Institution
Swedish Museum of Natural History
Archive•Stockholm, Sweden•
About: Swedish Museum of Natural History is a archive organization based out in Stockholm, Sweden. It is known for research contribution in the topics: Zircon & Population. The organization has 762 authors who have published 4177 publications receiving 165350 citations. The organization is also known as: National Museum of Natural History & NRS.
Topics: Zircon, Population, Genus, Monophyly, Metamorphism
Papers published on a yearly basis
Papers
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TL;DR: The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly, and provides more output options than previously, including samples of ancestral states, site rates, site dN/dS rations, branch rates, and node dates.
Abstract: Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
18,718 citations
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Conrad L. Schoch1, Keith A. Seifert, Sabine M. Huhndorf2, Vincent Robert3 +157 more•Institutions (59)
TL;DR: Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation.
Abstract: Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
4,116 citations
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University of Bergen1, Academy of Sciences of the Czech Republic2, Charles University in Prague3, University of Nottingham4, Boise State University5, Goethe University Frankfurt6, Memorial University of Newfoundland7, Stockholm University8, University of Vienna9, University of Geneva10, Swedish Museum of Natural History11
TL;DR: The Plesovice zircon as discussed by the authors has a concordant U-Pb age with a weighted mean Pb-206/U-238 date of 337.13 +/- 0.37 Ma (ID-TIMS, 95% confidence limits, including tracer calibration uncertainty).
3,694 citations
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TL;DR: Cladistic analysis of amino acid sequence data, including evaluation of all equally or almost equally parsimonious cladograms, shows that much homoplasy (parallelisms and reversals) is present and that few or no well supported monophyletic groups of families can be demonstrated.
Abstract: Amino acid sequence data are available for ribulose biphosphate carboxylase, plastocyanin, cytochrome c, and ferredoxin for a number of angiosperm families. Cladistic analysis of the data, including evaluation of all equally or almost equally parsimonious cladograms, shows that much homoplasy (parallelisms and reversals) is present and that few or no well supported monophyletic groups of families can be demonstrated. In one analysis of nine angiosperm families and 40 variable amino acid positions from three proteins, the most parsimonious cladograms were 151 steps long and contained 63 parallelisms and reversals (consistency index = 0.583). In another analysis of six families and 53 variable amino acid positions from four proteins, the most parsimonious cladogram was 161 steps long and contained 50 parallelisms and reversals (consistency index = 0.689). Single changes in both data matrices could yield most parsimonious cladograms with quite different topologies and without common monophyletic groups. Presently, amino acid sequence data are not comprehensive enough for phylogenetic reconstruction among angiosperms. More informative positions are needed, either from sequencing longer parts of the proteins or from sequencing more proteins from the same taxa.
2,512 citations
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Technische Universität München1, Central Institution for Meteorology and Geodynamics2, University of Tartu3, Swedish Museum of Natural History4, University of Latvia5, Humboldt University of Berlin6, University of Ljubljana7, MeteoSwiss8, Trinity College, Dublin9, Autonomous University of Barcelona10, Norwegian University of Life Sciences11, Norwegian Meteorological Institute12, Finnish Meteorological Institute13, Czech Hydrometeorological Institute14, Environment Agency15, Wageningen University and Research Centre16, University of Oslo17
TL;DR: In this article, the authors used an enormous systematic phenological network data set of more than 125 000 observational series of 542 plant and 19 animal species in 21 European countries (1971-2000) and concluded that previously published results of phenological changes were not biased by reporting or publication predisposition.
Abstract: Global climate change impacts can already be tracked in many physical and biological systems; in particular, terrestrial ecosystems provide a consistent picture of observed changes. One of the preferred indicators is phenology, the science of natural recurring events, as their recorded dates provide a high-temporal resolution of ongoing changes. Thus, numerous analyses have demonstrated an earlier onset of spring events for mid and higher latitudes and a lengthening of the growing season. However, published single-site or single-species studies are particularly open to suspicion of being biased towards predominantly reporting climate change-induced impacts. No comprehensive study or meta-analysis has so far examined the possible lack of evidence for changes or shifts at sites where no temperature change is observed. We used an enormous systematic phenological network data set of more than 125 000 observational series of 542 plant and 19 animal species in 21 European countries (1971–2000). Our results showed that 78% of all leafing, flowering and fruiting records advanced (30% significantly) and only 3% were significantly delayed, whereas the signal of leaf colouring/fall is ambiguous. We conclude that previously published results of phenological changes were not biased by reporting or publication predisposition: the average advance of spring/summer was 2.5 days decade � 1 in Europe. Our analysis of 254 mean national time series undoubtedly demonstrates that species’ phenology is responsive to temperature of the preceding
2,457 citations
Authors
Showing all 771 results
Name | H-index | Papers | Citations |
---|---|---|---|
Philippe Grandjean | 93 | 540 | 34730 |
Martin J. Whitehouse | 80 | 554 | 26593 |
Peter R. Crane | 66 | 235 | 15690 |
Örjan Gustafsson | 66 | 236 | 14936 |
Pal Weihe | 63 | 207 | 14378 |
Peter K. Endress | 61 | 194 | 13410 |
Wilfried A. König | 58 | 410 | 12799 |
Else Marie Friis | 57 | 153 | 9404 |
Fredrik Ronquist | 54 | 122 | 76188 |
Thomas Pape | 53 | 317 | 10333 |
F. Combley | 52 | 312 | 14094 |
Alexander A. Nemchin | 51 | 184 | 8560 |
Cynthia A. de Wit | 49 | 114 | 29113 |
Stefan Bengtson | 48 | 140 | 6872 |
Per G. P. Ericson | 48 | 148 | 7602 |