Society of Systematic Biologists

Subject line: Tenure-track position: effect of global change on population-level evolutionary processes Body of message: We are seeking a tenure-track Assistant Professor in the Department of Biological Sciences, College of Environment and Life Sciences (CELS) with research interests in the effects of global change on population-level evolutionary processes. The anticipated appointment is August 1, 2011. Visit website: https://jobs.uri.edu to view complete details for job posting #6000230. Position is open until filled, with review of applications to begin October 1, 2010. Only electronic applications will be accepted. Documents to attach in PDF format to your letter of application: curriculum vitae which, through your record of experience, education, publications, research plan, and statement of teaching philosophy, demonstrates your potential for excellence in teaching and for developing a high quality, nationally recognized and externally-funded research program. Additionally, send copies of up to three published papers and arrange to have three letters of reference sent by October 1, 2010 to: Dr. Brad A. Seibel, Associate Professor, CELS-Bio, Center Biotech Life Science, University of Rhode Island, Kingston, RI 02881. Visit the department website: http://www.uri.edu/cels/bio/ for additional information. The University of Rhode Island is an Affirmative Action/Equal Employment Opportunity Employer and values diversity. URI is an E-Verify Employer. Evan Preisser, Assistant Professor Dept. of Biological Sciences, University of Rhode Island 9 E. Alumni Ave., Kingston RI 02881 USA 401 874-2120; preisser[at]uri.edu; http://cels.uri.edu/preisserlab/ Evan Preisser

I am looking for a lab technician. My lab studies sexual selection and speciation in stickleback fish, and we combine behavioral work with genetics, morphology and evolution. The position is split between fish husbandry and research support. Applications must be made through the MSU Human Resources website for job posting # 4087. https://jobs.msu.edu/applicants/jsp/shared/frameset/Frameset.jsp?time=1283375322611 Informal inquiries can be made to Jenny Boughman, boughman[at]msu.edu . Job description: Research Technician I -- Department of Zoology, Michigan State University Minimum requirements: A Bachelor's degree in biology or related field with knowledge of animal behavior, ecology, and evolution. Several months experience with husbandry of fish or ampibians, including care of adult and juvenile fish and embryos, and of setting up and maintaining large numbers of aquariums for freshwater fish and/or amphibians. Some experience and good ability for training and supervising assistants in care of fish and colony maintenance. Excellent organizational and communication skills. Must be dependable. Weekend and holiday work required. Desired qualifications: Ability to take charge and oversee animal husbandry and lab procedures. Understanding of campus animal care policy and procedures. Experience with the use of spreadsheet software (e.g., excel etc) and introductory statistics. Ability to learn new software programs. Job summary: Primary responsibility for maintaining large colony of stickleback fish, including caring for fish, keeping aquaria and lab clean. Provide support for ongoing experiments, including collection and analysis of morphological, genetic, and behavioral data on threespine sticklebacks. Supervise and train undergraduate assistants in fish husbandry and lab maintenance tasks. Order equipment, supplies, and materials and oversee maintaining supplies necessary for fish care and experiments in the lab. Maintain animal care records and lab records of animal and maintenance protocols, genetic crosses, supplies, orders, and maintain lab website and computer network. Some animal care experience required. Position to begin immediately. Salary $30,846 -- Jenny Boughman Associate Professor Zoology Michigan State University 203 Natural Science Bldg East Lansing MI 48824 517.353.8636 boughman[at]msu.edu http://www.zoology.msu.edu/all-faculty/janette-boughman.html Jenny Boughman

