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April 5, 2014

00:18

Radiation and Extinction - Investigating Clade Dynamics in Deep Time 10th-11th November 2014 - Linnean Society of London (UK) A two-day symposium and workshop bringing together a diverse array of researchers developing and applying methods for reconstructing deep-time macroevolutionary patterns in biodiversity, with a particular focus on analytical approaches that take advantage of the wealth of data available in the fossil record. Dan Rabosky (University of Michigan) will deliver the plenary talk, with additional confirmed presentations from Tracey Aze (University of Oxford), Natalie Cooper (Trinity College Dublin), Mario dos Reis (University College London), John Finarelli (University College Dublin), Matt Friedman (University of Oxford), Melanie Hopkins (American Museum of Natural History), Graeme Lloyd (University of Oxford), Emily Rayfield (University of Bristol), Marcello Ruta (University of Lincoln), Graham Slater (Smithsonian National Museum of Natural History), Jeroen Smaers (Stony Brook University), Tanja Stadler (ETH Zrich), Gavin Thomas (University of Sheffield), and Chris Venditti (University of Reading). Further details and registration here: http://bit.ly/PBxYty Dr. Anjali Goswami Reader in Palaeobiology Department of Genetics, Evolution, and Environment and Department of Earth Sciences University College London Darwin Building 218A Gower Street London WC1E 6BT +44 (0)20 7679 2190  www.goswamilab.com “Goswami, Anjali” via Gmail

Source: EVOLDIR
00:03
The Ecology and Evolution program at Sun Yet-Sen University (SYSU), a premiere institution in China, is seeking to expand its Ecology and Evolution program by recruiting 6-8 PIs. The positions, open rank, welcome qualified scientists of all nationalities. The EE program at SYSU, recently ranked first in China, plans to recruit in broad areas of modern ecological research and in the interface between ecology and evolution. SYSU has had long-standing ties with major universities in North America and their faculty members have strong research presence on campus. An International center established 2005 will be expanded into a new Open Laboratory in Ecology and Evolution as part of this growth. Salary and start-up package are highly competitive. The university is located in Guangzhou, a major metropolis in southern China. Guangzhou is one of the three most internationalized cities in the country and is home to many international schools from K to 12. For inquiry, please write to Hong Pang (Sun Yat-sen University, Lsshpang@mail.sysu.edu.cn) . For pre-application consultation, interested individuals are welcome to contact Fangliang He (University of Alberta, fhe@ualberta.ca), Chung-I Wu (University of Chicago, ciwu@uhicago.edu) or Antony Dean (University of Minnesota, deanx024@umn.edu). (SYSU; http://bit.ly/1je3CYv; http://bit.ly/1je3BE2) wuci via Gmail
Source: EVOLDIR

April 4, 2014

23:49

3-YEAR FUNDED PhD POSITION ON EVOLUTIONARY GENOMICS TITLE: How the loss of genes has shaped the genome as we know it SUPERVISOR: Antonio Marco ORGANIZATION: University of Essex LOCATION: Colchester, United Kingdom DEADLINE: April 30th, 2014 DESCRIPTION: Genomes are the product of a long evolutionary process. Many genes have multiple copies, reflecting the importance of gene duplication during genome evolution. The duplication of genes with regulatory functions has been associate with the development of novel functions. However, there is strong evidence that the loss of gene functions has also influenced the evolution of species. Gene loss is often associated with redundant functions, but the loss of non-redundant regulatory genes also happens with relative frequency. In recent years, the characterization of novel types of regulatory genes, such as microRNAs or long-non-coding RNAs, showed that gene loss is much more important that previously thought. Nevertheless, gene loss as a driving evolutionary force has not been systematically explored. This project aims to understand how gene losses have shaped genomes. A PhD student will compare the genomes of related species and characterize which genes have been lost in specific lineages. The work will focus in transcription factors as well as in other regulatory genes such as microRNAs. By analysing the function, evolutionary age and regulatory connections of lost genes, we will be able to generate a model of genome evolution by gene loss. The candidate will be trained in computational biology / bioinformatics, with a focus on evolutionary genetics and comparative genomics. No prior knowledge of computer programming is required, but the candidate will have the chance to learn one programming language and state-of-the-art computational approaches. Depending on the interest of the student, the project may also involve molecular genetics in Drosophila melanogaster. REFERENCES: - Marco A, Ninova M, Ronsaugen M, Griffiths-Jones S (2013) Clusters of microRNAs emerge by new hairpins in existing transcripts. Nucleic Acids Res, 41:7745-7752. - Marco A (2012) Regulatory RNAs in the light of Drosophila genomics. Brief Func Genomics, 11:356-365. - Hahn MW, Han MV, Han S-G (2007) Gene family evolution across 12 Drosophila genomes. PLoS Genetics 3:e197. CAMPUS: The School of Biological Sciences at University of Essex is one of the largest science departments in the University, with some 52 teaching and academic staff working in the areas of environmental microbiology, plant productivity, biophysics, biochemistry, organic chemistry, cell/molecular biology and evolution. This broad-based structure provides for a strong multidisciplinary environment involving collaboration between chemists, biochemists and biologists. Colchester campus is located in Wivenhoe Park, a picturesque and historic 200 acres parkland. The park was originally landscaped in the eighteenth century and was painted by celebrated landscape artist John Constable. The campus is only two miles from the historic centre of Colchester - England’s oldest recorded town, and one hour from London. It is a vibrant and international campus, hosting more than 9,000 students from more than 130 different nationalities. FUNDING: This scholarship will be to the value of 12,500 per annum plus UK tuition fees. Apply from the University web page at: http://bit.ly/PBqdE1 For any query, please, contact me at: amarco.bio@gmail.com http://amarco.net via Gmail

