| 1. |
- Olsson, Urban, 1954, et al.
(författare)
-
The Lanius excubitor (Aves, Passeriformes) conundrum – Taxonomic dilemma when molecular and non-molecular data tell different stories.
- 2010
-
Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 55:2, s. 347-357
-
Tidskriftsartikel (refereegranskat)abstract
- The phylogeny of 18 taxa in the Lanius excubitor complex, and the related species L. sphenocercus, L. ludovicianus and L. somalicus, was estimated based on the mitochondrial cytochrome b gene and the non-coding D-loop (in total ∼1.3 kb). According to the mitochondrial gene tree, Lanius excubitor s.l. is non-monophyletic, with some of its subspecies being more closely related to L. sphenocercus, L. ludovicianus, and L. somalicus. Also the division of the L. excubitor complex into a northern (L. excubitor) and a southern (L. meridionalis) species, as has been proposed based on morphological and ecological similarity and geographical distributions, is not compatible with the mitochondrial tree. Overall, genetic divergences among the ingroup taxa are small, indicating a recent radiation. A tree based on the nuclear ornithine decarboxylase (ODC) introns 6–7 is unresolved with respect to the ingroup, but provides strong support for a clade containing the Lanius excubitor complex, L. sphenocercus, L. ludovicianus and L. somalicus. We discuss the incongruence between the current taxonomy and the mitochondrial gene tree, and conclude that based on the latter the Lanius excubitor complex may be treated as at least six species, L. borealis, L. elegans, L. excubitor, L. lahtora, L. meridionalis, and L. uncinatus, but that other taxonomic treatments are also possible. However, uncertainty regarding to which extent the mitochondrial gene tree reflects the species phylogeny prevents us from recommending taxonomic change without further investigation. This study highlights the possible danger of relying on a single molecular marker, such as mitochondrial DNA, in taxonomic revisions and phylogenetic inference
|
|
| 2. |
|
|
| 3. |
|
|
| 4. |
- Tedersoo, L., et al.
(författare)
-
454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases
- 2010
-
Ingår i: New Phytologist. - : Wiley. - 0028-646X. ; 188:1
-
Tidskriftsartikel (refereegranskat)abstract
- Compared with Sanger sequencing-based methods, pyrosequencing provides orders of magnitude more data on the diversity of organisms in their natural habitat, but its technological biases and relative accuracy remain poorly understood. This study compares the performance of pyrosequencing and traditional sequencing for species’ recovery of ectomycorrhizal fungi on root tips in a Cameroonian rain forest and addresses biases related to multi-template PCR and pyrosequencing analyses. Pyrosequencing and the traditional method yielded qualitatively similar results, but there were slight, but significant, differences that affected the taxonomic view of the fungal community. We found that most pyrosequencing singletons were artifactual and contained a strongly elevated proportion of insertions compared with natural intra- and interspecific variation. The alternative primers, DNA extraction methods and PCR replicates strongly influenced the richness and community composition as recovered by pyrosequencing. Pyrosequencing offers a powerful alternative for the identification of ectomycorrhizal fungi in pooled root samples, but requires careful selection of molecular tools. A well-populated backbone database facilitates the detection of biological and technical artifacts. The pyrosequencing pipeline is available at http://unite.ut.ee/454pipeline.tgz.
|
|
| 5. |
- Gamboa, G., et al.
(författare)
-
Mg/Ca ratios in coralline algae record northwest Atlantic temperature variations and North Atlantic Oscillation relationships
- 2010
-
Ingår i: Journal of Geophysical Research-Oceans. - 0148-0227. ; 115
-
Tidskriftsartikel (refereegranskat)abstract
- [1] Climate variability in the North Atlantic has been linked in part to the North Atlantic Oscillation (NAO). The NAO influences marine ecosystems in the northwestern Atlantic and transport variability of the cold Labrador Current. Understanding historic patterns of NAO variability requires long-term and high-resolution climate records that are not available from instrumental data. Here we present the first century-scale proxy record of sea surface temperature (SST) variability from the Newfoundland shelf, a region from which other annual-resolution shallow marine proxies are unavailable. The 116 year record was obtained from three sites along the eastern Newfoundland shelf using laser ablation inductively coupled mass spectrometry-determined Mg/Ca ratios in the crustose coralline alga Clathromorphum compactum. The alga is characterized by a high Mg-calcite skeleton exhibiting annual growth increments and a century-scale lifespan. Results indicate positive correlations between interannual variations in Mg/Ca ratios and both station-based and gridded instrumental SST. In addition, the record shows high spatial correlations to SST across the Newfoundland shelf and the Gulf of St. Lawrence. Before 1950 the Mg/Ca proxy record reveals significant departures from gridded temperature records. While the Newfoundland shelf is generally considered a region of negative correlations to the NAO, the algal time series as well as a recent modeling study suggest a variable negative relationship with the NAO which is strongest after similar to 1960 and before the mid-1930s.
|
|
| 6. |
- Jafari, Gholamali, et al.
(författare)
-
Genetics of extracellular matrix remodeling during organ growth using the Caenorhabditis elegans pharynx model.
- 2010
-
Ingår i: Genetics. - : Oxford University Press (OUP). - 1943-2631. ; 186:3, s. 969-82
-
Tidskriftsartikel (refereegranskat)abstract
- The organs of animal embryos are typically covered with an extracellular matrix (ECM) that must be carefully remodeled as these organs enlarge during post-embryonic growth; otherwise, their shape and functions may be compromised. We previously described the twisting of the Caenorhabditis elegans pharynx (here called the Twp phenotype) as a quantitative mutant phenotype that worsens as that organ enlarges during growth. Mutations previously known to cause pharyngeal twist affect membrane proteins with large extracellular domains (DIG-1 and SAX-7), as well as a C. elegans septin (UNC-61). Here we show that two novel alleles of the C. elegans papilin gene, mig-6(et4) and mig-6(sa580), can also cause the Twp phenotype. We also show that overexpression of the ADAMTS protease gene mig-17 can suppress the pharyngeal twist in mig-6 mutants and identify several alleles of other ECM-related genes that can cause or influence the Twp phenotype, including alleles of fibulin (fbl-1), perlecan (unc-52), collagens (cle-1, dpy-7), laminins (lam-1, lam-3), one ADAM protease (sup-17), and one ADAMTS protease (adt-1). The Twp phenotype in C. elegans is easily monitored using light microscopy, is quantitative via measurements of the torsion angle, and reveals that ECM components, metalloproteinases, and ECM attachment molecules are important for this organ to retain its correct shape during post-embryonic growth. The Twp phenotype is therefore a promising experimental system to study ECM remodeling and diseases.
|
|
| 7. |
- Hoorn, C., et al.
(författare)
-
Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity
- 2010
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 330:6006, s. 927-931
-
Tidskriftsartikel (refereegranskat)abstract
- The Amazonian rainforest is arguably the most species-rich terrestrial ecosystem in the world, yet the timing of the origin and evolutionary causes of this diversity are a matter of debate. We review the geologic and phylogenetic evidence from Amazonia and compare it with uplift records from the Andes. This uplift and its effect on regional climate fundamentally changed the Amazonian landscape by reconfiguring drainage patterns and creating a vast influx of sediments into the basin. On this "Andean" substrate, a region-wide edaphic mosaic developed that became extremely rich in species, particularly in Western Amazonia. We show that Andean uplift was crucial for the evolution of Amazonian landscapes and ecosystems, and that current biodiversity patterns are rooted deep in the pre-Quaternary.
|
|
| 8. |
- Abarenkov, Kessy, et al.
(författare)
-
PlutoF—a web based workbench for ecological and taxonomic research, with an online implementation for fungal ITS sequences
- 2010
-
Ingår i: Evolutionary Bioinformatics. - 1176-9343. ; 6, s. 189-196
-
Tidskriftsartikel (refereegranskat)abstract
- DNA sequences accumulating in the International Nucleotide Sequence Databases (INSD) form a rich source of information for taxonomic and ecological meta-analyses. However, these databases include many erroneous entries, and the data itself is poorly annotated with metadata, making it difficult to target and extract entries of interest with any degree of precision. Here we describe the web-based workbench PlutoF, which is designed to bridge the gap between the needs of contemporary research in biology and the existing software resources and databases. Built on a relational database, PlutoF allows remote-access rapid submission, retrieval, and analysis of study, specimen, and sequence data in INSD as well as for private datasets though web-based thin clients. In contrast to INSD, PlutoF supports internationally standardized terminology to allow very specific annotation and linking of interacting specimens and species. The sequence analysis module is optimized for identification and analysis of environmental ITS sequences of fungi, but it can be modified to operate on any genetic marker and group of organisms. The workbench is available at http://plutof.ut.ee.
|
|
| 9. |
|
|
| 10. |
- Pendrill, Ann-Marie, 1952
(författare)
-
Students compete in European Union Science Olympiad 2010
- 2010
-
Ingår i: Physics Education. - 0031-9120 .- 1361-6552. ; 45:4, s. 318-320
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- In April 2010, young students from 21 countries competed in EUSO - the European Union Science Olympiad. Each country sent two teams of three students to an experimental science competition. The first day, the teams helped an alien find water on Earth, and the second day, the solved a criminal case.
|
|
