Lab Updates: March/April 2017

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The last couple of months have flown by with lots of goings on amongst all of us here on team MacroBird.

Data Collection

Throughout March, we were joined by two postgraduate students from the department of Animal and Plant Sciences, both undertaking projects utilising the data we are collecting from museum specimens.
As part of their research projects, both Jade and Sarah spent a few weeks with us at the Natural History Museum in Tring.

JadeJade’s project is looking at plumage diversity across parrots (the family Psittacidae)- one of the largest groups in our taxonomy. The photography side of our project has been initially focussing on the passerines, so this was also our first attempt at imaging birds outside this group using our current setup. Whilst the majority of passerines fit within our small photography calibration (with some obvious exceptions- the immense tail feathers of some birds of paradise, for example), the Psittacidae encompass a huge variety in size. From the tiny hanging parrots, measuring only a few centimeters in length to the huge scarlet macaw, only just fitting within the limits of our light tent. Working our way through the family also highlighted the extraordinary spectrum to be seen within its plumage- from bright, vivid primary colours, to pastel gradients and dark ombres… just amazing.

parrots

Photographing the Psittacidae also raised a couple of interesting issues we haven’t really had to consider before. As many species of parrots have made popular pets, a fairly significant proportion of the specimens within the museum’s collections were either bred or lived in captivity. As diet can be a factor in plumage colouration, birds kept in captivity may develop colour abnormalities that could produce erroneous results if included in our dataset.parrot As such, we have had to be extra careful in interpreting the information provided on specimen labels to try and ensure only wild specimens are included in our study.

For much the same reason as their proliferation in captivity, a number of species are now classed as endangered (extinct species are not currently being included in our study), including the wonderful kakapo, but can still be included in our research thanks to the museum’s distinct E&E collection. It’s a huge privilege to work with such rare material and whilst our attitudes to collecting today have, thankfully, evolved and are now held to modern ethical standards and legislation, it does bring home the importance of preserving these existing historical collections for future research.

Furnarius rufus

Our scan of a Rufous hornero bill alongside an example of nest built by ovenbirds of this genus. Photograph by Darios Anches, CC BY-SA 2.0

SarahSarah’s work, concerned with the scanning side of our project, will be focusing on the ovenbirds (Furnariidae), a large family of primarily South American passerines, widely known for their incredible nest-building skills. Despite approaching 90% of world bird species processed for the bill component of our study, the ovenbirds have remained one of the least represented taxa in our dataset as a result of re-curation. Sarah’s project gave us the opportunity to correct this, with us successfully having now scanned every available species from the NHM’s collections. With a renewed push on scanning, this has seen a new batch of 3D scans available for landmarking on our crowdsourcing site markmybird.org for citizen scientists (old and new!) to landmark for inclusion within our study.

Alongside these individual projects, our usual data-collection has been continuing at pace. With two set-ups, able to process a wider variety of specimen sizes, we have been steadily working our way through all possible passerine families. Ranging from birds of paradise to weavers, parrotbills to waxbills over the last few weeks alone, our completion percentage has seen a real jump to:

22,047 specimens photographed: we are selecting up to 6 specimens of each species, both male and female
132,480 photos taken: six photographs- dorsal, ventral and lateral in both UV and human visible spectrums- of every selected specimen (with a few additional ones for extra large birds)
Approaching 46% of world bird species

Mark My Bird & Beak of the Week

The number of citizen scientists now subscribed to our citizen science site is around the 1700 mark and we are slowly nearing our targets. Alongside our usual day-to-day landmarking and weekly twitter competition #beakoftheweek, we also held a markmybird-athon, linking with students from the University of South Florida, where Dr Jen Bright- one of our original postdocs- is now based, for an evening of landmarking. It’s great to see how our data and website are being used to assist in teaching, engaging with science or any number of other uses people can think of.

A large portion of our data is now available in full via the Natural History Museum’s data portal, with lots more of scans available via our own website– we hope this resource will be used by others for a range of uses and to assist in answering lots of questions beyond our current study. If you’ve used our data, we’d love to hear about it!

Other News

3D printed bills

In other goings on, our group took part in the University of Sheffield’s annual Discovery Night- a brilliant opportunity to present our project to future generations of researchers. We had a great time talking about macroevolution, the values of natural history collections, the joys of 3D printing and the importance of citizen science for wide-ranging projects such as ours.

You can learn more about the event and our offering in a recent blog post, here.

 

Lastly for this month, team PhD students Angela Chira and Emma Hughes both presented posters discussing their projects and findings to-date- congratulations all round!

Angela & Emma

 

 

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.

Happy New Year-ish!: Lab Updates January 2017

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It’s been another busy few months for all of us here on team MacroBird and time has flown since our last update at the end of the Summer. Team changes, data collection, paper writing, outreach and PhD-beginnings have kept us occupied as we start another year of all things macroevolution!

Data collection will be continuing throughout 2017 using the fantastic ornithology collections at the Natural History Museum at Tring. With two remaining research assistants and a new member joining the team, both scanning and photography will be pushing on over the coming months. Emma Hughes, one of our original RAs, is now based with the rest of the team in Sheffield, beginning a NERC-funded PhD exploring the impact of global change on avian diversity.

IMG_8589At the end of September we took part in Science Uncovered- the Natural History Museum’s European Researcher’s Night event- for the second year running. MacroBird PI Dr Gavin Thomas gave a talk about our research and crowdsourcing project whilst we demonstrated our use of the collections with our scanners, specimens and citizen science website. You can read more about the night here.


Data collecting in Tring: 3D scanning & UV photography

Having achieved approaching 90% of species processed (with over 75% successfully scanned), we’re well on our way to completing the scanning component of our project. The remaining species that are available within the Natural History Museum’s collections will be scanned over the coming months and added to our crowdsourcing site MarkMyBird, increasing the diversity of bills available to view and landmark through our galleries. Remaining target families include the Tyrant flycatchers (Tyrannidae) and Ovenbirds (Furnariidae).

Finches

Clockwise from top left: I’iwi or Scarlet honeycreeper (Drepanis coccinea), Brown-capped rosy finch (Leucosticte australis), Long-tailed rosefinch (Carpodacus sibiricus), Goldfinch (Carduelis carduelis)

As such, data collection has had a shift of focus in recent months as our efforts have been turned from scanning to photography. After some alterations to the equipment we are using whilst imaging the plumage (male and female) of every extant species in both the human visible and ultraviolet ranges we continue to photograph our way through the passerines. We are currently progressing through the brilliantly varied Fringillidae family, including everything from the European goldfinch (Carduelis carduelis) to the fascinating Hawaiian honeycreepers.

MarkMyBird 

Fratercula arctica- Atlantic puffinOur crowdsourcing site markmybird.org still needs you! We are aiming to scan the bills of as many as possible of the world’s 10,000 species of bird and now have almost 80% of this total uploaded and ready for you to view and landmark on our dedicated crowdsourcing website. In order to include these incredibly detailed 3D scans in our study, we need citizen scientists to help us ‘landmark’ these models, placing key points and traMagpie2cing curves and edges. The process allows you to get up close to this fascinating and massively variable area of avian anatomy and contribute to this wide ranging research. We have everything from extinct and endangered species to old favourites such as the Atlantic puffin (Fratercula arctica– left) and the Eurasian magpie (Pica pica– right) to explore. This month we reached a fantastic milestone, exceeding 1000 registered users on the site- brilliant stuff! 

#BeakoftheWeek

Our weekly twitter competition #BeakoftheWeek is still going strong with some especially unusual choices in recent weeks- including the little spotted kiwi (Apteryx owenii), as pictured below. Anyone is welcome to join in and have a guess every Wednesday- you might even be first to get the correct answer and make your way onto our extremely prestigious leader board.

kiwi

Publications

After over two years of data collection, thousands of 3D scans (and even more specimens assessed, measured and processed), the contributions of scores of citizen scientists and months of analysis, we’re thrilled to say that the first paper resulting from this project has been accepted for publication. The paper will available to read very soon and we’ll be sure to make lots of noise when the publication date arrives- watch this space!

Images

All scans (c) of Team Macrobird and The Natural History Museum (London and Tring)
Finch photographs: credits provided.

1000 citizen scientists- thank you!

facebooktwitterCitizen Science- Thank You

Since our crowdsourcing site markmybird.org launched in September 2015 we have had scores of brilliant citizen scientists offer their time, skills and curiosity to this research project.

This month our 1000th citizen science volunteer signed up to the site- a fantastic milestone!

This year will see the publication of our first paper resulting from this study, an achievement that has been aided in no small part by this generosity from interested individuals. Every landmarked scan has helped us reach this stage and will assist in increasing our understanding of avian evolution.

The work isn’t over yet though- data collection is still continuing in museum collections and more scans means more landmarking! Whether you want to learn more about research of this nature, wonder about the ways museum specimens are utilised in modern science, are interested in the amazing diversity of birds or just curious about what we’re up to, markmybird has lots to explore for everyone. No matter what your background, age or experience, anyone can sign-up and have a go, so head on over!

Science Uncovered 2016

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After having a great time showcasing our research last year, we were invited back to take part in the Natural History Museum’s offerings for European Researcher’s Night 2016.

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One of the best parts of our role as Research Assistants is the freedom to work with the museum’s collections everyday, moving across all taxa and, at times, preparation methods (study skins, spirit and skeleton specimens) as data collection requires. Without access to such incredible collections, wide-ranging studies such as ours simply wouldn’t be possible and the importance of highlighting the many uses of such diverse and well-maintained resources is becoming increasingly important. When they were collected, primarily during the heyday of Victorian exploration and collecting, nobody could have anticipated the ways in which these specimens would be used. Yet, by preserving them for future generations, this historical material can now be utilised in contemporary science projects, continuing to help us understand the evolving biodiversity of the planet.IMG_8576

There’s no better way to show this than with the real thing so we selected an array of study skins- exactly like those kept in the natural history museum’s ornithology research collections and used in our study- for people to explore up close. Alongside these were a selection of skulls from the museum’s handling collections, ranging from the large, stocky bill of the marabou stork and the curved, pointed bill of the kestrel to the filter feeding bill of a flamingo and the mud-probing bill of an ibis.

With our portable 3D scanner in tow, we were alsIMG_8578o able to give live scanning demonstrations with anyone welcome to have a go at creating their own 3D digital bill model- not as easy as it looks! By demonstrating how we move from a physical specimen to a detailed digital replica it becomes clear why this is only possible with study skins- it would be practically and logistically impossible to replicate this process with living birds in the field.

One of the great things about talking to the public about our research in particular is that anyone interested can actually become a citizen scientist and contribute to the study through the wonders of our crowdsourcing site markmybird.org. With over three-quarters of world bird species now uploaded, there are thousands of bills to explore up-close via our gallery as well as opportunities for anyone to have a go at landmarking our 3D scans, assisting with our analysis and helping answer key questions about avian evolution.

In addition to our stand, Principal Investigator Gavin Thomas gave a talk introducing our research and its reliance on ornithology collections. Situated in thIMG_8588e public galleries of the Natural History Museum at Tring- a Victorian zoological collection and display space donated to the NHM by its founder, Walter Rothschild- it was a great opportunity to highlight the value of largely unseen research collections and highlight the questions we are hoping to answer.

Alongside our offerings were demonstrations from expert taxidermists showing how museum specimens are preserved and the opportunity to see some of the manuscript treasures of the Natural History Museum being made available through the digitisation efforts of the amazing Biodiversity Heritage Library. There was also the opportunityscarlet rumped trogon drawing to talk to curators about contemporary museum issues: from a stand exploring the use of bird skins in helping identify material picked up by HM Customs, blocking aircraft engines or contaminating foods to discussions concerning how natural history museums deal with selecting (and declining) new acquisitions.

You can learn more about European Researcher’s Night here, the Natural History Museum at Tring here and us on our team website, twitter and crowdsourcing site!

 

 

Lab Updates August 2016

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It’s been another month of change here at Team MacroBird with two of our original team members moving on to adventures anew.

14100385_10104845417626067_3774523421000460044_nPost-doc Jen Bright (green t-shirt, thumbs up), geometric morphometrics whizz and all-round human-encyclopedia, is taking up a new post as Assistant Professor of Geosciences at the University of South Florida.

Research assistant Elliot Capp (cheesy grin, beard), mechscan master, brains behind #beakoftheweek and all round zoology ace is off to become a teacher extraordinaire.

To mark these departures, all of us on team MacroBird went on a trip to South Kensington to see the new Colour and Vision exhibition at the Natural History Museum. We saw the octopus Charles Darwin kept as a pet during the voyage of HMS Beagle, lots of very cool trilobites, some impressive iridescent butterflies, plenty of birds (Gouldian finches galore) and learnt that ‘cyborg artist’ is someone’s actual job title.

Colour & Vision

Data Collection in Tring: 3D scanning

With all this change on the horizon, we’ve been pushing to meet as many data collection targets as possible. This involves progressing through remaining large families and returning to those we moved on from whilst nearing completion.

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3D Scan of Mauritius Kestrel (Falco punctatus) from www.markmybird.org

One such example is the birds of prey which are, in general, great to scan. Although some genera have obstructing feathers and bristles, most have clear landmarks and well-defined ‘cutting edges’ that are clearly picked up by our scanners. One of the last non-passerine families in need of completing were the Falcons and Caracaras (Falconidae) – with all the larger species having already been imaged on the bigger of our two scanners (the R3X) we still had a number of significantly smaller, finer bills remaining. After what feels like months of Hummingbirds (Trochilidae) and Sunbirds (Nectariniidae), finishing a family with such chunky, nonlinear bills was a breeze!

On the other end of the scale, we had some really big species that needed our attention. Both the Rheas (Rheidae) and the Cassowaries (Casuariidae), two of the tallest and heaviest living birds, are primarily stored as either mounted taxidermy or in a compact, curled-up form within the collections due to their size and shape. Selecting a specimen suitable for scanning can be a real challenge as we need to access the bill from all angles in order to capture enough images to build a 3D model. Rather than simply rotating the specimen (as we do with small passerines for example) we have to get a bit creative and move the scanner around these huge specimens, carefully manoeuvring the long, brittle necks to ensure no damage is caused. In moments like this, such as scanning the last of the cassowaries (below), we realise just how peculiar parts of our job are…

cassowary

Data Collection in Tring: UV photography

This month we’ve been photographing the plumage of some really interesting species- with the Pittas (Pittidae) being a particular favourite.

The Pittas are a small family of charismatic birds found across Asia, Africa and Australasia. They are small-medium in size and stocky in form with very short tails and comparatively long legs. What really sets them apart from other species is their brightly coloured plumage (particularly interesting for this element of our research), in vivid shades of red, blue and purple. In the wild, Pittas are notoriously difficult to pinpoint as they are highly secretive and perhaps because of this, they often feature on lists of species birders particularly want to see (including one or two members of our team!). 

Being able to access these species within museum collections allows us to use an ultraviolet filter when photographing the specimens, which provides us with a different perspective of this fantastic plumage. Certain patches of colour positively glow- as you can see from our images of the Azure-breasted Pitta (Pitta steerii) below. 

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MarkMyBird and #BeakoftheWeek

We’ve recently been experiencing some technical problems with our crowd sourcing website markmybird– thank you to everyone for being so patient and for keeping us updated. Everything is now up-and-running again and we’ve uploaded more than a thousand new 3D bill models for you to view and landmark, even more reason to revisit or sign up and give citizen science a try!

black-winged stilt

Our weekly twitter competition #BeakoftheWeek has seen some great picks this month, including a number of first-time guessers and winners. Chris Packham was successful in spotting the black-winged stilt (above) in record time, followed by the hen harrier in his honour. There are still thousands of species to pick from so the competition is far from over, join us on twitter every Wednesday and give it a go.

Images

All images (c) of Team Macrobird and The Natural History Museum

 

Lab Updates July 2016

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HummingbirdsTime is flying on all sides of project MacroBird. We have some big changes on the horizon in coming months with scanning targets to meet, team members moving on and tweaks to some of our data collection processes.

This month we were joined by a second undergraduate from the Department of Plant and Animal Sciences at Sheffield. After being awarded a SURE (Sheffield Undergraduate Research Experience) grant, Louie Rombaut spent a fortnight with us at the Natural History Museum, shadowing our work and making use of the fantastic ornithology library collections. He will be using our scans to investigate hummingbird feeding behaviour for his summer project- it’s great to see the data being put to use already!

Data Collection in Tring: 3D scanning and UV photography

Hummingbirds have featured heavily in our lab updates for the last couple of months and July is no different. These long, sometimes curved and often extremely fine bills have really put our scanning equipment and skills to the test! As such an interesting family however, they are one of our priorities so we have continued to work through the huge number of species, alongside the equally varied and challenging tyrant flycatchers.

One of the things we don’t often talk about on this blog are the practicalities of working with museum specimens. For the scanning and photography sides of the project, we are using the birds in quite different ways- focussing on different aspects that require very different approaches for data collection.

Whilst the bill scanning uses only one specimen and is a steady, time-consuming process with the birds virtually static, the photography method requires us to sample up to six specimens of every species, rotating the birds to capture all angles of their plumage. Varying vastly in condition, size and preparation method, the research skins need to be handled securely and with care so having the right equipment to allow us to do this is really important.

Scanning

As you might expect, there isn’t a big market for this kind of product so there is a good amount of experimentation, testing and DIY involved. This month we have been working on a new ‘stand’ to support a wider variety of specimen sizes for photography and will begin putting it to the test next month.

MarkMyBird and #BeakoftheWeek

This scanning focus does mean there is now a wide variety of Trochilidae scans ready for landmarking on our crowdsourcing site MarkMyBird so, if you’re interested in seeing the variety of bill form within this fascinating family, head on over. You can always have a browse through our gallery to look at some interesting species or get a feel for the 3D models we are generating, it might just inspire you to sign-up and contribute to this vast study.

Frilled coquetteLophornis magnificus)

Frilled coquette (Lophornis magnificus)

There have been some great picks of species on #BeakoftheWeek lately, including this weeks challenge- the Apostlebird. You can read more about these mudnesters in our most recent blog post here.

We’ve also written about a #Beakoftheweek pick from a few weeks back- the reedhaunters– a pair of species first collected by Charles Darwin aboard HMS Beagle with a fascinating taxonomic and historical background, just a click away on our team blog.

John Gould's original illustrations of the Reedhaunters, with Limnoctites rectirostris thought to have been painted directly from the type specimen

John Gould’s original illustrations of the Reedhaunters

 

Images
– The Chilean Woodstars (Eulidia yarrellii), from ‘A monograph of the Trochilidæ, or family of humming-birds’ by John Gould. Courtesy of the Biodiversity Heritage Library: http://dx.doi.org/10.5962/bhl.title.51056
– Photograph of a bird being scanned and 3D scan of the frilled coquette, copyright Natural History Museum, London and Tring.
– John Gould’s illustrations of the Reedhaunters (Limnoctites rectirostris and Limnornis curvirostris) from The zoology of the voyage of H.M.S. Beagle. Courtesy of the Biodiversity Heritage Library: http://dx.doi.org/10.5962/bhl.title.14216

Lab Updates June 2016

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Team2

June saw team member Chris Moody (dog whisperer, last on the right) move on from his role as photographer-extraordinaire to challenges anew. Alongside our farewells to Chris, the usual data collection and analysis have been keeping us all busy..

We were also joined by an undergraduate from the Department of Plant and Animal Sciences at Sheffield, Will Wood, for a fortnight. After successfully being awarded a SURE (Sheffield Undergraduate Research Experience) grant, Will (who is interested in how UV plumage is affected by the environment, with a particular focus on South American suboscine passerines) came to shadow the team during data collection at the Natural History Museum, having a go at photography, scribing and using these amazing collections.

Data Collection in Tring: 3D Scanning

Haeckel HummingbirdsThis month we finally finished scanning the majority of the sunbirds (Nectariniidae), a massive task requiring lots of patience! We are still left with a number of large families with narrow, fine or bristly bills to occupy us, including the tyrant flycatchers (Tyrannidae).

A current target remains to continue working our way through the more than 300 species of hummingbird (Trochilidae). This month, we scanned some species of Lophornis, a genus of particularly tiny hummingbirds known as the coquettes. These fantastic birds have some of the most outlandish plumage, with the males displaying particularly colourful crests and markings.

Many of the hummingbirds have brilliant names, and some of our favourites from recent weeks include the festive coquette (Lophornis chalybeus), the bronze-tailed plumeleteer (Chalybura urochrysia), the blossomcrown (Anthocephala floriceps) and the glowing puffleg (Eriocnemis vestita).

To date we have scanned:

  • 7159 (71.64%) of species
  • 3338 (82.38%) of species from island families
  • 3893 (62.25%) of passerines
  • 3263 (81.03%) of non-passerines

Data Collection in Tring: UV and Visible Photography

The Common Starling (Sturnus vulgaris)

The Common Starling (Sturnus vulgaris)

One of the main families we have been photographing this month are the Starlings (Sturnidae) – displaying some of the most impressive iridescence we’ve come across yet. Even the Common Starling (Sturnus vulgaris), with its white feather tips and glossy greenish, blue, and purple sheen, has beautiful, complex plumage when viewed up close.

Lamprotornis Starlings. Above Left: Superb Starling (Lamprotornis superbus), Above Right: Burchell's Starling (Lamprotornis australis), Below: Emerald Starling (Lamprotornis iris)

Lamprotornis Starlings. Above Left: Superb Starling (L. superbus), Right: Burchell’s Starling (L. australis), Below: Emerald Starling (L. iris)

Our process of imaging each specimen requires a series of single dorsal, ventral and lateral shots. These static images don’t necessarily display this extraordinary iridescence in all its variety (as with these photographs taken in the field) but will allow us to compare and assess the extent to which, if at all, these species utilise UV reflecting plumage.

To date we have reached:

  • 69 (35.57%) of families
  • 2654 (26.56%) of species
  • 12264 specimens: we are selecting up to 6 specimens of each species, both male and female
  • 75384 photographs: six photographs- dorsal, ventral and lateral in both UV and human visible spectrums- of every selected specimen

Mark My Bird

Our crowdsourcing site markmybird.org has now exceeded 840 registered landmarkers- with 3D bill models for over half of all extant world bird species available, there is a huge variety to view and landmark. As mentioned above, we have recently been working on scanning the bills of as many species of hummingbird as possible so these will soon be uploaded for people to explore with other new species regularly added as they are imaged from the museum’s collections. If you would like a go, simply visit our site markmybird.org and sign up, everyone’s efforts- however big or small- will help contribute to this huge research project.

#BeakoftheWeek

Our twitter competition #BeakoftheWeek has continued every Wednesday (plus the occasional surprise Thursday). Everyone is welcome to join in and have a go at guessing the species of bird from one of our fantastic 3D bill models. One of this month’s challenges was the straight-billed reedhaunter (Limnoctites rectirostris), pictured here (more on this bird at a later date). If you think you’ve got what it takes, have a guess and perhaps even make it into our leaderboard!

Publications

Cooper, N., Thomas, G.H., & FitzJohn, R.G. (2016). Shedding light on the ‘dark side’of phylogenetic comparative methods. Methods in Ecology and Evolution, 7(6): 693-699.

Images

Page from Ernest Haeckel’s Kunstformen der Natur (1904), showing a variety of hummingbirds (Trochilidae) is out of copyright

Common Starling (Sturnus vulgaris) taken by Koshy Koshy is licensed under CC BY 2.0

Lamprotornis Starlings
Above Left: Superb Starling (Lamprotornis superbus) taken by Sumeet Moghe is licensed under CC BY-SA 3.0 
Above Right: Burchell’s Starling (Lamprotornis australis) taken by Bernard DUPONT is licensed under CC BY-NC-SA 2.0
Below: Emerald Starling (Lamprotornis iris) taken by Doug Janson is licensed under CC BY-SA 3.0

 

Lab Updates May 2016

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May has been another busy month of data collection for team MacroBird with us reaching some big milestones on both the photography and 3D scanning sides of the project.

We also collaborated on a short video exploring the immense value of museum collections with the brilliant team at Eco Sapien– an organisation dedicated to spreading the word about all things related to biodiversity, conservation and the natural world. You can view the video, featuring our very own Dr Chris Cooney and a cameo from Emma Hughes, here:

Data Collection in Tring: 3D Scanning

Last week we celebrated reaching 80% of all bird species processed- that’s over 8000 specimens selected, retrieved from the collections and, where possible, databased, measured and 3D imaged! You can view many of these scanned species (approaching 7000) on our MarkMyBird gallery.

The streaked spiderhunter (Arachnothera magna). A member of the Nectariniidae family alongside the sunbirds, with a long, curved and finely pointed bill

The streaked spiderhunter (Arachnothera magna). A member of the Nectariniidae family alongside the sunbirds, with a long, curved and finely pointed bill

As with last month, we have continued to work on completing scanning the bills of all island species such as the fantails (Rhipiduridae) with their flat, triangular bills, and the bristly drongos (Dicruridae). Just to make life easier for ourselves, we have also turned our attention towards working through some of the remaining families with particularly hard to scan bills, such as the sunbirds (Nectariniidae) and hummingbirds (Trochilidae). With extremely fine tips, prominent bristles and long bills- such as the Streaked Spiderhunter (Arachnothera magna) pictured here- these species are time-consuming to both scan and select from the collections.

To date we have scanned:

  • 6994 (69.99%) of species
  • 3281 (80.97%) of species from island families
  • 3788 (63.33%) of passerines
  • 3203 (79.54%) of non-passerines

Data Collection in Tring: UV and Visible Photography

Plumage photography has continued at full pace and also reached some important milestones with well over 10,000 individual specimens now imaged- a huge achievement!

The Asian Paradise Flycatcher (Tersiphone paradisi). Right: Illustration taken from Birds of Asia by John Gould, courtesy of the Biodiversity Heritage Library, licensed under CC BY 2.0 Left: Photograph taken by Dr. Vijay Anand Ismavel MS MCh and licensed under CC BY-NC-SA 3.0

The Asian Paradise Flycatcher (Terpsiphone paradisi).

Amongst other families this month we have been photographing the beautiful Paradise Flycatcherspart of the monarch (Monarchidae) family. Found across Africa and Asia, the genus Terspiphone is sexually dimorphic- with colourful males featuring prominent tail streamers and primarily monochrome or rufous females. 

Another interesting feature exhibited by some species within this family are colour morphs. For example, the male Madagascar Paradise Flycatchers (Terpsiphone mutata) have both a nominate white morph and a rufous morph.

To date we have reached:

  • 67 (34.54%) of families completed
  • 2452 (24.54%) of species
  • 11209 specimens: we are selecting up to 6 specimens of each species, both male and female
  • 67254 photographs: six photographs- dorsal, ventral and lateral in both UV and human visible spectrums- of every selected specimen

Mark My Bird

Our crowdsourcing site markmybird.org has now exceeded 820 registered landmarkers. With over 5000 3D bill models uploaded and ready for landmarking, and more added regularly as each family is scanned from museum specimens, there is lots to be done! If you would like to see the amazing diversity of bill form up close, you can visit our site markmybird.org and have a go at landmarking, contributing directly to this huge study.

If you are new to citizen science, aren’t sure what we mean by landmarking or just want to see the process in action, Elliot has also produced a video taking you step-by-step through the landmarking process. Any questions, queries or comments- let us know!

Twitter and #BeakoftheWeek

Our twitter competition #BeakoftheWeek has continued every Wednesday- all are welcome to join in and have a guess, perhaps even beating our current contenders to the top slots!

We post regular blogs about some of our favourite species chosen for the weekly challenge over on our website, this month including the fascinating Tawny Frogmouth (Podargus strigoides).

Publications

IMG_3522RAs Zoë, Emma, and Elliot wrote an article for the Spring edition of the Natural History Museum’s evolve magazine. Exploring the role of the museum’s collections and citizen science in our research, the article includes photographs of some of our favourite unusual bills from the ornithology research collections taken by Chris and Lara.

Zoë is also lead author on a paper detailing the rediscovery and identification of a (thought to be) long lost owl specimen collected by Charles Darwin on the famous second voyage of HMS Beagle. During research into the zoological collection of Robert FitzRoy- Darwin’s captain during the South American voyage- a specimen thought to be Asio flammeus galapagoensis was found to contain a tiny metal tag hidden amongst its tarsal feathers indicating a different species and backstory. The paper explores how, by tracking a specimen through original voyage manuscript data and on through historical museum registers and catalogues, specimens such as this can be traced back to their original collectors and correct identifications.

Varley, Z., Cooper, J. and Prys-Jones, R., Rediscovery of a long misattributed and misidentified Darwin Beagle bird specimen (2016) Bull. B.O.C., 2016 136(1)

Images

Streaked Spiderhunter (Arachnothera magna) taken by Lip Kee is licensed under CC BY-SA 2.0

The Asian Paradise Flycatcher (Terpsiphone paradisi)
Right: Illustration taken from Birds of Asia by John Gould, courtesy of the Biodiversity Heritage Library, licensed under CC BY 2.0
Left: Photograph taken by Dr. Vijay Anand Ismavel MS MCh and licensed under CC BY-NC-SA 3.0

Evolve front cover (c) Natural History Museum, London