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

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.

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.

Screen Shot 2016-09-09 at 10.04.13

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

Lab Updates March 2016

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March has been a busy month for all on team MacroBird. Data collection, based at the Natural History Museum’s ornithology research collections in Tring, has continued for both the 3D scanning and photography components of our study.

Data Collection in Tring: 3D Scanning

Overall, we have achieved scanning 60% of all of the world’s bird species – that’s 6000 bills! In addition, we have scanned 74% of species that feature on our island families list, and are currently working our way through the pigeons (Columbidae) and babblers (Timaliidae). With around 500 scannable species left (with suitable specimens available for scanning in the museum’s collection), we hope to have worked our way through the list by the end of May. Our next aim will be to scan 100% of all non-passerine species.

Species scanned plot

The larger of our two scanners, the R3X, has been working brilliantly with its new lenses, allowing us to scan much finer bills and keep our scanning productivity at full speed. Currently preoccupied with the huge number of aforementioned pigeon species, we will be moving on to scanning raptors on this shortly.

Noisy friarbird (Philemon corniculatus)

Noisy friarbird (Philemon corniculatus)

An interesting island family that we have worked through this month are the honeyeaters (Meliphagidae). Honeyeaters are small-medium passerines, largely found in Australia and New Guinea. This group contains the fantastically named ‘Friarbirds‘ that have featherless heads which give them an almost vulture-like appearance. We also worked through the woodpeckers (Picidae) which have one of the easiest bills to scan – the majority are pale and their chisel-like shape means it doesn’t take too many rotations to scan the entire bill. One thing we didn’t realise was quite how variable in size the woodpecker bill is, going from the large 9.5cm bill of the Imperial Woodpecker (Campephilus imperialis) to the tiny 1.5cm bill of the African Piculet (Sasia africanus).

To date we have scanned:

  • 6323 (63.26%) of species
  • 2028 (96.99%) of genera
  • 3006 (74.19%) of species from island families
  • 3332 (55.85%) of passerines
  • 2988 (74.20%) of non-passerines

Data Collection in Tring: UV and Visible Photography

Blue-winged leafbird (Chloropsis cochinchinensis)

Blue-winged leafbird (Chloropsis cochinchinensis)

As mentioned in last month’s updates, the photography component of our project – imaging the plumage of as wide a range of the 10,000 species of birds as possible in both the human visible and ultraviolet spectrum – is now well underway.

This month has seen us continue to target our priority list of species, focussing primarily on passerine families, including the beautiful Australasian robins (Petroicidae) and the fantastically colourful leafbirds (Chloropseidae).

To date we have photographed:

  • 37 (19.07%) of families completed
  • 1808 (18.09%) of species
  • 8102 specimens: we are selecting up to 6 specimens of each species, both male and female
  • 48612 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 750 registered landmarkers, with over 100 new participants this month alone! The fantastic efforts of these citizen scientists has seen our overall landmarking progress reach 35%, contributing vital data as we proceed further into the analysis stages of the project.

This doesn’t mean the chance to contribute to the study is over, far from it! There are still thousands of these fantastic 3D models of bills in need of landmarking. With new species being added as each family is scanned from museum specimens, you can learn more about this research or join in and have a go yourself by visiting our website www.markmybird.org.

In May we will be holding a Mark-My-Bird-athon at the University of Sheffield – more news on this to follow..

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Conferences

Chris gave a talk at the Yorkshire Naturalists Union annual conference. Chris’s talk, and those of the other speakers, are covered in this vlog by Eco Sapien.

Publications

Brulez, K., Mikšík, I., Cooney, C.R., Hauber, M.E., Lovell, P.G., Maurer, G., Portugal, S.J., Russell, D., Silas James, Reynolds, S.J. & Cassey, P. (2016). Eggshell pigment composition covaries with phylogeny but not with life history or with nesting ecology traits of British passerinesEcology and evolution.

Twitter and #BeakoftheWeek

Our twitter competition #BeakoftheWeek has continued every Wednesday, with Tim Blackburn and Paul Sweet remaining at the top of our leaderboard- all are welcome to have a go and perhaps even beat 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 fabulous Twelve-Wired Bird of Paradise (Seleucidis melanoleucus) and the striking King Eider (Somateria spectabilis).

 

Images

Blue-winged leafbird (Chloropsis cochinchinensis) taken by Dr. Vijay Anand Ismavel MS MCh is licensed under CC BY-NC-SA 3.0

Noisy friarbird (Philemon corniculatus) taken by Leo is licensed under CC BY-NC-SA 2.0

MMB banner (c) Jen Bright

Lab Updates: It’s been a while!

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Straight-billed reedhaunter (Limnoctites rectirostris)

Straight-billed reedhaunter (Limnoctites rectirostris)

Data Collection in Tring: 3D Scanning

We have achieved our target of scanning a species from every genus that is both available to us in Tring’s collection and scannable, giving us excellent coverage across the bird family tree. The last remaining species were those from the Extinct and Endangered, and Type collections. Specimens are classed as a Type if they were the example used for officially describing and naming a new species- they are some of the most important in any natural history collection. One of the most interesting Type specimens we have scanned in recent months was collected by Darwin himself on the second Voyage of the Beagle, the straight-billed reedhaunter (Limnoctites rectirostris), an ovenbird from South America.

Our largest scanner, the R3X, had been largely redundant before Christmas as we had scanned nearly all species with bills large enough for it to scan. This meant that the only scanner we had working was the MechScan which tackles bills from the size of  a grain of rice to about 50mm in length. With only one scanner in action our rate decreased quite considerably. However, we now have some new lenses for the R3X allowing us to scan bills from about 35mm upwards and so both scanners are now running at full speed!

Currently we are working on completing families containing species that live on islands such as white-eyes, finches, sunbirds and storm-petrels.

To date we have scanned:

  • 5766 (57.70%) of species
  • 2029 (97.03%) of genera
  • 3144 (52.70%) of passerines
  • 2613 (64.89%) of non-passerines

Data Collection in Tring: Visible and UV Photography

The end of 2015 also saw the photography component of our project start in full force, with the ambitious aim of imaging the plumage colouration and pattern of as many of the 10,000 extant species of bird as possible, in both the visible and ultraviolet spectrum. We are targeting selected families to begin with, such as woodpeckers, tyrant flycatchers and cotingas, but hope to get as wide a coverage as possible by using the Natural History Museum’s incredible collections.

In the first few months we have been able to photograph approximately 900 species, and as we are selecting multiple males and females from each species, this equates to upwards of 4000 specimens. We take photographs of the bird at dorsal, lateral and ventral angles in both the visible and UV spectrums, meaning a total of 6 images per specimen, so overall we have taken around 25,000 individual photographs to date!

With almost 9% of world bird species imaged, this is a brilliant start!

Great Jacamar (Jacamerops aurea) in the ultraviolet (UV) spectrum

Great Jacamar (Jacamerops aurea) in the ultraviolet (UV) spectrum

Great Jacamar (Jacamerops aurea) in human visible spectrum

Great Jacamar (Jacamerops aurea) in the human visible spectrum

 

 

 

 

 

 

 

Mark My Bird

Since Mark My Bird launched we’ve had fantastic input from citizen scientists with over 650 registered landmarkers now contributing to our study – thank you! We have so far uploaded 3500 scans of species from around the world for people to view up close and landmark, providing essential data for our analysis. With almost 12,000 bills landmarks, this is a brilliant start to the enormous task ahead.

If you haven’t signed up yet and would be interested to learn more about the crowdsourcing side of our work, explore the 3D models we are generating or actually have a go at landmarking, visit our website www.markmybird.org.

Our stand at Science Uncovered, NHM Tring.

Our stand at Science Uncovered, NHM Tring.

Science Uncovered

At the end of September, Team MarkMyBird took part in the Natural History Museum’s annual Science Uncovered event (part of European Researcher’s Night) at the Tring museum site – home to the incredible ornithology research collections that are essential for our data collection. This was a great opportunity to talk about our research and answer questions from museum visitors of all ages. You can read about our stand and the event itself in our blog post.

Conferences

Angela attended the EMPSEB21 (European Meeting of PhD Students in Evolutionary Biology) conference in Scotland (8th-12th September 2015) and presented some of her PhD research about  the perks of using variable-rates models of trait evolution.

In November, Jen gave a talk at the 3 Days of 3D conference at the Naturalis Biodiversity Centre in Leiden, The Netherlands (2-4th November 2015).

Publications

Edwards, D. P., Gilroy, J. J., Thomas, G. H., Uribe, C. A. M., & Haugaasen, T. (2015). Land-Sparing Agriculture Best Protects Avian Phylogenetic Diversity. Current Biology, 25(18), 2384-2391.

The paper also featured in an article in the guardian!

Twitter and #BeakoftheWeek

Our weekly Twitter competition #BeakoftheWeek is still going strong with Tim Blackburn and Paul Sweet leading the way. If you’d like to know more about some of the birds featured in #BeakoftheWeek, check out our blogs exploring some of our favourites as the competition runs on.

Other News: New Research Assistants!

Two new research assistants, Zoë and Lara, joined our research group towards the end of last year. Lara’s background is in Zoology and she completed her postgraduate studies in Biological Photography and Imaging. Zoë previously worked as a Curatorial Assistant for Bird Group at Tring NHM and read Art History and subsequently Museum Studies at University. You can find out more about the MarkMyBird research group here.

Zoë getting to grips with 3D scanning

Zoë getting to grips with 3D scanning

Lara learning how to take linear morphometric measurements

Lara learning how to take linear morphometric measurements

 

 

 

 

 

 

 

 

 

Images

Straight-billed reedhaunter (Limnoctites rectirostris) taken by Cláudio Dias Timm is licensed under CC BY-NC-SA 2.0

All other images (c) Natural History Museum, London.

August Updates: A charm of hummingbirds!

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Species level coverage: 42.87%

Species level coverage: 42.87%

Data Collection in Tring: 3D Scanning

We should finish our target of scanning a species from every genus over the coming month. The remaining specimens needed will require us to recalibrate one of our scanners, the MechScan, to a larger scanning volume. The final genera to target will be those whose species are locked away in the Extinct and Endangered collection.

Our main achievement this month has been to finish scanning every available hummingbird genus – the third largest avian family (according to our taxonomy) after tyrant-flycatchers and parrots! One of the species we came across was the tooth-billed hummingbird (Androdon aequatorialis), which as its name suggests has a beak filled with small tooth-like serrations – very different from the other hummingbirds we have scanned so far!

3D scan of a tawny frogmouth (Podargus strigoides skull

3D scan of a tawny frogmouth (Podargus strigoides) skull

At present, we have been unable to obtain scans for 60 genera. Most often these have been obscure monotypic genera with only one species that are missing from Tring’s collection. This seems to be the case for neotropical groups like the ovenbirds and tyrant-flycatchers. Other genera we have been unable to scan are those with very ‘fluffy’ species, for example owls, frogmouths and nightjars. Groups such as these pose a particular problem because the feathers around the beak hide important landmarks at the top and sides of the upper mandible which are essential for downstream analyses. Thankfully these problematic groups are in the minority. Even so, we have scanned all available skulls from these groups from the skeleton collection as an alternative.

To date we have scanned:

  • 4284 (42.87%) of species
  • 1913 (91.49%) of genera
  • 2138 (35.72%) of passerines
  • 2143 (53.22%) of non-passerines

Mark My Bird

We have set our launch date for our new crowdsourcing website ‘Mark My Bird’ as the 21st September! Mark My Bird is a web-based landmarking platform that will greatly speed up the process of post-processing our 3D scans. Keep an eye out on our website and twitter feed for updates on how to get involved!
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Conferences

This month Gavin gave a talk describing the divergence and macroevolutionary pathways that generated the diversity of avian bill morphologies, at the Systematics Association Biennial conference at the University of Oxford Museum of Natural History (26-28th August 2015).

Analysis

Emma spent a week adding to Chris C’s spectrophotometric measurements of bird plumage to improve coverage across the avian radiation, with the aim being to capture the extremes of avian plumage ‘colourspace’.

Twitter and #BeakoftheWeek

We had two new winners in our weekly #BeakoftheWeek competition – well done to Will and Patrick. You can always check out the Beak of the Week leaderboard to see previous winners, beaks and blogs about each species. And remember – you’ve got to be in it to win it!

Lab Updates July 2015

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Data Collection in Tring: 3D Scanning

We are nearing our target of scanning a species from every genus!

Phylogeny showing genus level coverage >87.61%:   Purple=Scanned, Yellow=Not Scanned

Phylogeny showing genus level coverage: 87.61%
Purple=Scanned, Yellow=Not Scanned

Our main focus this month has been to continue with scanning a species from every genus. We have now sampled over 87% of genera – up from 70% in June. One of the families we worked through this month was the long-tailed tits (Aegithalidae), which included the pygmy tit (Psaltria exilis). With a beak length of just under 5.5mm, it has the smallest beak we have scanned to date!

We also spent a couple of days scanning species of genera that are held in the restricted extinct and endangered collections, such as the California condor (Gymnogyps californianus), giant ibis (Thaumatibis gigantea) and the Philippine eagle (Pithecophaga jefferyi).

Our large scanner, the R3X, spent a week tackling all the remaining species housed in the large skins collection (minus three cassowary and rhea species).

To date we have scanned:

  • 4197 (42.00%) of species
  • 1832 (87.61%) of genera
  • 2084 (34.93%) of passerines
  • 2110 (52.40%) of non-passerines

Mark My Bird

Thank you very much to everyone who tested out our new data crowdsourcing website and provided such valuable feedback. The final few tweaks are currently being made and (fingers crossed) the website will be going live at the start of September – exciting! Mark My Bird is  a web-based landmarking platform that will greatly speed up the process of post-processing our 3D scans. Keep an eye out on our website and twitter feed for updates on how to get involved!

Conferences

Jen gave a talk at the Craniocervical Systems in Vertebrates conference in Ghent, Belgium (7th-10th July 2015) and bought back some lovely Belgian sweets for us all to enjoy.

Publications

Unrelated to birds entirely, Jen was the third author on a paper about fish (available here). The study was led by University of Bristol PhD student Lucy Brunt, and used an engineering method called Finite Element Analysis (usually used to test the strength of things like bridges and cars) to look at how muscle forces affect jaw development in zebrafish. It’s important for developing animals (humans included!) to use their muscles in order to develop proper joint shapes, and this study showed how cell and joint growth can go wrong if the muscles aren’t working properly.

The beautiful plumage of the himalayan monal (Lophophorus impejanus )

The beautiful plumage of the himalayan monal (Lophophorus impejanus)

Analysis

Back in Sheffield, Jen has also been busy landmarking more bird beaks that will eventually be used to build an initial ‘bill morphospace’. In contrast, Chris C has been focusing on bird feathers rather than bills by taking spectrophotometric measurements of bird plumage colouration in an attempt to capture the extremes of avian plumage ‘colourspace’ – very cool! The Himalayan monal (Lophophorus impejanus) and the vulturine guineafowl (Acryllium vulturinum) are just two of the species that Chris has found which have rather unusual plumage colouration.

Twitter and #BeakoftheWeek

We are nearing 500 followers on twitter! We had four new winners in our weekly #BeakoftheWeek competition – well done to Alison, Beth, TD James and Keith. You can always check out the Beak of the Week leaderboard to see previous winners, beaks and blogs about each species. And remember – you’ve got to be in it to win it!

Images

Himalayan monal (Lophophorus impejanus) by Francesco Veronesi is licensed under CC BY-NC-SA 2.0