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[dinosaur] Sauropod turtle stomp + penguin genomes + tail regeneration + Andrias





Ben Creisler
bcreisler@gmail.com

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Some recent mainly non-dino papers:

This article was originally posted in a free preprint form but it is also now published in a formal (paywalled) way not yet mentioned:


Christian PÃntener, Jean-Paul Billon-Bruyat, Daniel Marty & GÃraldine Paratte (2019)
Under the feet of sauropods: a trampled coastal marine turtle from the Late Jurassic of Switzerland?
Swiss Journal of Geosciences (advance online publication)
DOI: https://doi.org/10.1007/s00015-019-00347-0
https://link.springer.com/article/10.1007/s00015-019-00347-0


Recent excavations from the "PalÃontologie A16" project brought to light thousands of dinosaur footprints and numerous turtle remains from the Late Jurassic of Porrentruy (Swiss Jura Mountains). While most fossil turtles (Thalassochelydia) were found in marly layers that were deposited in a coastal marine paleoenvironment, the dinosaur (theropod and sauropod) tracks were found in laminites that were deposited in a tidal flat environment. Despite extensive exploration, very few body fossils were found in these dinosaur track-bearing laminites. On one occasion, a sub-complete turtle shell (Plesiochelys bigleri) was discovered within the laminites, embedded just beneath an important sauropod track level. The state of preservation of this specimen suggests that the turtle died on the tidal flat and was quickly buried. This is the first evidence that these turtles occasionally visited tidal flat paleoenvironments. Moreover, the particular configuration of the fossil turtle suggests that the shell was possibly trodden on by a large sauropod dinosaur.


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Hailin Pan, Theresa L Cole, Xupeng Bi, Miaoquan Fang, Chengran Zhou, Zhengtao Yang, Daniel T Ksepka, Tom Hart, Juan L Bouzat, Lisa S Argilla, Mads F Bertelsen, P Dee Boersma, Charles-Andrà Bost, Yves Cherel, Peter Dann, Steven R Fiddaman, Pauline Howard, Kim Labuschagne, Thomas Mattern, Gary Miller, Patricia Parker, Richard A Phillips, Petra Quillfeldt, Peter G Ryan, Helen Taylor, David R Thompson, Melanie J Young, Martin R Ellegaard, M Thomas P Gilbert, Mikkel-Holger S Sinding, George Pacheco, Lara D Shepherd, Alan J D Tennyson, Stefanie Grosser, Emily Kay, Lisa J Nupen, Ursula Ellenberg, David M Houston, Andrew Hart Reeve, Kathryn Johnson, Juan F Masello, Thomas Stracke, Bruce McKinlay, Pablo GarcÃa Borboroglu, De-Xing Zhang & Guojie Zhang (2019)
High-coverage genomes to elucidate the evolution of penguins.
GigaScience 8(9): giz117
doi: https://doi.org/10.1093/gigascience/giz117
https://academic.oup.com/gigascience/article/8/9/giz117/5571031

Background

Penguins (Sphenisciformes) are a remarkable order of flightless wing-propelled diving seabirds distributed widely across the southern hemisphere. They share a volant common ancestor with Procellariiformes close to the Cretaceous-Paleogene boundary (66 million years ago) and subsequently lost the ability to fly but enhanced their diving capabilities. With â20 species among 6 genera, penguins range from the tropical GalÃpagos Islands to the oceanic temperate forests of New Zealand, the rocky coastlines of the sub-Antarctic islands, and the sea ice around Antarctica. To inhabit such diverse and extreme environments, penguins evolved many physiological and morphological adaptations. However, they are also highly sensitive to climate change. Therefore, penguins provide an exciting target system for understanding the evolutionary processes of speciation, adaptation, and demography. Genomic data are an emerging resource for addressing questions about such processes.

Results

Here we present a novel dataset of 19 high-coverage genomes that, together with 2 previously published genomes, encompass all extant penguin species. We also present a well-supported phylogeny to clarify the relationships among penguins. In contrast to recent studies, our results demonstrate that the genus Aptenodytes is basal and sister to all other extant penguin genera, providing intriguing new insights into the adaptation of penguins to Antarctica. As such, our dataset provides a novel resource for understanding the evolutionary history of penguins as a clade, as well as the fine-scale relationships of individual penguin lineages. Against this background, we introduce a major consortium of international scientists dedicated to studying these genomes. Moreover, we highlight emerging issues regarding ensuring legal and respectful indigenous consultation, particularly for genomic data originating from New Zealand Taonga species.

Conclusions

We believe that our dataset and project will be important for understanding evolution, increasing cultural heritage and guiding the conservation of this iconic southern hemisphere species assemblage.

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Lorenzo Alibardi (2019)
Tail regeneration in Lepidosauria as an exception to the generalized lack of organ regeneration in amniotes.
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution (advance online publication)
doi: https://doi.org/10.1002/jez.b.22901
https://onlinelibrary.wiley.com/doi/10.1002/jez.b.22901


The present review hypothesizes that during the transition from water to land, amniotes lost part of the genetic program for metamorphosis utilized in larvae of their amphibian ancestors, a program that in extant fish and amphibians allows organ regeneration. The direct development of amniotes, with their growth from embryos to adults, occurred with the elimination of larval stages, increases the efficiency of immune responses and the complexity of nervous circuits. In amniotes, Tâcells and macrophages likely eliminate embryonicâlarval antigens that are replaced with the definitive antigens of adult organs. Among lepidosaurians numerous lizard families during the Permian and Triassic evolved the process of tail autotomy to escape predation, followed by tail regeneration. Autotomy limits inflammation allowing the formation of a regenerative blastema rich in the immunosuppressant and hygroscopic hyaluronic acid. _expression_ loss of developmental genes for metamorphosis and segmentation in addition to an effective immune system, determined an imperfect regeneration of the tail. Genes involved in somitogenesis were likely lost or are inactivated and the axial skeleton and muscles of the original tail are replaced with a nonsegmented cartilaginous tube and segmental myotomes. Lack of neural genes, negative influence of immune system, and isolation of the regenerating spinal cord within the cartilaginous tube impede the production of nerve and glial cells, and a stratified spinal cord with ganglia. Tissue and organ regeneration in other body regions of lizards and other reptiles is relatively limited, like in the other amniotes, although the cartilage shows a higher regenerative capability than in mammals.

HIGHLIGHTS
Direct development of reptiles exclude a larval stage and metamorphosis.
Among amniotes only lizards regenerate a large organ, the tail.
It is hypothesized that tail regeneration evolved in association to autotomy.
Tail regeneration occurs after formation of an immunosuppressed soft blastema.
Signaling pathways of coding and non coding genes determines tail regeneration.

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Free pdf:

Samuel T. Turvey, Melissa M. Marr, Ian Barnes, Selina Brace, BenjaminTapley, Robert W. Murphy , Ermi Zhao & Andrew A. Cunningham (2019)Historical museum collections clarify the evolutionary history of cryptic species radiation in the world's largest amphibians.
Ecology and Evolution (advance online publication)
doi: https://doi.org/10.1002/ece3.5257
https://onlinelibrary.wiley.com/doi/10.1002/ece3.5257Â

Free pdf:
https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.5257Â


Inaccurate taxonomic assessment of threatened populations can hinder conservation prioritization and management, with humanâmediated population movements obscuring biogeographic patterns and confounding reconstructions of evolutionary history. Giant salamanders were formerly distributed widely across China, and are interpreted as a single species, Andrias davidianus. Previous phylogenetic studies have identified distinct Chinese giant salamander lineages but were unable to associate these consistently with different landscapes, probably because population structure has been modified by humanâmediated translocations for recent commercial farming. We investigated the evolutionary history and relationships of allopatric Chinese giant salamander populations with NextâGeneration Sequencing methods, using historical museum specimens and late 20thâcentury samples, and retrieved partial or nearâcomplete mitogenomes for 17 individuals. Samples from populations unlikely to have been affected by translocations form three clades from separate regions of China, spatially congruent with isolation by either major river drainages or mountain ranges. PlioceneâPleistocene divergences for these clades are consistent with topographic modification of southern China associated with uplift of the QinghaiâTibet Plateau. General Mixed Yule Coalescent model analysis indicates that these clades represent separate species: Andrias davidianus (Blanchard, 1871) (northern Yangtze/Sichuan), Andrias sligoi (Boulenger, 1924) (Pearl/Nanling), and an undescribed species (Huangshan). Andrias sligoi is possibly the world's largest amphibian. Inclusion of additional reportedly wild samples from areas of known giant salamander exploitation and movement leads to increasing loss of biogeographic signal. Wild Chinese giant salamander populations are now critically depleted or extirpated, and conservation actions should be updated to recognize the existence of multiple species.


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