Preparation of Mitotic Chromosomes with the Squash Technique

Plant chromosomes are usually obtained from meristematic tissue of active root tips through the conventional squash method. Nevertheless, cytogenetic work usually implies a great effort and some modifications of standard procedures need to be evaluated. In this chapter, we describe our outline for handling chromosomes using the squash method. By using these protocols, high-quality chromosome spreads are obtained, which allow chromosome counting, building karyotypes, and assessing chromosomal landmarks, and enable genome mapping by fluorochrome banding and in situ hybridization techniques.

The Nuclear 35S rDNA World in Plant Systematics and Evolution: A Primer of Cautions and Common Misconceptions in Cytogenetic Studies

The ubiquitous presence of rRNA genes in nuclear, plastid, and mitochondrial genomes has provided an opportunity to use genomic markers to infer patterns of molecular and organismic evolution as well as to assess systematic issues throughout the tree of life. The number, size, location, and activity of the 35S rDNA cistrons in plant karyotypes have been used as conventional cytogenetic landmarks. Their scrutiny has been useful to infer patterns of chromosomal evolution and the data have been used as a proxy for assessing species discrimination, population differentiation and evolutionary relationships. The correct interpretation of rDNA markers in plant taxonomy and evolution is not free of drawbacks given the complexities derived from the lability of the genetic architecture, the diverse patterns of molecular change, and the fate and evolutionary dynamics of the rDNA units in hybrids and polyploid species. In addition, the terminology used by independent authors is somewhat vague, which often complicates comparisons. To date, no efforts have been reported addressing the potential problems and limitations involved in generating, utilizing, and interpreting the data from the 35S rDNA in cytogenetics. This review discusses the main technical and conceptual limitations of these rDNA markers obtained by cytological and karyological experimental work, in order to clarify biological and evolutionary inferences postulated in a systematic and phylogenetic context. Also, we provide clarification for some ambiguity and misconceptions in terminology usually found in published work that may help to improve the usage of the 35S ribosomal world in plant evolution.

Interstitial Arabidopsis-Type Telomeric Repeats in Asteraceae

Tandem repeats of telomeric-like motifs at intra-chromosomal regions, known as interstitial telomeric repeats (ITR), have drawn attention as potential markers of structural changes, which might convey information about evolutionary relationships if preserved through time. Building on our previous work that reported outstanding ITR polymorphisms in the genus Anacyclus, we undertook a survey across 132 Asteraceae species, focusing on the six most speciose subfamilies and considering all the ITR data published to date. The goal was to assess whether the presence, site number, and chromosomal location of ITRs convey any phylogenetic signal. We conducted fluorescent in situ hybridization (FISH) using an Arabidopsis-type telomeric sequence as a probe on karyotypes obtained from mitotic chromosomes. FISH signals of ITR sites were detected in species of subfamilies Asteroideae, Carduoideae, Cichorioideae, Gymnarhenoideae, and Mutisioideae, but not in Barnadesioideae. Although six small subfamilies have not yet been sampled, altogether, our results suggest that the dynamics of ITR formation in Asteraceae cannot accurately trace the complex karyological evolution that occurred since the early diversification of this family. Thus, ITRs do not convey a reliable signal at deep or shallow phylogenetic levels and cannot help to delimitate taxonomic categories, a conclusion that might also hold for other important families such as Fabaceae.

Interstitial Telomeric-like Repeats (ITR) in Seed Plants as Assessed by Molecular Cytogenetic Techniques: A Review

The discovery of telomeric repeats in interstitial regions of plant chromosomes (ITRs) through molecular cytogenetic techniques was achieved several decades ago. However, the information is scattered and has not been critically evaluated from an evolutionary perspective. Based on the analysis of currently available data, it is shown that ITRs are widespread in major evolutionary lineages sampled. However, their presence has been detected in only 45.6% of the analysed families, 26.7% of the sampled genera, and in 23.8% of the studied species. The number of ITR sites greatly varies among congeneric species and higher taxonomic units, and range from one to 72 signals. ITR signals mostly occurs as homozygous loci in most species, however, odd numbers of ITR sites reflecting a hemizygous state have been reported in both gymnosperm and angiosperm groups. Overall, the presence of ITRs appears to be poor predictors of phylogenetic and taxonomic relatedness at most hierarchical levels. The presence of ITRs and the number of sites are not significantly associated to the number of chromosomes. The longitudinal distribution of ITR sites along the chromosome arms indicates that more than half of the ITR presences are between proximal and terminal locations (49.5%), followed by proximal (29.0%) and centromeric (21.5%) arm regions. Intraspecific variation concerning ITR site number, chromosomal locations, and the differential presence on homologous chromosome pairs has been reported in unrelated groups, even at the population level. This hypervariability and dynamism may have likely been overlooked in many lineages due to the very low sample sizes often used in cytogenetic studies.

Molecular Evolution of rbcL in Orthotrichales (Bryophyta): Site Variation, Adaptive Evolution, and Coevolutionary Patterns of Amino Acid Replacements

Molecular evolution of the large subunit of the RuBisCO enzyme is understudied in early diverging land plants. These groups show morphological and eco-physiological adaptations to the uneven and intermittent distribution of water in the terrestrial environment. This might have prompted a continuous fine-tuning of RuBisCO under a selective pressure modifying the species-specific optima for photosynthesis in contrasting microdistributions and environmental niches. To gain a better insight into the molecular evolution of RuBisCO large subunits, the aim of this study was to assess the pattern of evolutionary change in the amino acid residues in a monophyletic group of Bryophyta (Orthotrichaceae). Tests for positive, neutral, or purifying selection at the amino acid level were assessed by comparing rates (ω) of non-synonymous (d_N) and synonymous (d_S) nucleotide substitutions along a Maximum Likelihood phylogenetic tree. Molecular adaptation tests using likelihood ratio tests, reconstruction of ancestral amino acid sites, and intra-protein coevolution analyses were performed. Variable amino acid sites (39) were unevenly distributed across the LSU. The residues are located on rbcL sites that are highly variable in higher plants and close to key regions implying dimer-dimer (L₂L₂), RuBisCO-activase interactions, and conformational functions during catalysis. Ten rbcL sites (32, 33, 91, 230, 247, 251, 255, 424, 449 and 475) have been identified by the Bayesian Empirical Bayes inference to be under positive selection and under adaptive evolution under the M8 model. The pattern of amino acid variation suggests that it is not lineage specific, but rather representative of a case of convergent evolution, suggesting recurrent changes that potentially favor the same amino acid substitutions that are likely optimized the RuBisCO activity.

Dissimilar molecular and morphological patterns in an introgressed peripheral population of a sand dune species (Armeria pungens, Plumbaginaceae)

Introgression is a poorly understood evolutionary outcome of hybridisation because it may remain largely undetected whenever it involves the transfer of small parts of the genome from one species to another. Aiming to understand the early stages of this process, a putative case from the southernmost border of the Armeria pungens range from its congener A. macrophylla is revisited following the discovery of a subpopulation that does not show phenotypic signs of introgression and resembles typical A. pungens. We analysed morphometrics, nuclear ribosomal DNA ITS and plastid DNA (trnL-trnF) sequences, genome size, 45S and 5S rDNA loci-FISH data and nrDNA IGS sequences. Within the study site, most individuals match morphologies of either of the two hybridising species, particularly the new subpopulation, with intermediate phenotypes being scarce. This pattern does not fully fit molecular evidence revealing two ITS ribotypes co-occurring intragenomically in most plants from the study site and one single plastid haplotype. Genome size and structural features of the IGS sequences both indicate that A. pungens from the study site is genetically more similar to its sympatric congener than to the remainder of its conspecifics. Introgression of A. macrophylla into A. pungens and plastid capture explain all the evidence analysed. However, important features to understand the origin and fate of the introgressed population, such as the degree and direction of introgression, which are important for understanding early stages of hybridisation in plants with low reproductive barriers, should be addressed with new data.

Unique Epigenetic Features of Ribosomal RNA Genes (rDNA) in Early Diverging Plants (Bryophytes)

Introduction: In plants, the multicopy genes encoding ribosomal RNA (rDNA) typically exhibit heterochromatic features and high level of DNA methylation. Here, we explored rDNA methylation in early diverging land plants from Bryophyta (15 species, 14 families) and Marchantiophyta (4 species, 4 families). DNA methylation was investigated by methylation-sensitive Southern blot hybridization in all species. We also carried out whole genomic bisulfite sequencing in Polytrichum formosum (Polytrichaceae) and Dicranum scoparium (Dicranaceae) and used available model plant methyloms (Physcomitrella patents and Marchantia polymorpha) to determine rDNA unit-wide methylation patterns. Chromatin structure was analyzed using fluorescence in situ hybridization (FISH) and immunoprecipitation (CHIP) assays. Results: In contrast to seed plants, bryophyte rDNAs were efficiently digested with methylation-sensitive enzymes indicating no or low levels of CG and CHG methylation in these loci. The rDNA methylom analyses revealed variation between species ranging from negligible (<3%, P. formosum, P. patens) to moderate (7 and 17% in M. polymorpha and D. scoparium, respectively) methylation levels. There were no differences between coding and noncoding parts of rDNA units and between gametophyte and sporophyte tissues. However, major satellite repeat and transposable elements were heavily methylated in P. formosum and D. scoparium. In P. formosum rDNA, the euchromatic H3K4m3 and heterochromatic H3K9m2 histone marks were nearly balanced contrasting the angiosperms data where H3K9m2 typically dominates rDNA chromatin. In moss interphase nuclei, rDNA was localized at the nucleolar periphery and its condensation level was high. Conclusions: Unlike seed plants, the rRNA genes seem to escape global methylation machinery in bryophytes. Distinct epigenetic features may be related to rDNA expression and the physiology of these early diverging plants that exist in haploid state for most of their life cycles.

Inter- and intraspecific hypervariability in interstitial telomeric-like repeats (TTTAGGG)n in Anacyclus (Asteraceae)

Background and Aims

Interstitial telomeric repeat (ITR) sites, consisting of tandem repeats of telomeric motifs localized at intrachromosomal sites, have been reported in a few unrelated organisms including plants. However, the causes for the occurrence of ITRs outside of the chromosomal termini are not fully understood. One possible explanation are the chromosomal rearrangements involving telomeric sites, which could also affect the location of other structural genome elements, such as the 45S rDNA. Taking advantage of the high dynamism in 45S rDNA loci previously found in Anacyclus (Asteraceae, Anthemideae), the occurrence and patterns of variation of ITRs were explored in this genus with the aim of finding common underlying causes.

Methods

In total, 132 individuals from 44 populations of nine species were analysed by fluorescence in situ hybridization using an Arabidopsis-type telomeric sequence as a probe.

Key results

Variable presence of ITR sites was detected in six out of nine species of Anacyclus, ranging from two to 45 sites and showing contrasting chromosomal locations and a differential presence of the ITR site on homologous chromosome pairs. At the intraspecific level, the ranges were as large as 0-12 ITR sites. Although only 26 % of the total observed ITR sites were localized in chromosomes bearing 45S rDNA loci, all cases of interstitial 45S rDNA reported in a previous work co-occurred with ITRs in close proximity in the same chromosome arms.

Conclusions

High levels of ITR polymorphism within a single species have not been previously reported in plants and suggest that this pattern might have been overlooked due to insufficient sampling. Although ancient Robertsonian translocations or the amplification of terminal 45S rDNA sites cannot, on their own, explain all of the levels of variability in ITRs reported here, there are suggestions that they may have been involved in the evolutionary history of this genus or its ancestors in Anthemideae.

Conserved Organisation of 45S rDNA Sites and rDNA Gene Copy Number among Major Clades of Early Land Plants

Genes encoding ribosomal RNA (rDNA) are universal key constituents of eukaryotic genomes, and the nuclear genome harbours hundreds to several thousand copies of each species. Knowledge about the number of rDNA loci and gene copy number provides information for comparative studies of organismal and molecular evolution at various phylogenetic levels. With the exception of seed plants, the range of 45S rDNA locus (encoding 18S, 5.8S and 26S rRNA) and gene copy number variation within key evolutionary plant groups is largely unknown. This is especially true for the three earliest land plant lineages Marchantiophyta (liverworts), Bryophyta (mosses), and Anthocerotophyta (hornworts). In this work, we report the extent of rDNA variation in early land plants, assessing the number of 45S rDNA loci and gene copy number in 106 species and 25 species, respectively, of mosses, liverworts and hornworts. Unexpectedly, the results show a narrow range of ribosomal locus variation (one or two 45S rDNA loci) and gene copies not present in vascular plant lineages, where a wide spectrum is recorded. Mutation analysis of whole genomic reads showed higher (3-fold) intragenomic heterogeneity of Marchantia polymorpha (Marchantiophyta) rDNA compared to Physcomitrella patens (Bryophyta) and two angiosperms (Arabidopsis thaliana and Nicotiana tomentosifomis) suggesting the presence of rDNA pseudogenes in its genome. No association between phylogenetic position, taxonomic adscription and the number of rDNA loci and gene copy number was found. Our results suggest a likely evolutionary rDNA stasis during land colonisation and diversification across 480 myr of bryophyte evolution. We hypothesise that strong selection forces may be acting against ribosomal gene locus amplification. Despite showing a predominant haploid phase and infrequent meiosis, overall rDNA homogeneity is not severely compromised in bryophytes.

Non-functional plastid ndh gene fragments are present in the nuclear genome of Norway spruce (Picea abies L. Karsch): insights from in silico analysis of nuclear and organellar genomes

Many genes have been lost from the prokaryote plastidial genome during the early events of endosymbiosis in eukaryotes. Some of them were definitively lost, but others were relocated and functionally integrated to the host nuclear genomes through serial events of gene transfer during plant evolution. In gymnosperms, plastid genome sequencing has revealed the loss of ndh genes from several species of Gnetales and Pinaceae, including Norway spruce (Picea abies). This study aims to trace the ndh genes in the nuclear and organellar Norway spruce genomes. The plastid genomes of higher plants contain 11 ndh genes which are homologues of mitochondrial genes encoding subunits of the proton-pumping NADH-dehydrogenase (nicotinamide adenine dinucleotide dehydrogenase) or complex I (electron transport chain). Ndh genes encode 11 NDH polypeptides forming the Ndh complex (analogous to complex I) which seems to be primarily involved in chloro-respiration processes. We considered ndh genes from the plastidial genome of four gymnosperms (Cryptomeria japonica, Cycas revoluta, Ginkgo biloba, Podocarpus totara) and a single angiosperm species (Arabidopsis thaliana) to trace putative homologs in the nuclear and organellar Norway spruce genomes using tBLASTn to assess the evolutionary fate of ndh genes in Norway spruce and to address their genomic location(s), structure, integrity and functionality. The results obtained from tBLASTn were subsequently analyzed by performing homology search for finding ndh specific conserved domains using conserved domain search. We report the presence of non-functional plastid ndh gene fragments, excepting ndhE and ndhG genes, in the nuclear genome of Norway spruce. Regulatory transcriptional elements like promoters, TATA boxes and enhancers were detected in the upstream regions of some ndh fragments. We also found transposable elements in the flanking regions of few ndh fragments suggesting nuclear rearrangements in those regions. These evidences support the hypothesis that, at least in Picea, ndh translocations from the plastid to the nuclear genome have occurred, and that there might have been a functional machinery at some time during evolution to accommodate them within a nuclear-encoded environment, or attempts to form it.

Evolutionary site-number changes of ribosomal DNA loci during speciation: complex scenarios of ancestral and more recent polyploid events

Several genome duplications have been identified in the evolution of seed plants, providing unique systems for studying karyological processes promoting diversification and speciation. Knowledge about the number of ribosomal DNA (rDNA) loci, together with their chromosomal distribution and structure, provides clues about organismal and molecular evolution at various phylogenetic levels. In this work, we aim to elucidate the evolutionary dynamics of karyological and rDNA site-number variation in all known taxa of subtribe Vellinae, showing a complex scenario of ancestral and more recent polyploid events. Specifically, we aim to infer the ancestral chromosome numbers and patterns of chromosome number variation, assess patterns of variation of both 45S and 5S rDNA families, trends in site-number change of rDNA loci within homoploid and polyploid series, and reconstruct the evolutionary history of rDNA site number using a phylogenetic hypothesis as a framework. The best-fitting model of chromosome number evolution with a high likelihood score suggests that the Vellinae core showing x = 17 chromosomes arose by duplication events from a recent x = 8 ancestor. Our survey suggests more complex patterns of polyploid evolution than previously noted for Vellinae. High polyploidization events (6x, 8x) arose independently in the basal clade Vella castrilensis-V. lucentina, where extant diploid species are unknown. Reconstruction of ancestral rDNA states in Vellinae supports the inference that the ancestral number of loci in the subtribe was two for each multigene family, suggesting that an overall tendency towards a net loss of 5S rDNA loci occurred during the splitting of Vellinae ancestors from the remaining Brassiceae lineages. A contrasting pattern for rDNA site change in both paleopolyploid and neopolyploid species was linked to diversification of Vellinae lineages. This suggests dynamic and independent changes in rDNA site number during speciation processes and a significant lack of correlation between 45S and 5S rDNA evolutionary pathways.

Incomplete sequence homogenization in 45S rDNA multigene families: intermixed IGS heterogeneity within the single NOR locus of the polyploid species Medicago arborea (Fabaceae)

BACKGROUND AND AIMS

Ribosomal sequences have become the classical example of the genomic homogenization of nuclear multigene families. Despite theoretical advantages and modelling predictions that support concerted evolution of the 45S rDNA, several reports have found intragenomic polymorphisms. However, the origins and causes of these rDNA polymorphisms are difficult to assess because seed plants show a wide range of 45S rDNA loci number variation, especially in polyploids. Medicago arborea is a tetraploid species that has a single 45S rDNA locus. This feature makes this species a suitable case study to assess the fate of ribosomal IGS homogenization in polyploid species showing nucleolus organizer region (NOR) reduction.

METHODS

The intergenic spacer (IGS) region was amplified by long PCR and the fragments were cloned and sequenced by a primer-walking strategy. The physical mapping of the whole and partial IGS variants was assessed by fluorescent in situ hybridization (FISH) and fibre-FISH methods on mitotic chromosomes and extended DNA fibres, respectively.

KEY RESULTS

Two IGS fragments of 4·8 and 3·5 kb were obtained showing structural features of functional sequences. The shorter variant appears to be a truncated copy of the 4·8 kb fragment that lacks the duplication of the transcription initiation site region and the entire D region. The physical localization of the two IGS variants on metaphase chromosomes and extended DNA fibres using FISH corroborated their joint presence within the same locus. In addition, no spatial structure of the two variants was detected within the NOR.

CONCLUSIONS

The results suggest that full sequence homogenization is not operating within the NOR locus of M. arborea. The structure of the NOR locus reported here departs from the models of IGS heterogeneity present in plants and caution against assuming the widespread belief that intragenomic ribosomal heterogeneity is mainly due to sequence variation between paralogous loci.

Amplification, contraction and genomic spread of a satellite DNA family (E180) in Medicago (Fabaceae) and allied genera

BACKGROUND AND AIMS

Satellite DNA is a genomic component present in virtually all eukaryotic organisms. The turnover of highly repetitive satellite DNA is an important element in genome organization and evolution in plants. Here we assess the presence and physical distribution of the repetitive DNA E180 family in Medicago and allied genera. Our goals were to gain insight into the karyotype evolution of Medicago using satellite DNA markers, and to evaluate the taxonomic and phylogenetic signal of a satellite DNA family in a genus hypothesized to have a complex evolutionary history.

METHODS

Seventy accessions from Medicago, Trigonella, Melilotus and Trifolium were analysed by PCR to assess the presence of the repetitive E180 family, and fluorescence in situ hybridization (FISH) was used for physical mapping in somatic chromosomes.

KEY RESULTS

The E180 repeat unit was PCR-amplified in 37 of 40 taxa in Medicago, eight of 12 species of Trigonella, six of seven species of Melilotus and in two of 11 Trifolium species. Examination of the mitotic chromosomes revealed that only 13 Medicago and two Trigonella species showed FISH signals using the E180 probe. Stronger hybridization signals were observed in subtelomeric and interstitial loci than in the pericentromeric loci, suggesting this satellite family has a preferential genomic location. Not all 13 Medicago species that showed FISH localization of the E180 repeat were phylogenetically related. However, nine of these species belong to the phylogenetically derived clade including the M. sativa and M. arborea complexes.

CONCLUSIONS

The use of the E180 family as a phylogenetic marker in Medicago should be viewed with caution. Its amplification appears to have been produced through recurrent and independent evolutionary episodes in both annual and perennial Medicago species as well as in basal and derived clades.

Patterns of genetic variability and habitat occupancy in Crepis triasii (Asteraceae) at different spatial scales: insights on evolutionary processes leading to diversification in continental islands

BACKGROUND AND AIMS

Archipelagos are unique systems for studying evolutionary processes promoting diversification and speciation. The islands of the Mediterranean basin are major areas of plant richness, including a high proportion of narrow endemics. Many endemic plants are currently found in rocky habitats, showing varying patterns of habitat occupancy at different spatial scales throughout their range. The aim of the present study was to understand the impact of varying patterns of population distribution on genetic diversity and structure to shed light on demographic and evolutionary processes leading to population diversification in Crepis triasii, an endemic plant from the eastern Balearic Islands.

METHODS

Using allozyme and chloroplast markers, we related patterns of genetic structure and diversity to those of habitat occupancy at a regional (between islands and among populations within islands) and landscape (population size and connectivity) scale.

KEY RESULTS

Genetic diversity was highly structured both at the regional and at the landscape level, and was positively correlated with population connectivity in the landscape. Populations located in small isolated mountains and coastal areas, with restricted patterns of regional occupancy, were genetically less diverse and much more differentiated. In addition, more isolated populations had stronger fine-scale genetic structure than well-connected ones. Changes in habitat availability and quality arising from marine transgressions during the Quaternary, as well as progressive fragmentation associated with the aridification of the climate since the last glaciation, are the most plausible factors leading to the observed patterns of genetic diversity and structure.

CONCLUSIONS

Our results emphasize the importance of gene flow in preventing genetic erosion and maintaining the evolutionary potential of populations. They also agree with recent studies highlighting the importance of restricted gene flow and genetic drift as drivers of plant evolution in Mediterranean continental islands.

Relationships of the woody Medicago species (section Dendrotelis) assessed by molecular cytogenetic analyses

BACKGROUND AND AIMS

The organization of rDNA genes in the woody medic species from the agronomically important Medicago section Dendrotelis was analysed to gain insight into their taxonomic relationships, to assess the levels of infraspecific variation concerning ribosomal loci in a restricted and fragmented insular species (M. citrina) and to assess the nature of its polyploidy.

METHODS

Fluorescence in situ hybridization (FISH) was used for physical mapping of 5S and 45S ribosomal DNA genes in the three species of section Dendrotelis (M. arborea, M. citrina, M. strasseri) and the related M. marina from section Medicago. Genomic in situ hybridization (GISH) was used to assess the genomic relationships of the polyploid M. citrina with the putatively related species from section Dendrotelis.

KEY RESULTS

The diploid (2n = 16) M. marina has a single 45S and two 5S rDNA loci, a pattern usually detected in previous studies of Medicago diploid species. However, polyploid species from section Dendrotelis depart from expectations. The tetraploid species (2n = 32) M. arborea and M. strasseri have one 45S rDNA locus and two 5S rDNA loci, whereas in the hexaploid (2n = 48) M. citrina four 45S rDNA and five 5S rDNA loci have been detected. No single chromosome of M. citrina was uniformly labelled after using genomic probes from M. arborea and M. strasseri. Instead, cross-hybridization signals in M. citrina were restricted to terminal chromosome arms and NOR regions.

