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Background Most, if not all, green plant (Virdiplantae) species including angiosperms and ferns are polyploids themselves or have ancient polyploid or whole genome duplication signatures in their genomes. Polyploids are not only restricted to our major crop species such as wheat, maize, potato and the brassicas, but also occur frequently in wild species and natural habitats. Polyploidy has thus been viewed as a major driver in evolution, and its influence on genome and chromosome evolution has been at the centre of many investigations. Mechanistic models of the newly structured genomes are being developed that incorporate aspects of sequence evolution or turnover (low-copy genes and regulatory sequences, as well as repetitive DNAs), modification of gene functions, the re-establishment of control of genes with multiple copies, and often meiotic chromosome pairing, recombination and restoration of fertility. Scope World-wide interest in how green plants have evolved under different conditions – whether in small, isolated populations, or globally – suggests that gaining further insight into the contribution of polyploidy to plant speciation and adaptation to environmental changes is greatly needed. Forward-looking research and modelling, based on cytogenetics, expression studies, and genomics or genome sequencing analyses, discussed in this Special Issue of the Annals of Botany, consider how new polyploids behave and the pathways available for genome evolution. They address fundamental questions about the advantages and disadvantages of polyploidy, the consequences for evolution and speciation, and applied questions regarding the spread of polyploids in the environment and challenges in breeding and exploitation of wild relatives through introgression or resynthesis of polyploids. Conclusion Chromosome number, genome size, repetitive DNA sequences, genes and regulatory sequences and their expression evolve following polyploidy – generating diversity and possible novel traits and enabling species diversification. There is the potential for ever more polyploids in natural, managed and disturbed environments under changing climates and new stresses.

Chromosome identification is essential for linking sequence and chromosomal maps, verifying sequence assemblies, showing structural variations and tracking inheritance or recombination of chromosomes and chromosomal segments during evolution and breeding programs. Unfortunately, identification of individual chromosomes and chromosome arms has been a major challenge for some economically important crop species with a near-continuous chromosome size range and similar morphology. Here, we developed oligonucleotide-based chromosome-specific probes that enabled us to establish a reference chromosome identification system for oil palm (Elaeis guineensis Jacq., 2n = 32). Massive oligonucleotide sequence pools were anchored to individual chromosome arms using dual and triple fluorescent in situ hybridization (EgOligoFISH). Three fluorescently tagged probe libraries were developed to contain, in total 52,506 gene-rich single-copy 47-mer oligonucleotides spanning each 0.2-0.5 Mb across strategically placed chromosome regions. They generated 19 distinct FISH signals and together with rDNA probes enabled identification of all 32 E. guineensis chromosome arms. The probes were able to identify individual homoeologous chromosome regions in the related Arecaceae palm species: American oil palm (Elaeis oleifera), date palm (Phoenix dactylifera) and coconut (Cocos nucifera) showing the comparative organization and concerted evolution of genomes in the Arecaceae. The oligonucleotide probes developed here provide a valuable approach to chromosome arm identification and allow tracking chromosome transfer in hybridization and breeding programs in oil palm, as well as comparative studies within Arecaceae.

Enset (Ensete ventricosum) is a multipurpose crop extensively cultivated in southern and southwestern Ethiopia for human food, animal feed, and fiber. It has immense contributions to the food security and rural livelihoods of 20 million people. Several distinct enset landraces are cultivated for their uses in traditional medicine. These landraces are vulnerable to various human-related activities and environmental constraints. The genetic diversity among the landraces is not verified to plan conservation strategy. Moreover, it is currently unknown whether medicinal landraces are genetically differentiated from other landraces. Here, we characterize the genetic diversity of medicinal enset landraces to support effective conservation and utilization of their diversity. We evaluated the genetic diversity of 51 enset landraces, of which 38 have reported medicinal value. A total of 38 alleles across the 15 simple sequence repeat (SSR) loci and a moderate level of genetic diversity (He = 0.47) were detected. Analysis of molecular variation (AMOVA) revealed that only 2.4% of the total genetic variation was contributed by variation among the medicinal and non-medicinal groups of landraces, with an FST of 0.024. A neighbor-joining tree showed four separate clusters with no correlation to the use-values of the landraces. Except for two, all “medicinal” landraces with distinct vernacular names were found to be genetically different, showing that vernacular names are a good indicator of genetic distinctiveness in these specific groups of landraces. The discriminant analysis of the principal components also confirmed the absence of distinct clustering between the two groups. We found that enset landraces were clustered irrespective of their use-value, showing no evidence for genetic differentiation between the enset grown for ‘medicinal’ uses and non-medicinal landraces. This suggests that enset medicinal properties may be restricted to a more limited number of genotypes, might have resulted from the interaction of genotype with the environment or management practice, or partly misreported. The study provides baseline information that promotes further investigations in exploiting the medicinal value of these specific landraces.

Pararetroviruses, taxon Caulimoviridae, are typical of retroelements with reverse transcriptase and share a common origin with retroviruses and LTR retrotransposons, presumably dating back 1.6 billion years and illustrating the transition from an RNA to a DNA world. After transcription of the viral genome in the host nucleus, viral DNA synthesis occurs in the cytoplasm on the generated terminally redundant RNA including inter- and intra-molecule recombination steps rather than relying on nuclear DNA replication. RNA recombination events between an ancestral genomic retroelement with exogenous RNA viruses were seminal in pararetrovirus evolution resulting in horizontal transmission and episomal replication. Instead of active integration, pararetroviruses use the host DNA repair machinery to prevail in genomes of angiosperms, gymnosperms and ferns. Pararetrovirus integration – leading to Endogenous ParaRetroViruses, EPRVs – by illegitimate recombination can happen if their sequences instead of homologous host genomic sequences on the sister chromatid (during mitosis) or homologous chromosome (during meiosis) are used as template. Multiple layers of RNA interference exist regulating episomal and chromosomal forms of the pararetrovirus. Pararetroviruses have evolved suppressors against this plant defense in the arms race during co-evolution which can result in deregulation of plant genes. Small RNAs serve as signaling molecules for Transcriptional and Post-Transcriptional Gene Silencing (TGS, PTGS) pathways. Different populations of small RNAs comprising 21–24 nt and 18–30 nt in length have been reported for Citrus, Fritillaria, Musa, Petunia, Solanum and Beta. Recombination and RNA interference are driving forces for evolution and regulation of EPRVs.

Among transposable elements (TEs), the LTR retrotransposons are abundant followed by non-LTR retrotransposons in plant genomes, the lateral being represented by LINEs and SINEs. Computational and molecular approaches were used for the characterization of Brassica LINEs, their diversity and phylogenetic relationships. Four autonomous and four non-autonomous LINE families were identified and characterized from Brassica. Most of the autonomous LINEs displayed two open reading frames, ORF1 and ORF2, where ORF1 is a gag protein domain, while ORF2 encodes endonuclease (EN) and a reverse transcriptase (RT). Three of four families encoded an additional RNase H (RH) domain in pol gene common to 'R' and 'I' type of LINEs. The PCR analyses based on LINEs RT fragments indicate their high diversity and widespread occurrence in tested 40 Brassica cultivars. Database searches revealed the homology in LINE sequences in closely related genera Arabidopsis indicating their origin from common ancestors predating their separation. The alignment of 58 LINEs RT sequences from Brassica, Arabidopsis and other plants depicted 4 conserved domains (domain II-V) showing similarity to previously detected domains. Based on RT alignment of Brassica and 3 known LINEs from monocots, Brassicaceae LINEs clustered in separate clade, further resolving 4 Brassica-Arabidopsis specific families in 2 sub-clades. High similarities were observed in RT sequences in the members of same family, while low homology was detected in members across the families. The investigation led to the characterization of Brassica specific LINE families and their diversity across Brassica species and their cultivars.

Long terminal repeat retrotransposons represent a major component of plant genomes and act as drivers of genome evolution and diversity. Musa is an important fruit crop and also used as a starchy vegetable in many countries. BAC sequence analysis by dot plot was employed to investigate the LTR retrotransposons from Musa genomes. Fifty intact LTR retrotransposons from selected Musa BACs were identified by dot plot analysis and further BLASTN searches retrieved 153 intact copies, 61 truncated, and a great number of partial copies/remnants from GenBank database. LARD-like elements were also identified with several copies dispersed among the Musa genotypes. The predominant elements were the LTR retrotransposons Copia and Gypsy, while Caulimoviridae (pararetrovirus) were rare in the Musa genome. PCR amplification of reverse transcriptase (RT) sequences revealed their abundance in almost all tested Musa accessions and their ancient nature before the divergence of Musa species. The phylogenetic analysis based on RT sequences of Musa and other retrotransposons clustered them into Gypsy, Caulimoviridae, and Copia lineages. Most of the Musa-related elements clustered in their respective groups, while some grouped with other elements indicating homologous sequences. The present work will be helpful to understand the LTR retrotransposons landscape, giving a complete picture of the nature of the elements, their structural features, annotation, and evolutionary dynamics in the Musa genome.

Summary Sequence data and genomic in situ hybridization identify the New World diploid Panicum capillare as an ancestral genome of the Old World tetraploid cereal broomcorn millet, P. miliaceum., Panicum miliaceum (broomcorn millet) is a tetraploid cereal, which was among the first domesticated crops, but is now a minor crop despite its high water use efficiency. The ancestors of this species have not been determined; we aimed to identify likely candidates within the genus, where phylogenies are poorly resolved. Nuclear and chloroplast DNA sequences from P. miliaceum and a range of diploid and tetraploid relatives were used to develop phylogenies of the diploid and tetraploid species. Chromosomal in situ hybridization with genomic DNA as a probe was used to characterize the genomes in the tetraploid P. miliaceum and a tetraploid accession of P. repens. In situ hybridization showed that half the chromosomes of P. miliaceum hybridized more strongly with labelled genomic DNA from P. capillare, and half with labelled DNA from P. repens. Genomic DNA probes differentiated two sets of 18 chromosomes in the tetraploid P. repens. Our phylogenetic data support the allotetraploid origin of P. miliaceum, with the maternal ancestor being P. capillare (or a close relative) and the other genome being shared with P. repens. Our P. repens accession was also an allotetraploid with two dissimilar but closely related genomes, the maternal genome being similar to P. sumatrense. Further collection of Panicum species, particularly from the Old World, is required. It is important to identify why the water-efficient P. miliaceum is now of minimal importance in agriculture, and it may be valuable to exploit the diversity in this species and its ancestors.

†Background and Aims The genus Nicotiana includes diploid and tetraploid species, with complementary ecological, agronomic and commercial characteristics. The species are of economic value for tobacco, as ornamentals, and for secondary plant-product biosynthesis. They show substantial differences in disease resistance because of their range of secondary products. In the last decade, sexual hybridization and transgenic technologies have tended to eclipse protoplast fusion for gene transfer. Somatic hybridization was exploited in the present investigation to generate a new hybrid combination involving two sexually incompatible tetraploid species. The somatic hybrid plants were characterized using molecular, molecular cytogenetic and phenotypic approaches. †Methods Mesophyll protoplasts of the wild fungus-resistant species N. debneyi (2n ¼ 4x ¼ 48) were electrofused with those of the ornamental interspecific sexual hybrid N. × sanderae (2n ¼ 2x ¼ 18). From 1570 protoplast-derived cell colonies selected manually in five experiments, 580 tissues were sub-cultured to shoot regeneration medium. Regenerated plants were transferred to the glasshouse and screened for their morphology, chromosomal composition and disease resistance. †Key Results Eighty-nine regenerated plants flowered; five were confirmed as somatic hybrids by their intermediate morphology compared with parental plants, cytological constitution and DNA-marker analysis. Somatic hybrid plants had chromosome complements of 60 or 62. Chromosomes were identified to parental genomes by genomic in situ hybridization and included all 18 chromosomes from N. × sanderae, and 42 or 44 chromosomes from N. debneyi. Four or six chromosomes of one ancestral genome of N. debneyi were eliminated during culture of electrofusion-treated protoplasts and plant regeneration. Both chloroplasts and mitochondria of the somatic hybrid plants were probably derived from N. debneyi. All somatic hybrid plants were fertile. In contrast to parental plants of N. × sanderae, the seed progeny of somatic hybrid plants were resistant to infection by Peronospora tabacina, a trait introgressed from the wild parent, N. debneyi. †Conclusions Sexual incompatibility between N. × sanderae and N. debneyi was circumvented by somatic hybridization involving protoplast fusion. Asymmetrical nuclear hybridity was seen in the hybrids with loss of chromosomes, although importantly, somatic hybrids were fertile and stable. Expression of fungal resistance makes these somatic hybrids extremely valuable germplasm in future breeding programmes in ornamental tobacco.

The plant genome is organized into chromosomes that provide the structure for the genetic linkage groups and allow faithful replication, transcription and transmission of the hereditary information. Genome sizes in plants are remarkably diverse, with a 2350-fold range from 63 to 149,000 Mb, divided into n=2 to n= approximately 600 chromosomes. Despite this huge range, structural features of chromosomes like centromeres, telomeres and chromatin packaging are well-conserved. The smallest genomes consist of mostly coding and regulatory DNA sequences present in low copy, along with highly repeated rDNA (rRNA genes and intergenic spacers), centromeric and telomeric repetitive DNA and some transposable elements. The larger genomes have similar numbers of genes, with abundant tandemly repeated sequence motifs, and transposable elements alone represent more than half the DNA present. Chromosomes evolve by fission, fusion, duplication and insertion events, allowing evolution of chromosome size and chromosome number. A combination of sequence analysis, genetic mapping and molecular cytogenetic methods with comparative analysis, all only becoming widely available in the 21st century, is elucidating the exact nature of the chromosome evolution events at all timescales, from the base of the plant kingdom, to intraspecific or hybridization events associated with recent plant breeding. As well as being of fundamental interest, understanding and exploiting evolutionary mechanisms in plant genomes is likely to be a key to crop development for food production.

This special Highlight section of Annals of Botany contains seven papers that show the rapid progress in understanding the genetics related to plant evolution – identifying genes that have immediate effects on reproductive behaviour and diversity, and that directly lead to further diversification and eventually speciation. Understanding the genetic effects and genes that enable these processes is critical for both wild ecosystems and crop species. The study of plant genetics is moving forward at an unprecedented rate: for most of the last century geneticists had a few phenotypes to work with, but by the early 1990s there were hundreds of isozyme and then DNA markers allowing fine mapping of plant genomes in carefully constructed crosses. By the year 2000, with the results from DNA sequencing, there were hundreds of genes known from their DNA and research could move from marker discovery to functional genomics, relating these gene sequences to single-gene, Mendelian phenotypes, some of which have surprising consequences. For some years now, both simple characters and groups of genes have been related to complex phenotypes through QTL (quantitative trait locus) analysis, and mutation or transgenic approaches. Taxonomy has continued its development from a descriptive aspect of botanical research to having a strong phylogenetic and evolutionary basis, including DNA sequences to complement morphological analysis. The interpretation of the results from experimental hybridization has also been helpful in defining species and their relationships. However, results from hybridization can be misleading, with many exceptions in both directions to the simplistic concept that two plants that hybridize are the same species. Many characters, ranging from polyploidy to sexual incompatibility, prevent hybrids being made within a species, while otherwise well-defined species form hybrids that are among the most successful and dominant genotypes in many environments, and in some cases become species themselves. As our understanding of genetics has increased, ever more features of plant behaviour have been shown to be under close genetic control; this Highlight brings together seven outstanding articles showing the nature – and range – of genetic effects on speciation and domestication. While most Highlight issues featuring manuscripts on a particular important topic are planned a year or more in advance, these papers were submitted by chance around the same time, and have been published together in this issue to show the rapid advances in the area of understanding genetic effects on divergence and speciation. The review by Rieseberg and Blackman (2010) identifies no less than 41 genes that have been considered to lead to reproductive isolation of populations. Interestingly, the genes are very diverse, and include those which have prezygotic and postzygotic effects. Simple geographical isolation is not seen as the only widespread cause of speciation and the cessation of gene flow between populations; nevertheless, both larger and smaller features of geography lead to isolation of populations, and He et al. (2010) are able to show an example where the genetic structure of a species, Banksia hookeriana, is not solely dependent on the structure of a landscape, in this case where the population is located on sand dune crests physically separated by uninhabitable hollows. Occasional long-distance dispersal of seeds or movement of individuals from one population to another maintains connectivity within the species and prevents isolation. In contrast, Nomura et al. (2010) provide insight into the phylogeny and implications of habitat diversity. Farfugium (Asteraceae) is a monophyletic group associated with a wide range of habitats, including forest understorey (sciophytes), coastal crags (heliophytes) and riverbeds (rheophytes) in an archipelago in east Asia. They conclude that isolation on islands and subsequent parallel adaptation events followed migration over Quaternary land-bridges along the distribution range. Uninformative DNA sequence variation coupled with highly divergent morphologies suggest that adaptive diversification was rapid. The other four papers make conclusions related to the genetic diversification and selection seen in crop plants. The Tehuacan Valley in Mexico provides a remarkable ‘natural laboratory’ for study of human selection effects on plants, because there are well over 100 native plant species where artificial selection is being practiced and these silvicultural and cultivated populations co-exist with wild populations. Parra et al. (2010) study the cactus Stenocereus puinosus and find that despite selection for larger and sweeter fruit, there are high levels of gene flow that have promoted morphological divergence and moderate genetic structure between wild and managed populations, while conserving genetic diversity. Hence, despite strong selection, there is no evident genetic bottleneck that might limit breeders of the fruit in future, unlike that seen in many other domesticated species. As noted above, hybridization or polyploidy – speciation by whole-genome duplication – can lead to new, and reproductively isolated, species in a single event. Evidence of evolutionarily recent polyploidy events is seen in half of all plants, and contributes significantly to plant biodiversity. Shi et al. (2010) look at ancient events, or paleopolyploidy, that may be inferred from genomic data and their analysis of the nuclear genomes of kiwi fruit (Actinidia) and related Ericales shows evidence for at least two paleopolyploidy events. Their results provide evidence that gene-family methods are able to reliably uncover ancient polyploid speciation events. Soybean, Glycine max, is an important tetraploid crop, but there are still gaps in its domestication history. Guo et al. (2010) carry out an extensive study of the diversity of soybean from its South China centre of origin using molecular markers, and propose a single origin with a moderately severe genetic bottleneck during domestication. Wild soybeans in this region have an unexploited and valuable gene pool for future breeding, but, unlike the situation in Stenocereus, it will require careful study and extensive crossing with selection to introduce this diversity into the germplasm pool available to plant breeders. The final paper in the Highlight presents an important example of how diversity from a wild species can be used in one of the world's three most important grain crops. Rice, Oryza sativa, requires fertilization to set seed, but the temperatures experienced during hot weather (over 32–36 °C) induce sterility. Considering that such temperatures are rarely reached in the early morning, Ishimaru et al. (2010) introgressed an early-morning flowering (EMF) trait from wild rice, O. officinalis, where anthesis occurs soon after sunrise. Although the temperature effect on sterility itself was similar in the two rice species, the avoidance of high temperatures by a few hours caused by the early-morning flowering trait leads to significantly increased fertility in the line with introgression of the EMF trait. Together, these seven papers add considerably to our understanding of genetics in a broad evolutionary context. The results are of significance for wild species, with implications for whole ecosystems, and indeed the species used as examples in these papers are those of coastal, island and duneland systems that are particularly threatened by changes including urban ‘development’, sea-level alterations, storm frequencies and temperature. The crop papers show how knowledge of the mechanisms of evolution and associated genes can impact on our exploitation of biodiversity in crops and their wild relatives.

Individual plant species thrive in specific environments, some growing well across a wide area, others being restricted to survival in very narrow ecological niches. Within a niche, a species must compete for space, light and other resources with the same and other species. Many decades of work on crops has advanced our understanding of characteristics related to crop production and agronomy, with many studies involving the partitioning of components to the smallest part that can be measured, extensive experimental studies in both controlled and natural environments, linkage mapping or association genetics allowing the underlying genes or quantitative trait loci (QTLs) to be identified, and modelling of the effects of the genes on plant development. Now, with extensive segregating populations for most agricultural and many model species, high-throughput DNA sequencing is accelerating discovery of gene alleles related to functional traits, while DNA-based markers have increasing application in breeding programmes. This Highlight section of Annals of Botany shows the novel and rapid advances now being made in the identification and characterization of functional traits in ecology, identifying genes that enhance plant adaptation to ecological niches within ecosystems. There are many contrasts with crop studies that make this work particularly challenging, particularly because of the enormous biodiversity within a natural ecosystem (both within individual species and in the number of interacting species) and the variation in the environment. As in many areas of evolutionary biology, Darwin (1859) put in place an understanding of trait variation and selection. Later, pioneers in population genetics and G × E (genotype-by-environment) studies have demonstrated many aspects of plant adaptation to their environment, leading to understanding of endemism and applications in ecosystem modelling. Now, the underlying traits are being investigated both within and between species using observational, experimental, genetic and modelling methods, as is shown within the five papers highlighted here. The results have clear predictive value for ecosystems, with importance for short-term management strategies and longer-term approaches, for example in mitigation of climate changes. A small number of plants flourish when moved to a different environment, and are highly productive: a desirable outcome for crops, but not for plants that become invasive. One can argue that some invasives occupy niches where plants have hardly thrived, the obvious example being the Eichornia species of water hyacinth, native to South America, but now forming dense mats and clogging the surfaces of water courses across sub-tropical Asia and Africa. Drenovsky et al. (2012) review dynamic approaches to understating key functional traits that make a species invasive, and in particular consider how global environmental change will affect non-native plant invasions. These authors emphasize the need for research at scales from the individual to the ecosystem, and their review points to the range of science-based policies that need to be implemented to cope with the devastating impacts that invasive species are having on important ecosystems, whether in terms of preventing future invasions or mitigating the spread of invasive through interventions including restoration ecology. Mondoni et al. (2012) study a novel aspect of the seed germination trait, considering the impact of climate change on timing of germination in alpine species. In the extreme short seasons of the alpine ecosystem, vegetative reproduction and the spread of clones is widespread, and seed germination has often been considered rare, albeit of genetic importance. In contrast, migration of plants is normally (although not universally) through seed dispersal, and migration can include the response of species to the movement of their optimum environment because of climate change. Taking an experimental approach, the authors show that seeds of many alpine species are closely adapted to their current environment. For six of the eight species they study from an ice-free site at 2500 m, timing of seedling emergence is shifted to the less-favourable autumn season under conditions where the autumn is warmer. Seed dormancy factors can affect the nature and rate of species' migration and establishment in ways that are not related to the success of the vegetative plant. A different aspect of ecological genetics is studied in the work by Milla et al. (2012). Kin co-operation and rivalry has long been studied by ecologists in mammalian species, with extensive modelling being used to examine the advantages to individuals and species of competition or co-operation for dissemination of their own genes. The occurrence of co-operation between related plant genotypes is more controversial, and in this report the authors find no evidence for kin recognition and modification of growth strategies based on relatedness in pot-based experiments with siblings (1/2 related), cousins (1/8 related) and unrelated plants of the legume Lupinus angustifolius. Clearly, more examples are required to investigate whether kin co-operation does occur in plants, particularly given the importance of monocultures to agricultural production, and the significance of genetic homogeneity for disease epidemiology in both natural and agricultural environments. The abundance of angiosperm trees since the Cretaceous and their replacement of the previously dominant gymnosperms, except in some extreme ecosystems, has been widely discussed. A number of models involving water transport, reproduction and vegetative growth have been developed to explain the success of angiosperms. In this issue, Lusk et al. (2012) collect data from seedlings of conifers and angiosperms in five temperate rainforests. A modelling approach then shows that leaf structure, and particularly the superior light interception of angiosperm seedlings over the gymnosperms, gives them a substantial competitive advantage: it seems that the small number of larger leaves giving high light interception are important. The advantage is particularly high in light-limited environments, so gymnosperms continue to be successful in environments where other factors limit growth, and the authors conclude that traits related to seedling competitive ability are an important advantage for angiosperm trees. The final paper in this Highlight compares the behaviour of two successful species that co-occupy a single niche despite contrasting traits and hence strategies for survival. Surprisingly, in a seasonally dry tropical forest, both evergreen and deciduous angiosperm trees are successful, while in most environments the successful species tend to follow similar growth strategies within a niche. Fu et al. (2012) show that numerous fundamental traits, including stem hydraulic efficiency, photosynthetic rate, xylem cavitation resistance and leaf turgour-loss-point water potential, differ between the species. Thus a suite of characters have co-evolved in each species to cope with the seasonally dry tropical environment, and both strategies are equally successful. More generally, crop biologists will need to consider different solutions to environmental challenges, and it is probable that several approaches will be equally valuable in increasing the robustness of whole systems to environmental instability. These five articles show how understanding of plant traits and their significance for interactions with the environment is advancing using a range of approaches. The articles emphasize the impact that the ecosystem research is having on both fundamental knowledge of plant growth and development, and on the management strategies required for communities that are so critical in providing ecosystem services. I am sure the area will continue to develop, but I also hope that the lessons will be used in development of policies in a shorter timescale.

Retrotransposons make up a major fraction — sometimes more than 40% — of all plant genomes investigated so far. We have isolated the reverse transcriptase domains of the Ty1-copia group elements from several species, ranging in genome size from some 100 Mbp to 23 000 Mbp, and determined the distribution patterns of these retrotransposons on metaphase chromosomes and within interphase nuclei by DNA:DNA in situ hybridization. With some exceptions, the reverse transcriptase domains were distributed over the length of the chromosomes. Exclusion from rDNA sites and some centromeres (e.g., slash pine, 23 000 Mbp, or barley, 5500 Mbp) is frequent, whereas many species exclude retrotransposons from other sites of heterochromatin (e.g., intercalary and centromeric sites in broad bean). In contrast, in the plant Arabidopsis thaliana, widely used for plant molecular genetic studies because of its small genome (c. 100 Mbp), the Ty1-copia group reverse transcriptase gene domains are concentrated in the centromeric regions, collocalizing with the 180 bp satellite sequence pAL1. Unlike the pAL1 sequence, however, the Ty1-copia signal is also detectable as weaker, diffuse hybridization along the lengths of the chromosomes. Possible mechanisms for evolution of the contrasting distributions are discussed. Understanding the physical distribution of retrotransposons and comparisons of the distribution between species is critical to understanding their evolution and the significance for generation of the new patterns of variability and in speciation.

The Ty1-copia group of LTR retrotransposons has been studied extensively in yeast and Drosophila, the organisms in which they were first discovered, and more recently in higher plant and vertebrate species. Their properties, such as copy number, sequence homogeneity, transcriptional and transpositional activity vary greatly between these different hosts. We will try to resolve these apparent discrepancies between these properties, explain any fundamental differences in the biology of the Ty1-copia group between hosts, and propose a general model for LTR retrotransposon evolution.

Background and Aims Diploid and polyploid Urochloa (including Brachiaria, Panicum and Megathyrsus species) C4 tropical forage grasses originating from Africa are important for food security and the environment, often being planted in marginal lands worldwide. We aimed to characterize the nature of their genomes, the repetitive DNA and the genome composition of polyploids, leading to a model of the evolutionary pathways within the group including many apomictic species. Methods Some 362 forage grass accessions from international germplasm collections were studied, and ploidy was determined using an optimized flow cytometry method. Whole-genome survey sequencing and molecular cytogenetic analysis were used to identify chromosomes and genomes in Urochloa accessions belonging to the ‘brizantha’ and ‘humidicola’ agamic complexes and U. maxima. Key Results Genome structures are complex and variable, with multiple ploidies and genome compositions within the species, and no clear geographical patterns. Sequence analysis of nine diploid and polyploid accessions enabled identification of abundant genome-specific repetitive DNA motifs. In situ hybridization with a combination of repetitive DNA and genomic DNA probes identified evolutionary divergence and allowed us to discriminate the different genomes present in polyploids. Conclusions We suggest a new coherent nomenclature for the genomes present. We develop a model of evolution at the whole-genome level in diploid and polyploid accessions showing processes of grass evolution. We support the retention of narrow species concepts for Urochloa brizantha, U. decumbens and U. ruziziensis, and do not consider diploids and polyploids of single species as cytotypes. The results and model will be valuable in making rational choices of parents for new hybrids, assist in use of the germplasm for breeding and selection of Urochloa with improved sustainability and agronomic potential, and assist in measuring and conserving biodiversity in grasslands.