Comparative genome analysis is a powerful tool that can facilitate the reconstruction of the evolutionary history of the genomes of modern-day species. The model plant Arabidopsis thaliana with its n = 5 genome is thought to be derived from an ancestral n = 8 genome. Pairwise comparative genome analyses of A. thaliana with polyploid and diploid Brassicaceae species have suggested that rapid genome evolution, manifested by chromosomal rearrangements and duplications, characterizes the polyploid, but not the diploid, lineages of this family. In this study, we constructed a low-density genetic linkage map of Arabidopsis lyrata ssp. lyrata (A. l. lyrata; n = 8, diploid), the closest known relative of A. thaliana (MRCA approximately 5 Mya), using A. thaliana-specific markers that resolve into the expected eight linkage groups. We then performed comparative Bayesian analyses using raw mapping data from this study and from a Capsella study to infer the number and nature of rearrangements that distinguish the n = 8 genomes of A. l. lyrata and Capsella from the n = 5 genome of A. thaliana. We conclude that there is strong statistical support in favor of the parsimony scenarios of 10 major chromosomal rearrangements separating these n = 8 genomes from A. thaliana. These chromosomal rearrangement events contribute to a rate of chromosomal evolution higher than previously reported in this lineage. We infer that at least seven of these events, common to both sets of data, are responsible for the change in karyotype and underlie genome reduction in A. thaliana.

BACKGROUND: The microsatellite,(GATA)n has been frequently used for DNA fingerprinting. However, very few attempts have been made to analyze (GATA)n-containing loci in rice. RESULTS: Three polymorphic (GATA)n-harboring loci viz. OS1A6, OS1H10 and OS2E7, containing 7-13 repeat motifs were identified from a genomic library of a cultivated rice, Oryza sativa var. Basmati-370 using oligonucleotide probe (GATA)4. When (GATA)n flanking primers were used to screen 26 wilds (representing different genomes of rice), 16 cultivars, 47 Indian elite rice varieties and 37 lines resistant/susceptible to bacterial blight, up to 22 alleles were obtained at an individual locus. Also, interestingly the bacterial blight resistant lines clustered into a separate group from the remaining rice genotypes, when a dendrogram was constructed based on the polymorphism obtained at the three loci. This may be due to the partial homology of the clones OS1H10 and OS2E7 to regions encoding O. longistaminata receptor kinase-like protein and pathogenesis-related protein. The ability of these O. sativa flanking primers to amplify DNA of maize, wheat, barley and oat indicates that these (GATA)n-containing loci are conserved across different cereal genera. CONCLUSIONS: The large allele number obtained reveals the potential of (GATA)n-containing loci as powerful tools to detect simple sequence length polymorphism (SSLP). The (GATA)n-flanking primers were not only useful in distinguishing between closely related genotypes, but could also be used for cross-species amplification and are also conserved across different cereal genera. These loci could also cluster the bacterial blight resistant/susceptible lines into different groups based on the resistance genes present in them.

As a starting point for a phylogenetic study of self-incompatibility (SI) in crucifers and to elucidate the genetic basis of transitions between outcrossing and self-fertilizing mating systems in this family, we investigated the SI system of Arabidopsis lyrata. A. lyrata is an outcrossing close relative of the self-fertile A. thaliana and is thought to have diverged from A. thaliana approximately 5 million years ago and from Brassica spp 15 to 20 million years ago. Analysis of two S (sterility) locus haplotypes demonstrates that the A. lyrata S locus contains tightly linked orthologs of the S locus receptor kinase (SRK) gene and the S locus cysteine-rich protein (SCR) gene, which are the determinants of SI specificity in stigma and pollen, respectively, but lacks an S locus glycoprotein gene. As described previously in Brassica, the S haplotypes of A. lyrata differ by the rearranged order of their genes and by their variable physical sizes. Comparative mapping of the A. lyrata and Brassica S loci indicates that the S locus of crucifers is a dynamic locus that has undergone several duplication events since the Arabidopsis--Brassica split and was translocated as a unit between two distant chromosomal locations during diversification of the two taxa. Furthermore, comparative analysis of the S locus region of A. lyrata and its homeolog in self-fertile A. thaliana identified orthologs of the SRK and SCR genes and demonstrated that self-compatibility in this species is associated with inactivation of SI specificity genes.

It is estimated that 5 million years of evolution separate Arabidopsis thaliana from its close relative Arabidopsis lyrata. The two taxa differ by many characteristics, and together they exemplify the differentiation of angiosperms into self-fertilizing and cross-fertilizing species as well as annual and perennial species. Despite their disparate life histories, the two species can be crossed to produce viable and vigorous hybrids exhibiting heterotic effects. Although pollen sterile, the hybrids produce viable ovules and were used as female parent in backcrosses to both parental species. The resulting backcross plants exhibited transgressive variation for a number of interesting developmental and growth traits as well as negative nuclear/cytoplasmic interactions. Moreover, the genesis of a fertile amphidiploid neospecies, apparently by spontaneous somatic doubling in an interspecific hybrid, was observed in the laboratory. The mechanisms responsible for the generation of amphiploids and the subsequent evolution of amphiploid genomes can now be studied through direct observation using the large arsenal of molecular tools available for Arabidopsis.

Variation in repeat number at 20 microsatellite loci of Arabidopsis thaliana was studied in a worldwide sample of 42 ecotypes to investigate the pattern and level of polymorphism in repetitive sequences in natural plant populations. There is a substantial amount of variation at microsatellite loci despite the selfing nature of this plant species. The average gene diversity was 0.794 and the average number of alleles per locus was 10.6. The distribution of alleles was centered around the mean of repeat number at most loci, but could not be regarded as normal. There was a significantly positive correlation between the number of repeats and the amount of variation. For most loci, the observed number of alleles was between the expected values of the infinite allele and stepwise mutation models. The two models were rejected by the sign test. Linkage disequilibrium was detected in 12.1% of the pairwise comparisons between loci. In phylogenetic tree, there was no association between ecotype and geographic origin. This result is consistent with the recent expansion of A. thaliana throughout the world.

Genetic variation was studied in quantitative traits and molecular markers in six natural Scandinavian populations of Arabidopsis thaliana. Only two of the populations had several molecular marker haplotypes and significant between-family variance components in quantitative traits. There was no genetic variation in the other four populations. The differentiation between the populations was high in both molecular markers and quantitative traits, with FST estimates of above 0.60 in almost all traits. The patterns of variation of the neutral markers and morphological and phenological traits were consistent in all the analyses, as opposed to what has been found in predominantly outcrossing species. The general picture of the level and distribution of genetic variance agrees with the information from other predominantly inbreeding species.

The rotational properties of a mixture of two distinguishable Bose gases that are confined in a ring potential provide novel physical effects that we demonstrate in this study. Persistent currents are shown to be stable for a range of the population imbalance between the two components at low angular momentum. At higher values of the angular momentum, even small admixtures of a second species of atoms make the persistent currents highly fragile.

In this study we investigate natural selection in a pine phylogeny. DNA sequences from 18 nuclear genes were used to construct a very well supported species tree including 10 pine species. This tree is in complete agreement with a previously reported supertree constructed from morphological and molecular data but there are discrepancies with previous chloroplast phylogenies within the section Pinus. A significant difference in evolutionary rate between Picea and Pinus was found, which could potentially indicate a lower mutation rate in Picea, but other scenarios are also possible. Several approaches were used to study selection patterns in a set of 21 nuclear genes in pines and in some cases in Picea and Pseudotsuga. The overall pattern suggests efficient purifying selection resulting in low branch specific dn/ds ratios with an average of 0.22, which is similar to other higher plants. Evidence for purifying selection was common and found on at least 55% of the branches. Evidence of positive selection at several sites was found in a phytocyanin homolog and significant differences in dn/ds among the branches in the gene tree in dehydrin 1. Several genes suitable for further phylogenetic analysis at various levels of divergence were identified.

The perennial outcrossing Arabidopsis lyrata is becoming a plant model species for molecular ecology and evolution. However, its evolutionary history, and especially the impact of the climatic oscillations of the Pleistocene on its genetic diversity and population structure, is not well known. We analyzed the broad-scale population structure of the species based on microsatellite variation at 22 loci. A wide sample in Europe revealed that glaciations and postglacial colonization have caused high divergence and high variation in variability between populations. Colonization from Central Europe to Iceland and Scandinavia was associated with a strong decrease of genetic diversity from South to North. On the other hand, the Russian population included in our data set may originate from a different refugium probably located more to the East. These genome-wide patterns must be taken into account in studies aiming at elucidating the genetic basis of local adaptation. As shown by sequence data, most of the loci used in this study do not evolve like typical microsatellite loci and show variable levels of homoplasy: this mode of evolution makes these markers less suitable to investigate the between-continent divergence and more generally the worldwide evolution of the species. Finally, a strong negative correlation was detected between levels of within-population diversity and indices of differentiation such as F(ST). We discuss the causes of this correlation as well as the potential bias it induces on the quantification and interpretation of population structure.Heredity advance online publication, 17 October 2007; doi:10.1038/sj.hdy.6801057.