CONCLUSIONS

FISH results support the close taxonomic interrelationship between M. arborea and M. strasseri. In these tetraploid species, NOR loci have experienced a diploidization event through physical loss of sequences, a cytogenetic feature so far not reported in other species of the genus. The high number of rDNA loci and GISH results support the specific status for the hexaploid M. citrina, and it is suggested that this species is not an autopolyploid derivative of M. arborea or M. strasseri. Further, molecular cytogenetic data do not suggest the hypothesis that M. arborea and M. strasseri were involved in the origin of M. citrina. FISH mapping can be used as an efficient tool to determine the genomic contribution of M. citrina in somatic hybrids with other medic species.

Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants

The internal transcribed spacers (ITS) of the nuclear ribosomal 18S-5.8S-26S cistron continue to be the most popular non-plastid region for species-level phylogenetic studies of plant groups despite the early warnings about their potential flaws, which may ultimately result in incorrect assumptions of orthology. It has been gradually realized that the alternative target regions in the nuclear genome (low-copy nuclear genes, LCNG) are burdened with similar problems. The consequence is that, to date, developing useful LCNG for non-model organisms requires an investment in time and effort that hinders its use as a real practical alternative for many labs. It is here argued that ITS sequences, despite drawbacks, can still produce insightful results in species-level phylogenetic studies or when non-anonymous nuclear markers are required, provided that a thoughtful use of them is made. To facilitate this, two series of guidelines are proposed. One helps to circumvent problems of ITS amplification from the target organism, including spurious results from contaminants, paralogs and pseudogenes, as well as detection of sequencing artifacts. The other series helps to find out causes for unresolved clades in phylogenetic reconstruction, to integrate gene phylogenies, to distinguish horizontal transfer from lineage sorting, and to reveal if ITS phylogeny is not a good estimate of organism phylogeny.

A Phylogeographic Split in Buxus balearica (Buxaceae) as Evidenced by Nuclear Ribosomal Markers: When ITS Paralogues Are Welcome

Sequences from the ribosomal nuclear internal transcribed spacers (ITS) have been widely used to infer evolutionary hypotheses across a broad range of living organisms. Intraspecific sequence variation is assumed to be absent or negliable in most species, but few detailed studies have been conducted to assess the apportionment of ITS sequence variation within and between plant populations. Buxus balearica was chosen as a model species to assess the levels of infraspecific and intragenomic ITS variation in rare and endangered species occurring in disjunct populations around the Mediterranean basin. Intragenomic polymorphic sites were detected for western and eastern accessions of B. balearica and in two accessions of the sister species B. sempervirens. Overall, 19 different ribotypes were found in B. balearica after sequencing 48 clones, whereas 15 ribotypes were detected in 19 clones of B. sempervirens. The integrity and secondary structure stability of the ribosomal sequences suggest that they are not pseudogenes. The high number of ribotypes recovered through cloning suggested that some sequences could be chimeric or generated in vivo by partial homogenization through gene conversion or unequal crossing-over. Average sequence divergence among B. balearica clones was 0.768%, and the most divergent sequences differed by 1.62%. Available evidence does not suggest that B. balearica paralogues have been obtained from other extant Buxus species through interspecific hybridization. The presence of several ribosomal sequences in box implies that the molecular forces driving the concerted evolution of this multigene family are not fully operational in this genus. Phylogenetic analyses of cloned ITS sequences from B. balearica displayed very poor resolution and only two clades received moderate bootstrap support. Despite the marked intragenomic sequence divergence found, ribosomal data suggest a clear phylogeographic split in B. balearica between western and eastern accessions. The distinct, nonchimeric sequences that are postulated as being present in each biogeographic group suggest that box populations from Anatolia (eastern Mediterranean) are relict.

New method of DNA isolation from two food additives suitable for authentication in polymerase chain reaction assays

Locust bean gum and guar gum are galactomannans used as additives (E 410 and E 412, respectively) in the food industry as stabilizing agents. Analytical discrimination between the two additives in gums and foods is now feasible by molecular techniques. However, only complex and time-consuming DNA isolation protocols are available to date. We have developed simple improved protocols to obtain enough DNA suitable for PCR amplification from a few milligrams of commercial E 410 and E 412 additives (containing more than 75% polysaccharides). The suspension of additives in water or 10 mM Tris-HCl, pH 8.5, efficiently recovers DNA suitable for authentication in PCR assays. However, the Tris method was much more efficient for the extraction of DNA from E 410 than for E 412 additives. Conversely, the water method was the most suitable for detecting DNA extracted from E 412 or from E 410/E 412 mixtures. Combined with the use of the two specific ribosomal primer pairs previously designed, our methods are well-suited for a fast and simple high-throughput sample treatment of commercial gums for molecular certification.

Identification of two additives, locust bean gum (E-410) and guar gum (E-412), in food products by DNA-based methods

Locust bean gum (E-410) and guar gum (E-412) are high molecular weight galactomannans used by the food industry as versatile food additives. The compounds, although chemically closely related, do not have the same functional properties when used in foods, and the substitution or unadvertised addition of either could change the desired qualities of the product. Analytical discrimination between E-410 and E-412 is technically difficult since they only differ in their galactose: mannose ratios, being 1 : 4 and 1 : 2 for locust bean gum and guar gum, respectively. A qualitative DNA-based method is reported for the authentication of additives E-410 and E-412 in finished food products (ice cream, dehydrated desserts, milk derivatives, dehydrated soups, salad dressing, marmalade and meat) from small quantities of food. DNA sequences from the nuclear ribosomal spacers of Ceratonia siliqua and Cyamopsis tetragonoloba, the plant sources of E-410 and E-412, respectively, were used to design polymerase chain reaction primers specific for each additive (PA23/PA21 and PG22/PG21). Twenty-two foods were analysed for the presence of E-410 and E-412 additives by this single-step polymerase chain reaction-based method. Positive DNA amplifications with the E-410 and/or E-412 primers were obtained in all 19 samples reported to contain either additive.

Genetic variability in a narrow endemic snapdragon (Antirrhinum subbaeticum, Scrophulariaceae) using RAPD markers

Antirrhinum subbaeticum is an endangered species inhabiting fragmented limestone cliffs. In the last 3 years, a drastic population decline has been observed in three of four known populations and the estimated number of surviving individuals is now close to 400. A RAPD study was conducted to evaluate the levels of genetic variation present in this species to improve conservation guidelines. Thirty-nine polymorphic products identified 66.1% of the samples by unique RAPD multilocus profiles. A cluster analysis grouped the samples into two broad groups corresponding to northern or southern provenances. AMOVA analysis showed that only 17.7% of the genetic diversity was partitioned within populations. These results are in contrast to data available for other Antirrhinum species. This genetic structure could be explained by the predominant selfing behaviour exhibited by A. subbaeticum as opposed to the allogamy of other congeners. Genetic diversity within populations does not seem to be strongly related to population size and historical factors could be responsible for the very low levels of genetic diversity found in one population. Given the low genetic diversity within populations, it is suggested that an extensive sampling of individuals be made for recovering appropriate levels of the gene pool for ex situ preservation. However, translocation of individuals to the genetically weakened Bogarra population from other sources is not recommended.

Seed germination and reproductive features of Lysimachia minoricensis (Primulaceae), a wild-extinct plant

Lysimachia minoricensis is one of the few Mediterranean endemic plants (Minorca, Balearic islands) that has gone extinct in the wild but which persists as extant germplasm or cultivated plants in several botanical gardens. Reproductive features (seed set, number of seeds per capsule, seed weight) and germination responses to constant temperatures, sea water and dry-heat pre-treatments were investigated to determine the extent to which they may have influenced the extinction of the species. Seed set in Lysimachia is not dependent on pollinators, suggesting a functional selfer breeding system. Most plants produced a large mean number of fruits (23.2) and seeds (466), and the mean production of seeds per individual was estimated to be almost 1,100. Overall, no highly specific requirements were observed for seed germination. Seed germination was not inhibited in the dark, and a high germinability (over 87% in all cases) was recorded in most experiments, with the exception of those performed at low temperatures (5 and 10 degrees C). These data suggest that fertility and seed viability were not the major causes of extinction. The high reproductive performance of L. minoricensis is in striking contrast to its status as a wild-extinct plant, suggesting that extrinsic factors were responsible for its extinction.

Testing taxonomic and biogeographical relationships in a narrow Mediterranean endemic complex (Hippocrepis balearica) using RAPD markers

Analyses of RAPD profiles from 17 populations of the Hippocrepis balearica complex revealed a highly structured geographic pattern, not only among continental-insular areas but also within the eastern Balearic islands. In marked contrast to previous morphometric results, a clear separation between continental and insular samples was found, and intermediates between H. balearica and H. valentina samples were not detected. Molecular data indicated that western and eastern Balearic populations of the complex (H. grosii and H. balearica) were more closely related to each other than to continental populations (H. valentina). Multivariate analyses of the RAPD data clearly indicated that the similarities between continental and eastern Balearic samples of the H. balearica complex recovered by morphometric methods are due either to parallel evolution or to retention of plesiomorphic features.

Why nuclear ribosomal DNA spacers (ITS) tell different stories in Quercus

The molecular systematics of Quercus (Fagaceae) was recently assessed by two teams using independently generated ITS sequences. Although the results disagreed in several remarkable features, the phylogenetic trees for either hypothesis were highly supported by bootstrap resampling. We have reanalyzed the ITS sequences used by both teams (eight taxa) to reveal the underlying patterns of this divergence. Within species, conspicuous length and G + C% divergence were evident in most sequence comparisons. In addition, a high rate of substitutions and deletions involving highly conserved motifs in both ITS spacers were present in a set of sequences. This was coupled with a less thermodynamic stability in the RNA structure, lacking conserved hairpins that are putatively involved in the processing of the RNA transcripts. Compelling evidence suggests that the divergent ITS alleles reported by one team are pseudogenes, i.e., nonfunctional paralogous loci. The hypothesis that the contrasting phylogenetic histories drawn from Quercus using ITS data are not strictly related to technical differences between laboratories, but that they have rather been generated from the analysis of paralogous sequences, best reconciles the available data. The risk of incorporating ITS paralogues in plant evolutionary studies which can distortion the phylogenetic signal should caution molecular systematists. Without a detailed inspection of some basic features of the sequence, including the integrity of the conserved motifs and the thermodynamic stability of the secondary structures of the RNA transcripts, errors in evolutionary inferences could be easily overlooked.

Study of the evolutionary relationships among Limonium species (Plumbaginaceae) using nuclear and cytoplasmic molecular markers

The genus Limonium, due to the patchiness of the natural habitats of its species as well as the high frequency of hybridization and polyploidy and the possibility of reproduction by apomixis, provides an example of all the principal mechanisms of rapid speciation of plants. As an initial study of evolution in this genus, we have analyzed intra- and interspecific variability in 17 species from section Limonium, the largest in the genus, based on RFLPs of cpDNA and nuclear rDNA ITS sequences. In the cpDNA analysis, 21 restriction enzymes were used, resulting in 779 fragments, 490 of which were variable and 339 parsimony informative. L. furfuraceum exhibited two relatively divergent cpDNA haplotypes. The relationships found among the species based on cpDNA restriction fragments were coincident using different methods of phylogenetic analysis. Due to the presumed reticulate evolution in the genus Limonium, the comparison of these results with data from the nuclear DNA was necessary; ITS sequences were analyzed. The final alignment contained 488 characters, of which 198 were variable and 156 parsimony informative. Two relatively divergent ITS types were present at the intraindividual level in L. delicatulum, a triploid species. Each type was related to ITS from different groups of diploid Limonium species, one with a base haploid chromosome number n = 8 (represented by L. cossonianum) and the other with n = 9 (represented by L. minutum). The different phylogenetic inference methods used for the analysis of ITS sequences rendered very similar topologies. In general, the relationships among the species studied were coincident with those obtained with the chloroplast genome. Both nuclear and cytoplasmic markers support the polyphyly of section Limonium, with at least two species, L. narbonense and L. vulgare, clearly divergent from the rest. Moreover, the remaining subsections into which section Limonium is currently divided seem to be artificial.

Molecular evidence for the compilospecies model of reticulate evolution in Armeria (Plumbaginaceae)

Cladistic analyses of the nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequences from 55 samples corresponding to 34 taxa in the genus Armeria reveal that ITS sequence diversity among and within species utterly conflicts with patterns of morphological similarity. Three facts are apparent from the results here reported: (1) different samples of a single subspecies, A. villosa subsp. longiaristata, appear in three of the five major clades; (2) samples of at least one of the six subspecies of A. villosa appear in four of the five major clades; and (3) the composition of major clades shows greater congruence with the geographic origin of plants than with the traditional systematic arrangement based primarily on morphology. Specifically, the clades here termed Ia, II, III, and IV each encompass terminals restricted to geographically delimited areas. There are alternative explanations for the ITS pattern, but the most likely one is that nucleotide positions supporting the major clades are due, in some of the samples, to concerted evolution following horizontal transfer (gene flow) rather than to recency of common ancestry. This interpretation is consistent with previous systematic and experimental evidence and implies that reticulation in Armeria may be extensive. Harlan and de Wet (1963, Evolution 17:497-501) proposed the compilospecies concept to account for situations in which a genetically "aggressive" species captures portions of the genome of other sympatric species by means of extensive introgression. Evidence of extensive reticulation, ecological diversification, and geographic pattern indicates that A. villosa may fit the compilospecies concept, which is here supported on molecular grounds for the first time.

Nuclear ribosomal DNA (nrDNA) concerted evolution in natural and artificial hybrids of Armeria (Plumbaginaceae)

Nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequences from artificial hybrids and backcrosses between Armeria villosa ssp. longiaristata and A. colorata were studied to assess the possible effects of concerted evolution in natural hybrids. F1 artificial hybrids show the expected pattern of additive polymorphisms for five of the six variable sites as estimated from direct sequences. However, homogenization of polymorphism is already observed in the F2, and is biased towards A. colorata except for one site. In backcrosses, an expected tendency towards homogenization of polymorphic sites in the direction of the recurrent parent is observed for five sites, although this does not necessarily imply concerted evolution. Conversely, the sixth site appears to elude such a mechanism and thus provides additional support for the occurrence of biased concerted evolution. Our findings are relevant to interpreting phylogeographic patterns involving gene flow and are also consistent with the hypothesis of a hybrid origin of A. villosa ssp. carratracensis.