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Extended Data Fig. 5 in Isolation of an archaeon at the prokaryote eukaryote interface

Extended Data Fig. 5 | Amino acid, cofactor and nucleotide biosynthesis capacities of MK-D1 and other Asgard archaea. Genomes that encode proteins for the synthesis of amino acids,cofactors and nucleotides from pyruvate or acetyl-CoA (dark blue) and synthesis from other intermediates (light blue) are indicated. Those without complete pathways from pyruvate and/or acetyl-CoA are indicated in white.Halodesulfovibrio sp.strain MK-HDV and Methanogenium sp.strain MK-MG isolated in this study are also shown.

Fig. 2 in Isolation of an archaeon at the prokaryote eukaryote interface

Fig. 2 | Syntrophic amino acid utilization of MK-D1. a, Genome-based metabolic reconstruction of MK-D1.Metabolic pathways identified (coloured or black) and not identified (grey) are shown.For identified pathways,each step (solid line) or process (dotted) is marked by whether it is oxidative (red), reductive (blue),ATP-yielding (orange) or ATP-consuming (purple).Wavy arrows indicate exchange of compounds:formate,H2, amino acids,vitamin B12, biotin, lipoate and thiamine pyrophosphate (TPP),which are predicted to be metabolized or synthesized by the partnering Halodesulfovibrio and/or Methanogenium. Biosynthetic pathways are indicated with a yellow background.Metatranscriptomics-detected amino-acid-catabolizing pathways are indicated (black dots above amino acids).DHDH,4,5-dihydroxy- 2,6-dioxohexanoate;DHDG,2-dehydro-3-deoxy-d-gluconate;DHDG6P, 3-dehydro-3-deoxy-d-gluconate 6-phosphate;Ac-CoA,acetyl-CoA;uro, urocanate;Fo-Glu,formyl glutamate;CH3=H4F,methylene-tetrahydrofolate; CH≡H4F,methenyl-tetrahydrofolate;Fo-H4F,formyl-tetrahydrofolate;2OB, 2-oxobutyrate;Prop-CoA,propionyl-CoA;ACAC,acetoacetate; GB-CoA, γ-amino-butyryl-CoA;But-CoA,butyryl-CoA;Fd,ferredoxin;XSH/X-S-S-X, thiol/disulfide pair; TCA,tricarboxylic acid cycle;PPP,pentose-phosphate pathway.b–e, NanoSIMS analysis of a highly purified MK-D1 culture incubated with a mixture of 13C- and 15N-labelled amino acids.b, Green fluorescent micrograph of SYBR Green I-stained cells.Aggregates are MK-D1,and filamentous cells are Methanobacterium sp. strain MO-MB1 (fluorescence can be weak owing to the high rigidity and low permeability of the cell membrane (Extended Data Fig.2m,n; see also ref.49). c, NanoSIMS ion image of 12C (cyan). d, NanoSIMS ion image of 12C15N/12C14N (magenta).e, Overlay image of b–d. d, The colour bar indicates the relative abundance of 15N expressed as 15N/14N. Scale bars 5 µm.The NanoSIMS analysis was performed without replicates due to its slow growth rate and low cell density.However,to ensure the reproducibility,we used two different types of highly purified cultures of MK-D1 (see Methods).Representative of n = 8 recorded images.The iTAG analysis of the imaged culture is shown in Supplementary Table 1.

Fig. 4 in Isolation of an archaeon at the prokaryote eukaryote interface

Fig. 4 | Phylogeny of MK-D1 and catabolic features of Asgard archaea. a, Maximum-likelihood tree (100 bootstrap replicates) of MK-D1 and select cultured archaea,eukaryotes and bacteria based on 31 ribosomal proteins that are conserved across the three domains (Supplementary Tables 7,8). Bootstrap values around critical branching points are also shown.We used 14,024 sites of the alignment for tree construction.b, The presence or absence of amino acid degradation,electron metabolism,fermentation,C1 metabolism,sulfur metabolism and aerobic respiration in individual genomes are shown (complete pathway,full circle; mostly complete pathway,half circle).For amino acid metabolism,pathways that are exclusively used for catabolism or degradation are in bold.Glycine metabolism through pyruvate (top) or formate (bottom). Butyrate metabolism is reversible (fermentation or β-oxidation); however,butyryl-CoA dehydrogenases tend to be associated with EtfAB in the genomes,suggesting formation of an electron-confurcating complex for butyrate fermentation.Propionate was determined by the presence of methylmalonyl-CoA decarboxylase,biotin carboxyl carrier protein and pyruvate carboxylase.Propionate metabolism is also reversible;however,no member of the Asgard archaea encodes the full gene set for syntrophic degradation.Alcohol dehydrogenases can have diverse substrate specificities. See Supplementary Note 5 for abbreviations.

Fig. 1 in Isolation of an archaeon at the prokaryote eukaryote interface

Fig. 1 | Growth curves and photomicrographs of the cultured Lokiarchaeota strain MK-D1. a, Growth curves of MK-D1 in anaerobic medium supplemented with casamino acids (CA) alone; casamino acids with 20 amino acids (AAs) and powdered milk (PM); or peptone with powdered milk. Results are also shown for cultures fed with 10- and 100-fold dilution of casamino acids,20 amino acids and powdered milk.b, c, Fluorescence images of cells from enrichment cultures after 8 (b) and 11 (c) transfers stained with DAPI (violet) and hybridized with nucleotide probes that target MK-D1 (green) and Bacteria (red). Pie charts show the relative abundance of microbial populations based on SSU rRNA gene-tag sequencing (iTAG) analysis.d, A fluorescence image of cells from enrichment cultures after 11 transfers hybridized with nucleotide probes that target MK-D1 (green) and Methanogenium (red).The FISH experiments were performed three times with similar results.e, SEM image of a highly purified co-culture of MK-D1 and Methanogenium. White arrows indicate Methanogenium cells.We observed four different co-cultures with Methanogenium. Representative of n = 40 recorded images.The detailed iTAG-based community compositions of cultures corresponding to each of the images are shown in Supplementary Table 1. Scale bars,10 µm (b, c) and 5 µm (d, e).

opencc-by-4.0Jan 2020View details →

TinySOL: an audio dataset of isolated musical notes

TinySOL ======= Version 6.0, February 2020.     Created By -------------- Carmine-Emanuele Cella (1), Daniele Ghisi (1), Vincent Lostanlen (2), Fabien Lévy (3), Joshua Fineberg (4), Yan Maresz (5) (1): UC Berkeley (2): New York University (3): Columbia University (4): Boston University (5): Conservatoire de Paris   Description --------------- TinySOL is a dataset of 2913 samples, each containing a single musical note from one of 14 different instruments: <ol> <li>Bass Tuba</li> <li>French Horn</li> <li>Trombone</li> <li>Trumpet in C</li> <li>Accordion</li> <li>Contrabass</li> <li>Violin</li> <li>Viola</li> <li>Violoncello</li> <li>Bassoon</li> <li>Clarinet in B-flat</li> <li>Flute</li> <li>Oboe</li> <li>Alto Saxophone</li> </ol>   These sounds were originally recorded at Ircam in Paris (France) between 1996 and 1999, as part of a larger project named Studio On Line (SOL). Although SOL contains many combinations of mutes and extended playing techniques, TinySOL purely consists of sounds played in the so-called "ordinary" style, and in absence of mute. TinySOL can be used for creative purposes insofar at the use complies with the Creative Commons Attribution 4.0 International license (see below). TinySOL can be used for education and research purposes. In particular, it can be employed as a dataset for training and/or evaluating music information retrieval (MIR) systems, for tasks such as instrument recognition or fundamental frequency estimation. For this purpose, we provide an official 5-fold split of TinySOL. This split has been carefully balanced in terms of instrumentation, pitch range, and dynamics. For the sake of research reproducibility, we encourage users of TinySOL to adopt this split and report their results in terms of average performance across folds.   Data Files -------------- TinySOL contains 2913 audio clips as WAV files, sampled at 44.1 kHz, with a single channel (mono), at a bit depth of 16. This is equivalent to the audio quality of a compact disc. Audio clips vary in duration between two and ten seconds. Every audio file has a file path of the form: <FAMILY>/<INSTRUMENT>/ordinario/<INSTR>-ord-<PITCH>-<DYN>-<INSTANCE>-<MISC>.wav where: <ul> <li><FAMILY> corresponds to the instrument family: "Brass", "Keyboards" (includes accordion), "Strings", and "Winds" (i.e., woodwinds).</li> <li><INSTRUMENT> is the full name of the instrument.</li> <li>"ordinario" denotes the ordinary playing technique. This is in contrast with the rest of the SOL dataset, which also encompasses extended playing techniques.</li> <li><INSTR> is the abbreviation of the instrument.</li> <li>"ord" is the abbreviation of "ordinario".</li> <li><PITCH> denotes the pitch of the musical note. This pitch is encoded in the American standard pitch notation: pitch class (C means "do") followed by pitch octave. According to this convention, A4 has a fundamental frequency of 440 Hz.</li> <li><DYN> denotes the intensity dynamics, ranked from pp (pianissimo) to ff (fortissimo).</li> <li><INSTANCE> contains additional information, when applicable. For example, for bowed string instruments, the same pitch may sometimes be achieved on different positions and different strings, resulting in small timbre differences. In this case the label "1c", "2c", "3c", or "4c" denotes the string which is being bowed. (The letter c originates from the word "corde", which means string in French.) By convention, the first string is the one with the highest pitch when played as an open string. Furthermore, on some wind instruments, the same note was played multiple times, e.g. at multiple durations. In this case, we use the label "alt1", "alt2", etc. to denote alternative instances of the note. If none of these tags apply, the <INSTANCE> field becomes "N", which stands for "Not Applicable".</li> <li><MISC> contains additional information, if applicable. In TinySOL, some pitches were never recorded (about 1% of the whole dataset), and thus missing from the chromatic scale. In this case, the <MISC> tag contains a letter "R", to denote the fact that the corresponding WAV file has been obtained by transforming a different audio clip via some digital frequency transposition (similar to Auto-Tune). The letter "R" stands for "resampled". Furthermore, some pitches (about 20% of the whole dataset) were slightly out of tune in comparison with the A440 tuning standard. Again, we applied some digital frequency transposition to correct them and put them exactly in tune. The amount of frequency transposition is measured in "cents" of an equal-tempered semitone. The letter "T" stands for "tuned". Because we employed a high-fidelity algorithm for frequency transposition, and because the amount of digital frequency transposition is small, the timbre of pitch-corrected notes remains faithful to the instrument. If none of these tags apply, the <MISC> field becomes "N", which stands for "natural"; in this case, the note is distributed exactly as it was recorded in the studio.</li> </ul> For example, "Strings/Violin/ordinario/Vn-ord-D#7-mf-1c-T22d_R100u" corresponds to: <ul> <li>a violin sound ;</li> <li>played in the ordinary playing technique ;</li> <li>at pitch D#7 (approximately 2489 Hz) ;</li> <li>with mezzoforte dynamics ;</li> <li>on the first string ; and</li> <li>resampled from a D7 by raising pitch by a semitone, i.e. 100 cents (R100u)</li> <li>lowered by 22 cents (T22d) to match the A440 tuning standard.</li> </ul>   Metadata File ------------------- The TinySOL_metadata.csv file contains 2913 rows, one for each audio clip. It can be opened by a text editor or by a spreadsheet software application. It contains 13 columns: <ol> <li>Path to the WAV file, in UNIX filesystem format. For Windows compatibility, replace the slashes ("/") by backslashes ("\"). Ex: "Brass/BTb/BTb-ord-A#1-ff-N.wav"</li> <li>Fold ID. Either equal to 0, 1, 2, 3, or 4.</li> <li>Family. Ex: "Brass"</li> <li>Instrument abbreviation. Ex: "BTb"</li> <li>Instrument name in full. Ex: "Bass Tuba"</li> <li>Technique abbreviation. Always equal to "ord" in the case of TinySOL.</li> <li>Technique name in full. Always equal to "ordinario" in the case of TinySOL.</li> <li>Pitch. Ex: "A#1"</li> <li>Pitch ID in MIDI format. Ex: 34. Integer in the range 0-127.</li> <li>Dynamics. Ex: "ff".</li> <li>Dynamics ID. Integer. pp maps to 0 and ff maps to 4. The higher, the louder.</li> <li>Instance ID. Integer in the range 0-4</li> <li>String ID. Equal to 1, 2, 3, 4, or empty if not applicable.</li> <li>"Needed digital retuning". TRUE if the file has been pitch-shifted with digital audio effects; FALSE otherwise.</li> </ol>   Conditions of Use ------------------------ TinySOL was created in 2020 by Carmine-Emanuele Cella, Daniele Ghisi, Vincent Lostanlen, Fabien Lévy, Joshua Fineberg, and Yan Maresz. TinySOL is a derivative of SOL. We wish to thank Hugues Vinet, Greg Beller, and all coordinators of the Ircam Forum for their authorization to upload TinySOL to Zenodo. TinySOL is offered free of charge under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) license: https://creativecommons.org/licenses/by/4.0/ The dataset and its contents are made available on an "as is" basis and without warranties of any kind, including without limitation satisfactory quality and conformity, merchantability, fitness for a particular purpose, accuracy or completeness, or absence of errors. Subject to any liability that may not be excluded or limited by law, the authors are not liable for, and expressly exclude all liability for, loss or damage however and whenever caused to anyone by any use of the TinySOL dataset or any part of it. We encourage TinySOL users to subscribe to the Ircam Forum so that they can have access to larger versions of SOL. While downloading full version of SOL requires premium membership (for a yearly fee), a medium-sized version named OrchideaSOL is made available free of charge to all members. Note, however, that TinySOL is the only subset of SOL which is released under a Creative Commons License. For more information, please visit: https://forum.ircam.fr/   Versions ----------- 1.0 was released on January 31st, 2020. 2.0 and 3.0 were released the same day, after fixing an issue in the metadata related to file paths. 4.0 was released on February 7th, 2020. The file structure of the tar.gz file was simplified so as to improve the interoperability with the mirdata Python package. 5.0 was released on February 23th, 2020. New audio samples were added (from 2478 to 2913) and more details were supplied regarding retuning. 6.0 was released the same day, after fixing an issue in the metadata related to file paths.   Feedback ------------- Please help us improve TinySOL by sending your feedback to: carmine.cella@berkeley.edu For issues regarding the metadata encoding, the five-fold split, or the TinySOL module in mirdata, please write to: vincent.lostanlen@nyu.edu In case of a problem, please include as many details as possible.

opennotspecifiedOct 2019View details →

Distribution. Widely distributed through out tropical Africa from Senegal E to ex treme W Uganda and E DR Congo, with isolated populations in W Angola, SE Ken ya, and N, NE & SE Tanzania; also on Bioko I. in Family Hipposideridae (Old World Leaf-nosed Bats)

Distribution. Widely distributed through out tropical Africa from Senegal E to ex treme W Uganda and E DR Congo, with isolated populations in W Angola, SE Ken ya, and N, NE & SE Tanzania; also on Bioko I.

opennotspecifiedOct 2019View details →

Distribution. SE Africa from SE Zambia, S Malawi, W Mozambique, Zimbabwe, and N Botswana to Swaziland and C & E South Africa, and isolated records from Uganda and Tanzania; there are also apparently records from Togo, Benin, C Nigeria, NE Egypt, and Lesotho, but they need validation and are not mapped here. in Rhinolophidae

Distribution. SE Africa from SE Zambia, S Malawi, W Mozambique, Zimbabwe, and N Botswana to Swaziland and C & E South Africa, and isolated records from Uganda and Tanzania; there are also apparently records from Togo, Benin, C Nigeria, NE Egypt, and Lesotho, but they need validation and are not mapped here.

opencc-zeroJun 2020View details →

Data from: Between an ocean and a high place: coastal drainage isolation generates endemic cryptic species in the Cape Kurper Sandelia capensis (Anabantiformes: Anabantidae), Cape Region, South Africa

This study investigated the range-wide phylogenetics and biogeography of the Cape Kurper Sandelia capensis, a primary freshwater fish endemic to, and widespread within, the Cape Floristic Region (CFR) of South Africa. Maximum likelihood, Bayesian phylogenetic, and haplotype network analyses, based on two mitochondrial and two nuclear genes, revealed the existence of three reciprocally monophyletic, deeply divergent and allopatric clades that likely represent cryptic species. The West Coast Clade is largely confined to the Langvlei, Verlorenvlei, Berg, and Diep rivers, the Klein River Clade is endemic to the Klein River, and the South Coast Clade is found everywhere else in the range of S. capensis sensu lato. It was hypothesized that divergences within S. capensis sensu lato likely occurred because of (1) isolation of coastal drainages by persistent drainage divides and/or (2) vicariance of current tributaries by the drowning of their confluences by high sea levels. The current distribution of lineages could be due to historical range expansion and gene flow via (1) river capture or some other mode of transdivide dispersal, and/or (2) dispersal during periods of low sea level via paleoriver confluences of currently isolated coastal rivers. Comparison of BEAST2 estimated divergence times with the timing of climatic, geological, and geomorphological events supported long-term coastal drainage isolation, punctuated by rare transdivide dispersal events and limited paleoriver dispersal, as the best explanation of current phylogeographic and divergence patterns in S. capensis. Hydrological barriers that block upstream passage in palaeotributaries could hypothetically explain why S. capensis failed to disperse through certain palaeoriver confluences. There were several sites where biogeographic patterns have likely been confounded by human translocation of S. capensis. Alien fish predators and water extraction may threaten the three cryptic species more severely than previously realized, due to their smaller population sizes and inhabitation of only a portion of the range previously ascribed to S. capensis sensu lato. The preponderance of cryptic diversity and endemism in the CFR suggests that additional undescribed cryptic species of obligate freshwater fishes may be found in short coastal river systems around the world, especially in regions with a history of geological stability and a narrow continental shelf.

opencc-zeroAug 2020View details →

Septicemia of Subterranean Termites Coptotermes curvignathus Caused by Disturbance of Bacteria Isolated from Termite Gut and Its Foraging Pathways

Microbial pathogens continue to attract a great deal of attention to manage termite population. Every bacterium has its own mode of action and in fact, the mechanisms used by bacteria to attack termites remains elusive at the moment. Hence, the objective of this study was to evaluate the susceptibility of subterranean termites Coptotermes curvignathus to opportunistic pathogens using culturable aerobic bacteria isolated from the termite gut and its foraging pathways. Bacterial suspensions were prepared in concentrations of 103, 106, and 109 CFU/mL and introduced to the termites via oral-contact and physical contact treatment. The data shows that contact method acted slower and gave lower mortality, compared to oral-contact method. C. curvignathus were highly susceptible to Serratia marcescens and Pseudomonas aeruginosa. Serratia marcescens showed the highest mortality percentage of 68% and 54% at bacterial concentration of 109 CFU/mL via oral-contact and contact method, respectively. S. marcescens was also defined as the bacteria with the highest ability to induce high mortality of C. curvignathus with the lowest concentration of bacterial suspension at a given time under laboratory condition. The results of this study indicate that P. aeruginosa and S. marcescens in particular may be attractive candidates worth further examination as a possible biocontrol agent against C. curvignathus in the field and, to evaluate environmental and ecological risks of the biocontrol.

opencc-zeroAug 2020View details →

Data from: Gene flow at the leading range edge - the long-term consequences of isolation in European Beech (Fagus sylvatica L. Kuhn)

Aim: Isolation is expected to lead to negative impacts on populations due to a reduction in effective population size and gene flow, exacerbating the effects of genetic drift, which might be stronger in peripheral and fragmented populations. Fagus sylvatica (European beech) in southern Sweden presents a gradient of isolation towards the leading range edge of the species. We sought to determine the impact of long-term isolation on genetic diversity and population genetic structure within populations of this species. Location: Samples were obtained from 14 sites towards the northern edge of the native range of beech in Sweden. Taxon: Fagaceae Methods: Using historical sources, we obtained area- and distance-based measures of isolation. We measured genetic diversity and structure by using nuclear microsatellite marker data, and performed parentage analysis to estimate external pollen-mediated gene flow. We implemented a partial least squares regression to determine the effects of isolation on each of the genetic diversity estimators and the measures of external pollen-mediated gene flow. Results: Long-term isolation generally had a negative impact on genetic diversity, which is exacerbated over time, further affecting progeny and suggesting that isolated populations are subject to strong genetic drift, possibly due to the combination of founder events and persistent small population sizes. Bayesian cluster analysis revealed that isolation was also acting as a barrier to gene flow in the north-eastern distribution of beech. Main conclusions: Isolation at the leading range edge of beech in Sweden has created gradients of contemporary gene flow within the species. The long-term cumulative effects of isolation on this wind-pollinated tree species and its negative impacts on genetic diversity and gene flow, could lead to inbreeding depression and higher extinction risk where populations remain small and isolated.

opencc-zeroAug 2020View details →

Monitoring and traceability of genetically modified soybean event GTS 40-3-2 during soybean protein concentrate and isolate preparation

To evaluate DNA fragmentation and GMO quantification during soybean protein concentrate and isolate preparation, genetically modified soybean event GTS 40-3-2 (RRS) was blended with conventional soybeans at mass percentages of 0.9%, 2%, 3%, 5%, and 10%. Qualitative PCR and real-time PCR were used to monitor the taxon-specific lectin and exogenous cp4 epsps target levels in all of the main products and by-products, which has practical significance for RRS labelling threshold and traceability. Along the preparation chain, the majority of DNA was distributed in main products, and the DNA degradation was noticed. From a holistic perspective, the lectin target degraded more than cp4 epsps target during both of the two soybean proteins preparations. Therefore, the transgenic contents in the final protein products were higher than the actual mass percentages of RRS in raw materials. Our results are beneficial to the improvement of GMO labelling legislation and the protection of consumer rights.

Seminal fluid protein divergence among populations exhibiting postmating prezygotic reproductive isolation

Despite holding a central role for fertilisation success, reproductive traits often show elevated rates of evolution and diversification. The rapid evolution of seminal fluid proteins (Sfps) within populations is predicted to cause mis-signalling between the male ejaculate and female reproductive tract between populations resulting in postmating prezygotic (PMPZ) isolation. Crosses between populations of Drosophila montana show PMPZ isolation in the form of reduced fertilisation success in both noncompetitive and competitive contexts. Here we test whether male ejaculate proteins deriving from either the accessory glands or the ejaculatory bulb differ between populations using liquid chromatography tandem mass spectrometry. We find more than 150 differentially abundant proteins between populations which may contribute to PMPZ isolation. These proteins include a number of proteases and peptidases, and several orthologs of D. melanogaster Sfps, all known to mediate fertilisation success and which mimic PMPZ isolation phenotypes. Males of one population typically produced greater quantities of Sfps and the strongest PMPZ isolation occurs in this direction. The accessory glands and ejaculatory bulb have different functions and the ejaculatory bulb contributes more to population differences than the accessory glands. Proteins with a secretory signal, but not Sfps, evolve faster than non-secretory proteins although the conservative criteria used to define Sfps may have impaired the ability to identify rapidly evolving proteins. We take advantage of quantitative proteomics data from three Drosophila species to determine shared and unique functional enrichments of Sfps that could be subject to selection between taxa and subsequently mediate PMPZ isolation. Our study provides the first high throughput quantitative proteomic evidence showing divergence of reproductive proteins implicated in the emergence of PMPZ isolation between populations.

Data from: Isolated trees support lower bird taxonomic richness than trees within habitat patches but similar functional diversity

Large isolated trees are keystone structures that can help maintain biodiversity in fragmented landscapes, with evidence that open areas with isolated trees may support similar levels of taxonomic diversity to nearby patches of habitat. However, it is not clear if isolated trees can support the same diversity of ecological functions as trees in habitat patches. We compared species richness, community composition and functional diversity of birds in trees at forest edges and isolated trees. Twenty isolated trees and ten edge trees of American muskwood (Guarea guidonia) were selected, and sampled on 11 occasions, each of 20 minutes, over four months. All individual birds that landed at trees were recorded using a standardized protocol. Species richness was, on average, almost twice as high at edge trees than at isolated trees. Taxonomic composition differed between edge and isolated trees, with many forest-dependent birds restricted to edge trees, and some open-area birds restricted to isolated trees. Overall functional diversity was similar at edge and isolated trees, but some ecological functions (e.g. frugivory) were less frequent, while others (e.g. granivory) were more frequent at isolated compared to edge trees. Isolated trees are important for supporting many ecological functions in modified areas. However, the maintenance of forest patches is essential to complement the provision of such functions in modified landscapes.

Data from: Learning to see the wood for the trees: machine learning, decision trees and the classification of isolated theropod teeth

Taxonomic identification of fossils based on morphometric data traditionally relies on the use of standard linear models to classify such data. Machine learning and decision trees offer powerful alternative approaches to this problem but are not widely used in palaeontology. Here, we apply these techniques to published morphometric data of isolated theropod teeth in order to explore their utility in tackling taxonomic problems. We chose two published datasets consisting of 886 teeth from 14 taxa and 3020 teeth from 17 taxa, respectively, each with five morphometric variables per tooth. We also explored the effects that missing data have on the final classification accuracy. Our results suggest that machine learning and decision trees yield superior classification results over a wide range of data permutations, with decision trees achieving accuracies of 96% in classifying test data in some cases. Missing data or attempts to generate synthetic data to overcome missing data seriously degrade all classifiers predictive accuracy. The results of our analyses also indicate that using ensemble classifiers combining different classification techniques and the examination of posterior probabilities is a useful aid in checking final class assignments. The application of such techniques to isolated theropod teeth demonstrate that simple morphometric data can be used to yield statistically robust taxonomic classifications and that lower classification accuracy is more likely to reflect preservational limitations of the data or poor application of the methods.

Data from: Genetic structure in Orkney island mice: isolation promotes morphological diversification

Following human occupation, the house mouse has colonized numerous islands, exposing the species to a wide variety of environments. Such a colonization process, involving successive founder events and bottlenecks, may either promote random evolution or facilitate adaptation, making the relative importance of adaptive and stochastic processes in insular evolution difficult to assess. Here, we jointly analyse genetic and morphometric variation in the house mice (Mus musculus domesticus) from the Orkney archipelago. Genetic analyses, based on mitochondrial DNA and microsatellites, revealed considerable genetic structure within the archipelago, suggestive of a high degree of isolation and long-lasting stability of the insular populations. Morphometric analyses, based on a quantification of the shape of the first upper molar, revealed considerable differentiation compared to Western European populations, and significant geographic structure in Orkney, largely congruent with the pattern of genetic divergence. Morphological diversification in Orkney followed a Brownian motion model of evolution, suggesting a primary role for random drift over adaptation to local environments. Substantial structuring of human populations in Orkney has recently been demonstrated, mirroring the situation found here in house mice. This synanthropic species may thus constitute a bio-proxy of human structure and practices even at a very local scale.

opencc-by-4.0Oct 2020View details →

Isolated Ti(III) Species on the Surface of a Pre-active Ziegler Natta Catalyst. Dataset related to publication. Version: 1

Origin of the data: Experimental spectroscopic measurements; Computer modelling.  Data type: experimental measurements, models. The obtained data are in txt, DCS, DTA, SPC and PAR format. Data generated by a machine. Information on the machine: firm which produced the machine: BRUKER; version of the machine: ESP 300E for measurements at X-band frequency  and Elexys E580 for measurements at Q-band frequency. Methodology used to collect the data and to process the data: EPR Spectroscopy Analytical and procedural information: EPR Spectroscopy Definitions of variables: Magnetic field and temperature. Units of measurement: milli Tesla (mT), Kelvin (K), Megahertz (MHz). Abbreviation mg70 for the data related to the binary system MgCl2/TiCl4, Abbreviation mg21  for the data related to the ternary system MgCl2/TiCl4/monoether Abbreviation mg36  for the data related to the ternary system MgCl2/TiCl4/diester. Specialized abbreviations: EPR – Electron Paramagnetic Resonance, CW– Continuous Wave, ESE – Electron Spin Echo, ESEEM – Electron Spin Echo Envelope Modulation, HYSCORE – Hyperfine Sublevel Correlation, ZN catalyst – Ziegler-Natta catalyst, ID – internal donor. To read the data, OriginPro 9.0 and Matlab R2019a have been used on Windows platform. For simulation Easyspin 5.2.28 simulation package has been used.  To read the data, also Python can be used based on the convenience of the users. To process the data, OriginPro 9.0 and Matlab R2019a have been used in Windows platform. Python can also be used based on the convenient of users. Where to get OriginPro 9.0, Matlab R2019a and Easyspin 5.2.28:  <ul> <li>MATLAB R2019a: <a href="https://nl.mathworks.com/downloads/web_downloads/select_release?mode=gwylf">https://nl.mathworks.com/downloads/web_downloads/select_release?mode=gwylf</a></li> <li>OriginPro 9.0: <a href="https://www.originlab.com/index.aspx?go=PRODUCTS/Origin">https://www.originlab.com/index.aspx?go=PRODUCTS/Origin</a></li> <li>Easyspin 5.2.28: <a href="https://easyspin.org/easyspin/documentation/index.html">https://easyspin.org/easyspin/documentation/index.html</a></li> </ul> Where to get the licenses: For MATLAB R2019a the website to download the licence is: <a href="https://nl.mathworks.com/downloads/web_downloads/select_release?mode=gwylf">https://nl.mathworks.com/downloads/web_downloads/select_release?mode=gwylf</a> For OriginPro 9.0: <a href="https://www.originlab.com/index.aspx?go=PURCHASE/LicensingOptions">https://www.originlab.com/index.aspx?go=PURCHASE/LicensingOptions</a>

opencc-zeroOct 2020View details →

Contrasting effects of host tree isolation on population connectedness in two tropical epiphytic bromeliads

Premise of the study Conversion of primary forests to pastures is a major cause of habitat fragmentation in the tropics. Fragmentation is expected to impede gene flow for many plant species that are restricted to remaining forest fragments. Epiphytes may be especially vulnerable to this effect of forest fragmentation because they depend on host trees. However, trees that remain in pastures may enhance connectivity across the landscape for epiphyte species that can thrive on such trees. To investigate this possibility, we studied the genetic structures of two such species on isolated pasture trees and surrounding forest, in relation to their local abundances in different habitat types and aspects of their reproductive biology including pollen and seed dispersal agents, and looked for evidence of increased or diminished gene flow. Methods We used microsatellite markers to assess geographic patterns of genetic diversity and differentiation in two epiphytic bromeliads, Catopsis nitida and Werauhia tonduziana, in the Monteverde region of Costa Rica. Key results About 85% of the FST value for Catopsis nitida was found among pastures within regions, while for Weruahia tonduziana, about 80% of the FST value was contributed by differences between regions, indicating much more gene flow within regions, relative to C. nitida. Conclusions Although there was substantial genetic differentiation among epiphyte populations, those on isolated pasture trees were not substantially less diverse than those in adjacent forests, suggesting that pasture trees may serve as "stepping stones" that help these species maintain their genetic connectedness and diversity at larger geographic scales.

opencc-zeroOct 2020View details →

Morning glory species co-occurrence is associated with asymmetrically decreased and cascading reproductive isolation

Hybridization between species can affect the strength of the reproductive barriers that separate those species. Two extensions of this effect are: (1) the expectation that asymmetric hybridization or gene flow will have asymmetric effects on reproductive barrier strength and (2) the expectation that local hybridization will affect only local reproductive barrier strength and could therefore alter within-species compatibility. We tested these hypotheses in a pair of morning glory species that exhibit asymmetric gene flow from highly selfing Ipomoea lacunosa into mixed-mating I. cordatotriloba in regions where they co-occur. Because of the direction of this gene flow, we predicted that reproductive barrier strength would be more strongly affected in I. cordatotriloba than I. lacunosa. We also predicted that changes to reproductive barriers in sympatric I. cordatotriloba populations would affect compatibility with allopatric populations of that species. We tested these predictions by measuring the strength of a reproductive barrier to seed set across the species' ranges. Consistent with our first prediction, we found that sympatric and allopatric I. lacunosa produce the same number of seeds in crosses with I. cordatotriloba, whereas crosses between sympatric I. cordatotriloba and I. lacunosa are more successful than crosses between allopatric I. cordatotriloba and I. lacunosa. This difference in compatibility appears to reflect an asymmetric decrease in the strength of the barrier to seed set in sympatric I. cordatotriloba, which could be caused by I. lacunosa alleles that have introgressed into I. cordatotriloba. We further demonstrated that changes to sympatric I. cordatotriloba have decreased its ability to produce seeds with allopatric populations of the same species, in line with our second prediction. Thus, in a manner analogous to cascade reinforcement, we suggest that introgression associated with hybridization not only influences between-species isolation but can also contribute to isolation within a species.

opencc-zeroDec 2019View details →

Characterization, functional properties and antioxidant activities of macromolecular extracts isolated from Porphyra yezoensis

Porphyra yezoensis is one of the most economical seaweed species in China. Determining how to make full use of mature P. yezoensis and exploring new ways to increase the value of its resources are important subjects of research for the development of the laver breeding industry. In this study, we provide a simple method to comprehensively extract the bioactive substances from P. yezoensis. The characteristics, functional properties and antioxidant activities of two types of biopolymer extract from P. yezoensis were studied and analyzed relatively. Based on the characterization of water-soluble concentrate (WPC) and alkali-soluble concentrate (APC), obtained via chemical analysis, FT-IR, TGA and differential scanning calorimetry (DSC), they both had typical polysaccharide and protein characteristics and steady composition. APC showed higher nitrogen solubility, water holding capacity and foaming ability. APC could not only be used as a protein supplement; it also performs well in improving the properties of foods in terms of water-holding and fat-absorption. The emulsifying activity and oil-holding capacity of WPC were observed to be higher than those of APC; thus, WPC has the potential to be used as an emulsifier. Surprisingly, WPC and APC have radical scavenging capacity in vitro, which broadens the direction of their application.