[ECOLOG-L] Government Shutdown: Who to contact
Dear ECOLOG members, I am a recent graduate looking for postdocs and jobs, mostly within the federal government where I hope to establish a career. This government shutdown puts the breaks on interviews, potential interviews (USAJOBS referrals), and jobs from being posted. This poses an emotional and financial burden on me and my family. I am sure there are other ECOLOG members in the same boat, or similar due to the shutdown. I am for the most part a political novice. My question to the more politically minded members out there, who do I contact to let them know the burden the shutdown is posing on citizens and to encourage them to work towards ending the shutdown? I am currently living in Southern Michigan but looking for jobs/postdocs across the US. Cheers, Ed Krynak
[ECOLOG-L] Rare taxa: Summary
Thanks for all the great comments and/or publications. Following is a list of all the comments and publications. If this list spurs more thoughts, comments and recommended publications, awesome! -- Ed It seems like you are talking about a statistically rare species with respect to a sample. I would recommend looking at McCune and Grace's Analysis of Ecological Communities. Of course, there are many cases (eg. calculation of species richness, evenness or diversity measures) when you would not want to delete any rare species. The removal of rare taxa, at least in my view, is more a statistical thing than an ecological thing. What I mean is the taxa are removed to avoid skewing a site based on a small number of taxa. There are different ways to define rare. In my own work, some species are legitimately rare, others are made rarer by disturbance, and some are database-rare, meaning that we simply didn't identify or encounter it often. What do these things mean? In practice, maybe much the same, but the question is whether you're trying to detect rare things or not. If so, dropping them from analysis makes little sense. I use ordination a lot, and that technique does really poorly with zeros (non-occurrence records) in the dataset. I frequently will combine taxa to a higher level (genera) or maybe even functional type. That frequently helps with my analyses by making fewer analytical objects (columns in the database). I don't have any great references for this, but Bruce McCune has talked about this I know. I define rare as <1% relative read abundance in any one sample (speaking in OTU language). In microbiome research, singletons or taxa <1% relative read abundance probably aren't having a huge effect on the function of the bacterial community, but then again, some are finding that rarer taxa do have influence on community function... generally speaking they are talking those organisms not "rare" as I define above, but "rarer" meaning not in the "core" microbiome... but there again, everyone defines a core differently... Personally, I say it is context dependent and you have to defend your rationale. ; ) Now that I have thoroughly muddied the waters 1.Cao, Y., Williams, D. D. & Williams, N. E. How important are rare species in aquatic community ecology and bioassessment? Limnol. Oceanogr. 43, 1403–1409 (1998). 2.Marchant, R. How important are rare species in aquatic community ecology and bioassessment? A comment on the conclusions of Cao et al. Limnol. Oceanogr. 44, 1840–1841 (1999). 3.Cao, Y. & Williams, D. D. Rare species are important in bioassessment (Reply to the comment by Marchant). Limnol. Oceanogr. 44, 1841–1842 (1999). Cao, Y., Larsen, D. P. & Thorne, R. S.-J. Rare species in multivariate analysis for bioassessment: some considerations. Journal of the North American Benthological Society 20, 144–153 (2001). Jain, M. et al. The importance of rare species: a trait-based assessment of rare species contributions to functional diversity and possible ecosystem function in tall-grass prairies. Ecology and Evolution 4, 104– 112 (2014). Ostermiller, J. D. & Hawkins, C. P. Effects of Sampling Error on Bioassessments of Stream Ecosystems: Application to RIVPACS-Type Models. Journal of the North American Benthological Society 23, 363–382 (2004). Poos, M. S. & Jackson, D. A. Addressing the removal of rare species in multivariate bioassessments: The impact of methodological choices. Ecological Indicators 18, 82–90 (2012). Dorado, J., et al. (2011). "Rareness and specialization in plant– pollinator networks." Ecology 92(1): 19-25. Hopkins, G. W., et al. (2002). "Identifying rarity in insects: the importance of host plant range." Biological Conservation 105(3): 293- 307. Kunin, W. E. and K. J. Gaston, Eds. (1997). The biology of rarity: causes and consequences of rare-common differences. London, Chapman & Hall. Lesica, P., et al. (2006). "Rare plants are common where you find them." Am. J. Bot. 93(3): 454-459. Rabinowitz, D. (1981). Seven forms of rarity. The Biological Aspects of rare Plant Conservation. H. Synge. New York, Wiley: 205-217. Molina, R., Horton, T. R., Trappe, J. M. & Marcot, B. G. Addressing uncertainty: How to conserve and manage rare or little-known fungi. Fungal Ecology 4, 134–146 (2011). Ramirez, K. S. et al. Detecting macroecological patterns in bacterial communities across independent studies of global soils. Nature Microbiology 3, 189–196 (2018). Shade, A. & Gilbert, J. A. Temporal patterns of rarity provide a more complete view of microbial diversity. Trends in Microbiology 23, 335–340 (2015). Shade, A., McManus, P. S. & Handelsman, J. Unexpected Diversity during Community Succession in the Apple Flower Microbiome. mBio 4, e00602-12 (2013). Shade, A. et al. Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity. mBio 5, e01371-14 (2014).
[ECOLOG-L] Rare taxa
In my analyses I often have to decide whether to keep or drop rare taxa, and how to define rare. What publications would you consider an authority on this issue that discusses pros/cons of removing/keeping rare taxa and (same or different pub) how to define rare. I have done a web of science search on this, but I would like your opinion, as an experienced community ecologist in the field, as to what you consider excellent publications on this topic. You can respond to the list, or email me directly: ekry...@uwo.ca
Re: [ECOLOG-L] Graduate School Funding Advice
Hi Jordan, Travis is right (I actually went to school with Travis), your best option is finding a program that will fund you. For a M.S., it is harder to find a program that will fund you well enough to live off of, but not impossible. When you said in this area were you referring to living area, or area of study? If you are only looking in your local area, you will find it even more difficult. Start looking nationally, and internationally. If you don't find a program, don't get discouraged. Funding comes in waves, as does new research projects and openings for students. If there isn't something this year, there may be next year or the year following. My advice (this is how I found a M.S. and a PhD program) is to start reading journal articles on topics that you are interested in. Contact the authors and let them know you've read such and such paper and ask them if they have funding for a student. If not, ask if they have contacts who do have funding. Also, keep a lookout on this and other listservs. Keep that up until you find something. In the interim, look for internships doing any research and especially research in your area of study (but any type of field work/research will get you a leg up in your marketability). You'll have fun, gain great experience, and perhaps great contacts. Don't give up and best of luck! Cheers, Ed Krynak
[ECOLOG-L] MSc - Identifying ecological indicators for monitoring the Tobacco Creek Model Watershed
Motivated M.Sc. student sought for a unique opportunity in the Department of Geography at Western University to conduct research as part of an interuniversity collaboration to develop an integrated aquatic monitoring and management framework for the Tobacco Creek Model Watershed Manitoba, Canada. Student project will be focused on development of indicators of aquatic ecosystem health and ecological thresholds to land use activities for use in watershed assessment and management. Student responsibilities will include designing and executing experiments and analyzing and reporting research outcomes. Applicants are expected to have a strong background in aquatic ecology, environmental science or related discipline and interest in designing experiments and conducting field and lab work. Ability to work as part of a team is a must. The successful candidate will be based at Western University in London, Ontario with opportunities for lab exchange placements at the Canadian Rivers Institute at the University of New Brunswick in Fredericton, New Brunswick and the Canadian Centre for Inland Waters in Burlington Ontario. The candidate will also be required to conduct fieldwork in southern Manitoba as part of their thesis research. Required qualifications: #61623; B.Sc. in Aquatic Ecology, Environmental Science or related discipline #61623; Meet enrollment requirements of the Dept of Geography at The University of Western Ontario (http://geography.ssc.uwo.ca/grad) Additional desired qualifications: #61623; Experience with ArcGIS #61623; Experience conducting aquatic fieldwork #61623; Knowledge of univariate and multivariate statistical analyses #61623; Demonstrated written oral communication skills #61623; Valid drivers license Please send your CV, a list of two references (along with contact phone and email), and a cover letter summarizing qualifications and research interests to Dr. Adam Yates at adam.ya...@uwo.ca. Start date is September 2013 with employment opportunity as a research assistant from May through August 2013. Review of applications will begin February 1, 2013 and continue until the position is filled.
[ECOLOG-L] e-Reader results
First my original message, followed by votes for types of readers, and then a selection of comments. If the comments seemed to be repeats, I did not place them here. Feel free to email me if you have questions (or additional comments), but for the most part, what you see here is what I know. iPad seems to be the winner, unfortunately out of my Grad student salary range. Thanks to all who participated.-- Ed ORIGINAL MESSAGE: Does anyone have an e-reader/e-ink device they recommend for journal articles? The ability to make highlights and/or notes is very desirable. Thank you, Ed Krynak ekry...@uwo.ca VOTES: iPad x 7 Kindle x 3 Sony x 2 Nook x 2 ECTO Jetbook x 2 Samsung Galaxy Tab x 1 Onyx Boox M92 x 1 iPhone x 1 COMMENTS: KINDLE and a comment for Ectaco Jetbook and Kyobo Mirasol (see Samsung Galaxy tab for additional comment on the kindle DX) -- I have the Kindle DX which is the largest screen (approx. 8 x 10). I really like it. I think for pdf files/figures you need the largest screen. Yes you can take notes, but I have found that it is easiest for me to write notes elsewhere (or imbed them in the pdf itself). The real difference with a lot of ereaders is the technology. The black and white Kindles (not the fire) use actual ink and the screen really looks like a printed page. Other ereaders I think are better if you'd like to use it for more than just reading (or reading in color). Just keep in mind that the resolution of the pdf is a function of the file itself not the ereader, and therefore the journal articles rarely look as crisp as books, etc. Definitely ereader is the way to go, mine has hundreds of articles (and some books, including textbooks) and weighs less than a pound. -- I have used the Amazon Kindle Touch for looking at journal pdfs and I would NOT recommend it. It is difficult to find a good resolution to be able to easily read the text and also scroll through the paper. Moving around on the pdf and flipping pages is also very buggy with the e-ink device. You CAN highlight and make notes on it. I have not personally used the Amazon Kindle Fire tablet, but have colleagues who have, and they give it good reviews. It has all of the features you mentioned, but is about twice the cost. -- I was really interested in this topic and did a wide review. All the economical ereaders (nook touch, kindle touch, kobo, etc) are really jumpy/flashy when handling pdfs, and certainly lack pinch zones and smooth scrolling. IMO, this really distracts from the reading experience, having suffered the Nook 1st gen for a long time and its deplorable pdf abilities. For much more $$$, the Ectaco Jetbook and Kyobo Mirasol (both colour E-inks) seem to be the ultimate solution. I've no experience with either, but the few youtube reviews show dazzling pdf abilities (smooth, fluid scrolling). -- I haven't looked into the Nooks, but I currently have a Kindle Touch that seems to be the best of the Kindle family for reading PDFs. Other versions have trouble zooming and moving PDFs left and right to view. There are limited highlighting and note-taking capabilities, and I've heard that it's possible to transfer the notes with the PDF back to your computer, though I haven't figured out how to do that yet. SAMSUNG GALAXY TAB (with Kindle DX comment) -- I use dropbox to keep .pdf's available on the tablet and my office computer and laptop. Usually I download the files from my desktop as it's easier to manage being connected to the library etc. and then drag them into the dropbox folder, things sync nicely. The tab is a backlit and has pretty vibrant colors which is good for me as a lot of the papers I read have maps with color gradients etc. that you need the full color for. I've read papers on a Kindle DX and the formatting was occasionally off and if I wanted color figures I was out of luck. With the Samsung tab I read papers using the free adobe reader app which you can use to highlight text and type in annotations. Typing on the touchscreen is a bit cumbersome if you want to make anything more than a short note, but it is getting more reasonable as I've gotten accustomed to it. It fits into a jacket pocket and seems really durable (it's no worse for the wear after 3 months of pretty regular use and mild abuse), the 7 size and backlit screen may be hard on the eyes if you're really looking for e-ink. IPAD 3 -- It is a bit expensive, but the iPad 3 is probably the best for viewing science articles. You can highlight and save notes, just like on your computer. Plus, when you sync with a computer, it saves all of your notes in a common folder. --I've been very happy with my first gen iPad and the app GoodReader. It has good file management with various cloud access for easy transfer of pdfs. The annotation tools are robust, from simple highlighting to notes. It's probably the most used app on my iPad. SONY --When I
[ECOLOG-L] e-Reader for academic papers
Does anyone have an e-reader/e-ink device they recommend for journal articles? The ability to make highlights and/or notes is very desirable. Thank you, Ed Krynak ekry...@uwo.ca
