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December 19, 2014

*Two year Postdoc opportunity in* ** *Statistical and Population Genomics* ** *Miguel Pérez-Enciso (**)* ** *Centre for Research in Agricultural Genomics (CRAG)* *Campus UAB, 08193 Bellaterra, Barcelona, Spain* ** *JOB DESCRIPTION* A two year postdoc position is available within the recently funded project ‘Next generation tools to exploit genome diversity in domestic species’. Two research topics are possible, or a mixture of both: 1- Use of sequence data in genomic selection. We will investigate by simulation, but using real sequence data, what are the potential advantages of sequence over high density genotyping under realistic genetic architectures. 2- To develop a population genetics model that mimic domestication and breed structure in livestock. Focusing in the pig species and using genomewide sequence data, the goal is to adjust a population genetics model that can be used as neutral model to test for selection. ** *THE RESEARCH TEAM* The PhD project wil be supervised by Miguel Pérez-Enciso (ICREA professor,;, in cooperation with S.E. Ramos-Onsins. Recent related publications include: Pérez-Enciso M. et al. On genetic differentiation between domesticpigs and Tibetan wild boars. Nature Genetics (correspondence), accepted. Nevado, N., et al. 2014. Re-sequencing studies of non-model organisms using closely-related reference genomes: optimal experimental designs and bioinformatics approaches for population genomics. Mol. Ecol. 23: 1764–1779. Pérez-Enciso, M. 2014. Genomic relationships computed from either next generation sequence or array SNP data. J. Anim. Breed. Genet. 131:85-96. Ramírez O, et al. 2014. Genome data from a sixteenth century pig illuminate modern breed relationships. Heredity doi: 10.1038/hdy.2014.81 Groenen et al. 2012. Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491:393-8. The research will be developed in the recently built Centre for Research in Agricultural Genomics (, based on campus of Universitat Autonoma of Barcelona (, Spain. ** *SALARY AND CONDITIONS* Annual gross salary is 29k €, the contract is available for one year and extendable to an additional year. The position is available starting May 2015 or as agreed. Candidates interested in the position should email me ( their CV and names of two persons who can provide references. Miguel Perez-Enciso ICREA professor Centre for Research in Agricultural Genomics (CRAG) and Facultat de Veterinaria UAB Campus Universitat Autonoma Barcelona Bellaterra E-08193 Spain Tel: +34 935636600 ext 3346 Fax: +34 935636601, based on campus of Universitat Autonoma of Barcelona (, Spain. ** *SALARY AND CONDITIONS* Annual gross salary is 29k €, the contract is available for one year and extendable to an additional year. The position is available starting May 2015 or as agreed. Candidates interested in the position should email me ( their CV and names of two persons who can provide references. Miguel Perez-Enciso ICREA professor Centre for Research in Agricultural Genomics (CRAG) and Facultat de Veterinaria UAB Campus Universitat Autonoma Barcelona Bellaterra E-08193 Spain Tel: +34 935636600 ext 3346 Fax: +34 935636601 miguel via Gmail
Research Associate Position in Single Cell Phylogenomics University of British Columbia Vancouver, Canada The Department of Botany seeks a well-trained highly motivated and enthusiastic individual interested in exploring the evolutionary biology of complex microbial life and their organelles using single cell genomics methods coupled with phylogenomic analyses as a Research Associate. The applicant must have a PhD or equivalent and at least three additional years of research experience. Expertise in eukaryotic biodiversity and evolutionary history, and the application of single cell genomics methods (genomic and transcriptomic datasets) and phylogenic analyses are essential. The applicant must have excellent written and oral communication skills and be highly organised. Basic molecular biology and analyses techniques are also highly desirable. The candidate must have a proven record of publication in significant journals in the field. [If there are particular duties and/or experience the applicants should have, please add them here. These will be used to prove why other applicants do not meet the criteria.] The position is available starting May 15 2015 for an initial period of one year with a possibility for extension subject to a satisfactory performance and funding. To apply, please send a cover letter outlining research experience and interest, a curriculum vitae and the names and contact information for 3 referees to Patrick Keeling, Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, B. C. V6T 1Z4, Canada. Fax (604) 822-6089. Closing date is Friday, January 23, 2015. UBC hires on the basis of merit and is strongly committed to equity and diversity within its community. We especially welcome applications from visible minority group members, women, Aboriginal persons, persons with disabilities, persons of minority sexual orientations and gender identities, and others with the skills and knowledge to productively engage with diverse communities. Canadians and permanent residents of Canada will be given priority. “Keeling, Patrick” via Gmail
