EcoEvo@TCD will be taking a short break for the summer so we won’t be updating the blog through July and August. Between us I think we’re attending five or six conferences, giving almost 20 talks and posters, and visiting three different continents, all for SCIENCE! Some of us are also taking a well-earned break. I am currently hiking around the wilds of Yellowstone attempting to spot wolves, bison, and moose, and aiming not to get eaten by bears! When we get back we’ll report on the highlights of conference season and bring you more ecology and evolution related news, views and advice.
I hope you all have a safe, fun and productive summer! See you September!
Last month I spent a month in Mbuluzi Game Reserve in Swaziland attempting to build a walk-in trap that will allow me to capture vultures. I want to be able to tag the birds with GPS trackers and ask a host of interesting questions from which a flood of Nature papers will follow.
Step 1 – Clear the areaStep 2 – Create some support for the polesStep 3 – Erect the frameStep 4 – Add the meshStep 5 – bait the area (this sickly Waterbuck had died)Step 6 – record everything that comes downStep 7 – play the waiting game (perching African White-backed Vultures)
We’ll have to wait for the vultures to get habituated to the area before adding the front to the trap. Once this happens we can proceed. So this is a ‘to be continued’…
Did you know that otter’s penises are shrinking? I didn’t. Until I was informed of that by my scientist girlfriend. I can no longer look at otters the same way again. Science ruins everything.
I used to enjoy life. The future promised to us by Back to the Future was so close! That all ended the day I started going out with a scientist.
I’m now a cynic. I don’t trust anything that isn’t peer reviewed and even then, what’s the impact factor of the journal? I even know some journals by name now! About 50% of the time I can say “Congrats on getting published in PNAS” without laughing.
Nights out with scientists are different to nights with any other group of people. While most people like to leave their work behind them, scientists take theirs with them and just get slightly louder while they discuss it. It must be how Robin Ince feels when he goes for dinner over at Brian Cox‘s, but instead of talking about the Higgs Boson the topics range from the plight of the buff tailed bumblebee to dinosaur biomechanics. Who knew dinosaurs could be so boring? I didn’t. Until I started dating a scientist.
Peer review is a twisted system. It’s a place where people can be just downright mean to others and get away with it. It seems that the point of peer review is not just to ensure that only the best research gets published in the best journals, but to make those whose work isn’t good enough feel stupid and embarrassed that they thought their puny intellect was capable of appearing in a journal as glorious as the almighty [redacted]!
I must admit, it hasn’t ALL been bad, I no longer think everything gives me cancer (who knew The Daily Mail wasn’t a reliable source?!) That’s right, this blog PROBABLY won’t cause cancer.
I now look forward to being told that my blog doesn’t ask a question, didn’t have a hypothesis and had no supporting data. I haven’t even cited anything. I’m ok with those inevitable criticisms. If they get me down I just have to keep reminding myself, only two more years until we get hoverboards.
It has been estimated that less than 10% of global spending on health research is devoted to diseases or conditions that account for 90% of the global disease burden. These are mostly diseases of the world’s poorest people. The general public, and funding agencies, often equate third world diseases with the big three killers; HIV/Aids, tuberculosis and malaria. There is, however, a group of conditions known as neglected tropical diseases (NTDs) which have an even wider impact. They include some of the most common helminth parasites that, while don’t often kill, result in morbidity and debilitation. One of these, the large human roundworm Ascaris lumbricoides, is the focus of research by Professor Celia Holland at Trinity College Dublin.
A. lumbricoides infects over a billion people globally, mainly in tropical and sub-tropical regions. Infection occurs through the faecal-oral route. Poor sanitation results in soil becoming a reservoir for infectious eggs and ascarisis included within the group known as soil-transmitted helminths or geohelminths. This is why, sometimes, the salad is not the safest bet. Once swallowed the infective ova hatch in the small intestine. From the small intestine they migrate to the proximal colon, through the mucosa and onto the liver and eventually the lungs. In the lungs they penetrate the alveolar space, move into the pharynx where they are swallowed and returned back to the small intestine. The migratory route of ascaris and other related helminths may be an evolutionary holdover from a skin penetrating ancestor.
The discovery of the ascaris life cycle in humans is one of those great anecdotes that pepper medical history. In 1922 Japanese paediatrician, Shimesu Koino, infected both a volunteer and himself with ascaris eggs. He realised the larvae were migrating when he found large numbers of larvae in his sputum. Put plainly, he coughed up baby nematodes that had penetrated his lungs. Not a methodology likely to get past ethics committees today.
Worldwide, severe ascaris infections cause approximately 60,000 deaths per year, with serious health consequences observed in a further 122 million people. Children from preschool age to adolescents carry the greatest worm burdens. Ascariasis is the disease associated with ascaris infection and symptoms include appetite loss, lactose maldigestion and impaired weight gain. As children are at vulnerable stages of growth and development, these nutritional deficits lead to stunted growth, diminished physical fitness and impaired memory and cognition. Other symptoms of adult worms include abdominal distension and pain, nausea and diarrhoea. In heavy infections entangled worms have been known to cause intestinal blockages. The migrating larvae cause their own set of problems which include acute lung inflammation, difficulty in breathing and fever.
Ascariasis and other neglected infectious diseases are diseases that result from poverty but also help to perpetuate it. Children cannot develop to their full potential, and infected adults are not as productive as they could be. The good news is that there is a renewed momentum in combating these diseases. The World Health Organization (WHO), and public-private partnerships are linking their efforts to combat NTDs in a more coordinated and systematic way. The Bill and Melinda Gates Foundation have to date committed more than US$1.02 billion in grants to organizations working to address NTDs and have named ascaris as one of their newly targeted diseases. The WHO has set out a strategy for eliminating morbidity from soil transmitted helminths in children by 2020.
This makes Professor Holland’s new book “Ascaris: The Neglected Parasite”, a timely and important contribution to the fight against NTDs. The book is the first on ascaris in over 20 years and presents a wealth of new insights. The 16 chapters from top authors from around the world include detailed information on the biology, epidemiology, host and parasite genetics and public health and clinical aspects of A. lumbricoides and the closely related A. sum, an economically important parasite of pigs. As any researcher new to a field knows, having up to date research collected and summarised in an assessable format, with lists of lovely, lovely references, is a gift. This is the third book Professor Holland is senior editor on, the others being “Toxocara the enigmatic parasite” and “The Geohelminths: Ascaris, Trichuris and Hookworm”.
Jaws has a lot to answer for. While I doubt there was ever a time that sharks weren’t seen as a threat, that threat was only threatening to sailors and those who chose to traverse the oceans. Then Jaws comes along and suddenly sharks become the enemy to anyone foolhardy enough to set foot in briny water.
This isn’t to say that sharks aren’t dangerous. Earlier this year a man was killed by a shark in New Zealand in a vicious attack that left a community stunned. Yet this was a rare event, one of the (on average) 4 fatal attacks that happen each year globally. To put this into context the World Health Organisation estimate that 388 thousand people die from downing each year, yet people fear the sharks much more than they fear the water.
One of the problems is that when people think of sharks they inevitably think of something like this:
When really they should be thinking of something more like this:
This is a catshark (also known as dogfish for some reason) and there are over 150 species of which the largest is only about 1.6m and most never reach more than 80cm. They feed on invertebrates and small fish and are completely harmless.
Even the two largest shark species in the world, the whale shark and the basking shark, are harmless. They are planktivores and have teeth that could barely break skin, let along tear anyone apart.
All these sharks, despite their differences, have one thing in common: they are well known to most people. Who hasn’t watched a documentary on ‘killer sharks’ or seen David Attenborough extol the wonders of the whale shark, or simply found a dogfish washed up on the beach?
Yet many of the over 470 shark species are rarely seen by humans. They live in the depths of the ocean and are only occasionally seen as bycatch. Examples include the frilled shark (Chlamydoselachus anguineus), which was caught during the survey of Rockall Bank that I wrote about recently; the cookiecutter shark (Isistius brasiliensis) which feeds by taking bites shaped like a cookie cutter out of prey as they swim past; and my new favourite species, the dwarf lanternshark (Etmopterus perryi) which is thought to be the world’s smallest shark at only 21 cm total length. I think it’s just adorable!
On the other end of the cuteness scale is the goblin shark (Mitsukurina owstoni) which looks like something out of a very strange nightmare:
Like so many of these species, little is known about the life-history of the goblin shark. Many deep sea animals live at low abundances, spreading out so as to reduce competition for the scant food that is available at depths. This means our chances of catching specimens are low. Additionally, most are caught by fishermen who generally have little interest in filling their freezers with species that won’t bring in a profit, so it is only when something really strange is caught that animals are brought back for study. Hence the importance of surveys (hey, I’m back to making the point of my last post!) where scientific importance is allowed to trump commerce.
I could continue that theme, but I won’t. Instead I’ll end by asking that you look beyond Hollywood and tacky ‘documentaries’ to see the beauty and variety of sharks. Sharks are incredibly diverse and fascinating creatures yet we know very little about most of them. They can be scary – I certainly would be cautious about going in the water with a great white – but we are much more a threat to them than they are to us. It is estimated that over 100 million sharks are killed each year, a horrifying and unsustainable number. There is the very real threat that many species will go extinct if we continue to exploit them at current levels. Who’s the bigger threat?
There’s an international celebrity star of the Victorian age directly above my office. He’s lived there long enough to see his museum home gradually shrink around him to such an extent that he no longer fits out the door. He will spend the rest of his days eavesdropping on undergraduate lectures, seminar presentations and NERD club meetings. Prince Tom adds a flavour of exoticism and royal blue blood to our Zoology Museum’s collections.
Tom was an Indian elephant caught from the wild and presented as a gift from the ruler of Nepal to Queen Victoria’s second son, the Duke of Edinburgh. Along with a tortoise companion, Tom accompanied the Duke on his visit to New Zealand in 1870. He lived and worked with the sailors aboard H.M.S. Galatea, partaking in the manual work of hoisting sails and enjoying his daily crew rations of rum – the quantities of which were up scaled so they were befitting an animal of his size.
As one of the first elephantine visitors to the land of kiwis, Tom sparked quite a publicity stir in New Zealand. Tom’s decidedly non-teetotaller ways were of particular interest; one journalist remarked that Tom “indulged in alcoholic stimulants, of which a temperance advocate might say, he was far too fond”. Tom was also noted for his gentle ways; bending down to offer rides to his adoring public and happy to accept treats of buns, biscuits and lollies.
Upon his return from the colonies, Tom was loaded onto a train at Plymouth bound for London. While he was, by now, accustomed to maritime transport, confinement in a train carriage was an entirely different matter. Amidst his attempt to escape, Tom crushed the Royal Marine corporal who had been entrusted as his carer. Clearly health and safety practices of the Victorian era did not stretch to include protocols for the safe transport of slightly tipsy elephants.
Tom was relocated to Dublin Zoo in June 1872 where he quickly became a star attraction. He gave rides to children and was, for a time, effectively given free-reign of the zoo (just a touch different to how the elephants are looked after today!) Tom’s most famous trick was to buy his own snacks from the food stands. He learned to collect coins in his trunk and hand them over in exchange for his favourite treats.
A few close encounters when Tom broke loose and “endangered himself and others” put an end to his free reign at the zoo and he spent his last few years confined to his house and small yard. He died in 1882 aged roughly 15; evidently his years of heavy drinking and fondness for pastries were not conducive to prolonging his longevity. His body was transported by barge from the Zoo to Trinity College where he was dissected “with the aid of shears, ropes and pulleys”, how I would have loved to attend that anatomy lecture!
Tom’s skeleton has remained in our Zoology Museum ever since. His celebrity status continues long after his death as he is now one of the main attractions of our new museum guided tours which start today. So if you’re around Dublin, come along and meet Tom for yourself, hear stories about our other famous animals and learn about our extraordinary collections which date back to the voyages of Captain Cook in the late 18th century. You never know what unusual tales lurk behind our taxidermied and skeletal remains.
As I mentioned in a former blog post, we invited François Gould (@PaleoGould) to enlighten us about the murky world of geometric morphometrics. His talk and workshop were eventually described by some people (@SiveFinlay – to protect her identity) as “the best day of [their] PhD so far!” I will clumsily try to summarize our awesome day of morphometrics.
What?
François emphasized the importance of seeing geometric morphometrics (hereafter let’s be familiar and just call it morphometrics) as a toolkit of methods for shape variation analysis more than a discipline in itself. So one can use this toolkit to describe and analyse the variation of shape defined as the “aspects of geometry invariant to rotation translation and reflection”. To get your head around this definition, one example François gave which I found really useful is that if you drop a pile of A4 papers, they will still have the same shape even if some sneaky ones tried to rotate, translate or reflect while falling on the floor.
As a practical example, understanding shape variation allows you to study superiority, competition and opportunism in the evolutionary radiation of Dinosaurs.
How?
So here’s where we get to all the technical mumbo jumbo at the heart of morphometrics. As François explained to us, it is way easier to think about morphometric ideas than to formally explain the mathematics behind them and many knowledgeable morphometricians are still arguing about the theory underpinning morphometric methods. I don’t have the talent or the knowledge to talk about so I’ll leave it up to the experts here, here and here.
However, I’d like to show you the general methods and share some of François’ comments.
So, regarding the different analyses you can do, the most common approach is to use landmarks; homologous points on a biological object. You place them on the different items you want to analyse using either 2D images or 3D scans. The trick with working with landmarks lies in paying attention to their homology and their number (some of the debates and details about this crucial step can be found here or here). Then you can “translate, rotate and scale the shapes with a least squares fit” in order to compare your different objects (that’s the Procrustes method, named after the mythological blacksmith who distorted his victims to fit an iron bed, who said morphometricians weren’t cultured?). Depending on your question, the resolution of your images and your study objects, alternative methods could be more appropriate to deal with novel structures or curves but again, I’ll pass you on to the excellent literature on this topic.
Here’s one of the examples François showed us from his studies. You want to compare these femur heads? (picture courtesy of François Gould)Landmark them and then pile ’em up using a Procrustes transformation (easy: just translate, rotate and scale all these bad boys). (picture courtesy of François Gould)
This is an excellent summary, both theoretical and practical, which details some of the amazing possibilities when using this toolkit of methods.
Before embarking on your own morphometric analyses, here are François’ useful questions (slightly paraphrased!) which you should ask yourself:
1) What the heck are you doing? You can use morphometrics for data exploration or for hypothesis testing; make sure you know what your question is before you start collecting your data.
2) How are you gonna do that? Many tools exist to analyse shape, from old-school calipers to a CT scanner. All give good results depending on what your question is.
3) What analyses are you gonna use? Again, that all depends on the crucial first step but after François’ talk I recommend this nice review which will help you find out what’s the best fit for your question.
I gratefully thank François Gould as most of the information in this post comes from his workshop (the slides from which can be found here) and the rich discussions we had (plus the massive amount of morpho chat he had with other people and where I sneaked in to absorb some of his extensive morphometric knowledge).
The term “algae” does not refer to a single taxonomic group but instead comprises a diverse array of species, from prokaryotic cyanobacteria to many types of unicellular and multicellular eukaryotes. It’s well known that algae make great contributions to sustaining the diversity and productivity of our natural world. It has been estimated that the number of algae species could range from 30,000 to more than 1 million. So it’s not surprising to find that algae, so high in diversity and abundance, have significantly altered the appearance of our planet.
Just as plants add colour to our terrestrial world, algae are responsible for the diverse colours of many aquatic systems. Without the existence of macroalgae, most marine zones would be barren places and we would miss the beauty of park-like intertidal zones and magnificent marine forests comprised of gigantic algae such as the Giant kelp (Macrocystis pyrifera). In the shallow zone of rivers and lakes, attached filamentous macroalgae can flourish when the pressure of competition from aquatic plants is low, making the river and lake much greener than it would be otherwise. Microalgae also play their own role in dyeing the environment. In marine areas with high concentrations of phytoplankton, the existence of large amounts of chlorophyll absorbs the red and blue portions of the light spectrum and reflects green light. Therefore, sea water in these regions is not blue but appears as different shades; from blue-green to green. Attached microalgae, such as some benthic diatom species, can easily occupy diverse substrates, such as stones and aquatic plants, and decorate that substrate with their own colour. Despite their tiny volumes, only several μm in length or diameter, the adherent strength of these algae is quite strong and it is not easy to remove them from the substrate (as I found out when helping Lindsay with her field experiments!).
Some people might say they prefer multicoloured coral reefs to algae. However, even the beautiful colours of coral reefs depend on Symbiodinium, one group of dinoflagellate algae which live in a symbiotic relationship with coral polyps. However, this relationship is not absolutely stable and severe environmental stress can sometimes weaken the symbiotic bond. Increased sea water temperatures and ocean acidification can cause coral polyps to expel their algae. As a consequence, the corals lose both their color and any phototrophic capabilities and eventually become boringly white; a process termed coral bleaching.
Bleached coral reefHealthy coral
Algae are also responsible for the beautiful colours of some sea slug species. In contrast to the harmonious symbioses between algae and corals, some sea slugs directly consume algae and use the algae’s pigment to produce remarkable body colors which can either be apatetic or aposematic in their functions.
Sometimes, however, algal colouration is not always welcome. Blooms of intensively growing algae can produce very ugly and unpleasant colours. Cyanobacterial blooms are one of the most common environmental problems in freshwater systems including eutrophic lakes, reservoirs and the backwater zone of rivers. During bloom periods, lake surfaces can be partly or fully occupied by cyanobacterial cells, creating an unappealing dark blue-green colour.
A cyanobacterial bloom in Chao Hu, the fifth largest freshwater lake in China
Other algal groups, such as some dinoflagellates, are commonly found in marine blooms. The colours of algal blooms in marine systems are more diverse depending on the type and density of bloom species. However, one kind of bloom, Noctiluca scintillans, is especially unattractive. Proliferation of this species creates a bloody red colour remarkably similar to the one described in Exodus, which may be one of the earliest recorded instances of a red tide (“… and all the waters that were in the river turned to blood. And the fish that were in the river died, and the water stank …”).
A Noctiluca scintillans bloom off the coast of eastern Australia
What do you study that? It’s a common question, and one that’s often hard to answer. Some subjects have obvious and immediate uses (medicinal drug development is an obvious one) but others have less clear goals. Much, if not most, of science proceeds through slow increments building on past knowledge, without any grander desire than to find out why something is the way it is. Even discoveries that have revolutionised our lives were seen as small curiosities when first discovered. When asked about the use of electricity following its discovery Michael Faraday is said (erroneously) to have claimed “…one day you can tax it”.
Ecology is one area where the immediate uses are often hard to pin down. Surveys of animals are lovely, but what really is the point? In these economically-straitened times such questions demand an answer, if only because without one those surveys will no longer be funded. A recent survey by Marine Scotland brilliantly highlights their importance, discovering new species and new habitat which has major implications for fishing in the area.
They report the presence of extensive deep sea coral reefs and at least two new species of chemosynthetic clam which is a strong indication of the presence of cold seeps. Cold seeps are areas in the deep ocean where chemicals seep from the crust into the water. They were first discovered in 1983 and use hydrogen sulphide, rather than sunlight, as the basis of their ecosystem. The seep found by Marine Scotland is the first in near-UK waters and only the third in the North-East Atlantic, so it is a significant (and fantastic!) discovery.
The report also found evidence of extensive habitat loss due to bottom trawling. Bottom trawling is arguably one of the most destructive forms of fishing, taking not just the target fish but also any habitat that dares to rise above the sea bed. Rocks, sponges and corals all get caught and what is left behind is a barren plateau that can take years to recover. Due to the presence of the rare habitats found by the survey, as well as the clear evidence of fishing activity in the area, the report strongly recommended closure of fishing grounds in the survey area.
No one knew what, if anything, they would find when they left shore. They could have found nothing of importance but instead they found a type of habitat that has not been found in the region before and at least two new species; information that has led to commercially-significant recommendations.
This is the result of just one of the thousands of surveys done each year. Some of those surveys may not be useful now, some may be (like this one), and some may have a use in the future than can’t be predicted. Surveys aren’t glamorous, but they are extremely useful, and they are a perfect example of why not having narrow goals isn’t always a bad thing.
The word “Morphometrics” was already mentioned on this blog here and here. It’s a horrible term which nevertheless describes a really cool field in evolutionary science…
Today we’re having a workshop with François Gould (@PaleoGould) so hopefully everyone will know more about all things morpho by the end of the day. I won’t go into the juicy details of procrustes analyses, elliptic Fourier transform or other Bezier polynomials (see Zelditch and colleagues “Geometric Morphometrics” book or Julien Claude’s excellent “Morphometrics with R” for further details about these friendly terms). Instead, I’d like to talk about one aspect of data collection.
In a simplistic way, morphometric data can be sorted into two categories. Two dimensional data, such as linear measurements or shape outlines, can be obtained in many ways, from trusty calipers (which are digital these days) to computer measurements of landmarks placed on pictures (see here for a nice list of usable software). The second type of data is obviously 3D data which, again, may be collected in many ways using fancy technology from digital microscribes to medical CT-scanners.
3D scanner
I use a surface 3D scanner like this one which has a fairly well defined list of pros and cons.
-Firstly, it is way more time consuming to scan specimens than to use either 2D methods or a 3D microscribe. My scanner takes roughly one hour per skull.
-Secondly, the scanner is quite expensive even though the final scans aren’t always completely accurate and may have problems of poor quality.
Despite these problems, I’ve found that, in the end, the list of pros is much longer!
-It is really easy to use the scanner and, even if the price is not cheap, it’s far from unaffordable.
-The data you get from a scan is easily transportable and therefore easily sharable; think about posting or e-mailing a skull! I think this point is really important when you are studying fossils. You can usually find skulls of most living primates in any natural history museum but fossils are really rare and specimens are only housed in a few places so access to 3D scans would be a great asset to interested researchers.
-Another point linked to this sharing idea: it is more scientifically friendly since you can put your scans into online supplementary materials and publish them with your papers.
-Furthermore, even if it’s a less technical point, 3D scans look pretty amazing and are excellent illustrations for your papers like this 3D ring-tailed Lemur skull:
This list of pros and cons can continue on ad infinitum and ultimately all morphometric methods have both advantages and disadvantages of one kind or another. Aside from all these technical details, I think that the best part of using a scanner is the chance to play with lasers! It’s just so cool to be measuring skulls in a museum with a normal set of calipers while your scanner spits out lasers in all directions and then, by magic, the giant lemur (Megaladapis) on the desk is there staring out from your computer screen.
Megaladapis – the skull in the American Museum of Natural History is about 30cm long but only 50MB on my computer!
