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).

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http://onlinelibrary.wiley.com/doi/10.1002/ece3.1303/abstract

Abstract

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 – www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.

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PS:

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 🙂

It is conference-summer – BES-TEG in YORK 2014

The Sun is shining, birds are singing and most scientists have nothing better to do than jetting around the globe to attend conferences. Yes, it is summer indeed. Here is some advertising for the 2014 Tropical Ecology – Early Carer Meeting of the British Ecological Society. This year the fun is happening in York. As many people seem to be on vacation the deadline for abstracts has been extended to the 14th of July. See the attached Documents ( BES-TEG 2014 Flyer ,BES_TEG Key speakers ) for more information. I will be there as well… .

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Dear All,

The British Ecology Society – Tropical Ecology Group (BES-TEG) are organizing a 7th early career meeting scheduled to take place at the University of York, on the 14th and 15th of August 2014. Day one will focus on Ecology and Ecosystem Processes while day two will focus on Practical Applications and Links to Policy; such as conservation, livelihood, policy and development. All early-career researchers, both PhD and Post-Docs, are welcome to present their tropical ecology related research as a poster and/or oral presentation. The deadline for abstract submission has been extended to Monday the 14th of July 2014.

Please find attached the flyer and conference document for detailed information.

It would be appreciated if this flyer circulates within your department. Students are encouraged to come to York for what should be a really interesting few days in August.

An event website has been set up for registration

http://www.eventbrite.co.uk/o/british-ecological-society-tropical-ecology-group-bes-teg-6217007537

Interesting Paper: Global warming and invertebrate colouring

Just now another very interesting paper has been published in Nature Communications, which was written by former colleagues of mine from the University of Marburg.

Global warming favours light-coloured insects in Europe

As we all know many insect species like butterflies, bees or dragonflies have their main activity pattern during the day due to their ectotherm thermoregulation. Body colour is an important aspect of this thermoregulation as darker ( more blackish) individuals usually heat up faster. Therefore darker insects have an advantage compared to brighter insects in cooler climates as they heat up more rapidly and can forage earlier. This pattern can be mapped on a larger scale using occurrence data and has been known as “thermal melanism hypothesis” in macroecology. The authors go a step further from here as they  not only display a new biogeographic pattern previously unknown to science ( colouring gradient of European dragonflies and butterflies from south to north), but they also demonstrate how this mechanistic link between a macroecological pattern and a functional trait can be used to forecast the effect of climate change on insects.

From Zeuss et al. (2014): Shift in colour value for (a) the raw data; (b) the phylogenetic component (P); and (c) the specific component (S). Red indicates an increase in colour lightness; blue indicates a decrease in colour lightness. The diameter of each dot indicates the extent of the shift (n=1,845). The distribution of the shifts shows for the specific component a clear trend towards higher (that is, lighter-coloured) values (peak of the distribution positive; zero indicated by black line). The phylogenetic component suggests that the shifts in colour lightness have a strong phylogenetic background leading to a complex geographic mosaic in the response of assemblages to climate change. The inserted histograms show the mean change in colour lightness calculated for 1,000 alternative phylogenetic trees and are positive throughout, indicating that uncertainties in the phylogenetic hypotheses are unlikely to affect our conclusion of a general shift towards lighter assemblages. The distributional information used in the analysis is often based on a large time span, that is, the distributional information published in 1988 summarizes data until that year using information even from the beginning of the twentieth century. Rugs at the abscissa indicate observed values.

Possible critics: A definite next step in the analysis would be to include real measurements of optical colour rather than RGB values of scanned pictures. The colour values used in this study were all derived from scientific taxonomic drawings of those insects and thus biased by subjectivity of the respective artist. Nevertheless this bias should be consistent (if the same artist has sketched the images) so it should not influence the colouring gradient.  It is also interesting to note that many insects ( I know this for instance from my work with bugs and hoverflies) can adapt their body colouring to their habitat or differ quite a lot within a population. Differing melanism in body color and wing colouration might be related to the climatic niche they occur in, but the insects themselves might also possess phenotypic plasticity to adapt for instance to different habitats and background (Hochkirch et al. 2008). This pattern certainly needs more investigations in the future.

The article has been published as open access paper, so give it a try 😉

• Hochkirch, A., Deppermann, J. and Gröning, J. (2008), Phenotypic plasticity in insects: the effects of substrate color on the coloration of two ground-hopper species. Evolution & Development, 10: 350–359.

