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

Ben Creisler
[email protected]

===

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 Püntener, Jean-Paul Billon-Bruyat, Daniel Marty & Géraldine
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://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1007_s00015-2D019-2D00347-2D0&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=8B7cpAaykYtVYI4WyPBOKCyz04p5xOnZfRhcvaUTuy8&s=LoZ7TNCbmSOYUDWwhMmL-2fm7FRQI8qv06BcrovvfAU&e= 
https://urldefense.proofpoint.com/v2/url?u=https-3A__link.springer.com_article_10.1007_s00015-2D019-2D00347-2D0&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=8B7cpAaykYtVYI4WyPBOKCyz04p5xOnZfRhcvaUTuy8&s=5m1Ohj31QgUR8AgMHpr7rNDVliM5oBF86mt2ZvT6EWw&e= 


Recent excavations from the "Paléontologie 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.


====

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-André 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 García Borboroglu, De-Xing
Zhang & Guojie Zhang (2019)
High-coverage genomes to elucidate the evolution of penguins.
GigaScience 8(9): giz117
doi: https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1093_gigascience_giz117&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=8B7cpAaykYtVYI4WyPBOKCyz04p5xOnZfRhcvaUTuy8&s=iXj2YORXyqan5h-e0c3BrGOwbjbmWtGr_1dEPKHAABk&e= 
https://urldefense.proofpoint.com/v2/url?u=https-3A__academic.oup.com_gigascience_article_8_9_giz117_5571031&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=8B7cpAaykYtVYI4WyPBOKCyz04p5xOnZfRhcvaUTuy8&s=1hnrTVkxiNSkkTAY3dfS08EaJS0C-NK72uKP7JsZIps&e= 

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 ∼20 species among 6 genera, penguins range from the
tropical Galápagos 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.

====

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://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1002_jez.b.22901&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=8B7cpAaykYtVYI4WyPBOKCyz04p5xOnZfRhcvaUTuy8&s=zaHIJLPNqFPwrC2rLGY3-r267lkGRZZ1hTzXu5EPZ-8&e= 
https://urldefense.proofpoint.com/v2/url?u=https-3A__onlinelibrary.wiley.com_doi_10.1002_jez.b.22901&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=8B7cpAaykYtVYI4WyPBOKCyz04p5xOnZfRhcvaUTuy8&s=0mwoEYWRObC-WA4K0ZdjACMkZEvXntDIHbI7kp7C2ZI&e= 


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, T‐cells and macrophages likely
eliminate embryonic‐larval 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.

==========


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://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1002_ece3.5257&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=8B7cpAaykYtVYI4WyPBOKCyz04p5xOnZfRhcvaUTuy8&s=PvWiEeQd3a0DU6Mv4kTWK-ui-jEXbUHANfGcY2Gj40Y&e= 
https://urldefense.proofpoint.com/v2/url?u=https-3A__onlinelibrary.wiley.com_doi_10.1002_ece3.5257&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=8B7cpAaykYtVYI4WyPBOKCyz04p5xOnZfRhcvaUTuy8&s=Z49Qp7-EHL65VhgldfXGv4heVE12ecAKBAILGwpuo3U&e= 

Free pdf:
https://urldefense.proofpoint.com/v2/url?u=https-3A__onlinelibrary.wiley.com_doi_pdf_10.1002_ece3.5257&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=8B7cpAaykYtVYI4WyPBOKCyz04p5xOnZfRhcvaUTuy8&s=SFJHpShmA2TpIu2F43XcGHcUCWviVhVsl8KmwK-EPDY&e= 


Inaccurate taxonomic assessment of threatened populations can hinder
conservation prioritization and management, with human‐mediated 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 human‐mediated translocations for recent commercial farming. We
investigated the evolutionary history and relationships of allopatric
Chinese giant salamander populations with Next‐Generation Sequencing
methods, using historical museum specimens and late 20th‐century samples,
and retrieved partial or near‐complete 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.
Pliocene–Pleistocene divergences for these clades are consistent with
topographic modification of southern China associated with uplift of the
Qinghai‐Tibet 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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