Using light to describe the ancient world

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Pink feathers on a living dinosaur

Feather pigments in the Pink-headed duck were recently analysed with Raman spectroscopy. Image adapted from: Henrik Grönvold (1858–1940).  Journal of the Bombay Natural History Society Volume 18. The Pink-headed Duck Rhodonessa caryophyllacea = Rhodonessa caryophyllacea (Pink-headed Duck)

Feather pigments in the Pink-headed duck were recently analysed with Raman spectroscopy. Image adapted from: Henrik Grönvold (1858–1940). Journal of the Bombay Natural History Society Volume 18. The Pink-headed Duck Rhodonessa caryophyllacea = Rhodonessa caryophyllacea (Pink-headed Duck)

Birds are living dinosaurs. Modern birds and extinct beast-footed dinosaurs (i.e. theropods) have many traits in common because they inherited these traits from the same ancestor, e.g. s-shaped necks, fused clavicles (…wishbones) and feathers. Many living birds have brightly coloured feathers, which leads us to wonder if ancient dinosaurs also had colourful plumage. One way we can answer this is by studying living dinosaurs (…birds). If two closely related birds have red feather pigments, like Northern and Desert cardinals, then we would suppose that they inherited this pigment trait from a recent shared ancestor. The more-distantly related two birds are that share the same trait, the older the ancestor must be that they inherited the trait from. If we can find two very distantly related birds with brightly coloured feathers then we might think they inherited that trait from an ancestor that was alive during the Age of Dinosaurs.

Cardinals and ducks are very distant relatives.

Dr Helen James from the Smithsonian Institution National Museum of Natural History and I have been studying bird species that have carotenoid-pigmented plumage. Carotenoids are responsible for most of the red, orange, yellow and pink colours we see in feathers. In our search we discovered that the Pink-headed Duck (Rhodonessa caryophyllacea) has carotenoid-pigmented plumage. These pigments are rare among ducks and a few years ago we discovered the only other known occurrence: the pink ‘ears’ of the Pink-eared Duck (Malacorhynchus membranaceous). In fact, these occurrences are so rare that when we model the evolution of carotenoids in duck feathers our results tell us that pink feathers in each species evolved independently and were not inherited from ancient dinosaurs. This is still a bit puzzling and it suggests that we need to dig deeper. Maybe into the genetics of feather pigmentation. If the same “carotenoid feather pigment” genes are found in cardinals and ducks, it may mean that ancient dinosaurs had brightly coloured feathers as well.

Thomas DB, James HF. 2016. Nondestructive Raman spectroscopy confirms carotenoid-pigmented plumage in the Pink-headed Duck. The Auk 133: 147-154

3D printed moa bone

A 3D printed moa bone held next to a screen shot of the 3D digital version. The 3D moa bone can be viewed at The moa bone was 3D printed by Tim Carr, Chief Ninja of Mind Kits (twitter: @mindkits). The moa bone was made available for scanning by Neville Hudson at the University of Auckland Geological Collections. is a digital gallery that allows you to explore some of New Zealand’s fauna through 3D models, wildlife images and audio. I add content to both and illuminatingfossils (although has been receiving a little more attention lately…).

Check it out:

Guest article at March of the Fossil Penguins

Fossil bird expert Dr Dan Ksepka kindly let me write a guest article for his blog, March of the Fossil Penguins. You can check it out here:

#Introducing R

R is an incredibly useful programming language that I often use in my research. For example, I use have used R to analyse XRF spectra, to study feather colours, and to look at the possibility of red-feathered dinosaurs.

If you are interested in learning to use R then check out my Introduction to R slides, which can be accessed from Slideshare. These slides provide a basic intro, including a few statistical tests for you to work with. In a future set of slides I will include the code for my spectral analyses.

#Living the dream

My academic journey so far.

My academic journey so far.

I have recently started a new position at Massey University in Auckland: Lecturer of Vertebrate Zoology (!!!!!). This is an amazing opportunity and I can’t wait to sink my teeth in. I wanted to take this opportunity to give a big thank you to everyone who has helped me along the way, and to name but a tiny fraction:

University of Otago: Professor Ewan Fordyce, Professor Russell Frew, Dr Marc Schallenberg

University of Cape Town: Professor Anusuya Chinsamy-Turan

Smithsonian Institution National Museum of Natural History: Dr Helen James, Dr Matthew Carrano, Dr Gary Graves, Dr Carla Dove, Christopher Milensky, Christina Gebhard, Brian Schmidt, Jacob Saucier

Arizona State University: Professor Kevin McGraw

And a very special thank you to Cushla McGoverin, Joanne Thomas, Murray Thomas, Hollie Steel, Dan Ksepka, Mark Clements and Brandon Gellis


It’s busy times at the moment and there are big plans afoot. Sorry blog, but we might be trains in the night for a little while longer.

#A problem with sand dunes

The West Coast National Park in the Western Cape of South Africa is a great place for spotting wildlife. In the southern reaches of the National Park, which is the distant background of this photo, lies the the Geelbek Dune system. Fossils recovered from the Geelbek Dunes have provided great insight into the ancient wildlife of the region.

The West Coast National Park in the Western Cape of South Africa is a great place for spotting wildlife. The Geelbek Dune System lies in the southern reaches of the National Park, which is the distant background of this photo. Fossils recovered from the Geelbek Dunes have provided great insight into the ancient wildlife of the region.

How old is a fossil from a sand dune? Fossils recovered from dune fields help us to reconstruct ancient environments. But how ancient is ancient? Thanks to Steno we know that the fossils are younger than the sand dunes they are buried in, and we know that the dune system is younger than the rocks underneath. But sand dunes are dynamic, shifting and reforming with every gust of wind and every drop of rain. Fossils can be winnowed out from depth and settle in newly formed layers, or simply be transported to the dune surface to sit alongside modern debris. Our usual methods for reading the age of a fossil are less reliable in dune environments – for an analogy, imagine pulling clothes out of a tumble dryer and trying to decide what order you first put them in.

We can try and solve this problem in a few different ways. One approach is to use  relative dating. When we don’t have the ability to place an absolute age on a fossil assemblage – fossil A is 12,000 years old and fossil B is 10,000 years old – we can instead place fossils in  an order of deposition – fossil A is older than fossil B. Relative ages are useful for tracking changes in ancient environments, and importantly, these ages can tell us about the natural disintegration of fossils over time.

Fossil ‘survivorship’ in the Geelbek Dune systems was the focus of a 2008 study by Nicholas Conard, Steven Walker and Andrew Kandel. Here the authors gathered an assemblage of fossils, placed them into size categories, and assigned a relative age to each one. Conard and colleagues observed that both dense and porous bones stood the test of time at Geelbek, in contrast to the standing paradigm, which states that dense fossil bones have a better chance of being preserved as fossils. Importantly, this means there is a good chance that tiny animals are also preserved from the ancient environment represented in the Geelbek Dunes assemblage. There is a big question looming over this conclusion though – how were the fossils assigned a relative age?

Conard and colleagues used colour, heft and other physical parameters to gauge the extent to which minerals had grown on and in the fossils. The authors reasoned that bones that had more minerals had been in the ground for longer, and hence where older. So, fossil bones were sorted into ‘mineralisation categories’ based on the perceived amounts of secondary minerals, and ‘mineralisation category’ became a proxy for burial duration.

This is where spectroscopy comes in. Professor Anusuya Chinsamy-Turan, my postdoc advisor at the University of Cape Town, spoke to Dr Kandel after he presented this work at a conference in Cape Town. Andrew and Anusuya agreed that studying the chemistry of the Geelbek fossils might make the ‘mineralisation categories’ (and the assessment of relative age in a dune system) a little more robust. Andrew brought the very precious fossils from Iziko South African Museum to the University of Cape Town, where I analysed the bones with a handheld x-ray fluorescence spectrometer. We were interested to see if the concentration of mineral forming elements agreed with the mineralisation category that had been assigned to each fossil.

Fossil bones from the Geelbek Dune system, sorted by mineralisation category. X-ray fluorescence was use to assess the elemental concentrations of mineral forming elements on these bones. The physically assessed mineralisation categories, and the chemical assessments from XRF, did not always agree. Image from Thomas et al. 2012. Permission for image use granted bythrough Rightslink.

Fossil bones from the Geelbek Dune system, grouped by mineralisation category. X-ray fluorescence was used to assess the elemental concentrations of mineral forming elements in these bones. The physically assessed mineralisation categories, and the chemical assessments from XRF, did not always agree. Image from Thomas et al. 2012. Permission for image use granted through Rightslink.

Well, we found a loose correlation between the mineralisation categories and the XRF data  (Thomas et al. 2012). To the original five categories we added a zeroth – modern bone. X-ray fluorescence spectra could distinguish the lower categories (zero to three) from the higher categories (four to five), but it couldn’t separate out individual categories. We were able to see a range of elemental concentrations, but the chemical data was not a strong match for the physically assessed ‘mineralisation categories’. From a chemical perspective, the ‘mineralisation categories’ did not reflect mineral accumulation.

So what does this mean? The original conclusion about bone ‘survivorship’ is mostly valid – there are both dense and porous fossils with very high elemental concentrations of mineral forming elements, and hence they have may been buried the longest. Unfortunately, I don’t think physically assessed ‘mineralisation categories’ can give accurate relative ages by themselves. Fortunately, x-ray fluorescence is non-destructive and portable, so we could easily supplement the physical assessments with chemical data. Together, these assessments can help assign relative ages to fossils recovered from sand dunes.

Conard NJ, Walker SJ, Kandel AW. 2008. How heating and cooling and wetting and drying can destroy dense faunal elements and lead to differential preservation. Palaeogeography, Palaeoclimatology, Palaeoecology 266: 236-245

Thomas DB, Chinsamy A, Conard NJ, Kandel AW. 2012 Chemical investigation of mineralisation categories used to assess taphonomy. Palaeogeography, Palaeoclimatology, Palaeoecology 361-362: 104-110

Behind the curtain at the Smithsonian

A week ago I was at the 72nd Annual meeting of the Society of Vertebrate Paleontology. Some of the research presented there has been showing up online – like T. rex eating Triceratops, and descriptions of giant sea creatures. I presented research I am working on at the Smithsonian and it lead to some great conversations with some very interesting people – including two incredible paleoartists, Tyler Keilor and Julius Csotonyi. Before I talk about the conference, I just want to give a bit of background to my work, and mention the mind-blowing collections at the Smithsonian.

I am based in the Division of Birds, in the National Museum of Natural History. Without a doubt, the Natural History Museum is one of the greatest places on Earth. The specimens on display in the public galleries are a small fraction of the amazing things that have been collected over the years. I have the incredible privilege of being among the relatively few people that gets to step behind the curtain and see the wonders that are not on public display.

A large part of the Division of Birds is occupied with the study skin collection and this is what I want to talk about here. I have been working with these skins quite a bit lately and so it is only fair that I do my part to add to the collections. So, under the tutelage of Carla Dove, James Whatton, Chris Milensky, Brian Schmidt, and mostly, Christina Gebhard, I have been learning to prepare birds as study skins. The study skin collection receives many visiting researchers every year, from within the United States and around the world, so it is important to maintain and grow the collection. I am part of a small class of novices that are being trained in the sacred art of preparing study skins. How does this relate to the spectroscopy of fossils? All in good time. First, let me tell my story about how a simple lad from Thames, New Zealand has helped to grow one of the most important natural history collections in the world.

It began in earnest with a male house sparrow, Passer domesticus. I will skip the prologue and move to the part where the sparrow is sitting in front of me on a long table in the Museum prep lab. Our small group of trainees, each equipped with a house sparrow, is clustered either around Brian or Christina, who are also seated with a bird. Brian and Christina, and Chris, working at the high bench on the other side of the room, tell us the number of birds they have prepared and the time it would take them to produce a study skin from an inert sparrow. Thousands and 15 to 30 minutes. We would spend three hours that morning moving through the first set of steps, converting our deceased seed eater into a feather pelt. A quick break for lunch – a true testament of appetite after our mornings activities – and we were ready for the final steps. Cotton wool to fill, cotton thread to seal. For the second time that day the sparrows looked like silently sleeping woodland creatures. The finishing steps involved carefully pinning the bird to a spongy plastic board, making sure the tail was evenly fanned and the head and wings were perfectly straight. After a few days the pins were removed and the sparrow was set in an immortal pose.

Anne Wiley and I have just received the house sparrows that will be prepared as study skins. Anne is a Peter Buck postdoctoral fellow and studies isotopes from seabird tissues. Photo credit: Christina Gebhard.

On the left, foreground to background, are myself, Brian Schmidt and Megan Spitzer (just visible behind Brian). Anne Wiley is sitting opposite me and Hanneke Meijer is sitting across from Megan. It is not a coincidence that I am sitting near Brian, our tutor – preparing study skins is crazy challenging. Photo credit: Christina Gebhard.

The study skins are filled with cotton. I don’t think I need to go into the details. Photo credit: Christina Gebhard.

A final and critical step involves pinning the specimens. This controls the final appearance of the study skin. Photo credit: Christina Gebhard.

These study skins are eternal with proper care, and many tens of thousands of birds have been prepared in the museum’s long history. You might think this is morbid – I have no comment either way, but I will leave you with the following thought. Below is a bird that I have used in my studies. My methods are non-destructive and they use instruments that were built inside of the last decade. This bird was collected in 1883, decades before the technique I use was even discovered, let alone designed into a computerised instrument. This specimen was available to researchers 100 years before I was born and I expect it will outlive me by at least as long. So, there is a very long term, possibly eternal value to these specimens. I find it easy to see the value of these historic collections in a modern world that is pushing species to extinction.

Some birds in the collection are really old – this red-capped robin was collected from Australia in 1883.

Thanks Christina for inspiring this post!

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