• Zeuss, D. et al. (2014) Global warming favours light-coloured insects in Europe. Nat. Commun. 5:3874

BIOFRAG – Biodiversity responses to Forest Fragmentation

Another interesting project closely related to PREDICTS is the BIOFRAG Project, which tries to construct a global database of research papers dealing with Forest Fragmentation and its impacts on Biodiversity taxa. One final goal of the BIOFRAG project is the development of a new fragmentation index using watersheds delineation algorithm and fragment descriptors in order to characterize Fragment traits. I am very interested in seeing the final outcome of this approach and maybe I even find the time to implement their algorithm in LecoS for QGIS as soon as it is released. Their database paper, lead authored by Marion Pfeifer, was just released to the public as open-access paper. You can read it in full here.

Pfeifer et al. (2014) BIOFRAG – a new database for analyzing BIOdiversity responses to forest FRAGmentation. Ecology and Evolution. doi: 10.1002/ece3.1036

If you consider of contributing data then more information can be found on the BIOFRAG blog and all researchers involved with forest fragmentation research should consider contributing to them and also to PREDICTS   (see here) if you haven’t already done so. And as usual: If you were studying in Africa, then please get in touch with me! I will contact you as soon as I return from my Fieldwork in Kenya and Tanzania at the end of May.

Out in the field – Working in the agricultural Mosaic of the Taita Hills

And here are some news from my current field work that is part of my Thesis. After spending some quiet, but exiting days in Nairobi (maybe later more about that) I finally arrived in Wundanyi, Taita Hills, where a substantial part of my work will be conducted along the CHIESA transect. Suited in the coastel area in proximity to Mombasa the Taita Hills are renown for their extraordinary bird diversity and endemic species and as such are considered to be part of the Eastern Arc Mountains Diversity hotspot. The Taita hills encompass a variety of different land-use forms, but the majority of them surely are tropical homegardens as most of the “Taita” people are subsistence farmers growing crops in the highly fertile soil of the mountain slopes. Besides homegardens there are riverine forests in the valleys, shrubland vegetation in the lower altitudes, exotic tree plantations and of course the remaining indigenous forests remaining on the Taita hills mountain tops. Every last forest part is known well and was traditionally protected by the locals as part of their culture. However in the later centuries the remaining forest area became more and more scarcer and even during my visits in some of the forest fragments with the highest biodiversity value (Chawia, Ngangao) I saw frequent signs of fuelwood and timber extraction. Clearly a lack of funding for biodiversity protection seems to be the problem, but also an economic perspective and opportunities such as ecotourism might enhance locals perception if and how these last forest parts should be protected.

Past Funding

Cloud Forest Vuria

Woodland

My work in the Taita hills is all about birds. Specifically I am conducting avian diversity and abundance assessments along an altitudinal transect encompassing a variety of different land-use systems. Although avian assessments have been conducted in Taita many times before, they were often restricted to the forest fragments and for instance didn’t look at the bird diversity in homegardens in different altitudes. The resulting data will just be used for my thesis as validation dataset, but I am hoping that it has maybe some value on its own as well. Initial results show that especially the homegarden in Taita support quite a high diversity of birds, which is even similar to levels in the remaining forest fragments (although the community is somewhat different and biotic homogenization is likely on-going).

It can be quite challenging to conduct avian research in tropical human-dominated landscapes. Not only do you have to arrange for transport to the specific transect areas and lodging (in my case provided by the University of Helsinki Research station in Wundanyi), but also account for the frequent interruption by children and farmers asking what you are doing. Furthermore it is not an easy task to count birds in for instance a maize or sugarcane plantation due to the limited accessibility and my intention not to damage the farmers crops. Most of the farmers however happily provide access to their land and are very interested in what kind of research this “Mzungu” is doing on their farm. From my own experience here I can tell that the Taita people are very kind and it is a pleasure to work with them on their land. They are very respectful and even walking around late at night or very early in the morning seems to be no problem here (in contrast to for instance Nairobi or Mombasa).

Speckled Mousebird

Female Chameleon

In the end my sampling goes on quite well and much better than I expected. Although it is technically raining season and long heavy rains can be expected every day, the mornings were exceptionally dry and weather was mostly favourable for ornithological research. Generally this time of the year in East Africa is especially interesting for bird assessments as many local bird species are in their breeding plumage and nesting, but also because European migrants are often still around or on their way back to Europe (for instance I saw and heard an European Willow Warbler some days ago). Lets see what else the next weeks will have for be in terms of avian diversity.

Interesting Paper and Data: Global Forest Loss (Hansen et al. 2013)

Just some moments ago (on the 15th of November 2013, so not yet in Europe 😀 ) a new very interesting paper came out in Science presenting a new High-resolution dataset of global forest loss in the last decade. It is written by the authors of already existing widely used datasets, such as GLCF and CARPE, in corporation with Google.

Hansen et al. (2013), High-Resolution Global Maps of 21st-Century Forest Cover Change

“In this study, Earth observation satellite data were used to map global forest loss (2.3 million square kilometers) and gain (0.8 million square kilometers) from 2000 to 2012 at a spatial resolution of 30 meters. The tropics were the only climate domain to exhibit a trend, with forest loss increasing by 2101 square kilometers per year.”

Not surprisingly only the tropical rain-forest was found to posses a negative trend in the last decade. Most likely because of shifting agriculture, clash-and-burn practices and large scale deforestations due to monoculture cultivation of Palmoil, Soy and Jatropha. Quite impressively they used over  654,178 Landsat images in a time-series analysis to in characterize forest extent and change in the time from 2000 to 2012. Google apparently helped out with the computation (cloud-computing). And the best thing is: You can view the data

Google Viewer of Hansens et al. 2013 forest loss dataset

online via Google.

Online view of Global Forest Change

At the bottom you can find a Data download link, which makes the whole thing very interesting for follow-up research! Check it out!

EDIT: Apparently download is not yet available for the public. Will keep you updated!

Peer reviewed Videos

JoVE (Journal of visualized Experiments) just opened up a whole new section called Environment, which is potentially interesting for all ecologists and environmentalists. I really like the idea of peer reviewed videos in science and i am sure its gonna be the next frontier line. For instance, why read about a 3-4 pages long method paper on how to correctly sample insects in forests when you could just watch and listen so someone who demonstrates it?

Check it out!

Interesting Paper: Impact of Fragmentation on Plant-Frugivore networks redundancy

Jörg Albrecht, my former co-supervisor at the University of Marburg finally published his first results from his PhD. I was eagerly waiting for this publication as i also helped to raise a lot of data as a volunteer ornithologist while working on my bachelor thesis. Looking back i remember many nice beautiful moments like sitting in a camouflaged tent early in the morning counting frugivorous birds in the very core zone of Bialowieza forest. Bisons, Mooses, wildcats, the sound of howling wolfs in the morning were among the nice experiences i took with me. It was definitely a nice period of my life and i congratulate Jörg for publishing this nice paper! Published in the renown Journal of Ecology you can now access the paper in early-view:

Albrecht  et al. 2013 – Logging and forest edges reduce redundancy in plant–frugivore networks in an old-growth European forest

For those of you who want a little appetizer of what the paper is about. The paper itself incorporates information gained from many recently developed techniques for ecological network analysis to draw conclusions using general ecological theory (Optimal Foraging Theory). The optimal Foraging Theory developed by MacArthur (1955) hasn’t yet much appeared in the ecological network literature, which is a shame as it allows predictions about changing plant/animal specialization patterns in the light of habitat perturbations.  Here is a little summary, but i still recommend to read the full paper as both methods and conclusions are quite sophisticated 🙂

• 2 years of recorded plant-frugivorous interactions in Europe’s last old-growth lowland forest (Białowieza, Eastern Poland)
• Hypothesis (Summarized from the 3 expectations in the paper): Increased competition at Forest edges (caused by logging) compared to the interior forest leads to higher, respectively lower, redundancy in plant-frugivore networks. (But better read the paper!)
• To fully understand the extent of this study you need to dive deep into the study design and purpose. It uses state of the art statistical network-analysis techniques to calculate network redundancy and interaction specialization. Two and a half pages alone explain the data gathering and analysis, while the results sections is nearly half a page long 🙂
• Despite the small sample size (which was/is a major critical point) the results show that the networks redundancy was reduced at forest edges due to shifting dietary specialization of the interacting partners. As i remember from the data collection Black-caps and Blackbirds dominated in most of the assessed trees, which leads to an asymmetry in the interaction network. As shown in the paper this might be due to forest fragmentation.
• Possible Critic:The sampling effort of 10 studysites, which were sampled over 2 years might not be enough to detect real properties of ecological networks. However so far every study investigating ecological networks worked with incomplete data. I also don’t really trust the whole separation of species in specialist and generalists based on available literature. Although much is known up to now, both foraging and behavioral patterns of birds might change due to forest fragmentation and therefore such classification might be inaccurate depending on the study sites properties.
• Why is the study of interest?  Up to now not much is known about how temperate Plant-frugivore interactions change in the face of habitat perturbation. Most of the available literature was conducted in the tropics or didn’t incorporated whole interaction networks. Probably due to the geographical bias, most of the available literature furthermore failed to detect an effect on network stability as this study shows.

So, enough advertising 😉

Interesting paper: The spatial road disturbance index

Following current papers and newly proposed methods is always exciting. Especially when someone proposes a new technique for conservation planning, which

Daily car victims: frogs

includes the habitat fragmentation caused by roads. The decrease of road-less areas in Europe certainly has an impact on a wide range of species (Selva et al. 2011), especially if they inhabit large home-ranges and frequently move between for instance forest patches. To give an example: Conservation NGOs in Germany are currently celebrating the return of wolves in east German forests. While this is certainly a good thing it requires a lot of future management actions (possible compensation of farmers, education of the public, …) and furthermore the high fragmentation of east German landscapes might also alter wolf behavior and migration. Many other animals are also affected by fast moving traffic (see the picture of the poor frog) and therefore i am certain that roads will become more and more important in future conservation area prioritizations and landscape planing.

In their recent paper Freudenberger et al (2013) shed light on the current fragmentation of an east German state and introduce a new landscape metric called the spatial road disturbance index (SPROADI). The SPROADI is an aggregated index, which integrates  the (1) traffic intensity on the habitat intersecting road, (2) density and distribution of roads in a landscape and (3) overall fragmentation caused by roads. Mathematically the new index is just a weighted sum of the three equally weighted subindices, which were previously categorized using available quantitative data. While this is certainly not perfect (data maybe biased and thus has to be normalized beforehand, correlations with subindices) i think that due to its simplicity and easy understanding it might become a handy index for landscape planners and biologists conducting impact assessments for roads. Although i am not entirely convinced by the mathematics behind this new index (next rainy sunday i will put some thoughts behind it) i recommend interested people to give their paper a try.

• Freudenberger et al. “Spatial road disturbance index (SPROADI) for conservation planning: a novel landscape index, demonstrated for the State of Brandenburg, Germany”. Landscape Ecology (2013): 1-17. DOI: http://dx.doi.org/10.1007/s10980-013-9887-8
• Selva, Nuria, et al. “Roadless and low-traffic areas as conservation targets in Europe.” Environmental management 48.5 (2011): 865-877.

Genetic barrier detection in landscape genetics

Hey,

currently i am working with micro-satellite data from several local populations of Tanzanian elephants and i was wondering if there are somehow borders between my populations that prevent migration and therefore gene-flow. As elephants usually are animals that live quite long (if not killed by poaching right after reaching maturity), detecting actual barriers in field-observations might be difficult and requires a lot of effort. And that is where landscape genetic techniques come into the picture.

As early as in 1973, a french Guy called Monmonier (Monmonier 1973) came up with a very nice idea of barrier-detection using graph-theory and gis-techniques such as Vorronoi tessellations. Although previously intended to be used in a purely geographical context  its nowadays has been extended and can be used in multiple cases including population genetics.

What i did:

• I downloaded the program Barrier. Then i calculated centroids of my sampling locations and loaded everything into Barrier
• I then bootstrapped my Microsatellite-data 100x times (Chao et al. 2008) and created pairwise-distance matrices using the D index introduced by Jost (Jost 2008). So i end up with a list of 100 “dist” objects in R.
• I saved the list of dist-matrices into a txt-file and loaded it into Barrier to conduct a barrier significance test (Using replicates of the same matrix).

Genetic Barrier detection using pairwise population differentiation indices with bootstrapped Microsatellite-data.

As you can see especially Point 4 (red arrow -> a national park in central Tanzania) seems to be more genetically isolated than the other sampling locations (the strength of the red lines represent contribution of the bootstrapped barriers). However the whole result was a bit disappointing for me (no really clear barrier) and additional analysis using the popular program structure as well as traditional population differentiation indices like Fst, G’st and Jost’D revealed that the population structure of elephants is indeed quite complex. Still i really like this technique and I’m curious about other use-cases.

In this case I used the very simple and straight-forward program barrier by Manni et al (2004) to produce the above graphic. However the popular R-package adegenet (Jombart 2008) also has a method – monmonier – for genetic barrier detection. See the R graphical website for an example. Still it would be great to see such feature in a real GIS-environment like GRASS or QGIS. Has anyone heard of any extensions or plugins that add landscape genetic methodologies to these programs? I don’t have much time to code right now, but basically all it needs are some point coordinates (from a point layer) and a matrix displaying distance between the points. Great stuff 🙂

References:

• Monmonier, M. (1973) Maximum-difference barriers: an alternative numerical regionalization method. Geographic Analysis, 3, 245–261.
• Manni,F., Guérard, E. & Heyer, E. (2004). Geographic patterns of (genetic, morphologic, linguistic) variation: how barriers can be detected by “Monmonier’s algorithm”. Human Biology, 76(2): 173-190.
• Jombart T. (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24: 1403-1405
• Chao, A. et al. (2008). A Two-Stage probabilistic approach to Multiple-Community similarity indices. Biometrics, 64:1178-1186
• Jost, L. (2008), GST and its relatives do not measure differentiation. Molecular Ecology, 17: 4015-4026.