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August 24, 2014
For those of you who do not understand the notation:
Homo apriorius ponders the probability of a specified hypothesis, while Homo pragamiticus is interested by the probability of observing particular data. Homo frequentistus wishes to estimate the probability of observing the data given the specified hypothesis, whereas Homo sapients is interested in the joint probability of both the data and the hypothesis. Homo bayesianis estimates the probability of the specified hypothesis given the observed data.
August 23, 2014
Working Title: Research Curator, Ichthyology Position: Natural Science Research Curator II Vacancy Number: 60034991 Description of Work: This position of Research Curator, Ichthyology, has several areas of responsibility, including: 1. Development of original scientific research programs in ichthyological systematics (taxonomy, phylogenetics), genomics, ecology, and/or related fields; research programs may have local, regional, and/or international focus and will include pursuit of external research funding, data generation and analyses, and publication/dissemination of results; some aspects of this research should, ideally, include collaborations with other agencies, universities, and/or citizen scientists. 2. Curatorial responsibilities for the Ichthyology Research Collection, including maintenance and growth of collection, migrating collections data to databse format, specimen loan activities, and setting curatorial best-practice guidelines for collection. 3. Operational management and administration of the Icthyology unit, a subdivision of the Research & Collections section; duties include supervision of laboratory with oversight of equipment, budgets, and personnel. 4. Participation in science communication initiatives, including participation in Museum educational programming, delivering public science-based presentations, interacting with Museum visitors, serving as a role model for students and citizen scientists, and creating programmatic themes that raise the science literacy of visitors. A successful candidate will have the following knowledge, skills and abilities: (1) Considerable taxonomic/systematic knowledge in Ichthyology, in general, and of North Carolina and South Eastern United States fishes, specifically (2) Experience applying principles and practices of research, with special expertise in at least one aspect of fish systematics (taxonomy, phylogenetics), genomics, ecology, and/or related fields (3) A demonstrated mastery of materials, equipment, and techniques used in relevant research (laboratory based protocols and fieldwork) and specimen collection curatorial activities (4) A demonstrated track record of effective and creative science communication to diverse audiences (5) Experience managing/supervising research projects, a research laboratory, and/or personnel (6) Experience in preparing grant proposals to fund biological research and/or administering budgets supporting research or collections- related activities (7) Experience in publishing technical science papers in peer- reviewed journals Training and Experience Requirements: Required: A Master’s degree in biology, zoology, or related science field and three years of experience in specialty area; or an equivalent combination of education and experience. Preferred: A Ph.D. in biology, zoology, or related science field. Applicants should attach: a current CV; contact information for 3 personal references; and a vision statement outlining their short and long term research goals, their approach to collection curation, and their philosophy and objectives regarding science communication. For more information and application instructions, see: http://bit.ly/1qCjFA5 Jason R. Cryan, Ph.D. Deputy Museum Director, Research & Collections North Carolina Museum of Natural Sciences 11 W. Jones Street Raleigh, NC 27601 Phone: (919) 707-9933 Fax: (919) 715-2614 email: firstname.lastname@example.org Museum Website: http://bit.ly/1krSgkd Research Website: www.planthopper.com “Cryan, Jason R” “Stuart, Bryan” via Gmail
MOLECULAR EVOLUTION Faculty Position, Princeton University Princeton University seeks candidates for a tenured or tenure track faculty position in the area of Molecular Evolution to join a growing collaborative program across the broad interface of evolution, ecology, molecular biology and genomics. We are interested in scientists whose research focuses on questions that integrate across this interface, with the aim of offering novel conceptual advances. The position will be shared between the Department of Ecology & Evolutionary Biology and the Department of Molecular Biology. We seek colleagues who will enthusiastically contribute to a climate of interdisciplinary collaboration, excellence and diversity. The candidate should share our commitment to a mentoring process that attracts students of all ethnicities, nationalities, and genders. Applicants should write a vision statement, no longer than two pages, that outlines one or more major unsolved problems in their field and how they plan to address them. In this respect, the vision statement should go beyond a summary of the applicant’s prior and current research. Applications, including the vision statement, curriculum vitae, three reprints, and contact information for three references can be submitted online via http://bit.ly/1dfwjBL, Req #1400594. Screening of applications will begin October 31, 2014. Princeton University is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability status, protected veteran status, or any other characteristic protected by law. This position is subject to the University’s background check policy. The direct link to the online posting of Job Req #1400594 http://bit.ly/1pss50S (If the site does not come up, click twice or search Req#.) Thank you, Diane Carlino Department Manager Ecology and Evolutionary Biology Princeton University 104A Guyot Hall 609-258-5810 email@example.com Diane Carlino via Gmail
Background: Branched polymers of glucose are universally used for energy storage in cells, taking the form of glycogen in animals, fungi, Bacteria, and Archaea, and of amylopectin in plants. Some enzymes involved in glycogen and amylopectin metabolism are similarly conserved in all forms of life, but some, interestingly, are not. In this paper we focus on the phylogeny of glycogen branching and debranching enzymes, respectively involved in introducing and removing of the ?(1?6) bonds in glucose polymers, bonds that provide the unique branching structure to glucose polymers. Results: We performed a large-scale phylogenomic analysis of branching and debranching enzymes in over 400 completely sequenced genomes, including more than 200 from eukaryotes. We show that branching and debranching enzymes can be found in all kingdoms of life, including all major groups of eukaryotes, and thus were likely to have been present in the last universal common ancestor (LUCA) but have been lost in seemingly random fashion in numerous single-celled eukaryotes. We also show how animal branching and debranching enzymes evolved from their LUCA ancestors by acquiring additional domains. Furthermore, we show that enzymes commonly perceived as orthologous, such as human branching enzyme GBE1 and E. coli branching enzyme GlgB, are in fact related by a gene duplication and consequently paralogous. Conclusions: Despite being usually associated with animal liver glycogen and plant starch, energy storage in the form of branched glucose polymers is clearly an ancient process and has probably been present in the last universal common ancestor of all present life. The evolution of the enzymes enabling this form of energy storage is more complex than previously thought and illustrates the need for explicit phylogenomic analysis in the study of even seemingly ?simple? metabolic enzymes. Patterns of conservation in the evolution of the glycogen/starch branching and debranching enzymes hint at some as yet unknown mechanisms, as mutations disrupting these patterns lead to a variety of genetic diseases in humans and other mammals.
August 22, 2014
AustralianNationalUniversity.GeneticDiversity ARC Laureate Fellowship PhD scholarship - Genetic Diversity The Fenner School of Environment and Society at the Australian National University is seeking applications from highly qualified and motivated candidates for a PhD scholarship for research on ecological surrogates. Purpose Professor David Lindenmayer’s ARC Laureate Fellowship research program is examining surrogate ecology, particularly when and where it might work to improve environmental management. We are seeking an outstanding candidate to join a team working on biodiversity surrogates. Genetic diversity is an often overlooked aspect of biodiversity. This PhD program will evaluate genetic indicators and their use in biodiversity conservation. Aspects of the project may include assessing the use of genetic indicators for monitoring genetic diversity and assessing the impacts of management interventions and natural disturbance on genetic diversity and connectivity. This project will be focused on an exciting and novel aspect of biodiversity monitoring and as such provides scope for the student to develop ideas based around the topic of genetic indicators. The successful applicant will need to be highly motivated and capable of writing high-level scientific articles for leading international journals. Experience in population genetics is highly desirable. The successful candidate will be awarded a post-graduate scholarship stipend as part of an Australian Research Council Laureate Fellowship held by Professor David Lindenmayer. The scholarship will support the PhD program for 3 years, with a possible extension for a further 6 months. The successful candidate will need to commence their project no later than November 2014. The position is supported by an ARC Laureate Fellowship with a stipend of $29,844 per annum, tax-free for 3 years paid in fortnightly instalments. Other benefits The Fenner School of Environment and Society has a large, dynamic community of PhD students who are provided with modern office facilities and computer and statistical support. Students are encouraged to collaborate widely and attend national and international conferences. The successful candidate will become part of the Environmental Decisions Group - a network of some of the world’s leading applied environmental scientists that provides travel support for national and international collaboration. Duration Three years full-time with a possible six month extension. Supervision The project will be supervised by ARC Laureate Fellow Professor Lindenmayer and a supervisory panel that matches the candidate’s skills. Candidate requirements Bachelors degree with first-class honours, or a research Masters degree from a recognised university. Australian and New Zealand citizens; permanent residents of Australia; international students who hold an International Postgraduate Research Scholarship (IPRS). Selection is based on academic merit and the candidate’s research proposal. The successful candidate will have experience in environmental science and management, ecology or similar. Application process and closing date Interested individuals are invited to discuss the project with Professor David Lindenmayer (02 6125 0654 or firstname.lastname@example.org) and must submit a CV and a one page statement of possible research directions they would pursue in their project to email@example.com by 5pm 19 September 2014. The successful candidate would be expected to commence their doctoral program no later than November 2014. firstname.lastname@example.org via Gmail
PhD scholarships at the Australian Centre for Ancient DNA, Adelaide, Australia Project 1: Epigenetic modifications in adaptation to climate change Project 2: Phylogenomic analysis of the impacts of climate change, population fragmentation and localised extinctions We have 2 PhD positions available at the Australian Centre for Ancient DNA (ACAD), School of Earth & Environmental Sciences, at the University of Adelaide. For more information about ACAD, check out http://bit.ly/1wjI463 for links to Twitter, Facebook, our blog, recent publications and the official website. The positions are open to both international and domestic students with a strong academic achievement in either of the following areas: evolutionary biology, bioinformatics, or molecular biology. Competitive scholarships are also available via the University of Adelaide Graduate Centre for domestic (http://bit.ly/1ktxIHU) and international students (http://bit.ly/1iMxKwV). Both the Australian Department of Immigration and University of Adelaide expect international applicants to meet the English Language Proficiency (ELP) requirements. The ELP is based on high scores in IELTS (International English Language Testing System) or TOEFL (Test of English as a Foreign Language). For further information please refer to http://bit.ly/1ktxIY8. The projects are described below. There is the potential for fieldwork, and training in ancient DNA, bioinformatics, genomics, and population genetics. Interested applicants are encouraged to send a resume, a cover letter, and the contact details of 3 referees to Dr Bastien Llamas (email@example.com). 1) The role of epigenetic modifications in bovid adaptation to environmental change (Australian Research Council grant LP130100646). Supervision: Dr Bastien Llamas and Prof Alan Cooper. This project will use a novel experimental system to explore the potentially important role of epigenetics in long-term evolution and how animals adapt to rapid climate change. Bones of ancient bison and cattle preserved in permafrost or caves will be analysed for epigenetic markers using advanced Next Generation Sequencing approaches, and the patterns contrasted over a 30,000-year record of major climatic and environmental shifts. It has strong potential to reveal key loci for climate adaptation in modern cattle. Most previous genetic research has been blind to epigenetic marks, and this study promises to be a major advance in addressing this issue, with considerable implications for conservation genetics and the cattle industry. 2) Using phylogenomics to record the impacts of climate change, extinction and population fragmentation (Australian Research Council grant DP140104233). Supervision: Dr Julien Soubrier and Prof Alan Cooper. We will use ancient DNA from permafrost-preserved Steppe bison bones and bovid exome capture systems to build a detailed record of the genomic impacts of rapid climate and environmental change at the end of the Pleistocene (30-11 kyr). The project will analyse how ancestral genetic diversity is distributed amongst surviving bison populations, and the role of nuclear loci under selection and drift. It will create a novel temporal dataset of genomic adaptation and evolution, and will generate critical data for studies of evolutionary processes such as extinctions, speciation and conservation biology and management. via Gmail
Global analysis of saliva as a source of bacterial genes for insights into human population structure and migration studies
Background: The genetic diversity of the human microbiome holds great potential for shedding light on the history of our ancestors. Helicobacter pylori is the most prominent example as its analysis allowed a fine-scale resolution of past migration patterns including some that could not be distinguished using human genetic markers. However studies of H. pylori require stomach biopsies, which severely limits the number of samples that can be analysed. By focussing on the house-keeping gene gdh (coding for the glucose-6-phosphate dehydrogenase), on the virulence gene gtf (coding for the glucosyltransferase) of mitis-streptococci and on the 16S-23S rRNA internal transcribed spacer (ITS) region of the Fusobacterium nucleatum/periodonticum-group we here tested the hypothesis that bacterial genes from human saliva have the potential for distinguishing human populations. Results: Analysis of 10 individuals from each of seven geographic regions, encompassing Africa, Asia and Europe, revealed that the genes gdh and ITS exhibited the highest number of polymorphic sites (59% and 79%, respectively) and most OTUs (defined at 99% identity) were unique to a given country. In contrast, the gene gtf had the lowest number of polymorphic sites (21%), and most OTUs were shared among countries. Most of the variation in the gdh and ITS genes was explained by the high clonal diversity within individuals (around 80%) followed by inter-individual variation of around 20%, leaving the geographic region as providing virtually no source of sequence variation. Conversely, for gtf the variation within individuals accounted for 32%, between individuals for 57% and among geographic regions for 11%. This geographic signature persisted upon extension of the analysis to four additional locations from the American continent. Pearson correlation analysis, pairwise Fst-cluster analysis as well as UniFrac analyses consistently supported a tree structure in which the European countries clustered tightly together and branched with American countries and South Africa, to the exclusion of Asian countries and the Congo. Conclusion: This study shows that saliva harbours protein-coding bacterial genes that are geographically structured, and which could potentially be used for addressing previously unresolved human migration events.
Background: Vertebrate mitogenomes are economically organized and usually lack intergenic sequences other than the control region. Intergenic spacers located between the tRNAThr and tRNAPro genes (“T-P spacers”) have been observed in several taxa, including gadiform species, but information about their biological roles and putative functions is still lacking. Results: Sequence characterization of the complete European hake Merluccius merluccius mitogenome identified a complex T-P spacer ranging in size from 223–532 bp. Further analyses of 32 gadiform species, representing 8 families and 28 genera, revealed the evolutionary preserved presence of T-P spacers across all taxa. Molecular complexity of the T-P spacers was found to be coherent with the phylogenetic relationships, supporting a common ancestral origin and gain of function during codfish evolution. Intraspecific variation of T-P spacer sequences was assessed in 225 Atlantic cod specimens and revealed 26 haplotypes. Pyrosequencing data representing the mito-transcriptome poly (A) fraction in Atlantic cod identified an abundant H-strand specific long noncoding RNA of about 375 nt. The T-P spacer corresponded to the 5’ part of this transcript, which terminated within the control region in a tail-to-tail configuration with the L-strand specific transcript (the 7S RNA). Conclusions: The T-P spacer is inferred to be evolutionary preserved in gadiform mitogenomes due to gain of function through a long noncoding RNA. We suggest that the T-P spacer adds stability to the H-strand specific long noncoding RNA by forming stable hairpin structures and additional protein binding sites.
POST-DOCTORAL POSITION IN MICROBIAL GENOMICS A post-doctoral position is available in the laboratory of Jesse Shapiro (www.shapirolab.ca) at the University of Montreal (UdeM), starting in autumn 2014. About the lab. Our current research theme is microbial adaptation over recent (“human”) time scales. We aim to answer the following types of questions: What are the ecological and evolutionary mechanisms of adaptation? How do these mechanisms interact? What are the genomic changes that underlie microbial phenotypes of clinical and environmental importance? How does speciation work in bacteria? We are a diverse and international group of scientists, working on natural systems ranging from human gut-associated bacteria to bloom-forming freshwater cyanobacteria, using a combination of wet- lab and dry-lab approaches, rooted in population genomics, and located in the wonderful city of Montreal. About the position. We are looking for an excellent quantitative/computational biologist to work on a Canadian Institutes of Health Research (CIHR) funded project entitled “Genomic analysis of cholera transmission and microevolution.” This is a multi-disciplinary collaboration, involving researchers at UdeM, The Massachusetts General Hospital and The International Centre for Diarrhoeal Disease Research, Bangladesh. The aims of the project are (1) to identify Vibrio cholerae variants associated with symptomatic disease using (and developing) genome-wide association studies (GWAS), (2) to map cholera transmission events with a genomic-epidemiological approach, and (3) to quantify within-patient V. cholerae genetic diversity and its impact on disease and transmission. Within the scope of this project, the candidate will have the opportunity to work on the aspects that best suit their interests and skills. Desired candidate. The candidate must have a high level of training (PhD) with expertise in computational biology, population genetics and/or genomics, as evidenced by first-author publications. The ability to work in a collaborative, interdisciplinary research environment is essential. A strong computational or quantitative background is also essential. Applying. To apply, please send (1) a brief letter of research interests, (2) your CV, (3) contact information for three references, and (4) a publication representative of your work to: firstname.lastname@example.org. Selected publications from the lab: Shapiro BJ & Polz MF. (2014) Ordering microbial diversity into ecologically and genetically cohesive units. Trends in Microbiology 22: 235-247. PMID: 24630527 Farhat M, Shapiro BJ et al. (2013) Genomic Analysis Identifies Targets of Convergent Positive Selection in Drug-Resistant Mycobacterium tuberculosis. Nature Genetics 45: 1183-1189. PMID: 23995135 Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, Szabò G, Polz MF, Alm EJ. (2012) Population Genomics of Early Events in the Ecological Differentiation of Bacteria. Science 336: 48-51. PMID: 22491847 B. Jesse Shapiro Canada Research Chair // Chaire de recherche du Canada Microbial Evolutionary Genomics // Génomique microbienne évolutionnaire Assistant Professor // Professeur adjoint Department of Biological sciences // Département de sciences biologiques Université de Montréal www.shapirolab.ca Jesse Shapiro via Gmail
August 21, 2014
Research interns are needed to assist in a multi-disciplinary, multi-investigator, experimental study ecology and evolution in Trinidad. The research is led by Professor David Reznick at the University of California, Riverside. We seek to integrate multiple biological fields for the study of the interactions between ecological and evolutionary processes in Trinidadian streams. Duties of the position include assisting in monthly censuses of fish populations (guppies) in montane streams. The monthly censuses include long hours of laboratory time. Qualifications: We seek interns who are entertaining the possibility of pursing graduate studies in some area of ecology and evolution and who wish to gain some field research experience before entering graduate school. Research will take place in semi-remote areas of Trinidad sometimes under bad weather conditions. Applicants must be able to live and work well with others. Research will also involve carrying heavy packs over slippery and steep terrain. Applicants must be in good physical condition and be able to meet the demands of field research under these conditions. Ability to drive a standard transmission vehicle is desirable but not required. Applicants with first-aid/first responder training, skills in automobile maintenance, and construction skills are highly desirable. Please address these skills when applying. Interns will be required to spend a minimum of 3-months in Trinidad, with possibility of extension. Starting dates are flexible, starting as early as November 2014. We will cover travel expenses and living expenses. Applicants should send cover letter, CV and the names, phone numbers and e-mail addresses of three or more professional references to David Reznick (gupy @ ucr.edu) and Andrs Lpez-Sepulcre (alopez @ biologie.ens.fr ). At least two of the references should be academics. Andrs Lpez-Sepulcre via Gmail
The Lakehead University Paleo-DNA Laboratory Practical DNA Training Program. Please post the following information about the training program on the EvolDir website and direct it towards evolutionary biologists: Practical DNA Training Program: A two-week (9 business days) intensive laboratory-based training program designed to teach participants the fundamentals of molecular techniques including DNA extraction, amplification (using PCR), sequencing and interpretation. This training program is offered at various times throughout the year and we will work with you to find a suitable time for training. The next two scheduled courses for the Practical DNA Training Program are October 14 - 24, 2014 and November 10 - 20, 2014. For more information please contact us at 807-343-8877 or email@example.com or visit our website www.ancientdna.com and click on ‘Training Programs’. Thank you. Karen. Karen Maa Administrative Assistant Paleo-DNA Laboratory 1294 Balmoral Street, 3rd Floor Thunder Bay, Ontario P7B 5Z5 Telephone: 1-866-DNA-LABS or 1-807-343-8616 Karen Maa via Gmail
The implications of a Silurian and other thylacocephalan crustaceans for the functional morphology and systematic affinities of the group
