Some recent non-dino papers:
Jens C.D. Kosch & Lindsay E. Zanno (2020)
Sampling impacts the assessment of tooth growth and replacement rates in archosaurs: implications for paleontological studies.
PeerJ 8:e9918
doi: https://doi.org/10.7717/peerj.9918
https://peerj.com/articles/9918/
Birds exhibit remarkable variation in plumage patterns, both within individual feathers and among plumage patches. Differences in the size, shape, and location of pigments and structural colors comprise important visual signals involved in mate choice, social signaling, camouflage, and many other functions. While ornithologists have studied plumage patterns for centuries, recent technological advances in digital image acquisition and processing have transformed pattern quantification methods, enabling comprehensive, detailed datasets of pattern phenotypes that were heretofore inaccessible. In this review, we synthesize recent and classic studies of plumage patterns at different evolutionary and organismal scales and discuss the various roles that plumage patterns play in avian biology. We dissect the role of plumage patches as signals within and among species. We also consider the evolutionary history of plumage patterns, including phylogenetic comparative studies and evolutionary developmental research of the genetic architecture underlying plumage patterns. We also survey an expanding toolbox of new methods that characterize and quantify the size, shape, and distribution of plumage patches. Finally, we provide a worked example to illustrate a potential workflow with dorsal plumage patterns among subspecies of the Horned Lark (Eremophila alpestris) in western North America. Studies of plumage patterning and coloration have played a prominent role in ornithology thus far, and recent methodological and conceptual advances have opened new avenues of research on the ecological functions and evolutionary origins of plumage patterns in birds.
=====
Free pdf:
Mehdi Behroozi, Xavier Helluy, Felix StrÃckens, Meng Gao, Roland Pusch, Sepideh Tabrik, Martin Tegenthoff, Tobias Otto, Nikolai Axmacher, Robert Kumsta, Dirk Moser, Erhan Genc & Onur GÃntÃrkÃn (2020)
Event-related functional MRI of awake behaving pigeons at 7T.
Nature Communications 11, Article number: 4715
DOI: https://doi.org/10.1038/s41467-020-18437-1
https://www.nature.com/articles/s41467-020-18437-1
Animal-fMRI is a powerful method to understand neural mechanisms of cognition, but it remains a major challenge to scan actively participating small animals under low-stress conditions. Here, we present an event-related functional MRI platform in awake pigeons using single-shot RARE fMRI to investigate the neural fundaments for visually-guided decision making. We established a head-fixated Go/NoGo paradigm, which the animals quickly learned under low-stress conditions. The animals were motivated by water reward and behavior was assessed by logging mandibulations during the fMRI experiment with close to zero motion artifacts over hundreds of repeats. To achieve optimal results, we characterized the species-specific hemodynamic response function. As a proof-of-principle, we run a color discrimination task and discovered differential neural networks for Go-, NoGo-, and response execution-phases. Our findings open the door to visualize the neural fundaments of perceptual and cognitive functions in birds--a vertebrate class of which some clades are cognitively on par with primates.
News:
How researchers look at the bird brain in action
=====
Free pdf:
Jens C.D. Kosch & Lindsay E. Zanno (2020)
Sampling impacts the assessment of tooth growth and replacement rates in archosaurs: implications for paleontological studies.
PeerJ 8:e9918
doi: https://doi.org/10.7717/peerj.9918
https://peerj.com/articles/9918/
Dietary habits in extinct species cannot be directly observed; thus, in the absence of extraordinary evidence, they must be reconstructed with a combination of morphological proxies. Such proxies often include information on dental organization and function such as tooth formation time and tooth replacement rate. In extinct organisms, tooth formation times and tooth replacement rate are calculated, in part via extrapolation of the space between incremental lines in dental tissues representing daily growth (von Ebner Line Increment Width; VEIW). However, to date, little work has been conducted testing assumptions about the primary data underpinning these calculations, specifically, the potential impact of differential sampling and data extrapolation protocols. To address this, we tested a variety of intradental, intramandibular, and ontogentic sampling effects on calculations of mean VEIW, tooth formation times, and replacement rates using histological sections and CT reconstructions of a growth series of three specimens of the extant archosaurian Alligator mississippiensis. We find transect position within the tooth and transect orientation with respect to von Ebner lines to have the greatest impact on calculations of mean VEIWâa maximum number of VEIW measurements should be made as near to the central axis (CA) as possible. Measuring in regions away from the central axis can reduce mean VEIW by up to 36%, causing inflated calculations of tooth formation time. We find little demonstrable impact to calculations of mean VEIW from the practice of subsampling along a transect, or from using mean VEIW derived from one portion of the dentition to extrapolate for other regions of the dentition. Subsampling along transects contributes only minor variations in mean VEIW (<12%) that are dwarfed by the standard deviation (SD). Moreover, variation in VEIW with distance from the pulp cavity likely reflects idiosyncratic patterns related to life history, which are difficult to control for; however, we recommend increasing the number of VEIW measured to minimize this effect. Our data reveal only a weak correlation between mean VEIW and body length, suggesting minimal ontogenetic impacts. Finally, we provide a relative SD of mean VEIW for Alligator of 29.94%, which can be used by researchers to create data-driven error bars for tooth formation times and replacement rates in fossil taxa with small sample sizes. We caution that small differences in mean VEIW calculations resulting from non-standardized sampling protocols, especially in a comparative context, will produce inflated error in tooth formation time estimations that intensify with crown height. The same holds true for applications of our relative SD to calculations of tooth formation time in extinct taxa, which produce highly variable maximum and minimum estimates in large-toothed taxa (e.g., 718-1,331 days in Tyrannosaurus).
===
Nicholas A. Mason & Rauri C.K. Bowie (2020)
Plumage patterns: Ecological functions, evolutionary origins, and advances in quantification.
The Auk: ukaa060
doi: https://doi.org/10.1093/auk/ukaa060
https://academic.oup.com/auk/advance-article-abstract/doi/10.1093/auk/ukaa060/5906268
Plumage patterns: Ecological functions, evolutionary origins, and advances in quantification.
The Auk: ukaa060
doi: https://doi.org/10.1093/auk/ukaa060
https://academic.oup.com/auk/advance-article-abstract/doi/10.1093/auk/ukaa060/5906268
Birds exhibit remarkable variation in plumage patterns, both within individual feathers and among plumage patches. Differences in the size, shape, and location of pigments and structural colors comprise important visual signals involved in mate choice, social signaling, camouflage, and many other functions. While ornithologists have studied plumage patterns for centuries, recent technological advances in digital image acquisition and processing have transformed pattern quantification methods, enabling comprehensive, detailed datasets of pattern phenotypes that were heretofore inaccessible. In this review, we synthesize recent and classic studies of plumage patterns at different evolutionary and organismal scales and discuss the various roles that plumage patterns play in avian biology. We dissect the role of plumage patches as signals within and among species. We also consider the evolutionary history of plumage patterns, including phylogenetic comparative studies and evolutionary developmental research of the genetic architecture underlying plumage patterns. We also survey an expanding toolbox of new methods that characterize and quantify the size, shape, and distribution of plumage patches. Finally, we provide a worked example to illustrate a potential workflow with dorsal plumage patterns among subspecies of the Horned Lark (Eremophila alpestris) in western North America. Studies of plumage patterning and coloration have played a prominent role in ornithology thus far, and recent methodological and conceptual advances have opened new avenues of research on the ecological functions and evolutionary origins of plumage patterns in birds.
=====
Free pdf:
Mehdi Behroozi, Xavier Helluy, Felix StrÃckens, Meng Gao, Roland Pusch, Sepideh Tabrik, Martin Tegenthoff, Tobias Otto, Nikolai Axmacher, Robert Kumsta, Dirk Moser, Erhan Genc & Onur GÃntÃrkÃn (2020)
Event-related functional MRI of awake behaving pigeons at 7T.
Nature Communications 11, Article number: 4715
DOI: https://doi.org/10.1038/s41467-020-18437-1
https://www.nature.com/articles/s41467-020-18437-1
Animal-fMRI is a powerful method to understand neural mechanisms of cognition, but it remains a major challenge to scan actively participating small animals under low-stress conditions. Here, we present an event-related functional MRI platform in awake pigeons using single-shot RARE fMRI to investigate the neural fundaments for visually-guided decision making. We established a head-fixated Go/NoGo paradigm, which the animals quickly learned under low-stress conditions. The animals were motivated by water reward and behavior was assessed by logging mandibulations during the fMRI experiment with close to zero motion artifacts over hundreds of repeats. To achieve optimal results, we characterized the species-specific hemodynamic response function. As a proof-of-principle, we run a color discrimination task and discovered differential neural networks for Go-, NoGo-, and response execution-phases. Our findings open the door to visualize the neural fundaments of perceptual and cognitive functions in birds--a vertebrate class of which some clades are cognitively on par with primates.
News:
How researchers look at the bird brain in action
====
Free pdf:
Alejandro PÃrez-Ramos and Borja Figueirido (2020)
Toward an "Ancient" Virtual World: Improvement Methods on X-ray CT Data Processing and Virtual Reconstruction of Fossil Skulls.
Frontiers in Earth Science 8: 345
doi: https://doi.org/10.3389/feart.2020.00345
https://www.frontiersin.org/articles/10.3389/feart.2020.00345/full
This article focuses on new virtual advances to solve technical problems usually encountered by paleontologists when using X-ray computed tomography (XCT), such as (i) the limited scanning envelope (i.e., field of view of CT systems/machines) to acquire data on large structures; (ii) the use in the same study of biological objects acquired with different types of computed tomography systems (medical and laboratory XCTs and laboratory high-resolution XÎCT) and therefore different resolutions; and (iii) matrix removal within the fossil (e.g., cranial cavities, intratrabecular cavities, among other cavities). All these problems are very common in paleontology, and therefore, solving them is important to save effort and the time invested in data processing. In this article, we propose various solutions to tackle these issues, based on new technical advances focused on improving and processing the images obtained from XCT. Other aspects include image filtering and histogram calibration to remove background noise and artifacts. Such artifacts can result from dense mineral inclusion occurring during the fossilization process or derived from anthropogenic restoration of the sample. Accordingly, here, we provide a protocol to acquire data on samples with size that exceed the scanning envelope of the X-ray tomography machine, joining the parts with enough accuracy, and we propose the use of the interpolation "bicubic" method. Moreover, using this method, it is possible to use medical/laboratory XCT data together with XÎCT data and therefore opening new ways to manipulate the acquired data within the image stack. Another advantage is the use of plugins for quantitative analysis, which require data with isometric voxels, such as the plugin BoneJ of the software ImageJ. We also deal with the problem of removing the exogenous material that usually fills the internal cavities of fossils by means of using filters based on edge detection by gradient. Applying this method, it is possible to segment the non-bony matrix parts more quickly and efficiently. All of this is exemplified using five fossil skulls belonging to the cave bear group (Ursus spelaeus sensu lato), an iconic fossil species from the Pleistocene of Eurasia.
=====
Toward an "Ancient" Virtual World: Improvement Methods on X-ray CT Data Processing and Virtual Reconstruction of Fossil Skulls.
Frontiers in Earth Science 8: 345
doi: https://doi.org/10.3389/feart.2020.00345
https://www.frontiersin.org/articles/10.3389/feart.2020.00345/full
This article focuses on new virtual advances to solve technical problems usually encountered by paleontologists when using X-ray computed tomography (XCT), such as (i) the limited scanning envelope (i.e., field of view of CT systems/machines) to acquire data on large structures; (ii) the use in the same study of biological objects acquired with different types of computed tomography systems (medical and laboratory XCTs and laboratory high-resolution XÎCT) and therefore different resolutions; and (iii) matrix removal within the fossil (e.g., cranial cavities, intratrabecular cavities, among other cavities). All these problems are very common in paleontology, and therefore, solving them is important to save effort and the time invested in data processing. In this article, we propose various solutions to tackle these issues, based on new technical advances focused on improving and processing the images obtained from XCT. Other aspects include image filtering and histogram calibration to remove background noise and artifacts. Such artifacts can result from dense mineral inclusion occurring during the fossilization process or derived from anthropogenic restoration of the sample. Accordingly, here, we provide a protocol to acquire data on samples with size that exceed the scanning envelope of the X-ray tomography machine, joining the parts with enough accuracy, and we propose the use of the interpolation "bicubic" method. Moreover, using this method, it is possible to use medical/laboratory XCT data together with XÎCT data and therefore opening new ways to manipulate the acquired data within the image stack. Another advantage is the use of plugins for quantitative analysis, which require data with isometric voxels, such as the plugin BoneJ of the software ImageJ. We also deal with the problem of removing the exogenous material that usually fills the internal cavities of fossils by means of using filters based on edge detection by gradient. Applying this method, it is possible to segment the non-bony matrix parts more quickly and efficiently. All of this is exemplified using five fossil skulls belonging to the cave bear group (Ursus spelaeus sensu lato), an iconic fossil species from the Pleistocene of Eurasia.
=====
Samantha Presslee, Kirsty Penkman, Roman Fischer, Eden Richards-Slidel, John Southon, Carolina Acosta Hospitaleche, Matthew Collins & Ross MacPhee (2020)
Assessment of different screening methods for selecting palaeontological bone samples for peptide sequencing.
Journal of Proteomics 103986
doi: https://doi.org/10.1016/j.jprot.2020.103986
https://www.sciencedirect.com/science/article/abs/pii/S1874391920303547
Highlights
Assessment of different screening methods for selecting palaeontological bone samples for peptide sequencing.
Journal of Proteomics 103986
doi: https://doi.org/10.1016/j.jprot.2020.103986
https://www.sciencedirect.com/science/article/abs/pii/S1874391920303547
Highlights
ATR-FTIR, Chiral amino acid (AA) analysis and MALDI-ToF MS were tested as screening methods for palaeoproteomics.
Am/P was shown to be the best criterion to assess protein survival when using ATR-FTIR.
AA analysis and MALDI-ToF MS results show a good correlation with protein survival
Abstract
Ancient proteomics is being applied to samples dating further and further back in time, with many palaeontological specimens providing protein sequence data for phylogenetic analysis as well as protein degradation studies. However, fossils are a precious material and proteomic analysis is destructive and costly. In this paper we consider three different techniques (ATR-FTIR, MALDI-ToF MS and chiral AA analysis) to screen fossil material for potential protein preservation, aiming to maximise the proteomic information recovered and saving costly time consuming analyses which may produce low quality results. It was found that splitting factor and C/P indices from ATR-FTIR were not a reliable indicator of protein survival as they are confounded by secondary mineralisation of the fossil material. Both MALDI-ToF MS and chiral AA analysis results were able to successfully identify samples with surviving proteins, and it is therefore suggested that one or both of these analyses be used for screening palaeontological specimens.
Significance
This study has shown both chiral amino acid analysis and MALDI-ToF MS are reliable screening methods for predicting protein survival in fossils. Both these methods are quick, cheap minimally destructive (1âmg and 15âmg respectively) and can provide crucial additional information about the endogeneity of the surviving proteins. It is hoped that the use of these screening methods will encourage the examination of a wide range of palaeontological specimens for potential proteomic analysis. This in turn will give us a better understanding of protein survival far back in time and under different environmental conditions.