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November 22, 2013
Dear colleagues, This is a reminder that the registration deadline for the International Symposium ‘Ecology & Evolution of Marine Parasites and Diseases’ is coming closer. If you would like to attend, please do not forget to register before 1 December 2013! International Symposium ‘Ecology & Evolution of Marine Parasites and Diseases’ at the NIOZ Royal Netherlands Institute for Sea Research on Texel in the Netherlands from 10-14 March 2014 The budding fields of marine ecological and evolutionary parasitology lack a platform that fosters the exchange among the divergent questions and approaches taken to understand the role of parasitism and disease in marine ecosystems. This symposium intends to fill this void with the aim to: - collect and synthesise our current knowledge on marine parasites and diseases. - facilitate the exchange of ideas and collaborations among researchers from different fields. - identify important future research avenues. We are delighted to announce that the following invited speakers have confirmed to join the symposium: Robert Poulin (University of Otago, NZ), Mark Bertness (Brown University, USA), Kevin Lafferty (USGS & UC Santa Barbara, USA), Corina Brussard (NIOZ & University of Amsterdam, NL), Carolyn Friedman (University of Washington, USA), David Marcogliese (Environment Canada, CA). Themes of the symposium: • Biogeography and macroecology • Phylogeography and population genetics • Local adaptation and co-evolutionary dynamics • Direct and indirect effects of diseases on marine populations and communities • Parasites in marine food webs and effects on ecosystem functioning • Drivers of epidemics and emerging diseases • Diseases in marine reserves and in marine conservation efforts For further information and registration got to: http://bit.ly/18UWoRH. Kind regards Mathias Wegner & David Thieltges Mathias Wegner AWI Waddenseastation Sylt Hafenstrasse 43 25992 List/Sylt +49 4651 9564-205 +49 4651 9564-200 Mathias.Wegner@awi.de http://bit.ly/1bZ1rqb Mathias Wegner via Gmail
November 21, 2013
The International Max Planck Research School (IMPRS) for Organismal Biology offers several fully-funded PhD positions. The IMPRS is based in southern Germany and is jointly organized by the Max Planck Institute for Ornithology in Seewiesen and Radolfzell and the University of Konstanz. Outstanding students of all nationalities with a deep commitment to basic research in Organismal Biology are invited to apply. More than 25 internationally recognized research groups actively participate in the PhD program and offer challenging, cutting-edge PhD projects in the fields of Behavioral Biology, Ecology, Evolutionary Biology, Physiology, and Neurobiology. For a list of all available PhD projects visit http://bit.ly/18czeMc. All students accepted to the program will be supported by stipends or contracts. The program offers a dedicated teaching program, high quality research experience, and outstanding research facilities in an inspiring research and living environment. The working language is English. Each PhD student receives individual supervision and mentoring and is guided in her/his research work by a PhD advisory committee. Deadline for the application is January 15, 2014. Interviews with the applicants are scheduled for Mid-March. Candidates accepted into the program may start latest September 2013. The Max Planck Society and the University of Konstanz are equal opportunity employers. Qualification: Applicants should hold a MSc or equivalent degree in biology or a related discipline at the point of enrollment. Queries should be mailed to the program office: IMPRS@uni-konstanz.de Application: For the online application process visit http://bit.ly/17SXPjm . More information at www.orn.mpg.de/IMPRS and http://on.fb.me/18czeMdwww.orn.mpg.de/IMPRS and http://on.fb.me/18czeMd . IMPRS via Gmail
A thematic Parmenides fellowship is open at the Parmenides Center for the Conceptual Foundations of Science (Mnich, Germany) under the supervision of Prof. Ers Szathmry. The successful candidate will carry out his/her own research agenda in the fields described below. The position is for a minimum of 1 year to a maximum of 3 years. The successful applicant will receive a stipend of 2500 EUR per month (net). The proposed project can start as soon as a suitable candidate is identified, but not later than the 1st January, 2014. Origin and evolution of adaptive immune systems: The project will involve the development of a conceptual framework and detailed evolutionary scenario to place the origin and evolution of adaptive immune systems in the framework of the major evolutionary transitions. Individual steps of the evolutionary pathway will be investigated with the help of mathematical and simulation models. We seek applicants with an interest in both theoretical evolutionary biology and immunology, with experience in using a range of computational, bioinformatics and mathematical techniques to answer evolutionary questions. The ideal candidate will have 5+ years of postdoctoral experience, a track record in publishing in international scholarly journals and fluency in English. Past experience in the supervision of MSc/PhD students is an advantage. Candidates should submit an application consisting of a CV with full list of publications, a motivation letter (1 page) and a proposed workplan (max 3 pages). The deadline for applications is 15th December, 2013. Applications should be sent by email to Ers Szathmry, email@example.com. Carsten Freitger Projektmanagement Parmenides Stiftung Kirchplatz 1 82049 Pullach Tel +49.89.4520935.0 Fax +49.89.4520935.31 Mobil +49.173.5403274 firstname.lastname@example.org Carsten Freitger via Gmail
DataDryad.org is a curated general-purpose repository that makes the data underlying scientific publications discoverable, freely reusable, and citable. Dryad has integrated data submission for a growing list of journals; submission of data from other publications is also welcome.