Background: Thylacocephala is a group of enigmatic extinct arthropods. Here we provide a full description of the oldest unequivocal thylacocephalan, a new genus and species Thylacares brandonensis, which is present in the Silurian Waukesha fauna from Wisconsin, USA. We also present details of younger, Jurassic specimens, from the Solnhofen lithographic limestones, which are crucial to our interpretation of the systematic position of Thylacocephala. In the past, Thylacocephala has been interpreted as a crustacean ingroup and as closely related to various groups such as cirripeds, decapods or remipeds. Results: The Waukesha thylacocephalan, Thylacares brandonensis n. gen. n. sp., bears compound eyes and raptorial appendages that are relatively small compared to those of other representatives of the group. As in other thylacocephalans the large bivalved shield encloses much of the entire body. The shield lacks a marked optical notch. The eyes, which project just beyond the shield margin, appear to be stalked. Head appendages, which may represent antennulae, antennae and mandibles, appear to be present. The trunk is comprised of up to 22 segments. New details observed on thylacocephalans from the Jurassic Solnhofen lithographic limestones include antennulae and antennae of Mayrocaris bucculata, and endites on the raptorial appendages and an elongate last trunk appendage in Clausocaris lithographica. Preserved features of the internal morphology in C. lithographica include the muscles of the raptorial appendage and trunk. Conclusions: Our results indicate that some ‘typical’ thylacocephalan characters are unique to the group; these autapomorphies contribute to the difficulty of determining thylacocephalan affinities. While the new features reported here are consistent with a eucrustacean affinity, most previous hypotheses for the position of Thylacocephala within Eucrustacea (as Stomatopoda, Thecostraca or Decapoda) are shown to be unlikely. A sister group relationship to Remipedia appears compatible with the observed features of Thylacocephala but more fossil evidence is required to test this assertion. The raptorial appendages of Thylacocephala most likely projected 45 degrees abaxially instead of directly forward as previously reconstructed. The overall morphology of thylacocephalans supports a predatory mode of life.
—_000_87FCC0D1FF47BB4E8B42E4989C746A862B9E0C80EXCHMBOX6exchuc_ Content-Type: text/plain; charset=”Windows-1252” Content-Transfer-Encoding: quoted-printable Position Description A postdoctoral position is available in the Department of Entomology at the University of California Riverside to work on the genetic and molecular basis of insecticide resistance in glassy winged sharpshooter (GWSS) - the primary vector of the bacteria Xylella fastidiosa, which causes Pierce’s Disease in grapevines. Recent insecticidal control failures and corresponding surges in GWSS numbers have raised serious concerns about the status of insecticide susceptibility in Californian populations of GWSS. The successful candidate will (1) determine the current resistance status of GWSS in California agricultural and nursery settings, (2) elucidate the genetic and molecular underpinnings of any resistance, and (3) design tools and assays for use in an integrated insecticide resistance management plan. Additionally, the postdoc is encouraged to develop new lines of work (e.g. population genomics, ecological modeling, etc.) on GWSS. The project, funded by the California Department of Food and Agriculture, is a collaborative effort headed by Drs. Frank Byrne, Rick Redak, and Bradley White. The postdoc will be supervised by Dr. White, but will also work closely with the other PIs. After completion of the project, the postdoc will have substantial experience designing and conducting bioassays, analyzing next-generation sequencing data, and communicating policy recommendations to growers. As such, the position represents an excellent opportunity to acquire a unique combination of skills that serve as good training for various positions in academia, industry, and government. We are looking for someone with expertise in evolutionary biology, insect ecology, vector biology, insect toxicology, and/or agricultural entomology. Familiarity with next-generation sequencing analysis is a positive, but not required. Regardless of prior experience, we expect the candidate to develop a wide-knowledge base and skillset. The position is for one year with the possibility of renewal for up to three years total. Salary will be commensurate with experience level. For additional information about the White Laboratory please navigate to http://bit.ly/17xDZQ5 To Apply A minimum qualification is a PhD or equivalent in Biology, Entomology, or a related discipline. Applicants with multiple, first-author publications are preferred. To apply, please send a brief description of previous research (1 page), a CV, and contact information for three references to firstname.lastname@example.org. A start date in Fall 2014 is ideal, but negotiable. Position is open until filled. Additional Information The White Lab is housed in the relatively new Entomology Building at UCR. We have access to state of the art genomic and bioinformatics core facilities and are part of the Center for Disease Vector Control (CDVR), which is composed of a diverse and highly talented group of scientists studying insect vectors of animal, human, and plant diseases. Substantial resources for field experiments are available through the Agricultural Experiment Station (AES) facilities. UCR is an affirmative action and equal opportunity employer with a commitment to workforce diversity. AA/EOE Bradley J. White Assistant Professor Center for Disease Vector Research Department of Entomology University of California Riverside, CA 92521 —_000_87FCC0D1FF47BB4E8B42E4989C746A862B9E0C80EXCHMBOX6exchuc_ Content-Type: text/html; charset=”Windows-1252” Content-Transfer-Encoding: quoted-printable
A postdoctoral position is available in the Department of Entomology at the University of California Riverside to work on the genetic and molecular basis of insecticide resistance in glassy winged sharpshooter (GWSS) - the primary vector of the bacteria Xylella fastidiosa, which causes Pierce’s Disease in grapevines. Recent insecticidal control failures and corresponding surges in GWSS numbers have raised serious concerns about the status of insecticide susceptibility in Californian populations of GWSS. The successful candidate will (1) determine the current resistance status of GWSS in California agricultural and nursery settings, (2) elucidate the genetic and molecular underpinnings of any resistance, and (3) design tools and assays for use in an integrated insecticide resistance management plan. Additionally, the postdoc is encouraged to develop new lines of work (e.g. population genomics, ecological modeling, etc.) on GWSS.
The project, funded by the California Department of Food and Agriculture, is a collaborative effort headed by Drs. Frank Byrne, Rick Redak, and Bradley White. The postdoc will be supervised by Dr. White, but will also work closely with the other PIs. After completion of the project, the postdoc will have substantial experience designing and conducting bioassays, analyzing next-generation sequencing data, and communicating policy recommendations to growers. As such, the position represents an excellent opportunity to acquire a unique combination of skills that serve as good training for various positions in academia, industry, and government.
We are looking for someone with expertise in evolutionary biology, insect ecology, vector biology, insect toxicology, and/or agricultural entomology. Familiarity with next-generation sequencing analysis is a positive, but not required. Regardless of prior experience, we expect the candidate to develop a wide-knowledge base and skillset. The position is for one year with the possibility of renewal for up to three years total. Salary will be commensurate with experience level.
For additional information about the White Laboratory please navigate to http://bit.ly/17xDZQ5
A minimum qualification is a PhD or equivalent in Biology, Entomology, or a related discipline. Applicants with multiple, first-author publications are preferred. To apply, please send a brief description of previous research (1 page), a CV, and contact information for three references to email@example.com. A start date in Fall 2014 is ideal, but negotiable. Position is open until filled.
The White Lab is housed in the relatively new Entomology Building at UCR. We have access to state of the art genomic and bioinformatics core facilities and are part of the Center for Disease Vector Control (CDVR), which is composed of a diverse and highly talented group of scientists studying insect vectors of animal, human, and plant diseases. Substantial resources for field experiments are available through the Agricultural Experiment Station (AES) facilities.
UCR is an affirmative action and equal opportunity employer with a commitment to workforce diversity. AA/EOE
Bradley J. White
Center for Disease Vector Research
Department of Entomology
University of California
Riverside, CA 92521—_000_87FCC0D1FF47BB4E8B42E4989C746A862B9E0C80EXCHMBOX6exchuc via Gmail
Postdoctoral position in Systematics and Evolution A two-year postdoctoral position in Systematics and Evolution is available in the Department of Zoology, Swedish Museum of Natural History, Stockholm. Project description “Species-level phylogeny and delimitation in a biodiversity hotspot” Madagascar is well known for its high level of endemism, basically across every organism group. The combination with severe habitat degradation has “rewarded” the island with a top placement among biodiversity hotspots. The increased evolutionary research interest last twenty years has focused on vertebrates and surprisingly little is yet known about the colonization and speciation history of most insect groups. Using Hydradephagan water beetles as model organisms this project will use dated phylogenetic frameworks to analyze colonization and speciation patterns across replicated endemic radiations and clades with representatives but seemingly without radiations. Intraspecific genetic variation will be sampled to estimate parameters in the multispecies coalescent model as a window into the speciation process. The project also includes evaluation of species delimitation methods on endemic radiations with non-reciprocally monophyletic species in gene-trees. Tasks The position is part of a research project and group (Bergsten Systematic Entomology Lab: http://bit.ly/1uZz1FZ) at the Swedish Museum of Natural History on the taxonomy, faunistics, phylogeny, colonization, speciation and evolutionary history of Hydradephagan water beetles on Madagascar. The work includes DNA labwork, fieldwork, data analyses, help with supervision of student projects, article- and grant writing. The DNA labwork will be conducted at the Molecular Systematics Laboratory at the Swedish Museum of Natural History. Qualifications To be qualified for the postdoctoral position the applicant needs to have a PhD degree (or have a PhD thesis ready with a date fixed within 2014 for thesis defense) in Systematics/Phylogenetics/Evolutionary Biology or similar direction of studies. The PhD degree should have been received no more than six years before the deadline for applications. Criteria for selection Among qualified applicants selection is made according to scientific merits, quality of the PhD thesis, personal skills, the applicant´s documented knowledge in subjects of relevance for the research area, ability to master English language (both spoken and written), analytical ability, creativity, initiative, independence, teamwork and ability to cooperate. Previous experience with molecular (DNA) lab work and knowledge of relevant theory and methods (phylogenetic, dating, species delimitation, biogeographic and diversification rate analyses) weigh heavily. Experience with entomological fieldwork, taxonomic work and French language (spoken in Madagascar) are consider as additional qualifications. Terms of employment The position is for two years full time. Start of position should be in 2014 but exact date up to negotiation with the successful candidate. The position is financed by a grant from the Swedish Research Council, VR. For more information, please contact Johannes Bergsten (firstname.lastname@example.org). Union representative is Bodil Kajrup, SACO-S. Both can be reached at telephone number + 46 8 519 540 00. To be included in the application Maximum one A4-page of personal presentation and your reasons for applying (letter of intent). Curriculum vitae with publication list. Copy of three selected publications. Copy of PhD thesis and PhD degree certificate or date of scheduled defense within 2014. Also provide a list of two persons who may act as references (with telephone numbers and e-mail addresses). Please send your application, marked with dnr 2.3.1-603-2014, to email@example.com or to Swedish Museum of Natural History, P. O. Box 50007, SE-104 05 Stockholm, Sweden, no later than September 9, 2014. Johannes Bergsten, PhD Senior Curator / Förste Intendent Research Division Swedish Museum of Natural History Box 50007 SE-104 05 Stockholm SWEDEN Visiting Address: Frescativägen 40 Phone: +46 8 5195 4192 Fax: +46 8 5195 4212 E-mail: firstname.lastname@example.org http://bit.ly/1AA3fQ2 Johannes Bergsten via Gmail
The Washington Area Phylogenetics Consortium is pleased to announce the Fourth annual Frontiers in Phylogenetics Symposium “Genome-Scale Phylogenetics: Analysing the Data” Sponsored by the National Museum of Natural History, Smithsonian Institution, and the Washington Area Phylogenetics Consortium Location: Warner Brothers Theatre, National Museum of American History, Washington, DC Time and Date: 9 AM to 5 PM, Monday September 15, 2014 REGISTRATION IS FREE BUT REQUIRED. Please visit the link below to register. http://bit.ly/FIPSymposium 8:00 Coffee and Continental Breakfast Service in Constitution Café 9:00 Introductions Michael Braun, National Museum of Natural History 9:05 Welcome to the Smithsonian John Kress, Interim Undersecretary for Science, Smithsonian Institution 9:15 Overview and Logistics Guillermo Ortí, George Washington University 9:25 Phylogenomics and Next-Generation Inferences: the Future of Phylogenetics in an Era of Big Data Lacey Knowles, University of Michigan 10:05 Break 10:30 Deep Metazoan Phylogeny and the Utility of Taxon-Specific Ortholog Sets Kevin Kocot, University of Queensland, Brisbane 11:10 A Phylogenomic View on the Early History of Gnasthostome Evolution: Is One Tree Enough? Ingo Ebersberger, Goethe University, Frankfurt 11:50 Lunch Break 1:30 Distinguishing Methodological and Biological Causes of Gene Tree Discordance in Phylogenomic Datasets Derrick Zwickl, University of Arizona 2:10 Filtering and Partitioning Strategies for Phylogenomic Analyses David Swofford, Duke University and National Evolutionary Synthesis Center 2:50 Break 3:10 Genome-scale Phylogenetics in the Presence of Hybridization and Incomplete Lineage Sorting Luay Nakhleh, Rice University 3:50 Joint Inference of Gene Trees and Species Trees at the Genomic Scale Bastien Boussau, University Claude Bernard, Lyon 4:30 Round Table Discussion With All Speakers Any questions or for more information contact Brian Coyle Coyleb@si.edu “Coyle, Brian J.” via Gmail
August 20, 2014
Dear EvolDir Community, We are pleased to announce the RNA-seqlopedia: http://bit.ly/1z4tj30 The RNA-seqlopedia is meant as a resource for researchers trying to utilize RNA-seq protocols for their research, including de novo assembly of transcriptomes as well as quantification of gene expression. The site focuses on multiple aspects of RNA-seq work including experimental design, molecular protocols, and bioinformatic analyses. We realize that the site does not yet cover all aspects of transcriptomic analysis, and undoubtedly contains errors or dated information that will be modified. We will continue to update the site and add to its content, particularly via input from the scientific community, so we request your input! We hope that the RNA-seqlopedia will prove to be a useful research resource for those interested in transcriptomic analyses using second (and third) generation sequencing. The site was made possible by a grant from the NIH National Center for Research Resources, and is being created and maintained by the Cresko Lab at the University of Oregon. If you have any feedback or suggestions, please write us. Sincerely, Clay Small Julian Catchen Susie Bassham Bill Cresko William A. Cresko, Ph.D. Associate Professor of Biology Director, Institute of Ecology and Evolution University of Oregon http://bit.ly/1pMIFIC; @wcresko email@example.com via Gmail
*Postdoctoral position in Evolutionary Genomics and Molecular and Cellular biology * */Molecular and cellular mechanisms of hyper-resistance to stress in the ameiotic bdelloid rotifer Adineta vaga/*** ** A 3-year postdoctoral research position is available in the group of Biochemistry, Biophysics and Molecular Genetics of Micro-organisms at the life Science Institute (ISV) of the Catholic University of Louvain (UCL, Belgium) to take part in a collaborative ARC research program with the Research Units in Environmental and Evolutionary Biology (URBE) and in Cellular Biology (URBC) at the University of Namur (UNamur, Be). This postdoc position is embedded within the research project entitled: /Asexuality and ‘immortality’, bdelloid rotifers as an evolutionary ‘scandal’ and a model system in biology. /This project is funded during 5 years and will start in October 2014. *Project:* Bdelloid rotifers are micro-organisms (animals) that have recently attracted much interest in the scientific community because of their ancient asexuality and their extreme resistance to stress, such as desiccation and high doses of ionizing radiation. They are capable to survive when their genome is shattered into small fragments and repair the DNA double strands breaks (DSBs) (see Hespeels et al., 2014). Repeated cycles of chromosomal repair are thought to promote allelic recombination and gene conversion in the absence of meiosis. Moreover desiccation and the induced DNA DSBs are also thought to provide a unique opportunity to acquire horizontally transferred genes, thereby contributing to the adaptive success of these organisms. In this project, the mechanisms that make bdelloid rotifers unique in terms of evolutionary strategy and hyper-resistance to stress will be investigated based on genomic data recently obtained by our consortium for the bdelloid rotifer /Adenita vaga/ (see Flot et al, 2013, Nature 500:453-7). Genomic approaches will be used to study the dynamics of /A. vaga/ genome during cycles of desiccation/rehydration/radiationand to decipher the genetic expression program that governs the different stages of its life-style. Molecular and cellular approaches will be developed to unveil and characterize the mechanisms that allow /A. vaga/ to repair its shattered chromosomes and generate genetic diversity,as well as its dependence with respect to oxidative stress response. Finally, conditions for horizontal gene transfer and RNA interference will be investigated, opening the way to the development of reverse genetic strategies. The ultimate prospect of the project is to establish bdelloid rotifers as a new model system for the understanding of fundamental biological processes such as DNA repair, cell survival and senescence. *PIs of the consortium:* Prof. Bernard Hallet (ISV, UCL), Prof. Karine Van Doninck (URBE, UNamur), Dr. Florence Debacq-Chainiaux (URBC, UNamur)** The involved consortium brings together experts in the fields of evolutionary biology and genomics (K. Van Doninck, URBE, UNamur), DNA recombination and genome plasticity (B. Hallet, ISV, UC) and oxidative stress response (F. Debacq-Chainiaux, URBC, UNamur). The appointed candidate will be expected to share its research time on both sites under the supervision of the three PIs of the consortium. The universities are at a distance of 35km from each other and easily connected by train. *Contacts:* Prof. Bernard Hallet, Bernard.firstname.lastname@example.org Universit Catholique de Louvain. Institut des Sciences de la Vie (ISV) http://bit.ly/1qTDNQl Prof. Karine Van Doninck, email@example.com University of Namur, Laboartory of Evolutionary Genetics and Ecology (http://bit.ly/1qTDQf8) *Qualifications:* We are looking for a post-doc with a strong interest and background in evolutionary genomics and molecular and cell biology. Expertise in the field of DNA repair and recombination, chromosome structure and dynamics, and/or genomics (NGS approach) is a valuable asset. Additional experience in cell biology techniques like DNA transfection, immuno-localization, fluorescence hybridization and microscopy will be a benefit. Priority will be given to candidates with a proven track record (with several publications as a first author) who will express their motivation in developing their autonomy and their interest for new challenges. *Application://* The position is available to both foreign nationals and Belgian citizens under ‘international mobility’ status, meaning that they may not have resided in Belgium for more than 12 months over the past 3 years preceding the appointment. The duration is for 2 years (with a possible 1-year renewal) starting on the *1^st of October 2014. *The closing date for applications is *^September 5th 2014.* Interested applicants should send a cover letter (briefly describing research experience, interests, and career goal), a curriculum vitae (with list of publications), and the names of three references (With address, phone number and E mail) to Bernard HALLET (Bernard.firstname.lastname@example.org) via Gmail
Postdoctoral Research Associate: Mechanistic Phylogenetic Models for Amino Acid Substitution Temple University An NSF-funded postdoctoral research position is available in the research group of David Liberles (Temple University from November, 2014; currently at University of Wyoming). The position is guaranteed for 1 year with the possibility of extension with successful performance. The successful candidate will be expected to relocate to Philadelphia, PA, USA and a start date as soon as possible after 11/1/14 is desired. The research project involves the construction and phylogenetic implementation of mechanistic models for amino acid substitution in C++. The ideal candidate will have a strong background in mathematics and statistics, strong C++ programming skills, and experience with phylogenetic methods. Knowledge of proteins and/or evolutionary biology is a plus. To apply, please send a cover letter that describes your background, motivation, and interests as well as a full CV to email@example.com. Please also arrange to have 3 letters of recommendation sent directly by the letter writer to the above email address as well. International applicants are encouraged to apply and will be given full consideration. “David A. Liberles” via Gmail
Ph.D. Student: Mechanistic Phylogenetic Models for Amino Acid Substitution Temple University An NSF-funded Ph.D. student position is available in the research group of David Liberles (Temple University from November, 2014; currently at University of Wyoming). The successful candidate will be expected to enroll in the Ph.D. program at Temple University in spring semester, 2015. The research project involves the construction and phylogenetic implementation of mechanistic models for amino acid substitution in C++. The ideal candidate will have prior programming coursework or experience, a strong background in mathematics, and interest in evolutionary biology. Students with any number of primary backgrounds, including biology and mathematics will be considered. To apply, please send a cover letter that describes your background, motivation, and interests as well as a full CV to firstname.lastname@example.org. I will guide the successful candidate through the Ph.D. application process at Temple University. International applicants are encouraged to apply and will be given full consideration. “David A. Liberles” via Gmail
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology