Eco‐genetic additivity of diploids in allopolyploid wild wheats

Underpinnings of the distribution of allopolyploid species (hybrids with duplicated genome) along spatial and ecological gradients are elusive. As allopolyploid speciation combines the range of genetic and ecological characteristics of divergent diploids, allopolyploids initially show their additivity and are predicted to evolve differentiated ecological niches to establish in face of their competition. Here, we use four diploid wild wheats that differentially combined into four independent allopolyploid species to test for such additivity and assess the impact of ecological constraints on species ranges. Divergent genetic variation from diploids being fixed in heterozygote allopolyploids supports their genetic additivity. Spatial integration of comparative phylogeography and modelling of climatic niches supports ecological additivity of locally adapted diploid progenitors into allopolyploid species which subsequently colonised wide ranges. Allopolyploids fill suitable range to a larger extent than diploids and conservative evolution following the combination of divergent species appears to support their expansion under environmental changes.     

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.     

Unraveling reticulate evolution in North American dryopteris (dryopteridaceae)

ABSTRACT: BACKGROUND: The thirteen species of Dryopteris in North America have long been suspected of having undergone a complicated history of reticulate evolution via allopolyploid hybridization. Various explanations for the origins of the allopolyploid taxa have been suggested, and though most lines of evidence have supported the so-called "semicristata" hypothesis, contention over the group's history has continued in several recent, conflicting studies. RESULTS: Sequence data from nine plastid and two nuclear markers were collected from 73 accessions representing 35 species of Dryopteris. Sequences from each of the allopolyploids are most closely related to their progenitor species as predicted by the "semicristata" hypothesis. Allotetraploid D. campyloptera appears to be derived from a hybrid between diploid D. expansa and D. intermedia; D. celsa, from diploid D. ludoviciana x D. goldiana; and D. carthusiana and D. cristata, from diploid "D. semicristata" x D. intermedia and D. ludoviciana, respectively. Allohexaploid D. clintoniana appears to be derived from D. cristata x D.goldiana. The earliest estimated dates of formation of the allopolyploids, based on divergence time analyses, were within the last 6 Ma. We found no evidence for recurrent formation of any of the allopolyploids. The sexual allopolyploid taxa are derived from crosses between parents that show intermediate levels of genetic divergence relative to all pairs of potential progenitors. In addition, the four allotetraploids are transgressive with respect to geographic range relative to one or both of their parents (their ranges extend beyond those of the parents), suggesting that ecological advantages in novel habitats or regions may promote long-term regional coexistence of the hybrid taxa with their progenitors. CONCLUSIONS: This study provides the first thorough evaluation of the North American complex of woodferns using extensive sampling of taxa and genetic markers. Phylogenies produced from each of three datasets (one plastid and two nuclear) support the "semicristata" hypothesis, including the existence of a missing diploid progenitor, and allowed us to reject all competing hypotheses. This study demonstrates the value of using multiple, biparentally inherited markers to evaluate reticulate complexes, assess the frequency of recurrent polyploidization, and determine the relative importance of introgression vs. hybridization in shaping the histories of such groups.     

Sequence polymorphism in polyploid wheat and their d-genome diploid ancestor

Sequencing was used to investigate the origin of the D genome of the allopolyploid species Triticum aestivum and Aegilops cylindrica. A 247-bp region of the wheat D-genome Xwye838 locus, encoding ADP-glucopyrophosphorylase, and a 326-bp region of the wheat D-genome Gss locus, encoding granule-bound starch synthase, were sequenced in a total 564 lines of hexaploid wheat (T. aestivum, genome AABBDD) involving all its subspecies and 203 lines of Aegilops tauschii, the diploid source of the wheat D genome. In Ae. tauschii, two SNP variants were detected at the Xwye838 locus and 11 haplotypes at the Gss locus. Two haplotypes with contrasting frequencies were found at each locus in wheat. Both wheat Xwye838 variants, but only one of the Gss haplotypes seen in wheat, were found among the Ae. tauschii lines. The other wheat Gss haplotype was not found in either Ae. tauschii or 70 lines of tetraploid Ae. cylindrica (genomes CCDD), which is known to hybridize with wheat. It is concluded that both T. aestivum and Ae. cylindrica originated recurrently, with at least two genetically distinct progenitors contributing to the formation of the D genome in both species.     

Postglacial population expansion of Japanese macaques (<Emphasis Type="Italic">Macaca fuscata</Emphasis>) inferred from mitochondrial DNA phylogeography

We investigated the diversity and phylogeography of mitochondrial DNA (mtDNA) in Japanese macaques (Macaca fuscata), an endemic species in Japan that has the northernmost distribution of any non-human primate species. DNA samples from 135 localities representing the entire range of this species were compared. A total of 53 unique haplotypes were observed for the 412-bp partial mtDNA control region sequence, with length variation distinguishing the two subspecies. Clustering analyses suggested two putative major haplogroups, of which one was geographically distributed in eastern Japan and the other in western Japan. The populations in the east showed lower mtDNA diversity than those in the west. Phylogeographical relationships of haplotypes depicted with minimum spanning network suggested differences in population structure. Population expansion was significant for the eastern but not the western population, suggesting establishment of the ancestral population was relatively long ago in the west and recent in the east. Based on fossil evidence and past climate and vegetation changes, we inferred that the postulated population expansion may have taken place after the last glacial period (after 15,000 years ago). Mitochondrial DNA showed contrasting results in both variability and phylogenetic status of local populations to those of previous studies using protein variations, particularly for populations in the periphery of the range, with special inference on habitat change during the glacial period in response to cold adaptation. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Allopolyploidy in the Thalloid Liverwort Corsinia (Marchantiales)

The thalloid liverwort Corsinia coriandrina includes morphologically similar haploid and polyploid populations with an allopatric geographical distribution. Haploid and polyploid colonies of the Old World, and one polyploid colony from Texas have been analysed. The polyploid, monoecious cytotype has a wider geographical range and ecological tolerance than the haploid, dioecious cytotype which appears to be restricted to southern Europe and Macaronesia. Similarity coefficients between the two Old World cytotypes based on isozyme data show them to be more genetically divergent than suggested by their morphology, and to fit the definition of sibling species. Fixed heterozygosity in six of eight enzyme loci suggests an alloploid origin of the Old World polyploids. The haploid cytotype could be one of the putative parents. Alleles in the polyploid that were not detected in the haploid are presumably derived from an unknown progenitor. The polyploid New World colony shows significant genetic divergence; it represents a different allopolyploid sibling species. Accordingly, at least two independent origins of the polyploid must be supposed; one in the Old World; the other in the New World. The presumed autopolyploid origin of polyploid liverworts is once more challenged by our analysis of polyploid Corsinia. Indeed, autopolyploidy has still not been documented conclusively in any polyploid liverwort.     

Evolution of the perennial soybean polyploid complex (Glycine subgenus Glycine): a study of contrasts

Glycine subgenus Glycine , the sister group to the cultivated soybean and its progenitor, have received considerable study over several decades. The combination of biosystematic data and an extensive germplasm collection has provided a strong foundation for molecular systematic studies in the group, including those on allopolyploids. These studies have shown that the various polyploid taxa known from the subgenus are all part of a single large allopolyploid complex, linked by shared diploid genomes. Many elements of the complex have arisen recently, and most show evidence of recurrent origins. However, there are also many dissimilarities among even closely related polyploids. Polyploids differ from one another in such ways as number of origins, amount of allelic diversity harboured at different loci, bidirectional vs. unidirectional origins, retention of ribosomal gene homoeologues, success as measured by geographical range and abundance, and patterns of gene expression.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 583–597.     

