contribute more to total reproductive isolation in plants than do postzygotic barriers, in which hybrid offspring are selected against. Adaptive divergence in response to ecological factors such as pollinators and habitat commonly drives the evolution of prezygotic barriers, but the evolutionary forces responsible for the development of intrinsic postzygotic barriers are virtually unknown and frequently result in polymorphism of incompatibility factors within species. Polyploid speciation, in which the entire genome is duplicated, is particularly frequent in plants, perhaps because polyploid plants often exhibit ecological differentiation, local dispersal, high fecundity, perennial life history, and self-fertilization or asexual reproduction. Finally, species richness in plants is correlated with many biological and geohistorical factors, most of which increase ecological opportunities.

Polyploids are often geographically segregated from their diploid progenitors, but the extent of sympatry and the consequences for reproductive isolation and coexistence are rarely quantified. •In this study, we document the distribution and co-occurrence of diploid and tetraploid Chamerion angustifolium among 57 populations within the diploid-tetraploid contact zone in the Canadian Rocky Mountains. Rates of hybrid mating in mixed-ploidy populations were inferred from the frequency of triploid offspring in open-pollinated seed families. •Twenty-three of 57 populations sampled contained a single cytotype; 20 (87%) were tetraploid and three (13%) were diploid. Thirty-four populations (60%) contained multiple ploidies. Diploid and tetraploid plants occurred in all mixed-ploidy populations; triploids occurred in 13 populations and averaged 1.4% of plants per population. The proportion of tetraploids in a population was negatively related to elevation (partial regression: F = 27.2, P <0.0001) and latitude (partial regression: F = 17.4, P < 0.0001). Triploids were detected in seed from all eight mixed-ploidy populations sampled ( = 3.7% of seed per population), comprising 7% of that expected with random mating (G = 2589.2, df = 1, P <0.0001, n = 2628), and were more often produced by diploid maternal parents than tetraploid parents. •Our results indicate that tetraploids regularly coexist with diploids in the contact zone and that this coexistence is likely promoted by both strong reproductive isolation and asymmetric intercytotype mating between diploid and tetraploid C. angustifolium.

Ecological differentiation is recognized as an important factor for polyploid speciation, but little is known regarding whether the ecological niches of cytotypes differ between areas of sympatry and areas where single cytotypes occur (i.e. niche displacement).Ecological niches of four groups of Senecio carniolicus sensu lato (s.l.) (western and eastern diploid lineages, tetraploids and hexaploids) were characterized via Landolt indicator values of the accompanying vascular plant species and tested using multivariate and univariate statistics.The four groups of S. carniolicus s.l. were ecologically differentiated mainly with respect to temperature, light and soil (humus content, nutrients, moisture variability). Niche breadths did not differ significantly. In areas of sympatry hexaploids shifted towards sites with higher temperature, less light and higher soil humus content as compared with homoploid sites, whereas diploids and tetraploids shifted in the opposite direction. In heteroploid sites of tetraploids and the western diploid lineage the latter shifted towards sites with lower humus content but higher aeration.Niche displacement can facilitate the formation of stable contact zones upon secondary contact of polyploids and their lower-ploid ancestors and/or lead to convergence of the cytotypes' niches after they have attained non-overlapping ranges. Niche displacement is essential for understanding ecological consequences of polyploidy.© The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Polyploidy (the state of having more than two genome copies) is widely distributed in flowering plants and can vary within species, with polyploid races often associated with broad ecological tolerances. Polyploidy may influence within-species variation in seed development, germination and establishment. We hypothesized that interactions between polyploidy and the seed developmental environment would affect subsequent dormancy, germination and early growth traits, particularly in stressful environments. Using seeds developed in a common garden under ambient and warmed conditions, we conducted germination trials under drought and temperature stress, and monitored the subsequent growth of seedlings. The study species, Themeda triandra, is a widespread, keystone, Australian native grass and a known polyploid complex. Tetraploid plants produced heavier, more viable seeds than diploids. Tetraploids were significantly more dormant than diploids, regardless of seed developmental environment. Non-dormant tetraploids were more sensitive to germination stress compared to non-dormant diploids. Finally, tetraploid seedlings were larger and grew faster than diploids, usually when maternal plants were exposed to developmental temperatures atypical to the source environment. Seed and seedling traits suggest tetraploids are generally better adapted to stressful environments than diploids. Because tetraploid seeds of T. triandra are more dormant they are less likely to germinate under stress, and when they do germinate, seedling growth is rapid and independent of seed developmental environment. These novel results demonstrate that polyploidy, sometimes in interaction with developmental environment and possibly also asexuality, can have within-species variation in seed and seedling traits that increase fitness in stressful environments.© 2020 German Society for Plant Sciences and The Royal Botanical Society of the Netherlands.

DNA ploidy levels were estimated using DAPI-flow cytometry of silica-dried specimens of the European mountain plant Senecio carniolicus (Asteraceae), covering its entire distribution area in the Eastern Alps (77 populations, 380 individuals) and the Carpathians (five populations, 22 individuals). A complex pattern of ploidy level variation (2x, 4x, 5x, 6x, and 7x cytotypes) was found in this species, which has been considered uniformly hexaploid. Hexaploids predominated in the Eastern Alps and was the only cytotype found in the Carpathians, while odd ploidy levels (5x, 7x) constituted a small fraction of the samples (<1.3%). Tetraploids occurred in two disjunct areas, which correspond with putative Pleistocene refugia for silicicolous alpine plants. Diploids occurred in large portions of the Alps but were absent from areas most extensively glaciated in the past. Intrapopulational cytotype mixture was detected in 22 populations-the majority involving diploids and hexaploids-with intermediate ploidy levels mostly lacking, suggesting limited gene flow and the evolution of reproductive isolation. Significant and reproducible intracytotype variation in nuclear DNA content was observed. Higher genome size in western diploids might be due to ancient introgression with the closely related S. incanus or to different evolutionary pathways in the geographically separated diploids.

Whole genome duplication is considered to be a significant contributor to angiosperm speciation due to accumulation of rapid, strong interploid reproductive isolation. However, recent work suggests that interploid reproductive isolation may not be complete, especially among higher order cytotypes. This study evaluates postzygotic reproductive isolation among three cytotypes within a polyploid complex. We conducted reciprocal crosses using two diploid and two hexaploid populations each crossed to tetraploid populations spanning the geographic and phylogenetic range of the Campanula rotundifolia polyploid complex. Interploid and intrapopulation crosses were scored for fruit set, seed number, germination proportion and pollen viability. Postzygotic isolation was calculated for each cross as the product of these fitness components. A subset of offspring was cytotyped via flow cytometry. Postzygotic isolation was significantly lower in tetraploid-hexaploid crosses than diploid-tetraploid crosses, mostly due to substantially higher germination among tetraploid-hexaploid crosses. Tetraploid-hexaploid crosses produced pentaploids exclusively, whereas diploid-tetraploid crosses produced both triploids and tetraploids in high frequencies. Postzygotic isolation was weaker among higher order polyploids than between diploids and tetraploids, and unreduced gametes may facilitate diploid-tetraploid reproduction. This incomplete postzygotic isolation could allow ongoing interploid gene flow, especially among higher order polyploids, which may slow divergence and speciation in polyploid complexes.© 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

The prevalence and recurrence of polyploidization in plant species make it one of the most important evolutionary events in plants, and as a result, polyploidization is an extensively investigated research field. Due to the rapid development of sequencing technologies, there is increased evidence to support that polyploidization plays an important role in the diversification of plant species, evolution of genes, and the domestication of crops. Here, we reviewed the influence of polyploidization on various aspects of plant evolution, mainly focused on polyploid origin, characteristics, subsequent genome divergence, and its impact on gene function innovation and crop domestication. The occurrence of many independent polyploidization events in plants was found to be tightly associated with the timing of extreme climate events or natural disasters on earth, leading to mass extinction while possibly facilitating increased polyploidization. Following allo-polyploidization, a distinct phenomenon known as sub-genome dominance occurred during sub-genome evolution, which was found to be associated with the methylation of transposons. Extensive gene fractionations (lost) following polyploidization were reported in almost all paleo-polyploids, and the evolutionary fates of multi-copy genes, such as sub-/neo- functionalization, were further proposed to illustrate their underlying mechanisms. Moreover, polyploidization was found to significantly impact species diversification, with subsequent effects on crop domestication and the development of traits with agronomic importance. Based on the progress of plant polyploidization studies, we discussed several main topics that might further improve our understanding of polyploid evolution and that are likely contribute to the application of polyploidization in crop breeding in the near future.