Breaking down taxonomic barriers in polyploidy research

Effects of polyploidization and their evolutionary implications are revealed by heritable polyploidy in the haplodiploid wasp Nasonia vitripennis

Recurrent polyploidization occurred in the evolutionary history of most Eukaryota. However, how neopolyploid detriment (sterility, gigantism, gene dosage imbalances) has been overcome and even been bridged to evolutionary advantage (gene network diversification, mass radiation, range expansion) is largely unknown, particularly for animals. We used the parasitoid wasp Nasonia vitripennis, a rare insect system with heritable polyploidy, to begin addressing this knowledge gap. In Hymenoptera the sexes have different ploidies (haploid males, diploid females) and neopolyploids (diploid males, triploid females) occur for various species. Although such polyploids are usually sterile, those of N. vitripennis are reproductively capable and can even establish stable polyploid lines. To assess the effects of polyploidization, we compared a long-established polyploid line, the Whiting polyploid line (WPL) and a newly generated transformer knockdown line (tKDL) for fitness traits, absolute gene expression, and cell size and number. WPL polyploids have high male fitness and low female fecundity, while tKDL polyploids have poor male mate competition ability and high fertility. WPL has larger cells and cell number reduction, but the tKDL does not differ in this respect. Expression analyses of two housekeeping genes indicated that gene dosage is linked to sex irrespective of ploidy. Our study suggests that polyploid phenotypic variation may explain why some polyploid lineages thrive and others die out; a commonly proposed but difficult-to-test hypothesis. This documentation of diploid males (tKDL) with impaired competitive mating ability; triploid females with high fitness variation; and hymenopteran sexual dosage compensation (despite the lack of sex chromosomes) all challenges general assumptions on hymenopteran biology. We conclude that polyploidization is dependent on the duplicated genome characteristics and that genomes of different lines are unequally suited to survive diploidization. These results demonstrate the utility of N. vitripennis for delineating mechanisms of animal polyploid evolution, analogous to more advanced polyploid plant models.

Comparative and Phylogenetic Analysis of Complete Plastomes among Aristidoideae Species (Poaceae)

Aristidoideae is a subfamily in the PACMAD clade of family Poaceae, including three genera, Aristida, Stipagrostis, and Sartidia. In this study, the plastomes of Aristida adscensionis and Stipagrostis pennata were newly sequenced, and a total of 16 Aristidoideae plastomes were compared. All plastomes were conservative in genome size, gene number, structure, and IR boundary. Repeat sequence analysis showed that forward and palindrome repeats were the most common repeat types. The number of SSRs ranged from 30 (Sartidia isaloensis) to 54 (Aristida purpurea). Codon usage analysis showed that plastome genes preferred to use codons ending with A/T. A total of 12 highly variable regions were screened, including four protein coding sequences (matK, ndhF, infA, and rpl32) and eight non-coding sequences (rpl16-1-rpl16-2, ccsA-ndhD, trnY-GUA-trnD-GUC, ndhF-rpl32, petN-trnC-GCA, trnT-GGU-trnE-UUC, trnG-GCC-trnfM-CAU, and rpl32-trnL-UAG). Furthermore, the phylogenetic position of this subfamily and their intergeneric relationships need to be illuminated. All Maximum Likelihood and Bayesian Inference trees strongly support the monophyly of Aristidoideae and each of three genera, and the clade of Aristidoideae and Panicoideae was a sister to other subfamilies in the PACMAD clade. Within Aristidoideae, Aristida is a sister to the clade composed of Stipagrostis and Sartidia. The divergence between C₄ Stipagrostis and C₃ Sartidia was estimated at 11.04 Ma, which may be associated with the drought event in the Miocene period. Finally, the differences in carbon fixation patterns, geographical distributions, and ploidy may be related to the difference of species numbers among these three genera. This study provides insights into the phylogeny and evolution of the subfamily Aristidoideae.

When it only takes one to tango: assessing the impact of apomixis in the fern genus Pteris

PREMISE

Apomixis (asexual reproduction by seed, spore, or egg) has evolved repeatedly across the tree of life. Studies of animals and angiosperms show that apomictic lineages are often evolutionarily short-lived and frequently exhibit different distributions than their sexual relatives. However, apomixis is rare in these groups. Less is known about the role of apomixis in the evolution and biogeography of ferns, in which ~10% of species are apomictic. Apomixis is especially common in the fern genus Pteris (34-39% of species); however, because of the limited taxonomic and geographic sampling of previous studies, the true frequency of apomixis and its associations with geography and phylogeny in this lineage remain unclear.

METHODS

We used spore analyses of herbarium specimens to determine reproductive mode for 127 previously unsampled Pteris species. Then we leveraged biogeographic and phylogenetic analyses to estimate the global distribution and evolution of apomixis in Pteris.

RESULTS

Among all Pteris species examined, we found that 21% are exclusively apomictic, 71% are exclusively sexual, and 8% have conflicting reports. Apomixis is unevenly distributed across the range of the genus, with the Paleotropics exhibiting the highest frequency, and has evolved numerous times across the Pteris phylogeny, with predominantly East Asian and South Asian clades containing the most apomictic species.

CONCLUSIONS

Apomixis arises frequently in Pteris, but apomictic species do not appear to diversify. Species that encompass both apomictic and sexual populations have wider ranges than exclusively sexual or apomictic species, which suggests that sexual and apomictic ferns could occupy separate ecological niches.

The Plot Thickens: Haploid and Triploid-Like Thalli, Hybridization, and Biased Mating Type Ratios in Letharia

The study of the reproductive biology of lichen fungal symbionts has been traditionally challenging due to their complex lifestyles. Against the common belief of haploidy, a recent genomic study found a triploid-like signal in Letharia. Here, we infer the genome organization and reproduction in Letharia by analyzing genomic data from a pure culture and from thalli, and performing a PCR survey of the MAT locus in natural populations. We found that the read count variation in the four Letharia specimens, including the pure culture derived from a single sexual spore of L. lupina, is consistent with haploidy. By contrast, the L. lupina read counts from a thallus' metagenome are triploid-like. Characterization of the mating-type locus revealed a conserved heterothallic configuration across the genus, along with auxiliary genes that we identified. We found that the mating-type distributions are balanced in North America for L. vulpina and L. lupina, suggesting widespread sexual reproduction, but highly skewed in Europe for L. vulpina, consistent with predominant asexuality. Taken together, we propose that Letharia fungi are heterothallic and typically haploid, and provide evidence that triploid-like individuals are hybrids between L. lupina and an unknown Letharia lineage, reconciling classic systematic and genetic studies with recent genomic observations.

A Recently Formed Triploid Cardamine insueta Inherits Leaf Vivipary and Submergence Tolerance Traits of Parents

Contemporary speciation provides a unique opportunity to directly observe the traits and environmental responses of a new species. Cardamine insueta is an allotriploid species that appeared within the past 150 years in a Swiss village, Urnerboden. In contrast to its two progenitor species, Cardamine amara and Cardamine rivularis that live in wet and open habitats, respectively, C. insueta is found in-between their habitats with temporal water level fluctuation. This triploid species propagates clonally and serves as a triploid bridge to form higher ploidy species. Although niche separation is observed in field studies, the mechanisms underlying the environmental robustness of C. insueta are not clear. To characterize responses to a fluctuating environment, we performed a time-course analysis of homeolog gene expression in C. insueta in response to submergence treatment. For this purpose, the two parental (C. amara and C. rivularis) genome sequences were assembled with a reference-guided approach, and homeolog-specific gene expression was quantified using HomeoRoq software. We found that C. insueta and C. rivularis initiated vegetative propagation by forming ectopic meristems on leaves, while C. amara did not. We examined homeolog-specific gene expression of three species at nine time points during the treatment. The genome-wide expression ratio of homeolog pairs was 2:1 over the time-course, consistent with the ploidy number. By searching the genes with high coefficient of variation of expression over time-course transcriptome data, we found many known key transcriptional factors related to meristem development and formation upregulated in both C. rivularis and rivularis-homeolog of C. insueta, but not in C. amara. Moreover, some amara-homeologs of these genes were also upregulated in the triploid, suggesting trans-regulation. In turn, Gene Ontology analysis suggested that the expression pattern of submergence tolerant genes in the triploid was inherited from C. amara. These results suggest that the triploid C. insueta combined advantageous patterns of parental transcriptomes to contribute to its establishment in a new niche along a water-usage gradient.

Using species distribution models to locate the potential cradles of the allopolyploid Gypsophila bermejoi G. López (Caryophyllaceae)

Polyploidy has been an influential force in plant evolution, playing a crucial role in diversification. Differences in polyploid and diploid distributions have been long noted, with polyploid taxa especially abundant in harsh environments. These plants have higher photosynthetic rates and/or higher tolerance to water deficits. Moreover, there is data pointing to an increase in the rate of unreduced gamete formation by plants under conditions of stress. Accordingly, a higher frequency of polyploid individuals would be expected in populations living under extreme environments, a phenomenon that may be relevant when considering the origin of allopolyploid species. Hybridization between distinct autopolyploids is known to produce allopolyploids and hence, a high frequency of compatible autopolyploids in an area could enhance the formation of stable populations of the corresponding allopolyploid hybrid. Here we consider the allopolyploid species Gypsophila bermejoi G. López and its parental taxa G. struthium L. subsp. struthium and G. tomentosa L. We have used Species Distribution Models to locate areas with low bioclimatic suitability for both parental taxa during the Last Glacial Maximum (LGM), hypothesizing that the rate of tetraploid hybrid formation would be higher than expected where low suitability areas of both parental species overlap. We selected those areas taking into account the strict gypsophyllic nature of these taxa. There is data pointing to a post-glacial origin of the current G. bermejoi populations and according to our hypothesis, such locations could be centers for hybrid tetraploid formation or potential cradles of this species. Indeed, potential Mid-Holocene cradles were also identified in this manner. The evolution of bioclimatic suitability in both LGM and Mid-Holocene cradles was studied to assess the possible survival of the hybrids, and the current distribution of G. bermejoi proved to be consistent with our hypothesis.

First Report on Successful Triploidy Induction in Clarias gariepinus (Burchell, 1822) Using Electroporation

This study investigated the use of electric-shock in inducing triploidy in African catfish Clarias gariepinus. To achieve this, three voltages (9, 12, 21 V) were applied for different durations (3, 5, 10 min). The shock was initiated approximately three minutes after fertilization followed by incubation in ambient temperature. After incubation, hatchability and survival rates were determined while ploidy status of the treatment fishes was confirmed in one-month-old fingerlings using the exclusive triploid range of the erythrocyte major axis previously reported for the same species (11.9–14.9 μm) and by cytogenetic analysis of the chromosome. The results showed triploidy were achieved in 10 to 85% of the treatment groups. A consistent trend of decrease in hatchability and an increase in triploidy rate was observed with increased electroporation voltages and shock durations. The mean erythrocyte major axis length of triploid progenies (3n = 84) was observed to be between 11.3–14.6 μm and was higher than the range of 7.0–10.5 μm recorded for diploid progenies (2n = 56). It was concluded that electric shock can be used to induce triploidy in African catfish C. gariepinus.

Evolutionary history and structure of nuclear matrix constituent proteins, the plant analogues of lamins

Nuclear matrix constituent proteins (NMCPs), the structural components of the plant lamina, are considered to be the analogues of lamins in plants based on numerous structural and functional similarities. Current phylogenetic knowledge suggests that, in contrast to lamins, which are widely distributed in eukaryotes, NMCPs are taxonomically restricted to Streptophyta. At present, most information about NMCPs comes from angiosperms, and virtually no data are available from more ancestral groups. In angiosperms, the NMCP family comprises two phylogenetic groups, NMCP1 and NMCP2, which evolved from the NMCP1 and NMCP2 progenitor genes. Based on sequence conservation and the presence of NMCP-specific domains, we determined the structure and number of NMCP genes present in different Streptophyta clades. We analysed 91 species of embryophytes and report additional NMCP sequences from mosses, liverworts, clubmosses, horsetail, ferns, gymnosperms, and Charophyta algae. Our results confirm an origin of NMCPs in Charophyta (the earliest diverging group of Streptophyta), resolve the number and structure of NMCPs in the different clades, and propose the emergence of additional NMCP homologues by whole-genome duplication events. Immunofluorescence microscopy demonstrated localization of a basal NMCP from the moss Physcomitrella patens at the nuclear envelope, suggesting a functional conservation for basal and more evolved NMCPs.

Distribution and ecological segregation on regional and microgeographic scales of the diploid Centaurea aspera L., the tetraploid C. seridis L., and their triploid hybrids (Compositae)

Although polyploidy is considered a ubiquitous process in plants, the establishment of new polyploid species may be hindered by ecological competition with parental diploid taxa. In such cases, the adaptive processes that result in the ecological divergence of diploids and polyploids can lead to their co-existence. In contrast, non-adaptive processes can lead to the co-existence of diploids and polyploids or to differentiated distributions, particularly when the minority cytotype disadvantage effect comes into play. Although large-scale studies of cytotype distributions have been widely conducted, the segregation of sympatric cytotypes on fine scales has been poorly studied. We analysed the spatial distribution and ecological requirements of the tetraploid Centaurea seridis and the diploid Centaurea aspera in east Spain on a large scale, and also microspatially in contact zones where both species hybridise and give rise to sterile triploid hybrids. On the fine scale, the position of each Centaurea individual was recorded along with soil parameters, accompanying species cover and plant richness. On the east Spanish coast, a slight latitudinal gradient was found. Tetraploid C. seridis individuals were located northerly and diploid C. aspera individuals southerly. Tetraploids were found only in the habitats with strong anthropogenic disturbance. In disturbed locations with well-developed semi-fixed or fixed dunes, diploids and tetraploids could co-exist and hybridise. However, on a fine scale, although taxa were spatially segregated in contact zones, they were not ecologically differentiated. This finding suggests the existence of non-adaptive processes that have led to their co-existence. Triploid hybrids were closer to diploid allogamous mothers (C. aspera) than to tetraploid autogamous fathers (C. seridis). This may result in a better ability to compete for space in the tetraploid minor cytotype, which might facilitate its long-term persistence.

Polyploid lineages in the genus Porphyra

Whole genome duplication is now accepted as an important evolutionary force, but the genetic factors and the life history implications affecting the existence and abundance of polyploid lineages within species are still poorly known. Polyploidy has been mainly studied in plant model species in which the sporophyte is the dominant phase in their life history. In this study, we address such questions in a novel system (Porphyra, red algae) where the gametophyte is the dominant phase in the life history. Three Porphyra species (P. dioica, P. umbilicalis, and P. linearis) were used in comparisons of ploidy levels, genome sizes and genetic differentiation using flow cytometry and 11 microsatellite markers among putative polyploid lineages. Multiple ploidy levels and genome sizes were found in Porphyra species, representing different cell lines and comprising several cytotype combinations among the same and different individuals. In P. linearis, genetic differentiation was found among three polyploid lineages: triploid, tetraploid and mixoploids, representing different evolutionary units. We conclude that the gametophytic phase (n) in Porphyra species is not haploid, contradicting previous theories. New hypotheses for the life histories of Porphyra species are discussed.

Computation of the inverse additive relationship matrix for autopolyploid and multiple-ploidy populations

Rules to generate the inverse additive relationship matrix (A ^-1 ) are defined to enable the adoption restricted maximum likelihood (REML) and best linear unbiased prediction (BLUP) in autopolyploid populations with multiple ploidy levels. Many important agronomic, horticultural, ornamental, forestry, and aquaculture species are autopolyploids. However, the adoption of restricted maximum likelihood (REML), for estimating co/variance components, and best linear unbiased prediction (BLUP), for predicting breeding values, has been hampered in autopolyploid breeding by the absence of an appropriate means of generating the inverse additive relationship matrix (A ^-1 ). This paper defines rules to generate the A ^-1 of autopolyploid populations comprised of individuals of the same or different ploidy-levels, including populations exhibiting (1) odd-numbered ploidy levels (e.g. triploids), (2) sex-based differences in the probability that gametic genes are identical by descent and (3) somatic chromosome doubling. Inbreeding, due to double reduction, in autopolyploid founders in the absence of mating among relatives is also accounted for. A previously defined approach is modified, whereby rules are initially defined to build an inverse matrix of kinship coefficients (K ^-1 ), which is then used to generate A ^-1 . An R package (polyAinv; https://github.com/mghamilton/polyAinv ) to implement these rules has been developed and examples of analyses provided. The adoption of REML and BLUP methods made possible by these new rules has the potential to provide further insights into the quantitative genetic architecture of autopolyploid and multiple-ploidy populations, improve estimates of breeding values, and increase genetic gains made through recurrent selection.

