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!
Markmybird 4

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

Lab Updates June 2015

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Data Collection in Tring: 3D Scanning

Over the last month, our efforts have switched from scanning species from islands, to scanning a species from every genus.

Phylogeny showing genus level coverage >70%:   Blue=Scanned, Yellow=Not Scanned

Phylogeny showing genus level coverage >70%:  
Blue=Scanned, Yellow=Not Scanned

As a result, we have now 3D scanned at least one species from over 70% genera. This includes scanning nearly every genus from the largest avian family, the tyrant flycatchers (Tyrannidae). Tyrant flycatchers are one of the trickier species that we scan, as they have fine hooks at the beak tip and feathers around the beak that are particularly bristly and fluffy. Combined, these factors make each scan more noisy and so more difficult to align into the complete 3D model. Now the MechScan has finished with these, we can focus on some of the easier to scan genera and so increase the scanning rate.

Our larger scanner, the R3X, has also been targeting genera, but has additionally completed scanning 100% of the following families: kiwis (Apterygidae), skuas (Stercorariidae) and thick-knees (Burhinidae). We are hoping to take this scanner into the large skins collection during the next stint of data collection, and 3D scan the species with larger beaks that are too big to be housed in the main collection (e.g storks (Ciconiidae), pelicans (Pelecanidae), albatross (Diomedeidae)).

To date we have scanned:

  • 3534 (35.36%) Species
  • 1509 (72.17%) Genera
  • 1814 (30.40%) Passerines
  • 1717 (42.64%) NonPasserines

Mark My Bird

Our crowdsourcing website, Mark My Bird, is in the final stages of beta testing and so will be going live over the next few weeks! Mark My Bird 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 take part!

Conferences

Talks were given at two conferences this month. Firstly, Gavin and Chris C attended the EU Macro 2015 conference at the University of Copenhagen (14th-16th June), with Chris presenting an ignite talk on the projects initial findings. Chris also attended and presented at Evolution 2015 (26th-30th June) in Guarujá, Brazil. You can watch Chris giving his talk by clicking here.

Tweets

Analysis

Back in Sheffield, Jen has been landmarking more species to go into the projects initial morphospace.

Twitter and #BeakoftheWeek

The team’s twitter account has gained lots of new followers this month, mainly thanks to Gavin’s excellent tweeting during EUMacro, Chris’s conference talks, and our weekly #BeakoftheWeek competition. Elliot has constructed a wonderful new Beak of the Week leaderboard for the website. Here, you can also view images of previous ‘Beaks of the Week’, and links through to blogs about each species.

Other Lab News

Team member, Chris Moody got married. Congratulations Chris and Kathryn!

Team Macrobird making the most of the sparklers at the wedding.

Team Macrobird making the most of the sparklers at the wedding.