Salt‐tolerance diversity in diploid and polyploid cotton (Gossypium) species

The development of salt‐tolerant genotypes is pivotal for the effective utilization of salinized land and to increase global crop productivity. Several cotton species comprise the most important source of textile fibers globally, and these are increasingly grown on marginal or increasingly saline agroecosystems. The allopolyploid cotton species also provide a model system for polyploid research, of relevance here because polyploidy was suggested to be associated with increased adaptation to stress. To evaluate the genetic variation of salt tolerance among cotton species, 17 diverse accessions of allopolyploid (AD‐genome) and diploid (A‐ and D‐genome) Gossypium were evaluated for a total of 29 morphological and physiological traits associated with salt tolerance. For most morphological and physiological traits, cotton accessions showed highly variable responses to 2 weeks of exposure to moderate (50 mm NaCl) and high (100 mm NaCl) hydroponic salinity treatments. Our results showed that the most salt‐tolerant species were the allopolyploid Gossypium mustelinum from north‐east Brazil, the D‐genome diploid Gossypium klotzschianum from the Galapagos Islands, followed by the A‐genome diploids of Africa and Asia. Generally, A‐genome accessions outperformed D‐genome cottons under salinity conditions. Allopolyploid accessions from either diploid genomic group did not show significant differences in salt tolerance, but they were more similar to one of the two progenitor lineages. Our findings demonstrate that allopolyploidy in itself need not be associated with increased salinity stress tolerance and provide information for using the secondary Gossypium gene pool to breed for improved salt tolerance.     

When polyploidy and hybridization produce a fuzzy taxon: the complex origin of the insular neoendemic Neotinea commutata (Orchidaceae)

Polyploidy and hybridization often provide genetic and phenotypic variability upon which evolutionary forces can act and are therefore considered as fundamental evolutionary processes for diversification in vascular plants, resulting in plant adaptation to changing environmental conditions. However, polyploid speciation is a complex process, potentially involving ecological divergence between lineages of different ploidies and/or genetic mixing with parental species. In the present study, we investigated the origins and dynamics of the Sicilian endemic orchid Neotinea commutata and its relationships with putative parental species. Molecular, cytogenetic and morphometric analyses revealed that N. commutata is a tetraploid derived from hybridization between N. tridentata and N. lactea. However, we also found variation in chromosome number and genome content within N. commutata, indicating that other events, including the possible replacement of the diploid progenitor N. tridentata by N. commutata, may have contributed, or still be contributing, to the evolutionary dynamics of this neoendemic taxon, which appears to be partially reproductively isolated from its progenitors. Distributional data indicate that the allopolyploid N. commutata has been able to establish and spread on the island when compared with its putative parents. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 707–720.     

Multiple origins of allopolyploid <Emphasis Type="Italic">Aegilops triuncialis</Emphasis>

Polyploidization is a key component of plant evolution. The number of independent origins of polyploid species traditionally has been underestimated. The objective of this study was to ascertain the number of origins of a tetraploid Aegilops species. We screened 84 primer sets to identify genome-specific primer sets for the tetraploid wheat relative [Aegilops triuncialis (UUCC genome)] and its diploid progenitors [Ae. umbellulata (UU genome) and Ae. caudata (CC genome)]. Primer sets G12 and G43 were U genome-specific and D21 was a C genome-specific primer. DNA sequence comparison of the G43 locus was used to estimate the number of polyploidization events in the formation of Ae. triuncialis. Parsimony analysis of G43 data revealed at least two independent formations of Ae. triuncialis. In the chloroplast hotspot region, located between genes rbcL and petA, sequence analysis suggested that at least three polyploidization origins might have occurred independently. Ae. triuncialis appears to be a tetraploid derived from multiple origins with minimal genome change after its formation.     

