TimeTree 5: An Expanded Resource for Species Divergence Times

We present the fifth edition of the TimeTree of Life resource (TToL5), a product of the timetree of life project that aims to synthesize published molecular timetrees and make evolutionary knowledge easily accessible to all. Using the TToL5 web portal, users can retrieve published studies and divergence times between species, the timeline of a species’ evolution beginning with the origin of life, and the timetree for a given evolutionary group at the desired taxonomic rank. TToL5 contains divergence time information on 137,306 species, 41% more than the previous edition. The TToL5 web interface is now Americans with Disabilities Act-compliant and mobile-friendly, a result of comprehensive source code refactoring. TToL5 also offers programmatic access to species divergence times and timelines through an application programming interface, which is accessible at timetree.temple.edu/api. TToL5 is publicly available at timetree.org.     

TimeTree: a public knowledge-base of divergence times among organisms

Biologists and other scientists routinely need to know times of divergence between species and to construct phylogenies calibrated to time (timetrees). Published studies reporting time estimates from molecular data have been increasing rapidly, but the data have been largely inaccessible to the greater community of scientists because of their complexity. TimeTree brings these data together in a consistent format and uses a hierarchical structure, corresponding to the tree of life, to maximize their utility. Results are presented and summarized, allowing users to quickly determine the range and robustness of time estimates and the degree of consensus from the published literature. AVAILABILITY: TimeTree is available at http://www.timetree.net     

Transformer‐4 version 2.0.1, a free multi‐platform software to quickly reformat genotype matrices of any marker type,and archive them in the Demiurge information system

Transformer‐4 version 2.0.1 (T4) is a multi‐platform freeware programmed in java that can transform a genotype matrix in Excel or XML format into the input formats of one or several of the most commonly used population genetic software, for any possible combination of the populations that the matrix contains. T4 also allows the users to (i) draw allozyme gel interpretations for any number of diploid individuals, and then generate a genotype matrix ready to be used by T4; and (ii) produce basic reports about the data in the matrices. Furthermore, T4 is the only way to optionally submit ‘genetic diversity digests’ for publication in the Demiurge online information system ( http://www.demiurge-project.org ). Each such digest undergoes peer‐review, and it consists of a geo‐referenced data matrix in the tfm4 format plus any ancillary document or hyperlink that the digest authors see fit to include. The complementarity between T4 and Demiurge facilitates a free, safe, permanent, and standardized data archival and analysis system for researchers, and may also be a convenient resource for scientific journals, public administrations, or higher educators. T4 and its converters are freely available (at, respectively, http://www.demiurge-project.org/download_t4 and http://www.demiurge-project.org/converterstore ) upon registration in the Demiurge information system ( http://demiurge-project.org/register ). Users have to click on the link provided on an account validation email, and accept Demiurge's terms of use (see http://www.demiurge-project.org/termsofuse ). A thorough user's guide is available within T4. A 3‐min promotional video about T4 and Demiurge can be seen at http://vimeo.com/29828406 .     

BRENDA: a resource for enzyme data and metabolic information.

BRENDA (BRaunschweig ENzyme DAtabase), founded in 1987 by Dietmar Schomburg, is a comprehensive protein function database, containing enzymatic and metabolic information extracted from the primary literature. Presently, the database holds data on more than 40 000 enzymes and 4460 different organisms, and includes information about enzyme-ligand relationships with numerous chemical compounds. The collection of molecular and biochemical information in BRENDA provides a fundamental resource for research in biotechnology, pharmacology, medicinal diagnostics, enzyme mechanics, and metabolism. BRENDA is accessible free of charge to the academic community at http://www.brenda.uni-koeln.de/; commercial users need a license available from http://www.science-factory.com/     

The Mouse Gene Expression Database (GXD)

The Gene Expression Database (GXD) is a community resource of gene expression information for the laboratory mouse. By combining the different types of expression data, GXD aims to provide increasingly complete information about the expression profiles of genes in different mouse strains and mutants, thus enabling valuable insights into the molecular networks that underlie normal development and disease. GXD is integrated with the Mouse Genome Database (MGD). Extensive interconnections with sequence databases and with databases from other species, and the development and use of shared controlled vocabularies extend GXD's utility for the analysis of gene expression information. GXD is accessible through the Mouse Genome Informatics web site at http://www.informatics.jax.org/ or directly at http://www.informatics.jax.org/menus/expression_menu. shtml.     

