Instability of chromosome number and DNA methylation variation induced by hybridization and amphidiploid formation between <Emphasis Type="Italic">Raphanus sativus</Emphasis> L. and <Emphasis Type="Italic">Brassica alboglabra</Emphasis>Bailey

Background  

Distant hybridization can result genome duplication and allopolyploid formation which may play a significant role in the origin and evolution of many plant species. It is unclear how the two or more divergent genomes coordinate in one nucleus with a single parental cytoplasm within allopolyploids. We used cytological and molecular methods to investigate the genetic and epigenetic instabilities associated with the process of distant hybridization and allopolyploid formation, measuring changes in chromosome number and DNA methylation across multiple generations.     

Multispeed genome diploidization and diversification after an ancient allopolyploidization

Hybridization and genome doubling (allopolyploidy) have led to evolutionary novelties as well as to the origin of new clades and species. Despite the importance of allopolyploidization, the dynamics of postpolyploid diploidization (PPD) at the genome level has been only sparsely studied. The Microlepidieae (MICR) is a crucifer tribe of 17 genera and c. 56 species endemic to Australia and New Zealand. Our phylogenetic and cytogenomic analyses revealed that MICR originated via an intertribal hybridization between ancestors of Crucihimalayeae (n = 8; maternal genome) and Smelowskieae (n = 7; paternal genome), both native to the Northern Hemisphere. The reconstructed ancestral allopolyploid genome (n = 15) originated probably in northeastern Asia or western North America during the Late Miocene (c. 10.6–7 million years ago) and reached the Australian mainland via long‐distance dispersal. In Australia, the allotetraploid genome diverged into at least three main subclades exhibiting different levels of PPD and diversity: 1.25‐fold descending dysploidy (DD) of n = 15 → n = 12 (autopolyploidy → 24) in perennial Arabidella (3 species), 1.5‐fold DD of n = 15 → n = 10 in the perennial Pachycladon (11 spp.) and 2.1–3.75‐fold DD of n = 15 → n = 7–4 in the largely annual crown‐group genera (42 spp. in 15 genera). These results are among the first to demonstrate multispeed genome evolution in taxa descending from a common allopolyploid ancestor. It is suggested that clade‐specific PPD can operate at different rates and efficacies and can be tentatively linked to life histories and the extent of taxonomic diversity.     

Fast Diploidization in Close Mesopolyploid Relatives of Arabidopsis

Mesopolyploid whole-genome duplication (WGD) was revealed in the ancestry of Australian Brassicaceae species with diploid-like chromosome numbers (n = 4 to 6). Multicolor comparative chromosome painting was used to reconstruct complete cytogenetic maps of the cryptic ancient polyploids. Cytogenetic analysis showed that the karyotype of the Australian Camelineae species descended from the eight ancestral chromosomes (n = 8) through allopolyploid WGD followed by the extensive reduction of chromosome number. Nuclear and maternal gene phylogenies corroborated the hybrid origin of the mesotetraploid ancestor and suggest that the hybridization event occurred ~6 to 9 million years ago. The four, five, and six fusion chromosome pairs of the analyzed close relatives of Arabidopsis thaliana represent complex mosaics of duplicated ancestral genomic blocks reshuffled by numerous chromosome rearrangements. Unequal reciprocal translocations with or without preceeding pericentric inversions and purported end-to-end chromosome fusions accompanied by inactivation and/or loss of centromeres are hypothesized to be the main pathways for the observed chromosome number reduction. Our results underline the significance of multiple rounds of WGD in the angiosperm genome evolution and demonstrate that chromosome number per se is not a reliable indicator of ploidy level.     

Phylogeny, biogeography and adaptive radiation of Pachycladon (Brassicaceae) in the mountains of South Island, New Zealand

