Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes.

The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.

A new crocodilian from the Lower Cretaceous Crato Formation of north-eastern Brazil

A new mesosuchian crocoddian from the Nova Olinda Member of the Crato Formation (Lower Cretaceous, Aptian) of north-eastern Brazil is described. Susisuchus anatoceps gen. et sp. nov. is the first crocodillan to be reported from this formation. It is represented by an incomplete, partially articulated skeleton: the skull and mandible, partial postcranial axial skeleton, forelimbs and portions of the osteodermal skeleton. Preservation of soft tissues includes the skin surrounding both forelimbs and the digits of the right hand. The state of preservation of the specimen suggests that it was incorporated into the basin as a desiccated carcass. Susisuchus anatoceps is one of the oldest crocodilians with a eusuchian-type dorsal shield, comprising a tetraserial paravertebral shield and, either side of this, two sagittal rows of accessory osteoderms. It also possesses amphicoelous thoracic, lumbar and caudal vertebrae. This combination of postcranial features have never before been seen in a crocodilian and warrant the erection of a new family within Mesosuchia: Susisuchidae. Taxonomically, S. anatoceps is similar to a number of Lower Cretaceous mesosuchians previously considered to have given rise to eusuchians, most notably the Glen Rose crocodilian and a new, but as yet undescribed crocodillan from the Lower Cretaceous Winton Formation of western Queensland, Australia. Preliminary preparation of the Winton crocodilian indicates that it may belong to Susisuchidae, supporting the hypotheses of interchange between the vertebrate faunas of South America and Australia during the Lower Cretaceous.

Catchment-specific element signatures in estuarine crocodiles (Crocodylus porosus) from the Alligator Rivers Region, northern Australia

The concentrations of Na, K, Ca, Mg, Ba, Sr, Fe, Al, Mn, Zn, Pb, Cu, Ni, Cr, Co, Se, U and Ti were determined in the osteoderms and/or flesh of estuarine crocodiles (Crocodylus porosus) captured in three adjacent catchments within the Alligator Rivers Region (ARR) of northern Australia. Results from multivariate analysis of variance showed that when all metals were considered simultaneously, catchment effects were significant (P≤0.05). Despite considerable within-catchment variability, linear discriminant analysis (LDA) showed that differences in elemental signatures in the osteoderms and/or flesh of C. porosus amongst the catchments were sufficient to classify individuals accurately to their catchment of occurrence. Using cross-validation, the accuracy of classifying a crocodile to its catchment of occurrence was 76% for osteoderms and 60% for flesh. These data suggest that osteoderms provide better predictive accuracy than flesh for discriminating crocodiles amongst catchments. There was no advantage in combining the osteoderm and flesh results to increase the accuracy of classification (i.e. 67%). Based on the discriminant function coefficients for the osteoderm data, Ca, Co, Mg and U were the most important elements for discriminating amongst the three catchments. For flesh data, Ca, K, Mg, Na, Ni and Pb were the most important metals for discriminating amongst the catchments. Reasons for differences in the elemental signatures of crocodiles between catchments are generally not interpretable, due to limited data on surface water and sediment chemistry of the catchments or chemical composition of dietary items of C. porosus. From a wildlife management perspective, the provenance or source catchment(s) of 'problem' crocodiles captured at settlements or recreational areas along the ARR coastline may be established using catchment-specific elemental signatures. If the incidence of problem crocodiles can be reduced in settled or recreational areas by effective management at their source, then public safety concerns about these predators may be moderated, as well as the cost of their capture and removal. Copyright © 2002 Elsevier Science B.V.

International Workshop for Management and Trade of Caiman yacare, Gainsville, FL, 3-5 October 2002

A workshop was held 3-5 October 2002 in Gainesville, Florida, USA to discuss management, conservation and trade in Caiman yacare. Twenty five official participants represented the four yacare range states (Argentina, Bolivia, Brazil, Paraguay), Venezuela, USA, the meeting sponsors (US Fish and Wildlife Service, CITES Secretariat, Louisiana Fur and Alligator Council), TRAFFIC Sur America and Crocodile Specialist Group. A series of country reports detailing yacare management in the four range states were distributed in Spanish and English prior to the meeting and presentations on these and on general principles of crocodilian harvest, conservation and management provided the basis for the discussions. Three working groups considered: • Requirements and field techniques for field data collection. • Requirements and techniques for regulation of harvest. • Requirements and processes for regulation of trade and export. Written reports of working groups and a plenary drafting session were finalized during the meeting and distributed, with the country reports, to participants. The workshop drafted a framework for caiman management and regulation that could be used as a template and adapted for use in each range state. The meeting agreed to convene an ad-hoc working group of range state representatives to continue discussions on the harmonization of caiman management into the future.

大别－苏鲁造山带与华北陆块东部岩石层三维速度结构

The 3-D velocity images of the crest and upper mantle beneath the region of 112° -124°E, 28°-39°N including the Dabie-Sulu orogenic belt are reconstructed by using 36405 P-wave arrivals of 3437 regional and 670 distant earthquakes during the period from 1981 to 1996, and gridding the area of 0.5° * 0.5°. The results of tomography demonstrate that: 1. The results of tomographic imaging show a broad heterogeneity in P wave velocity structure for the lithosphere beneath the Dabie-Sulu orogenic belt. 2. In the Dabie orogenic belt, the velocity patterns in the crust are different among various tectonic units. The Dabie and Qinling orogenic belts are remarkable in the tomographic images, and in mm the Hongan and Dabie blocks in the Dabie orogenic belt are also imaged very distinguishably. 3. A velocity (about 5.9～6.0 km/s) layer exists in the Dabie block at depth between 15～25 km, which is coincident with the low-resistance layer at the depth of 12-23 km, being inferred to be the tectonic detachment zone and suggesting that the extension detachment structure was formed in the middle crust. Beneath the southern and northerm Dabie tectonic units, the north-dipping high-velocity (at level of 6.5 ～ 6.6 km/s) block was developed in the crust, which might be correlated with the UHP rockswith low content of the meta-ultramafic rocks. This result is in agreement with the geological observation on the surface. 4. The velocity image at 40 km depth reveals the features at the top of mantle and the configuration of the Moho discontinuity. The depth of the Moho changes slightly along the trend of the orogenic belt. It in Hongan block is less than 40 km, but it is different in the western and eastern parts of the Dabie block, the former is more than 40 km, and the latter less than or equal to 40 km. The remnant of the mountain root exists between the Shangcheng-Macheng fault and the line of Huoshan-Yuexi-Yingshan in the Dabie orogenic belt, and beneath the southern and northern Dabie tectonic units. However, the thickness of the Moho is about 40 km and there is no obvious changes, which suggest that the Dabie orogenic belt has been experienced quite in the gravity equilibration. The Moho's depth in the Sulu is less than 40 km. 5. There is a dipping slab-like high-velocity body in the uppermost mantle. It is sandwiched by slow velocities and exists beneath the Dabie-Sulu orogenic belt in the range of depths between the Moho discontinuity and 110 km at least. This high-velocity body outlines a picture of the slab interpreted as the remnant of the Triassic subducted YZ. 6. The Sulu orogenic belt displays "crocodilian" velocity structure, the upper crust of the Yangtze thrusted over the Huabei crest, and the Huabei crust indented into the Yangtze crust, where the ancient subduction zone of the Yangtze lithosphere located. Based on the previous geological data, this structure is not related with the collision between the Yangtze and Sino-Korean Blocks, but caused by the sinistral offset of the Tan-Lu Fault. Studied on the velocity structure of the eastern Huabei lithosphere indicates: 1. The 'present-day' lithosphere of the eastern Huabei is between 40-100 km thick with greatly thinned lithosphere around the Bohai Sea. Generally, thickness of the lithosphere in this region decreased eastwards. 2. The attenuation of the lithosphere is attributed to the strongly uplift of the asthenosphere. In the area between the Taihang Mountains and the Tan-Lu Fault, there is a 'lever' with red low velocity belt, it is clearly defined, transverse continuity, depth between 100-150 km, local variations visible, and an upwards trend towards the Bohai Sea. Generally, the velocity structure in the mantle beneath the lithosphere displays irregular column-shape consisting of alternating high and low velocities, and when cold high velocity ancient lithosphere connects with the hot low velocity mantle materials forming precipitous compact structure. More heat pathways from the mantle occur towards the Tan-Lu Fault. 3. The strongly irregular characteristics of the contact between the asthenosphere and the lithosphere is induced by the long-term hot, chemical erosion and alteration on the contact. 4. There are still preserved high velocity lithosphedc root beneath Huabei with 'block-shape' distribution and surrounded by hot materials. Results of our studies indicate that the evolution models of the eastern China mantle are characterized by the direct contact between the uplifted lithosphere and the Huabei Craton accompanying the upwelling of the deep mantle materials. At the contact betwen the lithosphere and the asthenosphere, the upwelled mantle materials replaced and altered the lower lithosphere forming the metasome through the hot and chemical modifications impacted on the Craton lithosphere, and changed it into the lithosphere gradually, resulting in the lithospheric thinning. Thus, the lithospheric thinning is the result of the upwelling of the asthenosphere.

Missed, not missing: phylogenomic evidence for the existence of Avian FoxP3

The Forkhead box transcription factor FoxP3 is pivotal to the development and function of regulatory T cells (Tregs), which make a major contribution to peripheral tolerance. FoxP3 is believed to perform a regulatory role in all the vertebrate species in which it has been detected. The prevailing view is that FoxP3 is absent in birds and that avian Tregs rely on alternative developmental and suppressive pathways. Prompted by the automated annotation of foxp3 in the ground tit (Parus humilis) genome, we have questioned this assumption. Our analysis of all available avian genomes has revealed that the foxp3 locus is missing, incomplete or of poor quality in the relevant genomic assemblies for nearly all avian species. Nevertheless, in two species, the peregrine falcon (Falco peregrinus) and the saker falcon (F. cherrug), there is compelling evidence for the existence of exons showing synteny with foxp3 in the ground tit. A broader phylogenomic analysis has shown that FoxP3 sequences from these three species are similar to crocodilian sequences, the closest living relatives of birds. In both birds and crocodilians, we have also identified a highly proline-enriched region at the N terminus of FoxP3, a region previously identified only in mammals.

Evolutionary history of trypanosomes from South American caiman (Caiman yacare) and African crocodiles inferred by phylogenetic analyses using SSU rDNA and gGAPDH genes

In this study, using a combined data set of SSU rDNA and gGAPDH gene sequences, we provide phylogenetic evidence that supports Clustering of crocodilian trypanosomes from the Brazilian Caiman yacare (Alligatoridae) and Trypanosoma grayi, a species that Circulates between African crocodiles (Crocodilydae) and tsetse flies. In a survey of trypanosomes in Caiman yacare from the Brazilian Pantanal, the prevalence of trypanosome infection was 35% as determined by microhaematocrit and haemoculture, and 9 cultures were obtained. The morphology of trypomastigotes from caiman blood and tissue imprints was compared with those described for other crocodilian trypanosomes. Differences in morphology and growth behaviour of caiman trypanosomes were corroborated by molecular polymorphism that revealed 2 genotypes. Eight isolates were ascribed to genotype Cay01 and 1 to genotype Cay02. Phylogenetic inferences based on concatenated SSU rDNA and gGAPDII sequences showed that caiman isolates are closely related to T. grayi, constituting a well-supported monophyletic assemblage (clade T. grayi). Divergence time estimates based on clade composition, and biogeographical and geological events were used to discuss the relationships between the evolutionary histories of crocodilian trypanosomes and their hosts.

Lactate sequestration by osteoderms of the broad-nose caiman, Caiman latirostris, following capture and forced submergence

Lactate accumulation in osteoderms; of the broad-nose caiman, Caiman latirostris, was determined following capture and surgery and after a period of forced submergence and related to concurrent values in blood. Control samples of bone and blood were taken after recovery from surgery and before submergence. In addition, samples of osteoderm were incubated in a lactate solution to determine equilibrium concentration, and additional samples were analyzed for elemental and CO2 concentrations. The composition of the osteoderms closely resembles that of typical vertebrate bone, with a high concentration of calcium and phosphate. Plasma and osteoderm lactate concentrations were both elevated following surgery and decreased significantly after 1 day of recovery. Submergence produced a typical lactate pattern in the plasma, with only a modest increase during the dive and then a sharp increase during recovery to a peak of 31.2 +/- 1.9 mumol ml(-1) after 1 h. When caimans were anesthetized 2 h after submergence, osteoderm lactate in the same animals was significantly increased to 14.8 mumol g(-1) wet mass. The ratio of the osteoderm: plasma lactate concentration after submergence was similar to the ratio observed in the incubated samples, suggesting that osteoderm lactate concentrations in vivo were equilibrated with circulating plasma levels. We conclude that caiman osteoderms sequester lactate during lactic acidosis and that the time course is fast enough to have benefit to these animals following normal anaerobic burst activity.