• Open Access close
• English close

Cruise QC flag: D (see further details). The Fair Data Use Statement for SOCAT can be found at hdl:10013/epic.48576.d001

We propose to use coherent X-ray scattering to study the dynamics of organic molecules during organic molecule deposition. Using X-ray photon correlation spectroscopy, we can measure the characteristic time scales over which the surface of the film evolves. To do this, we will study several organic molecules of different shapes to be particularly sensitive to rotational and vibrational degrees of freedom that are not present in inorganic film growth.

1. Species distribution modeling, which allows users to predict the spatial distribution of species with the use of environmental covariates, has become increasingly popular, with many software platforms providing tools to fit such models. However, the species observations used can have varying levels of quality and can have incomplete information, such as uncertain or unknown species identity. 2. In this paper, we develop two algorithms to classify observations with unknown species identities which simultaneously predict several species distributions using spatial point processes. Through simulations, we compare the performance of these algorithms using 7 different initializations to the performance of models fitted using only the observations with known species identity. 3. We show that performance varies with differences in correlation among species distributions, species abundance, and the proportion of observations with unknown species identities. Additionally, some of the methods developed here outperformed the models that didn't use the misspecified data. We applied the best-performing methods to a dataset of three frog species (Mixophyes). 4. These models represent a helpful and promising tool for opportunistic surveys where misidentification is possible or for the distribution of species newly separated in their taxonomy. Our study case dataset uses presence-only records from the online database of the Atlas of Living Australia. On this platform, any person that sees a frog in the wild can report the coordinates and other relevant information. We focused the analysis on the three northern species of Mixophyes genus that have been recently separated in Mahony et al. 2006. We cleaned our dataset by including only observations of adult specimens with date information and through verification by a specialist of these species, M. Mahony. The observations with known species labels were those for which we have associated genetic information as well as any observations reported after the taxonomic split in 2006. The rest of the observations were considered as having unknown species labels. We extracted relevant covariates for these species on a 5kmx5km grid from different sources: BBCVL, UC Davis Biogeo group and bom. A README file details the data files and an Rscript documents details of the steps of the analysis.

README file for packageDescribes all files in package and provides external links to additional documentation.SILVA-to-NCBI mappingContains a mapping of Genbank accession numbers to NCBI taxon ids and names. The accessions are those that are the reference sequences for SILVA clusters.accessions.tgzOTT amendmentsThe taxonomy amendments used in preparation of OTT. Includes all amendments in https://github.com/OpenTreeOfLife/amendments-1 at the time that we built the version of OTT described in the article. Each amendment is a json file that includes the change being proposed as well as sources that support the change.amendments.tgzmapping of source ids to OTT idsCumulative mapping of identifiers in sources to OTT identifiers. Format of each line is source:sourceid,OTTid.by_qid.tgzOTT version2.10This is the previous version of the Open Tree Taxonomy. It is included because we use the previous version during identifier assignment (ott2.10 required to build ott3.0). See the enclosed README for details on files and formats.ott2.10.tgzOTT version 3.0Version of the Open Tree Taxonomy described in the manuscript. See the enclosed README for details on files and formats.ott3.0.tgzseparation taxonomyThe 'separation taxonomy' described in the manuscript. Contains a list of taxa and a list of synonyms.separation.tgz Taxonomy and nomenclature data are critical for any project that synthesizes biodiversity data, as most biodiversity data sets use taxonomic names to identify taxa. Open Tree of Life is one such project, synthesizing sets of published phylogenetic trees into comprehensive summary trees. No single published taxonomy met the taxonomic and nomenclatural needs of the project. Here we describe a system for reproducibly combining several source taxonomies into a synthetic taxonomy, and we discuss the challenges of taxonomic and nomenclatural synthesis for downstream biodiversity projects.

composite depth: core fit between GIK12329-4 and GIK12329-6, original depth belongs to GIK12329-4 or GIK12329-6

The movie shows the region of the Antarctic Peninsula (land mask: dark grey; ice shelf: light grey). Sea ice cover (colour coded) is shown in a daily time series beginning 2000-03-01 for 12 month. Adult male southern elephant seals (white circle symbols) had been equipped with satellite transmitters at King George Island (South Shetland Islands). The individual symbols appear in red for the initial and terminal location of each seal.

Priority effects occur when a species or genotype with earlier arrival has an advantage such that its relative abundance in the community or population is increased compared with later-arriving species. Few studies have dealt with this concept in the context of within-species competition. Skeletonema marinoi is a marine diatom that shows a high degree of genetic differentiation between populations over small geographical distances. To test whether historical events such as priority effects may have been important in inducing these patterns of population differentiation, we performed microcosm experiments with successive inoculation of different S. marinoi strains. Our results show that even in the absence of a numerical advantage, significant priority effects were evident. We propose that priority effects may be an important mechanism in initiating population genetic differentiation. Priority effects_raw dataRaw data for growth curves and AsQ-PCR results referred to in the publication.

Calibrated ages of a high-resolution peat core from the Past Global Changes - Carbon in Peat on EArth through Time (PAGES_C-PEAT) Project.