Multiple ITS Copies Reveal Extensive Hybridization within Rheum (Polygonaceae), a Genus That Has Undergone Rapid Radiation

During adaptive radiation events, characters can arise multiple times due to parallel evolution, but transfer of traits through hybridization provides an alternative explanation for the same character appearing in apparently non-sister lineages. The signature of hybridization can be detected in incongruence between phylogenies derived from different markers, or from the presence of two divergent versions of a nuclear marker such as ITS within one individual.In this study, we cloned and sequenced ITS regions for 30 species of the genus Rheum, and compared them with a cpDNA phylogeny. Seven species contained two divergent copies of ITS that resolved in different clades from one another in each case, indicating hybridization events too recent for concerted evolution to have homogenised the ITS sequences. Hybridization was also indicated in at least two further species via incongruence in their position between ITS and cpDNA phylogenies. None of the ITS sequences present in these nine species matched those detected in any other species, which provides tentative evidence against recent introgression as an explanation. Rheum globulosum, previously indicated by cpDNA to represent an independent origin of decumbent habit, is indicated by ITS to be part of clade of decumbent species, which acquired cpDNA of another clade via hybridization. However decumbent and glasshouse morphology are confirmed to have arisen three and two times, respectively.These findings suggested that hybridization among QTP species of Rheum has been extensive, and that a role of hybridization in diversification of Rheum requires investigation

Effects of Natura 2000 on nontarget bird and butterfly species based on citizen science data

ABSTRACT The European Union's Natura 2000 (N2000), is one of the largest international networks of protected areas. One of its aims is to secure the status of a pre-determined set of (targeted) bird and butterfly species. However, also non-target species may benefit from N2000. We evaluated how the terrestrial component of this network relates to the abundance of non-targeted, more common bird and butterfly species using data from long-term volunteer-based monitoring programs in 9,602 sites for birds and 2,001 sites for butterflies. In almost half of the 155 bird species assessed, and particularly among woodland specialists, abundance increased with the proportion of N2000 sites in the landscape. The corresponding positive relationship was found for 27 of the 104 butterfly species, although most of these species were generalists. These positive relationships disappeared for most of the species when land-cover covariates were taken into account, hinting that land-cover is a primary factor defining the positive effects of the N2000 network. The increase in abundance with N2000 was correlated with the specialization index for bird species, but not for butterfly species. Although the N2000 network supports higher abundance of a large spectrum of species, the low number of specialist butterfly species showing a positive association stresses the need to implement management plan improving the quality of habitats of N2000 areas potentially harboring openland butterfly specialists. For a better understanding of the processes involved, we advocate for a standardized collection of data on N2000 sites. Article impact statement: Across Europe the abundance of a majority of nontarget birds and a quarter of nontarget butterflies increased with Natura 2000 coverage. This article is protected by copyright. All rights reservedpeerReviewe

Notulae to the Italian native vascular flora: 3.

In this contribution new data concerning the distribution of native vascular flora in Italy are presented. It includes new records, exclusions, and confirmations to the Italian administrative regions for taxa in the genera Asplenium, Bolboschoenus, Botrychium, Chamaerops, Crocus, Galeopsis, Grafia, Helosciadium, Hieracium, Juniperus, Leucanthemum, Lolium, Medicago, Phalaris, Piptatherum, Potamogeton, Salicornia, Salvia, Seseli, Silene, Spiraea, Torilis and Vicia. Rhaponticoides calabrica is proposed as synonym novum of R. centaurium. Furthermore, new combinations in the genera Galatella and Lactuca are proposed

The ITS1-5.8S-ITS2 Sequence Region in the Musaceae: Structure, Diversity and Use in Molecular Phylogeny

Genes coding for 45S ribosomal RNA are organized in tandem arrays of up to several thousand copies and contain 18S, 5.8S and 26S rRNA units separated by internal transcribed spacers ITS1 and ITS2. While the rRNA units are evolutionary conserved, ITS show high level of interspecific divergence and have been used frequently in genetic diversity and phylogenetic studies. In this work we report on the structure and diversity of the ITS region in 87 representatives of the family Musaceae. We provide the first detailed information on ITS sequence diversity in the genus Musa and describe the presence of more than one type of ITS sequence within individual species. Both Sanger sequencing of amplified ITS regions and whole genome 454 sequencing lead to similar phylogenetic inferences. We show that it is necessary to identify putative pseudogenic ITS sequences, which may have negative effect on phylogenetic reconstruction at lower taxonomic levels. Phylogenetic reconstruction based on ITS sequence showed that the genus Musa is divided into two distinct clades – Callimusa and Australimusa and Eumusa and Rhodochlamys. Most of the intraspecific banana hybrids analyzed contain conserved parental ITS sequences, indicating incomplete concerted evolution of rDNA loci. Independent evolution of parental rDNA in hybrids enables determination of genomic constitution of hybrids using ITS. The observation of only one type of ITS sequence in some of the presumed interspecific hybrid clones warrants further study to confirm their hybrid origin and to unravel processes leading to evolution of their genomes

Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence-Structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life

L). Some have advocated the use of the nuclear-encoded, internal transcribed spacer two (ITS2) as an alternative to the traditional chloroplast markers. However, the ITS2 is broadly perceived to be insufficiently conserved or to be confounded by introgression or biparental inheritance patterns, precluding its broad use in phylogenetic reconstruction or as a DNA barcode. A growing body of evidence has shown that simultaneous analysis of nucleotide data with secondary structure information can overcome at least some of the limitations of ITS2. The goal of this investigation was to assess the feasibility of an automated, sequence-structure approach for analysis of IT2 data from a large sampling of phylum Chlorophyta.Sequences and secondary structures from 591 chlorophycean, 741 trebouxiophycean and 938 ulvophycean algae, all obtained from the ITS2 Database, were aligned using a sequence structure-specific scoring matrix. Phylogenetic relationships were reconstructed by Profile Neighbor-Joining coupled with a sequence structure-specific, general time reversible substitution model. Results from analyses of the ITS2 data were robust at multiple nodes and showed considerable congruence with results from published phylogenetic analyses.Our observations on the power of automated, sequence-structure analyses of ITS2 to reconstruct phylum-level phylogenies of the green algae validate this approach to assessing diversity for large sets of chlorophytan taxa. Moreover, our results indicate that objections to the use of ITS2 for DNA barcoding should be weighed against the utility of an automated, data analysis approach with demonstrated power to reconstruct evolutionary patterns for highly divergent lineages

Crocins with high levels of sugar conjugation contribute to the yellow colours of early-spring flowering

Crocus sativus is the source of saffron spice, the processed stigma which accumulates glucosylated apocarotenoids known as crocins. Crocins are found in the stigmas of other Crocuses, determining the colourations observed from pale yellow to dark red. By contrast, tepals in Crocus species display a wider diversity of colours which range from purple, blue, yellow to white. In this study, we investigated whether the contribution of crocins to colour extends from stigmas to the tepals of yellow Crocus species. Tepals from seven species were analysed by UPLC-PDA and ESI-Q-TOF-MS/MS revealing for the first time the presence of highly glucosylated crocins in this tissue. beta-carotene was found to be the precursor of these crocins and some of them were found to contain rhamnose, never before reported. When crocin profiles from tepals were compared with those from stigmas, clear differences were found, including the presence of new apocarotenoids in stigmas. Furthermore, each species showed a characteristic profile which was not correlated with the phylogenetic relationship among species. While gene expression analysis in tepals of genes involved in carotenoid metabolism showed that phytoene synthase was a key enzyme in apocarotenoid biosynthesis in tepals. Expression of a crocetin glucosyltransferase, previously identified in saffron, was detected in all the samples. The presence of crocins in tepals is compatible with the role of chromophores to attract pollinators. The identification of tepals as new sources of crocins is of special interest given their wide range of applications in medicine, cosmetics and colouring industries.The laboratory is supported by the Spanish Ministerio de Ciencia e Innovacion (BIO2009-07803) and participates in the IBERCAROT network (112RT0445). Dr. Ahrazem was funded by FPCYTA through the INCRECYT Programme. 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