Evolution of clonality and polyploidy in a weevil system

The increased interest in asexual organisms calls for in-depth studies of asexual complexes that actively give rise to new clones. We present an extensive molecular study of the Otiorhynchus scaber (Coleoptera, Curculionidae) weevil system. Three forms have traditionally been recognized: diploid sexuals, triploid, and tetraploid parthenogens. All forms coexist in a small central area, but only the polyploid parthenogens have colonized marginal areas. Analyzing the phylogenetic relationship, based on three partial mitochondrial genes, of 95 individuals from 19 populations, we find that parthenogenesis and polyploidy have originated at least three times from different diploid lineages. We observe two major mitochondrial lineages, with over 2.5% sequence divergence between the most basal groups within them, and find that current distribution and phylogenetic relationships are weakly correlated. Quite unexpectedly, we also discover diploid clones that coexist with, and are morphologically indistinguishable from, the diploid sexual females. Our results support that these diploid clones are derived directly from the diploid sexuals. We also find that it is mainly an increase in ploidy level and not the benefits of asexual reproduction that confers to polyploid parthenogens the advantage over their diploid sexual relatives.     

Transcriptome and miRNAs analyses enhance our understanding of the evolutionary advantages of polyploidy

Polyploid organisms have more than two sets of chromosomes, including autopolyploid via intraspecific genome doubling, and allopolyploid via merging genomes of distinct species by hybridization. Polyploid organisms are widespread in plants, indicating that polyploidy has some evolutionary advantages over its diploid ancestor. Actually, polyploidy is always tightly associated with hybrid vigor and adaptation to adverse environmental conditions. However, why polyploidy can develop such advantages is poorly known. MicroRNAs (miRNAs) are endogenous ～21?nt small RNAs which can play important regulatory roles in animals and plants by targeting mRNAs for cleavage or translational repression. MicroRNAs are essential for cell development, differentiation, signal transduction, and show an adaptive response to biotic and abiotic stresses. Environmental stresses cause plants to over- or under-express certain miRNAs or synthesize new miRNAs to cope with stress. We have here reviewed our current knowledge on the molecular mechanisms, which can account for the evolutionary advantages of polyploidy over its diploid ancestor from genome-wide gene expression and microRNAs expression perspectives.     

Perspectives on polyploidy in plants – ancient and neo

It is timely to re-examine the phenomenon of polyploidy in plants. Indeed, the power of modern molecular technology to provide new insights, and the impetus of genomics, make polyploidy a fit, fashionable and futuristic topic for review. Some historical perspective is essential to understand the meaning of the terms, to recognize what is already known and what is dogma, and to frame incisive questions for future research. Polyploidy is important because life on earth is predominantly a polyploid phenomenon. Moreover, civilization is mainly powered by polyploid food – notably cereal endosperm. Ongoing uncertainty about the origin of triploid endosperm epitomizes our ignorance about somatic polyploidy. New molecular information makes it timely to reconsider how to identity polyploids and what is a polyploid state. A functional definition in terms of a minimal genome may be helpful. Genes are known that can raise or lower ploidy level. Molecular studies can test if, contrary to dogma, the relationship between diploids and polyploids is a dynamic two-way system. We still need to understand the mechanisms and roles of key genes controlling ploidy level and disomic inheritance. New evidence for genome duplications should be compared with old ideas about cryptopolyploidy, and new views of meiosis should not ignore premeiotic genome separation. In practice, new knowledge about polyploidy will be most useful only when it reliably predicts which crops can be usefully improved as stable autopolyploids and which genomes combined to create successful new allopolyloids.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 411–423.     

Chromosomes and polyploidy in Lenophyllum (Crassulaceae)

Gametic chromosome numbers of 22, 32, 33, and 44 in five species of Lenophyllum suggest that they may be polyploids on a basic 11, but this number has not been found. Three species have 8-12 distinctively large chromosomes that do not pair with each other in their hybrids and probably belong to the same genome. In hybrids of many polyploid Mexican Crassulaceae preferential pairing occurs between corresponding chromosomes of their multiple genomes, which indicates that they are autopolyploids. However, little or no preferential pairing occurs between chromosomes of Lenophyllum in its hybrids, and its species appear to be allopolyploids. The putative parents are unknown.     

Occurrence of polyploidy in the fishes

Polyploidy, the multiplication of entire setsof chromosomes beyond the normal set of two,has occurred extensively, independently, and isoften repeated in many groups of fish, from thesharks to the higher teleosts. While there areseveral ways that a polyploid fish can develop,environmental change and hybrid stabilizationmay play a large role in the initiation of anew polyploid species. Despite its prevalence,the importance of polyploidy in the evolutionof the fishes is unclear. Polyploidy is morecommon in the lower teleosts than the higherteleosts, possibly due to an advantage gainedthrough decreased specialization in the lowerteleosts, a decreased viability of polyploidyin the higher fish, or both. Polyploid fishcould gain an advantage over diploid fishthrough increased heterozygosity, divergence ofduplicate genes, and/or increased expression ofkey physiological proteins. While polyploidfish do not differ considerably from diploidsphenotypically, they may be at a disadvantage,or certain advantages may be lessened due to anoverall decrease in cell number. This papersummarizes all polyploid species of fish knownto-date, and discusses the possible roles andpathways for establishment of polyploidy in theevolution of the fishes.     

Extensive variation in chromosome number and genome size in sexual and parthenogenetic species of the jumping‐bristletail genus Machilis (Archaeognatha)

Parthenogenesis in animals is often associated with polyploidy and restriction to extreme habitats or recently deglaciated areas. It has been hypothesized that benefits conferred by asexual reproduction and polyploidy are essential for colonizing these habitats. However, while evolutionary routes to parthenogenesis are manifold, study systems including polyploids are scarce in arthropods. The jumping‐bristletail genus Machilis (Insecta: Archaeognatha) includes both sexual and parthenogenetic species, and recently, the occurrence of polyploidy has been postulated. Here, we applied flow cytometry, karyotyping, and mitochondrial DNA sequencing to three sexual and five putatively parthenogenetic Eastern‐Alpine Machilis species to investigate whether (1) parthenogenesis originated once or multiply and (2) whether parthenogenesis is strictly associated with polyploidy. The mitochondrial phylogeny revealed that parthenogenesis evolved at least five times independently among Eastern‐Alpine representatives of this genus. One parthenogenetic species was exclusively triploid, while a second consisted of both diploid and triploid populations. The three other parthenogenetic species and all sexual species were diploid. Our results thus indicate that polyploidy can co‐occur with parthenogenesis, but that it was not mandatory for the emergence of parthenogenesis in Machilis. Overall, we found a weak negative correlation of monoploid genome size (Cx) and chromosome base number (x), and this connection is stronger among parthenogenetic species alone. Likewise, monoploid genome size decreased with elevation, and we therefore hypothesize that genome downsizing could have been crucial for the persistence of alpine Machilis species. Finally, we discuss the evolutionary consequences of intraspecific chromosomal rearrangements and the presence of B chromosomes. In doing so, we highlight the potential of Alpine Machilis species for research on chromosomal and genome‐size alterations during speciation.     

Population genetic structure,migration, and polyploidy origin of a medicinal species Gynostemma pentaphyllum (Cucurbitaceae)

Gynostemma pentaphyllum, a member of family Cucurbitaceae, is a perennial creeping herb used as a traditional medicinal plant in China. In this study, six polymorphic nSSR and four EST‐SSR primers were used to genotype 1,020 individuals in 72 wild populations of G. pentaphyllum. The genetic diversity and population structure were investigated, and ecological niche modeling was performed to reveal the evolution and demographic history of its natural populations. The results show that G. pentaphyllum has a low level of genetic diversity and high level of variation among populations because of pervasive asexual propagation, genetic drift, and long‐term habitat isolation. Results of the Mantel test demonstrate that the genetic distance and geographic distance are significantly correlated among G. pentaphyllum natural populations. The populations can be divided into two clusters on the basis of genetic structure. Asymmetrical patterns of historical gene flow were observed among the clusters. For the contemporary, almost all the bidirectional gene flow of the related pairs was symmetrical with slight differences. Recent bottlenecks were experienced by 34.72% of the studied populations. The geographic range of G. pentaphyllum continues to expand northward and eastward from Hengduan Mountains. The present distribution of G. pentaphyllum is a consequence of its complex evolution. Polyploidy in G. pentaphyllum is inferred to be polygenetic. Finally, G. pentaphyllum is a species in need of protection, so in situ and ex situ measures should be considered in the future.     

Nuclear DNA variation, chromosome numbers and polyploidy in the endemic and indigenous grass flora of New Zealand

BACKGROUND AND AIMS: Little information is available on DNA C-values for the New Zealand flora. Nearly 85 % of the named species of the native vascular flora are endemic, including 157 species of Poaceae, the second most species-rich plant family in New Zealand. Few C-values have been published for New Zealand native grasses, and chromosome numbers have previously been reported for fewer than half of the species. The aim of this research was to determine C-values and chromosome numbers for most of the endemic and indigenous Poaceae from New Zealand. SCOPE: To analyse DNA C-values from 155 species and chromosome numbers from 55 species of the endemic and indigenous grass flora of New Zealand. KEY RESULTS: The new C-values increase significantly the number of such measurements for Poaceae worldwide. New chromosome numbers were determined from 55 species. Variation in C-value and percentage polyploidy were analysed in relation to plant distribution. No clear relationship could be demonstrated between these variables. CONCLUSIONS: A wide range of C-values was found in the New Zealand endemic and indigenous grasses. This variation can be related to the phylogenetic position of the genera, plants in the BOP (Bambusoideae, Oryzoideae, Pooideae) clade in general having higher C-values than those in the PACC (Panicoideae, Arundinoideae, Chloridoideae + Centothecoideae) clade. Within genera, polyploids typically have smaller genome sizes (C-value divided by ploidy level) than diploids and there is commonly a progressive decrease with increasing ploidy level. The high frequency of polyploidy in the New Zealand grasses was confirmed by our additional counts, with only approximately 10 % being diploid. No clear relationship between C-value, polyploidy and rarity was evident.     

Effects of polyploidy and reproductive mode on life history trait expression

Ploidy elevation is increasingly recognized as a common and important source of genomic variation. Even so, the consequences and biological significance of polyploidy remain unclear, especially in animals. Here, our goal was to identify potential life history costs and benefits of polyploidy by conducting a large multiyear common garden experiment in Potamopyrgus antipodarum, a New Zealand freshwater snail that is a model system for the study of ploidy variation, sexual reproduction, host–parasite coevolution, and invasion ecology. Sexual diploid and asexual triploid and tetraploid P. antipodarum frequently coexist, allowing for powerful direct comparisons across ploidy levels and reproductive modes. Asexual reproduction and polyploidy are very often associated in animals, allowing us to also use these comparisons to address the maintenance of sex, itself one of the most important unresolved questions in evolutionary biology. Our study revealed that sexual diploid P. antipodarum grow and mature substantially more slowly than their asexual polyploid counterparts. We detected a strong negative correlation between the rate of growth and age at reproductive maturity, suggesting that the relatively early maturation of asexual polyploid P. antipodarum is driven by relatively rapid growth. The absence of evidence for life history differences between triploid and tetraploid asexuals indicates that ploidy elevation is unlikely to underlie the differences in trait values that we detected between sexual and asexual snails. Finally, we found that sexual P. antipodarum did not experience discernable phenotypic variance‐related benefits of sex and were more likely to die before achieving reproductive maturity than the asexuals. Taken together, these results suggest that under benign conditions, polyploidy does not impose obvious life history costs in P. antipodarum and that sexual P. antipodarum persist despite substantial life history disadvantages relative to their asexual counterparts.     

Wide variation in ploidy level and genome size in a New Zealand freshwater snail with coexisting sexual and asexual lineages

Natural animal populations are rarely screened for ploidy-level variation at a scale that allows detection of potentially important aberrations of common ploidy patterns. This type of screening can be especially important for the many mixed sexual/asexual systems in which sexuals are presumed to be dioecious diploids and asexuals are assumed to be triploid and all-female. For example, elevation of ploidy level above triploidy can be a source of genetic variation and raises the possibility of gene flow among ploidy levels and to asexual lineages. We used flow cytometry and mtDNA sequencing to characterize ploidy level and genome size in Potamopyrgus antipodarum, a New Zealand freshwater snail where obligate sexual (presumed diploid and dioecious) and obligate apomictic asexual (presumed triploid and nearly all female) individuals frequently coexist. We documented the widespread occurrence and multiple origins of polyploid males and individuals with >3× ploidy, and find that both are likely to be descended from asexual females. Our survey also suggested the existence of extensive variation in genome size. The discovery of widespread variation in ploidy level and genome size in such a well-studied system highlights the importance of broad, extensive, and ecologically representative sampling in uncovering ploidy level and genome-size variation in natural populations.     

The evolution of unisexuality in Calligrapha leaf beetles: molecular and ecological insights on multiple origins via interspecific hybridization

Interspecific hybridization is a well-established cause of unisexual origins in vertebrates. This mechanism is also suspected in other apomictic taxa, but compelling evidence is rare. Here, we evaluate this mechanism and other hypotheses for the evolutionary origins of unisexuality through an investigation of Calligrapha leaf beetles. This group provides an intriguing subject for studies of unisexual evolution because it presents a rare insect example of multiple apomictic thelytokous species within a primarily bisexual genus. To investigate unisexual evolution, this study conducts the first molecular systematic analysis of Calligrapha. This involved the collection and analysis of about 3000 bp of DNA sequences--representing RNA and protein-coding loci from mitochondrial and nuclear genomes--from 54 specimens of 25 Calligrapha species, including four unisexual tetraploid taxa. Phylogenetic and molecular clock analyses indicated independent and single evolutionary origins of each of these unisexual species during the Pleistocene. Significant phylogenetic incongruence was detected between mitochondrial and nuclear datasets and found to be especially associated with the asexual taxa. This pattern is expected when unisexual lineages arise via interspecific hybridization and thus represent genetic mosaics that possess certain nuclear alleles from the paternal species lineage and mitochondrial DNA (mtDNA) alleles from the maternal parent. Analyzing the mtDNA and nuclear relatedness of unisexuals with corresponding haplotypes of bisexual Calligrapha species allowed the putative identification of these maternal and paternal species lineages for each unisexual species. Strong phenotypic similarities between unisexual taxa and their paternal parent species supported a model that involves both backcrosses of interspecific hybrids with a paternal parent and unreduced gametes. This model accounts for the origins of apomixis, polyploidy, and an overrepresentation of paternal nuclear alleles (and associated phenotypes) in unisexuals. This model is also consistent with the tetraploid karyotypes of unisexual Calligrapha, in which three sets of chromosomes (of presumed paternal ancestry) are quite morphologically homogeneous compared to the fourth. Especially intriguing was a consistent association of unisexual species with the host plant of the paternal parent but never with the maternal host. The statistical implausibility of these patterns occurring by chance further supports our inference of parental species. Moreover, it points to a potentially critical role for host-association in the formation and preservation of unisexual lineages. These findings suggest that ecological factors are critical for the diversification of unisexual as well as bisexual taxa and thus point out new research directions in the area of ecological speciation.     

Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae)

To study the consequences of hybridization and genome duplication on polyploid genome evolution and adaptation, we used independently formed hybrids (Spartina x townsendii and Spartina x neyrautii) that originated from natural crosses between Spartina alterniflora, an American introduced species, and the European native Spartina maritima. The hybrid from England, S. x townsendii, gave rise to the invasive allopolyploid, salt-marsh species, Spartina anglica. Recent studies indicated that allopolyploid speciation may be associated with rapid genetic and epigenetic changes. To assess this in Spartina, we performed AFLP (amplified fragment length polymorphism) and MSAP (methylation sensitive amplification polymorphism) on young hybrids and the allopolyploid. By comparing the subgenomes in the hybrids and the allopolyploid to the parental species, we inferred structural changes that arose repeatedly in the two independently formed hybrids. Surprisingly, 30% of the parental methylation patterns are altered in the hybrids and the allopolyploid. This high level of epigenetic regulation might explain the morphological plasticity of Spartina anglica and its larger ecological amplitude. Hybridization rather than genome doubling seems to have triggered most of the methylation changes observed in Spartina anglica.     

Morphofunctional characterization and ploidy levels of cells in the bivalve digestive gland, with special reference to somatic polyploidy

This study investigates the histological organization and ploidy levels of the digestive gland cells in 29 species of marine, brackish water, and freshwater bivalves belonging to 5 subclasses. In all species studied, the digestive gland epithelium consists of two types of differentiated cells: digestive and basophilic. The nuclei of digestive cells contain the diploid quantity of DNA. Basophilic (secretory) cells often remain diploid also; however, in a number of species all or some of the cells showed an increase in the quantity of DNA per nucleus up to 4c. Tetraploidy of basophilic cells in several species of the subclass Anomalodesmata seems to be due to carnivory. In other species, no apparent correlation was found between selective polyploidy of basophilic cells and environmental conditions or biology traits of the bivalves. Additionally, there was no relationship between the occurrence of polyploid cells and the lifespan of the investigated species. In the bivalve mollusks, somatic polyploidy appears to be an adaptation; it is neither a tissue growth strategy nor a component of the cytodifferentiation program.     

Repeated regions in mitochondrial genomes: Distribution, origin and evolutionary significance

All complete or nearly complete mitochondrial genomes of Metazoa (2819) have been subject to bioinformatic analysis to investigate the distribution and features of repeated and palindromic sequences. Repeats are ubiquitous, with 29.9% of genomes containing at least one and 1.95% of total genome length being repeated. Repeat boundaries were tested for the presence of secondary structure motifs, consensus sequences or small repeats, features generally reported as associated with duplications. No significant relationship was detected, suggesting the non ubiquitousness of such features. A mechanism related to gene conversion is proposed to explain the origin of small interspersed repeats.     

New chromosome numbers, meiotic behaviour and pollen fertility in American taxa of Lupinus (Leguminosae): contributions to taxonomic and evolutionary studies

Original chromosome determinations are presented for 20 American Lupinus taxa, including, for the first time, unifoliolate species, together with first data on meiotic behaviour and pollen fertility for some South American species. Most of the Brazilian multifoliolate L. lanatus, L. rubriflorus, L. multiflorus, L. paranensis, L. bracteolaris and L. reitzii and unifoliolate L. crotalarioides, L. guaraniticus and L. velutinus accessions analysed presented regular chromosome pairing. Meiotic indexes and estimations of pollen viability were higher than 90% for all species and accessions analysed, reflecting the generally regular meiotic behaviour of these plants. Chromosome numbers were determined for the first time for the eastern South‐American species L. guaraniticus, L. crotalarioides, L. paranensis, L. paraguariensis and L. velutinus (n = 18 or 2n = 36) and for the Andean L. ballianus, L. eanophyllus, L. huaronensis, L. semperflorens, plus another eight taxa (2n = 48) from Peru and Bolivia, and L. bandelierae (2n = 36) from Bolivia. Chromosome numbers were confirmed for L. lanatus, L. rubriflorus (2n = 36), L. bracteolaris (2n = 34) and L. microphyllus (2n = 48). In the three accessions of the North American unifoliolate species, L. cumulicola and L. villosus, a chromosome number (2n = 52) previously unknown among American taxa was found. The results of the study, plus published data, support the suggestions that south‐eastern South American species are a group cytologically differentiated from the Andean as well as from most other American ones, and that the Brazilian and the North American unifoliolate Lupinus had independent origins. © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society, 2006, 150 , 229–240.     

Rate variation among nuclear genes and the age of polyploidy in Gossypium

Molecular evolutionary rate variation in Gossypium (cotton) was characterized using sequence data for 48 nuclear genes from both genomes of allotetraploid cotton, models of its diploid progenitors, and an outgroup. Substitution rates varied widely among the 48 genes, with silent and replacement substitution levels varying from 0.018 to 0.162 and from 0.000 to 0.073, respectively, in comparisons between orthologous Gossypium and outgroup sequences. However, about 90% of the genes had silent substitution rates spanning a more narrow threefold range. Because there was no evidence of rate heterogeneity among lineages for any gene and because rates were highly correlated in independent tests, evolutionary rate is inferred to be a property of each gene or its genetic milieu rather than the clade to which it belongs. Evidence from approximately 200,000 nucleotides (40,000 per genome) suggests that polyploidy in Gossypium led to a modest enhancement in rates of nucleotide substitution. Phylogenetic analysis for each gene yielded the topology expected from organismal history, indicating an absence of gene conversion or recombination among homoeologs subsequent to allopolyploid formation. Using the mean synonymous substitution rate calculated across the 48 genes, allopolyploid cotton is estimated to have formed circa 1.5 million years ago (MYA), after divergence of the diploid progenitors about 6.7 MYA.     

Gene duplication and evolutionary novelty in plants

Duplication is a prominent feature of plant genomic architecture. This has led many researchers to speculate that gene duplication may have played an important role in the evolution of phenotypic novelty within plants. Until recently, however, it was difficult to make this connection. We are now beginning to understand how duplication has contributed to adaptive evolution in plants. In this review we introduce the sources of gene duplication and predictions of the various fates of duplicates. We also highlight several recent and pertinent examples from the literature. These examples demonstrate the importance of the functional characteristics of genes and the source of duplication in influencing evolutionary outcome.     

Plant species diversity and polyploidy in islands of natural vegetation isolated in extensive cultivated lands

Natural polyploidy is often related to a longer life span, vegetative reproduction and higher competitive ability. In this paper, we test the possibility that these characteristics may favour the survival of polyploid taxa under conditions of long-term habitat fragmentation. In islands of natural vegetation isolated in extensive vineyards located in the South of France and in a large neighbouring area of natural vegetation, plant species richness and the relative abundance of polyploid taxa were assessed according to island size, isolation and vegetation structure. High species richness was observed, with numerous species restricted to the islands, suggesting that these may constitute refugia. However, species richness was not related to island size or to degree of isolation except for the flora of the woody areas. A very positive effect of area fragmentation on plant richness was observed, which is probably attributable to relatively low species overlap among the islands. Particularly high species richness was observed in open areas, provided that these were not extensively colonized by shrubs which seem to be responsible for local extinction of many annual taxa. Polyploids, which comprised mostly perennial herbs and woody species, were predominant in all the islands and in the large reference area. In open habitats invaded by shrubby species, a higher relative frequency of polyploids was observed in islands than in the reference area. Moreover, polyploid taxa were present in a larger number of islands than the diploid taxa, which were often restricted to a single island, suggesting that, after a long period of isolation, the polyploids may still have a lower probability of extinction. Evidence was obtained from vegetation structure analysis that diploid and polyploid annual herbs were restricted to open habitats and were both eliminated by shrubby species. Conversely, the diploid perennial herbs were also significantly affected by shrub colonization whereas the polyploids were mostly present in shrubby areas. This suggests that the higher competitive ability of polyploid perennial herbs may constitute a critical factor responsible for their wider distribution over the islands. We report the implications of our findings on conservation strategies, more particularly for a Mediterranean flora.