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September 3, 2015

01:41

–_000_ED2874FFBF4A4E8FB447FE67E48F4B90albanyedu_ Content-Type: text/plain; charset=“us-ascii” Content-Transfer-Encoding: quoted-printable Tenure-track faculty position in Ecology and Evolution of Infectious Diseases at the University at Albany, SUNY The Department of Biological Sciences (http://bit.ly/1rqUKk3), University at Albany, invites applications for a tenure-track position at the Assistant Professor level. The Department seeks a candidate whose research will advance conceptual understanding of ecological and evolutionary aspects of infectious diseases. Possible research themes may include, but are not limited to: pathogen transmission and spread, host-pathogen interactions, vector biology or pathogen variation and evolution. Applicants should have wide interests in disease biology. The successful candidate will contribute to the Department’s graduate program in Ecology and Evolutionary Biology (EEB) and will be expected to teach at the undergraduate and graduate levels in courses appropriate to their expertise. Local opportunities for collaboration include faculty in the Life Sciences (http://bit.ly/1wiWPFJ), the RNA Institute (http://bit.ly/1rqUKk5), and the School of Public Health (http ://www.albany.edu/sph), as well as the New York State Department of Health (http://bit.ly/1wiWNxC). Initial salary and start-up funds are competitive. Applicants must have a Ph.D. from a university accredited by the U.S. Department of Education or an internationally recognized accrediting organization, at least three years of post-doctoral experience, and a strong publication record. Professional Rank and Salary Range: Assistant Professor, salary competitive and commensurate with qualifications. Start Date: September 1, 2016 The Jeanne Clery Disclosure of Campus Security Policy and Campus Crime Statistics Act, or Clery Act, mandates that all Title IV institutions, without exception, prepare, publish and distribute an Annual Security Report. This report consists of two basic parts: disclosure of the University’s crime statistics for the past three years; and disclosures regarding the University’s current campus security policies. The University at Albany’s Annual Security Report is available in portable document format [PDF] by clicking this link http://bit.ly/1ijDJur THE UNIVERSITY AT ALBANY IS AN EO/AA/IRCA/ADA EMPLOYER Please apply online via http://bit.ly/1ObsPAY via Gmail

Source: EVOLDIR
01:11
We have an open position for an ornithologist at Georgia College that may be of interest to the EvolDir community. ASSISTANT PROFESSOR OF BIOLOGY (Ornithology) The Department of Biological and Environmental Sciences at Georgia College & State University invites applications for a tenure track position in Biology. We seek a highly trained individual who is committed to liberal arts education, can demonstrate excellence in teaching and research, and possesses the ability to work with a culturally diverse student population. A primary teaching responsibility will be Ornithology, with other teaching opportunities including introductory courses in the biological sciences, core curriculum and other upper level courses in the candidate’s area of expertise. The candidate will have the opportunity to develop an independent research program. There are two undergraduate majors within the Department of Biological and Environmental Sciences. We currently have 23 full time faculty in the department with about 470 undergraduate biology majors, 110 environmental science majors, and an M.S. program in biology with approximately 35 students pursuing thesis and non-thesis degrees. For more information about the department visit us at http://bit.ly/1ijBC9X Knowledge/Skills and Abilities: Ability to teach Ornithology, Field Ornithology, Comparative Vertebrate Anatomy, introductory biology and upper division courses in area of specialization. Ability to contribute to the core curriculum. Ability to engage undergraduates and graduates in ornithology-related research. Ability to work collegially and effectively with university students, faculty, and staff as well as the surrounding community. Demonstrable ability to work collegially and effectively with individuals of diverse backgrounds. Minimum Qualifications: Ph.D. preferred (ABD with a completion by August 1, 2016 considered) in Biological Sciences or related field. Research experience (demonstrated by publication record). Undergraduate teaching experience. Must meet SACSCOC accreditation requirements stated in C.S. 3.7.1 (www.sacscoc.org (faculty credentials)) Preferred Qualifications: We are particularly interested in candidates who can utilize and enhance the existing ornithology research collections of study skins and skeletons for their teaching and research. At least two years of experience teaching undergraduate courses preferred. The unit is especially interested in candidates who can work collegially and effectively with individuals of diverse backgrounds and whose experience, research, teaching, and service can contribute to the diversity and excellence of the academic community. Interested candidates should apply online at http://bit.ly/1OboKgj and include a letter of application, vitae, 1-page teaching philosophy, 1-page research statement, unofficial transcripts and 3 confidential letters of recommendation. Review of applications will begin November 15, 2015, and continue until the position is filled. Position start date is August 1, 2016. The College: Encompassing the arts and humanities, social and behavioral sciences, sciences and mathematics, fine and performing arts, and select professional programs, the College of Arts and Sciences is the largest of the university’s four colleges. Approximately 185 full-time faculty in twelve departments teach approximately 3,000 students with arts and science majors. Most of the core curriculum and many service courses to the other colleges are taught by Arts and Sciences faculty. Arts and Sciences Mission: The fundamental mission of the College of Arts and Sciences is to promote critical reflection and advancement of knowledge by teaching the core curriculum and offering rigorous and comprehensive major programs that challenge students to address the analytical, historical, cultural, and philosophical foundations of their discipline; and to graduate students with the ability to think critically and creatively; act with ethical awareness; communicate effectively in a free and open exchange of ideas; and prepared to contribute productively, responsibly, and ethically to our state, our nation and the global community. Diversifying our curriculum geographically, temporally, and thematically is a high priority, so evidence of comparative and cross-cultural scholarship is particularly welcome. Evidence of methodological innovation and creative teaching strategies is highly desirable. In keeping with the University’s mission we especially encourage applicants who will further our goal of cultural, ethnic, racial, and gender diversity. Georgia College is known for combining the educational experiences typical of esteemed private liberal arts colleges with the affordability of public universities. The university’s main campus is a residential learning community that emphasizes undergraduate education and offers a select number of graduate programs. GC faculty and staff are dedicated to engaging students in the learning process through high impact pedagogies and fostering excellence in the classroom and beyond. Georgia College seeks to endow its graduates with a passion for achievement, intellectual curiosity, and exuberance for learning and critical thinking. Our values include an emphasis on acting from a foundation of respect for self and others, fostering responsible leaders and global citizens, and cultivating relationships that enhance collaborative approaches to solving problems. Hiring preference will be given to faculty and administrators who demonstrate an understanding of Georgia College’s mission and who are enthusiastic about working closely with high-achieving students within www.sacscoc.org (faculty credentials)) Preferred Qualifications: We are particularly interested in candidates who can utilize and enhance the existing ornithology research collections of study skins and skeletons for their teaching and research. At least two years of experience teaching undergraduate courses preferred. The unit is especially interested in candidates who can work collegially and effectively with individuals of diverse backgrounds and whose experience, research, teaching, and service can contribute to the diversity and excellence of the academic community. Interested candidates should apply online at http://bit.ly/1OboKgj and include a letter of application, vitae, 1-page teaching philosophy, 1-page research statement, unofficial transcripts and 3 confidential letters of recommendation. Review of applications will begin November 15, 2015, and continue until the position is filled. Position start date is August 1, 2016. The College: Encompassing the arts and humanities, social and behavioral sciences, sciences and mathematics, fine and performing arts, and select professional programs, the College of Arts and Sciences is the largest of the university’s four colleges. Approximately 185 full-time faculty in twelve departments teach approximately 3,000 students with arts and science majors. Most of the core curriculum and many service courses to the other colleges are taught by Arts and Sciences faculty. Arts and Sciences Mission: The fundamental mission of the College of Arts and Sciences is to promote critical reflection and advancement of knowledge by teaching the core curriculum and offering rigorous and comprehensive major programs that challenge students to address the analytical, historical, cultural, and philosophical foundations of their discipline; and to graduate students with the ability to think critically and creatively; act with ethical awareness; communicate effectively in a free and open exchange of ideas; and prepared to contribute productively, responsibly, and ethically to our state, our nation and the global community. Diversifying our curriculum geographically, temporally, and thematically is a high priority, so evidence of comparative and cross-cultural scholarship is particularly welcome. Evidence of methodological innovation and creative teaching strategies is highly desirable. In keeping with the University’s mission we especially encourage applicants who will further our goal of cultural, ethnic, racial, and gender diversity. Georgia College is known for combining the educational experiences typical of esteemed private liberal arts colleges with the affordability of public universities. The university’s main campus is a residential learning community that emphasizes undergraduate education and offers a select number of graduate programs. GC faculty and staff are dedicated to engaging students in the learning process through high impact pedagogies and fostering excellence in the classroom and beyond. Georgia College seeks to endow its graduates with a passion for achievement, intellectual curiosity, and exuberance for learning and critical thinking. Our values include an emphasis on acting from a foundation of respect for self and others, fostering responsible leaders and global citizens, and cultivating relationships that enhance collaborative approaches to solving problems. Hiring preference will be given to faculty and administrators who demonstrate an understanding of Georgia College’s mission and who are enthusiastic about working closely with high-achieving students within an academic community dedicated to the advancement of knowledge through learning and scholarship. Georgia is an Open Records state. The finalist will be required to submit to a background investigation. GCSU is an Affirmative Action/Equal Opportunity Institution committed to cultural, racial, and ethnic communities and to compliance with the Americans with Disabilities Act. It is expected that successful candidates share these commitments. Persons who need reasonable accommodations under the Americans with Disabilities Act to participate in the application process should contact the Division of Human Resources at 478-445-5596. gretchen ionta via Gmail
Source: EVOLDIR
01:11
POST-DOC POSITION IN EVOLUTIONARY ECOLOGY AT U SHERBROOKE, U LAVAL & UQAM (WINTER 2016) A postdoc position is available as part of a FRQNT project on “adaptation to insularity and the role of behaviour in the dynamics of a metapopulation of deer mice Peromyscus maniculatus in Northwest Ontarioâ€�. The project will involve laboratory work with high-throughput SNPs genotyping and next generation sequencing, bioinformatics and fieldwork. The postdoc will be involved in all the aspects of the project, from data collection to publication. She/he will be part of a team of researchers composed of Denis Réale and Steven Kembel (Université du Québec À Montréal), Dany Garant (Université de Sherbrooke), Louis Bernatchez (Université Laval), and 2 PhD students. Requirement : PhD in ecological genetics. A candidate with an experience on SNPs, next generation sequencing and bioinformatics is preferred. We are seeking a very autonomous, highly motivated, productive person, who will be willing to gain experience both in the lab and in the field. The candidate will be based in Sherbrooke University (with Dany Garant), will do extensive lab works in Laval University (in Louis Bernatchez’ lab), and frequent visits to UQAM (Montréal). Fieldwork will be conducted near Kenora (Northwest Ontario) in July and August 2016. Although the candidate will work in francophone Universities, French is not required. The position is available for one year starting in January 2016, with possibility of renewal depending on research progress. To apply please send your CV, statement of research interests, and letters from at least two references, before October 10, to Denis Réale (reale.denis@uqam.ca) or by mail to Denis Reale, Département des Sciences Biologiques, Université du Québec À Montréal, CP 8888 succursale centre-ville, Montréal, Quebec, H3C3P8. Denis Réale Professeur Groupe de Recherche en Ecologie Comportementale et Animale Département des Sciences Biologiques Université du Québec À Montréal CP 8888, succursale centre-ville Montreal, Québec, Canada, H3C 3P8 Tel: 514 987 3000 (2265#) Fax: 514 987 4746 Denis Réale via Gmail
Source: EVOLDIR
00:41
PhD Studentship opportunity -€Institute of Biodiversity Animal Health and Comparative Medicine (IBAHCM) / School of Life Sciences (SLS), University of Glasgow. Supervisor: Dr. Martin Llewellyn (Advisors: Prof. Mario Grijalva; Prof. Bjorn Andersson; Prof. Erin Landguth) Populations genomics to guide interventions against Neglected Tropical Diseases: Ecological and landscape genomics of Trypanosoma cruzi and associated vectors in Ecuador. An NIH funded project is currently underway in Southern Ecuador to establish the landscape drivers of Trypanosoma cruzi (parasite) and Rhodnius ecuadoriensis (vector) genomic diversity and population connectivity. Research partners on this project include the Center for Infectious Disease Research at Catholic University, Quito, Ecuador (Prof., Mario Grijalva); Ohio University, USA (Prof., Mario Grijalva); the University of Montana, USA (Dr. Erin Landguth); The Karolinska Instute, Sweden (Prof. Bjorn Anderson) and the IBAHCM / SLS Glasgow (Dr. Martin Llewellyn) Funding is in place for a three-year PhD studentship to accompany this NIH project at the University of Glasgow. Under the supervision of Dr. Martin Llewellyn and via integration with the project team the student have the opportunity to take the lead on population genomic analyses of both vectors and parasites, as well as to contribute to fieldwork activities and undertake training in spatial analyses, as well some wet lab activities (sequence library preparation etc). Finally, there is an opportunity to integrate into other ongoing research in the Dr. Llewellyn’s lab (Current webpage: http://bit.ly/1NOHN2R) UK/EU students holding a 2:1 degree (or equivalent GPA) and above should apply. A good level of computer competency is vital; familiarity with R, linux/unix systems preferable; prior experience handling NGS data (including familiarity with python, perl etc) a bonus. Some Spanish language would be helpful. For further details email – martllewellyn@gmail.com Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office. Martin Llewellyn via Gmail
Source: EVOLDIR
00:27

This is a multi-part message in MIME format. via Gmail

Source: EVOLDIR

September 2, 2015

23:56

The University of Oregon Institute of Ecology and Evolution (http://bit.ly/15YnlBz) and the Department of Biology invite applications for a tenure-related position (Assistant Professor) in evolutionary biology. We are particularly interested in candidates who use statistical, genomic and/or phylogenetic approaches to study fundamental evolutionary processes at the molecular level, but candidates with exemplary records in other areas of evolutionary biology are also invited to apply. The successful candidate will have an outstanding research program and a commitment to excellence in teaching at the undergraduate and graduate levels. Ph.D. required. Interested persons should apply online to the University of Oregon IE2 SEARCH at http://bit.ly/1JAdmap. Applicants should submit a cover letter, a curriculum vitae, statement of research accomplishments and future research plans, a description of teaching experience and philosophy, and three letters of recom mendation. Submission of up to 3 selected reprints is encouraged. To be assured of consideration, application materials should be uploaded by October 1, 2015, but the search will remain open until the position is filled. The University of Oregon is an equal opportunity, affirmative action institution committed to cultural diversity and compliance with the ADA. The University encourages all qualified individuals to apply, and does not discriminate on the basis of any protected status, including veteran and disability status. http://bit.ly/1LWlJ6a via Gmail

Source: EVOLDIR
15:42

Over the weekend, out of the blue, Dan Whaley commented on an earlier blog post of mine (Altmetrics, Disqus, GBIF, JSTOR, and annotating biodiversity data. Dan is the project lead for hypothes.is, a tool to annotate web pages. I was a bit dismissive as hypothes.is falls into the "stick note" camp of annotation tools, which I've previously been critical of.

However, I decided to take another look at hypothes.is and it looks like a great fit to another annotation problem I have, namely augmenting and correcting OCR text in BioStor (and, by extension, BHL). For a subset of BioStor I've been able to add text to the page images, so you can select that text as you would on a web page or in a PDF with searchable text. If you can select text, you can annotate it using hypothes.is. Then I discovered that not only is hypothes.is a Chrome extension (which immediately limits who will use it), you can add it to any web site that you publish. So, as an experiment I've added it to BioStor, so that people can comment on BioStor using any modern browser.

So far, so good, but the problem is I'm relying on the "crowd" to come along and manually annotate the text. But I have code that can take text and extract geographic localities (e.g., latitude and longitude pairs), specimen does, and taxonomic names. What I'd really like to do is be able pre-process the text, locate these features, then programmatically add those as annotations. Who wants to do this manually when a computer can do most of it?

Hypothesi.is, it turns out, has an API that, while a bit *cough* skimpy on documentation, enables you to add annotations to text. So now I could pre-process the text, and just ask people to add things that have been missed, or flag errors on the automated annotations.

This is all still very preliminary, but as an example here's a screen shot of a page in BioStor together with geographic annotations displayed using hypothes.is (you can see this live here: http://biostor.org/reference/147608/page/1 (make sure you click on the widgets at the top right of the page to see the annotations):

The page shows two point localities that have been extracted from the text, together with a static Google Map showing the localities (hypothesis.is supports Markdown in annotations, which enables links and images to be embedded).

Not only can we write annotations, we can also read them, so if someone adds an annotation (e.g., highlights a specimen code that was missed, or some text that OCR has messed up) we could retrieve that and, for example, index the corrected text to improve findability.

Lots still to do, but these early experiments are very encouraging.

Source: iPhylo
11:00

There seems to be increased interest in the notion that evolutionary history is worthy of management and conservation (see, e.g. Frishkoff et al. 2014; Diniz-Filho et al. 2013). The basic quantity seems to be “phylogenetic diversity” (PD) or the sum of the edge lengths connecting a candidate set of species (Faith 1992). Given a tree or network, one can produce many measures of current (or expected) (contributions to) PD, and these can be modified by other axes of value and expected costs and benefits of interventions. The technical side of the field seems to me to be in some disarray; there are overlapping terms and definitions, weak connections to other literatures (particularly community ecology), and under-tested assumptions. My presentation will offer little or no new data, but I will draw on the work of others in an attempt to partially organize the technical side of the field as I see it. Key issues concerning mapping traits and geographic scale are taken up in the following two presentations in this series.

Source: Phyloseminar
06:17

I have just added another dataset to our database. This one is of considerable interest, because it is a complex one. As the authors note, it is likely to contain ancient hybrid speciation, recent introgression and deep coalescence. Thus, identifying recent hybrids will be problematic.
Michael L. Moody and Loren H. Rieseberg (2012) Sorting through the chaff, nDNA gene trees for phylogenetic inference and hybrid identification of annual sunflowers (Helianthus sect. Helianthus). Molecular Phylogenetics and Evolution 64: 145–155.There are 29 accessions from 13 species, with data for 11 loci in 5 linkage groups (a total of 8,077 aligned nucleotides). The accessions have sequences for either 1 or 2 of the alleles, and sometimes 3 (the latter are likely to be the result of PCR artifacts). The authors have also tried to identify recombinant sequences. Three of the species are previously identified hybrid taxa.

Unfortunately, adding this dataset to the database has also been problematic, because there are internal inconsistencies. For complete consistency, Figure 1 of the paper should agree with its own Table 1, and the GenBank data should agree with both of them. Unfortunately, this three-way consistency exists for only 2 of the 11 loci. For the rest, in 7 instances the dataset is the odd one out, in 4 cases it is the table, and in four instances it is the figure. For the data discrepancies, in 2 cases a sequence is missing, in 1 case there is an extra sequence, and for the remaining 2 pairs it is likely that there is mis-labelling of the sequences.

It is therefore not immediately obvious to what extent this counts as a "gold standard" dataset. I have included it because of its intrinsic interest, but obviously with a caveat emptor warning. Sadly, this sort of situation has been all too common in my search for suitable datasets.

06:00
Background: Acariformes is the most species-rich and morphologically diverse radiation of chelicerate arthropods, known from the oldest terrestrial ecosystems. It is also a key lineage in understanding the evolution of this group, with the most vexing question whether mites, or Acari (Parasitiformes and Acariformes) is monophyletic. Previous molecular studies recovered Acari either as monophyletic or non-monophyletic, albeit with a limited taxon sampling. Similarly, relationships between basal acariform groups (include little-known, deep-soil 'endeostigmatan' mites) and major lineages of Acariformes (Sarcoptiformes, Prostigmata) are virtually unknown. We infer phylogeny of chelicerate arthropods, using a large and representative dataset, comprising all main in- and outgroups (228 taxa). Basal diversity of Acariformes is particularly well sampled. With this dataset, we conduct a series of phylogenetically explicit tests of chelicerate and acariform relationships and present a phylogenetic framework for internal relationships of acariform mites. Results: Our molecular data strongly support a diphyletic Acari, with Acariformes as the sister group to Solifugae (PP =1.0; BP = 100), the so called Poecilophysidea. Among Acariformes, some representatives of the basal group Endeostigmata (mainly deep-soil mites) were recovered as sister-groups to the remaining Acariformes (i. e., Trombidiformes + and most of Sarcoptiformes). Desmonomatan oribatid mites (soil and litter mites) were recovered as the monophyletic sister group of Astigmata (e. g., stored product mites, house dust mites, mange mites, feather and fur mites). Trombidiformes (Sphaerolichida + Prostigmata) is strongly supported (PP =1.0; BP = 98–100). Labidostommatina was inferred as the basal lineage of Prostigmata. Eleutherengona (e. g., spider mites) and Parasitengona (e. g., chiggers, fresh water mites) were recovered as monophyletic. By contrast, Eupodina (e. g., snout mites and relatives) was not. Marine mites (Halacaridae) were traditionally regarded as the sister-group to Bdelloidea (Eupodina), but our analyses show their close relationships to Parasitengona. Conclusions: Non-trivial relationships recovered by our analyses with high support (i.e., basal arrangement of endeostigmatid lineages, the position of marine mites, polyphyly of Eupodina) had been  proposed by previous underappreciated morphological studies. Thus, we update currently the accepted taxonomic classification to reflect these results: the superfamily Halacaroidea Murray, 1877 is moved from the infraorder Eupodina Krantz, 1978 to Anystina van der Hammen, 1972; and the subfamily Erythracarinae Oudemans, 1936 (formerly in Anystidae Oudemans, 1902) is elevated to family rank, Erythracaridae stat. ressur., leaving Anystidae only with the nominal subfamily. Our study also shows that a clade comprising early derivative Endeostigmata (Alycidae, Nanorchestidae, Nematalycidae, and maybe Alicorhagiidae) should be treated as a taxon with the same rank as Sarcoptiformes and Trombidiformes, and the scope of the superfamily Bdelloidea should  be changed. Before turning those findings into nomenclatural changes, however, we consider that our study calls for (i) finding shared apomorphies of the early derivative Endeostigmata clade and the clade including the remaining Acariformes; (ii) a well-supported hypothesis  for Alicorhagiidae placement; (iii) sampling the families Proterorhagiidae, Proteonematalycidae and Grandjeanicidae not yet included in molecular analyses; (iv) undertake a denser sampling of clades traditionally placed in Eupodina, Anystina (Trombidiformes) and Palaeosomata (Sarcoptiformes), since consensus networks and Internode certainty (IC) and IC All (ICA) indices indicate high levels of conflict in these tree regions. Our study shows that regions of ambiguous alignment may provide useful phylogenetic signal when secondary structure information is used to guide the alignment procedure and provides an R implementation to the Bayesian Relative Rates test.
06:00
Background: In the short-term, organisms acclimate to stress through phenotypic plasticity, but in the longer term they adapt to stress genetically. The mutations that accrue during adaptation may contribute to completely novel phenotypes, or they may instead act to restore the phenotype from a stressed to a pre-stress condition. To better understand the influence of evolution on the diversity and direction of phenotypic change, we used Biolog microarrays to assay 94 phenotypes of 115 Escherichia coli clones that had adapted to high temperature (42.2 °C). We also assayed these same phenotypes in the clones’ ancestor under non-stress (37.0 °C) and stress (42.2 °C) conditions. We explored associations between Biolog phenotypes and genotypes, and we also investigated phenotypic differences between clones that have one of two adaptive genetic trajectories: one that is typified by mutations in the RNA polymerase β-subunit (rpoB) and another that is defined by mutations in the rho termination factor. Results: Most (54 %) phenotypic variation was restorative, shifting the phenotype from the acclimated state back toward the unstressed state. Novel phenotypes were more rare, comprising between 5 and 18 % of informative phenotypic variation. Phenotypic variation associated statistically with genetic variation, demonstrating a genetic basis for phenotypic change. Finally, clones with rpoB mutations differed in phenotype from those with rho mutations, largely due to differences in chemical sensitivity. Conclusions: Our results contribute to previous observations showing that a major component of adaptation in microbial evolution experiments is toward restoration to the unstressed state. In addition, we found that a large deletion strongly affected phenotypic variation. Finally, we demonstrated that the two genetic trajectories leading to thermal adaptation encompass different phenotypes.

September 1, 2015

23:46

Tenure-track faculty position in Ecology at The University of Pennsylvania. The Department of Biology at the University of Pennsylvania invites applications for a tenure-track faculty position in Ecology. The appointment will be at the level of Assistant Professor. We are searching broadly for a community or ecosystem ecologist working at any spatial scale, from local to global, and using theoretical and/or empirical approaches. Areas of interest include, but are not limited to, mechanisms of community assembly, coexistence, diversity, adaptation and the interplay between biotic and abiotic processes in the face of climate and land-use change. We welcome applicants working on any domain of life, from micro- to macroscopic. We are especially interested in candidates who utilize novel approaches that span levels of biological organization or transcend traditional boundaries. Penn’s Department of Biology has a long-standing tradition of maintaining an integrated research and educational program across all basic biological sciences, from Ecology and Evolution, Plant Sciences, Molecular and Cellular Biology, Genomics, to Neuroscience. The Department values interdisciplinary research, collaboration, and collegiality, and has a vision emphasizing Life in its Natural Context. Candidates are expected to have demonstrated excellence and productivity in research and will be expected to excel in undergraduate and graduate teaching. Interested candidates should submit materials online at http://bit.ly/1KGj5Qg and include a curriculum vitae, concise statements of research and teaching interests, a short annotated description of up to five publications, and the name and contact information of at least three referees. Recommenders will be contacted by the University with instructions on how to submit a letter to the website. Review of applicants will begin September 11, 2015 and continue until the position is filled. The Department of Biology is strongly committed to Penn’s Action Plan for Faculty Diversity and Excellence and to creating a more diverse faculty (for more information see: http://bit.ly/1eC8Ath). The University of Pennsylvania is an equal opportunity employer. Minorities, women, individuals with disabilities, and protected veterans are encouraged to apply. via Gmail

Source: EVOLDIR
23:29

PhD Student Position studying the genetic basis of adaptation to environmental change Monash University, Melbourne Australia An opportunity is available for two PhD students to join Carla Sgr’s research group in the School of Biological Sciences at Monash University, in Melbourne, Australia. We are seeking creative and motivated students who wish to carry out original research on the genetic basis of adaptation to environmental change. Individuals with a background in evolutionary biology, quantitative genetics or evolutionary genetics are invited to apply. Those with strong quantitative and computational skills are particularly encouraged. Specific projects are flexible, potentially interdisciplinary, and include opportunities to carry out new research in experimental evolutionary biology. Specific research plans will be developed in collaboration with each successful candidate, and tailored to match their individual interests and strengths. To find out more about the interests of my group, please visit www.carlasgrolab.org. Successful candidates will be fully funded for 3.5 years, for full time research, and with no teaching requirements. The annual stipend is approximately $25,000 AUD, tax-free, and additional expenses for research, coursework, and conference attendance (once per year) will also be covered. Both Australian/NZ domestic and international students are eligible to apply. Domestic candidates will be invited to apply for an Australian Postgraduate Award, and if successful, will be awarded an annual tax-free stipend of approximately $25,000 AUD. Top ranked candidates receive a top-up scholarship of $5,000 and students moving interstate or from NZ are eligible for a one-off moving scholarship of $3,000. All Monash PhD students also receive approximately $3,000 worth of travel funds to attend conferences during their degree. Monash University is a member of Australia’s Group of Eight coalition, and is internationally recognized for excellence in research and teaching. The School of Biological Sciences is home to a collegial and interdisciplinary research environment, with strengths in ecology, genetics and evolutionary biology. The Monash doctoral program includes additional training opportunities beyond the research program that enhance employability post degree. Monash is located in Melbourne, one of the most liveable cities in the world and a cultural and recreational hub. To apply, please send a CV, academic transcript, and a brief outline of research interests and goals to carla.sgro@monash.edu. Informal inquiries are also welcome at the same address. Applicants must hold a Bachelor’s degree with first-class honours, or a master’s degree. Review of applications will begin immediately, and short-listed candidates will be contacted to set up phone/Skype interviews. Dr Carla M. Sgr Associate Professor and ARC Future Fellow School of Biological Sciences Building 18, Monash University Clayton Campus Wellington Rd, Clayton 3800 Melbourne, Victoria Australia Email: carla.sgro@monash.edu http://bit.ly/1hx3WVJwww.carlasgrolab.org. Successful candidates will be fully funded for 3.5 years, for full time research, and with no teaching requirements. The annual stipend is approximately $25,000 AUD, tax-free, and additional expenses for research, coursework, and conference attendance (once per year) will also be covered. Both Australian/NZ domestic and international students are eligible to apply. Domestic candidates will be invited to apply for an Australian Postgraduate Award, and if successful, will be awarded an annual tax-free stipend of approximately $25,000 AUD. Top ranked candidates receive a top-up scholarship of $5,000 and students moving interstate or from NZ are eligible for a one-off moving scholarship of $3,000. All Monash PhD students also receive approximately $3,000 worth of travel funds to attend conferences during their degree. Monash University is a member of Australia’s Group of Eight coalition, and is internationally recognized for excellence in research and teaching. The School of Biological Sciences is home to a collegial and interdisciplinary research environment, with strengths in ecology, genetics and evolutionary biology. The Monash doctoral program includes additional training opportunities beyond the research program that enhance employability post degree. Monash is located in Melbourne, one of the most liveable cities in the world and a cultural and recreational hub. To apply, please send a CV, academic transcript, and a brief outline of research interests and goals to carla.sgro@monash.edu. Informal inquiries are also welcome at the same address. Applicants must hold a Bachelor’s degree with first-class honours, or a master’s degree. Review of applications will begin immediately, and short-listed candidates will be contacted to set up phone/Skype interviews. Dr Carla M. Sgr Associate Professor and ARC Future Fellow School of Biological Sciences Building 18, Monash University Clayton Campus Wellington Rd, Clayton 3800 Melbourne, Victoria Australia Email: carla.sgro@monash.edu http://bit.ly/1hx3WVJ carla.sgro@monash.edu via Gmail

Source: EVOLDIR
17:26

@mathmomike wrote:

Does anyone know references or previous work to the following three questions:

  1. Consider the graph G_NNI of unrooted binary phylogenetic trees on leaf set {1,..,n} where two trees form an edge if they are one NNI apart. Similarly G_SPR (where trees are joined if they are one SPR apart). Both these graphs are regular (each tree has the same number of neighbors) so if you start anywhere then after a while you will be at each tree with (asymptotically) uniform probability - the question is what is the mixing time (time to be near uniform as a function of n) for this random walk? Note I'm not talking about data (or Bayesian methods) here - just a pure mixing time question regarding this discrete graph. Does anyone know a paper that studies this (I think I saw one once, but all my papers/notes got lost in the 2010/2011 earthquakes here!).

  2. There are various notions of the centre of a tree - e.g. the "centroid" (explained very nicely in the recent Tanglegrams paper by Matsen/Billey/Kas/Konvalinka paper on ArXiv). However does anyone know any paper that discusses what we might call a 'leaf-centroid'. Given a tree T call a vertex v of T a leaf-centroid if each of the components of T-v contains at most half of the leaves of T. If T has no vertices of degree 2 then (just like the centroid) a tree either has a unique leaf-centroid or two adjacent leaf centroids. However even for this class ( trees without vertices of degree 2) the leaf-centroid can be different from the centroid! Just wondering if anyone has seen this notion mentioned or studied before?

  3. Anyone know an early (pre-1960s) reference to the simple but fundamental result: A collection C of nonempty subsets of X (including X) forms a hierarchy (nested family) if and only if C is the set of clusters of a rooted X-tree? It may be implicit in Linneaus (or even Aristotle!) but some more explicitly mathematical statement would be good.

Any advice will help for a book ('mathematical phylogeny') that I'm now half-way through writing I might ask a few further questions over the coming month or two.

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06:00
Background: Eurypterids are a diverse group of chelicerates known from ~250 species with a sparse Ordovician record currently comprising 11 species; the oldest fully documented example is from the Sandbian of Avalonia. The Middle Ordovician (Darriwilian) fauna of the Winneshiek Lagerstätte includes a new eurypterid species represented by more than 150 specimens, including some juveniles, preserved as carbonaceous cuticular remains. This taxon represents the oldest described eurypterid, extending the documented range of the group back some 9 million years. Results: The new eurypterid species is described as Pentecopterus decorahensis gen. et sp. nov.. Phylogenetic analysis places Pentecopterus at the base of the Megalograptidae, united with the two genera previously assigned to this family by the shared possession of two or more pairs of spines per podomere on prosomal appendage IV, a reduction of all spines except the pair on the penultimate podomere of appendage V, and an ornamentation of guttalate scales, including angular scales along the posterior margin of the dorsal tergites and in longitudinal rows along the tergites. The morphology of Pentecopterus reveals that the Megalograptidae are representatives of the derived carcinosomatoid clade and not basal eurypterids as previously interpreted. Conclusions: The relatively derived position of megalograptids within the eurypterids indicates that most eurypterid clades were present by the Middle Ordovician. Eurypterids either underwent an explosive radiation soon after their origination, or earlier representatives, perhaps Cambrian in age, remain to be discovered. The available instars of Pentecopterus decorahensis suggest that eurypterids underwent extreme appendage differentiation during development, a potentially unique condition among chelicerates. The high degree of appendage specialization in eurypterids is only matched by arachnids within chelicerates, supporting a sister taxon relationship between them.
04:52

A little over a week ago I was at the 6th International Barcode of Life Conference, held at Guelph, Canada. It was my first barcoding conference, and was quite an experience. Here are a few random thoughts.

AttendeesIt was striking how diverse the conference crowd was. Apart from a few ageing systematists (including veterans of the cladistics wars), most people were young(ish), and from all over the world. There clearly something about the simplicity and low barrier to entry of barcoding that has enabled its widespread adoption. This also helps give barcoding a cohesion, no matter what the taxonomic group or the problem you are tackling, you are doing much the same thing as everybody else (but see below). While ageing systematists (like myself) may hold their noses regarding the use of a single, short DNA sequence and a tree-building method some would dismiss as "phenetic", in many ways the conference was a celebration of global-scale phylogeography.

Awesome drone footage from #DNAbarcodes2015. Thanks to everyone who helped make this conference so fantastic!!! https://t.co/37nYuIxGuz

— Mike Wright (@MIKEisWRIGHT20) August 22, 2015

Standards aren't enoughAnd yet, standards aren't enough. I think what contributes to DNA barcoding's success is that sequences are computable. If you have a barcode, there's already a bunch of barcodes sequences you can compare yours to. As others add barcodes, your sequences will be included in subsequent analyses, analyses which may help resolve the identity of what you sequenced.

To put this another way, we have standard image file formats, such as JPEG. This means you can send me a bunch of files, safe in the knowledge that because JPEG is a standard I will be able to open those files. But this doesn't mean that I can do anything useful with them. In fact, it's pretty hard to do anything with images part from look at them. But if you send me a bunch of DNA sequences for the same region, I can build a tree, BLAST GenBank for similar sequences, etc. Standards aren't enough by themselves, to get the explosive growth that we see in barcodes the thing you standardise on needs to be easy to work with, and have a computational infrastructure in place.

Next generation sequencing and the hacker cultureClassical DNA barcoding for animals uses a single, short mtDNA marker that people were sequencing a couple of decades ago. Technology has moved on, such that we're seeing papers such as An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. As I've argued earlier (Is DNA barcoding dead?) this misses the point about the power of standardisation on a simple, scalable method.

At the same time, it was striking to see the diversity of sequencing methods being used in conference presentations. Barcoding is a broad church, and it seemed like it was a natural home for people interested in environmental DNA. There was excitement about technologies such as the Oxford Nanopore MinION™, with people eager to share tips and techniques. There's something of a hacker culture around sequencing (see also Biohackers gear up for genome editing), just as there is for computer hardware and software.

Community

So this happened #dnabarcodes2015 pic.twitter.com/EQ6OqNSTjn

— Kevin Morey (@moreykev94) August 21, 2015 The final session of the conference started with some community bonding, complete with Paul Hebert versus Quentin Wheeler wielding light sables. If, like me, you weren't a barcode, things started getting a little cult-like. But there's no doubt that Paul's achievement in promoting a simple approach to identifying organisms, and then translating that into a multi-million dollar, international endeavour is quite extraordinary.

After the community bonding, came a wonderful talk by Dan Janzen. The room was transfixed as Dan made the case for conservation, based on his own life experiences, including Area de Conservación Guanacaste where he and Winnie Hallwachs have been involved since the 1970s. I sat next to Dan at a dinner after the conference, and showed him iNaturalist, a great tool for documenting biodiversity with your phone. He was intrigued, and once we found pictures taken near his house in Costa Rica, he was able to identify the individual animals in the photos, such as a bird that has since been eaten by a snake.

Dark taxaMy own contribution to the conference was a riff on the notion of dark taxa, and mostly consisted of me trying think through how to respond to DNA barcoding. Two graphs, three responses from Roderic Page The three responses to barcoding that I came up with are:
  1. By comparison to barcoding, classical taxonomy is digitally almost invisible, with great chunks of the literature still not scanned or accessible. So, one response is to try and get the core data of taxonomy digitised and linked as fast as possible. This is why I built BioStor and BioNames, and why I continually rant about the state of efforts to digitise taxonomy.
  2. This is essentially President Obama's "bucket" approach, maybe the sane thing to do is see barcoding as the future and envisage what we could do in a sequence only world. This is not to argue that we should ignore the taxonomic literature as such, but rather lets start with sequences first and see what we can do. This is the motivation for my Displaying a million DNA barcodes on Google Maps using CouchDB, and my experiments with Visualising Geophylogenies in Web Maps Using GeoJSON. These barely scratch the surface of what can be done.
  3. The third approach is to explore how we integrate taxonomy and barcoding at global scale, in which case linking at specimen level (rather, than, say using taxonomic names) seems promising, albeit requiring a massive effort to reconcile multiple specimen identifiers.

Summary

@rdmpage Thanks for spreading the word! Looks like an interesting conference, which is a rare thing indeed.

— Nakensnegl (@kueda) August 23, 2015 Yes, the barcoding conference was that rare thing, a well organised (including well-fed), interesting, indeed eye-opening, conference.

Source: iPhylo
03:26
PhD position in theory/analysis of gene regulation A PhD position is available in the group of Prof. Erik van Nimwegen at the Biozentrum of the University of Basel and Swiss Institute of Bioinformatics (http://bit.ly/1FfckPo). We are looking for highly motivated individuals with strong mathematical and computational skills that are interested to perform theoretical and computational research in the area of gene regulation. Our research group is highly interdisciplinary, involving both an experimental section where researchers with a background in molecular biology are experimentally studying genome evolution and gene regulation at the single cell level in bacteria, and a theoretical section where researchers with backgrounds in theoretical physics, computer science, and applied mathematics are using techniques from Bayesian probability, evolutionary theory, dynamical systems theory, and stochastic processes, to study the function and evolution of genome-wide regulatory networks in cells. We are particularly interested in uncovering the principles by which genome-wide regulatory networks specify and maintain cell identity in multi-cellular organisms, how cells control and exploit the noise in gene regulatory processes, and how gene regulation evolves. A list of our group’s publications can be found http://bit.ly/1MZBckp . Our lab also takes part in a number of collaborative projects within Switzerland including StoNets, which studies the ways in which cells control and exploit stochasticity in gene regulatory networks, and BrainStemX, which studies the gene regulatory networks underlying mammalian forebrain development. The precise topic of the PhD research project will be determined jointly with the candidate and candidates that display initiative and independence will be given priority. Candidates should have strong mathematical and computational skills, and experience in such areas as stochastic processes, dynamical systems theory, and Bayesian statistics is a plus. Candidates do not necessarily have to have a biological background but should have a strong desire to directly work with experimental biological data and collaborate with experimental biologists. The candidates should have a good knowledge of English. German is helpful but not necessary. The salary is generous and is set according to the guidelines of the Swiss National Science Foundation. The start date will by mutual arrangement. Basel is a very international city and a center of life science research, with over 900 life science research companies in the area, including Novartis and Roche. Several other academic institutions are also in the city, including the Friedrich Miescher Institute, the ETH Zurich Biosystems Science and Engineering Department, and the Swiss Tropical Institute. The city is less than 5km from both France and Germany and an hour and a half from the Swiss Alps. To apply, please send a single pdf containing your application letter, CV, and the names of two references to erik.vannimwegen-at-unibas.ch Review of applications will begin immediately. Thomas Julou via Gmail
Source: EVOLDIR
03:26
Post-doc position in computational genomics/gene regulatory networks A post-doctoral position is available in the group of Prof. Erik van Nimwegen (http://bit.ly/1FfckPo) at the Biozentrum of the University of Basel and Swiss Institute of Bioinformatics. We are looking for highly motivated individuals with strong mathematical and computational skills that are interested to perform theoretical research in computational genomics, genome-wide regulatory networks, and stochastic gene regulation in single cells. Our research group is highly interdisciplinary, involving both an experimental section where researchers with a background in molecular biology are experimentally studying genome evolution and gene regulation at the single cell level in bacteria, and a theoretical section where researchers with backgrounds in theoretical physics, computer science, and applied mathematics are using techniques from Bayesian probability, evolutionary theory, dynamical systems theory, and stochastic processes, to study the function and evolution of genome-wide regulatory networks in cells. We are particularly interested in uncovering the principles by which genome-wide regulatory networks specify and maintain cell identity in multi-cellular organisms, how cells control and exploit the noise in gene regulatory processes, and how gene regulation evolves. A list of our groups publications can be found at http://bit.ly/1MZBckp . Our lab also takes part in a number of collaborative projects within Switzerland including StoNets, which studies the ways in which cells control and exploit stochasticity in gene regulatory networks, and BrainStemX, which studies the gene regulatory networks underlying mammalian forebrain development. For this position we are in particular looking for candidates that are interested in developing methods for the analysis of next-generation sequencing data, including RNA-seq, single-cell RNA-seq, and ChIP-seq data. The precise topic of the research project will be determined jointly with the candidate and candidates that display initiative and independence will be given priority. Candidates should have strong mathematical and computational skills, and experience in such areas as stochastic processes, dynamical systems theory, and Bayesian statistics is a plus. Experience with next-generation sequencing data is desirable but not strictly required. Candidates do not necessarily have to have a biological background but should have a strong desire to directly work with experimental biologists. The candidates should have a good knowledge of English. German is helpful but not necessary. The salary is generous and is set according to the guidelines of the Swiss National Science Foundation. The start date will be by mutual arrangement. Basel is a very international city and a center of life science research, with over 900 life science research companies in the area, including Novartis and Roche. Several other academic institutions are also in the city, including the Friedrich Miescher Institute, the ETH Zurich Biosystems Science and Engineering Department, and the Swiss Tropical Institute. The city is less than 5km from both France and Germany and an hour and a half from the Swiss Alps. To apply, please send a single pdf containing your application letter, CV, and the names of two references to erik.vannimwegen-at-unibas.ch Review of applications will begin immediately. Thomas Julou via Gmail
Source: EVOLDIR
03:26
Free summer school (July 3rd-9th 2016): Introduction to the concepts and methods of networks in evolutionary studies (sequence similarity networks, genome networks and bipartite graphs) This summer school will be held in Roscoff, France, between July 3rd 2016 (date of arrival) and July 9th (date of departure) (http://bit.ly/1FfckPh). This school is designed in priority for biologists and bio-informaticians (completing a PhD degree or currently post-doctoral fellows), who wish to learn the bases of network analyses. The main notions (regarding various types of networks, the relevance of their analyses, and some bases in graph theory) will be introduced by short theoretical classes, followed by practical case-studies, introducing the basics in programming required to run such network analyses as well as to use the existing software/tools. Our goal is that, by the end of this summer school, all applicants will be qualified to perform network analyses of their own datasets. More precisely, we will focus on the following concepts and methods: - Introgressive evolution and large-scale diversity studies. - Construction and analysis of sequence similarity networks (construction and sorting of connected components, definition of gene families, search for composite genes, implementation of centrality measures) - Construction and analysis of genome networks (construction of weighted genome networks, implementation of their diameter, shortest paths, analyses of labeled nodes, etc.) - Construction and analysis of gene-genome bipartite graphs (detection of connected components, and their articulation points, and twins) In addition, conferences on networks and evolution will be delivered by leading scientists during this school. Expected speakers feature : Fernando Baquero, Robert Beiko, Marco Fondi, Michel Habib, Philippe Huneman, Mattis List, Philippe Lopez, and Marc-Andr Slosse. This summer school is funded by ERC grant (FP7/2007-2013 Grant Agreement # 615274). Hence, registration is free, housing and food (breakfast, lunch and dinner) are also fully covered. Applicants will only need to fund their travel to Roscoff. 10 places only are available, with a mandatory requirement: applicants must show basic computer skills (i.e. to be familiar with Linux environment and with at least one programming language, preferably R or Python). Applications are to be submitted asap, and no later than January 15th 2016, by email to : eric.bapteste@upmc.fr , and contain a brief letter describing why this class will be of significant interest for the applicant and his/her future studies. Applicants will be selected based on their motivation, and their resume, including the names of two scientific referees. We are excited to meet you soon in Roscoff. Eric Bapteste + Philippe Lopez Bapteste Eric via Gmail
Source: EVOLDIR

August 30, 2015

16:30

Last week I blogged about Spinach and the iron fallacy. I analysed an early set of data by Thomas Richardson (1848), who calculated the amount of iron in combusted ash for various vegetables and fruits, and showed that spinach is not at all unusual in its constituents. The idea that spinach is rich in iron is untrue, and the story about a mis-placed decimal point seems to be nothing more than an urban myth.

In the meantime, Joachim Dagg, at the Natural History Apostilles blog, has reanalysed Richardson's data and revealed that The first source for the spinach-iron myth is likely to have been a somewhat inappropriate attempt to combine his data for the percent iron values in relation to the ash with the percent values of the ashes in in relation to the fresh matter.

So, I have recalculated the phylogenetic network using these "adjusted" values. I used the percent values of the chemical constituents in relation to the pure ash (raw ash minus carbonic acid, charcoal and sand), and combined them with the percent values of the ashes. The issue here is that radish roots and leaves have the largest ash values, followed by cherry stems and spinach. This leads to an over-statement of the chemical contents. In particular, the iron content moves spinach from being ranked sixth to second (behind radish foliage, which is not usually eaten).