Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens.

In the recent years, many protocols aimed at reproducibly sequencing reduced-genome subsets in non-model organisms have been published. Among them, RAD-sequencing is one of the most widely used. It relies on digesting DNA with specific restriction enzymes and performing size selection on the resulting fragments. Despite its acknowledged utility, this method is of limited use with degraded DNA samples, such as those isolated from museum specimens, as these samples are less likely to harbor fragments long enough to comprise two restriction sites making possible ligation of the adapter sequences (in the case of double-digest RAD) or performing size selection of the resulting fragments (in the case of single-digest RAD). Here, we address these limitations by presenting a novel method called hybridization RAD (hyRAD). In this approach, biotinylated RAD fragments, covering a random fraction of the genome, are used as baits for capturing homologous fragments from genomic shotgun sequencing libraries. This simple and cost-effective approach allows sequencing of orthologous loci even from highly degraded DNA samples, opening new avenues of research in the field of museum genomics. Not relying on the restriction site presence, it improves among-sample loci coverage. In a trial study, hyRAD allowed us to obtain a large set of orthologous loci from fresh and museum samples from a non-model butterfly species, with a high proportion of single nucleotide polymorphisms present in all eight analyzed specimens, including 58-year-old museum samples. The utility of the method was further validated using 49 museum and fresh samples of a Palearctic grasshopper species for which the spatial genetic structure was previously assessed using mtDNA amplicons. The application of the method is eventually discussed in a wider context. As it does not rely on the restriction site presence, it is therefore not sensitive to among-sample loci polymorphisms in the restriction sites that usually causes loci dropout. This should enable the application of hyRAD to analyses at broader evolutionary scales

18S rDNA Phylogeny of Lamproderma and Allied Genera (Stemonitales, Myxomycetes, Amoebozoa)

The phylogenetic position of the slime-mould genus Lamproderma (Myxomycetes, Amoebozoa) challenges traditional taxonomy: although it displays the typical characters of the order Stemonitales, it appears to be sister to Physarales. This study provides a small subunit (18S or SSU) ribosomal RNA gene-based phylogeny of Lamproderma and its allies, with new sequences from 49 specimens in 12 genera. We found that the order Stemonitales and Lamproderma were both ancestral to Physarales and that Lamproderma constitutes several clades intermingled with species of Diacheopsis, Colloderma and Elaeomyxa. We suggest that these genera may have evolved from Lamproderma by multiple losses of fruiting body stalks and that many taxonomic revisions are needed. We found such high genetic diversity within three Lamproderma species that they probably consist of clusters of sibling species. We discuss the contrasts between genetic and morphological divergence and implications for the morphospecies concept, highlighting the phylogenetically most reliable morphological characters and pointing to others that have been overestimated. In addition, we showed that the first part (∼600 bases) of the SSU rDNA gene is a valuable tool for phylogeny in Myxomycetes, since it displayed sufficient variability to distinguish closely related taxa and never failed to cluster together specimens considered of the same species

How 'alpine' are nivicolous myxomycetes? A worldwide assessment of altitudinal distribution

Abstract: Nivicolous myxomycetes constitute an ecologically well defined group of organisms occurring at the edge of melting winter snow cover. They often are considered and described as alpine species, occurring exclusively or most frequently in the alpine belt. We reviewed and synthesized available published data on the altitudinal occurrences of nivicolous myxomycetes in 22 massifs worldwide and attributed the records to main altitudinal belts (montane/subalpine/alpine) defined for particular areas. Based on this comparative analysis we attempted to analyze and discuss general views on the altitudinal/biogeographical properties of nivicolous myxomycetes. Our study indicates that the altitudinal distribution of nivicolous mycomycetes extends over montane, subalpine and alpine belts. The most abundant records were found in the forest (montane) belt, while the alpine belt had the lowest number of occurrences. Although this picture might be biased to some extent by better average exploration of lower areas, it shows clearly that this ecological group-even though connected with mountainous habitats-does not form an alpine element. Therefore they should not be considered alpine species. Based on the available data it also could be hypothesized that nivicolous myxomycetes form a widely distributed biogeographical mountain element instead of an alpine or arctic-alpine element. Based on our conclusions we also emphasize the need for precise and cautious use of the notion of ''alpines'', which appears to be confusingly overused in the myxomycete studies

Obserwacje statusu mikoryzowego Polygonum viviparum w polskich Tatrach (Karpaty Zachodnie)

Polygonum viviparumis one of very few herbaceous plants known to form ectomycorrhiza; in the Tatra Mts. it is one of dominants in the alpine zone, but also descends down to the feet of the massif. Specimens of this plant were collected from 5 sites at the altitude range 900– 2150 m, from granite and limestone. It allowed an estimation of the ectomycorrhizal diversity as well as preliminary ecological observations. Roots were also stained in order to check potential presence of arbuscular mycorrhizal colonization. Ectomycorrhizae were present in all specimens (with 2–5 morphotypes observed on single plants). In total, 17 morphotypes were observed and briefly described. The most widespread were the mycorrhiza of Cenococcum geophilum and a brightly coloured morphotype resembling the ectomycorrhizae of Russula sp. No important differences in ectomycorrhizal colonization between low and high localities were found. Observed general differences in abundance and diversity of mycorrhiza in P. viviparum between sites could most probably be connected with plant community composition (presence/absence of ectomycorrhizal shrubs maintaining ectomycorrhizal fungi), although mycorrhizae were present also in sites devoid of other ectomycorrhizal plants. Structures associated to arbuscular colonization (vesicles, hyphal coils) were occassionally observed, but without formation of arbuscules.Polygonum viviparum jest jednym z nielicznych gatunków roślin zielnych, które tworzą ektomikoryzę. W Tatrach rdest żyworodny należy do gatunków dominujących w piętrze alpejskim, występuje również niżej sięgając do podnóży masywu. Celem badań była wstępna analiza różnorodności ektomikoryz tworzonych przez ten gatunek w Tatrach oraz ogólna analiza jej zależności od warunków ekologicznych takich jak wysokość nad poziom morza oraz skład zbiorowisk roślinnych. Korzenie P. viviparum były również dodatkowo badane pod kątem obecności kolonizacji endomikoryzowej. Próby korzeni zebrano z 5 stanowisk na podłożu granitowym i wapiennym, rozmieszczonych w przedziale wysokości 900–2150 m n.p.m. Ektomikoryzy były obecne na wszystkich badanych okazach Polygonum viviparum; na pojedynczych roślinach obserwowano 2–5 morfotypów. W sumie zaobserwowano i krótko scharakteryzowano 17 morfotypów ektomikoryz. Najbardziej rozpowszechnione we wszystkich próbach były mikoryza Cenococcum geophilum oraz niezidentyfikowany, jasno zabarwiony morfotyp przypominający mikoryzy Russula sp. Nie stwierdzono znaczących różnic w poziomie kolonizacji ektomikoryzowej pomiędzy stanowiskami różniącymi się położeniem nad poziomem morza. Zaobserwowane różnice w liczebności i różnorodności mikoryz P. viviparum na poszczególnych stanowiskach wiązać można najprawdopodobniej ze składem gatunkowym zbiorowisk roślinnych – obecnością krzewinek ektomikoryzowych spełniających zasadniczą rolę w utrzymywaniu populacji grzybów ektomikoryzowych. Należy jednak podkreślić, że ektomikoryzy obserwowano również na stanowiskach, gdzie P. viviparum było jedynym potencjalnym symbiontem ektomikoryzowym. Regularnie obserwowano kolonizację korzeni Polygonum przez grzyby endofityczne. W kilku korzeniach odnotowano obecność struktur charakterystycznych dla mikoryzy arbuskularnej (pęcherzyki, peletony), jednak nie towarzyszyły im wykształcone arbuskule

Cochlearia polonica Frohl. (Brassicaceae), a narrow endemic species of southern Poland: history of conservation efforts, overview of current population resources and genetic structure of populations

Cochlearia polonica Fröhl. (Brassicaceae) is one of the rarest species in the Polish and European flora and a taxon endemic to a very small area in southern Poland. Due to industrial activities and subsequent transformation of habitats it was extinct in all natural localities around 1994. The persistence of the species was ensured thanks to the active protection efforts including a series of transplantations based on the material from the last and decreasing natural population. The history of conservation efforts of C. polonica provides a model example of successful active protection in the European flora. Here, we provide a complete review comprising the following aims: (i) outline of the discovery and taxonomic conceptions on C. polonica, (ii) review of conservation efforts aimed at preserving its populations, (iii) description of the existing population resources, and (iv) analysis of the genetic structure of all existing populations based on previously published data and new, supplementary results

Low genetic diversity in the endangered population of Viola uliginosa in its locus classicus at Rzaska near Cracow [southern Poland] as revealed by AFLP markers

An extremely endangered population of Viola uliginosa Besser at the classical locality of this taxon has been studied. The AFLP analysis was based on 18 specimens of V. uliginosa (about 10% of preserved individuals); additionally, two individuals of V. riviniana were included in the data set as the out group. A high genetical uniformity of the whole population (similarity indexes close to 1) was detected. It was not correlated significantly with the spatial distribution of the plants. The study serves as a basis for practical conservation measures and at the same time as a starting point for a more extensive research on the genetical variability of the species throughout its range

Nuclear ribosomal ITS DNA sequence alignment of Ranunculus glacialis s.l.

The file contains the alignment of sequences used for the BEAST analysis of nuclear ribosomal ITS (Internal transcribed Spacer region containing ITS1, 5.8S gene and ITS 2) DNA variation in Ranunculus glacialis s.l