The lab of Célio F. B. Haddad has an opening for a postdoctoral position in biology of amphibians. The lab is located within the Department of Zoology at Universidade Estadual Paulista, State of São Paulo, Brazil, and maintains close interactions with an exceptionally large and diverse group of labs that work on amphibians over the world. Haddad’s lab is seeking a postdoctoral fellow to develop a project with *Brachycephalus*, an endemic genus of tiny frogs from the Atlantic Forest of Brazil. The fellowship will be provided by FAPESP (more information in Start date should be immediate. Candidates should have experience with these amphibians and some required qualifications: 1) Ph.D. in Zoology or related field, obtained no more than one year ago; 2) experience with amphibians, including publications with the target taxonomic group; 3) skills to work with GIS and molecular evolutionary analysis; 4) availability to plan and to do fieldwork; 5) availability to live at Rio Claro, State of São Paulo, Brazil, during the execution of the project; 6) fluent English and personal interest to learn Portuguese; 7) exclusive dedication to the project. The selected candidate should work on the specific project “Diversification of *Brachycephalus *(Anura: Brachycephalidae): evolutionary patterns and processes”. To apply, please send a CV, a statement of the academic background and research interests and two recommendation letters to The deadline for applications is January 18, 2015. The successful applicants will be contacted by e-mail to an interview, if necessary. The result will be disclosed by e-mail until January 25, 2015. Célio F. B. Haddad Professor Department of Zoology Universidade Estadual Paulista (UNESP) Rio Claro, SP, Brazil Célio Fernando Baptista Haddad via Gmail
The International Max Planck Research School (IMPRS) for Organismal Biology offers several fully funded PhD positions. The IMPRS is based in southern Germany and is jointly organized by the Max Planck Institute for Ornithology in Seewiesen and Radolfzell and the University of Konstanz. Outstanding students of all nationalities with a deep commitment to basic research in Organismal Biology are invited to apply. More than 25 internationally recognized research groups actively participate in the PhD program and offer challenging, cutting-edge PhD projects in the fields of Behavioral Biology, Ecology, Evolutionary Biology, Physiology, and Neurobiology. The aim of the IMPRS is to provide first-class training and education for outstanding doctoral students from all over the world in a stimulating research environment. The competitive doctoral program provides its fellows with an excellent starting platform for a successful career in the fields of animal behaviour, ecology, evolution, physiology, and neurobiology. For 2015, we offer the following PhD projects: Evolutionary Genetics of the Embryo Mortality Puzzle in the Zebra Finch Ecological genomics in urbanizing burrowing owls Comparative Analysis of Sexual Selection in Parrots of the World Early Sexual Development of the Chicken Brain Collective Animal Behaviour Computational Approaches to the Experimental Study of Animal Collectives Two open PhD positions for own proposal elaboration within Organismal Biology For a list of all available PhD projects visit Our Offer All students accepted to the program will be supported by stipends or contracts. The program offers a dedicated teaching program, high quality research experience, and outstanding research facilities in an inspiring research and living environment. The working language is English. Each PhD student receives individual supervision and mentoring and is guided in her/his research work by a PhD advisory committee. The Max Planck Society and the University of Konstanz are equal opportunity employers. Your application Outstanding students of all nationalities with a deep commitment to basic research in Organismal Biology are invited to apply. Deadline for the application is January 15, 2015. Interviews with the applicants are scheduled for March 23-26, 2015. Candidates accepted into the program may start latest September 2015. Qualification: Applicants should hold a MSc or equivalent degree in biology or a related discipline at the point of enrollment. Queries should be mailed to the program office: Application: You can only apply via the three-tier electronical application process on the Institutes webpage. For more information visit More information at and and Mggi Hieber Ruiz via Gmail
One Research Fellow position at the Biosciences Department in Swansea University to study the genetic and epigenetic basis of fish domestication (salary scale: 32,277 to 37,394 per annum (pro rata if part time) together with USS pension benefits). Swansea University is one of the top 30 Universities in the UK and the Biosciences Department has ranked 8 in the UK in the recently published Research Excellence Framework (REF), with 93.8% of the research outputs considered as being world leading (4*) or of international excellence (3*). We are looking for 1 Postdoctoral Research Fellow to work on an exciting project that will use a multidisciplinary, cutting-edge approach to bridge, for the first time, the behavioural, genetic and environmental (epigenetic) components of fish undergoing domestication and disentangle the role of domestication in disease resistance. See details on how to apply in the link below: The Research Fellow position is available for 42 months starting approximately April 2015. Applicants are expected to match the following criteria: - Have a PhD in a relevant field (e.g. Biology, Ecology, Genetics). - Not be awarded their first PhD less than 2 years to the starting date of the position. - Have published, confirmed accepted or in press, at least 5 papers in ISI accredited peer-reviewed journals by the starting date of the position. Desirable criteria are: experience working on fish behaviour, genetics/genomics background, experience programming in R/Python Informal enquiries can be directed to Sonia Consuegra ( Carlos Garcia de Leaniz ( Dr. Sonia Consuegra Dept Biosciences College of Science Swansea University Singleton Park SA2 8PP Swansea Tel. +44 (0) 1792 602931 Email. “CONSUEGRA S.” via Gmail

December 18, 2014

One reason I'm excited by the launch of the NHM data portal is that it opens up opportunities to link publications about specimens i the NHM to the record of the specimens themselves. For example, consider specimen 1977.3097, which is in the new portal as (possibly the ugliest URL ever).

This specimen is of the bat Pteralopex acrodonta, shown in the image to the right (by William N. Beckon, taken from the EOL page for this species). This species was described in the following paper:
Hill JE, Beckon WN (1978) A new species of Pteralopex Thomas, 1888 (Chiroptera: Pteropodidae) from the Fiji Islands. Bulletin of the British Museum (Natural History) Zoology 34(2): 65–82. paper is in my BioStor project, and if you visit BioStor you'll see see that BioStor has extracted a specimen code (BM(NH) 77.3097) and also has a map of localities extracted from the paper.

Looking at the paper we discover that BM(NH) 77.3097 is the type specimen of Pteralopex acrodonta:
HOLOTYPE. BM(NH) 77.3097. Adult . Ridge about 300 m NE of the Des Voeux Peak Radio Telephone Antenna Tower, Taveuni Island, Fiji Islands, 16° 50½' S, 179° 58' W, c. 3840ft (1170 m). Collected 3 May 1977 by W. N. Beckon, died 6-7 May 1977. Caught in mist net on ridge summit : bulldozed land with secondary scrubby growth, adjacent to primary forest. Original number 104. Skin and skull.Note that the NHM data portal doesn't know that 1977.3097 is the holotype, nor does it have the latitude and longitude. Hence, if we can link 1977.3097 to BM(NH) 77.3097 we can augment the information in the NHM portal.

This specimen has also been cited in a subsequent paper:
Helgen, K. M. (2005, November). Systematics of the Pacific monkey‐faced bats (Chiroptera: Pteropodidae), with a new species of Pteralopex and a new Fijian genus . Systematics and Biodiversity. Informa UK Limited. doi:10.1017/s1477200005001702You can read this paper in BioNames. In this paper Helgen creates a new genus, Mirimiri for Pteralopex acrodonta, and cites the holotype (as BMNH 1977.3097). Hence, if we could extract that specimen code from the text and link it to the NHM record we could have two citations for this specimen, and note that the taxon the specimen belongs to is also known as Mirimiri acrodonta.

Imagine being able to do this across the whole NHM data portal. The original description of this bat was published in a journal published by the NHM (and part of a volume contributed by the NHM to the Biodiversity Heritage Library). With a *cough* little work we could join up these two NHM digital resources (specimen and paper) to provide a more detailed view what we know about this specimen. From my perspective this cross-linking between the different digital assets of an institution such as the NHM (as well as linking to external data such as other publications, GenBank sequences, etc.) is where the real value of digitisation lies. It has the potential to be much more than simply moving paper catalogues and publications online.
Source: iPhylo

The International Society for Evolution, Medicine, & Public Health meeting March 19-21 in Arizona now has support for travel awards, thanks to the National Evolutionary Synthesis Center, the Triangle Center for Evolution and Medicine, and donations to the Foundation for Evolution, Medicine, & Public Health. Meeting details at Details below. *Student travel awards* Travel awards of $500 to $1,000 US dollars (possibly more depending on applications) each to students to defray a portion of the costs of lodging and travel to the ISEMPH inaugural meeting. -The applicant must be a student in good standing as an undergraduate, graduate student, postdoctoral fellow, veterinary student, medical student or medical resident, in a degree program at an accredited university. -$5,000 of the available awards are committed for support of students from under-represented groups in science, including women, thanks to funding from the National Evolutionary Synthesis Center and Tri-CEM. If you would like to be considered for one of the awards for students from underrepresented groups, please indicate that in your statement. -Students presenting papers or posters at the conference are prioritized; followed by students who are co-authors of papers or posters to be presented at the conference. However, students who will not be presenting are still encouraged to apply and will be supported if possible. Travel distance and overall costs are also considered when making awards. Submission Deadline: January 10, 2015 Notification: January 31, 2015 Application information at *Faculty travel awards* Funding is available from the National Evolutionary Synthesis Center (NESCent) and the Triangle Center for Evolutionary Medicine (TriCEM) to support travel by faculty from under-represented groups in science to the International Society for Evolution, Medicine, & Public Health meeting in Arizona March 19-21. Applicants must be from an under-represented group in science and be on the faculty at a Minority Serving Institution or Historically Black College or University. Submission Deadline: January 8, 2015 Notification: January 15, 2015 Apply at via Gmail

The Behaviour Ecology and Evolution Research (BEER) Centre at Durham University is delighted to be hosting the Association for the Study of Animal Behaviour’s Postgraduate Workshop and Easter Conference 18-20 March 2015. The Easter ASAB conferences expressly welcome submissions from students to present their research findings in spoken or poster presentations, with prizes! The Conference (Thursday 19th - Friday 20th March) will be preceded on Wednesday 18th March by a Postgraduate Workshop, focussing on ‘Careers Outside Academia’. Please join us for our reception on Wednesday 18th March for BEER beer and The Trial of Chimpanzee Jack. Plenary speakers: Dr Tristram Wyatt, University of Oxford, and Dr Paula Stockley, University of Liverpool. Email: Twitter: @asabeaster2015 Abstract and early bird registration deadline: 9 Feb 2015 Website: See you there! Dr Joanna (Jo) M Setchell Director of Research Reader in Evolutionary Anthropology Department of Anthropology Durham University, UK The Behaviour, Ecology and Evolution Research (BEER) Centre: are hosting ASAB Easter 2015: Editor-in-Chief, International Journal of Primatology “SETCHELL J.M.” via Gmail
—_000_FBE5B4773C60E147B791856BB8B128C901001971BELLATRIXuniver_ Content-Type: text/plain; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable Hello EvolDirers, We are excited to announce the 2nd annual election for the board of the International Network of Next-Generation Ecologists (INNGE) We’re looking for the most enthusiastic, creative and skilled early-career scientists to serve on the board. The call is available via this Google form ( The form must be filled before January 8th with the following information. 1. your name 2. your society (if applicable) 3. your country 4. your vision for INNGE, how would you like to see INNGE evolve over the coming years ( and to stay abreast of developments via the INNGE blog, Facebook, and Twitter. Please do not hesitate to contact us if you have any questions regarding the elections or the bylaws, or any other aspect regarding INNGE. With best wishes, Rachel White (on behalf of INNGE’s Governing Board) INNGE Governing Board member and Membership Coordinator via Gmail
Clark Honors College, University of Oregon Asst./Assoc./Full Professor of Evolutionary Sciences 1. Position: The Robert D. Clark Honors College (CHC) at the University of Oregon (UO) invites applications for a tenure-track position in evolutionary sciences. This position may carry the rank of Assistant Professor, Associate Professor, or Full Professor and a salary commensurate with experience. Start date September 16, 2015. The position is a full-time, nine-month academic year appointment. 2. Essential Functions: We are particularly interested in individuals whose research interests include evolution, genetics, statistics, quantitative analysis, and historical science, and whose teaching interests would add breadth to our Honors College science curriculum. The successful candidate will have a research affiliation with UO’s research centers, institutes (such as the Institute of Ecology and Evolution) and/or with their disciplinary department(s), and will have teaching and service responsibilities primarily within the Clark Honors College, including shared responsibility for its introductory science curriculum. Clark Honors College courses in all fields are taught in a seminar format. Candidates should show evidence of excellence in teaching and mentoring undergraduates, as well as an outstanding research program. 3. Minimum and Preferred Qualifications: Ph.D. in physics, biology or related natural science field. Evidence of superior scholarship and teaching. Commitment to teaching state of the art courses with up-to-date approaches. Preference will be given to those with experience working in an Honors College or in a competitive liberal arts college. Candidates who promote and enhance diversity are encouraged to apply. About science in the CHC: The CHC functions as a liberal arts college of about 800 undergraduate students and 20 arts and sciences faculty within the larger University of Oregon community. The mission of the CHC is to provide high-achieving students the best of both an intensive small college experience and a major research university education, and to foster lively conversation across the arts and sciences. Our curriculum currently requires at least one course in science taught in the Honors College format, with a heavy emphasis on science literacy and critical thinking, writing, and speaking. Roughly 1/3 of our students are in science majors or minors, and all complete a research thesis in the course of the CHC curriculum. 4. Description of the University and Community: The CHC at the University of Oregon (UO) is a highly competitive, small liberal arts college of approximately 800 students featuring small classes and close interaction between students and faculty. It emphasizes interdisciplinary scholarship and independent research in a tight-knit, dynamic community. The University of Oregon is located in Eugene, Oregon, home to more than 155,000 people and Oregon’s third largest city. Within only a few hours’ drive are ocean beaches, lakes, rivers, forests, high desert, and the Cascade and Coast mountain ranges. The Willamette River runs through the heart of the city and joins the McKenzie River north of town. Mild winters, long growing seasons, and few drastic weather changes are characteristic. Eugene has a high percentage of professionals, including doctors, lawyers, architects, and educators, and is home to the Hult Center for the Performing Arts, which regularly hosts the Oregon Bach Festival, the Eugene Symphony, the Eugene Ballet, and the Eugene Opera, among other cultural offerings. 5. Application Procedure and Closing Dates: Application review begins on January 1, 2015. Applications submitted by that date will be ensured consideration. The position will remain open, and qualified candidates in the pool will remain active, until the position is filled. The finalist for this position must successfully complete a criminal background check. Submit the application materials to: . The successful candidate will support and enhance a diverse learning and working environment. A complete application must include the following: 1. A cover letter demonstrating how you meet the qualifications and addressing your interest in the position. 2. A current CV including a publication list, research and teaching statements. 3. Three letters of reference. 4. Submission of 1-3 selected reprints is encouraged, as well as evidence of effective teaching. 6. AAEO Statement: The University of Oregon is an equal opportunity, affirmative action institution committed to cultural diversity and compliance with the ADA. The University encourages all qualified individuals to apply, and does not discriminate on the basis of any protected status, including veteran and disability status. Colleen Dietz via Gmail
A competitive fully-funded PhD studentship will be available to study comparative ecological genomics of freshwater fishes with Kathryn Elmer and Colin Adams through the University of Glasgow College of Medical, Veterinary and Life Sciences Doctoral Training Programme (CMVLS-DTP). Details are available at: See the project entitled “Comparative ecological genomics of environmental heterogeneity” under the section “Food Security (Crop Science and Animal Health)”. Note that the application is to the CMVLS-DTP and not to the project, but the project will be available to the successful candidates. This Doctoral Training Programme aims to deliver high quality, collaborative research and training for PhD students within the Biosciences. The competition is open to all UK students and EU nationals who reside in the UK. Deadline for applications is Friday 16 January 2015 Dr. Kathryn Elmer is interested in the genetic basis of biodiversity and ecological diversification and is based in the Evolutionary Analysis Group. Prof. Colin Adams studies fish biology and ecology and is Director of the Scottish Centre for Ecology and the Natural Environment (SCENE). Both faculty are based in the Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Scotland. Please see the website for details on the CMVLS-DTP and feel free to contact Kathryn Elmer with informal inquiries in advance of the deadline. Kathryn Elmer via Gmail

December 17, 2014

Dear colleague, Grenoble, at the heart of the French Alpes, will host an outstanding international scientific event in the field of systems biology: The conference /*Perspectives in Environmental and Systems Biology */will bring together more than 150 scientists from all over the world, including biologists, physicians, health professionals, environmental scientists, and specialists in mathematical and computational modeling. The conference is organized by the Grenoble Federal Research Structure /Environmental and Systems Biology/ on the campus of the University Grenoble Alpes on *April 13-15, 2015*. /*Perspectives in Environmental and Systems Biology*/ will emphasize the inter- and cross-disciplinary character of systems biology, and integrate contributions of various classical disciplines ranging from molecular and cellular biology to medicine and ecology, informatics and applied mathematics. It will discuss topics such as multi-scale approaches, the analysis of networks, computational modelling, systems biology in medicine, and synthetic biology. More than 25 distinguished scientists have already accepted to present their view of systems biology. Retrieve the conference program on the dedicated website: or download it directly here We cordially invite you to join this major event in Grenoble. The scientific committee Uwe Schlattner, President *Registration* For your registration, click here Preferential rate before December 31st, 2014: *Student:* 140 EUR - *Regular:* 280 EUR /The price includes coffee breaks and lunches on April 13, 14 and 15. Participation at the Welcome Dinner requires separate registration./ *Abstract Submission* All abstracts must be submitted electronically by February 28th, 2015 *Travel award* The scientific committee will bestow travel awards for students and postdoctoral fellows for attending the conference as presenting author. Each travel award may be used for waiving registration fee and travel costs and will not exceed 500 EUR. Application can be made when submitting abstract. Advisors are expected to recommend their trainee by detailing his/her excellent achievements in a separate email to the scientific committee ( ) Irene Till-Bottraud Directrice Laboratoire d’Ecologie Alpine, CNRS UMR 5553 Universite Joseph Fourier BP 53 X 38041 Grenoble cedex France Tel : (33) 04 76 51 45 24Fax : (33) 04 76 51 42 79 E-Mail : Irne Till-Bottraud via Gmail
*John Maynard Smith Prize 2015: Call for Nominations* Every year the European Society for Evolutionary Biology (ESEB) distinguishes an outstanding young evolutionary biologist with a prize named after John Maynard Smith (1920 - 2004), eminent scientist, great mentor, author of many books on evolution, and a former President of ESEB. Nomination: The prize is open to any field of evolutionary biology. The candidates for the 2015 prize must have begun their PhD study after January 1, 2008. The nomination of the candidate may be by a colleague or self-nominated. The nominations should be sent as a single PDF file to Ute Friedrich at the ESEB office . The nomination should include a brief justification, the candidate’s CV and list of publications (indicating three most significant papers), a short description of future research plans, and a letter from the candidate approving the nomination. A letter of reference from another colleague (or two in case of self-nomination) should be sent directly to Ute Friedrich. Nominations should arrive no later than January 15, 2015. Please take care to limit the size of attachments (total via Gmail
We propose a catalysis meeting to advance theoretically-grounded, empirical study of scientific collaborations designed to achieve synthesis. Synthesis is the integration of diverse theories, methods and data across spatial or temporal scales, scientific phenomena, and forms of expertise to increase the generality, parsimony, applicability, or empirical soundness of scientific explanations. It generates emergent explanations beyond the scope of any one discipline, dataset or method. It counterbalances scientific specialization, capitalizes on existing data, and can be used to address complex problems. Synthesis centers are an increasingly vital component of science policy, rising in number, size, and prominence nationally and globally. Despite this, our understanding of synthesis-group collaborations and their performance are inadequate to advance knowledge, inform policy and guide practice. This meeting will draw together scientists who lead and conduct synthetic research with a diverse group of experts on scientific collaboration and research evaluation. Our aim is to advance understanding of synthesis and develop new approaches for investigating it empirically, longitudinally and comparatively.
Source: NESCent
The Natural History Museum has released their data portal ( As of now it contains 2,439,827 of the Museum's 80 million specimens, so it's still early days. I gather that soon this data will also appear in GBIF, ending the unfortunate situation where data from one of the premier natural history collections in the world was conspicuous by its absence.

I've not had a chance to explore it in much detail, but one thing I'm keen to do is see whether I can link citations of NHM specimens in the literature (e.g., articles in BioStor) with records in the NHM portal. Being able to dip this would enable all sorts of cool things, such as being able to track what researchers have said about particular specimens, as well as develop citation metrics for the collection.

Source: iPhylo
On a recent trip to the Natural History Museum, London, the subject of DNA barcoding came up, and I got the clear impression that people at the NHM thought classical DNA barcoding was pretty much irrelevant, given recent developments in sequencing technology. For example, why sequence just COI when you can use shotgun sequencing to get the whole mitogenome? I was a little taken aback, although this is a view that's getting some traction, e.g. [1,2]. There is also the more radical view that focussing on phylogenetics is itself less useful than, say, "evolutionary gene networks" based on massive sequencing of multiple markers [3].

At the risk of seeming old-fashioned in liking DNA barcoding, I think there's a bigger issue at stake (see also [4]). DNA barcoding isn't simply a case of using a single, short marker to identify animal species. It's the fact that it's a globalised, standardised approach that makes it so powerful. In the wonderful book "A Vast Machine" [5], Paul Edwards talks about "global data" and "making data global". The idea is that not only do we want data that is global in coverage ("global data"), but we want data that can be integrated ("making data global"). In other words, not only do we want data from everywhere in the world, say, we also need an agreed coordinate system (e.g., latitude and longitude) in order to put each data item in a global context. DNA barcoding makes data global by standardising what a barcode is (a given fragment of COI), and what metadata needs to be associated with a sequence to be a barcode (e.g., latitude and longitude) (see, e.g. Guest post: response to "Putting GenBank Data on the Map"). By insisting on this standardisation, we potentially sacrifice the kinds of cool things that can be done with metagenomics, but the tradeoff is that we can do things like put a million barcodes on a map:

To regard barcoding as dead or outdated we'd need an equivalent effort to make metagenomic sequences of animals global in the same way that DNA barcoding is. Now, it may well be that the economics of sequencing is such that it is just as cheap to shotgun sequence mitogenomes, say, as to extract single markers such as COI. If that's the case, and we can get a standardised suite of markers across all taxa, and we can do this across museum collections (like Hebert et al.'s [6] DNA barcoding "blitz" of 41,650 specimens in a butterfly collection), then I'm all for it. But it's not clear to me that this is the case.

This also leaves aside the issue of standardising other things's much as the metadata. For instance, Dowton et al. [2] state that "recent developments make a barcoding approach that utilizes a single locus outdated" (see Collins and Cruickshank [4] for a response). Dowton et al. make use of data they published earlier [7,8]. Out of curiosity I looked at some of these sequences in GenBank, such as JN964715. This is a COI sequence, in other words, a classical DNA barcode. Unfortunately, it lacks a latitude and longitude. By leaving off latitude and longitude (despite the authors having this information, as it is in the supplemental material for [7]) the authors have missed an opportunity to make their data global.

For me the take home message here is that whether you think DNA barcoding is outdated depends in part what your goal is. Clearly barcoding as a sequencing technology has been superseded by more recent developments. But to dismiss it on those grounds is to miss the bigger picture of what is a stake, namely the chance to have comparable data for millions of samples across the globe.

  1. TAYLOR, H. R., & HARRIS, W. E. (2012, February 22). An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. Molecular Ecology Resources. Wiley-Blackwell. doi:10.1111/j.1755-0998.2012.03119.x
  2. Dowton, M., Meiklejohn, K., Cameron, S. L., & Wallman, J. (2014, March 28). A Preliminary Framework for DNA Barcoding, Incorporating the Multispecies Coalescent. Systematic Biology. Oxford University Press (OUP). doi:10.1093/sysbio/syu028
  3. Bittner, L., Halary, S., Payri, C., Cruaud, C., de Reviers, B., Lopez, P., & Bapteste, E. (2010). Some considerations for analyzing biodiversity using integrative metagenomics and gene networks. Biol Direct. Springer Science + Business Media. doi:10.1186/1745-6150-5-47
  4. Collins, R. A., & Cruickshank, R. H. (2014, August 12). Known Knowns, Known Unknowns, Unknown Unknowns and Unknown Knowns in DNA Barcoding: A Comment on Dowton et al. Systematic Biology. Oxford University Press (OUP). doi:10.1093/sysbio/syu060
  5. Edwards, Paul N. A Vast Machine: Computer Models, Climate Data, and the Politics of Global Warming. MIT Press ISBN: 9780262013925
  6. Hebert, P. D. N., deWaard, J. R., Zakharov, E. V., Prosser, S. W. J., Sones, J. E., McKeown, J. T. A., Mantle, B., et al. (2013, July 10). A DNA “Barcode Blitz”: Rapid Digitization and Sequencing of a Natural History Collection. (S.-O. Kolokotronis, Ed.)PLoS ONE. Public Library of Science (PLoS). doi:10.1371/journal.pone.0068535
  7. Meiklejohn, K. A., Wallman, J. F., Pape, T., Cameron, S. L., & Dowton, M. (2013, October). Utility of COI, CAD and morphological data for resolving relationships within the genus Sarcophaga (sensu lato) (Diptera: Sarcophagidae): A preliminary study. Molecular Phylogenetics and Evolution. Elsevier BV. doi:10.1016/j.ympev.2013.04.034
  8. Meiklejohn, K. A., Wallman, J. F., Cameron, S. L., & Dowton, M. (2012). Comprehensive evaluation of DNA barcoding for the molecular species identification of forensically important Australian Sarcophagidae (Diptera). Invertebrate Systematics. CSIRO Publishing. doi:10.1071/is12008

Source: iPhylo
Background: Synonymous codon usage bias (SCUB) is an inevitable phenomenon in organismic taxa, generally referring to differences in the occurrence frequency of codons across different species or within the genome of the same species. SCUB happens in various degrees under pressure from nature selection, mutation bias and other factors in different ways. It also attaches great significance to gene expression and species evolution, however, a systematic investigation towards the codon usage in Bombyx mori (B. mori) has not been reported yet. Moreover, it is still indistinct about the reasons contributing to the bias or the relationship between the bias and the evolution of B. mori. Results: The comparison of the codon usage pattern between the genomic DNA (gDNA) and the mitochondrial DNA (mtDNA) from B. mori suggests that mtDNA has a higher level of codon bias. Furthermore, the correspondence analysis suggests that natural selection, such as gene length, gene function and translational selection, dominates the codon preference of mtDNA, while the composition constraints for mutation bias only plays a minor role. Additionally, the clustering results of the silkworm superfamily suggest a lack of explicitness in the relationship between the codon usage of mitogenome and species evolution. Conclusions: Among the complicated influence factors leading to codon bias, natural selection is found to play a major role in shaping the high bias in the mtDNA of B. mori from our current data. Although the cluster analysis reveals that codon bias correlates little with the species evolution, furthermore, a detailed analysis of codon usage of mitogenome provides better insight into the evolutionary relationships in Lepidoptera. However, more new methods and data are needed to investigate the relationship between the mtDNA bias and evolution.
Background: There is great interest in understanding the genomic underpinnings of social evolution, in particular, the evolution of eusociality (caste-containing societies with non-reproductives that care for siblings). Subsociality is a key precursor for the evolution of eusociality and characterized by prolonged parental care and parent-offspring interaction. Here, we provide the first transcriptomic data for the small carpenter bee, Ceratina calcarata. This species is of special interest because it is subsocial and in the same family as the highly eusocial honey bee, Apis mellifera. In addition, some C. calcarata females demonstrate alloparental care without reproduction, which provides a unique opportunity to study worker behaviour in a non-eusocial species. Results: We uncovered similar gene expression patterns related to maternal care and sibling care in different groups of females. This agrees with the maternal heterochrony hypothesis, specifically, that changes in timing of offspring care gene expression are related to worker behaviour in incipient insect societies. In addition, we also detected some similarity to caste-related gene expression patterns in highly eusocial honey bees, and uncovered large lifetime changes in gene expression that accompany shifts in reproductive and maternal care behaviour. Conclusions: For Ceratina calcarata, we found that transcript expression profiles were most similar between sibling care and maternal care females. The maternal care behaviour exhibited post-reproductively by Ceratina mothers is concordant in terms of transcript expression with the alloparental care exhibited by workers. In line with theoretical predictions, our data are consistent with the maternal heterochrony hypothesis for the evolutionary development of worker behaviour in subsocial bees.
Background: In bacteria, cell size affects chromosome replication, the assembly of division machinery, cell wall synthesis, membrane synthesis and ultimately growth rate. In addition, cell size can also be a target for Darwinian evolution for protection from predators. This strong coupling of cell size and growth, however, could lead to the introduction of growth defects after size evolution. An important question remains: can bacterial cell size change and/or evolve without imposing a growth burden? Results: The directed evolution of particular cell sizes, without a growth burden, was tested with a laboratory Escherichia coli strain. Cells of defined size ranges were collected by a cell sorter and were subsequently cultured. This selection-propagation cycle was repeated, and significant changes in cell size were detected within 400 generations. In addition, the width of the size distribution was altered. The changes in cell size were unaccompanied by a growth burden. Whole genome sequencing revealed that only a few mutations in genes related to membrane synthesis conferred the size evolution. Conclusions: In conclusion, bacterial cell size could evolve, through a few mutations, without growth reduction. The size evolution without growth reduction suggests a rapid evolutionary change to diverse cell sizes in bacterial survival strategies.
Gould Award announcement The Society for the Study of Evolutions Committee for the Stephen J. Gould Award for the Improvement for the Understanding of Evolution is soliciting nominations for the Award for 2015. With this annual award the Society for the Study of Evolution recognizes, promotes, and rewards individuals who have increased public understanding of evolutionary biology and its place in modern science. The award will include a cash prize of $5,000 and the expectation that the recipient will present the Public Outreach Seminar at the Evolution Meeting (expenses for travel/lodging and registration would be covered by the SSE). The awardee should be a leader in evolutionary thought and in public outreach who can deliver an inspiring lecture for both professionals and the broader public at the 2015 meetings of the Society in San Paolo, Brazil. Nominations should include the CV of the nominee along with a 1-2 page letter describing why this individual is worthy of the award. Please send nominations via e-mail to the Chair of the Committee, Steve Palumbi, at Please submit names of nominees by December 18. All nominations will be treated confidentially and will be evaluated by members of the Committee and the Council for the Society. An awardee will be announced in early February. Stephen R. Palumbi Harold A Miller Director, Hopkins Marine Station Jane and Marshall Steel Professor of Biology Stanford University Steve Palumbi via Gmail