New papers on Kyrgyzsaurus, Madygenerpeton, and Longisquama

Alifanov, V. R. and E. N. Kurochkin. 2011..Kyrgyzsaurus bukhanchenkoi gen. et sp. nov., a new reptile from the Triassic of southwestern Kyrgyzstan. Paleontological Journal 45(6):639-647.
[DOI: 10.1134/S0031030111060025] [link]

Description of a reptile fossil with skin preservation discovered in 2006. Comes form the same locality as Sharovipteryx and Longisquama. The authors interpret the specimen as a member of drepanosaurs, a Late Triassic group of archosauromorphs. This paper represents one of the last contributions of the Russian palaeornithologist Evgenii N. Kurochkin who passed away recently.

Buchwitz, M., C. Foth, I. Kogan, and S. Voigt. 2012 in press. On the use of osteoderm features in a phylogenetic approach on the internal relationships of the Chroniosuchia (Tetrapoda: Reptiliomorpha). Palaeontology. [DOI: 10.1111/j.1475-4983.2012.01137.x] [link]

Includes a graphic reconstruction of Madygenerpeton (drawing by Frederik Spindler).

Buchwitz, M. and S. Voigt. 2012 in press. The dorsal appendages of the Triassic reptile Longisquama insignis: reconsideration of a controversial integument type. Paläontologische Zeitschrift.
[DOI: 10.1007/s12542-012-0135-3] [Link]

More thorough description/ graphic documentation compared to Voigt et al.(2009) and considers some aspects of diapsid skin evolution.

A palaeodictyopteran and other relics from Madygen

Béthoux, O., S. Voigt, and J. W. Schneider. 2010. A Triassic palaeodictyopteran from Kyrgyzstan. Palaeodiversity 3: 9-13. [pdf 1.5 Mb]

Despite the substantial collection and study of insect fossils from the Madygen Formation (see overview in Shcherbakov 2008a) there are still unkown elements of the entomofauna left. Béthoux et al. (2010) describe a wing of a not yet reported group of insects from lacustrine shales of the northwestern ouctrop area of the Madygen Fm. (which also yielded Sharovipteryx and Longisquama).

Ruling out all alternatives on the basis of wing venation data, they come to the conclusion that reliquia spec. nov. was a late member of Palaeodictyoptera, an order-rank group according to conventional classification schemes that was previously thought to have died out during the Middle or Late Permian.

Béthoux et al. suggest that the disappearance of ancient insect groups in equatorial realms is linked to the Late Paleozoic aridisation in these areas that triggered the migration to wetter higher latitude ecosystems, such as the Madygen lake environment. The relatively late occurence of paleodictyopterans in Madygen is also in agreement with Shcherbakov's (2008b) hypothesis that the renewal of Triassic entomofaunas was asynchronous, starting in the lower latitudes and spreading to the higher latitudes.

Other Madygen relics?

Apart from modern groups, such as dipterans and hymenopterans among insects as wells as lissamphibians and archosaurs among tetrapods there are further relict forms, such as the choniosuchian Madygenerpeton or the basal cynodont Madysaurus. As hinted by Béthoux et al. the question to what degree and why Madygen functioned as a refugium is still to be answered.

Maths in Paleontology (I): Data

''In every special doctrine of nature only so much science proper can be found as there is mathematics in it.'' - Immanuel Kant, Metaphysical Foundations of Natural Science (1786)

Warningly the maths professor who got the unthankful task to teach us first-semester scientists-to-be some basic basics of his field chose Kant's statement as the first in his first lecture on "higher" maths. However, when I started my studies in geology and paleontology, there was another saying among old school geology teachers: "A bad mathematician makes a good geologist."

Many a fellow student were rather willing to believe in these latter words than in the inconvenient alternative. (I always considered this believe as outdated and I got the feeling that geology as a science might have been shaped not only by the talents of its protagonists but also by their limitations in terms of exactness and rigorousity.)

Luckily you were not necessarily considered as a bad geologist if you were interested in maths and the notion that modern geoscience involves maths and exact methods (e.g. methods of quantitative data analysis, databases, multivariate statistics and geostatistics, geoinformatics and geographic information systems, 3D and 4D modelling, remote sensing) was clearly on the rise. Perhaps from a biologists' point of view this story would be different, but, to tell you the truth, some of the biology-based paleontologists I got to know are not much living on the exact side either.

Apart from microscopy seminars, field, and lab practicals which teach you ways of data acquisition some classes in statistics and data analysis during first semesters of study give you an idea about the structure of data and ways how to sample and how to deal with data in order to find new knowledge, e.g. a relationship between two phenomena previously not considered to be related.

At the very beginning you will learn that there are different types of data used in paleontology and that you have to bring your data into shape for any kind of mathematical analysis tools, i.e. arrange them as a data table such as the following:

Specimen	Class	State of XYZ	No. of UVW	size L [mm]	size M [cm²]
A	a	Aa	2	12.1	234
B	b	B	3	13.3	87
...	...	...	...	...	...
X	x	X	...	...	...

Normally lines of the table represent samples (or groups of samples or taxa) whereas columns may represent various features or measures. Such features may be the belonging to a certain class or category or the presence, absence, or specificity of a feature. Measured values as entries may have a discrete contribution (e.g. natural numbers such as the number of teeth or segments or body chambers) or a continuous distribution (e.g. length, area, angle, temperature measurements).

Various data relevant for paleontologists can be arranged as tables, such as morphological and microstructural data, stable isotope and other geochemical data, geographical, sedimentological, and stratigraphic data, as well as taphonomic and paleoecological data. Some of these data have a special structure and can be referred to one of the following types:


Compositional data...

... add up to 100%. Chemical compositions of fossils or faunal compositions are compositional data:

Community	Trilobites	Brachiopods	Echinoderms	Poriferans	Nautiloids
A	23 [%]	42	17	5	13
B	10	15	5	50	20
...	...	...	...	...	...
X	...	...	...	...	...

These data require careful considerations and a special kind of maths because all variables are (necessarily) correlated and thus an alleged dependence, e.g. of brachiopod and echinoderm abundances, can be obscured by variation in another group.


Spatially or temporally correlated data

‘Spatial correlation’ means that values for data points close to each other are more similar than values of more distant data points – e.g. the faunal composition of an ecosystem from Arizona is rather like that of a Nevada community than that of a Massachusetts community.

Locality	Easting (X)	Northing (Y)	Facies	Archosaurs [%]	Rhynchosaurs [%]
A	5687	0487	lacustrine	23	45
B	6485	0808	fluviatile	34	38
C	6800	1490	fluviatile	40	37
...	...	...	...	...	...

Geostatistics is the usual method to deal with spatially correlated data. Spatial correlation can also occur on much smaller scales, e. g. the shape and size of two skull bones in contact to each other can show a stronger dependence than the shape and size of bones that are more distant to each other.

In paleontology temporal correlation is quite abundant, especially if your study considers different stratigraphic ages or sedimentological field data:

Population	Horizon	Ar/Ar age [Ma]	Facies	δ18O [‰]	Average size [mm]
A	1	210 ± 1	deltaic	-2.0	5.2
B	2a	N/A	distal shelf	1.4	6.4
C	2c	207 ± 2	?	2.1	6.8
D	4	200 ± 1	deltaic	-2.2	6.0

As in stockmarket analytics methods of time series analysis can be applied to interpret temporally correlated data (i.e. time series). Such data may be relevant for your study as they often indicate evolutionary trends (biological evolution in the stricter sense but also evolution of paleoenvironments), cyclic processes with a certain periodicity, and/or they can form the basis for relating contemporaneous processes in the geological past (e.g. stratigraphic correlation of separate sedimentary successions).


Orientation data

For elongated fossils such as conical shells or long bones the orientation of the fossil long axis towards the geographical cordinate system can be measured using a compass (with inclinometer). In a similar way the orientation of bedding planes can be documented. Such measurements are often used for the purpose of deducing the former transport direction of a ancient sediment transport and depostion system (such as a river, delta, or alluvial fan). A data table with orientation data may look like that:

Specimen No.	Description	Length [cm]	Horizon	Azimuth>	Dip
1	long bone	21	1	N 20° E	0°
2	rib	12	1	N 10° W	5°
3	calamite stem	80	2a	N 15° E	0°
...	...	...	...	...	...

“Azimuth” refers to the angle towards north. Orientation data are distributed on a halfsphere. Mean values (e.g. the average orientation of long bones) and other distribution parameters cannot be derived directly from the averaging of orientation angles but vector arithmetics has to be applied.


Cladistic data

Phylogeny on the basis of morphology conventionally involves cladistic methods, especially in the field of vertebrate paleontology which deals with a particular character-rich group that is deemed suitable for cladistic approaches employing certain kinds of analysis software specialized for the calculation of phylogenetic trees (e.g. PAUP, WinClada).

In cladistic datasets lines represent taxa, mostly species or genera of the group of interest, and columns represent characters (ordered by number), i. e. features of the skeleton which are variable among the included taxa:

Taxon	1	2	3	4	5	6	7	8	9	10
A-saurus	0	0	0	0	0	0	1	0	?	0
B-raptor	?	0	1	?	0	0	1	1	0	0
C-onyx	1	1	0	?	-	1	-	1	0	1
D-ops	1	1	2	1	1	1	1	0	1	1
E-mimus	0	-	2	1	1	2	0	0	1	1

One of the main issues in cladistics is the definition of characters and the correct (unbiased) coding of morphological information. You can include qualitative differences ("bone X contacts bone Y but not bone Z" = character state “0”; "bone X contacts bones Y and Z" = character state “1”) and quantitative differences ("length of metatarsal 3 larger than or as large as length of metatarsal 4" = character state "0"; "mt3 is shorter than mt4" = "1"). Sometimes mixed character states like "0 or 1 [but not 2]" occur in a taxon and are coded accordingly.


Missing data...

...occur all the time in paleontology ... either because specimens are not complete enough or because their geological age cannot be exactly determined or because specimens are too rare or valuable to use them for a destructive analysis method or because they are for some reason no longer accessible. "N/A" ("not applicable") or empty entries or question marks often symbolize missing data.


Some introductory literature:

Borradaile, G. J. 2003. Statistics of Earth Science Data. Springer, Berlin, 280 pages. ISBN 3540436030

Swan, A. R. H. and M. Sandilands. 1995. Introduction to geological data analysis. Blackwell, Oxford, 446 pages. ISBN 0632032243

Three recent papers on chroniosuchians

Buchwitz M, Voigt S. 2010. Peculiar carapace structure of a Triassic chroniosuchian implies evolutionary shift in trunk flexibility. Journal of Vertebrate Paleontology 30: 1697-1708. [Link]

Schoch RR, Voigt S, Buchwitz M. 2010. A chroniosuchid from the Triassic of Kyrgyzstan and analysis of chroniosuchian relationships. Zoological Journal of the Linnaean Society 160: 515-530. [Link]

Klembara J, Clack J, Čerňanský A. 2010. The anatomy of palate of Chroniosaurus dongusensis (Chroniosuchia, Chroniosuchidae) from the Upper Permian of Russia. Palaeontology 53: 1147-1153. [Link]

The redescription of the Chroniosaurus dongusensis palate by Klembara and colleagues adds further data to the morphological dataset provided by Clack and Klembara (2009) in their revision of C. dongusensis on the basis of a new specimen (which is the most complete of any yet known chroniosuchian). According to the updated phylogenetic analysis from the 2010 paper Chroniosaurus as the only included chroniosuchian taxon formed the sister group of embolomeres.

Schoch and colleagues (me included) describe Madygenerpeton pustulatus, a new species of chroniosuchians from the Middle to Late Triassic of Central Asia with a highly derived skull morphology and a carapace that was chroniosuchid-like in many aspects. The find shows that one lineage of chroniosuchids survived the Permian-Triassic boundary (by 20 or so million years).

The authors discuss characteristics uniting chroniosuchians with "higher reptiliomorphs" and unlike the approach of Klembara and colleagues their cladistic analysis, which includes five chroniosuchian taxa, results in a position of chroniosuchians somewhat closer to amniotes than to embolomeres. Chroniosaurus comes out as the closest relative of Madygenerpeton (both share the characteristic ornamentation of the skull and osteoderms besides other features).

Buchwitz & Voigt consider the functionality of chroniosuchian carapaces, comparing them to archosaur osteoderm systems. They argue that chroniosuchian carapaces basically served terrestrial locomotion but that the higher lateral flexibility of the Madygenerpeton osteoderm system was linked to a secondary increase in undulation swimming capability.

Reference:
Clack JA, Klembara J. 2009. An articulated specimen of Chroniosaurus dongusensis, and the morphology and relationships of the chroniosuchids. Special Papers in Palaeontology 81: 15-42. [Link]

Madygenerpeton pustulatus: first description finally out

Schoch, R. R., S. Voigt, and M. Buchwitz. 2010. A chroniosuchid from the Triassic of Kyrgyzstan and analysis of chroniosuchian relationships. Zoological Journal of the Linnean Society 160(3): 515-530. [Abstract]

Perception of deep time by geologists and biologists

Following the Darwin Year a colloquium lecture by zoologist Prof. Wolfgang Maier from Tübingen dedicated to "Darwin and deep time" discussed Charles Darwin’s role as a geologist who (among others) introduced the concept of deep time (a term later coined for million to several billion year long time ranges in geology) to biology.

Darwin did this by translating a hierarchy of (anatomical) similarity into a tree scheme that linked organisms from successive time slices with thousands of generations separating each two slices (see the scheme from Darwin’s "Origin of Species": [link]). The time slices can be related to certain units of the geological time scale.

Deep time correspondents in stratigraphy …

The problem of imagining time ranges far outside the scale of human experience has been approached by geologists with the method and concepts of stratigraphy: Strata of rock can be interpreted as a succession of time slices. Relative ages and age differences often manifest in an amount of rock which is loosely corresponding to certain a time span if similar rockforming processes are underlying. The relationship between the duration of a process and the amount of materal it creates can be inferred from direct observation of recent systems, allowing the assignment of absolute time (in years or millions of years) to a succession of strata. Given that long-term geological processes are rarely gradual, a more reliable absolute age is provided by radiometric dating.

If you would ask a geologist how he/ she percieves deep time I suppose he/ she would explain that it becomes clear from the slowness of present-day geological processes on the one hand and from the vast amount of products of such processes on the other hand.

… and phylogenetics

The evolution of organisms yields another approximation of deep time: The passing of time manifests in the hierarchical distinctness of living systems. Seeing how slow evolution works in a human being’s life span and how much change in anatomy/ biochemistry etc. must have occurred since last common ancestor of mouse and elephant or of mouse and lemon tree, leads to another way of percieving long time spans.

Regarding a certain distinctness and species richness of a group as a product of a certain number of character changes and speciation events (which is more or less well correlated with time) was probably enhanced by the more quantitative look at phylogenetics since the introduction of cladistics and molecular methods.

When I was attending a workshop on molecular paleobiology in 2008 specialists of that field were using the expression “(addressing) deep time problems” synonymous to phylogenetics of higher systematic groups, i.e. as the study of evolutionary changes that occurred deep down in the tree of animals and other organisms – opposed to let’s say the comparative analysis of human and neanderthal genomes or the radiation of Darwin finches.

The viewpoints of paleontologists…

But how do (present-day) paleontologists percieve deep time? You would expect them to share the view of both, phylogeneticists and stratigraphers, as most of them are taught at least a bit about both fields. However, for a paleontological fieldworker who employs the study of fossils as a means to understand and describe geological processes and paleoenvironmental contexts the flow of time is much easier grasped as a series of events preserved in a succession of rocks (and not as a phylogenetic tree scheme).

On the other hand, as a consequence of the so-called paleobiological revolution, you don’t need to be a field worker to contribute to the understanding of ancient organisms. In fact many aspects of paleobiology require mere laboratory and magazine work and you can spend a lifetime on that without ever considering rocks – naturally the perspective of such a modern paleobiologist on deep time will be strictly that of a phylogeneticist.

…can lead to conflicts?

These different perceptions on deep time and evolution are probably the background why cladistics was (and still is) met with some scepticism by “old school paleontologists” (or by “Eastern Europe school paleontologists”): Instead of considering all kinds of data for phylogenetic hypothesis-making I am supposed to use merely data from the (anatomical, molecular, etc.) comparison of organisms, as if evolution does not manifest in other ways in the geological record.

One could argue that it is possible to integrate other data, i.e. stratigraphic ages and palaeobiogeographical relations, in a cladistic analysis or at least in the discussion of its results, and so assure that hypotheses from the tree perspective on evolution are tested under consideration of independent data.

The idea to use time directly as a character in a parsimony analysis with consecutive time slices as character states may be epistemically unsound, as it is problematic to justify any kind of model assumption how time is weighted with respect to anatomical characters (and implicitly would this mean a post-hoc failure if proximity in time is regarded as indicative for degree of relationship?).

An a posteriori fit to other data – e.g. looking which of the equally parsimonious morphology-only-based time-calibrated trees has shorter lineages of no record (ghost lineages) – might be a better approach, but is still hard to swallow for some people who have problems with parsimony analyses on the basis of (too) small character samples (i.e. with inherent biases due to sample size/ character poorness or ambivalence of fossils).