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[dinosaur] Turtle origin time tree + hatchling Araripemys + snake origins + placental attachment + more





Ben Creisler
bcreisler@gmail.com



Some recent non-dino papers:

"mid-late Triassic origin for crown turtles and a mid-Carboniferous split of turtles from their sister group, Archosauria"



H. Bradley Shaffer, Evan McCartney-Melstad, Thomas J. Near, Genevieve G. Mount & Phillip Q. Spinks (2017)
Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines).
Molecular Phylogenetics and Evolution 115: 7–15
doi: https://doi.org/10.1016/j.ympev.2017.07.006
http://www.sciencedirect.com/science/article/pii/S1055790317305110

Highlights

We estimate divergence times for living turtles and archosaurs using genomic data.
We present a turtle-specific target capture array for 539 nuclear loci across turtles.
Our array is 2.4 times more variable than a recently published UCE data set.
Our phylogeny is congruent with a recent analysis based on UCEs.
We provide crown age estimates for all living turtle families except Chelidae.
The chronogram provides a temporal scaffold for testudine evolution and conservation.

Abstract

Accurate time-calibrated phylogenies are the centerpiece of many macroevolutionary studies, and the relationship between the size and scale of molecular data sets and the density and accuracy of fossil calibrations is a key element of time tree studies. Here, we develop a target capture array specifically for living turtles, compare its efficiency to an ultraconserved element (UCE) dataset, and present a time-calibrated molecular phylogeny based on 539 nuclear loci sequenced from 26 species representing the breadth of living turtle diversity plus outgroups. Our gene array, based on three fully sequenced turtle genomes, is 2.4 times more variable across turtles than a recently published UCE data set for an identical subset of 13 species, confirming that taxon-specific arrays return more informative data per sequencing effort than UCEs. We used our genomic data to estimate the ages of living turtle clades including a mid-late Triassic origin for crown turtles and a mid-Carboniferous split of turtles from their sister group, Archosauria. By specifically excluding several of the earliest potential crown turtle fossils and limiting the age of fossil calibration points to the unambiguous crown lineage Caribemys oxfordiensis from the Late Jurassic (Oxfordian, 163.5–157.3 Ma) we corroborate a relatively ancient age for living turtles. We also provide novel age estimates for five of the ten testudine families containing more than a single species, as well as several intrafamilial clades. Most of the diversity of crown turtles appears to date to the Paleogene, well after the Cretaceous-Paleogene mass extinction 66 mya.

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Gustavo R. Oliveira & Alexander W.A. Kellner (2017)
Rare hatchling specimens of Araripemys Price, 1973 (Testudines, Pelomedusoides, Araripemydidae) from the Crato formation, Araripe Basin.
Journal of South American Earth Sciences (advance online publication)
doi: https://doi.org/10.1016/j.jsames.2017.07.014
http://www.sciencedirect.com/science/article/pii/S0895981117301815

Highlights

Anatomical conservative features during early ontogenetic stages in Araripemys.
Araripemys indicates tolerance to distinct salinities.

Abstract

Hatchling turtles are rare in the fossil record. Here we report two incomplete juvenile specimens of the genus Araripemys from the Aptian (ca. 110 Ma) Crato Formation (Araripe Basin, Brazil). Although the description of this material does not completely elucidate the ontogeny of this taxon, the analysis of these specimens yield relevant information about diagnostic features of the genus, showing their presence in hatchling such as: skull with nearly oval shape in dorsal view; closely spaced orbits; cervical vertebrae with long vertebral body indicating the presence of a long neck; the extension and the angle of curvature of the axillary (obtuse angle); and unguals arrow-shaped. The small size of the specimens (40–50 mm) and their poor degree of ossification including unfused costal bones indicate that both represent hatchling individuals. The paleoenvironment of the Crato Formation was similar to mangroves, which is corroborated by the presence of juvenile turtles and fishes, anurans and insects. Araripemys barretoi was also recorded in the Romualdo Formation, which represents a lagoon. The fact that this turtle is found in these quite distinct paleoenvironments suggests that this species could be tolerant to distinct salinities levels.



