Did Archaeopteryx Really Have Black Plumage?

Not surprisingly, the latest Archaeopteryx study has kicked up quite a stir within the media and scientific realms, considering the iconic status it has attained since discovery some 150 years past. This latest paper by Carney et al. and published in the journal Nature Communications claims to have resolved the plumage colour of a feather possibly from  Archaeopteryx, a pretty neat little addition to the reconstruction of this critical species. They use methods employed during previous studies, namely the morphological or structural analysis of melanin-bearing organelles within feathers called melanosomes to infer that Archaeopteryx possessed an entirely black plumage.

The notorious black feather (Image Copyright: WitmerLab at Ohio University)

There is no doubt that the structures are in fact melanosomes, and no doubt that melanosomes contribute to plumage colour. But the question is, how much do they contribute to the plumage colour..? Well, I don’t know. In fact, no-one knows, at least in extinct avian theropods. The authors don’t discuss this either. It has however been discussed elsewhere in similar studies, albeit only qualitatively and in passing.

One comment is from Zhang et al. 2010: “Melanosomes are lyosome-related organelles of pigment cells in which melanins are stored and are responsible in part for the colours exhibited by modern birds.”

And Li et al. 2010: “Other molecular pigments such as carotenoids and porphyrins also produce plumage colours but are not preserved morphologically, thus we cannot address their possible effects here.”

That seems like a pretty big caveat. It’s like saying if you mix green, yellow and red paint in unknown quantities, you get red every time. Or something similar, I suck at analogies. The point is, if in modern birds, there are other significant structures that dictate or contribute towards plumage colour, does it make sense to try and predict colour when these are absent?

UPDATE: Ryan has been kind enough to clarify this point in a comment below.

Furthermore, the 95% confidence intervals the authors use are practically useless. Look at the ordination provided in Figure 4 (not sure if I can copy it here, so won’t..).  These 95% confidence ellipses mean nothing in the slightest, or at least nothing meaningful. What they should have shown is an envelope includes 95% of all points within a sample, so that when you insert data ‘blind’, if it falls within a completely discriminated envelope, you can be 95% certain that it belongs to that group (i.e., 95 times out of 100, a blind data point will be correct). The envelopes shown in figure 4 clearly do not show this (if you don’t have access to the paper, ask me for a copy, or take my word for it). As a result, the points calculated for the particular Archaeopteryx feather analysed could really be grey or black, or maybe brown at a push (the number of colour choices is simply overwhelming..).

So was Archaeopteryx lithographica black?

Probably, probably not.

Carney et al. (2012) New evidence on the colour and nature of the isolated Archaeopteryx feather, Nature, DOI: 10.1038/ncomms1642

Li et al. (2010) Plumage patterns of an extinct dinosaur, Science, 327, 1369-1372

Negro et al. (2009) Porphyrins and pheomelanins contribute to the reddish juvenal plumage of black-shouldered kites, Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, 153(3), 296-299

Zhang et al. (2010) Fossilized melanosomes and the colour of Cretaceous dinosaurs and birds, Nature, 463, 1075-1078

What is a Fossil Species..?

What do we currently understand by a ‘species’?

Naming species, also known as alpha taxonomy, forms the fundamental basis and core of systematic analysis (e.g., for biodiversity, macroevolutionary and ecological studies). Since the origin of the species concept, there has been heated and continuous debate as to what exactly constitutes a species. The discovery of DNA as an evolutionary tool sparked a vigorous new line of discussion into what precisely defines a species. Even to this day, despite a wealth of theoretical, empirical and philosophical studies, there is still a lack of consensus in the way of rigorously defining a species unit. This is not to say that there isn’t a general idea of what a species is (ask any biologist or palaeontologist); in fact most people reading this will probably have a pretty good idea of what they define a species as. But there is not total agreement, not by a long shot. Furthermore, most if not all current species concepts are explicitly based on extant organisms which can be directly observed in their every day life, and also just happen to provide a near-endless supply of DNA. But what about fossils? I’ve outlined the critical importance of using fossils in conjunction with pretty much any systematic analysis before (here), but how do palaeontologists actually recognise and delimit fossil species? This is a pretty serious issue, considering the DNA of fossil organisms has always decayed long before exhumation (except in exceptional circumstances), and fossil remains typically only represent a biased sample of the organism it once was.

What are the current species concepts?

For biologists, the species problem can be framed as: “What level of divergence (morphological, genetic, etc.) between populations constitutes species diagnosis?” This can be modified slightly according to whichever species concept is being applied (see below). Using DNA as a sole basis for species delimitation is fraught with issues, including but not limited to the concept of paralogy, lateral gene transfer (transfection), arbitrary delimitation protocols, lack of data (e.g., in tropical species), and often a lack of training or instrumentation (in third world countries mainly). The relative issues and benefits of morphological and/or DNA-based analysis is a tale for another time though. Currently, there is no single ‘silver bullet’ technique for species delimitation (although many DNA taxonomists will try and pretend there is..). What we actually have are a series of non-independent concepts that actually apply to different stages of the speciation process (de Quieroz 2007 discusses this in a most brilliant manner). Here are a couple of examples:

Biological Species Concept: This is the one most people will have heard of. Species are defined by reproductive isolation, or the ability to produce fertile offspring. Obvious issues with this are if you’re asexual, and how do you know if two organisms (within reason) can or cannot mate if they are not sympatric. Also, reproductive isolation is not always congruent with morphological divergence, so is inadequate with purely morphological data sets.

Phylogenetic Species Concept: This refers to diagnosability based on the monophyly of a population. This invariably invokes the use of DNA. Genetic population divergence goes through three stages: polyphyly, paraphyly and finally reciprocal monophyly, giving two or more irreducible clusters of diagnosable organisms with a traceable pattern of ancestry and descent.

Genealogical Species Concept: This is the use of multiple gene marker distributions to delimit putative species by identifying periods of complete lineage sorting. Essentially this means that the incongruence from coalescence (the point in time where gene variants unite in a gene genealogy) no longer affects delimitation.

A currently widely used method is DNA barcoding. Some molecular systematists deem this as a powerful enough tool to entirely replace standard Linnaean taxonomy, although (obviously) there are numerous vocal objections. DNA barcoding operates on the assumption that there is a threshold for species delimitation based on a single gene, which is the entirely arbitrary 10 times greater genetic divergence (interspecific) than intraspecificity, leading to the concept of reciprocal monophyly. It works sometimes, but is fraught again with theoretical and empirical problems. (I love the idea that molecular systematists will go to the tropics with the aim of identifying unique or diverse haplotypes in insects etc., by killing as many organisms as possible; “We’ve found a unique haplotype! We must therefore preserve this beetle at all costs!”, as the decapitated beetle floats around the dissection palate..)

How do these concepts relate to fossils?

Every single one of these concepts rely on either direct observational data (e.g., sympatry for the BSC), or the use of DNA. Few modern studies rely solely on morphology to delimit species (annoyingly, seeing as it is directly coupled with behaviour, ecology etc.; DNA is just, well, DNA..). So really, with regards to fossils, in which phenotype is the only aspect preserved (and ecology etc. accordingly inferred), as well as the spatio-temporal context in which it exists, how can these concepts be applied? Well, they can’t really. So what can palaeontologists do..?

How are fossil species delimited?

In principle, there are two different methods of species delimitation: a discovery-based approach, and a hypothesis-based approach. The former makes no a priori assumptions regarding the putative species in a sample, only delimiting subsequent to analysis (e.g., DNA barcoding/taxonomy, cladistics). The latter requires an a priori assumption of what species already exist within a sample, with the analysis being a validation test. It varies in papers as to whether a full or partial cladistic analysis is carried out (if at all) when the focus if the paper is the erection and description of a new species. By partial analysis, I simply mean that the authors observe the synapomorphies of a specific clade and see if their specimen(s) match or not. This is a pretty horrendous breach of taxonomy and cladistic methodology, as it ignores the fact the every single character placement and it’s polarity is influenced by the addition of new species (in fact, this is the principal method by which cladograms are initially constructed). Full analysis is the dominantly used method, thankfully, given the accessibility of free software and relative simplicity in executing cladistic analysis (although there may be issues in obtaining and extracting previous data sets, but that’s another tale too. For someone else.) This leads us on to the next part.

Bring on Cladistics

Cladistics is the method that sytematists use to forge a hierarchical grouping of taxa into discrete subsets, or clades, for the inference of common ancestry between species and groups. A clade is defined by a node (or sometimes a branch) – the point of intersection of two or more branches – that represents the common ancestry and speciation of all subsequent taxa. Each node is represented by one or more shared derived characters (synapomorphies) between all branches, and hence taxa, emanating from the node. If the taxa in question are species (i.e., terminal branches), then the minimum required number of synapomorphies to give a sister taxa relationship is one, and the minimum number of required autapomorphies (unique derived characters) to ‘split’ the branch into two separately recognised entities, is one. That is, cladistics can recognise discrete units, including species, on the basis of a single unique character, regardless of the size of the initial character set. There are statistical methods of assessing the strength or support of this (e.g., pseudo-replication analyses, branch decay tests), but the point remains that a species can be delimited through cladistic analysis based on the possession of a single unique character. [this is a really simple overview, there are numerous web-pages and texts out there that describe cladistic methodology in more detail; just search.]

It seems that there are two main methods of delimiting fossil species: qualitatively, whereby the fossil simply looks different but the differences are not broken down into discrete characters; and quantitatively, where the species name is supported by x number of autapomorphies, and the strength or support of the diagnosis is a function of x, and is testable through cladistic methods. This is pretty much the only method available to palaeontologists given the relative paucity of fossil data. But then how many autapomorphies are required to be interpreted as a ‘strong’, or valid, diagnosis? And to what extent are species therefore comparable? It’s a problematic issue, that I haven’t actually came across much at all in the published literature. If I’m mistaken, please do point me in the right direction! What is perhaps required though, is a rigorous species concept that is directly compatible with the full range of fossil diversity, and that extant taxa can be integrated in to.

One thing to consider though is that species are treated as discrete entities when these concepts are applied; is this the correct approach  when really a lineage on which an organism sits is by definition, continuous? What do we gain by stamping an arbitrary and highly subjective boundary on this continuum? A method of classification. It has heuristic value in systematics, but it seems that the fundamental treatment of species as discrete units may need some consideration. Furthermore, speciation is a pretty stochastic and deterministic process, and the application of delimitation criteria must be flexible to account for the variation between lineages. Unless someone comes up with something really neat. Like..

Future prospects? Geometric Morphometrics. 3D automated species recognition software, based on robust statistical delimitation procedures. It’s awesome. Watch this space!

Disclaimer: I’ve probably missed out huge amounts here; this is such a massively studied field, that it’s been difficult to even shrink down to these couple of paltry pages! Comments as always are more than welcome! There are simply too many references to list here too. If people would like to read more about the subject, drop me an email (jon.tenannt.2[at]gmail.com), and I’ll happily whizz a few papers [legally..] your way, depending on taste!

Final thought: with respect to all of the work that has gone into validating ‘species’, what has been done to test the validity of higher taxonomic units, such as Family and Order, or even the Genus..?

For reading all that, here’s a snap of the Iguanodon specimen on display at the museum in Oxford, England.

Surprised American for scale

Evolution in the Reconstruction of Diplodocus

Diplodocus  has always held a significant position in the hearts of dinosaur palaeontologists, as it was one of the very first genera to ever be formally recognised and described. Following, are some images and attempted reconstructions from Hutchinson (1917), and by comparison some excellent recent research by Taylor et al. (2009) on posture in Diplodocus carnegiei (or carnegii). I just figured it would be cool to show how mechanical interpretations and life reconstructions had changed over the years, since from dinosaurs were first mounted to now where more complex biomechanical modelling procedures are being utilised.

Mounted skeleton model of Diplodocus carnegiei in the Reptile Gallery at the British Museum of Natural History, Hutchinson (1917) (click for larger image)

The following is a model reconstruction made from plaster based on the above skeleton. The tail rests on the ground, the neck is concave downwards and held-sub-horizontally, and the limbs are situated laterally to the trunk. Hutchinson (1917) explicitly says that despite this odd arrangement, Diplodocus did not crawl around on the ground like a lizard or crocodile.

Model of Diplodocus carnegiei, as restored by Hutchinson (1917). Try and ignore that it's head looks like a duck.. (click for larger image)

Following the above reconstruction, there is a simple reconstruction of the pelvic girdle and hind-limb provided. The femur and the tibia/fibula are perpendicular, with the pes also perpendicular to that to rest on a substrate. It pretty much looks like the ischium gouged a furrow whenever the animal tried to walk in this reconstruction.

Pelvic girdle and hindlimb of Diplodocus carnegiei in posterior (caudal) aspect, Hutchinson (1917) (click for larger image)

By comparison, more recent reconstructions are quite different. The following is just one of many illustrations by the talented Scott Hartman (follow @skeletaldrawing on Twitter). Note the distinct differences in posture: the legs are held vertically under (and slightly lateral) to the trunk, elevating the main body. Accordingly, the neck and tail both become more horizontal, acting as respective cantilevers with respect to the main body and the centre of gravity. Much more detail regarding stance and posture can be found on the wonderful SV-POW blog here, and in many formal publications.

Diplodocus carnegiei, based on specimen CM 84, Copyright: Scott Hartman (click for larger image)

Following on from reconstructions like above, the next step is to reconstruct the range of motion to discern possible ecological functions of various skeletal elements and domains. This has been done rather successfully by H. Mallison with Plateosaurus (Part 1 and Part 2). Hutchinson (1917) attempted a very rudimentary interpretation of this, as shown below.

Simplified illustration of the functional domains in Diplodocus carnegiei showing articulation points (above), and the range of humeral motion (below), Hutchinson (1917)

Yeah, ok, it’s pretty basic. Some progress has been made in this field with sauropods however, notably that from Taylor et al. (2009) with regards to Brachiosaurus brancai, as shown below (edit: the Tendaguru Brachiosaurus brancai is now regarded as Giraffatitan brancai, Taylor, 2009; see comment below). Obviously Brachiosaurus is not Diplodocus, but it illustrates the point nicely.

Reconstructions of Brachiosaurus brancai in a drinking (left) and browsing (right) posture (Taylor et al., 2009) (click for larger image) Edit: Note that these are not 'actual life poses', but examples of 'what if' deviations from a previously suggested 'neutral' model (see comment below).

Digital reconstruction is proving to be a pretty useful tool in imaging and interpreting life positions of dinosaurs and other extinct organisms. More recently, vertebrate palaeontologists, combined with mechanical modellers and zoologists have began to map muscles on to these digital skeletons using modern analogues and the ‘extant phylogenetic bracket‘ theory, to gain a significantly more detailed reconstruction and make more valid interpretations about extinct archosaur mechanics.

As computing technology has developed, palaeontologists have kept pace and are finding ever more elaborate methods to aid in understanding the mechanics, physiology, and ecology of extinct organisms. It’s an exciting field, with lots of promise for the future!

Note: I feel like a tit. Spent a whole year working/studying in the NHM London, and don’t have a single photo of the focal Diplodocus specimen there, Dippy. Oops.

Bates, K. T., Maidment, S. C., Allen, V. and Barrett, P. M. (2012) Computational modelling of locomotor muscle moment arms in the basal dinosaur Lesothosaurus diagnosticus: assessing convergence between birds and basal ornithischians, Journal of Anatomy, doi: 10.1111/j.1469-7580.2011.01469.x

Mallison, H. (2010) The digital Plateosaurus I: body mass, mass distribution and posture assessed using CAD and CAE on a digitally mounted complete skeleton, Palaeontologia Electronica, 13.2.8A

Mallison, H. (2010) The digital Plateosaurus II: an assessment of the range of motion of the limbs and vertebral column and of previous reconstructions using a digital skeletal mount, Acta Palaeontologica Polonica, 55(3), 433-458

Taylor, M. P., Wedel, M. J. and Naish, D. (2009) Head and neck posture in sauropod dinosaurs inferred from extant animals, Acta Palaeontologica Polonica, 54(2), 213-220

Middle-Earth gets a Geological Makeover

As if J. R. R. Tolkien wasn’t brilliant enough with his creation of Middle-Earth, it appears that using his numerous maps and illustrations provided, supplemented by observations from within the texts themselves, a geological reconstruction can be achieved! I recently came across this old article from the Proceedings of the J. R. R. Tolkien Centenary Conference, Oxford, England, 1992, and figured it was worth sharing.

The first attempt at a geological history of Middle-Earth was Margaret Howes in 1967 in a piece entitled “The Elder Ages and Later Glaciations off the Pleistocene Epoch”. Here, she endeavoured to recapitulate the successive geomorphologies from the time when Morgoth (the real bad guy in Middle-Earth) was overthrown to beyond the time when Aragorn adopted rule over Gondor. However, this work has been recognised as being too far adrift from Tolkien’s original creations, drawing in too much from Earth’s own recent geological history.

This work was truly over-shadowed by that of Robert Reynolds, who in 1974 wrote his “The geomorphology of Middle-Earth”. This actually incorporated the theory of plate tectonics to the entirety of Middle-Earth (Fig. 1).

Fig. 1 Reynold' tectonic reconstruction of Middle-Earth (click for larger image)

The extension of this by the authors of the article is presented in Figure 2. They revise the number of tectonic plates, as well as apply modern boundary terminology (e.g., strike-slip, triple-junction etc.). The result really is quite a nice read of the fusion of a modern day description of tectonics with a seminal creation that has inspired generations, and hopefully will inspire more to come. It’s great to come across Mount Doom being described as a “hotspot” – it really adds a slant to the old “volcano lair” for bad guys. It also helps to answer questions which I’m sure plagued geologists throughout the books and films, such as ‘where did the mythril come from?’, and ‘how did the mountains surrounding Mordor get such a weird shape?’. All in all, it’s an impressive article that successfully increases the dimensionality of a masterpiece.

Fig 2. Current interpretation of the principal tectonic features of Middle-Earth (click for larger image)

If anyone would like the complete original article, I’d be happy to send a scanned version – it really is quite a spectacular piece of Middle-Earth metadata.

Howes, M. M. (1967) The Elder Ages and the later glaciations of the Pleistocene Epoch, Tolkien Journal, 3(2), 3-15

Reynolds, R. C. (1974) The geomorphology of Middle-Earth, The Swansea Geographer, 11, 67-71

Sarjeant, W. A. S. (1992) The geology of Middle-Earth, Proceedings of the J. R. R. Tolkien Centenary Conference

Quantitative Shape Analysis 2: Data Collection – easier than you think!

“If you want to inspire confidence, give plenty of statistics. It does not matter that they should be accurate, or even intelligible, as long as there is enough of them.” Lewis Carroll (1832-1898)

 

The last post on this series gave an introduction to the background and significance of quantitative shape analysis. I conveyed the use of landmarks, or geometric co-ordinates, as the basis for statistical analysis of shape. The last article finished by stating this article would discuss different methods of geometric morphometric analysis, but I forgot one crucial step: Data Collection! Here, I present a simple and efficient way of collecting data for use as the basis for a range of geometric morphometric analyses.

Following is an example of data collection from a simple coursework study I did last year, looking at cranial allometry in carnivores. Firstly, you need a target or hypothesis for your analysis. The target here was to use exemplar carnivorous mammal species to look at shape variation in the skull, and to interpret in terms of form and dietary function. The first decision to make is what points to use as your landmark data. I’ll use a hypothetical skull as an example.

Chosen selection of landmarks - you can chose any, as long as they are topographically correspondent between all specimens as described in the last post

 

Each one of these landmarks represents a specific topographically correspondent point amongst all specimens in the sample. For the sake of simplicity in this example, assume that the lower jaw and the cranium are a single module. The landmarks can be defined as such:

Cranial landmarks (right-lateral aspect; red)

1. Posterior extremity of occipital margin (type 3)

2. Tympanic aperture (centre) (type 1)

3. Posteroventral extremity of occipital condyle (type 3)

4. Ventral extremity of dorsal postorbital process (type 3)

5. Rostral extremity of orbital periphery (type 3)

6. Mid-point on ventral maxillary margin between premolars and canines (type 3)

7. Ventral deflection in dorsal margin (maximum curvature) [rostral to postorbital] (type 2)

8. Dorsal expansion in dorsal margin (maximum curvature) [posterior to external nares] (type 2)

9. Anterior extremity of premaxilla (type 3)

10. Dorsal extremity of dorsal margin (type 3)

11. Ventral extremity of zygamatic arch-jugal suture (type 1)

12. Position of distal border on posterior-most tooth (maxillary) (type 1)

 

Lower jaw landmarks (right-lateral aspect; blue)

13. Posterior extremity of angular process (type 3)

14. Posterior-most (distal) extent of dentary molars (type 3)

15. Mid-point on ventral dentary margin between premolars and canines (type 3)

16. Anterior extremity of dentary (type 3)

17. Point of posterodorsal deflection of ventral margin, culminating in angular process (type 2)

18. Ventral pinnacle of coronoid process (dentary) (type 2)

 

This is just a hypothetical example to show landmark positions and how to define them. Real data is freely available for almost anything on the internet. A series of sample images can be easily obtained through MorphBank, for example. If anyone reading this would like, I can send them a copy of the images I used for this coursework as a trial data set – just drop me a quick message with your email address.

Converting these landmarks into usable geometric data is possible through a number of image modification programs. A good one to use is ImageJ, freely available on the web. An important thing to note at this point is that within your image collection, every one you import into this program or any other must be angularly identical, or as close as possible (e.g., all of a precise lateral view of a skull).

Using ImageJ you can simply import an image with pre-defined landmarks as above, use the ‘Point’ tool to click on the landmark, hit ctrl-m (or use the Analyse-Measure tab), and hey-presto, you have the two-dimensional geometric co-ordinate of that point in a table! Consecutive points can then be added to this table for each specimen. Do this for all points per sample in a pre-defined numerical sequence (as indicated above), then simply export to an Excel spread-sheet. A rather nifty thing you can then do is plot them as a graph, and you’ll see a landmark representation of your image (awesomeness of this depends on how many landmarks you use). Repeat for all samples, and you have a comparable data set. Simple eh! Note that this can be done free of scale, so you don’t need to measure any lengths or inter-landmark distances. A future post will cover how to compensate for this in quantitative shape analysis. What you want to end up with at this stage is a single spread-sheet, with a labelled tab for each specimen, and containing a series of geometric co-ordinates that are topographically related between specimens.

There are of course more techniques using more complex software and data imaging methods (using surface or outline data, laser scans etc.), but typically these will not be accessible to the general public. The above procedure is a convenient and free method of obtaining a decent and workable initial data set, without having to spend endless time in a museum collection or laboratory.

So, now you know the procedure, nothing should stop anyone from going out there and collecting a data set, constructing a series of landmarks and digitally obtaining their geometric co-ordinates. Right? Next time, I’ll actually discuss how to assemble this data into a format that you can use to input to some free software, and several analyses you can then conduct with this software (e.g., Principal Components Analysis).