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August 16, 2014

01:28

Lecturer in Evolutionary Biology, University of York The Department of Biology at University of York is seeking to appoint a Lecturer in Evolutionary Biology (equivalent to Assistant Professor) who has an excellent publication record and can demonstrate a reputation for internationally recognised research. Your research interests will complement existing strengths in the Department of Biology, which range from genome organisation to global change biology and which use theoretical, analytical and experimental approaches. You should have a PhD or equivalent and be able to demonstrate a strong commitment to the promotion of teaching and learning. You will be expected to participate actively in research supervision, management and administration. York is one of the most successful universities in the UK. With world-class activity across the spectrum from the physical sciences, life sciences, and social sciences to the humanities, we have been recognised as one of the top 100 universities in the world, gaining outstanding results in official assessments of our research and teaching. The Department of Biology is the first biology department in Britain to receive a Gold Athena Swan Award which recognises success in supporting the careers of women in science. You are invited to make an informal enquiry to Professor Ian Graham (Head, Department of Biology; (+44) 01904 328507), Professor Jane Hill (Jane.Hill@york.ac.uk) or Professor Michael Brockhurst (Michael.Brockhurst@york.ac.uk). Interviews will be held on Thursday 23 October 2014. http://bit.ly/1qejN8L via Gmail

Source: EVOLDIR
00:26
Dear all, I am using FSTAT to calculate various F-statistics. However, I am struggling to find my Fst p-values. I have found a couple of papers online, both of which contradict the other. Can anyone please point me in the right direction? Thanks in advance, Samantha Beck (bsp22a@bangor.ac.uk) Molecular Ecology & Fisheries Genetics Laboratory Bangor University North Wales Samantha Beck via Gmail
Source: EVOLDIR
00:26

Job: Genetics Research Assistant_Omaha’s Henry Doorly Zoo & Aquarium Applications are invited for a Laboratory Technician in the Conservation Genetics Department at Omaha’s Henry Doorly Zoo & Aquarium (http://bit.ly/1uZQqeE). The Laboratory Technician will participate in ongoing molecular and bioinformatics research. Importantly, the technician will utilize sophisticated computer programs during the analysis of datasets from next generation sequencing. This technician will develop high-throughput solutions to improve scalability of in-house genetic interpretation tools. The technician will be responsible for developing a pipeline for genomic analyses and database monitoring and maintenance. Early-career technicians will have the opportunity to gain on-the-job training regarding bioinformatics. Duties: The Laboratory Technician will confer with research staff to determine data needs and programming requirements and to provide assistance with database-related research activities. Importantly, the technician will utilize bioinformatics techniques to analyze or manipulate large datasets from next generation sequencing in a Unix/Linux environment. Sophisticated computer programs will be used to gather, analyze, and track data regarding biological functions or characteristics in order to gain a better understanding of computational evolutionary biology and comparative genomics. The technician will develop high throughput solutions to improve scalability of in-house genetic interpretation tools. Duties will involve writing or modifying existing computer code to perform analysis of high-throughput sequencing data including the analysis of whole genome sequencing data. The technician will need to develop a pipeline for genomic analyses as well as a system for monitoring database performance and perform any necessary maintenance, upgrades, or repairs. Ultimately the technician will complete statistical analyses and prepare reports on related findings. Additionally, the technician will assist multiple research projects as well as routine maintenance within the laboratory. Participation in group activities such as grant preparation and reporting, literature searches, and manuscript writing efforts will be expected. All laboratory staff will maintain cleanliness and sanitation while complying with safety procedures in their employed laboratories. Duties will include non-research activities such as facility maintenance and outside work. Qualifications: Ideally, the Laboratory Technician will have a thorough knowledge of bioinformatics, molecular genetics and related techniques, and have a good understanding of biological sciences. Experience in bioinformatics and next-generation sequencing is highly preferred. A Bachelor’s degree in the Genomics, Genetics, Bioinformatics or Computer Science or related field is required. Ideal candidates will have a proficiency in Linux, programming experience in at least one of the following programming languages: C, C++, Java, Perl, or Python. Knowledge of parallel processing and computing and the use of R statistic software would be beneficial. Early-career technicians will have the opportunity to gain on-the-job training regarding bioinformatics. Start Date: flexible Location: Omaha, Nebraska, USA. Please visit http://bit.ly/1pz5Nu6 for full job description and to submit an application. Applicants should include a cover letter describing previous experience, a resume, and the names and contact information for two references. Review of applications will begin immediately and will continue until the position is filled. Applications can also be sent to Dr. Edward Louis Jr. at genetics@omahazoo.com genetics@omahazoo.com via Gmail

Source: EVOLDIR
00:26

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ZW0gaXMgYW4gRXF1YWwgT3Bwb3J0dW5pdHkgRW1wbG95ZXI8bzpwPjwvbzpwPjwvc3Bhbj48L2k+ PC9iPjwvcD4NCjxwIGNsYXNzPSJNc29Ob3JtYWwiPjxzcGFuIHN0eWxlPSJmb250LWZhbWlseTom cXVvdDtDYWxpYnJpJnF1b3Q7LCZxdW90O3NhbnMtc2VyaWYmcXVvdDsiPjxvOnA+Jm5ic3A7PC9v OnA+PC9zcGFuPjwvcD4NCjxwIGNsYXNzPSJNc29Ob3JtYWwiPjxvOnA+Jm5ic3A7PC9vOnA+PC9w Pg0KPC9kaXY+DQo8L2Rpdj4NCjwvYm9keT4NCjwvaHRtbD4NCg= —_000_A67A4FDB38492D42875EEF0058E1163324FD13FFBIOEXCHbiotamue via Gmail

Source: EVOLDIR

August 15, 2014

09:01
If we view biodiversity data as part of the "biodiversity knowledge graph" then specimens are a fairly central feature of that graph. I'm looking at ways to link specimens to sequences, taxa, publications, etc., and doing this across multiple data providers. Here are some rough notes on trying to model this in a simple way.

For simplicity let's suppose that we have this basic model:



A specimen comes from a locality (ideally we have the latitude and longitude of that locality), it is assigned to a taxon, we have data derived from that specimen (e.g., one or more DNA sequences), and we have one or more publications about that specimen (e.g., a paper that publishes a taxon name for which the specimen is a type, or a paper that publishes a sequence for which the specimen is a voucher).

NCBI
In GenBank we have sequences that have accession numbers, and these are linked to taxa (identified by NCBI tax ids). A nice feature of sequence databases is that taxa are explicitly defined by extension, that is, a taxon is the set of sequences assigned to a given taxon. Most (but not all, see Miller et al. doi:10.1186/1756-0500-2-101) sequences are also linked to a publication, which will usually have a PubMed id (PMID), and sometimes a DOI. Many sequences are also georeferenced (see Guest post: response to "Putting GenBank Data on the Map"). Most sequences aren't linked to a voucher specimen, but there is the implict notion of a source (in RDF-speak, many specimens are "blank nodes" Blank nodes for specimens without URI). Some sequences are associated with a specimen that has a museum code, and some are explicitly linked to the specimen by a URL.

DNA barcodes
Barcodes, as represented in BOLD are similar to sequences in GenBank. We have explicit taxa ("BINs") each of which has a URL, some also having DOIs. Most barcodes are georeferenced. There's some ambiguity about whether the URL for a barcode record identifies the barcode sequence, the specimen, or both. There may be a voucher code for the specimen. Some barcodes are linked to publications, but not (as far as I can see) in the data obtained from the API. Some barcodes are linked to the corresponding record in GenBank (which may or may not be supressed, see Dark taxa even darker: NCBI pulls (some) DNA barcodes from GenBank (updated)).

GBIF
At it's core GBIF has occurrence records (many of these are specimen-based, but the majority of data in GBIF is actually observation-based), each of which has a unique id, and which is linked to a taxon, also with a unique id. As with the sequence databases, a taxon is a set of occurrences that have been assigned to that taxon. Many records in GBIF are georeferenced. There are limited cross links to other database - some occurrences list associated GenBank sequences. Some GBIF occurrences actually are sequences (e.g., the European Molecular Biology Laboratory Australian Mirror and the soon to be indexed Geographically tagged INSDC sequences), and barcodes are also making their way into GBIF (e.g., Zoologische Staatssammlung Muenchen - International Barcode of Life (iBOL) - Barcode of Life Project Specimen Data). Links to publications are limited.

Museums and herbaria
Some individual natural history collections which are online provide specimen-level web pages and URLs (some even have DOIs, see DOIs for specimens are here, but we're not quite there yet), and some museums list associated GenBank sequences. In the diagram I've not linked the specimens to a taxon, because most specimens are tagged by a name, not an explicit taxon concept (unlike NCBI, BOLD, or GBIF).

Literature
Literature databases (represented here by BioStor, but could be other sources such as ZooKeys, for example) may contain articles that mention specimen codes. These articles may also mention taxon names, and geographic localities (including coordinates) (see, for example, Linking GBIF and the Biodiversity Heritage Library. Mining text for names, specimens, and localities is fairly easy, but linking these together is harder (i.e., this specimen is of this taxon, and was found at this locality).

Linking together
If we have these separate sources and this trivial model, then we can imagine trying to tie information about the same specimen together across the different databases. Why might we want to do this. Here are three reasons:

  1. Augmentation Combining information can enhance our understanding of a specimen. Perhaps a specimen in GBIF is a geographic outlier. A publication that mentions the specimen includes it in a new taxon, perhaps discovered by sequencing DNA extarcted from that specimen. Linking this information together resolves the problematic distribution.
  2. Provenance What is the evidence that a particular specimen belongs to a particualr taxon, or was collected at a particular locality? If we connect specimens to the literature we we can review the evidence for ourselves. If we have sequences we can run BLAST, build a tree, and see if we should rethink our classification of that sequence. Imagine being able to browse GBIF and see the evidence for each dot on the map?
  3. Citation Mentions in the literature, use as vouchers for DNA barcoding or other forms of sequencing can be thought of a "citation" of that specimen. Museums hosting that material could use metrics base don this to demonstrate the value of their collection (see also The impact of museum collections: one collection ≈ one Nobel Prize).
Making the links
All this is well and good, the trick is to actually make the links. Here things get horribly messy very quickly. Museum specimens are cited in inconsistent ways, we don't have widely used unique, resolvable specimen identifiers, and even if we did have these identifiers we don't have a global discovery mechanism for matching voucher codes to identifiers. GBIF would be an obvious part of a "global discovery mechanism" (bit like CrossRef but for specimens), GBIF can have multiple records for the same specimen. Sometimes this is because GBIF not only aggregates data from primary sources (such as museums) but also other aggregations which may themselves already include specimens harvested from primary sources. GBIF can also have multiple records because museums keep messing with their databases, try new variants of the Darwin Core triple, etc., resulting in records that look "new" to GBIF. Whole collections can be duplicate din this way.

One way to tackle this multiplicity of specimen records is to think in terms of "clusters" of specimens that are, in some sense, the same thing across multiple databases. For example, clustering a set of duplicated GBIF records together with the sequences derived from those specimens, perhaps including a DNA barcode, and a list of papers that mention that specimen. This is represented by the yellow bar through the diagram, it connects all the different pieces of information about a specimen into a single cluster. More *cough* later.

Source: iPhylo
06:00
Background: Social information use is usually considered to lead to ecological convergence among involved con- or heterospecific individuals. However, recent results demonstrate that observers can also actively avoid behaving as those individuals being observed, leading to ecological divergence. This phenomenon has been little explored so far, yet it can have significant impact on resource use, realized niches and species co-existence. In particular, the time-scale and the ecological context over which such shifts can occur are unknown. We examined with a long-term (four years) field experiment whether experimentally manipulated, species-specific, nest-site feature preferences (symbols on nest boxes) are transmitted across breeding seasons and affect future nest-site preferences in a guild of three cavity-nesting birds. Results: Of the examined species, resident great tits (Parus major) preferred the symbol that had been associated with unoccupied nest boxes in the previous year, i.e., their preference shifted towards niche space previously unused by putative competitors and conspecifics. Conclusions: Our results show that animals can remember the earlier resource use of conspecifics and other guild members and adjust own decisions accordingly one year after. Our experiment cannot reveal the ultimate mechanism(s) behind the observed behaviour but avoiding costs of intra- or interspecific competition or ectoparasite load in old nests are plausible reasons. Our findings imply that interspecific social information use can affect resource sharing and realized niches in ecological time-scale through active avoidance of observed decisions and behavior of potentially competing species.
01:11

We would like to invite submissions for a special issue on ‘The evolution of behavioural mechanisms’ in the journal Current Zoology, to appear early next year: http://bit.ly/XlXZ4u Possible subtopics include (but are not limited to) the following: - Neuroendocrine mechanisms of behaviour - The evolution of learning - Fixed versus flexible behaviour - Heuristics and rules of thumb - Mood, emotion and cognitive biases - Information processing and neural networks - Constraints on adaptive behaviour All submissions (including original research articles, reviews and opinion pieces) will be considered but preference will be given to those that explicitly integrate evolutionary and mechanistic perspectives. Manuscripts will be subject to the usual peer review process and editorial revision. Note that there are no publication charges. If you wish to contribute an article, please send a provisional title and abstract to madorganiser@gmail.com by 1 September 2014. We will then invite selected authors to submit full articles by 1 November 2014. Best wishes Tim James A. R. Marshall, Tim W. Fawcett & Andrew D. Higginson Guest Editors, ‘The Evolution of Behavioural Mechanisms’ http://bit.ly/XlXZ4u Functional studies of animal behaviour traditionally ignore the psychological and physiological mechanisms involved. Yet often, mechanistic details can crucially affect the behaviour we observe. For a more complete understanding of animal behaviour, we need to study the adaptive value of the underlying mechanisms and the constraints on their evolution. This special issue of Current Zoology will showcase an emerging line of research that directly addresses the evolution of behavioural mechanisms. How do animals reach adaptive solutions? What information-processing rules do they use? Why is behaviour sometimes irrational? Why are cognitive systems biased? How do animals deal with uncertainty? When is flexible behaviour favoured over rigid behaviour? These questions are central to understanding how selection shapes behaviour. The special issue will cover theoretical and empirical research, integrate functional and mechanistic approaches, and draw on insights from a range of sub-disciplines to offer a diversity of perspectives on animal behaviour. via Gmail

Source: EVOLDIR
01:11

Lab & Field technician, Egan Lab at Rice University The Egan lab at Rice University in Houston, Texas, is seeking a temporary research technician, starting immediately. The Egan lab works on many different aspects of evolutionary biology, including behavior, evolutionary ecology, genetics and genomics. Current projects include understanding the roles of ecology and the genome during the evolution of new biological species. Most work is done using insects from natural populations. Duties will included (1.) the performance of basic molecular biology lab techniques, including DNA and RNA extractions, sample prep for high-throughput sequencing, (2.) implementing and maintaining experiments in the lab, greenhouses, or field settings, (3.) insect husbandry in the lab, and (4.) responsibility for day-to-day lab logistics, including purchasing, shipping, and receiving supplies, as well as working closely with undergraduate and graduate researchers. Important skills include: 1. strong attention to detail and careful record keeping 2. ability to work independently, as well as with others 3. strong molecular techniques and experience 4. ability to work in the field, sometimes under challenging conditions Required: 1. bachelor’s degree or higher in Biology or related field 2. 1+ year of research experience outside of class requirements Position is for 40 hours per week for 12 months at a minimum of $13.51/hour plus full benefits, with the possibility of renewal contingent on performance and the availability of funding. See Rice HR website for further details: http://bit.ly/1m0xTJM. Please follow the following links for further information about the Egan lab (http://bit.ly/XlXYO4), the Department of BioSciences (http://bit.ly/1m0xTJN), or Rice University (http://www.rice.edu). Applicants should include in one merged PDF file:(1.) a 1-page cover letter describing previous experience, (2.) a resume/CV, (3) unofficial transcripts from your undergraduate institution, and (4.) the names and contact information of two references. Review of applications will begin immediately and will continue until the position is filled. Applications should be sent to Scott Egan (scott.p.egan@rice.edu) with Lab & Field Technician” in the Subject line. Questions may be directed to the same email address. via Gmail

Source: EVOLDIR
00:56
Scott Nichols lab at the University of Denver is accepting applications from graduate students for admission in September 2015. We primarily use sponges and choanoflagellates as research models to address fundamental questions about early animal evolution. In particular, we are interested in questions related to the evolution of multicellularity and animal body plan diversification. Current projects range from studies of cell adhesion and developmental morphogenesis, to comparative genomics and gene expression. Students are encouraged to develop their own research ideas. The University of Denver (DU) is located minutes outside of the urban center of Denver, which is a vibrant city on the edge of the Rocky Mountains. Cultural, culinary, and outdoor opportunities abound. Many students choose to live within walking distance of the campus and there are excellent public transportation options including a municipal bus system and a light-rail system. The closest remote mountain areas and ski resorts are within a 45 minute drive. Students are guaranteed full tuition offset, health benefits, and a competitive living stipend for either two (MS) or five (PhD) years. Because DU is a private, non-profit institution, there are *no additional fees for out of state or international applicants*. Prospective applicants and first year students are also strongly encouraged to apply to the NSF predoctoral fellowship program (deadline Nov 4, 2014), and I am happy to discuss this option with you in advance. The Department of Biological Sciences offers both a Masters and PhD program, and students are invited to apply to either. The department does not offer a laboratory rotation system in the first year, instead successful applicants are admitted directly to the research laboratory where they will work. I often encourage students to enter the Masters program initially, because it is possible to transition to the PhD program at the end of the first year if desired. To learn more about the application process, please go to the Department of Biological Sciences homepage and read under Degree Programs . Applicants should contact Scott Nichols directly at scott.nichols@du.edu well before the January 1st (2015) application deadline. Please provide a brief description of your background and interests and your reasons for considering the Nichols lab for graduate training. Scott Nichols, Ph.D. Assistant Professor of Biological Sciences 2101 E. Wesley Ave SG Mudd #288 University of Denver Denver, CO 80208 email: sa.nichols321@gmail.com lab homepage: nicholslab.wikidot.com phone: 303-871-5658 Scott Nichols via Gmail
Source: EVOLDIR
00:39
Chairperson, Department of Plant Biology Michigan State University Michigan State University invites applications and nominations for the position of Chairperson of the Department of Plant Biology. The Chair would lead an internationally recognized department with a long history of university commitment to excellence in the Plant Sciences. The Department has more than 30 faculty members, strong graduate and undergraduate programs, and a supportive administrative and technical staff. It is built on the concept of integrating all sub-disciplines of plant biology, ranging from evolution and ecology to cellular, molecular and genomic biology. Research is conducted in modern research facilities on campus and at field sites across Michigan and throughout the world. The department includes faculty affiliated with the Kellogg Biological Station, the MSU Department of Energy Plant Research Laboratory, and the Great Lakes Bioenergy Research Center. The Chair is expected to provide leadership and to promote a creative environment that fosters innovation and excellence in research and teaching/educational programs in Plant Biology. Candidates must possess an established record of strong scholarship in a relevant field, proven academic leadership, and strong interpersonal skills. Continuation of an active research program is encouraged and will be supported. Candidates should be qualified to hold the rank of tenured Full Professor. Applicants should submit: a complete curriculum vitae; a statement of interest highlighting specific strengths related to this position, including research and administrative experience and accomplishments; and the names of three references (who will be contacted only with your permission). Every effort will be made to maintain confidentiality until a list of candidates for interviewing is determined. All materials should be assembled into one PDF and uploaded to: https://jobs.msu.edu for position #9727. Review of applications will begin October 15, 2014, and will continue until the position is filled. Questions regarding the position may be sent to the Chair of the search committee, at PLBChairsearch@plantbiology.msu.edu. MSU is an affirmative-action, equal-opportunity employer and is committed to achieving excellence through diversity. The University actively encourages applications of women, persons of color, veterans, and persons with disabilities, and we endeavor to facilitate employment assistance to spouses or partners of candidates for faculty and academic staff positions. “LaClair, Stacy” via Gmail
Source: EVOLDIR
00:24
Evolutionary Biologist: We invite applications for a tenure-track Assistant/Associate Professor of Biology in Evolutionary Biology to begin August 2015. We prefer taxonomic expertise in plants or fungi, but candidates with interests in other organisms will also be considered. Research interests should complement those of current faculty. This appointment will be at the rank of Assistant or Associate Professor (depending on qualifications). Applicants must have a Ph.D. in a relevant discipline (post-doctoral experience preferred), teaching experience, and demonstrated commitment to excellence in teaching as well as scholarship involving undergraduates. Teaching responsibilities will include lower division courses (introductory biology, or new sophomore level courses in genetics or cell biology), one or more upper division courses in area(s) of expertise, and departmental service courses for majors or non-majors. The average teaching load is 10-12 contact hours/semester (including labs); a common course load is 3 lectures and 4 labs per academic year. Faculty also mentor senior capstone projects (literature reviews or research projects). We seek a collegial scholar-teacher whose research interests complement existing expertise in the department. We expect the successful candidate to establish an active research program with undergraduates. The research program must be successful and feasible in our liberal arts college setting; it should also be attractive to our student body, which includes many preparing for professional school in the health professions (e.g., optometry, physical therapy, pharmacy) as well as some pursuing teaching, environmental biology, and other professional work in the life sciences. Our research facilities include a greenhouse, and start-up funds are provided. Pacific University is particularly interested in candidates who can contribute, through their research, teaching, or service, to the diversity and excellence of the academic community. Minimum requirements for the position include a Ph.D. In Biology, or equivalent terminal research-based degree; one academic year of college or university teaching experience (TA or instructor); and two years research experience in evolution. Education, teaching and research may be gained concurrently. Pacific University is an independent, comprehensive university in Forest Grove, Oregon (about 25 miles west of Portland). The Biology department is part of the College of Arts and Sciences (ca. 1700 students), a liberal arts undergraduate college where faculty and staff are committed to an intimate, personalized education. The University also includes a College of Health Professions (including Physical Therapy, Occupational Therapy, Physician Assistant Studies, Pharmacy, Dental Science and Professional Psychology), a College of Optometry, a College of Business, and a College of Education. The Biology Department currently has 10 permanent faculty members and 2 laboratory support staff. We are committed to learning through discovery in both the laboratory and the classroom. We graduate 35-50 majors each year. Many of our graduates pursue graduate or professional study in the health sciences or careers in teaching, biology research, or environmental biology. Application materials Please submit: 1. A cover letter that addresses your preparation/promise to teach in a liberal arts college with many pre-health professions students 2. CV 3. A teaching philosophy, with a separate section identifying courses you would feel qualified and comfortable teaching (upper and lower division) 4. A research statement, which should include a brief summary of prior research, a research plan for a liberal arts institution, and an argument for how your research program at Pacific would attract and involve undergraduates. Selection criteria will include feasibility of research plan and fit to our department and student body. 5. Unofficial graduate and undergraduate transcripts 6. Arrange for three letters of reference (at least one of which speaks directly to teaching ability and experience) to be submitted directly. 7. In October, candidates on our short list may be requested to submit evidence of teaching experience and excellence, such as teaching evaluations, reports from observers, or examples of teaching materials; please do not include these materials with your initial application. Please combine application materials 1-4 into a single file (.pdf or .doc), in the order listed above, with the following naming: Last name, First name, Evolution 2014. Send applications electronically to Patty Larkins (address below); put Evolutionary Biology 2014 as the subject in your e-mail. Patty Larkins, plarkins@pacificu.edu Administrative Assistant, School of Natural Sciences, Pacific University Review of applications will begin October 3 and continue until the position is filled. Contact Dr. Stacey Halpern (Biology Department Chair) with questions. NOTICE OF NONDISCRIMINATION POLICY | It is the policy of Pacific University not to discriminate on the basis of sex, physical or mental disability, race, color, national origin, sexual orientation, age, religious preference or disabled veteran or Vietnam Era status in admission and access to, or treatment in employment, educational programs or activities as required by Title IX of the Education Amendments of 1972, section 504 of the Rehabilitation Act of 1973, Title VII of the Civil Rights Act of 1964, the Age Discrimination Act, the Americans with Disabilities Act of 1990, or any other classification protected under state or federal law, or city ordinance. Questions or complaints may be directed to the Vice President for Academic Affairs, 2043 College Way, Forest Grove, OR 97116, provost@pacificu.edu. Patty Larkins | Administrative Assistant | School of Natural Sciences Pacific University | 2043 College Way | Forest Grove, OR 97116 p: 503.352.1492 | f: 503.352.2933 | plarkins@pacificu.edu “Larkins, Patty” via Gmail
Source: EVOLDIR

August 14, 2014

23:52
I am looking for an excellent candidate for a postdoc grant application to work on NZ manuka (Myrtaceae) population genetics. Please note this is not for a postdoc position for which I already have funding, however I need an applicant for a project proposal that is already written. In brief, I had a candidate until yesterday when this person was offered another position. I now have a well developed and exciting project proposal that just misses a strong candidate. The deadline for proposal in August 29th 2014, however I will be attending conferences from August 17th to 26th, so there is a bit of urgency (apologies for this). A summary of the proposal is below. I am looking for a candidate with strong leadership skills who completed a PhD and would be available in the next few months and for 2 to 3 years, with expertise in population genetics/genomics, molecular marker development and genome analysis, and plant biology. The quality of the applicant’s CV is crucial, so the usual criteria will apply (publications, awards and distinction etc…). Project summary Manuka honey is among New Zealand’s premium export products, largely due to the presence of the unique compound methylglyoxal (MG) which has strong, proven antimicrobial activity. A compound (dihydroxyacetone) present in the nectar is the precursor for MG. Manuka (Leptospermum scoparium) is a NZ native species found across a range of habitats, and key traits for manuka honey production are highly variable in natural populations. However, little is known about the interplay of manuka genetics, growth site and climate in regulating these traits. To address this lack of information, we will first determine genetic variability in manuka from sites around NZ, focussing our sampling on regions favoured by beekeepers. This will allow us to develop genetic markers for selection of plants and verification of population-of-origin of commercially available plants and future cultivars. Additionally, we will collect data on variability in key traits of interest, using replicates across multiple seasons and sites, to determine the interplay of genetic and environmental influences on trait variability. Using high-resolution genotyping, we will look for regions of the manuka genome associated with trait variation and develop genetic markers for desirable traits. A deeper understanding of the natural genetic resources available in manuka and of the relative influences of genetic and environmental factors on traits of interest to beekeepers will inform the choice of plants for plantations and assist in development of best management practices. If successful the postdoc will be based in Palmerston North, New Zealand at the New Zealand Institute for Plant & Food Research Ltd (Plant & Food Research). Thank you David David Chagné Scientist T: +64 6 953 7751 F: +64 6 953 7701 david.chagne@plantandfood.co.nz http://bit.ly/1ozoWgc The New Zealand Institute for Plant & Food Research Limited Postal Address: Plant & Food Research Palmerston North Private Bag 11600, Manawatu Mail Centre, Palmerston North, 4442, New Zealand Physical Address: Plant & Food Research Palmerston North Batchelar Road, FISC Building, Palmerston North, 4474, New Zealand David Chagne via Gmail
Source: EVOLDIR
11:58

Scott Handley wrote:

Hello Phylobabble community!

I am assisting in the organization of a Workshop on Molecular Evolution which will be held in Cesky Krumlov, Czech Republic in January 2015. I have helped to organize this event before, but this year we are renewing the program and I am working with several new people to design something that we believe will be of interest to many in the phyologenetics/molecular evolution communities. More details below!

We also organize a Workshop on Genomics immediately prior to the Molecular Evolution Workshop for those interested in those sorts of topics: http://evomics.org/workshops/workshop-on-genomics/2015-workshop-on-genomics-cesky-krumlov/

2015 Workshop on Molecular Evolution, Český Krumlov, Czech Republic

Dates: 25 January - 7 February, 2015

Application Deadline: 15 October, 2014 is the preferred application deadline, after which time people will be admitted to the course following application review by the admissions committee. However, later applications will certainly be considered for admittance or for placement on a waiting list.

Registration Fee: $1500 USD. Fee includes opening reception and access to all course material, but does not include other meals or housing. Special discounted pricing has been arranged for hotels, pensions and hostels. Information regarding housing and travel will be made to applicants following acceptance.

APPLY HERE: http://evomics.org/registration-form...cesky-krumlov/

Useful Links: Direct Link to the Full Workshop Schedule: http://evomics.org/workshops/worksho...cesky-krumlov/ General Workshop information:http://evomics.org Frequently Asked Questions (FAQ) about the Workshop and Český Krumlov can be found here: http://evomics.org/workshops/faq/

Workshop Overview:

The 2015 Workshop on Molecular Evolution brings together an international collection of faculty members and Workshop participants to study and discuss current ideas and techniques for exploring molecular evolution. The Workshop on Molecular Evolution consists of a series of lectures, demonstrations and computer laboratories that cover theoretical and conceptual aspects of molecular evolution with a strong emphasis on data analysis.

The Workshop has a strong focus on molecular phylogenetics, and covers all aspects of phylogenetic workflows, including marker selection, phylogeny reconstruction, time-calibration, as well as detection of natural selection, phylogeography, diversification rates, and trait evolution patterns. A majority of the schedule is dedicated to hands-on learning activities designed by faculty and the workshop team. This interactive experience provides Workshop participants with the practical experience required to meet the challenges presented by modern evolutionary sciences.

Co-directors: Walter Salzburger, Michael Matschiner, Jan Stefka and Scott Handley

For more information and online application see the Workshop web site - http://evomics.org

Posts: 1

Participants: 1

Read full topic

11:49
Update: Angelique Hjarding and her co-authors have responded in a guest post on iPhylo.
The quality and fitness for use of GBIF-mobilised data is a topic of interest to anyone that uses GBIF data. As an example, a recent paper on African chameleons comes to some rather alarming conclusions concerning the utility of GBIF data:

Hjarding, A., Tolley, K. A., & Burgess, N. D. (2014, July 10). Red List assessments of East African chameleons: a case study of why we need experts. Oryx. Cambridge University Press (CUP). doi:10.1017/s0030605313001427
Here's the abstract (unfortunately the paper is behind a paywall):

The IUCN Red List of Threatened Species uses geographical distribution as a key criterion in assessing the conservation status of species. Accurate knowledge of a species’ distribution is therefore essential to ensure the correct categorization is applied. Here we compare the geographical distribution of 35 species of chameleons endemic to East Africa, using data from the Global Biodiversity Information Facility (GBIF) and data compiled by a taxonomic expert. Data screening showed 99.9%of GBIF records used outdated taxonomy and 20% had no locality coordinates. Conversely the expert dataset used 100%up-to-date taxonomy and only seven records (3%) had no coordinates. Both datasets were used to generate range maps for each species, which were then used in preliminary Red List categorization. There was disparity in the categories of 10 species, with eight being assigned a lower threat category based on GBIF data compared with expert data, and the other two assigned a higher category. Our results suggest that before conducting desktop assessments of the threatened status of species, aggregated museum locality data should be vetted against current taxonomy and localities should be verified. We conclude that available online databases are not an adequate substitute for taxonomic experts in assessing the threatened status of species and that Red List assessments may be compromised unless this extra step of verification is carried out.
The authors used two data sets, one from GBIF, the other provided by an expert to compute the conservation status for each chameleon species endemic to Kenya and/or Tanzania. After screening the GBIF data for taxonomic and geographic issues, a mere 7% of the data remained - 93% of the 2304 records downloaded from GBIF were discarded.

This study raises a number of questions, some of which I will touch on here. Before doing so, it's worth noting that it's unfortunate that neither of the two data sets used in this study (the data downloaded from GBIF, and the expert data set assembled by Colin Tilbury) are provided by the authors, so our ability to further explore the results is limited. This is a pity, especially now that citable data repositories such as Dryad and Figshare are available. The value of this paper would have been enhanced if both datasets were archived.

Below is Table 1 from the paper, "Museums from which locality records for East African chameleons were obtained for the expert and GBIF datasets":

MuseumExpert datasetGBIFAfrika Museum, The NetherlandsxAmerican Museum of Natural History, USAxBishop Museum, USAxBritish Museum of Natural History, UKxBrussels Museum of Natural Sciences, BelgiumxCalifornia Academy of Sciences, USAxDitsong Museum, South AfricaxxLos Angeles County Museum of Natural History, USAxMuseum für Naturkunde, GermanyxMuseum of Comparative Zoology (Harvard University), USAxNaturhistorisches Museum Wien, AustriaxSmithsonian Institution, USAxSouth African Museum, South AfricaxTrento Museum of Natural Sciences, ItalyxUniversity of Dar es Salaam, TanzaniaxZoological Research Museum Alexander Koenig, Germanyx

It is striking that there is virtually no overlap in data sources available to GBIF and the sources used by the expert. Some of the museums have no presence in GBIF, including some major collections (I'm looking at you, The Natural History Museum), but some museums do contribute to GBIF, but not their herpetology specimens. So, GBIF has some work to do in mobilising more data (Why is this data not in GBIF? What are the impediments to that happening?). Then there are museums that have data in GBIF, but not in a form useful for this study. For example, the American Museum of Natural History has 327,622 herpetology specimens in GBIF, but not one of these is georeferenced! Given that there are records in GenBank for AMNH specimens that are georeferenced, I suspect that the AMNH collection has deliberately not made geographic coordinates available, which raises the obvious question - why?

GBIF coverage
I had a quick look at GBIF to get some idea of the geographic coverage of the relevant herpetology collections (or animal collections if herps weren't separated out). Below are maps for some of these collections. The AMNH is empty, as is the smaller Zoological Research Museum Alexander Koenig collection (which supplied some of the expert data).

American Museum of Natural History, USA
Bishop Museum, USA
California Academy of Sciences, USA
Ditsong Museum, South Africa
Los Angeles County Museum of Natural History, USA
Museum für Naturkunde, Germany
Museum of Comparative Zoology (Harvard University), USA
Smithsonian Institution, USA
Zoological Research Museum Alexander Koenig, Germany

Some collections are relevant, such as the California Academy of Sciences, but a number of the collections in GBIF simply don't have georeferenced data on chameleons. Then there are several museums that are listed as sources for the expert database and which contribute to GBIF, but haven't digitised their herp collections, or haven't made these available to GBIF.

Taxonomy
The other issue encountered by Hjarding et al. 2014 is that the GBIF taxonomy for chameleons is out of date (2302 of 2304 GBIF-sourced records needed to be updated). Chameleons are a fairly small group, and it's not like there are hundreds of new species being discovered each year (see timeline in BioNames), 2006 was a bumper year with 12 new taxonomic names added. But there has been a lot of recent phylogenetic work which has clarified relationships, and as a result species get shuffled around different genera, resulting in a plethora of synonyms. GBIF's taxonomy has lagged behind current research, and also manages to horribly mangle the chameleon taxonomy is does have. For example, the genus Trioceros is not even placed within the chameleon family Chamaeleonidae but is simply listed as a reptile, which means anyone searching for data on the family Chamaeleonidae will all the Trioceros species.

Summary
The use case for this study seems one of the most basic that GBIF should be able to meet - given some distributions of organisms, compute an assessment of their conservation status. That GBIF-mobilised data is so patently not up to the task in this case is cause for concern.

However, I don't see this is simply a case of expert data set versus GBIF data, I think it's more complicated than that. A big issue here is data availability, and also the extent of data release (assuming that the AMNH is actively withholding geographic coordinates for some, if not most of its specimens). GBIF should be asking those museums that provide data why they've not made georeferenced data available, and if its because the museums simply haven't been able to do this, then how can it help this process? It should also be asking why museums which are part of GBIF haven't mobilised their herpetology data, and again, what can it do to help? Lastly, in an age of rapid taxonomic change driven by phylogenetic analysis, GBIF needs to overhaul the glacial pace at which it incorporates new taxonomic information.
Source: iPhylo
06:04
06:04

We describe new methods for characterizing gene tree discordance in phylogenomic data sets, which screen for deviations from neutral expectations, summarize variation in statistical support among gene trees, and allow comparison of the patterns of discordance induced by various analysis choices. Using an exceptionally complete set of genome sequences for the short arm of chromosome 3 in Oryza (rice) species, we applied these methods to identify the causes and consequences of differing patterns of discordance in the sets of gene trees inferred using a panel of 20 distinct analysis pipelines. We found that discordance patterns were strongly affected by aspects of data selection, alignment, and alignment masking. Unusual patterns of discordance evident when using certain pipelines were reduced or eliminated by using alternative pipelines, suggesting that they were the product of methodological biases rather than evolutionary processes. In some cases, once such biases were eliminated, evolutionary processes such as introgression could be implicated. Additionally, patterns of gene tree discordance had significant downstream impacts on species tree inference. For example, inference from supermatrices was positively misleading when pipelines that led to biased gene trees were used. Several results may generalize to other data sets: we found that gene tree and species tree inference gave more reasonable results when intron sequence was included during sequence alignment and tree inference, the alignment software PRANK was used, and detectable "block-shift" alignment artifacts were removed. We discuss our findings in the context of well-established relationships in Oryza and continuing controversies regarding the domestication history of O. sativa. [gene trees; multilocus data; Oryza; phylogenomics; phylogeny reconstruction; species trees.]

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