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April 8, 2014
Wednesday, 12:00 PM at NESCent, Ninth Street and Main Street, Erwin Mill Building, 2024 W. Main Street, Suite A200. For more information, call 919-668-4551
A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility
Background: Protein sites evolve at different rates due to functional and biophysical constraints. It is usually considered that the main structural determinant of a site’s rate of evolution is its Relative Solvent Accessibility (RSA). However, a recent comparative study has shown that the main structural determinant is the site’s Local Packing Density (LPD). LPD is related with dynamical flexibility, which has also been shown to correlate with sequence variability. Our purpose is to investigate the mechanism that connects a site’s LPD with its rate of evolution. Results: We consider two models: an empirical Flexibility Model and a mechanistic Stress Model. The Flexibility Model postulates a linear increase of site-specific rate of evolution with dynamical flexibility. The Stress Model, introduced here, models mutations as random perturbations of the protein’s potential energy landscape, for which we use simple Elastic Network Models (ENMs). To account for natural selection we assume a single active conformation and use basic statistical physics to derive a linear relationship between site-specific evolutionary rates and the local stress of the mutant’s active conformation.We compare both models on a large and diverse dataset of enzymes. In a protein-by-protein study we found that the Stress Model outperforms the Flexibility Model for most proteins. Pooling all proteins together we show that the Stress Model is strongly supported by the total weight of evidence. Moreover, it accounts for the observed nonlinear dependence of sequence variability on flexibility. Finally, when mutational stress is controlled for, there is very little remaining correlation between sequence variability and dynamical flexibility. Conclusions: We developed a mechanistic Stress Model of evolution according to which the rate of evolution of a site is predicted to depend linearly on the local mutational stress of the active conformation. Such local stress is proportional to LPD, so that this model explains the relationship between LPD and evolutionary rate. Moreover, the model also accounts for the nonlinear dependence between evolutionary rate and dynamical flexibility.
Source: BMC Evolutionary Biology
Brian Foley wrote:
Over the weekend I was reading _Neanderthal Man_ by Svante Paabo . This book discusses comparative genomics of humans and close relatives, including the complete genome of Pan paniscus published in Nature in 2012, and the complete genome of an Altai Neanderthal in 2014. It is clear from the phylogenetic trees and other comparisons in these papers that the complete genomes can be analyzed, for example to show diversity within the Major Histocompatibility Complex in comparison to diversity in other regions of the genomes.
However, when I attempt to download the MHC region from each of the genomes to do some of my own comparisons, I find that it is not easy to get the data. The genomes are not well assembled and annotated on the public sites, so I cannot just search for the MHC gene region in Pan troglodytes, Altai Neanderthal genome, or Pan paniscus genome.
Does anyone here know if the annotated genomes are available at some other site? Papers discussing the genomes seem to indicate that the authors have access to annotation to determine which genes and gene families are shared between modern humans and Neanderthals.
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[A pdf of this ad is available at http://bit.ly/R03O4n] The Cartwright Lab at Arizona State University in Tempe, AZ is seeking multiple Postdoctoral Research Associates in the areas of Evolutionary Genomics, Statistics, and Bioinformatics to develop methodologies and study evolutionary questions related to mutation and short-read sequencing. Successful applicants will join a rapidly growing and well-funded lab involved on a variety of active research projects and collaborations. Current projects include (1) the analysis of cilliate mutation accumulation lines, (2) the development of software for de-novo mutation detection from traditional and single-cell sequencing datasets, (3) the analysis of non-pathogenic somatic mutation patterns in mammals and plants, (4) the study of indel patterns across the tree of life, (5) characterizing mutations and fitness-landscapes of metabolically engineered microbes, (6) population genetics of malaria parasites, (7) the construction of phylogenies from short-read, whole genome datasets, and (8) simulation techniques for molecular evolution research. The Cartwright Lab is part of the Center for Evolutionary Medicine and Informatics (CEMI), one of 10 research centers in Arizona State University’s Biodesign Institute. Research in the Cartwright Lab covers many different questions in population genetics and molecular evolution, at the interface of biology, statistics, and computer science. A majority of our research involves developing, implementing, and applying novel methodologies to study genomic datasets. Members have the opportunity to develop both dry-lab and wet-lab research programs through interactions with both national and international collaborations. As part of this project, the Postdoctoral Research Associates are expected to be able to: 1) Assemble microbial or metazoan genomes from short-read sequences and identify variable sites and regions. 2) Develop novel, high-throughput methodologies to study mutations from next generation sequencing of related individuals and cells. 3) Work closely with collaborators to customize methodologies to specific experimental designs. Required Qualifications: Ph.D. in genomics, bioinformatics, or a related field Desired Qualifications: Experience working with genomes and evolutionary analyses; Knowledge of programming languages including R, Python, and C++; Knowledge of statistical methodologies; Experience with short-read sequencing Application must contain: (1) Resume, (2) Cover Letter, (3) Names, addresses, and phone numbers of three professional references Deadline for applications is May 1, 2014. Applications will continue to be accepted and considered until the job is filled/closed. For more information see http://bit.ly/1ioG1RD or http://bit.ly/R03LFM. To apply, forward one document that includes a cover letter, detailed CV, and names of 3 references to email@example.com. Please put the job title in the subject line of the letter. Arizona State University is an Equal Opportunity/Affirmative Action employer. A background check is required for employment. A pdf of this ad is available at http://bit.ly/R03O4n via Gmail
PhD position-Laval University-Systems Biology A four year PhD position in evolutionary systems biology is available at Laval University. The project will be tailored to the candidates interests and will have to touch upon current research interests of the laboratory, which include i) evolution and robustness of protein interaction networks; ii) evolution of signalling networks and crosstalk among posttranslational modifications; iii) gene duplication and the evolution of network complexity. See recent publications: Landry et al. Cell (2013); Diss et al. Cell Reports (2013); Freschi et al. PLoS Genetics (2013); Diss et al. Current Opinion in Biotechnology (2013); Freschi et al. Molecular Systems Biology (2011); Gagnon-Arsenault et al. J Proteomics (2013); Moses and Landry, Trends in Genetics (2010); Diss et al. JEZ B (2014); Leducq et al. PLoS Genetics (2012); Levy et al. Phil Trans Roy Soc (2012); Landry et al. Trends in Genetics (2009); Tarassov et al. Science (2008); Applicants must have i) a strong background in genetics or molecular biology or biochemistry or proteomics or bioinformatics (or their combination), and an expertise in or a strong interest for evolutionary biology and ii) a MSc degree in any relevant field of the life sciences. The Landry laboratory is a dynamic, international and interdisciplinary research group with broad interests in integrative biology, systems biology, molecular evolution, bioinformatics and ecological genomics. Laval University is one of the most important research universities in Canada and is located in Quebec City, a lively city with a vibrant culture that offers an exceptional quality of life. Interested applicants should send a CV with a list of publications and accomplishments, a low-resolution copy of official academic transcripts, a statement of interest (1 page) and the names of three referees in a single PDF file to Christian.firstname.lastname@example.org. Christian Landry via Gmail
PhD position-Laval University-Ecological Genomics A four year PhD position in ecological genomics is available at Laval University. The project will exploit a new study system we recently developed for the study of adaptation and ecological speciation using the budding yeast Saccharomyces paradoxus. The candidate will use genomic tools (whole-genome sequencing, high-throughput phenotypic profiling, QTL analyses, association mapping) to study the molecular bases of phenotypic divergence between incipient species and identify genes involved in hybrid incompatibilities. The project will combine experimental molecular biology, bioinformatics approaches and possibly field work. See recent publications: Leducq et al., Proc Soc B (2014); Charron et al., FEMS Yeast Research (2014); Leducq et al., PLoS Genetics (2012); Landry and Aubin-Horth, Adv Exp Med Biol. (2014); Verta et al., Molecular Ecology (2013); Pavey et al., Trends in Ecology and Evolution (2012); Fontanillas et al., Molecular Ecology (2010); Brown et al., Molecular Ecology (2008); Lynch et al. PNAS (2008); Landry et al., Molecular Ecology (2006); Landry et al. Heredity (2007); Landry et al. Science (2007); Applicants must have i) a strong background in evolutionary genetics and/or evolutionary ecology plus a strong interest for using genomics and bioinformatics tools and ii) a MSc degree in any relevant field of the life sciences. The Landry laboratory is a dynamic, international and interdisciplinary research group with broad interests in integrative biology, systems biology, molecular evolution, bioinformatics and ecological genomics. Laval University is one of the most important research universities in Canada and is located in Quebec City, a lively city with a vibrant culture that offers an exceptional quality of life. Interested applicants should send a CV with a list of publications and accomplishments, a low-resolution copy of official academic transcripts, a statement of interests (1 page) and the names of three referees in a single PDF file to Christian.email@example.com. Christian Landry via Gmail
ICBB.2014_Symposium:Butterfly.behaviour We are organising a symposium for the International Conference on the Biology of Butterflies, 2014 in Turku, Finland (August 11-14th) and encourage submissions for talks and posterson ‘Behavioural and neurological aspects of ecological adaptation and speciation’ Symposium theme: A major goal of evolutionary biology has been to characterize the adaptations between populations that contribute to ecological divergence and speciation. Although most studies have concentrated on structural adaptations, such as colour pattern, shifts in behaviour may be especially important in generating both reproductive and ecological isolation. These behavioural differences may be genetically determined or acquired (learnt), may involve sensory adaptations, changes in life history, or adaptive changes in brain size, structure or connectivity. This symposium will take a broad approach to examining the role of behavioural and neurological change in ecological adaptation and speciation. We hope to attract talks spanning the following topics: The role of behavioural plasticity in ecological diversification The genetic architecture of adaptive behaviours Behavioural aspects of reproductive isolation Neural basis of adaptive behaviours Ecological correlates of neural diversification **During abstract submission please select ‘BEHAVIOURAL ECOLOGY’ from the drop down box for the main topic area of your abstract.** Invited Speakers: Prof. Steven Reppert (U. Massachusetts): Neuroethology of monarch butterfly migration Prof. Emilie Snell-Rood (U. Minnesota): Nutrition as a constraint on life history and brain evolution: a comparative study across butterflies Dr. Erica Westerman (U. Chicago): Perceptual biases and visual attraction: the role of perception in reproductive isolation Dr. Maaike De Jong (U. Bristol): Ecological genetics of life history and host plant adaptation in the Glanville fritillary butterfly More details: Conference information: http://bit.ly/17ARV8Y Abstract submission: http://bit.ly/OM9lul Many thanks and we hope to see you in Turku, Stephen Montgomery (Stephen.Montgomery@cantab.net) & Richard Merrill (R.Merrill@zoo.cam.ac.uk) Dr. Stephen Montgomery Research Fellow The Royal Commission for the Exhibition of 1851 Dept. of Genetics, Evolution and Environment University College London http://bit.ly/1iozrKW Stephen Montgomery via Gmail
VOLUNTEER FIELD ASSISTANT sought immediately for 4-6 weeks (starting mid-April 2014), to help with a study of paper wasp (Polistes) behavioural ecology in southern Spain. The work will involve helping a postdoctoral researcher/PhD student to census and observe colonies as part of experiments to elucidate the basis of helping behaviour in these wasps, which live in small colonies of via Gmail
http://bit.ly/PXvO7H Thanks, James Mathematical modelling of key transitions in social insect systems Our research is about trying to understand the functioning of biological systems through the use of mathematical models. Dr Childs is a population biologist who develops data-driven models to understand population dynamics and natural selection. Dr Marshall is a computational biologist with interests in social evolution and social insect behaviour. We have been awarded a studentship to facilitate a new collaboration. Research pursued by the student may address any topic that lies at the interface of our interests, though we are particularly interested in the following two questions: 1) Can we detect critical transitions in social insect systems? Ecologists have become increasingly interested in using ideas from nonlinear dynamics to forecast qualitative changes in the behaviour of natural communities (e.g. via critical slowing down). Using this framework, we would like to develop methods to forecast the occurrence of economically important phenomena in social insect systems (e.g. colony collapse disorder). 2) What inﬂuences the evolutionary stability of unicolonial ant species? Some ant species form huge unicolonial populations. The existence of such supercolonies is surprising: since the relatedness of individuals within them is nearly zero, kin selection theory predicts they should be evolutionarily unstable. We would like to develop models to explore the demographic and ecological factors that favour such colonies in evolutionary time. The studentship is fully funded and open to residents of the UK/EU. We are looking for students with a strong background in mathematics, physics, or computer science. Contact Dr Childs for further information. James A. R. Marshall Behavioural and Evolutionary Theory Lab Department of Computer Science and Kroto Research Institute University of Sheffield http://bit.ly/1ecElzb James Marshall via Gmail
Associate Professor in Vertebrate Zoology (anatomy/evolution) A permanent position as associate professor in vertebrate zoology is open at the University Museum of Bergen, the Natural History Collections (http://bit.ly/1klT6Sx). We are seeking a researcher within vertebrate zoology with special competence in vertebrate skeletal morphology (osteology). The successful applicant should also have competence in one or several of the new scientific methods; i.e. isotopes, trace elements or DNA and be able to apply these in research on modern as well as sub-fossil skeletal material. The comprehensive collections of skeletal material from prehistory and present time are important data for research within faunal- and environmental history, morphological adaptation or evolutionary relationships. The successful applicant is expected to document research at international level in zoology/osteology at in least one of these methods. He/she is supposed to work within faunal- and environmental history. The position is connected to the osteology collections. The University Museum of Bergen hold two comprehensive collections of vertebrate skeletons; one recent collection of c.15000 specimens (fish, amphibians, reptiles, birds and mammals) from Norway and a national collection of sub-fossil bones, mainly from the post glacial and from archaeological excavations. The successful applicant will have scientific responsibility for the modern skeletal collection. He/she is expected to participate in developing the collections through own research, but also by national and international cooperation as well as improvement of databases and home pages. The successful applicant is also expected to participate in teaching and in the development of zoological exhibitions at the University museum. A more detailed description of the position and information about necessary documentation which must be enclosed in the application can be found further down on this page. Additional information can be obtained from the head of the Natural History Collections, associate professor Kari Loe Hjelle, phone (+47) 55583323 / e-mail firstname.lastname@example.org. http://bit.ly/1qiZjMs Bjarte Henry Jordal via Gmail
PhD position in plant population genetics available at the Laboratory of Evolutionary Botany, University of Neuchatel http://bit.ly/1qiZjMC The main objective of this PhD project is to infer the evolution of selected diploid/polyploid Aegilops wild wheats in space and time. Dated phylogenies will provide a robust framework to address the comparative phylogeography of their genomes and their inhabiting transposable elements. The work combines knowledge from high-throughput sequencing, genotyping, bioinformatics, population genetics and evolutionary ecology. Field work will be conducted to complement existing data. We seek a highly motivated student with strong interest in evolutionary genomics. Skills in treating large datasets with varied statistical tools are relevant. The fellow will interact within a network of researchers and particularly with Prof. N. Salamin at the University of Lausanne, and needs to have collaborative abilities. For more information please contact Christian Parisod (email@example.com) Please send your complete application (letter describing motivation and ideas for this project, CV incl. publication list and contact details of at least two references) as one single pdf to firstname.lastname@example.org Application received before April 28th will be given full consideration. Expected start date is June 1st 2014 or at earliest convenience thereafter. Christian Parisod and Fran?ois Felber Christian Parisod Evolutionary Botany, University of Neuchatel Rue Emile-Argand 11, 2000 Neuchatel, Switzerland Phone: +41 (0)32 718 2344, Fax: +41 (0)32 718 3001 e-mail: email@example.com http://bit.ly/1km2Hc4 Christian Parisod via Gmail
Symposium proposals for ESEB 2015: potential gender bias Further to our recent call for symposium proposals for ESEB 2015 in Lausanne next year, we wish to encourage potential symposium organisers to take diversity (of gender, nationality and age) into account when proposing speakers for their symposium. As ESEB members will be aware, research shows clearly that (gender) bias in academia is usually not the result of intentional acts of exclusion, but rather the effect of more subtle mechanisms like implicit bias. Substantial concern has been raised about gender bias among invited speakers for symposia at previous ESEB (and other) meetings. The organisers of ESEB 2015 acknowledge this concern and wish to ensure that symposia selected for ESEB in Lausanne draw participants (both invited and those selected for inclusion when abstracts are reviewed) as broadly as possible to reflect the full research strengths of the fields represented. We thus encourage prospective symposium organisers to account for potential implicit bias before inviting speakers or submitting their proposals. Balance in terms of gender, nationality and age will be included as one criterion used by the scientific committee when selecting symposia. Further information about the symposia can be found at: http://bit.ly/1rIZnbY For symposium submission, please go to: http://bit.ly/1rIZm7V The organisers and the scientific committee of ESEB 2015. John Pannell via Gmail
Postdoctoral researcher position available in computational global change ecology. Dr Daniel Reuman is recruiting into his lab in the University of Kansas Department of Ecology and Evolutionary Biology and the Kansas Biological Survey. Research will focus on software aspects of two large projects: 1) Ramifications of metapopulation synchrony through the complex North Sea and North Atlantic metacommunities in the face of climate change; and 2) Revealing the mechanisms linking the structure, functioning, and dynamics of whole ecological communities using likelihood. The researcher will be expected to contribute to software development for both projects, collaborating with teams of biologists, statisticians, and modellers and pursuing independent research questions. The position could be suitable for scientists from diverse training backgrounds. See http://bit.ly/1ebXgdx for details or to apply. Contact firstname.lastname@example.org with questions. Daniel C. Reuman Senior Lecturer, Department of Life Sciences Imperial College London http://bit.ly/1jpHLgR Visiting Assistant Professor, Laboratory of Populations, Rockefeller University Grand Challenges in Ecosystems and the Environment initiative, member Director, MSc in Quantitative Biology http://bit.ly/1cnn41p Director, MRes in Biodiversity Informatics and Genomics http://bit.ly/PJXNYS +44 (0)20 7594 2401 “Reuman, Dan” via Gmail
An undergraduate student (Aime Rankin) doing a project with me on citation and impact of museum collections came across a paper I hadn't seen before:
Strasser, B. J. (2011, March). The Experimenter’s Museum: GenBank, Natural History, and the Moral Economies of Biomedicine. Isis. University of Chicago Press. doi:10.1086/658657
Unfortunately the paper is behind a paywall, but here's the abstract (you can also get a PDF here):
Today, the production of knowledge in the experimental life sciences relies crucially on the use of biological data collections, such as DNA sequence databases. These collections, in both their creation and their current use, are embedded in the experimentalist tradition. At the same time, however, they exemplify the natural historical tradition, based on collecting and comparing natural facts. This essay focuses on the issues attending the establishment in 1982 of GenBank, the largest and most frequently accessed collection of experimental knowledge in the world. The debates leading to its creation—about the collection and distribution of data, the attribution of credit and authorship, and the proprietary nature of knowledge—illuminate the different moral economies at work in the life sciences in the late twentieth century. They offer perspective on the recent rise of public access publishing and data sharing in science. More broadly, this essay challenges the big picture according to which the rise of experimentalism led to the decline of natural history in the twentieth century. It argues that both traditions have been articulated into a new way of producing knowledge that has become a key practice in science at the beginning of the twenty-first century.
It's well worth a read. It argues that sequence databases such as Genbank are essentially the equivalent of the great natural history museums of the 19th Century. There are several ironies here. One is that some early advocates of molecular biology cast it as a modern, experimental science as opposed to mere natural history. However, once the amount of molecular data became too great for individuals to easily manage, and once it became clear that many of the questions being asked required a comparative approach, the need for a centralised database of sequences (the "experimenter's museum" of the title of the paper) became increasingly urgent. Another irony is that the clash between molecular and morphological taxonomy overlooks these striking similarities in history (collecting ever increasing amounts of data eventually requiring centralisation).
Bruno Strasser's article also discusses the politics behind setting up GenBank, including the inevitable challenge of securing funding, and the concerns of many individual scientists about the loss of control over their data. A final irony is that, having gone through this process once with the formation of the big museums in the 19th century, we are going through it again with the wrangling over aggregating the digitised versions of the content of those museums.
Update: See also
Strasser, B. J. (2008, October 24). GENETICS: GenBank--Natural History in the 21st Century? Science. American Association for the Advancement of Science (AAAS). doi:10.1126/science.1163399 (via Guanyang Zhang).
Associate Professor in Systematic Botany A permanent position as associate professor in systematic botany is open at the University Museum of Bergen, the Natural History Collections (DNS),(http://bit.ly/1klT6Sx). We are seeking an active researcher focusing on plant evolution, who has expertise in systematics of vascular plants and phylogenetics. Relevant fields of research are evolutionary relationships, taxonomy and species diversity of vascular plants, and evolutionary processes generating biodiversity. Applicants must be able to document research with international standards within one or more of these fields. This position entails the scientific responsibility for a botanic garden that is more than a century old; the Museum Garden. The successful applicant will also be scientifically responsible for the botanical exhibitions at the museum, and will take part in the development of new natural history exhibitions which are currently being planned. He or she will also be expected to take part in the teaching of botany at UiB. A more detailed description of the position and information about necessary documentation which must be enclosed in the application can be found further down on this page. Additional information can be obtained from the head of the Natural History Collections, associate professor Kari Loe Hjelle, phone (+47) 55583323 / e-mail email@example.com. http://bit.ly/1qiM9iH Bjarte Henry Jordal via Gmail
The Research Group of Plant Ecological Genomics of the Department for Botany and Biodiversity Research at the University of Vienna, Austria is recruiting a Lab Technical Assistant in Molecular Biology An up to 5-years position funded by the Austrian Science Fund (FWF) is immediately available in a research project on the evolution of wild polyploid orchids (see http://bit.ly/1qiImlm). Our exciting research makes use of an array of state-of-the-art genomic and epigenomic techniques. Apart from playing a key role in optimizing and performing parts of laboratory protocols, the Assistant will take care of orders and lab equipment. S/he will also maintain databases of protocols and samples. We are looking for a highly focused and motivated candidate that searches for exciting research opportunities and has an excellent previous record. The successful candidate must have excellent organization and communication skills, and to work in a multinational team. S/he is expected to have a degree in a related discipline (e.g., molecular biology, biochemistry) and to be able to demonstrate previous experience with molecular laboratory duties. Experience with RNA work and/or NGS library preparation will be considered as an important advantage. The Assistant should be willing to learn continuously new methodologies with the support of the rest of the team. The working language in our laboratory is English; German skills are therefore not essential, but they are highly desirable to allow a proper communication with people from outside the team. The position offers a competitive salary (according to experience min. 27,000 per year before tax for full time, including social and health security), and opportunities for career development/further training. If preferable for the successful candidate, 30 hours a week employment is also possible. To be considered please send your application per email to firstname.lastname@example.org including your CV, a cover letter explaining why would this job fit your qualifications, experience and expectations (up to two pages), and the names and contacts of three referees. Please note: Incomplete applications will not be considered. Screening of applications will begin immediately and will continue until the position is filled. The latest preferred start date is June 1st, 2014. email@example.com via Gmail
Dear all, My name is Emma Chance and I am a final year student at the University of Manchester working on my dissertation project. I have created a website to help people beginning or switching to using MorphoJ, for analysing geometric morphometric data, get started with fewer difficulties and have a greater understanding into the rationale and purpose behind a few of the key statistical analyses. I would really appreciate it if you could take a look at my website, and spend no longer than 5 minutes of your time to answer a quick survey about how useful you have found my resource and any improvements that I could make. Thank you very much for your time. Kind regards, Emma Chance http://bit.ly/1mXC6PO firstname.lastname@example.org via Gmail
Dear Evoldir Members, I’m wondering if anyone could point me toward some recent comprehensive reviews, dedicated websites, or specific bodies of work on intron sequence evolution in protein-encoding genes? I am especially interested in conceptual papers and/or any that might include new tools for finding and comparing specific sequence themes independently of intron length, potential miRNA encoding regions, miRNA target sites, etc. thanks in advance for any help you can give. Bruce Turner email@example.com via Gmail
I have developed a series of active learning lessons in evolutionary biology (undergraduate level). A list and brief description of the lessons are provide at http://bit.ly/1irERpV I am interested in having folks test these lessons and provide feedback. There are descriptions of two lessons available for download with more coming depending on interest. Andrew Martin Professor University of Colorado A mind once stretched by a new idea never regains its original dimensions. Andrew Martin via Gmail
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology