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

Multilocus DNA analysis supports Didymodon gelidus (Musci, Pottiaceae) as a distinct endemic of the austral polar region

The taxonomic position of the Antarctic subendemic species Didymodon gelidus Cardot is controversial, notably because of its notorious sterile condition. Considering the overall appearance and the reddish coloration of the plants, the leaf areolation, reaction of the leaf lamina with KOH, and the presence of multicellular axillary gemmae, this species was considered to be conspecific with the Holarctic D. brachyphyllus (Sull.) R. H. Zander. As a result, the latter was established as a bipolar species. Recent detailed morphological and anatomical studies have revealed a number of features which enable recognition of D. gelidus and D. brachyphyllus, including the shape of leaves, leaf apices and basal leaf cells, as well as costal anatomy. Here, within a larger-scale project focused on the evolution and biogeographical connections of Antarctic endemic mosses, we analyzed the genetic relationships of D. gelidus and D. brachyphyllus to confront the morphology-based conclusions. We selected five geographically distinct collections per species and applied a multilocus DNA analysis based on nuclear (ITS) and plastid (atpIH, trnLF, trnG, rps4) sequences to assess the genetic differentiation of these two taxa. We also placed their lineages in a wider phylogenetic context using an extended sampling of Didymodon taxa and select other representatives of Pottiaceae. Our results showed a clear genetic differentiation of the Southern Hemisphere (D. gelidus) and Northern Hemisphere (D. brachyphyllus) plants. Moreover, the phylogenetic analysis showed that D. gelidus formed a strongly supported clade on its own which was distantly related to D. brachyphyllus. Accordingly, the two taxa do not represent geographical vicariants. Didymodon gelidus must be considered a distinct endemic species of the austral polar region, having its optimal occurrence in the Antarctic and weakly penetrating northward to South Georgia and Îles Kerguelen in the Subantarctic. The relatively isolated phylogenetic position of D. gelidus likely suggests its old age

A Brief Review of Molecular Techniques to Assess Plant Diversity

Massive loss of valuable plant species in the past centuries and its adverse impact on environmental and socioeconomic values has triggered the conservation of plant resources. Appropriate identification and characterization of plant materials is essential for the successful conservation of plant resources and to ensure their sustainable use. Molecular tools developed in the past few years provide easy, less laborious means for assigning known and unknown plant taxa. These techniques answer many new evolutionary and taxonomic questions, which were not previously possible with only phenotypic methods. Molecular techniques such as DNA barcoding, random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), microsatellites and single nucleotide polymorphisms (SNP) have recently been used for plant diversity studies. Each technique has its own advantages and limitations. These techniques differ in their resolving power to detect genetic differences, type of data they generate and their applicability to particular taxonomic levels. This review presents a basic description of different molecular techniques that can be utilized for DNA fingerprinting and molecular diversity analysis of plant species

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