We investigated transmission ratio distortion within an Icelandic population of Arabidopsis lyrata using 16 molecular markers unlinked to the S-locus. Transmission ratio distortion was found more often than expected by chance at the gametic level, but not at the genotypic or zygotic level. The gametic effect may be due to meiotic drive or selection acting postmeiotically. At the gametic level, 10.9% of the tests were significant, which is substantially lower than earlier observed in an interpopulation cross (allowing for differences in power)-suggesting that the high level of transmission ratio distortion in the interpopulation cross is due to population divergence. It is also substantially lower than previously observed in intrapopulation crosses at the self-incompatibility locus, suggesting inherent fitness differences of the self-incompatibility alleles. We discuss the possible role of deleterious alleles accumulating at loci under balancing selection. Zygotic effects play a larger role in the interpopulation cross than in the intrapopulation crosses suggesting that Dobzhansky-Muller incompatibilities may be accumulating between the widely diverged populations.Heredity advance online publication, 17 October 2007; doi:10.1038/sj.hdy.6801066.

We investigate universal properties of strongly confined particles that turn out to be dramatically different from what is observed for electrons in atoms and molecules. For a large class of harmonically confined systems, such as small quantum dots and optically trapped atoms, many-body particle addition and removal energies, and energy gaps, are accurately obtained from single-particle eigenvalues. Transport blockade phenomena are related to the derivative discontinuity of the exchange-correlation functional. This implies that they occur very generally, with Coulomb blockade being a particular realization of a more general phenomenon. In particular, we predict a van der Waals blockade in cold atom gases in traps.

To determine whether population differentiation in flowering time is consistent with differences in current selection, we quantified phenotypic selection acting through female reproductive success on flowering phenology and floral display in two Scandinavian populations of the outcrossing, perennial herb Arabidopsis lyrata in two years. One population was located in an alpine environment strongly affected by grazing, whereas the other was close to sea level and only moderately affected by herbivory. Multiple regression models indicated directional selection for early end of flowering in one year in the lowland population, and directional selection for early start of flowering in one year in the alpine population. As expected, there was selection for more inflorescences in the lowland population. However, in the alpine population, plants with many inflorescences were selectively grazed and the number of inflorescences produced was negatively related to female fitness in one year and not significantly related to female fitness in the second year. The results are consistent with the hypothesis that genetic differentiation in flowering phenology between the study populations is adaptive, and indicate that interactions with selective grazers may strongly influence selection on floral display in A. lyrata.

The ex situ conservation of plant genetic resources in gene banks involves the selection of accessions to be conserved and the maintenance of these accessions for current and future users. Decisions concerning both these issues require knowledge about the distribution of genetic diversity within and between accessions sampled from the gene pool, but also about the changes in variation of these samples as a result of regenerations. These issues were studied in an existing gene bank collection of a cross-pollinating crop using a selection of groups of very similar Dutch white cabbage accessions, and additional groups of reference material representing the Dutch, and the global white cabbage gene pool. Six accessions were sampled both before and after a standard regeneration. 30 plants of each of 50 accessions plus 6 regeneration populations included in the study were characterised with AFLPs, using scores for 103 polymorphic bands. It was shown that the genetic changes as a result of standard gene bank regenerations, as measured by AFLPs, are of a comparable magnitude as the differences between some of the more similar accessions. The observed changes are mainly due to highly significant changes in allele frequencies for a few fragments, whereas for the majority of fragments the alleles occur in similar frequencies before and after regeneration. It is argued that, given the changes of accessions over generations, accessions that display similar levels of differentiation may be combined safely.

Most conifer species occur in large continuous populations, but radiata pine, Pinus radiata, occurs only in five disjunctive natural populations in California and Mexico. The Mexican island populations were presumably colonized from the mainland millions of years ago. According to Axelrod (1981), the mainland populations are relicts of an earlier much wider distribution, reduced some 8000 years ago, whereas according to Millar (1997, 2000), the patchy metapopulation-like structure is typical of the long-term population demography of the species. We used 19 highly polymorphic microsatellite loci to describe population structure and to search for signs of the dynamics of population demography over space and time. Frequencies of null alleles at microsatellite loci were estimated using an approach based on the probability of identity by descent. Microsatellite genetic diversities were high in all populations [expected heterozygosity (H(e))= 0.68-0.77], but the island populations had significantly lower estimates. Variation between loci in genetic differentiation (F(ST)) was high, but no locus deviated statistically significantly from the rest at an experiment wide level of 0.05. Thus, all loci were included in subsequent analysis. The average differentiation was measured as F(ST)= 0.14 (SD 0.012), comparable with earlier allozyme results. The island populations were more diverged from the other populations and from an inferred common ancestral gene pool than the mainland ones. All populations showed a deficiency of expected heterozygosity given the number of alleles, the mainland populations more so than the island ones. The results thus do not support a recent important contraction in the mainland range of radiata pine.

To support conservation policies for old Dutch grasslands that are still in agricultural use, morphological variation and AFLP-based (amplified fragment length polymorphism-based) genetic diversity was studied in perennial ryegrass and white clover populations and compared with the diversity in reference varieties. In addition, AFLP variation was also studied in grasslands located in nature reserves. From principal component analysis (PCA), it appeared that date of ear emergence in perennial ryegrass and characters related to plant vigour in white clover were the main morphological characters separating the reference varieties from the old Dutch grassland populations, and some of the grassland populations from each other. In both species, intrapopulation variation was lower for the reference varieties. Lower heterogeneity within the reference varieties was also found in the AFLP analysis. All common AFLP's observed in old Dutch grasslands could also be found in the reference varieties and nature reserves. Only a small number of low-frequency alleles found in old Dutch grasslands were absent from the other two groups. However, band frequencies of markers could vary considerably between populations, which may have been caused by selection. Analysis of the AFLP data by PCA distinguished the majority of reference varieties from the old Dutch grasslands, and showed genetic differentiation only between some grasslands. Comparison of old Dutch grasslands with grasslands in nature reserves indicated that basically the same range of genetic variation is covered by the two groups. Our study indicates that the Netherlands harbour a more or less continuous population for major parts of the diversity of perennial ryegrass and white clover. It was concluded that no specific conservation measures are presently needed to maintain genetic diversity of perennial ryegrass and white clover occurring in old Dutch grasslands.

ABSTRACT: BACKGROUND: Transposable Elements (TEs) make up the majority of plant genomes, and thus understanding TE evolutionary dynamics is key to understanding plant genome evolution. Plant reproductive systems are diverse and mating type variation is one factor among many hypothesized to influence TE evolutionary dynamics. Here, we collected a large TE-display data set in self-fertilizing Arabidopsis thaliana, and compared it to data gathered in outcrossing Arabidopsis lyrata. We analyzed seven TE families in four natural populations of each species to tease apart the effects of mating system, demography, transposition, and selection in determining patterns of TE diversity. RESULTS: Measures of TE band differentiation were largely consistent across TE families. However, patterns of diversity in A. thaliana Ac elements differed significantly from that other TEs, perhaps signaling a lack of recent transposition. Across TE families, we estimated higher allele frequencies and lower selection coefficients on A. thaliana TE insertions relative to A. lyrata TE insertions. CONCLUSIONS: The differences in TE distributions between the two Arabidopsis species represents a synthesis of evolutionary forces that include the transposition dynamics of individual TE families and the demographic histories of populations. There are also species-specific differences that could be attributed to the effects of mating system, including higher overall allele frequencies in the selfing lineage and a greater proportion of among population TE diversity in the outcrossing lineage.

Chloroplast microsatellites (cpSSRs) provide a powerful tool to study the genetic variation and evolution of plants. We have investigated the usefulness of 39 primer pairs tagging cpSSR loci on a set of eight different genera of Leguminosae (Papilionoideae subfamily) and five species belonging to the genus Phaseolus. Thirty-six 'universal' primer pairs were retrieved from the literature, one was re-designed and a further two were designed de novo. The cpSSR loci analysed were highly polymorphic across the individuals examined. Twenty-seven primer pairs were polymorphic in the overall sample, 18 within Phaseolus, and 16 in both P. vulgaris and P. coccineus. Analysis of the plastome sequences of four Leguminosae species (obtained from GenBank) showed that in the loci targeted by universal primer pairs:(i) the originally tagged cpSSRs can be lost;(ii) other cpSSRs can be present; and (iii) polymorphism arises not only from differences in the numbers of cpSSR repeats, but often from other insertion/deletion events. Multilocus linkage disequilibrium analysis suggests that homoplasy is not a major problem in our dataset, and principal component analysis indicates intelligible relationships among the species considered. Our study demonstrates that this set of chloroplast markers provides a useful tool to study the diversity and the evolution of several legumes, and particularly P. vulgaris and P. coccineus.