Repeated Polyploidy Drove Different Levels of Crossover Suppression between Homoeologous Chromosomes in Brassica napus Allohaploids

Allopolyploid species contain more than two sets of related chromosomes (homoeologs) that must be sorted during meiosis to ensure fertility. As polyploid species usually have multiple origins, one intriguing, yet largely underexplored, question is whether different mechanisms suppressing crossovers between homoeologs may coexist within the same polyphyletic species. We addressed this question using Brassica napus, a young polyphyletic allopolyploid species. We first analyzed the meiotic behavior of 363 allohaploids produced from 29 accessions, which represent a large part of B. napus genetic diversity. Two main clear-cut meiotic phenotypes were observed, encompassing a twofold difference in the number of univalents at metaphase I. We then sequenced two chloroplast intergenic regions to gain insight into the maternal origins of the same 29 accessions; only two plastid haplotypes were found, and these correlated with the dichotomy of meiotic phenotypes. Finally, we analyzed genetic diversity at the PrBn locus, which was shown to determine meiotic behavior in a segregating population of B. napus allohaploids. We observed that segregation of two alleles at PrBn could adequately explain a large part of the variation in meiotic behavior found among B. napus allohaploids. Overall, our results suggest that repeated polyploidy resulted in different levels of crossover suppression between homoeologs in B. napus allohaploids.     

Geographical range,heat tolerance and invasion success in aquatic species

Species with broader geographical ranges are expected to be ecological generalists, while species with higher heat tolerances may be relatively competitive at more extreme and increasing temperatures. Thus, both traits are expected to relate to increased survival during transport to new regions of the globe, and once there, establishment and spread. Here, we explore these expectations using datasets of latitudinal range breadth and heat tolerance in freshwater and marine invertebrates and fishes. After accounting for the latitude and hemisphere of each species’ native range, we find that species introduced to freshwater systems have broader geographical ranges in comparison to native species. Moreover, introduced species are more heat tolerant than related native species collected from the same habitats. We further test for differences in range breadth and heat tolerance in relation to invasion success by comparing species that have established geographically restricted versus extensive introduced distributions. We find that geographical range size is positively related to invasion success in freshwater species only. However, heat tolerance is implicated as a trait correlated to widespread occurrence of introduced populations in both freshwater and marine systems. Our results emphasize the importance of formal risk assessments before moving heat tolerant species to novel locations.     

Nuclear DNA amount and genome downsizing in natural and synthetic allopolyploids of the genera Aegilops and Triticum

Recent molecular studies in the genera Aegilops and Triticum showed that allopolyploidization (interspecific or intergeneric hybridization followed by chromosome doubling) generated rapid elimination of low-copy or high-copy, non-coding and coding DNA sequences. The aims of this work were to determine the amount of nuclear DNA in allopolyploid species of the group and to see to what extent elimination of DNA sequences affected genome size. Nuclear DNA amount was determined by the flow cytometry method in 27 natural allopolyploid species (most of which were represented by several lines and each line by several plants) as well as 14 newly synthesized allopolyploids (each represented by several plants) and their parental plants. Very small intraspecific variation in DNA amount was found between lines of allopolyploid species collected from different habitats or between wild and domesticated forms of allopolyploid wheat. In contrast to the constancy in nuclear DNA amount at the intraspecific level, there are significant differences in genome size between the various allopolyploid species, at both the tetraploid and hexaploid levels. In most allopolyploids nuclear DNA amount was significantly less than the sum of DNA amounts of the parental species. Newly synthesized allopolyploids exhibited a similar decrease in nuclear DNA amount in the first generation, indicating that genome downsizing occurs during and (or) immediately after the formation of the allopolyploids and that there are no further changes in genome size during the life of the allopolyploids. Phylogenetic considerations of the origin of the B genome of allopolyploid wheat, based on nuclear DNA amount, are discussed.     

Plant chemical defense allocation constrains evolution of tolerance to community change across a range boundary

Because transplant experiments show that performance usually decreases across species range boundaries, some range limits might develop from factors and processes that prevent adaptation to stressful environments. Here, we determined whether an ecological cost of plant defense involving stress associated with changes in the local plant community may contribute to range limit development in the upland mustard species Boechera stricta. In a common garden experiment of 499 B. stricta plants, performance decreased and a multivariate axis of community structure increased across the boundary, indicating increased stress associated with the community change. There was also significant genetic variation (evolutionary potential) among marker‐inferred inbred lines of B. stricta for tolerance to the stress; however, lines with high basal levels of glucosinolate toxins had lower tolerance to the change in community structure. We suggest that defense allocation, which is also needed across the range, may impede adaptation to the stress associated with the community change and thus contribute to range limit development.     

Evolution of RAG-1 in polyploid clawed frogs

Possible genetic fates of a gene duplicate are silencing, redundancy, subfunctionalization, or novel function. These different fates can be realized at the DNA, RNA, or protein level, and their genetic determinants are poorly understood. We explored molecular evolution of duplicated RAG-1 genes in African clawed frogs (Xenopus and Silurana) (1) to examine the fate of paralogs of this gene at the DNA level in terms of recombination, positive selection, and gene degeneration and in the absence of extensive recombination among alleles at different paralogs, (2) to test phylogenetic hypotheses about the origins of polyploid species. We found that recombination between different RAG-1 paralogs is infrequent, that degeneration of some paralogs has occurred via stop codons and frameshift mutations, and that this degeneration occurred in paralogs inherited from only one diploid progenitor species. Simulations and phylogenetic analyses of RAG-1 and mitochondrial DNA support one origin of extant tetraploids in Xenopus and at least one origin in Silurana, five allopolyploid origins of extant octoploids, and two allopolyploid origins of extant dodecaploids. In allopolyploid species, which inherit a complete genome from two different ancestors, genes inherited from the same ancestor have a longer period of coevolution than genes inherited from different ancestors. Because of this, gene ancestry could potentially influence gene fate: interacting paralogs derived from the same lower ploidy ancestor might have similar genetic destinies.     

Natural variation for fertile triploid F1 hybrid formation in allohexaploid wheat speciation

The tempo, mode, and geography of allopolyploid speciation are influenced by natural variation in the ability of parental species to express postzygotic reproductive phenotypes that affect hybrid fertility. To shed light on the impact of such natural variations, we used allohexaploid Triticum aestivum wheats’ evolution as a model and analyzed the geographic and phylogenetic distributions of Aegilops tauschii (diploid progenitor) accessions involved in the expression of abnormality and fertility in triploid F₁ hybrids with Triticum turgidum (tetraploid progenitor). Artificial-cross experiments and chloroplast-DNA-based evolutionary analyses showed that hybrid-abnormality-causing accessions had limited geographic and phylogenetic distributions, indicative that postzygotic hybridization barriers are underdeveloped between these species. In contrast, accessions that are involved with fertile triploid F₁ hybrid formation have wide geographic and phylogenetic distributions, indicative of a deep evolutionary origin. Wide-spread hybrid-fertilizing accessions support the theory that T. aestivum speciation occurred at multiple sites within the species range of Ae. tauschii, in which existing conditions enabled natural hybridization with T. turgidum. Implications of our findings on how natural variation in the ability of Ae. tauschii to express those postzygotic reproductive phenotypes diversified and contributed to the speciation of T. aestivum are discussed. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Identification of homologous, homoeologous and paralogous sequence variants in an outbreeding allopolyploid species based on comparison with progenitor taxa

The combination of homologous, homoeologous and paralogous classes of sequence variation presents major challenges for SNP discovery in outbreeding allopolyploid species. Previous in vitro gene-associated SNP discovery studies in the allotetraploid forage legume white clover (Trifolium repens L.) were vulnerable to such effects, leading to prohibitive levels of attrition during SNP validation. Identification of T. occidentale and T. pallescens as the putative diploid progenitors of white clover has permitted discrimination of the different sequence variant categories. Amplicons from selected abiotic stress tolerance-related genes were obtained using mapping family parents and individuals from each diploid species. Following cloning, progenitor comparison allowed tentative assignment of individual haplotypes to one or other sub-genome, as well as to gene copies within sub-genomes. A high degree of coincidence and identity between SNPs and HSVs was observed. Close similarity was observed between the genome of T. occidentale and one white clover sub-genome, but the affinity between T. pallescens and the other sub-genome was weaker, suggesting that a currently uncharacterised taxon may be the true second progenitor. Selected validated SNPs were attributed to individual sub-genomes by assignment to and naming of homoeologous linkage groups, providing the basis for improved genetic trait-dissection studies. The approach described in this study is broadly applicable to a range of allopolyploid taxa of equivocal ancestry.     

