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October 11, 2014
Dear EvolDir Members, if you have seen our announcement of three weeks ago and you have a study that satisfies the criteria specified then (see below), we would be very grateful, if you could contact us in the next week. Thank you Margarita Lpez-Uribe email@example.com> Shalene Jha firstname.lastname@example.org Antonella Soro email@example.com As part of a meta-analysis on bee population genetics, I request information regarding population differentiation indices in bees. This request is part of a collaborative study between myself, Shalene Jha (Assistant Professor in the Department of Integrative Biology at the University of Texas at Austin), and Margarita Lpez-Uribe (Postdoctoral Researcher at North Carolina State University). So far, we have examined studies acquired through the Web of Science, but we would like to increase our sample size with the incorporation of additional studies (published or unpublished). Specifically, we are looking for data sets where bee population genetics analyses have been conducted with: at least 5 microsatellite markers at least 20 unrelated individual per population at least 5 populations If you have one or more data sets that satisfy these criteria and are willing to contribute, please provide us with the reference to your work (if published) and the Fst estimator with 95% CI. We would also be interested in Gst (Hedrick 1995) and Josts D (Jost 2008) if you have those available, too. Your contribution would obviously be acknowledged and your publication(s) cited. Wed like to publicly thank the individuals whom weve already contacted directly and who generously offered their data. Thank you very much in advance Antonella Soro firstname.lastname@example.org Antonella Soro via Gmail
October 10, 2014
Doctoral Research Fellowship in Speciation Genetics A PhD position is available at the Department of Biosciences (IBV), Faculty of Mathematics and Natural Sciences, University of Oslo (UiO). The PhD project is part of a larger research program on the ‘Evolvability of genomic architecture during hybrid speciation’. Far from being an evolutionary dead end, hybridization may even generate lineages that can speciate even under the most constraining of conditions. The Italian sparrow (Passer italiae) is the first documented case of hybrid speciation in birds (Hermansen et al. 2011). This hybrid species originated from past events of hybridization between two divergent parental species, the house sparrow (P. domesticus) and the Spanish sparrow (P. hispaniolensis) some thousands of years ago. The Italian sparrow is both phenotypically and genetically variable across the Italian peninsula and its genome is a composite mosaic of DNA from both parentspecies’ genomes. But little is known about the consequences of such major genomic rearrangements on the evolutionary potential of hybrid species and how hybridization in general may favor novel evolutionary trajectories. This project integrates ecological and molecular approaches to develop an understanding of the evolution of genomic architecture during hybridization events and its evolutionary implications, using the Italian sparrow as the model system. The successful candidate will be allowed to choose aspects of the evolutionary genetics and genomics of the larger study as best fits her/his skills and research interests. She/he will also be encouraged to develop additional, complementary avenues of research. Interested candidates should have a Master degree or equivalent in a relevant field of biology, such as in genetics, genomics and/or bioinformatics. Documented knowledge in evolutionary biology is required. A good command of English and laboratory experience is likewise required. In addition, a special interest in the field of speciation and previous fieldwork or bird handling experience would be advantageous. The position is affiliated with the Centre for Ecological and Evolutionary Synthesis (CEES), and research will be conducted in close collaboration with Prof. Saetre and his group at CEES. The research team will also include other scientists from Norway, the US and Switzerland. The working language will be English. Fieldwork may be conducted at a variety of locations, including Norway, Italy and other Mediterranean countries. The appointment is for 3 years, but may be extended to 4 years conditional on 25% teaching obligations and approval from the Department of Biosciences. Candidates interested in a 4-year position should state so, in which case previous teaching experience would be considered a merit. Application deadline: Octiber 31st Expected starting date: January-February 2015 Informal enquiries can be made to Fabrice Eroukhmanoff and Glenn-Peter Saetre: email@example.com firstname.lastname@example.org For more information and how to apply: http://bit.ly/1qaNo3A Fabrice Eroukhmanoff Research Fellow Department of Biosciences, CEES University of Oslo Norway Fabrice.email@example.com Fabrice Eroukhmanoff via Gmail
Dear all, I am a historian of scientific thought. My research focuses on Neo-Lamarckian evolutionary principles. There has been a lot of recent work in this regard, what with epigenetic mechanisms and the like. I am currently revising a manuscript and seeking input from the broader evolutionary biology community. Basically, the central thesis is that Darwin and Wallace were wrong and that their work should be re-evaluated. The main issue is that the ideas of both Darwin and Wallace were due to work conducted on islands, and it is a well-known fact that evolution on islands is dominated by the forces of drift. Moreover, since most work predating the work of Darwin and Wallace was conducted in mainland European populations, it would have behooved them to stick to what others have been studying. I think this would clearly have been more relevant to the scientific community at the time. I am looking forward to hearing your thoughts and opinions on these ideas. Sincerest regards, Charlie Dawson firstname.lastname@example.org via Gmail
Recovering species demographic history from multi-model inference: the case of a Neotropical savanna tree species
Background: Glaciations were recurrent throughout the Quaternary and potentially shaped species genetic structure worldwide by affecting population dynamics. Here, we implemented a multi-model inference approach to recover the distribution dynamics and demographic history of a Neotropical savanna tree, Tabebuia aurea (Bignoniaceae). Exploring different algorithms and paleoclimatic simulations, we used ecological niche modelling to generate alternative hypotheses of potential demographic changes through the last glacial cycle and estimated genetic parameters using coalescent modelling. Results: Comparing predictions from demographic hypotheses with genetic parameters of modern populations, our findings revealed a likely scenario of population decline, with spatial displacement towards Northeast Brazil from the last glacial maximum to the mid-Holocene. Subsequently, populations expanded in response to the return of the climatically suitable conditions in Central-West Brazil. Nevertheless, a wide historical refugium across Central Brazil likely maintained large populations connected throughout time. The expected genetic signatures from such predicted distribution dynamics are also corroborated by spatial genetic structure observed in modern populations. Conclusion: By exploring uncertainties inherent in multiple working hypotheses, we have shown that multi-model inference is a fruitful and efficient approach to recover the nature, timing and geographical context of the Tabebuia aurea population dynamic in response to the Quaternary climate changes.
Erick Matsen wrote:
From Gascuel & co--www.ncbi.nlm.nih.gov Searching for virus phylotypes. F Chevenet, M Jung, M Peeters, T de Oliveira and O Gascuel, Bioinformatics (Oxford, England), Mar 2013 1
Large phylogenies are being built today to study virus evolution, trace the origin of epidemics, establish the mode of transmission and survey the appearance of drug resistance. However, no tool is available to quickly inspect these phylogenies and combine them with extrinsic traits (e.g. geographic location, risk group, presence of a given resistance mutation), seeking to extract strain groups of specific interest or requiring surveillance.
News to me!
Background: Although the genetic heritage of aboriginal Siberians is mostly of eastern Asian ancestry, a substantial western Eurasian component is observed in the majority of northern Asian populations. Traces of at least two migrations into southern Siberia, one from eastern Europe and the other from western Asia/the Caucasus have been detected previously in mitochondrial gene pools of modern Siberians. Results: We report here 166 new complete mitochondrial DNA (mtDNA) sequences that allow us to expand and re-analyze the available data sets of western Eurasian lineages found in northern Asian populations, define the phylogenetic status of Siberian-specific subclades and search for links between mtDNA haplotypes/subclades and events of human migrations. From a survey of 158 western Eurasian mtDNA genomes found in Siberia we estimate that nearly 40% of them most likely have western Asian and another 29% European ancestry. It is striking that 65 of northern Asian mitogenomes, i.e. ~41%, fall into 19 branches and subclades which can be considered as Siberian-specific being found so far only in Siberian populations. From the coalescence analysis it is evident that the sequence divergence of Siberian-specific subclades was relatively small, corresponding to only 0.6-9.5 kya (using the complete mtDNA rate) and 1–6 kya (coding region rate). Conclusions: The phylogeographic analysis implies that the western Eurasian founders, giving rise to Siberian specific subclades, may trace their ancestry only to the early and mid-Holocene, though some of genetic lineages may trace their ancestry back to the end of Last Glacial Maximum (LGM). We have not found the modern northern Asians to have western Eurasian genetic components of sufficient antiquity to indicate traces of pre-LGM expansions.
MULTIMEDIA SPECIALIST (PHILADELPHIA) The Center for Biodiversity at Temple University (Philadelphia) is interested in hiring a Multimedia Specialist. Duties include, but are not limited to, graphics illustration for publication, image and video editing, web site design and editing, and assisting the center in other activities. The successful applicant should be proficient in multimedia design and production, and familiarity with web programming (HTML and/or PHP coding) is preferred. A bachelor’s degree is preferred. The Center for Biodiversity is located in the new Science, Education, and Research Center (SERC building) on Temple’s main campus (http://bit.ly/10Z0cVa). Interested persons should send an e-mail to email@example.com, stating their interest in this position, and attach a curriculum vitae that also contains contact information for three references. The e-mail may be addressed to the director, S. Blair Hedges (http://bit.ly/1vT6hvF). Review of applications will begin on November 1 and continue until the position is filled. Temple University is located in the heart of historic Philadelphia and is the sixth largest provider of graduate school education in the USA. Situated in close proximity to New York City and Washington DC, Philadelphia is the birthplace of America and home to many academic and research institutions as well as numerous cultural attractions. via Gmail
Dear Colleagues (with apologies for duplicate postings): *PLEASE DISTRIBUTE TO OTHER LISTS AS YOU THINK APPROPRIATE*: I am asking for help in locating active tissue/cell line cryopreservation programs for endangered species. The extant population of the Catarina Pupfish, *Megupsilon apodus*, now consists solely of two males at the Dallas aquarium; the single known natural population was wiped out in the 1990$B!G(Bs. The species is essentially already extinct. I have been trying to find a program that would be interested in establishing and preserving cell lines or even simply storing tissue samples from one or both of the last surviving individuals. I thought I had located one such program associated with the San Diego zoo. What follows is the text of an e-mail I sent that program on 6 October: $B!H(BSan Diego Zoo Institute for Conservation Research 15600 San Pasqual Valley Road Escondido, California 92027 The unique $B!H(BCatarina Pupfish,$B!I(B *Megupsilon aporus*, is now effectively extinct, because the captive refugium population previously maintained by the Dallas Aquarium now consists of two males and 0 females. The single known natural population, confined to a single spring in central Mexico, was wiped out in the early 1990$B!G(Bs when the habitat was completely destroyed, and the two Dallas individuals are the last representatives of the species on the planet. I am therefore asking if your $B!H(Bfrozen zoo$B!I(B program would be interested in adding biological material from *M. apodus* to your collection. Assuming that is the case, I would appreciate it if you would let me know the steps that need to be taken so that this may be accomplished. I am not well versed in tissue culture and related techniques, but I suspect that the technology does exist to derive cell lines from the extant animals and cryopreserve them. Put more simply, we need to know just what to do next. It is my understanding that the surviving two *M. apodus* males will shortly be in the possession of Dr. Chris Martin at Berkeley. He is planning to attempt to hybridize them with females of a related species, *Cyprinodon alverezi *(which has been accomplished by others in the past*) *and hopes to eventually to use new genome editing tools to selectively remove the *C. alverezi* genes from the hybrid lineage. I believe that it will very likely be possible for him to take tissue samples (perhaps from fin clips) from one or both males that could be used to initiate cell lines. Among the many ways in which *M. apodus* is unusual or unique is its multiple sex chromosome system, which was the first example to be described in vertebrates. While similar systems have subsequently been described in other fish species, the enormous Y chromosome of *M. apodus* has no known equivalent, and it should be of great interest to students of sex chromosome evolution. Even if the species itself cannot be restored by contemporary conservation efforts, it would be extremely worthwhile to preserve its cells so that its Y chromosome will be available to cytogeneticists in the future. $B!H(B This e-mail has thus far elicited no response. While I do realize that only a few days have passed since I sent it, I would have thought that the obvious urgency of the situation would have merited at least a formal acknowledgement of receipt. I am concerned that my information may not be correct, or that I addressed it to the wrong person, and that precious time may be wasted. Consequently, I$B!G(Bm asking for help in locating other programs and/or finding the proper routes to approach them, or in networking that might lead to these goals. Any help would be greatly appreciated. Bruce Turner Bruce Turner via Gmail
Reminder: Call for Symposia closing on October 19, 2014 Dear Colleague, The Society for Molecular Biology and Evolution is now accepting proposals for symposium topics for the 2015 annual meeting, taking place in Vienna July 12th-16th 2015. For each accepted symposium the society provides substantial financial support to facilitate symposia organizers to attract outstanding invited speakers (up two invited speakers per symposium): - free registration for invited speakers - free accommodation for invited speakers - up to 1900€ travel support To submit your proposal please follow the instructions in the guide to applicants available at: http://bit.ly/1pnLk6L Return your completed submission to firstname.lastname@example.org by Sunday October 19, 2014. The subject line should read: Symposium submission Successful applications will be confirmed by December 5, 2014 and a call for abstracts will follow. We hope to see you all in Vienna! Kind regards, Julia Hosp On behalf of the local organizing committee Website: http://smbe2015.at via Gmail
The Hernandez Lab at UCSF has an open position available for a computational specialist/programmer. In our computational lab, we use detailed simulations, modeling, and analysis of high throughput genome sequencing data in humans and other mammals. Research projects in the group focus on developing novel techniques for applying principals of population and evolutionary genomics to medical resequencing studies, analysis of the patterns of global genetic diversity across several whole genome sequencing data sets, quantifying the genetic basis of asthma in admixed populations, and the genomics of host-pathogen interactions. The successful candidate will be expected to work with members of the group to implement and optimize algorithms for various projects, as well as maintain a Linux server. Basic Qualifications: - BA/BS/MS in computer science or related computational field. - Experience implementing efficient algorithms in a research setting. - Proficiency in C/C++ and perl/python. - The ideal candidate will also be proficient in managing Linux workstations, familiarity with the Sun Grid Engine queuing system, and ability to write parallelized code (MPI, pthreads, and/or openCL). UCSF is an Equal Opportunity/Affirmative Action Employer, and the Hernandez Lab is committed to increasing diversity in the sciences. Applications from women and minorities are highly encouraged. Applicants should email a short statement on education/experience/career goals, CV, and the names and email addresses of one-three references as a single pdf file to Ryan Hernandez . Informal inquiries are also welcome. via Gmail
BIODIVERSITY LABORATORY SPECIALIST (PHILADELPHIA) The Center for Biodiversity at Temple University (Philadelphia) is interested in hiring a Biodiversity Laboratory Specialist. The successful applicant will be responsible for organizing and carrying out research in biodiversity, specifically to maintain a molecular biology laboratory including a frozen tissue collection, collect and analyze DNA sequence data from a diversity of vertebrate species (mostly amphibians and reptiles), and to assist the center and work with students and other users of the laboratory. The successful candidate will also work with whole organisms, the databasing of collections, and organization of project data. A bachelor’s or master’s degree is preferred. The Center for Biodiversity is located in the new Science, Education, and Research Center (SERC building) on Temple’s main campus (http://bit.ly/10Z0cVa). Interested persons should send an e-mail to email@example.com, stating their interest in this position, and attach a curriculum vitae that also contains contact information for three references. The e-mail may be addressed to the director, S. Blair Hedges (http://bit.ly/1vT6hvF). Review of applications will begin on November 1 and continue until the position is filled. Temple University is located in the heart of historic Philadelphia and is the sixth largest provider of graduate school education in the USA. Situated in close proximity to New York City and Washington DC, Philadelphia is the birthplace of America and home to many academic and research institutions as well as numerous cultural attractions. via Gmail
This is a multipart message in MIME format. via Gmail
—Apple-Mail-5-777428471 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=”us-ascii” Graduate Opportunities at the University of Kansas in Medusozoan Evolution. The Cartwright Lab at the University of Kansas seeks PhD applicants for fall 2015. The lab investigates medusozoan evolution using developmental, genomic and phylogenetic approaches. More recently, the lab has been focusing on investigating the evolution of the the parasitic group, Myxozoa. Students must be highly motivated, have a demonstrated ability to work independently and show a keen interest medusozoan evolution. The Ecology and Evolutionary Biology program at the University of Kansas offers five years of guaranteed support through a combination of graduate teaching assistantships, research assistantships, and university fellowships. For more information, please go to: http://bit.ly/10Z0ewd and http://eeb.ku.edu/. Interested students should contact Dr. Cartwright (firstname.lastname@example.org) describing your background and research interests. Paulyn Cartwright Associate Professor Department of Ecology and Evolutionary Biology University of Kansas Lawrence, KS 66045 —Apple-Mail-5-777428471 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=”us-ascii”
Graduate Opportunities at the University of Kansas in Medusozoan Evolution.
The Cartwright Lab at the University of Kansas seeks PhD applicants for fall 2015. The lab investigates medusozoan evolution using developmental, genomic and phylogenetic approaches. More recently, the lab has been focusing on investigating the evolution of the the parasitic group, Myxozoa. Students must be highly motivated, have a demonstrated ability to work independently and show a keen interest medusozoan evolution.
The Ecology and Evolutionary Biology program at the University of Kansas offers five years of guaranteed support through a combination of graduate teaching assistantships, research assistantships, and university fellowships. For more information, please go to: http://bit.ly/10Z0ewd and http://eeb.ku.edu/. Interested students should contact Dr. Cartwright (email@example.com) describing your background and research interests.Paulyn CartwrightAssociate ProfessorDepartment of Ecology and Evolutionary BiologyUniversity of KansasLawrence, KS 66045
—Apple-Mail-5-77742847 via Gmail
Postdoctoral Positions in Computational/Evolutionary Genomics at UCSF The Hernandez Lab at UCSF has two postdoctoral positions available. The research projects are flexible, and will focus on the particular interests of the candidates. Research projects will likely focus on developing novel techniques for applying principals of population and evolutionary genomics to medical resequencing studies. Ongoing collaborations involve comprehensive studies of patterns of global genetic diversity as part of several whole genome sequencing projects, the genetic basis of asthma in admixed populations, and the genomics of host-pathogen interactions. Successful candidates will be expected to develop novel computational/statistical methods for addressing specific biological hypotheses, and to perform analyses of large-scale genomics data. Ideal candidates will have a background in a quantitative field (such as computer science, statistics, applied mathematics, bioinformatics, or related), experience in performing genet ics/genomics research, and a strong track-record of accomplishment in research. Basic Qualifications: - Ph.D. in bioinformatics, computer science, statistics, genetics, molecular biology, applied mathematics, or a related field. - Research experience (with first-author publications) in population genetics or a related field. - Proficiency in programming, ideally in C or C++, scripting languages such as perl/python, and familiarity with R. - Comfortable with large data sets, computer clusters, and databases. UCSF is an Equal Opportunity/Affirmative Action Employer, and the Hernandez Lab is committed to increasing diversity in the sciences. Applications from women and minorities are highly encouraged. Applicants should send a short research statement (including past, present, and future goals), CV, and the names and email addresses of at least two references as a single pdf file to Ryan Hernandez . Informal inquiries are also welcome. via Gmail
Reminder Population and Conservation Genomics Workshop Plant and Animal Genome XXIII International Conference http://bit.ly/14sBoDh January 10-14, 2015 Town and Country Convention Centre, San Diego, California The annual Population and Conservation Genomics workshop will be held at the Plant and Animal Genome XXIII International conference. The workshop is scheduled on Saturday, January 10, 2015. You are invited to attend this Workshop and submit abstracts for oral presentations on any population and conservation genomics aspect of both plants and animals. The topics may include: population genomic diversity and structure; molecular evolution; adaptive molecular genetic variation; natural selection and local adaptation; candidate-gene and genome-wide population studies; application of genomics in conservation and management of genetic resources; genomic effects of domestication, management practices, fragmentation, bottlenecks, climate and environment change, and transgenic deployment; and gene conservation; etc. The workshop has a slot for six invited speakers. A number of invited presentations will be selected from the submitted abstracts. Please send your abstract of no more than 250 words by e-mail to Om Rajora (Om.Rajora@unb.ca) as an attached Word file no later than October 17, 2014. You will be notified by October 24th whether your abstract has been selected for an oral presentation. Thereafter, the selected presenters will need to submit their abstract to the PAG website. Authors whose abstracts are not selected for oral presentations are highly encouraged to present a poster at the conference. Inquiries and Abstract Submission For information and questions regarding the Population and Conservation Genomics workshop, please contact Om Rajora at the following coordinates. Dr. Om P. Rajora, Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB E3B 5A3, Canada. E-mail: Om.Rajora@unb.ca Tel: (506) 458-7477 Fax: (506) 453-3538 Om Rajora via Gmail
ASSISTANT/ASSOCIATE PROFESSOR IN CROP FUNCTIONAL GENOMICS DEPARTMENT OF SOIL AND CROP SCIENCES COLORADO STATE UNIVERSITY FT. COLLINS, COLORADO 80523 The Department of Soil and Crop Sciences (SCS) at Colorado State University is recruiting for a tenure-track Assistant/Associate Professor in the field of Crop Functional Genomics. We seek a dynamic, motivated scientist to lead an innovative research program that employs functional genomics approaches to discover and characterize genes controlling traits that are important for crop production and utilization. The intended focus of the position is in wheat, though opportunities exist for research in other areas and crops. Candidates are sought with demonstrated capacity to integrate modern whole-genome approaches and techniques to further gene discovery and characterization for agronomic, pest resistance, and crop utilization objectives. The successful candidate will advance Colorado State University’s and SCS’s land-grant mission and will contribute to programs of the College of Agricultural Sciences (CAS) by conducting research and teaching that is responsive to local or regional production constraints, global food security, and the rapidly expanding technological capacity in crop genomics. This tenure track position is a 60% research, 30% teaching, and 10% outreach appointment on a 9-month contract. Information regarding the department, its programs, and degrees offered can be viewed at http://bit.ly/1m69sPU. The successful applicant will be expected to develop a nationally and internationally recognized research program using cutting-edge technologies in the arena of crop functional genomics, specifically to identify genes and characterize the mechanisms by which genes affect important agronomic, pest resistance, or end-use quality traits. Potential research topics include, but are not limited to, gene discovery and characterization via TILLING or genome editing methods, comparative genomics, integration of functional genomics techniques with other genotype to phenotype approaches (such as QTL analysis and genome-wide association studies), fine mapping and gene cloning, and plant transformation for validation of gene function. The successful candidate will teach an alternate-year undergraduate level course in applications of plant biotechnology and an alternate-year graduate level course in the candidate’s primary area of expertise. Required Qualifications: - Completion of PhD or equivalent degree by date of hire. Degree emphasis in a relevant field such as (but not limited to) plant breeding, plant genetics, genomics, or biotechnology. - Demonstrated ability and experience in the conduct of innovative field- and/or laboratory-based studies that incorporate functional genomics approaches relevant in agronomic or horticultural crops. Preferred Qualifications: - Demonstrated success in publication of research findings. - Demonstrated success in preparation of competitive grant proposals. - Post-doctoral (or equivalent) research experience, preferably with wheat or other grass species. - Effective communication skills, with an emphasis on presenting and disseminating research information. - Demonstrated excellence in teaching. - Ability to advance the department’s commitment to diversity and inclusion through research, teaching, and outreach with relevant programs, goals and activities. Applications will be accepted until the position is filled; however, to ensure full consideration applications should be submitted by December 31, 2014. The anticipated starting date for the position is August 15, 2015, but is negotiable. Interested individuals should submit the following application materials on-line at http://bit.ly/1w8Qh8F: (1) a cover letter addressing required and preferred qualifications; (2) a curriculum vitae; (3) a statement of research background and interests; (4) a statement of teaching experience and philosophy; (5) PDF copies of up to three relevant publications; and (6) a list of three professional references whom we may contact at a future date for a letter of recommendation. References will not be contacted without prior notification to a candidate. Interested candidates may contact Search Committee Chair Dr. Scott Haley (firstname.lastname@example.org) for questions about the position or SCS Office Manager Jeannie Roberts (email@example.com) for questions about the search process Colorado State University, located in Fort Collins, Colorado, is situated on nearly 5,000 acres of land, including the main campus, a foothills campus, the Agricultural Research Development & Education Center (ARDEC), and a mountain campus (Pingree Park). Colorado State University research and Cooperative Extension faculty also conduct programs at several off-campus research centers throughout the state. Fort Collins is an award-winning city located on the Front Range of the Rocky Mountains. Easy access to hiking, skiing, rafting and other outdoor sports is a great advantage to CSU students, faculty and staff. Read more about the university and community at http://bit.ly/1va19q5. Colorado State University is committed to providing an environment that is free from discrimination and harassment based on race, age, creed, color, religion, national origin or ancestry, sex, gender, disability, veteran status, genetic information, sexual orientation, gender identity or expression, or pregnancy. Colorado State University is an equal opportunity/equal access/affirmative action employer fully committed to achieving a diverse workforce and complies with all Federal and Colorado State laws, regulations, and executive orders regarding non-discrimination and affirmative action. The Office of Equal Opportunity is located in 101 Student Services. Colorado State University is committed to providing a safe and productive learning and living community. To achieve that goal, we conduct background investigations for all final candidates being considered for employment. Background checks may include, but are not limited to, criminal history, national sex offender search and motor vehicle history. via Gmail
Dear colleagues, Transmitting Science offers a new course which migth could be of interest for some members of this list: “GEOMETRIC MORPHOMETRICS IN R “. January 26-30, 2015; 35 hourse on-site. Dr. JULIEN CLAUDE (Institut des Sciences de l’Évolution de Montpellier, France). WEBPAGE: http://bit.ly/1w8Qfxx PROGRAM: 1. An Introduction to R / Image Processing / Organizing Morphometric Data. - Some Basics in R: The R Environment. R objects, Assigning, Indexing. Generating Data in R. 2D and 3D Plots in R; Interacting with the Graphs. - Organizing Data for Morphometrics: Data-frame, Array and List. Converting and Coercing Objects. Read and Write Morphometric Data in R. - Image Processing in R: Reading Various Image Files. Obtaining Image Properties. Modifying Image Properties: Contrast, Channels, Saturation Directly from R or by Interfacing R with Imagemagick. - Simple Tests, Simple Linear Modelling, Alternatives to Linear Modeling, an example using traditional morphometrics. Defining size and shape using PCA and log-shape ratio approaches. Getting stats and test outputs. Testing assumptions of linear modeling. Testing for allometry and isometry. Solutions when assumptions of linear modeling are not met. 2. Landmark data. - Acquiring Landmark Data in R. - Plotting Landmark Configurations in 2 and in 3D: Using Different Symbols and Setting the Graphical Parameters. Labeling Landmarks. - Geometric Transformation with Landmark Configurations: Translation. Scaling using Baseline or Centroid Size. Rotation. - Superimposing and Comparing Two Shapes: 2.4.1. Baseline Superimposition. Ordinary Least Squares Superimposition. Resistant Fit. - Representing Shape Differences: Plotting Superimposed Shape with Wireframe. Lollipop Diagrams and Vector Fields. Thin Plate Splines and Warped Shapes. - Superimposing More Than Two Shapes. Baseline Registration. Full Generalized Procrustes Analysis. Partial Generalized Procrustes Analysis. Dimensionality of Superimposed Coordinates. - Exploring Shape Variation and Testing Hypotheses: PCA. Multivariate Linear Modeling (Multivariate Regression and MANOVA). Allometry free approaches (Burnaby correction). Linear discriminant and Canonical Analysis. 3. Outlines. - Acquiring outline Data in R: Fourier Analysis. Principles. Fourier Analysis of the Tangent Angle. Radius Fourier Analysis. Elliptic Fourier Analysis. Reduction of Shape Variables. Statistical Analysis of Shape Variation with Fourier Analysis. Exploring Shape Variation and Testing Hypotheses. PCA. Multivariate Linear Modeling (Multivariate Regression and MANOVA). Canonical Analysis. - Combining Landmarks and Curves: Hybrid Methods between Fourier and Procrustes Analysis. Sliding Semi Landmarks. - Solutions for Open Curves 4. Specific Applications. - Testing Measurement Error. - Partitional Clustering: K-means, Partition Around Medoids. Mclust. Combining Genetic, Geographic and Morphometric Data. - Modularity / Integration Studies: Two-block Partial Least Squares. Testing Among Various Sets of Modules. Fluctuating Asymmetry and Directional Asymmetry. Inter-Individual and Intra-Individual Variation. Object and Matching Symmetry. - Phylogenetic Data: The Problem of Phylogenetic Non-independence. Plotting the Tree in the Shape Space, Testing Evolutionary Models, Estimating Ancestral Character States. Morphological Disparity Through Time Diagram. - Bending Energy, Uniform and Non-uniform Shape Variation. PLACE: Facilities of the Centre of Restauració i Interpretació Paleontologica, Els Hostalets de Pierola, Barcelona (Spain). Organized by: Transmitting Science, the Institut Catalá de Paleontologia Miquel Crusafont and the Centre of Restauració i Interpretació Paleontologica. With best regards Soledad De Esteban Trivigno, PhD. Course Director Transmitting Science Soledad De Esteban Trivigno via Gmail
October 9, 2014
Phylodynamic methods are widely used to estimate demographic parameters and historical population dynamics from genealogies of individuals sampled from a population. In this phyloseminar, I will describe how we can understand genealogies in terms of basic demographic or ecological processes, and how these concepts can be used to develop statistical models for inference. In particular, I will discuss some similarities and differences between the two main modeling frameworks in phylodynamics: the coalescent and birth-death models. I will also briefly introduce some of the latest statistical methods currently used to fit these models to genealogies. I will end by discussing one of the main challenges facing the field---adequately representing the structure of complex, heterogenous populations in phylodynamic models.
Ecological niche and phylogeography elucidate complex biogeographic patterns in Loxosceles rufescens (Araneae, Sicariidae) in the Mediterranean Basin
Background: Understanding the evolutionary history of morphologically cryptic species complexes is difficult, and made even more challenging when geographic distributions have been modified by human-mediated dispersal. This situation is common in the Mediterranean Basin where, aside from the environmental heterogeneity of the region, protracted human presence has obscured the biogeographic processes that shaped current diversity. Loxosceles rufescens (Araneae, Sicariidae) is an ideal example: native to the Mediterranean, the species has dispersed worldwide via cohabitation with humans. A previous study revealed considerable molecular diversity, suggesting cryptic species, but relationships among lineages did not correspond to geographic location. Results: Delimitation analyses on cytochrome c oxidase subunit I identified 11 different evolutionary lineages, presenting two contrasting phylogeographic patterns: (1) lineages with well-structured populations in Morocco and Iberia, and (2) lineages lacking geographic structure across the Mediterranean Basin. Dating analyses placed main diversification events in the Pleistocene, and multiple Pleistocene refugia, identified using ecological niche modeling (ENM), are compatible with allopatric differentiation of lineages. Human-mediated transportation appears to have complicated the current biogeography of this medically important and synanthropic spider. Conclusions: We integrated ecological niche models with phylogeographic analyses to elucidate the evolutionary history of L. rufescens in the Mediterranean Basin, with emphasis on the origins of mtDNA diversity. We found support for the hypothesis that northern Africa was the center of origin for L. rufescens, and that current genetic diversity originated in allopatry, likely promoted by successive glaciations during the Pleistocene. We corroborated the scenario of multiple refugia within the Mediterranean, principally in northern Africa, combining results from eight atmosphere?ocean general circulation models (AOGCMs) with two different refugium-delimitation methodologies. ENM results were useful for providing general views of putative refugia, with fine-scale details depending on the level of stringency applied for agreement among models.
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology
Molecular Biology and Evolution