Quick notes on yet another attempt to marry the task of editing a taxonomic classification with versioning it in GitHub.
The idea of dumping the whole GBIF classification into GitHub as a series of nested folders looks untenable. So, maybe there's another way to tackle the problem.
Let's imagine that we dump, say, the GBIF classification down to family-level as a series of nested folders (i.e., we recreate the classification on disk). For each family we then create a bunch of files and store them in that folder. For example, we could have the classification in Darwin Core Archive format (basically, delimited text). Let's also create a graph that corresponds to that classification, using a format for which we have tools available for visualising and editing.
For example, I've created a Graph Modelling Language (GML) file for the Pinnotheridae here. Using software such as yEd I can load this file, display it, and edit it. For example, below is a compact tree layout of the graph:
This image is a bitmap, if you opened the GML file in yEd it would be interactive, and you could zoom in, alter the layout, edit the graph, etc.
Looking at the graph there are a few oddities, such as "orphan" genera that lack any species, and some names that appear very similar. For example, there is an orphan genus Glassella, and a similar genus Glassellia (note the "i") with a single species Glassellia costaricana. A little digging in BioNames shows that Glassellia is a misspelling of Glassella. The original description appears in:
E Campos, M K Wicksten (1997) A New Genus For The Central American Crab Pinnixa costaricana Wicksten, 1982 (Crustacea: Brachyura: Pinnotheridae). Proceedings of the Biological Society of Washington 110(1): 69–73. http://biostor.org/reference/81137So, we have one genus that appears twice due to a typo. Furthermore, there are nodes in the graph for the taxa Glassellia costaricana and Pinnixa costaricana, but these are the same thing (the names are synonyms, albeit Glassellia costaricana has the genus misspelt). So, we could delete Pinnixa costaricana, delete the mispelling Glassellia, fix the misspelling in Glassellia costaricana, and move it to the correctly spelt Glassella. There are other problems with this classification, but let's leave them for the moment.
Now, imagine that after editing I use the graph to regenerate the DWCA file, which now has the edited classification. I then commit the changes to GitHub, and anyone else (including GBIF) could grab the DWCA and, for example, replace their Pinnotheridae classification with the edited version.
We could also go further, and add what i think is a missing component of the GBIF classification, namely a link to the nomenclators. For example, in an ideal world we would have each name in the classification linked to a stable identifier for the name provided by a nomenclator, and that nomenclator would know, for example, that Pinnixa costaricana and Glassella costaricana were objective synonyms. If we had those links then we could automatically detect cases such as this where logically you can have either Pinnixa costaricana or Glassella costaricana in the same classification, but not both.
There are some wrinkles to figure out, for example it would be nice to compute the difference between the original and edited graphs in terms of graph operations (not simply the difference as text files) so we could do things like list nodes that have been moved or deleted. I did some work on this a while back (Page, R. D., & Valiente, G. (2005).BMC Bioinformatics, 6(1), 208. doi:10.1186/1471-2105-6-208), something like that tool might do the trick.
There is an element here of trying to coerce a problem into a form that can existing tools can solve, but in a way that's what makes it attractive. If we can use things that already exist then we can move from talking about it to actually doing it.
Conference: Symbioses (Yosemite, CA) Dear Colleagues, The Fourth annual Symbiosis Workshop will take place on May 3-4, 2014 at the Sierra Nevada Research Institute, Yosemite National Park. This is an integrative meeting of biologists focusing on symbiosis research Co-organized by Mnica Medina (UC Merced) and Joel Sachs (UC Riverside) Keynote speaker: Dr. John Pringle from Stanford University. Aiptasia, a model system for dinoflagellate-cnidarian symbiosis Information about our meeting: Why: Our goal is to better integrate scientists that focus on symbiosis research. We plan to continue annual workshops at Yosemite as this site is both beautiful and secluded. This will be our 4th annual meeting and we are now attracting scientists from all over the country and overseas. Who: The meeting is small by design (~50 participants) and we seek to focus on scientists interested in both cooperation and symbiosis. In the past we have covered a range of symbiosis topics from ecology and evolution to molecular mechanisms in different model and non-model systems. We would like to make room for a diverse group of people so we will initially accept up to 3 lab members per group (including the PI) on a first come first served basis. When: The meeting will be held May 3-4, 2014, though we make accommodation arrangements available for attendees to arrive on Friday the 2nd to provide opportunities to enjoy the park. Since time at the conference is limited, we ask attendees to submit an abstract and a preference (talk versus poster). Priority will be given to those presenting. Abstract and early bird registration are due on January 15th, 2014. Where: SNRI has a set of cabins in Wawona and all within a short walk of the conference room. Costs: See details in the registration page. We will only be able to accept credit card payments this year. Link to meeting information: http://bit.ly/18pYFYK Registration link: http://bit.ly/IhH5eT Please direct any questions to the organizers: Monica Medina, email@example.com, Joel Sachs firstname.lastname@example.org Becca Fenwick (SNRI) email@example.com Joel Lawrence Sachs via Gmail
Biodiversity Research Centre, The University of British Columbia Fellowship Opportunity The next application deadline is January 13, 2014. As a part of our NSERC CREATE training program in biodiversity research, we seek applicants for a 2-year postdoctoral fellowship in the U.B.C. Biodiversity Research Centre (http://bit.ly/IhFPZb). The Centre is made up of over 50 faculty members with interests in ecology, evolution, systematics, biodiversity and conservation. Preference will be given to candidates with bold ideas, demonstrated research ability, and strong communication skills. The successful candidate will be expected to conduct original research on core problems in biodiversity, foster interactions within the Centre, run a seminar series, and organize a retreat. Postdoctoral fellows funded by the Biodiversity Research Centre typically interact with several lab groups. Candidates are welcome to contact potential collaborating labs in the Centre to inquire about current and potential research activities, but it is not necessary to apply to work with a specific faculty member. Starting date, 1 September 2014. Salary $43,000 per yr. Research stipend: $7,000 per yr. Send curriculum vitae, three letters of reference, and a statement of overall scientific goals and interests (approximately 2 pages) to the address below. Applications and Reference letters will be accepted electronically; reference letters must be sent directly by the referee. Search Chair, Biodiversity Research Centre, U.B.C., 6270 University Blvd., Vancouver, B.C., Canada V6T 1Z4. (Fax 604-822-2416, e-mail firstname.lastname@example.org). Closing date for application, 13 January 2014. The University of British Columbia hires on the basis of merit and is committed to employment equity. We encourage all qualified candidates to apply. Lebby Balakshin via Gmail
—_000_CEB24EFBFBBBweiganggenectrhuntercunyedu_ Content-Type: text/plain; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable Positions for 1-2 graduate students at Ph.D. Level are available in the lab of Dr Weigang Qiu in the Department of Biological Sciences at Hunter College of the City University of New York, located at the 68th Street/Lexington Avenue in Manhattan, New York City. The successful applicants are expected to develop new statistical methods and computational algorithms to test adaptive and non-adaptive mechanisms of genome evolution in bacterial pathogens of Lyme disease. Up-to-date research projects, lab activities, and publications of the Qiu Lab are described on the lab website: http://bit.ly/1aI5KTX. Applicants should have a Bachelor’s degree in either Biology with computer-programming experience in Linux/Unix environment, or Computer Science with college-level biology courses. The applicants are expected to apply to the Ecology, Evolutionary Biology, and Behavior (EEB) subprogram within the Biology Program at the Graduate Center (GC), City University of New York and meet all admission requirements. The Biology Program at CUNY GC is described at http://bit.ly/1aw0iVd. The deadline for application is January 1, 2014. Application package can be found at http://bit.ly/1aI5KTZ. Prior to filing a formal application, the applicant should contact Dr. Weigang Qiu by email (email@example.com) with the subject line “Potential grad student”. Dr Qiu will make recommendations to apply after determining eligibility. Biology Program’s statement on student support and benefit is quoted below: “Each student admitted for doctoral study in Biology will have financial support for five full years of study, assuming the student remains in good academic standing and progresses on schedule in his/her doctoral research. The support includes tuition, $25,000/year living allowance, and low-cost health benefits. First-year graduate students do not teach undergraduate class sections, but there is a small service component related to lab rotations and professional development. The living allowance in years 2-5 may include salary for teaching at one of the senior CUNY colleges.” via Gmail
Postdoctoral Fellowship position: Comparative transcriptomics and proteomics of successful and unsuccessful aquatic invasive species We are offering an exciting opportunity for a Post-doctoral Fellow (PDF) interested in applications of advanced molecular biology to the study of aquatic invasive species (AIS). The position is part of the Canadian Aquatic Invasive Species Network (CAISN), composed of 30 faculty nationwide from 12 partner universities and six federal laboratories; funding will cover a competitive salary for one year, renewable for a second year. Techniques to be used will include massively parallel (NextGen) sequencing of cDNA coupled with micro-fluidics, quantitative real-time PCR to quantify genome-level gene transcription in invasive populations. The goal is to identify genes that are correlated with the successful invasion and spread of AIS. The PDF will also explore the role and function of the identified genes using proteomic methods to quantify final protein concentrations in targeted species for quantitative comparisons between successful and unsuccessful AIS. This work will rely on recently acquired genomics and proteomics infrastructure and equipment in the Environmental Genomics Facility at the Great Lakes Institute for Environmental Research (GLIER), University of Windsor. Join us at the Great Lakes Institute for Environmental Research for an outstanding interdisciplinary PDF experience, where you will be mentored by our team of internationally renowned researchers and have unmatched hands-on access to cutting edge genomics and proteomics facilities. Applications should include a curriculum vitae and names and contact information of three references. All inquiries should be directed to Dr. Hugh MacIsaac, CAISN Director, firstname.lastname@example.org Hugh MacIsaac Professor and Director, NSERC Canadian Aquatic Invasive Species Network II Great Lakes Institute for Environmental Research University of Windsor, Windsor, ON, Canada N9B 3P4 ph. (519) 253-3000 ext. 3754 (office), 2734 (lab) ph. (519) 817-9689 (cell), fax (519) 971-3616 http://bit.ly/1ejvlEn http://www.caisn.ca Hugh MacIsaac via Gmail
Subject: Journal of Evolutionary Biology; Graduate student prize starts 2014 The European Society for Evolutionary Biology & the Journal of Evolutionary Biology editorial team have decided to instigate an annual prize for the best paper by a graduate student published in the journal in a calendar year. This is aimed at recognising outstanding graduate research, so the paper should primarily arise from a significant piece of work which was included in a Masters or PhD thesis. The prize will be conferred at the nearest ESEB Congress and announced in the journal and online. The award will include an invitation to attend the Congress (fees and travel included), and a cash prize of 250. We expect the corresponding or senior (first) author to be the graduate student primarily responsible for the research and paper writing, and the supervisor will be asked to confirm this for shortlisted papers. We expect papers to be submitted at the latest within five years of starting a PhD project. When papers are accepted we will ask if the paper is eligible to be considered for the award, and that all the authors agree to this. The prize will be selected by the Deciding Editors of the journal, and we expect the first award to be for a paper published in 2014. If you have any queries about this, please address them to the JEB team at email@example.com Mike Ritchie Centre for Biological Diversity, School of Biology, University of St Andrews, Fife. Scotland KY16 9TH UK Phone: 0 (44 outside UK) 1334 463495 Some websites: Lab: http://bit.ly/1b9rz1H Uni: http://bit.ly/19JB5SP Google: http://bit.ly/1b9rBq5 CBD: http://bit.ly/19JB4yd Michael Ritchie via Gmail
ALIFE 14: THE FOURTEENTH INTERNATIONAL CONFERENCE ON THE SYNTHESIS AND SIMULATION OF LIVING SYSTEMS July 31st - August 2nd, 2014 Javits Center, Manhattan, New York, NY, USA http://alife14.org Sponsored by the International Society for Artificial Life (ISAL) January 15, 2014 — Workshop/tutorial proposal deadline February 1, 2014 — Science visualization competition deadline March 31, 2014 — Paper/abstract submission deadline We cordially invite you to submit papers to ALIFE 14: The Fourteenth International Conference on the Synthesis and Simulation of Living Systems. Since its inception in 1987, ALIFE has been the leading biyearly international conference in the field of Artificial Life via Gmail
November 20, 2013
Good afternoon, I am sending an inquiry to the Evolution community to bring partners to our Consortium. My colleagues and I are in the midst of building a partnership between multiple professional organizations and institutions to support Quantitative Undergraduate Biology Education and Synthesis (QUBES). Currently, our partners include NIMBioS, ABLE, BIO-SIGMAA, SMB, KSMB, BioQUEST, NARST, SUMS4Bio, and other invested individuals. QUBES was gathered to support and give stakeholder feedback on the creation of QUBES Hub, and online social-networking and repository focused on quantitative biology education. This Hub would link together the massive amounts of excellent quantitative biology education material in one place, with the benefit of user ratings and tags to sort through information. I am happy to communicate more specific information upon request. Please e-mail me: ceaton “at” unity.edu if you represent an organization that would be interested in joining the partnership. At this time we do not have a list serve for potential users, but be on the lookout for an email to that effect within a few months. Cheers, Carrie Carrie Diaz Eaton Program Chair BIO-SIGMAA Associate Professor of Mathematics Center for Biodiversity, Unity College http://bit.ly/1djqOol Carrie Eaton via Gmail
