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May 6, 2015
Primates are highly charismatic and often serve as flagship species in conservation efforts. They are also the closest living relatives of humans, and therefore hold the keys to resolving many questions about human evolution and ecology. However, the slow life histories of primates, combined with their complex social systems, their behavioral plasticity, and the challenging field conditions in which primate researchers must work, have severely limited analyses of mortality and fertility in wild, unprovisioned primate populations. This in turn limits comparative analyses that can shed light on the population dynamics and the social and ecological adaptations that have shaped both human and nonhuman primate evolution. We propose a Primate Life Histories Working Group to compare mortality and fertility schedules across taxa, to evaluate a set of hypotheses about the roles that phylogeny, ecology, and behavior play in shaping primate mortality and fertility patterns, and to examine whether life history theory predicts which vital rates are most variable across species. Using unique, individual-based life history data that have been collected from wild populations by nine working group participants over a minimum of 19 years, we will develop age-specific mortality and fertility schedules and create population projection matrices for each species. Our immediate goals are to test current hypotheses about the evolution of life histories in order to advance our understanding of primate evolution. Our longer-term goal is to move toward a collaborative, shared databank allowing analyses of irreplaceable life history data on wild primates.
April 23, 2015
The identification and explanation of long-term evolutionary trends in higher taxa and biological communities is an important goal of biological research. Body size is the single most important ecological characteristic of metazoa and the variable most easily applied to analysis of evolutionary trends across distantly related taxa. The proposed working group will bring together paleobiologists studying body size evolution in deep time and across higher taxa with biologists studying the distribution of body sizes in living organisms from the community to global scale. The working group will initiate a community-wide database of body sizes through the Phanerozoic, an effort that requires standardized data on body size across higher taxa. The working group will also catalyze collaborations between paleobiologists and biologists to develop the theory necessary to investigate long-term dynamics in body-size evolution across diverse living and extinct metazoan lineages. The workshop will provide a venue for members to address the relationships between the pattern of body size evolution and the distribution of body sizes in extant organisms. How well can macroevolutionary patterns be inferred from macroecological ones? How well do those patterns reflect evolutionary mechanisms, whether driven or passive? Ultimately, the resulting database will become a broadly applicable and dynamic resource for macroevolutionary research, with real potential to help future workers shed light on the forces that have shaped the evolutionary trajectory of animal life on Earth.
April 12, 2015
Although the Indian and Pacific Oceans (hereafter Indo-Pacific) have long been recognized as containing the majority of marine biodiversity, their vastness poses substantial challenges for empirical research. Syntheses of published data, however, can expand the geographic scope of inference. We plan to examine the recent evolution of Indo-Pacific taxa by drawing upon all available population genetic data. We have two immediate research goals: 1) compile and analyze existing datasets for multiple species using consistent and uniform methods of analysis that represent the best current practice in population genetics to better determine oceanographic and geographic features as well as biological traits correlated with population structure. These results will inform our understanding of evolutionary processes in the region and provide information directly relevant to managers and conservation organizations. We will also: 2) conduct the first large scale multispecies investigation to infer the geography of speciation among Indo-Pacific taxa that incorporates population genetic inferences, thus testing predictions of competing biogeographic hypotheses using a novel approach. These research goals are underpinned by the creation of a database that would become publicly accessible to facilitate future studies. In addition, we plan to develop a virtual collaboration space that will support international collaborations in genetic-based research, training, and education throughout the region.
March 15, 2015
February 26, 2015
Evolutionary biology is a foundational and integrative science for medicine, but few physicians or medical researchers are familiar with its most relevant principles. While undergraduate students have increasing opportunities to learn about the interface of evolution, health, and disease, most premedical students have scant room for electives in their schedules, few premed prerequisite courses incorporate evolutionary thinking, and no medical school develops these competencies. The overarching goal of this Working Group is to lay the groundwork for future endeavors by providing testable models and pathways for infusing premedical and medical education with evolutionary thinking. This Working Group, an interdisciplinary, international, and intergenerational group of physicians, scientists, educators, and students, will 1) define core competencies in evolutionary biology for physicians and other health professionals; 2) investigate the ability of current curricula to prepare health professionals to meet these standards; 3) identify âteachable momentsâ that provide opportunities to integrate evolutionary principles into premedical and medical curricula; 4) design model curricula and learning experiences that can advance evolutionary education for health professionals; and 5) provide open access to these resources and disseminate them. The Working Group will be supported by an Advisory Committee of senior academic leaders and stakeholders. These efforts will not be sufficient in themselves, but they will establish the intellectual platform from which educational interventions on student learning, and scientific and clinical problem solving, can be developed and tested.
Americans are far less accepting of human evolution than other realms of evolution; yet, human evolution and our common ancestry with other animals are increasingly relevant to medicine and our daily lives. We propose a NESCent working group made up of scientists, educators, and a journalist that will be devoted to enhancing communication of these health-related applications of human evolution to diverse audiences. Planned activities include discussion of methodological approaches designed to best communicate these ideas, design of teacher workshops, writing publications geared to each of these audiences, and discussion regarding collaboration with museums (in particular, the Smithsonian Institution) and zoos. In these activities, we will take a systematic scholarly approach using evidence-based methods to foster communication of principles of human evolution to these diverse audiences.
February 22, 2015
It is easily demonstrable that organisms with rapid, appropriate plastic responses to environmental change will prevail over genotypes with fixed phenotypes. It is also accepted that the general dearth of organisms successful across a wide environmental range indicates fundamental limits to or costs of plasticity. The nature of constraining factors has been broadly discussed (DeWitt et al. 1998), and numerous studies have been done to quantify them. However, a curious pattern has emerged: although hypothesized to be widespread, costs are absent more often than they are detected. The issue of costs of plasticity (CoP) lies at the intersection of a range of evolutionary and ecological questions: What are the limits to plasticity? Are CoP associated with life history tradeoffs? Are CoP expected in all environments? Does plasticity enhance invasiveness? etc. This working group will address two fundamental questions. 1) Are the expectations that costs of plasticity should be universal well-founded (i.e., the Âno free lunchÂ principle)? Several authors have proposed that, in situations where the intensity of selection for adaptive plasticity is strong, there should be corresponding pressure to ameliorate costs. 2) Independently of the answer to the first question, Are analytical and experimental methods for detecting CoP appropriate or sufficiently sensitive? CoP have most often been studied using common garden style plasticity experiments and analyzed via van TienderenÂs (1991) multiple regression approach.
February 10, 2015
A working group to solve problems in model selection and phylogeny in mixed multi-factor meta-analysis
Meta-analysis is a statistical technique used for syntheses of results from numerous independent studies. Increasingly, evolutionary biologists need to perform meta-analysis in which the effects of numerous explanatory variables on a response variable of interest are considered, taking into account the evolutionary history of the species in the dataset. However, such analyses require analysis of numerous complex statistical models, and methods for such analyses have not been previously developed. Our working group is developing these methods and applying them to understand local adaptation, context-dependency, and the influence of evolutionary relationships on outcomes of symbiosis between plants and mycorrhizal fungi.
January 14, 2015
When a seed germinates determines the seasonal environment experienced by a plant throughout its life, and germination phenology is one of the very first phenotypes expressed by plants during ontogeny. As such, germination phenology is subject to extremely strong natural selection, especially during early stages of adaptation. Moreover, germination co-evolves with seed dispersal, mating system, and reproductive strategy to determine plant life cycles and demographic dynamics of plant populations. This working group will test the importance of germination adaptations in delimiting species niche and range limits, both in the past and in response to changed environments. More generally, this topic pertains to the identification of key traits associated with adaptation to environmental change, and the role that early life-stage traits and traits associated with habitat selection contribute to these dynamics. The focus on germination provides a clear and tractable system for addressing general evolutionary and ecological questions concerning the interactions between ontogeny and adaptation, trait coevolution, and the roles of habitat selection and organismal responses to their environment in niche evolution. It also will contribute tangibly to efforts to predict plant responses to environmental change. The group will compile and analyze a comprehensive data set on germination and dormancy, combined with data on niche breadth, geographic range, and life history, in order to test hypotheses concerning trait coevolution and species range limits. The group will also theoretically explore interactions between ontogeny and adaptation, theoretically model trait coevolution via habitat selection and bet hedging, and develop phenological models of integrated life histories that include germination in order to predict plant responses to environmental change.
January 13, 2015
Humans are vulnerable to a number of unique musculoskeletal maladies as a consequence of our evolutionary history. Although walking on our extended hind limbs is the hallmark adaptation characterizing our species it nevertheless makes us vulnerable to a wide range of serious joint and soft tissue problems. When viewed from an evolutionary perspective many of these medical issues become understandable and, indeed, novel methods of diagnosis and treatment can emerge. The proposed collaborative, a working group of paleoanthropologists, comparative anatomists, biomechanical engineers, and physicians will create new analytical approaches and new ways of viewing the disorders that uniquely plague our species. The results of this work include the development and implementation of a model curriculum, the creation of a website, and the publication of an edited volume. The disorders directly related to our way of walking include chronically sprained ankles, hernias, osteoporotic fractures of the hip, spine, and forearm, obstetric problems, knee problems, foot disorders, fatigue fractures, and many others. By understanding how our anatomy changed in order to walk upright, and why these changes occurred, we gain a better understanding of why these adaptations sometimes go awry resulting in disorders and pain.
December 17, 2014
We propose a catalysis meeting to advance theoretically-grounded, empirical study of scientific collaborations designed to achieve synthesis. Synthesis is the integration of diverse theories, methods and data across spatial or temporal scales, scientific phenomena, and forms of expertise to increase the generality, parsimony, applicability, or empirical soundness of scientific explanations. It generates emergent explanations beyond the scope of any one discipline, dataset or method. It counterbalances scientific specialization, capitalizes on existing data, and can be used to address complex problems. Synthesis centers are an increasingly vital component of science policy, rising in number, size, and prominence nationally and globally. Despite this, our understanding of synthesis-group collaborations and their performance are inadequate to advance knowledge, inform policy and guide practice. This meeting will draw together scientists who lead and conduct synthetic research with a diverse group of experts on scientific collaboration and research evaluation. Our aim is to advance understanding of synthesis and develop new approaches for investigating it empirically, longitudinally and comparatively.
December 9, 2014
Wednesday, 12:00 PM at NESCent, Ninth Street and Main Street, Erwin Mill Building, 2024 W. Main Street, Suite A200. For more information, call 919-668-4551
December 7, 2014
Making science more reproducible has enormous potential to accelerate scientific advance, including for practicing individuals. Despite this, the tools and approaches that are already available are rarely taught. To address this, we are organizing a 4-day workshop aimed at developing, and later teaching, a short course curriculum for tools, resources, and practices for reproducible science. A part of the workshop will also be devoted to addressing gaps that hinder the broad adoption of such resources.
December 2, 2014
November 25, 2014
Andrew Roger wrote:
I'm wondering if those of you developing phylogenetic software tools have thought much about the problem of how we will develop software tools that are able to handle both large numbers of taxa (>100) and large numbers of sites (super-matrices of 50,000 positions and more) but at the same time implement complex substitution models. I think the problem is especially acute for complex 'site-heterogeneous' mixture models such as Lartillot's CAT models or even ones with a set number of classes (e.g. 10-60 as in Lartillot and Gascuel's C-series models) or models that involve large matrices such as codon models or the covarion-type models. Additional computational complexity is introduced by partitioned models where different parameters are allowed to be estimated for different partitions (e.g. edgelengths for different genes in a super-matrix). My concern is that currently large complex data sets cannot be analyzed with the best substitution models currently because the the computational time required to evaluate the likelihoods are prohibitive even with relatively small data sets. Tree-searching becomes nearly impossible under these conditions because of the time required.
I have been using DIVERGE (DetectIng Variability in Evolutionary Rates among GEnes) to test for divergence in function across different clades of a protein superfamily.
I have noticed that when using the 2001 algorithm and the 1999 algorithm (although to a lesser extent) I get negative values for thetaML = the Maximum likelihood estimate of the coefficient of functional divergence (normally lies between 0 and 1). I then get an LRT theta value (likelihood ratio test against the null) of '-1.#IND00' or 'not a number'.
I emailed the developer but had no response yet. I suspect it may have something to do with short branch lengths or something like that...
Has anyone ever used DIVERGE and have some insight as to why this might happen?
Graduate Opportunity Spatial Genomic Analysis of North American Mountain Pine Beetle Outbreaks We are recruiting a graduate student to investigate the spatial genomic patterns among outbreak populations of mountain pine beetle across North America. This will involve collaborative work among a number of Canada Universities and Canadian Forest Service conducted under funding to the TRIA project (see http://bit.ly/15dxHnm). The work will build upon previous spatial genetic studies (e.g., Samarasekera et al 2012; Janes et al 2014) by using a genotype-by-sequencing approach to explore genomic differences among outbreak populations across North America and to identify loci under local selection. Results of this study will improve our understanding of the genetic differences among mountain pine beetle outbreaks and provide much needed information for the ongoing management and predictive modeling of future outbreaks. The qualified student will conduct the majority of their course work and research at the Prince George campus of the University of Northern BC, but will also have the opportunity to engage in courses and meetings involving TRIA members from other Canadian Universities. UNBC is a small, dynamic research intensive university (www.unbc.ca). Situated in the geographic centre of British Columbia, the Prince George area offers an affordable quality of life and an abundant of summer and winter outdoor recreation activities. Please see our website for more information on the Natural Resources and Environmental Studies Graduate Program including degree requirements and expectations (www.unbc.ca/nres/). Qualifications: This is a challenging, but rewarding project requiring a range of interests and aptitudes. Preferably, the successful applicant will have a degree in biology or ecology. Previous experience and coursework in insect biology, population genetic and/or molecular ecology are an asset. The student should be willing to work in a collaborative environment with multiple University and Government research partners. Ideally the graduate student will begin in May 2015, although earlier or later start dates will be considered. We anticipate a competitive stipend (~20,000/year) and full funding to support lab and other research activities. For further information please contact Brent Murray (firstname.lastname@example.org; 1-250-960-5638; http://bit.ly/1plOi2gwww.unbc.ca). Situated in the geographic centre of British Columbia, the Prince George area offers an affordable quality of life and an abundant of summer and winter outdoor recreation activities. Please see our website for more information on the Natural Resources and Environmental Studies Graduate Program including degree requirements and expectations (www.unbc.ca/nres/). Qualifications: This is a challenging, but rewarding project requiring a range of interests and aptitudes. Preferably, the successful applicant will have a degree in biology or ecology. Previous experience and coursework in insect biology, population genetic and/or molecular ecology are an asset. The student should be willing to work in a collaborative environment with multiple University and Government research partners. Ideally the graduate student will begin in May 2015, although earlier or later start dates will be considered. We anticipate a competitive stipend (~20,000/year) and full funding to support lab and other research activities. For further information please contact Brent Murray (email@example.com; 1-250-960-5638; http://bit.ly/1plOi2g). Samarasekera NG, Bartell N, Lindgren BS, Cooke JEK, Davis CS, James PMA, Coltman DW, Mock KE, and Murray BW. (2012) Spatial Genetic Structure of the Mountain Pine Beetle (Dendroctonus ponderosae) Outbreak in Western Canada: Historical patterns and contemporary dispersal. Molecular Ecology, 21:2931-2948. Janes JK, Li Y, Keeling CI, Yuen MMS, Boone CK, Cooke JEK, Bohlmann J, Huber PW, Murray BW, Coltman DW and Sperling FAH (2014) How the mountain pine beetle (Dendroctonus ponderosae) breached the Canadian Rocky Mountains. Molecular Biology and Evolution advanced press, April 22, 2014; doi: 10.1093/molbev/msu135 Brent Murray via Gmail
Dear colleagues, We are excited to invite submissions to the symposium “Cooperation without kinship: from genomes to mutualism” to be held at the 15th Congress of the European Society for Evolutionary Biology (ESEB), August 10-14 2015 in Lausanne, Switzerland. While kin selection is a powerful explanation for some cooperation, there are many cases where relatedness is simply not possible, such as cooperation between species. More generally, these cases are forms of “egalitarian” cooperation and include examples as diverse as genes in a genome, nuclear and organellar genomes within cells, and species in symbiosis and mutualisms. Without relatedness, the key hurdle in egalitarian coalitions is conflict suppression. Conflict suppression mechanisms have been studied in all the key examples of egalitarian coalitions, including the suppression of transposable elements in genomes, and cheaters in mutualisms. However, these systems are rarely discussed together. We hope to bring together researchers from across these diverse systems to stimulate interactions and seek general principles underlying the evolution of egalitarian cooperation. We have two great invited speakers: - Toby Kiers, Vrije Universiteit Amsterdam, http://bit.ly/1y7Z3WM - Justin Blumenstiel, University of Kansas, http://bit.ly/1C9m9kT General details of ESEB 2015 can be found here: http://bit.ly/1rIZnbW Abstract submission and registration are due January 10th, 2015. In the meantime, please don’t hesitate to get in touch if you have any questions! All the best, Arvid Agren, firstname.lastname@example.org Kevin Foster, email@example.com via Gmail
Dear evoldir A PhD studentship is available by competition to study the molecular evolution of tyrosine kinases, jointly supervised by me (Dr Ed Hollox) and Prof Nick Brindle at the University of Leicester. Further details at http://bit.ly/1bRFqnL Project outline: Although multicellularity has evolved several times in eukaryotes, its evolution in metazoa is of particular interest, because of the range of distinct cell types observed in metazoans leading to highly complex and mobile organisms. Tyrosine kinases (Y kinases) are an important family of proteins involved in mediating cell-cell signalling. They evolved from serine-threonine kinases (ST kinases) around 600 million years ago and are found only in metazoans and choanoflagellates. Y kinases are thought to be critical in enabling the evolution of multicellularity in metazoans by developing an extra signalling space for cell-cell communication (1). It is not known how the tyrosine kinase signalling system evolved, and what biochemical constraints on the protein sequence space there were in the evolution of tyrosine kinases. This multidisciplinary project combines bioinformatics, evolutionary genetic analysis, experimental evolution and biochemistry to determine how Y kinases evolved. The initial step, supervised by Ed Hollox, will infer ancestral pre-Y kinase and proto-Y kinase domain sequences from Kinbase, a highly curated database. The second step will be investigation of the biochemistry of the transition between pre-Y and proto-Y kinase domain using an in-vitro evolution system in the lab of Nick Brindle. This project is available for a PhD studentship is available as part of the Midlands Integrative Biosciences Training Partnership, http://bit.ly/1C9m94x Eligibility: British nationals who have lived in the UK all their lives are eligible. Also eligible are non-British nationals who have settled status AND have been resident in the UK for 3 years immediately prior to the date of the start of the course. EU nationals who have been ordinarily resident in the UK and Islands for three years immediately prior to the date of start of the course; EU nationals not resident in the UK are eligible for matched funding studentships only. Ed Hollox, PhD Lecturer in Genetics, University of Leicester Research group pages http://bit.ly/1k2YVjk Departmental staff page http://bit.ly/Qq1zqZ Room G6, Department of Genetics, **** note new office *** Adrian Building University Road, Leicester LE1 7RH UK Tel: +44 (0)116 252 3407 (office G6) +44 (0)116 223 1366 (lab G3) “Hollox, Ed (Dr.)” via Gmail
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology
Molecular Biology and Evolution