[show abstract][hide abstract] ABSTRACT: Polyploidy in higher plants is a major source of genetic novelty upon which selection may act to drive evolution, as evidenced by the widespread success of polyploid species in the wild. However, research into the effects of polyploidy can be confounded by the entanglement of several processes: genome duplication, hybridisation (allopolyploidy is frequent in plants) and subsequent evolution. The discovery of the chemical agent colchicine, which can be used to produce artificial polyploids on demand, has enabled scientists to unravel these threads and understand the complex genomic changes involved in each. We present here an overview of lessons learnt from studies of natural and artificial polyploids, and from comparisons between the 2, covering basic cellular and metabolic consequences through to alterations in epigenetic gene regulation, together with 2 in-depth case studies in Senecio and Glycine. See also the sister article focusing on animals by Arai and Fujimoto in this themed issue.
Cytogenetic and Genome Research 06/2013; · 1.84 Impact Factor
[show abstract][hide abstract] ABSTRACT: The conservation of unique populations of animals is critical in order to preserve valuable genetic diversity and, where populations are free-living, maintain their irreplaceable influence upon habitat ecology. An accurate assessment of genetic diversity and structure within and between populations is crucial in order to design and implement conservation strategies in natural and domesticated species. Moreover, where it is possible to identify relic populations that are related to a structured breed an ideal opportunity presents itself to model processes that reveal historical factors that have shaped genetic diversity. The origins of native UK mountain and moorland ponies are uncertain, but they may have directly descended from prehistoric populations and potentially harbour specific adaptations to the uplands of Britain and Ireland. To date, there have been no studies of population structure and genetic diversity present within a free-living group of ponies in the Carneddau mountain range of North Wales. Herein, we describe the use of microsatellites and SNPs together with analysis of the mitochondrial control region to quantify the extent and magnitude of genetic diversity present in the feral Carneddau pony and relate this to several recognised British and Irish pony breeds. Our results establish that the feral Carneddau ponies represent a unique and distinctive population that merits recognition as a defined population and conservation priority. We discuss the implications for conservation of this population as a unique pool of genetic diversity adapted to the British uplands and potentially of particular value in maintaining the biodiversity of these habitats.
Ecology and Evolution 04/2013; 3(4):934-47. · 1.18 Impact Factor
[show abstract][hide abstract] ABSTRACT: Perennial ryegrass (Lolium perenne L.) is the most important forage crop in temperate livestock agriculture. Its nutritional quality has significant impact on the quality of meat and milk for human consumption. Evidence suggests that higher energy content in forage can assist in reducing greenhouse gas emissions from ruminants. Increasing the fatty acid content (especially α-linolenic acid, an omega-3 fatty acid) may thus contribute to better forage, but little is known about the genetic basis of variation for this trait. To this end, quantitative trait loci (QTLs) were identified associated with major fatty acid content in perennial ryegrass using a population derived from a cross between the heterozygous and outbreeding high-sugar grass variety AberMagic and an older variety, Aurora. A genetic map with 434 restriction-associated DNA (RAD) and SSR markers was generated. Significant QTLs for the content of palmitic (C16:0) on linkage groups (LGs) 2 and 7; stearic (C18:0) on LGs 3, 4 and 7; linoleic (C18:2n-6) on LGs 2 and 5; and α-linolenic acids (C18:3n-3) on LG 1 were identified. Two candidate genes (a lipase and a beta-ketoacyl CoA synthase), both associated with C16:0, and separately with C18:2n-6 and C18:0 contents, were identified. The physical positions of these genes in rice and their genetic positions in perennial ryegrass were consistent with established syntenic relationships between these two species. Validation of these associations is required, but the utility of RAD markers for rapid generation of genetic maps and QTL analysis has been demonstrated for fatty acid composition in a global forage crop.
[show abstract][hide abstract] ABSTRACT: Human activity and climate change are increasingly driving species, which were once separate together, leading to the potential for gene flow. Hybridization between diverged species brings together two genomes which have evolved to meet different adaptive requirements. The unique combination of these traits in a hybrid may be beneficial or maladaptive, but either way it results in increased phenotypic variation. A percentage of hybrid individuals may, therefore, find themselves able to exploit environmental niches which their progenitors cannot, leading to invasive hybrid swarms becoming established in new habitats. Previous research into hybrids, most famously that of Loren Rieseberg and co-workers (Rieseberg et al. 1999, 2003) in sunflowers, demonstrated that hybridization can give rise to transgressive segregation of adaptive traits, wherein the combination of favourable alleles from both parents in hybrids can enable them to outperform either. However, the question still remains as to how much of the competitive ability of hybrids is a direct result of admixture and how much is the result of selection after the fact. In this issue of Molecular Ecology, (Czypionka et al. 2012) describe their study of transcriptional changes resulting from hybridization in a fish hybrid termed invasive sculpins (Cottus). Using gene expression microarray assays, they compare gene expression in both wild and lab-reared invasive hybrids to the progenitor species and experimentally produced F(2) hybrids. They demonstrate that whilst hybridization alone does result in higher variance in gene expression (some of which is transgressive), many of the transgressive changes distinguishing the invasives appear to have come about subsequent to the initial natural hybridization event. They speculate that initial success of the hybrids in their new habitat is facilitated by hybridization, but that optimization of the invasive phenotype and removal of maladaptive traits rapidly reduces the variation in gene expression seen in early hybrids.
[show abstract][hide abstract] ABSTRACT: Senecio cambrensis is one of a few allopolyploid plant species known to
have originated in the recent past and, therefore, provides excellent material for
analysing allopolyploid speciation. This allohexaploid species originated in the
UK within the last 100 years following hybridization between diploid S. squalidus
and tetraploid S. vulgaris. In this chapter, we first describe the events leading up to
hybridization between these two species, focusing mainly on the origin and spread
of S. squalidus in the UK. We then consider alternative pathways by which S.
cambrensis might have originated and conclude that current evidence suggests an
origin via formation of the triploid hybrid (S. x baxteri) followed by chromosome
doubling. We next review our investigations into levels of genetic diversity and
also changes to gene expression and the possible causes of this (epigenetic effects)
during the origin of S. cambrensis. High levels of genetic diversity, assessed by
surveys of allozyme and AFLP variation, have been recorded in S. cambrensis, and
it is likely that intergenomic recombination was an important generator of this
diversity. Our studies of ‘resynthesized’ S. cambrensis have shown that the initial
genome merger (hybridization) producing S. x baxteri generates genome-wide,
non-additive alterations to parental patterns of gene expression and DNA methylation, with genome duplication resulting in a secondary burst of both
transcriptional and epigenetic modification. In synthetic allohexaploid lines of S.
cambrensis phenotypic changes become apparent from the second to fifth generations,
possibly as a consequence of recombination or epigenetic effects; these
include changes in ray flower form and emergence of self-incompatible individuals.
We conclude by considering the future of S. cambrensis from the standpoint
of it being a model species for further study of allopolyploid speciation, and
second its long-term success in the wild. Ongoing work to produce a draft reference
genome for S. squalidus will underpin future research in S. cambrensis,
enabling a more thorough survey of changes to DNA methylation, small RNA
activity and promoter binding in the hybrids, as well as comparison with the
related allotetraploid S. eboracensis to determine the effects of genome dosage.
The future of the species in the wild is currently uncertain. The population in
Edinburgh that represented a separate origin of the species in the wild during the
1970s is now extinct, and there has been a marked decline in the number of
populations and individuals of the species in its heartland, North Wales, since the
1980s. An analysis of how its ecology compares with those of its parents is
lacking. However, it appears to share the same habitats in the wild with its parents,
which might have contributed to its decline. Although S. cambrensis may become
extinct in the wild in the near future, the potential will remain for it to originate
again in the UK providing that conditions prevail for its parents to hybridize.
[show abstract][hide abstract] ABSTRACT: Pollen-pistil interactions are an essential prelude to fertilization in angiosperms and determine compatibility/incompatibility. Pollen-pistil interactions have been studied at a molecular and cellular level in relatively few families. Self-incompatibility (SI) is the best understood pollen-pistil interaction at a molecular level where three different molecular mechanisms have been identified in just five families. Here we review studies of pollen-pistil interactions and SI in the Asteraceae, an important family that has been relatively understudied in these areas of reproductive biology.
We begin by describing the historical literature which first identified sporophytic SI (SSI) in species of Asteraceae, the SI system later identified and characterized at a molecular level in the Brassicaceae. Early structural and cytological studies in these two families suggested that pollen-pistil interactions and SSI were similar, if not the same. Recent cellular and molecular studies in Senecio squalidus (Oxford ragwort) have challenged this belief by revealing that despite sharing the same genetic system of SSI, the Brassicaceae and Asteraceae molecular mechanisms are different. Key cellular differences have also been highlighted in pollen-stigma interactions, which may arise as a consequence of the Asteraceae possessing a 'semi-dry' stigma, rather than the 'dry' stigma typical of the Brassicaceae. The review concludes with a summary of recent transcriptomic analyses aimed at identifying proteins regulating pollen-pistil interactions and SI in S. squalidus, and by implication the Asteraceae. The Senecio pistil transcriptome contains many novel pistil-specific genes, but also pistil-specific genes previously shown to play a role in pollen-pistil interactions in other species.
Studies in S. squalidus have shown that stigma structure and the molecular mechanism of SSI in the Asteraceae and Brassicaceae are different. The availability of a pool of pistil-specific genes for S. squalidus offers an opportunity to elucidate the molecular mechanisms of pollen-pistil interactions and SI in the Asteraceae.
Annals of Botany 07/2011; 108(4):687-98. · 3.45 Impact Factor
[show abstract][hide abstract] ABSTRACT: What happens to the expression of homeologous gene copies during the formation of new allopolyploid hybrids and their subsequent evolution? Recent studies have shown that hybridisation may relax transcriptional regulation and enable subsequent allopolyploid generations to develop novel patterns of parental gene expression.
Current biology: CB 04/2011; 21(7):R254-5. · 10.99 Impact Factor
[show abstract][hide abstract] ABSTRACT: The merger of two or more divergent genomes within an allopolyploid nucleus can facilitate speciation and adaptive evolution in flowering plants. Widespread changes to gene expression have been shown to result from interspecific hybridisation and polyploidy in a number of plant species, and attention has now shifted to determining the epigenetic processes that drive these changes. We present here an analysis of cytosine methylation patterns in triploid F(1) Senecio (ragwort) hybrids and their allohexaploid derivatives. We observe that, in common with similar studies in Arabidopsis, Spartina and Triticum, a small but significant proportion of loci display nonadditive methylation in the hybrids, largely resulting from interspecific hybridisation. Despite this, genome duplication results in a secondary effect on methylation, with reversion to additivity at some loci and novel methylation status at others. We also observe differences in methylation state between different allopolyploid generations, predominantly in cases of additive methylation with regard to which parental methylation state is dominant. These changes to methylation state in both F(1) triploids and their allohexaploid derivatives largely mirror the overall patterns of nonadditive gene expression observed in our previous microarray analyses and may play a causative role in generating those expression changes. These similar global changes to DNA methylation resulting from hybridisation and genome duplication may serve as a source of epigenetic variation in natural populations, facilitating adaptive evolution. Our observations that methylation state can also vary between different generations of polyploid hybrids suggests that newly formed allopolyploid species may display a high degree of epigenetic diversity upon which natural selection can act.
[show abstract][hide abstract] ABSTRACT: Homoploid hybrid speciation is the origin of a hybrid species without change in chromosome number. Although currently thought to be a rare form of speciation, especially relative to the more common allopolyploid hybrid speciation, it is feasible that many examples of homoploid hybrid species will be discovered in the future now that genetic resources are readily available for testing their occurrence. In this review, we focus on the speed of homoploid hybrid speciation, the importance of ecological and spatial isolation in the process, and the nature of genetic changes that occur in a new hybrid during its origin and establishment in the wild. With reference mainly to the extensive work carried out on homoploid hybrid species of Helianthus, and to our own work on the very recently originated diploid hybrid species Senecio squalidus, we review evidence showing: (1) that new fertile homoploid hybrid species can originate very quickly, although a longer period is likely to be required before the species becomes fully stabilized both genomically and phenotypically; (2) ecological divergence of the hybrid species from its parents is key to successful establishment, and that this can occur even in the absence of post-zygotic isolation caused by chromosomal and/or genetic sterility barriers; (3) transgressive changes in phenotypic traits and gene expression are of great importance in adapting homoploid hybrid species to habitats that are ecologically and spatially divergent from those of the parents; (4) adaptive differences distinguishing a homoploid hybrid species from its parental species are likely to be maintained in the face of parental gene flow, and evolve in concert across populations representing multiple origins of the species; (5) in the absence of parental gene flow, i.e., under conditions of geographical isolation, rapid genetic divergence of the hybrid species is likely to be enhanced due to the combined effects of founder events, genetic drift and selection.
[show abstract][hide abstract] ABSTRACT: The plant nucleus is a highly ordered and dynamic structure, with a considerable level of variation between species in terms of genome size, genome organisation, chromosome territories and patterns associated with developmental changes. Diploids naturally represent the simplest state of affairs, but in the plant world more than 70% of species may have been involved in polyploidisation events at some stage during their evolution. Autopolyploids have multiple sets of chromosomes from a single species, and aside from the complexities of meiosis we may expect them to accommodate their polysomic state as well as their disomic relatives. Allopolyploids are at the other extreme, with multiple sets of chromosomes from 2 or more species, embedded in the cytoplasm of the maternal parent following hybridisation, and this presents the nucleus of nascent allopolyploids with certain zones of conflict. Nature has found ways to make the accommodation, and recent developments in molecular analysis have now opened a window for the experimenter to view the process of this adjustment, and to see how rapidly it takes place and what processes are involved. The nature of the resolution of nuclear conflicts in diploid hybrids and in allopolyploids is discussed.
Cytogenetic and Genome Research 12/2009; 126(4):376-89. · 1.84 Impact Factor
[show abstract][hide abstract] ABSTRACT: Hybridization is an important cause of abrupt speciation. Hybrid speciation without a change in ploidy (homoploid hybrid speciation) is well-established in plants but has also been reported in animals and fungi. A notable example of recent homoploid hybrid speciation is Senecio squalidus (Oxford ragwort), which originated in the UK in the 18th Century following introduction of hybrid material from a hybrid zone between S. chrysanthemifolius and S. aethnensis on Mount Etna, Sicily. To investigate genetic divergence between these taxa, we used complementary DNA microarrays to compare patterns of floral gene expression. These analyses revealed major differences in gene expression between the parent species and wild and resynthesized S. squalidus. Comparisons of gene expression between S. aethnensis, S. chrysanthemifolius and natural S. squalidus identified genes potentially involved in local environmental adaptation. The analysis also revealed non-additive patterns of gene expression in the hybrid relative to its progenitors. These expression changes were more dramatic and widespread in resynthesized hybrids than in natural S. squalidus, suggesting that a unique expression pattern may have been fixed during the allopatric divergence of British S. squalidus. We speculate that hybridization-induced gene-expression change may provide an immediate source of novel phenotypic variation upon which selection can act to facilitate homoploid hybrid speciation in plants.
[show abstract][hide abstract] ABSTRACT: Senecio squalidus is a diploid hybrid species which originated in the British Isles following the introduction of material collected from a hybrid zone on Mount Etna, Sicily, approximately 300 years ago. Introduced hybrid material was cultivated in the Oxford Botanic Garden and gave rise to the stabilized diploid hybrid species, which later spread throughout much of the UK and into some parts of Ireland. Unusually for an invasive species, S. squalidus has a strong system of sporophytic self-incompatibility (SSI) that may have become modified as a result of its recent hybrid origin and spread. First, S. squalidus contains relatively few S alleles (between 2 and 6 S alleles within individual UK populations) compared to other species with SSI (estimates average ~17 S alleles per population). This most probably reflects the population bottleneck experienced by introduced hybrid material. Second, dominance relationships among S. squalidus S alleles are more extensive than those reported in other species with SSI. Third, although pseudo-self-compatibility occurs sporadically in S. squalidus, it is not widespread, indicating that SSI is maintained in the species despite potential mate availability restrictions imposed by low numbers of S alleles. Surveys of other forms of genetic diversity in S. squalidus show that allozyme variation is reduced relative to that within the progenitor species, but Randomly Amplified Polymorphic DNA variation is relatively high. Both types of genetic variation show little or no pattern of isolation-by-distance between populations in keeping with the recent range expansion of the species. During its spread in the British Isles, S. squalidus has hybridized with the native self-compatible (SC) tetraploid species, S. vulgaris, which has led to the origin of three new SC hybrid taxa: a radiate form of S. vulgaris (var. hibernicus), a tetrapoid hybrid species (S. eboracensis) and an allohexaploid (S. cambrensis).
[show abstract][hide abstract] ABSTRACT: Interspecific hybridization is an important mechanism of speciation in higher plants. In flowering plants, hybrid speciation is usually associated with polyploidy (allopolyploidy), but hybrid speciation without genome duplication (homoploid hybrid speciation) is also possible, although it is more difficult to detect. The combination of divergent genomes within a hybrid can result in profound changes to both genome and transcriptome. Recent transcriptomic studies of wild and resynthesized homoploid and allopolyploid hybrids have revealed widespread changes to gene expression in hybrids relative to expression levels in their parents. Many of these changes to gene expression are 'non-additive', i.e. not simply the sum of the combined expression levels of parental genes. Some gene expression changes are far outside the range of gene expression in either parent, and can therefore be viewed as 'transgressive'. Such profound changes to gene expression may enable new hybrids to survive in novel habitats not accessible to their parent species. Here, we give a brief overview of hybrid speciation in plants, with an emphasis on genomic change, before focusing discussion on findings from recent transcriptomic studies. We then discuss our current work on gene expression change associated with hybrid speciation in the genus Senecio (ragworts and groundsels) focusing on the findings from a reanalysis of gene expression data obtained from recent microarray studies of wild and resynthesized allopolyploid Senecio cambrensis. These data, showing extensive non-additive and transgressive gene expression changes in Senecio hybrids, are discussed in the light of findings from other model systems, and in the context of the potential importance of gene expression change to hybrid speciation in plants.
Philosophical Transactions of The Royal Society B Biological Sciences 07/2008; 363(1506):3055-69. · 6.23 Impact Factor
[show abstract][hide abstract] ABSTRACT: Polyploidy, or the presence of two or more diploid parental genome sets within an organism, is found to an amazing degree in higher plants. In addition, many plant species traditionally considered to be diploid have recently been demonstrated to have undergone rounds of genome duplication in the past and are now referred to as paleopolyploids. Polyploidy and interspecific hybridisation (with which it is often associated) have long been thought to be important mechanisms of rapid species formation. The widespread occurrence of polyploids, which are frequently found in habitats different from that of their diploid progenitors, would seem to indicate that polyploidy is associated with evolutionary success in terms of the ability to colonise new environmental niches. A flurry of recent genomic studies has provided fresh insights into the potential basis of the phenotypic novelty of polyploid species. Here we review current knowledge of genetic, epigenetic, and transcriptional changes associated with polyploidy in plants and assess how these changes might contribute to the evolutionary success of polyploid plants. We conclude by stressing the need for field-based experiments to determine whether genetic changes associated with polyploidy are indeed adaptive.
Current Biology 06/2008; 18(10):R435-44. · 9.49 Impact Factor
[show abstract][hide abstract] ABSTRACT: How does having more than one genome give plant species an advantage when it comes to adaptive evolution? Recent molecular studies have shown that altered patterns of gene expression may offer polyploids a broader phenotypic range than that of their progenitors.
Current Biology 12/2007; 17(21):R927-9. · 9.49 Impact Factor
[show abstract][hide abstract] ABSTRACT: Allopolyploidy, which involves genome doubling of an interspecific hybrid is an important mechanism of abrupt speciation in flowering plants [1-6]. Recent studies show that allopolyploid formation is accompanied by extensive changes to patterns of parental gene expression ("transcriptome shock") [7-15] and that this is likely the consequence of interspecific hybridization rather than polyploidization . To investigate the relative impacts of hybridization and polyploidization on transcription, we compared floral gene expression in allohexaploid Senecio cambrensis with that in its parent species, S. vulgaris (tetraploid) and S. squalidus (diploid), and their triploid F1 hybrid, S. x baxteri . Major changes to parental gene expression were associated principally with S. x baxteri, suggesting that the polyploidization event responsible for the formation of S. cambrensis had a widespread calming effect on altered gene expression arising from hybridization . To test this hypothesis, we analyzed floral gene expression in resynthesized lines of S. cambrensis and show that, for many genes, the "transcriptome shock" observed in S. x baxteri is calmed ("ameliorated") after genome doubling in the first generation of synthetic S. cambrensis and this altered expression pattern is maintained in subsequent generations. These findings indicate that hybridization and polyploidization have immediate yet distinct effects on large-scale patterns of gene expression.
Current Biology 09/2006; 16(16):1652-9. · 9.49 Impact Factor
[show abstract][hide abstract] ABSTRACT: Interspecific hybridization is an important process through which abrupt speciation can occur. In recent years, genetic changes associated with hybrid speciation have been identified through a variety of techniques, including AFLP/SSR mapping, GISH/FISH and cDNA-AFLP differential display. However, progress in using microarray technology to analyse whole genome/transcriptome changes associated with hybrid speciation has been limited due to the lack of extensive sequence data for many hybrid species and the difficulties in extrapolating results from commercially available microarrays for model species onto nonmodel hybrid taxa. Increasingly therefore researchers studying nonmodel systems are turning to the development of 'anonymous' cDNA microarrays, where the time and cost of producing microarrays is reduced by printing unsequenced cDNA clones, and sequencing only those clones that display interesting expression patterns. Here we describe the creation, testing and preliminary use of anonymous cDNA microarrays to study changes in floral transcriptome associated with allopolyploid speciation in the genus Senecio. We report a comparison of gene expression between the allohexaploid hybrid, Senecio cambrensis, its parental taxa Senecio squalidus (diploid) and Senecio vulgaris (tetraploid), and the intermediate triploid (sterile) hybrid Senecioxbaxteri. Anonymous microarray analysis revealed dramatic differences in floral gene expression between these four taxa and demonstrates the power of this technique for studies of the genetic impact of hybridization in nonmodel flowering plants.
[show abstract][hide abstract] ABSTRACT: Abrupt speciation through interspecific hybridisation is an important mechanism in angiosperm evolution. Flowering plants therefore offer excellent opportunities for studying genetic processes associated with hybrid speciation. Novel molecular approaches are now available to examine these processes at the level of both genome organization and gene expression - transcriptomics. Here, we present an overview of the molecular technologies currently used to study hybrid speciation and how they are providing new insights into this mode of speciation in flowering plants. We begin with an introduction to hybrid speciation in plants, followed by a review of techniques, such as isozymes and other markers, which have been used to study hybrid species in the past. We then review advances in molecular techniques that have the potential to be applied to studies of hybrid species, followed by an overview of the main genomic and transcriptomic changes suspected, or known, to occur in newly formed hybrids, together with commentary on the application of advanced molecular tools to studying these changes.
New Phytologist 03/2005; 165(2):411-23. · 6.74 Impact Factor
[show abstract][hide abstract] ABSTRACT: Interspecific hybridization has resulted in the recent origin of several hybrid Senecio taxa at diploid, tetraploid and hexaploid levels. As part of research aimed at constructing and comparing genomic maps of each of these taxa and their parents, we have isolated microsatellite loci from genomic DNA libraries of S. vulgaris and S. squalidus. Primers of 35 loci amplified microsatellites resolved in agarose gels from one or more of S. vulgaris, S. squalidus, S. aethnensis and S. chrysanthemifolius. Approximately 71% of primers amplified a product in all four species. A survey of microsatellite variation in S. chrysanthemifolius over a subset of 14 loci resolved 2–11 alleles per locus in polyacrylamide gels with expected heterozygosity (HE) ranging from 0.26 to 0.87.