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June 4, 2015

May 31, 2015

22:00
With consequences for disease severity, resistance or clearance of a pathogen infection by an individual can be enhanced by a previous exposure to that pathogen, occurring either within an individual or even in its parents. This form of immune memory, traditionally thought the province of the vertebrate adaptive immune response, can also arise from innate immune pathways of vertebrates and invertebrates, and through distinct pathways in plants and bacteria. Researchers studying this phenomenon rarely interact across taxonomic boundaries, however, and use a preponderance of disparate terms to describe this innate immune mediated memory, including immune memory, immune priming, trained immunity, and systemic acquired resistance. This catalysis meeting will facilitate a synthesis of disparate researchers to better understand commonalities among these different forms of innate immune memory and key consequences for disease. We will use this opportunity to produce a broad interest synthesis manuscript elaborating upon specific avenues by which an improved understanding of innate immune memory will inspire future research, with direct and indirect benefits for human health. First, better understanding of how vertebrate immune memory works in retaining specific memory stands to improve vaccine design and delivery. Second, the specificity of immune memory could be manipulated to leave harmful pests, vectors, and human parasites susceptible to pathogen mediated biocontrol, while improving the health of beneficial organisms such as agricultural plants, animals, and pollinators that ensure human food security. Our approach aims to identify model systems functionally analogous to human innate immune memory that maximize our flexibility to interrogate the genetics, constraints, and functional manipulations of innate immune memory. Finally, this synthesis will elucidate fundamental concepts underlying host-pathogen evolution and the limits of immunological plasticity.
Source: NESCent

May 27, 2015

06:25

@josephwb wrote:

Fellow phylo-dorks,

I was wondering if anyone had hard numbers (or a paper reference) for the energy consumption required by large phylogenetic analyses (or comparable computational problems from other fields). Perhaps @rdmpage, @ematsen, @alexei_drummond, @Alexis_RAxML, @mtholder, @phylorich, or @beerli might be able to help me out?

Thanks! JWB.

Posts: 3

Participants: 2

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May 26, 2015

22:30

Charles Darwin's most poetic published words concern his image of the Tree of Life. However, he did not claim to have originated the image. For example, Alfred Russel Wallace had already used it. Recently, the Natural History Apostilles blog has mentioned another important predecessor of both Englishmen, the Frenchman Charles Naudin, who deserves wider recognition.

Darwin's well-known words from On the Origin of Species (1859) are:
The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species ... As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications.Wallace seems to have developed the Tree of Life metaphor quite independently (1855. On the law which has regulated the introduction of new species. Annals and Magazine of Natural History, 2nd series 16: 184-196):
"the analogy of a branching tree [is] the best mode of representing the natural arrangement of species ... a complicated branching of the lines of affinity, as intricate as the twigs of a gnarled oak ... we have only fragments of this vast system, the stem and main branches being represented by extinct species of which we have no knowledge, while a vast mass of limbs and boughs and minute twigs and scattered leaves is what we have to place in order, and determine the true position each originally occupied with regard to the others."Darwin freely admitted having read Wallace's work. Moreover, he was well aware of the other of his predecessors, Charles Naudin, because on p.167 of his 'Books Read' and 'Books to be Read' notebook of 1852-1860 (see Darwin Online CUL-DAR128) he recorded:
"Revue Horticol Imp. 1852. p. 102. Naudin Consid. Phil, sur l'espèce"Charles Naudin's words are these, roughly translated from the original French (1852. Considérations philosophiques sur l'espèce et la variété. Revue Horticole, 4th series 1: 102-109) [NB. the long convoluted sentences are in the original]:
This doctrine of inbreeding among organic beings of same family, the same class, and perhaps of the same kingdom, is not new; men of talent, both in France as well as abroad, among them our learned Lamarck, have supported it with all of the authority of their names. We do not deny that, on more than one occasion, they have reasoned upon assumptions which were not adequately supported by observation, that they did sometimes apply to the facts forced interpretations, that finally resulted in exaggerations that have mainly helped to push their ideas. But these defects in details do not diminish the greatness and perfect rationality of the whole system that, alone, reflects, by the community of origin, the great fact of the organizational community of the other living beings of the same kingdom, the primary basis of our rankings of species into genera, families, orders and phyla. In the opposing system now in vogue, in this system which involves many partial and independent creations we recognize or think we recognize as distinct species, one is forced to be logical, to admit the similarities exhibited by these species are only fortuitous coincidence, that is to say an effect without a cause, concluding that the reason is not acceptable. In our own [system], on the contrary, these similarities are both the consequence and proof of a relationship, not metaphorical, but real, that they hold a common ancestor, which they left at times more or less remote and through a series of intermediaries greater or fewer in number; so they express the true relationships between species by saying that the sum of their mutual similarities is the expression of their degree of relationship, as the sum of the differences is that of the distance they are from the common stock from which they derive their origin.Considered from this point of view, the plant kingdom would present, not as a linear series whose terms would increase or decrease in organizational complexity, according as we consider starting with one end or the other; it would not be more of a disordered tangle of intersecting lines, like a geographical map, whose regions, different in shape and size, would touch by a greater or lesser number of points; it would be a tree the roots of which, mysteriously hidden in the depths of cosmological time, would have given birth to a limited number of successively divided and subdivided stems. These first stems would represent the primordial types of the kingdom; their last ramifications would be the current species.It follows from there that a perfect and rigorous classification of the other organized beings of the same kingdom, of the same order, of the same family, if something other than the family tree even of the species, indicates the relative age of each, its degree of speciation and the line of ancestors from which it descended. Thereby would be represented, in a manner of some sort so palpable and material, the different degrees of relationship of the species, such as that of groups of varying degrees, dating back to the primordial kinds. Such a classification, summarized in a graphical table, would be seized with much facility by the mind through the eyes, and present the most beautiful application of this principle generally accepted by naturalists: that nature is avaricious [stingy?] of causes and prodigal of effects.This is quite clearly a description of a modern phylogenetic tree, and the taxonomic consequences of adopting that conception.

It is, however, rather a pity that he explicitly rejects a network ("a disordered tangle of intersecting lines") as a suitable model, along with the chain ("a linear series").

01:14
Genomics Week @ CIBIO-InBIO June 15-19, 2015 | CIBIO-InBIO, Vairao, Portugal >From June 15 to 19, CIBIO-InBIO will host a Genomics Week, taking place at Vairão Campus. The programme for this week includes: · on June 15-17, the advanced course “Genotyping by Sequencing (GBS): principles, approaches and applicationsâ€� [Registration required]; and · on June 18-19, a “Genomics Seminarâ€� [No registration required]. ADVANCED COURSE GENOTYPING BY SEQUENCING (GBS): PRINCIPLES, APPROACHES AND APPLICATIONS June 15-17, 2015 | Room 2 - Vairão Campus This course aims to give attendees a broad overview of Genotyping-by-Sequencing (GBS), including the principles of how data are obtained by the various different approaches, and their advantages and disadvantages. There will be a question and answer session to help determine the right approach for different study systems or special cases, such as degraded DNA. There will also be practical data-analysis sessions, where attendees will be guided through example data processing with various analysis tools. INTENDED AUDIENCE The course will be open to a maximum number of 20 participants. Priority will be given to: I. 1st year PhD students attending the BIODIV Doctoral Programme; II. Other BIODIV PhD students; III. PhD students attending other courses; IV. Other candidates. REGISTRATION Registration deadline: June 4, 2015 GENOMICS SEMINAR June 18-19, 2015 | Auditorium - Vairão Campus During this two-day seminar, five major topics in genomics research will be covered: 1. Environmental Genomics; 2. Phylogenomics; 3. Conservation/Population Genomics; 4. AgriGenomics; One Health Genomics. Participation in this seminar is free and the number of attendees is limited to the capacity of the auditorium. To know more about this event, please visit CIBIO-InBIO’s website [http://bit.ly/1SzFZf5]. References 1. mailto:divulgacao@cibio.up.pt 2. http://cibio.up.pt/ 3. http://on.fb.me/1Ecb3H2 CIBIO Divulgação via Gmail
Source: EVOLDIR
00:33
PR~Statistics Genetic data analysis using R (statistics course) 3^rd€- 7^th August 2015 - There are 4 last places left on this course The course is being delivered by Dr. Thibaut Jombart who has contributed towards a number of R packages (adegenet, adephylo, geography, outbreaker, Outbreakertools, bmmix, episerve (author) and ade4 and phylobase (contributor) and Caitlin Collins (Imperial College London) who also contributes to the R packages adegenet, Outbreakertools and episerve) This 5 day course will be held at SCENE (Scottish Centre for Ecology and the Natural Environment), Glasgow, United Kingdom from August 3rd - 7th 2015 This course will provide an extensive overview of exploratory methods for the analysis of genetic data using the R software. We will address a number of key problems in population genetics, such as: How to examine genetic diversity using phylogenetic trees as well as multivariate methods, identify genetic clusters, and unravel spatial genetic patterns. Participants will be provided with the theoretical background and statistical methodology necessary to approach each problem from a number of different angles (considering, for example, univariate and multivariate approaches). Hands-on practical sessions will then provide an opportunity to highlight the pros and cons of methods introduced by the lectures, while conferring to participants advanced knowledge of the R packages adegenet, ape, and phangorn. Altogether, the aim of this course is to equip participants with powerful resources for tackling increasingly common challenges in genetic data analysis. Course timetable: Day 1: Intro to phylogenetic reconstruction Lecture 1a: Reconstructing phylogenies from genetic sequence data. Three main approaches covered: distance-based phylogenies; maximum parsimony; and likelihood-based approaches. Lecture 1b: Short R refresher. Practical 1: Phylogenetic reconstruction using R. Three main approaches plus rooting a tree; assessing/testing for a molecular clock; and bootstrapping. Main packages: ape, phangorn. Day 2: Intro to multivariate analysis of genetic data Lecture 2: Key concepts in multivariate analysis. Focus on using factorial methods for genetic data analysis. Practical 2: Basics of multivariate analysis of genetic data in R. Topics include: data handling, population genetic tests of population structure (PCA, PCoA). Main packages: adegenet, ade4, ape. Day 3: Exploring group diversity Lecture 3: Approaches to identifying and describing genetic clusters. Topics include: hierarchical clustering, K-means, population-level multivariate analysis (between-group-PCA, DA, DAPC). Practical 3: Applying the approaches covered in morning lecture and emphasising their strengths and weaknesses. Main packages: adegenet, ade4. Day 4: Genome-Wide Association Studies (GWAS) Lecture 4: Intro to GWAS study design and statistical approaches: univariate, regression-based and multivariate analysis. Practical 4: Applying each class of methods covered in morning lecture, with emphasis on their strengths and weaknesses. Main packages: adegenet, glmnet. Day 5: Spatial genetic structures Class 1: Discussing the origin and significance of spatial genetic patterns, and how to test for them. Practical: Visualising and analysing spatial genetic data. Topics: spatial density estimates, Moran/Mantel tests, mapping principal components in PCA, spatial PCA. Main packages: adegenet, adehabitat, ade4. Cost is £490 for the 5 days including lunches and refreshments or £665 for an all-inclusive option which includes the addition of accommodation, breakfast, lunch, dinner and refreshments. For further details or questions or to register please email oliverhooker@prstatistics.co.uk or visit http://bit.ly/1v1Pet4 Please feel free to distribute this material among colleagues if you think it is suitable Additional upcoming courses; BIOINFORMATICS FOR BIOLOGISTS AND GENETICISTS; APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS; SPATIAL ANALYSIS OF ECOLOGICAL DATA USING R; ADVANCING IN R; STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR; “oliverhooker@prstatistics.co.uk” via Gmail
Source: EVOLDIR
00:33
The Eckert Lab in the Department of Biology at Queens University in Canada is seeking an enthusiastic post-doctoral researcher with expertise in population genetics and bioinformatics to investigate the population genetics of species range limits in plants. The position is funded for one year with potential renewal for a second year. The candidate will use a mix of RNAseq and RADseq to develop a large number of SNP markers for two species of plants that are the subjects of ongoing research: Rhinanthus minor (Orobanchaceae) and Decodon verticillatus (Lythraceae). In addition to collaborating with graduate students on the population-genetic components of their projects, there will plenty of opportunity to develop independent research. One option of particular interest is to investigate the shift from sexuality to obligate asexuality in Decodon verticillatus at its northern range limit in eastern North America (see Dorken et al. 2004 Proc Roy Soc Lond B 271:2375; Eckert 2002 Evol Ecol 15:501; Dorken & Eckert 2001 J Ecol 89:339). In addition to marker develop and analyses to test for genomic signatures of long-term asexuality, this project will involve fieldwork in lakes and wetlands in late summer and early autumn. Applicants are expected to have completed PhD training in evolutionary biology, population genetics and marker development along with the requisite bioinformatics skills (fluency in BASH, Python and R are essential). Experience working with plants in the greenhouse and field or a strong desire to learn these skills is desirable. A valid drivers license and passport are required. Salary is $40,000 CDN/year plus benefits. The position is open immediately and applications will be considered until a suitable candidate is found. Fieldwork starts 1 July 2015. To apply, please email your CV, a 1-page description of past research accomplishments, relevant skills and future goals, plus the names and e-mail addresses of at least 3 references to Dr. Chris Eckert (chris.eckert@queensu.ca). Informal enquiries are also welcome. For more about our research: http://bit.ly/1du9pve Queens University is medium-sized research-intensive institution (http://bit.ly/1LBiXiy) located in beautiful downtown Kingston, on the shores of eastern Lake Ontario. We enjoy a very diverse, collegial department (http://bit.ly/1c6j4TR) and excellent quality of life with easy access to the outdoors. Queens University invites applications from all qualified candidates. Queen’s is committed to employment equity and diversity in the workplace and welcomes applications from women, visible minorities, Aboriginal peoples, persons with disabilities, and persons of any sexual orientation or gender identity. Posting date: 25 May 2015 Christopher Eckert via Gmail
Source: EVOLDIR

May 25, 2015

23:29

Dear Evoldir, The 2015 Summer of V’s series of meetings at the University of St Andrews, Scotland, covers the Four V’s of Data Science - Veracity, Variety, Velocity and Volume. Meetings are explicitly aimed at all Faculties of the University, including evolutionary biologists. Everyone is very welcome to attend one, all or any number of meetings, whether you are based at St Andrews or elsewhere. Attendance is free. Meetings begin with a buffet lunch, then a talk from a prestigious invited speaker, followed by contributions from local researchers. The next meeting is on Monday 6th July, 12:30-4 PM. The programme includes: o Professor PETER CHRISTEN, Australian National University (http://bit.ly/1Fcxi0M), “Advanced record linkage methods: scalability, classification, and privacy”. o Dr AILEEN FYFE, School of History, University of St Andrews. o Dr LEN THOMAS, Centre for Research into Ecological and Environmental Modeling and School of Mathematics and Statistics, University of St Andrews. There will also be a discussion panel. For registration and further details, please see: http://bit.ly/1HHj2Db This IDIR Summer of V’s meeting is scheduled to fit with the International Environmental ‘Omics Synthesis Conference (IEOS2015), also at St Andrews. Attendees are welcome to attend one or both meetings. IEOS2015 requires separate registration (http://bit.ly/1HHj0eI).=0A We look forward to seeing you on 6th July. Thank you, Summer of V’s Organising Committee - Dr Daniel Barker db60@st-andrews.ac.uk, Professor Aaron Quigley aquigley@st-andrews.ac.uk, Professor Simon Dobson Simon.Dobson@st-andrews.ac.uk http://bit.ly/1HHj2Db The University of St Andrews is a charity registered in Scotland : No SC013532 via Gmail

Source: EVOLDIR
18:00
Background: Tribe Orchideae dominates the orchid flora of the temperate Northern Hemisphere but its representatives in East Asia had been subject to less intensive phylogenetic study than those in Eurasia and North America. Although this situation was improved recently by the molecular phylogenetic study of Jin et al., comparatively few species were analyzed from the species-rich and taxonomically controversial East Asian Amitostigma alliance. Here, we present a framework nrITS tree of 235 accessions of Orchideae plus an in-depth analysis of 110 representative accessions, encompassing most widely recognized species within the alliance, to elucidate their relationships. Results: We used parsimony, likelihood and Bayesian approaches to generate trees from data for two nuclear (rITS, low-copy Xdh) and four chloroplast (matK, psbA-trnH, trnL-F, trnS-trnG) markers. Nuclear and plastid data were analyzed separately due to a few hard incongruences that most likely reflect chloroplast capture. Our results suggest key phylogenetic placements for Sirindhornia and Brachycorythis, and confirm previous assertions that the Amitostigma alliance is monophyletic and sister to the Eurasian plus European clades of subtribe Orchidinae. Seven robust clades are evident within the alliance, but none corresponds precisely with any of the traditional genera; the smaller and more morphologically distinct genera Tsaiorchis, Hemipilia, Neottianthe and Hemipiliopsis are monophyletic but each is nested within a polyphyletic plexus of species attributed to either Ponerorchis or the most plesiomorphic genus, Amitostigma. Two early-divergent clades that escaped analysis by Jin et al. undermine their attempt to circumscribe an expanded monophyletic genus Ponerorchis. Conclusions: We provide a new framework on the complex phylogenetic relationships between Amitostigma and other genera traditionally included in its alliance; based on which, we combine the entire Amitostigma alliance into a morphologically and molecularly circumscribed Amitostigma sensu latissimo that also contains seven molecularly circumscribed sections. Our molecular trees imply unusually high levels of morphological homoplasy, but these will need to be quantified via a future group-wide review of the alliance based on living plants if morphology is to be fully integrated into our classification.

May 24, 2015

16:30

We are often told that flying is the safest way to travel, at least as far as the use of commercial airlines is concerned. In an early stand-up comedy routine, Shelley Berman noted: "Statistics prove that flying is the safest way to travel. I don't know how much consideration they've given to walking!" Well, actually, they have included walking.

Governments like to keep a track of these things, and the Department for Transport in Great Britain has released statistics on "Passenger casualty rates for different modes of travel" for 2003-2012. These modes include:
  • Air (passenger casualties in accidents involving UK registered airline aircraft)
  • Rail (passenger casualties involved in train accidents and accidents occurring through movement of railway vehicles)
  • Water (passenger casualties on UK registered merchant vessels)
  • Bus or coach (passenger casualties)
  • Car (driver and passenger casualties)
  • Van (driver and passenger casualties)
  • Motorcycle (driver and passenger casualties)
  • Pedal cycle
  • Pedestrian
The data are yearly averages for Great Britain from 2003-2012 inclusive, standardized as persons per billion passenger kilometres. The data are provided separately for the number of people killed, seriously injured, or slightly injured.

As usual, we can employ a phylogenetic network as a form of exploratory data analysis for these data. I first used the manhattan distance to calculate the similarity of the seven transportation modes for which there are complete data, followed by a Neighbor-net analysis to display the between-mode similarities as a phylogenetic network. So, modes that are closely connected in the network are similar to each other based on their accident figures across the ten years, and those that are further apart are progressively more different from each other.


The probability of incidents increases from right to left in the graph.

Some notable conclusions from the data are:
  • The probabilities of being killed, seriously injured or even slightly injured are all minuscule for air travel compared to anything else. This is a topic explored more thoroughly in an earlier blog post (A network analysis of airplane disasters).
  • You are much more likely to be injured in a bus than in a truck, but more likely to be killed in the truck than in the bus.
  • You are slightly more likely to be killed walking than cycling, but much more likely to be injured cycling.
  • A motorbike is the most effective way to get killed or seriously injured in Britain.

The walking versus cycling data are likely to surprise many people, but the average data across the 10 years are clear:

Pedestrian
Pedal cycle
Motorcycle Killed
31
27
92 Seriously injured
328
550
1,043 Slightly injured
1,245
3,190
2,997
Danny Yee (Walking and cycling: relative risks) provides one explanation:
People who wouldn't even contemplate wearing special high-visability clothing or a helmet for a walk to the shops do so when cycling the same route.

May 23, 2015

01:20
THIRD INTERNATIONAL ENVIRONMENTAL ‘OMICS SYNTHESIS CONFERENCE **important updates** **postgrads submitting abstracts entitled to full registration bursary (first-come-first-serve)** **talk abstracts due 29 May, poster abstracts due 6 June** University of St Andrews 6-8 July 2015 http://bit.ly/1Kbg9rU ABSTRACTS AND REGISTRATION ABSTRACT (TALK) DEADLINE: 29 May 2015 (extended from 25 May) REGISTRATION DEADLINE: 6 June 2015 The aim of this conference is to bring together researchers and organisations from a range of disciplines with shared interests in the development of new approaches for data handling, generation and analysis in environmental omics. Science areas of interest include bioinformatics, DNA-barcoding, genomics, metagenomics, metabarcoding, transcriptomics, proteomics, metabolomics, epigenetics, evolutionary and ecological omics, phylogenetics, study of ancient DNA and anthropology, new tools, resources and training, and beyond as applied to the study of the natural environmental and environmentally relevant organisms and systems. It is our hope is that the resulting interaction and exchange of ideas will lead to novel approaches, new collaborations and the consolidation of a wider integrated environmental omics community. EOS and this conference is supported by Natural Environmental Research Council (NERC) through its Mathematics and Informatics for Environmental Omics Data Synthesis programme and the UK Science and Technology Facilities Council (STFC) Global Challenges programme. Professor Thomas R. Meagher School of Biology, Sir Harold Mitchell Building University of St Andrews St Andrews KY16 9TH UK +44(0)1334 463364 office +44(0)7793356889 mobile +44(0)1334 463366 fax http://bit.ly/1IUL9NW Thomas Meagher via Gmail
Source: EVOLDIR
01:02
Dear All, I have just uploaded a new version of DAMBE. The main news is that (distance-based method + pairwise alignment) performs much better than (maximum likelihood method + multiple alignment) based on extensive sequence simulations of amino acid, codon and nucleotide sequences of increasing sequence divergence. The difference in performance disappears only when sequences are easily aligned or when sequences experienced full substitution saturation (when no method can recover any true tree or subtrees). The function for (distance-based method + pairwise alignment) can be accessed by clicking ‘Phylogenetics|Distance-based methods|Phylogenetics with pairwise alignment’. If you wish to compare the performance by doing simulation yourself, here are the associated functions: 1. Do sequence simulation with indels, and save the resulting unaligned sequences into a FASTA file (The indels introduced in simulation leads to different sequence lengths. Make sure that some sequences will not accumulate so many deletions that only a few AA, codon or nucleotides are left). If you take a tree with 24 OTUs and simulate 100 sets, then the FASTA file will be >S1 Sequence… >S2 Sequence… … S20 Sequence… >S1 Sequence… >S2 Sequence… … S20 Sequence… … 2. To use DAMBE to reconstruct 100 trees from these 100 sets of sequences, start DAMBE and click 'File|Open file with multiple datasets’ to read in the file (You will be asked to enter “Number of sequences per set” and you should enter 24 if there are 24 OTUs per set of data. This is needed because FASTA files have no internal structure to indicate the beginning and ending of each set of sequences). In the dialogbox on what job to perform, click 'Distance-based phylogenetics’ and click 'Run’. In the following dialog boxes, just keep default values. 3. To analyze the sequences by ML method, e.g., (PROML and DNAML in PHYLIP), you can use DAMBE to do batch alignment and then save to PHYLIP format. That is, you click 'File|Open file with multiple datasets’ to read in the file and enter the number OTUs (e.g., 24). In the dialog box on what job to perform, click 'Align multiple sets of sequences’. You may use either the built-in alignment tool (ClustalW) or use external alignment programs (I often use mafft.bat). Once the sequences are aligned, you may save them to PHYLIP format. If you have simulated 100 sets of AA sequences, then it is better to save the 100 sets of sequences into multiple files and run PROML in a parallel fashion (otherwise it may take months). In DAMBE, once the alignment is done, you will be presented with the option of saving the multiple sets to one file or to multiple files. 4. If, in your simulation of 100 sets of sequences, the simulation program produce 100 separate files, each with 24 sequences, then you click 'File|Read multiple files for batch processing’. The rest is the same. 5. Once you have produced the trees in a file, e.g., outtree from PHYLIP, paste the “true tree” (the tree used in simulation) into the file as the first tree. You need to know which methods recover more true trees/subtrees. Click 'Phylogenetics|Robinson- Foulds analysis on trees’. This will compare the 100 reconstructed tree against the first tree (the true tree). By the way, DAMBE has a good codon alignment function that align codon sequences with a 64-by-64 score matrix. It is quite good. If you simulate codon sequences, then you should align them by codon instead of by nucleotide because aligning by codon is not only faster (the sequences are three times shorter), but also more accurate. There are also a number of minor bug fixes in this release. For those who do not know what DAMBE is: it is a comprehensive software package for data analysis in molecular biology and evolution, freely available at: http://bit.ly/16O3JAO Best Xuhua http://bit.ly/1bVebhK http://bit.ly/16O3JAP Xuhua Xia Professor Biology Department University of Ottawa Rm 278 Gendron 30 Marie Curie, Ottawa, Ontario Canada K1N 6N5 Tel: (613) 562-5800 ext 6886 Xuhua Xia via Gmail
Source: EVOLDIR
01:02
A fixed term full-time Postdoctoral position (Level A) is available at the School of BioSciences (Faculty of Science), University of Melbourne. The Research Fellow will be responsible for designing, executing, and analysing field and laboratory experiments, as part of the research project “The dark side of night: species and community impacts of night lighting”, which is funded by an ARC Discovery grant. The research is part of an international collaboration between the University of Melbourne (Dr Theresa Jones and Prof Mark Elgar), the University of Exeter (Prof Kevin Gaston) and the Netherlands Institute of Ecology (Prof Marcel Visser). The position is located at The University of Melbourne and reports to the Chief Investigator. Salary: $64,863* - $88,016 p.a. (*PhD entry Level $81,998 p.a.) plus 9.5% superannuation For further information please visit the website: http://bit.ly/1JJ4cvq . Dr Theresa Jones Senior Lecturer - The Behaviour and Evolution Group The School of BioSciences, The University of Melbourne Victoria 3010, Australia Tel: +61 (0)3 90359576 Theresa Melanie Jones via Gmail
Source: EVOLDIR
01:02
A PhD position at the School of Biological Science at the University of Portsmouth (UK) Supervisor: Rocio Perez-Barrales and W. Scott Armbruster Project title: Pollination competition and facilitation as ecological driver of floral diversity and evolution in Mediterranean Linum (Linaceae) Most plants in communities tent to interact indirectly by sharing pollinators, and these interactions can bring positive or negative effects to plant fitness. At community level, most of the research has focused on whether sharing pollinators is beneficial or costly for plants. This is surprising because the sign and net effect of the interaction is context dependent. For example, adjustments in flowering phenology of species can support the pollinator community during the entire blooming season and increase the residence time of pollinators. In contrast, co-flowering species can compete for the pollinator service, and the strength of these negative interactions may be a density dependent process in a spatially explicit context. All these processes are not mutually exclusive, and they vary temporally and spatially; in the longer term, they can structure species composition and combinations of different floral traits. This PhD project will (i) evaluate how facilitation and competition for pollinator service can structure plant communities by looking at (ii) rates of intra-specific pollen flow and inter-specific pollen flow to (iii) quantify the selective value of these complex interactions as drivers of floral evolution, speciation and differentiation of traits directly linked with female and male fitness. The research will be conducted in Mediterranean communities of flax species (Linum, Linaceae) in Spain, where often several species co$B!>(Bflower and share pollinators. We are looking for enthusiastic, independent and dynamic candidates with strong interest in plant-animal interactions. Candidates must have a good Master’s degree, or good degree in Biology or Environmental Biology, with a background in Plant Population Biology, Ecology and Evolution. The candidate should be familiar with the package R for data analysis of ecological and molecular data, and flexible to work in a team and independently. It is expected that (s)he will be an active part of preparation of grant proposal and manuscripts. The candidate will gain skills both in the field and the lab. The fieldwork will be conducted in Spain, and it would be beneficial for the candidate to speak Spanish. The lab work and greenhouse experiments will be conducted in the facilities of The University of Portsmouth. In addition the candidate will have access to the Graduate School Development Programme and Department Postgraduate Researcher Training, and will join the Biodiversity and Evolution research team at the School of Biological Science. Application should be sent before the 4th June on line at http://bit.ly/1F2g9G5, but please contact me before applying at rocio.barrales@port.ac.uk Rocio Perez-Barrales Lecturer in Evolutionary Biology School of Biological Sciences University of Portsmouth Rocio Perez-Barrales via Gmail
Source: EVOLDIR

May 22, 2015

23:26

Dear colleagues, Recognizing that the difficult funding situation may have made the attendance of SMBE 2015 in Vienna for some people impossible, the Institute of Population Genetics has made 10 fellowships for SMBE attendance available. The fellowships entail a free registration to SMBE 2015 and will be awarded on a first come, first served basis with special attention given to the different time zones. In order to apply, please send a short email with the subject “conference fellowship” to office@smbe2015.at explaining your need for the fellowship and a proof for the recently rejected grant. Please note that travel grants count as well as grants submitted by the advisors. Conference website: http://bit.ly/1Ho9nMv julia.hosp@gmail.com via Gmail

Source: EVOLDIR
18:00
Background: Phylogeographic research has advanced in South America, with increasing efforts on taxa from the dry diagonal biomes. However, the diversification of endemic fauna from the semiarid Caatinga biome in northeastern Brazil is still poorly known. Here we targeted saxicolous lizards of the Tropidurus semitaeniatus species group to better understand the evolutionary history of these endemic taxa and the Caatinga. We estimated a time-calibrated phylogeny for the species group based on two mitochondrial and two nuclear genes and jointly estimated the species limits and species tree within the group. We also devoted a denser phylogeographic sampling of the T. semitaeniatus complex to explore migration patterns, and the spatiotemporal diffusion history to verify a possible role of the São Francisco River as a promoter of differentiation in this saxicolous group of lizards. Results: Phylogenetic analysis detected high cryptic genetic diversity, occurrence of unique microendemic lineages associated with older highlands, and a speciation history that took place during the Pliocene-Pleistocene transition. Species delimitation detected five evolutionary entities within the T. semitaeniatus species group, albeit with low support. Thus, additional data are needed for a more accurate definition of species limits and interspecific relationships within this group. Spatiotemporal analyses reconstructed the geographic origin of the T. semitaeniatus species complex to be located north of the present-day course of the São Francisco River, followed by dispersal that expanded its distribution towards the northwest and south. Gene flow estimates showed higher migration rates into the lineages located north of the São Francisco River. Conclusions: The phylogenetic and population structures are intrinsically associated with stable rock surfaces and landscape rearrangements, such as the establishment of drainage basins located to the northern and southern distribution ranges. The T. semitaeniatus complex preserved high genetic diversity during range expansion, possibly as a result of frequent long-distance dispersal events. Our results indicate that both the current course of the São Francisco River and its paleo-courses had an important role in promoting diversification of the Caatinga endemic T. semitaeniatus species group.
06:00
Background: Although males and females need one another in order to reproduce, they often have different reproductive interests, which can lead to conflict between the sexes. The intensity and frequency of male-male competition for fertilization opportunities is thought to be an important contributor to this conflict. The nematode genus Caenorhabditis provides an opportunity to test this hypothesis because the frequency of males varies widely among species with different mating systems. Results: We find evidence that there is strong inter- and intra-sexual conflict within C. remanei, a dioecious species composed of equal frequencies of males and females. In particular, some C. remanei males greatly reduce female lifespan following mating, and their sperm have a strong competitive advantage over the sperm of other males. In contrast, our results suggest that both types of conflict have been greatly reduced within C. elegans, which is an androdioecious species that is composed of self-fertilizing hermaphrodites and rare males. Using experimental evolution in mutant C. elegans populations in which sperm production is blocked in hermaphrodites (effectively converting them to females), we find that the consequences of sexual conflict observed within C. remanei evolve rapidly within C. elegans populations experiencing high levels of male-male competition. Conclusions: Together, these complementary data sets support the hypothesis that the intensity of intersexual conflict varies with the intensity of competition among males, and that male-induced collateral damage to mates can evolve very rapidly within populations.
01:30

PanAm EVODEVO V UC Berkeley 5-9 August 2015 [http://bit.ly/1D23EcV] COME ONE, COME ALL! EvoDevo2015 is coming together as the most exciting evodevo event of the year. If you have already registered and submitted your abstract, THANK YOU! We received over 200 submissions. The organizing committee will be selecting abstracts for oral presentations and you will be notified in the next couple of weeks. THERES SOMETHING FOR EVERYONE: Invited talks and the Contributed Sessions are selected to ensure taxonomic diversity and to include a wide variety of innovative tools and techniques for studying evodevo, demonstrating the international nature of the field and highlighting the exciting breath and depth of studies encompassed by the field of Evolutionary Developmental Biology. [http://bit.ly/1ISEHHw] PRESENT YOUR LATEST FINDINGS: While abstract submission for oral presentations is closed, we are accepting abstracts for poster presentations and registrations until July 22nd, 2015. PICTURES ARE WORTH A THOUSAND WORDS!!! THE POSTER SESSION will extend the entire duration of the meeting, and will include large blocks of time (outdoors, with sunshine, food and drink!) for presenters to interact with the community surrounding their latest data. Use this forum to engage in direct conversation with your fellow scientists: students, postdocs and faculty will be presenting their latest data in the form of creative posters and interactive displays. DO NOT MISS the opportunity to be part of this historic event. Register now for the first biennial meeting of the PanAmerican Society for Evolutionary Developmental Biology! 5-9 August Berkeley, California via Gmail

Source: EVOLDIR
00:07

Evolutionary Medicine We are looking for a brave, ambitious, fun and skilled post-doc with a very strong background in evolutionary biology who is interested in real time evolution in a US hospital setting. We want to do evolutionary risk analyses with a view to understanding the clinical decisions which drive resistance evolution. It is our contention that much of the conventional wisdom in this area has a very poor evidence base, and that understanding what is going on quantitatively will make possible evidence-based resistance management. This project is a collaboration between an Infectious Disease physician with a very strong background in evolutionary biology (Woods MD/PhD) and an evolutionary biologist with a strong interest in hospital infections (Read PhD), and will be primarily focused on data generated by clinicians during patient care. The position is based in the University of Michigan Hospital, Ann Arbor, with the expectation of considerable time at the Center for Infectious Disease Dynamics, Penn State. Here’s the formal stuff: RESEARCH FELLOW Job Summary The Department of Internal Medicine, Division of Infectious Diseases is seeking a post-doctoral applicant to take the lead on development, implementation and analysis of ecological and evolutionary models of antibiotic resistance, which could include agent-based models and compartmental dynamical model, including model fitting and parameter estimation. Additionally, the application will be expected to gather and critical synthesize literature for metanalyses, as well as take the lead on writing of manuscripts for publication. This is a collaborative project between the labs of Robert Woods at the University of Michigan and Andrew Read at Pennsylvania State University. The position will be based at the University of Michigan, with some time spent at the Center of Infectious Disease Dynamics at Penn State. Required Qualifications Ph.D. required. Experience coding in R or python is a requirement. Significant publication track record in this area, ideally with post-doctoral experience. Desired Qualifications Experience fitting microbiological data to ecological and evolutionary models, and a track record of collaboration with mathematicians, statisticians, biologists, and public health officials is an advantage. Full details and application process at http://bit.ly/1HlOUb6 Informal inquiries to Bob Woods (robertwo@med.umich.edu) or me (a.read@psu.edu). via Gmail

Source: EVOLDIR

May 21, 2015

23:49

The INRA laboratory UMR 1290 Bioger (Thiverval-Grignon, France) has a two-year open position for a research engineer in genomics and bioinformatics in the team EGIP (Evolution and Genomics of Plant Pathogen Interactions). Position: We are seeking a motivated applicant interested in providing computational and bio-informatics expertise to different fungal genomics projects developed in the team (Illumina sequencing data handling, de novo genome assembly, polymorphism detection, genome annotation, transcriptomics). The applicant will work as a member of a multidisciplinary team with evolutionary biologists, geneticists, and plant pathologists with skills in bioinformatics and fungal genome analysis. Genome annotation will be performed in close collaboration with the JGI-DOE Mycocosm project. The contract may include a stay at the JGI office in Walnut Creek near San Francisco, CA, USA. Required qualifications: Master in biology or computer science; bioinformatics experience or working knowledge of bioinformatics tools; good understanding of Linux and solid programming experience; good practice of scientific English. Please send a CV and letter(s) of recommendation to Dr Marc-Henri Lebrun (marc-henri.lebrun@versailles.inra.fr). The position is open and review of applications will continue until the position is filled. BIOGER is located on the ground of the AgroParisTech School for Engineers in Agriculture at Thiverval-Grignon. The Campus is located in the country side South-West of Paris, close to a railway station easily connected to Gare Montparnasse (http://bit.ly/1F59Anc). via Gmail

Source: EVOLDIR