The Bushley lab in the Department of Plant Biology at The University of Minnesota-Twin Cities will have an opening for a graduate student starting in Fall 2014. Major projects in the lab focus on how fungal secondary metabolites shapes the interaction of fungi with plants and other organisms. Using a combination of next generation sequencing, natural products chemistry, molecular genetics, and metabolomics, we examine the evolution, diversity, and functions of fungal secondary metabolites, particularly nonribosomal peptide synthetases (NRPSs) and polyketide synthetases (PKSs). Current research is focused on population genomic analyses and fine-scale evolution of NRPS secondary metabolites among strains of the beetle pathogen Tolypocladium inflatum. Future research projects include 1) a comparative genomic and transcriptomic approach to identify genes, secondary metabolites, and regulatory networks that allow fungi in the genera Fusarium and Beauveria to interact with distinct hosts (insects, plants, and other fungi), and 3) examining the roles of root and leaf endophytic fungi in mediating resistance to nematodes and other insect pests. The Bushley lab is a diverse, interdisciplinary, and stimulating research environment that values diverse ethnic, cultural, and gender backgrounds. The University of Minnesota-College is home to a vibrant academic community with strong expertise in mycology, genetics, host-microbe interactions, and natural products chemistry. The university recently hired 4 new faculty in mycology, adding additional expertise to an already strong program. Students will have the opportunity to interact with other mycology labs [Kennedy,May,Figuroa,Bates,Shilling, and Kistler] as well as strong programs in plant and microbial biology at the University of Minnesota. Students can apply through either The Department of Plant Biology or The Department of Ecology, Evolution, and Behavior which both offer competitive stipends, tuition waivers, and health benefits for full-time graduate students. Applications should be submitted by December 2, 2013 for Fall 2014 entry. http://bit.ly/1eVY2tu http://bit.ly/1fEPEjh Prospective students are expected to have a passion for fungi and interests in evolutionary biology, comparative genomics, and/or natural products chemistry. Research experience/interest in molecular biology, next-generation sequencing, and computational biology are a plus. Please see the lab website for more information: http://bit.ly/1e1IgKp Contact Dr. Kathryn Bushley (firstname.lastname@example.org). Please send a CV, a brief outline of your research interests and goals, and contact information for references. Kathryn E. Bushley Postdoctoral Researcher 2082 Cordley Hall Department of Botany and Plant Pathology Oregon State University Corvallis, OR 97331 office: (541) 737-5284 cell: (541) 908-0116 “Kathryn E. Bushley” via Gmail
Analyses of mitochondrial amino acid sequence datasets support the proposal that specimens of Hypodontus macropi from three species of macropodid hosts represent distinct species
Background: Hypodontus macropi is a common intestinal nematode of a range of kangaroos and wallabies (macropodid marsupials). Based on previous multilocus enzyme electrophoresis (MEE) and nuclear ribosomal DNA sequence data sets, H. macropi has been proposed to be complex of species. To test this proposal using independent molecular data, we sequenced the whole mitochondrial (mt) genomes of individuals of H. macropi from three different species of hosts (Macropus robustus robustus, Thylogale billardierii and Macropus [Wallabia] bicolor) as well as that of Macropicola ocydromi (a related nematode), and undertook a comparative analysis of the amino acid sequence datasets derived from these genomes. Results: The mt genomes sequenced by next-generation (454) technology from H. macropi from the three host species varied from 13,634 bp to 13,699 bp in size. Pairwise comparisons of the amino acid sequences predicted from these three mt genomes revealed differences of 5.8% to 18%. Phylogenetic analysis of the amino acid sequence data sets using Bayesian Inference (BI) showed that H. macropi from the three different host species formed distinct, well-supported clades. In addition, sliding window analysis of the mt genomes defined variable regions for future population genetic studies of H. macropi in different macropodid hosts and geographical regions around Australia. Conclusions: The present analyses of inferred mt protein sequence datasets clearly supported the hypothesis that H. macropi from M. robustus robustus, M. bicolor and T. billardierii represent distinct species.
Background: The increasing number of assembled mammalian genomes makes it possible to compare genome organisation across mammalian lineages and reconstruct chromosomes of the ancestral marsupial and therian (marsupial and eutherian) mammals. However, the reconstruction of ancestral genomes requires genome assemblies to be anchored to chromosomes. The recently sequenced tammar wallaby (Macropus eugenii) genome was assembled into over 300,000 contigs. We previously devised an efficient strategy for mapping large evolutionarily conserved blocks in non-model mammals, and applied this to determine the arrangement of conserved blocks on all wallaby chromosomes, thereby permitting comparative maps to be constructed and resolve the long debated issue between a 2n = 14 and 2n = 22 ancestral marsupial karyotype. Results: We identified large blocks of genes conserved between human and opossum, and mapped genes corresponding to the ends of these blocks by fluorescence in situ hybridization (FISH). A total of 242 genes was assigned to wallaby chromosomes in the present study, bringing the total number of genes mapped to 554 and making it the most densely cytogenetically mapped marsupial genome. We used these gene assignments to construct comparative maps between wallaby and opossum, which uncovered many intrachromosomal rearrangements, particularly for genes found on wallaby chromosomes X and 3. Expanding comparisons to include chicken and human permitted the putative ancestral marsupial (2n = 14) and therian mammal (2n = 19) karyotypes to be reconstructed. Conclusions: Our physical mapping data for the tammar wallaby has uncovered the events shaping marsupial genomes and enabled us to predict the ancestral marsupial karyotype, supporting a 2n = 14 ancestor. Futhermore, our predicted therian ancestral karyotype has helped to understand the evolution of the ancestral eutherian genome.
Superiority of a mechanistic codon substitution model even for protein sequences in Phylogenetic analysis
Background: Nucleotide and amino acid substitution tendencies are characteristic of each species, organelle, and protein family. Hence, various empirical amino acid substitution rate matrices have needed to be estimated for phylogenetic analysis: JTT, WAG, and LG for nuclear proteins, mtREV for mitochondrial proteins, cpREV10 and cpREV64 for chloroplast-encoded proteins, and FLU for influenza proteins. On the other hand, in a mechanistic codon substitution model, in which each codon substitution rate is proportional to the product of a codon mutation rate and the ratio of fixation depending on the type of amino acid replacement, mutation rates and the strength of selective constraint on amino acids can be tailored to each protein family with additional 11 parameters. As a result, in the evolutionary analysis of codon sequences it outperforms codon substitution models equivalent to empirical amino acid substitution matrices. Is it superior even for amino acid sequences, among which synonymous substitutions cannot be identified? Results: Nucleotide mutations are assumed to occur independently of codon positions but multiple nucleotide changes in infinitesimal time are allowed. Selective constraints on the respective types of amino acid replacements are tailored to each gene with a linear function of a given estimate of selective constraints, which were estimated by maximizing the likelihood of an empirical amino acid or codon substitution frequency matrix, each of JTT, WAG, LG, and KHG. It is shown that the mechanistic codon substitution model with the assumption of equal codon usage yields better values of Akaike and Bayesian information criteria for all three phylogenetic trees of mitochondrial, chloroplast, and influenza-A hemagglutinin proteins than the empirical amino acid substitution models with mtREV, cpREV64, and FLU, which were designed specifically for those protein families, respectively. The variation of selective constraint across sites fits the datasets significantly better than variable codon mutation rates, confirming that substitution rate variations across sites detected by amino acid substitution models are caused primarily by the variation of selective constraint against amino acid substitutions rather than the variation of codon mutation rate. Conclusions: The mechanistic codon substitution model is superior to amino acid substitution models even in the evolutionary analysis of protein sequences.
There is a fairly scathing editorial in Nature [The new zoo. (2013). Nature, 503(7476), 311–312. doi:10.1038/503311b ] that reacts to a recent paper by Dubois et al.:
Dubois, A., Crochet, P.-A., Dickinson, E. C., Nemésio, A., Aescht, E., Bauer, A. M., Blagoderov, V., et al. (2013). Nomenclatural and taxonomic problems related to the electronic publication of new nomina and nomenclatural acts in zoology, with brief comments on optical discs and on the situation in botany. Zootaxa, 3735(1), 1. doi:10.11646/zootaxa.3735.1.1
To quote the editorial:
...there might be more than a disinterested concern for scientific integrity at work here. A typical reader of the Zootaxa paper (not that there are typical readers of a 94-page work on the minutiae of nomenclature protocol) might reasonably conclude that the authors have axes to grind. Exhibits A–E: the high degree of autocitation in the Zootaxa paper; the admission that some of the authors were against the ICZN amendments; that they clearly feel that their opinions regarding the amendments have been disregarded; the ad hominem attacks on ‘wealthy’ publishers as opposed to straitened natural-history societies; and the use of emotive and occasionally intemperate language that one does not associate with the usually dry and legalistic tone of debate on this subject. (The online publisher BioMed Central, based in London, gets a particular pasting, to which it has responded; see http://blogs.biomedcentral.com/bmcblog/2013/11/15/the-devil-may-be-in-the-detail-but-the-longview-is-also-worth-a-look/.)
One of many recommendations made in the diatribe is that journals should routinely have on their review boards those expert in the business of nomenclature — in other words, a cadre of people who are, unlike ordinary mortals, qualified to interpret the mystic strictures of the code. A typical reader is again entitled to ask whom, apart from themselves, the authors think might be suitable candidates.
Ouch! But Dubois et al.'s paper pretty much deserves this reaction - it's a reactionary rant that is breathtaking in it's lack of perspective. From the abstract:
As shown by several examples discussed here, an electronic document can be modified while keeping the same DOI and publication date, which is not compatible with the requirements of zoological nomenclature. Therefore, another system of registration of electronic documents as permanent and inalterable will have to be devised.
So, we have an identifier system for publications which currently has 63,793,212 registered DOIs (see CrossRef), includes key journals such as Zootaxa and ZooKeys, and which has tools to support versioning of papers (see CrossMark) but hey, let's have our own unique system. After all, zoological nomenclature is special, and our community has such a good track record of maintaining our own identifier system (LSIDs anyone?).
Now that the financial crisis faced by the ICZN has been averted by a three-year bail-out by the National University of Singapore (for three years at least), maybe the guardians of scientific names can focus on providing tools and services of value to the broader scientific community (or, indeed, taxonomists). As it stands, the ICZN can say little about the majority of animal names. Much better to focus on that than trying to rail against the practices of modern publishing.
—_000_1DD85342C7274CA1962F215BD0B99EE2ugaedu_ Content-Type: text/plain; charset=”Windows-1252” Content-Transfer-Encoding: quoted-printable Post-Doctoral Position Available in Computational Genomics - University of Georgia, Athens, USA A 3-year postdoctoral position is available immediately to conduct bioinformatic analyses within the context of a collaborative NSF-funded project to sequence the genome of Aegilops tauschii, the D-genome donor to bread wheat. The successful candidate will participate in the annotation of the Ae. tauschii genome and develop new algorithms and approaches to investigate the structural and functional evolution of the Ae. tauschii genome. The position is based in the labs of Dr. Katrien M. Devos, Institute of Plant Breeding, Genetics and Genomics, and Dept. of Plant Biology, and Dr. Jeffrey L. Bennetzen, Dept. of Genetics at the University of Georgia, Athens. The post-doc with be part of and closely collaborate with a team of geneticists and bioinformaticians located across different institutions nationally and internationally. Requirements: A PhD in bioinformatics, computer science, genetics or other relevant topic; a strong background in statistics; proficient in one or more scripting languages; experience with the analysis of large biological data sets. Individuals interested in the position should send (1) a cover letter summarizing their research interests and expertise relevant to the project (2) a Curriculum Vitae, and (3) the names and contact information for at least three people who can provide recommendations. The application should be sent as a single pdf file to Katrien M. Devos (email@example.com). Salary will be commensurate with appropriate experience and the position includes health and retirement benefits. Review of applications will start on November 1st and will continue until a suitable applicant has been found. The University of Georgia is an equal opportunity, affirmative action employer. —_000_1DD85342C7274CA1962F215BD0B99EE2ugaedu_ Content-Type: text/html; charset=”Windows-1252” Content-ID: Content-Transfer-Encoding: quoted-printable
Post-Doctoral Position Available in Computational Genomics - University of Georgia, Athens, USAA 3-year postdoctoral position is available immediately to conduct bioinformatic analyses within the context of a collaborative NSF-funded project to sequence the genome of Aegilops tauschii, the D-genome donor to bread wheat. The successful candidate will participate in the annotation of the Ae. tauschii genome and develop new algorithms and approaches to investigate the structural and functional evolution of the Ae. tauschii genome. The position is based in the labs of Dr. Katrien M. Devos, Institute of Plant Breeding, Genetics and Genomics, and Dept. of Plant Biology, and Dr. Jeffrey L. Bennetzen, Dept. of Genetics at the University of Georgia, Athens. The post-doc with be part of and closely collaborate with a team of geneticists and bioinformaticians located across different institutions nationally and internationally.Requirements: A PhD in bioinformatics, computer science, genetics or other relevant topic; a strong background in statistics; proficient in one or more scripting languages; experience with the analysis of large biological data sets.Individuals interested in the position should send (1) a cover letter summarizing their research interests and expertise relevant to the project (2) a Curriculum Vitae, and (3) the names and contact information for at least three people who can provide recommendations. The application should be sent as a single pdf file to Katrien M. Devos (firstname.lastname@example.org). Salary will be commensurate with appropriate experience and the position includes health and retirement benefits. Review of applications will start on November 1st and will continue until a suitable applicant has been found. The University of Georgia is an equal opportunity, affirmative action employer.
UW-Madison MS and PhD positions on molecular adaptation of invasive insects Position Description: MS and/or PhD research assistantships are available to assess how invasive insects adapt to novel environments. Insect pests can be viewed as model systems in which to explore fundamental concepts in ecology and evolutionary biology. They are especially promising candidates to study mechanisms of rapid evolution at the genetic level, as many insect pests have shown a remarkable ability to cope with pesticides, novel climatic space, and novel host plants. While there are significant challenges in determining adaptation at the genetic level and in finding ways to forecast future changes, there are strong incentives (ecological, economic and social) to do this research. Students will combine population genomics approaches with field ecology and manipulative experiments to understand the evolutionary mechanisms of adaptation. Training will focus on the use of landscape genomics approaches to relate spatial and temporal variation in the environment to adaptive and neutral genetic variation. Information on University, Department, Lab, and City: The University of Wisconsin-Madison is one of the major research universities in the United States. This project will be supported in the Department of Entomology and under the supervision of Dr. Sean Schoville. Madison consistently ranks as one of the best places in the United States to live, work, and study. It is Wisconsin’s capital city, with a vibrant population of approximately 230,000 that combines small town charm with a variety of leisure and cultural opportunities. Stipend/Salary: Current annual stipend levels are $20,808 per year before taxes, plus tuition remission and health care benefits. Financial support is available for two years. The start date for the project is September 2014. Qualifications: A BS or BA degree in entomology, biology or a related discipline is required. We are looking for motivated students interested in pursuing a MS or PhD degree at UW-Madison. Students with an MS degree will be given preference in admissions to the PhD program. The preferred candidate will have prior research experience and have some knowledge of population genetics. Candidates should have interests in entomology, evolutionary ecology, and working in both the field and laboratory. Excellent writing and verbal communication skills are expected, as well as the ability to work collaboratively. Application Process: Applications will be reviewed upon receipt and review will continue until candidates are chosen. The application deadline is Jan 2, 2014. The University of Wisconsin-Madison is an equal opportunity/affirmative action employer. We promote excellence through diversity and encourage all qualified individuals to apply. Interested applicants are asked to e-mail the following documents listed below to our Student Services Coordinator Sara Rodock (email@example.com) (in ONE PDF file please). Please specify in your letter when you would be available to start. Required Documents: -The “Entomology; University of Wisconsin-Madison Graduate Application Cover Sheet” which can be found at: http://bit.ly/1dgGDvU - A well-crafted cover letter outlining research interests, academic and professional backgrounds - Resume/CV - Copies of transcripts (unofficial copies acceptable at this point) - GRE scores if available - Names and contact addresses of three references Thanks! Sara Sara (Lorence) Rodock Student Services Coordinator Plant Pathology, Entomology and Forest & Wildlife Ecology University of Wisconsin-Madison 276 Russell Labs, 1630 Linden Dr Madison WI 53706 P: 608-262-9926 F: 608-262-9922 firstname.lastname@example.org Sara Rodock via Gmail
Research Associate / Senior Research Associate: Bioinformatics and Comparative Genomics : London, United Kingdom * * * * UCL Division of Biosciences ResearchResearch Associate/Senior Research Associate: Bioinformatics and Comparative Genomics This appointment is full time on UCL Grade 7/8. The salary range will be £32,375 – £39,132 Grade 7 & £40,216 – £47,441 Grade 8, inclusive of London Allowance. The Telford Lab is seeking an experienced bioinformatician to lead the computational aspects of an interdisciplinary project funded by an ERC advanced grant. The Research Associate or Senior Research Associate (depending on experience) will use next-gen sequencing data to perform de novo assembly and annotation of genomes and transcriptomes of several members of a phylum of marine worms with an unexpected evolutionary history. They will develop methods to make sense of the genome resources from this newly identified phylum of deuterostome. Supported by the experimental teammates, the Research Associate/Senior Research Associate will integrate the genomes/transcriptomes with new and existing data on morphology, ultrastructure and developmental genetics in these and related species. The successful candidate will work in close collaboration with the PI and 3 experimentalists, and will be involved in the supervision of a newly hired computational biology PhD student. To be appointed at the higher grade the successful candidate will hold an independent research reputation, with evidence of national recognition of achievement within the appropriate subject area. Funding is available until 31st May 2018 in the first instance. To be appointed, the successful applicant must have a PhD (or about to be awarded) in Bioinformatics/Computer Science or related subject and a proven track record of high quality research in bioinformatics/molecular evolution/biology/comparative genomics. For further details about the vacancy and how to apply online please go to http://bit.ly/17KP4gE and search on Reference Number 1377153. Informal enquiries on the post can be directed to Professor Max Telford (email@example.com). For informal enquiries regarding the application process, please contact Christine Davis (firstname.lastname@example.org). Closing Date: 14th December 2013. Latest time for the submission of applications: 4pm. We particularly welcome female applicants and those from an ethnic minority, as they are under-represented within University College London at this level. UCL Taking Action for Equality Max Telford Professor of Zoology Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK. Tel: +44 (0)20 7679 2554 (Internal: 32554) Fax: +44 (0)20 7679 7096 http://bit.ly/17LNPIR a new open access journal EvoDevo: http://bit.ly/187penq Telford & Littlewood: Animal Evolution. OUP Software to align Nucleotide sequence according to Amino Acid translation TranslatorX Files and software for downloading: Mrimpatient: If you cant wait to see latest result of MrBayes analysis. Xstem and Ystem: Software for 2y structure data in rRNA phylogenetic analyses. MtZoa and MtHydro : new amino acid substitution matrices Hacked version of MrBayes using these matrices Xenoturbella You Tube video The Linnean Society of London “Telford, Max” via Gmail»»>
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