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Re: [dinosaur] Placental mammal evolution in Cretaceous + nocturnal vision in birds + more




Also, add these, just out:

Tuo Qiao, Benedict King, John A. Long, Per E. Ahlberg& Min Zhu  (2016) 
Early Gnathostome Phylogeny Revisited: Multiple Method Consensus. 
PLoS ONE 11(9): e0163157. 
doi:10.1371/journal.pone.0163157
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0163157

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Jeremy J. Klingler (2016) 
On the Morphological Description of Tracheal and Esophageal Displacement and Its Phylogenetic Distribution in Avialae. 
PLoS ONE 11(9): e0163348. 
doi:10.1371/journal.pone.0163348
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0163348





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On Tue, Sep 20, 2016 at 12:16 PM, Ben Creisler <bcreisler@gmail.com> wrote:

Ben Creisler
bcreisler@gmail.com


Some recent non-dino papers that may be of interest:



Mark S. Springer, Christopher A. Emerling, Robert W. Meredith, Jan E. Janečka, Eduardo Eizirik, William J. Murphy (2016)

Waking the undead: implications of a soft explosive model for the timing of placental mammal diversification.

Molecular Phylogenetics and Evolution (advance online publication)

doi:  http://dx.doi.org/10.1016/j.ympev.2016.09.017

http://www.sciencedirect.com/science/article/pii/S1055790316302421


 

Highlights


By contrast with ghost lineages, zombie lineages occur when a crown fossil is older than a molecular divergence time.

Rate transference errors in rates of molecular evolution can drag estimated divergence times backward or forward.

Timetree analyses that address rate transference problems support the long fuse model of placental mammal diversification.



Abtract


The explosive, long fuse, and short fuse models represent competing hypotheses for the timing of placental mammal diversification. Support for the explosive model, which posits both interordinal and intraordinal diversification after the KPg mass extinction, derives from morphological cladistic studies that place Cretaceous eutherians outside of crown Placentalia. By contrast, most molecular studies favor the long fuse model wherein interordinal cladogenesis occurred in the Cretaceous followed by intraordinal cladogenesis after the KPg boundary. Phillips (2016) proposed a soft explosive model that allows for the emergence of a few lineages (Xenarthra, Afrotheria, Euarchontoglires, Laurasiatheria) in the Cretaceous, but otherwise agrees with the explosive model in positing the majority of interordinal diversification after the KPg mass extinction. Phillips (2016) argues that rate transference errors associated with large body size and long lifespan have inflated previous estimates of interordinal divergence times, and further suggests that most interordinal divergences are positioned after the KPg boundary when rate transference errors are avoided through the elimination of calibrations in large-bodied and/or long lifespan clades. Here, we show that rate transference errors can also occur in the opposite direction and drag forward estimated divergence dates when calibrations in large-bodied/long lifespan clades are omitted. This dragging forward effect results in the occurrence of more than half a billion years of ‘zombie lineages’ on Phillips’ preferred timetree. By contrast with ghost lineages, which are a logical byproduct of an incomplete fossil record, zombie lineages occur when estimated divergence dates are younger than the minimum age of the oldest crown fossils. We also present the results of new timetree analyses that address the rate transference problem highlighted by Phillips (2016) by deleting taxa that exceed thresholds for body size and lifespan. These analyses recover all interordinal divergence times in the Cretaceous and are consistent with the long fuse model of placental diversification. Finally, we outline potential problems with morphological cladistic analyses of higher-level relationships among placental mammals that may account for the perceived discrepancies between molecular and paleontological estimates of placental divergence times.

 


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Yonghua Wu, Elizabeth A. Hadly, Wenjia Teng, Yuyang Hao, Wei Liang, Yu Liu & Haitao Wang (2016)
Retinal transcriptome sequencing sheds light on the adaptation to nocturnal and diurnal lifestyles in raptors.
Scientific Reports 6, Article number: 33578 (2016)
doi:10.1038/srep33578

Owls (Strigiformes) represent a fascinating group of birds that are the ecological night-time counterparts to diurnal raptors (Accipitriformes). The nocturnality of owls, unusual within birds, has favored an exceptional visual system that is highly tuned for hunting at night, yet the molecular basis for this adaptation is lacking. Here, using a comparative evolutionary analysis of 120 vision genes obtained by retinal transcriptome sequencing, we found strong positive selection for low-light vision genes in owls, which contributes to their remarkable nocturnal vision. Not surprisingly, we detected gene loss of the violet/ultraviolet-sensitive opsin (SWS1) in all owls we studied, but two other color vision genes, the red-sensitive LWS and the blue-sensitive SWS2, were found to be under strong positive selection, which may be linked to the spectral tunings of these genes toward maximizing photon absorption in crepuscular conditions. We also detected the only other positively selected genes associated with motion detection in falcons and positively selected genes associated with bright-light vision and eye protection in other diurnal raptors (Accipitriformes). Our results suggest the adaptive evolution of vision genes reflect differentiated activity time and distinct hunting behaviors.

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Jeremy J. Klingler (2016) 
On the Morphological Description of Tracheal and Esophageal Displacement and Its Phylogenetic Distribution in Avialae. 
PLoS ONE 11(9): e0163348. 
doi:10.1371/journal.pone.0163348


This research examines the evolution and phylogenetic distribution of a peculiar and often overlooked character seen in birds, herein called tracheal and esophageal displacement. Tracheal and esophageal displacement refers to an asymmetrically situated trachea and/or esophagus along the length of the neck. This contrasts with what would be perceived as the “normal” (midsagittal) placement of these organs, wherein the two organs are situated along the ventral midline of the neck with no deviation. A total of forty-two bird species were examined (thirty-six of which came from dissections whereas six came from comments from previous literature or personal observations), as well as turtles, lizards, crocodylians, and mammals. This study found that essentially all birds have a laterally displaced trachea and/or esophagus. Lizards and mammals were seen to have normal, midsagittally placed tracheae and esophagi. Crocodylians were interesting in that alligators were defined by a normally situated trachea and esophagus whereas some crocodiles were characterized by displacement. In birds, the displacement may occur gradually along the neck, or it may happen immediately upon exiting the oropharynx. Displacement of these organs in birds is the result of a heavily modified neck wherein muscles that restrict mobility of the trachea and esophagus in lizards, alligators, and mammals (e.g., m. episternocleidomastoideus, m. omohyoideus, and m. sternohyoideus) no longer substantially restrict positions of the trachea and esophagus in birds. Rather, these muscles are modified in ways which may assist with making tracheal movements. The implications of this study may provide interesting insights for future comparisons in extinct taxa.

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L. Alibardi (2016)
The Process of Cornification Evolved From the Initial Keratinization in the Epidermis and Epidermal Derivatives of Vertebrates: A New Synthesis and the Case of Sauropsids.
International Review of Cell and Molecular Biology (advance online publication)



During land adaptation of the integument in tetrapods, an efficient stratum corneum was originated through the evolution of numerous corneous proteins in addition to the framework of intermediate filament-keratins present in keratinocytes. The new genes for corneous proteins were originated in a chromosome region indicated as epidermal differentiation complex (EDC), a locus with no apparent relationship to keratin genes. The addition of EDC proteins to IF-keratins transformed the process of epidermal keratinization present in anamniotes into a new process of cornification in the epidermis and skin appendages of amniotes, including hairs and feathers. In sauropsids among other EDC proteins a peculiar type of small proteins evolved a central region of 34 amino acids conformed as beta-sheets that, differently from the other EDC proteins, allowed the formation of long polymers of filamentous proteins customarily termed beta-keratins but in the present review reclassified as EDC corneous beta proteins. To the initial beta-sheets present in the corneous beta proteins specific N- and C-regions were later added in the proteins of different sauropsids in relation to the evolution of the corneous layer and skin appendages. Cornification contributed to the evolutive success of amniotes in the terrestrial environment.