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December 17, 2014
The Natural History Museum has released their data portal (http://data.nhm.ac.uk/). As of now it contains 2,439,827 of the Museum's 80 million specimens, so it's still early days. I gather that soon this data will also appear in GBIF, ending the unfortunate situation where data from one of the premier natural history collections in the world was conspicuous by its absence.
I've not had a chance to explore it in much detail, but one thing I'm keen to do is see whether I can link citations of NHM specimens in the literature (e.g., articles in BioStor) with records in the NHM portal. Being able to dip this would enable all sorts of cool things, such as being able to track what researchers have said about particular specimens, as well as develop citation metrics for the collection.
On a recent trip to the Natural History Museum, London, the subject of DNA barcoding came up, and I got the clear impression that people at the NHM thought classical DNA barcoding was pretty much irrelevant, given recent developments in sequencing technology. For example, why sequence just COI when you can use shotgun sequencing to get the whole mitogenome? I was a little taken aback, although this is a view that's getting some traction, e.g. [1,2]. There is also the more radical view that focussing on phylogenetics is itself less useful than, say, "evolutionary gene networks" based on massive sequencing of multiple markers .
At the risk of seeming old-fashioned in liking DNA barcoding, I think there's a bigger issue at stake (see also ). DNA barcoding isn't simply a case of using a single, short marker to identify animal species. It's the fact that it's a globalised, standardised approach that makes it so powerful. In the wonderful book "A Vast Machine" , Paul Edwards talks about "global data" and "making data global". The idea is that not only do we want data that is global in coverage ("global data"), but we want data that can be integrated ("making data global"). In other words, not only do we want data from everywhere in the world, say, we also need an agreed coordinate system (e.g., latitude and longitude) in order to put each data item in a global context. DNA barcoding makes data global by standardising what a barcode is (a given fragment of COI), and what metadata needs to be associated with a sequence to be a barcode (e.g., latitude and longitude) (see, e.g. Guest post: response to "Putting GenBank Data on the Map"). By insisting on this standardisation, we potentially sacrifice the kinds of cool things that can be done with metagenomics, but the tradeoff is that we can do things like put a million barcodes on a map:
To regard barcoding as dead or outdated we'd need an equivalent effort to make metagenomic sequences of animals global in the same way that DNA barcoding is. Now, it may well be that the economics of sequencing is such that it is just as cheap to shotgun sequence mitogenomes, say, as to extract single markers such as COI. If that's the case, and we can get a standardised suite of markers across all taxa, and we can do this across museum collections (like Hebert et al.'s  DNA barcoding "blitz" of 41,650 specimens in a butterfly collection), then I'm all for it. But it's not clear to me that this is the case.
This also leaves aside the issue of standardising other things's much as the metadata. For instance, Dowton et al.  state that "recent developments make a barcoding approach that utilizes a single locus outdated" (see Collins and Cruickshank  for a response). Dowton et al. make use of data they published earlier [7,8]. Out of curiosity I looked at some of these sequences in GenBank, such as JN964715. This is a COI sequence, in other words, a classical DNA barcode. Unfortunately, it lacks a latitude and longitude. By leaving off latitude and longitude (despite the authors having this information, as it is in the supplemental material for ) the authors have missed an opportunity to make their data global.
For me the take home message here is that whether you think DNA barcoding is outdated depends in part what your goal is. Clearly barcoding as a sequencing technology has been superseded by more recent developments. But to dismiss it on those grounds is to miss the bigger picture of what is a stake, namely the chance to have comparable data for millions of samples across the globe.
Background: Synonymous codon usage bias (SCUB) is an inevitable phenomenon in organismic taxa, generally referring to differences in the occurrence frequency of codons across different species or within the genome of the same species. SCUB happens in various degrees under pressure from nature selection, mutation bias and other factors in different ways. It also attaches great significance to gene expression and species evolution, however, a systematic investigation towards the codon usage in Bombyx mori (B. mori) has not been reported yet. Moreover, it is still indistinct about the reasons contributing to the bias or the relationship between the bias and the evolution of B. mori. Results: The comparison of the codon usage pattern between the genomic DNA (gDNA) and the mitochondrial DNA (mtDNA) from B. mori suggests that mtDNA has a higher level of codon bias. Furthermore, the correspondence analysis suggests that natural selection, such as gene length, gene function and translational selection, dominates the codon preference of mtDNA, while the composition constraints for mutation bias only plays a minor role. Additionally, the clustering results of the silkworm superfamily suggest a lack of explicitness in the relationship between the codon usage of mitogenome and species evolution. Conclusions: Among the complicated influence factors leading to codon bias, natural selection is found to play a major role in shaping the high bias in the mtDNA of B. mori from our current data. Although the cluster analysis reveals that codon bias correlates little with the species evolution, furthermore, a detailed analysis of codon usage of mitogenome provides better insight into the evolutionary relationships in Lepidoptera. However, more new methods and data are needed to investigate the relationship between the mtDNA bias and evolution.
Background: There is great interest in understanding the genomic underpinnings of social evolution, in particular, the evolution of eusociality (caste-containing societies with non-reproductives that care for siblings). Subsociality is a key precursor for the evolution of eusociality and characterized by prolonged parental care and parent-offspring interaction. Here, we provide the first transcriptomic data for the small carpenter bee, Ceratina calcarata. This species is of special interest because it is subsocial and in the same family as the highly eusocial honey bee, Apis mellifera. In addition, some C. calcarata females demonstrate alloparental care without reproduction, which provides a unique opportunity to study worker behaviour in a non-eusocial species. Results: We uncovered similar gene expression patterns related to maternal care and sibling care in different groups of females. This agrees with the maternal heterochrony hypothesis, specifically, that changes in timing of offspring care gene expression are related to worker behaviour in incipient insect societies. In addition, we also detected some similarity to caste-related gene expression patterns in highly eusocial honey bees, and uncovered large lifetime changes in gene expression that accompany shifts in reproductive and maternal care behaviour. Conclusions: For Ceratina calcarata, we found that transcript expression profiles were most similar between sibling care and maternal care females. The maternal care behaviour exhibited post-reproductively by Ceratina mothers is concordant in terms of transcript expression with the alloparental care exhibited by workers. In line with theoretical predictions, our data are consistent with the maternal heterochrony hypothesis for the evolutionary development of worker behaviour in subsocial bees.
Background: In bacteria, cell size affects chromosome replication, the assembly of division machinery, cell wall synthesis, membrane synthesis and ultimately growth rate. In addition, cell size can also be a target for Darwinian evolution for protection from predators. This strong coupling of cell size and growth, however, could lead to the introduction of growth defects after size evolution. An important question remains: can bacterial cell size change and/or evolve without imposing a growth burden? Results: The directed evolution of particular cell sizes, without a growth burden, was tested with a laboratory Escherichia coli strain. Cells of defined size ranges were collected by a cell sorter and were subsequently cultured. This selection-propagation cycle was repeated, and significant changes in cell size were detected within 400 generations. In addition, the width of the size distribution was altered. The changes in cell size were unaccompanied by a growth burden. Whole genome sequencing revealed that only a few mutations in genes related to membrane synthesis conferred the size evolution. Conclusions: In conclusion, bacterial cell size could evolve, through a few mutations, without growth reduction. The size evolution without growth reduction suggests a rapid evolutionary change to diverse cell sizes in bacterial survival strategies.
Gould Award announcement The Society for the Study of Evolutions Committee for the Stephen J. Gould Award for the Improvement for the Understanding of Evolution is soliciting nominations for the Award for 2015. With this annual award the Society for the Study of Evolution recognizes, promotes, and rewards individuals who have increased public understanding of evolutionary biology and its place in modern science. The award will include a cash prize of $5,000 and the expectation that the recipient will present the Public Outreach Seminar at the Evolution Meeting (expenses for travel/lodging and registration would be covered by the SSE). The awardee should be a leader in evolutionary thought and in public outreach who can deliver an inspiring lecture for both professionals and the broader public at the 2015 meetings of the Society in San Paolo, Brazil. Nominations should include the CV of the nominee along with a 1-2 page letter describing why this individual is worthy of the award. Please send nominations via e-mail to the Chair of the Committee, Steve Palumbi, at email@example.com. Please submit names of nominees by December 18. All nominations will be treated confidentially and will be evaluated by members of the Committee and the Council for the Society. An awardee will be announced in early February. Stephen R. Palumbi Harold A Miller Director, Hopkins Marine Station Jane and Marshall Steel Professor of Biology Stanford University Steve Palumbi via Gmail
Computational Biologist - Research & Development 23andMe Mountain View, CA, United States Do you wish that your work had a more direct impact on people? Are you excited about the potential of human genetics to make a real difference in the world? At 23andMe, we believe that genetics is on the cusp of huge advances, and that our unique database of hundreds of thousands of genotypes and almost two hundred million phenotype data points gives us an incredible opportunity to advance not only biomedical research, but our understanding of ourselves. We are looking for a colleague with extensive training and experience in computational biology to join our highly productive, world-class research team. This person will be involved in the analysis of human genetic data and the development of product features that depend on a mix of computational skills, statistical knowledge, creativity, and biological insight. The scope and breadth of our vision means that most of the necessary techniques have yet to be developed anywhere in the world. This person is also expected to participate in the communication and public relations efforts of the company. QUALIFICATIONS: - PhD in Computational Biology or related field (eg, Genetics, Computer Science, Engineering, Physics, Math, Bioinformatics) - Strong bioinformatics and biostatistics background - Background in algorithm development - Proficiency with scripting languages (eg, Python, R, bash) - Enthusiasm for working in a highly collaborative environment ALSO VALUABLE: - Evolutionary or population genetics research experience - Demonstrated record of developing and distributing tools for the analysis and visualization of genomics data - Experience with C/C++ Experience mentoring other scientists and familiarity with epidemiological principles are highly desirable. Apply online: http://bit.ly/1szeN0H ABOUT US 23andMe is the leading personal genetics company. We are dedicated to helping individuals understand their own genetic information through DNA analysis technologies and web-based interactive tools. Our mission is to personalize health care by making and supporting meaningful discoveries through genetic research. Combining web development, computer science, genetics, social media, and informatics, 23andMe is at the forefront of a new era in personal genetics. Kasia Bryc via Gmail
—Apple-Mail=_975A4FE6-3B15-476B-9CA4-7AA827601258 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii DARWIN FELLOW The Graduate Program in Organismic and Evolutionary Biology at University of Massachusetts Amherst announces a two-year POSTDOCTORAL FELLOWSHIP/LECTURESHIP. OEB draws together more than 80 faculty from the Five Colleges (University of Massachusetts Amherst and Smith, Hampshire, Mount Holyoke and Amherst Colleges), offering unique training and research opportunities in the fields of ecology, organismic and evolutionary biology. Our research/lecture position provides recent PhD’s an opportunity for independent research with an OEB faculty sponsor, as well as experience mentoring graduate students and teaching a one-semester undergraduate biology course. The successful candidate will have a recent PhD in a field relevant to ecology, organismic or evolutionary biology and proven teaching skills. Position subject to availability of funds. To apply online, please go to http://bit.ly/1qZcTLk and submit a CV, statements of research and teaching interests, and arrange for 3 letters of reference and a letter of support from your proposed OEB faculty sponsor. A list of OEB faculty and additional information is available at http://bit.ly/1vYlB89 . Applicants should apply by the priority deadline of January 26, 2015 in order to ensure consideration. The position is expected to start in August 2015. Questions about this search may be sent to: firstname.lastname@example.org The University of Massachusetts Amherst is an Affirmative Action/Equal Opportunity Employer of women, minorities, protected veterans and individuals with disabilities and encourages applications from these and other protected group members —Apple-Mail=_975A4FE6-3B15-476B-9CA4-7AA827601258 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-asciiDARWIN FELLOWThe Graduate Program in Organismic and Evolutionary Biology at University of Massachusetts Amherst announces a two-year POSTDOCTORAL FELLOWSHIP/LECTURESHIP. OEB draws together more than 80 faculty from the Five Colleges (University of Massachusetts Amherst and Smith, Hampshire, Mount Holyoke and Amherst Colleges), offering unique training and research opportunities in the fields of ecology, organismic and evolutionary biology. Our research/lecture position provides recent PhD’s an opportunity for independent research with an OEB faculty sponsor, as well as experience mentoring graduate students and teaching a one-semester undergraduate biology course. The successful candidate will have a recent PhD in a field relevant to ecology, organismic or evolutionary biology and proven teaching skills. Pos ition subject to availability of funds. To apply online, please go to http://bit.ly/1vYlB8a; and submit a CV, statements of research and teaching interests, and arrange for 3 letters of reference and a letter of support from your proposed OEB faculty sponsor. A list of OEB faculty and additional information is available at http://bit.ly/1qZcTLo;. Applicants should apply by the priority deadline of January 26, 2015 in order to ensure consideration. The position is expected to start in August 2015. Questions about this search may be sent to: email@example.comThe University of Massachusetts Amherst is an Affirmative Action/Equal Opportunity Employer of women, mino rities, protected veterans and individuals with disabilities and encourages applications from these and other protected group members
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A 2-year postdoc position is available at SLU, Alnarp: Plant Resistance Ecology: A new tool to engineer pollination In strawberries herbivore-damaged plants deter pollinators, leading to reduced pollination success. However, wild plant genotypes, as well as domesticated varieties, differ in their resistance against herbivores. The aim of this postdoc project is to investigate whether pollination success is improved when wild strawberries evolve stronger resistance, and during plant breeding for improved resistance in domesticated varieties. The postdoc will have access to a large common garden with 100 wild plant genotypes (Fragaria vesca), and several domesticated varieties (Fragaria x ananassa, F. vesca, F. viridis, F. moschata), that differ in their resistance against herbivores. The full ad can be downloaded here: http://bit.ly/1vYlARM Johan Johan A. Stenberg Associate Professor Sveriges lantbruksuniversitet Swedish University of Agricultural Sciences Department of Plant Protection Biology PO Box 102, SE-230 53 ALNARP Visiting address: Sundsvgen 14 Mobile: +46 70 622 00 42 firstname.lastname@example.org, www.slu.se/stenberg Johan A Stenberg via Gmail
The Williams and Clark labs at Cornell University have an opening for a postdoctoral fellow in computational genetics and genomics. Key research topics center on analyses of identity by descent (IBD) sharing within and between populations, and include potential development of novel methods to detect IBD segments. In addition to this general topic area, candidates with distinct but related research interests are encouraged to apply. The Clark and Williams labs are in the Biological Statistics and Computational Biology Department at Cornell University, and maintain close connections to neighboring genetics and genomics labs on campus. Postdocs will benefit from a collaborative environment with many opportunities to interact with the vibrant genetics community at Cornell. Initial appointment is for two years with the possibility of extension and includes competitive salary and benefits. Start date is flexible and can be immediate. Qualifications: Candidates are expected to have a Ph.D. in computational biology, computer science, statistics, genetics, applied mathematics, or related disciplines. Strong quantitative and programming experience (ideally in C or C++) are essential skills. Informal inquiries and applications are welcome via email sent to both alw289 cornell.edu and ac347 cornell.edu. To apply, email a CV, one page statement of research interests and experience, and email addresses for at least two references. Applications will be reviewed immediately and continue until the positions are filled. http://bit.ly/1makgwW http://bit.ly/1wJPbC4 via Gmail
This is the final week to apply for a postdoc position that integrates field work and genomics in Anopheles mosquitoes. Applications submitted before Friday (Dec 19) will be considered. I am seeking a postdoctoral fellow to join the Malaria Programme at the Wellcome Trust Sanger Institute and lead our field-based effort to carry out large-scale genetic analyses of vector/parasite interactions. The fellow will be required to coordinate and manage very large-scale collection and rearing of wild mosquito larvae to adults in field based insectaries, followed by P. falciparum infection and preservation for genome sequencing. The postdoc will be trained on bioinformatic analyses of the data, and carry out functional testing in the lab on genes of interest. Considerable scope to incorporate microbial genetics into the project exists, and candidates from this background will also be considered. The ideal applicant will be interested and able to spend several months at a time in African countries (likely Uganda, Burkina Faso, Mali, but others are possible), and will be extremely organised with the ability to work independently, troubleshoot problems, and plan own work to a high standard, both at Sanger and in the field. The fellow will also join the 1000 Anopheles genomes project, which you can read about here http://bit.ly/1wJLoos More about my group here http://bit.ly/1DLeJoX http://bit.ly/1wJLoou Job description and online application: http://bit.ly/1DLeJFg For further information, please contact me at email@example.com Thank you, Mara Lawniczak Mara Lawniczak via Gmail
*BEACON Center for the Study of Evolution in Action* *BEACON Distinguished Postdoctoral Fellows Program* ** BEACON is an NSF Science and Technology Center headquartered at Michigan State University with partners at North Carolina A&T State University, University of Idaho, University of Texas at Austin, and University of Washington. BEACON brings together biologists, computer scientists, and engineers to study evolutionary dynamics using biological and computational techniques and to apply evolutionary principles to engineering problems. We seek outstanding post-doctoral scholars to pursue interdisciplinary research on evolution in action with BEACON faculty members, in the fields of biology, computer science, and/or engineering. Applicants will propose a research project within the scope of BEACONs mission and must have two BEACON faculty sponsors who will serve as research mentors should the fellowship be awarded. One sponsor must be MSU faculty; the other sponsor may be from any of the five BEACON institutions. Preference is given for interdisciplinary research. The post-doc fellow will be based at Michigan State University in East Lansing. Please see our website (http://bit.ly/18YLdLp) for information about BEACON mission, participants and ongoing research projects. Applicants must submit the following, in a single PDF, to BEACON Managing Director Danielle Whittaker via email (firstname.lastname@example.org): 1.CV 2.A two-page description of their research plan 3.A one-page summary of their doctoral research 4.Letters of support from two BEACON sponsors (one must be from MSU) 5.Two additional letters of recommendation Fellowships last two years and include a salary of $50,000/year and modest funds to support research and travel. The successful applicant will help foster collaborations among faculty and disciplines and serve as a professional model for pre-doctoral trainees. A Ph.D. in biology, computer science, engineering or related fields is required. Current MSU graduate students or postdocs are not eligible for this fellowship. US citizens or permanent residents only. Minority applicants are especially encouraged to apply. MSU is an Equal Opportunity/Affirmative Action Employer. The deadline for applications is January 15, 2015. Danielle J. Whittaker, Ph.D. Managing Director BEACON Center for the Study of Evolution in Action 567 Wilson Road, Room 1441E Michigan State University East Lansing, MI 48824 (517) 884-2561 email@example.com http://bit.ly/GN0Rhx “Danielle J. Whittaker” via Gmail
Last call - GRC conference SPECIATION 2015 Dear colleagues, A few places are still available for SPECIATION 2015, a new Gordon Research Conference (GRC) devoted entirely to speciation research, which will be held from March 15 to 20, 2015, at the Four Points Sheraton Harbor Resort in the beautiful coastal city of Ventura, California. The conference will be the world’s largest on speciation research and will feature an unprecedented mosaic of interrelated talks by invited researchers, as detailed in the conference program appended below. The GRC conferences on speciation, of which this will be the very first, will raise to a trans-Atlantic level a tradition of international conferences on speciation research that has been initiated by the European Research Networking Programme ‘Frontiers of Speciation Research’. The two conferences that have been held so far, SPECIATION 2010 and SPECIATION 2013, helped facilitate bridge-building between disparate approaches to speciation research and attracted more than 150 participants on each occasion. SPECIATION 2015 will continue this tradition of scientific bridge-building and promote integrative perspectives that interface empirical insights with theoretical advances and bring together developments in ecology, systematics, and genetics. Reflecting the aims of the GRC conference series, and committed to a pluralistic perspective on the field, we have selected invited scientists based on their complementary expertise in different areas of speciation research. In this way, the conference will provide a platform for comparing and orchestrating different approaches to speciation research. In addition to about 30 invited presentations, the conference will prominently feature a rich poster session, as well as selected poster introductions. The topics that will be covered at the conference include the biodiversity crisis, mechanisms of reproductive isolation, genetic constraints, ecological drivers, genomic signatures, behavioral mechanisms, species cohesion, hybrid zones, macro-ecological explanations, as well as integrative and synthetic perspectives on speciation. Each of a total of nine conference sessions will feature 3 or 4 invited presentations, with ample time for discussion. Registration is open at http://bit.ly/16s5mvF until the few remaining open slots have been completely filled. With many thanks and best wishes, ke Brnnstrm & Ulf Dieckmann Overview of invited presentations; for the full program see http://bit.ly/16s5mvF. Session 1: Biodiversity Crisis and Speciation Roger Butlin (University of Sheffield, United Kingdom) “Local Adaptation and Speciation” Michael Rosenzweig (University of Arizona) “Speciation Rates at the Paleontological Scale: Is Autonomous Regulation Important?” Session 2: Mechanisms of Reproductive Isolation Loren Rieseberg (University of British Columbia, Canada) “Sexual Selection and Plant Speciation” ke Brnnstrm (Ume University, Sweden) “Phenotypic Plasticity and Reproductive Isolation” Chris Jiggins (University of Cambridge, United Kingdom) “Multiple Mechanisms of Reproductive Isolation in Heliconius Butterflies” Leonie Moyle (Indiana University) “Postmating Sexual Selection and the Evolution of Reproductive Isolation: Tales from Two Kingdoms” Session 3. Genetic Constraints Reinhard Buerger (University of Vienna, Austria) “On the Evolution of Assortative Mating in Spatially Structured Populations” Sara Via (University of Maryland) “Genetic Constraints on Speciation-with-Gene-Flow?” Sergey Gavrilets (University of Tennessee) “Models of Speciation: Where Are We Now?” Session 4. Ecological Drivers Ulf Dieckmann (International Institute for Applied Systems Analysis, Austria) “Robust Adaptive Speciation” Rees Kassen (University of Ottawa, Canada) “Species Interactions and Diversification in a Model Adaptive Radiation” Michael Doebeli (University of British Columbia, Canada) “Two Little-Known Facts About Speciation Models, and an Empirical Example” Session 5. Genomic Signatures Jeffrey Feder (University of Notre Dame) “Genomics, Ecological Adaptation, and Divergence: A Case Study Involving the Apple Maggot Fly” Anna Qvarnstrm (Uppsala University, Sweden) “Mechanisms of Speciation Driving Genome Divergence” Louis Bernatchez (Laval University, Canada) “Think Globally: Investigating Ecological Speciation by Means of an Integrative Biology Framework” Session 6. Behavioral Mechanisms Erik Svensson (Lund University, Sweden) “Behaviour as a Facilitator or Constraint on Population Divergence and Speciation” Jenny Boughman (Michigan State University) “Sexual Selection and the Dynamic Process of Speciation” Glenn-Peter Saetre (University of Oslo, Norway) “A Fruitful Affair: Speciation by Hybridisation in Sparrows” Rebecca Safran (University of Colorado, Boulder) “The Role of Sexual Selection in Speciation: An Integrative Perspective” Session 7. Species Cohesion and Hybrid Zones James Mallet (Harvard University) “Large Fractions of the Genome Are Exchanged Between Heliconius Species via Natural Hybrids” Kerstin Johannesson (University of Gothenburg, Sweden) “Reproductive Barriers in Littorina” Axel Meyer (University of Konstanz, Germany) “Repeated Parallel Sympatric Speciation in the Adaptive Radiations of Crater Lake Cichlid Fish from Nicaragua” Session 8. Macro-Ecological Explanations of Biodiversity Rampal Etienne (University of Groningen, Netherlands) “Inference on Diversification from Phylogenies” Stephen Hubbell (University of California, Los Angeles) “The Potential of Red-Queen Host-Pathogen Dynamics to Drive Speciation” Akira Sasaki (Graduate University for Advanced Studies, Sokendai, Japan) “Discrete Species Packing and Evolved Neutrality in a Continuous Niche Space” Hans Metz (Leiden University, Netherlands) “Branching for Multivariate Traits” Session 9. Toward a Synthetic Understanding of Speciation Ole Seehausen (University of Bern, Switzerland) “Exploring Causes of Very Large Variation in Rates of Speciation Among Closely Related Lineages: Ecology, Contingency and Constraint” Xavier Thibert-Plante (Ume University, Sweden) “Insights on Ecological Speciation from Two New Case Studies” Dolph Schluter (University of British Columbia, Canada) “Speciation, Ecological Opportunity, and Latitude” Ulf Dieckmann Program Director Evolution and Ecology Program International Institute for Applied Systems Analysis A-2361 Laxenburg Austria Email firstname.lastname@example.org Phone +43 2236 807 386 Phone secretary +43 2236 807 231 Fax +43 2236 807 466 or +43 2236 71313 Web http://bit.ly/17j1ut8 Online reprints http://bit.ly/17j1utc FishACE Network http://bit.ly/17j1sS3 FinE Network http://bit.ly/17j1ute FroSpects Network http://bit.ly/17j1sS5 DIECKMANN Ulf via Gmail
The Centre for Ecology & Conservation at the University of Exeter’s Penryn Campus is offering a range of Scholarships to students wishing to undertake a Masters degree. Our portfolio of programmes includes: MSc Evolutionary and Behavioural Ecology MSc Applied Ecology MSc Conservation and Biodiversity MSc Conservation Science and Policy We are offering the following awards that include some with a specific geographic focus and others that are open to all applicants: Award Value Description Conservation, Ecology and Evolution Masters Distinction Scholarships 5,000 The Conservation, Ecology and Evolution Masters Distinction Scholarships are available for top performing students enrolling on the MSc Conservation and Biodiversity, MSc Conservation Science and Policy, MSc Evolutionary and Behavioural Ecology or MSc Applied Ecology. Masters Distinction Scholarships 5,000 Masters Distinction Scholarships are available for top performing students who accept a place to study an eligible taught Masters programme. Africa Masters Excellence Awards 2,000 The Africa Masters Excellence Awards are available for top performing applicants who are resident of an African country and who accept a place to study an eligible taught Masters programme. China Masters Excellence Awards 2,000 The China Masters Excellence Awards are available for top performing applicants who are resident of China and who accept a place to study an eligible taught Masters programme. US Masters Excellence Awards 2,000 The US Masters Excellence Awards are available for top performing applicants who are resident of the US and who accept a place to study an eligible taught Masters programme. The application deadline for all of the awards is 30 April 2015. For additional information see: http://bit.ly/1wJw0sk Prof DJ Hosken University of Exeter, Cornwall Tremough, Penryn TR10 9FE UK 01326 371843 D.J.Hosken@exeter.ac.uk http://bit.ly/1bMLIqH DJ Hosken via Gmail
Dear EvolDir users, (sorry for repost, some users pointed out no contact information) I’m currently assembling a database for a meta-analysis looking at the performance of extra-pair young in versus within-pair young in birds. I would appreciate your help in getting the data that was not published (e.g. due to lack of significant results, low statistical power etc). The types of data I would require include mainly differences between the extra-pair and within-pair young in any phenotypic traits (morphology, physiology, genetics, sex-ratio, life-history etc). The form of these differences should ideally be means in respective groups (within-pair and extra-pair young) and respective sample sizes but if for some reasons original means are not available any form of sigificance testing is acceptable. Of course - I would gladly accept original data if only you could share them with me - that would make calculation of relevant effect sizes the easiest. The data of particular interest are differences measured in several consecutive breeding seasons (accompanied by indication of geographical location and year ID) or measures taken in differing conditions (e.g. different experimental treatments, different climatic regimes etc.) Please contact me if you find my explanations unclear, I’ll be happy to explain everything in more detail if needed. Best regards Szymon Drobniak Jagiellonian University, Institute of Environmental Sciences email@example.com firstname.lastname@example.org via Gmail
Dear colleagues, It is our pleasure to announce a Symposium on ‘Genomics of local adaptation’ (see Abstract below) that will take place during the next ESEB meeting, August 10th-14th 2015 in Lausanne, Switzerland (www.unil.ch/eseb2015). The Symposium is organized by Dr. Santiago C. Gonzlez-Martnez (Madrid, Spain) and Prof. Martin Lascoux (Uppsala, Sweden) and the invited speakers are Prof. Outi Savolainen (Oulu, Finland; http://bit.ly/1GOxxjj) and Prof. Thomas Mitchell-Olds (Durham, USA; http://bit.ly/1GOxyUh). We hope to see you in Lausanne! Deadline for Abstract submission is January 10th, 2015 Genomics of Local Adaptation The study of how organisms adapt to different environments is one of the major challenges in evolutionary biology. Recent genome and transcriptome sequencing has allowed fast progress in our understanding of the genomic signatures of local adaptation, including the genetic architecture of fitness traits, and the identification of ecologically-relevant gene variation. Genome-wide molecular studies have addressed classical questions on local adaptation, such as the role of new mutation vs. standing variation or the geographical distribution of adaptive polymorphisms. They are also starting to produce the empirical information needed to assess the potential for evolutionary responses of keystone plants and animals in the face of impending climate change, a major societal concern, and to push forward the field from mostly descriptive studies towards the construction of prediction models. Recently, genome-wide studies have also produced detailed knowledge on covariance of allelic effects and adaptive gene networks. Nevertheless, ecological genomic studies of local adaptation also bring about new challenges related to sampling issues, the production of reliable genomic data in many individuals, the analysis of large and particularly complex datasets, and the understanding of twww.unil.ch/eseb2015). The Symposium is organized by Dr. Santiago C. Gonzlez-Martnez (Madrid, Spain) and Prof. Martin Lascoux (Uppsala, Sweden) and the invited speakers are Prof. Outi Savolainen (Oulu, Finland; http://bit.ly/1GOxxjj) and Prof. Thomas Mitchell-Olds (Durham, USA; http://bit.ly/1GOxyUh). We hope to see you in Lausanne! Deadline for Abstract submission is January 10th, 2015 Genomics of Local Adaptation The study of how organisms adapt to different environments is one of the major challenges in evolutionary biology. Recent genome and transcriptome sequencing has allowed fast progress in our understanding of the genomic signatures of local adaptation, including the genetic architecture of fitness traits, and the identification of ecologically-relevant gene variation. Genome-wide molecular studies have addressed classical questions on local adaptation, such as the role of new mutation vs. standing variation or the geographical distribution of adaptive polymorphisms. They are also starting to produce the empirical information needed to assess the potential for evolutionary responses of keystone plants and animals in the face of impending climate change, a major societal concern, and to push forward the field from mostly descriptive studies towards the construction of prediction models. Recently, genome-wide studies have also produced detailed knowledge on covariance of allelic effects and adaptive gene networks. Nevertheless, ecological genomic studies of local adaptation also bring about new challenges related to sampling issues, the production of reliable genomic data in many individuals, the analysis of large and particularly complex datasets, and the understanding of the limitations associated with these analyses. This Symposium will welcome original research in model and non-model species as well as the presentation of novel methodological approaches. Invited speakers: Outi Savolainen (University of Oulu, Finland) and Thomas Mitchell-Olds (Duke University, USA) via Gmail
—_000_C87C1C21E904CA429965ADABCB2CB0C451BF8596exchange22_ Content-Type: text/plain; charset=”iso-8859-1” Content-Transfer-Encoding: quoted-printable A 4-year PhD position is available at SLU, Alnarp: Plant Resistance Ecology: A new tool to engineer biological control of herbivores Several plant traits are important for plants’ interactions with herbivores and parasitoids. One very important plant trait is resistance against herbivores. A general question to investigate is how herbivore-parasitoid interactions are affected when resistance in wild plants evolves, and when domestic plants are bred for increased resistance. Horticultural plants are often dependent on biological control of herbivores provided by parasitoids. This ecosystem service may be affected if resistance increases or declines during plant breeding. Knowledge regarding such plant effects opens up novel opportunities to actively breed for improved biocontrol. Similarly, plant resistance evolution in natural populations may lead to altered trophic interactions which could affect the level of herbivory experienced by the plant. The aim of this PhD project is to investigate how plant resistance against herbivores affects plant-herbivore-parasitoid interactions in wild and domesticated strawberry. The PhD student will have access to a large common garden with 100 wild plant genotypes (Fragaria vesca), and several domesticated varieties (Fragaria x ananassa, F. vesca, F. viridis, F. moschata), that differ in their resistance against herbivores. The full ad can be downloaded here: http://bit.ly/1GOxxjb Johan Johan A. Stenberg Associate Professor Sveriges lantbruksuniversitet Swedish University of Agricultural Sciences Department of Plant Protection Biology PO Box 102, SE-230 53 ALNARP Visiting address: Sundsvgen 14 Mobile: +46 70 622 00 42 email@example.com, www.slu.se/stenberg —_000_C87C1C21E904CA429965ADABCB2CB0C451BF8596exchange22_ Content-Type: text/html; charset=”iso-8859-1” Content-Transfer-Encoding: quoted-printable
December 16, 2014
************************************************************************* PHD STUDENTSHIPS IN EVOLUTION AND GENOMICS IMPERIAL COLLEGE LONDON and partner organisations ************************************************************************* Science and Solutions for a Changing Planet (SSCP) is an exciting Doctoral Training Programme supported by the Natural Environmental Research Council and led by Imperial College London in association with 6 core partners and 27 partners from the business and policy world. Projects on evolution and genomics for the October 2015 start are listed below. For a full list with links to project descriptions and instructions on how to apply, visit: http://bit.ly/1GOsKy8 ELIGIBILITY: To be eligible for a full award a student must have: - Settled status in the UK, meaning they have no restrictions on how long they can stay, - Been ordinarily resident’ in the UK for 3 years prior to the start of the studentship. This means they must have been normally residing in the UK (apart from temporary or occasional absences) - Not been residing in the UK wholly or mainly for the purpose of full-time education. (This does not apply to UK or EU nationals). IF YOU’RE NOT ELIGIBLE: We welcome queries from students who do not meet these eligibility criteria for discussion of alternative potential funding sources. CONTACTS: For project-related queries and to apply, contact individual supervisors. For general queries about evolutionary PhD projects at Imperial College London, contact Prof. Tim Barraclough (firstname.lastname@example.org). CLOSING DATE for applications 19th January 2015. The positions are competitive-funded: each project will put forward their best student applicant, then a subset of projects (roughly one quarter) will be funded based on the quality of the students. List of supervisors and projects in Evolution for 2015 Dr Ben Raymond (email@example.com) Assessing “evolution-proof” bacterial treatments in model systems: do anti-virulence drugs have better consequences for the evolution of resistance and virulence than antibiotics? Dr David Orme (firstname.lastname@example.org, Dr Robin Freeman and Dr Monika Bhm, ZSL) Monitoring species from space: objective assessments and dynamics of extinction risk Dr James Rosindell (email@example.com) Modelling of dispersal, speciation and extinction on islands Dr Samraat Pawar (firstname.lastname@example.org) Biological Limits to Acclimation and Adaptation to Climate change Dr Sarah Knowles (email@example.com) Ecology and fitness effects of the gut microbiota in wild mice Prof Alfried Vogler (firstname.lastname@example.org) Metagenomics and museum collections to characterize declining pollination webs Dr Alan Paton (Royal Botanic Gardens Kew, Prof. Tim Barraclough, Life Sciences) Evolution of pollination syndromes in South African and Madagascan species of Plectranthus (Lamiaceae) Dr Bente Klitgaard (Royal Botanic Gardens Kew, Prof. Tim Barraclough, Life Sciences) Neotropical plant evolution: Adding pieces to the jigsaw Dr Jason Hodgson (email@example.com) The relationship between tsetse flies, trypanosomiasis, and development in rural Africa Dr Martin Bidartondo (firstname.lastname@example.org) The diversity, physiology and evolution of fungal symbiosis in land plants Prof Tim Barraclough (email@example.com) Modelling the dynamics, evolution and ecosystem functioning of microbial communities Prof Vincent Savolainen (firstname.lastname@example.org) Ecological genomics of the evolution of species on islands via Gmail
It has been noted before that we have a wide range of mathematical techniques available for producing data-display networks, most notably the many variants of splits graphs (see Huson & Scornavacca 2011). For example, NeighborNets and Consensus networks are commonly encountered in the phylogenetics literature, and Reduced median networks and Median-joining networks are commonly used for haplotype networks in population biology.
However, there are few techniques used to produce evolutionary networks. Studies of reticulate evolutionary histories, which include recombination networks, hybridization networks, introgression networks and HGT networks, have no unifying theme as yet. So, the biological literature has many papers in which biologists struggle with reticulate evolutionary histories using ad hoc collections of techniques, which often boil down to simply presenting incongruent phylogenetic trees from different datasets (see Morrison 2014a).
So, maybe a brief look at the current state of play with evolutionary networks would be useful. There are enough worthwhile techniques out there for people to be using them more often than they are.
Almost all current phylogenetic methods assume that the basic building unit is a non-recombining sequence block, for which the evolutionary history is strictly tree-like. We tend to call these blocks "genes" and their history "gene trees", but this is just for semantic convenience. In practice, we first collect data for various loci, and we then simply make the assumption that there is recombination between the loci but not within them. This is basically the assumption of independence between loci. At the limit, each nucleotide along a chromosome has a tree-like history, but for aggregations of nucleotides it is all assumptions.
Furthermore, we assume that there are no data errors that will confound any reconstruction of the phylogenetic trees. Possible sources of error include: incorrect data (e.g. contamination), inappropriate sampling (taxa or characters), and model mis-specification. Any of these errors will lead to stochastic variation at best and to bias at worst.
Reticulate evolutionary processes lead to gene trees that are not all congruent. However, there are two other processes that have been widely recognized as also producing gene-tree incongruence, but which do not involve reticulation in the strict sense: incomplete lineage sorting (deep coalescence; ancestral polymorphism), and gene duplication-loss.
Many studies have now shown that stochastic variation due to ILS can be very large (see Degnan & Rosenberg 2009), and that this varies in relation to both the population sizes of the taxa and the times between divergence events. The expectation of completely congruent gene trees is thus very naive, even when the evolutionary history of the taxa has been strictly tree-like. A number of methods have been developed to reconstruct species trees in the face of ILS (Nakhleh 2013).
DL involves gene duplication (which can be repeated to create gene families) followed by selective gene loss. The phylogenetic history of the genes is usually presented as an unfolded species tree, where each gene copy has its own part of the tree. A number of methods have been developed to reconstruct gene DL histories given a "known" species tree, which is called gene-tree reconciliation (Szöllősi et al 2015). However, our interest here is in the reverse process, in which reconstructed but incongruent gene trees are combined into a single species tree, given a model of duplication and selective loss, which is called species-tree inference (which is the same as cophylogeny reconstruction; Drinkwater & Charleston 2014).
Known biological processes such as recombination, reassortment, hybridization, introgression and horizontal gene transfer all create reticulate phylogenetic histories. However, it is a moot point as to whether these processes can be distinguished from each other solely in the context of an evolutionary network (Holder et al. 2001; Morrison 2015). These evolutionary processes operate by distinct biological mechanisms, but the evolutionary patterns that they create can all be rather similar. The processes all result in gene flow among contemporaneous organisms (usually called horizontal flow or transfer), whereas other evolutionary processes involve gene flow from parent to offspring (usually called vertical inheritance), including ILS and DL. These gene flows create incongruent gene histories, which we may detect directly in the data or via reconstructed gene trees. The patterns of incongruence do not necessarily allow us to infer the causal process.
There are a number of differences in pattern, but the consistency of these is doubtful. Polyploid hybridization produces the most distinctive pattern, because there is duplication of the genome in the hybrid. However, subsequent aneuploidy will serve to obscure this pattern. Homoploid hybridization nominally involves 50% of the genome coming from difference sources, while introgression ultimately involves a smaller percentage. However, in practice, genome mixtures vary continuously from 0 to 50%. HGT also involves a small percentage of the genome, but in theory it also can vary from 0 to 50%. Reassortment produces mixtures of viral genes, which can occur in such a great number that reconstructing the history is severely problematic.
So, in the absence of independent experimental evidence, distinguishing one form of evolutionary network from another is almost a matter of definition. This has become increasingly obvious in the methodological literature, where semantic confusion abounds.
For example, a network produced directly from a set of characters has usually been called a "recombination network", while one produced from a set of trees has usually been called a "hybridization network", irrespective of what processes the gene trees represent. Furthermore, models that add reticulation events to DL trees have usually referred to the horizontal gene flow as "HGT", whereas models that add reticulation events to ILS trees have usually referred to the horizontal gene flow as "hybridization" (Morrison 2014a). Studies of horizontal gene flow during human evolution have usually referred to "admixture", which is a more process-neutral term.
In many, if not most, cases we might all be better off if network methods simply distinguish gene flow among contemporaries (horizontal) from gene inheritance between generations (vertical), rather than trying to infer a process — process inference can often best take place after network construction. This does not help anthropologists, of course, who are dealing with evolutionary networks where oblique gene flow is possible (so that they do not have Time inconsistency in evolutionary networks).
There seems to be a dichotomy of purposes to current method development, which are neatly summarized by the contrasting theoretical views of Mindell (2013) and Morrison (2014b). These views each recognize that evolutionary history involves both vertical and horizontal processes, but they reconstruct the resulting evolutionary patterns as a species tree and a species network, respectively. Obviously, this blog is dedicated to the latter point of view, but it is the former one (the so-called Tree of Life) that seems to currently dominate the literature.
Focussing on gene-tree inference, Szöllősi et al (2015) provide a comprehensive review of the various models that have been used to describe the dependence between gene trees and species trees. Essentially, gene trees are contained within the species tree, and they may differ from it in relative branch lengths and/or topology. The differences between genes and species are the result of population-level processes, often modeled using the coalescent. These authors recognize four current classes of probabilistic model that combine different evolutionary processes:
Extending these ideas to infer networks (rather than species trees) is a bit more tricky, and most of the work to date has involved combining hybridization and ILS. There has been no recent summary of the ideas. However, calculating the parsimony score of a network, given a set of gene-tree topologies, has been beed addressed by Yu et al (2011); and Yu et al (2013a) have extended these ideas to heuristically search the network space for the optimal network (the one that minimizes the number of extra reticulation lineages in a species tree). Furthermore, methods for computing the likelihood of a phylogenetic network, given a set of gene-tree topologies, have been devised by Yu et al (2012, 2013b); and Yu et al (2014) have extended these ideas to heuristically search for the maximum-likelihood network for limited cases of introgression or hybridization (since they differ only in degree).
There are also several methods that simply use gene-tree incongruence to infer reticulation events in a species network (Huson et al. 2010). Basically, these methods combine gene trees into "hybridization networks" by minimizing the number of reticulations required for reconciliation, measured either by counting the reticulations or calculating the network level. The combinatorial optimization can be based on trees, triplets or clusters, using parsimony as the optimality criterion. These methods model homoploid hybridization by assuming that reticulation is the sole cause of all gene-tree incongruence. This means that they are likely to overestimate the amount of reticulation in a dataset when other processes are co-occurring.
The most completely developed network methods involve data for allopolyploid hybrids. Here, there are multiple copies of each gene, one in each copy of the genome, so that allopolyploid hybrids have more copies than do their diploid parent taxa. To construct a hybridization network topology, Huber et al (2006) developed a parsimony method based on first estimating a multi-labeled gene tree, and then searching for the single-labeled network that best accommodates the multiple gene patterns. The model has been extended to heuristically include ILS (Marcussen et al 2012), as well as dates for the internal nodes (Marcussen et al 2015). Jones et al. (2013) have also developed models that incorporate ILS in a bayesian context, but only for the case of a single hybridization event between two diploid species (an allotetraploid).
Species-tree inference for a pair of gene phylogenies that may be networks not trees, has been considered in terms of parsimony by Drinkwater & Charleston (2014).
This brings us to the matter of introgression. The massive recent influx of genome-scale data for hominids has lead to the development of methods explicitly for the analysis of what is termed admixture among the lineages. These methods basically work by constructing a phylogenetic tree that includes admixture events, the topology inference being based on allele frequencies. There has been no formal comparison of the methods, and not much application to non-humans. Three such methods have been produced so far (Patterson et al 2012; Pickrell & Pritchard 2012; Lipson et al 2013).
Recombination has somewhat been the poor cousin to other causes of reticulation, as most network methods assume it to be absent. Nevertheless, Gusfield (2014) has recently provided an ample survey of the study methods available to date.
Degnan JH, Rosenberg NA (2009) Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends in Ecology & Evolution 24: 332-340.
Drinkwater B, Charleston MA (2014) An improved node mapping algorithm for the cophylogeny reconstruction problem. Coevolution 2: 1-17.
Gusfield D (2014) ReCombinatorics: the Algorithmics of Ancestral Recombination Graphs and Explicit Phylogenetic Networks. MIT Press, Cambridge.
Holder MT, Anderson JA, Holloway AK (2001) Difficulties in detecting hybridization. Systematic Biology 50: 978-982.
Huber KT, Oxelman B, Lott M, Moulton V (2006) Reconstructing the evolutionary history of polyploids from multilabeled trees. Molecular Biology & Evolution 23: 1784-1791.
Huson D, Rupp R, Scornavacca C (2010) Phylogenetic Networks: Concepts, Algorithms, and Applications. Cambridge University Press, Cambridge.
Huson DH, Scornavacca C (2011) A survey of combinatorial methods for phylogenetic networks. Genome Biology & Evolution 3: 23-35.
Jones G, Sagitov S, Oxelman B (2013) Statistical inference of allopolyploid species networks in the presence of incomplete lineage sorting. Systematic Biology 62: 467-478.
Lipson M, Loh P-R, Levin A, Reich D, Patterson N, and Berger B (2013) Efficient moment-based inference of population admixture parameters and sources of gene flow. Molecular Biology & Evolution 30: 1788-1802.
Marcussen T, Heier L, Brysting AK, Oxelman B, Jakobsen KS (2015) From gene trees to a dated allopolyploid network: insights from the angiosperm genus Viola (Violaceae). Systematic Biology 64: 84-101.
Marcussen T, Jakobsen KS, Danihelka J, Ballard HE, Blaxland K, Brysting AK, Oxelman B (2012) Inferring species networks from gene trees in high-polyploid north American and Hawaiian violets (Viola, Violaceae). Systematic Biology 61: 107-126.
Mindell DP (2013) The Tree of Life: metaphor, model, and heuristic device. Systematic Biology 62: 479-489.
Morrison DA (2014a) Phylogenetic networks: a review of methods to display evolutionary history. Annual Research and Review in Biology 4: 1518-1543.
Morrison DA (2014b) Is the Tree of Life the best metaphor, model or heuristic for phylogenetics? Systematic Biology 63: 628-638.
Morrison DA (2015, in press) Pattern recognition in phylogenetics: trees and networks. In: Elloumi M, Iliopoulos CS, Wang JTL, Zomaya AY (eds) Pattern Recognition in Computational Molecular Biology: Techniques and Approaches. Wiley, New York.
Nakhleh L (2013) Computational approaches to species phylogeny inference and gene tree reconciliation. Trends in Ecology & Evolution 28: 719-728.
Patterson NJ, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, Genschoreck T, Webster T, Reich D (2012) Ancient admixture in human history. Genetics 192: 1065-1093.
Pickrell JK, Pritchard JK (2012) Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genetics 8: e1002967.
Szöllősi GJ, Tannier E, Daubin V, Boussau B (2015) The inference of gene trees with species trees. Systematic Biology 64: e42-e62.
Yu Y, Barnett RM, Nakhleh L (2013a) Parsimonious inference of hybridization in the presence of incomplete lineage sorting. Systematic Biology 62: 738-751.
Yu Y, Degnan JH, Nakhleh L (2012) The probability of a gene tree topology within
a phylogenetic network with applications to hybridization detection. PLoS Genetics 8:
Yu Y, Dong J, Liu KJ, Nakhleh L (2014) Maximum likelihood inference of reticulate evolutionary histories. Proceedings of the National Academy of Sciences of the USA 111: 16448-16453.
Yu Y, Ristic N, Nakhleh L (2013b) Fast algorithms and heuristics for phylogenomics
under ILS and hybridization. BMC Bioinformatics 14: S6.
Yu Y, Than C, Degnan JH, Nakhleh L (2011) Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting. Systematic Biology 60: 138-149.
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
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology