[dinosaur] Tuatara genome + reptile teeth

Ben Creisler
[email protected]

Some recent non-dino papers:

Neil Gemmell, Kim Rutherford, Stefan Prost, Marc Tollis, David J Winter, J.
Robert Macey, David L Adelson, Alexander Suh, Terry Bertozzi, José Grau,
Chris Organ, Paul Gardner, Matthieu Muffato, Mateus Patricio, Konstantinos
Billis, Fergal J Martin, Paul Flicek, Bent Petersen, Lin Kang, Pawel
Michalak, Thomas Buckley, Melissa A Wilson, Yuanyuan Cheng, Hilary Miller,
Ryan K Schott, Melissa Jordan, Richard Newcomb, José Ignacio Arroyo, Nicole
Valenzuela, Timothy A. Hore, Jaime Renart, Valentina Peona, Claire Peart,
Vera Warmuth, LU ZENG, Daniel Kortschak, Joy M. Raison, Valeria Velásquez
Zapata, Zhiqiang Wu, Didac Santesmasses, Marco Mariotti, Roderic Guigo,
Shawn Rupp, Victoria Twort, Nicolas Dussex, Helen R. Taylor, Hideaki Abe,
James Paterson, Daniel G. Mulcahy, Vanessa Gonzalez, Charles G. Barbieri,
Dustin P. DeMeo, Stephan Pabinger, Oliver A. Ryder, Scott V. Edwards,
Steven Salzberg, Lindsay Mickelson, Nicola Nelson, Clive Stone & Ngatiwai
Trust Board (2019)
The tuatara genome: insights into vertebrate evolution from the sole
survivor of an ancient reptilian order.
bioRxiv (preprint)
doi: https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1101_867069&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=qj8gMkpBt7_-S4qY_mLrJn8kOlDlJ_BZH5KveiLpY0I&s=VR3VukrQ4rgGolWPJjyDfUxMCmcJlTptNhNTC9EOZQo&e= 
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_content_10.1101_867069v1&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=qj8gMkpBt7_-S4qY_mLrJn8kOlDlJ_BZH5KveiLpY0I&s=W2HYCtuw4uJJjVdXEbi8HeBdLw92pY83tEZN0Q6YAcc&e= 

Free pdf:
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_content_biorxiv_early_2019_12_08_867069.full.pdf&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=qj8gMkpBt7_-S4qY_mLrJn8kOlDlJ_BZH5KveiLpY0I&s=yq7cKXaWh2qJCXW6fYmHrmEp1j7EJuyKeppqC5TXXdo&e= 



The tuatara (Sphenodon punctatus), the only living member of the archaic
reptilian order Rhynchocephalia (Sphenodontia) once widespread across
Gondwana, is an iconic and enigmatic terrestrial vertebrate endemic to New
Zealand. A key link to the now extinct stem reptiles from which dinosaurs,
modern reptiles, birds and mammals evolved, the tuatara provides exclusive
insights into the ancestral amniotes. The tuatara genome, at ~5 Gbp, is
among the largest vertebrate genomes assembled. Analysis of this genome and
comparisons to other vertebrates reinforces the uniqueness of the tuatara.
Phylogenetic analyses indicate tuatara diverged from the snakes and lizards
~250 MYA. This lineage also shows moderate rates of molecular evolution,
with instances of punctuated evolution. Genome sequence analysis identifies
expansions of protein, non-protein-coding RNA families, and repeat
elements, the latter of which show an extraordinary amalgam of reptilian
and mammalian features. Sequencing of this genome provides a valuable
resource for deep comparative analyses of tetrapods, as well as for tuatara
biology and conservation. It also provides important insights into both the
technical challenges and the cultural obligations associated with genome
sequencing.

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Free pdf:

Jacob D. Gardner, Michel Laurin & Chris L. Organ (2019)
The Relationship Between Genome Size and Metabolic Rate in Extant
Vertebrates.
bioRxiv 659094 (preprint)
doi: https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1101_659094&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=qj8gMkpBt7_-S4qY_mLrJn8kOlDlJ_BZH5KveiLpY0I&s=vEJjafSxMBW0dgFqd7XA-ZKutgL4oECVWpeqsoyCqNg&e= 
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_content_10.1101_659094v2&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=qj8gMkpBt7_-S4qY_mLrJn8kOlDlJ_BZH5KveiLpY0I&s=QxHajxrgI4dWGk7PDOE5AwHwUq9naPYylzAXmhON28Y&e= 

Free pdf:
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_content_biorxiv_early_2019_12_08_659094.full.pdf&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=qj8gMkpBt7_-S4qY_mLrJn8kOlDlJ_BZH5KveiLpY0I&s=8-Cc-w5x6MeSA41zHH_ZkUDyU64ex3a8izqgYjwZ3rQ&e= 


Genome size has long been hypothesized to affect metabolic rate in various
groups of animals. The mechanism behind this proposed association is the
nucleotypic effect, in which large nucleus and cell sizes influence
cellular metabolism through surface area-to-volume ratios. Here, we provide
a review of the recent literature on the relationship between genome size
and metabolic rate. We also conduct an analysis using phylogenetic
comparative methods and a large sample of extant vertebrates. We find no
evidence that the effect of genome size improves upon models in explaining
metabolic rate variation. Not surprisingly, our results show a strong
positive relationship between metabolic rate and body mass, as well as a
substantial difference in metabolic rate between endothermic and
ectothermic vertebrates, controlling for body mass. The presence of
endothermy can also explain elevated rate shifts in metabolic rate whereas
genome size cannot. We further find no evidence for a punctuated model of
evolution for metabolic rate. Our results do not rule out the possibility
that genome size affects cellular physiology in some tissues, but they are
consistent with previous research suggesting little support for a direct
functional connection between genome size and basal metabolic rate in
extant vertebrates.

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Marie Landova Sulcova, Oldrich Zahradnicek, Jana Dumkova, Hana Dosedelova,
Jan Krivanek, Marek Hampl, Michaela Kavkova, Tomas Zikmund, Martina
Gregorovicova, David Sedmera, Jozef Kaiser, Abigail S. Tucker & Marcela
Buchtova (2019)
Developmental mechanisms driving complex tooth shape in reptiles.
Developmental Dynamics (advance online publication)
doi: https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1002_dvdy.138&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=qj8gMkpBt7_-S4qY_mLrJn8kOlDlJ_BZH5KveiLpY0I&s=aWhmFSgAdQ-WFdXTQ3ERTIr4HTwB7Yjl1p12Niyn8EU&e= 
https://urldefense.proofpoint.com/v2/url?u=https-3A__anatomypubs.onlinelibrary.wiley.com_doi_10.1002_dvdy.138&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=qj8gMkpBt7_-S4qY_mLrJn8kOlDlJ_BZH5KveiLpY0I&s=wCt1W4Dax8AuG33msm3olXlIuw0O_Ub4AIOZ0eVhLh8&e= 


Background

In mammals, odontogenesis is regulated by transient signaling centers known
as enamel knots (EKs), which drive the dental epithelium shaping. However,
the developmental mechanisms contributing to formation of complex tooth
shape in reptiles are not fully understood. Here, we aim to elucidate
whether signaling organizers similar to EKs appear during reptilian
odontogenesis and how enamel ridges are formed.

Results

Morphological structures resembling the mammalian EK were found during
reptile odontogenesis. Similar to mammalian primary EKs, they exhibit the
presence of apoptotic cells and no proliferating cells. Moreover,
expression of mammalian EK‐specific molecules (SHH, FGF4 and ST14) and
GLI2‐negative cells were found in reptilian EK‐like areas. 3D analysis of
the nucleus shape revealed distinct rearrangement of the cells associated
with enamel groove formation. This process was associated with
ultrastructural changes and lipid droplet accumulation in the cells
directly above the forming ridge, accompanied by alteration of membranous
molecule expression (Na/K‐ATPase) and cytoskeletal rearrangement (F‐actin).

Conclusions

The final complex shape of reptilian teeth is orchestrated by a combination
of changes in cell signaling, cell shape and cell rearrangement. All these
factors contribute to asymmetry in the inner enamel epithelium development,
enamel deposition, ultimately leading to the formation of characteristic
enamel ridges.