A broad research programme in Arabidopsis thaliana has provided estimates of selection on specific alleles in specific contexts, and identified geographic patterns of alleles in genes linked to timing of flowering. A closely related field has successfully captured many key axes of the evolution of timing of flowering in other monocarpic species through statistical and demographic modelling of large empirical databases. There has as yet been no synthesis between these two fields. Here we examine ways in which the two fields inform each other, and how this synergy will shape our knowledge of life-history evolution as a whole.

* It is not clear to what extent the orthologues of genes that are adaptively important in one species also contribute to adaptive variation in others. Here, we examine Arabidopsis lyrata to assess the functional and evolutionary significance of natural variation in an orthologue of the gene RPW8 known to be a major determinant of powdery mildew resistance in Arabidopsis thaliana.* We assessed the sequence variation at RPW8 and the associated resistance reaction in populations of A. lyrata ssp. petraea. Neutrality tests were performed to understand the importance of local adaptation in maintaining variation at the locus.* Highly truncated RPW8 proteins were frequent in all populations and were associated with an increased risk of susceptibility. Haplotypes encoding full-length proteins were highly significantly associated with resistance. There were no signatures of selection at the species-wide level, but some evidence for positive selection in two populations.* RPW8 in A. lyrata appears to have a role in powdery mildew resistance, similar to its orthologue in A. thaliana. Unlike A. thaliana, A. lyrata contains a genetic component that can act independently of RPW8 to confer resistance to powdery mildew pathogens. Infrequent local selective sweeps may favour different alleles in different populations, and thereby contribute to the maintenance of species-wide variation at the locus.

Microsatellites consisting of AT repeats are highly polymorphic in rice genomes and can be used to distinguish between even closely related japonica cultivars in Japan. Polymorphisms of 20 microsatellite loci were determined using 59 japonica cultivars, including both domestic and modern Japanese cultivars. Although the polymorphisms of these 20 microsatellite loci indicated that the Japanese cultivars were genetically quite similar, microsatellites consisting of AT repeats showed high gene diversity even among such closely related cultivars. Combinations of these hypervariable microsatellites can be employed to classify individual cultivars, since the microsatellites were stable within each cultivar. An identification system based on these highly polymorphic microsatellites could be used to maintain the purity of rice seeds by eliminating contamination. A parentage diagnosis using 17 polymorphic microsatellite loci clearly demonstrated that plants which carried desired chromosome regions had been selected in breeding programs. Thus, these hypervariable microsatellites consisting of AT repeats should promote the selection of plants which carry desired chromosomes from genetically similar parents. Backcrossing could also help to eliminate unnecessary chromosome regions with microsatellite polymorphisms at an early stage in breeding programs.

Volatile organic compounds have been reported to serve some important roles in plant communication with other organisms, but little is known about the biological functions of most of these substances. To gain insight into this problem, we have compared differences in floral and vegetative volatiles between two closely related plant species with different life histories. The self-pollinating annual, Arabidopsis thaliana, and its relative, the outcrossing perennial, Arabidopsis lyrata, have markedly divergent life cycles and breeding systems. We show that these differences are in part reflected in the formation of distinct volatile mixtures in flowers and foliage. Volatiles emitted from flowers of a German A. lyrata ssp. petraea population are dominated by benzenoid compounds in contrast to the previously described sesquiterpene-dominated emissions of A. thaliana flowers. Flowers of A. lyrata ssp. petraea release benzenoid volatiles in a diurnal rhythm with highest emission rates at midday coinciding with observed visitations of pollinating insects. Insect feeding on leaves of A. lyrata ssp. petraea causes a variable release of the volatiles methyl salicylate, C(11)- and C(16)-homoterpenes, nerolidol, plus the sesquiterpene (E)-beta-caryophyllene, which in A. thaliana is emitted exclusively from flowers. An insect-induced gene (AlCarS) with high sequence similarity to the florally expressed (E)-beta-caryophyllene synthase (AtTPS21) from A. thaliana was identified from individuals of a German A. lyrata ssp. petraea population. Recombinant AlCarS converts the sesquiterpene precursor, farnesyl diphosphate, into (E)-beta-caryophyllene with alpha-humulene and alpha-copaene as minor products indicating its close functional relationship to the A. thaliana AtTPS21. Differential regulation of these genes in flowers and foliage is consistent with the different functions of volatiles in the two Arabidopsis species.

Detecting the signature of adaptation on nucleotide variation is often difficult in species that like Arabidopsis thaliana might have a complex demographic history. Recent re-sequencing surveys in this species provided genome-wide information that would mainly reflect its demographic history. We have used a large empirical data set (LED) as well as multilocus coalescent simulations to analyse sequence variation at loci involved in the phenylpropanoid pathway of this species. We surveyed and examined DNA sequence variation at nine of these loci (about 19.7 kb) in 23 accessions of A. thaliana and one accession of its closely related species Arabidopsis lyrata. Nucleotide variation was lower at nonsynonymous sites than at silent sites in all loci, indicating generalized functional constraint at the protein level. No association between variation and position in the metabolic pathway was detected. When the data were contrasted against the standard neutral model, significant deviations for silent variation were detected with Tajima's D, Fu's F(S) and Fay and Wu's H multilocus test statistics. These deviations were in the same direction than in previous large-scale multilocus analyses, suggesting a genome-wide effect. When the nine-locus data set was contrasted against the large empirical data set, the level (Watterson's theta) and pattern of variation (Tajima's D) detected in these loci did not deviate either at the single-locus or multilocus level from the corresponding empirical distributions. These results would support an important role of the demographic history of A. thaliana in shaping nucleotide variation at the nine studied phenylpropanoid loci. The potential and limitations of the empirical distribution approach are discussed.

The polymerase chain reaction has been a boon to the study of molecular ecology and population genetics of birds. But the nagging truth is that for many bird species, the number of polymerase chain reaction (PCR) primer pairs that one can pick off the shelf and expect to amplify their target loci with ease is frustratingly small. Now, studying DNA sequence variation in natural populations of birds just got a whole lot easier. This issue of Molecular Ecology reports a large-scale bioinformatics search for exonic sequences conserved between the chicken and zebra finch genomes and flanking polymorphic introns that has generated a staggering 242 PCR primer pairs that readily amplify their single-copy target loci in five avian species spanning ~100 million years of avian evolution (Backström et al. 2008). As proof of principle, these primers have also been used to survey the genomic landscape in over 110 kb of intronic sequence in the collared flycatcher, a model species in ecology and evolution. These resources pave the way for easy multilocus study of evolving populations and lineages of birds, and bring the goal of quickly turning nonmodel species in to ecological genomic models tantalizingly close.

What genetic and epigenetic changes underlie adaptation and divergence? Arabidopsis thaliana and its relatives are increasingly being employed to address such central questions of evolutionary biology. For example, comparative, genomic and classical genetic approaches are revealing mechanisms underlying processes relevant to speciation, including mating system evolution, the effects of ploidy and other chromosomal differences, and the roles that specific genes might play in Dobzhansky-Muller type incompatibilities. The considerable body of knowledge and resources available for A. thaliana and improvements in tools and technology applied to its close relatives are opening doors for combining experimental and comparative analyses to elucidate fundamental mechanisms of evolution.

Extensive intraspecific variation in the chloroplast trnL(UAA)-trnF(GAA) spacer of model plant Arabidopsis lyrata is caused by multiple copies of a tandemly repeated trnF pseudogene undergoing parallel independent changes in copy number. Linkage disequilibrium and secondary structure analyses indicate that the diversification of pseudogene copies is driven by complex processes of structurally mediated illegitimate recombination. Disperse repeats sharing similar secondary structures interact, facilitating reciprocal exchange of structural motifs between copies via intramolecular and intermolecular recombinations, forming chimeric sequences and iterative expansion and contraction in pseudogene copy numbers. Widely held assumptions that chloroplast sequence evolution is simple and structural changes are informative are violated. Our findings have important implications for the use of this highly variable region in Brassicaceae studies. The reticulate evolution and nonindependent nucleotide substitution render the pseudogene inappropriate for standard phylogenetic reconstruction, but over short evolutionary timescales they may be useful for assessing gene flow, hybridization and introgression.