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August 23, 2014
Background: Branched polymers of glucose are universally used for energy storage in cells, taking the form of glycogen in animals, fungi, Bacteria, and Archaea, and of amylopectin in plants. Some enzymes involved in glycogen and amylopectin metabolism are similarly conserved in all forms of life, but some, interestingly, are not. In this paper we focus on the phylogeny of glycogen branching and debranching enzymes, respectively involved in introducing and removing of the ?(1?6) bonds in glucose polymers, bonds that provide the unique branching structure to glucose polymers. Results: We performed a large-scale phylogenomic analysis of branching and debranching enzymes in over 400 completely sequenced genomes, including more than 200 from eukaryotes. We show that branching and debranching enzymes can be found in all kingdoms of life, including all major groups of eukaryotes, and thus were likely to have been present in the last universal common ancestor (LUCA) but have been lost in seemingly random fashion in numerous single-celled eukaryotes. We also show how animal branching and debranching enzymes evolved from their LUCA ancestors by acquiring additional domains. Furthermore, we show that enzymes commonly perceived as orthologous, such as human branching enzyme GBE1 and E. coli branching enzyme GlgB, are in fact related by a gene duplication and consequently paralogous. Conclusions: Despite being usually associated with animal liver glycogen and plant starch, energy storage in the form of branched glucose polymers is clearly an ancient process and has probably been present in the last universal common ancestor of all present life. The evolution of the enzymes enabling this form of energy storage is more complex than previously thought and illustrates the need for explicit phylogenomic analysis in the study of even seemingly ?simple? metabolic enzymes. Patterns of conservation in the evolution of the glycogen/starch branching and debranching enzymes hint at some as yet unknown mechanisms, as mutations disrupting these patterns lead to a variety of genetic diseases in humans and other mammals.
August 22, 2014
AustralianNationalUniversity.GeneticDiversity ARC Laureate Fellowship PhD scholarship - Genetic Diversity The Fenner School of Environment and Society at the Australian National University is seeking applications from highly qualified and motivated candidates for a PhD scholarship for research on ecological surrogates. Purpose Professor David Lindenmayer’s ARC Laureate Fellowship research program is examining surrogate ecology, particularly when and where it might work to improve environmental management. We are seeking an outstanding candidate to join a team working on biodiversity surrogates. Genetic diversity is an often overlooked aspect of biodiversity. This PhD program will evaluate genetic indicators and their use in biodiversity conservation. Aspects of the project may include assessing the use of genetic indicators for monitoring genetic diversity and assessing the impacts of management interventions and natural disturbance on genetic diversity and connectivity. This project will be focused on an exciting and novel aspect of biodiversity monitoring and as such provides scope for the student to develop ideas based around the topic of genetic indicators. The successful applicant will need to be highly motivated and capable of writing high-level scientific articles for leading international journals. Experience in population genetics is highly desirable. The successful candidate will be awarded a post-graduate scholarship stipend as part of an Australian Research Council Laureate Fellowship held by Professor David Lindenmayer. The scholarship will support the PhD program for 3 years, with a possible extension for a further 6 months. The successful candidate will need to commence their project no later than November 2014. The position is supported by an ARC Laureate Fellowship with a stipend of $29,844 per annum, tax-free for 3 years paid in fortnightly instalments. Other benefits The Fenner School of Environment and Society has a large, dynamic community of PhD students who are provided with modern office facilities and computer and statistical support. Students are encouraged to collaborate widely and attend national and international conferences. The successful candidate will become part of the Environmental Decisions Group - a network of some of the world’s leading applied environmental scientists that provides travel support for national and international collaboration. Duration Three years full-time with a possible six month extension. Supervision The project will be supervised by ARC Laureate Fellow Professor Lindenmayer and a supervisory panel that matches the candidate’s skills. Candidate requirements Bachelors degree with first-class honours, or a research Masters degree from a recognised university. Australian and New Zealand citizens; permanent residents of Australia; international students who hold an International Postgraduate Research Scholarship (IPRS). Selection is based on academic merit and the candidate’s research proposal. The successful candidate will have experience in environmental science and management, ecology or similar. Application process and closing date Interested individuals are invited to discuss the project with Professor David Lindenmayer (02 6125 0654 or firstname.lastname@example.org) and must submit a CV and a one page statement of possible research directions they would pursue in their project to email@example.com by 5pm 19 September 2014. The successful candidate would be expected to commence their doctoral program no later than November 2014. firstname.lastname@example.org via Gmail
PhD scholarships at the Australian Centre for Ancient DNA, Adelaide, Australia Project 1: Epigenetic modifications in adaptation to climate change Project 2: Phylogenomic analysis of the impacts of climate change, population fragmentation and localised extinctions We have 2 PhD positions available at the Australian Centre for Ancient DNA (ACAD), School of Earth & Environmental Sciences, at the University of Adelaide. For more information about ACAD, check out http://bit.ly/1wjI463 for links to Twitter, Facebook, our blog, recent publications and the official website. The positions are open to both international and domestic students with a strong academic achievement in either of the following areas: evolutionary biology, bioinformatics, or molecular biology. Competitive scholarships are also available via the University of Adelaide Graduate Centre for domestic (http://bit.ly/1ktxIHU) and international students (http://bit.ly/1iMxKwV). Both the Australian Department of Immigration and University of Adelaide expect international applicants to meet the English Language Proficiency (ELP) requirements. The ELP is based on high scores in IELTS (International English Language Testing System) or TOEFL (Test of English as a Foreign Language). For further information please refer to http://bit.ly/1ktxIY8. The projects are described below. There is the potential for fieldwork, and training in ancient DNA, bioinformatics, genomics, and population genetics. Interested applicants are encouraged to send a resume, a cover letter, and the contact details of 3 referees to Dr Bastien Llamas (email@example.com). 1) The role of epigenetic modifications in bovid adaptation to environmental change (Australian Research Council grant LP130100646). Supervision: Dr Bastien Llamas and Prof Alan Cooper. This project will use a novel experimental system to explore the potentially important role of epigenetics in long-term evolution and how animals adapt to rapid climate change. Bones of ancient bison and cattle preserved in permafrost or caves will be analysed for epigenetic markers using advanced Next Generation Sequencing approaches, and the patterns contrasted over a 30,000-year record of major climatic and environmental shifts. It has strong potential to reveal key loci for climate adaptation in modern cattle. Most previous genetic research has been blind to epigenetic marks, and this study promises to be a major advance in addressing this issue, with considerable implications for conservation genetics and the cattle industry. 2) Using phylogenomics to record the impacts of climate change, extinction and population fragmentation (Australian Research Council grant DP140104233). Supervision: Dr Julien Soubrier and Prof Alan Cooper. We will use ancient DNA from permafrost-preserved Steppe bison bones and bovid exome capture systems to build a detailed record of the genomic impacts of rapid climate and environmental change at the end of the Pleistocene (30-11 kyr). The project will analyse how ancestral genetic diversity is distributed amongst surviving bison populations, and the role of nuclear loci under selection and drift. It will create a novel temporal dataset of genomic adaptation and evolution, and will generate critical data for studies of evolutionary processes such as extinctions, speciation and conservation biology and management. via Gmail
Background: Vertebrate mitogenomes are economically organized and usually lack intergenic sequences other than the control region. Intergenic spacers located between the tRNAThr and tRNAPro genes (?T-P spacers?) have been observed in several taxa, including gadiform species, but information about their biological roles and putative functions is still lacking. Results: Sequence characterization of the complete European hake Merluccius merluccius mitogenome identified a complex T-P spacer ranging in size from 223?532?bp. Further analyses of 32 gadiform species, representing 8 families and 28 genera, revealed the evolutionary preserved presence of T-P spacers across all taxa. Molecular complexity of the T-P spacers was found to be coherent with the phylogenetic relationships, supporting a common ancestral origin and gain of function during codfish evolution. Intraspecific variation of T-P spacer sequences was assessed in 225 Atlantic cod specimens and revealed 26 haplotypes. Pyrosequencing data representing the mito-transcriptome poly (A) fraction in Atlantic cod identified an abundant H-strand specific long noncoding RNA of about 375?nt. The T-P spacer corresponded to the 5? part of this transcript, which terminated within the control region in a tail-to-tail configuration with the L-strand specific transcript (the 7S RNA). Conclusions: The T-P spacer is inferred to be evolutionary preserved in gadiform mitogenomes due to gain of function through a long noncoding RNA. We suggest that the T-P spacer adds stability to the H-strand specific long noncoding RNA by forming stable hairpin structures and additional protein binding sites.
POST-DOCTORAL POSITION IN MICROBIAL GENOMICS A post-doctoral position is available in the laboratory of Jesse Shapiro (www.shapirolab.ca) at the University of Montreal (UdeM), starting in autumn 2014. About the lab. Our current research theme is microbial adaptation over recent (“human”) time scales. We aim to answer the following types of questions: What are the ecological and evolutionary mechanisms of adaptation? How do these mechanisms interact? What are the genomic changes that underlie microbial phenotypes of clinical and environmental importance? How does speciation work in bacteria? We are a diverse and international group of scientists, working on natural systems ranging from human gut-associated bacteria to bloom-forming freshwater cyanobacteria, using a combination of wet- lab and dry-lab approaches, rooted in population genomics, and located in the wonderful city of Montreal. About the position. We are looking for an excellent quantitative/computational biologist to work on a Canadian Institutes of Health Research (CIHR) funded project entitled “Genomic analysis of cholera transmission and microevolution.” This is a multi-disciplinary collaboration, involving researchers at UdeM, The Massachusetts General Hospital and The International Centre for Diarrhoeal Disease Research, Bangladesh. The aims of the project are (1) to identify Vibrio cholerae variants associated with symptomatic disease using (and developing) genome-wide association studies (GWAS), (2) to map cholera transmission events with a genomic-epidemiological approach, and (3) to quantify within-patient V. cholerae genetic diversity and its impact on disease and transmission. Within the scope of this project, the candidate will have the opportunity to work on the aspects that best suit their interests and skills. Desired candidate. The candidate must have a high level of training (PhD) with expertise in computational biology, population genetics and/or genomics, as evidenced by first-author publications. The ability to work in a collaborative, interdisciplinary research environment is essential. A strong computational or quantitative background is also essential. Applying. To apply, please send (1) a brief letter of research interests, (2) your CV, (3) contact information for three references, and (4) a publication representative of your work to: firstname.lastname@example.org. Selected publications from the lab: Shapiro BJ & Polz MF. (2014) Ordering microbial diversity into ecologically and genetically cohesive units. Trends in Microbiology 22: 235-247. PMID: 24630527 Farhat M, Shapiro BJ et al. (2013) Genomic Analysis Identifies Targets of Convergent Positive Selection in Drug-Resistant Mycobacterium tuberculosis. Nature Genetics 45: 1183-1189. PMID: 23995135 Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, Szabò G, Polz MF, Alm EJ. (2012) Population Genomics of Early Events in the Ecological Differentiation of Bacteria. Science 336: 48-51. PMID: 22491847 B. Jesse Shapiro Canada Research Chair // Chaire de recherche du Canada Microbial Evolutionary Genomics // Génomique microbienne évolutionnaire Assistant Professor // Professeur adjoint Department of Biological sciences // Département de sciences biologiques Université de Montréal www.shapirolab.ca Jesse Shapiro via Gmail
August 21, 2014
Research interns are needed to assist in a multi-disciplinary, multi-investigator, experimental study ecology and evolution in Trinidad. The research is led by Professor David Reznick at the University of California, Riverside. We seek to integrate multiple biological fields for the study of the interactions between ecological and evolutionary processes in Trinidadian streams. Duties of the position include assisting in monthly censuses of fish populations (guppies) in montane streams. The monthly censuses include long hours of laboratory time. Qualifications: We seek interns who are entertaining the possibility of pursing graduate studies in some area of ecology and evolution and who wish to gain some field research experience before entering graduate school. Research will take place in semi-remote areas of Trinidad sometimes under bad weather conditions. Applicants must be able to live and work well with others. Research will also involve carrying heavy packs over slippery and steep terrain. Applicants must be in good physical condition and be able to meet the demands of field research under these conditions. Ability to drive a standard transmission vehicle is desirable but not required. Applicants with first-aid/first responder training, skills in automobile maintenance, and construction skills are highly desirable. Please address these skills when applying. Interns will be required to spend a minimum of 3-months in Trinidad, with possibility of extension. Starting dates are flexible, starting as early as November 2014. We will cover travel expenses and living expenses. Applicants should send cover letter, CV and the names, phone numbers and e-mail addresses of three or more professional references to David Reznick (gupy @ ucr.edu) and Andrs Lpez-Sepulcre (alopez @ biologie.ens.fr ). At least two of the references should be academics. Andrs Lpez-Sepulcre via Gmail
The Lakehead University Paleo-DNA Laboratory Practical DNA Training Program. Please post the following information about the training program on the EvolDir website and direct it towards evolutionary biologists: Practical DNA Training Program: A two-week (9 business days) intensive laboratory-based training program designed to teach participants the fundamentals of molecular techniques including DNA extraction, amplification (using PCR), sequencing and interpretation. This training program is offered at various times throughout the year and we will work with you to find a suitable time for training. The next two scheduled courses for the Practical DNA Training Program are October 14 - 24, 2014 and November 10 - 20, 2014. For more information please contact us at 807-343-8877 or email@example.com or visit our website www.ancientdna.com and click on ‘Training Programs’. Thank you. Karen. Karen Maa Administrative Assistant Paleo-DNA Laboratory 1294 Balmoral Street, 3rd Floor Thunder Bay, Ontario P7B 5Z5 Telephone: 1-866-DNA-LABS or 1-807-343-8616 Karen Maa via Gmail
The implications of a Silurian and other thylacocephalan crustaceans for the functional morphology and systematic affinities of the group
Background: Thylacocephala is a group of enigmatic extinct arthropods. Here we provide a full description of the oldest unequivocal thylacocephalan, a new genus and species Thylacares brandonensis, which is present in the Silurian Waukesha fauna from Wisconsin, USA. We also present details of younger, Jurassic specimens, from the Solnhofen lithographic limestones, which are crucial to our interpretation of the systematic position of Thylacocephala. In the past, Thylacocephala has been interpreted as a crustacean ingroup and as closely related to various groups such as cirripeds, decapods or remipeds. Results: The Waukesha thylacocephalan, Thylacares brandonensis n. gen. n. sp., bears compound eyes and raptorial appendages that are relatively small compared to those of other representatives of the group. As in other thylacocephalans the large bivalved shield encloses much of the entire body. The shield lacks a marked optical notch. The eyes, which project just beyond the shield margin, appear to be stalked. Head appendages, which may represent antennulae, antennae and mandibles, appear to be present. The trunk is comprised of up to 22 segments. New details observed on thylacocephalans from the Jurassic Solnhofen lithographic limestones include antennulae and antennae of Mayrocaris bucculata, and endites on the raptorial appendages and an elongate last trunk appendage in Clausocaris lithographica. Preserved features of the internal morphology in C. lithographica include the muscles of the raptorial appendage and trunk. Conclusions: Our results indicate that some ‘typical’ thylacocephalan characters are unique to the group; these autapomorphies contribute to the difficulty of determining thylacocephalan affinities. While the new features reported here are consistent with a eucrustacean affinity, most previous hypotheses for the position of Thylacocephala within Eucrustacea (as Stomatopoda, Thecostraca or Decapoda) are shown to be unlikely. A sister group relationship to Remipedia appears compatible with the observed features of Thylacocephala but more fossil evidence is required to test this assertion. The raptorial appendages of Thylacocephala most likely projected 45 degrees abaxially instead of directly forward as previously reconstructed. The overall morphology of thylacocephalans supports a predatory mode of life.
—_000_87FCC0D1FF47BB4E8B42E4989C746A862B9E0C80EXCHMBOX6exchuc_ Content-Type: text/plain; charset=”Windows-1252” Content-Transfer-Encoding: quoted-printable Position Description A postdoctoral position is available in the Department of Entomology at the University of California Riverside to work on the genetic and molecular basis of insecticide resistance in glassy winged sharpshooter (GWSS) - the primary vector of the bacteria Xylella fastidiosa, which causes Pierce’s Disease in grapevines. Recent insecticidal control failures and corresponding surges in GWSS numbers have raised serious concerns about the status of insecticide susceptibility in Californian populations of GWSS. The successful candidate will (1) determine the current resistance status of GWSS in California agricultural and nursery settings, (2) elucidate the genetic and molecular underpinnings of any resistance, and (3) design tools and assays for use in an integrated insecticide resistance management plan. Additionally, the postdoc is encouraged to develop new lines of work (e.g. population genomics, ecological modeling, etc.) on GWSS. The project, funded by the California Department of Food and Agriculture, is a collaborative effort headed by Drs. Frank Byrne, Rick Redak, and Bradley White. The postdoc will be supervised by Dr. White, but will also work closely with the other PIs. After completion of the project, the postdoc will have substantial experience designing and conducting bioassays, analyzing next-generation sequencing data, and communicating policy recommendations to growers. As such, the position represents an excellent opportunity to acquire a unique combination of skills that serve as good training for various positions in academia, industry, and government. We are looking for someone with expertise in evolutionary biology, insect ecology, vector biology, insect toxicology, and/or agricultural entomology. Familiarity with next-generation sequencing analysis is a positive, but not required. Regardless of prior experience, we expect the candidate to develop a wide-knowledge base and skillset. The position is for one year with the possibility of renewal for up to three years total. Salary will be commensurate with experience level. For additional information about the White Laboratory please navigate to http://bit.ly/17xDZQ5 To Apply A minimum qualification is a PhD or equivalent in Biology, Entomology, or a related discipline. Applicants with multiple, first-author publications are preferred. To apply, please send a brief description of previous research (1 page), a CV, and contact information for three references to firstname.lastname@example.org. A start date in Fall 2014 is ideal, but negotiable. Position is open until filled. Additional Information The White Lab is housed in the relatively new Entomology Building at UCR. We have access to state of the art genomic and bioinformatics core facilities and are part of the Center for Disease Vector Control (CDVR), which is composed of a diverse and highly talented group of scientists studying insect vectors of animal, human, and plant diseases. Substantial resources for field experiments are available through the Agricultural Experiment Station (AES) facilities. UCR is an affirmative action and equal opportunity employer with a commitment to workforce diversity. AA/EOE Bradley J. White Assistant Professor Center for Disease Vector Research Department of Entomology University of California Riverside, CA 92521 —_000_87FCC0D1FF47BB4E8B42E4989C746A862B9E0C80EXCHMBOX6exchuc_ Content-Type: text/html; charset=”Windows-1252” Content-Transfer-Encoding: quoted-printable
A postdoctoral position is available in the Department of Entomology at the University of California Riverside to work on the genetic and molecular basis of insecticide resistance in glassy winged sharpshooter (GWSS) - the primary vector of the bacteria Xylella fastidiosa, which causes Pierce’s Disease in grapevines. Recent insecticidal control failures and corresponding surges in GWSS numbers have raised serious concerns about the status of insecticide susceptibility in Californian populations of GWSS. The successful candidate will (1) determine the current resistance status of GWSS in California agricultural and nursery settings, (2) elucidate the genetic and molecular underpinnings of any resistance, and (3) design tools and assays for use in an integrated insecticide resistance management plan. Additionally, the postdoc is encouraged to develop new lines of work (e.g. population genomics, ecological modeling, etc.) on GWSS.
The project, funded by the California Department of Food and Agriculture, is a collaborative effort headed by Drs. Frank Byrne, Rick Redak, and Bradley White. The postdoc will be supervised by Dr. White, but will also work closely with the other PIs. After completion of the project, the postdoc will have substantial experience designing and conducting bioassays, analyzing next-generation sequencing data, and communicating policy recommendations to growers. As such, the position represents an excellent opportunity to acquire a unique combination of skills that serve as good training for various positions in academia, industry, and government.
We are looking for someone with expertise in evolutionary biology, insect ecology, vector biology, insect toxicology, and/or agricultural entomology. Familiarity with next-generation sequencing analysis is a positive, but not required. Regardless of prior experience, we expect the candidate to develop a wide-knowledge base and skillset. The position is for one year with the possibility of renewal for up to three years total. Salary will be commensurate with experience level.
For additional information about the White Laboratory please navigate to http://bit.ly/17xDZQ5
A minimum qualification is a PhD or equivalent in Biology, Entomology, or a related discipline. Applicants with multiple, first-author publications are preferred. To apply, please send a brief description of previous research (1 page), a CV, and contact information for three references to email@example.com. A start date in Fall 2014 is ideal, but negotiable. Position is open until filled.
The White Lab is housed in the relatively new Entomology Building at UCR. We have access to state of the art genomic and bioinformatics core facilities and are part of the Center for Disease Vector Control (CDVR), which is composed of a diverse and highly talented group of scientists studying insect vectors of animal, human, and plant diseases. Substantial resources for field experiments are available through the Agricultural Experiment Station (AES) facilities.
UCR is an affirmative action and equal opportunity employer with a commitment to workforce diversity. AA/EOE
Bradley J. White
Center for Disease Vector Research
Department of Entomology
University of California
Riverside, CA 92521—_000_87FCC0D1FF47BB4E8B42E4989C746A862B9E0C80EXCHMBOX6exchuc via Gmail
Postdoctoral position in Systematics and Evolution A two-year postdoctoral position in Systematics and Evolution is available in the Department of Zoology, Swedish Museum of Natural History, Stockholm. Project description “Species-level phylogeny and delimitation in a biodiversity hotspot” Madagascar is well known for its high level of endemism, basically across every organism group. The combination with severe habitat degradation has “rewarded” the island with a top placement among biodiversity hotspots. The increased evolutionary research interest last twenty years has focused on vertebrates and surprisingly little is yet known about the colonization and speciation history of most insect groups. Using Hydradephagan water beetles as model organisms this project will use dated phylogenetic frameworks to analyze colonization and speciation patterns across replicated endemic radiations and clades with representatives but seemingly without radiations. Intraspecific genetic variation will be sampled to estimate parameters in the multispecies coalescent model as a window into the speciation process. The project also includes evaluation of species delimitation methods on endemic radiations with non-reciprocally monophyletic species in gene-trees. Tasks The position is part of a research project and group (Bergsten Systematic Entomology Lab: http://bit.ly/1uZz1FZ) at the Swedish Museum of Natural History on the taxonomy, faunistics, phylogeny, colonization, speciation and evolutionary history of Hydradephagan water beetles on Madagascar. The work includes DNA labwork, fieldwork, data analyses, help with supervision of student projects, article- and grant writing. The DNA labwork will be conducted at the Molecular Systematics Laboratory at the Swedish Museum of Natural History. Qualifications To be qualified for the postdoctoral position the applicant needs to have a PhD degree (or have a PhD thesis ready with a date fixed within 2014 for thesis defense) in Systematics/Phylogenetics/Evolutionary Biology or similar direction of studies. The PhD degree should have been received no more than six years before the deadline for applications. Criteria for selection Among qualified applicants selection is made according to scientific merits, quality of the PhD thesis, personal skills, the applicant´s documented knowledge in subjects of relevance for the research area, ability to master English language (both spoken and written), analytical ability, creativity, initiative, independence, teamwork and ability to cooperate. Previous experience with molecular (DNA) lab work and knowledge of relevant theory and methods (phylogenetic, dating, species delimitation, biogeographic and diversification rate analyses) weigh heavily. Experience with entomological fieldwork, taxonomic work and French language (spoken in Madagascar) are consider as additional qualifications. Terms of employment The position is for two years full time. Start of position should be in 2014 but exact date up to negotiation with the successful candidate. The position is financed by a grant from the Swedish Research Council, VR. For more information, please contact Johannes Bergsten (firstname.lastname@example.org). Union representative is Bodil Kajrup, SACO-S. Both can be reached at telephone number + 46 8 519 540 00. To be included in the application Maximum one A4-page of personal presentation and your reasons for applying (letter of intent). Curriculum vitae with publication list. Copy of three selected publications. Copy of PhD thesis and PhD degree certificate or date of scheduled defense within 2014. Also provide a list of two persons who may act as references (with telephone numbers and e-mail addresses). Please send your application, marked with dnr 2.3.1-603-2014, to email@example.com or to Swedish Museum of Natural History, P. O. Box 50007, SE-104 05 Stockholm, Sweden, no later than September 9, 2014. Johannes Bergsten, PhD Senior Curator / Förste Intendent Research Division Swedish Museum of Natural History Box 50007 SE-104 05 Stockholm SWEDEN Visiting Address: Frescativägen 40 Phone: +46 8 5195 4192 Fax: +46 8 5195 4212 E-mail: firstname.lastname@example.org http://bit.ly/1AA3fQ2 Johannes Bergsten via Gmail
The Washington Area Phylogenetics Consortium is pleased to announce the Fourth annual Frontiers in Phylogenetics Symposium “Genome-Scale Phylogenetics: Analysing the Data” Sponsored by the National Museum of Natural History, Smithsonian Institution, and the Washington Area Phylogenetics Consortium Location: Warner Brothers Theatre, National Museum of American History, Washington, DC Time and Date: 9 AM to 5 PM, Monday September 15, 2014 REGISTRATION IS FREE BUT REQUIRED. Please visit the link below to register. http://bit.ly/FIPSymposium 8:00 Coffee and Continental Breakfast Service in Constitution Café 9:00 Introductions Michael Braun, National Museum of Natural History 9:05 Welcome to the Smithsonian John Kress, Interim Undersecretary for Science, Smithsonian Institution 9:15 Overview and Logistics Guillermo Ortí, George Washington University 9:25 Phylogenomics and Next-Generation Inferences: the Future of Phylogenetics in an Era of Big Data Lacey Knowles, University of Michigan 10:05 Break 10:30 Deep Metazoan Phylogeny and the Utility of Taxon-Specific Ortholog Sets Kevin Kocot, University of Queensland, Brisbane 11:10 A Phylogenomic View on the Early History of Gnasthostome Evolution: Is One Tree Enough? Ingo Ebersberger, Goethe University, Frankfurt 11:50 Lunch Break 1:30 Distinguishing Methodological and Biological Causes of Gene Tree Discordance in Phylogenomic Datasets Derrick Zwickl, University of Arizona 2:10 Filtering and Partitioning Strategies for Phylogenomic Analyses David Swofford, Duke University and National Evolutionary Synthesis Center 2:50 Break 3:10 Genome-scale Phylogenetics in the Presence of Hybridization and Incomplete Lineage Sorting Luay Nakhleh, Rice University 3:50 Joint Inference of Gene Trees and Species Trees at the Genomic Scale Bastien Boussau, University Claude Bernard, Lyon 4:30 Round Table Discussion With All Speakers Any questions or for more information contact Brian Coyle Coyleb@si.edu “Coyle, Brian J.” via Gmail
August 20, 2014
Dear EvolDir Community, We are pleased to announce the RNA-seqlopedia: http://bit.ly/1z4tj30 The RNA-seqlopedia is meant as a resource for researchers trying to utilize RNA-seq protocols for their research, including de novo assembly of transcriptomes as well as quantification of gene expression. The site focuses on multiple aspects of RNA-seq work including experimental design, molecular protocols, and bioinformatic analyses. We realize that the site does not yet cover all aspects of transcriptomic analysis, and undoubtedly contains errors or dated information that will be modified. We will continue to update the site and add to its content, particularly via input from the scientific community, so we request your input! We hope that the RNA-seqlopedia will prove to be a useful research resource for those interested in transcriptomic analyses using second (and third) generation sequencing. The site was made possible by a grant from the NIH National Center for Research Resources, and is being created and maintained by the Cresko Lab at the University of Oregon. If you have any feedback or suggestions, please write us. Sincerely, Clay Small Julian Catchen Susie Bassham Bill Cresko William A. Cresko, Ph.D. Associate Professor of Biology Director, Institute of Ecology and Evolution University of Oregon http://bit.ly/1pMIFIC; @wcresko email@example.com via Gmail
*Postdoctoral position in Evolutionary Genomics and Molecular and Cellular biology * */Molecular and cellular mechanisms of hyper-resistance to stress in the ameiotic bdelloid rotifer Adineta vaga/*** ** A 3-year postdoctoral research position is available in the group of Biochemistry, Biophysics and Molecular Genetics of Micro-organisms at the life Science Institute (ISV) of the Catholic University of Louvain (UCL, Belgium) to take part in a collaborative ARC research program with the Research Units in Environmental and Evolutionary Biology (URBE) and in Cellular Biology (URBC) at the University of Namur (UNamur, Be). This postdoc position is embedded within the research project entitled: /Asexuality and ‘immortality’, bdelloid rotifers as an evolutionary ‘scandal’ and a model system in biology. /This project is funded during 5 years and will start in October 2014. *Project:* Bdelloid rotifers are micro-organisms (animals) that have recently attracted much interest in the scientific community because of their ancient asexuality and their extreme resistance to stress, such as desiccation and high doses of ionizing radiation. They are capable to survive when their genome is shattered into small fragments and repair the DNA double strands breaks (DSBs) (see Hespeels et al., 2014). Repeated cycles of chromosomal repair are thought to promote allelic recombination and gene conversion in the absence of meiosis. Moreover desiccation and the induced DNA DSBs are also thought to provide a unique opportunity to acquire horizontally transferred genes, thereby contributing to the adaptive success of these organisms. In this project, the mechanisms that make bdelloid rotifers unique in terms of evolutionary strategy and hyper-resistance to stress will be investigated based on genomic data recently obtained by our consortium for the bdelloid rotifer /Adenita vaga/ (see Flot et al, 2013, Nature 500:453-7). Genomic approaches will be used to study the dynamics of /A. vaga/ genome during cycles of desiccation/rehydration/radiationand to decipher the genetic expression program that governs the different stages of its life-style. Molecular and cellular approaches will be developed to unveil and characterize the mechanisms that allow /A. vaga/ to repair its shattered chromosomes and generate genetic diversity,as well as its dependence with respect to oxidative stress response. Finally, conditions for horizontal gene transfer and RNA interference will be investigated, opening the way to the development of reverse genetic strategies. The ultimate prospect of the project is to establish bdelloid rotifers as a new model system for the understanding of fundamental biological processes such as DNA repair, cell survival and senescence. *PIs of the consortium:* Prof. Bernard Hallet (ISV, UCL), Prof. Karine Van Doninck (URBE, UNamur), Dr. Florence Debacq-Chainiaux (URBC, UNamur)** The involved consortium brings together experts in the fields of evolutionary biology and genomics (K. Van Doninck, URBE, UNamur), DNA recombination and genome plasticity (B. Hallet, ISV, UC) and oxidative stress response (F. Debacq-Chainiaux, URBC, UNamur). The appointed candidate will be expected to share its research time on both sites under the supervision of the three PIs of the consortium. The universities are at a distance of 35km from each other and easily connected by train. *Contacts:* Prof. Bernard Hallet, Bernard.firstname.lastname@example.org Universit Catholique de Louvain. Institut des Sciences de la Vie (ISV) http://bit.ly/1qTDNQl Prof. Karine Van Doninck, email@example.com University of Namur, Laboartory of Evolutionary Genetics and Ecology (http://bit.ly/1qTDQf8) *Qualifications:* We are looking for a post-doc with a strong interest and background in evolutionary genomics and molecular and cell biology. Expertise in the field of DNA repair and recombination, chromosome structure and dynamics, and/or genomics (NGS approach) is a valuable asset. Additional experience in cell biology techniques like DNA transfection, immuno-localization, fluorescence hybridization and microscopy will be a benefit. Priority will be given to candidates with a proven track record (with several publications as a first author) who will express their motivation in developing their autonomy and their interest for new challenges. *Application://* The position is available to both foreign nationals and Belgian citizens under ‘international mobility’ status, meaning that they may not have resided in Belgium for more than 12 months over the past 3 years preceding the appointment. The duration is for 2 years (with a possible 1-year renewal) starting on the *1^st of October 2014. *The closing date for applications is *^September 5th 2014.* Interested applicants should send a cover letter (briefly describing research experience, interests, and career goal), a curriculum vitae (with list of publications), and the names of three references (With address, phone number and E mail) to Bernard HALLET (Bernard.firstname.lastname@example.org) via Gmail
Postdoctoral Research Associate: Mechanistic Phylogenetic Models for Amino Acid Substitution Temple University An NSF-funded postdoctoral research position is available in the research group of David Liberles (Temple University from November, 2014; currently at University of Wyoming). The position is guaranteed for 1 year with the possibility of extension with successful performance. The successful candidate will be expected to relocate to Philadelphia, PA, USA and a start date as soon as possible after 11/1/14 is desired. The research project involves the construction and phylogenetic implementation of mechanistic models for amino acid substitution in C++. The ideal candidate will have a strong background in mathematics and statistics, strong C++ programming skills, and experience with phylogenetic methods. Knowledge of proteins and/or evolutionary biology is a plus. To apply, please send a cover letter that describes your background, motivation, and interests as well as a full CV to email@example.com. Please also arrange to have 3 letters of recommendation sent directly by the letter writer to the above email address as well. International applicants are encouraged to apply and will be given full consideration. “David A. Liberles” via Gmail
Ph.D. Student: Mechanistic Phylogenetic Models for Amino Acid Substitution Temple University An NSF-funded Ph.D. student position is available in the research group of David Liberles (Temple University from November, 2014; currently at University of Wyoming). The successful candidate will be expected to enroll in the Ph.D. program at Temple University in spring semester, 2015. The research project involves the construction and phylogenetic implementation of mechanistic models for amino acid substitution in C++. The ideal candidate will have prior programming coursework or experience, a strong background in mathematics, and interest in evolutionary biology. Students with any number of primary backgrounds, including biology and mathematics will be considered. To apply, please send a cover letter that describes your background, motivation, and interests as well as a full CV to firstname.lastname@example.org. I will guide the successful candidate through the Ph.D. application process at Temple University. International applicants are encouraged to apply and will be given full consideration. “David A. Liberles” via Gmail
Faculty Position in Genomics The Genome, Cell, and Developmental Biology Program at Indiana University invites applications for a tenured/tenure-track faculty position in Genomics at the level of assistant professor. Candidates should have well-developed research programs that apply cutting-edge genomic approaches to investigate the molecular mechanisms underlying important aspects of eukaryotic biology, including gene regulation, epigenetics, development, or evolution. More senior candidates with outstanding credentials in research and extramural funding may also be considered. The Department of Biology (http://bit.ly/1cfCtA9) and affiliated departments and programs represent more than 60 research labs housed in 3 adjacent buildings, providing ample opportunities for collaboration. The applicant will have access to outstanding resources including state-of-the-art facilities for genomics and bioinformatics, light and electron microscopy, flow cytometry, biophysical instrumentation, and computing. Applicants must hold a Ph.D. degree and have relevant postdoctoral experience with a strong record of research accomplishments. Faculty members are expected to establish vigorous well-funded research programs and to participate in undergraduate/graduate education. Applications received by October 15, 2014 will be assured of full consideration. Applicants should submit a cover letter, CV, research statement (past, present, and planned), up to three PDFs of re-prints/pre-prints, and arrange for three letters of references to be submitted at http://bit.ly/1n8sv7E. Please address inquires to Jennifer Tarter at 812-856-3984; email@example.com; 1001 E. Third Street, Bloomington, IN 47405-3700. Indiana University is an equal employment and affirmative action employer and a provider of ADA services. All qualified applicants will receive consideration for employment without regard to age, ethnicity, color, race, religion, sex, sexual orientation or identity, national origin, disability status or protected veteran status. Jennifer Tarter Administrative Assistant to the Chair Department of Biology Indiana University “Tarter, Jennifer A” via Gmail
"Open post-doc position on birds and climate change in University of Helsinki The Zoology Unit of the Finnish Museum of Natural History is inviting applications for a position of a Post-doctoral Researcher for a fixed term of 2 years and 8 months into the project The combined effect of climate change and habitat protection on population changes and range shifts in birds. The preferred starting time is 1 January 2015. More details can be found from this link: http://bit.ly/1ocfARV" Best wishes, Aleksi Lehikoinen Aleksi Lehikoinen, Docent, intendentti - curator Linnustonseuranta - Monitoring Team, The Helsinki Lab of Ornithology Luonnontieteellinen keskusmuseo - Finnish Museum of Natural History PL 17 - P.O. Box 17 00014 Helsingin yliopisto - University of Helsinki Finland puh. - tel. +358-9-19128851 mobile phone +358-45-1375732 firstname.lastname@example.org Aleksi Lehikoinen via Gmail
August 19, 2014
The Department of Biology at Stanford University invites applications for a tenure-track Assistant Professor in Evolution. We seek outstanding applicants engaged in answering broad basic questions in Evolution. We welcome a wide spectrum of applicants and will consider both theoretical and empirical evolutionary biologists. Applicants working at the interface of Evolution and Ecology and/or other areas of Biology are encouraged to apply. The successful candidate will hold a Ph.D., and is expected to develop a vigorous research program and to participate in the Department’s teaching activities at both the undergraduate and graduate levels. More information about the Department and the University can be found at http://stanford.io/1vfKoa3. All applicants should submit a cover letter, a curriculum vitae including publication list, a statement of research accomplishments and future plans, a description of teaching experience, and three letters of reference. All materials must be submitted electronically to AcademicJobsOnline . Inquiries may be directed to Faculty Searches, Dept. of Biology, 371 Serra Mall, Stanford, CA 94305, or to email@example.com. Applicant materials must be received by October 15, 2014. The appointment would begin September 1, 2015. Stanford University is an equal opportunity employer and is committed to increasing the diversity of its faculty. It welcomes nominations of and applications from women and members of minority groups, protected veterans and individuals with disabilities, as well as others who would bring additional dimensions to the universitys research, teaching, and clinical mission. firstname.lastname@example.org via Gmail
Phylogeneticists treat the tree image as having special meaning for themselves. Conceptually, the tree is used as a metaphor for phylogenetic relationships among taxa, and mathematically it is used as a model to analyze phenotypic and genotypic data to uncover those relationships. Irrespective of whether this metaphor / model is adequate or not, it has a long history as part of phylogenetics (Pietsch 2012). Of particular interest ihas been Charles Darwin's reference to the "Tree of Life" as a simile, since that is clearly the key to the understanding of phylogenetics by the general public.
The principle on which phylogenetic trees are based seems to be the same as that for human genealogies. That is, phylogenies are conceptually the between-species homolog of within-species genealogies. As far as Western thought is concerned, human genealogies make their first important appearance in the Bible, with a rather specific purpose. The Bible contains many genealogies, mostly presented as chains of fathers and sons. For example, Genesis 5 lists the descendants of Adam+Eve down to Noah and his sons, which can be illustrated as a pair of chains (as shown in the first figure); and the rest of Genesis gets from there down to Moses' family, for which the genealogy can be illustrated as a complex tree.
The genealogy as listed in Genesis 5.
Cain's lineage was terminated by the Flood.
However, the theologically most important genealogies are those of Jesus, as recorded in Matthew 1:2-16 and Luke 3:23-38. Matthew apparently presents the genealogy through Joseph, who was Jesus' legal father; and Luke apparently traces Jesus' bloodline through Mary's father, Eli. These two lineages coalesc in David+Bathsheba, and from there they have a shared lineage back to Abraham. Their importance lies in the attempt to substantiate that Jesus' ancestry fulfils the biblical prophecies that the Messiah would be descended from Abraham (Genesis 12:3) through Isaac (Genesis 17:21) and Jacob (Genesis 28:14), and that he would be from the tribe of Judah (Genesis 49:8), the family of Jesse (Isaiah 11:1) and the house of David (Jeremiah 23:5).
That is, these genealogies legitimize Jesus as the prophesied Messiah. Following this lead, subsequent use of genealogies has commonly been to legitimize someone as a monarch, so that royal genealogies have been of vital political and social importance throughout recorded history (see the example in the next figure). This importance was not lost on the rest of the nobility, either, so that documented genealogies of most aristocratic families allow us to identify the first-born son of the first-born son, etc, and thus legitimize claimants to noble titles — genealogies are a way for nobles to assert their nobility.
The genealogy of the current royal family of Sweden.
The lineage of the recent monarchs is highlighted as a chain, with an aborted side-branch dashed.
If we focus solely on the line of descent involved in legitimization, then genealogies can be represented as a chain (as shown in the genealogy above). However, if we include the rest of the paternal lines of descent then family genealogies can be represented as a tree. However, if we include some or all of the maternal lineages as well, then family genealogies can be represented as a network. For example, the biblical genealogies only rarely name women, but where females are specifically named the genealogies actually form a reticulated network. Jacob produced offspring with both Rachel and Leah, who were his first cousins; and Isaac and Rebekah were first cousins once removed. Even Moses was the offspring of parents who were, depending on the biblical source consulted, either nephew-aunt, first cousins, or first cousins once removed. These relationships cannot be represented in a tree. (See also the complex genealogy of the Spanish branch of the Habsburgs, who were kings of Spain from 1516 to 1700.)
This idea of genealogical chains, trees and networks was straightforward to transfer from humans to other species. Originally, biologists stuck pretty much to the idea of a chain of relationships among organisms, as presented in the early part of Genesis. Human genealogies were traced upwards to Adam and from there to God, and thus species relationships were traced upwards to God via humans. However, by the second half of the 1700s both trees and networks made their appearance as explicit suggestions for representing biological relationships. In particular, Buffon (1755) and Duchesne (1766) presented genealogical networks of dog breeds and strawberry cultivars, respectively.
However, these authors did not take the conceptual leap from within-species genealogies to between-species phylogenies. Indeed, they seem to have explicitly rejected the idea, confining themselves to relationships among "races". It was Charles Darwin and Alfred Russel Wallace, a century later, who first took this leap, apparently seeing the evolutionary continuum that connects genealogies to phylogenies. In this sense, they both took ideas that had been "in the air" for several decades, but previously applied only within species, and applied them to the origin of species themselves. [See the Note below.] Both of them, however, confined themselves to genealogical trees rather than using networks. It seems to me that it was Pax (1888) who first put the whole thing together, and produced inter-species phylogenetic networks (along with some intra-species ones).
In this sense, the biblical Tree of Life has only a peripheral relevance to phylogenetics. Darwin used it as a rhetorical device to arouse the interest of his audience (Hellström 2011), but it was actually the biblical genealogies that were of most practical importance to his evolutionary ideas. Apart from anything else, the original biblical tree was actually the lignum vitae (Tree of Eternal Life) not the arbor vitae (Tree of Life). Similarly, the tree from which Adam and Eve ate the forbidden fruit was the lignum scientiae boni et mali (Tree of Knowledge of Good and Evil), not the arbor scientiae (Tree of Knowledge) that was subsequently used as a metaphor for human knowledge.
Note. Along with phylogenetic trees, Darwin and Wallace did not actually originate the idea of natural selection, which had previously been discussed by people such as James Hutton (1794), William Charles Wells (1818), Patrick Matthew (1831), Edward Blyth (1835) and Herbert Spencer (1852). However, this discussion had been in relation to within-species diversity, whereas Wallace and Darwin applied the idea to the origin of between-species diversity (i.e. the origin of new species).
Buffon G-L de. 1755. Histoire naturelle générale et particulière, tome V. Paris: Imprimerie
Duchesne A.N. 1766. Histoire naturelle des fraisiers. Paris: Didot le Jeune & C.J. Panckoucke.
Hellström N.P. 2011. The tree as evolutionary icon: TREE in the Natural History Museum, London. Archives of Natural History 38: 1-17.
Pax F.A. 1888. Monographische übersicht über die arten der gattung Primula. Bot. Jahrb. Syst. Pflanzeng. Pflanzengeo. 10:75-241.
Pietsch T.W. 2012. Trees of life: a visual history of evolution. Baltimore: Johns Hopkins University Press.
Natural selection adapts organisms to their past environments and has no ability to foresee the future. When the environment changes, adaptations to past environments can misfire in the current environment, producing a mismatch that can only be solved by subsequent evolution or by modifying the current environment. Mismatches are an inevitable consequence of evolution in changing environments. They are especially relevant to human affairs, since modern human environments are so radically different from ancestral human environments. In addition, countless species are becoming mismatched to their environments thanks to anthropogenic environmental changes at a planetary scale. Waiting for subsequent genetic evolution to correct mismatches is not an option for problems requiring immediate solutions. This working group will develop a rigorous methodology for identifying evolutionary mismatches and finding the right environmental interventions, or âwhat to do about it,â in both humans and nonhuman species. The focus on mismatch emerged from the recent NESCent catalysis meeting titled âThe Nature of Regulation: How Evolutionary Theory Can Inform the Regulation of Large-scale Human Social Interactionsâ which was organized in collaboration with the Evolution Institute. The working group will continue the collaboration, including a novel organizational structure that nests the working group within larger groups that provide both an informed audience and enables meaningful input from a distance.
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology