Lab Updates February 2017

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It’s been an exciting few weeks for all of us here at Team Macrobird with February seeing the first paper from our project published in Nature. We’re thrilled to finally have this out in print after over two years of data collection, analysis and the hard work of citizen scientists from around the world. We’ve already received some wonderful feedback and mentions in publications from the New York Times to the Yorkshire Post. You can learn more about the paper and our findings in our recent blog post or view it in full here.Nature issueAlongside this, the first portion of our data has now been made available via the Natural History Museum’s Data Portal– a dedicated space to ensure the museum’s collections, research and associated data is accessible to everyone. Whilst our website markmybird.org provides a gallery of approaching 8,000 3D scans, the data portal provides more in-depth data for an initial 2,028 specimens, comprising raw scan data and multiple landmarks for each as well as an adjoining spreadsheet featuring sex, museum registration number and taxonomic details. By making this data freely available we hope that more questions regarding beak shape can be investigated and answered by researchers, students and anyone with an interest well into the future.

NHM Data Portal

We’ve also had a new research assistant join our team collecting data at the Natural History Museum at Tring- Michael Jardine will be helping photograph the plumage of the world’s birds for the next six months. So too, Yichen He began his PhD towards the end of last year, working with PI Gavin Thomas to characterise phenotypic data for MicroCT scans of zebra finches.

Data collection: 3D scanning & UV photography

Whilst our first paper explores bill shape at genus level, we are still aiming to build a far more comprehensive dataset of bill and plumage information- covering as many of the approximately 10,000 extant species of bird as possible. This means data collection will be continuing full force, using the Natural History Museum’s ornithology collections at Tring.

Scanning has been going ahead in small increments this month with a number of new world warblers, australian robins and ovenbird species soon to be added to our site. Next month however, we aim to have a new push to complete the Furnariidae- more on this later.

sulphur crested cockatooIn contrast, towards the end of this month we moved over to having two photography light tents in operation for the first time. Not only will this increase the number of specimens we are able to image but the new, second light tent will also allow us to photograph larger passerines and many of the non-passerine families we choose to focus on.

Even better, this month we reached a significant milestone- with 25% of all world bird species imaged. This equates to a whopping:

12265 specimens photographed: we are selecting up to 6 specimens of each species, both male and female
73590 photos taken: six photographs- dorsal, ventral and lateral in both UV and human visible spectrums- of every selected specimen
22.68% of families
29.41% of genera
25.94% of species

MarkMyBird

Having only just celebrated the 1000th volunteer signing up to our crowdsourcing site markmybird.org last month, February has seen an amazing increase in new members with many first-time landmarkers contributing to our ongoing study through citizen science. We now have in excess of 1400 registered users with over 1000 bills landmarked this month alone, brilliant stuff!

great billed hermit

Landmarks placed along the beak edge of the Great-billed hermit (Phaethornis malaris), a species of hummingbird.

However, with scans for almost 80% of world bird species uploaded and ready to view on our website, the hard work isn’t over yet! If you’ve just heard about our project, have an interest in ornithology, are interested in the way historical museum specimens are used in modern science or are just curious to see what it involves to become a citizen scientist, head on over! We’ve even made a short video, showing the basics of landmarking a bill from beginning to end:

#BeakoftheWeek

Maui parrotbillOur twitter competition #BeakoftheWeek takes place every Wednesday- a chance to test your bird identifying skills against our 3D models. A favourite pick from this month was the Maui parrotbill (Pseudonestor xanthophrys), an unusual and misleading bill shape that really kept people guessing! Everyone is welcome to join in and a place on our leaderboard (as well as bragging rights) is up for grabs…

Other news

Macrobird post-doc Chris Cooney was lucky enough to undertake a research visit to the University of Chicago- spending time with Trevor Price and his lab group before scanning some hard-to-find species from the collections at the world famous Field Museum. You can read more about Chris’ American adventure here.

Finally, congratulations are in order for Will Wood and Louie Rombaut, both of whom undertook summer research projects last year as part of the University SURE (Sheffield Undergraduate Research Experience) scheme. Both Will and Louie spent time with us collecting data at the Natural History Museum in Tring and presented their findings at a recent open evening.

louie, will, chris

Mega-evolutionary dynamics of the adaptive radiation of birds

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Nature bills

The idea to 3D scan the bills of the world’s 10,000 bird species from museum collections has always seemed like an ambitious undertaking. However, after two years of data collection, months of analysis and the input of hundreds of citizen scientists, the first study resulting from our work was published in Nature last month.

This initial, wide-ranging exploration of bill diversity, compared over 2000 species from across all genera, considering the full range of present-day bill shapes.

The diversity we see in bill shape today is extraordinary and studying this characteristic can tell us a lot about species and how they interact with their environment- from foraging, hunting and eating food, to preening and nest building. Traditional methods of gathering information relating to bill form have often relied on length, depth and width measurements alone, missing many key elements of shape, such as curvature. By 3D scanning bills, we have been able to capture far more detailed information, providing a true reflection of bill diversity.

It would have been impossible to collect this information from birds in the wild so our study has been reliant on the incredible ornithology collections at Manchester Museum and the Natural History Museum in Tring. These archives of biodiversity have allowed us to create fantastically detailed models through access to such a broad variety of species, alongside curatorial expertise and work space.

One of the most novel aspects of our study was the way in which much of our initial data- the 3D scans- was processed through the input of citizen scientists from around the world. With each scan requiring landmarking by at least 3 different people, this in itself was a huge task and one that would not have been possible without such a collaborative effort. By helping us place key points and trace edges on every scanned bill, online volunteers assisted in turning these hugely complex 3D models into data that could then be analysed.

From this we have been able to highlight that the majority of bill diversification evolved quickly and, once extremes of shape were reached, the amount of change slowed down significantly as birds began to fill increasingly narrow ecological niches. As a result of this initial fast change and huge variety of form, birds have been able to exploit the equally wide range of habitats and sources of food.

The full paper can be read here and, excitingly, has also received some fantastic press attention, including a discussion of our findings with project PI Dr Gavin Thomas on both the Nature podcast and BBC Inside Science (interview starts at 20:00 minutes) – if you prefer a good listen, rather than a good read. A selection of our online coverage is listed here:

Audubon – Post-docs Dr Chris Cooney and Dr Jen Bright spoke to Audubon magazine about our findings and how they build upon our previous understanding of bill diversity.
BBC Science & Environment – ‘How birds of a feather evolved together’
New York Times – ‘Finding the Speed of Evolution in a Study of Bird Beaks’
Natural History Museum – Our study wouldn’t have been possible without the incredible ornithology collections at the Natural History Museum. This statement highlights our reliance on this resource as well as how our data can be used in the future.
University of Sheffield – A summary of our project and findings as part of the Department of Animal & Plant Sciences at the University of Sheffield.

If reading about our work has caught your interest, it’s not too late to contribute. Our crowdsourcing site markmybird.org is still very much up-and-running as we continue to increase our data relating to all extant species. Whether you want to browse our scan gallery or have a go at landmarking, everyone is welcome.

Chicago: lab visits, bird collections & the field museum

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Chris in Chicago

In early January, I headed stateside to begin a month-long visit to the University of Chicago with the main aim of spending some time working with Trevor Price, a world-leading expert on speciation, species diversity and colour vision in birds. Trevor began his research career studying Darwin’s finches on the Galapagos Islands with Peter and Rosemary Grant, and since then has gone on to have a long and distinguished career working on a huge range of Chris scanquestions related to the ecology and evolution of birds. Many of these insights were synthesised in his 2008 book “Speciation in birds”, which discusses the factors regulating the formation of new bird species for almost every conceivable angle. The wide-ranging nature of Trevor’s approach to understanding bird evolution is also reflected in the diversity of his lab group, whose current research interests stretch from understanding competitive interactions between ants and birds in the Indian Himalayas through to the role of chromosomal rearrangements in the formation of new bird species. The opportunity to spend time in such a vibrant research group that is doing so much exciting research was a great privilege, and I would like to say a big thank you to Trevor Price and his lab group for their hospitality and for the huge amount of inspiring discussions during his visit. A special thank you must also go to Macrobird PI Gavin Thomas, who encouraged and supported me in this visit from first to last. Thank you to everyone who made the visit such a success!

Field Museum

Aside from talking all things evolutionary with Trevor Price and his lab group, while in Chicago I also took the opportunity to visit the world-famous Field Museum of Natural history and add to the ever-expanding 3D beak-shape dataset. The Field Museum is one of the most prominent public museums in the world and is also home to one of the largest collections of natural history specimens. Like many natural history collections, a vast number of these specimens are birds, providing the perfect opportunity to locate and scan several hard-to-find species that are not represented in UK collections. In total I managed to add an extra 18 species to the dataset while out in Chicago, including several species of parrot (such as the blue-headed macaw, Primolius couloni) and Newell’s shearwater (Puffinus newelli) .

Chicago skyline

As a slight aside, one interesting—and perhaps slightly unfortunate—fact about the Field Museum is that every year their bird collection grows significantly owing to the fact that many hundreds of thousands of migrating birds perish after colliding with buildings in Chicago’s famous skyline. Many of these unfortunate birds are collected by museum volunteers or members of the public and then passed on to the Museum, who endeavour to preserve as many as possible in an effort to make the best of a bad situation. Because of the scale of the problem, the City of Chicago now takes steps to prevent as many bird collisions as possible, by modifying buildings and people’s behaviour, including encouraging workers to ensure office lights remain off overnight during migration periods. Again, the opportunity to spend time working at the Field Museum and to learn more about the role of the Museum in the fight against bird collisions was a huge privilege – a big thank you to Shannon Hackett, John Bates, Ben Marks at the Field Museum and Graham Slater at the University of Chicago for making that possible.