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January 13, 2015

22:30

BLAST is a computer program that searches a database for similarity matches to a given query sequence, either DNA or amino acid. It is most commonly used to search the GenBank database for matches to any new sequence that we might happen to have, in the hope that we will find one or more homologous sequences.

To most of us BLAST is a black box, in the sense that we have little idea about the details of how it does what it does. So, maybe we should at least look at what it does, just in case we ever need to know.

About 10 years ago I was working with some EST data. For those of you not old enough to know, ESTs consist of short DNA reads from arbitrary primers. In the hope of identifying the coding gene represented by each EST, BLASTX is used to search the GenBank protein database using each translated nucleotide query (in all six possible reading frames). BLASTX produces an E-value for each matching sequence, representing the strength of the match to the query. An E-value is not a probability (as they can vary from 0 to infinity), but at p=0.050 the expected E-value happens to be E=0.051. There is no consensus for what E-value should serve as indicating a "significant" match.

I decided to find out what happens if a DNA query sequence varies in either length or GC content. I used both random sequences (which were thus not in GenBank) as well as real sequences (which were in GenBank). The short answer is that the BLASTX results vary a lot. I never published these results because I figured the first thing a referee would do is ask me to explain BLASTX's behaviour, and I did not have an explanation (and still don't).

I present the results here for what they are still worth. Obviously, the results are not restricted to EST data, but apply any time that we use BLASTX.

Experimentation

The content of GenBank is quite different today to what it was back in late 2003, and so maybe the results will vary if the work was to be repeated. For reference, the first graph shows the GC content of the GenBank protein-coding sequences at the time of my work. Also, it is possible that BLASTX is different as well — I used v. 2.2.6 with default parameters (BLOSUM62, edge correction, length correction, SEG filtering, universal genetic code, gap penalty 11+k). Maybe some intrepid soul will be inspired to find out what happens nowadays.


Random sequences

I generated sets of 1,000 replicate "ESTs" using the perl script Randseq by M. Raymer (5/27/2003). These sets varied in DNA length (100–1,000 nt) and in GC content (0–94%), but were otherwise random sequences of nucleotides. These sequences are not expected to be homologous to anything already in GenBank, and should thus form BLASTX matches only by random chance.

The results for varying the sequence length are shown in the next graph, with each point representing the mean E-value observed. The lines represent four somewhat different GC contents; and the anticipated E-value for random data (0.051) is also shown. Clearly, very few points are near the expected value. The lines all show the same shape, with a minimum E-value near 450 nt, and rising slowly with longer lengths and rising rapidly with shorter lengths.


A more detailed assessment of the results for varying the GC content is shown in the third graph. The lines represent two somewhat different sequence lengths; and the anticipated E-value for random data (0.051) is also shown. It is clear that the E-value is capable of varying by up to seven orders of magnitude in response to variation in the GC content of the sequence.


Real sequences

I used the sequences contained in the Poxvirux Orthologous Clusters database (POCs), which used to be available at: http://athena.bioc.uvic.ca/pbr/POCs/pocs.html. This has since been replaced by the Viral Orthologous Clusters database (VOCs). These virus protein sequences are expected to already be in GenBank, and they should thus form good BLASTX matches.

The POCs database could be queried by both sequence length and GC content, and it was the only such database that I could find at the time. For each combination of length (in 50-nt bands) and GC-value (in 10% bands) I gathered a minimum of 20 sequences. There were few sequences for the shortest lengths, so I chopped up the longest sequences (longer then needed) to increase the sample size. There were also few sequences at the greatest GC values, so I used sequence AE004437.1 from GenBank (a Halobacterium sp.) to increase the sample size.

The results are shown in the final graph, with each point representing the mean E-value observed. The E-values are all small, since they represent actual database matches. Clearly, variation in sequence length can lead to orders of magnitude variation in E-value, while variation in GC content has an effect only at longer sequence lengths.


Conclusions

For a program that is supposed to produce comparable results, no matter what the sequence, these BLASTX results are disquieting. After all, BLAST is one of the most cited programs ever (see Massive citations of bioinformatics in biology papers), and yet I suspect that most people do not realize that it behaves like this.

The random sequences assess the effect of false positives. That they vary so much in E-value is amazing. Clearly, BLASTX E-values are not comparable between sequences. It is interesting that GC content seems to have a bigger effect than sequence length — for any given GC content the effect of length is relatively small for sequences longer than c. 600 nt. However, variation in GC content can produce orders of magnitude of effect at any given sequence length.

The real sequences assess the effect of true positives. That they vary in E-value is also not good — the E-values all represent true database matches (and presumably exact ones). Nevertheless, the effect of variation in sequence length and GC content is repeated for these real sequences. However, variation in GC content only has a large effect for the longer sequences, and instead it is the sequence length that produces the orders of magnitude variation in E-value.

You can make of this what you will.

22:00
Humans are vulnerable to a number of unique musculoskeletal maladies as a consequence of our evolutionary history. Although walking on our extended hind limbs is the hallmark adaptation characterizing our species it nevertheless makes us vulnerable to a wide range of serious joint and soft tissue problems. When viewed from an evolutionary perspective many of these medical issues become understandable and, indeed, novel methods of diagnosis and treatment can emerge. The proposed collaborative, a working group of paleoanthropologists, comparative anatomists, biomechanical engineers, and physicians will create new analytical approaches and new ways of viewing the disorders that uniquely plague our species. The results of this work include the development and implementation of a model curriculum, the creation of a website, and the publication of an edited volume. The disorders directly related to our way of walking include chronically sprained ankles, hernias, osteoporotic fractures of the hip, spine, and forearm, obstetric problems, knee problems, foot disorders, fatigue fractures, and many others. By understanding how our anatomy changed in order to walk upright, and why these changes occurred, we gain a better understanding of why these adaptations sometimes go awry resulting in disorders and pain.
Source: NESCent
09:10

Erick Matsen wrote:

I had no idea that this was coming down the pipe, but was excited to see a paper come out describing Phycas (http://www.phycas.org) from its authors, including @mtholder. Code is at https://github.com/plewis/phycas.

www.ncbi.nlm.nih.gov Phycas: Software for Bayesian Phylogenetic Analysis. PO Lewis, MT Holder and DL Swofford, Systematic biology, Jan 9 2015

Phycas is open source, freely available Bayesian phylogenetics software written primarily in C++ but with a Python interface. Phycas specializes in Bayesian model selection for nucleotide sequence data, particularly the estimation of marginal likelihoods, central to computing Bayes Factors. Marginal likelihoods can be estimated using newer methods (Thermodynamic Integration and Generalized Steppingstone) that are more accurate than the widely used harmonic mean estimator. In addition, Phycas supports two posterior predictive approaches to model selection: Gelfand-Ghosh and Conditional Predictive Ordinates. The GTR family of substitution models, as well as a codon model, are available, and data can be partitioned with all parameters unlinked except tree topology and edge lengths. Phycas provides for analyses in which the prior on tree topologies allows polytomous trees as well as fully resolved trees, and provides for several choices for edge length priors, including a hierarchical model as well as the recently described compound Dirichlet prior, which helps avoid overly informative induced priors on tree length.

I haven't played with Phycas, but I can describe what I think of as its "killer feature," which is the ability to use a prior incorporating polytomous trees. That means that the software can return trees that look like this:

where I've put an arrow pointing at the polytomy. In this case, the polytomy shows three descendants of a given lineage.

I would argue that such a representation is a more honest one (a "shrunken" estimate for @nicolas_lartill and friends). That is, if there is not information to resolve an internal node, then an unresolved tree is returned. One often sees such nodes when people collapse nodes in ML trees that have low bootstrap support. However, I think that it's better than that because it's rolled into the actual inference, meaning that the overall likelihoods are properly estimated. In a field where we are already in statistically tenuous territory with the number of discrete parameters being on the order of the number of independent data points (to say nothing of the discrete estimation part) having fewer parameters when appropriate is refreshing.

In the Bayesian phylogenetics world, not allowing such multifurcations can cause some trouble, as was the subject of some research in the mid-2000's. A good culmination of that work is this paper by Z Yang:

www.ncbi.nlm.nih.gov Fair-balance paradox, star-tree paradox, and Bayesian phylogenetics. Z Yang, Molecular biology and evolution, Aug 2007

The star-tree paradox refers to the conjecture that the posterior probabilities for the three unrooted trees for four species (or the three rooted trees for three species if the molecular clock is assumed) do not approach 1/3 when the data are generated using the star tree and when the amount of data approaches infinity. It reflects the more general phenomenon of high and presumably spurious posterior probabilities for trees or clades produced by the Bayesian method of phylogenetic reconstruction, and it is perceived to be a manifestation of the deeper problem of the extreme sensitivity of Bayesian model selection to the prior on parameters. Analysis of the star-tree paradox has been hampered by the intractability of the integrals involved. In this article, I use Laplacian expansion to approximate the posterior probabilities for the three rooted trees for three species using binary characters evolving at a constant rate. The approximation enables calculation of posterior tree probabilities for arbitrarily large data sets. Both theoretical analysis of the analogous fair-coin and fair-balance problems and computer simulation for the tree problem confirmed the existence of the star-tree paradox. When the data size n --> infinity, the posterior tree probabilities do not converge to 1/3 each, but they vary among data sets according to a statistical distribution. This distribution is characterized. Two strategies for resolving the star-tree paradox are explored: (1) a nonzero prior probability for the degenerate star tree and (2) an increasingly informative prior forcing the internal branch length toward zero. Both appear to be effective in resolving the paradox, but the latter is simpler to implement. The posterior tree probabilities are found to be very sensitive to the prior.

The point of this work is that if the data truly doesn't have any signal concerning an unresolved node, and we use a Bayesian phylogenetic inference package that doesn't allow multifurcations (every one except for Phycas as far as I know) the data set may (with non-vanishing probability) give very high confidence that one of the resolutions is correct. This is shown in this figure from Yang's paper (click to expand):

Pasted image1004x856 472 KB

See the deep red in the corners? That's showing that in replicate data sets there is a substantial probability that one of the resolutions will be very highly supported.

So, I can't comment on Phycas' usability, runtimes, etc, and Conditional Predictive Ordinates sound nice, but for me, proper support for polytomies is the headlining feature of Phycas. If anyone tries it out, please post here!

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05:05
—_000_D0D99B072787Emaslotmanagtamuedu_ Content-Type: text/plain; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable A post-doctoral position is available in the Slotman laboratory in the Department of Entomology at Texas A&M University (http://bit.ly/1q2xluC). Our lab focuses on the evolutionary and behavioral genetics/genomics of disease transmitting mosquitoes. The post-doc will conduct NIH-funded research into the genomic basis of outdoor feeding preference of the African malaria mosquito An. gambiae. This mosquito generally prefers feeding indoors, but after years of indoor-based vector control on Bioko Island has shifted its behavior towards a preference for outdoor feeding. We are taking a whole genome Pool-seq approach to map genetic differences between indoor and outdoor host-seeking An. gambiae mosquitoes on Bioko. In addition, the successful candidate will be expected to contribute to ongoing research into the genetic basis of attraction of An. gambiae to human hosts. The ideal candidate will have a background in population genetics, experience with analyzing next-generation sequencing data, and familiarity with R and Python (or Perl). The Texas A&M System is an Equal Opportunity/Affirmative Action/Veterans/Disability Employer committed to diversity. The position is available for two years available immediately, but start date is open to negotiation. If you are interested in applying for this position please send a cover letter, CV, PDFs of representative publications, and contact information for three references to maslotman@tamu.edu. —_000_D0D99B072787Emaslotmanagtamuedu_ Content-Type: text/html; charset=”us-ascii” Content-ID: Content-Transfer-Encoding: quoted-printable
Source: EVOLDIR
04:22
Dear Colleagues, Abstracts for oral presentations are being sought for a phylogenetics symposium titled “Untangling information, noise, and phylogenetic reconstruction in genome scale data”, a part of SMBE 2015 (July 12-16) in Vienna, Austria. Abstracts are due Feb 8, 2015 at the SMBE 2015 submission website (http://bit.ly/1xIlYts) Invited Speakers: Tandy Warnow (University of Illinois, Champaign-Urbana) Olivier Gascuel, Le Laboratoire dInformatique, de Robotique et de Microlectronique de Montpellier, France Organizers: Khidir Hilu, Virginia Tech (hilukw@vt.edu) Jeffery Townsend, Yale University (jeffrey.townsend@yale.edu) Arindam RoyChoudhury, Columbia University (ar2946@cumc.columbia.edu) A brief summary of the symposium theme: Phylogenetic information and noise are central components in successful tree reconstruction as they can invariably impact tree resolution, support, and accuracy. As we attempt to resolve deeper, shorter internodes and estimate short branch lengths in the tree of life with genome-scale data sets, the magnitude of impact of these two components is accentuated considerably, as is the prevalence of conflicts among gene trees. These phylogenetic issues are greatly entangled with intrinsic gene features, e.g. gene mode and tempo of evolution, and are exacerbated by historic depth. A high rate of nucleotide substitution can obscure phylogenetic information, and sometimes yields noise at deep historic times. However, fast rates and genome-scale datasets also potentially yield much more information if modeled accurately, taxa are sufficiently sampled, and substitution rate is not so fast. Thus, our symposium will be relevant to molecular evolution, phylogenetics and genomics. Recruited speakers will address theoretical and empirical studies relating to: 1) assessment of suitability of genomic regions across a spectrum of nucleotide substitution rates and selection pressure to resolve phylogenetic trees; 2) comparison between whole genome vs. optimal genes approaches; 3) evaluation of the effectiveness of current approaches/algorithms used in discerning sources of signal, noise and conflicts among phylogenetic trees; 4) fast methods and algorithms for dating and phylogenetic reconstruction of large genomic data. Best regards, Arindam RoyChoudhury “RoyChoudhury, Arindam” via Gmail
Source: EVOLDIR
04:22

—_000_8CF4BD0AE46C7142B6EFA932141BB91ECB2C32BAuwmbx06uwluse_ Content-Type: text/plain; charset=”iso-8859-1” Content-Transfer-Encoding: quoted-printable The link to the previously (Jan 4) advertised postdoc to study sexual selection and hybridisation in lizards is now unfortunately broken. To access information about this position (Official Records Number: NPA 2014/747) and two other postdoc opportunities in my group at Lund University, please see information posted on Jan 5 on the following link (which allows you to continue to the list of vacancies and the application system): http://bit.ly/1C235kd Apologies for any confusion caused. Dr Tobias Uller Wallenberg Academy Fellow Department of Biology Lund University —_000_8CF4BD0AE46C7142B6EFA932141BB91ECB2C32BAuwmbx06uwluse_ Content-Type: text/html; charset=”iso-8859-1” Content-Transfer-Encoding: quoted-printable

The link to the previously (Jan 4) advertised postdoc to study sexual selection and hybridisation in lizards is now unfortunately broken. To access information about this position (Official Records Number: NPA 2014/747) and two other postdoc opportunities in my group at Lund University, please see information posted on Jan 5 on the following link (which allows you to continue to the list of vacancies and the application system): http://bit.ly/1C235kd Apologies for any confusion caused. Dr Tobias Uller Wallenberg Academy Fellow Department of Biology Lund University —_000_8CF4BD0AE46C7142B6EFA932141BB91ECB2C32BAuwmbx06uwluse via Gmail
Source: EVOLDIR
03:23
Nutritional stress and thermal adaptation Applications are invited for a PhD fellowship/scholarship at Graduate School of Science and Technology, Aarhus University, Denmark, within the Bioscience programme. The position is available from 1 May 2015 or later. Title: Nutritional stress and thermal adaptation Research area and project description: Evolutionary genetics, ecophysiology and molecular biology. The PhD student should study effects of variable nutritional regimes and interactions between nutrition, temperature and genotype on stress resistance and life history traits using Drosophila as a model organism. It is intended to use rearing and test conditions that are ecological relevant making the studies of strong interest from ecological and evolutionary perspectives. Relevant molecular work should complement organismal phenotypic analyses, possibly followed up by the application of relevant “omics” techniques. The work will be done under the supervision of Prof. Volker Loeschcke (AU) in collaboration with Prof. MSO Torsten N. Kristensen from Aalborg University and in interaction with PhD students/post-docs Mads F. Schou and Tommaso Manenti and supported by grants from the Danish Natural Research Council (the project will be funded by grants of Natural Science Research Council to Volker Loeschcke (2/3) and Torsten Nygaard Kristensen (1/3). Qualifications and specific competences: A Master’s degree in Bioscience, Biotechnology or similar or a bachelor’s degree in a relevant subject are possible backgrounds. A strong interest in experimental as well as analytical work is required, and experience with the model organism Drosophila is an advantage. Place of Employment and Place of Work: The place of employment is Department of Bioscience, Aarhus University, Denmark, and the place of work is the section for Genetics, Ecology and Evolution, Ny Munkegade 114-116, 8000 Aarhus C, or for part of the time at Department of Biotechnology, Chemistry and Environmental Engineering, Section of Biology and Environmental Science, Aalborg University, Fredrik Bajers Vej 7H, DK-9220 Aalborg East, Denmark Contacts: Applicants seeking further information are invited to visit http://bit.ly/1Bhqf8p or contact: Volker Loeschcke, phone: +45 2899 2368, e-mail: volker@bios.au.dk, or Torsten Nygaard Kristensen, phone: +45 61463375, email: tnk@bio.aau.dk, for further information about the position. Torsten Nygrd Kristensen via Gmail
Source: EVOLDIR
03:23

Two field assistant positions to study oxidative stress in relation to social status in house sparrows in Switzerland. We are seeking for two (2) research assistants for the upcoming breeding season to join a project investigating the impact of oxidative stress and social status on the development of reproductive strategies in house sparrow. The research will be conducted in Bern, Switzerland. The work will start on 1st of April and will continue through early/mid July. Our project investigates how males with different positions in a dominance hierarchy allocate their antioxidant resources to the protection of their sperm vs. the protection of their somatic functions, and how such allocation strategies affect the quality of the sperm they produce. The project is based at the University of Neuchatel, Switzerland (PI Prof. Fabrice Helfenstein, PhD student Alfonso Rojas), but will be conducted at Hasli, Bern, Switzerland. The work of the volunteers will consist in carrying out an experiment in aviaries with house sparrows. This includes assisting the PhD student with catching and banding birds, behavioural observations, sample collection, data management and data analysis. During the conduct of the experiment we work 7 days a week and 10-12 hours a day. Qualifications: (1) BSc or higher in Biology or similar qualification (2) Ability to work and live in small groups and sociable personality (3) Fluent in English (French and/or German are a plus, but not essential) (4) Ability to endure long working days (5) Knowledge in observing & handling birds is a plus (6) Driving license. This is a volunteer field assistant position, thus the applicant should cover his/her travel expenses and food. Accommodation expenses will be covered (up to 500.-CHF/month). Applications - including a CV and a letter of motivation (1 pg.) - should be send to both: Fabrice Helfenstein: fabrice.helfenstein@unine.ch and Alfonso Rojas: alf.roja@gmail.com Please use “Volunteer Assistant in Switzerland” as the subject and note your availability during this time period in the body of the e-mail. Applications received until 15th of February 2014 will be given full consideration. Do not hesitate to contact us for further information. via Gmail

Source: EVOLDIR
02:44

Dear colleagues, it is our pleasure to invite you to submit abstracts to our symposium about **Origins and Evolution of Molecular Innovation** ! Our guest invited speaker is Prof. M. Mar Albà from the UPF in Barcelona. This symposium will be a part of the 2015 Society for Molecular Biology and Evolution Meeting (http://smbe2015.at/). The meeting will be held in the Hofburg Palace in Vienna, Austria. More details about the destination can be found here: http://bit.ly/1BORVzD The deadline for registration is Feb. 8, 2015. You may find registration information and a link to the registration portal here: http://bit.ly/1Hs3vnD Symposium description: Generally, the field of molecular evolution is dominated by studies of descent with accumulation of slight modifications. However, larger changes are also possible, in which entirely new molecular features originate for the first time. We will consider rapid or spontaneous molecular innovations of diverse kinds (structures, functions, interactions, networks), with a preference for the most dramatic leaps between the absence and the presence of the molecular traits or features in question. Timely examples of great interest in the community include (i) de novo emergence of new genes, protein domains, regulatory regions and (ii) neo-functionalization, e.g. via the acquisition of new and adaptive binding activities. The symposium will not only address well-documented examples of spontaneous emergence of novel molecular traits, but also cover findings relevant to the processes of innovation and its aftermath. These include (but are not limited to) the roles of promiscuity (e.g. in the emergence of novel enzymatic functions) and stochasticity across different organization levels. We look forward to seeing you in Vienna! Joanna Masel (masel@u.arizona.edu) Rafik Neme (rneme@evolbio.mpg.de) Erich Bornberg-Bauer (ebb@wwu.de) via Gmail

Source: EVOLDIR
02:25

Post-Doctoral Fellow (PDF) in Functional Conservation Genomics A collaborative research program on caribou conservation is seeking a conservation geneticist, molecular ecologist, molecular biologist or bioinformatician with strong quantitative skills for ecotype characterization of Canadian caribou. The relationship among sub-species and ecotypes will be examined in assessing the reconstruction of population histories across Canada. This project is a partnership between academic and provincial government agencies with significant engagement with industrial partners. The PDF will use a large DNA dataset to expand into functional gene characterization and mitogenomics of caribou representative of nation-wide sampling efforts. The PDF will be expected to take a leadership role in coordinating a team of graduate and undergraduate students and liaise with project partners. The salary is $40,000/year and the position will be filled as soon as a suitable candidate is found. Applicants should submit a CV, a statement of research interests, and the names and contact information for three references. Please submit applications to: Dr. Paul J. Wilson Canada Research Chair in DNA Profiling, Forensics & Functional Genomics Trent University, 1600 West Bank Drive, Peterborough, ON, K9J7B8 Phone 705.748.1011 ext. 7259; Fax 705.748.1003 Website: http://bit.ly/1IpeRtb pawilson@trentu.ca or Dr. Micheline Manseau Natural Resources Institute, University of Manitoba 70 Dysart Road, Winnipeg, MB, R3T 2N2 Phone 204.474.9889; Fax 204.261.0038 Website: www.lecol-ck.ca Micheline.Manseau@pc.gc.ca Post-Doctoral Fellow (PDF) in Landscape Genomics A collaborative research program on caribou conservation is seeking a researcher with strong quantitative skills to complement a research team examining the spatial genetic/genomic dynamics of Canadian boreal caribou. This project is a partnership between academic, federal and provincial government agencies and the private sector and builds on a multi-year dataset. The PDF will use project data to characterize the spatial genetic structure and landscape/environmental variables influencing caribou herds, ecotypes and associated subspecies based on genetic structure using mitogenomics, SNP analyses and functional gene profiles. The research will assess the potential impacts of anthropogenic activities, e.g. mining and protected areas, on caribou genetic structure by developing predictive genetic structure models within defined conservation units or targeted areas-of-interest for development or protection. The PDF will be expected to take a leadership role in coordinating a team of graduate and undergraduate students and liaise with project partners. The salary is $40,000/year + benefits and the position will be filled as soon as a suitable candidate is found. Applicants should submit a CV, a statement of research interests, and the names and contact information for three references. Please submit applications to: Dr. Paul J. Wilson Canada Research Chair in DNA Profiling, Forensics & Functional Genomics Trent University, 1600 West Bank Drive, Peterborough, ON, K9J7B8 Phone 705.748.1011 ext. 7259; Fax 705.748.1003 Website: http://bit.ly/1IpeRtbwww.lecol-ck.ca Micheline.Manseau@pc.gc.ca Post-Doctoral Fellow (PDF) in Landscape Genomics A collaborative research program on caribou conservation is seeking a researcher with strong quantitative skills to complement a research team examining the spatial genetic/genomic dynamics of Canadian boreal caribou. This project is a partnership between academic, federal and provincial government agencies and the private sector and builds on a multi-year dataset. The PDF will use project data to characterize the spatial genetic structure and landscape/environmental variables influencing caribou herds, ecotypes and associated subspecies based on genetic structure using mitogenomics, SNP analyses and functional gene profiles. The research will assess the potential impacts of anthropogenic activities, e.g. mining and protected areas, on caribou genetic structure by developing predictive genetic structure models within defined conservation units or targeted areas-of-interest for development or protection. The PDF will be expected to take a leadership role in coordinating a team of graduate and undergraduate students and liaise with project partners. The salary is $40,000/year + benefits and the position will be filled as soon as a suitable candidate is found. Applicants should submit a CV, a statement of research interests, and the names and contact information for three references. Please submit applications to: Dr. Paul J. Wilson Canada Research Chair in DNA Profiling, Forensics & Functional Genomics Trent University, 1600 West Bank Drive, Peterborough, ON, K9J7B8 Phone 705.748.1011 ext. 7259; Fax 705.748.1003 Website: http://bit.ly/1IpeRtb pawilson@trentu.ca or Dr. Micheline Manseau Natural Resources Institute, University of Manitoba 70 Dysart Road, Winnipeg, MB, R3T 2N2 Phone 204.474.9889; Fax 204.261.0038 Website: www.lecol-ck.ca Micheline.Manseau@pc.gc.ca Jill Lalor Research Technician Trent University Genomics Lab A112 and Wilson Lab C254 2140 East Bank Drive Peterborough, ON K9J 7B8 705-748-1011 ext 6657 via Gmail

Source: EVOLDIR
02:06
Dear colleagues and friends, This is to announce the meeting that Jonathan Wendel, Scot Jackson, Olivier Panaud, Michael Purugganan and myself are organizing in Barcelona very soon, in March (17-18), on plant genome evolution. The meeting is entitled “Evolution of plant phenotypes, from genomes to traits” and will be divided in three scientific sessions: 1. Mechanisms generating genome variability, with special emphasis on polyploidy and TEs; 2. Evolution of plant phenotypes: wild and domesticated species; 3. Domestication and plant improvement: Putting science into practice in the aid of the human condition. We have a group of excellent speaker from the US, the EU, Israel and Japan that will ensure a fantastic discussion on these exciting and timely scientific questions. The registration will be available very soon at the price of only 100 euro (which includes the lunch onsite for the two days of the conference). Please visit the webpage of the meeting (http://bit.ly/1u23Fdi) for more information on the meeting. Hope to see you in Barcelona! Best wishes, Josep Olivier Panaud via Gmail
Source: EVOLDIR
02:06

Dear Colleagues, Don’t forget the application deadline for the course “Systematics and Biology of Hydrozoa” is this week. The 2-week workshop held in Panama is aimed for at a graduate student level, but is open to any researcher wishing to learn more about hydrozoa, including collection managers, people involved in bioinventories and surveys and advanced undergraduates with appropriate preparation. Find out more at: http://bit.ly/1u23EWT logy_Tropical_Hydrozoa.html Or Contact one of us Dr. Rachel Collin CollinR@si.edu Dr. MariaPia Miglietta miglietm@tamug.edu via Gmail

Source: EVOLDIR
01:23
PhD studentship: Next-generation sequencing approaches to short-tandem repeat sequence variation: mutation processes, haplotype evolution and forensic application A fully funded four-year BBSRC CASE PhD Studentship is available with Prof Mark Jobling and Dr Jon Wetton to use next-generation sequencing (NGS) to study the internal structure of human short-tandem repeats. These markers are universally used in forensic analysis, but genotyping considers only allele length, and not allele sequence. The next decade promises to bring the power of NGS to bear on forensic identification, yet little is known about what new opportunities and problems sequence data will bring. The project will address the following questions: i) What is the internal sequence variability of autosomal and Y-STRs in human populations? ii) How are sequence variants (e.g. variant repeats, microdeletions) related to linked SNP variation? iii) What does the information from (i) and (ii) add to our understanding of microgeographic variation? iv) What can we learn about STR mutation processes from an appreciation of sequence variability? v) How can information from (iii) and (iv) be used in a forensic context? Close collaboration with Key Forensic Services Ltd. (http://bit.ly/1y88Aip) is an essential part of the project, and the student will spend 3-6 months in their laboratories on the University of Warwick campus. For further details and how to apply, see: http://bit.ly/14u9fhK Prof Mark A. Jobling Wellcome Trust Senior Research Fellow in Basic Biomedical Science Department of Genetics Room G5, Adrian Building University of Leicester University Road Leicester LE1 7RH UK tel.: +44 (0)116 252 3427 mob.: +44 (0)7955 882334 fax: +44 (0)116 252 3378 email: maj4@le.ac.uk web: http://bit.ly/1y88B5S Mark Jobling via Gmail
Source: EVOLDIR
01:03
A position is available for a Research Associate (Postdoc) to conduct research on fish biology, disease and bioinformatics, in the topic: Minimising the Impacts of Intensive Aquaculture in the face of Climate Change Institutions Involved:Cardiff University,Swansea Universityand Aberystwyth University Collaborators:Natural Resources Wales (NRW), Cardiff Harbour Authority (CHA), Wye & Usk Foundation (WUF), Natural Aptitude, Fishgen, Skillfish, Pontus Aqua, CIBIO Worldwide demand for fish and shellfish has increased 9% annually over the last few decades and is expected to reach c. 180 million tons by 2015, most of which will have to come from farmed fish, as the majority of wild fisheries are either stagnant or grossly over-exploited. However, to achieve long-term sustainability and meet food security demands, aquaculture needs to diversify and to step-up the domestication of aquatic species, which will have to thrive on less food, less space, and less water, all compounded by warmer temperatures and disease. The AquaWales Research Cluster combines academic (Swansea, Cardiff and Aberystwyth Universities) and non-academic participants, including stakeholders and local government involved in policy and regulation, and will target these challenges by capitalising on the diverse and complementary expertise of the group (from behavioural ecology to genomics, citizen-science and fisheries policy). We will use a multidisciplinary approach to disentangle the basis of domestication and the response to crowding (stress and parasite susceptibility), an aspect often neglected in breeding programs, and to investigate the potential effects of climate change on the risk of expansion and establishment of non-native aquatic species associated with aquaculture and fisheries using state-of-the-art methods. Specific aims include to: 1. bridge, for the first time, the behavioural, genetic and environmental (epigenetic) components of fish undergoing domestication 2. disentangle the role of domestication in disease resistance in response to stress and temperature change, and 3. model pathways of introduction and dispersal of aquaculture-related invasive species (AIS) under different environmental conditions, combining state-of-the-art methods for early detection (environmental DNA) and citizen science. The Research Associate will work in collaboration with a Research Associate based at Swansea and 2 PhDs affiliated with this research cluster; the Research Associate must also be prepared to work for short periods of time in Swansea and/or Aberystwyth. The main tasks of the Research Associate will be to work on the relationship between domestication and disease resistance under stressful conditions of crowding and disease in tilapia and salmon, developing infection protocols, culture assay methods and performing genomic/transcriptomic analyses. The successful candidate will have a PhD in related subject area or relevant industrial experience, experience in two of the following fields, fish behaviour, epidemiology, genetics/genomics background or experience programming in R/Python and proven ability to publish in international journals. This is a full-time position, fixed-term until 30 September 2018 Salary: 31,342 - 37,394 per annum (Grade 6).It is not anticipated that an appointment will be made above 6.31, currently 32,277 per annum. Closing data for application: Wednesday 21st January, 2015 Please use the following link to apply: Cardiff University - Job details Cardiff University - Job details Job Details: Vacancy Number 2951BRResearch AssociateA position View on krb-sjobs.brassring.com For additional information please contact: CableJ@cardiff.ac.uk and/or orozco-terwengelpa@cardiff.ac.uk Pablo Orozco-terWengel via Gmail
Source: EVOLDIR
00:46

We are currently seeking to fill one permanent Program Director position in the Systematics and Biodiversity Science cluster in the Division of Environmental Biology at the National Science Foundation in Arlington, Virginia. The deadline for submitting applications is February 9, 2015. Additional details about the position and application process can be found below and on the following web page: http://1.usa.gov/1u1kwCQ Simon Malcomber, Ph.D. Program Director, Systematics and Biodiversity Science Division of Environmental Biology National Science Foundation 4201 Wilson Boulevard, Room 640.04 Arlington, VA 22230 Tel: 703-292-8227 Email: smalcomb@nsf.gov via Gmail

Source: EVOLDIR

January 12, 2015

23:54

A postdoctoral position in evolutionary genomics is available in the newly established Vicoso group at the Institute of Science and Technology, Austria. The general focus of the lab is the evolution of sex chromosomes, which we approach using a combination of experimental and computational approaches. Questions that motivate our research include: why do some Y/W chromosomes degenerate while other remain homomorphic; what forces drive some species to acquire global dosage compensation, while others only compensate specific genes; what are the frequency and molecular dynamics of sex-chromosome turnover? The successful applicant will apply comparative genomics analyses to a wide variety of species, and combine them with population DNA and gene expression data, to achieve a better understanding of the evolutionary and molecular forces driving sex chromosome differentiation. Candidates wishing to work on a specific project in sex chromosome evolution are also encouraged to apply. Applicants should have obtained, or anticipate obtaining by the start date, a PhD in biology, genetics, bioinformatics, or a related field. A strong background in one or more the following areas is highly desired: • comparative genomics • molecular evolution • population genetics • bioinformatics The initial appointment is for one year, with the possibility of extension and a minimum salary of 49,070 Euros per year (gross). IST Austria is a young and vibrant international institute dedicated to basic research and graduate education in the natural and mathematical sciences, located on the outskirts of Vienna (www.ist.ac.at). The official language of the institute is English. Aside from the evolution cluster at IST Austria, Vienna is home to a large community of evolutionary biologists: http://bit.ly/1pSDzd6. To apply, send a summary of research interests, CV, up to three relevant publications/manuscripts, and the names and contact information for three references to Beatriz Vicoso (bvicoso@ist.ac.at). The start date is negotiable, but an earlier start would be preferred. Beatriz Vicoso Assistant Professor IST Austria website: http://bit.ly/1yea1dHwww.ist.ac.at). The official language of the institute is English. Aside from the evolution cluster at IST Austria, Vienna is home to a large community of evolutionary biologists: http://bit.ly/1pSDzd6. To apply, send a summary of research interests, CV, up to three relevant publications/manuscripts, and the names and contact information for three references to Beatriz Vicoso (bvicoso@ist.ac.at). The start date is negotiable, but an earlier start would be preferred. Beatriz Vicoso Assistant Professor IST Austria website: http://bit.ly/1yea1dH email: bvicoso@ist.ac.at via Gmail

Source: EVOLDIR
16:17
The taxonomic rank and phylogenetic relationships of the pipizine flower flies (Diptera: Syrphidae: Pipizini) were estimated based on DNA sequence data from three gene regions (COI, 28S and 18S) and 111 adult morphological characters. Pipizini has been treated as a member of the subfamily Eristalinae based on diagnostic adult morphological characteristics, while the larval feeding mode and morphology is shared with members of the subfamily Syrphinae. We analysed each dataset, both separately and combined, in a total evidence approach under maximum parsimony and maximum likelihood. To evaluate the influence of different alignment strategies of rDNA 28S and 18S genes on the resulting topologies, we compared the topologies inferred from a multiple alignment using fast Fourier transform (MAFFT) program with those topologies resulting from aligning the secondary structure of these rDNA genes. Total evidence analyses resolved pipizines as a sister group of the subfamily Syrphinae. Although the structural alignment and the MAFFT alignment differed in the inferred relationships of some clades and taxa, there was congruence in the placement of pipizines. The homogeneous morphology of the Pipizini clade in combination with their unique combination of characters among the Syrphidae suggest a change of rank to subfamily. Thus, we propose to divide Syrphidae into four subfamilies, including the subfamily Pipizinae stat. rev.
Source: Cladistics
00:04
STATS COURSE ‘SPATIAL ANALYSIS OF ECOLOGICAL DATA USING R’ A repeat of the course titled ‘SPATIAL ANALYSIS OF ECOLOGICAL DATA USING R’ has been arranged for 16th – 20th November 2015 This course will cover the concepts and R tools that can be used to analyse spatial data in ecology covering elementary and advanced spatial analysis techniques applicable to both plants and animals. The course is aimed at PhD students and post docs (although people at any stage of their career are welcome) with basic to moderate knowledge in R. It will be held at SCENE (Scottish Centre for Ecology and the Natural Environment), Glasgow, United Kingdom. Course content is as follows and will be based on biological/ecological data and relevant to evolutionary biologists particularly those studying behavior, habitat use and ecological speciation. Module 1 Introductory lectures; key questions in spatial ecology, the main types of data on species distributions, concepts, challenges and different types of environmental data; useful concepts from statistics; GLM’s Module 2 Density estimation, spatial autocorrelation, Smoothing, Kernel Smoothers, Kriging, Trend-fitting (linear, generalised linear, generalised additive models) Module 3 Habitat preference, Resource selection functions, MaxEnt: What’s it all about? Overview and caveats related to Niche models Module 4 Analysing grid data, Poisson processes, Occupancy models, Use-availability designs Module 5 Analysing telemetry data, Presence-only data, Spatial and serial autocorrelation, partitioning variation by mixed effects models Module 6 Analysing transect data, Detection functions for point and line transects, Using covariates in transect models Module 7 Advanced methods, Generalised Estimation Equations for difficult survey designs, GAM’s for habitat preference, Dealing with boundary effects using soap smoothers, Spatial point processes with INLA Module 8 Prediction, Validation by resampling, Generalised Functional Responses for species distribution, quantifying uncertainty, dealing with the effects of population density Module 9 Applications, Designing protected areas, thinking about critical habitat, representing uncertainty Module 10 Round-table discussions about the analysis requirements of attendees (option for them to bring their own data). Cost is £475 for the 5 days including lunches and refreshments or £675 for an all-inclusive option which includes the addition of accommodation, all meals and refreshments. For further details or questions please email oliverhooker@prstatistics.co.uk or visit http://bit.ly/1v1Pet4 - upcoming courses; ANALYSIS OF STABLE ISOTOPE DATA USING SIA-R; AN INTRODUCTION TO USING GIS IN ECOLOGICAL FIELD STUDIES; APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS; ADVANCING IN R Oliver Hooker PhD research student University of Glasgow +44 (0) 1360 870 510 +44 (0) 7966 500 340 o.hooker.1@research.gla.ac.uk Oliver Hooker via Gmail
Source: EVOLDIR

January 11, 2015

23:28
STATS COURSE ‘ADVANCING IN R’ A repeat of the course titled ‘ADVANCING IN R’ has been arranged for 30th November – 4th December 2015 The content designed to bridge the gap between basic R coding and more advanced statistical modelling. The course is aimed at PhD students and post docs (although people at any stage of their career are welcome) with basic to moderate knowledge in R. It will be held at SCENE (Scottish Centre for Ecology and the Natural Environment), Glasgow, United Kingdom. Course content is as follows and will be delivered by two evolutionary biologists and based on biological/ecological data thus highly relevant to evolutionary biologists. Module 1 Data manipulation & visualization using {dplyr} and {ggplot} Module 2 Univariate regression, diagnostics & plotting fits Module 3 Adding additional continuous predictors (multiple regression); scaling & collinearity Module 4 Adding factorial (categorical) predictors & incorporating interactions (ANCOVA) Module 5 Model selection & simplification (likelihood ratio tests, AIC) Module 6 Predicting on the basis of coefficients Module 7 Mixed effects model in theory and in practice Module 8 Generalised linear models in theory and practice Module 9 Nonlinear models (polynomial & mechanistic models) Module 10 Mored advanced topics & combinig methods (e.g. nonlinear mixed effect models (NLME) & generalised linear mixed effects models (GLMM). Cost is £460 for the 5 days including lunches and refreshments or £635 for an all-inclusive option which includes the addition of accommodation, all meals and refreshments. There is also the possibility (depending on time) to have casual one to one discussion regarding your own research so you are encouraged to bring data with you however this cannot be guaranteed. For further details or questions please email oliverhooker@prstatistics.co.uk or visit http://bit.ly/1v1Pet4 - upcoming courses; ANALYSIS OF STABLE ISOTOPE DATA USING SIA-R; AN INTRODUCTION TO USING GIS IN ECOLOGICAL FIELD STUDIES; APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS; SPATIAL ANALYSIS OF ECOLOGICAL DATA USING R Oliver Hooker PhD research student University of Glasgow +44 (0) 1360 870 510 +44 (0) 7966 500 340 o.hooker.1@research.gla.ac.uk Oliver Hooker via Gmail
Source: EVOLDIR