Friday, June 28, 2013

Research as it happens I: Museum of the Rockies

Museums at their best are living institutions that serve science in addition to public education. I took this photograph today in the Hall of Growth and Behavior at the exemplary Siebel Dinosaur Complex of the Museum of the Rockies (Bozeman, MT).
Introduction – what am I doing?
 I presently have five major research projects on the go; two are descriptive monographs, one is a descriptive article, and the last are works on tyrannosaurid ontogeny.
On Monday, June 24 (2013), I began a two-week research trip at the paleontology collections of the Museum of the Rockies (Bozeman, MT), where my goal is to complete the text and photographic plates for a monographic description of a new taxon of tyrannosaurid. I’ve arrived with a manuscript that is 426 pages long (double spaced!), and I expect it to leap up over my time here.
The goal of this entry is to give non-paleontologists a sense of what types of activities are actually required to produce a formal anatomical description, which I present in a question and answer format.
Why am I doing this?
Descriptive works are a part of the discovery venture of science; the outcome for paleontology will be new information about a long-extinct organism from a vanished ecosystem. The quality and completeness of the fossils promises a level of detail that is usually not seen, which will help to improve our understanding of variation among tyrannosaurids in general.
My personal motivation is that I want to learn everything that I can about how this group of dinosaurs grew and evolved for a longer-term project that will attempt to synthesize those sets of information. A synthesis of ontogeny (growth) and phylogeny (evolution) can provide the footing to explain how evolutionary changes occurred between ancestors and their descendants.
Why should anyone care?
Descriptions of new species of extinct organisms inevitably expand humanity’s understanding of nature, and serves to incrementally displace and reduce the influence of superstition upon people. Extinct animals are a reminder that our day-to-day concerns are limited to the current moment of our lives, the mere skin of history stretched thin over a vast and knowable summit of geological time.
What is a monograph?
A monograph is a detailed and lengthy formal scientific description of a specimen or specimens that is unconstrained by the short traditional page length of a typical journal article. Monographs are sometimes measured in the hundreds of pages, including the one I am drafting on this visit.
Why take this approach?
In my view, the days are over where short descriptions are sufficient enough to describe new species (I too am guilty of this approach), especially if a growth series is available. We have to take the opportunity to accurately assess variation and clear the noise from the signals of phylogeny and ontogeny. These goals require detail. We also have to make the effort to keep up with the volume of data that is scattered among many publications.
How long have you been working on this particular project?
In total, this project so far has required two previous research trips; the first took a month and the second was for two weeks. In total, I expect that it will have taken me two full months to write the description and produce the series of photographic plates while the specimens are in hand.
How does the writing process proceed?
This project has been a two-pass experience. During the first month-long visit, I drafted the entire ~300 page manuscript. With that raw description in hand, at home I then read it alongside other descriptive works (e.g., Russell, 1970, Brusatte et al., 2012) and phylogenetic studies (e.g., Currie et al., 2003; Brusatte et al., 2010). Along the way, I made certain to take note of all of the osteological features and phylogenetic characters that are mentioned in those works and include them in the manuscript for comparison with the new fossils.
This part of the process is written by hand as marginalia; on this collections visit and during the previous one, I systematically proceed page by page, comparing each note with the specimens, and adding those data to the manuscript. This has resulted in an expanded description that will make it useful for researchers to readily understand how the new species compares with other fossils.
In addition to adding the marginalia, I am also adding specimens to the description. During the first month I spent the first three weeks writing up the entire growth series of specimens until I realized that I was running out of time. For the last week I only wrote up the type (reference) specimen, leaving much of the palate and the entire mandibular ramus without comparative description. I am rectifying that deficit on this trip.
What have I accomplished so far?
In four days I have written 57 pages in expanding the anatomical descriptions of the ectopterygoid, articular, surangular, and angular; today I’ve largely finished writing up the prearticular, which has brought the page count of the manuscript to 483. The pterygoid, splenial, intercoronoid, dentary, dentition, and lesions are left for me to complete. Beyond that, I have the photographic plates to prepare and label.
What is the level of commitment required to do this?
The level of commitment is quite high; usually collections visits are from 9:00 am to 6:00 pm, but depending on the institution the day can start as early as 7:30 am and end at 10:00 pm. Some research trips can extend over weekends. I take every moment that is made available to me.
This sort of work is solitary; it requires long hours of isolation and intense focus. My best hours are in the morning, whereas the afternoon interval of 2:00 pm-5:00 pm is a slog. There is also the emotional cost of an extended time away from family, and the literal expense of personal money if research funds are not available.
What do I expect to accomplish?
1)   Complete the osteological description of the type specimen and the referred specimens in the context of a growth series.
2)   Document the lesions on the skull and jaws.
3)   Complete the sets of measurements for each specimen.
4)   Complete a draft of each photographic plate with labels.
I still have a little over a week to accomplish these goals…

At work on the monograph in January, 2013. Photograph by Holly Woodward.
References cited

--> -->
Brusatte, S. L., T.D. Carr, andM.A. Norell.  2012. The osteology of Alioramus, a gracile and long-snouted tyrannosaurid (Dinosauria: Theropoda) from the Late Cretaceous of Mongolia. Bulletin of the American Museum of Natural History 366: 1-197.

Brusatte, S.L., M.A. Norell, T.D. Carr, G.M. Erickson, J.R. Hutchinson, A.M. Balanoff, G.S. Bever, J.N. Choiniere, P.J. Makovicky, and X. Xu. 2010. Tyrannosaur paleobiology: new research on ancient exemplar organisms. Science 329: 1481-1485.

Currie, P.J. 2003. Cranial anatomy of tyrannosaurid dinosaurs from the late Cretaceous
Alberta, Canada. Acta Palaeontologica Polonica 48: 191–226.

Currie, P.J., J.H. Hurum, and K. Sabath. 2003. Skull structure and evolution in
tyrannosaurid dinosaurs. Acta Palaeontologica Polonica 48: 227–234.

Russell, D.A. 1970. Tyrannosaurs from the Late Cretaceous of western Canada. National Museum of Natural Science Publications in Palaeontology 1: 1-34.

Wednesday, June 26, 2013

Osteology II: Craniofacial frame and openings in dorsal view

The craniofacial skeleton of a subadult Albertosaurus libratus seen in dorsal view, 
© Dino Pulerà. Labels emphasize the overall structure of the skull and are explained below. Carbon dust plate by Mr. Dino Pulerà.
When viewed from above, the function of the tyrannosaurid skull is starkly clear: it is a supreme biological weapon honed by natural selection that is adapted to effortlessly aim, strike, and grip living animals with immobilizing power.
Directional terms
Lateral: A point of reference toward or at the side of a given structure (in this case, the craniofacial skeleton).
Medial: A point of reference toward or at the rostrocaudal midline of a given structure (in this case, the craniofacial skeleton).
Rostrolateral: A direction or point of reference that is both ahead of and external to another point of reference. Variation: caudolateral.
Rostromedial: A direction or point of reference that is both ahead of and internal to another point of reference. Variation: caudomedial.
AOFEN - Antorbital fenestra: In dorsal view, the antorbital fenestra is a long and narrow slot that extends along the lateral surface of the snout. It is surrounded ventrally and rostrally by the maxilla; medially and dorsally by the nasal rostrally, and by the lacrimal caudally; and the jugal contributes to its caudoventral corner. A wide axial strut separates the contralateral fenestrae dorsally, which is dominated by the nasal rostrally, but with caudolateral contributions by the lacrimals.
AOR – Antorbital region: When seen from above, the antorbital region narrows as it extends rostrally from the orbital region to form the parallel-sided snout.
BN - Bony naris: In dorsal view, the bony naris is a long and narrow opening situated somewhat toward the dorsal midline. It is enclosed rostrolaterally and ventrally by the premaxilla, caudolaterally and ventrally by the nasal, and medially and dorsally by the nasal.
DTFEN - Dorsotemporal fenestra: The dorsotemporal fenestra is a hole through the dorsal skull roof that permits the adductor (jaw-closing) muscles access to a high surface area of attachment. This fenestra is the largest opening that is seen in dorsal view, and it easily exceeds all others in terms of length, width, and cross sectional area. The fenestra narrow medially and it widens rostrally and caudally as it extends laterally.
The fenestra is surrounded by several bones, including: the frontal rostromedially; the postorbital rostrolaterally; the squamosal caudolaterally and caudally; the prootic caudomedially; the laterosphenoid rostromedially; and also the parietal rostromedially, between the laterosphenoid and frontal.
The dorsotemporal fenestra differs from the other openings described previously in that its circumference does not lie in a single plane; for example, the squamosal and postorbital are situated dorsal to the level of the prootic and laterosphenoid. The fenestra is a side effect of looking down into an irregular tunnel composed of many bones. Regardless, the dorsotemporal fenestra has a large cross sectional area in the horizontal plane, which indicates in the living animal a high bite force exerted from each side of the head.

LTFEN - Laterotemporal fenestra: In dorsal view, only the ventral part of this opening can be seen, where it is reduced to a narrow slot.
NB – Narial bar: When viewed from above, the narial bar is much a much wider structure than it appears to be in lateral view. The proximal end of the bar is wide and vaulted, and it gradually narrows and flattens as it extends rostroventrally to the dorsal surface of the premaxilla. The narial bar is dominated by the nasal, whereas the premaxilla is limited to the rostral end of the bar. The tip of each premaxilla is gripped laterally and medially by the nasal; the medial slip of the nasal is not seen in all tyrannosaurids.
OFEN - Orbital fenestra: In dorsal view, the orbital fenestra is a small triangular opening situated toward the lateral surface of the skull that is surrounded laterally and rostromedially by the jugal; medially and dorsally by the lacrimal rostrally, and the frontal caudally; and caudolaterally by the postorbital.
OR – Orbital region: When seen from above, the orbital region is much smaller than it appears in lateral view. It is roofed by the frontal, prefrontal, lacrimal, postorbital, and nasal; it is bounded caudally by the postorbital and jugal, ventrally by the jugal, and rostrally by the lacrimal, although some of these are not in the plane of view.
ORTR – Orbitotemporal region: In dorsal view, the orbitotemporal region surrounds the dorsotemporal and orbital fenestrae. This region has a complex three dimensional shape and it includes many bones, including the jugal, maxilla lacrimal, prefrontal, frontal, parietal, postorbital, squamosal, prootic, laterosphenoid, supraoccipital, basioccipital, quadratojugal, pterygoid, epipterygoid, and ectopterygoid (the last three bones are not illustrated here).
TR - Temporal region: When seen from above, the temporal region is the largest part - over half - of the orbitotemporal region. Its size directly reflects the great amount of adductor musculature that was present in life. In contrast to the dominant temporal region, the small orbital region is virtually a bare necessity required for aiming the snout and exerting the massive bite forces stored in the caudal quarter to third of the skull.
UTB - Upper temporal bar: In dorsal view, the upper temporal bar is a very narrow strut that extends between the relatively thin paroccipital complex (parietal + squamosal + otoccipital) caudally and the stable dorsal skull roof rostromedially. The squamosal forms the caudal part of the bar, whereas the postorbital completes it rostrally.
The squamosal is apposed to the rostrolateral surface of the paroccipital process of the otoccipital, and it extends rostrally along that structure as a tapering fingerlike process that fits into a long and deeply incised groove between the parietal above and the prootic below. The surface area of the connection between the squamosal and otoccipital is quite high, ensuring a stable contact between their otherwise lightly textured and gently undulating surfaces. Rostrolaterally the squamosal receives the squamosal process of the postorbital into a long and deep cleft in its lateral surface.
The postorbital extends rostromedially to articulate with the frontal along a complex and stable contact with the frontal dorsally and the laterosphenoid caudoventrally. Rostrally the postorbital and frontal abut each other, whereas caudal to this they are secured to each other by prominent and complementary ridges and slots. Caudoventrally the laterosphenoid inserts a stout process into a deep, cup-like process in the medial surface postorbital below the frontal. In some large adult tyrannosaurines, the postorbital and lacrimal are joined to each other above the orbital fenestra (Currie, 2003). In these cases, the upper temporal is incorporated into the orbital region.

References cited
Currie, P. J. 2003. Cranial anatomy of tyrannosaurid dinosaurs from the late Cretaceous Alberta, Canada. Acta Palaeontologica Polonica 48:191-226.

Tuesday, June 25, 2013

A note on the taxonomy used in this blog

The current consensus of the phylogenetic relationships of Tyrannosauridae. Pairs of sister species are subordinate members of a common ancestor that establishes the genus name. This approach maximizes the information content of the Linnean binomial names, where phylogenetic (sister group relationship) and morphological similarity (synapomorphy) is emphasized.

I am alone among my fellow tyrannosauroid colleagues, where I do not use the generic names Gorgosaurus or Tarbosaurus. My reason is that taxonomic names (i.e., genera) should be used to reflect phylogenetic relationships between pairs of sister species. This approach maximizes the information content of the name.
The cladogram above shows the present consensus on tyrannosaurid phylogenetic relationships, where Albertosaurus libratus and A. sarcophagus are sister species, and Tyrannosaurus rex and T. bataar are also sister species.  If A. libratus is bumped up to the genus Gorgosaurus, and if T. bataar is bumped up to Tarbosaurus, then the information content regarding its sister species relationship is lost. Also, the generic status implies a greater morphological and phylogenetic distance between the sister species than actually exists.
Notice the taxa that are not paired with sister species (Bistahieversor, Alioramus, Teratophoneus, Daspletosaurus), which mark successive lineages that contain multiple species (more than two). In these cases, generic status for each species is reasonable to emphasize their phylogenetic and morphological distinctiveness.
It has been argued that bestowing a genus name for every species makes communication more efficient. However, this is not truly expedient if the sister group relationship still needs to be spelled out. It also runs against the grain of using binomials in the first place.
In short, I'll adjust the taxonomy the day it is shown that A. libratus and A. sarcophagus, or T. bataar and T. rex, are no longer sister species. Until then, I stand apart with - I think - a defensible conviction.

Sunday, June 23, 2013

Osteology I: Craniofacial frame and openings in lateral view

Composite skull of a subadult Albertosaurus libratus in right lateral view with the major openings and struts labeled,
© Dino Pulerà. Abbreviations are defined below. Carbon dust plate by Mr. Dino Pulerà.

The osteology series of this blog is a primer for enthusiasts who are not necessarily paleontologists, but who want to know the definitions of the anatomical terms that they read about in technical articles and books. This series will begin with the craniofacial skeleton, followed by its individual bones, and then it will move on to the mandibular ramus, and so on.
Each entry of this section will start with a labeled figure, where spaces will be indicated by a leader line ending with a dot, and structures with lines that end in an arrowhead. The descriptions will be organized alphabetically, where each term will be defined and described. The spaces and structures will be based on the literature; novel terms will not appear here. Hopefully this approach will result in a clear and useful guide to derived tyrannosauroid (Bistahieversor + Tyrannosauridae) osteology.
Institutional abbreviations: AMNH FARB, American Museum of Natural History Fossil Amphibians and Reptiles (New York); ROM, Royal Ontario Museum (Toronto); TMP, Royal Tyrrell Museum of Palaeontology (Drumheller); USNM, United States National Museum (Washington).
A note on the figure
The figure of Albertosaurus libratus seen in this entry is a colorized version of the grayscale carbon dust plate that appeared in Carr (1999). This illustration is a composite of several specimens: AMNH FARB 5664, postorbital; ROM 1247, maxilla, nasals, lacrimal, jugal, braincase; ROM 1422, premaxilla, squamosal; TMP 1990.036.0500, premaxilla; USNM 12814, palatine, quadratojugal. The rationale for the decision to draft a composite was to present an approximation of what a “large stage 1” A. libratus would look like, where each of the specimens included are of the same relative maturity (Carr, 1999). The length of the skull is approximately 750 mm.
My illustrator, Mr. Dino Pulerà, and I worked closely together on this illustration. I first drafted a line drawing in pencil that was traced from photographs of the specimens, which Dino then transferred onto illustration board. He then covered the board in frisket (a sheet of low tack removable adhesive plastic), and cut out the space of the skull, leaving covered the spaces that extend through the skull (e.g., bony naris, antorbital fenestra). At that point illustration commenced, where Dino applied layers of graphite dust by brush onto the exposed board surface, gradually blocking out the form and shadows. By the convention of scientific illustration, the light source is from the upper left and skulls are usually depicted in right lateral view.
Once the form of the skull was achieved by brush, the intensive process in adding details began. To ensure accuracy Dino worked with the specimens (AMNH FARB, ROM) in hand illuminated with a single light source, and with me acting as art director over his shoulder. This approach ensured every detail seen in the specimens would be included in the image. Carbon dust has an advantage over line-and-stipple and coquille board in that the entire surface of a bone can be rendered, where no detail is lost to the low resolution and extensive white highlights that compromise the other approaches. With carbon dust, only the tooth (coarseness) of the board limits the level of detail in the illustration. This part of the process took the greatest amount of time, between 40 and 80 hours. In the end, the frisket was peeled and the image scanned for digital cleanup and layout.
Directional terms are used throughout the osteological entries, and they are defined here.
Caudal: A point of reference at or toward the back of the skull.
Dorsal: A point of reference at or toward the top (upper surface) of the skull.
Rostral: A point of reference at or toward the front of the skull.
Ventral: A point of reference at or toward the bottom (lower edge) of the skull.
AOFEN – Antorbital fenestra: In terms of area, the antorbital fenestra (“window ahead of the eye”) is the largest opening of the skull. It is surrounded rostrodorsally, rostrally, and rostroventrally by the maxilla, caudoventrally by the jugal, and caudally and caudodorsally by the lacrimal. This large space is an osteological correlate for the paranasal sinus that extended laterally from the nasal airway to breach the bony enclosure of the snout. Several bones can be seen within the antorbital fenestra, including the conjoined pterygoid, palatine, and vomer. Also, the bony choana and palatine fenestra can be seen as gaps below and between the palatal bones.
The antorbital fenestra splits the facial skeleton into a set of dorsoventrally shallow struts; the dorsal strut is formed by the conjoined lacrimal, maxilla, and nasal, which form the dorsal skull roof in this region. The ventral strut is formed by the jugal and maxilla on each side of the snout.
AOR – Antorbital region: This region is equivalent to the vernacular term ‘snout’, the region of the face ahead of the orbital fenestra. The antorbital region is flanked laterally by (from caudal to rostral) the lacrimal, maxilla, and premaxilla; dorsally it is covered by the nasal; and ventrally and medially it is composed of (rostrally to caudally) the vomer, palatines, and pterygoids. The antorbital region is an open structure that is penetrated by several large openings, including the bony naris, antorbital fenestra, bony choana, and palatine fenestra. Importantly, this region also includes the teeth that extend from its lower margin and continue across the front. The outer surface of this region is coarse, especially its dorsal surface where primary ornamental structures are located. The coarse surface surrounds the smooth antorbital fossa.
Functionally the antorbital region is complex; it includes the nasal airway, pneumatic sinuses, the palate, the upper jaw, ornamental structures, and a concentration of openings for tactile sensory nerves. Taken together, it is reasonable to regard the antorbital region as simultaneously a massive fingertip, shield, signal platform, nasal passage, and penetrating pincer.
BCH – Bony choana: This opening corresponds to the vernacular ‘internal nostril’, the bony caudal end of the nasal passage. In life, soft tissue would have extended this passage further caudally. The bony choana is surrounded rostrolaterally by the maxilla; rostromedially by the vomer; and caudolaterally, caudally, and caudomedially by the palatine.
BN – Bony naris: The bony naris corresponds to the vernacular ‘nostril’, the rostral end of the nasal passage. In life, soft tissue would have positioned the external opening toward the rostroventral region of the bony naris. The bony naris is surrounded rostrodorsally, rostrally, and rostrolaterally by the premaxilla, and caudolaterally, caudally, and caudodorsally by the nasal.
LTB – Lower temporal bar: The lower temporal bar forms the ventral boundary of the laterotemporal fenestra, and it is composed rostrally by the jugal and caudally by the quadratojugal. The presence of this bar is typical of the diapsid condition seen in amniotes. The jugal component is formed by a pair of caudally extending processes that extend deep to a single rostrally extending paddle-like process of the quadratojugal. The lower temporal bar forms much the ventral margin of the skull in the temporal region. It is also an important strut that extended lateral to the jaw-closing muscles and connects the suborbital region with the suspensorium (quadrate + quadratojugal + squamosal).
LTFEN – Laterotemporal fenestra: This fenestra opens onto the adductor chamber, a space through which the jaw closing muscles extended, as well as structures associated with the outer and middle ears. This opening is typical of diapsid amniotes. The laterotemporal fenestra is surrounded rostrodorsally by the postorbital, rostroventrally by the jugal, caudoventrally by the quadratojugal, and caudodorsally by the squamosal. Parts of several structures can be seen through the fenestra, including the parietal, laterosphenoid, prootic, otoccipital, quadrate, and pterygoid.
The fenestra in derived tyrannosauroids is distinct in that a large rostrally extending flange composed of the squamosal above and quadratojugal below nearly cuts the fenestra into a pair of subordinate openings. However, in no tyrannosauroids is the opening so completely separated.
NB – Narial bar: The narial bar is the strut that encloses the bony naris dorsally and rostrodorsally. It is comprised by the nasal rostrally, and by the nasal and premaxilla caudally, where the premaxilla extends along the lateral surface of the nasal, eventually tapering and stopping at the dorsal margin of the bony naris.
OFEN – Orbital fenestra: The orbital fenestra surrounds the former location of the eyeball and its associated structures. It is surrounded dorsally by the frontal (sometimes excluded by the conjoined postorbital and lacrimal), rostrodorsally, rostrally, and rostroventrally by the lacrimal, ventrally by the jugal, and caudally and caudodorsally by the postorbital. Although the prefrontal is seen in lateral view in the rostrodorsal corner of the orbit, it does not contribute to the margin of the fenestra.
In large tyrannosauroids such as Bistahieversor and Tyrannosaurus, the fenestra is keyhole shaped, with a circular dorsal region and a triangular ventral region. The upper part surrounded the eyeball, whereas the ventral region did not. Parts of several structures can be seen through the fenestra, including the mesethmoid, orbitosphenoid, sphenoid rostrum, prefrontal, and pterygoid.
ORTR – Orbitotemporal region: This region surrounds the orbital and laterotemporal fenestrae, and comprises approximately the caudal half of the craniofacial skeleton.
PALFEN – Palatine fenestra: This opening occurs between the pterygoid and palatine and it is seen within the antorbital fenestra.
POB – Postorbital bar: This wide bar separates the laterotemporal and orbital fenestrae, and so forms their rostral and caudal margins, respectively. The postorbital forms the rostrodorsal half of the structure, whereas the jugal forms its caudoventral part. The postorbital bar flanks the adductor chamber laterally, and only its rostrodorsal part encloses the caudodorsal corner of the orbital region.
TR – Temporal region: The temporal region represents the caudal half of the orbitotemporal region and it surrounds the adductor chamber, through which extended the adductor musculature in life. The temporal region is comprised by the braincase medially, the suspensorium caudolaterally, and the postorbital and jugal rostrolaterally. The space is crossed medially by the vertical strut formed by the quadrate and pterygoid, which separates the medial tympanic (middle ear) space from the lateral channel for the adductor musculature.
UTB – Upper temporal bar: The upper temporal bar bounds the laterotemporal fenestra dorsally and connects the suspensorium with the postorbital bar. The squamosal forms the caudal part of the bar and extends medial to the postorbital, which forms the rostral part of the bar.  The squamosal receives the postorbital in a deep, v-shaped groove. When articulated, the squamosal has the appearance of splitting into a pair of processes above and below the postorbital. In most cases the dorsal process extends to the rostral end of the bar, whereas the ventral bar stops short of it.

References cited
Carr, T. D.  1999.  Craniofacial Ontogeny in Tyrannosauridae (Dinosauria, Coelurosauria). Journal of Vertebrate Paleontology 19:497-520.