Aim To report analyses and propose hypotheses of adaptive radiation that explain distributional patterns of the alpine genus Pachycladon Hook.f. – a morphologically diverse genus from New Zealand closely related to Arabidopsis thaliana. Location South Island, New Zealand. Methods Morphological and nrDNA ITS sequence phylogenies were generated for Pachycladon. An analysis is presented of species distributional patterns and attributes. Results Phylogenetic analyses of morphological characters and nrDNA ITS sequence data were found to be congruent in supporting three New Zealand clades for Pachycladon. Monophyletic groups identified within the genus are geographically distinct and are associated with different geological parent materials. Distribution maps, latitude and altitude range, and data on geological parent material are presented for the nine named and one unnamed species of Pachycladon from New Zealand. Main conclusions (a) Panbiogeographic hypotheses accounting for the origin and present‐day distribution of Pachycladon in New Zealand are not supported.
(b) Species diversity and distributions of Pachycladon are explained by a Late Tertiary–Quaternary adaptive radiation associated with increasing specialization to geological substrates. Pachycladon cheesemanii Heenan & A.D.Mitch. is morphologically similar to the closest overseas relatives. It is a geological generalist and has wide latitudinal and altitudinal ranges, and we suggest it resembles the ancestral form of the genus in New Zealand. Pachycladon novae‐zelandiae (Hook.f.) Hook.f. and P. wallii (Carse) Heenan & A.D.Mitch. are a southern South Island group that predominantly occurs on Haast Schist, are polycarpic, have lobed leaves, and lateral inflorescences. Pachycladon enysii (Cheeseman) Heenan & A.D.Mitch., P. fastigiata (Hook.f.) Heenan & A.D.Mitch., and P. stellata (Allan) Heenan & A.D.Mitch. are restricted to greywacke in the eastern South Island, and are facultatively monocarpic, have serrate leaves, and stout terminal inflorescenes.
(c) Present distributions of Pachycladon species may relate to Pleistocene climate change. Pachycladon enysii reaches the highest altitude of New Zealand species of Pachycladon and is most common in the Southern Alps in Canterbury. We propose that this species survived on nunataks at the height of the last glaciation. In contrast, P. fastigiata grows at a lower altitude and is absent from the high mountains of the Southern Alps. We suggest it was extirpated from this area during the last glaciation.     

Inferring the mode of origin of polyploid species from next‐generation sequence data

Many eukaryote organisms are polyploid. However, despite their importance, evolutionary inference of polyploid origins and modes of inheritance has been limited by a need for analyses of allele segregation at multiple loci using crosses. The increasing availability of sequence data for nonmodel species now allows the application of established approaches for the analysis of genomic data in polyploids. Here, we ask whether approximate Bayesian computation (ABC), applied to realistic traditional and next‐generation sequence data, allows correct inference of the evolutionary and demographic history of polyploids. Using simulations, we evaluate the robustness of evolutionary inference by ABC for tetraploid species as a function of the number of individuals and loci sampled, and the presence or absence of an outgroup. We find that ABC adequately retrieves the recent evolutionary history of polyploid species on the basis of both old and new sequencing technologies. The application of ABC to sequence data from diploid and polyploid species of the plant genus Capsella confirms its utility. Our analysis strongly supports an allopolyploid origin of C. bursa‐pastoris about 80 000 years ago. This conclusion runs contrary to previous findings based on the same data set but using an alternative approach and is in agreement with recent findings based on whole‐genome sequencing. Our results indicate that ABC is a promising and powerful method for revealing the evolution of polyploid species, without the need to attribute alleles to a homeologous chromosome pair. The approach can readily be extended to more complex scenarios involving higher ploidy levels.     

Genetic diversity patterns in Curcuma reflect differences in genome size

The relationships between genome size and the systematic and evolutionary patterns in vascular plants are equivocal, although a close relationship between genome size and evolutionary patterns has been previously reported. However, several studies have also revealed the dynamic nature of genome size evolution and its considerable ‘ups’ and ‘downs’. Thus, in this study, the phylogenetic relationships among three previously revealed genome size groups and among species of the highly polyploid genus Curcuma were evaluated using AFLP. Our results suggest two main lineages within Indian Curcuma reflecting evolution of genome size. The first one includes hexaploids and higher polyploids of the previously recognized genome size group I, and the second one includes mainly hexaploids of genome size groups II and III. Within genome size group I, relationships among species seem to be influenced by reticulate evolution and higher polyploids are likely to be of allopolyploid origin. Reproductive systems in Indian Curcuma vary considerably among ploidy levels and these differences considerably affect morphological and genetic variation. In general, clonally reproducing species are expected to exhibit low genotypic diversity, but, at the same time, species of allopolyploid origin are expected to maintain higher levels of heterozygosity compared with their progenitors. We investigated intra‐populational genetic variability in Curcuma spp. to evaluate whether mode of reproduction or ploidy represent the main factor influencing the degree of genetic diversity. We found that hexaploid species exhibited significantly higher genetic diversity than higher polyploids (9x, 15x). Our results suggest that this genetic diversity pattern is largely influenced by the mode of reproduction, as higher polyploids reproduce exclusively vegetatively, whereas hexaploids reproduce mainly sexually. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 165 , 388–401.     

