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New Paper: Local factors mediate the response of biodiversity to land use on two African mountains

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.


New paper: A first global assessment of remaining biodiversity intactness

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 ( ) with a number of nice articles in the BBC and the Guardian.

Biodiversity intactness of ecological assemblages for species abundance. Source: Newbold et al. 2016

Biodiversity intactness of ecological assemblages for species abundance. Source: Newbold et al. 2016

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

To all editors, reviewers and authors: time to move on regarding land sparing

Interesting read:
J. Fischer on the land-sharing/land-sparing debate.

Ideas for Sustainability

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…

View original post 793 more words

Interesting Paper: Land-Sparing Agriculture Best Protects Avian Phylogenetic Diversity

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.



Source: From Edwards et al. 2015

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.

Further reading:

Edwards, D. P., Gilroy, J. J., Thomas, G. H., Uribe, C. A. M., & Haugaasen, T. (2015). Land-Sparing Agriculture Best Protects Avian Phylogenetic Diversity. Current Biology.

Assessing habitat specialization using IUCN data

Since quite some time ecological models have tried to incorporate both continuous and discrete characteristics of species into their models. Newbold et al. (2013) demonstrated that functional traits affect the response of tropical bird species towards land-use intensity. Tropical forest specialist birds seem to decrease globally in probability of presence and abundance in more intensively used forests. This patterns extends to many taxonomic groups and the worldwide decline of “specialist species” has been noted before by Clavel et al. (2011).

From Newbold et al. 2013

(a) Probabilities of presence of tropical bird species in in different disturbed forests and (b) ratios of abundance in light and intensive disturbed forests relative to undisturbed forests. Forest specialists are disproportionally affected in intensively used forests. Figure from Newbold et al. 2013 doi:

But how to acquire such data on habitat specialization? Ether you assemble your own exhaustive trait database or you query information from some of the openly available data sources. One could for instance be the IUCN redlist, which not only has expert-validated data on a species current threat status, but also on population size and also on a species habitat preference. Here IUCN follows its own habitat classification scheme ( ). The curious ecologist and conservationist should keep in mind however, that not all species are currently assessed by IUCN.

There are already a lot of scripts available on the net from which you can get inspiration on how to query the IUCN redlist (Kay Cichini from the biobucket explored this already in 2012 ). Even better: Someone actually compiled a whole r-package called letsR full of web-scraping functions to access the IUCN redlist. Here is some example code for Perrin’s Bushshrike, a tropical bird quite common in central Africa

# Install package

# Perrin's or Four-colored Bushshrike latin name
name <- 'Telophorus viridis'

# Query IUCN status

#>Species        Family Status Criteria Population Description_Year
#>Telophorus viridis MALACONOTIDAE LC Stable 1817
#>Angola, Congo, The Democratic Republic of the Congo, Gabon, Zambia

# Or you can query habitat information

#>Species Forest Savanna Shrubland Grassland Wetlands Rocky areas Caves and Subterranean Habitats
#>Telophorus viridis      1       1         1         0        0           0                               0
#> Desert Marine Neritic Marine Oceanic Marine Deep Ocean Floor Marine Intertidal Marine Coastal/Supratidal
#>      0              0              0                       0                 0                         0
#>  Artificial/Terrestrial Artificial/Aquatic Introduced Vegetation Other Unknown
#>                      1                  0                     0     0       0

letsR also has other methods to work with the spatial data that IUCN provides ( ), so definitely take a look. It works by querying the IUCN redlist api for the species id ( Sadly the habitat function does only return the information if a species is known to occur in a given habitat, but not if it is of major importance for a particular species (so if for instance a Species is known to be a “forest-specialist” ). Telophorus viridis for instance also occurs in savannah and occasionally artificial habitats like gardens ( ).

So I just programmed my own function to assess if forest habitat is of major importance to a given species. It takes a IUCN species id as input and returns ether “Forest-specialist”, if forest habitat is of major importance to a species, “Forest-associated” if a species is just known to occur in forest or “Other Habitats” if a species does not occur in forests at all. The function works be cleverly querying the IUCN redlist and breaking up the HTML structure at given intervals that indicate a new habitat type.

Find the function on gist.github (Strangely WordPress doesn’t include them as they promised)

How does it work? You first enter the species IUCN redlist id. It is in the url after you have queried a given species name. Alternatively you could also download the whole IUCN classification table and match your species name against it 😉 Find it here. Then simply execute the function with the code.

name = 'Telophorus viridis'
data <- read.csv('all.csv')
# This returns the species id
#> 22707695

# Then simply run my function
#> 'Forest-specialist'

The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts

New article in which I am also involved. I have told the readers of the blog about the PREDICTS initiative before. Well, the open-access article describing the last stand of the database has just been released as early-view article. So if you are curious about one of the biggest databases in the world investigating impacts of anthropogenic pressures on biodiversity, please have a look. As we speak the data is used to define new quantitative indices of global biodiversity decline valid for multiple taxa (and not only vertebrates like WWF living planet index).


Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species’ threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project – and avert – future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups – including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems – We make site-level summary data available alongside this article. The full database will be publicly available in 2015.

I know that I haven’t been particular active on this blog in the last months. I am currently quite busy with writing my Thesis and programming. I am gonna make it up later 🙂

Annual Forest Loss – A comparison between global forest loss datasets

The start of this year was marked by the publication of two new global datasets for environmental analysis. My impression is that both of those datasets will be of increasing importance in ecological analysis in the future (even though their value for conservation biology has been actively criticized, see Tropek et al. 2014). Thus there is a need to assess the accuracy of their forest loss detection over time and if they are consistent.

The first dataset is the already famous Global Forest Map published by Hansen et al. (2013) in Science end of last year. The temporal span of their dataset goes back from the year 2000 up to the year 2012 and by using only Landsat data in a temporal time-series analysis they got a pretty decent high-resolution land-cover product. Although the resolution of the Hansen dataset is great (30m global average coming from Landsat) Hansen et al. decided to only publish the year 2000 baseline with the forest cover. They provide us with aggregated loss, gain and loss per year layers though, but nevertheless the user has no option to reproduce a similar product for the year 2012.

The other dataset is the combined published result from a 4 year long monitoring by the japanese satellite ALOS-PALSAR. They decided to release a global forest cover map at a 50m spatial resolution, which in contrast to Hansen can be acquired for the whole time-frame of the ALOS-PALSAR mission. It thus has a temporal coverage of the whole globe from the year 2007 until 2010. The data can be acquired on their homepage after getting an account. The ALOS PALSAR data has a nice temporal span and can be downloaded for multiple years, thus in theory allowing to make temporal comparisons and predictions about future land-use trends. However I am a bit concerned about the accuracy of their classifications as I have found multiple errors already in the area I am working in.

Classification Errors with the ALOS PALSAR dataset. Suddenly there are huge waterbodies in the Savanna near Kilimanjaro

Classification Errors with the ALOS PALSAR dataset. Suddenly there are huge waterbodies (blue) in the Savanna near Kilimanjaro

Because I am interested in using the ALOS PALSAR dataset in my analysis (how often do you get a nice spatial-temporal dataset of forest cover) I made a comparison between the forest loss detected in my area of interest for both datasets. It should be noted that is a comparison between different satellite sensors as well and not only by classification algorithms. So we are not comparing products from the same data source.

So what is the plan for our comparison:

  • We downloaded the whole ALOS PALSAR layers for all years covered of the area around Kilimanjaro in northern Tanzania (N00, E035). We then extracted only the forest cover (Value == 1) and calculate the difference between years to acquire the forest loss for the year 2008,2009 and 2010 respectively.
  • From the Google Engine app we downloaded the “loss per year” dataset and cropped it to our area of interest. Furthermore we are only interested in the aggregated Forest loss in the years 2008, 2009 and 2010 which we have available in the ALOS PALSAR dataset. We furthermore resampled the Hansen dataset up to 50m to match up with the ALOS PALSAR resolution.

The Result:

I haven’t found a fancy way to display this simple comparison, so here comes just the result table. As predicted (if you look at it visually),the ALOS PALSAR algorithm overshots the amount of forest loss a lot.

year 2007-2008 2008-2009 2009-2010
Hansen Forest Loss cells 262 304 529
ALOS PALSAR Forest Loss cells 26995 24970 16297
Equal cells in both 17 30 131


So which one is right? I personally trust Hansens data a lot more. Especially because I found them to be pretty consistent in my area of study. For me the ALOS PALSAR data is not useable yet until the authors have figured out ways to improve their classification. It can be concluded that users should not forget that those Forest Cover products are ultimately just the result of a big un-supervised algorithm who doesn’t discriminate between right and wrong. Without validation and careful consideration of the observer you might end up having wrong results.

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