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April 21, 2015

18:00
Background: The genomes of eukaryotes vary enormously in size, with much of this diversity driven by differences in the abundances of transposable elements (TEs). There is also substantial structural and phylogenetic diversity among TEs, such that they can be classified into distinct classes, superfamilies, and families. Possible relationships between TE diversity (and not just abundance) and genome size have not been investigated to date, though there are reasons to expect either a positive or a negative correlation. This study compares data from 256 species of animals, plants, fungi, and “protists” to determine whether TE diversity at the superfamily level is related to genome size. Results: No simple relationship was found between TE diversity and genome size. There is no significant correlation across all eukaryotes, but there is a positive correlation for genomes below 1,000Mbp and a negative correlation among land plants. No relationships were found across animals or within vertebrates. Some TE superfamilies tend to be present across all major groups of eukaryotes, but there is considerable variance in TE diversity in different taxa. Conclusions: Differences in genome size are thought to arise primarily through accumulation of TEs, but beyond a certain point (~500Mbp), TE diversity does not increase with genome size. Several possible explanations for these complex patterns are discussed, and recommendations to facilitate future analyses are provided.
11:00

Adding to the work reported in Gire, et al (Science, 2014) which sequenced Ebola viruses from the first three weeks of the epidemic in Sierra Leone, we here present analyses of 150 additional viral genomes sampled from EVD cases at Kenema Government Hospital between the months of June to September 2014. We describe continued evidence for sustained human-to-human transmission with no additional zoonotic events, and preliminary results concerning new lineages from Guinea. We also characterize the epidemiological history of the limited number of exported viruses from the country. We also observe a slowing of the viral substitution rate over the course of the outbreak, consistent with the increased effect of purifying selection as the outbreak continues over time. These findings allow a closer view of viral evolution during its extended time in human populations and provide critical insights into the movement of the virus through the region.

This is the first talk in a pair of talks from collaborators Daniel Park and Gytis Dudas concerning their analysis of Ebola virus sequences.

Source: Phyloseminar
07:49

Playing with the my "material examined" tool I've been working on, I wondered whether I could make use of it in, say, a spreadsheet. Imagine that I have a spreadsheet of museum codes and want to look those up in GBIF. I could create a service for Open Refine but Open Refine is a bit big and clunky, you have to fire up a Java application and point your browser at it, and Open Refine isn't as intuitive or as flexible as a spreadsheet.

It turns that Google Spreadsheets supports custom functions, including importing JSDON from a remote data source. Following How to import JSON data into Google Spreadsheets in less than 5 minutes here's what to do:

  1. Create a new Google Spreadsheet.
  2. Click on Tools -> Script Editor.
  3. Click Create script for Spreadsheet.
  4. Delete the placeholder content and paste the code from this script.
  5. Rename the script to ImportJSON.gs and click the save button.
  6. Back in the spreadsheet, in a cell, you can type “=ImportJSON()” and begin filling out it’s parameters.

Lets imagine we have a spreadsheet with a specimen code in cell A1, e.g. "FMNH 187122".

To call the material examined service, we need a function like this:

=ImportJSON(CONCATENATE("http://bionames.org/~rpage/material-examined/service/api.php?code=",A1,"&match&extend=10"), "/hits/key,/hits/scientificName", "noHeaders")

Paste this into cell B1 (i.e., just to the right of the specimen code) and after a short delay you should see something like this:

The three parameters supplied to ImportJSON are are the query URL, written as a spreadsheet function that grabs the specimen code from cell A1, a list of the bits of data we want to extract from the result (expressed as JSON paths), and some options (in this case, don't show the headers). ImportJSON will grab the specimen code in cell A1, add it to the query URL, then output the results. You should see something like this:

The first column is the GBIF occurrence ID, the second is the scientific name (you can add more JSON paths to get more fields).

Note that we have multiple rows as there is more than one specimen with the code "FMNH 187122" in GBIF. Now, we can ask the material examined service to return only certain taxa (such as mammals) by adding the "scientificName" parameter:

=ImportJSON(CONCATENATE("http://bionames.org/~rpage/material-examined/service/api.php?code=",A10,"&scientificName=",B10,"&match&extend=10"), "/hits/key,/hits/scientificName", "noHeaders")

If you put the specimen code in cell A10, and the higher taxon "Mammalia" in cell B10, and paste the function above into cell C10, then you should see something like this:

Note that now we have a single row with the mammal specimen.

It's a little bit fussy (you need to get the ImportJSON script, and mess a bit with the parameters but it's quick and flexible, and you get all the power of a spreadsheet to help clean the data before trying to match it to GBIF. Plus you can do it all in your browser.

Source: iPhylo
03:59

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Source: EVOLDIR
01:12
This may be of interest - note impending abstract deadline Please distribute within your department ABSTRACT SUBMISSION DEADLINE: 30TH APRIL 2015 Dear colleagues, As you already know the XV European Congress of Ichthyology, organized by the Interdisciplinary Centre of Marine and Environmental Research, will take place from the 7th to 11th September 2015 in Porto Portugal. This is an international congress promoted by the European Ichthyological Societythat has been held on a three-year cycle since 1973. Recent meetings have been able to attract around 250-300 researchers from around the world. The congress will focus on fish as a subject of research in several biological sciences. The scientific program will include sessions following four main topics: I) Phylogeny, systematic and genetics; II) Ecology, conservation and invasive species; III) Life cycles, migration and connectivity; and IV) Physiology, behaviour and toxicology. Two special symposia have also been organized: V) Otoliths as a powerful tool to study fishes; and VI) Mediterranean fish biodiversity. The congress will be organized with parallel oral sessions and poster exhibitions. The congress will include several invited plenary lectures made by world renowned fish researchers: Drs. Jeffrey Leis (Australia), Joana Robalo (Portugal), Kenneth Able (USA), Marino Vachhi (Italy), Miguel Pineda(Spain), Neil Metcalfe (UK), Rui Oliveira (Portugal) and Steven Campana (Canada). The abstract submission deadline is fast approaching on the 30th of April 2015. It is mandatory to register first to access the on-line submission form. However, you do not need to pay until the early and late registration dates on the 15th and 30th of June 2015, respectively. The registration feeshave been kept low to attract as much as possible early career researchers (250 €) and graduate students (150 €). Members of the EIS have a 20% discount. Students will also have the opportunity to compete for awards for best oral and poster presentations. The congress will be held at the Hotel HF Ipanema Park, a 5 stars hotel. A complete buffet lunch, including water, juices and wines, is available in the conference hotel for 15 € per day, but to a limited number of persons. However, within short walking distance (less than 5 minutes) you have other light and inexpensive options, such as a Japanese restaurant, a Pizzeria and a few snack-bars. Please also check out the organized social program. We have schedule events for each conference day for both participants and accompanying persons. Some of them are free, but you will need to book them through the online registration. In 2014 Porto was elected the best European destination by European citizens (http://bit.ly/1DH4L54), and I am sure that you will be delighted with the city, people and food (and of course Port wine). Our international airport is served by several regular and low-cost airlines companies. But train and car are other options. Bookings for accommodation with special prices for other HF Hotels are also now open. Some low-cost accommodations are now also available on the webpage. We strongly recommend “Casa Diocesana Seminário do Vilar” with single and double rooms ranging from 25 to 39 € per day with breakfast included. September is still part of the summer season for tourism in Porto so try to reserve your accommodation in advance. If you need any help, feel free to contact us. Further, and regularly, updated information can be found at the congress webpage (http://bit.ly/1DH4L55). Please follow our latest news onFacebook (http://on.fb.me/1HczdrK) and Twitter (http://bit.ly/1DH4L57). We would greatly appreciate if you kindly forward this information to your colleagues and students in your University, Institute and/or national and international networks. Please also accept our apologies for cross-postings. We hope to see you in Porto in early September. On behalf of the Organizing Committee Prof. Alberto Teodorico Correia, ECIXV Chair Dr Lukas Rüber | Naturhistorisches Museum der Burgergemeinde Bern | Bernastrasse 15 | 3005 Bern | Switzerland phone: +41 (0)31 350 72 82 | email: lukas.ruber@nmbe.ch XV European Congress of Ichthyology, 7-11 September 2015, Porto, Portugal http://bit.ly/1DH4L55 Lukas Ruber via Gmail
Source: EVOLDIR
00:58
POSTDOCTORAL RESEARCH ASSOCIATE Host-Pathogen Evolution/Amphibian Conservation The Voyles lab is seeking a Postdoctoral Research Associate to participate in an NSF funded project investigating the evolution of virulence in an amphibian disease system. The successful applicant will also collaborate with project PIs at Tulane University, and UC Berkeley. Outcomes of this work will likely help shape conservation strategies for amphibians in the region. The successful applicant will be primarily based in Panama. Potential projects may include (1) field studies focused on understanding infection patterns in amphibian communities at multiple sites in Western Panama, (2) laboratory infection experiments, and (3) analyses of host and pathogen genetic and immunological data. Research experience in infectious disease, including field and laboratory skills, are expected, as are skills in data analysis and writing. Proficiency in conversational Spanish and prior experience leading field teams in tropical regions are preferred. This is a two year position, with the extension to a second year being contingent upon satisfactory progress. The position is available starting summer, 2015 (negotiable start date). Review of applications will begin May 1 2015 and continue until a suitable candidate is found. To apply, please send (1) a cover letter, (2) CV, (3) statement of research interests/experiences, and (4) names and contact information for three references to Dr. Jamie Voyles (jvoyles@nmt.edu or jamie.voyles@gmail.com). For more information about this and other research projects going on in our laboratories, please visit our websites at: http://bit.ly/1EmGlRP http://bit.ly/1DH1SRC http://bit.ly/1EmGlRS Corinne L. Richards Zawacki, Ph.D. email:cori@tulane.edu Ken and Ruth Arnold Early Career Professor in Science and Engineering Assistant Professor, Department of Ecology and Evolutionary Biology Tulane University, New Orleans, Louisiana “At night I went out into the dark and saw a glimmering star and heard a frog and nature seemed to say, well do not these suffice?” - Ralph Waldo Emerson Cori Zawacki via Gmail
Source: EVOLDIR

April 20, 2015

23:37

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Source: EVOLDIR

April 19, 2015

16:30

Phylogenetic networks were developed as a professional tool for displaying complicated evolutionary histories. However, this does no mean that such networks cannot be used elsewhere.

As an example, Pete Buchholz produces drawings of dinosaurs as the artist Ornithischophilia at the DeviantArt web site. Among these drawings are some phylogenies, and two of them are networks.

The first one is labelled Citrus is complicated, and refers to the origin of citrus cultivars.


The phylogenetic tree at the left is sourced from the American Journal of Botany, while the network at the right is from information in Wikipedia. The combination of the two appears to be original to the artist. The network is read from left to right — for example, the Limequat is a hybrid of the Key Line and the Kumquat. Compared to the original Wikipedia text, the picture speaks a thousand words.

The second network is labelled Apples are complicated, and refers to the origin of some of the apple cultivars.


No source is given for the information, but I assume that it also comes from Wikipedia. Note that, as before, the network is read from left to right, but this time there is a time scale at the top. The artist refers to it as a "spaghetti diagram", and notes that:
Colors are based on the major parent that the "story" revolves around; purple for Honeycrisp, Yellow for Golden Delicious, Red for Jonathan, Maroon for Red Delicious, Orange for Cox's Orange Pippin, Teal for McIntosh, Green for Granny Smith, and Blue for Topaz.
06:00
Background: Correct species identification is crucial in different fields of biology, and in conservation. The endemic West African frog family Odontobatrachidae currently contains a single described species, Odontobatrachus natator. From western Guinea to western Ivory Coast it inhabits forests around waterfalls or cascades. Based on more than 130 specimens from 78 localities, covering the entire distributional range, we investigated the molecular diversity of these frogs. Results: Our analyses included mitochondrial and nuclear genes, including a concatenated alignment of 3527 base pairs. We detected high level of genetic differentiation with five distinct lineages or operational taxonomic units (OTUs). These OTUs were also identified by two different species delimitation approaches, Generalized Mixed Yule Coalescent (GMYC) and cluster algorithm. All OTUs occur in parapatry in the Upper Guinean forests. One OTU, assigned to the “true” Odontobatrachus natator, covers the largest distribution, ranging from the border region of western Sierra Leone-Guinea to eastern Liberia. Two OTUs are restricted to western Guinea (Fouta Djallon and foothills), while two others occur in eastern Guinea and the border region of Guinea-Liberia-Ivory Coast. The OTU representing O. natator consists of two divergent subclades: one restricted to the Freetown Peninsula (Sierra Leone) and the other covering all populations further inland. Environmental niche models indicated that the restricted Freetown Peninsula population is separated by unsuitable habitat from remaining populations. Conclusion: Geographic isolation of OTUs and molecular differences comparable to species level differentiation in other frog families indicate that O. natator contains cryptic species diversity. Respective distribution patterns most probably resulted from repeated changes of forest cover (contraction and expansion) over evolutionary timescales. The survival within forest refugia that have persisted through multiple drier periods and subsequent dispersal during wetter times may best explain the observed geographic distributions of OTUs. According to the IUCN Red List range criteria each OTU should be classified as “Endangered.” If the Freetown Peninsula “natator” population is recognized as a distinct species it would warrant recognition as “Critically Endangered.” The identification of cryptic lineages in highlights the urgent need to protect these frogs, all of which are endemic to small areas within the Upper Guinean biodiversity hotspot.

April 18, 2015

23:34
Ten permanent positions in Bioinformatics and Biostatistics at Institut Pasteur (Paris) The new direction of Institut Pasteur has defined bioinformatics and systems biology as strategic priorities. A Center for Bioinformatics, Biostatistics and Integrative Biology has been recently created on the Parisian Campus. The objective of this center is to federate and strengthen capacities in bioinformatics in different yet complementary research areas developed within the Institute, such as genomics of hosts and pathogens, biology of infection, evolutionary genetics, population genetics, structural biology or health biology. In this framework, Institut Pasteur proposes 10 permanent positions in bio-informatics and biostatistics for 2015. People will be affiliated to the new center and to the Hub of bioinformatics and biostatistics and will be supervised by the director of the Center. They may be assigned for most of their time to research units and / or platforms to work on different projects while being close to the data and experimental biology. To apply (deadline: May 15) and know more on these positions: http://bit.ly/1JhUQUS Olivier Gascuel via Gmail
Source: EVOLDIR
06:00
Background: Long-established protein-coding genes may lose their coding potential during evolution (“unitary gene loss”). Members of the Poaceae family are a major food source and represent an ideal model clade for plant evolution research. However, the global pattern of unitary gene loss in Poaceae genomes as well as the evolutionary fate of lost genes are still less-investigated and remain largely elusive. Results: Using a locally developed pipeline, we identified 129 unitary gene loss events for long-established protein-coding genes from four representative species of Poaceae, i.e. brachypodium, rice, sorghum and maize. Functional annotation suggested that the lost genes in all or most of Poaceae species are enriched for genes involved in development and response to endogenous stimulus. We also found that 44 mutated genomic loci of lost genes, which we referred as relics, were still actively transcribed, and of which 84% (37 of 44) showed significantly differential expression across different tissues. More interestingly, we found that there were totally five expressed relics may function as competitive endogenous RNA in brachypodium, rice and sorghum genome. Conclusions: Based on comparative genomics and transcriptome data, we firstly compiled a comprehensive catalogue of unitary gene loss events in Poaceae species and characterized a statistically significant functional preference for these lost genes as well showed the potential of relics functioning as competitive endogenous RNAs in Poaceae genomes.

April 17, 2015

03:45
The adverts for our pending academic positions at the CEC http://bit.ly/1aetX5b are now live: For Professor in Biosciences (Ref: P48365) and For (3 positions) Lecturer/Senior Lecturer/Associate Professor in Biosciences (Ref: P48364) Applicants should be broadly aligned with one or more of our key areas (ecology, conservation, evolution, behaviour). However we are particularly interested in strengthening our activities in disease, population and community ecology as well as ecological and evolutionary genomics. Interest from independent research fellows are also welcomed. Interested applicants should contact either Brendan Godley (B.J.Godley@exeter.ac.uk) or Nina Wedell (N.Wedell@exeter.ac.uk). See: http://bit.ly/1Dqkoh8 http://bit.ly/1DqkqFO Prof DJ Hosken University of Exeter, Cornwall Tremough, Penryn TR10 9FE UK 01326 371843 D.J.Hosken@exeter.ac.uk http://bit.ly/1bMLIqH DJ Hosken via Gmail
Source: EVOLDIR
00:58

–089e0158c78a5a1ad00513d42624 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Research Officer Bangor University - School of Biological Sciences Fixed Term Contract, Salary Range: £31,342 - £37,394 p.a. Applications are invited for the above 21-month fulltime BBSRC/NERC-funded post working in the School of Biological Sciences at Bangor University, as part of a collaborative project including Bristol University and The Genome Analysis Centre (TGAC), Norwich. Duties will include bioinformatic, molecular and morphological studies of hybridisation between native and introduced tilapia fish populations from Tanzania, including analysis of full genome sequences. The post-holder will join a thriving research group at Bangor University working in the area of genetics, morphology, behaviour and conservation of African cichlid fish in implementation of this exciting collaborative project. We aim (1) to assess the extent and predictability of introgressive hybridization following introduction of exotic Oreochromis (mainly Nile tilapia) species into the range of native species in Tanzania, using genomic data; 2) to estimate the nature and basis of genomic introgression, including the types of genes most likely to introgress into native and exotic phenotypes and to estimate whether introgression of certain regions is predictable; 3) to develop a quick economical diagnostic test of the extent of introgression, using a SNP-chip based on 100 polymorphisms selected using the full genome sequences and chosen as diagnostic of the pure strains to allocate a ‘hybrid score’ to each individual and then to use this to calibrate phenotypic methods to diagnose hybrids; 4) to estimate the relative growth and ecological niche of pure native and exotic genotypes, as well as a range of hybrids and relate to phenotype to allow us to predict the likely outcome of the introduction 5) to enhance the genomic resources for Tilapia strain improvement through bioinformatics (sequences of a range of native species), tissue/ sperm cryopreservation in collaboration with WorldFish and advising the Tanzanian Government agencies on the identification of candidate stocks for in-situ conservation. The post holder will be responsible for conducting, analysing and publishing a series of genomic studies based on tissue samples obtained from Tanzania in a parallel project funded by the Leverhulme Trust. This will involve basic molecular and morphological laboratory studies and advanced bioinformatic analyses. Candidates should be educated to PhD standard (or equivalent) and have previous experience of molecular laboratory work and quantitative analysis of biological data, preferably including genome sequences. The successful candidate will be expected to commence on or before 1st July 2015. Applications will only be accepted via the on-line recruitment website, jobs.bangor.ac.uk. However, in cases of access issues due to disability, paper application forms are available by telephoning 01248 383865. Closing date for applications: Monday, 18th May 2015. For further details and specific enquiries contact Prof. George Turner ( george.turner@bangor.ac.uk). – via Gmail

Source: EVOLDIR

April 16, 2015

18:00
Background: Bayesian relaxed-clock dating has significantly influenced our understanding of the timeline of plant evolution. This approach requires the use of priors on the branching process, yet little is known about their impact on divergence time estimates. We investigated the effect of branching priors using the iconic cycads. We conducted phylogenetic estimations for 237 cycad species using three genes and two calibration strategies incorporating up to six fossil constraints to (i) test the impact of two different branching process priors on age estimates, (ii) assess which branching prior better fits the data, (iii) investigate branching prior impacts on diversification analyses, and (iv) provide insights into the diversification history of cycads. Results: Using Bayes factors, we compared divergence time estimates and the inferred dynamics of diversification when using Yule versus birth-death priors. Bayes factors were calculated with marginal likelihood estimated with stepping-stone sampling. We found striking differences in age estimates and diversification dynamics depending on prior choice. Dating with the Yule prior suggested that extant cycad genera diversified in the Paleogene and with two diversification rate shifts. In contrast, dating with the birth-death prior yielded Neogene diversifications, and four rate shifts, one for each of the four richest genera. Nonetheless, dating with the two priors provided similar age estimates for the divergence of cycads from Ginkgo (Carboniferous) and their crown age (Permian). Of these, Bayes factors clearly supported the birth-death prior. Conclusions: These results suggest the choice of the branching process prior can have a drastic influence on our understanding of evolutionary radiations. Therefore, all dating analyses must involve a model selection process using Bayes factors to select between a Yule or birth-death prior, in particular on ancient clades with a potential pattern of high extinction. We also provide new insights into the history of cycad diversification because we found (i) periods of extinction along the long branches of the genera consistent with fossil data, and (ii) high diversification rates within the Miocene genus radiations.
17:43

@rob_lanfear wrote:

Hi All,

I am putting together a collection of alignments with metadata (https://github.com/roblanf/PartitionedAlignments), and I'm looking for advice on file formats. The point of the collection is to make it simpler to test software and compare methods, by providing a well-annotated, tested set of published alignments that are all CC0.

The problem is formats. Each dataset has an alignment, various definitions of sites (i.e. which locus and genome each site comes from), taxon sets (e.g. outgroups), and other metadata (e.g. DOIs for the original study and data set, estimate of the age of the root of the tree, etc). Alignment formats are notoriously varied, so I'd like to stick with one of the standard formats (Nexus, phylip, FASTA), plus at most one more file for metadata (e.g. YAML, CSV).

I'd be happy to hear anyone's thoughts on the various pros and cons of any options.

Cheers,

Rob

Posts: 3

Participants: 3

Read full topic

17:43

@rob_lanfear wrote:

Hi All,

I am putting together a collection of alignments with metadata (https://github.com/roblanf/PartitionedAlignments), and I'm looking for advice on file formats. The point of the collection is to make it simpler to test software and compare methods, by providing a well-annotated, tested set of published alignments that are all CC0.

The problem is formats. Each dataset has an alignment, various definitions of sites (i.e. which locus and genome each site comes from), taxon sets (e.g. outgroups), and other metadata (e.g. DOIs for the original study and data set, estimate of the age of the root of the tree, etc). Alignment formats are notoriously varied, so I'd like to stick with one of the standard formats (Nexus, phylip, FASTA), plus at most one more file for metadata (e.g. YAML, CSV).

I'd be happy to hear anyone's thoughts on the various pros and cons of any options.

Cheers,

Rob

Posts: 3

Participants: 3

Read full topic

17:24
A phylogenetic analysis of the early branching lineages of the monocotyledons is performed using data from two plastid genes (rbcL and matK), five mitochondrial genes (atp1, ccmB, cob, mttB and nad5) and morphology. The complete matrix includes 93 terminals representing Acorus, the 14 families currently recognized within Alismatales, and numerous lineages of monocotyledons and other angiosperms. Total evidence analysis results in an almost completely resolved strict consensus tree, but all data partitions, genomic as well as morphological, are incongruent. The effects of RNA editing and potentially processed paralogous sequences are explored and discussed. Despite a decrease in incongruence length differences after exclusion of edited sites, the major data partitions remain significantly incongruent. The 14 families of Alismatales are all found to be monophyletic, but Acorus is found to be included in Alismatales rather than being the sister group to all other monocotyledons. The placement is strongly supported by the mitochondrial data, atp1 in particular, but it cannot be explained as an artifact caused by patterns of editing or by sampling of processed paralogues.
Source: Cladistics

April 15, 2015

23:25

ARC Postdoctoral Research Associate Human Evolutionary Genetics Australian Centre for Ancient DNA (ACAD), The University of Adelaide Salary: 1.0 FTE, Level A, AU$76,283-81,836 per annum plus up to 17 % Superannuation applies. Project: Biomedical population genetics of ancient human DNA A 3 year post-doctoral position is available on a project using bioinformatics techniques to analyse ancient human biomedical and genomic information, with a focus on the origins and spread of diseases. The position will head an internationally competitive research team working closely with Harvard, Max Planck Institutes, Sanger Centre and UCSD, to develop and apply field leading population genetics approaches. The aim of the program is to trace the evolution and spread of biomedically relevant markers through ancient populations and genomes, using existing and newly generated data. The position will work closely with the new ACAD-Australian National Data Service Online Ancient Genome Repository (OAGR) for ancient human genome and microbiome data, as well as population genetics specialists, archaeologists, and ancient DNA researchers from around the world. The project is situated within the ACAD and will combine state state-of-the-art genetics, bioinformatics, and genomics tools, and is funded by the Australian Research Council (ARC) for a period of 3 years with immediate start. The project is embedded in an ARC Laureate FL140100260 Using ancient genomes and microbiomes to reconstruct human history to Prof. Alan Cooper. The successful applicant will head a team that utilises anthropological and archaeological collections to generate paleogenomics data. While the position focuses on bioinformatics and population genetics analyses, there is scope for the generation of new ancient human data using the large collections of material available at ACAD and collaborators. S/he will develop and integrate analytical methods and pipelines for the analysis of large ancient genomic datasets, and co-supervise a group of postgraduate students in collaboration with overseas colleagues and the Universitys School of Mathematical Sciences. Applicants should have completed a PhD in biomedical genetics, population genetics, bioinformatics, biostatistics, ancient DNA or any relevant discipline, and preferentially have a keen interest in human evolution, disease, and archaeology. The successful appointee will have evidence of strong oral and written communication and organisation skills, demonstrated abilities to publish in scientific journals, present research at international conferences/committees, but also to present research in a meaningful and appealing format to the public. The applicant is expected to be passionate about research, capable of working both independently and as part of a larger team, and have demonstrated leadership skills. Experience with postgraduate student supervision is desirable. Enquires about the job specifications should be directed to Dr Laura Weyrich (laura.weyrich@adelaide.edu.au) or Prof Alan Cooper (alan.cooper@adelaide.edu.au). Interested applicants are encouraged to send a CV including a cover letter detailing, background experience and motivation, and addressing the key selection criteria of the job aspects above. Note applicants are invited to formally apply through the University of Adelaides job listing page at http://bit.ly/1CQmByA. For more information about ACAD, check out (http://bit.ly/1wjI463) for links to Twitter, Facebook, YouTube, our blog, recent publications and our official website. Prof. Alan Cooper, ARC Laureate Fellow Darling Blg (DP 418), Rm 209b University of Adelaide North Terrace Campus South Australia 5005 Australia Email: alan.cooper@adelaide.edu.au Ph: 61-8-8313-5950/3952 Fax: 61-8-8313-4364 http://bit.ly/1wjI463 - blogs, YouTube, Twitter http://bit.ly/1cxzV5T - Official Website CRICOS Provider Number 00123M alan.cooper@adelaide.edu.au via Gmail

Source: EVOLDIR
10:20

The six finalists for the GBIF Ebbe Nielsen Challenge have been announced by GBIF: “The creativity and ambition displayed by the finalists is inspiring’, said Roderic Page, chair of the Challenge jury and the GBIF Science Committee, who introduced the Challenge at GBIF’s 2014 Science Symposium in October.

“My biggest hope for the Challenge was that the biodiversity community would respond with innovative—even unexpected—entries,” Page said. “My expectations have been exceeded, and the Jury is eager to see what the finalists can achieve between now and the final round of judging.”The finalists all receive a €1,000 prize, and now have the possibility to refine their work and compete for the grand prize of €20,000 (€5000 for second place). As the rather cheesy quote above suggests, I think the challenge has been a success in terms of the interest generated, and the quality of the entrants. While the finalists bask in glory, it's worth thinking about the future of the challenge. If it is regarded as a success, should it be run in the same way next year? The first challenge was very open in terms of scope (pretty much anything that used GBIF data), would it be better to target the challenge on a more focussed area? If so, which area needs the nost attention. Food for thought.

Source: iPhylo
10:02

I've put together a working demo of some code I've been working on to discover GBIF records that correspond to museum specimen codes. The live demo is at http://bionames.org/~rpage/material-examined/ and code is on GitHub.

To use the demo, simply paste in a specimen code (e.g., "MCZ 24351") and click Find and it will do it's best to parse the code, then go off to GBIF and see what it can find. Some examples that are fun include MCZ 24351, KU:IT:00312, MNHN 2003-1054, and AMS I33708-051

It's proof of concept at this stage, and the search is "live", I'm not (yet) storing any results. For now I simply want to explore how well if can find matches in GBIF.

By itself this isn't terribly exciting, but it's a key step towards some of the things I want to do. For example, the NCBI is interested in flagging sequences from type specimens (see http://dx.doi.org/10.1093/nar/gku1127 ), so we could imagine taking lists of type specimens from GBIF and trying to match those to voucher codes in GenBank. I've played a little with this, unfortunately there seem to be lots of cases where GBIF doesn’t know that a specimen is, in fact, a type.

Another thing I’m interested in is cases where GBIF has a georeferenced specimen but GenBank doesn’t (or visa versa), as a stepping stone towards creating geophylogenies. For example, in order to create a geophylogeny for Agnotecous crickets in New Caledonia (see GeoJSON and geophylogenies ) I needed to combine sequence data from NCBI with locality data from GBIF.

It’s becoming increasingly clear to me that the data supplied to GBIF is often horribly out of date compared to what is in the literature. Often all GBIF gets is what has been scribbled in a collection catalogue. By linking GBIF records to specimen codes cited that are cited in the literature we could imagine giving GBIF users enhanced information on a given occurrence (and at the same time get citation counts for specimens The impact of museum collections: one collection ≈ one Nobel Prize).

Lastly, if we can link specimens to sequences and the literature, then we can populate more of the biodiversity knowledge graph

Source: iPhylo