Spatio‐temporal patterns of genome evolution in allotetraploid species of the genus Oryza

Despite knowledge that polyploidy is widespread and a major evolutionary force in flowering plant diversification, detailed comparative molecular studies on polyploidy have been confined to only a few species and families. The genus Oryza is composed of 23 species that are classified into ten distinct ‘genome types’ (six diploid and four polyploid), and is emerging as a powerful new model system to study polyploidy. Here we report the identification, sequence and comprehensive comparative annotation of eight homoeologous genomes from a single orthologous region (Adh1–Adh2) from four allopolyploid species representing each of the known Oryza genome types (BC, CD, HJ and KL). Detailed comparative phylogenomic analyses of these regions within and across species and ploidy levels provided several insights into the spatio‐temporal dynamics of genome organization and evolution of this region in ‘natural’ polyploids of Oryza. The major findings of this study are that: (i) homoeologous genomic regions within the same nucleus experience both independent and parallel evolution, (ii) differential lineage‐specific selection pressures do not occur between polyploids and their diploid progenitors, (iii) there have been no dramatic structural changes relative to the diploid ancestors, (iv) a variation in the molecular evolutionary rate exists between the two genomes in the BC complex species even though the BC and CD polyploid species appear to have arisen <2 million years ago, and (v) there are no clear distinctions in the patterns of genome evolution in the diploid versus polyploid species.     

Analysis of phylogenetic relationships of Brassicaceae species based on Chs sequences

Sequences of nuclear chalcone synthase gene (Chs) were analyzed for species of the Brassicaceae family to reconstruct phylogenetic relationships. The phylogeny for 106 species of 60 genera was reconstructed, and assigned to 24 tribes, using maximum parsimony, maximum likelihood, and neighbor-joining methods. Most of the tribes can be assigned to the major lineages (Lineages I–III) suggested by Beilstein et al. (2006). The tribe Camelineae was not monophyletic. Conringia planisiliqua together with Orychophragmus violaceus would not be recognized as a new tribe proposed by the previous studies, and C. planisiliqua should be a member of tribe Isatideae. The genera delimitation and monophyly of the expanded Solms-laubachia were also confirmed by our data. Furthermore, one parent of inter-tribal allopolyploid Pachycladon appeared to be most closely associated with Crucihimalaya, Transberingia and tribes Boechereae and Halimolobeae, another parent was proved to be in tribe Smelowskieae.     

Isozymes,Speciation and Evolution in the Polyploid Complex Cochlearia L. (Brassicaceae)

Within the genus Cochlearia L. sect. Cochlearia three isozyme systems (aspartate aminotransferase, leucine aminopeptidase and phosphoglucomutase) have been analysed at the populational level for eleven species with different ploidy levels. Nine loci complexes were resolved with a total of 33 alleles from 89 populations. In general, polyploids displayed higher numbers of alleles per species and per population. A notable exception is diploid C. pyrenaica with as many alleles as some polyploids. Data support: (1) the origin of tetraploid C. officinalis from C. pyrenaica s.l., particularly from C. aestuaria; (2) the allopolyploid origin of octoploid C. anglica from C. officinalis; (3) the allopolyploid origin of hexaploid inland taxa C. polonica, C. tatrae and C. bavarica via hybridization between C. pyrenaica and C. officinalis; (4) a putative allopolyploid origin of hexaploid coastal species C. danica by hybridization between C. pyrenaica s.l. and C. officinalis accompanied by a shift in chromosome complement. A scenario summarizing our present understanding of the evolution within Cochlearia sect. Cochlearia is presented.     

Phylogeny and evolutionary history of Leymus (Triticeae; Poaceae) based on a single-copy nuclear gene encoding plastid acetyl-CoA carboxylase

Background  

Single- and low- copy genes are less likely subject to concerted evolution, thus making themselves ideal tools for studying the origin and evolution of polyploid taxa. Leymus is a polyploid genus with a diverse array of morphology, ecology and distribution in Triticeae. The genomic constitution of Leymus was assigned as NsXm, where Ns was presumed to be originated from Psathyrostachys, while Xm represented a genome of unknown origin. In addition, little is known about the evolutionary history of Leymus. Here, we investigate the phylogenetic relationship, genome donor, and evolutionary history of Leymus based on a single-copy nuclear Acc1 gene.     

Structure and evolution of <Emphasis Type="Italic">Apetala3</Emphasis>, a sex-linked gene in <Emphasis Type="Italic">Silene latifolia</Emphasis>

Background  

The evolution of sex chromosomes is often accompanied by gene or chromosome rearrangements. Recently, the gene AP3 was characterized in the dioecious plant species Silene latifolia. It was suggested that this gene had been transferred from an autosome to the Y chromosome.     

Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization

Background  

The mechanism by which duplicate genes originate – whether by duplication of a whole genome or of a genomic segment – influences their genetic fates. To study events that trigger duplicate gene persistence after whole genome duplication in vertebrates, we have analyzed molecular evolution and expression of hundreds of persistent duplicate gene pairs in allopolyploid clawed frogs (Xenopus and Silurana). We collected comparative data that allowed us to tease apart the molecular events that occurred soon after duplication from those that occurred later on. We also quantified expression profile divergence of hundreds of paralogs during development and in different tissues.     

Compact genomes and complex evolution in the genus <Emphasis Type="Italic">Brachypodium</Emphasis>

The temperate annual grass Brachypodium distachyon is a diploid species with a chromosome base number of 5. It is strikingly different from other Eurasian species of the genus, which are perennial and often polyploid, with the diploids typically having base numbers of 8 or 9. Previously, phylogenies indicated that B. distachyon split from the other species early in the evolution of the genus, while its genome sequence revealed that extensive synteny on a chromosomal scale had been maintained with rice, a tropical grass with a base number of 12. Here we show evidence that B. distachyon may have a homoploid origin, involving ancestral interspecific hybridisation, although it does not appear to be a component of any of the perennial Eurasian allopolyploids. Using a cytogenetic approach, we show that dysploidy in Brachypodium has not followed a simple progression.     

Genome structure and apomixis in Phoenicaulis (Brassicaceae; Boechereae)

Apomixis in crucifer (Brassicaceae) species is rare, reported in just four genera (Boechera, Draba, Erysimum, and Parrya), and one intergeneric hybrid (Raphanobrassica). It is well studied only in Boechera, where it is widespread among 100+ recognized species. However, its occurrence in related genera of the tribe Boechereae has not been documented previously. Here we analyzed genome evolution, mode of reproduction, and fertility of the monospecific Boechereae genus Phoenicaulis (P. cheiranthoides), endemic to the northwestern United States. We discovered that the species encompasses diploid (2n = 2x = 14), triploid (2n = 3x = 21), and tetraploid (2n = 4x = 28) populations. Comparative chromosome painting analyses revealed that the three karyotypes are essentially structurally identical, differing only in the presence of a largely heterochromatic chromosome (Het) in the triploid and tetraploid cytotypes. The genome structure of Phoenicaulis appeared identical to that of Boechera species previously analyzed, suggesting genomic stasis despite the morphological and molecular divergence of the two genera. This genome colinearity extended to the presence and structure of the Het chromosomes, which are closely associated with apomictic reproduction in Boechera. Interestingly, all three cytotypes of Phoenicaulis proved to be apomictic, regardless of the presence or absence of a Het chromosome, and sexual populations have yet to be identified.     

A high frequency of allopolyploid speciation in the gymnospermous genus Ephedra and its possible association with some biological and ecological features

The origin and evolution of polyploids have been studied extensively in angiosperms and ferns but very rarely in gymnosperms. With the exception of three species of conifers, all natural polyploid species of gymnosperms belong to Ephedra, in which more than half of the species show polyploid cytotypes. Here, we investigated the origin and evolution of polyploids of Ephedra distributed in the Qinghai–Tibetan Plateau (QTP) and neighbouring areas. Flow cytometry (FCM) was used to measure the ploidy levels of the sampled species that are represented by multiple individuals from different populations, and then, two single‐copy nuclear genes (LFY and DDB2) and two chloroplast DNA fragments were used to unravel the possible origins and maternal donors of the polyploids. The results indicate that the studied polyploid species are allopolyploids, and suggest that allotetraploidy is a dominant mode of speciation in Ephedra. The high percentage of polyploids in the genus could be related to some of its biological attributes such as vegetative propagation, a relatively high rate of unreduced gamete formation, and a small genome size relative to most other gymnosperms. Significant ecological divergences between allotetraploids and their putative progenitors were detected by PCAs and anova and Tukey's tests, with the exception of E. saxatilis. The overlap of geographical distributions and ecological niches of some diploid species could have provided opportunities for interspecific hybridization and allopolyploid speciation.     

Phylogenetic relationships in genus <Emphasis Type="Italic">Arachis</Emphasis> based on ITS and 5.8S rDNA sequences

Background  

The genus Arachis comprises 80 species and it is subdivided into nine taxonomic sections (Arachis, Caulorrhizae, Erectoides, Extranervosae, Heteranthae, Procumbentes, Rhizomatosae, Trierectoides, and Triseminatae). This genus is naturally confined to South America and most of its species are native to Brazil. In order to provide a better understanding of the evolution of the genus, we reconstructed the phylogeny of 45 species using the variation observed on nucleotide sequences in internal transcribed spacer regions (ITS1 and ITS2) and 5.8 S of nuclear ribosomal DNA.     

Reconstructing the evolutionary history of the radiation of the land snail genus <Emphasis Type="Italic">Xerocrassa</Emphasis> on Crete based on mitochondrial sequences and AFLP markers

Background  

A non-adaptive radiation triggered by sexual selection resulted in ten endemic land snail species of the genus Xerocrassa on Crete. Only five of these species and a more widespread species are monophyletic in a mitochondrial gene tree. The reconstruction of the evolutionary history of such closely related species can be complicated by incomplete lineage sorting, introgression or inadequate taxonomy. To distinguish between the reasons for the nonmonophyly of several species in the mitochondrial gene tree we analysed nuclear AFLP markers.