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

Lab Updates April 2016

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Data Collection in Tring: 3D Scanning

Overall we have scanned 67% of the world’s birds! You can view many of these 6700 species on our MarkMyBird gallery.

Yellow-throated Longclaw (Macrornyx croceus)

Yellow-throated Longclaw (Macrornyx croceus)

Our current target is to scan every species from our list of ‘island bird families’. The remaining island families we are yet to complete such as fantails, monarchs and drongos are quite difficult to scan owing to their dark shiny bills, and rictal bristles that obscure the sides of the gape of the bill and so this has slowed down our progress a little. However, we have also been targeting some easier to scan bird families to keep things moving such as the pipits and wagtails (Motacillidae). As well as having bills that are easy to scan, many have incredibly long hind claws (such as the aptly named yellow-throated longclaw, Macrornyx croceus) which are thought to be an adaptation to help them walk through grass.

To date we have scanned:

  • 6688 (66.93%) of species
  • 3153 (77.81%) of species from island families
  • 3532 (59.20%) of passerines
  • 3153 (78.30%) of non-passerines

Data Collection in Tring: UV and Visible Photography

Ribbon-tailed Astrapia (Astrapia mayeri)

Ribbon-tailed Astrapia (Astrapia mayeri)

On the photography side of the project this month we have been lucky enough to work on the birds of paradise. With such an incredible variety of colours, amazing iridescence and some of the most extravagant feathers, this plumage is incredible to see up close (and a practical challenge to image at times!).

It’s particularly fascinating to see first hand just how vivid much of this structural colour remains in historical skins and it will be of particular interest to see how these photographs fare in our later analysis.

We continue to progress through the Passerine families and are currently working our way through the bright and colourful Oriolidae.

To date we have reached:

  • 51 (26.29%) of families completed
  • 2108 (21.09%) of species
  • 9583 specimens: we are selecting up to 6 specimens of each species, both male and female
  • 57498 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 790 registered landmarkers. The fantastic efforts of these citizen scientists has seen our overall landmarking progress reach 40%, 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.

We have a new mailing list for MarkMyBird where we send out a monthly research highlight for our landmarkers. This month you can see how accurate your shoebill mark up was! You can sign up to our mailing list here.

Publications

Raptor skull change with size

Raptor skull change with size

Jen was lead author on a paper published this month in PNAS investigating shape change in birds of prey. As the skulls of birds of prey increase in size, they do so in a predictable way. The bills are tightly linked to this change in skull size – one cannot change without the other – indicating a constraint on how the bill can evolve. If this constraint is broken, it could have important implications for avian groups that exhibit high bill diversity, such as the passerines, particularly in families that have undergone rapid and explosive radiations, including the Darwin’s finches and Hawaiian honeycreepers. You can read more on the University of Sheffield’s press release, or by reading the full paper below:  

Bright, J.A., Marugán-Lobón, J., Cobb, S.N. and Rayfield, E.J. (2016). The shapes of bird beaks are highly controlled by nondietary factors. Proceedings of the National Academy of Sciences.

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 Grey-necked Picathartes (Picathartes oreas).

Images
Yellow-throated longlaw (Macrornyx croceus) taken by Carmelo López Abad is licensed under CC BY-NC-SA 3.0

Ribbon-tailed Astrapia (Astrapia mayeri) by markaharper1 is licensed under CC BY-SA 2.0

MMB banner (c) Jen Bright

Raptor gif (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!
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.