The role of triploids in the origin and evolution of polyploids of Turnera sidoides complex (Passifloraceae, Turneroideae)

Triploids can play an important role in polyploid evolution. However, their frequent sterility is an obstacle for the origin and establishment of neotetraploids. Here we analyzed the microsporogenesis of triploids (x = 7) and the crossability among cytotypes of Turnera sidoides, aiming to test the impact of triploids on the origin and demographic establishment of tetraploids in natural populations. Triploids of T. sidoides exhibit irregular meiotic behavior. The high frequency of monovalents and of trivalents with non-convergent orientations results in unbalanced and/or non-viable male gametes. In spite of abnormalities in chromosome pairing and unbalanced chromosome segregation, triploids are not completely sterile and yielded up to 67% of viable pollen. Triploids that originated by the fusion of 2n × n gametes of the same taxon showed more regular meiotic behavior and higher fertility than triploids from the contact zone of diploids and tetraploids or triploids of hybrid origin. The reproductive isolation of T. sidoides cytotypes of different ploidy level is not strict and the 'triploid block' may be overcome occasionally. Triploids of T. sidoides produce diploid and triploid progeny suggesting that new generations of polyploids could originate from crosses between triploids or from backcrosses with diploids. The capability of T. sidoides to multiply asexually by rhizomes, would enhance the likelihood that a low frequency of neopolyploids can be originated and maintained in natural populations of T. sidoides.

Congruent population structure across paralogous and nonparalogous loci in Salish Sea chum salmon (Oncorhynchus keta)

Whole-genome duplications are major evolutionary events with a lasting impact on genome structure. Duplication events complicate genetic analyses as paralogous sequences are difficult to distinguish; consequently, paralogs are often excluded from studies. The effects of an ancient whole-genome duplication (approximately 88 MYA) are still evident in salmonids through the persistence of numerous paralogous gene sequences and partial tetrasomic inheritance. We use restriction site-associated DNA sequencing on 10 collections of chum salmon from the Salish Sea in the USA and Canada to investigate genetic diversity and population structure in both tetrasomic and rediploidized regions of the genome. We use a pedigree and high-density linkage map to identify paralogous loci and to investigate genetic variation across the genome. By applying multivariate statistical methods, we show that it is possible to characterize paralogous loci and that they display similar patterns of population structure as the diploidized portion of the genome. We find genetic associations with the adaptively important trait of run-timing in both sets of loci. By including paralogous loci in genome scans, we can observe evolutionary signals in genomic regions that have routinely been excluded from population genetic studies in other polyploid-derived species.

The Case of the Missing Ancient Fungal Polyploids

Polyploidy-the increase in the number of whole chromosome sets-is an important evolutionary force in eukaryotes. Polyploidy is well recognized throughout the evolutionary history of plants and animals, where several ancient events have been hypothesized to be drivers of major evolutionary radiations. However, fungi provide a striking contrast: while numerous recent polyploids have been documented, ancient fungal polyploidy is virtually unknown. We present a survey of known fungal polyploids that confirms the absence of ancient fungal polyploidy events. Three hypotheses may explain this finding. First, ancient fungal polyploids are indeed rare, with unique aspects of fungal biology providing similar benefits without genome duplication. Second, fungal polyploids are not successful in the long term, leading to few extant species derived from ancient polyploidy events. Third, ancient fungal polyploids are difficult to detect, causing the real contribution of polyploidy to fungal evolution to be underappreciated. We consider each of these hypotheses in turn and propose that failure to detect ancient events is the most likely reason for the lack of observed ancient fungal polyploids. We examine whether existing data can provide evidence for previously unrecognized ancient fungal polyploidy events but discover that current resources are too limited. We contend that establishing whether unrecognized ancient fungal polyploidy events exist is important to ascertain whether polyploidy has played a key role in the evolution of the extensive complexity and diversity observed in fungi today and, thus, whether polyploidy is a driver of evolutionary diversifications across eukaryotes. Therefore, we conclude by suggesting ways to test the hypothesis that there are unrecognized polyploidy events in the deep evolutionary history of the fungi.

Gene copy silencing and DNA methylation in natural and artificially produced allopolyploid fish

Allelic silencing is an important mechanism for coping with gene dosage changes in polyploid organisms that is well known in allopolyploid plants. Only recently, it was shown in the allotriploid fish Squalius alburnoides that this process also occurs in vertebrates. However, it is still unknown whether this silencing mechanism is common to other allopolyploid fish, and which mechanisms might be responsible for allelic silencing. We addressed these questions in a comparative study between Squalius alburnoides and another allopolyploid complex, the Amazon molly (Poecilia formosa). We examined the allelic expression patterns for three target genes in four somatic tissues of natural allo-anorthoploids and laboratory-produced tri-genomic hybrids of S. alburnoides and P. formosa. Also, for both complexes, we evaluated the correlation between total DNA methylation level and the ploidy status and genomic composition of the individuals. We found that allelic silencing also occurs in other allopolyploid organisms besides the single one that was previously known. We found and discuss disparities within and between the two considered complexes concerning the pattern of allele-specific expression and DNA methylation levels. Disparities might be due to intrinsic characteristics of each genome involved in the hybridization process. Our findings also support the idea that long-term evolutionary processes have an effect on the allele expression patterns and possibly also on DNA methylation levels.