Biodiversity of living benthic foraminifera: How many species are there?

In ecological studies involving the analysis of  2.4 million living (stained) individual tests, to date  2140 species of benthic foraminifera have been recorded. Of these 602 species are agglutinated, 341 porcelaneous and 1197 hyaline. The numbers of species in the major environments are: marginal marine 701 (in  1.5 million individuals), shelf 989 (in  0.6 million individuals) and deep sea 831 (in  0.3 million individuals). 381 species occur in more than one major environment. Overall  33% have abundance of > 10% while  67% are of minor abundance (< 10%). The majority of species are rare, most are endemic and very few are cosmopolitan (5% or less). To estimate the potential total number of living species the following factors need to be quantified: the proportion of species already named (here considered unlikely to be less than 50% of the potential total), the number of species currently known to be dead but for which living representatives may yet to be found (assumed to be 5% = 107 species), and the proportion of species that are synonyms (10–25% = 214 to 535 species). Assuming that 50% of species have already been named (2140 + 107 = 2247), the potential total ranges from  3959 to  4280 species for 10% synonymy to  3210 to  3531 species for 25% synonymy.     

WebACT--an online companion for the Artemis Comparison Tool

SUMMARY: WebACT is an online resource which enables the rapid provision of simultaneous BLAST comparisons between up to five genomic sequences in a format amenable for visualization with the well-known Artemis Comparison Tool (ACT). Comparisons can be generated on-the-fly using sequences directly retrieved via EMBL database queries, or by entering or uploading user sequences. Furthermore, pre-computed comparisons are available between all publicly available, completed prokaryotic genomes and plasmids currently contained within the Genome Reviews database (372 sequences, representing 175 different species). The system is designed to minimize the volume of downloaded data and maximize performance. Genome sequences, annotation and pre-computed comparisons are stored in a relational database allowing flexible querying based on user-defined sequence regions, from whole genome to a defined region flanking a specified gene. Comparison and sequence files, whether computed online or retrieved from the database of pre-computed genome comparisons, can be viewed online using ACT and are available for download. AVAILABILITY: Freely accessible at http://www.webact.org. SUPPLEMENTARY INFORMATION: User guide and worked examples are available at http://www.webact.org/WebACT/docs.     

Is sex necessary?

Fungal sexual reproductive modes have markedly high diversity and plasticity, and asexual species have been hypothesized to arise frequently from sexual fungal species. A recent study on the red yeasts provides further support for the notion that sexual ancestors may give rise to shorter-lived asexual species. However, presumed asexual species may also be cryptically sexual, as revealed by other recent studies.See research article: http://www.biomedcentral.com/1471-2148/11/249     

The scent of your enemy is my friend? The acquisition of large carnivore scent by a smaller carnivore

Scent marking is critical to intraspecific communication in many mammal species, but little is known regarding its role in communication among different species. We used 4 years of motion-triggered video to document the use of scent marking areas—termed “community scrapes”—by pumas (Puma concolor) (http://www.momo-p.com/showdetail-e.php?movieid=momo160812pc01a) and other carnivore species. We found that gray foxes (Urocyon cinereoargenteus) routinely rubbed their cheeks on puma scrapes (http://www.momo-p.com/showdetail-e.php?movieid=momo160812uc01a), and tested a series of hypotheses to determine its function. We found that gray foxes selected puma scrapes over other objects, and cheek rubbing by foxes was also correlated with how recently a puma had visited the scrape, suggesting that foxes were intent upon accumulating fresh puma scent. Cheek rubbing by foxes was not correlated with their breeding season or with how recently another fox had visited the site. Finally we found a cascading pattern in the occurrence of pumas, coyotes (Canis latrans) and gray foxes at community scrapes, suggesting that gray foxes may use puma scent to deter predation. This is the first published study to find evidence of a subordinate species using the scent of a dominant species to communicate with heterospecifics. The behavioral cascade we found in scent marking patterns also suggests that scent marking could be a mechanism that impacts the distribution and abundance of species. Additional videos pertaining to this article include http://www.momo-p.com/showdetail-e.php?movieid=momo160812uc02a, and http://www.momo-p.com/showdetail-e.php?movieid=momo160812uc03a.     

Gene set analysis in the cloud

Cloud computing offers low cost and highly flexible opportunities in bioinformatics. Its potential has already been demonstrated in high-throughput sequence data analysis. Pathway-based or gene set analysis of expression data has received relatively less attention. We developed a gene set analysis algorithm for biomarker identification in the cloud. The resulting tool, YunBe, is ready to use on Amazon Web Services. Moreover, here we compare its performance to those obtained with desktop and computing cluster solutions. AVAILABILITY AND IMPLEMENTATION: YunBe is open-source and freely accessible within the Amazon Elastic MapReduce service at s3n://lrcv-crp-sante/app/yunbe.jar. Source code and user's guidelines can be downloaded from http://tinyurl.com/yunbedownload.     

Lack of discrimination of sex and maturity of conspecifics in the copulation attempts of the male stalk-eyed fly,Sphyracephala detrahens (Diptera: Diopsidae)

Among insects, males have evolved the ability to discriminate potential mates to avoid vain mating attempts. In Diptera, courtship and mating behaviors of species that do not discriminate potential mates have rarely been studied. In this study, we investigated copulation attempts of the stalk-eyed fly, Sphyracephala detrahens males, which do not engage in any observable pre-copulatory courtship behavior. We found that sexually mature males attempted to copulate with mature males and immature adults of both sexes, as frequently as with mature females. Successful copulation only occurred with mature females. Immature females rejected mounting males by vibrating their bodies and immature and mature males by incurving their abdomen downward. Comparison of the cuticular hydrocarbon components of individuals of different sexes and maturity levels indicated that the cuticular hydrocarbon profiles were similar regardless of the sex and sexual maturity. Therefore, we suggest that visual or chemical information are of little use for males S. detrahens in discriminating receptive conspecific mates. Since elaborate mate discrimination behaviors lead to additional time and energy costs when discrimination is difficult, S. detrahens may increase reproductive success simply by increasing the number of copulation attempts. Digital video images related to this article are available at http://www.momo-p.com/showdetail-e.php?movieid=momo211123sd01a, http://www.momo-p.com/showdetail-e.php?movieid=momo211123sd02a, http://www.momo-p.com/showdetail-e.php?movieid=momo211123sd03a, and http://www.momo-p.com/showdetail-e.php?movieid=momo211123sd04a.

     

The apoptosis database

The apoptosis database is a public resource for researchers and students interested in the molecular biology of apoptosis. The resource provides functional annotation, literature references, diagrams/images, and alternative nomenclatures on a set of proteins having 'apoptotic domains'. These are the distinctive domains that are often, if not exclusively, found in proteins involved in apoptosis. The initial choice of proteins to be included is defined by apoptosis experts and bioinformatics tools. Users can browse through the web accessible lists of domains, proteins containing these domains and their associated homologs. The database can also be searched by sequence homology using basic local alignment search tool, text word matches of the annotation, and identifiers for specific records. The resource is available at http://www.apoptosis-db.org and is updated on a regular basis.     

A novel deconvolution method for modeling UDP-N-acetyl-D-glucosamine biosynthetic pathways based on 13C mass isotopologue profiles under non-steady-state conditions

This article is a response to Wang and Luo. See correspondence article http://www.biomedcentral.com/1741-7007/10/30/ [WEBCITE] and the original research article http://www.biomedcentral.com/1741-7007/9/24 [WEBCITE].     

Tackling thermosensation with multidimensional phenotyping

Ring species, in which two different forms coexist in one region while being connected by a long chain of interbreeding populations encircling a geographic barrier, provide clear demonstrations of the evolution of one species into two. Known ring species are rare, but now Monahan et al. propose an intriguing new approach to discovering them: focus first on geography to find potential barriers. See research article http://www.biomedcentral.com/1741-7007/10/20     

Protein kinase C-α negatively regulates EGF-induced PLC- activity through direct phosphorylation

Phospholipase C- is a PLC isozyme that contains a CDC25 homology domain and a pair of RA domains in addition to a conserved PLC catalytic domain. PLC- is activated by both growth factors and GPCR ligands in a distinct manner. Growth factors such as EGF stimulate PLC- in an RA2 domain-dependent manner through Ras and Rap. On the other hand, several GPCR ligands that are linked with Ga₁₂ or Ga₁₃ can activate PLC- by associating with GTP-RhoA. GTP-RhoA binds with the region in the PLC- Y domain. Gs-linked ligands such as PGE1 and adrenaline stimulate PLC- by cAMP-dependent activation of Epac and Rap2B. PLC- is important for cardiac development and function. In addition, several lines of evidence indicate that PLC- promotes cell growth in an activity-dependent or -independent manner. In particular, PLC--dependent suppression of EGF receptor downregulation contributes to its growth promoting activity. Proper regulation of PLC- activity is essential for preventing tumor formation. Our previous report indicated that EGF-dependent ubiquitination of PLC- is required for the control of PLC--dependent cell growth. Recently, we found that PLC- is phosphorylated by growth factor stimulation, and this is another mechanism of the negative regulation. PLC- is phosphorylated by PKC-α upon stimulation with growth factors such as EGF and PDGF. The EGF-induced phosphorylation of PLC- was abolished by PKC inhibitors and by the expression of the dominant negative mutant of PKC-α. Furthermore, PKC-α was found to phosphorylate PLC- directly in vitro, suggesting that PLC- is a substrate of PKC-α in cells. In addition, PLC- was co-immunoprecipitated with PKC-α in an EGF-dependent manner. Immunocytochemical studies showed that PLC- co-localized with PKC-α in the plasma membrane after EGF stimulation. In addition, inhibition of PKC activity enhanced PLC--mediated PIP₂ hydrolysis, suggesting that PKC-α negatively regulates PLC- activity. Taken together, these results suggest for the first time that PLC- is regulated by PKC-α-dependent phosphorylation.     

Morphological differentiation of Icelandic Redpolls,Acanthis flammea islandica

Capsule The analyses support the grouping of the three Acanthis species, although a large split is observed between the A. hornemanni subspecies.

Aims To investigate the morphological variation in A. f. islandica among different periods of the year and its morphological differentiation from the other subspecies A. f. flammea and A. f. rostrata, and also from the redpoll species, A. cabaret and the two subspecies of A. hornemanni, exilipes and hornemanni.

Methods The subspecies status of the Icelandic population was evaluated with Amadon's rule, by comparing its variation of traits to the distribution of the traits in different species/subspecies of the group.

Results A. f. islandica is characterized by intermediate wing, bill and tail lengths. Based on the 75% rule, wing length and bill depth can be used to discriminate A. f. islandica from both extreme morphs of redpolls (currently classified as different species); A. hornemanni and A. cabaret, and tail and wing length can distinguish A. f. islandica from its conspecifics A. f. flammea. The overall morphological divergence within the redpoll complex is not supported by association to the studied nuclear markers.

Conclusion The taxonomic status of the three redpoll species is supported by Amadon's rule, however the subspecies status of the Icelandic Redpoll remains unclear.