morphometrics Archives

08/05/201505/05/2015

Looks can be deceiving

We are all taught not to judge a book by its cover, it’s what inside that counts. Our new paper published in PeerJ shows that the same is true for tenrecs.

These cute Madagascar natives are often used as an example of a mammal family with high morphological diversity. It’s easy to see why: there are tenrecs which resemble shrews, moles, hedgehogs and even otters. These differences are even more remarkable when you consider that tenrecs are more closely related to elephants and aardvarks than they are to any of the small, “insectivore” mammals. One of only four native mammal clades in Madagascar, it appears that tenrecs have undergone an adaptive radiation to fill otherwise vacant, small mammal niches, evolving convergent similarities to other groups in the process.

Tenrecs are clearly very diverse in their appearance. However, prior to our study, no one had tested whether this apparently high diversity was more than skin deep. We tested whether tenrecs were more morphologically diverse than their closest relatives, the golden moles.

We measured the morphology of tenrec skulls and compared their diversity to the shape of golden mole skulls. This meant spending hours poking around the collections of natural history museums and many more hours placing landmarks on skull pictures for 2D geometric morphometrics analyses (Spotify was my friend!)

Pictures of an otter shrew tenrec (Potamogale velox) skull showing that landmarks (points) and semilandmarks (curves) that we used to summarise skull shape. See the paper for more information. — Pictures of an otter shrew tenrec (*Potamogale velox*) skull showing that landmarks (points) and semilandmarks (curves) that we used to summarise skull shape. See the paper for more information.

Tenrecs occupy a wider range of ecological niches (fossorial, arboreal, terrestrial and aquatic) than golden moles so we expected that tenrecs would be more morphologically diverse than their cousins. However, we found that tenrec skulls only have more diverse shapes than golden moles when we compared them in lateral (sideways) view but not dorsal or ventral views. These results show the importance of measuring morphology in many different views to gain a more complete understanding of overall morphological diversity.

The tenrec family includes species which convergently resemble many other, un-related small mammals. However, most tenrecs (19 out of the 31 tenrec species in our analysis) belong to the shrew-like Microgale tenrec genus. So, although many people tend to focus on the strange and unusual species (such as the otter shrew, hedgehog tenrec or the bizarre lowland streaked tenrec), most tenrecs are small, shrewy-type creatures that look very similar.

We tested whether the similarities among the Microgale tenrecs might be masking higher morphological diversity in the rest of the family. We repeated our analyses to compare the diversity of golden mole skulls to a sub-set of the tenrec family (including just 5 of the 19 Microgale species). In this case, tenrec skulls were more morphologically diverse than golden mole skulls in all comparisons (skulls in dorsal, ventral and lateral view).

Overall, our results indicate that, while there are clear physical differences among tenrec family members, the majority of tenrecs are quite morphologically similar to each other so morphological diversity in the family as a whole is not as big as it first appears. Of course comparing skull diversity is just one aspect of overall morphology – analysing the shape of other traits such as limbs could yield different results – but our study represents the first step towards a greater understanding of the ecological and evolutionary diversity of tenrecs.

It’s also testimony to the fact that you should never judge a tenrec by its cover.

Author: Sive Finlay, @SiveFinlay

08/11/201307/11/2013

Trophy Hunters

Antler collection at Harvard's Museum of Comparative Zoology — Antler collection at Harvard’s Museum of Comparative Zoology

It may be an inconvenient truth in these conservation-focused times but we owe a debt of gratitude to the trophy hunters; the army officers and colonial-types who killed animals for sport and prestige. Without their considerable efforts, the vaults of natural history museums would be devoid of the skeletons and skins which form the bases of both exhibitions and many PhD and MSc. theses. Of course, were it not for the over-zealous efforts of hunters perhaps many charismatic animal species wouldn’t be so endangered now but let’s focus on the positives here…

Naturally, if you’re a hunter looking for a prize, bigger is usually better. It’s far more impressive to have a stag or bear’s head mounted on your wall than a hedgehog or shrew – although I would like to hear the embellished stories which might arise from tales of killing your first hedgehog! Similarly, if you are a taxidermist or museum collections manager in many ways it is easier to prepare and preserve large rather than small mammal specimens.

These collection trends are all well and good if you’re interested in the charismatic species. I, however, am studying the little shrewy-type things; hedgehogs, moles, shrews, golden moles and tenrecs – fascinating species but not prized possessions for your trophy case. Even in some of the world’s largest natural history museums it’s difficult to find intact skulls and skeletons of some of these creatures. Combined with the inherent delicate nature of these animals (some tenrecs’ limbs are tiny!) compiling a complete morphometric data set of the groups remains challenging.

Tenrec limbs with a pen for scale; teeny tiny tenrecs!

For the museum collections of these little critters that do exist; I am eternally grateful to the progenitors of carefully handwritten labels accompanying the skulls and skeletons on which my PhD research depends. Adventurers such as Major Forsyth, G.K., Creighton, and C.J., Raxworthy who donated specimens from their tropical voyages deserve special thanks in any research which arises from their collective efforts. However, I am also grateful to the back-yard naturalists, the people who collected and preserved the seemingly ordinary, every-day species of common shrews and hedgehogs which are no less important to ecological and evolutionary research than their exotic counterparts. I benefitted greatly from their collective efforts during my recent trip to Chicago’s Field Museum.

Whether naturalists or trophy hunters, the individuals immortalised by museum specimen labels couldn’t possibly have envisaged all of the diverse future research which would be based on their prized collections. It’s an important reminder that, despite the inherent appeal of flagship species, the lesser-spotted or common-something-or-others are just as deserving of our attention and study. Even if you don’t have the equipment or inclination to start posting skeletal remains of common species to your local natural history museum, there are still plenty of ways of contributing to the study of “ordinary” wildlife. Don’t be dazzled by the allure of large-animal trophy hunting and remember that, when it comes to understanding the natural world, bigger is not always better.

Author:

Sive Finlay: sfinlay[at]tcd.ie

@SiveFinlay

Photo Credits

Sive Finlay

21/06/201321/06/2013

Morphometrics are fantastic!

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.

Screen Shot 2013-06-21 at 10.23.11 — Here’s one of the examples François showed us from his studies. You want to compare these femur heads?
(picture courtesy of François Gould)

Screen Shot 2013-06-21 at 10.23.56 — 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).

Author

Thomas Guillerme: guillert[at]tcd.ie

Photo credits

François Gould (@PaleoGould)

14/06/201314/06/2013

An army of skeletons with lasers

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.

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.

Screen Shot 2013-06-13 at 14.46.10 — Megaladapis – the skull in the American Museum of Natural History is about 30cm long but only 50MB on my computer!

Author

Thomas Guillerme: guillert[at]tcd.ie

Photo credit

Thomas Guillerme

22/03/201322/03/2013

Morphological convergence and disparity in Malagasy tenrecs

“I wish to register a complaint…” the first six months of my PhD have passed by far too quickly. As the date of departure for my first major data collection trip looms, I’m navigating the exciting but unnerving transition from the planning to action stages of my project. Fortunately the members of NERD club were on hand to very kindly listen to my ramblings and provide excellent ideas to add to and modify my research.

Here’s the plan so far…

Evolutionary studies have long-been concerned with understanding patterns of variation in morphological diversity. Two aspects of morphological variation which attract particular interest are convergence – the independent evolution of similar morphologies in phylogenetically distant species – and disparity –the range or significance of morphology in a given sample of organisms.

Morphological variation among tenrecs is particularly interesting – they appear to be both disparate from each other and convergent with other species such as hedgehogs, shrews, moles and otters. However, previous studies have neither quantified the degree of convergence or disparity among tenrecs nor attempted to identify reasons for the occurrence of these patterns. My aim is to fill these significant gaps in our understanding of the evolution of such a fascinating mammalian group.

I work with morphometric data compiled from museum collections of tenrecs and the mammals which they convergently resemble (my data collection involves traveling to museums in London, Washington DC, New York and Boston – oh the trials of PhD life!) I use calipers to take linear measurements and also photograph the species’ skulls and limbs. I use geometric morphometric techniques (this article is a great introduction to the murky world of morphometrics) to statistically analyse the degree of morphological (dis)similarity among tenrecs and other species.

I will plot the morphometric data from my species in a “morphospace”, something similar to Brusatte et al.’s 2008 paper on dinosaur morphology. This graphical interpretation will be useful for measuring both convergence among tenrecs and other species and disparity within tenrecs.

In morphospace plots, morphologically similar species sit closer together than dissimilar species. However, from a convergent evolution perspective these patterns are only interesting if morphologically close species are also phylogenetically distant. I will combine and modify existing approaches (e.g. Stayton 2008 and Muschick et al., 2012) to quantify the amount of convergence among tenrecs and other species and also determine whether tenrecs have evolved a higher degree of convergence than expected by random chance. Similarly, if tenrecs are significantly disparate from each other I expect that the range and variance of their morphological variation will be both greater than random evolution models and also significantly different from their nearest sister taxa, the Golden Moles (e.g. Harmon et al., 2003).

Many texts claim that convergent phenotypes evolve in animals that fill similar ecological niches. However, morphological and ecological convergences don’t necessarily go hand in hand so, while this idea is certainly very plausible in tenrecs, it is important to test the assumption. Fortunately relevant data on physical habitat characteristics, species range maps, life history traits and overlaps with potential competitors and predators are readily available from a range of sources (e.g. PanTheria, LANDSAT and the IUCN) so I can model the ecological similarities among tenrecs and other species. It will be very interesting to determine whether morphological convergence and ecological similarities truly correlate.

So that’s my plan for at least the next six months or so. Interspersed with working in major museum collections while taking a break to tap dance in a parade down Constitution Avenue in Washington DC, I think there are interesting times ahead.

Author

Sive Finlay: sfinlay[at]tcd.ie

Photo credits

http://www.digimorph.org/specimens/Hemicentetes_semispinosus/body/