Refinement of the karyological aspects of Psidium guineense (Swartz, 1788): a comparison with Psidium guajava (Linnaeus, 1753)

Euploidy plays an important role in the evolution and diversification of Psidium Linnaeus, 1753. However, few data about the nuclear DNA content, chromosome characterization (morphometry and class) and molecular markers have been reported for this genus. In this context, the present study aims to shed light on the genome of Psidium guineense Swartz, 1788, comparing it with Psidium guajava Linnaeus, 1753. Using flow cytometry, the nuclear 2C value of Psidium guineense was 2C = 1.85 picograms (pg), and the karyotype showed 2n = 4x = 44 chromosomes. Thus, Psidium guineense has four chromosome sets, in accordance with the basic chromosome number of Psidium (x = 11). In addition, karyomorphometric analysis revealed morphologically identical chromosome groups in the karyotype of Psidium guineense. The high transferability of microsatellites (98.6%) further corroborates with phylogenetic relationship between Psidium guajava and Psidium guineense. Based on the data regarding nuclear genome size, karyotype morphometry and molecular markers of Psidium guineense and Psidium guajava (2C = 0.95 pg, 2n = 2x = 22 chromosomes), Psidium guineense is a tetraploid species. These data reveal the role of euploidy in the diversification of the genus Psidium.

Speciation by genome duplication: Repeated origins and genomic composition of the recently formed allopolyploid species Mimulus peregrinus

Whole genome duplication (polyploidization) is a mechanism of “instantaneous” species formation that has played a major role in the evolutionary history of plants. Much of what we know about the early evolution of polyploids is based upon studies of a handful of recently formed species. A new polyploid hybrid (allopolyploid) species Mimulus peregrinus, formed within the last 140 years, was recently discovered on the Scottish mainland and corroborated by chromosome counts. Here, using targeted, high‐depth sequencing of 1200 genic regions, we confirm the parental origins of this new species from M. x robertsii, a sterile triploid hybrid between the two introduced species M. guttatus and M. luteus that are naturalized and widespread in the United Kingdom. We also report a new population of M. peregrinus on the Orkney Islands and demonstrate that populations on the Scottish mainland and Orkney Islands arose independently via genome duplication from local populations of M. x robertsii. Our data raise the possibility that some alleles are already being lost in the evolving M. peregrinus genomes. The recent origins of a new species of the ecological model genus Mimulus via allopolyploidization provide a powerful opportunity to explore the early stages of hybridization and genome duplication in naturally evolved lineages.

Natural pathways to polyploidy in plants and consequences for genome reorganization

The last decade highlighted polyploidy as a rampant evolutionary process that triggers drastic genome reorganization, but much remains to be understood about their causes and consequences in both autopolyploids and allopolyploids. Here, we provide an overview of the current knowledge on the pathways leading to different types of polyploids and patterns of polyploidy-induced genome restructuring and functional changes in plants. Available evidence leads to a tentative 'diverge, merge and diverge' model supporting polyploid speciation and stressing patterns of divergence between diploid progenitors as a suitable predictor of polyploid genome reorganization. The merging of genomes at the origin of a polyploid lineage may indeed reveal different kinds of incompatibilities (chromosomal, genic and transposable elements) that have accumulated in diverging progenitors and reduce the fitness of nascent polyploids. Accordingly, successful polyploids have to overcome these incompatibilities through non-Mendelian mechanisms, fostering polyploid genome reorganization in association with the establishment of new lineages. See also sister article focusing on animals by Collares-Pereira et al., in this themed issue.

Autopolyploidy differentially influences body size in plants, but facilitates enhanced accumulation of secondary metabolites, causing increased cytosine methylation

Whole genome duplication leads to autopolyploidy and brings about an increase in cell size, concentration of secondary metabolites and enhanced cytosine methylation. The increased cell size offers a positive advantage to polyploids for cell-surface-related activities, but there is a differential response to change in body size across species and taxonomic groups. Although polyploidy has been very extensively studied, having genetic, ecological and evolutionary implications, there is no report that underscores the significance of native secondary metabolites vis-à-vis body size with ploidy change. To address this problem we targeted unique diploid-autotetraploid paired sets of eight diverse clones of six species of Cymbopogon- a species complex of aromatic grasses that accumulate qualitatively different monoterpene essential oils (secondary metabolite) in their vegetative biomass. Based on the qualitative composition of essential oils and the plant body size relationship between the diploid versus autotetraploid paired sets, we show that polyploidy brings about enhanced accumulation of secondary metabolites in all cases, but exerts differential effects on body size in various species. It is observed that the accumulation of alcohol-type metabolites (e.g. geraniol) does not inhibit increase in body size with ploidy change from 2× to 4× (r = 0.854, P < 0.01), but aldehyde-type metabolites (e.g. citral) appear to drastically impede body development (r = -0.895). Such a differential response may be correlated to the metabolic steps involved in the synthesis of essential oil components. When changed to tetraploidy, the progenitor diploids requiring longer metabolic steps in production of their secondary metabolites are stressed, and those having shorter metabolite routes better utilize their resources for growth and vigour. In situ immunodetection of 5-methylcytosine sites reveals enhanced DNA methylation in autopolyploids. It is underpinned that the qualitative composition of secondary metabolites found in the vegetative biomass of the progenitor diploid has a decisive bearing on the body size of the derived autotetraploids and brings about an enhancement in genome-wide cytosine methylation.

A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses

BACKGROUND

Polyploidy is important from a phylogenetic perspective because of its immense past impact on evolution and its potential future impact on diversification, survival and adaptation, especially in plants. Molecular population genetics studies of polyploid organisms have been difficult because of problems in sequencing multiple-copy nuclear genes using Sanger sequencing. This paper describes a method for sequencing a barcoded mixture of targeted gene regions using next-generation sequencing methods to overcome these problems.