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Christopher A. Emerling (2017)
Genomic regression of claw keratin, taste receptor and light-associated genes provides insights into biology and evolutionary origins of snakes.
Molecular Phylogenetics and Evolution 115: 40–49
doi: https://doi.org/10.1016/j.ympev.2017.07.014   
http://www.sciencedirect.com/science/article/pii/S1055790317300131

earlier version (free pdf):
http://www.biorxiv.org/content/biorxiv/early/2017/04/15/127654.full.pdf

Highlights

Snakes have lost/inactivated claw keratins.
Different serpents have lost different numbers of taste receptors.
The earliest snakes lost numerous light-associated genes.
Evolutionary analyses suggest dim-light adaptation in snakes preceded leg loss.

Abstract

Regressive evolution of anatomical traits often corresponds with the regression of genomic loci underlying such characters. As such, studying patterns of gene loss can be instrumental in addressing questions of gene function, resolving conflicting results from anatomical studies, and understanding the evolutionary history of clades. The evolutionary origins of snakes involved the regression of a number of anatomical traits, including limbs, taste buds and the visual system, and by analyzing serpent genomes, I was able to test three hypotheses associated with the regression of these features. The first concerns two keratins that are putatively specific to claws. Both genes that encode these keratins are pseudogenized/deleted in snake genomes, providing additional evidence of claw-specificity. The second hypothesis is that snakes lack taste buds, an issue complicated by conflicting results in the literature. I found evidence that different snakes have lost one or more taste receptors, but all snakes examined retained at least one gustatory channel. The final hypothesis addressed is that the earliest snakes were adapted to a dim light niche. I found evidence of deleted and pseudogenized genes with light-associated functions in snakes, demonstrating a pattern of gene loss similar to other dim light-adapted clades. Molecular dating estimates suggest that dim light adaptation preceded the loss of limbs, providing some bearing on interpretations of the ecological origins of snakes.
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Free pdf:

Bjarke Jensen, Signe Vesterskov, Bastiaan J. Boukens, Jan M. Nielsen, Antoon F. M. Moorman, Vincent M. Christoffels & Tobias Wang (2017)

Morpho-functional characterization of the systemic venous pole of the reptile heart.

Scientific Reports 7, Article number: 6644 (2017)

doi:10.1038/s41598-017-06291-z

https://www.nature.com/articles/s41598-017-06291-z




Mammals evolved from reptile-like ancestors, and while the mammalian heart is driven by a distinct sinus node, a sinus node is not apparent in reptiles. We characterized the myocardial systemic venous pole, the sinus venosus, in reptiles to identify the dominant pacemaker and to assess whether the sinus venosus remodels and adopts an atrium-like phenotype as observed in mammals. Anolis lizards had an extensive sinus venosus of myocardium expressing Tbx18. A small sub-population of cells encircling the sinuatrial junction expressed Isl1, Bmp2, Tbx3, and Hcn4, homologues of genes marking the mammalian sinus node. Electrical mapping showed that hearts of Anolis lizards and Python snakes were driven from the sinuatrial junction. The electrical impulse was delayed between the sinus venosus and the right atrium, allowing the sinus venosus to contract and aid right atrial filling. In proximity of the systemic veins, the Anolis sinus venosus expressed markers of the atrial phenotype Nkx2-5 and Gja5. In conclusion, the reptile heart is driven by a pacemaker region with an _expression_ signature similar to that of the immature sinus node of mammals. Unlike mammals, reptiles maintain a sinuatrial delay of the impulse, allowing the partly atrialized sinus venosus to function as a chamber.



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Free pdf:

Oliver W. Griffith, Arun R. Chavan, Stella Protopapas, Jamie Maziarz, Roberto Romero, and Gunter P. Wagner (2017)
Embryo implantation evolved from an ancestral inflammatory attachment reaction. 
Proceedings of the National Academy of Sciences (advance online publication) 
doi:10.1073/pnas.1701129114 
http://www.pnas.org/content/early/2017/07/25/1701129114.full.pdf



Significance

 

Our data suggest that implantation in eutherians is derived from an ancestral inflammatory reaction to embryo attachment in the therian ancestor. These results explain the paradoxical role of inflammation at the beginning and the end of pregnancy in humans: Inflammation is necessary for implantation and parturition, but for most of pregnancy, inflammation threatens the continuation of pregnancy. We argue that the role of inflammation during implantation is an ancestral response to the embryo as a foreign body. By changing the way investigators think about implantation, we expect this research to contribute to new ways to study and treat implantation disorders, the most vulnerable step of assisted reproductive technology, in women.

 


Abstract


The molecular changes that support implantation in eutherian mammals are necessary to establish pregnancy. In marsupials, pregnancy is relatively short, and although a placenta does form, it is present for only a few days before parturition. However, morphological changes in the uterus of marsupials at term mimic those that occur during implantation in humans and mice. We investigated the molecular similarity between term pregnancy in the marsupials and implantation in eutherian mammals using the gray short-tailed opossum (Monodelphis domestica) as a model. Transcriptomic analysis shows that term pregnancy in the opossum is characterized by an inflammatory response consistent with implantation in humans and mice. This immune response is temporally correlated with the loss of the eggshell, and we used immunohistochemistry to report that this reaction occurs at the materno–fetal interface. We demonstrate that key markers of implantation, including Heparin binding EGF-like growth factor and Mucin 1, exhibit _expression_ and localization profiles consistent with the pattern observed during implantation in eutherian mammals. Finally, we show that there are transcriptome-wide similarities between the opossum attachment reaction and implantation in rabbits and humans. Our data suggest that the implantation reaction that occurs in eutherians is derived from an attachment reaction in the ancestral therian mammal which, in the opossum, leads directly to parturition. Finally, we argue that the ability to shift from an inflammatory attachment reaction to a noninflammatory period of pregnancy was a key innovation in eutherian mammals that allowed an extended period of intimate placentation.



News:


https://phys.org/news/2017-07-marsupials-taught-embryo-implantation-women.html


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Free pdf:

Michael R. Rampino & Yoram Eshet (2017)
The fungal and acritarch events as time markers for the latest Permian mass extinction: An update.
Geoscience Frontiers (advance online publication)
doi: https://doi.org/10.1016/j.gsf.2017.06.005
http://www.sciencedirect.com/science/article/pii/S1674987117301226


Highlights

1. The latest Permian mass extinction is marked by a fungal event in marine and non-marine sections
2. The latest Permian mass extinction is marked by an acritarch event in marine sediments.
3. The fungal event and the arcritarch events represent disaster ecologies that were dominant in the wake of the severe mass extinction on land and in the sea.
4. Reduviasporonites represents wood-degrading fungus, and does not have an algal origin.

Abstract

The latest Permian extinction (252 Myr ago) was the most severe in the geologic record. On land, widespread Late Permian gymnosperm/seed-fern dominated forests appear to have suffered rapid and almost complete destruction, as evidenced by increased soil erosion and changes in fluvial style in deforested areas, signs of wildfires, replacement of trees by lower plants, and almost complete loss of peat-forming and fire-susceptible vegetation. Permian–Triassic boundary strata at many sites show two widespread palynological events in the wake of the forest destruction: The fungal event, evidenced by a thin zone with >95% fungal cells (Reduviasporonites) and woody debris, found in terrestrial and marine sediments, and the acritarch event, marked by the sudden flood of unusual phytoplankton in the marine realm. These two events represent the global temporary explosive spread of stress-tolerant and opportunistic organisms on land and in the sea just after the latest Permian disaster. They represent unique events, and thus they can provide a time marker in correlating latest Permian marine and terrestrial sequences.

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