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February 20, 2014
Hi All, We are looking for a cell biologist in the Biology Department at the University of Hawaii at Hilo. We are especially interested in someone who can work with others in the department that have expertise in ecology and evolutionary biology and help build a growing bioinformatics/genomics program. http://bit.ly/1fiYiC1 Title: Assistant Professor (Biology/Cell Biology) Position Number: 0082909 Hiring Unit: College of Arts & Sciences Location: UH Hilo Date Posted: January 15, 2014 Closing Date: March 15, 2014 Salary Information: Commensurate with qualifications and experience. Monthly Type: 9 Month Tenure Track: Tenure Full Time/Part Time: Full Time Temporary/Permanent: Permanent Funding: General Other Conditions: - Appointment to begin approximately August 2014, pending position clearance and availability of funding. Duties and Responsibilities 1. Teach undergraduate courses in Cell Biology, Cell and Molecular Biology, and Introductory Biology for majors. Develop an independent research program in area of expertise that is supported by extramural funding; advise students; participate in departmental governance and related University and community service. The University of Hawai`i at Hilo also offers the opportunity for participation in graduate programs. Minimum Qualifications 1. Ph.D. from an accredited college or university in a biological science discipline appropriate to the position, teaching experience in biological sciences, research experience in area of expertise in cell biology, and demonstrated ability to work with students from diverse cultural backgrounds. Desirable Qualifications 1. Demonstrated teaching experience at the college or university level in undergraduate courses in areas related to Cell Biology, Biochemistry, Molecular Biology, and Introductory Biology. Demonstrated record of student advising and training; a successfully funded research program in area of expertise in animal cell biology, and the ability to develop a research program in the Hawaiian or Pacific region that complements existing department strengths in plant ecology and evolution, with the potential to obtain extramural funding. To Apply: Submit a cover letter indicating the position title and position number and how you satisfy the minimum and desirable qualifications, a curriculum vitae, academic transcripts, and statements of research and teaching interests. Please note that copies of transcripts are acceptable for application; however, original documents issued by a university registrar are required upon hire. Provide contact information for three (3) references. Electronic submissions are preferred and may be sent to email@example.com. Address: 1. Dr. Jonathan Awaya 2. University of Hawai`i at Hilo 3. Biology Department 4. 200 W. Kawili St. 5. Hilo, HI 96720 Inquiries: 1. Dr. Jonathan Awaya; firstname.lastname@example.org Dr. Donald Price Director TCBES Graduate Program Professor of Biology Science and Technology Building 109 University of Hawaii at Hilo Hilo, HI 96720 808-932-7178 email@example.com http://bit.ly/1d348Do http://bit.ly/1fiYjWF http://bit.ly/1d347zd Donald Price via Gmail
STATISTICAL GENETICS AND BIOINFORMATICS Open position at Institut Pasteur (Paris, France) In the framework of the LabEx consortium Milieu Intrieur (MI), *a position in statistical genetics and bioinformatics is open from March 2014* at the Institut Pasteur in Paris. The goal of the MI consortium is to define the naturally-occurring variation of the human immune responses to an unprecedented scale. Thousands of aspects of the variation of the immune response (i.e., gene expression, protein variation, cellular phenotypes, etc.) to pathogens and immune stimuli are being defined in a large cohort of 1000 healthy individuals. The integration of these datasets with the degree of genome-wide variation of the human genome, variation in microbiota, and a number of demographic variables will allow us to evaluate the respective impact of genetic, environmental and sociocultural factors on the inter-individual variability of the immune response, which in turn can account for differences in susceptibility to infectious disease, and response to therapeutic treatment and vaccines. The candidate will be responsible for data analyses in the context of this project and will work in a multidisciplinary team that integrates human genetics, population genetics, immunology, evolutionary biology and systems biology. This ambitious project needs cutting-edge and innovative methods for the statistical analyses of the data. We look for a candidate with strong experience in large-scale data analyses (data mining), and advanced tools in statistical inference (e.g., linear and generalised linear models, Bayesian statistics, MCMC algorithms, etc.). We expect the candidate to have a strong interest in the development of new statistical approaches. Knowledge of genomics and biology is not necessary but will be appreciated. *Requirements:*The applicant should have a PhD, or equivalent degree, in Biostatistics, Bioinformatics or Statistical Genetics, or several years of experience in these fields. Team spirit and dynamism are essential. Salary will depend on previous experience. *Contact*: To apply, send your CV and a letter describing your research interests and skills (in a single pdf file) to Dr Lluis Quintana-Murci, Unit of Human Evolutionary Genetics, Institut Pasteur, by e-mail: firstname.lastname@example.org Lluis Quintana-Murci via Gmail
February 19, 2014
A Postdoctoral Researcher position is being offered in the Department of Ecology and Evolutionary Biology at the University of Connecticut. The applicant will be a member of a research group interested in genome biology, integrative genomics, scientific databasing, and bioinformatics. RESPONSIBILITIES: - Perform scientific research as part of a collaborative project focused on the sequencing, assembly, annotation, and analysis of three conifer genomes. - Apply computational approaches to analyze RNA-Seq expression data - Develop and apply comparative genomics methods - Collaborate with biologists to characterize and study novel gene families - Develop and support tools to enable the extraction of information from large, complex genomes - Provide bioinformatics training to other team members REQUIREMENTS: To be eligible, applicants must have received a Ph.D. in computational biology, bioinformatics, computer science, genetics, or a related discipline involving significant computational experience. The ideal candidate will have: - Training in statistics and genetics - Fluency in Unix computing environments (shell scripting) - Programming experience (Perl/Python/Java) - Experience with next generation sequence analysis (RNA-Seq) - Familiarity with version control systems PREFERENCES: Highly motivated individuals with a strong background in genetics and computational biology, and a record of scientific productivity are encouraged to apply. HOW TO APPLY: Interested applicants should submit a letter of interest, statement of research interest and experience, curriculum vita, and contact information of three professional references. Please send all materials to Jill Wegrzyn (email@example.com) firstname.lastname@example.org via Gmail
*Identifying the determinants of genetic evolvability* Keywords: rates of evolution, gene duplication, evolvability, transcriptomics A three-years PhD position funded by the Royal Society is available at the University of Sheffield, in the department of Animal and Plant Sciences. The candidate will work under the supervision of Pascal-Antoine Christin (http://bit.ly/1jTJ7hA), and will investigate the rates of molecular evolution in plants. During the course of evolution, novel adaptive traits emerge through alterations in the expression patterns and/or catalytic properties of enzymes, which arise through random mutations in the regulatory regions and/or coding regions. The ability of genes to quickly change the properties of the encoded enzymes are likely to affect the evolutionary potential of species adapting to changing conditions. Rates of molecular evolution vary both among species and among genes of a given species. What are the factors explaining this variation? Does faster molecular evolution facilitates the evolution of novel adaptations? These questions will be addressed using comparative analyses applied to transcriptome data generated in this project through high-throughput RNA sequencing. The research will involve a combination of lab work and computer analyses, potentially including the development of new analytical methods. The student will integrate into a thriving department and will receive training in plant evolution, RNA sequencing, and methods to study molecular evolution. Applications are invited from candidates with interests in molecular evolution and the use of large genetic datasets to address important questions in evolutionary biology. The review of applications will start on the 3rd of March 2014 and will continue until the position is filled. The project is opened to UK/EU students. Informal inquiries can be addressed to Pascal-Antoine Christin: email@example.com Formal applications should be made using our online application form: http://bit.ly/1bsr64U via Gmail
Background: Spider silks are spectacular examples of phenotypic diversity arising from adaptive molecular evolution. An individual spider can produce an array of specialized silks, with the majority of constituent silk proteins encoded by members of the spidroin gene family. Spidroins are dominated by tandem repeats flanked by short, non-repetitive N- and C-terminal coding regions. The remarkable mechanical properties of spider silks have been largely attributed to the repeat sequences. However, the molecular evolutionary processes acting on spidroin terminal and repetitive regions remain unclear due to a paucity of complete gene sequences and sampling of genetic variation among individuals. To better understand spider silk evolution, we characterize a complete aciniform spidroin gene from an Argiope orb-weaving spider and survey aciniform gene fragments from congeneric individuals. Results: We present the complete aciniform spidroin (AcSp1) gene from the silver garden spider Argiope argentata (Aar_AcSp1), and document multiple AcSp1 loci in individual genomes of A. argentata and the congeneric A. trifasciata and A. aurantia. We find that Aar_AcSp1 repeats have >98% pairwise nucleotide identity. By comparing AcSp1 repeat amino acid sequences between Argiope species and with other genera, we identify regions of conservation over vast amounts of evolutionary time. Through a PCR survey of individual A. argentata, A. trifasciata, and A. aurantia genomes, we ascertain that AcSp1 repeats show limited variation between species whereas terminal regions are more divergent. We also find that average dN/dS across codons in the N-terminal, repetitive, and C-terminal encoding regions indicate purifying selection that is strongest in the N-terminal region. Conclusions: Using the complete A. argentata AcSp1 gene and spidroin genetic variation between individuals, this study clarifies some of the molecular evolutionary processes underlying the spectacular mechanical attributes of aciniform silk. It is likely that intragenic concerted evolution and functional constraints on A. argentata AcSp1 repeats result in extreme repeat homogeneity. The maintenance of multiple AcSp1 encoding loci in Argiope genomes supports the hypothesis that Argiope spiders require rapid and efficient protein production to support their prolific use of aciniform silk for prey-wrapping and web-decorating. In addition, multiple gene copies may represent the early stages of spidroin diversification.
Source: BMC Evolutionary Biology
There is a great post by Jeni Tennison on the Open Data Institute blog entitled Five Stages of Data Grief. It resonates so much with my experience working with biodiversity data (such as building BioNames, or exploring data errors in GBIF) that I've decide to reproduce it here.
Five Stages of Data Grief
As organisations come to recognise how important and useful data could be, they start to think about using the data that they have been collecting in new ways. Often data has been collected over many years as a matter of routine, to drive specific processes or sometimes just for the sake of it. Suddenly that data is repurposed. It is probed, analysed and visualised in ways that haven’t been tried before.
Data analysts have a maxim:
If you don’t think you have a quality problem with your data, you haven’t looked at it yet.
Every dataset has its quirks, whether it’s data that has been wrongly entered in the first place, automated processing that has introduced errors, irregularities that come from combining datasets into a consistent structure or simply missing information. Anyone who works with data knows that far more time is needed to clean data into something that can be analysed, and to understand what to leave out, than in actually performing the analysis itself. They also know that analysis and visualisation of data will often reveal bugs that you simply can’t see by staring at a spreadsheet.
But for the people who have collected and maintained such data — or more frequently their managers, who don’t work with the data directly — this realisation can be a bit of a shock. In our last ODI Board meeting, Sir Tim Berners-Lee suggested that the data curators need to go through was something like the five stages of grief described by the Kübler-Ross model.
So here is an outline of what that looks like.Denial
This can’t be right: there’s nothing wrong with our data! Your analysis/code/visualisation must be doing something wrong.
At this stage data custodians can’t believe what they are seeing. Maybe they have been using the data themselves but never run into issues with it because they were only using it in limiting ways. Maybe they had only ever been collecting the data, and not actually using it at all. Or maybe they had been viewing it in a form where the issues with data quality were never surfaced (it’s hard to spot additional spaces, or even zeros, when you just look at a spreadsheet in Excel, for example).
So the first reason that they reach for is that there must be something wrong with the analysis or code that seems to reveal issues with the data. There may follow a wild goose chase that tries to track down the non-existent bug. Take heart: this exercise is useful in that it can pinpoint the precise records that are causing the problems in the first place, which forces the curators to stop denying them.Anger
Who is responsible for these errors? Why haven’t they been spotted before?
As the fact that there are errors in the data comes to be understood, the focus can come to rest on the people who collect and maintain the data. This is the phase that the maintainers of data dread (and can be a reason for resisting sharing the data in the first place), because they get blamed for the poor quality.
This painful phase should eventually result in an evaluation of where errors occur — an evaluation that is incredibly useful, and should be documented and kept for the Acceptance phase of the process — and what might be done to prevent them in future. Sometimes that might result in better systems for data collection but more often than not it will be recognised that some of the errors are legacy issues or simply unavoidable without massively increasing the maintenance burden.Bargaining
What about if we ignore these bits here? Can you tweak the visualisation to hide that?
And so the focus switches again to the analysis and visualisations that reveal the problems in the data, this time with an acceptance that the errors are real, but a desire to hide the problems so that they’re less noticeable.
This phase puts the burden on the analysts who are trying to create views over the data. They may be asked to add some special cases, or tweak a few calculations. Areas of functionality may be dropped in their entirety or radically changed as a compromise is reached between utility of the analysis and low quality data to feed it.Depression
This whole dataset is worthless. There’s no point even trying to capture this data any more.
As the number of exceptions and compromises grows, and a realisation sinks in that those compromises undermine the utility of the analysis or visualisation as a whole, a kind of despair sets in. The barriers to fixing the data or collecting it more effectively may seem insurmountable, and the data curators may feel like giving up trying.
This phase can lead to a re-examination of the reasons for collecting and maintaining the data in the first place. Hopefully, this process can aid everyone in reasserting why the data is useful, regardless of some aspects that are lower quality than others.Acceptance
We know there are some problems with the data. We’ll document them for anyone who wants to use it, and describe the limitations of the analysis.
In the final stage, all those involved recognise that there are some data quality problems, but that these do not render the data worthless. They will understand the limits of analyses and interpretations that they make based on the data, and they try to document them to avoid other people being misled.
The benefits of the previous stages are also recognised. Denial led to double-checking the calculations behind the analyses, making them more reliable. Anger led to re-examination of how the data was collected and maintained, and documentation that helps everyone understand the limits of the data better. Bargaining forced analyses and visualisations to be focused and explicit about what they do and don’t show. Depression helped everyone focus on the user needs from the data. Each stage makes for a better end product.
Of course doing data analysis isn’t actually like being diagnosed with a chronic illness or losing a loved one. There are things that you can do to remedy the situation. So I think we need to add a sixth stage to the five stages of data grief described above:Hope
This could help us spot errors in the data and fix them!
Providing visualisations and analysis provides people with a clearer view about what data has been captured and can make it easier to spot mistakes, such as outliers caused by using the wrong units when entering a value, or new categories created by spelling mistakes. When data gets used to make decisions by the people who capture the data, they have a strong motivation to get the data right. As Francis Irving outlined in his recent Friday Lunchtime Lecture at ODI, Burn the Digital Paper, these feedback loops can radically change how people think about data, and use computers within their organisations.
Making data open for other people to look at provides lots more opportunities for people to spot errors. This can be terrifying — who wants people to know that they are running their organisation based on bad-quality data? — but those who have progressed through the five stages of data grief find hope in another developer maxim:
Given enough eyeballs, all bugs are shallow.
The more people look at your data, the more likely they are to find the problems within it. The secret is to build in feedback mechanisms which allow those errors to be corrected, so that you can benefit from those eyes and increase your data quality to what you thought it was in the first place.
—Apple-Mail=_9845EC27-DEDF-4B96-A0EF-0CEE55823506 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 POSTDOC POSITION IN PLANT EVOLUTIONARY BIOLOGY There is an opening for a postdoctoral position at the Instituto de Biologa, of the Universidad Nacional Autnoma de Mxico, Mexico City, in the lab of Dr. Susana Magalln The main research topic in our lab is plant macroevolution, investigated in a phylogenetic context. We seek candidates with bioinformatic abilities in phylogenetic, evolutionary and comparative biology; as well as knowledge of plant biology and/or the fossil record. The research project on which the successful candidate will work is part of an ongoing study on the timing and rate of evolution of flowering plants, with a special focus on the effect of differential use of fossil calibrations, and of alternative molecular clock methods. The successful candidate will play a key role in conducting molecular clock and comparative biology analyses; and contribute to teach these methods to graduate students. The postdoctoral position will start on September 1st, 2014, for a one-year period. There is the possibility to renew for a second year, on the basis of obtained results. The position is funded by the Postdoctoral Fellowship Program of the Coordination for Scientific Research, Universidad Nacional Autnoma de Mxico. It is granted on the basis of academic merits, CV and publication record, among a pool of candidates. Candidates should: 1. Have obtained his/her PhD degree by the date of hire (September 1st, 2014), and no earlier than 3 years previous to the date of hire. 2. Be 36 years old or younger by the date of hire. 3. Have experience publishing scientific papers. 4. Proficiency in Spanish is highly desirable. To apply, please submit: 1. An application letter including research interests and goals, and suitability for the proposed research topic. 2. A full CV. 3. PDFs of publications. 4. Names and contact information of two potential academic references. Inquiries and application materials should be submitted to: Dr. Susana Magalln: firstname.lastname@example.org Deadline: March 3rd, 2014 Dr. Susana Magalln Instituto de Biologa, Universidad Nacional Autnoma de Mxico email@example.com (52-55) 5622-9087 http://bit.ly/MbSPl7 —Apple-Mail=_9845EC27-DEDF-4B96-A0EF-0CEE55823506 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1POSTDOC POSITION IN PLANT EVOLUTIONARY BIOLOGYThere is an opening for a postdoctoral position at the Instituto de Biologa, of the Universidad Nacional Autnoma de Mxico, Mexico City, in the lab of Dr. Susana MagallnThe main research topic in our lab is plant macroevolution, investigated in a phylogenetic context. We seek candidates with bioinformatic abilities in phylogenetic, evolutionary and comparative biology; as well as knowledge of plant biology and/or the fossil record. The research project on which the successful candidate will work is part of an ongoing study on the timing and rate of evolution of flowering plants, with a special focus on the effect of differential use of fossil calibrations, and of alternative molecular clock methods. The successful candidate will play a key role in conducting molecular clock and comparative biology analyses; and contribute to teach these methods to graduate students.The postdoctoral position will start on September 1st, 2014, for a one-year period. There is the possibility to renew for a second year, on the basis of obtained results.The position is funded by the Postdoctoral Fellowship Program of the Coordination for Scientific Research, Universidad Nacional Autnoma de Mxico. It is granted on the basis of academic merits, CV and publication record, among a pool of candidates.Candidates should:1. Have obtained his/her PhD degree by the date of hire (September 1st, 2014), and no earlier than 3 years previous to the date of hire.2. Be 36 years old or younger by the date of hire.3. Have experience publishing scientific papers.4. Proficiency in Spanish is highly desirable.To apply, please submit:1. An application letter including research interests and goals, and suitability for the proposed research topic.2. A full CV.3. PDFs of publications.4. Names and contact information of two potential academic references.Inquiries and application materials should be submitted to:Dr. Susana Magalln: firstname.lastname@example.orgDeadline: March 3rd, 2014Dr. Susana MagallnInstituto de Biologa, Universidad Nacional Autnoma de Mxicos.email@example.com(52-55) 5622-9087http://bit.ly/MbSPl7
Laboratory Technician Position The Rockman Lab at New York University seeks a full-time research technician to participate in ongoing projects addressing the genetic basis of phenotypic variation. The position is available immediately. The responsibilities of the technician include isolation and purification of RNA and DNA from several species of nematode and annelid, construction of Illumina sequencing libraries (for RNA-seq, DNA-seq, & RAD-seq), and RNA labeling and hybridization for microarray experiments. The ideal candidate will have experience working with RNA, familiarity with standard equipment used for library construction (e.g., the bioanalyzer), demonstrated ability to troubleshoot molecular methods, and an interest in evolutionary genetics. The position represents an opportunity to engage with PhD students and postdoctoral researchers working on a range of questions in empirical evolutionary genetics. For information about the lab, see the website at http://bit.ly/MbSQ8F . New York University is located in Greenwich Village, convenient by train or subway from the entire New York metro area. NYU is an equal opportunity employer. Salary is commensurate with experience. Applicants should submit a cover letter and CV to Matt Rockman at firstname.lastname@example.org . Matthew Rockman Department of Biology and Center for Genomics & Systems Biology New York University 12 Waverly Place, 8th Floor New York, NY 10003 (212) 998 8490 email@example.com via Gmail
—001a11c2c1022bc75b04f2b3df62 Content-Type: text/plain; charset=ISO-8859-1 Lecturer in Ecology Brandeis University The Biology Department and the Environmental Studies Program of Brandeis University seek a Lecturer in Ecology and related topics, starting Fall 2014. This will be a two-year, part-time (0.6 FTE) appointment, with benefits and with the potential for renewal. The successful candidate will hold a Ph.D. degree in a branch of ecology. Teaching duties comprise three courses per year, including some combination of Ecology, Conservation Biology, Animal Behavior, Field Biology, or similar topics. These courses are primarily intended for Biology and Environmental Studies majors and minors. Brandeis University places emphasis on interdisciplinary programs and working closely with individual students. The Lecturer in Ecology will become an active participant in the advising of students, supervision of senior theses, and development of curriculum in the Environmental Studies Program. First consideration will be given to applications received by March 21, 2014. Applications, which should be submitted through AcademicJobsOnline at http://bit.ly/1dKIGr0, should include a letter outlining interests and evidence of effective undergraduate teaching, along with curriculum vitae, and the names of three referees. Evidence of teaching should include a list of courses and the institutions at which they were taught, and a syllabus from one of those courses. Brandeis University is an equal opportunity employer, committed to building a culturally diverse intellectual community, and strongly encourages applications from women and minority candidates. I HOPE THAT THIS IS THE CORRECT FORMAT! via Gmail
We are advertising an unestablished lectureship position in Ecology and Evolution. This appointment is to cover research leave funded by external (ERC) grants, but it is expected that the successful applicant will divide their time between research and teaching, as do all academic staff. This is not just a teaching appointment. The position is available for a fixed period of 36 months full time equivalent. It may be held either full time for a period of three years, or part time for a longer period (e.g. 5 years at 0.6 FTE). The advertisement has been placed in Nature to appear in w/b 24 February, and it is already available at Nature online (http://bit.ly/1ePHwFX). It is on the University web site (http://bit.ly/O7VKgy) and jobs.ac.uk (http://bit.ly/1ePHwG1) Further particulars are available at http://bit.ly/O7VKgE Please bring this opportunity to the attention of anyone who you think may be interested. We are particularly keen to attract applications from as many women as possible, as we have a historic imbalance in the number of women holding academic staff positions. Please contact me if you have any questions Chris Jiggins Reader in Evolution and Biological Diversity Department of Zoology University of Cambridge Tel: (+44)(0)1223 769021 Mob: (+44)(0) 7549-524-481 http://bit.ly/13gZCQc http://bit.ly/18EOGKU Fellow of St John’s College, Director of Studies in Biological Sciences Cambridge, UK. CB2 1TP firstname.lastname@example.org via Gmail
February 18, 2014
Job: REU summer research positions for Project Baseline The lab of Steve Franks at Fordham University is offering Research Experiences for Undergraduates (REU positions) through Project Baseline in summer 2014. Multiple positions are available. Project Baseline is an NSF-funded, nationwide effort to create a seed bank for studies of plant evolutionary responses to climate change. REU students will assist with seed and data collection efforts in the field, and will also conduct independent research related to the goals of the project and to plant evolutionary ecology. The positions are based at Fordham University in New York City, but field work and collections will take place throughout the eastern United States. For more on the Franks lab, see http://bit.ly/1nMr8eQ. For more on Project Baseline, see http://bit.ly/1bKxADx. Applicants must be currently enrolled and in good standing at an accredited college or university, have some undergraduate education in biology, ecology or a related field, or equivalent experience, and be willing to travel for extended periods of time, carry equipment, and work in the field under potentially adverse conditions. Desirable: 1) Research or field experience, 2) Interest in plant ecology, evolution, or global change, 3) Background in or willingness to learn plant identification, 4) Evidence of dedication, motivation, ability to work in a team, communication skills, and attention to detail, 5) a current valid driver’s license. Successful applicants will receive a stipend, and costs of transportation and housing/camping during field work will be provided. The positions will run from around late-May through mid-August, and exact start and end dates are flexible. Interested applicants should submit, as a single pdf: 1) a brief cover letter describing their qualifications and research interests; 2) a rsum or CV and 3) contact information of two references. Applications should be submitted by March 14, 2014 by email to the Project Baseline postdoc for the eastern region, Dr. Jennifer Weber ( email@example.com). Inquiries may be sent to this address or to Dr. Steve Franks (firstname.lastname@example.org). *Fordham University is an equal opportunity/affirmative action institution. Qualified applicants of all backgrounds and career goals are encouraged to apply.* Jennifer Weber http://bit.ly/1nMr8eU Postdoctoral Researcher http://bit.ly/1bKxADx Fordham University Bronx, NY email@example.com via Gmail
UZurich.FieldAssitant.Birds_behaviour_Spain Field assistant position to study mobbing behaviour in birds, in southern Spain (Crdoba & Guadix). For the upcoming field season (15th April - June 2014) I am are looking for a highly motivated field volunteer to join my field project investigating mobbing behaviour in birds. The study site is located in Guadix and Crdoba, south of Spain. We will work in average 6 days per week in the field depending on the workload of the experiments. The field work can be physically strenuous at times as temperatures in June can be above 35C. This project is part of a larger project ongoing since 2010 to understand the evolution of family living in birds. Thus, we closely collaborate with two other research teams, sharing both the study sites and the field station. Qualifications: (1) , BSc/MSc in Biology, Ecology or similar qualification; (2) Able to cope with “strenuous” conditions in the field (we work in a semi-arid area); (3) Ability to work in team and independently; (4) Motivated to learn about birds, and animal behaviour; (5) Knowledge in observing & handling birds is a plus; (6) Driving licence is a plus; (7) Fluent in English and/or Spanish or Portuguese; (8) Previous knowledge of experimental fieldwork is an advantage. We will cover for the accommodation and the food as well as travel costs up to 300 Euros. Applications - including a CV, a letter of motivation (1 page) and names of 2 referees - should be send to Filipe Cristovo: firstname.lastname@example.org. Applications received until 3rd March 2014 will be given full consideration. email@example.com via Gmail
Over the past two years I have published a number of posts in which I have used a data-display network as a multivariate data summary, comparable to an ordination (eg. PCA) or a cluster analysis (eg. UPGMA). This is a form of exploratory data analysis.
Here, I wish to point out that a multivariate data summary is not always necessary, even when the data are multivariate in form.
As an example, I will use the official census data on retail book sales in the USA. The monthly data are provided by the United States Census Bureau for the years 1992-2013 at:
The data include census code 4512, which covers "Book Stores, General", "Specialty Book Stores" and "College Book Stores". The data notes say: "Estimates are shown in millions of dollars, and are based on data from the Monthly Retail Trade Survey, Annual Retail Trade Survey, and administrative records." I downloaded the data on 17 February 2014.
These data are multivariate. For example, if each year is taken as a sample object, then there are data for 12 variables for each sample (one for each month). Any multivariate data analysis can therefore be applied to this dataset.
In the usual manner, I have used the manhattan distance and a neighbor-net network. Years that are closely connected in the network are similar to each other based on the 12 monthly sales figures, and those that are further apart are progressively more different from each other. All that the data show is a gradient clockwise from the top. That is, sales rose from 1992, reached a peak in 2007, and then declined again.
This same pattern could be displayed more simply by graphing the yearly averages, as shown in the next graph. A network is complete over-kill in this case. I presume that the recent decrease in retail book sales has something to do with the rise of e-book sales.
Finally, we could also plot the monthly sales, while we are at it. The peaks in late summer and at Christmas as very distinct. Presumably people are buying books to read in summer, and to give away at Christmas.
Background: The neuropeptide Kiss and its receptor KissR are key-actors in the brain control of reproduction in mammals, where they are responsible for the stimulation of the activity of GnRH neurones. Investigation in other vertebrates revealed up to 3 Kiss and 4 KissR paralogs, originating from the two rounds of whole genome duplication in early vertebrates. In contrast, the absence of Kiss and KissR has been suggested in birds, as no homologs of these genes could be found in current genomic databases. This study aims at addressing the question of the existence, from an evolutionary perspective, of the Kisspeptin system in birds. It provides the first large-scale investigation of the Kisspeptin system in the sauropsid lineage, including ophidian, chelonian, crocodilian, and avian lineages. Results: Sauropsid Kiss and KissR genes were predicted from multiple genome and transcriptome databases by TBLASTN. Phylogenetic and syntenic analyses were performed to classify predicted sauropsid Kiss and KissR genes and to re-construct the evolutionary scenarios of both gene families across the sauropsid radiation.Genome search, phylogenetic and synteny analyses, demonstrated the presence of two Kiss genes (Kiss1 and Kiss2 types) and of two KissR genes (KissR1 and KissR4 types) in the sauropsid lineage. These four genes, also present in the mammalian lineage, would have been inherited from their common amniote ancestor. In contrast, synteny analyses supported that the other Kiss and KissR paralogs are missing in sauropsids as in mammals, indicating their absence in the amniote lineage. Among sauropsids, in the avian lineage, we demonstrated the existence of a Kiss2-like gene in three bird genomes. The divergence of these avian Kiss2-like sequences from those of other vertebrates, as well as their absence in the genomes of some other birds, revealed the processes of Kiss2 gene degeneration and loss in the avian lineage. Conclusion: These findings contribute to trace back the evolutionary history of the Kisspeptin system in amniotes and sauropsids, and provide the first molecular evidence of the existence and fate of a Kiss gene in birds.
Source: BMC Evolutionary Biology
Research Officer Bangor University -School Of Biological Sciences (Ref: BU00475) Salary: £30,726 p.a. (on Grade 7) We seek a highly motivated postdoctoral researcher for a two year, full-time post carrying out research on the evolution of rattlesnake venom. The project aims to investigate the intrinsic and extrinsic causes of variation in venom composition in the Mohave rattlesnake, investigating the genome-level mechanisms responsible for different venoms, and the interrelationships between venom variation, gene flow among populations, and dietary variation. The position is funded by a two-year Leverhulme Trust grant awarded to Dr Wolfgang Wüster in the School of Biological Sciences. The successful applicant will join an established team working on the evolution of snake venoms and their composition, embedded in the Molecular Ecology and Fisheries Genetics Laboratory (MEFGL – http://bit.ly/1gyPw34) in the modern Environment Centre Wales Building. Duties will include responsibility for the day-to-day running of the project, data acquisition and analysis, and playing a leading role in the publication of the results. Candidates should be educated to PhD standard and have previous experience of relevant molecular genetics techniques. The interviews will be held on the 20th March and the successful candidate will be expected to commence on 1 May 2014 or as soon as possible thereafter. Applications will only be accepted via our on-line recruitment website, please click the APPLY button below. However, in cases of access issues due to disability, paper application forms are available by telephoning 01248 383865. Closing date for applications: Friday 14 March 2014. Informal enquiries can be made by contacting Dr Wolfgang Wüster, e-mail: firstname.lastname@example.org, tel: (01248) 382301. Dr. Wolfgang Wüster - Senior Lecturer School of Biological Sciences Bangor University Environment Centre Wales Bangor LL57 2UW Wales, UK Tel: +44 1248 382301 Fax: +44 1248 382569 E-mail: email@example.com http://bit.ly/1e38Pwp Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 Wolfgang Wuster via Gmail
Dear colleagues, We are pleased to announce the 4th International Conference on Invasive Spartina , *Rennes France July 7-10 (2014)*. Cordgrasses (Spartina, Poaceae) are perennial plants playing an important role in salt marsh sediment dynamics where they are considered as “ecosystem engineers”. Multiple cases of species introduction outside their native range had important evolutionary and ecological consequences on several continents (hybridization with native species, polyploid speciation, biological invasion, shifts in species interaction…). Due to the rapid expansion of some Spartina species, their adaptative potential, their tolerance to various pollutants and their high biomass, they have been used in wetland restoration programs, shoreline stabilization, in phytoremediation and are also considered as a potential bio-energy source for biofuel production. By bringing together international experts from complementary areas, this conference aims at promoting knowledge exchanges and discussion on the developments accomplished during the last decade in both fundamental biology (evolutionary history of the genus, impacts on ecosystems, evolution of the communities impacted by the invasions) and applied research (management and control of the invasive populations). The contribution of the recent technological developments and advanced genomic approaches to the understanding and use of /Spartina/ will be most particularly explored. Registration is now open, the link is http://bit.ly/1cTY68b *Some key dates: * Abstract submission deadline for oral presentations: 31 march 2014 * Abstract submission deadline for posters: 31 march 2014 * Early registration deadline 12 May. * Best regards, The Scientific Committee: **AINOUCHE Malika Univ. Rennes 1 (France) AYRES Debra Univ. California , Davis (USA) BORTOLUS Alejandro , Centro Nacional Patagonico - CONICET, Chubut (Argentina) CASTILLO Jesus Univ. Sevilla (Spain) GRAY Alan (Centre for Ecology and Hydrology, UK) PATTEN Kim Washington Sate Univ. USA MORRIS Jim Univ. South Carolina, Columbia, USA PENNINGS Steve Univ. Houston, TX (USA) SALMON Armel Univ. Rennes 1 (France) STRONG Donald Univ. California , Davis (USA) Malika Ainouche Prof. Univ. Rennes 1 UMR CNRS 6553 Ecobio Bt 14A Campus de Bealieu 35 042 Rennes cedex (France) Tel (33) 2 23 23 51 11 Malika Ainouche via Gmail»»»»»
"Charles Darwin: history and legacy" is a weekend course from the University of Cambridge Institute of Continuing Education. The course will take place from 21 to 23 March at Madingley Hall, an elegant 16th century mansion located three miles west of Cambridge. Taught by an esteemed scientist over a series of weekend sessions, the course will provide an excellent insight into Darwin’s enduring impact. Course description Darwin’s legacy extends into many branches of modern biology and other life sciences with varying degrees of acceptance and controversy. The course will conclude with a discussion of how the theory of natural selection and evolution has become a ‘universal’ concept of Darwinism and how environmental adaptation can be ascribed to other disciplines including literature, music, mathematics and many more. The tutor: Craig Gershater Craig JL Gershater has, for most of his career, worked as a research scientist in the pharmaceutical industry specialising in microbial biochemistry, biotechnology, computer control systems and applied mathematics. He holds degrees in biochemistry, mathematics and microbiology and has done PhD research into fungal enzymology. He has worked extensively in industry, managing research and development programmes in the USA, Europe and New Zealand, and in academia, in particular at Cambridge and London universities. Currently he works in the field of synthetic biology and is lecturer in applied statistics. More recently Craig, as a Cambridge City Guide, has undertaken numerous tours of Cambridge, many on the topic of the scientific heritage of the University. He is also a qualified and prize-winning Institute of Tourist Guiding Blue Badge guide for the south of England and offers tours throughout the region. He provides many courses to the Institute of Continuing Education, covering topics including the scientific heritage of Cambridge, Darwin, Newton and Leonardo da Vinci as well as Victorian, Edwardian, and interwar-years science. Additional details This course will run from 21 to 23 March. It will begin on Friday evening and disperse after lunch on Sunday. Accommodation is available in Madingley Hall for the duration of the course (typically the Friday and Saturday nights, but an extra night is available on the Sunday if desired). The course cost is 240, which includes dinner on Friday and Saturday and lunch on Saturday and Sunday. Accommodation, including breakfast on Saturday and Sunday, is available for 110 or 90 per person for two people sharing. You can find full details about this course, including the timetable, on its page on our website: http://bit.ly/1cTY680 James Burton Marketing Assistant Institute of Continuing Education, University of Cambridge Madingley Hall, Madingley, Cambridge CB23 8AQ T: +44 (0)1223 746421 E: firstname.lastname@example.org W: www.ice.cam.ac.uk * 140 years of continuing education at Cambridge 1873-2013 * * Become a Friend of Madingley Hall: http://bit.ly/1cTY682www.ice.cam.ac.uk * 140 years of continuing education at Cambridge 1873-2013 * * Become a Friend of Madingley Hall: http://bit.ly/1cTY682 James Burton via Gmail
We are pleased to announce the National Science Foundation’s Integrative Graduate Education and Research Traineeship (NSF-IGERT) Symposium on Deep Genomics on April 3-5, 2014 in Tucson, Arizona. Symposium website: http://bit.ly/1eL9suQ The University of Arizona IGERT Program in Comparative Genomics is sponsoring an international meeting on Deep Genomics. The symposium’s theme this year encompasses broad scale comparative inferences in the three areas of our training program, including comparative and evolutionary genomics of divergent species, genomics of development, traits, and related interaction networks originating early in evolutionary history, and computational challenges associated with genomics at a broad phylogenetic scale. The meeting will take place at the Marriott University Park Hotel adjacent to the University of Arizona campus in Tucson on Thursday-Saturday, April 3-5, 2014. The format of the meeting will allow considerable time for informal discussion and interaction among participants. Participation by graduate students and postdoctoral fellows is strongly encouraged, and discounted rates for registration will be available. REGISTRATION Early registration deadline: March 14, 2014 Faculty: $150, Students and Postdocs: $75 Late registration deadline: March 26, 2014 Faculty: $175, Students and Postdocs: $90 KEYNOTE SPEAKER Kenneth Wolfe - University College Dublin, Ireland CONFIRMED SPEAKERS Robert Beiko - Dalhousie University, Canada William Cresko - University of Oregon Miklos Csuros - Universite de Montreal, Canada Patrick Degnan - University of Illinois Dannie Durand - Carnegie Mellon University Veronica Hinman - Carnegie Mellon University Erin Kelleher - University of Houston Junhyong Kim - University of Pennsylvania Laura Landweber - Princeton University Li-Jun Ma - University of Massachusetts Michael Nodine - Gregor Mendel Institute, Austria Robert Reed - Cornell University Shin-Han Shiu - Michigan State University Joseph Thornton - University of Chicago Travish Wheeler - HHMI Janelia Farm POSTER SESSION The symposium will feature a poster session. Please refer to the website for more information: http://bit.ly/ItwI8q Please contact Dr. Michael Sanderson, email@example.com, with all scientific queries. Please contact Mrs. Pennie Liebig, firstname.lastname@example.org, with all registration or administrative queries. We hope to see you in April! via Gmail
Dear colleague, Please fill out our online survey to assess landscapes for ecological and evolutionary processes contributing to biodiversity conservation. The survey shows you 15 simple habitat patterns and asks you to rank their conservation value according to a criterion of your choice, for a type of organism or biodiversity that you know well, at particular spatial scales. Follow this link to see the survey and take part if you can: http://bit.ly/1fcLld2 We’ll use the results to compare expert assessments with outputs from simulation models. This is an important part of validating the models, as well as looking at agreement among experts. The findings should ultimately feed in to policy advice. Thanks in advance for your help, Richard Gunton and Dirk Schmeller. The SCALES project (http://bit.ly/1cTQYsc) Richard Gunton via Gmail
Dear all, Applications are now open for a 3-year Graduate Teaching Studentship in the School of Environment & Life Sciences, University of Salford, Greater Manchester, UK. The title of my proposed project is: *Endocrine disruption effects on the sexual differentiation of the brown shrimp Crangon crangon: a field test and characterization of a biomarker* http://bit.ly/1gyATwE The goals of this project are: (1) to determine the effects of endocrine disrupting chemicals (EDc) on the sexual differentiation of the brown shrimp *C. crangon* and (2) to characterize an effective ED biomarker in this species. The successful candidate will: 1) Perform field sampling of *C. crangon* in contaminated and non-contaminated sites; 2) Determine its sex (morphologically and through gonadal histological analyses); 3) Analyse sex ratios and sexual differentiation in the populations under study; 4) Test the use of vitellogenin (Vtg) as an effective ED biomarker (using recently developed protocols which, for example, employ LC-MS-MS, liquid chromatography tandem mass spectrometry). Successful applicants need to register for a PhD at the University of Salford and from the scheme they will gain experience of teaching in Higher Education while performing their research project. Details on the fellowship can be found here: http://bit.ly/1gyAVVB and here: http://bit.ly/1e2YuRd The closing date for application is 31st March 2014. Please feel free to contact me at: C.Benvenuto@salford.ac.uk Kind regards, Chiara *Dr. Chiara Benvenuto* Lecturer in Zoology* |* School of Environment & Life Sciences Room 317, Peel Building, University of Salford, Salford M5 4WT, UK *t:* +44 (0)161-295-5141 *| m: *+44 (0)7544-290-311 *C.Benvenuto@salford.ac.uk* | http://bit.ly/1gyAWbT http://bit.ly/1e2YuRg email@example.com via Gmail
The Barcode of Life
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology
Molecular Biology and Evolution