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May 9, 2015

00:37
Postdoc in bioinformatics A postdoc position is available on a project to study the evolutionary dynamics of genomes and transcriptomes. The postdoc will work in collaboration on two projects: (1) Evo-devo genomics, in the Robinson-Rechavi lab: evolutionary study of the duplication history of chordate genomes, including de novo assembly of a Mediterranean amphioxus genome from PacBio long reads, and comparative transcriptomics analysis from RNA-seq: (2) Evolution of sex chromosomes, in the Pannell and Perrin labs: assembly and polymorphism analysis of sex chromosomes from plants and amphibians. The postdoc would be expected to take a leading position on the bioinformatics of the genomics of non-model organisms, and to participate actively in evolutionary analyses and interpretation. The postdoc will work closely with other bioinformaticians and evolutionary genomicists on both projects. In the medium term, the postdoc will be expected to develop his or her own subproject and publications. The position will be in co-supervision between Profs Marc Robinson-Rechavi, John Pannell and Nicolas Perrin, all three in the Department of Ecology and Evolution. Prof Robinson-Rechavi is also a group leader at the Swiss Institute of Bioinformatics, and the postdoc will also be a full member of the SIB. The starting contract will be for 1 year, starting as soon as possible, renewable for up to five years; the postdoc will participate in some undergraduate and/or masters teaching, in English or in French. The ideal candidate would have a doctorate degree in bioinformatics, genomics, or a related field; a good command of Unix and another programming language; hands-on experience with genomic data; and an interest in pursuing research on non model organisms. Experience with the R language and cluster computing would be beneficial. Funds for the position are available immediately, and our preference would be to appoint someone to the position this summer, if possible. Full applications, which should include a cover letter, a CV, and the contact information of 3 referees, should be sent to marc.robinson-rechavi@unil.ch as a single PDF document. Informal enquiries should be directed to marc.robinson-rechavi@unil.ch; john.pannell@unil.ch; and/or nicolas.perrin@unil.ch. Deadline for applications: all applications received by May 22, 2015, will be given full consideration, but the position will remain open until the right candidate has been appointed. For background on the labs in which you would be working, please see: Robinson-Rechavi lab: http://bit.ly/1xmcvV6 Pannell lab: http://bit.ly/1xmcujX Perrin lab: http://bit.ly/1BDu34l John Richard Pannell via Gmail
Source: EVOLDIR

May 8, 2015

23:51
–_000_2B0B68B37515B9468BC274F705F374B9580277C4TIS102uopnetply_ Content-Type: text/plain; charset=“us-ascii” Content-Transfer-Encoding: quoted-printable “The evolution of trade-offs in mating behaviour and physiology” University of Plymouth, UK School of Biological Sciences Applications are invited for a three-year PhD studentship, fully funded for EU/UK students. The studentship will start on October 1st 2015. Supervisors: Dr Michael Thom (University of Plymouth) Dr Mark Briffa (Plymouth) Prof. Calvin Dytham (University of York) Prof. Helen White-Cooper (University of Cardiff) Summary: For male animals, successful reproduction involves a number of key processes including mate searching, courtship, copulation, and sperm competition. Many of these are energetically expensive, time-consuming, or otherwise incompatible and as a result males are unlikely to be able to maximise performance in all of them simultaneously. How males value the different processes will depend on both physical and social environment, with males expected to plastically adjust their relative investment in each to maximise their reproductive success under prevailing conditions. Using the model species Drosophila melanogaster, this project will explore how these different components of the male reproductive process are traded off under simultaneous variation in biotic (e.g. population density, sex ratio) and abiotic (e.g. nutritional composition, food distribution) conditions. The student will be based at Plymouth, but will conduct histological work on the rate and fidelity of spermatogene sis with Prof. Helen White-Cooper at Cardiff. In addition to the empirical studies on behaviour and sperm production, the student will have the opportunity to learn the programming language C++, and will use this to develop an agent-based model exploring the evolution of ecological plasticity in mating behaviour and physiology - this will be overseen by Prof. Calvin Dytham at York. If you wish to discuss this project further informally, please contact Dr Thom on michael.thom@plymouth.ac.uk. See http://bit.ly/1Pwk2sI for further details via Gmail
Source: EVOLDIR
23:34
–_000_D582A68C4BD8AE40901401A5A25E215D4569138AMAILSERVERnrmse_ Content-Type: text/plain; charset=“iso-8859-1” Content-Transfer-Encoding: quoted-printable Dear everyone, This is a reminder that the deadline for abstract submission expires on the 15th of May. Please submit your abstract for a talk or poster here: http://bit.ly/1chQse2 The 7th European Congress of Mammalogy will be held in Stockholm, Sweden, between 17-21 August 2015. Visit the conference website to find out more about the conference as well as to register (registration is open until the 15th of June): http://bit.ly/1tLnI5u The conference will cover a broad range of topics in mammal biology, including Species Interactions, Population Genetics, Conservation Biology and Ecology & Landscapes. List of Plenary & Keynote speakers: David Macdonald, University of Oxford Heikki Henttonen, Finnish Forest Research Institute Anjali Goswami, University College London Xavier Lambin, University of Aberdeen Jennifer Leonard, Doana Biological Station Tim Clutton-Brock, University of Cambridge Henrik Andrn, Swedish University of Agricultural Sciences Mike Bruford, Cardiff University Ian Barnes, Natural History Museum London Bodil Elmhagen, Stockholm University Kjell Danell, Swedish University of Agricultural Sciences Nigel Yoccoz, Tromso University Greger Larson, Oxford University Urs Breitenmoser, Bern University Selina Brace, Natural History Museum London Arild Landa, Norwegian Institute for Nature Research The aim of the European Congresses of Mammalogy is to foster communication between researchers working on issues of mammalian biology in the European arena, as well as providing a venue for the broad dissemination of European mammal research. The relaxed and friendly atmosphere of these congresses provides an excellent opportunity to hear the latest developments in various fields of mammalogy, to share research experience and expertise, and to develop new and closer contacts with colleagues from different countries. Facebook: http://on.fb.me/1chQsuh Twitter: https://twitter.com/ECMSthlm2015 Instagram: http://bit.ly/1FbbHeu –_000_D582A68C4BD8AE40901401A5A25E215D4569138AMAILSERVERnrmse_ Content-Type: text/html; charset=“iso-8859-1” Content-Transfer-Encoding: quoted-printable
Source: EVOLDIR
11:25

@rdmpage @BioDivLibrary @bouchoutdec Why aren't you creating an iphylo blog what metrics you expect to see so you will not be disappointed?

— Donat Agosti (@myrmoteras) May 1, 2015 There are no requirements for signing up. A signature is first and foremost a statement of support for open data . Each signatory can determine how best to make progress towards the goal. Some recommendations are included in the declaration. We hope that signatories will become early adopters of the open access approach, that they will promote change in their institutions, societies and journals, and will position themselves and their institutions as leaders. (from http://www.bouchoutdeclaration.org/faqs/)I've put off writing this post about the Bouchout Declaration for a number of reasons. I attended the meeting that launched the declaration last year, and from my perspective that was a frustrating meeting. Much talk about "Open Biodiversity Knowledge Management" with nobody seemingly willing or able to define it (see The vision thing - it's all about the links for some comments I made before attending the meeting), and as much as the signing of the Boechout Declaration provided good theatre, it struck me as essentially an empty gesture. Public pronouncements are all well and good, but are ultimately of little value unless backed up by action. We have institutions that have signed the declaration yet have much of their intellectual output locked behind paywalls (e.g., JSTOR Global Plants). So much for being open.

So, since Donat challenged me, here's what I'd like to see happen. I'd like to see metrics of "openness" that we can use to evaluate just how open the signatories actually are. These metrics could be viewed as ways to try and persuade institutions into sharing data and other information, as a league table we can use to apply pressure, or as a way to survey the field and see what the impediments are to being open (are they financial, legal, cultural, resource, etc.).

Below are some of the things I think we could "score" the openness of biodiversity institutions.

Is the collection digitised and in GBIF?Simple criterion that is easy to measure. If an institution has specimens or other biological material, is data and or metadata on the collection freely available? What fraction of the collection has been digitised? How good is that digitsation (e.g., what fraction has been georeferenced?). We could define digitisation more broadly to include imaging and sequencing (both are methods of converting analogue specimens into digital objects).

Are the institutional publications digitised? Are they open access?Some institutions have a history of digitising their in-house publications and making them freely available online (e.g., the AMNH), some even make them fully citable with CrossRef DOIs (e.g., the Australian Museum). But some institutions have, sadly, signed over their publications to commercial publishers or archives that charge for access (e.g., Kew's publications have been digitised by JSTOR, which limits their accessibility). As a foot note, I suspect that those institutions that lost confidence in their in-house publishing operations and outsourced them are the ones who have ended up loosing control of their intellectual output, some of which is now closed off (e.g., some of the NHM London's journals are now the property of Cambridge University Press). Those institutions that maintained a culture of in-house publishing are the ones at the vanguard of digitising and opening up those publications.

Does the institution take part on the Biodiversity Heritage Library?There are at least two ways to participate in the Biodiversity Heritage Library (BHL), one is by becoming a member and start scanning books from institutional libraries. The other is by granting permission to BHL to scan institutional publications. BHL is often viewed as an archive of "old" literature, but in fact it has some very recent content. Some farsighted organisations have let BHL scan their journals, contributing to BHL becoming an indispensable resource for biodiversity research.

Do institution staff publish in open access journals?A while ago I complained about how few new species descriptions were in open access journals (The top-ten new species described in 2010 and the failure of taxonomy to embrace Open Access publication). A measure of openness is whether an institution encourages its staff to publish their work in open access journals, and to make their data freely available as well. Some prefer to chase Nature and Science papers, but I'd like to think we could prioritise openness over journal impact factor.

These are just some of the more obvious things that could be used to measure openness. At the same time, it would be useful to develop ways to show the benefits of being open. For example, I've long argued that we could develop citation tracking for specimens. This gives researchers a means to track provenance of information (who said what about the identity of a specimen), and it also gives institutions a way to measure the impact of their collections. Doing this at scale is only going to be possible if collections are digitised, specimens have identifiers of some sort, and we can text mine the literature and associated data for those identifiers (in other words, the data and publications need to be open). So, perhaps on way to help make the case for being open is to develop metrics that are useful for the institutions themselves.

I guess I would have been much more enthusiastic about the Bouchout Declaration if these sort of things had been in place at the start. Anyone can sign a document. Ideas are cheap, execution is everything.

Source: iPhylo
01:50
ZHAW symposium 2015: “Life in Numbers 2: Genomics and Evolution of Microbial Pathogens” Date: 1 September 2015 Place: Wädenswil (Zürich lake), Switzerland Organizers: Maria Anisimova and Theo Smits Summary: With > 28’000 microbial genomes sequenced today, a broader range of researchers can step into NGS genomics without the prior knowledge of the complexity involved. This one-day conference is organised in two sections: “Genomics in practice” and “Evolutionary genomics”; with the aim to promote the dialogue between the community of microbiologists interested in genome analyses and their practical applications (e.g., in medicine or agriculture) and the community of bioinformatics method developers. During this conference the microbiology community will be able to bring their practical problems to the attention of method developers, prompting the exchange of ideas and leading to new methodologies and applications. The conference will facilitate the translation of academic results in pathogen genomics and bioinformatics to solving practical problems in microbiology. The conference is in line with the current strategy of ZHAW to expand applied genomics and bioinformatics research and its visibility in this field. The event will take place during the joint ZHAW-SIB summer school GEMP2015 (on a similar topic), and its participants will also attend the conference and will benefit from the invited talks and research discussions. Program and registration: http://bit.ly/1zIHocS “Anisimova Maria (anis)” via Gmail
Source: EVOLDIR

May 7, 2015

01:25
Hi Brian, below is an announcement of our NSF FuturePhy conference series, with ways to participate. Would appreciate it going out on EvolDir. You can probably do the links in a more elegant manner, or just send it with the full urls. Thanks, Mark *Announcement: FuturePhy Conferences and Workshops on Phylogenetics* FuturePhy is an NSF-sponsored, three-year program of conferences, workshops and hackathons on the Tree of Life. The project aims to promote novel, integrative data analyses and visualization, interdisciplinary syntheses of phylogenetic sciences, and cross-cutting uses of phylogenetics to develop and address new research questions and applications. The first phase of this mission is critical: to bring together a broad community of people from diverse backgrounds who are active in phylogenetics research, who use the tree of life in research or education, who will benefit in applied or practical ways from a comprehensive tree of life, or who come from a background that offers new perspectives on defining, addressing or transcending key challenges in phylogenetics. Help accelerate progress in all aspects of phylogenetics research by joining FuturePhy today. Diverse opportunities will be available to attend FuturePhy sessions in person or virtually, and to link FuturePhy to existing projects and initiatives. We invite you to participate in the project in several ways: 1. Register on http://futurephy.org Scientists from all aspects of the phylogenetic sciences, educators, members of the tree-using community, and others interested in phylogenetics are welcome. 2. Contribute to the discussion forum on http://futurephy.org This is the best way to log your interest and contribute ideas. 3. See our main themes, comment on them and take the survey to rank them: http://svy.mk/1KNNF88 4. Email contact@futurephy.org with ideas or comments 5. Tweet to the FuturePhy community: @FuturePhy 6. Comment in the FuturePhy thread on http://bit.ly/1ciDOFe via Gmail
Source: EVOLDIR
01:09
  We are seeking Evolutionary Biologists for the newly founded equal opportunities committee of the ESEB. Why an equal opportunities committee? The representation of women in academia remains low in most fields in science and engineering, despite near equal gender ratios at graduation. The problem is often phrased as the “Leaky Pipeline” problem, which describes the attrition of women from science at various stages along the academic career trajectory. Among the many contributing factors are unconscious biases that we have about the ability of men and women to perform a given scientific task. For example, a recent study found that fewer women give invited talks at the ESEB congress than might be expected. As a consequence, ESEB audiences are exposed to fewer top quality female speakers than are available, which reinforces gender stereotypes. Furthermore, ESEB student members experience fewer female role models than they could; this may demotivate young women to pursue an academic career in our field. Similar problems exist for other underrepresented groups (for example, ethnicities). The ESEB Equal Opportunities committee will target these and similar problems. Our aims are to: 1) to ensure equal opportunities in all activities and facets of ESEB 2) to increase awareness of the problem of underrepresented groups 3) to produce “best practice guidelines” for both ESEB as a society, the congress, and the journal 4) to monitor status and progress of underrepresented groups in our society and field The committee has a budget and an important task of committee members is to review applications and decide how to best spend our budget. The committee members will also work on guidelines and on monitoring. We are hoping to create a diverse committee with people who can bring diverse points of view and experience. If you have experience with improving participation of underrepresented groups, you are especially welcome to apply. If you are interested to bring yourself in and work forward to these goals as a committee member, please send an email with a very brief description of how you would like to help to julia.schroeder@gmail.com and pspennings@gmail.com Deadline is 20.05.2015 If you are interested to apply for money to improve participation of underrepresented groups, we’d be interested to hear from you too, although we need to form a committee before we post a formal call for proposals. Best wishes, Julia Schroeder and Pleuni Pennings Julia Schroeder Group Leader Evolutionary Biology Max Planck Institute for Ornithology Seewiesen, Germany +49 1721838836 Julia Schroeder via Gmail
Source: EVOLDIR

May 6, 2015

22:00
Primates are highly charismatic and often serve as flagship species in conservation efforts. They are also the closest living relatives of humans, and therefore hold the keys to resolving many questions about human evolution and ecology. However, the slow life histories of primates, combined with their complex social systems, their behavioral plasticity, and the challenging field conditions in which primate researchers must work, have severely limited analyses of mortality and fertility in wild, unprovisioned primate populations. This in turn limits comparative analyses that can shed light on the population dynamics and the social and ecological adaptations that have shaped both human and nonhuman primate evolution. We propose a Primate Life Histories Working Group to compare mortality and fertility schedules across taxa, to evaluate a set of hypotheses about the roles that phylogeny, ecology, and behavior play in shaping primate mortality and fertility patterns, and to examine whether life history theory predicts which vital rates are most variable across species. Using unique, individual-based life history data that have been collected from wild populations by nine working group participants over a minimum of 19 years, we will develop age-specific mortality and fertility schedules and create population projection matrices for each species. Our immediate goals are to test current hypotheses about the evolution of life histories in order to advance our understanding of primate evolution. Our longer-term goal is to move toward a collaborative, shared databank allowing analyses of irreplaceable life history data on wild primates.
Source: NESCent
18:00
Background: Feathers and hair consist of cornified epidermal keratinocytes in which proteins are crosslinked via disulfide bonds between cysteine residues of structural proteins to establish mechanical resilience. Cysteine-rich keratin-associated proteins (KRTAPs) are important components of hair whereas the molecular components of feathers have remained incompletely known. Recently, we have identified a chicken gene, named epidermal differentiation cysteine-rich protein (EDCRP), that encodes a protein with a cysteine content of 36%. Here we have investigated the putative role of EDCRP in the molecular architecture and evolution of feathers. Results: Comparative genomics showed that the presence of an EDCRP gene and the high cysteine content of the encoded proteins are conserved among birds. Avian EDCRPs contain a species-specific number of sequence repeats with the consensus sequence CCDPCQ(K/Q)(S/P)V, thus resembling mammalian cysteine-rich KRTAPs which also contain sequence repeats of similar sequence. However, differences in gene loci and exon-intron structures suggest that EDCRP and KRTAPs have not evolved from a common gene ancestor but represent the products of convergent sequence evolution. mRNA in situ hybridization demonstrated that chicken EDCRP is expressed in the subperiderm layer of the embryonic epidermis and in the barbule cells of growing feathers. This expression pattern supports the hypothesis that feathers are evolutionarily derived from the subperiderm. Conclusions: The results of this study suggest that convergent sequence evolution of avian EDCRP and mammalian KRTAPs has contributed to independent evolution of feathers and hair, respectively.
18:00
Background: Consumer-resource interactions constitute one of the most common types of interspecific antagonistic interaction. In natural communities, complex species interactions are likely to affect the outcomes of reciprocal co-evolution between consumers and their resource species. Individuals face multiple enemies simultaneously, and consequently they need to adapt to several different types of enemy pressures. In this study, we assessed how protist predation affects the susceptibility of bacterial populations to infection by viral parasites, and whether there is an associated cost of defence on the competitive ability of the bacteria. As a study system we used Serratia marcescens and its lytic bacteriophage, along with two bacteriovorous protists with distinct feeding modes: Tetrahymena thermophila (particle feeder) and Acanthamoeba castellanii (surface feeder). The results were further confirmed with another study system with Pseudomonas and Tetrahymena thermophila. Results: We found that selection by protist predators lowered the susceptibility to infections by lytic phages in Serratia and Pseudomonas. In Serratia, concurrent selection by phages and protists led to lowered susceptibility to phage infections and this effect was independent from whether the bacteria shared a co-evolutionary history with the phage population or not. Bacteria that had evolved with phages were overall more susceptible to phage infection (compared to bacteria with history with multiple enemies) but they were less vulnerable to the phages they had co-evolved with than ancestral phages. Selection by bacterial enemies was costly in general and was seen as a lowered fitness in absence of phages, measured as a biomass yield. Conclusions: Our results show the significance of multiple species interactions on pairwise consumer-resource interaction, and suggest potential overlap in defending against predatory and parasitic enemies in microbial consumer-resource communities. Ultimately, our results could have larger scale effects on eco-evolutionary community dynamics.
06:00
Background: Our aim is to understand the evolution of species-rich plant groups that shifted from tropical into cold/temperate biomes. It is well known that climate affects evolutionary processes, such as how fast species diversify, species range shifts, and species distributions. Many plant lineages may have gone extinct in the Northern Hemisphere due to Late Eocene climate cooling, while some tropical lineages may have adapted to temperate conditions and radiated; the hyper-diverse and geographically widespread genus Hypericum is one of these. Results: To investigate the effect of macroecological niche shifts on evolutionary success we combine historical biogeography with analyses of diversification dynamics and climatic niche shifts in a phylogenetic framework. Hypericum evolved cold tolerance c. 30 million years ago, and successfully colonized all ice-free continents, where today ~500 species exist. The other members of Hypericaceae stayed in their tropical habitats and evolved into ~120 species. We identified a 15–20 million year lag between the initial change in temperature preference in Hypericum and subsequent diversification rate shifts in the Miocene. Conclusions: Contrary to the dramatic niche shift early in the evolution of Hypericum most extant species occur in temperate climates including high elevations in the tropics. These cold/temperate niches are a distinctive characteristic of Hypericum. We conclude that the initial release from an evolutionary constraint (from tropical to temperate climates) is an important novelty in Hypericum. However, the initial shift in the adaptive landscape into colder climates appears to be a precondition, and may not be directly related to increased diversification rates. Instead, subsequent events of mountain formation and further climate cooling may better explain distribution patterns and species-richness in Hypericum. These findings exemplify important macroevolutionary patterns of plant diversification during large-scale global climate change.
03:17
Job Title: Research Assistant EcoHealthAlliance seeks an organized, self-motivated research assistant for our programs on emerging disease ecology, evolution, and modeling. The research assistant will assist senior research scientists on our USAID-funded PREDICT and NIH-funded projects examine the dynamics of pathogen transmission within and among wildlife populations, livestock, and humans; as well as the risk of spillover, patterns of infection, co-phylogenetic and phylogenetic relationships, and phylodynamics of emerging zoonotic diseases. The candidate should be self-motivated and proactive. Description and Responsibilities Reporting to senior research scientists this position will: - Work on modeling and other projects that broadly integrate evolutionary, ecological, and biodiversity data into emerging disease and zoonotic disease models. - Liaise with scientists to generate hypotheses and to assist with development of models and plan avenues of scientific investigation - Provide modeling and analytical support to EcoHealth Alliance scientists - Participate in and/or coordinate science and other meetings - Assist in project management and provide administrative support for project managers - Lead administration of grant proposals and reporting including contracting, coordinating invoicing, payments, and reports - Assist with finances, reimbursements, and expense coding - Take minutes and generate draft agendas for meetings - Assist with grant and manuscript writing - Have responsibility for some grant management and program coordination Qualifications - Minimum of B.S./B.A. in: Biology, Ecology, Evolutionary Biology, Public Health, or related field in the life sciences; Master$B!G(Bs degree preferred - Strong quantitative analytical skills - Experience with basic statistical analyses, particularly using R - Previous experience writing grants and with grant administration - Ability to conduct literature reviews, data collation and cleaning, and exploratory data analyses - Excellent oral and written communication skills - Publications in peer-reviewed scientific journals - Proven ability to work independently - A strong sense of team spirit and diplomacy - Previous experience in public health or infectious diseases - Cultural sensitivity - Fluency in English - Experience with phylogenetic and evolutionary analyses is a strong plus. Particularly, phylogenetic tools in R (e.g. ape, picante, geiger, etc.); software for building phylogenetic trees (including Geneious, and other programs for alignment and building likelihood and Bayesian trees); and molecular evolution (esp. BEAST) EcoHealth Alliance offers a competitive salary and a comprehensive benefit package including health, dental, and vision coverage, and a 403(b) pension plan. EcoHealth alliance is an equal opportunity employer. For further information about EcoHealth Alliance, please visit our website: http://bit.ly/1c4nPAV How to Apply: Send an email a single attachment labeled with your first and last name only ($B!H(Bfirst last.pdf$B!I(B) in PDF format containing with (a) a cover letter, (b) CV, and © three references to jobs@ecohealthalliance.org with “EHA RA SPRING 2015” in the subject line. Emails without the subject line or with multiple attachments will not be received. No formal text is required within the body of your email, since emails will not be evaluated. All inquires will receive an automatic response confirming receipt. Applicants will be evaluated and only appropriate candidates will be contacted. Thank you for your interest in EcoHealth Alliance! Aleksei Chmura via Gmail
Source: EVOLDIR
03:01

Investigating insertion and deletion in genomic inference via Gmail

Source: EVOLDIR
02:13
We are pleased to announce and invite you to the forthcoming edition of ConGen! 7th ConGen- Population Genomic Data Analysis Course: Recent Application of Next Gen Sequence Data to Understand Genetic Population Structure and Detect Natural Selection 31-Aug/ 5-Sept 2015, Flathead Lake Biological Station, Montana, USA Applications for 2015 edition are now open! Objective: To provide training in conceptual and practical aspects of data analysis for the population and evolutionary genomics of natural and managed populations. Emphasis will be on next generation sequence data analysis (RADs, exon capture, and whole genome sequence analyses) and interpretation of output from recent novel statistical approaches and software programs. The course also will allow daily discussions among young researchers (student participants) and >10 leaders in population genomics (instructors) to help develop the next generation of conservation and evolutionary geneticists. We will identify and discuss developments needed to improve data analysis approaches. This course will cover analysis methods including the coalescent, Bayesian, approximate Bayesian, and likelihood-based approaches. Who should apply: Ph.D. students, post-docs, and population biologists with a background of at least one semester university-level course in population genetics and a course in population ecology. Applicants must have a basic background in population genetic data analysis, including testing for Hardy-Weinberg proportions and gametic disequilibrium. Participation will be limited to 25-30 people allowing efficient instruction with hands-on computer exercises during the course. Priority will be given to persons with their own data to analyze (for example graduate students well into their degree program). Deadline for early bird application is 1 July, 2015 Course/Workshop Format: For each subject, we typically provide 30-45 minutes of background, theory, discussion and introduction to concepts. Immediately following, we will conduct data analyses together for 30-60 minutes using relevant software programs and real data sets. Evening hands-on computer sessions and lodging together of the instructors and students in the same location (the beautiful Flathead Lake field station) will allow for extensive exchange and facilitate learning. For detailed information (on instructors etc.) see http://bit.ly/1OZMGrq [dinner at McD (Large)] Field trip dinner with instructors in Glacier National Park “Luikart, Gordon” via Gmail
Source: EVOLDIR
02:13
Hey U.S. people going to Brazil for Evolution 2015: DO YOUR VISA NOW. IT’S A HUGE PAIN, at least for those of us that haven’t been to Brazil before. And it will take POSSIBLY 15 BUSINESS DAYS PLUS MAILING TIME ETC. Before too much griping, note that the aforementioned pain exists only because the U.S. does the same thing to Brazilians. So it won’t be easier until there is some mutual agreement reached between the governments. Since I blew half the day figuring it out, I will post the list of documents and basic procedure below. Of course you are responsible for your own decisions and I might have something wrong, I am not a lawyer, yadda yadda. GOAL: US citizens need a tourist visa for Brazil. They need approval stamped ON THEIR PASSPORT before they leave the U.S. TIME: The Atlanta Consulate says processing time is 15 business days (!). In other words, DO IT NOW. REQUIRED DOCUMENTS, which you will mail to the closest Brazilian consulate in the U.S. (unless you make an appointment at a consulate in person) ==== 1. U.S. passport. Yes, you will MAIL your precious passport to the consulate, they will stamp it and mail it back. No, this isn’t tremendously clear in the instructions. The passport must: 1a. be signed (make sure you sign it) 1b. have at least 6 months left on it from the time you enter Brazil 1c. have at least 2 blank pages 1d. You should scan / copy / iPhone photo your passport for backup before you mail it off 2. Plane tickets with ticket numbers for entry and exiting Brazil. 3. The invitation letter from the Evolution 2015 meeting, which you can get as a PDF after you register, by logging into http://bit.ly/1AE44WQ 4. A recent passport-type photo with a neutral expression. No glare, so take your glasses off. I got two at Walgreens for $12. 5. Fill out the online visa application, then print it out, then (a) glue on the passport photo, (b) sign it, and © also hand-write Contact Person and their phone number handwritten. The online application asks for a bunch of information including: - passport number etc. - hotel. The conference hotel is: Casa Grande Hotel Resort & Spa Telefone (Phone #): 55 13 3389-4000 Av Miguel Stéfano, 1001 - CEP: 11440-530. Enseada Guarujá/SP – Brasil Tel.: (55 13) 3389.4000. Fax.: (55 13) 3389.4023 http://bit.ly/1OZMIzt hotel@casagrandehotel.com.br (notes: SP = the state of São Paulo; CEP is I think the equivalent of zip code) 6. Recent bank statement showing “sufficient funds” to be a tourist. Your guess is as good as mine what that means, I am just printing out my checking account statement showing I have slightly more than $0. 7. You have to pay US$160.00, *not* with a check, but *only* with a U.S. Postal Service Money Order made out to “Consulate of Brasil”. Make sure to write your name on the money order. http://bit.ly/1AE42hz Note: The U.S. Post Office ONLY takes ATM/Debit, or cash, for Money Orders. No credit cards, no checks. 8. I am throwing in my hotel reservation and the extra passport photo because, why the heck not. 9. Pre-stamped, pre-addressed return envelope, with USPS tracking number. At the Post Office I got USPS Priority Mail each way, this comes with tracking numbers and $50 insurance., about $7 each way. Take the above stack of documents to the Post Office, and mail them to the local consulate with a USPS tracking number. ==== INSTRUCTIONS PAGES – the relevant info is spread over many pages. The best pages seem to be those *for the specific consulate that serves your region*, since there are differences between consulates. I recommend printing out all of these pages, reading them, and taking them to the Post Office in case questions come up. The most important thing is the address of the consulate. These were for the Atlanta, GA consulate, yours might be different and might have different instructions: ==== http://bit.ly/1OZMIzx http://bit.ly/1AE44WR http://bit.ly/1OZMIzB http://bit.ly/1AE44WV http://bit.ly/1OZMGrl http://bit.ly/1AE42hz ============================ Other folks – please post corrections/updates if you have any. NOTES: Tracy Heath reports that “The ‘sufficient funds’ requirement seems to only be for people in the Atlanta and Miami consulate jurisdictions.” Jeremy Brown says “For those still working on this, also bear in mind that some consulates allow you to mail things in and some require that you show up in person (or hire someone to show up on your behalf). I hired an agency to go to the consulate in Houston for me.” Nick says: Googling does turn up a lot of companies that will do the visa for you, probably you still have to get together the documents etc. Cheers, Nick Nick Matzke via Gmail
Source: EVOLDIR
02:13
Postdoctoral Fellow in Evolution & Medicine: Education Resources Development and Online Learning Reference #11183 Full-time The Center for Evolution & Medicine (CEM) at Arizona State University (ASU) invites applications for a Postdoctoral Fellow in Education Resources Development and Online Learning. Anticipated start date is August 3, 2015. This is a full-time (1.0) benefits-eligible, fiscal year (July 1 - June 30) appointment. Renewal is possible on an annual basis contingent on satisfactory performance, availability of resources, and the needs of the program. For additional information and policies regarding postdoctoral scholars at ASU, please see http://bit.ly/1AE42hI. The successful candidate will help curate existing online resources in evolutionary medicine, participate in the development and delivery of new innovative evolutionary medicine courses, both in-person and online, and will evaluate and study the impact and effectiveness of these resources and courses. The fellow will help develop a project plan to build courses that will initially be offered to ASU and ASU online students and later to medical personnel all over the world. This is an exciting opportunity to work with an interdisciplinary faculty in a growing field of study to develop, implement, and research innovative curriculum and other resources related to evolution and medicine. While specific technology expertise is not required, an ideal candidate would demonstrate a strong interest in the applications of technology in higher education, and would have an aptitude for developing and assessing new approaches to learning and how they are best supported by new technologies. This, together with experience in curriculum development and teaching, will allow the Education Resources Fellow to provide disciplinary and pedagogical expertise in creating innovative and rigorously assessed learning experiences. The Fellow may have supervisory responsibilities that include the training and mentoring of staff and/or student interns. This Postdoctoral Fellows Program is a service and training program designed for early career scientist-teachers who are interested in an academic pathway involving curriculum development, teaching, and educational programming in the interdisciplinary field of Evolutionary Medicine. As a training opportunity fellows will receive mentorship to support their development as educators throughout the duration of the fellowship and have an opportunity to participate in the ASU Science Education Group, the Evidenced-based Teaching Seminar series, as well as the Biology Education Research Lab. Candidates must have a Ph.D. in anthropology, biology or other natural science or science education field that provides an extensive background in evolutionary biology. Cross-training and experience in education is desirable. Candidates with experience in the following are preferred: developing and assessing education resources; conducting educational research; and using developing digital resources for online and classroom use. The successful candidates will have a commitment to science education, must have outstanding writing and organizational skills, demonstrated capacity for independence and innovation, and the ability to work as part of a team. Arizona State University is a dynamic, progressive university dedicated to interdisciplinary collaborations, to rethinking university education, and to integrating excellence in both research and teaching. The Center for Evolution and Medicine at Arizona State University’s Tempe campus is a university-wide presidential initiative whose mission is to establish evolutionary biology as an essential basic science for medicine, worldwide. The Center will bring leading scientists to ASU to join existing faculty in research that demonstrates the power of evolutionary biology to address problems in medicine and public health. The new courses and degrees they create will begin to meet the growing demand for such experiences, and will educate a generation of future researchers and health professionals. Many of these experiences will be at ASU, and some will be in conjunction with the new Mayo medical school, but others will be available online open access worldwide, providing the authoritative content that has long been needed to bridge the gap between evolutionary biology and medicine. To apply, please email a single pdf document containing a letter of application that states your interest in and qualifications for the position, a curriculum vitae, names of three references, and an item of choice that represents your approach to teaching in undergraduate science classroom to evmedsearch@asu.edu. The initial closing date for receipt of complete applications is June 30, 2015; applications will be reviewed weekly thereafter until the search is closed. A background check is required for employment. Arizona State University is an equal opportunity/affirmative action employer committed to excellence through diversity. Women and minorities are encouraged to apply (http://bit.ly/1OZMIzD). For more information on ASU’s non-discrimination policy, visit ACD 401. For additional information on the Center for Evolution & Medicine, visit http://bit.ly/1AE42hK. For additional information on the position, please contact Kathleen Holladay, Assistant Director, at kholladay@asu.edu. Kathleen Holladay via Gmail
Source: EVOLDIR

May 5, 2015

22:30

It is obvious that there is a big cultural difference between biologists and computationalists, irrespective of whether we think its a good idea or not. This follows simply from the nature of the activities in the two professions — the activities are different and therefore different personalities are attracted to those professions.

Some of these differences are well known. For example, computations require algorithmic repeatability, along with proof that the algorithms achieve the explicitly stated goal. This means that computationalists have to be pedants in order to succeed. On the other hand, no-one can be pedantic and succeed in biology. Biodiversity is a concept that makes it clear that there are no rules to biological phenomena — any generalization that you can think of will turn out to have numerous exceptions. In the biological sciences we do not look for universal "laws" (as in the physical sciences), because there are none; and if you can't handle that fact then you should not try to become a biologist.

This leads to a further difference between the two professions that I think is sometimes poorly appreciated. In general, computationalists focus on patterns, whereas biologists focus on processes. Many processes can produce the same patterns, and therefore the same computations can be used to detect those patterns; and this is of interest to people who are developing algorithms. On the other hand, in biology processes can produce many different patterns, so that patterns are often unpredictable. Biologists are aware that patterns and processes can be poorly connected, and the biological interest is primarily on understanding the processes, because these are frequently more generalizable than are the patterns.

As a simple example of this dichotomy, consider the following diagram (from Loren H. Rieseberg and Richard D. Noyes. 1998. Genetic map-based studies of reticulate evolution in plants. Trends in Plant Science 3: 254-259). It shows the eight haploid chromosomes of a particular plant species.


Perusal of the figure will lead you to identify the pattern, and this is straightforward to detect computationally. Each chromosomal segment is triplicated, but the triplicates are arranged arbitrarily and are sometimes segmented.

On its own this is of little biological interest. The interest lies in the processes that led to the pattern. These processes could produce an infinite number of similar patterns, and so predicting the exact pattern in this species is impossible. We use abduction to proceed from the pattern to the processes (see What we know, what we know we can know, and what we know we cannot know).

We appear to be looking at a case of allopolyploidy (the nuclear genome is hexaploid) followed by recombination. Neither of these processes necessarily produces patterns that can be predicted in detail.

So, the computation focuses on the pattern and the biology on the process. Sometimes biologists forget this, and naively interpret patterns as inevitably implying a particular process. And sometimes computationalists naively expect patterns to be predictable when they are not.

00:52
14th Annual General Meeting of the FoS and Symposium on"Conservation of the Natural and Cultural Heritage of Socotra" September 11-13, 2015 @ CIBIO-InBIO, Vairo, Portugal The Annual General Meeting of the Friends of Soqotra (FoS) is a great opportunity to meet other FoS members and fellow-travellers, to discuss the latest results of scientific research on the Soqotra Archipelago, to learn about ongoing projects, and to share information about FoS activities over the last year. Both members and non-members are very welcome to participate in the meetings. Between 2001 and 2014 the AGM has been held in different European countries. The 13th Annual General Meeting of FoS and Symposium entitled “Biodiversity and Culture of Socotra” was held on 19 - 21 September 2014 in Rome, Italy. In 2015 the 14th Annual General Meeting of the FoS and Symposium entitled “Conservation of the Natural and Cultural Heritage of Socotra” will take place on September 11-13 in Portugal hosted by CIBIO-InBIO’s CONGEN [http://bit.ly/1Ecb3GY] group. A discussion workshop relating current pressures to the heritage of Socotra and elaboration of a response plan will also take place during this meeting. IMPORTANT DATES Abstract submission deadline: June 30, 2015 Abstract acceptance / Early registration deadline: July 30, 2015 Further information about this event can be found here: http://bit.ly/1Ib8Ml8. CIBIO - Centro de Investigao em Biodiversidade e Recursos Genticos/ InBIO Laboratrio Associado, Universidade do Porto Campus Agrrio de Vairo Rua Padre Armando Quintas 4485-661 Vairo Portugal t: +351 252 660 411 Ext. 285 f: +351 252 661 780 e: divulgacao@cibio.up.pt w: http://cibio.up.pt f: http://on.fb.me/1Ecb3H2 CIBIO Divulgao via Gmail
Source: EVOLDIR
00:52
Dear Colleagues, The 11th International Plant Molecular Biology meeting will take place this year at Iguassu Falls from October 25th - 30th. Several talks and sessions will address key issues on plant evolution. The scientific program is very exciting and top questions in the field will be addressed. Visit the website at . Registration is open with reduced price until June 30th. Abstracts are accepted until July 31st. With our best regards, Marie-Anne On behalf of the Bilateral Organizing Committee and IPMB Board Rita Ulloa (INGEBI, Argentina), Marie-Anne Van Sluys (Universidade de Sao Paulo, Brazil) Fernando Carrari (INTA, Argentina), Marcio C. Silva-Filho ( Universidade de Sao Paulo - Brazil) mavsluys@usp.br via Gmail
Source: EVOLDIR