I know that it has been a while since I posted anything here. The daily responsibilities and effort required for my PhD program are taking quite a toll on the time I have available for other non-phd matters (for instance curating this blog). I apologize for this and hope to post some more tutorials and discussion post in the future. However at the moment my personal research reserved 105% of my available time. But the scientific blogosphere is generally in a bit of a crisis I heard.
Anyway, today I just want to quickly share the exciting news that my MSc thesis I conducted at the Center for Macroecology, Evolution and Climate has passed scientific peer review and is now in early view in Animal Conservation. I am quite proud of this work as it represents the first lead-author paper I managed to publish that involved primary research and data collection.
Short breakdown: During my masters and also now in my PhD I am extensively working with the PREDICTS database, which is a global project aiming at collating local biodiversity estimates in different land-use systems across the entire world. The idea for this work came as I realized that many of the categories in the PREDICTS database are affected by some level of subjectivity. Local factors – such as specific land-use forms, vegetation conditions and species assemblage composition – could alter general responses of biodiversity to land use that have been generalized across larger scales. Thus the simple idea was to compare ‘PREDICTS-style’ model predictions with independent biodiversity estimates raised at the same local scale. But see abstract and paper below.
Jung et al (2016) – Local factors mediate the response of biodiversity to land use on two African mountains
Land-use change is the single biggest driver of biodiversity loss in the tropics. Biodiversity models can be useful tools to inform policymakers and conservationists of the likely response of species to anthropogenic pressures, including land-use change. However, such models generalize biodiversity responses across wide areas and many taxa, potentially missing important characteristics of particular sites or clades. Comparisons of biodiversity models with independently collected field data can help us understand the local factors that mediate broad-scale responses. We collected independent bird occurrence and abundance data along two elevational transects in Mount Kilimanjaro, Tanzania and the Taita Hills, Kenya. We estimated the local response to land use and compared our estimates with modelled local responses based on a large database of many different taxa across Africa. To identify the local factors mediating responses to land use, we compared environmental and species assemblage information between sites in the independent and African-wide datasets. Bird species richness and abundance responses to land use in the independent data followed similar trends as suggested by the African-wide biodiversity model, however the land-use classification was too coarse to capture fully the variability introduced by local agricultural management practices. A comparison of assemblage characteristics showed that the sites on Kilimanjaro and the Taita Hills had higher proportions of forest specialists in croplands compared to the Africa-wide average. Local human population density, forest cover and vegetation greenness also differed significantly between the independent and Africa-wide datasets. Biodiversity models including those variables performed better, particularly in croplands, but still could not accurately predict the magnitude of local species responses to most land uses, probably because local features of the land management are still missed. Overall, our study demonstrates that local factors mediate biodiversity responses to land use and cautions against applying biodiversity models to local contexts without prior knowledge of which factors are locally relevant.
Anthropogenic land use is one of the dominant drivers of ongoing biodiversity loss on a global scale and it has often been asked how much biodiversity loss is “too much” for sustaining ecosystem function. Our new paper in the journal Science came out last week and attempts to quantify for the first time the global biodiversity intactness within the planetary boundary framework. I am absolutely delighted to have contributed to this study and it received quite a bit of media attention so far ( https://www.altmetric.com/details/9708902 ) with a number of nice articles in the BBC and the Guardian.
In our study we calculated the Biodiversity intactness index (BII) first proposed by Scholes and Biggs (2005) for the entire world using the local biodiversity estimates from the PREDICTS project and combined them with the best available down-scaled land-use information to date. We find that many terrestrial biomes are already well beyond the proposed biodiversity planetary boundary (previously defined and set as a precautionary 10% reduction of biodiversity intactness). Unless these ongoing trends are decelerated and stopped in the near future it is likely that biodiversity loss might corroborate national and international biodiversity conservation targets, ecosystem functioning and long-term sustainable development.
- Newbold, Tim, et al. “Has land use pushed terrestrial biodiversity beyond the planetary boundary? A global assessment.” Science 353.6296 (2016): 288-291. DOI: 10.1126/science.aaf2201
Scholes, R. J., and R. Biggs. “A biodiversity intactness index.” Nature 434.7029 (2005): 45-49. DOI: 10.1038/nature03289
As I can see my QGIS plugin LecoS is still widely used and downloaded from the QGIS plugin hub. I have noticed that some people already started referencing ether my blog or the QGIS repository in their outputs, which is fine, but after thinking about it for a while I thought why not make a little descriptive article out of it (being an upstart PhD scholar and scientist an’ all). I am now happy to announce that this article has passed scientific peer-review and is now been published in early view in the Journal of Ecological Informatics.
LecoS — A python plugin for automated landscape ecology analysis
The quantification of landscape structures from remote-sensing products is an important part of many analyses in landscape ecology studies. This paper introduces a new free and open-source tool for conducting landscape ecology analysis. LecoS is able to compute a variety of basic and advanced landscape metrics in an automatized way. The calculation can furthermore be partitioned by iterating through an optional provided polygon layer. The new tool is integrated into the QGIS processing framework and can thus be used as a stand-alone tool or within bigger complex models. For illustration a potential case-study is presented, which tries to quantify pollinator responses on landscape derived metrics at various scales.
The following link provided by Elsevier is still active until the 23 of January 2016. If you need a copy later on and don’t have access to the journal (sorry, I didn’t have the money to pay for open-access fees), then feel free to ether contact me or you can read an earlier prePrint of the manuscript on PeerJ.
So if you are using LecoS in any way for your work, it would be nice if you could reference it using the citation below. That shows me that people are actively using it and gives me incentives to keep on developing it in the future.
Martin Jung, LecoS — A python plugin for automated landscape ecology analysis, Ecological Informatics, Volume 31, January 2016, Pages 18-21, ISSN 1574-9541, http://dx.doi.org/10.1016/j.ecoinf.2015.11.006.
The full sourcecode of LecoS is released on github.
Today I just want to share with you two (new – granted this one is already 2 years old) services that aim to make voluntary or open work more visible and credible. Many researchers often do a lot of work that is not really valued or even accounted for in academic hiring processes or funding proposals. Such as for instance the very process of participating as a (voluntary) reviewer for a peer-reviewed journal. Those of you who have done such a review know that it is often a tremendous amount of work (to do it properly). At least for me it costs several hours of work on a day that I could in return spend on my work instead. I am not criticising peer-review here ( also because of a lack of alternatives), but I often wondered if there is a way to get credit for your past peer-reviews. And there actually is a way as I have just found out. Publons is a website that allows you create a free profile page, where you can list your past reviews. They have a mailing verification system in place and are in direct contact with journals to check if you have actually done a review or not. You don’t have to publish the contents of your review, but you obviously can decide to do so (for instance if it was a particular well written study or just love embracing the openness). Give it a try.
The other service I want to introduce is called Depsy and was just started today. It a website that promotes innovative and highly used scientific software for researchers by scanning github, citations, download rates and dependencies. Why is that helpful and very important? Consider for instance that you developed a piece of software, make it openly available and even provide a reference so that users can cite you. However your work might just be incorporated into others (such as the rgdal package that just wraps up access to the gdal and proj4 libraries) or is not cited due to pure convenience. For instance I really wonder if most of the users of ggplot2 in R ever called citation(“ggplot2”) and actually cited it in their work. Depsy is dedicating open-source projects their own page ( here for instance the one for ggplot2), which evaluate the overall impact of the software and how it has been (re)used since its release. Very cool and nice idea and I hope that this new service will finally provide credit for all those programmers out there so that maybe one day creating open-source scientific software will be properly valued.
J. Fischer on the land-sharing/land-sparing debate.
By Joern Fischer
Synopsis of this blog post: We don’t need sparing or sharing but both; and how exactly this should happen in any given landscape requires a (more holistic) interdisciplinary approach to be answered. Editors, reviewers and authors should recognize this and prioritise work that goes substantially beyond trading off sparing vs. sharing.
It’s no great secret that I’m not the biggest fan of the framework on land sparing and land sharing – though I do recognize that it does have an academic value, and it is an internally consistent, elegant framework. Those who know how to use this framework carefully do good science with it. But most users over-interpret it, which I find increasingly upsetting. So this blog post is a call to editors, reviewers and authors to be more critical about fundamental assumptions that are regularly being made by many authors, but hardly ever spelt out, or…
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For a long time I have been kinda reluctant to jump on the Smartphone/Touchscreen train, which might be due to the fact that I am rather conservative with regards to software. In the same way I choose my Linux distribution (Debian for the extra stability and often outdated , but proofed versions), I prefer to choose the tools surrounding me. Stability and function always meant a lot more to me than cultural trends or taste. Nevertheless in the last month I decided to purchase my first device with a touchscreen, a tablet running Android for my daily use and so that I do not have to take the notebook with me during every travel. I have never really used sth. like this before so please excuse the following over exaggerated praises as this whole world of using apps (as in application) is pretty new to me. In the short time I used my new tabet, I already managed to find some really useful apps, which I would like to share with you (feel free to recommend others):
Doing any kind of research usually requires you to read broadly and read a lot! Most of the time I stumble across new literature by reading blogs, tweets and following researchers who work on similar issues related to mine. Of course I occasionally check out different journal homepages as well and scroll down the list of abstracts from the latest issues. Working or being registered at a scientific institution enables you to read papers from all kinds of journals, not only those directly related to your main field of research. I promptly registered to many journals including some that are only in a very general way related to my field of study. In Browzine published new issues are highlighted with a red dot, so you can be sure never to miss a new paper from your favourite journal. In addition you can save any downloaded papers directly to your dropbox or mendeley account. Cons: Some opensource journals (peerJ) and preprint hosters (biorxiv) are missing? Also it seems as if not every institution has made a deal with the app publisher.
This one probably is not a new one to you. Evernote has been around for a while and simply does a splendid job of organizing your thoughts. You can drop whole websites, simple txt’s and pictures together to build your own little collection of paste-it posts. I usually also keep their web interface open on my desktop PC and all notes are synchronized with my mobile device.
If you are not running windows / evernote on your production machine, than usually you go with ether Zotero or mendeley as literature management software of your choice. I got used to mendeley and their nice plugin for Libreoffice, which enables to insert and manage references directly from mendeley. This really paid off when I noticed that there is also a mendeley app, which syncs with your mendeley account. Why is that useful? Well, I can for instance manage all my references and tons of pdfs on my PC, sync them to my mendeley account and then have them readily available for reading and commenting on my mobile device. Not to mention that it integrates quite well with other providers such as the mentioned above Browzine.
Excellent file browser which I really would like to have open all the time. You can browse all the files on your device (even the hidden once), social and remote service (like cloud hoster, ftp or network servers) are integrated. The ES File explorer is organized in windows, which enables you to switch quickly between for instance your dropbox and pictures. Very good discovery!
- Google calendar and mail
I tried almost every calender and mail app that is available in the google play store, but in the end I still stuck with the default google calendar and mail. The reasons: Ease of navigations, no annoying adds or popups which want to persuade you to buy a “pro” version and especially working sync with a wide range of accounts, contacts and events(!). Obviously the google apps have kinda of a homeplay game on android compared to other alternatives. Having the same kind of interface for the calendar on both the tablet and my personal computer was really, what made the deal in the end. Google mail also is quite easy to use and manage, especially for people like me with multiple mail accounts.
This one is really handy, especially for people who often get lost. It lets you access the popular openstreemap maps and navigate through it with your touchscreen. If you enable GPS you can see your current location and calculate the optimal route to your destination. Out of internet? No problem, the app lets you download and store whole geographic regions so that you can access openstreetmaps mapping and routing even while you are have no internet. Quite good if you are lost on the way to a conference and don’t want to use your precious bandwidth.
This one is an output from the Jetz lab at Yale university. You can use the application to find out the species that you just saw on your morning stroll around the park/coast/reserve. Based on species range maps it calculates the number of species, which can be potentially discovered in the current area. The little pictures also help a lot with the identification.
That´s it. But feel welcome to comment and suggest other nice (free) apps. I should explicitly mention that I am not related or employed by any of the apps´s providers.
A quick post to highlight a new publication in this weeks issue of Current Biology. Edwards et al. went for another piece on the land-sharing/land-sparing debate and presented a very nice case study. Land-sharing is often defined as combining “sustainable” agricultural production with higher biodiversity outcomes often at the tradeoff of harvesting less and loss of natural habitats. Land-sparing on the other hand attempts to prevent remaining natural habitat from being used by humans, but instead intensify production and increase yield from other areas, thus reducing their potential for wildlife-friendly farming. They combined field work from the Choco-andres region (Taxonomic focus: Birds) with simulation models to investigate which strategy might benefit biodiversity the most. Contrary to many other previous publications they focused on phylogenetic richness (PD) rather than “species richness”. Based on landscape simulation models they could show that PD decreases steadily with greater distance to forests, which is interesting because it demonstrates that land-sharing strategies might only be successful, if sufficient amounts of natural habitat are in close proximity, that can act as source habitat for dispersing species.
According to their analysis some species seem to benefit more from land-sparing strategies than others. Specific evolutionary traits thus might be ether beneficial or detrimental for surviving in intensive human land use such as agriculture. They conclude that land-sharing might be of limited benefit without the simultaneous protection of nearby blocks of natural habitat, which can only be achieved with a co-occurring land-sharing strategy.