Source: EVOLDIR
23:34
Reminder Professor in Evolutionary Biology The Institute of Ecology and Evolution of the University of Bern, Switzerland, announces a vacancy for a professorship (open rank) in Evolutionary Biology. Applications are sought from individuals with an outstanding research record in theoretical and/or experimental evolution. Candidates with a strong background in evolutionary genomics are also encouraged to apply. The candidate should have a doctorate in a relevant field, several years of postdoctoral and teaching experience, an interest in developing, testing and teaching evolutionary theory and in collaborating with other researchers of our institute. Senior researchers are also encouraged to apply. Hiring level, from tenure-track Assistant Professor to Full Professor, will be commensurate with experience. The new faculty member will have responsibility for part of the teaching of evolutionary biology at undergraduate and graduate levels. All graduate teaching and advanced undergraduate teaching are in English. The application should include a letter of motivation, a CV with a short research plan for the next 5 years, funding history, list of previous teaching and supervised MSc and PhD students, a list of publications, and the names and contact information for three references. Applications from women are strongly encouraged. Appointment will be either to tenure track or tenured, commensurate with experience. The earliest starting date for the position is August 1st 2015. Applications must be submitted by April 10th 2014 as one PDF file to info@natdek.unibe.ch, and should be addressed to the Faculty of Science, University of Bern, Prof. Silvio Decurtins, Dean, Sidlerstrasse 5, 3012 Bern, Switzerland. You can contact director@iee.unibe.ch for further information about the position. More information about the institute can be found on iee.unibe.ch Laurent Excoffier via Gmail
Source: EVOLDIR
18:00
Background: Manchurochelys manchoukuoensis is an emblematic turtle from the Cretaceous Yixian Formation of Liaoning, China, a geological rock unit that is famous for yielding perfectly preserved skeletons of fossil vertebrates, including that of feathered dinosaurs. Manchurochelys manchoukuoensis was one of the first vertebrates described from this fauna, also known as the Jehol Biota. The holotype was lost during World War II and only one additional specimen has been described since. Manchurochelys manchoukuoensis is a critical taxon for unraveling the phylogenetic relationships of Cretaceous pancryptodires from Asia, a group that is considered to be of key importance for the origin of crown-group hidden-neck turtles (Cryptodira). Results: A new specimen of Manchurochelys manchoukuoensis is described here from the Jiufotang Formation of Qilinshan, Chifeng, Inner Mongolia, China. This is the third specimen described and expands the range of this taxon from the Yixian Formation of the Fuxin-Yixian Basin in Liaoning to the Jiufotang Formation of the Chifeng-Yuanbaoshan Basin. A possible temporal extension of the range is less certain. The new finding adds to our understanding of the morphology of this taxon and invites a thorough revision of the phylogeny of Macrobaenidae, Sinemydidae, and closely allied forms. Conclusions: Our comprehensive phylogenetic analyses of Cretaceous Asian pancryptodires yielded two main competing hypotheses: in the first these taxa form a paraphyletic grade, whereas in the second they form a monophyletic clade. The inclusion of problematic tree changing taxa, such as Panpleurodires (stem + crown side-neck turtles) has a major influence on the phylogenetic relationships of Sinemydidae and closely allied forms. Manchurochelys manchoukuoensis nests within Sinemydidae together with Sinemys spp. and Dracochelys bicuspis in the majority of our analyses.
09:58

Boronian wrote:

Dear babblers, in the past I followed the "total evidence" approach quite doubtlessly, especially when only DNA regions of one genome type (cp, n, mt) were involed. I merely checked if the (good supported) backbone nodes in all trees from individual markers agreed. They mostly did, so I didn't bother any further and created the supermatrix with respective partitioning.

My question is: Is there any standard procedure or common practice I missed, to decide on a quantitative basis if one is allowed to combine the data sets?

I found hints to a couple of tools that should provide such tests [e.g. concaterpillar - couldn't make it run with recent RAxML and is only for amino acid data(?); arn - a package from Farris (yes, THE Farris), which I couldn't locate], but none of them seemed to be working for me.

I then calculated Robinson Foulds distances between the individual trees and the tree from the supermatrix, but I am unsure what distance value should be considered as a threshold (if this is at all a good way to go for my aim).

Please let me know if you have hints in this respect, especially some automizable thing (in R?) would be nice.

Cheers

Posts: 10

Participants: 5

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09:24

Erick Matsen wrote:

I was following a reference chain and came across the PhD thesis of Jonathan Laserson, who was a Daphne Koller student and now works at Google.

The thesis is interesting. It's quite ambitious: in one chapter he sets up a Bayesian inference algorithm for a tree of cells (cc @mathmomike) that explicitly models sequencing error. On the other hand, I can't see how he got any of this to work efficiently for the sizes of data sets discussed, and his software, called ImmuniTree, is not to be found on the web.

@jeetsukumaran and others may know this fellow from his Genovo de novo assembly software for mixed populations.

Posts: 2

Participants: 2

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06:22
Following on from the previous post Rethinking annotating biodiversity data, here are some more thoughts on annotating biodiversity data.

Annotations as sticky notes
I get the sense that most people think of annotations as "sticky notes" that someone puts on data. In other words, the data is owned by somebody, and anyone who isn't the owner gets to make comments, which the owner is free to use or ignore as they see fit. With this model, the focus is on how the owner deals with the annotations, and how they manage the fact that their data may have changed since the annotations were made.

This model has limitations. For a start, it privileges the "owner", and puts annotators at their mercy. For example, I posted an issue regarding a record in the Museum of Comparative Zoology Herpetology database (see https://github.com/mcz-vertnet/mcz-subset-for-vertnet/issues/1). VertNet has adopted GitHub to manage annotations of collection data, which is nice, but it only works if there's someone at the other end ready to engage with people like me who are making annotations. I suspect this is mostly not going to be the case, so why would I bother annotating the data? Yes, I know that VertNet has only just set this up, but that's missing the point. Supporting this model requires customer support, and who has the resources for that? If I don't get the sense that someone is going to deal with my annotation, why bother?

So, the issues here are that the owner gets all the rights, the annotators have none, and in practice the owners might not be in a position to make use of the annotations anyway.

Wikis
OK, if the owner/annotator model doesn't seem attractive, what about wikis? Let's put the data on a wiki and let folks edit it, that'll work, right? There's a lot to be said in favour of wikis, but there's a disadvantage to the basic wiki model. On a wiki, there is one page for an item, and everyone gets to edit that same page. The hope is that a consensus will emerge, but if it doesn't then you get edit wars (e.g., When taxonomists wage war in Wikipedia). If you've made an edit, or put your data on a wiki, anyone can overwrite it. Sure, you can roll back to an earlier version, but so can anyone else.

Wikis bring tools for community editing, but overturn ownership completely, so the data owner, or indeed any individual annotator has no control over what happens to their contributions. Why would an expert contribute if someone else can undo all their hard work?

Social data
So, if sticky notes and wikis aren't the solution, what is? I've been looking at Fluidinfo lately. There's an interview here, and a book here. The company has gone quiet lately (apparently focussing on enterprise customers), but what matters here is the underlying idea, namely "social data".

Fluidinfo's model is that it is a database of objects (representing things or concepts), and anyone can add data to those objects (they are "openly writable"). The key is that every tag is linked to the user, and by default you can only add, edit, or delete your own tags. This means that if a data provider adds, say a bibliographic reference to the database, I can edit it by adding tags, but I can't edit the data provider's tags. To make this a bit more concrete, suppose we have a record for the article with the DOI 10.1163/187631293X00262. We can represent the metadata from CrossRef like this:

{
"_id": "10.1163/187631293X00262",
"crossref/doi" : "10.1163/187631293X00262",
"crossref/title" : "A taxonomic review of the pondskater...",
"crossref/journal" : "Insect Systematics & Evolution",
"crossref/issn" : [ "1399-560X", "1876-312X"]
}

Note the use of the namespace "crossref" in the tags. This is data that, notionally, CrossRef "owns" and can edit, and nobody else. Now, as I've discussed earlier (Orwellian metadata: making journals disappear) some publishers have an annoying habit of retrospectively renaming journals. This article was published in Entomologica Scandinavica, which has since been renamed Insect Systematics & Evolution, and CrossRef gives the latter as the journal name for this article. But most citations to the article will use the old journal name. Under the social data model, I can add this information (in bold):

{
"_id": "10.1163/187631293X00262",
"crossref/doi" : "10.1163/187631293X00262",
"crossref/title" : "A taxonomic review of the pondskater...",
"crossref/journal" : "Insect Systematics & Evolution",
"crossref/issn" : ["1399-560X", "1876-312X"],
"rdmpage/journal" : "Entomologica Scandinavica","rdmpage/issn" : ["0013-8711" ]
}

My tags have the namespace "rdmpage", so they are "mine". I haven't overwritten the "crossref" tags. Somebody else could add their own tags, and of course, CrossRef could update their tags if they wish. We can all edit this object, we don't need permission to do so, and we can rest assured that our own edits won't be overwritten by somebody else.

This model can be quite liberating. If you are a data provider/owner, you don't have to worry about people trampling over your data, because you (and any users of your data) can simply ignore tags not in your namespace ("ignore those rdmpage' tags, that Rod Page chap is clearly a nutter"). Annotators are freed from their reliance on data providers doing anything with the annotations they created. I don't care whether CrossRef decides to revert the journal name Insect Systematics & Evolution to Entomologica Scandinavica for earlier article (or not), I can just use the "rdmpage/journal" (if it exists) to get what I think is the appropriate journal name. My annotations are immediately usable. Because everyone gets to edit in their own namespace, we don't need to form a consensus, so we don't need the version control feature of wikis to enable roll backs, there are no more edit wars (almost).

Implementation
A key feature of the Fluidinfo social data model is that the data is stored in a single, globally accessible place. Hence we need a global annotation store. Fluidinfo itself doesn't seem to have a publicly accessible database, I guess in part because managing one is a major undertaking (think Freebase). Despite Nicholas Tollervey's post (FluidDB is not CouchDB (and FluidDB's secret sauce)), I think CouchDB is exactly the way I'd want to implement this (it's here, it works, and it scales). The "secret sauce" is essentially application logic (every key has a namespace corresponding to a given user).

The more I think about this model the more I like it. It could greatly simplify the task of annotating biodiversity data, and avoid what I fear are going to be the twin dead ends of sticky note annotation and wikis.
Source: iPhylo
02:21
The link in the email is giving problems. Currently it is http://bit.ly/1jDTglD“ It needs to be (i.e. With the “ removed at the end) http://bit.ly/1jDTglD Can you repost this email? Thanks, Jenny “A few weeks ago I posted the following query “Does anyone have a user-friendly way of inputting data into CLUMPP and DISTRUCT? CLUMPP averages results across STRUCTURE simulations once K has been selected, and DISTRUCT produces the STRUCTURE figure.The challenge is that both are command-line programs, and DISTRUCT mac version seems broken (however, I assume PC version is OK). Dent Earl and Bridgett vonHoldt produced an great solution for processing STRUCTURE output. A similar solution for CLUMPP and DISTRUCT would be most welcome. (Earl, D. A., vonHoldt, B. M., 2011. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4, 359-361, doi:10.1007/s12686-011-9548-7.)” Many thanks to those who replied. Their answers are found at http://bit.ly/1jDTglD Thanks, Jenny ***** ** New UQ email address** j.ovenden@uq.edu.au Jennifer Ovenden http://bit.ly/1eYVhrV http://bit.ly/MV3SQf From: Richard Coleman Date: Thursday, 3 April 2014 6:52 pm To: Jennifer Ovenden Subject: Fwd: Other: CLUMPP_and_DISTRUCT.answers Hi Jenny, Thanks for asking this question! I am going through the exact same issue at this very moment. I was wondering if you had a working link to the answers you compiled? The link that is provided leads to an empty page. Regards, Richard - via Gmail
Source: EVOLDIR
01:59
PhD student seeking a male roommate to share a double room at the upcoming joint CSZ/CSEE Genomes to Biomes Meeting in Montreal,Canada, 25-29 May 2014. Student plans to stay for the entire meeting, including the night of 29 May (departure 30 May). Anyone interested in sharing should contact Roohollah Abbasi: roohollahabbasi@gmail.com Jeffrey Marcus via Gmail
Source: EVOLDIR
01:40
Dear Colleagues, Registration for the Ontario Ecology, Ethology, and Evolution Colloquium closes this Monday, April 7. OE3C 2014 is hosted by the University of Guelph and will be held on May 8-10. We are still accepting abstract submissions for oral or poster presentations, especially from undergraduate or graduate students and post-docs. Abstract guidelines, conference logistics, and instructions about registration can be found on our website: http://bit.ly/MwFZhq Please contact us at oe3c2014@gmail.com with any questions. We hope to see you in May! Kate Eisen http://bit.ly/MwFZhq oe3c2014@gmail.com OE3C 2014  via Gmail
Source: EVOLDIR
01:40
SUMMER COURSE ON MARINE GENOMICS AT THE MARINE BIOLOGICAL STATION OF ROSCOFF (F) Second announcement >From May 25th - June 7th, 2014 the 10th Summer Course on Marine Evolutionary & Ecological Genomics will take place at the Station Biologique de Roscoff, Roscoff, France. Aims: The two week course, which consists of lectures, tutorials and computer labs, aims to highlight the crucial role of marine genomics for the understanding of the marine environment and for an efficient use of its resources. It takes place at the Biological Station, a vibrant research community of 273 scientists and support personnel, located in the old town and fishing port of Roscoff, Brittany, France. Advanced PhD students and junior postdocs are encouraged to apply. The course includes lectures, tutorials and computer based exercises on the following topics. * Genomics - next generation sequencing, database searching, basic skills in data handling and bioinformatics * Population genomics - diversity, structure, connectivity and gene flow, assignment, effective population size, population dynamics, adaptive variation * Environmental genomics - environment - genome interactions, ecogenomics, metagenomics and metagenetics * Functional genomics - genome structure, molecular evolution at the functional level, genomic architecture, functional networks * Comparative genomics - whole genome comparisons, concatenated phylogenies, genome organization, annotating genomic information, co-evolution The course covers all aspects of life in the ocean. Target group PhD students (at least in their second year) and junior postdocs with a solid knowledge in phylogenetics and/or population genetics. 18 participants will be selected on the following criteria: 1. Relevance of the course for their PhD or post-doc project 2. Background and experience 3. We aim at training people with different research backgrounds; not more than one person per institute will be considered. We implement a gender policy. The selected persons will be notified by mid April and will have to confirm attendance within 7 days. There is a waiting list in case of non-confirmations and cancellations. Teaching staff : Jonas Colln, SB-Roscoff, FR Simon Creer, U Bangor, UK Yves Desdevises, UPMC, Banuyls, FR Jakob Hemmer-Hansen, DTU-Aqua, DK Erica Leder, U Turku, Fi Frdric Partensky, SB-Roscoff, FR Daniel Vaulot, SB-Roscoff, FR Filip Volckaert, KULeuven, BE Mathias Wegner, GEOMAR, Kiel and AWI-Sylt, GE Organizing committee Jonas Colln, SB-Roscoff, FR Damien Guiffant, SB-Roscoff, FR Matthias Obst, Univ. Gothenburg, SW Jeanine Olsen, Univ Groningen, NL Filip Volckaert, KU Leuven, BE For information and application please check http://bit.ly/Pf8qCX. The application deadline is April 8 2014. Filip Volckaert via Gmail
Source: EVOLDIR
01:04

Application Deadline Approaching, 11 April 2014 Human Genome Analysis, Genetic Analysis of Multifactorial Diseases Venue: Wellcome Trust Genome Campus, Hinxton, Cambridge, UK When: 23 - 29 July 2014 Course organiser: Daniel Weeks (University of Pittsburgh, USA) Course instructors: Heather Cordell (Institute of Genetic Medicine, Newcastle University, UK) Janet Sinsheimer (University of California, Los Angeles, USA) Eric Sobel (University of California, Los Angeles, USA) Joe Terwilliger (Columbia University, New York, USA) Simon Heath (Centre Nacional d’Anlisi Genmica (CNAG), Barcelona, Spain) Guest speakers: Cornelia van Duijn (Erasmus University Medical Center, The Netherlands) Dajiang Liu (Penn State College of Medicine, USA) Dorret Boomsma (VU University Amsterdam, The Netherlands) Eris Moses (The University of Western Australia) Philippe Froguel (Imperial College London, UK) Summary: This advanced course covers statistical methods currently used to map disease susceptibility genes, with an emphasis on (but not limited to) methods that can analyse family data or a combination of families and individuals. Discussions of the latest statistical methodology are complemented by practical hands-on computer exercises using state-of-the-art software. The statistical basics behind each method will be carefully explained so that participants with a non-statistical background can understand. We will discuss fundamental issues needed to increase success in gene mapping studies including: optimal study design, power to detect linkage and association, determining the most appropriate statistical methods and software, interpretation of statistical results and trouble shooting. We will also cover the basic principles of statistical inference, hypothesis testing, population and quantitative genetics and Mendelian inheritance. Our interactive and intensive educational program will enable one to better carry out sophisticated statistical analyses of genetic data, and will also improve one’s interpretation and understanding of the results. All the software used is freely available, so that skills learned can be easily applied after the course. Teaching will take the form of lectures by invited speakers, informal tutorials, hands-on computer sessions, and analysis of disease family data sets. There will also be an opportunity to discuss participants’ own data sets. Registration fee and bursaries: Registration (including accommodation and all meals) 890. Limited bursaries are available covering up to 50% of the registration fee. Full details: http://bit.ly/1la3qtk via Gmail

Source: EVOLDIR
00:44

—Apple-Mail=_FD55AEC6-C0FE-4C36-9B48-1E84C0CFB53F Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=windows-1252 Understanding evolutionary rates on the avian tree of life Two post-doctoral and four postgraduate research assistant positions in macroevolution/trait evolution in birds. Two postdoctoral research associate positions and four postgraduate research assistant positions are available to work on macroevolution and trait evolution in birds. The posts are funded by a European Research Council consolidator grant to Gavin Thomas in the Department of Animal and Plant Sciences at the University of Sheffield. The successful applicants will join a new research team collecting novel, high-resolution morphometric data on bird bill shape using 3D structured white-light digitisation and plumage colour using visible and UV spectrum digital photography. Postdoctoral Research Associates (two posts): The project is focused on modelling phenotypic evolution of species traits in birds at broad phylogenetic and spatial scales. The aims are to test how and why phenotypic evolutionary rates vary and to ask how that variation has shaped both the avian tree of life and global distributions of species and traits. The exact directions of the research will be partially dependent on the skills and interests of the successful applicant(s). Applicants must have a PhD with emphasis on macroevolutionary/phylogenetic approaches to evolutionary biology or similar. Expertise in modelling evolutionary processes on phylogenies, 3D surface morphometrics, or measuring plumage colour with digital photography would be advantageous. Full details are available from, and formal applications should be made, via University of Sheffield job’s pages Postgraduate Research Assistants (four posts): The postgraduate post-holder(s) will be responsible for generating and processing high-resolution morphometric data on bird bills using 3D structured white-light digitisation and plumage colour using visible and UV spectrum digital photography. Data collection will rely on extensive museum collections in the UK and elsewhere. Applicants must have a good first degree in biology, ideally with a substantial evolutionary biology component. However, candidates with other backgrounds will be considered. A masters degree in an evolutionary biology discipline would be an advantage. Potential applicants with a PhD are also eligible to apply. Experience in working with museum collections would be an advantage but is not essential and training will be provided. Up to four positions are available initially as fixed-term one-year contracts with funding available to extend by an additional 1-2 years for suitable candidates. Further details are available from, formal applications should be made via University of Sheffield job’s pages Informal enquiries for all posts are encouraged and should be sent by email (gavin.thomas@sheffield.ac.uk) with an outline or your research interests, CV and or/link to a personal webpage. In addition to the above posts one PhD studentship on the same grant is available and details will be advertised very soon. Gavin Thomas —Apple-Mail=_FD55AEC6-C0FE-4C36-9B48-1E84C0CFB53F Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=windows-1252 Understanding evolutionary rates on the avian tree of life

Two post-doctoral and f our postgraduate research assistant positions in macroevolution/trait evolution in birds.

Two postdoctoral research associate positions and four postgraduate research assistant positions are available to work on macroevolution and trait evolution in birds. The posts are funded by a European Research Council consolidator grant to Gavin Thomas in the Department of Animal and Plant Sciences at the University of Sheffield. The successful applicants will join a new research team collecting novel, high-resolution morphometric data on bird bill shape using 3D structured white-light digitisation and plumage colour using visible and UV spectrum digital photography.

Postdoctoral Research Associates (two posts): The project is focused on modelling phenotypic evolution of species traits in birds at broad phylogenetic and spatial scales. The aims are to test how and why phenotypic evolutionary rates vary and to ask how th at variation has shaped both the avian tree of life and global distributions of species and traits. The exact directions of the research will be partially dependent on the skills and interests of the successful applicant(s). Applicants must have a PhD with emphasis on macroevolutionary/phylogenetic approaches to evolutionary biology or similar. Expertise in modelling evolutionary processes on phylogenies, 3D surface morphometrics, or measuring plumage colour with digital photography would be advantageous.

Full details are available from, and formal applications should be made, via University of Sheffield job’s pages  

Postgraduate Research Assistants (four posts): The postgraduate post-holder(s) will be responsible for generating and processing high-resolution morphometric data on bird bills using 3D structured white-light digitisation a nd plumage colour using visible and UV spectrum digital photography. Data collection will rely on extensive museum collections in the UK and elsewhere. Applicants must have a good first degree in biology, ideally with a substantial evolutionary biology component. However, candidates with other backgrounds will be considered. A masters degree in an evolutionary biology discipline would be an advantage. Potential applicants with a PhD are also eligible to apply. Experience in working with museum collections would be an advantage but is not essential and training will be provided. Up to four positions are available initially as fixed-term one-year contracts with funding available to extend by an additional 1-2 years for suitable candidates.

Further details are available from, formal applications should be made via University of Sheffield job’s pages 

Informal enquiries for all posts are encouraged and should be sent by email (gavin.thomas@sheffield.ac.uk) with an outline or your research interests, CV and or/link to a personal webpage.

In addition to the above posts one PhD studentship on the same grant is available and details will be advertised very soon.

Gavin Thomas —Apple-Mail=_FD55AEC6-C0FE-4C36-9B48-1E84C0CFB53 via Gmail

00:44
—MIRAPOINT_PART2_533dd251 Content-Language: en-US Content-Type: multipart/alternative; boundary=”_000_EA6D12614D434644AD1134AEC074B58F118E8871EX1VMadirhullac_” —_000_EA6D12614D434644AD1134AEC074B58F118E8871EX1VMadirhullac_ Content-Type: text/plain; charset=”iso-8859-1” Content-Transfer-Encoding: quoted-printable Bioinformatics Research Fellow in Evolutionary & Environmental Genomics This is an exciting new Research Fellow position for a bioinformatician to work with staff in Evolutionary and Environmental Genomics. We are looking to work with a bioinformatics colleague and scientist, this is not a technical post. We have quite a number of projects, most already with data, on which you could take the lead. We would additionally welcome the development of new projects in collaboration with staff in the group. We anticipate that for the right candidate this could be a very productive fellowship in terms of publications and collaborations. Please feel free to discuss the position with Dave Lunt. The advert is below: Reference: FS0093 Campus: Hull Faculty: Faculty of Science and Engineering Department: School of Biological, Biomedical and Environmental Sciences Salary: 31,644 to 36,661 per annum, Post type: fixed term, full time Closing date: Sunday 27 April 2014 Applicants with a strong background in bioinformatics, comparative genomics, or evolutionary and population genomics are invited to apply for the position of Postdoctoral Research Fellow within the School of Biological, Biomedical, and Environmental Sciences at the University of Hull, UK. The post-holder will work closely with members of the Evolutionary and Environmental Genomics (EEG) group to analyze genomic datasets from a diverse range of projects and develop new collaborative research programmes. Previous expertise of work with eukaryotic genome assembly, RADseq, metabarcoding, or population genomics would be advantageous. The position is funded by The School of Biological, Biomedical, and Environmental Sciences for two years and will be central to the developing research agenda of this active group. Existing expertise within the EEG Group encompasses phylogenetics, network ecology, bioinformatics, speciation genetics, molecular evolution, and population genetics. It is anticipated that the new Bioinformatics Fellow will complement and extend these existing skills. The EEG Group is very research active and currently comprises six members of academic staff along with postdocs, research students, and technicians. The post-holder will also be involved in undergraduate and postgraduate bioinformatics teaching. This may include undergraduate metabarcoding practicals, postgraduate training days in bioinformatics, and similar. This will be an exciting career opportunity for a research fellow wishing to broaden their experience with different research systems, develop methods and novel bioinformatics approaches, forge new collaborations, and maintain a very substantial publication record. The successful applicant will have completed a PhD in a relevant biological subject area (e.g. bioinformatics, evolutionary biology, population genetics) and have proven ability to carry out large-scale data analysis using bioinformatic approaches. An excellent understanding of the science underlying the work of the EEG group would be advantageous. This is a full time position for 24 months in the first instance. Candidates are encouraged to discuss this role informally with Dr Dave Lunt, Tel: +44 (0)1482 465514, Email: dave.lunt@gmail.com For information about the position and research of the EEG group visit: http://bit.ly/1fEivmo For information about the School visit: http://bit.ly/1q36WZ6 To apply see http://bit.ly/1q36U3G Dr. Bernd Hnfling Lecturer in Ecology and Evolution Director of Postgraduate Studies Evolutionary Biology Group Department of Biological Sciences University of Hull Hull, HU6 7RX UK E-mail: b.haenfling@hull.ac.uk Tel: 0044-1482-465804 Fax: 0044-1482-465458 http://bit.ly/1q36WZc —_000_EA6D12614D434644AD1134AEC074B58F118E8871EX1VMadirhullac_ Content-Type: text/html; charset=”iso-8859-1” Content-Transfer-Encoding: quoted-printable
Source: EVOLDIR
00:26

Dear EvoDir members: Please, find here below a summary of the answers I got from all of you about question on DNA stain. Thank you very much for your very useful suggestions! Cheers, Filippo — via Gmail

Source: EVOLDIR
00:07

A field assistant is required to help with research on speciation in Heliconius butterflies. We are studying the genetic basis of traits causing reproductive isolation between a pair of recently diverged sister species ( http://bit.ly/OgJqtx). The field assistant will help to collect data for QTL mapping of the genomic regions involved in the production of colour patterns, pheromones and host plant choice. The field assistant will be required from June - December 2014, but the exact dates are flexible and shorter time periods could be considered. The assistant will work with a postdoctoral researcher in Tarapoto, Peru (a medium sized town at the Amazonian/Andean ecotone). The field assistant’s primary tasks will be to help run experiments on captive populations of butterflies and to collect wild butterflies to supplement captive stocks. The field assistant will develop an excellent practical knowledge of Heliconius butterflies and their host plants (Passifloraceae). S/he will improve his/her understanding of evolutionary ecology and genetics, be actively involved in experimental design, preliminary data analysis, and likely gain co-authorship on a published study. The project will provide excellent preparation for a PhD on tropical biodiversity. The field assistant’s return airfare to Peru and accommodation will be covered, in addition to a small stipend for food and basic living costs. Applicants should hold an undergraduate or Master’s degree in Life Sciences with an interest in Evolutionary Biology, and have a passion for natural history and biodiversity. The successful applicant will need to be independent and comfortable in a culturally challenging environment. Spanish language skills are highly desirable but not essential. Latin Americans are particularly encouraged to apply. Interested candidates should write to Neil Rosser (neil.rosser@york.ac.uk) before 1st May 2014. neil.rosser@york.ac.uk via Gmail

Source: EVOLDIR

April 3, 2014

23:49
Hello all, This is a reminder that talk abstract submissions for the 2014 Galaxy Community Conference are due this Friday, April 4. See http://bit.ly/gcc2014abs for details. This is a great opportunity to share your work in high-throughput biology. Accepted abstracts will be considered for the GigaScience “Galaxy: Data Intensive and Reproducible Research” series (announced for GCC2013). BGI is also continuing to cover the article processing charges until the end of the year Poster abstracts are being accepted until April 25. Early registration (save a bundle, really) is also open. Thanks, and I do hope you’ll join us in Baltimore, Dave C, on behalf of the GCC2014 Organizing Committee 2014 Galaxy Community Conference (GCC2014) http://bit.ly/1hJrJkj June 30 - July 2, 2014 Homewood Campus Johns Hopkins University Baltimore, Maryland, United States On Sat, Feb 22, 2014 at 3:29 PM, Dave Clements wrote: > > The 2014 Galaxy Community Conference (GCC2014, http://bit.ly/1hJrJkj) features two full days of presentations, discussions, poster sessions, lightning talks and birds-of-a-feather, all about data-intensive biology and the tools that support it. GCC2014 also includes a Training Day with five concurrent tracks and in-depth coverage of thirteen different topics. > > GCC2014 will be held at the Homewood Campus of Johns Hopkins University, in Baltimore, Maryland, United States, from June 30 through July 2, 2014. > > Galaxy is an easily extensible data integration and analysis platform for life sciences research that supports hundreds of bioinformatics analysis tools. Galaxy is open-source and can be locally installed or run on the cloud. There are hundreds of local installs, and over 50 publicly accessible servers around the world. > > Early registration is now open. Early combined registration (Training Day + main meeting) starts at $140 for post-docs and students. Registration is capped this year at 250 participants, and we expect to hit that limit. Registering early assures you a place at the conference and also a spot in the Training Day workshops you want to attend. > > You can also book affordable conference housing at the same time you register. See the conference Logistics page for details on this and other housing options. > > Abstract submission for both oral presentations and posters is also open. Abstract submission for oral presentations closes April 4, and poster submission closes April 25. The GigaScience “Galaxy: Data Intensive and Reproducible Research” series (announced for GCC2013) is continuing to take submissions for this year’s meeting and beyond. BGI is also continuing to cover the article processing charges until the end of the year, and for more information see their latest update. > > Thanks, and hope to see you in Baltimore! > > The GCC2014 Organizing Committee via Gmail
Source: EVOLDIR
23:27

The end of extended early registration for the 8th International Wolbachia Conference is approaching fast: submission of poster and oral presentations will be possible exclusively until 4 April 2014; no exceptions will be made. Furthermore, 15% late registration charge will be added to the conference fees afterwards. Late registration (without possibility to submit presentations) will close on 23 May 2014. The conference will be held from 6 to 11 June 2014 in Innsbruck, Austria. Please register now to get hold of the remaining presentation slots. Conference topics will include, inter alia, - ecology, evolution, and development - phenotypes, diversity, and distribution - cell biology - genetics & genomics - applications in pest control and disease management - other reproductive parasites than Wolbachia. Visit the conference website at http://bit.ly/1hl3CYz or proceed directly to the registration page at http://bit.ly/1at0pwr. Please also consider subscribing to our newsletter to be constantly informed about important news on the meeting: http://bit.ly/1hl3AQo Kind regards from Innsbruck, Wolfgang Arthofer on behalf of the WOLBACHIA 2014 Organizing Committee *8^th International Wolbachia Conference * *Wolfgang Arthofer Organising Committe* Molecular Ecology Group, University of Innsbruck Technikerstr. 25, 6020 Innsbruck, Austria Phone +43 (0) 512 507 51751 Fax +43 (0) 512 507 51799 office@wolbachia2014.org http://bit.ly/1hl3CYz WOLBACHIA 2014 logo office@wolbachia2014.org via Gmail

Source: EVOLDIR
18:00
Background: Polytypism in aposematic species is unlikely according to theory, but commonly seen in nature. Ranitomeya imitator is a poison frog species exhibiting polytypic mimicry of three congeneric model species (R. fantastica, R. summersi, and two morphs of R. variabilis) across four allopatric populations (a "mimetic radiation"). In order to investigate chemical defenses in this system, a key prediction of Müllerian mimicry, we analyzed the alkaloids of both models and mimics from four allopatric populations. Results: In this study we demonstrate distinct differences in alkaloid profiles between co-mimetic species within allopatric populations. We further demonstrate that R. imitator has a greater number of distinct alkaloid types than the model species and more total alkaloids in all but one population. Conclusions: Given that R. imitator is the more abundant species in these populations, R. imitator is likely driving the majority of predator-learned avoidance in these complexes. The success of Ranitomeya imitator as a putative advergent mimic may be a direct result of differences in alkaloid sequestration. Furthermore, we propose that automimicry within co-mimetic species is an important avenue of research.