A northern glacial refugium for bank voles (Clethrionomys glareolus).

peer reviewedThere is controversy and uncertainty on how far north there were glacial refugia for temperate species during the Pleistocene glaciations and in the extent of the contribution of such refugia to present-day populations. We examined these issues using phylogeographic analysis of a European woodland mammal, the bank vole (Clethrionomys glareolus). A Bayesian coalescence analysis indicates that a bank vole population survived the height of the last glaciation (≈25,000–10,000 years B.P.) in the vicinity of the Carpathians, a major central European mountain chain well north of the Mediterranean areas typically regarded as glacial refugia for temperate species. Parameter estimates from the fitted isolation with migration model show that the divergence of the Carpathian population started at least 22,000 years ago, and it was likely followed by only negligible immigration from adjacent regions, suggesting the persistence of bank voles in the Carpathians through the height of the last glaciation. On the contrary, there is clear evidence for gene flow out of the Carpathians, demonstrating the contribution of the Carpathian population to the colonization of Europe after the Pleistocene. These findings are consistent with data from animal and plant fossils recovered in the Carpathians and provide the clearest phylogeographic evidence to date of a northern glacial refugium for temperate species in Europe

Characterization of Bacteria in Biopsies of Colon and Stools by High Throughput Sequencing of the V2 Region of Bacterial 16S rRNA Gene in Human

BACKGROUND: The characterization of the human intestinal microflora and their interactions with the host have been identified as key components in the study of intestinal disorders such as inflammatory bowel diseases. High-throughput sequencing has enabled culture-independent studies to deeply analyze bacteria in the gut. It is possible with this technology to systematically analyze links between microbes and the genetic constitution of the host, such as DNA polymorphisms and methylation, and gene expression. METHODS AND FINDINGS: In this study the V2 region of the bacterial 16S ribosomal RNA (rRNA) gene using 454 pyrosequencing from seven anatomic regions of human colon and two types of stool specimens were analyzed. The study examined the number of reads needed to ascertain differences between samples, the effect of DNA extraction procedures and PCR reproducibility, and differences between biopsies and stools in order to design a large scale systematic analysis of gut microbes. It was shown (1) that sequence coverage lower than 1,000 reads influenced quantitative and qualitative differences between samples measured by UniFrac distances. Distances between samples became stable after 1,000 reads. (2) Difference of extracted bacteria was observed between the two DNA extraction methods. In particular, Firmicutes Bacilli were not extracted well by one method. (3) Quantitative and qualitative difference in bacteria from ileum to rectum colon were not observed, but there was a significant positive trend between distances within colon and quantitative differences. Between sample type, biopsies or stools, quantitative and qualitative differences were observed. CONCLUSIONS: Results of human colonic bacteria analyzed using high-throughput sequencing were highly dependent on the experimental design, especially the number of sequence reads, DNA extraction method, and sample type

Histoire évolutive du campagnol roussâtre (Myodes glareolus) en Eurasie

L’objectif général de cette thèse était de comprendre l’histoire évolutive du campagnol roussâtre (Myodes glareolus) en Eurasie à l’aide de la génétique moléculaire et des méthodes développées en phylogéographie et en génétique des populations mais aussi, par une approche multidisciplinaire impliquant des données morphologiques, paléontologiques, géologiques, paléoenvironnementales, écologiques et éthologiques. Un patron phylogéographique complexe et unique a été mis en évidence par la découverte de cinq lignées méditerranéennes et quatre lignées continentales pour cette espèce. Chacune de ces lignées présente une histoire évolutive particulière et permet de jeter un éclairage nouveau sur certains concepts et processus phylogéographiques. Le patron phylogéographique d’une espèce peut être perçu comme un système en perpétuelle évolution, les réponses des organismes face aux changements environnementaux pouvant être très variables en termes de contraction, expansion, différenciation et extinction. La découverte de plusieurs lignées de campagnols roussâtres en péninsule ibérique, italienne et en Europe centrale révèle la complexité phylogéographique rencontrée au niveau de certaines régions refuges. La fragmentation du milieu durant les glaciations aurait conduit à structurer l’espace géographique en îles d’habitat ou îles continentales (les refuges glaciaires) qui ont joué et jouent encore un rôle majeur dans l’émergence et l’évolution de la diversité génétique intraspécifique. Dans cette optique, cette thèse de doctorat révèle que les populations méditerranéennes s’avèrent être les garantes des plus hautes valeurs de diversité et de richesse intraspécifique malgré le fait qu’elles occupent une petite partie de l’aire de distribution de l’espèce.Les régions méditerranéennes ont vu la contraction et l’expansion de nombreuses populations d’espèces tempérées au fil des refroidissements et réchauffements du Pleistocène. A côté de cette stratégie de survie des populations face aux changements climatiques, notre étude montre que certaines populations situées dans des refuges glaciaires nordiques ont été capables de survivre in situ aux glaciations, en recherchant localement les conditions environnementales les plus favorables ou en s’adaptant à un nouvel environnement. En Russie, les populations de campagnols roussâtres ont subi une diminution drastique de leur diversité génétique et une extinction de plusieurs populations, suite aux changements brutaux des ceintures de végétation dans cette région durant les changements climatiques. Néanmoins, il existe un signal d’expansion post-glaciaire large et rapide pour ces populations ce qui montre leur capacité d’expansion sur de très longues distances dès que l’habitat leur redevient plus favorable. Finalement, l’étude d’une lignée de campagnol roussâtre introgressée par l’ADN mitochondrial d’une autre espèce, nous a permis d’aborder la question de l’hybridation interspécifique chez les mammifères. La découverte de cette lignée largement étendue géographiquement et, dans certaines régions, très probablement soumise à la sélection naturelle, démontre que l’hybridation interspécifique peut aussi être source de diversité et d’adaptation chez les mammifères

Comparative phylogeography of forest rodents (Apodemus sylvaticus, A. flavicollis and Clethrionomys glareolus) in the western Palearctic region: how the same quaternary climatic changes led to different evolutionary histories

peer reviewe

Characterization of bacteria in biopsies of colon and stools by high throughput sequencing of the V2 region of bacterial 16S rRNA gene in human.

BackgroundThe characterization of the human intestinal microflora and their interactions with the host have been identified as key components in the study of intestinal disorders such as inflammatory bowel diseases. High-throughput sequencing has enabled culture-independent studies to deeply analyze bacteria in the gut. It is possible with this technology to systematically analyze links between microbes and the genetic constitution of the host, such as DNA polymorphisms and methylation, and gene expression.Methods and findingsIn this study the V2 region of the bacterial 16S ribosomal RNA (rRNA) gene using 454 pyrosequencing from seven anatomic regions of human colon and two types of stool specimens were analyzed. The study examined the number of reads needed to ascertain differences between samples, the effect of DNA extraction procedures and PCR reproducibility, and differences between biopsies and stools in order to design a large scale systematic analysis of gut microbes. It was shown (1) that sequence coverage lower than 1,000 reads influenced quantitative and qualitative differences between samples measured by UniFrac distances. Distances between samples became stable after 1,000 reads. (2) Difference of extracted bacteria was observed between the two DNA extraction methods. In particular, Firmicutes Bacilli were not extracted well by one method. (3) Quantitative and qualitative difference in bacteria from ileum to rectum colon were not observed, but there was a significant positive trend between distances within colon and quantitative differences. Between sample type, biopsies or stools, quantitative and qualitative differences were observed.ConclusionsResults of human colonic bacteria analyzed using high-throughput sequencing were highly dependent on the experimental design, especially the number of sequence reads, DNA extraction method, and sample type

Association between coverage and the number of OTUs.

<p>(A) The number of OTUs sampled as a function of number of reads. The data points represent mean ± SD of five randomized samplings. (B) Coverage to detect OTU with different frequencies with ≥95% of confidence. The data points were estimated based on the binomial distribution (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016952#s4" target="_blank">Materials and Methods</a>). The x axis is shown in logarithmic scale.</p

Association between coverage and UniFrac distances at different coverage.

<p>(A) Weighted and (B) unweighted UniFrac distances. For ‘Between individuals’ each data point includes 36 distances calculated from 6 samples of individual B and 6 samples of individual C. For ‘Within same individual’ each data point includes 18 distances (9 within sample B and 9 within sample C). Mean ± SD.</p

UniFrac distances between the seven biopsies and two sampling types of stools.

<p>Weighted distances are shown in the cells below the diagonal and unweighted distances are shown above the diagonal. Significance was tested with each UniFrac distance between that of two extractions from the same anatomic region (Mean ± SD, weighted: 0.084±0.027, unweighted: 0.415±0.068).</p><p>* p<0.05,</p><p>** p<0.01,</p><p>*** p<0.001,</p><p>**** p<0.0001. Significant p values after Bonferroni correction ( =  1.67×10⁻³) are underlined.</p