Dear list: My request for protocols for getting DNA out of bone and formalin-fixed generated lots of response. Thanks for your time and information! Below is a collection of all the responses so far. I can't comment on the efficacy of any one of them yet, but I'm working on it. Thanks, Steve ** If you are not having success I suspect your problems are one/some of the below a) There is absolutely no DNA in the samples - in particular if the material was in formalin for more than ca. 12-24 hours it will have been heavily crosslinked, and even fragmented if it was in unbuffered formalin b) There is DNA but the primers you are using are targeting too big a fragment. How old are the samples and how long were the fixed ones fixed, and how long ago where they fixed? In general, a simply and effective bone protocol is that by Rohland et al, attached. If that doesn't work, and you are using really short PCRs (ca 100bp) my guess is it won't work. For formalin, I once did a lot of work on it. Please see the extremely tedious paper that I wrote as a result. As you will gather from it, heat + alkali can help matters (the Shi 2004 paper I cite), but in general by increasing yield only. If there is no DNA...it won't do much. Happy to help with any specific questions. ** Hi Steve, Dealing with formalin-fixed material is not an easy task, as you might already know. We recently published a paper using a new method based on Tetramethylsilane (TMS)-Chelex to reduce costs compared with Fang et al. (2002). Most importantly, we observed that neither an indigestible matrix of cross-linked protein nor soluble PCR inhibitors impede PCR success when dealing with formalin-fixed material. Instead, amplification success from formalin-fixed tissue appears to depend on the presence of unmodified DNA in the extracted sample. We were not able to get DNA sequences out of every sample, but we provide a 'test' to check if DNA will be useful for PCR. You can obtain a pdf of our paper at http://www.icm.csic.es/scimar/index.php/secId/6/IdArt/3907/ I hope this helps. Cheers, ** Dear Steve, Take a look on this article ( http://www.pnas.org/content/105/40/15464.figures-only). The authors extracted DNA from museum specimens (mostly bones) of the giant tortoises of Galapagos. Take care ** Hi Steve, I think you're wasting your time with formalin-fixed tissues, as this issue has appeared on EvolDir about twice or thrice a year for fifteen years...but you should be able to get DNA from the carapace. For ideas, see Biotechniques. 1999 Jun;26(6):1086-8. Microsatellite locus amplification using deer antler DNA. O'Connell A, Denome RM. PMID: 10376147 [PubMed - indexed for MEDLINE] also http://oldwww.wii.gov.in/ars/2006/imran_khan.htm ** http://oldwww.wii.gov.in/ars/2006/imran_khan.htm>If you are interested in using a kit to do the extraction, there is an excellent protocol on the Qiagen website for extraction of DNA from bone. It is called "Purificant of total DNA form compact animal bone using the DNeasy Blood and Tissue Kit". I recently used it to extract over 40 toe bone specimens from a mouse species with a lot of success. If not I also have a standard ethanol precipitation method that I have used with success in bones as well. Let me know if you would like that. ** I would suggest you post your message on the ancient DNA forum at: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=ancient-dna Several people worked on Museum specimen. I work on bones so let me know if you want a few protocols. Usually the one from Hofreiter & Rohland is the one most aDNA people use. ** Steve, I saw your message this morning on Evoldir. Coincidentally, I am working on a very similar problem with the goal of extracting DNA from turtle claws. We have had success with fresh tissue and we have been able to amplify a 630 bp fragment from the mtDNA control region of painted turtles. During the past month, we have been conducting experiments where we expose claws to buffered formalin for 48 hours followed by 4-5 days in 70% EtOH (modeling museum protocol), and then attempting extraction using a modified protocol from the Qiagen blood and tissue kit (basically the addition of DTT, additional proteinase K, and longer digestion times). So far the results are not too encouraging but we are actively trying some different things and have some claws from specimens of different collection date from the Field Museum that we will test once we're confident in a protocol. ** Dear Steve, There are many methods that can be used for extraction and almost all of them work but it is also a matter of how are you testing the extracts to determine their success. With degraded DNA you have a few problems that have to addressed; 1) Quantity 2) Quality 3) Inhibition If you are trying to quantify using real-time qPCR then you have to solve the other two problems first as these will both affect your ability to amplify the DNA thus quantify. If you are determining the concentration in other ways you may also get background or contaminating DNA that may not contaminate the PCR but are there as background DNA because the sample has sat in a museum for a long time. If you are determining success based on PCR amplification (success or failure) then you also have to consider 2 and 3 first. To overcome quantity you add as much material as you can to ensure quantity is abundant. Some people have used up to 5g. Once you have resolved all the other problems then you can optimize quantity because 5g is a lot of material and sometimes too much of a very valuable sample. I regularly use between 10-50mg of bone material. There are a number of problems with degraded DNA that affect their quality. 1) Fragmentation 2) modification 3) cross-links All degraded DNA will be fragmented with single stranded and double stranded DNA breaks. Most research agree that 200bp is the norm in nDNA. So if you are trying to determine success by PCR your primers have to amplify less than 200bp. 200bp is the amount of DNA that wraps around the histone complex and in a way protect the DNA where the breaks more frequently occur in the inter-linker regions between the histone complexes (Look at the Apoptotic 200bp ladder for proof). All degraded DNA is modified this is where you get abasic (AP) sites due to depurination and depyrimidation, modified bases where the amine is lost through deamination. There is also oxidative damage generating hydantoins amongst many other types of modified bases. Some of these will prevent your DNA from being amplified. Some of these will generate miscoding lesions where the sequence is not authentic due to an incorrect base pair generating an erroneous sequence. Some researcher have incorporated repair methods to overcome this step (as have I). The other form of damage is cross-links which can occur between the DNA and other molecules like metals and proteins (amongst others). There has been some research to develop methods of cleaving these cross-links off to allow the DNA to be analysed. All of these have to be considered for degraded DNA. Finally there is inhibition. If you do not resolve this problem first you will not be able to do anything. Inhibition is going to be unique to the site, the collection or even the sample. It must be determined if you have it (spiked PCR) or ensure you have removed it through various purification systems. So with these points in mind go back to the methods in the literature and you will find they will work. The most common methods in degraded DNA studies are proteinase K methods and Guanidinium thiocyanate but there are other chaotropic salt methods that can also work very well. I can give you dozens of methods of extracting degraded DNA that I have personally used but without considering these factors you will not succeed with any of them. Let me know if you need any more information on any of these points or reference papers on any of these points. ** Hi Steve, It is almost impossible to get anything out of a formalin fixed specimen (I tried most of the available protocols on a muscle sample that was only 5 years old and got nothing and I have heard the same thing from most people that I contacted). As for getting DNA out of bone or alcohol fixed specimens, your luck should be better (although if the samples have been stored in a hot place, DNA will degrade much faster). Have you tried any of the bone protocols yet? Your best bets are the two attached. Also you need to be sure that you are doing all of your DNA extraction and PCR set up in a lab far from any labs that work on turtles (in my ancient DNA lab, we do all our work in the morning or on days that we don't go to the modern lab unless we go to the gym to shower before returning to the ancient lab). Finally, you need to be sure that your PCR primers are sensitive to low amounts of DNA and that they amplify products less than 200 bp in length (BSA added to your PCR also helps yield). The ancient DNA literature might be of help to you in terms of suggestions and recommendations for avoiding contamination from modern DNA. Good luck! ** Hey Steve, for the extraction of bone samples from museum specimens I can strongly recommend the latest version of the silica based protocol from Nadin Rohland and Michael Hofreiter. I attached the pdf. ** Hi Steve, I've used the Shedlock extraction protocol with success on seahorses and use the guanidinium non-destructive method on parrotfish bones from archaeological sites (1300 AD jaw bones and teeth). Have you tried these? Also, I would suggest you cut down your PCR product to ~150 bp...you may be getting DNA but its too short and degraded to amplify in large pieces. I amplify 150-250 bp fragments and piece them together. Design short primers, test them on modern good quality DNA to make sure they work, then use a good quality hot start Taq, touchdown PCR (like 65 - 45 C) for 65 cycles, with short extension times (30s denature, 30s annealing, 30 extension - will prolong the life of the taq over the large number of cycles), and relatively high MgCl2 (2.5 mM), high primer concentration 0.5 mM, and high dntp concentration (.25 mM) and BSA at 1 mg/ml. That way if there's any DNA in your PCR, it will work...but be very careful of contamination :) Hope that helps and feel free to write back with questions, -- Steve Kimble PhD student, Department of Forestry and Natural Resources Purdue University skimble[at]purdue.edu sjkimble[at]gmail.com 205.337.4843 http://web.ics.purdue.edu/~rodw/Steve%20Kimble.htm steve kimble

The Promislow lab at the University of Georgia is seeking an enthusiastic, independent postdoctoral researcher to study the genetic architecture of aging in Drosophila. Current projects include studies on aging in molecular networks, and on natural genetic variation for somatic mutation rate. The goal of these projects is to better understand the causes and consequences of aging in natural populations. The successful candidate will apply genetic and genomic approaches to the study of aging in flies. Specific experiments will include large-scale analyses of genomic and metabolomic networks, in vivo measures of somatic mutation rate, and genome wide association studies to map variation in network structure and mutation rate. Preference will be given to candidates with experience in population genetics, genomics, and/or systems biology & network analysis. The position is initially available for two years, and may be extended. The postdoc will be among a dynamic, interactive group of evolutionary geneticists at the University of Georgia in Athens, GA. Applications should be sent by Sept. 17, 2010 by email to Daniel Promislow (promislow[at]uga.edu). Applicants are requested to send a single PDF file that includes a cover letter, a CV and one or two representative publications. Applicants should also arrange for three letters of recommendation to be sent by email. The University of Georgia is an Equal Opportunity/Affirmative Action Employer. Daniel Promislow

Hello, In an old posting from Evoldir I found someone pointing out that multiplexing dyes for AFLPs was problematic because of interference between dyes. I would like to get some feedback from anyone who might have experienced the same problems or who maybe have found a solution around this. Thank you, gruberloo2[at]yahoo.com karlgruber[at]daad-alumni.de

Dear all, I'm writing to announce that the next Systematics Association biennial meeting will be held at Queen's University Belfast from the 4-8 July 2011. We are currently working on arranging the details of the event, and we hope to have some more information on the Systematics Association website (www.systass.org) very soon. In particular, we have started arranging the scientific program for the biennial, and are keen to involve as wide a cross-section of the systematics community as possible. If you wold like to arrange a symposium, or have suggestions for symposium topics you would like to see at next year's meeting, please get in touch with me, the Programme Secretary, soon. We look forward to seeing some of you in Belfast next year, Yours, James Cotton James Cotton Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge. CB10 1SA UK 01223 494864 james.cotton[at]sanger.ac.uk

Background: We have analyzed the complete mitochondrial genomes of 22 Pan paniscus (bonobo, pygmy chimpanzee) individuals to assess the detailed mitochondrial DNA (mtDNA) phylogeny of this close relative of Homo sapiens. Results: We identified three major clades among bonobos that separated approximately 540,000 years ago, as suggested by Bayesian analysis. Incidentally, we discovered that the current reference sequence for bonobo likely is a hybrid of the mitochondrial genomes of two distant individuals. When comparing spectra of polymorphic mtDNA sites in bonobos and humans, we observed two major differences: (i) Of all 31 bonobo mtDNA homoplasies, i.e. nucleotide changes that occurred independently on separate branches of the phylogenetic tree, 13 were not homoplasic in humans. This indicates that at least a part of the unstable sites of the mitochondrial genome is species-specific and difficult to be explained on the basis of a mutational hotspot concept. (ii) A comparison of the ratios of non-synonymous to synonymous changes (dN/dS) among polymorphic positions in bonobos and in 4902 Homo sapiens mitochondrial genomes revealed a remarkable difference in the strength of purifying selection in the mitochondrial genes of the F0F1-ATPase complex. While in bonobos this complex showed a similar low value as complexes I and IV, human haplogroups displayed 2.2 to 7.6 times increased dN/dS ratios when compared to bonobos. Conclusions: Some variants of mitochondrially encoded subunits of the ATPase complex in humans very likely decrease the efficiency of energy conversion leading to production of extra heat. Thus, we hypothesize that the species-specific release of evolutionary constraints for the mitochondrial genes of the proton-translocating ATPase is a consequence of altered heat homeostasis in modern humans.

Background: Patterns of spatial variation in discrete phenotypic traits can be used to draw inferences about the adaptive significance of traits and evolutionary processes, especially when compared to patterns of neutral genetic variation. Population divergence in adaptive traits such as color morphs can be influenced by both local ecology and stochastic factors such as genetic drift or founder events. Here, we use quantitative color measurements of males and females of Skyros wall lizard, Podarcis gaigeae, to demonstrate that this species is polymorphic with respect to throat color, and the morphs form discrete phenotypic clusters with limited overlap between categories. We use divergence in throat color morph frequencies and compare that to neutral genetic variation to infer the evolutionary processes acting on islet- and mainland populations. Results: Geographically close islet- and mainland populations of the Skyros wall lizard exhibit strong divergence in throat color morph frequencies. Population variation in throat color morph frequencies between islets was higher than that between mainland populations, and the effective population sizes on the islets were small (Ne:s < 100). Population divergence (FST) for throat color morph frequencies fell within the neutral FST-distribution estimated from microsatellite markers, and genetic drift could thus not be rejected as an explanation for the pattern. Moreover, for both comparisons among mainland-mainland population pairs and between mainland-islet population pairs, morph frequency divergence was significantly correlated with neutral divergence, further pointing to some role for genetic drift in divergence also at the phenotypic level of throat color morphs. Conclusions: Genetic drift could not be rejected as an explanation for the pattern of population divergence in morph frequencies. In spite of an expected stabilising selection, throat color frequencies diverged in the islet populations. These results suggest that there is an interaction between selection and genetic drift causing divergence even at a phenotypic level in these small, subdivided populations.

The monthly review of the EvolDir is available from the EvolDir website - http://life.biology.mcmaster.ca/~brian/evoldir.html. For more information or for help send mail to Golding[at]McMaster.CA. Please see the above website for instructions for the EvolDir. This includes ways to limit/reduce the messages you receive from the EvolDir. A reminder: The userid for the web site user list is `evoldir' and the password is `2EvolBulletins'. [ This was done to limit the access of spammers (e.g. SpeakOut.Com and others). ] Brian Golding

Job: Engineering Support Job ID: 635089 Location: Albuquerque, NM About Sandia Sandia National Laboratories is the nation's premier science and engineering lab for national security and technology innovation. We are a world-class team of scientists, engineers, technologists, post docs, and visiting researchers all focused on cutting-edge technology, ranging from homeland defense, global security, biotechnology, and environmental preservation to energy and combustion research, computer security, and nuclear defense. To learn more, visit California Website: http://ca.sandia.gov/casite/ or New Mexico Website: http://www.sandia.gov/. Department Description The Bioenergy and Defense Technologies department, which is part of Sandia's Biological and Materials Sciences Center, supports mission areas in biodefense, emerging infectious disease, and biofuels. The department conducts fundamental research in cell biology, immunology, and microbiology and develops advanced measurement technologies, such as fluorescence microscopy, vibrational spectroscopies, and x-ray and neutron scattering. Current research projects include understanding receptor activation and cell signaling processes, pathogenesis, and plant physiology, as well as algal biochemistry and cultivation characterization for biofuels applications. We conduct research for the National Institutes of Health, the Department of Homeland Security, the Department of Defense, U.S. industry, and Sandia's Laboratory Directed Research & Development program. To learn more, visit http://bio.sandia.gov. How to Apply Visit http://tinyurl.com/233kmec, follow the instructions to upload a resume, and complete the submission process to indicate your interest in this position. Job Details SUMMARY: Run routine data pipeline programs and database tools to analyze sequence data DUTIES: - Use existing applications, such as, alignment programs, sequence assemblers and BLAST to perform routine analytical tasks - Collaborate with scientific staff to use software specifications for data pipelines - Maintain daily operation of ?omics-oriented pipelines Required - Bachelors degree in Bioinformatics, Computer Science, Computer Engineering, or four years of relevant software engineering experience or education - Ability to operate in a UNIX/Linux operating environment - Fluency in object-oriented Perl, and one or more relational database management systems. Knowledge of one or more programming languages such as C++, C#, R, Java. Familiarity with web technologies such as HTML, CSS, PHP, Ajax - Programming expertise in statistical analyses software packages, such as SAS, MATLAB, Mathematica and/or the R Project for Statistical Computing, languages and tools Desired - Parallel and grid-based computing programming experience - Ability to support production data management and software pipeline operation - Ability to provide support to senior-level scientific staff Security Clearance Sandia is required by DOE directive to conduct a pre-employment background review that includes personal reference checks, law enforcement record and credit checks, and employment and education verifications. Applicants for employment must be able to obtain and maintain the appropriate DOE security clearance if required for a position. Applicants offered employment with Sandia are subject to a federal background investigation to meet the requirements for employment including access to classified information or matter. Substance abuse or illegal drug use, falsification of information, criminal activity, serious misconduct or other indicators of untrustworthiness can cause a clearance to be denied by the DOE, rendering the inability to perform the duties assigned and resulting in termination of employment. Citizenship Sandia is a Department of Energy (DOE) national laboratory; as such, many of our jobs require a DOE security clearance, which requires U.S. citizenship. If this position requires a Department of Energy (DOE)-granted security clearance, U.S. citizenship and employee eligibility for clearance processing will be required at the time of hire. If you hold dual citizenship and you accept a job offer for a position that requires a DOE-granted security clearance, you may be asked by DOE to renounce your foreign citizenship and retain only your U.S. citizenship. Benefits At Sandia you will receive many benefits as a valued employee of a premier national multi-program engineering and science research laboratory. In our Total Rewards package you will enjoy competitive pay, great benefits, a stimulating, positive environment and learning opportunities that will help build your career. More information may be found on our Careers website. EEO Sandia National Laboratories is an Equal Opportunity Employer M/F/D/V. Erin Quinn Talent Acquisition Sandia National Laboratories/CA Telephone (925) 294-2460 http://sandia.gov/careers/ "Quinn, Erin Elizabeth"

Postdoctoral position in plant ecology, evolution, and conservation at the Center for Conservation and Sustainable Development, Missouri Botanical Garden A Postdoctoral position is available at the Center for Conservation and Sustainable Development (CCSD) of the Missouri Botanical Garden (MBG) to participate in ongoing projects about determinants of plant diversity (alfa, beta, and gamma diversity) and size of species geographic ranges, the effects of climate change on plants spatial distribution, and the conservation status of plant species. The post holder will also be expected to develop new projects by integrating into spatial analyses plant data contained in the MBG's herbarium and TROPICOS database (http://tropicos.org/) with other types of information such as quantitative local vegetation inventories (i.e., plant plots), phylogenies, and geographic environmental data. See website for description of ongoing research at CCSD (http://www.mobot.org/plantscience/ccsd/) and MBG in general (http://www.mobot.org/plantscience/default.asp). Applicants should have excellent writing and communications skills as well as an eagerness to produce and publish scientific results. Candidates should have a strong background in one or more of the following fields: ecology, evolution, systematics, spatial analysis, inferential statistics, or bioinformatics. Applicants should furthermore have experience with one or more of the following tools: the R statistical environment, ESRI software or species distribution models. Computer simulation skills are particularly desirable. Fluency in Spanish is a plus. The Postdoctoral fellow will be based in St. Louis where a vibrant community of systematists, ecologists, and evolutionary biologists interact through partnerships among MBG, Washington University, University of Missouri-St. Louis and Saint Louis University. Funding for this position is available for two years, extendable to three years subject to review after one year. The starting annual salary range is anticipated to be between $30,000-$34,000. The Missouri Botanical Garden offers a comprehensive benefits package. To be considered, applicants should apply on-line (http://www.mobot.org/jobs/mbgjobs.asp#J053), and submit a brief statement of research interests, a CV, copies of relevant publications or manuscripts, and three letters of recommendation from people familiar with their research to tracy.breckenridge[at]mobot.org before 31st October 2010. IvᮠJim鮥z Assistant Curator Center for Conservation and Sustainable Development Missouri Botanical Garden P.O. Box 299 St. Louis, MO 63166 ivan.jimenez[at]mobot.org http://www.mobot.org/MOBOT/Research/curators/jimenez.shtml Ivan Jimenez

Postdoctoral position, University of Rochester A postdoctoral position is currently available in the laboratory of Daniel Garrigan in the Biology Department at the University of Rochester. The Garrigan laboratory focuses on using population genomics data to address questions about speciation in natural populations. The candidate for this position will be involved in one (or more) of several projects involving genome assembly and alignment, and the statistical analysis of population structure, gene flow and natural selection using data from a variety of model taxa, including primates and Drosophila. The successful candidate should have a strong background in population genetics and bioinformatics. Knowledge of programming languages and proficiency in unix-based computational environments is desirable. The group interacts and collaborates with other laboratories in the department, including those of Daven Presgraves, Allen Orr, and John Jaenike. Please direct inquiries and electronic applications (please attach a pdf of a CV, copies of relevant publications and two letters of recommendation) to Daniel Garrigan at dgarriga[at]bio.rochester.edu. The starting date is negotiable and the compensation level will depend upon experience. Daniel Garrigan Department of Biology University of Rochester Rochester, NY dgarriga[at]bio.rochester.edu

--_000_D3FE8797E7E80F40BA869D851974620B02872EF0120ADOITEX701ex_ Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: quoted-printable Resubmit of earlier email, with correct format for subject line. Has anyone used IDT's MAX fluorophore in multiplex with AB's LIZ size standard? I can't find data on the abs/emission spectra for LIZ. VIC (538/554) is compatible with LIZ, but IDT doesn't offer VIC, and recommend either HEX (538/555), JOE (529/555), or MAX (524/557), instead. The Yale sequencing center says that while HEX is not compatible with LIZ, JOE is; this is perplexing given that HEX and VIC have nearly identical spectral characteristics. I'd prefer to buy HEX or MAX because they're considerably cheaper than JOE. Anyone want to weigh in on this? Thanks, Bob Marra Robert E. Marra, Ph.D. Forest Pathologist Department of Plant Pathology and Ecology Connecticut Agricultural Experiment Station 123 Huntington Street, P.O. Box 1106 New Haven CT 06504-1106 http://www.ct.gov/caes/cwp/view.asp?a=3D2812&q=3D394858 E-mail: robert.marra@ct.gov Phone: (203) 974-8508 Fax: (203) 974-8502 Please consider the environment before printing this e-mail ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ This information may be confidential and/or privileged. If you received this in error, please inform the sender and remove any record of this message. Note that messages to or from the State of Connecticut domain may be subject to Freedom of Information statutes and regulations. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --_000_D3FE8797E7E80F40BA869D851974620B02872EF0120ADOITEX701ex_ Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: quoted-printable

Resubmit of earlier email, with correct format for subject line.

 

Has anyone used IDT’s MAX fluorophore in multiplex with AB’s LIZ size standard?   I can’t find data on the abs/emission spectra for LIZ.  VIC (538/554) is compatible with LIZ, but IDT doesn’t offer VIC, and recommend either HEX (538/555), JOE (529/555), or MAX (524/557), instead.  The Yale sequencing center says that while HEX is not compatible with LIZ, JOE is; this is perplexing given that HEX and VIC have nearly identical spectral characteristics.  I’d prefer to buy HEX or MAX because they’re considerably cheaper than JOE.  Anyone want to weigh in on this?

Thanks,

Bob Marra

 

 

 

Robert E. Marra, Ph.D.

Forest Pathologist

Department of Plant Pathology and Ecology

Connecticut Agricultural Experiment Station

123 Huntington Street, P.O. Box 1106

New Haven CT 06504-1106

 

http://www.ct.gov/caes/cwp/view.asp?a=2812&q=394858">http://www.ct.gov/caes/cwp/view.asp?a=3D2812&q=3D394858

 

E-mail: robert.marra[at]ct.gov& lt;mailto:robert.marra[at]ct.gov>

Phone:  (203) 974-8508

Fax:  (203) 974-8502

 

Please consider the environment before printing this e-mail

 

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This information may be confidential and/or privileged. If you received this in error, please inform the sender and remove any record of this message.  Note that messages to or from the State of Connecticut domain may be subject to Freedom of Information statutes and regulations. 

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Assistant Professor in Biological Mathematics The College of William and Mary The Department of Biology at The College of William and Mary invites applications for a tenure-track position at the level of Assistant Professor in Biological Mathematics beginning Fall, 2011. The successful candidate will develop a productive, externally funded research program in biological mathematics, broadly construed, that includes collaborations with both faculty and students in the Department of Biology and, potentially, the Program in Neuroscience. Collaboration with faculty in the Departments of Applied Science and Mathematics is also encouraged. Typical teaching duties will be one course per semester; the successful candidate will develop and teach a sophomore level course in mathematical biology suitable for Biology majors and an advanced course that incorporates student research projects. In addition, the successful candidate will help to develop quantitative elements for introductory and advanced Biology courses in collaboration with the instructors of such courses. The assignment to teach a particular course might be substituted partially or entirely by collaborative work with other faculty members to develop and integrate biological mathematics into courses from the introductory to advanced level. An interest in and ability to teach biostatistics is preferred, but this need not be the research focus of the successful candidate. A Ph.D. is required and postdoctoral experience is desirable. Applications should include a curriculum vitae, a statement of current and future research interests, and a statement of teaching interests and experience and should be submitted electronically as a single PDF to http://jobs.wm.edu. The system will also prompt you for the names and emails of a minimum of three referees familiar with your research and/or teaching who will be asked to provide a reference letter. Questions should be addressed to Margaret Saha (mssaha[at]wm.edu). Review of applications will begin on November 1, 2010 and will continue until an appointment is made. The College of William and Mary is an EEO/AA Employer and is committed to improving diversity. Dr. John Swaddle Professor, Biology Director, Environmental Science and Policy Program Millington Hall, Room 220 College of William & Mary Williamsburg, VA 23187-8795 Office: 757.221.2231 Fax: 757.221.6483 http://jpswad.people.wm.edu/ John Swaddle

Buckler Lab for Maize Genetics and Diversity A USDA-ARS Lab with Cornell's Institute for Genomic Diversity Job Description Postdoc in Grass Bioinformatics Position Overview: Postdoc will process and analyze next generation sequencing data from Tripsacum dactyloides, maize's perennial relative, and switchgrass, a potential perennial biofuel grass. They will conduct analysis and develop software for an ongoing research program focused on the natural variation inherent in perennial grass genomes for the dissection of complex traits. The research will focus specifically on (1) identifying the novel genes in perennial grasses that are lacking in maize, (2) identify the alleles involved in adaptation of perennial grasses to North American environments. Our longer term goal is to support the development of high performance perennial grass crops. Responsibilities: * Develop the analysis pipelines for genotype by sequencing without the aid of a reference genome, using next generation sequencing libraries from Tripsacum and switchgrass. * Construct high density genetic, diversity, and QTL maps of Tripsacum and switchgrass to facilitate the identification of key genes. * Develop analytic approaches for combining next generation sequencing with higher ploidy organisms. Qualifications: Applicant must have Ph.D. in statistical genetics, population genetics, bioinformatics or a related field and demonstrated skills in bioinformatics, programming and the analysis of next generation DNA sequence data. Knowledge of PERL, Java, and C required. This is position is a two year appointment at a highly competitive salary. Applicants for this position MUST be U.S. permanent residents or citizens. Please email your current CV to sjm336[at]cornell.edu Sara Miller Administrator, Buckler Lab Institute for Genomic Diversity Cornell University 607.255.1809 sjm336[at]cornell.edu sara.miller[at]cornell.edu

The Field Museum of Natural History's Division of Insects is preparing for extensive research laboratory and collection renovations, which will integrate and compactorize its entire pinned collection in one collection room over the next several months. Starting September 15, 2010, the insect collection rooms will have to be closed to allow installation of compactors and cabinets and renovation of research labs. >From now until May 1, 2011, please * contact us before scheduling any visits to determine whether we can accommodate you and * postpone all new loan requests and specimen return shipments. If our reopening date becomes significantly earlier or later than that, we will circulate an update. Our newly renovated collection and research areas will better serve the entomological community and our training efforts by providing additional work space, better access to the collection and research facilities, and enhanced long-term collection expansion space. Thank you for your cooperation and patience during this construction phase. We apologize for the lack of advance notice, but we got short notice of the final approval of the funding. Margaret K. Thayer, Ph.D. mthayer[at]fieldmuseum.org Associate Curator, Zoology and Head, Division of Insects Fieldiana Associate Editor (Zoology) http://www.fieldmuseum.org/fieldiana/ Field Museum of Natural History 1400 South Lake Shore Drive Chicago IL 60605-2496, USA PHONE: +1-312-665-7741 (direct) FAX: +1-312-665-7754 FMNH personal web page: http://tinyurl.com/4g4zz Austral Staphylinidae with Staphyliniformia databases: http://tinyurl.com/3a39n7 Beetle Tree of Life project: http://tinyurl.com/38yryf Division of Insects collection database: http://tinyurl.com/2mnc9j mthayer[at]fieldmuseum.org

Looking for support for a sabbatical, grad student, postdoc, or meeting? NESCent welcomes your proposals. The next deadline is December 1.

Background: The grape powdery mildew fungus, Erysiphe necator, was introduced into Europe more than 160 years ago and is now distributed everywhere that grapes are grown. To understand the invasion history of this pathogen we investigated the evolutionary relationships between introduced populations of Europe, Australia and the western United States (US) and populations in the eastern US, where E. necator is thought to be native. Additionally, we tested the hypothesis that populations of E. necator in the eastern US are structured based on geography and Vitis host species. Results: We sequenced three nuclear gene regions covering 1803 nucleotides from 146 isolates of E. necator collected from the eastern US, Europe, Australia, and the western US. Phylogeographic analyses show that the two genetic groups in Europe represent two separate introductions and that the genetic groups may be derived from eastern US ancestors. Populations from the western US and Europe share haplotypes, suggesting that the western US population was introduced from Europe. Populations in Australia are derived from European populations. Haplotype richness and nucleotide diversity were significantly greater in the eastern US populations than in the introduced populations. Populations within the eastern US are geographically differentiated; however, no structure was detected with respect to host habitat (i.e., wild or cultivated). Populations from muscadine grapes, V. rotundifolia, are genetically distinct from populations from other Vitis host species, yet no differentiation was detected among populations from other Vitis species. Conclusions: Multilocus sequencing analysis of the grape powdery mildew fungus is consistent with the hypothesis that populations in Europe, Australia and the western US are derived from two separate introductions and their ancestors were likely from native populations in the eastern US. The invasion history of E. necator follows a pattern consistent with plant-mediated dispersal, however, more exhaustive sampling is required to make more precise conclusions as to origin. E. necator shows no genetic structure across Vitis host species, except with respect to V. rotundifolia.

Background: The human FOXI1 gene codes for a transcription factor involved in the physiology of the inner ear, testis, and kidney. Using three interspecies comparisons, it has been suggested that this may be a gene under human-specific selection. We sought to confirm this finding by using an extended set of orthologous sequences. Additionally, we explored for signals of natural selection within humans by sequencing the gene in 20 Europeans, 20 East Asians and 20 Yorubas and by analysing SNP variation in a 2 Mb region centered on FOXI1 in 39 worldwide human populations from the HGDP-CEPH diversity panel. Results: The genome sequences recently available from other primate and non-primate species showed that FOXI1 divergence patterns are compatible with neutral evolution. Sequence-based neutrality tests were not significant in Europeans, East Asians or Yorubas. However, the Long Range Haplotype (LRH) test, as well as the iHS and XP-Rsb statistics revealed significantly extended tracks of homozygosity around FOXI1 in Africa, suggesting a recent episode of positive selection acting on this gene. A functionally relevant SNP, as well as several SNPs either on the putatively selected core haplotypes or with significant iHS or XP-Rsb values, displayed allele frequencies strongly correlated with the absolute geographical latitude of the populations sampled. Conclusions: We present evidence for recent positive selection in the FOXI1 gene region in Africa. Climate might be related to this recent adaptive event in humans. Of the multiple functions of FOXI1, its role in kidney-mediated water-electrolyte homeostasis is the most obvious candidate for explaining a climate-related adaptation.

Background: Ecological speciation is a process in which a transiently resource-polymorphic species divides into two specialized sister lineages as a result of divergent selection pressures caused by the use of multiple niches or environments. Ecology-based speciation has been studied intensively in plant-feeding insects, in which both sympatric and allopatric shifts onto novel host plants could speed up diversification. However, while numerous examples of species pairs likely to have originated by resource shifts have been found, the overall importance of ecological speciation in relation to other, non-ecological speciation modes remains unknown. Here, we apply phylogenetic information on sawflies belonging to the 'Higher' Nematinae (Hymenoptera: Tenthredinidae) to infer the frequency of niche shifts in relation to speciation events. Results: Phylogenetic trees reconstructed on the basis of DNA sequence data show that the diversification of higher nematines has involved frequent shifts in larval feeding habits and in the use of plant taxa. However, the inferred number of resource shifts is considerably lower than the number of past speciation events, indicating that the majority of divergences have occurred by non-ecological allopatric speciation; based on a time-corrected analysis of sister species, we estimate that a maximum of c. 20% of lineage splits have been triggered by a change in resource use. In addition, we find that postspeciational changes in geographic distributions have led to broad sympatry in many species having identical host-plant ranges. Conclusion: Our analysis indicates that the importance of niche shifts for the diversification of herbivorous insects is at present implicitly and explicitly overestimated. In the case of the Higher Nematinae, employing a time correction for sister-species comparisons lowered the proportion of apparent ecology-based speciation events from c. 50-60% to around 20%, but such corrections are still lacking in other herbivore groups. The observed convergent but asynchronous shifting among dominant northern plant taxa in many higher-nematine clades, in combination with the broad overlaps in the geographic distributions of numerous nematine species occupying near-identical niches, indicates that host-plant shifts and herbivore community assembly are largely unconstrained by direct or indirect competition among species. More phylogeny-based studies on connections between niche diversification and speciation are needed across many insect taxa, especially in groups that exhibit few host shifts in relation to speciation.