Birds in space… (multidimensiaonal trait-space that is)

movieAn animated rotation of a plot of cloud forest bird species in their multidimensional trait space, showing vectors of trait variables, and spiders linking groups defined from a separate clustering analysis.

A small success in R yesterday, I finally managed to generate a 3d movie of the arrangement of species in the multidimensional trait space I am currently working with, for cloud forest birds in the Colombian Andes.  The output above uses the “rgl” and “vegan” packages to produce a series of .png files that animate the plot rotation, and for the conversion to video requires “imagemagick” to be installed (which in turn requires Xcode and macports to get it all happening).  I found great help for getting my initial code just for 3d plots to work on stack overflow.

It is not executable, but below is what my code looks like. Continue reading

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Presentation: Land-use, Climate Change and Avian Ecosystem Services in the Montane Neotropics: Managing for Resilience.


A 3d plot generated in R, showing a simulated landscape, onto which I mapped the estimated functional richness of Villeger et al (2008), calculated for our community of Andean cloud forest birds.

The second presentation I gave at ATBC in Cairns this year was in the Symposium entitled “Intelligent design: Managing landscapes to improve the future of biodiversity conservation (organised by David P. Edwards & Roman Carrasco)”.  I presented some preliminary results of my current work in Colombia:

Abstract: The cloud forest avifauna of the Colombian Andes provides a stark example of the tropical biodi – versity crisis: high diversity and restricted distributions coincide with narrow climatic niches and in- tensive land-clearing. Birds provide critical ecosystem services in these forests, including pollina- tion, insect control, and seed dispersal, important for regeneration and carbon storage. Work else- where shows tropical species shifting up-slope, tracking their thermal niches in response to climate change. Yet we do not know how resilient avian ecosystem services are to range-shifts: do source assemblages contain the redundancy and response diversity to absorb shifts, or should we expect cascading changes to key services? Nor do we know how land-use will influence these processes: are modified landscapes permeable to shifting species? Do their assemblages provide services similar to those of primary forest?

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ATBC 2014 Trip 1: “Gondwanan relicts and upland bird endemics of the Australian Wet Tropics”

tooth_billAt the association for tropical biology and Conservation (ATBC) meeting held in Cairns this year I will have the pleasure of co-guiding with Dr. David Edwards from Sheffield University a conference field trip entitled: “Gondwanan relicts and upland bird endemics of the Australian Wet Tropics”

From the ATBC website: “Home to the highest levels of terrestrial biodiversity in Australia, the Australian Wet Tropics World Heritage Area supports a unique combination of endemic and Gondwanan flora and fauna. We will leave Cairns early and drive up the coastal escarpment to the submontane and montane rainforests of Mount Lewis for dawn.  Here, we will find species such as Victoria’s Riflebird at their upper altitudinal limits, and as we ascend further, species such as Bridled Honeyeater, Atherton Scrubwren, Fernwren, and the enigmatic Chowchilla are common, with a chance of Tooth-billed and Golden Bowerbirds, all species threatened by climate change. We will descend for lunch at the well-known Kingfisher Park birding lodge, for good views of many species, including endemic Macleay’s Honeyeater ( From here, we will drive south along the Atherton Tablelands, passing through the edge of the gulf savannah and a large wetland.  As we approach Cairns we will take an afternoon walk in the rainforests of the Douglas Track at Speewah, where we will have further chances of Victoria’s Riflebird, Bower’s Shrike-Thrush, Pied Monarch, and Wompoo Fruit-dove”.

Should be fun!

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Null Models In Ecology: book download

Null models, love them or hate them, are a huge topic, but one nicely summarised by Gotelli and Graves.  They managed to do so in a way that I am finding accessible, and applicable to real-world analyses questions.  Happily, copyright has been returned to the authors, and I have just discovered that one can now download the whole thing, albeit chapter by chapter, here:

or here:


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Presentation: “Rapid Population Shifts in Australia’s Tropical Montane Avifauna: Monitoring Responses to Climate Change”.

GHR_plot.001Plot showing the observed up-slope shift and slight increase in population size of Grey-headed Robins, (Heteromyias albispecularis) based on 15  years of monitoring in the Australian Wet Tropics.

At ATBC in Cairns this year I am lucky enough to have the opportunity to present two papers.  The first, entitled “Rapid Population Shifts in Australia’s Tropical Montane Avifauna: Monitoring Responses to Climate Change” is in the Symposium entitled “Impacts of climate change on tropical birds: Current knowledge and pressing uncertainties” (organised by Jeffrey D. Brawn & Cagan Sekercioglu), and draws on the results of a large collaborative project at the Centre For Tropical Biodiversity and Climate Change where I did my PhD, completed in 2011, and first short Post Doc, completed in 2013.

Abstract:Montane tropical rainforests are critical reservoirs of endemic bird diversity, while narrow thermal tolerances and restricted distributions make these faunas particularly vulnerable to climate change.  In the Australian Wet Tropics, climate niche modeling has been used to predict range contractions of cool-adapted upland endemic species, and expansion of lowland generalists.  Actually detecting these changes however has proved challenging, as population densities and hence patterns of distribution and abundance in rainforest birds are difficult to quantify.  Efforts focused at range margins face the challenge of detecting rare colonization events, and demonstrating absences at the trailing edge is similarly problematic.  By focusing on estimates of density and models of elevational abundance response, we have overcome some of these challenges for a suite of rainforest specialist species in the Australian Wet Tropics.

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birding in Colombia, by the numbers…


90: The number of days spent in Colombia on this last trip.

162: The (estimated) number of lifers (new birds) seen by me on the trip.

290: The number of species I personally measured while collecting morphological data for the functional trait matrix I am developing of cloud forest birds from the western cordillera of the Colombian Andes

2,912: The combined number of specimens measured by myself  and Alejandro Pinto, one of my collaborators at the Insituto Alexander von Humboldt.

24,295: the combined number of actual measurements carried out by us (by Alejandro at a rate 3 times faster than me, as he had digital calipers!).

19,750: the (estimated) number of kilometres traveled, including international flights from Oslo.

22,250: the (estimated) combined volume (in milliliters) of blackberry smoothies and hot chocolate consumed during my visit to Colombia.

Its been several weeks that I have been back in Norway, and time to get cracking with organising, and checking the morphological data I collected in Colombia, as well as sorting through the 7,000 photographs taken while I was visiting that amazing country.  Unfortunately the approach of summer means that the weather is steadily improving, and the arrival of migrant birds, and the increased activity of resident species adds to the appeal of spending more time outside, and less time in the office…

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Its is a short drive from Cali over the misty peaks of Los Farallones, past El Dieceocho, to the pacific slope of Colombia’s Western Cordillera.  But in this  distance, many things change, both in terms of the visible environment, and in more subtle ways.  In moving from the inter-andean valley to the pacific slope, one becomes acutely aware of the reason why the peaks of the Western Cordillera are so constantly shrouded in mist, and why here forests are so abundantly green and moss-hung.  This reason has a name: the Cocó-Darien.  Famous as the place that stopped the Pan-American Highway, with its impenetrable forests and up to ten metres of annual rainfall, the Chocó is a massive lung, harvesting and respiring great humid breaths of the moisture moving in from the warm pacific coast, and condensing it against the high peaks of the Andes.  In these forests, the almost constant rain humidity has allowed the growth and diversification of a massive profusion of life-forms, including many species not found anywhere else on the planet.

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