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