RESULTS

Using 64 3-bp barcodes, we successfully sequenced three chloroplast and two nuclear gene regions (each of which contained two gene copies with up to two alleles per individual) in a total of 60 individuals across 11 species of Australian Poa grasses. This method had high replicability, a low sequencing error rate (after appropriate quality control) and a low rate of missing data. Eighty-eight percent of the 320 gene/individual combinations produced sequence reads, and >80% of individuals produced sufficient reads to detect all four possible nuclear alleles of the homeologous nuclear loci with 95% probability.We applied this method to a group of sympatric Australian alpine Poa species, which we discovered to share an allopolyploid ancestor with a group of American Poa species. All markers revealed extensive allele sharing among the Australian species and so we recommend that the current taxonomy be re-examined. We also detected hypermutation in the trnH-psbA marker, suggesting it should not be used as a land plant barcode region. Some markers indicated differentiation between Tasmanian and mainland samples. Significant positive spatial genetic structure was detected at <100 km with chloroplast but not nuclear markers, which may be a result of restricted seed flow and long-distance pollen flow in this wind-pollinated group.

CONCLUSIONS

Our results demonstrate that 454 sequencing of barcoded amplicon mixtures can be used to reliably sample all alleles of homeologous loci in polyploid species and successfully investigate phylogenetic relationships among species, as well as to investigate phylogeographic hypotheses. This next-generation sequencing method is more affordable than and at least as reliable as bacterial cloning. It could be applied to any experiment involving sequencing of amplicon mixtures.

The evolutionary history of the allopolyploid Squalius alburnoides (Cyprinidae) complex in the northern Iberian Peninsula

Understanding the population structure, population dynamics and processes that give rise to polyploidy and helps to maintain it is central to our knowledge of the evolution of asexual vertebrates. Previous studies revealed high genetic diversity and several reproductive pathways in the southern populations of the Squalius alburnoides hybrid complex. In contrast, lower genetic variability and the associated limited chance of introducing new genetic combinations may threaten the survival of the northern Mondego populations. We analysed the genetic diversity and structure of nine populations of S. alburnoides in the Iberian Peninsula using microsatellite loci to provide further insights on the evolutionary history of this complex. Special attention was given to the less-studied northern populations (Mondego and Douro basins). Marked population structure, a high frequency of private alleles and a high diversity of some biotypes in the Douro basin indicate that some northern populations may not be at high risk of extinction, contrary to what was expected. The genetic diversity found in the northern Douro populations contradicts the general trend of remarkable genetic impoverishment northwards that occurs in other species and regions. The results indicate the possible existence of a glacial refugium in the Rabaçal River, corroborating findings in other species of this region. Historical events seem to have affected the geographical patterns of genetic variability found among and within the northern and southern populations of this complex and contributed to different patterns of genome composition. Therefore, historical events might have a major role in the long-term persistence of some polyploid hybrid taxa.

Complex distribution patterns, ecology and coexistence of ploidy levels of Allium oleraceum (Alliaceae) in the Czech Republic

BACKGROUND AND AIMS

Despite extensive study of polyploidy, its origin, and ecogeographical differences between polyploids and their diploid progenitors, few studies have addressed ploidy-level structure and patterns of ecogeographical differentiation at various spatial scales using detailed sampling procedures. The pattern of coexistence of polyploids in the geophyte Allium oleraceum at the landscape and locality scale and their ecology were studied.

METHODS

Flow cytometry and root-tip squashes were used to identify the ploidy level of 4347 plants from 325 populations sampled from the Czech Republic using a stratified random sampling procedure. Ecological differentiation among ploidy levels was tested by comparing sets of environmental variables recorded at each locality.

KEY RESULTS

Across the entire sampling area, pentaploids (2n = 5x = 40) predominated, while hexaploids (2n = 6x = 48) and tetraploids (2n = 4x = 32) were less frequent. The distribution of tetra- and hexaploids was partially sympatric (in the eastern part) to parapatric (in the western part of the Czech Republic) whereas pentaploids were sympatric with other cytotypes. Plants of different ploidy levels were found to be ecologically differentiated and the ruderal character of cytotypes increased in the direction 4x --> 5x --> 6x with the largest realized niche differences between tetra- and hexaploids. Most populations contained only one ploidy level (77 %), 22 % had two (all possible combinations) and 1 % were composed of three ploidy levels. The majority of 4x + 5x and 5x + 6x mixed populations occurred in sympatry with uniform populations of the participating cytotypes in sites with ecologically heterogeneous or marginal environment, suggesting secondary contact between cytotypes. Some mixed 4x + 6x populations dominated by tetraploids being sympatric and intermixed with uniform 4x populations might represent primary zones of cytotype contact. Almost no mixed accessions were observed on the fine spatial scale in mixed populations.

CONCLUSIONS

The results provide evidence for adaptive differences among ploidy levels, which may contribute to their complex distribution pattern. The prevalence of asexual reproduction, limited dispersal and equilibrium-disrupting processes may support local coexistence of cytotypes.

Body shape evolution among ploidy levels of the Squalius alburnoides hybrid complex (Teleostei, Cyprinidae)

Hybridization, ploidy level and genomic constitution may be important to respond to different environments, by producing different phenotypes and thus reducing competitive interaction. Through geometric morphometrics, we examined variation in body size and shape among biotypes of the Squalius alburnoides hybrid complex and their sperm donor (Squalius carolitertii). Results showed that S. carolitertii is significantly larger in size than the biotypes of the complex. No significant relationship was observed between ploidy and body size among S. alburnoides biotypes. Significant variation in body shape was found between S. carolitertii and S. alburnoides, and between tetraploids and the other biotypes. These differences in biotypes may reduce resource competition, highlighting the potential importance of resource availability favouring one biotype over another. In S. alburnoides, the adaptation to different trophic niches through modification of trophic morphology, body shapes, and feeding behaviour, may result from an increase in ploidy and genomic constitution. This adaptation may account also for the formation and maintenance of this nonsexual complex.

The role of hybridization in plant speciation

The importance of hybridization in plant speciation and evolution has been debated for decades, with opposing views of hybridization as either a creative evolutionary force or evolutionary noise. Hybrid speciation may occur at either the homoploid (i.e., between two species of the same ploidy) or the polyploid level, each with its attendant genetic and evolutionary consequences. Whereas allopolyploidy (i.e., resulting from hybridization and genome doubling) has long been recognized as an important mode of plant speciation, the implications of genome duplication have typically not been taken into account in most fields of plant biology. Recent developments in genomics are revolutionizing our views of angiosperm genomes, demonstrating that perhaps all angiosperms have likely undergone at least one round of polyploidization and that hybridization has been an important force in generating angiosperm species diversity. Hybridization and polyploid formation continue to generate species diversity, with several new allopolyploids having originated just within the past century or so. The origins of polyploid species-whether via hybridization between species or between genetically differentiated populations of a single species-and the immediate genetic consequences of polyploid formation are therefore receiving enthusiastic attention. The time is therefore right for a review of the role of hybridization in plant speciation.

Speciation towards tetraploidization after intermediate processes of non-sexual reproduction

Polyploidy, hybridization and variation in mating systems are central issues for a deeper understanding of animal evolution. The Iberian species Squalius alburnoides represents an example combining all three phenomena. Previous studies showed that S. alburnoides populations are mainly composed of triploid and diploid hybrid forms (mainly females), and that the tetraploid forms are rare or absent. Both populations from the Douro drainage reveal a distinct scenario: tetraploid individuals represent 85.6-97.5% of the population, with no sex ratio bias observed. Based on the flow cytometry measurements of blood and spermatozoa cells, microsatellite loci and experimental crosses, we describe here, for the first time, two symmetric allotetraploid populations (CCAA) that resumed normal meiosis after undergoing intermediate processes of non-sexual reproduction to give rise to a new sexually reproducing polyploid species. Prezygotic (habitat selection and assortative mating) and postzygotic mechanisms (nonviable embryos) are responsible for the reproductive isolation from other forms of the S. alburnoides complex (e.g. CA, CAA). This example illustrates how hybrid polyploid complexes may lead to speciation.

Sympatric diploid and hexaploid cytotypes of Senecio carniolicus (Asteraceae) in the Eastern Alps are separated along an altitudinal gradient

We explored the fine-scale distribution of cytotypes of the mountain plant Senecio carniolicus along an altitudinal transect in the Eastern Alps. Cytotypes showed a statistically significant altitudinal segregation with diploids exclusively found in the upper part of the transect, whereas diploids and hexaploids co-occurred in the lower range. Analysis of accompanying plant assemblages revealed significant differences between cytotypes along the entire transect but not within the lower part only, where both cytotypes co-occur. This suggests the presence of ecological differentiation between cytotypes with the diploid possessing the broader ecological niche. No tetraploids were detected, indicating the presence of strong crossing barriers.

Glacial in situ survival in the Western Alps and polytopic autopolyploidy in Biscutella laevigata L. (Brassicaceae)

Past climatic changes and especially the ice ages have had a great impact on both the distribution and the genetic composition of plant populations, but whether they promoted speciation is still controversial. The autopolyploid complex Biscutella laevigata is a classical example of polyploidy linked to glaciations and is an interesting model to explore migration and speciation driven by climate changes in a complex alpine landscape. Diploid taxa survived the last glacial maximum in several never-glaciated areas and autotetraploids are clearly dominant in the central parts of the Alps; however, previous range-wide studies failed to identify their diploid ancestor(s). This study highlights the phylogeographical relationships of maternal lineages in the Western Alps and investigates the polyploidy process using plastid DNA sequences (trnS-trnG and trnK-intron) combined with plastid DNA length polymorphism markers, which were transferable among Brassicaceae species. Twenty-one distinct plastid DNA haplotypes were distinguished in 67 populations densely sampled in the Western Alps and main lineages were identified by a median-joining network. The external Alps harboured high levels of genetic diversity, while the Central Alps contained only a subset of haplotypes due to postglacial recolonization. Several haplotypes were restricted to local peripheral refugia and evidence of in situ survival in central nunataks was detected by the presence of highly differentiated haplotypes swamped by frequent ones. As hierarchical genetic structure pointed to an independent evolution of the species in different biogeographical districts, and since tetraploids displayed haplotypes belonging to different lineages restricted to either the northern or the southern parts of the Alpine chain, polytopic autopolyploidy was also apparent in the Western Alps.

Chromosomal stasis in diploids contrasts with genome restructuring in auto- and allopolyploid taxa of Hepatica (Ranunculaceae)

Polyploidization and chromosomal rearrangements are recognized as major forces in plant evolution. Their role is investigated in the disjunctly distributed northern hemisphere Hepatica (Ranunculaceae). Chromosome numbers, karyotype morphology, banding patterns, 5S and 35S rDNA localization in all known species were investigated and interpreted in a phylogenetic context established from nuclear internal transcribed spacer (ITS) and plastid matK sequences. All species had a chromosome base number of x = 7. The karyotype was symmetric and showed little variation among diploids with one locus each of 5S and 35S rDNA, except for interpopulational variation concerning 35S rDNA loci number and localization in H. asiatica. Tetraploids exhibited chromosomal changes, including asymmetry and/or loss of rDNA loci. Nuclear and plastid sequences resulted in incongruent topologies because of the positions of some tetraploid taxa. The diversification of Hepatica occurred not earlier than the Pliocene. Genome restructuring, especially involving 35S rDNA, within a few million yr or less characterizes evolution of both auto- and allopolyploids and of the diploid species H. asiatica, which is the presumptive ancestor of two other diploid species.

Cancer as an evolutionary and ecological process

Neoplasms are microcosms of evolution. Within a neoplasm, a mosaic of mutant cells compete for space and resources, evade predation by the immune system and can even cooperate to disperse and colonize new organs. The evolution of neoplastic cells explains both why we get cancer and why it has been so difficult to cure. The tools of evolutionary biology and ecology are providing new insights into neoplastic progression and the clinical control of cancer.

Diagnosing duplications – can it be done?

New genes arise through duplication and modification of DNA sequences on a range of scales: single gene duplication, duplication of large chromosomal fragments and whole-genome duplication. Each duplication mechanism has specific characteristics that influence the fate of the resulting duplicates, such as the size of the duplicated fragment, the potential for dosage imbalance, the preservation or disruption of regulatory control and genomic context. The ability to diagnose or identify the mechanism that produced a pair of paralogs has the potential to increase our ability to reconstruct evolutionary history, to understand the processes that govern genome evolution and to make functional predictions based on paralogy. The recent availability of large amounts of whole-genome sequence, often from several closely related species, has stimulated a wealth of new computational methods to diagnose gene duplications.

Evolutionary biology of cancer

Cancer is driven by the somatic evolution of cell lineages that have escaped controls on replication and by the population-level evolution of genes that influence cancer risk. We describe here how recent evolutionary ecological studies have elucidated the roles of predation by the immune system and competition among normal and cancerous cells in the somatic evolution of cancer. Recent analyses of the evolution of cancer at the population level show how rapid changes in human environments have augmented cancer risk, how strong selection has frequently led to increased cancer risk as a byproduct, and how anticancer selection has led to tumor-suppression systems, tissue designs that slow somatic evolution, constraints on morphological evolution and even senescence itself. We discuss how applications of the tools of ecology and evolutionary biology are poised to revolutionize our understanding and treatment of this disease.

Multiple origins of tetraploid taxa in the Eurasian Bufo viridis subgroup

We used Q-banding and analyzed nucleolar organizing regions (NORs) to study the cytogenetic evolution of tetraploids within the Palearctic Bufo viridis subgroup, the only known amphibian complex comprising di-, tri- and tetraploid bisexually reproducing taxa. We examined three diploid (2n) nominal taxa (Bufo viridis viridis, B. v. turanensis, B. v. kermanensis) from five Eurasian localities and six tetraploid (4n) nominal taxa (B. oblongus, B. o. danatensis, B. pewzowi pewzowi, B. p. taxkorensis, B. p. unicolor, B. p. strauchi) from eight Central Asian localities. Homeologous chromosomes of 2n and 4n toads exhibit a similar morphology. Silver-staining and in situ hybridization revealed terminal NORs in the long arms of chromosomes 6 in all 2n but in only two out of four chromosomes 6 in all 4n taxa. Q-banding and a rapidly evolving mitochondrial marker suggest at least two origination events for Asian 4n toads: "Western Central Asian tetraploids" (B. oblongus Nikolsky, 1896) exhibit distinct differences within some chromosome quartets, which are divisible into pairs of chromosomes and may be allopolyploid. In contrast, "Central Asian tetraploids" (B. pewzowi Bedriaga, 1898) showed homogenous Q-banding patterns within each quartet, suggesting autopolyploidy. In Northeastern Iran, we discovered a zone of either common ancestry or hybridization of 2n and Western Central Asian 4n toads. This raises intriguing questions about how diploid and tetraploid taxa may evolve by exchanging genetic material.

Placing Paleopolyploidy in Relation to Taxon Divergence: A Phylogenetic Analysis in Legumes Using 39 Gene Families

Young polyploid events are easily diagnosed by various methods, but older polyploid events become increasingly difficult to identify as chromosomal rearrangements, tandem gene or partial chromosome duplications, changes in substitution rates among duplicated genes, pseudogenization or locus loss, and interlocus interactions complicate the means of inferring past genetic events. Genomic data have provided valuable information about the polyploid history of numerous species, but on their own fail to show whether related species, each with a polyploid past, share a particular polyploid event. A phylogenetic approach provides a powerful method to determine this but many processes may mislead investigators. These processes can affect individual gene trees, but most likely will not affect all genes, and almost certainly will not affect all genes in the same way. Thus, a multigene approach, which combines the large-scale aspect of genomics with the resolution of phylogenetics, has the power to overcome these difficulties and allow us to infer genomic events further into the past than would otherwise be possible. Previous work using synonymous distances among gene pairs within species has shown evidence for large-scale duplications in the legumes Glycine max and Medicago truncatula. We present a case study using 39 gene families, each with three or four members in G. max and the putative orthologues in M. truncatula, rooted using Arabidopsis thaliana. We tested whether the gene duplications in these legumes occurred separately in each lineage after their divergence (Hypothesis 1), or whether they share a round of gene duplications (Hypothesis 2). Many more gene family topologies supported Hypothesis 2 over Hypothesis 1 (11 and 2, respectively), even after synonymous distance analysis revealed that some topologies were providing misleading results. Only ca. 33% of genes examined support either hypothesis, which strongly suggests that single gene family approaches may be insufficient when studying ancient events with nuclear DNA. Our results suggest that G. max and M. truncatula, along with approximately 7000 other legume species from the same clade, share an ancient round of gene duplications, either due to polyploidy or to some other process.