There are currently 0 users and 27 guests online.
March 12, 2015
Immunity, suicide or both? Ecological determinants for the combined evolution of anti-pathogen defense systems
Background: Parasite-host arms race is one of the key factors in the evolution of life. Most cellular life forms, in particular prokaryotes, possess diverse forms of defense against pathogens including innate immunity, adaptive immunity and programmed cell death (altruistic suicide). Coevolution of these different but interacting defense strategies yields complex evolutionary regimes. Results: We develop and extensively analyze a computational model of coevolution of different defense strategies to show that suicide as a defense mechanism can evolve only in structured populations and when the attainable degree of immunity against pathogens is limited. The general principle of defense evolution seems to be that hosts do not evolve two costly defense mechanisms when one is sufficient. Thus, the evolutionary interplay of innate immunity, adaptive immunity and suicide, leads to an equilibrium state where the combination of all three defense strategies is limited to a distinct, small region of the parameter space. The three strategies can stably coexist only if none of them are highly effective. Coupled adaptive immunity-suicide systems, the existence of which is implied by the colocalization of genes for the two types of defense in prokaryotic genomes, can evolve either when immunity-associated suicide is more efficacious than other suicide systems or when adaptive immunity functionally depends on the associated suicide system. Conclusions: Computational modeling reveals a broad range of outcomes of coevolution of anti-pathogen defense strategies depending on the relative efficacy of different mechanisms and population structure. Some of the predictions of the model appear compatible with recent experimental evolution results and call for additional experiments.
Background: Drosophila melanogaster often shows correlations between latitude and phenotypic or genetic variation on different continents, which suggests local adaptation with respect to a heterogeneous environment. Previous phenotypic analyses of latitudinal clines have investigated mainly physiological, morphological, or life-history traits. Here, we studied latitudinal variation in sleep in D. melanogaster populations from North and Central America. In parallel, we used RNA-seq to identify interpopulation gene expression differences. Results: We found that in D. melanogaster the average nighttime sleep bout duration exhibits a latitudinal cline such that sleep bouts of equatorial populations are roughly twice as long as those of temperate populations. Interestingly, this pattern of latitudinal variation is not observed for any daytime measure of activity or sleep. We also found evidence for geographic variation for sunrise anticipation. Our RNA-seq experiment carried out on heads from a low and high latitude population identified a large number of gene expression differences, most of which were time dependent. Differentially expressed genes were enriched in circadian regulated genes and enriched in genes potentially under spatially varying selection. Conclusion: Our results are consistent with a mechanistic and selective decoupling of nighttime and daytime activity. Furthermore, the present study suggests that natural selection plays a major role in generating transcriptomic variation associated with circadian behaviors. Finally, we identified genomic variants plausibly causally associated with the observed behavioral and transcriptomic variation.
Background: Social animals have the unique capability of mounting social defenses against pathogens. Over the last decades, social immunity has been extensively studied in species with obligatory and permanent forms of social life. However, its occurrence in less derived social systems and thus its role in the early evolution of group-living remains unclear. Here, we investigated whether lining nests with feces is a form of social immunity against microbial growth in the European earwig Forficula auricularia, an insect with temporary family life and facultative maternal care. Results: Using a total of 415 inhibition zone assays, we showed that earwig feces inhibit the growth of two GRAM+ bacteria, two fungi, but not of a GRAM- bacteria. These inhibitions did not result from the consumed food or the nesting environment. We then demonstrated that the antimicrobial activity against fungus was higher in offspring than maternal feces, but that this difference was absent against bacteria. Finally, we showed that family interactions inhibited the antibacterial activity of maternal feces against one of the two GRAM+ bacteria, whereas it had no effect on the one of nymphal feces. By contrast, antifungal activities of the feces were independent of mother-offspring interactions. Conclusion: These results demonstrate that social immunity occurs in a species with simple and facultative social life, and thus shed light on the general importance of this process in the evolution of group-living. These results also emphasize that defecation can be under selection for other life-history traits than simple waste disposal.
Background: Shelled pteropods are planktonic gastropods that are potentially good indicators of the effects of ocean acidification. They also have high potential for the study of zooplankton evolution because they are metazoan plankton with a good fossil record. We investigated phenotypic and genetic variation in pteropods belonging to the genus Cuvierina in relation to their biogeographic distribution across the world’s oceans. We aimed to assess species boundaries and to reconstruct their evolutionary history. Results: We distinguished six morphotypes based on geometric morphometric analyses of shells from 926 museum and 113 fresh specimens. These morphotypes have distinct geographic distributions across the Atlantic, Pacific and Indian oceans, and belong to three major genetic clades based on COI and 28S DNA sequence data. Using a fossil-calibrated phylogeny, we estimated that these clades separated in the Late Oligocene and Early to Middle Miocene. We found evidence for ecological differentiation among all morphotypes based on ecological niche modelling with sea surface temperature, salinity and phytoplankton biomass as primary determinants. Across all analyses, we found highly congruent patterns of differentiation suggesting species level divergences between morphotypes. However, we also found distinct morphotypes (e.g. in the Atlantic Ocean) that were ecologically, but not genetically differentiated. Conclusions: Given the distinct ecological and phenotypic specializations found among both described and undescribed Cuvierina taxa, they may not respond equally to future ocean changes and may not be equally sensitive to ocean acidification. Our findings support the view that ecological differentiation may be an important driving force in the speciation of zooplankton.
We invite you to the 10th Annual Meeting of the Canadian Society for Ecology and Evolution (CSEE) to be held in Saskatoon (SK, Canada)on 22-24 May 2015. This year, the theme of the conference is: ‘Ecology and Evolution of Managed Landscapes’. We have an exciting program of symposia, invited speakers, and field trips. Please see the conference website for details: http://bit.ly/1w7KGU0. Conference registration and the call for presentations are now open. Early bird fees and the presentation call end March 15th! Nous vous invitons à Saskatoon (SK, Canada), du 22 au 24 mai 2015 pour la 10e rencontre annuelle de la SCEE tenue par l’Université de la Saskatchewan. Cette année, le thème de la conférence est : «Écologie et évolution des paysages aménagés». Une gamme passionnante de symposia, conférenciers invités et excursions sur le terrain ont été organisés. Pour plus de détails, veuillez consulter le site internet de la conférence : http://bit.ly/1LOsl1s. L’inscription à la conférence et l’appel de présentations sont maintenant ouverts. Les frais d’inscription htive et l’appel de présentations se terminent le 15 mars 2015! Ciee-Icee@uregina.ca via Gmail
—Apple-Mail=_FB5E39FA-E2E7-43BD-A13F-79D8D79BD5AA Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Postdoc: Modeling Population Genetics for Suppression of Mosquito-Vectored Diseases PROJECT DESCRIPTION: Dengue is a mosquito-vectored disease that affects over 100 million people each year. With funding from the NIH, FNIH, and W. M. Keck Foundation, we have developed a set of mathematical models ranging from simple to complex, aimed at assisting the design and deployment of novel approaches for suppressing transmission of dengue by its major mosquito vector, Aedes aegypti. We are especially interested in evaluating the potential utility and risks associated with using genetically engineered, selfish genetic elements to drive genes into mosquito populations that render them incapable of transmitting dengue fever or decrease mosquito density. Our new work also extends to models relevant to suppressing malaria. New developments in molecular genetics promise to increase the efficiency of building gene drive systems with novel properties. The postdoc in this position will build a set of simple to complex models to examine the expected dynamics of these gene drive systems in mosquitoes and other taxa. The most detailed model that we have developed simulates the population dynamics and population genetics of Ae. aegypti in a city on the Amazon river, Iquitos, for which there are rich data sets on both mosquito dynamics and dengue epidemiology. An accompanying epidemiological model is currently under development. The goals of two other postdocs in our group are to expand the mosquito model and the human epidemiology model to encompass the entire city of about 400,000 people. The postdoc in this new position will also collaborate with the other postdocs to use these detailed models to test gene drive systems. In addition to working on model development and analysis, the person in this position will collaborate in an interdisciplinary research group composed of mosquito ecologists, disease epidemiologists, molecular biologists, biomathematicians, ethicists, and scientists from disease-endemic countries. The person in this position will have the opportunity to visit Iquitos to better understand one of the systems being modeled. Desirable skills include the ability to program in C++ or knowledge of a related programming language, and training in evaluation of mechanistic models. To apply: email a cover letter and CV to Fred_Gould@ncsu.edu For more details on the project see the following publications: Esvelt, K. M., A. L. Smidler, F. Catteruccia, G. M. Church. 2014. Concerning RNA-guided gene drives for the alteration of wild populations. eLife. 10.7554/eLife.03401. Oye, K. A. et al. 2014. Regulating gene drives. Science. 345:626-628 Published online 17 July 2014 Huang, Y., Lloyd, A.L., Legros, M., Gould, F. 2010. Gene-drive into insect populations with age and spatial structure: a theoretical assessment. Evol. Appl. ISSN 1752-4571. Gould, F., Huang, Y., Legros, M., Lloyd, A. L. 2008. A killer-rescue system for self-limiting gene drive of anti-pathogen constructs. Proc. Royal. Soc. Lond. B. 275:2823-2829. Magori, K., M. Legros, M. Puente, D. A. Focks, T. W. Scott, A. Lloyd, F, Gould. 2009. Skeeter Buster: a stochastic, spatially-explicit modeling tool for studying Aedes aegypti population replacement and population suppression strategies. PLoS Negl Trop Dis 3(9): e508. doi:10.1371/journal.pntd.0000508 Okamoto KW, Robert MA, Gould F, Lloyd AL (2014) Feasible Introgression of an Anti-pathogen Transgene into an Urban Mosquito Population without Using Gene-Drive. PLoS Negl Trop Dis 8(7): e2827. doi:10.1371/journal.pntd.0002827 —Apple-Mail=_FB5E39FA-E2E7-43BD-A13F-79D8D79BD5AA Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=us-ascii
Postdoc: Modeling Population Genetics for Suppression of Mosquito-Vectored Diseases
PROJECT DESCRIPTION: Dengue is a mosquito-vectored disease that affects over 100 million people each year. With funding from the NIH, FNIH, and W. M. Keck Foundation, we have developed a set of mathematical models ranging from simple to complex, aimed at assisting the design and deployment of novel approaches for suppressing transmission of dengue by its major mosquito vector, Aedes aegypti. We are especially interested in evaluating the potential utility and risks associated with using genetically engineered, selfish genetic elements to drive genes into mosquito populations that render them incapable of transmitting dengue fever or decrease mosquito density. Our new work also extends to models relevant to suppressing malaria.
New developments in molecular genetics promise to increase the efficiency of building gene drive systems with novel properties. The postdoc in this position will build a set of simple to complex models to examine the expected dynamics of these gene drive systems in mosquitoes and other taxa.
The most detailed model that we have developed simulates the population dynamics and population genetics of Ae. aegypti in a city on the Amazon river, Iquitos, for which there are rich data sets on both mosquito dynamics and dengue epidemiology. An accompanying epidemiological model is currently under development. The goals of two other postdocs in our group are to expand the mosquito model and the human epidemiology model to encompass the entire city of about 400,000 people. The postdoc in this new position will also collaborate with the other postdocs to use these detailed models to test gene drive systems.
In addition to working on model development and analysis, the person in this position will collaborate in an interdisciplinary research group composed of mosquito ecologists, disease epidemiologists, molecular biologists, biomathematicians, ethicists, and scientists from disease-endemic countries. The person in this position will have the opportunity to visit Iquitos to better understand one of the systems being modeled. Desirable skills include the ability to program in C++ or knowledge of a related programming language, and training in evaluation of mechanistic models.
To apply: email a cover letter and CV to Fred_Gould@ncsu.edu
For more details on the project see the following publications:
Esvelt, K. M., A. L. Smidler, F. Catteruccia, G. M. Church. 2014. Concerning RNA-guided gene drives for the alteration of wild populations. eLife. 10.7554/eLife.03401.
Oye, K. A. et al. 2014. Regulating gene drives. Science. 345:626-628 Published online 17 July 2014
Huang, Y., Lloyd, A.L., Legros, M., Gould, F. 2010. Gene-drive into insect populations with age and spatial structure: a theoretical assessment. Evol. Appl. ISSN 1752-4571.
Gould, F., Huang, Y., Legros, M., Lloyd, A. L. 2008. A killer-rescue system for self-limiting gene drive of anti-pathogen constructs. Proc. Royal. Soc. Lond. B. 275:2823-2829.
Magori, K., M. Legros, M. Puente, D. A. Focks, T. W. Scott, A. Lloyd, F, Gould. 2009. Skeeter Buster: a stochastic, spatially-explicit modeling tool for studying Aedes aegypti population replacement and population suppression strategies. PLoS Negl Trop Dis 3(9): e508. doi:10.1371/journal.pntd.0000508
Okamoto KW, Robert MA, Gould F, Lloyd AL (2014) Feasible Introgression of an Anti-pathogen Transgene into an Urban Mosquito Population without Using Gene-Drive. PLoS Negl Trop Dis 8(7): e2827. doi:10.1371/journal.pntd.0002827—Apple-Mail=_FB5E39FA-E2E7-43BD-A13F-79D8D79BD5A via Gmail
A postdoctoral position is available at the University of California - Davis to study the molecular mechanisms, phylogenetic patterns, and functional consequences of transcriptome evolution in Drosophila. The project is based on the integration of RNA-seq, ChIP-seq, transgenic manipulation of gene expression and DNA-protein binding, and quantitative phylogenetic analysis to understand the roles of gene cooption, gene duplication, and de novo gene origin in the evolution of tissue-specific regulatory circuits. This work involves a collaboration between the labs of Artyom Kopp (developmental genetics and evo-devo), David Begun (evolutionary and population genomics), and Brian Moore (phylogenetic and comparative analysis). Additional aspects of this project may range from cell type specification to the evolution of enhancer sequences. Postdocs will be encouraged to develop independent research reflecting their own interests, within the broad field of developmental and evolutionary genomics.Candidates should have demonstrated expertise in experimental molecular genetics and genomics, with an emphasis on RNA-seq and ChIP-seq analysis, genome annotation, and comparative genomics. Some experience in developmental biology and transgenic methods is also desirable. Initial appointment is for one year, extendable by mutual agreement. Our labs and the entire department provide a very supportive atmosphere. The broader research environment at UC - Davis offers postdoctoral fellows chances for collaboration with leading experts in fields ranging from cell and developmental biology to evolutionary genomics and phylogenetics. Northern California, where Davis is located, provides outstanding recreational opportunities. Interested applicants should contact Artyom Kopp (email@example.com) with a CV, a brief statement of research interests and experience, and the names of three references.
Title: Niche Evolution in wild or lab-reared insects (U. of Aberdeen, UK) I am seeking talented and motivated PhD students to investigate evolutionary causes and consequences of ecological niche divergence during adaptive radiations, range shifts, or in response to anthropogenic habitat modification. The student may choose to conduct fieldwork with wild or pest insect species in Northeast Scotland, or can apply their ideas in mesocosm experiments using lab-bred insects such as seed beetles (Callosobruchus maculates). See http://bit.ly/18dFqnX for ongoing projects in the laboratory, and contact Lesley Lancasterlesleylancaster@abdn.ac.uk to express interest in joining the lab. Together, we will brainstorm a project idea that fits with the ongoing work in my lab and with your unique research goals. Research training: The student will be provided with all relevant research training. Essential background required by the student: First / second undergraduate degree (or equivalent), or masters degree with commendation/distinction. Link to the project: http://bit.ly/1F1bMPx To apply online: http://bit.ly/18dFswb APPLICATIONS DUE: 30th April 2015. It is advised to email Lesley Lancaster (firstname.lastname@example.org) with informal inquiries prior to applying online. *KEY DETAILS*: This project advert is for a competitively-funded scheme for a limited number of Elphinstone PhD Scholarships (http://bit.ly/1j0ulZR). These scholarships are available to students of any nationality, and will cover all tuition and fees associated with pursuing a PhD at the University of Aberdeen. Living expenses are not covered in the scholarship, however, and thus applicants should be prepared to contribute approximately 45,000 pounds to cover living expenses for the duration of their PhD. It is not advised to take on part time work during an intensive PhD-ship, so ideal candidates are those with sufficient means to cover their expenses for the duration of their studies. Lesley Lancaster, PhD University of Aberdeen School of Biological Sciences Zoology Building, Tillydrone Ave. Aberdeen AB24 2TZ email@example.com +44 01224 274551 http://bit.ly/18dFqnX The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas clraichte ann an Alba, ir. SC013683. “Lancaster, Lesley” via Gmail
Dear EvolDir community, The Deep Carbon Observatory (DCO) is an international, multidisciplinary initiative aimed at exploring all aspect of carbon science. The Deep Carbon Observatory is trying to integrate different aspect of carbon science from all disciplines (including evolutionary biologist), and one of the main interest is to integrate knowledge trough time (in the evolutionary sense). Relevant questions are linked to the evolution of microorganisms and their metabolism, the origin of life and the co-evolution of biosphere with the geosphere. The Deep Carbon Observatory is hosting its second Early Career Scientist Workshop at the Centro De Vulcanologia e Avaliao de Riscos Geolgicos ( http://bit.ly/18dFsw4), University of the Azores, So Miguel (Portugal), 31 August-5 September 2015. This workshop will bring together the next generation of researchers active in deep carbon studies from around the world. This relatively small workshop (~40 scientists) of early career researchers will continue to foster collaboration and community within the growing DCO Science Network. This workshop is funded by the Deep Carbon Observatory, and aims to support financially as many participants as possible. There is no registration fee for this workshop (accommodation and meals will be provided), and successful applicants will be eligible for up to 100% reimbursement of travel costs. Applications are encouraged from senior graduate students, postdoctoral researchers, fellows, and newly appointed assistant professors working on all aspect of carbon science (visit the DCO website for major details, http://bit.ly/18dFsw6). More informations on the workshop and the application procedure are available at this link http://bit.ly/1F1bN61 Deadline for the application is May 1, 2015. Please pass this message along to those that may be interested. Donato Giovannelli, PI Second DCO Early Career Scientist Workshop [image: Immagine in linea 1] Donato Giovannelli, PhD a: Department of Marine and Coastal Science - IMCS Rutgers University 71 Dudley Rd, suite 208 08901 New Brunswick, NJ - USA *Follow me on Twitter @d_giovannelli * T: (+1) 848-932-3378 e: firstname.lastname@example.org email@example.com http://bit.ly/1F1bMPr Skype: Given95 Google Scholar Profile http://bit.ly/18dFsw9 firstname.lastname@example.org via Gmail
March 11, 2015
The potential for synthetic research based on aggregating, integrating, and re-using data is enormous, yet most resources remain interoperable. To realize this potential, software and databases that handle evolutionary trees (and their associated annotations) must be interoperable. Interoperability, in turn, requires tools based on common standards. In the past few years, evolutionary informaticists, with help from NESCent, have been building a software toolbox for solving interoperability problems, based on the EvoIO âstackâ of NeXML, CDAO and PhyloWS. This toolbox makes it possible to begin building a worldwide network of interoperable evolutionary resources. The HIP (Hackathons, Interoperability, Phylogenies) aims to use the hackathon mechanism (which we have helped to develop at NESCent) to grow this network directly, by adding links to it, and indirectly, by creating examples for others to follow. To support this project within a working-group budget, we leverage support from strategic partners. Each of the planned series of 3 hackathons will bring together scientific programmers with related challenges. The hackathons target early-career scientists, who often have the most technical expertise and the most potential to pass along their skills and enthusiasm.
Asymmetrical sexual isolation but no postmating isolation between the closely related species Drosophila suboccidentalis and Drosophila occidentalis
Background: During the speciation process several types of isolating barriers can arise that limit gene flow between diverging populations. Studying recently isolated species can inform our understanding of how and when these barriers arise, and which barriers may be most important to limiting gene flow. Here we focus on Drosophila suboccidentalis and D. occidentalis, which are closely related mushroom-feeding species that inhabit western North America and are not known to overlap in geographic range. We investigate patterns of reproductive isolation between these species, including premating, postmating prezygotic, and postzygotic barriers to gene flow. Results: Using flies that originate from a single population of each species, we find that the strength of premating sexual isolation between these species is asymmetric: while D. occidentalis females mate with D. suboccidentalis males at a reduced but moderate rate, D. suboccidentalis females discriminate strongly against mating with D. occidentalis males. Female hybrids will mate at high rates with males of either species, indicating that this discrimination has a recessive genetic basis. Hybrid males are accepted by females of both species. We do not find evidence for postmating prezygotic or postzygotic isolating barriers, as females use the sperm of heterospecific males and both male and female hybrids are fully fertile. Conclusions: Premating isolation is substantial but incomplete, and appears to be the primary form of reproductive isolation between these species. If these species do hybridize, the lack of postzygotic barriers may allow for gene flow between them. Given that these species are recently diverged and are not known to be sympatric, the level of premating isolation is relatively strong given the lack of intrinsic post-zygotic isolation. Further work is necessary to characterize the geographic and genetic variation in reproductive isolating barriers, as well as to determine the factors that drive reproductive isolation and the consequences that isolating barriers as well as geographic isolation have had on patterns of gene flow between these species.
Dear colleagues, please find enclosed an opening for four professorships in the newly created “Center for Integrated Breeding” at the Georg-August-University Goettingen. Further information can be found at http://bit.ly/1GqS1iK, or you can contact me (email@example.com). Please feel free to bring this opening to the attention of potential applicants. Thanks and best wishes Henner Simianer Dr. Henner Simianer Professor of Animal Breeding and Genetics Department of Animal Sciences Georg-August-University Goettingen Albrecht-Thaer-Weg 3, 37075 Goettingen Tel.: +49-551-395604, Fax: +49-551-395587 Email: firstname.lastname@example.org http://bit.ly/1C6d6lb The Faculty of Agricultural Sciences at the Georg-August University Göttingen seeks to fill four professorships within the framework of a new “Center for Integrated Breeding” at the earliest possible date. The professorships are part of a “Center for Integrated Breeding” which is unique in Europe. This center is presently in the development stage und will bring together knowledge from plant- and animal-breeding with contributions from natural sciences as well as social sciences in order to establish an internationally leading role in this field. The establishment of the Center is being supported by leading German companies in the fields of animal and plant breeding. The successful candidates are expected to show a strong interdisciplinary approach and the willingness to cooperate with other faculties. There are excellent opportunities for research in cooperation with companies internationally active in the fields of animal and plant breeding. In teaching, the professorships should contribute to the research orientated MSc-programme “Integrated Plant and Animal Breeding”, which is to be established, as well as to other programmes offered by the Faculty of Agricultural Sciences for BSc-, MSc- and PhD-students. Ability and willingness to teach in English are a prerequisite. The conditions for being appointed to a professorship are stated in 25 of the Niedersächsischen Hochschulgesetzes (NHG) vom 26.02.2007 (Nds. GVBl. S. 69). The University of Göttingen Public Law Foundation has the right to appoint professors. Details will be gladly explained upon request. Applications from abroad are expressly welcome. Under certain circumstances, the positions may be filled on a part-time basis. The University of Göttingen strives to increase its proportion of female staff in fields where women are underrepresented and expressly encourages qualified women to apply. The university plans to make the professorships part of the Programme for Women Professors jointly organised by the German federal government and regional states. Disabled persons with equivalent qualification will be given preference. Applications including a CV with a representation of the applicant’s academic education and career, publications and teaching record should be submitted electronically no later than April 19, 2015. Further information and the application portal: http://bit.ly/1GqS1iK Full Professor “Functional Breeding ’ genetics and improvement of functional traits by breeding” The successful candidate will cover the field of development and implication of breeding methods for the purpose of improving functional traits in livestock with a focus on poultry. Research should contribute to combining the necessary genetic performance of livestock with the expression of functional traits such as fertility, health, behaviour and resource efficiency under the aspect of animal welfare. To this purpose, modern genome-based approaches including methods of quantitative genetics should be utilised. Facilities for experimental research with animals are available. Temporary professor (W2) with tenure track “Breeding Informatics” The successful candidate will develop methods based on bioinformatics for the efficient use of data from genome sequencing, high-throughput phenotyping and high-throughput genotyping in animal and plant breeding. This entails the development of methods which combine bioinformatics approaches with concepts from quantitative genetics, statistical genetics and population genomics. The methods thus formulated should be tested with very large data sets (“Big Data”) stemming from practical breeding. Full Professor (W3) “Plant Breeding Methodology ” The successful candidate covers the discipline of Plant Breeding and all aspects of its role in crop production. A strong methodological focus on Quantitative Genetics / Population Genetics as well as Selection Theory is expected. At a later moment, the candidate will succeed Prof. Dr. Heiko Becker, Professor of Plant Breeding. Full Professor (W3) “Crop Plant Genetics” The successful candidate is familiar with all current trends in Crop Plant Genetics and she/he is capable of investigating and judging their potential in crop breeding sciences. Her/his research will focus on highly promising methods for use in practical plant breeding e.g. functional genomics emphasizing nutrient uptake or pest resistance, application of genomics, transcriptomics, proteomics and metabolomics, analysis of gene networks, epigenetics or control of recombination. “Simianer, Henner” via Gmail
Get new Ideas, learn new techniques, form new collaborations: 2015 Meeting of PanAm EvoDevo REGISTRATION NOW OPEN for the inaugural meeting of the Pan American Society for Evolutionary Developmental Biology ! Mark your calendars for 5-9 August, 2015, Register NOW before all 350 slots are filled! *The registration deadline is April 1, 2015. Click **here* * to register.* Join us in Berkeley, California for the first EvoDevo meeting in the Americas sponsored by a new professional society dedicated to supporting the EvoDevo field! A few meeting highlights: - *Confirmed speakers: *Chris Amemiya, Alexa Bely, Sean Carroll, Rachel Collin, Kim Cooper, Tamara Franz-Odendaal, Matt Gibson, Angela Hay, Vivian Irish, Catherine Linnen, Mark Martindale, Jose Xavier Neto, Natalia Pabn-Mora (Early Career Award Recipient), Richard Palmer, Rudy Raff (Pioneers Award recipient), Bob Reed, Matt Rockman, Neelima Sinha, Stacey D. Smith, Ralf Sommer, Mansi Srivastava, James Umen - *Contributed papers *selected from submitted abstracts: submit now to ensure you have a chance to present your work. - Small, friendly symposia with focused breakout groups and workshops - Engaging posters on display throughout the entire meeting - Poster awards and prizes for students and postdocs All details about registration, accommodations, child care, and the conference program are available at the following website: http://bit.ly/1D23EcV Support the Society and Become a Member!! To learn more about PASEDB, visit the following website: http://bit.ly/1ElPbx4 Chelsea D. Specht, PhD Associate Professor; Departments of Plant and Microbial Biology & Integrative Biology Curator of Monocots; University and Jepson Herbaria University of California, Berkeley 111 Koshland Hall, MC 3102 Berkeley, CA 94720 510.642.5601 email@example.com http://bit.ly/16diOlZ Chelsea Specht via Gmail
—_000_da86a51e750245469a03add6fd47519aexch15mr02tutempleedu_ Content-Type: text/plain; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable iGEM @ Temple University Assistant Director The Institute for Genomics and Evolutionary Medicine (iGEM) is seeking candidates for the position of the Assistant Director of iGEM (http://bit.ly/YVV0zL). He/she will assist the Director (Sudhir Kumar) in all matters related to operations, academics, and grants. The duties include assistance with writing grant applications and progress reports, development and management of shared institutional resources, developing and maintaining relationships with stakeholders or potential funding sources, and coordinating institute outreach. They will also be responsible for the coordination of activities such as: implementing systems and procedures, preparing reports and/or financial analyses, managing web presence, and organizing special events, workshops , and meetings. We are looking for candidates with knowledge of molecular and/or genomic biology, strong interpersonal skills, and excellent oral and written communication abilities. Proficiency with Microsoft word, power point, and excel is a must. While we seek candidates with doctoral degree who do not plan to pursue traditional research careers, applications from highly experienced candidates with bachelors and masters degrees will also be seriously considered. Interested candidates should send inquiries or their detailed resume to firstname.lastname@example.org (include a cover letter). The application deadline is March 31, 2015. Temple University is located in the heart of historic Philadelphia, and is the sixth largest provider of graduate school education in the USA. Situated between New York City and Washington DC, Philadelphia is home to a large biotech industry and has many outstanding academic, research, and cultural institutions. Temple University is an equal opportunity, equal access, affirmative action employer committed to achieving a diverse community (AA, EOE, m/f/d/v). ==============Sudhir Kumar, Ph.D. Director, iGEM@Temple http://bit.ly/YVV0zL email@example.com phone: 623-225-5230 —_000_da86a51e750245469a03add6fd47519aexch15mr02tutempleedu_ Content-Type: text/html; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable
Post-doctoral position in epigenetic management of stress and disease resistance in Atlantic salmon @ Swansea University Institutions: Swansea University, Cardiff University, University of Aberdeen, University of East Anglia Collaborators: Landcatch, Marine Harvest To meet global food demands, aquaculture is expected to intensify fish production, but stress during intensification can also compromise animal health, particularly during early life when the teleost immune system is being formed. Many farmed fish are already highly inbred and further intensification will likely make them more susceptible to infectious diseases and pathogens more detrimental. Stress during intensification could change the expression of genes via epigenetic programming, but knowledge of fish epigenomes is very limited. We are looking for 1 Postdoctoral Research Fellow to work on an exciting project that will use a multidisciplinary, cutting-edge approach to investigate how stress experienced during early life can change the epigenome and subsequently affect the ability of fish to respond to pathogens. The project will involve a BACI design to manipulate stress in Atlantic salmon during embryogenesis and assess its effects on subsequent gut health and fitness by carrying out a gut bacterial community profiling using metagenomics. As a fitness indicator it will also examine fluctuating asymmetry and challenge fry with Saprolegnia parasitica, a pervasive fish pathogen, and monitor fry survival in relation to expression of immune-related genes through RNAseq, and patterns of DNA methylation. Following fish from fertilization to first feeding, will allow for the first time to relate the effects of early stress to (1) health, (2) an indicator of fitness and (3) resistance to parasites, and examine these in relation to variation in the genome and the epigenome. A Research Fellow position is available at Swansea University for 22 months starting June 2015, starting salary approx. 31,000. Travelling to partner Universities (Cardiff and Aberdeen mainly) will be required to complete parts of the work. Applicants are expected to match the following criteria: - Have a PhD in a relevant field (e.g. Biology, Ecology, Genetics). - Have published, confirmed accepted or in press, at least 3-4 papers in ISI accredited peer-reviewed journals by the starting date of the position. (Applicants with longer periods of postdoctoral experience will be expected to have proportionally higher numbers). Desirable criteria are: experience working on fish, genetics/genomics background, experience programming in R/Python. Informal enquiries can be directed to: Carlos Garca de Leaniz (firstname.lastname@example.org) or Sonia Consuegra (email@example.com) “CONSUEGRA S.” via Gmail
A three-year postdoc funded by the ERC is available at the University of Sheffield (United Kingdom), in the department of Animal and Plant Sciences. The postdoc will work with Pascal-Antoine Christin (http://bit.ly/1jTJ7hA), in collaboration with Patrik Nosil (http://bit.ly/1kRiEUc) and Colin Osborne (http://bit.ly/1p8VKLD). * The project The goal of this project is to understand the history of mutations and subsequent gene flow under selection that led to the gradual emergence of novel physiological pathways, using C4 photosynthesis as a study system. Genome-wide data will be generated for grasses of the genus Alloteropsis collected throughout Africa and Asia and analysed in an ecological context coupled with phenotyping (conducted in parallel by other group members). * What we require The postdoc will be responsible for collecting the samples in the field, generating the genome-wide data, and leading hypothesis-driven analyses in an evolutionary context. He will perform innovative data analyses and disseminate the results of the project. Applications are invited from candidates with interests in populations genomics as a tool to address important questions in evolutionary biology. A PhD is required, as well as a demonstrated expertise in population genomics, or bioinformatics. Field work experience is preferred. * What we offer A three-year contract is offered, which might be renewed for two extra years. The successful candidate will have the opportunity to conduct fieldwork in Africa, Asia and Oceania. The postdoc will integrate in a dynamic team composed of multiple postdocs and PhD students, and will collaborate with groups studying evolution, genomics, ecology and physiology. Preferred start date: 1st May 2015. The position will remain open until a suitable candidate is found. For inquiries, contact Pascal-Antoine Christin by email (firstname.lastname@example.org) and include a CV and brief (1-page) statement of research interests. Further reading: Christin PA, et al. 2012. Adaptive evolution of C4 photosynthesis through recurrent lateral gene transfer. Current Biology 22: 445-449. Soria-Carrasco V, et al. 2014. Stick insect genomes reveal natural selection’s role in parallel speciation. Science 344: 738-742. via Gmail
Multiple sequence alignment software have not yet met their primary aim for evolutionary biologists: maximizing homology of characters. The proliferation of alignment methods have diverse optimization functions, along with assorted heuristics to search for the optimum alignment; and these methods produce detectably different multiple sequence alignments in almost all realistic cases (see The need for a new sequence alignment program). This leaves the phylogeneticists wondering what to do. In response, the majority of phylogeneticists use manual alignment or re-alignment at some stage in their procedures.
If our goal is to develop an automated procedure for homology assessment (see Multiple sequence alignment), then we need some means of evaluating the relative success of different alignment methods.
There are four suggestions for benchmarking strategies for sequence alignment (Iantorno S, Gori K, Goldman N, Gil M, Dessimoz C 2014. Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment. Methods in Molecular Biology 1079: 59-73):
Simulation-based approaches adopt a probabilistic model of sequence evolution to describe nucleotide substitution, deletion, and insertion rates, while keeping track of “true” relationships of homology between individual residue positions (see Do biologists over-interpret computer simulations?).
(a) The simulation and analysis methods are not independent. All observations drawn from simulated data depend on the assumptions and simplifications of the model used to generate the data. This means that the results are biased towards those analysis methods that most closely match the assumptions of the simulation model.
(b) Simulations cannot straightforwardly, if at all, account for all evolutionary forces. This means that the simulations are not realistic, and their relevance for the behaviour of real datasets is unknown. The biggest failing in this regard is that, at some stage in the simulation, insertions and deletions are assumed to occur at random along the sequence (IID), and nothing could be further from the truth. Sequence variation occurs as a result of tandem repeats, inverted repeats, substitutions, inversions, translocations, transpositions, deletions, and insertions; and there are strong spatial constraints on variation such as codons and stem-loops. Current simulation methods fall well short of modeling these patterns of sequence variation.
The key idea behind consistency-based benchmarks is that different good aligners should tend to agree on a common alignment (namely, the correct one) whereas poor aligners might make different kinds of mistakes, thus resulting in inconsistent alignments.
(a) Two wrongs don't make a right. That is, consistent methods may be collectively biased. Moreover, consistency is not independent of the set of methods used (some may be consistent with each other and not with others).
(b) Consistency scores are a feature of several methods, which means that the benchmark is not independent.
3. Structural benchmarks most commonly employ the superposition of known protein/RNA structures as an independent means of alignment, to which alignments derived from sequence analysis can then be compared (see Edgar RC 2010. Quality measures for protein alignment benchmarks. Nucleic Acids Research 38: 2145-2153). The best known of these include: BAliBASE, OXBench, PREFAB, SABmark, IRMBase, and BRAliBase.
(a) Datasets are limited to structurally conserved regions, and may not be relevant for other alignment objectives.
(b) Deriving the structure-based alignments is problematic. For example, there is inconsistency amongst different stuctural superpositions.
4. Given a reference tree, the more accurate is the tree resulting from a given alignment, then the more accurate the underlying alignment is assumed to be (see Dessimoz C, Gil M 2010. Phylogenetic assessment of alignments reveals neglected tree signal in gaps. Genome Biology 11: R37).
(a) False inversion of a proposition: Accurate alignments yield accurate trees, therefore accurate trees must be based on accurate alignments.
(b) Alignment is often involved in constructing the reference tree. If not, the tree may be trivial in terms of taxon relationships.
This evaluation leaves us in the invidious position of not yet having any benchmarking method that is relevant to homology assessment for multiple sequence alignments. This conclusion is at variance with other previous assessments (eg. Aniba MR, Poch O, Thompson JD 2010. Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. Nucleic Acids Research 38: 7353-7363).
We need to consider what such a method might look like, and how we might go about constructing it. If biologists can't give the bioinformaticians a concrete goal for homology alignment then they can expect nothing in return.
It seems clear that we need to follow the idea behind option 3, but base the alignments on homology rather than structure. I once made a start with compiling some suitable datasets (see Morrison DA 2009. A framework for phylogenetic sequence alignment. Plant Systematics and Evolution 282: 127-149); but this was a very minor effort.
As I see it, we need alignments that are explicitly annotated with the reasons for considering the columns to be homologous. One suggestion would be to have relatively short alignments with annotations for "known" features, such as tandem repeats, inverted repeats, substitutions, inversions, translocations, transpositions, deletions, insertions, or stem-loops. These all create sequence variation, and they provide evidence of the homology relations among the sequences. Presumably the alignments would vary in length and number of sequences, and in the complexity of the patterns.
Perhaps the biggest practical problem will be how to deal with alignments where the homology criteria conflict with each other. That is, there are different types of criteria used to recognize homology — ie. similarity, structure, ontogeny, congruence (see Morrison DA 2015. Is multiple sequence alignment an art or a science? Systematic Botany 40: 14-26) — and they do not necessarily agree with each other.
This would allow us to come up with a set of requirements to specify various categories of the database, based on each of the above features. We would then try to accumulate as many example datasets for each category as we can. The database will presumably have protein-coding sequences in one section and RNA-coding, introns, etc in another. This dichotomy is simplistic, but I feel that it needs to be that way in order to be of practical use. Within each of those two sections we would have subsets of varying degrees of difficulty (eg. different degrees of average sequence similarity, or distinct taxon subsets in the same alignment, or orphan sequences).
This organisational approach is similar to that originally adopted for BAliBase, but it was dropped by most of the databases developed subsequently. I believe that it is the best approach for our purposes.
There are also experimentally created datasets where the alignment is known because all of the ancestors were sequenced as well. These would be useful; but their limitation is that the sequence variation was generated more or less at random, and so it does not match normal evolutionary processes. These alignments are more likely to match the IID assumption of the current automated alignment methods.
There is one further issue with this approach. Bioinformaticians often state that a few carefully prepared datasets is of little practical use to them (as opposed to being of use to phylogeneticists). What they need is a large number of datasets, the more the better. This is because they are interested in the percent success of their algorithms, and this cannot be assessed with small sample sizes. So, each alignment probably does not need to have too many taxa or too much sequence length — it is the number of alignments that is important, not their individual sizes. This could be achieved by sub-dividing larger datasets.
The American Museum of Natural History seeks to hire a part-time Physical Anthropology Facilitator to work in the Sackler Educational Laboratory for Comparative Genomics and Human Origins. Primary responsibilities will be to communicate key concepts in human biology and evolution to the public, and teach middle and high school groups. Facilitation requires comprehensive knowledge of hominin and primate skeletal material, proficiency with fundamental molecular biology techniques (i.e. PCR, restriction digest, gel electrophoresis), and a working knowledge of basic neurobiology. Requirements are a Masters Degree in Physical Anthropology, Forensic Anthropology, Genetics, or Human Biology. The ideal candidate will have informal teaching experience in a museum, zoo, or after school program. Please see full listing and apply online here: http://bit.ly/1FKs39R Julia M. Zichello, PhD Manager, Sackler Educational Laboratory for Comparative Genomics and Human Origins American Museum of Natural History Central Park West at 79th Street New York, NY 10024 212.769.5138 Julia Zichello via Gmail
Dear colleagues, Registration is open for the course “THE USE OF PHYLOGENIES IN THE STUDY OF MACROEVOLUTION - 3rd edition”, Septiembre 28-October 2, 2015. Instructor: Dr. Juan Lpez Cantalapiedra (Museo de Ciencias Naturales, CSIC, Spain). New phylogenetic methods would allow us to draw on the information encapsulated in phylogenetic trees in order to address a wide range of questions on macroevolution. First, this course will introduce participants to the use, modification and representation of phylogenetic trees. Then, we will focus on the use of phylogenetic information to reconstruct ancestral characters and biogeographic histories, learning how to apply phylogenetic comparative methods. This course will also tackle trait evolution modelling and the assessment of phylogenetic signal. Finally, we will learn about the shape of phylogenetic trees and its evolutionary causes and how to estimate the rates of diversification throughout the evolutionary history of groups. Participants are encouraged to bring their data sets to use in the practical class. Important note: Please bear in mind that this course is not about reconstructing (building) phylogenetic trees. Software: Mesquite, TreeEdit, FigTree, BayesTraits (using BayesTraits Wrapper in R), Tracer, RASP and R (ape, TreeSim, TreePar, Geiger, OUwie, BioGeoBEARS). Place: Facilities of the CRIP at Els Hostalets de Pierola, Barcelona (Spain). Organized by: Transmitting Science, the Centre de Restauraci i Interpretaci Paleontologica and the Institut Catal de Paleontologia Miquel Crusafont. More information: http://bit.ly/1m2EgOB or writing to email@example.com Please feel free to distribute this information between your colleagues if you consider it appropriate. With best regards Soledad De Esteban Trivigno, PhD. firstname.lastname@example.org via Gmail
We invite undergraduate and graduate students interested in ecological research and hands-on study of the natural world to take our Spring and Summer 2015 field classes at the University of Michigan Biological Station. You will join a community of researchers on the shores of Douglas Lake near Pellston, Michigan. Spring classes are 2-4 weeks long (2-5 credits) and include Great Lakes Oceanography, Biology of Birds and Ethnobotany. Summer classes are 8 weeks long and feature organismal- (Biology of Insects, Biology of Fishes, Algae) and ecosystem- (Rivers, Lakes and Wetlands, Limnology, Field Botany and Forest Ecosystems) focused classes as well as Ecology, Evolution and Behavioral Ecology. We have rolling course admissions, but the DEADLINE for priority consideration for our FINANCIAL AID is March 16, 2015. More information available at: http://bit.ly/1wt362X. via Gmail
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology