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May 13, 2015
Dear EvolDir users: I’m a doctoral candidate in Mathematics Education at the University of Texas, Austin, conducting a study on biologists use of math to identify the main mathematical and statistical tools currently used in the field. The results of the study would help to inform the graduate and undergraduate curriculum in Biology and MathematicsXas well as the curriculum of related training programs outside of academiaXso that they would better align to student needs at their future workplace. The first part of the study consists of an online survey designed for biologists (from the areas of ecology, evolution, and behavior and developmental biology) that was piloted by faculty members and students at UT Austin, and has an average completion time of 9 minutes. I am emailing to ask for your participation in the survey. I can offer no compensation but I would be happy to share the results of the study, and make you eligible to win one of four $25 Amazon gift cardsXI know is not really not much, I am limited to a very small budget. The online survey is completely anonymous; you will just need to click on the link below to take it. http://bit.ly/1H2G0iC Thank you so much for taking the time to consider my request, and please let me know if you have any further questions. Pablo Duran Doctoral candidate in Mathematics Education The University of Texas at Austin Pablo Duran via Gmail
Postdoctoral position in evolutionary genomics at University of Helsinki The project The main goal of this Academy of Finland funded post-doctoral project is to address questions about the genetic underpinnings of quantitative trait variation within and among different populations of stickleback fishes. Large datasets (SNPs and full genome sequences) will be analysed with QTL- and association mapping, along with other population genomic approaches. Questions relating to phylogeographical relationships among different populations and species of sticklebacks, as well as the relative roles of selective and neutral processes underlying the inferred relationships, are also to be addressed within this project. Opportunities for collaborative projects with other unit members and research associates are possible. The candidate would be given freedom to pursue her/his own ideas and research interests within the general framework of the main project. Requirements We are looking for an ambitious postdoctoral researcher with strong enthusiasm towards science. The successful candidate should have PhD / post doctoral experience within the fields of evolutionary genetics/genomics, bioinformatics and/or animal breeding, with genuine interest towards addressing problems at the population level (rather than comparative genomics). Excellent bioinformatics skills and experience in handling both large marker datasets and full-genome sequence analyses (e.g. programming in C, or scripting language Python and/or Perl), as well as good written and verbal communication skills in English are required. Starting date The preferred starting date is 1st January 2016, but an earlier start date is negotiable (earliest possible start date: 1st October 2015). The employment contract includes a trial period of 4 months. Salary The salary will be based on level 5 of the demands level chart for teaching and research personnel in the salary system of Finnish universities. In addition, the appointee will be paid a salary component based on personal work performance. The total minimum salary at the beginning of the employment is 3127,54 euro/month. How to apply To apply, please send your CV with publication list and contact details of two references, and a letter (max 2 pages) with a description of your research interests and career goals. In particular, please provide clear motivation for your suitability as a candidate for this position. Send these documents as a single pdf-file to email@example.com Apply at latest 31 July 2015. Information For more information, please contact Prof. Juha Merilä (firstname.lastname@example.org), Tel: +358-40-8374165. More information about host groups research profile, please consult e.g. http://bit.ly/1G5eFjF About the host institute The University of Helsinki, founded in 1640, is one of the world’s leading universities for multidisciplinary research. The university has an international academic community of 40,000 students and staff members. The University of Helsinki offers comprehensive services to its employees, including occupational health care and health insurance, sports facilities, and opportunities for professional development. The International Staff Services office assists employees from abroad with their transition to work and life in Finland. The Department of Biosciences situated at the Viikki science park belongs to the Faculty of Biological and Environmental Sciences of University of Helsinki and is the largest research and teaching unit in biosciences in Finland. The department of is one of the largest departments of Helsinki University with its c. 25 million euro budget and over 400 staff members. It hosts research community of experimental, computational, and theoretical labs with common interest in Evolutionary Biology. Cutting edge infrastructure is available at all levels, including high-performance computer clusters, access to next-generation sequencing facilities, molecular biology labs and animal breeding facilities. Juha Merilä via Gmail
POSTDOC IN POPULATION/COMPUTATIONAL GENOMICS, Institut Pasteur A postdoctoral position in population/computational genomics is available in the Human Evolutionary Genetics Unit (Quintana-Murcis Lab), in the Department of Genomes and Genetics at Institut Pasteur in Paris. The lab combines large empirical datasets and computation approaches to study human population genetics, for more information see http://bit.ly/LRWdT1. Current work in the lab focuses on a wide range of topics, including (i) the study of the relative effects of demography and natural selection in the shaping of human genome variability using next-generation sequencing data, (ii) the genetic control of gene expression related to immunity-related processes, (iii) the influence of genetic variation and changes in lifestyle and ecologies of human populations on patterns of epigenetic variation. Our lab benefits from the large and outstanding community of researchers in population genetics, epigenetics, microbiology, immunology and computational biology at the Institut Pasteur, providing a working interdisciplinary research environment. Applicants must have a strong background in statistics and computer science and a desire to do research in genetics and evolutionary biology, or a strong background in theoretical population genetics with experience analyzing genomewide datasets. Programming skills and proficiency in unix-based computational environments are essential.The applicants will have the freedom to choose their own projects as long and they fit within the general interests of our lab. US citizens are encouraged to apply to the prestigious Pasteur Foundation Postdoctoral Fellowships (Deadline September 10, 2015). Detailed information can be found at http://bit.ly/1PFXgPf Informal inquiries as well as applications (including a CV, research statement, copies of relevant publications and contact information for at least two references) should be emailed to Lluis Quintana-Murci at . Lluis QUINTANA-MURCI Unit of Human Evolutionary Genetics, CNRS URA3012 Institut Pasteur 25, rue du Dr. Roux 75724 Paris Cedex 15 France Tel: +33 1 40 61 34 43 Fax: +33 1 45 68 87 27 e-mail: email@example.com Lab Website: http://bit.ly/LRWdT1 Lluis Quintana-Murci via Gmail
May 12, 2015
cE3c – Centre for Ecology, Evolution and Environmental Changes Advanced Course Climate Change: scenarios, impacts and responses organized by Maria Joao Cruz and Elisabeth Robert | July 13-17 2015 @ Lisbon, Portugal Climate Change: scenarios, impacts and responses Objectives: The goal of this short course is to introduce the students to the main climate change research concepts and prepare them to use available information on scenarios, impacts and adaptation. Specific goals include: Study climate change and socio-economic scenarios and have an overview of what are the predictions for Portugal, Europe and the World; Explore the main expected impacts of climate change in a range of sectors; Explore direct and indirect impacts on biodiversity; introduction vulnerability assessment methodologies; Study specific responses to climate change, namely Mitigation and Adaptation (including Ecosystem based Adaptation), looking at specific examples in a range of scales. Course Coordinators: Maria Joao Cruz (firstname.lastname@example.org) Elisabeth Robert (email@example.com) Researchers at the Centre for Ecology, Evolution and Environmental Changes (cE3c - http://bit.ly/1H2CkgO), Research Group CCIAM Intended audience This course will be open to a maximum number of 20 participants. Minimum formation: Bachelor in Biology or related area. The course is free for 1st year PhD students in the Doctoral programme in Biology (FCUL), Biodiversity, Genetics and Evolution (UL; UP) and Biology and Ecology of Global Changes (UL, UA). For information of fees for other participants see the programme details (access link below) Deadline for applications: June 19, 2015 Candidates should send a short CV and motivation letter to Ângela Antunes (email - firstname.lastname@example.org). For additional details about the programme of the course, fees and to know how to register, click here, and access the specific course http://bit.ly/1JbO0Tl For more information about the course, please contact: email@example.com Margarida Matos, PhD Centro de Ecologia, Evolução e Alterações Ambientais (cE3c - Centre for Ecology, Evolution and Environmental Changes) Faculdade de Ciências da Universidade de Lisboa Campo Grande, Edificio C2 - 5º Piso Phone: +351 217500000 ext. 22141 1749-016 Lisboa Portugal Margarida Matos via Gmail
Dear Colleagues, Registration is open for the course MULTIVARIATE DATA ANALYSIS FOR ECOLOGY AND EVOLUTION IN R. Date: January 18-22, 2016. Instructors: Dr. Dean Adams((Iowa State University, USA) and Dr. Antigoni Kaliontzopoulou (Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), Portugal). Course Webpage: http://bit.ly/1Fd0iZP This course is directed towards PhD students and researchers interested in exploring the potential of R language for multivariate analyses in ecology and evolution. The course will provide a general presentation of major statistical tools for multivariate analyses, including exploratory methods, multivariate GLM, methods for controlling for evolutionary and ecological non-independence, model selection and analysis of dispersion. The course will include a morning and an afternoon session. During the morning session, the instructors will discuss major themes in ecology and evolution and associate them to the statistical tools available for exploring specific scientific questions. The afternoon session will begin with a short (1h) demonstration of R code based on a worked, biological example and followed by practical training by the participants. At the end of the course, participants will each give a presentation on their research system, potentially including some analyses carried out during the course, or ideas of how they might incorporate the knowledge acquired during the course to their research. This course will be held in the Sabadell facilities of the Institut Català de Paleontologia (Barcelona, Spain) and is co-organized by Transmitting Science and the Institut Catalá de Paleontologia M. Crusafont. Place are limited and will be covered by strict registration order. please feel free to distribute this information between your colleagues if you consider it appropriate. With best regards Soledad De Esteban-Trivigno, PhD.firstname.lastname@example.org Transmitting Science http://bit.ly/1gdSpYn email@example.com via Gmail
A protocol for the delimitation of areas of endemism and the historical regionalization of the Brazilian Atlantic Rain Forest using harvestmen distribution data
The concept of areas of endemism (AoEs) has rarely been discussed in the literature, even though the use of methods to ascertain them has recently increased. We introduce a grid-based protocol for delimiting AoEs using alternative criteria for the recognition of AoEs that are empirically tested with harvestmen species distributions in the Atlantic Rain Forest. Our data, comprising 778 records of 123 species, were analysed using parsimony analysis of endemicity and endemicity analysis on four different grids (two cell sizes and two cell placements). Additionally, we employed six qualitative combined criteria for the delimitation of AoEs and applied them to the results of the numerical analyses in a new protocol to objectively delimit AoEs. Twelve AoEs (the most detailed delimitation of the Atlantic Rain Forest so far) were delimited, partially corroborating the main divisions previously established in the literature. The results obtained with the grid-based methods were contradictory and were plagued by artefacts, probably due to the existence of different endemism patterns in one cell or to a biogeographical barrier set obliquely to latitudinal and longitudinal axes, for example. Consequently, the congruence patterns found by them should not be considered alone; qualitative characteristics of species and clade distributions and abiotic factors should be evaluated together. Mountain slopes are the main regions of endemism, and large river valleys are the main divisions. Refuges, marine transgressions and tectonic activity seem to have played an important role in the evolution of the Atlantic Rain Forest.
This is a guest blog post, following on from his previous post, by:
Johann-Mattis ListCentre des Recherches Linguistiques sur l'Asie Orientale, Paris, France
All languages constantly change. Words are lost when speakers cease to use them, new words are gained when new concepts evolve, and even the pronunciation of the words changes slightly over time. Slight modifications that can barely be noticed during a person's lifetime sum up to great changes in the system of a language over centuries. When the speakers of a language diverge, their speech keeps on changing independently in the two communities, and at a certain point of time the independent changes are so great that they can no longer communicate with each other — what was one language has become two.
Demonstrating that two languages once were one is one of the major tasks of historical linguistics. If no written documents of the ancestral language exist, one has to rely on specific techniques for linguistic reconstruction (see the examples in this previous post). These techniques require us to first identify those words in the descendant languages that presumably go back to a common word form in the ancestral language. In identifying these words, we infer historical relations between them. The most fundamental historical relation between words is the relation of common descent. However, similarly to evolutionary biology, where homology can be further subdivided into the more specific relations of orthology, paralogy, and xenology, more specific fundamental historical relations between words can be defined for historical linguistics, depending on the underlying evolutionary scenario.
Homology and Cognacy in Linguistics and Biology
In evolutionary biology there is a rather rich terminological framework describing fundamental historical relations between genes and morphological characters. Discussions regarding the epistemological and ontological aspects of these relations are still ongoing (see the overview in Koonin 2005, but also this recent post by David). Linguists, in contrast, have rarely addressed these questions directly. They rather assumed that the fundamental historical relations between words are more or less self-evident, with only few counter-examples, which were largely ignored in the literature (Arapov and Xerc 1974; Holzer 1996; Katičić 1966). As a result, our traditional terminology to describe the fundamental historical relations between words is very imprecise and often leads to confusion, especially when it comes to computational applications that are based on software originally developed for applications in evolutionary biology.
As an example, consider the fundamental concept of homology in evolutionary biology. According to Koonin (2005: 311), it "designates a relationship of common descent between any entities, without further specification of the evolutionary scenario". The terms orthology, paralogy, and xenology are used to address more specific relations. Orthology refers to "genes related via speciation" (Koonin 2005: 311); that is, genes related via direct descent. Paralogy refers to "genes related via duplication" (ibid.); that is, genes related via indirect descent. Xenology, a notion which was introduced by Gray and Fitch (1983), refers to genes "whose history, since their common ancestor, involves an interspecies (horizontal) transfer of the genetic material for at least one of those characters" (Fitch 2000: 229); i.e. to genes related via descent involving lateral transfer.
In historical linguistics, the only relation that is explicitly defined is cognacy (also called cognation). Cognacy usually refers to words related via “descent from a common ancestor” (Trask 2000: 63), and it is strictly distinguished from descent involving lateral transfer (borrowing). The term cognacy itself, however, covers both direct and indirect descent. Hence, traditionally, German Zahn 'tooth' is cognate with English tooth, and German selig 'blessed' with English silly, and German Geburt 'birth' with English birth, although the historical processes that shaped the present appearance of these three word pairs are quite different. Apart from the sound shape, Zahn and tooth have regularly developed from Proto-Germanic *tanθ-; selig and silly both go back to Proto-Germanic *sæli- 'happy', but the meaning of the English word has changed greatly; Geburt and birth stem from Proto-Germanic *ga-burdi-, but the English word has lost the prefix as a result of specific morphological processes during the development of the English language (all examples follow Kluge and Seebold 2002, with modifications for the pronunciation of Proto-Germanic). Thus, of the three examples of cognate words given, only the first would qualify as having evolved by direct inheritance, while the inheritance of the latter two could be labelled as indirect, involving processes which are largely language-specific and irregular, such as meaning shift and morpheme loss. Trask (2000: 234) suggests the term oblique cognacy to label these cases of indirect inheritance, but this term seems to be rarely used in historical linguistics; and at least in the mainstream literature of historical linguistics I could not find even a single instance where the term was employed (apart from the passage by Trask).
In the table above (with modifications taken from List 2014: 39), I have tried to contrast the terminology used in evolutionary biology and historical linguistics by comparing to which degree they reflect fundamental historical relations between words or genes. Here, common descent is treated as a basic relation which can be further subdivided into relations of direct common descent, indirect common descent, and common descent involving lateral transfer. As one can easily see, historical linguistics lacks proper terms for at least half of the relations, offering no exact counterparts for homology, orthology, and xenology in evolutionary biology.
Cognacy in historical linguistics is often deemed to be identical with homology in evolutionary biology, but this is only true if one ignores common descent involving lateral transfer. One may argue that the notion of xenology is not unknown to linguists, since the borrowing of words is a very common phenomenon in language history. However, the specific relation which is termed xenology in biology has no direct counterpart in historical linguistics: the term borrowing refers to a distinct process, not a relation resulting from the process. There is no common term in historical linguistics which addresses the specific relation between such words as German kurz 'short' and English short. These words are not cognate, since the German word has been borrowed from Latin cŭrtus 'mutilated' (Kluge and Seebold 2002). They share, however, a common history, since Latin cŭrtus and English short both (may) go back to Proto-Indo-European *(s)ker- 'cut off' (Vaan 2008: 158). The specific history behind these relations is illustrated in the following figure.
A specific advantage of the biological notion of homology as a basic relation covering any kind of historical relatedness, compared to the linguistic notion of cognacy as a basic relation covering direct and indirect common descent, is that the former is much more realistic regarding the epistemological limits of historical research. Up to a certain point, it can be fairly reliably demonstrated that the basic entities in the respective disciplines (words, genes, or morphological characters) share a common history. Demonstrating that more detailed relations hold, however, is often much harder. The strict notion of cognacy has forced linguists to set goals for their discipline which may often be far too ambitious to achieve. We need to adjust our terminology accordingly and bring our goals into balance with the epistemological limits of our discipline. In order to do so, I have proposed to refine our current terminology in historical linguistics to the schema shown in the table below (with modifications taken from List 2014: 44):
Fifty Shades of Cognacy
In a recent blog post, David pointed to the relative character of homology in evolutionary biology in emphasizing that it "only applies locally, to any one level of the hierarchy of character generalization". Recalling his example of bat wings compared to bird wings, which are homologous when comparing them as forelimbs but who are analogous when comparing them as wings, we can find similar examples in historical linguistics.
If we consider words for 'to give' in the four Romance languages Portuguese, Spanish, Provencal and French, then we can state that both Portuguese dar and Spanish dar are homologous, as are Provencal douna and French donner. The former pair go back to the Latin word dare 'to give', and the latter pair go back to the Latin word donare 'to gift (give as a present)'. In those times when Latin was commonly spoken, both dare and donare were clearly separated words denoting clearly separated contexts and being used in clearly separated contexts. The verb donare itself was derived from Latin donum 'present, gift'. Similarly to English where nouns can be easily used as verbs, Latin allowed for specific morphological processes. In contrast to English, however, these processes required that the form of the noun was modified (compare English gift vs. to gift with Latin donum vs. donare).
What the ancient Romans (who spoke Latin as their native tongue) were not aware of is that Latin donum 'gift' and Latin dare 'to give' themselve go back to a common word form. This was no longer evident in Latin, but it was in Proto-Indo-European, the ancestor of the Latin language. Thus, Latin dare goes back to Proto-Indo-European *deh3- 'to give', and Latin donum goes back to Proto-Indo-European *deh3-no- 'that which is given (the gift)' (Meiser 1999; what is written as *h3 in this context was probably pronounced as [x] or [h]). The word form *deh3-no- is a regular derivation from *deh3-, so at the Indo-European level both forms are homologous, since one is derived from the other. That means, in turn, that Latin dare and donum are also homologs, since they are the residual forms of the two homologous words in Proto-Indo-European. And since Latin donare is a regular derivation of donum, this means, again, that Latin dare and donare are also homologous, as are the words in the four descendant languages, Portuguese dar, Spanish dar, Provencal douna, and French donner. Depending on the time depth we apply, we will arrive at different homology decisions. I have tried to depict the complex history of the words in the following figure:
Judging from the treatment in linguistic databases, many scholars do not regard these different "shades of homology" as a real problem. In most cases, scholars use a "lumping approach" and label as cognates all words that go back to a common root, no matter how far that root goes back in time (compare, for example, the cognate labeling for reflexes of Proto-Indo-European *deh3- in the IELex).
Importantly, this labeling practice, however, may be contrary to the models that are used to analyze the data afterwards. All computational analyses model language evolution as a process of word gain and word loss. The words for the analyses are sampled from an initial set of concepts (such as 'give', 'hand', 'foot', 'stone', etc.) which are translated into the languages under investigation. If we did not know about the deeper history of Latin dare and donare, we would assume a regular process of language evolution here: at some point, the speakers of Gallo-Romance would cease to use the word dare to express the meaning 'to give' and use the word donare instead, while the speakers of Ibero-Romance would keep on using the word dare. This well-known process of lexical replacement (illustrated in the graphic below), which may provide strong phylogenetic signals, is lost in the current encoding practice where all four words are treated as homologs. Our current practice of cognate coding masks vital processes of language change.
Historical linguistics needs a more serious analysis of the fundamental processes of language change and the fundamental historical relations resulting from these processes. In the last two decades a large arsenal of quantitative methods has been introduced in historical linguistics. The majority of these methods come from evolutionary biology. While we have quickly learned to adapt and apply these methods to address questions of language classification and language evolution, we have forgotten to ask whether the processes these methods are supposed to model actually coincide with the fundamental processes of language evolution. Apart from adapting only the methods from evolutionary biology, we should consider also adapting the habit of having deeper discussions regarding the very basics of our methodology.
Arapov MV, Xerc MM (1974) Математические методы в исторической лингвистике [Mathematical methods in historical linguistics]. Moscow: Nauka. German translation: Arapov, M. V. and M. M. Cherc (1983). Mathematische Methoden in der historischen Linguistik. Trans. by R. Köhler and P. Schmidt. Bochum: Brockmeyer.
Fitch WM (2000) Homology: a personal view on some of the problems. Trends in Genetics 16.5, 227-231.
Gray GS, Fitch WM (1983) Evolution of antibiotic resistance genes: the DNA sequence of a kanamycin resistance gene from Staphylococcus aureus. Molecular Biology and Evolution 1.1, 57-66.
Holzer G (1996) Das Erschließen unbelegter Sprachen. Zu den theoretischen Grundlagen der genetischen Linguistik. Frankfurt am Main: Lang
Katičić R (1966) Modellbegriffe in der vergleichenden Sprachwissenschaft. Kratylos 11, 49-67.
Kluge F, Seebold E (2002) Etymologisches Wörterbuch der deutschen Sprache. 24th ed. Berlin: de Gruyter.
List J-M (2014) Sequence Comparison in Historical Linguistics. Düsseldorf: Düsseldorf University Press.
Meiser G (1999) Historische Laut- und Formenlehre der lateinischen Sprache. Wissenschaftliche Buchgesellschaft: Darmstadt.
Vaan M (2008) Etymological Dictionary of Latin and the Other Italic Languages. Leiden and Boston: Brill.
Background: Haplodiploidy, where females develop from diploid, fertilized eggs and males from haploid, unfertilized eggs, is abundant in some insect lineages. Some species in these lineages reproduce by thelytoky that is caused by infection with endosymbionts: infected females lay haploid eggs that undergo diploidization and develop into females, while males are very rare or absent. It is generally assumed that in thelytokous wasps, endosymbionts merely diploidize the unfertilized eggs, which would then trigger female development. Results: We found that females in the parasitoid wasp Asobara japonica infected with thelytoky-inducing Wolbachia produce 0.7–1.2 % male offspring. Seven to 39 % of these males are diploid, indicating that diploidization and female development can be uncoupled in A. japonica. Wolbachia titer in adults was correlated with their ploidy and sex: diploids carried much higher Wolbachia titers than haploids, and diploid females carried more Wolbachia than diploid males. Data from introgression lines indicated that the development of diploid individuals into males instead of females is not caused by malfunction-mutations in the host genome but that diploid males are most likely produced when the endosymbiont fails to activate the female sex determination pathway. Our data therefore support a two-step mechanism by which endosymbionts induce thelytoky in A. japonica: diploidization of the unfertilized egg is followed by feminization, whereby each step correlates with a threshold of endosymbiont titer during wasp development. Conclusions: Our new model of endosymbiont-induced thelytoky overthrows the view that certain sex determination mechanisms constrain the evolution of endosymbiont-induced thelytoky in hymenopteran insects. Endosymbionts can cause parthenogenesis through feminization, even in groups in which endosymbiont-diploidized eggs would develop into males following the hosts’ sex determination mechanism. In addition, our model broadens our understanding of the mechanisms by which endosymbionts induce thelytoky to enhance their transmission to the next generation. Importantly, it also provides a novel window to study the yet-poorly known haplodiploid sex determination mechanisms in haplodiploid insects.
Source: BMC Evolutionary Biology
Background: When overlapping sets of genes encode multiple traits, those traits may not be able to evolve independently, resulting in constraints on adaptation. We examined the evolution of genetically integrated traits in digital organisms—self-replicating computer programs that mutate, compete, adapt, and evolve in a virtual world. We assessed whether overlap in the encoding of two traits – here, the ability to perform different logic functions – constrained adaptation. We also examined whether strong opposing selection could separate otherwise entangled traits, allowing them to be independently optimized. Results: Correlated responses were often asymmetric. That is, selection to increase one function produced a correlated response in the other function, while selection to increase the second function caused a complete loss of the ability to perform the first function. Nevertheless, most pairs of genetically integrated traits could be successfully disentangled when opposing selection was applied to break them apart. In an interesting exception to this pattern, the logic function AND evolved counter to its optimum in some populations owing to selection on the EQU function. Moreover, the EQU function showed the strongest response to selection only after it was disentangled from AND, such that the ability to perform AND was lost. Subsequent analyses indicated that selection against AND had altered the local adaptive landscape such that populations could cross what would otherwise have been an adaptive valley and thereby reach a higher fitness peak. Conclusions: Correlated responses to selection can sometimes constrain adaptation. However, in our study, even strongly overlapping genes were usually insufficient to impose long-lasting constraints, given the input of new mutations that fueled selective responses. We also showed that detailed information about the adaptive landscape was useful for predicting the outcome of selection on correlated traits. Finally, our results illustrate the richness of evolutionary dynamics in digital systems and highlight their utility for studying processes thought to be important in biological systems, but which are difficult to investigate in those systems.
Source: BMC Evolutionary Biology
Hi everyone, For a meta-analysis, we are looking for microsatellite (SSR) datasets from plants sampled in North-America. If you have such data available -either published or unpublished- are you willing to share it with us? Many thanks in advance, Patrick Meirmans Patrick Meirmans Institute for Biodiversity and Ecosystem Dynamics (IBED) University of Amsterdam Postal address: P.O. Box 94248, 1090GE Amsterdam Visiting address: Science Park 904, room C4.165, 1098XH Amsterdam Tel: +31 20 5258424 firstname.lastname@example.org http://bit.ly/1JE08KX Patrick Meirmans via Gmail
Three advanced courses from cE3c Portugal. via Gmail
Post-doctoral Position in nonhuman primate functional genomics A postdoctoral position in nonhuman primate functional genomics is available under the co-mentorship of Dr. Luis Barreiro (University of Montreal and at the Sainte-Justine Hospital Research Center) and Dr. Jenny Tung (Duke University). Collaborative projects between our labs focus on the biological consequences of social relationships and social stressors in primates, using genomic and computational tools. More details on some of our ongoing projects can be found at http://bit.ly/1bTGx7s or http://bit.ly/1JE06T7. Postdoctoral applicants should have a strong background in evolutionary, behavioral, or computational genomics. Strong data analysis skills, including programming and statistical modeling experience, are essential. Familiarity or experience with primate behavior or population genetics is a plus. The applicants will have the freedom to choose their own projects as long as they fit within the general interests of our collaborative research. Our labs offer congenial research environments that foster strong interdisciplinary training and collaborative exchange. This position is posted through the University of Montreal, with flexibility to be physically based either in Montreal or in North Carolina. To apply for the position please send an email to Luis Barreiro (email@example.com) and Jenny Tung (firstname.lastname@example.org) including a cover letter, current CV, and contact information for at least two references. *Luis Barreiro, PhD.* *Assistant Professor * *CHU Sainte-Justine/University of Montreal* *Canadian Research Chair in Functional and Evolutionary * *Genomics of the Immune System. * 3175, Cte Sainte-Catherine, *Phone# : 514-345-4931 ext. 2544* *e-mail: email@example.com firstname.lastname@example.org via Gmail
*MSc. Position in Ecological Genomics at University of New Brunswick Saint John: Striped Bass Adaptation (Fall 2015 or Winter 2016)* A position is available for a Masters of Science student to participate in an integrated Striped Bass genomics research program. The student will use ecologically divergent populations and full-genome re-sequencing to determine the genetic basis of adaptation. The student will be part of a lab of a new Canada Research Chair in Aquatic Molecular Ecology and Ecological Genomics at the University of New Brunswick in Saint John. Funding is available for a stipend or top-up bonus for students with funding. The student will use state-of-the-art laboratory equipment, including robotics, to streamline repetitive tasks and will have priority access to a high-powered computer with 1.5 TB of RAM for bioinformatics. The lab is located at the Canadian Rivers Institute ( http://bit.ly/1KDkZOw). Suitable candidates will have a solid quantitative background with experience in genetics and genomics lab work and/or bioinformatics. Candidates must have a positive attitude and willingness to work with a team. Experience in programing with R, Python or Perl computer languages is a plus. The position will begin in the fall term of 2015 or winter of 2016. Submit a Cover Letter, CV, contact information for three references and unofficial transcripts that include course names to Dr. Scott Pavey ( email@example.com). Application packages will be accepted until the position is filled. Scott Pavey via Gmail
*Research Assistant: Tropical Fieldwork Trinidad July 2015* A volunteer field assistant is required to help with a field-based project on behaviour in social wasps. This project combines behavioural experiments with next-generation sequencing to understand the molecular mechanisms behind sociality. Fieldwork will be conducted on the island of Trinidad, and will run from July-September. Research involves marking individual wasps, manipulations, conducting censuses, sample collections, and behavioural observations. Research is suited towards those with a keen interest in behavioural ecology, social evolution, and/or entomology. See link below: http://bit.ly/1He8Y4k *Dr Daisy Taylor* Post-doctoral Research Assistant School of Biological Sciences 24 Tyndall Avenue Bristol BS8 1TQ UK firstname.lastname@example.org DA Taylor via Gmail
Summer School on Evolutionary Developmental Biology Conceptual and Methodological Foundations 4th Edition: The Evolution of Developmental Processes Venice, 28 September 1 October 2015 Organizers: Alessandro Minelli, Gerd B. Mller and Giuseppe Fusco School director: Johannes Jaeger School sponsors: Istituto Veneto di Scienze, Lettere ed Arti, Venice and Konrad Lorenz Institute for Evolution and Cognition Research, Vienna. Location: Istituto Veneto di Scienze, Lettere ed Arti, Palazzo Franchetti, Venice Taching panel: J. Jaeger (School Director, CRG Barcelona), P. Beldade (Gulbenkian Institute, Lisbon), G.E. Budd (University of Uppsala), G. Fusco (University of Padova), R. Jenner (Natural History Museum, London), A. Khila (Institut de Gnomique Fonctionnelle de Lyon), A. McGregor (Oxford Brookes University), A. Minelli (University of Padova), C. Mirth (Instituto Gulbenkian de Ciencia, Oeiras, Portugal), G.B. Mller (Konrad Lorenz Institute, Vienna, and University of Vienna), A. Peel (University of Leeds) Deadline for applications: May 30th 2015 For details, visit Giuseppe Fusco Department of Biology University of Padova Via U. Bassi 58/B I-35131 Padova Italy tel. +39.049.827.6238 fax +39.049.827.6230 e-mail email@example.com webpage http://bit.ly/1MHIFBm Giuseppe Fusco via Gmail
May 10, 2015
Building non-model species genome curation communities
May 9, 2015
This is a multi-part message in MIME format. via Gmail
BIOINFORMATICIAN WITH FOCUS ON GENOME ANNOTATION Full time permanent position. The position is available as soon as possible. 6 months trial period. Uppsala University is an international research university focused on the development of science and education. Our most important assets are all the individuals who with their curiosity and their dedication makes Uppsala University one of Sweden’s most exciting work places. Uppsala University has 45.000 students, 6,800 employees and a turnover of SEK 6,300 million. Bioinformatics Infrastructure for Life Sciences (BILS; http://bils.se) is furthering life science research in Sweden by providing support in the field of bioinformatics. Over 45 experts are currently employed at multiple sites in Sweden, supporting projects in a wide array of areas such as genomics, transcriptomics, proteomics, metabolomics, statistics, and more. BILS is working closely together with SciLifeLab (http://bit.ly/17a7QLt), a national resource that facilitates research in molecular biosciences by providing access to advanced technologies and technical know-how. Through recent acquisitions, SciLifeLab is now the third largest sequencing center in Europe. The large amount of resources available makes Sweden one of the best countries in the world to perform life science research, and together with talented Swedish researchers this has placed Sweden at the forefront of fields such as comparative genomics and genome evolution. BILS is now looking for a new member to the genome assembly and annotation team to work with in particular annotation of eukaryote genomes. The team is placed at Uppsala University in the creative environment of the SciLifeLab Uppsala node “The Hub” where more than 20 bioinformaticians as well as core facilities and many different research groups are interacting. The team is working in close collaboration with Swedish research groups to supply genome assemblies and genome annotations of a high international standard. Job description: We are looking for an expert with a strong background in NGS bioinformatics and an interest in genome annotation. The work will involve helping Swedish genome annotation projects with anything from providing guidance in the setup and running of annotation projects to completely running the whole annotation process for the customer. The projects will differ in complexity from quick-running jobs of a few days to longer projects of several months and can focus on any type of organism, but mostly eukaryotes. A familiarity with scripting and automation of procedures in a Linux environment is of importance, as the work also will involve the maintenance and improvement of existing pipelines and methods. Qualifications: We seek a candidate with a PhD in bioinformatics, molecular biology, computer science or any related field with a strong competence in genome annotation or a related field such as transcriptomics. Experience from large eukaryote genome projects is valued highly. Proficiency in one or more scripting languages (e.g. Perl, Python, Ruby) is a necessity, with experience in Ensembl-API or Ensembl-Hive considered extra beneficial. The ability to drive projects and work in a collaborative, yet service-minded environment is a must. Excellent communication skills in both written and spoken English are required, since the candidate will collaborate with scientists of very different backgrounds. Emphasis will be placed on personal suitability for the position. Information: For questions regarding BILS, please check out our website at http://www.bils.se or contact the director of BILS, Bengt Persson (firstname.lastname@example.org). For questions regarding the position, please send an E-mail to Henrik Lantz (email@example.com). You are welcome to submit your application no later than June 1, 2015, UFV-PA 2015/1037. Use the link below to access the application form.We decline offers of recruitment and advertising help. We only accept the application the way described in the advertisement. http://bit.ly/1IYm5Gg via Gmail
Postdoc in bioinformatics A postdoc position is available on a project to study the evolutionary dynamics of genomes and transcriptomes. The postdoc will work in collaboration on two projects: (1) Evo-devo genomics, in the Robinson-Rechavi lab: evolutionary study of the duplication history of chordate genomes, including de novo assembly of a Mediterranean amphioxus genome from PacBio long reads, and comparative transcriptomics analysis from RNA-seq: (2) Evolution of sex chromosomes, in the Pannell and Perrin labs: assembly and polymorphism analysis of sex chromosomes from plants and amphibians. The postdoc would be expected to take a leading position on the bioinformatics of the genomics of non-model organisms, and to participate actively in evolutionary analyses and interpretation. The postdoc will work closely with other bioinformaticians and evolutionary genomicists on both projects. In the medium term, the postdoc will be expected to develop his or her own subproject and publications. The position will be in co-supervision between Profs Marc Robinson-Rechavi, John Pannell and Nicolas Perrin, all three in the Department of Ecology and Evolution. Prof Robinson-Rechavi is also a group leader at the Swiss Institute of Bioinformatics, and the postdoc will also be a full member of the SIB. The starting contract will be for 1 year, starting as soon as possible, renewable for up to five years; the postdoc will participate in some undergraduate and/or masters teaching, in English or in French. The ideal candidate would have a doctorate degree in bioinformatics, genomics, or a related field; a good command of Unix and another programming language; hands-on experience with genomic data; and an interest in pursuing research on non model organisms. Experience with the R language and cluster computing would be beneficial. Funds for the position are available immediately, and our preference would be to appoint someone to the position this summer, if possible. Full applications, which should include a cover letter, a CV, and the contact information of 3 referees, should be sent to firstname.lastname@example.org as a single PDF document. Informal enquiries should be directed to email@example.com; firstname.lastname@example.org; and/or email@example.com. Deadline for applications: all applications received by May 22, 2015, will be given full consideration, but the position will remain open until the right candidate has been appointed. For background on the labs in which you would be working, please see: Robinson-Rechavi lab: http://bit.ly/1xmcvV6 Pannell lab: http://bit.ly/1xmcujX Perrin lab: http://bit.ly/1BDu34l John Richard Pannell via Gmail
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology