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September 2, 2015

23:56

The University of Oregon Institute of Ecology and Evolution (http://bit.ly/15YnlBz) and the Department of Biology invite applications for a tenure-related position (Assistant Professor) in evolutionary biology. We are particularly interested in candidates who use statistical, genomic and/or phylogenetic approaches to study fundamental evolutionary processes at the molecular level, but candidates with exemplary records in other areas of evolutionary biology are also invited to apply. The successful candidate will have an outstanding research program and a commitment to excellence in teaching at the undergraduate and graduate levels. Ph.D. required. Interested persons should apply online to the University of Oregon IE2 SEARCH at http://bit.ly/1JAdmap. Applicants should submit a cover letter, a curriculum vitae, statement of research accomplishments and future research plans, a description of teaching experience and philosophy, and three letters of recom mendation. Submission of up to 3 selected reprints is encouraged. To be assured of consideration, application materials should be uploaded by October 1, 2015, but the search will remain open until the position is filled. 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. http://bit.ly/1LWlJ6a via Gmail

Source: EVOLDIR
15:42

Over the weekend, out of the blue, Dan Whaley commented on an earlier blog post of mine (Altmetrics, Disqus, GBIF, JSTOR, and annotating biodiversity data. Dan is the project lead for hypothes.is, a tool to annotate web pages. I was a bit dismissive as hypothes.is falls into the "stick note" camp of annotation tools, which I've previously been critical of.

However, I decided to take another look at hypothes.is and it looks like a great fit to another annotation problem I have, namely augmenting and correcting OCR text in BioStor (and, by extension, BHL). For a subset of BioStor I've been able to add text to the page images, so you can select that text as you would on a web page or in a PDF with searchable text. If you can select text, you can annotate it using hypothes.is. Then I discovered that not only is hypothes.is a Chrome extension (which immediately limits who will use it), you can add it to any web site that you publish. So, as an experiment I've added it to BioStor, so that people can comment on BioStor using any modern browser.

So far, so good, but the problem is I'm relying on the "crowd" to come along and manually annotate the text. But I have code that can take text and extract geographic localities (e.g., latitude and longitude pairs), specimen does, and taxonomic names. What I'd really like to do is be able pre-process the text, locate these features, then programmatically add those as annotations. Who wants to do this manually when a computer can do most of it?

Hypothesi.is, it turns out, has an API that, while a bit *cough* skimpy on documentation, enables you to add annotations to text. So now I could pre-process the text, and just ask people to add things that have been missed, or flag errors on the automated annotations.

This is all still very preliminary, but as an example here's a screen shot of a page in BioStor together with geographic annotations displayed using hypothes.is (you can see this live here: http://biostor.org/reference/147608/page/1 (make sure you click on the widgets at the top right of the page to see the annotations):

The page shows two point localities that have been extracted from the text, together with a static Google Map showing the localities (hypothesis.is supports Markdown in annotations, which enables links and images to be embedded).

Not only can we write annotations, we can also read them, so if someone adds an annotation (e.g., highlights a specimen code that was missed, or some text that OCR has messed up) we could retrieve that and, for example, index the corrected text to improve findability.

Lots still to do, but these early experiments are very encouraging.

Source: iPhylo
11:00

There seems to be increased interest in the notion that evolutionary history is worthy of management and conservation (see, e.g. Frishkoff et al. 2014; Diniz-Filho et al. 2013). The basic quantity seems to be “phylogenetic diversity” (PD) or the sum of the edge lengths connecting a candidate set of species (Faith 1992). Given a tree or network, one can produce many measures of current (or expected) (contributions to) PD, and these can be modified by other axes of value and expected costs and benefits of interventions. The technical side of the field seems to me to be in some disarray; there are overlapping terms and definitions, weak connections to other literatures (particularly community ecology), and under-tested assumptions. My presentation will offer little or no new data, but I will draw on the work of others in an attempt to partially organize the technical side of the field as I see it. Key issues concerning mapping traits and geographic scale are taken up in the following two presentations in this series.

Source: Phyloseminar
06:17

I have just added another dataset to our database. This one is of considerable interest, because it is a complex one. As the authors note, it is likely to contain ancient hybrid speciation, recent introgression and deep coalescence. Thus, identifying recent hybrids will be problematic.
Michael L. Moody and Loren H. Rieseberg (2012) Sorting through the chaff, nDNA gene trees for phylogenetic inference and hybrid identification of annual sunflowers (Helianthus sect. Helianthus). Molecular Phylogenetics and Evolution 64: 145–155.There are 29 accessions from 13 species, with data for 11 loci in 5 linkage groups (a total of 8,077 aligned nucleotides). The accessions have sequences for either 1 or 2 of the alleles, and sometimes 3 (the latter are likely to be the result of PCR artifacts). The authors have also tried to identify recombinant sequences. Three of the species are previously identified hybrid taxa.

Unfortunately, adding this dataset to the database has also been problematic, because there are internal inconsistencies. For complete consistency, Figure 1 of the paper should agree with its own Table 1, and the GenBank data should agree with both of them. Unfortunately, this three-way consistency exists for only 2 of the 11 loci. For the rest, in 7 instances the dataset is the odd one out, in 4 cases it is the table, and in four instances it is the figure. For the data discrepancies, in 2 cases a sequence is missing, in 1 case there is an extra sequence, and for the remaining 2 pairs it is likely that there is mis-labelling of the sequences.

It is therefore not immediately obvious to what extent this counts as a "gold standard" dataset. I have included it because of its intrinsic interest, but obviously with a caveat emptor warning. Sadly, this sort of situation has been all too common in my search for suitable datasets.

06:00
Background: Acariformes is the most species-rich and morphologically diverse radiation of chelicerate arthropods, known from the oldest terrestrial ecosystems. It is also a key lineage in understanding the evolution of this group, with the most vexing question whether mites, or Acari (Parasitiformes and Acariformes) is monophyletic. Previous molecular studies recovered Acari either as monophyletic or non-monophyletic, albeit with a limited taxon sampling. Similarly, relationships between basal acariform groups (include little-known, deep-soil 'endeostigmatan' mites) and major lineages of Acariformes (Sarcoptiformes, Prostigmata) are virtually unknown. We infer phylogeny of chelicerate arthropods, using a large and representative dataset, comprising all main in- and outgroups (228 taxa). Basal diversity of Acariformes is particularly well sampled. With this dataset, we conduct a series of phylogenetically explicit tests of chelicerate and acariform relationships and present a phylogenetic framework for internal relationships of acariform mites. Results: Our molecular data strongly support a diphyletic Acari, with Acariformes as the sister group to Solifugae (PP =1.0; BP = 100), the so called Poecilophysidea. Among Acariformes, some representatives of the basal group Endeostigmata (mainly deep-soil mites) were recovered as sister-groups to the remaining Acariformes (i. e., Trombidiformes + and most of Sarcoptiformes). Desmonomatan oribatid mites (soil and litter mites) were recovered as the monophyletic sister group of Astigmata (e. g., stored product mites, house dust mites, mange mites, feather and fur mites). Trombidiformes (Sphaerolichida + Prostigmata) is strongly supported (PP =1.0; BP = 98–100). Labidostommatina was inferred as the basal lineage of Prostigmata. Eleutherengona (e. g., spider mites) and Parasitengona (e. g., chiggers, fresh water mites) were recovered as monophyletic. By contrast, Eupodina (e. g., snout mites and relatives) was not. Marine mites (Halacaridae) were traditionally regarded as the sister-group to Bdelloidea (Eupodina), but our analyses show their close relationships to Parasitengona. Conclusions: Non-trivial relationships recovered by our analyses with high support (i.e., basal arrangement of endeostigmatid lineages, the position of marine mites, polyphyly of Eupodina) had been  proposed by previous underappreciated morphological studies. Thus, we update currently the accepted taxonomic classification to reflect these results: the superfamily Halacaroidea Murray, 1877 is moved from the infraorder Eupodina Krantz, 1978 to Anystina van der Hammen, 1972; and the subfamily Erythracarinae Oudemans, 1936 (formerly in Anystidae Oudemans, 1902) is elevated to family rank, Erythracaridae stat. ressur., leaving Anystidae only with the nominal subfamily. Our study also shows that a clade comprising early derivative Endeostigmata (Alycidae, Nanorchestidae, Nematalycidae, and maybe Alicorhagiidae) should be treated as a taxon with the same rank as Sarcoptiformes and Trombidiformes, and the scope of the superfamily Bdelloidea should  be changed. Before turning those findings into nomenclatural changes, however, we consider that our study calls for (i) finding shared apomorphies of the early derivative Endeostigmata clade and the clade including the remaining Acariformes; (ii) a well-supported hypothesis  for Alicorhagiidae placement; (iii) sampling the families Proterorhagiidae, Proteonematalycidae and Grandjeanicidae not yet included in molecular analyses; (iv) undertake a denser sampling of clades traditionally placed in Eupodina, Anystina (Trombidiformes) and Palaeosomata (Sarcoptiformes), since consensus networks and Internode certainty (IC) and IC All (ICA) indices indicate high levels of conflict in these tree regions. Our study shows that regions of ambiguous alignment may provide useful phylogenetic signal when secondary structure information is used to guide the alignment procedure and provides an R implementation to the Bayesian Relative Rates test.
06:00
Background: In the short-term, organisms acclimate to stress through phenotypic plasticity, but in the longer term they adapt to stress genetically. The mutations that accrue during adaptation may contribute to completely novel phenotypes, or they may instead act to restore the phenotype from a stressed to a pre-stress condition. To better understand the influence of evolution on the diversity and direction of phenotypic change, we used Biolog microarrays to assay 94 phenotypes of 115 Escherichia coli clones that had adapted to high temperature (42.2 °C). We also assayed these same phenotypes in the clones’ ancestor under non-stress (37.0 °C) and stress (42.2 °C) conditions. We explored associations between Biolog phenotypes and genotypes, and we also investigated phenotypic differences between clones that have one of two adaptive genetic trajectories: one that is typified by mutations in the RNA polymerase β-subunit (rpoB) and another that is defined by mutations in the rho termination factor. Results: Most (54 %) phenotypic variation was restorative, shifting the phenotype from the acclimated state back toward the unstressed state. Novel phenotypes were more rare, comprising between 5 and 18 % of informative phenotypic variation. Phenotypic variation associated statistically with genetic variation, demonstrating a genetic basis for phenotypic change. Finally, clones with rpoB mutations differed in phenotype from those with rho mutations, largely due to differences in chemical sensitivity. Conclusions: Our results contribute to previous observations showing that a major component of adaptation in microbial evolution experiments is toward restoration to the unstressed state. In addition, we found that a large deletion strongly affected phenotypic variation. Finally, we demonstrated that the two genetic trajectories leading to thermal adaptation encompass different phenotypes.

September 1, 2015

23:46

Tenure-track faculty position in Ecology at The University of Pennsylvania. The Department of Biology at the University of Pennsylvania invites applications for a tenure-track faculty position in Ecology. The appointment will be at the level of Assistant Professor. We are searching broadly for a community or ecosystem ecologist working at any spatial scale, from local to global, and using theoretical and/or empirical approaches. Areas of interest include, but are not limited to, mechanisms of community assembly, coexistence, diversity, adaptation and the interplay between biotic and abiotic processes in the face of climate and land-use change. We welcome applicants working on any domain of life, from micro- to macroscopic. We are especially interested in candidates who utilize novel approaches that span levels of biological organization or transcend traditional boundaries. Penn’s Department of Biology has a long-standing tradition of maintaining an integrated research and educational program across all basic biological sciences, from Ecology and Evolution, Plant Sciences, Molecular and Cellular Biology, Genomics, to Neuroscience. The Department values interdisciplinary research, collaboration, and collegiality, and has a vision emphasizing Life in its Natural Context. Candidates are expected to have demonstrated excellence and productivity in research and will be expected to excel in undergraduate and graduate teaching. Interested candidates should submit materials online at http://bit.ly/1KGj5Qg and include a curriculum vitae, concise statements of research and teaching interests, a short annotated description of up to five publications, and the name and contact information of at least three referees. Recommenders will be contacted by the University with instructions on how to submit a letter to the website. Review of applicants will begin September 11, 2015 and continue until the position is filled. The Department of Biology is strongly committed to Penn’s Action Plan for Faculty Diversity and Excellence and to creating a more diverse faculty (for more information see: http://bit.ly/1eC8Ath). The University of Pennsylvania is an equal opportunity employer. Minorities, women, individuals with disabilities, and protected veterans are encouraged to apply. via Gmail

Source: EVOLDIR
23:29

PhD Student Position studying the genetic basis of adaptation to environmental change Monash University, Melbourne Australia An opportunity is available for two PhD students to join Carla Sgr’s research group in the School of Biological Sciences at Monash University, in Melbourne, Australia. We are seeking creative and motivated students who wish to carry out original research on the genetic basis of adaptation to environmental change. Individuals with a background in evolutionary biology, quantitative genetics or evolutionary genetics are invited to apply. Those with strong quantitative and computational skills are particularly encouraged. Specific projects are flexible, potentially interdisciplinary, and include opportunities to carry out new research in experimental evolutionary biology. Specific research plans will be developed in collaboration with each successful candidate, and tailored to match their individual interests and strengths. To find out more about the interests of my group, please visit www.carlasgrolab.org. Successful candidates will be fully funded for 3.5 years, for full time research, and with no teaching requirements. The annual stipend is approximately $25,000 AUD, tax-free, and additional expenses for research, coursework, and conference attendance (once per year) will also be covered. Both Australian/NZ domestic and international students are eligible to apply. Domestic candidates will be invited to apply for an Australian Postgraduate Award, and if successful, will be awarded an annual tax-free stipend of approximately $25,000 AUD. Top ranked candidates receive a top-up scholarship of $5,000 and students moving interstate or from NZ are eligible for a one-off moving scholarship of $3,000. All Monash PhD students also receive approximately $3,000 worth of travel funds to attend conferences during their degree. Monash University is a member of Australia’s Group of Eight coalition, and is internationally recognized for excellence in research and teaching. The School of Biological Sciences is home to a collegial and interdisciplinary research environment, with strengths in ecology, genetics and evolutionary biology. The Monash doctoral program includes additional training opportunities beyond the research program that enhance employability post degree. Monash is located in Melbourne, one of the most liveable cities in the world and a cultural and recreational hub. To apply, please send a CV, academic transcript, and a brief outline of research interests and goals to carla.sgro@monash.edu. Informal inquiries are also welcome at the same address. Applicants must hold a Bachelor’s degree with first-class honours, or a master’s degree. Review of applications will begin immediately, and short-listed candidates will be contacted to set up phone/Skype interviews. Dr Carla M. Sgr Associate Professor and ARC Future Fellow School of Biological Sciences Building 18, Monash University Clayton Campus Wellington Rd, Clayton 3800 Melbourne, Victoria Australia Email: carla.sgro@monash.edu http://bit.ly/1hx3WVJwww.carlasgrolab.org. Successful candidates will be fully funded for 3.5 years, for full time research, and with no teaching requirements. The annual stipend is approximately $25,000 AUD, tax-free, and additional expenses for research, coursework, and conference attendance (once per year) will also be covered. Both Australian/NZ domestic and international students are eligible to apply. Domestic candidates will be invited to apply for an Australian Postgraduate Award, and if successful, will be awarded an annual tax-free stipend of approximately $25,000 AUD. Top ranked candidates receive a top-up scholarship of $5,000 and students moving interstate or from NZ are eligible for a one-off moving scholarship of $3,000. All Monash PhD students also receive approximately $3,000 worth of travel funds to attend conferences during their degree. Monash University is a member of Australia’s Group of Eight coalition, and is internationally recognized for excellence in research and teaching. The School of Biological Sciences is home to a collegial and interdisciplinary research environment, with strengths in ecology, genetics and evolutionary biology. The Monash doctoral program includes additional training opportunities beyond the research program that enhance employability post degree. Monash is located in Melbourne, one of the most liveable cities in the world and a cultural and recreational hub. To apply, please send a CV, academic transcript, and a brief outline of research interests and goals to carla.sgro@monash.edu. Informal inquiries are also welcome at the same address. Applicants must hold a Bachelor’s degree with first-class honours, or a master’s degree. Review of applications will begin immediately, and short-listed candidates will be contacted to set up phone/Skype interviews. Dr Carla M. Sgr Associate Professor and ARC Future Fellow School of Biological Sciences Building 18, Monash University Clayton Campus Wellington Rd, Clayton 3800 Melbourne, Victoria Australia Email: carla.sgro@monash.edu http://bit.ly/1hx3WVJ carla.sgro@monash.edu via Gmail

Source: EVOLDIR
17:26

@mathmomike wrote:

Does anyone know references or previous work to the following three questions:

  1. Consider the graph G_NNI of unrooted binary phylogenetic trees on leaf set {1,..,n} where two trees form an edge if they are one NNI apart. Similarly G_SPR (where trees are joined if they are one SPR apart). Both these graphs are regular (each tree has the same number of neighbors) so if you start anywhere then after a while you will be at each tree with (asymptotically) uniform probability - the question is what is the mixing time (time to be near uniform as a function of n) for this random walk? Note I'm not talking about data (or Bayesian methods) here - just a pure mixing time question regarding this discrete graph. Does anyone know a paper that studies this (I think I saw one once, but all my papers/notes got lost in the 2010/2011 earthquakes here!).

  2. There are various notions of the centre of a tree - e.g. the "centroid" (explained very nicely in the recent Tanglegrams paper by Matsen/Billey/Kas/Konvalinka paper on ArXiv). However does anyone know any paper that discusses what we might call a 'leaf-centroid'. Given a tree T call a vertex v of T a leaf-centroid if each of the components of T-v contains at most half of the leaves of T. If T has no vertices of degree 2 then (just like the centroid) a tree either has a unique leaf-centroid or two adjacent leaf centroids. However even for this class ( trees without vertices of degree 2) the leaf-centroid can be different from the centroid! Just wondering if anyone has seen this notion mentioned or studied before?

  3. Anyone know an early (pre-1960s) reference to the simple but fundamental result: A collection C of nonempty subsets of X (including X) forms a hierarchy (nested family) if and only if C is the set of clusters of a rooted X-tree? It may be implicit in Linneaus (or even Aristotle!) but some more explicitly mathematical statement would be good.

Any advice will help for a book ('mathematical phylogeny') that I'm now half-way through writing I might ask a few further questions over the coming month or two.

Posts: 1

Participants: 1

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06:00
Background: Eurypterids are a diverse group of chelicerates known from ~250 species with a sparse Ordovician record currently comprising 11 species; the oldest fully documented example is from the Sandbian of Avalonia. The Middle Ordovician (Darriwilian) fauna of the Winneshiek Lagerstätte includes a new eurypterid species represented by more than 150 specimens, including some juveniles, preserved as carbonaceous cuticular remains. This taxon represents the oldest described eurypterid, extending the documented range of the group back some 9 million years. Results: The new eurypterid species is described as Pentecopterus decorahensis gen. et sp. nov.. Phylogenetic analysis places Pentecopterus at the base of the Megalograptidae, united with the two genera previously assigned to this family by the shared possession of two or more pairs of spines per podomere on prosomal appendage IV, a reduction of all spines except the pair on the penultimate podomere of appendage V, and an ornamentation of guttalate scales, including angular scales along the posterior margin of the dorsal tergites and in longitudinal rows along the tergites. The morphology of Pentecopterus reveals that the Megalograptidae are representatives of the derived carcinosomatoid clade and not basal eurypterids as previously interpreted. Conclusions: The relatively derived position of megalograptids within the eurypterids indicates that most eurypterid clades were present by the Middle Ordovician. Eurypterids either underwent an explosive radiation soon after their origination, or earlier representatives, perhaps Cambrian in age, remain to be discovered. The available instars of Pentecopterus decorahensis suggest that eurypterids underwent extreme appendage differentiation during development, a potentially unique condition among chelicerates. The high degree of appendage specialization in eurypterids is only matched by arachnids within chelicerates, supporting a sister taxon relationship between them.
04:52

A little over a week ago I was at the 6th International Barcode of Life Conference, held at Guelph, Canada. It was my first barcoding conference, and was quite an experience. Here are a few random thoughts.

AttendeesIt was striking how diverse the conference crowd was. Apart from a few ageing systematists (including veterans of the cladistics wars), most people were young(ish), and from all over the world. There clearly something about the simplicity and low barrier to entry of barcoding that has enabled its widespread adoption. This also helps give barcoding a cohesion, no matter what the taxonomic group or the problem you are tackling, you are doing much the same thing as everybody else (but see below). While ageing systematists (like myself) may hold their noses regarding the use of a single, short DNA sequence and a tree-building method some would dismiss as "phenetic", in many ways the conference was a celebration of global-scale phylogeography.

Awesome drone footage from #DNAbarcodes2015. Thanks to everyone who helped make this conference so fantastic!!! https://t.co/37nYuIxGuz

— Mike Wright (@MIKEisWRIGHT20) August 22, 2015

Standards aren't enoughAnd yet, standards aren't enough. I think what contributes to DNA barcoding's success is that sequences are computable. If you have a barcode, there's already a bunch of barcodes sequences you can compare yours to. As others add barcodes, your sequences will be included in subsequent analyses, analyses which may help resolve the identity of what you sequenced.

To put this another way, we have standard image file formats, such as JPEG. This means you can send me a bunch of files, safe in the knowledge that because JPEG is a standard I will be able to open those files. But this doesn't mean that I can do anything useful with them. In fact, it's pretty hard to do anything with images part from look at them. But if you send me a bunch of DNA sequences for the same region, I can build a tree, BLAST GenBank for similar sequences, etc. Standards aren't enough by themselves, to get the explosive growth that we see in barcodes the thing you standardise on needs to be easy to work with, and have a computational infrastructure in place.

Next generation sequencing and the hacker cultureClassical DNA barcoding for animals uses a single, short mtDNA marker that people were sequencing a couple of decades ago. Technology has moved on, such that we're seeing papers such as An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. As I've argued earlier (Is DNA barcoding dead?) this misses the point about the power of standardisation on a simple, scalable method.

At the same time, it was striking to see the diversity of sequencing methods being used in conference presentations. Barcoding is a broad church, and it seemed like it was a natural home for people interested in environmental DNA. There was excitement about technologies such as the Oxford Nanopore MinION™, with people eager to share tips and techniques. There's something of a hacker culture around sequencing (see also Biohackers gear up for genome editing), just as there is for computer hardware and software.

Community

So this happened #dnabarcodes2015 pic.twitter.com/EQ6OqNSTjn

— Kevin Morey (@moreykev94) August 21, 2015 The final session of the conference started with some community bonding, complete with Paul Hebert versus Quentin Wheeler wielding light sables. If, like me, you weren't a barcode, things started getting a little cult-like. But there's no doubt that Paul's achievement in promoting a simple approach to identifying organisms, and then translating that into a multi-million dollar, international endeavour is quite extraordinary.

After the community bonding, came a wonderful talk by Dan Janzen. The room was transfixed as Dan made the case for conservation, based on his own life experiences, including Area de Conservación Guanacaste where he and Winnie Hallwachs have been involved since the 1970s. I sat next to Dan at a dinner after the conference, and showed him iNaturalist, a great tool for documenting biodiversity with your phone. He was intrigued, and once we found pictures taken near his house in Costa Rica, he was able to identify the individual animals in the photos, such as a bird that has since been eaten by a snake.

Dark taxaMy own contribution to the conference was a riff on the notion of dark taxa, and mostly consisted of me trying think through how to respond to DNA barcoding. Two graphs, three responses from Roderic Page The three responses to barcoding that I came up with are:
  1. By comparison to barcoding, classical taxonomy is digitally almost invisible, with great chunks of the literature still not scanned or accessible. So, one response is to try and get the core data of taxonomy digitised and linked as fast as possible. This is why I built BioStor and BioNames, and why I continually rant about the state of efforts to digitise taxonomy.
  2. This is essentially President Obama's "bucket" approach, maybe the sane thing to do is see barcoding as the future and envisage what we could do in a sequence only world. This is not to argue that we should ignore the taxonomic literature as such, but rather lets start with sequences first and see what we can do. This is the motivation for my Displaying a million DNA barcodes on Google Maps using CouchDB, and my experiments with Visualising Geophylogenies in Web Maps Using GeoJSON. These barely scratch the surface of what can be done.
  3. The third approach is to explore how we integrate taxonomy and barcoding at global scale, in which case linking at specimen level (rather, than, say using taxonomic names) seems promising, albeit requiring a massive effort to reconcile multiple specimen identifiers.

Summary

@rdmpage Thanks for spreading the word! Looks like an interesting conference, which is a rare thing indeed.

— Nakensnegl (@kueda) August 23, 2015 Yes, the barcoding conference was that rare thing, a well organised (including well-fed), interesting, indeed eye-opening, conference.

Source: iPhylo
03:26
PhD position in theory/analysis of gene regulation A PhD position is available in the group of Prof. Erik van Nimwegen at the Biozentrum of the University of Basel and Swiss Institute of Bioinformatics (http://bit.ly/1FfckPo). We are looking for highly motivated individuals with strong mathematical and computational skills that are interested to perform theoretical and computational research in the area of gene regulation. Our research group is highly interdisciplinary, involving both an experimental section where researchers with a background in molecular biology are experimentally studying genome evolution and gene regulation at the single cell level in bacteria, and a theoretical section where researchers with backgrounds in theoretical physics, computer science, and applied mathematics are using techniques from Bayesian probability, evolutionary theory, dynamical systems theory, and stochastic processes, to study the function and evolution of genome-wide regulatory networks in cells. We are particularly interested in uncovering the principles by which genome-wide regulatory networks specify and maintain cell identity in multi-cellular organisms, how cells control and exploit the noise in gene regulatory processes, and how gene regulation evolves. A list of our group’s publications can be found http://bit.ly/1MZBckp . Our lab also takes part in a number of collaborative projects within Switzerland including StoNets, which studies the ways in which cells control and exploit stochasticity in gene regulatory networks, and BrainStemX, which studies the gene regulatory networks underlying mammalian forebrain development. The precise topic of the PhD research project will be determined jointly with the candidate and candidates that display initiative and independence will be given priority. Candidates should have strong mathematical and computational skills, and experience in such areas as stochastic processes, dynamical systems theory, and Bayesian statistics is a plus. Candidates do not necessarily have to have a biological background but should have a strong desire to directly work with experimental biological data and collaborate with experimental biologists. The candidates should have a good knowledge of English. German is helpful but not necessary. The salary is generous and is set according to the guidelines of the Swiss National Science Foundation. The start date will by mutual arrangement. Basel is a very international city and a center of life science research, with over 900 life science research companies in the area, including Novartis and Roche. Several other academic institutions are also in the city, including the Friedrich Miescher Institute, the ETH Zurich Biosystems Science and Engineering Department, and the Swiss Tropical Institute. The city is less than 5km from both France and Germany and an hour and a half from the Swiss Alps. To apply, please send a single pdf containing your application letter, CV, and the names of two references to erik.vannimwegen-at-unibas.ch Review of applications will begin immediately. Thomas Julou via Gmail
Source: EVOLDIR
03:26
Post-doc position in computational genomics/gene regulatory networks A post-doctoral position is available in the group of Prof. Erik van Nimwegen (http://bit.ly/1FfckPo) at the Biozentrum of the University of Basel and Swiss Institute of Bioinformatics. We are looking for highly motivated individuals with strong mathematical and computational skills that are interested to perform theoretical research in computational genomics, genome-wide regulatory networks, and stochastic gene regulation in single cells. Our research group is highly interdisciplinary, involving both an experimental section where researchers with a background in molecular biology are experimentally studying genome evolution and gene regulation at the single cell level in bacteria, and a theoretical section where researchers with backgrounds in theoretical physics, computer science, and applied mathematics are using techniques from Bayesian probability, evolutionary theory, dynamical systems theory, and stochastic processes, to study the function and evolution of genome-wide regulatory networks in cells. We are particularly interested in uncovering the principles by which genome-wide regulatory networks specify and maintain cell identity in multi-cellular organisms, how cells control and exploit the noise in gene regulatory processes, and how gene regulation evolves. A list of our groups publications can be found at http://bit.ly/1MZBckp . Our lab also takes part in a number of collaborative projects within Switzerland including StoNets, which studies the ways in which cells control and exploit stochasticity in gene regulatory networks, and BrainStemX, which studies the gene regulatory networks underlying mammalian forebrain development. For this position we are in particular looking for candidates that are interested in developing methods for the analysis of next-generation sequencing data, including RNA-seq, single-cell RNA-seq, and ChIP-seq data. The precise topic of the research project will be determined jointly with the candidate and candidates that display initiative and independence will be given priority. Candidates should have strong mathematical and computational skills, and experience in such areas as stochastic processes, dynamical systems theory, and Bayesian statistics is a plus. Experience with next-generation sequencing data is desirable but not strictly required. Candidates do not necessarily have to have a biological background but should have a strong desire to directly work with experimental biologists. The candidates should have a good knowledge of English. German is helpful but not necessary. The salary is generous and is set according to the guidelines of the Swiss National Science Foundation. The start date will be by mutual arrangement. Basel is a very international city and a center of life science research, with over 900 life science research companies in the area, including Novartis and Roche. Several other academic institutions are also in the city, including the Friedrich Miescher Institute, the ETH Zurich Biosystems Science and Engineering Department, and the Swiss Tropical Institute. The city is less than 5km from both France and Germany and an hour and a half from the Swiss Alps. To apply, please send a single pdf containing your application letter, CV, and the names of two references to erik.vannimwegen-at-unibas.ch Review of applications will begin immediately. Thomas Julou via Gmail
Source: EVOLDIR
03:26
Free summer school (July 3rd-9th 2016): Introduction to the concepts and methods of networks in evolutionary studies (sequence similarity networks, genome networks and bipartite graphs) This summer school will be held in Roscoff, France, between July 3rd 2016 (date of arrival) and July 9th (date of departure) (http://bit.ly/1FfckPh). This school is designed in priority for biologists and bio-informaticians (completing a PhD degree or currently post-doctoral fellows), who wish to learn the bases of network analyses. The main notions (regarding various types of networks, the relevance of their analyses, and some bases in graph theory) will be introduced by short theoretical classes, followed by practical case-studies, introducing the basics in programming required to run such network analyses as well as to use the existing software/tools. Our goal is that, by the end of this summer school, all applicants will be qualified to perform network analyses of their own datasets. More precisely, we will focus on the following concepts and methods: - Introgressive evolution and large-scale diversity studies. - Construction and analysis of sequence similarity networks (construction and sorting of connected components, definition of gene families, search for composite genes, implementation of centrality measures) - Construction and analysis of genome networks (construction of weighted genome networks, implementation of their diameter, shortest paths, analyses of labeled nodes, etc.) - Construction and analysis of gene-genome bipartite graphs (detection of connected components, and their articulation points, and twins) In addition, conferences on networks and evolution will be delivered by leading scientists during this school. Expected speakers feature : Fernando Baquero, Robert Beiko, Marco Fondi, Michel Habib, Philippe Huneman, Mattis List, Philippe Lopez, and Marc-Andr Slosse. This summer school is funded by ERC grant (FP7/2007-2013 Grant Agreement # 615274). Hence, registration is free, housing and food (breakfast, lunch and dinner) are also fully covered. Applicants will only need to fund their travel to Roscoff. 10 places only are available, with a mandatory requirement: applicants must show basic computer skills (i.e. to be familiar with Linux environment and with at least one programming language, preferably R or Python). Applications are to be submitted asap, and no later than January 15th 2016, by email to : eric.bapteste@upmc.fr , and contain a brief letter describing why this class will be of significant interest for the applicant and his/her future studies. Applicants will be selected based on their motivation, and their resume, including the names of two scientific referees. We are excited to meet you soon in Roscoff. Eric Bapteste + Philippe Lopez Bapteste Eric via Gmail
Source: EVOLDIR

August 30, 2015

16:30

Last week I blogged about Spinach and the iron fallacy. I analysed an early set of data by Thomas Richardson (1848), who calculated the amount of iron in combusted ash for various vegetables and fruits, and showed that spinach is not at all unusual in its constituents. The idea that spinach is rich in iron is untrue, and the story about a mis-placed decimal point seems to be nothing more than an urban myth.

In the meantime, Joachim Dagg, at the Natural History Apostilles blog, has reanalysed Richardson's data and revealed that The first source for the spinach-iron myth is likely to have been a somewhat inappropriate attempt to combine his data for the percent iron values in relation to the ash with the percent values of the ashes in in relation to the fresh matter.

So, I have recalculated the phylogenetic network using these "adjusted" values. I used the percent values of the chemical constituents in relation to the pure ash (raw ash minus carbonic acid, charcoal and sand), and combined them with the percent values of the ashes. The issue here is that radish roots and leaves have the largest ash values, followed by cherry stems and spinach. This leads to an over-statement of the chemical contents. In particular, the iron content moves spinach from being ranked sixth to second (behind radish foliage, which is not usually eaten).


August 29, 2015

23:36
The Hughes Lab is seeking a Postdoctoral Scholar to work on PlantVillage. This position is in collaboration with the lab of Dr Marcel Salathe at EPFL, Switzerland who together with Hughes is the co-founder of PlantVillage. The position is available in the Centre for Infectious Disease Dynamics (www.cidd.psu.edu), The Pennsylvania State University, University Park Campus. PlantVillage (www.plantvillage.com) wants to impact global food production by making the knowledge needed to increase crop yields immediately available to all growers around the world. Agriculture was humanitys first and arguably most important knowledge society. It was knowledge that led to crop domestication and the many improvements in the subsequent 10,000 years, providing the foundation for modern civilization. But the knowledge is not available everywhere. The move towards universal access to broadband via mobile devices offers the promise of democratizing access. The smartphone platform PlantVillage is already doing that. PlantVillage makes available thousands of pages and images of high quality, science-based knowledge on plant health. This is free to anyone with a smartphone or Internet connection. We provide any grower, anywhere, the essential knowledge they need. In addition, we provide the world`s largest social network within a community platform of global experts. Post a question and the global community answers it. Using our platform, growers are not limited by their lack of access to knowledge and so can get the latest advice on nutrient delivery, pest management and cultivation, as well as where to source seeds and sell produce. The Postdoctoral Scholar position at Penn State involves the development of approaches that facilitate the automatic identification of plant diseases via smartphones. This involves codifying both the diseases and the decisions plant pathologists make. This is important for the development of eventual algorithms that automate disease diagnosis. The ideal candidate will have a range of applicable skills including plant pathology, image recognition of diseases, biostatistics and modeling disease in plants. The position also requires contributing to the PlantVillage database by collecting images of healthy and diseased plants as well as adding content to the PlantVillage library. The candidate should also engage in the community Q&A portion of PlantVillage as well as liaising with a diverse group of stakeholders interested in disease detection in crops. This position will involve travel to field sites both nationally and internationally to source images. Candidates should demonstrate a track record of publication; have extremely strong organizational, written, and oral communication skills; and be able to work both independently and as part of a collaborative team. This position is initially funded for one year, with the possibility of a second year. For further information, please feel free to contact Dr Hughes (dph14@psu.edu; +1 814- 863-6073). Interested applicants should upload a curriculum vitae, a 1-2 page statement of research interests that explicitly describes professional qualifications for this position, and contact information for three referees. Review of applicants is ongoing and the position will begin when a suitable candidate is selected. The Pennsylvania State University requires all applicants to register and complete the application form at the Penn State employment website at http://bit.ly/1KuA1ZTwww.cidd.psu.edu), The Pennsylvania State University, University Park Campus. PlantVillage (www.plantvillage.com) wants to impact global food production by making the knowledge needed to increase crop yields immediately available to all growers around the world. Agriculture was humanitys first and arguably most important knowledge society. It was knowledge that led to crop domestication and the many improvements in the subsequent 10,000 years, providing the foundation for modern civilization. But the knowledge is not available everywhere. The move towards universal access to broadband via mobile devices offers the promise of democratizing access. The smartphone platform PlantVillage is already doing that. PlantVillage makes available thousands of pages and images of high quality, science-based knowledge on plant health. This is free to anyone with a smartphone or Internet connection. We provide any grower, anywhere, the essential knowledge they need. In addition, we provide the world`s largest social network within a community platform of global experts. Post a question and the global community answers it. Using our platform, growers are not limited by their lack of access to knowledge and so can get the latest advice on nutrient delivery, pest management and cultivation, as well as where to source seeds and sell produce. The Postdoctoral Scholar position at Penn State involves the development of approaches that facilitate the automatic identification of plant diseases via smartphones. This involves codifying both the diseases and the decisions plant pathologists make. This is important for the development of eventual algorithms that automate disease diagnosis. The ideal candidate will have a range of applicable skills including plant pathology, image recognition of diseases, biostatistics and modeling disease in plants. The position also requires contributing to the PlantVillage database by collecting images of healthy and diseased plants as well as adding content to the PlantVillage library. The candidate should also engage in the community Q&A portion of PlantVillage as well as liaising with a diverse group of stakeholders interested in disease detection in crops. This position will involve travel to field sites both nationally and internationally to source images. Candidates should demonstrate a track record of publication; have extremely strong organizational, written, and oral communication skills; and be able to work both independently and as part of a collaborative team. This position is initially funded for one year, with the possibility of a second year. For further information, please feel free to contact Dr Hughes (dph14@psu.edu; +1 814- 863-6073). Interested applicants should upload a curriculum vitae, a 1-2 page statement of research interests that explicitly describes professional qualifications for this position, and contact information for three referees. Review of applicants is ongoing and the position will begin when a suitable candidate is selected. The Pennsylvania State University requires all applicants to register and complete the application form at the Penn State employment website at http://bit.ly/1KuA1ZT David Hughes: Hughes, is a behavioral ecologist who has studied social insects and their diseases in 11 countries on 5 continents. He has worked with diverse diseases as well as the behavior of healthy and infected ants under field (rain- and temperate forests) and laboratory conditions. In recent years he has become interested in plant diseases. www.hugheslab.com Penn State is an equal opportunity, affirmative action employer, and is committed to providing employment opportunities to all qualified applicants without regard to race, color, religion, age, sex, sexual orientation, gender identity, national origin, disability or protected veteran status. David Hughes CIDD, Dept Entomology & Biology, Penn State www.hugheslab.com www.plantvillage.com dhughes@psu.edu twitter: @zombieantguy, @plantvillage 814 863 6073 (Office) 814 777 7366 (Cell) David Hughes via Gmail
Source: EVOLDIR
14:39

@ss107 wrote:

The rate matrix (Q) for Jukes-Cantor generally is expressed as described here: https://en.wikipedia.org/wiki/Models_of_DNA_evolution#Most_common_models_of_DNA_evolution

The factor (1/4) comes because the base frequency is 0.25 in Jukes-Cantor analysis and μ is the rate of substitution.

The transition/probability matrix [P(t)] for any branch length (t) is the exponentiation of Q multiplied by t.

What I understand is: The matrix P will be entirely different if the substitution rate μ have two different values (say 0.25 and 1).

The question I have: Is there any restriction on the value of μ?

Related software packages like SeqGen/MrBayes expresses the rate matrix in terms of six rates {AC, AG, AT, CG, CT, GT} which all equals μ in this discussion.

From the examples from the related manuals, I think they normalize the rates such that their sum would be 1. That means, for JC, 6 μ = 1 always!

Generally, the substitution rates are taken as input either as percentages of the rate sum or they are scaled to the GT rate. I believe this information is not enough to decide the actual rate.

In simple terms, for JC, saying,

AC = AG = AT = CG = CT = GT

is not enough. You have to explicitly tell what the value is. Based on that value, the transition/probability matrix can change drastically.

If I always normalize the values then rate matrix for JC reduces to a matrix with static values.

I know some of my understanding is wrong. Where am I wrong?

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02:24
Post-doctoral position in molecular evolution Three two-year post-doctoral positions are available in the Ellegren lab at the Evolutionary Biology Centre, Uppsala University, Sweden (http://bit.ly/1IsgBil). Two positions are broadly defined as population genomics and one as molecular evolution (presented below), although there is some extent of overlap both in terms of concepts and data used among the positions. We are interested in how sequence evolution and evolution of base-composition are related to factors such as epigenetic modifications, life history and recombination. Avian genomes are in focus for our research (allowing analyses of highly heterogeneous recombination landscapes) and we perform whole-genome re-sequencing of population samples to obtain detailed estimates of the site-frequency spectrum. Examples of on-going work are studies of methylation in avian genomes based on whole-genome bisulfite sequencing and how methylation affects substitution patterns and gene expression, how GC-biased gene conversion give genomic signals mimicking those of selection (and how signals of gBGC and selection can be separated), and the link between life history and rates of diversity/divergence. The specific questions to be addressed will be decided in dialogue with the successful candidate and will depend on her/his interests and background. Recent publications from the group relating to the project include Weber et al 2014 Genome Biology 15:542 and 15:549; Mugal et al 2015 G3 5:441-447; Smeds et al 2015 Nature Communications 6:7330; Uebbing et al 2015 Mol Biol Evol, in press. Suitable background to this position is a PhD geared toward molecular evolution, population genetics, or bioinformatics. Experience from bioinformatic analyses of next-generation sequencing data is of merit. Start date is flexible, ideally before January 1, 2016. The position can be extended for up to two more years. For full consideration, please send application materials by September 18, 2015. Interested candidates should submit the following to Hans.Ellegren@ebc.uu.se - a cover letter stating research interests, - CV, including publication record - a short (1-2 page) description of research accomplishments, - email addresses and phone numbers of three references Please feel free to contact me at the above email address with questions. The venue for the position, the Evolutionary Biology Centre, is situated in central Uppsala. The working atmosphere is international with the great majority of PhD students and post-docs recruited from abroad. The Centre constitutes an exciting arena for multidisciplinary research in evolutionary biology in a broad sense, housing some 300 scientists and graduate students. The scientific environment with numerous seminars, journal clubs and social activities offer excellent possibilities for contacts and collaborations. Local platforms for high-performance computational analyses (http://bit.ly/SetGti), NGS, SNP genotyping and proteomic analyses (http://bit.ly/17a7QLt) ensure immediate access to state-of-the-art technology. Uppsala University is the oldest university in Scandinavia and the city of Uppsala is a vibrant student town with beautiful and easy accessible surroundings conveniently situated close to Stockholm. The Ellegren group is part of the Department of Evolutionary Biology (http://bit.ly/1DLY70Z), which is a branch of the larger Department of Ecology and Genetics (http://bit.ly/1L4KtWv). The Department of Evolutionary Biology houses 8 independent research groups and about 25 PhD students, 25 postdocs, and several bioinformaticians. A common theme is that we address key questions in evolutionary biology, like speciation, local adaptation, life history evolution, genome and molecular evolution, using genomic approaches. We have tight connections with several other research groups in the Department of Ecology and Genetics within the Evolutionary Biology Centre. Professor Hans Ellegren Department of Evolutionary Biology Evolutionary Biology Centre Uppsala University Norbyvägen 18D SE-752 36 Uppsala Sweden Email: Hans.Ellegren@ebc.uu.se LAB WEB PAGE: http://bit.ly/1IsgBil Hans Ellegren via Gmail
Source: EVOLDIR
02:09
ASSISTANT PROFESSOR IN COMPUTATIONAL BIOLOGY/GENOMICS The Department of Biology at Washington University in St. Louis (http://bit.ly/17dDCTv ) invites applications for a tenuretrack faculty position at the Assistant Professor level from candidates whose research employs computational and/or genomicscale approaches to answer important biological and/or evolutionary questions. We seek an innovative and accomplished scientist whose research program will complement and diversify existing departmental areas including epigenetics in plant/animal/microbial systems, developmental biology. The successful candidate will have an appointment at the rank of Assistant Professor in the Department of Biology and is expected to establish an externally funded research program. Contributions to both undergraduate and graduate teaching and research mentoring are required. Duties will also include writing research publications, serving as a formal advisor to undergraduate students, and participating in departmental committees and university service. Qualifications include a PhD degree and strong research, mentoring and teaching credentials. Competitive start-up funding, laboratory development resources and ancillary support commensurate with the candidate’s qualifications and needs are available with this position. Consideration of applicants will begin on October 1, 2015 and will continue until the position is filled. Applicants should submit the following materials in a single pdf file format: cover letter; current curriculum vitae; separate statements of research and teaching interests; and the names and contact information of three individuals who can serve as references upon request. Application materials must be submitted electronically to: computationalsearch@wustl.edu Questions regarding the search process should be directed to Douglas Chalker (dchalker@wustl.edu), Chair of the Search Committee. Washington University is committed to excellence through diversity, and we particularly encourage applications from persons from underrepresented groups. Washington University is an Affirmative Action Employer “Musick, Judy” via Gmail
Source: EVOLDIR
01:54
Two post-doctoral positions in population genomics Three two-year post-doctoral positions are available in the Ellegren lab at the Evolutionary Biology Centre, Uppsala University, Sweden (http://bit.ly/1IsgBil). Two positions are broadly defined as population genomics (presented below) and one as molecular evolution, although there is some extent of overlap both in terms of concepts and data used among the positions. 1. Population genomics We use flycatchers of the genus Ficedula to study evolutionary processes related to the evolution of heterogeneous genomic landscapes of species differentiation (e.g. Ellegren et al 2012 Nature 491:756-760). There is increasing evidence that genomic regions with elevated differentiation (‘differentiation islands’) can evolve by processes unrelated to speciation. For example, the concept of linked selection, which is particularly pronounced in low-recombining regions, will locally reduce the effective population size and thereby enhance genetic drift of segregating variants. Pursuing these studies using haplotype-based statistics and NGS-data from sequencing platforms generating long reads is one possible direction of research for the post-doc. Other directions include, for example, demographic analyses and studies of the recombination landscape. The specific questions to be addressed will be decided in dialogue with the successful candidate and will depend on her/his interests and background. Recent publications from the group relating to the project include Nadachowska-Brzyska et al 2015 Current Biology 25:1375-1380; Nater et al 2015 Systematic Biology, in press; Smeds et al. 2015 Nature Communications 6:7330; Suh et al 2015 PLoS Biology 13:1002224. 2. Population genomics The wolf was once widespread in Scandinavia, as well as in other parts of Europe, but long-term persecution led to its extinction by the 1960s. Two animals founded a new population in Sweden in the 1970s and a limited number of immigrants have subsequently become integrated with the population and it has grown to several hundreds of individuals. The population is highly inbred (inbreeding coefficient of newborns is currently 0.25 on average) and there are signs of inbreeding depression. We are now conducting whole-genome re-sequecning of 100 animals sampled from throughout the time period since the new population was founded. The post-doc will be responsible for analysing these data with the aims of investigating the rate of allelic loss, the extent and distribution of genomic regions identical-by-descent, the genomic contribution of each founder to the extant population, and to compare genetic relationships derived from the pedigree and genome sequence data. Several other research questions can apply as well. The project is a collaboration with Grimso Wildlife Research Station of the Swedish University of Agricultural Sciences. Suitable background to these position is a PhD geared toward evolutionary biology, population genetics, or bioinformatics. Experience from bioinformatic analyses of next-generation sequencing data is of merit. Depending on the direction of research to be taken, experience of demographic modeling, molecular evolutionary analyses or conservation biology could also be of merit. Start date is flexible, ideally before January 1, 2016. The positions can be extended for up to two more years. For full consideration, please send application materials by September 18, 2015. Interested candidates should submit the following to Hans.Ellegren@ebc.uu.se - a cover letter stating research interests, - CV, including publication record - a short (1-2 page) description of research accomplishments, - email addresses and phone numbers of three references Please feel free to contact me at the above email address with questions. The venue for the positions, the Evolutionary Biology Centre, is situated in central Uppsala. The working atmosphere is international with the great majority of PhD students and post-docs recruited from abroad. The Centre constitutes an exciting arena for multidisciplinary research in evolutionary biology in a broad sense, housing some 300 scientists and graduate students. The scientific environment with numerous seminars, journal clubs and social activities offer excellent possibilities for contacts and collaborations. Local platforms for high-performance computational analyses (http://bit.ly/SetGti), NGS, SNP genotyping and proteomic analyses (http://bit.ly/17a7QLt) ensure immediate access to state-of-the-art technology. Uppsala University is the oldest university in Scandinavia and the city of Uppsala is a vibrant student town with beautiful and easy accessible surroundings conveniently situated close to Stockholm. The Ellegren group is part of the Department of Evolutionary Biology (http://bit.ly/1DLY70Z), which is a branch of the larger Department of Ecology and Genetics (http://bit.ly/1L4KtWv). The Department of Evolutionary Biology houses 8 independent research groups and about 25 PhD students, 25 postdocs, and several bioinformaticians. A common theme is that we address key questions in evolutionary biology, like speciation, local adaptation, life history evolution, genome and molecular evolution, using genomic approaches. We have tight connections with several other research groups in the Department of Ecology and Genetics within the Evolutionary Biology Centre. Professor Hans Ellegren Department of Evolutionary Biology Evolutionary Biology Centre Uppsala University Norbyvägen 18D SE-752 36 Uppsala Sweden Email: Hans.Ellegren@ebc.uu.se LAB WEB PAGE: http://bit.ly/1IsgBil Hans Ellegren via Gmail
Source: EVOLDIR