Further evidence for cryptic north-western refugia in Europe? Mitochondrial phylogeography of the sibling species Pipistrellus pipistrellus and Pipistrellus pygmaeus

The geographic ranges of European plants and animals underwent periods of contraction and re-colonisation during the climatic oscillations of the Pleistocene. The southern Mediterranean peninsulas (Iberian, Italian and Balkan) have been considered the most likely refugia for temperate/warm adapted species. Recent studies however have revealed the existence of extra-Mediterranean refugia, including the existence of cryptic north-west European refugia during the Last Glacial Maxima (24-14.6 kyr BP). In this study we elucidated the phylogeographic history of two sibling bat species, Pipistrellus pipistrellus and P. pygmaeus in their western European range. We sequenced the highly variable mtDNA D-loop for 167 samples of P. pipistrellus (n = 99) and P. pygmaeus (n = 68) and combined our data with published sequences from 331 individuals. Using phylogenetic methodologies we assessed their biogeographic history. Our data support a single eastern European origin for populations of P. pygmaeus s.str., yet multiple splits and origins for populations of P. pipistrellus s.str., including evidence for refugia within refugia and potential cryptic refugia in north western Europe and in the Caucasus. This complex pattern in the distribution of mtDNA haplotypes supports a long history for P. pipistrellus s.str. in Europe, and the hypothesis that species with a broad ecological niche may have adapted and survived outside southern peninsula throughout the LGM.</p

First insight into dead wood protistan diversity: a molecular sampling of bright-spored Myxomycetes (Amoebozoa, slime-moulds) in decaying beech logs

Decaying wood hosts a large diversity of seldom investigated protists. Environmental sequencing offers novel insights into communities, but has rarely been applied to saproxylic protists. We investigated the diversity of bright-spored wood-inhabiting Myxomycetes by environmental sequencing. Myxomycetes have a complex life cycle culminating in the formation of mainly macroscopic fruiting bodies, highly variable in shape and colour that are often found on decaying logs. Our hypothesis was that diversity of bright-spored Myxomycetes would increase with decay. DNA was extracted from wood chips collected from 17 beech logs of varying decay stages from the Hainich-Dun region in Central Germany. We obtained 260 partial small subunit ribosomal RNA gene sequences of bright-spored Myxomycetes that were assembled into 29 OTUs, of which 65% were less than 98% similar to those in the existing database. The OTU richness revealed by molecular analysis surpassed that of a parallel inventory of fruiting bodies. We tested several environmental variables and identified pH, rather than decay stage, as the main structuring factor of myxomycete distribution

Two-Gene Phylogeny of Bright-Spored Myxomycetes (Slime Moulds, Superorder Lucisporidia)

<div><p>Myxomycetes, or plasmodial slime-moulds, are one of the largest groups in phylum Amoebozoa. Nonetheless, only ∼10% are in the database for the small subunit (SSU) ribosomal RNA gene, the most widely used gene for phylogenetics and barcoding. Most sequences belong to dark-spored Myxomycetes (order Fuscisporida); the 318 species of superorder Lucisporidia (bright-spored) are represented by only eleven genuine sequences. To compensate for this, we provide 66 new sequences, 37 SSU rRNA and 29 elongation factor 1-alpha (EF-1α), for 82% of the genera of Lucisporidia. Phylogenetic analyses of single- and two-gene alignments produce congruent topologies and reveal both morphological characters that have been overemphasised and those that have been overlooked in past classifications. Both classical orders, Liceida and Trichiida, and several families and genera are para/polyphyletic; some previously unrecognised clades emerge. We discuss possible evolutionary pathways. Our study fills a gap in the phylogeny of Amoebozoa and provides an extensive SSU rRNA sequence reference database for environmental sampling and barcoding. We report a new group I intron insertion site for Myxomycetes in one <i>Licea</i>.</p></div

SSU rRNA gene tree of Lucisporidia derived by Bayesian inference of 1325 nucleotide positions of 51 sequences, with <i>Ceratiomyxa fruticulosa</i> as outgroup.

<p>Species names are followed by GenBank accession number, except for sequences obtained during this study (in bold), whose accession numbers and collection sites are in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062586#pone.0062586.s004" target="_blank">Table S1</a>. Clades are highlighted and labelled according to current classification or as new. Bayesian posterior probabilities (BPP)/ML bootstrap replicates (MLB) are shown for each branch; dashes indicate a conflicting topology in the ML tree; a dot on the line indicates maximum support in both analyses. The scale bar indicates the fraction of substitutions per site. Credit photos: A, F, G, J–M: Michel Poulain; B–E, H, I, N–P: Alain Michaud.</p

Spore-like bodies.

<p><b>A.</b> Vertical section of the stalk and the base of the sporotheca of <i>Hemitrichia calyculata</i>, showing the stalk filled with spore-like bodies. Those are larger and clearer than the spores in the sporotheca above, without clear demarcation. <b>B.</b> Vertical section of the stalk and the base of the sporotheca of <i>Trichia decipiens</i>, showing the stalk filled with spore-like bodies and few capillitial filaments. <b>C.</b> Greater magnification of the spore-like bodies of <i>Trichia decipiens</i>. Scale and colours are approximate. Credit photos: Michel Poulain.</p

Four different capillitial threads in Trichiida.

<p><b>A.</b> Capillitial threads of <i>Trichia varia</i>: isolated threads sculptured with spiral bands, two very short ones are indicated by a black line. <b>B.</b> Capillitial threads of <i>Arcyria obvelata,</i> forming a network and sculptured with spines. <b>C.</b> Capillitial threads of <i>Oligonema flavidum</i>, short and in this case branched, smooth. Note the reticulate ornamentation of the spores, similar to that of <i>Oligonema schweinitzii</i> and <i>Trichia persimilis</i>. <b>D.</b> Capillitial threads of <i>Cornuvia serpula</i>, branched and ornamented with rings. Scale and colours are approximate. Credit photos: Michel Poulain.</p

Systematic treatment of the class Myxomycetes (according to [12]), number of genera and species (according to Nomenmyx, http://eumycetozoa.com/data/index.php, updated 20.7.12) and percentage of genera and species sequenced in this study.

<p>Systematic treatment of the class Myxomycetes (according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062586#pone.0062586-Poulain1" target="_blank">[12]</a>), number of genera and species (according to Nomenmyx, <a href="http://eumycetozoa.com/data/index.php" target="_blank">http://eumycetozoa.com/data/index.php</a>, updated 20.7.12) and percentage of genera and species sequenced in this study.</p

Bayesian phylogeny of Lucisporidia inferred from concatenated alignments of SSU rRNA and EF-1α genes, based on 41 sequences and 1705 positions, with <i>Ceratiomyxa fruticulosa</i> as outgroup.

<p>Clades are highlighted as in Fig. 1. Bayesian posterior probabilities (BPP)/ML bootstrap replicates (MLB) are shown for each branch; a dot on the line indicates maximum support in both analyses. In Trichiida, classical families (according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062586#pone.0062586-Poulain1" target="_blank">[12]</a>) are indicated by an ellipse with the initials (Arc = Arcyriidae; Dia = Dianemidae; Tri = Trichiidae). The scale bar indicates the fraction of substitutions per site.</p