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Daniel G. Peterson - One of the best experts on this subject based on the ideXlab platform.
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a bacterial artificial chromosome library for the australian saltwater crocodile crocodylus porosus and its utilization in gene isolation and genome characterization
BMC Genomics, 2009Co-Authors: Xueyan Shan, John Bunge, Daniel G. PetersonAbstract:Background Crocodilians (Order Crocodylia) are an ancient vertebrate group of tremendous ecological, social, and evolutionary importance. They are the only extant reptilian members of Archosauria, a monophyletic group that also includes birds, dinosaurs, and pterosaurs. Consequently, crocodilian genomes represent a gateway through which the molecular evolution of avian lineages can be explored. To facilitate comparative genomics within Crocodylia and between crocodilians and other archosaurs, we have constructed a bacterial artificial chromosome (BAC) library for the Australian saltwater crocodile, Crocodylus porosus. This is the first BAC library for a crocodile and only the second BAC resource for a crocodilian.
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a bacterial artificial chromosome library for the australian saltwater crocodile crocodylus porosus and its utilization in gene isolation and genome characterization
BMC Genomics, 2009Co-Authors: Xueyan Shan, John Bunge, David A Ray, Daniel G. PetersonAbstract:Crocodilians (Order Crocodylia) are an ancient vertebrate group of tremendous ecological, social, and evolutionary importance. They are the only extant reptilian members of Archosauria, a monophyletic group that also includes birds, dinosaurs, and pterosaurs. Consequently, crocodilian genomes represent a gateway through which the molecular evolution of avian lineages can be explored. To facilitate comparative genomics within Crocodylia and between crocodilians and other archosaurs, we have constructed a bacterial artificial chromosome (BAC) library for the Australian saltwater crocodile, Crocodylus porosus. This is the first BAC library for a crocodile and only the second BAC resource for a crocodilian. The C. porosus BAC library consists of 101,760 individually archived clones stored in 384-well microtiter plates. Not I digestion of random clones indicates an average insert size of 102 kb. Based on a genome size estimate of 2778 Mb, the library affords 3.7 fold (3.7×) coverage of the C. porosus genome. To investigate the utility of the library in studying sequence distribution, probes derived from CR1a and CR1b, two crocodilian CR1-like retrotransposon subfamilies, were hybridized to C. porosus macroarrays. The results indicate that there are a minimum of 20,000 CR1a/b elements in C. porosus and that their distribution throughout the genome is decidedly non-random. To demonstrate the utility of the library in gene isolation, we probed the C. porosus macroarrays with an overgo designed from a C-mos (oocyte maturation factor) partial cDNA. A BAC containing C-mos was identified and the C-mos locus was sequenced. Nucleotide and amino acid sequence alignment of the C. porosus C-mos coding sequence with avian and reptilian C-mos orthologs reveals greater sequence similarity between C. porosus and birds (specifically chicken and zebra finch) than between C. porosus and squamates (green anole). We have demonstrated the utility of the Crocodylus porosus BAC library as a tool in genomics research. The BAC library should expedite complete genome sequencing of C. porosus and facilitate detailed analysis of genome evolution within Crocodylia and between crocodilians and diverse amniote lineages including birds, mammals, and other non-avian reptiles.
Xueyan Shan - One of the best experts on this subject based on the ideXlab platform.
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a bacterial artificial chromosome library for the australian saltwater crocodile crocodylus porosus and its utilization in gene isolation and genome characterization
BMC Genomics, 2009Co-Authors: Xueyan Shan, John Bunge, Daniel G. PetersonAbstract:Background Crocodilians (Order Crocodylia) are an ancient vertebrate group of tremendous ecological, social, and evolutionary importance. They are the only extant reptilian members of Archosauria, a monophyletic group that also includes birds, dinosaurs, and pterosaurs. Consequently, crocodilian genomes represent a gateway through which the molecular evolution of avian lineages can be explored. To facilitate comparative genomics within Crocodylia and between crocodilians and other archosaurs, we have constructed a bacterial artificial chromosome (BAC) library for the Australian saltwater crocodile, Crocodylus porosus. This is the first BAC library for a crocodile and only the second BAC resource for a crocodilian.
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a bacterial artificial chromosome library for the australian saltwater crocodile crocodylus porosus and its utilization in gene isolation and genome characterization
BMC Genomics, 2009Co-Authors: Xueyan Shan, John Bunge, David A Ray, Daniel G. PetersonAbstract:Crocodilians (Order Crocodylia) are an ancient vertebrate group of tremendous ecological, social, and evolutionary importance. They are the only extant reptilian members of Archosauria, a monophyletic group that also includes birds, dinosaurs, and pterosaurs. Consequently, crocodilian genomes represent a gateway through which the molecular evolution of avian lineages can be explored. To facilitate comparative genomics within Crocodylia and between crocodilians and other archosaurs, we have constructed a bacterial artificial chromosome (BAC) library for the Australian saltwater crocodile, Crocodylus porosus. This is the first BAC library for a crocodile and only the second BAC resource for a crocodilian. The C. porosus BAC library consists of 101,760 individually archived clones stored in 384-well microtiter plates. Not I digestion of random clones indicates an average insert size of 102 kb. Based on a genome size estimate of 2778 Mb, the library affords 3.7 fold (3.7×) coverage of the C. porosus genome. To investigate the utility of the library in studying sequence distribution, probes derived from CR1a and CR1b, two crocodilian CR1-like retrotransposon subfamilies, were hybridized to C. porosus macroarrays. The results indicate that there are a minimum of 20,000 CR1a/b elements in C. porosus and that their distribution throughout the genome is decidedly non-random. To demonstrate the utility of the library in gene isolation, we probed the C. porosus macroarrays with an overgo designed from a C-mos (oocyte maturation factor) partial cDNA. A BAC containing C-mos was identified and the C-mos locus was sequenced. Nucleotide and amino acid sequence alignment of the C. porosus C-mos coding sequence with avian and reptilian C-mos orthologs reveals greater sequence similarity between C. porosus and birds (specifically chicken and zebra finch) than between C. porosus and squamates (green anole). We have demonstrated the utility of the Crocodylus porosus BAC library as a tool in genomics research. The BAC library should expedite complete genome sequencing of C. porosus and facilitate detailed analysis of genome evolution within Crocodylia and between crocodilians and diverse amniote lineages including birds, mammals, and other non-avian reptiles.
John Bunge - One of the best experts on this subject based on the ideXlab platform.
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a bacterial artificial chromosome library for the australian saltwater crocodile crocodylus porosus and its utilization in gene isolation and genome characterization
BMC Genomics, 2009Co-Authors: Xueyan Shan, John Bunge, Daniel G. PetersonAbstract:Background Crocodilians (Order Crocodylia) are an ancient vertebrate group of tremendous ecological, social, and evolutionary importance. They are the only extant reptilian members of Archosauria, a monophyletic group that also includes birds, dinosaurs, and pterosaurs. Consequently, crocodilian genomes represent a gateway through which the molecular evolution of avian lineages can be explored. To facilitate comparative genomics within Crocodylia and between crocodilians and other archosaurs, we have constructed a bacterial artificial chromosome (BAC) library for the Australian saltwater crocodile, Crocodylus porosus. This is the first BAC library for a crocodile and only the second BAC resource for a crocodilian.
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a bacterial artificial chromosome library for the australian saltwater crocodile crocodylus porosus and its utilization in gene isolation and genome characterization
BMC Genomics, 2009Co-Authors: Xueyan Shan, John Bunge, David A Ray, Daniel G. PetersonAbstract:Crocodilians (Order Crocodylia) are an ancient vertebrate group of tremendous ecological, social, and evolutionary importance. They are the only extant reptilian members of Archosauria, a monophyletic group that also includes birds, dinosaurs, and pterosaurs. Consequently, crocodilian genomes represent a gateway through which the molecular evolution of avian lineages can be explored. To facilitate comparative genomics within Crocodylia and between crocodilians and other archosaurs, we have constructed a bacterial artificial chromosome (BAC) library for the Australian saltwater crocodile, Crocodylus porosus. This is the first BAC library for a crocodile and only the second BAC resource for a crocodilian. The C. porosus BAC library consists of 101,760 individually archived clones stored in 384-well microtiter plates. Not I digestion of random clones indicates an average insert size of 102 kb. Based on a genome size estimate of 2778 Mb, the library affords 3.7 fold (3.7×) coverage of the C. porosus genome. To investigate the utility of the library in studying sequence distribution, probes derived from CR1a and CR1b, two crocodilian CR1-like retrotransposon subfamilies, were hybridized to C. porosus macroarrays. The results indicate that there are a minimum of 20,000 CR1a/b elements in C. porosus and that their distribution throughout the genome is decidedly non-random. To demonstrate the utility of the library in gene isolation, we probed the C. porosus macroarrays with an overgo designed from a C-mos (oocyte maturation factor) partial cDNA. A BAC containing C-mos was identified and the C-mos locus was sequenced. Nucleotide and amino acid sequence alignment of the C. porosus C-mos coding sequence with avian and reptilian C-mos orthologs reveals greater sequence similarity between C. porosus and birds (specifically chicken and zebra finch) than between C. porosus and squamates (green anole). We have demonstrated the utility of the Crocodylus porosus BAC library as a tool in genomics research. The BAC library should expedite complete genome sequencing of C. porosus and facilitate detailed analysis of genome evolution within Crocodylia and between crocodilians and diverse amniote lineages including birds, mammals, and other non-avian reptiles.
Christopher A. Brochu - One of the best experts on this subject based on the ideXlab platform.
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An Expanded Combined Evidence Approach to the Gavialis Problem Using Geometric Morphometric Data from Crocodylian Braincases and Eustachian Systems
2016Co-Authors: Maria Eugenia, Christopher A. Brochu, Leone Gold, Mark A. NorellAbstract:The phylogenetic position of the Indian gharial (Gavialis gangeticus) is disputed- morphological characters place Gavialis as the sister to all other extant Crocodylians, whereas molecular and combined analyses find Gavialis and the false gharial (Tomistoma schlegelii) to be sister taxa. Geometric morphometric techniques have only begun to be applied to this issue, but most of these studies have focused on the exterior of the skull. The braincase has provided useful phylogenetic information for basal crurotarsans, but has not been explored for the crown group. The Eustachian system is thought to vary phylogenetically in Crocodylia, but has not been analytically tested. To determine if gross morphology of the Crocodylian braincase proves informative to the relationships of Gavialis and Tomistoma, we used two- and three-dimensional geometric morphometric approaches. Internal braincase images were obtained using high-resolution computerized tomography scans. A principal components analysis identified that the first component axis was primarily associated with size and did not show groupings that divide the specimens by phylogenetic affinity. Sliding semi-landmarks and a relative warp analysis indicate that a unique Eustachian morphology separates Gavialis from other extant members of Crocodylia. Ontogenetic expansion of the braincase results in a more dorsoventrally elongate median Eustachian canal. Changes in the shape of the Eustachian system do provide phylogenetic distinctions between major Crocodylian clades. Each morphometric dataset, consisting of continuous morphological characters, was added independently to a combined cladistic analysis of discret
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An expanded combined evidence approach to the Gavialis problem using geometric morphometric data from Crocodylian braincases and Eustachian systems.
PLOS ONE, 2014Co-Authors: Maria Eugenia Leone Gold, Christopher A. Brochu, Mark A. NorellAbstract:The phylogenetic position of the Indian gharial (Gavialis gangeticus) is disputed - morphological characters place Gavialis as the sister to all other extant Crocodylians, whereas molecular and combined analyses find Gavialis and the false gharial (Tomistoma schlegelii) to be sister taxa. Geometric morphometric techniques have only begun to be applied to this issue, but most of these studies have focused on the exterior of the skull. The braincase has provided useful phylogenetic information for basal crurotarsans, but has not been explored for the crown group. The Eustachian system is thought to vary phylogenetically in Crocodylia, but has not been analytically tested. To determine if gross morphology of the Crocodylian braincase proves informative to the relationships of Gavialis and Tomistoma, we used two- and three-dimensional geometric morphometric approaches. Internal braincase images were obtained using high-resolution computerized tomography scans. A principal components analysis identified that the first component axis was primarily associated with size and did not show groupings that divide the specimens by phylogenetic affinity. Sliding semi-landmarks and a relative warp analysis indicate that a unique Eustachian morphology separates Gavialis from other extant members of Crocodylia. Ontogenetic expansion of the braincase results in a more dorsoventrally elongate median Eustachian canal. Changes in the shape of the Eustachian system do provide phylogenetic distinctions between major Crocodylian clades. Each morphometric dataset, consisting of continuous morphological characters, was added independently to a combined cladistic analysis of discrete morphological and molecular characters. The braincase data alone produced a clade that included crocodylids and Gavialis, whereas the Eustachian data resulted in Gavialis being considered a basally divergent lineage. When each morphometric dataset was used in a combined analysis with discrete morphological and molecular characters, it generated a tree that matched the topology of the molecular phylogeny of Crocodylia.
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a diagnosis of alligator mississippiensis bite marks with comparisons to existing Crocodylian datasets
Ichnos-an International Journal for Plant and Animal Traces, 2014Co-Authors: Stephanie K Drumheller, Christopher A. BrochuAbstract:Crocodylians are known to consume and modify bones, but actualistic observations of their bite marks have been limited to forensic case studies and surveys of two taxa: Crocodylus niloticus and Crocodylus porosus. To further explore patterns of Crocodylian bite mark expression, we conducted a survey of traces left by Alligator mississippiensis. We compared the results to pre-existing Crocodylian datasets regarding the potentially diagnostic traits of bisected marks, hook scores, and a lack of furrows. Mark type did not correlate with vital statistics of the sampled animals or collections protocol. Bisected marks were found in rates similar to those seen in one previous survey of C. niloticus, and rates of hook scoring and bone breakage were higher. These traces were all present in higher rates than those reported in C. porosus. Unlike results seen in Crocodylus, furrows were identified in the A. mississippiensis samples. Hook scores were also identified, but recent surveys of non-Crocodylian taxa have sho...
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a new horned crocodile from the plio pleistocene hominid sites at olduvai gorge tanzania
PLOS ONE, 2010Co-Authors: Christopher A. Brochu, Jackson K Njau, Robert J Blumenschine, Llewellyn D DensmoreAbstract:Background The fossil record reveals surprising crocodile diversity in the Neogene of Africa, but relationships with their living relatives and the biogeographic origins of the modern African Crocodylian fauna are poorly understood. A Plio-Pleistocene crocodile from Olduvai Gorge, Tanzania, represents a new extinct species and shows that high Crocodylian diversity in Africa persisted after the Miocene. It had prominent triangular “horns” over the ears and a relatively deep snout, these resemble those of the recently extinct Malagasy crocodile Voay robustus, but the new species lacks features found among osteolaemines and shares derived similarities with living species of Crocodylus. Methodology/Principal Findings The holotype consists of a partial skull and skeleton and was collected on the surface between two tuffs dated to approximately 1.84 million years (Ma), in the same interval near the type localities for the hominids Homo habilis and Australopithecus boisei. It was compared with previously-collected material from Olduvai Gorge referable to the same species. Phylogenetic analysis places the new form within or adjacent to crown Crocodylus. Conclusions/Significance The new crocodile species was the largest predator encountered by our ancestors at Olduvai Gorge, as indicated by hominid specimens preserving crocodile bite marks from these sites. The new species also reinforces the emerging view of high Crocodylian diversity throughout the Neogene, and it represents one of the few extinct species referable to crown genus Crocodylus.
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how the terror crocodile grew so big
Nature, 1999Co-Authors: Gregory M Erickson, Christopher A. BrochuAbstract:Deinosuchus is a giant Crocodylian from the Late Cretaceous period of North America. It was 8 to 10 metres long and weighed between 2,500 and 5,000 kg, three to five times more than the largest crocodiles alive today. How Deinosuchus attained sizes to rival its dinosaurian contemporaries, on which it undoubtedly preyed, has remained a mystery. Did it exhibit accelerated growth rates, like its dinosaurian cousins1, or did it simply maintain primitive reptilian rates for decades (as was once proposed to explain gigantism in dinosaurs2)? We find that growth indices from Deinosuchus skeletons reveal rates comparable to those of smaller Crocodylian taxa, indicating that the gigantic proportions were attained by prolonging development.
Gregory M Erickson - One of the best experts on this subject based on the ideXlab platform.
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ontogenetic bite force modeling of alligator mississippiensis implications for dietary transitions in a large bodied vertebrate and the evolution of Crocodylian feeding
Journal of Zoology, 2016Co-Authors: Paul M. Gignac, Gregory M EricksonAbstract:Crocodylians undergo substantial increases in size during ontogeny. The American alligator, Alligator mississippiensis, in particular traverses nearly four orders of body mass between hatching and senescence. Accompanying such changes are modifications in rostrodental morphology and feeding capabilities that facilitate major shifts in diet. How such anatomical changes relate to ecological niche occupation across sizes is not well understood. In this study, we focused on the effects of ontogenetic changes on the force-generating mechanisms for jaw closure to assess the impacts of scaling on feeding biomechanics. We developed dissection-based, musculoskeletal models of maximum bite-force generation throughout ontogeny and compared and tested their veracity with data from an A. mississippiensis developmental series, for which bite forces were directly measured. Through examinations of the scaling patterns within the parameters of our models, we discuss how muscle pennation and positive allometry in the American alligator jaw adductor system facilitate capture strategies and oral processing of prey, and contribute to developmental niche shifts in this large-bodied taxon. On the basis of conservation of the Crocodylian jaw adductor system, we argue that our findings are broadly applicable to crown Crocodylia and reflect an important, but often overlooked, aspect of the Crocodylian feeding ecomorphology: littoral, sit-and-wait predation is enhanced by posteroventrally displaced, exceptionally large, and forceful ventral pterygoideus muscles, in particular. Future studies on the ontogeny and evolution of feeding in Crocodylians should not neglect the functional and ecological implications of these muscles' contributions to diet.
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a comparative analysis of ontogenetic bite force scaling among Crocodylia
Journal of Zoology, 2014Co-Authors: Gregory M Erickson, Paul M. Gignac, Kent A Vliet, A K Lappin, John Brueggen, Grahame J W WebbAbstract:Interspecific adult bite forces for all extant Crocodylian species are now known. However, how bite forces scale during ontogeny across the clade has yet to be studied. Here we test the hypotheses that extant Crocodylians share positively allometric and statistically comparable developmental scaling coefficients for maximal bite-force capacity relative to body size. To do this, we measured bite forces in the Australian freshwater crocodile Crocodylus johnsoni and the Saltwater crocodile C. porosus, and determined how performance changed during ontogeny. We statistically compared these results with those for the American alligator Alligator mississippiensis using 95% prediction intervals and interpreted our findings in a phylogenetic context. We found no observable taxon-specific shifts in the intraspecific scaling of biomechanical performance. Instead, all bite-force values in our crocodylid dataset fell within the bounds of the A. mississippiensis 95% prediction intervals, suggesting similar bite-force capacity when same-sized individuals are compared. This holds true regardless of differences in developmental stage, potential adult body size, rostro-dental form, bone mineralization, cranial suturing, dietary differences or phylogenetic relatedness. These findings suggest that intraspecific bite-force scaling for Crocodylians with feeding ecologies comparable with those of extant forms has likely remained evolutionarily static during their diversification.
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how the terror crocodile grew so big
Nature, 1999Co-Authors: Gregory M Erickson, Christopher A. BrochuAbstract:Deinosuchus is a giant Crocodylian from the Late Cretaceous period of North America. It was 8 to 10 metres long and weighed between 2,500 and 5,000 kg, three to five times more than the largest crocodiles alive today. How Deinosuchus attained sizes to rival its dinosaurian contemporaries, on which it undoubtedly preyed, has remained a mystery. Did it exhibit accelerated growth rates, like its dinosaurian cousins1, or did it simply maintain primitive reptilian rates for decades (as was once proposed to explain gigantism in dinosaurs2)? We find that growth indices from Deinosuchus skeletons reveal rates comparable to those of smaller Crocodylian taxa, indicating that the gigantic proportions were attained by prolonging development.