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1.  Variation of osteocyte lacunae size within the tetrapod skeleton: implications for palaeogenomics 
Biology Letters  2011;7(5):751-754.
Recent studies have emphasized the ability to reconstruct genome sizes (C-values) of extinct organisms such as dinosaurs, using correlations between known genome sizes and bone cell (osteocyte lacunae) volumes. Because of the established positive relationship between cell size and genome size in extant vertebrates, osteocyte lacunae volume is a viable proxy for reconstructing C-values in the absence of any viable genetic material. However, intra-skeletal osteocyte lacunae size variation, which could cause error in genome size estimation, has remained unexplored. Here, 11 skeletal elements of one individual from each of four major clades (Mammalia, Amphibia, Aves, Reptilia) were examined histologically. Skeletal elements in all four clades exhibit significant differences in the average sizes of their lacunae. This variation, however, generally does not cause a significant difference in the estimated genome size when common phylogenetic estimation methods are employed. On the other hand, the spread of the estimations illustrates that this method may not be precise. High variance in genome size estimations remains an outstanding problem. Additionally, a suite of new methods is introduced to further automate the measurement of bone cells and other microstructural features on histological thin sections.
doi:10.1098/rsbl.2011.0173
PMCID: PMC3169053  PMID: 21411450
osteocyte lacunae; genome size; palaeogenomics; bone histology
2.  Variation, Variability, and the Origin of the Avian Endocranium: Insights from the Anatomy of Alioramus altai (Theropoda: Tyrannosauroidea) 
PLoS ONE  2011;6(8):e23393.
The internal braincase anatomy of the holotype of Alioramus altai, a relatively small-bodied tyrannosauroid from the Late Cretaceous of Mongolia, was studied using high-resolution computed tomography. A number of derived characters strengthen the diagnosis of this taxon as both a tyrannosauroid and a unique, new species (e.g., endocranial position of the gasserian ganglion, internal ramification of the facial nerve). Also present are features intermediate between the basal theropod and avialan conditions that optimize as the ancestral condition for Coelurosauria—a diverse group of derived theropods that includes modern birds. The expression of several primitive theropod features as derived character states within Tyrannosauroidea establishes previously unrecognized evolutionary complexity and morphological plasticity at the base of Coelurosauria. It also demonstrates the critical role heterochrony may have played in driving patterns of endocranial variability within the group and potentially reveals stages in the evolution of neuroanatomical development that could not be inferred based solely on developmental observations of the major archosaurian crown clades. We discuss the integration of paleontology with variability studies, especially as applied to the nature of morphological transformations along the phylogenetically long branches that tend to separate the crown clades of major vertebrate groups.
doi:10.1371/journal.pone.0023393
PMCID: PMC3154410  PMID: 21853125
3.  Implications of flexible-shelled eggs in a Cretaceous choristoderan reptile 
Flexible, or soft-shelled, eggs are almost unknown in the fossil record, leaving large gaps in our knowledge of the reproductive biology of many tetrapod clades. Here, we report two flexible-shelled eggs of the hyphalosaurid choristodere Hyphalosaurus baitaigouensis from the Early Cretaceous of China, one containing an embryo and the second associated with a neonate. Choristoderes are an enigmatic group of aquatic reptiles that survived the K–T extinction but died out in the Miocene. Hyphalosaurids, a specialized clade of Choristodera, resemble miniature plesiosaurs and are considered to be primarily aquatic in habit. Scanning electron microscopy of samples from the eggs reveals a thin, non-columnar external mineralized layer characterized by rounded nodes and tentatively identified poorly structured irregular pores, with an underlying amorphous layer presumably representing decomposed protein fibrils. While the relationships of Choristodera remain controversial, eggshell microstructure more closely resembles that of Lepidosauromorpha (the lineage including lizards) as opposed to that of Archosauromorpha (the lineage including birds and crocodiles).
doi:10.1098/rspb.2009.2035
PMCID: PMC2842823  PMID: 20018793
eggshell; embryo; paleontology; fossil; reptile
4.  A giant ornithomimosaur from the Early Cretaceous of China 
Ornithomimosaurs (ostrich-mimic dinosaurs) are a common element of some Cretaceous dinosaur assemblages of Asia and North America. Here, we describe a new species of ornithomimosaur, Beishanlong grandis, from an associated, partial postcranial skeleton from the Aptian-Albian Xinminpu Group of northern Gansu, China. Beishanlong is similar to another Aptian-Albian ornithomimosaur, Harpymimus, with which it shares a phylogenetic position as more derived than the Barremian Shenzhousaurus and as sister to a Late Cretaceous clade composed of Garudimimus and the Ornithomimidae. Beishanlong is one of the largest definitive ornithomimosaurs yet described, though histological analysis shows that the holotype individual was still growing at its death. Together with the co-eval and sympatric therizinosaur Suzhousaurus and the oviraptorosaur Gigantraptor, Beishanlong provides evidence for the parallel evolution of gigantism in separate lineages of beaked and possibly herbivorous coelurosaurs within a short time span in Central Asia.
doi:10.1098/rspb.2009.0236
PMCID: PMC2842665  PMID: 19386658
Ornithomimosauria; body-size evolution; phylogeny; faunal assemblage; Cretaceous; Central Asia
5.  A longirostrine tyrannosauroid from the Early Cretaceous of China 
The fossil record of tyrannosauroid theropods is marked by a substantial temporal and morphological gap between small-bodied, Barremian taxa, and extremely large-bodied taxa from the latest Cretaceous. Here we describe a new tyrannosauroid, Xiongguanlong baimoensis n. gen. et sp., from the Aptian–Albian Xinminpu Group of western China that represents a phylogenetic, morphological, and temporal link between these disjunct portions of tyrannosauroid evolutionary history. Xiongguanlong is recovered in our phylogenetic analysis as the sister taxon to Tyrannosauridae plus Appalachiosaurus, and marks the appearance of several tyrannosaurid hallmark features, including a sharp parietal sagittal crest, a boxy basicranium, a quadratojugal with a flaring dorsal process and a flexed caudal edge, premaxillary teeth bearing a median lingual ridge, and an expanded axial neural spine surmounted by distinct processes at its corners. Xiongguanlong is characterized by a narrow and elongate muzzle resembling that of Alioramus. The slender, unornamented nasals of Xiongguanlong are inconsistent with recent hypotheses of correlated progression in tyrannosauroid feeding mechanics, and suggest more complex patterns of character evolution in the integration of feeding adaptations in tyrannosaurids. Body mass estimates for the full-grown holotype specimen of Xiongguanlong fall between those of Late Cretaceous tyrannosaurids and Barremian tyrannosauroids, suggesting that the trend of increasing body size observed in North American Late Cretaceous Tyrannosauridae may extend through the Cretaceous history of Tyrannosauroidea though further phylogenetic work is required to corroborate this.
doi:10.1098/rspb.2009.0249
PMCID: PMC2842666  PMID: 19386654
China; Cretaceous; Dinosauria; Tyrannosauroidea; Xinminpu Group; Xiongguanlong baimoensis
6.  Was Dinosaurian Physiology Inherited by Birds? Reconciling Slow Growth in Archaeopteryx 
PLoS ONE  2009;4(10):e7390.
Background
Archaeopteryx is the oldest and most primitive known bird (Avialae). It is believed that the growth and energetic physiology of basalmost birds such as Archaeopteryx were inherited in their entirety from non-avialan dinosaurs. This hypothesis predicts that the long bones in these birds formed using rapidly growing, well-vascularized woven tissue typical of non-avialan dinosaurs.
Methodology/Principal Findings
We report that Archaeopteryx long bones are composed of nearly avascular parallel-fibered bone. This is among the slowest growing osseous tissues and is common in ectothermic reptiles. These findings dispute the hypothesis that non-avialan dinosaur growth and physiology were inherited in totality by the first birds. Examining these findings in a phylogenetic context required intensive sampling of outgroup dinosaurs and basalmost birds. Our results demonstrate the presence of a scale-dependent maniraptoran histological continuum that Archaeopteryx and other basalmost birds follow. Growth analysis for Archaeopteryx suggests that these animals showed exponential growth rates like non-avialan dinosaurs, three times slower than living precocial birds, but still within the lowermost range for all endothermic vertebrates.
Conclusions/Significance
The unexpected histology of Archaeopteryx and other basalmost birds is actually consistent with retention of the phylogenetically earlier paravian dinosaur condition when size is considered. The first birds were simply feathered dinosaurs with respect to growth and energetic physiology. The evolution of the novel pattern in modern forms occurred later in the group's history.
doi:10.1371/journal.pone.0007390
PMCID: PMC2756958  PMID: 19816582
7.  Avian-like breathing mechanics in maniraptoran dinosaurs 
In 1868 Thomas Huxley first proposed that dinosaurs were the direct ancestors of birds and subsequent analyses have identified a suite of ‘avian’ characteristics in theropod dinosaurs. Ossified uncinate processes are found in most species of extant birds and also occur in extinct non-avian maniraptoran dinosaurs. Their presence in these dinosaurs represents another morphological character linking them to Aves, and further supports the presence of an avian-like air-sac respiratory system in theropod dinosaurs, prior to the evolution of flight. Here we report a phylogenetic analysis of the presence of uncinate processes in Aves and non-avian maniraptoran dinosaurs indicating that these were homologous structures. Furthermore, recent work on Canada geese has demonstrated that uncinate processes are integral to the mechanics of avian ventilation, facilitating both inspiration and expiration. In extant birds, uncinate processes function to increase the mechanical advantage for movements of the ribs and sternum during respiration. Our study presents a mechanism whereby uncinate processes, in conjunction with lateral and ventral movements of the sternum and gastral basket, affected avian-like breathing mechanics in extinct non-avian maniraptoran dinosaurs.
doi:10.1098/rspb.2007.1233
PMCID: PMC2596187  PMID: 17986432
Aves; theropod; uncinate processes; ventilation; gastralia
8.  Growth patterns in brooding dinosaurs reveals the timing of sexual maturity in non-avian dinosaurs and genesis of the avian condition 
Biology Letters  2007;3(5):558-561.
The timing of sexual maturation in non-avian dinosaurs is not known. In extant squamates and crocodilians it occurs in conjunction with the initial slowing of growth rates as adult size is approached. In birds (living dinosaurs) on the other hand, reproductive activity begins well after somatic maturity. Here we used growth line counts and spacing in all of the known brooding non-avian dinosaurs to determine the stages of development when they perished. It was revealed that sexual maturation occurred well before full adult size was reached—the primitive reptilian condition. In this sense, the life history and physiology of non-avian dinosaurs was not like that of modern birds. Palaeobiological ramifications of these findings include the potential to deduce reproductive lifespan, fecundity and reproductive population sizes in non-avian dinosaurs, as well as aid in the identification of secondary sexual characteristics.
doi:10.1098/rsbl.2007.0254
PMCID: PMC2396186  PMID: 17638674
development; reproduction; histology; Aves; Theropoda
9.  Prey choice and cannibalistic behaviour in the theropod Coelophysis 
Biology Letters  2006;2(4):611-614.
Abstract
Direct evidence of prey choice in carnivorous dinosaurs is rare in the fossil record. The most celebrated example pertains to purported stomach contents in the carnivorous dinosaur Coelophysis bauri, which besides revealing prey choice, also points to cannibalistic behaviour as being commonplace (Colbert 1989, 1995). Here, we test this hypothesis by conducting the first comprehensive anatomical and histological examination of the famed Coelophysis ‘cannibals’. The results unequivocally show that the gut contents derive from early crocodylomorphs rather than juveniles of Coelophysis. These findings suggest that this taxon is not cannibalistic and bring into question the commonality of this behaviour among non-avian dinosaurs.
doi:10.1098/rsbl.2006.0524
PMCID: PMC1834007  PMID: 17148302
Coelophysis; prey choice; cannibalism; palaeobiology; Mesozoic; dinosaur
10.  Extreme convergence in the body plans of an early suchian (Archosauria) and ornithomimid dinosaurs (Theropoda) 
Living archosaurs comprise birds (dinosaurs) and crocodylians (suchians). The morphological diversity of birds and stem group dinosaurs is tremendous and well-documented. Suchia, the archosaurian group including crocodylians, is generally considered more conservative. Here, we report a new Late Triassic suchian archosaur with unusual, highly specialized features that are convergent with ornithomimid dinosaurs. Several derived features of the skull and postcranial skeleton are identical to conditions in ornithomimids. Such cases of extreme convergence in multiple regions of the skeleton in two distantly related vertebrate taxa are rare. This suggests that these archosaurs show iterative patterns of morphological evolution. It also suggests that this group of suchians occupied the adaptive zone that was occupied by ornithomimosaurs later in the Mesozoic.
doi:10.1098/rspb.2005.3426
PMCID: PMC1560254  PMID: 16600879
convergent evolution; Effigia; Shuvosaurus; suchian; Triassic; archosaur

Results 1-10 (10)