Pollen and seed morphology of Nordic Draba (Brassicaceae): phylogenetic and ecological implications

Pollen and seed morphology were examined in 54 diploid and allopolyploid populations representing 15 Nordic species of the taxonomically complex genus Draba. The pollen size was strongly correlated with chromosome number, but it was unreliable for inferring the exact ploidal level of individual populations. Five main pollen types were recognized based on sculpturing of the exine. Two populations of D. lactea had conspicuously different exine sculpturing, supporting a previous hypothesis based on molecular data that this hexaploid is polyphyletic and has been derived from various combinations of diploid species. The pollen morphological data are also consistent with the hypotheses that the 16-ploid D. corymbosa is an intersectional allopolyploid derived from the sections Draba and Chrysodraba , that the hexaploid D. cinerea is a progenitor of the decaploid D. arctica , and that D. crassifolia and D. adamsii represent isolated allopolyploid lineages. The seed size and weight were only weakly correlated with chromosome number, but showed a close relationship to habitat ecology. The largest seeds were observed in species typical of closed habitats, in which seedling establishment probably is limited by competition with mosses. The seed coat surface had a characteristic verrucate reticulum, but the differentiation among species was vague or absent. The seed size and colour, however, distinguish some species, e.g., in the D. alpina complex, which otherwise are morphologically very similar.     

Ecophysiological plasticity and local differentiation help explain the invasion success of Taraxacum officinale (dandelion) in South America

Plasticity and local adaptation have been suggested as two main mechanisms that alien species use to successfully tolerate and invade broad geographic areas. In the present study, we try answer the question if the mechanism for the broad distributional range of T. officinale is for phenotypic plasticity, ecotypic adaptation or both. For this, we used individuals of T. officinale originated from seeds collected in five localities along its latitudinal distribution range in the southern‐hemisphere. Seedlings were acclimated at 5 and 25°C for one month. After the acclimation period we evaluated ecophysiological and cytogenetic traits. Additionally, we assessed the fitness at each temperature by recording the seed output of individuals from different localities. Finally, we performed a manipulative experiment in order to assess the tolerance to herbivory and competitive ability between T. officinale from all origins and Hypochaeris scorzonerae a co‐occurring native species. Overall, individuals of T. officinale showed high plasticity and ecotypic adaptation for all traits assessed in this study. Changes both in physiology and morphology observed in T. officinale from different origins were mostly correlated, enhancing their ecophysiological performance in temperatures similar to those of their origin. Additionally, all localities showed the same chromosome number and ploidy level. On the other hand, all individuals showed an increase the seed output at 25°C, but those from northern localities increased more. T. officinale from all origins was not significantly affected by herbivory while native showed a negative effect. On the other hand, T. officinale exerted a strong negative effect on the native species, but this former not effected significantly to the invasive T. officinale. High plasticity and local adaptation in all ecophysiological traits, seed‐set and the low cytogenetic variability in T. officinale suggests that both strategies are present in this invasive plant species and are not mutually exclusive. Finally, higher tolerance to herbivory and competitive ability suggests that T. officinale could perform successfully in environments with different climatic conditions, and thus colonize and invade South‐America.     

Polymorphism and phylogeny of D-genome species of <Emphasis Type="Italic">Aegilops</Emphasis> L. Based on the results of analysis of the microsatellite loci of the chloroplast genome

A total of 14 chloroplast microsatellite markers were used for analysis of the variability and phylogeny of the cytoplasmic genome in 71 members of six species of goat grass with D-genomes. Greater species diversity was found in diploid species of Aegilops tauschii. Greater species variability among polyploid species was demonstrated for A. ventricosa. The haplotype of A. ventricosa considerably differs from haplotypes of A. tauschii. Analyzed samples of A. cylindrica have haplotypes similar to the haplotypes of A. tauschii.