PeerJ Preprints: Paleontologyhttps://peerj.com/preprints/index.atom?journal=peerj&subject=2200Paleontology articles published in PeerJ PreprintsA simplified correlation between vertebrate evolution and Paleozoic geomagnetismhttps://peerj.com/preprints/28002v32019-12-312019-12-31John P Staub
Background. Despite a fifty-year failure of paleontologists to find a viable connection between geomagnetic polarity reversals and evolutionary patterns, recent paleobiology databases show that the early appearance, radiation, and diversification of Paleozoic vertebrates tends to occur during periods having frequent collapses of the Earth’s geomagnetic field. The transition time during the collapse of the Earth’s protective magnetic shield can last thousands of years, and the effects on biota are unknown. Solar and cosmic radiation, volcanism, climate alteration, low-frequency electromagnetic fields, depletion of ozone, the stripping of atmospheric oxygen, and increasing production of Carbon14 in the stratosphere have been proposed as possible causes, but previous studies have found no effects.
Methods. Using published databases, we compiled a spreadsheet showing the first appearance of 2104 genera with each genus assigned to one of 8 major taxonomic groups. From Gradstein’s Geologic Time Scale 2012, we delineated 17 Paleozoic zones with either high or low levels of polarity reversals.
Results. From our compilation, 727 Paleozoic vertebrates represent the initial radiation and diversification of individual Paleozoic vertebrate clades. After compensating for sample-size and external geologic and sampling biases, the resulting Pearson’s correlation coefficient between the 727 genera and geomagnetic polarity zones equals 0.8, a result that suggests a strong relationship exists between Paleozoic vertebrates and geomagnetism.
Discussion. The question: is this apparent connection between geomagnetism and the evolution of Paleozoic vertebrate due to environmental or biologic factors. If biologic, why are vertebrates the only biota effected? And after an indeterminate period of time, how do vertebrates become immune to the ongoing effects of polarity reversals?
Background. Despite a fifty-year failure of paleontologists to find a viable connection between geomagnetic polarity reversals and evolutionary patterns, recent paleobiology databases show that the early appearance, radiation, and diversification of Paleozoic vertebrates tends to occur during periods having frequent collapses of the Earth’s geomagnetic field. The transition time during the collapse of the Earth’s protective magnetic shield can last thousands of years, and the effects on biota are unknown. Solar and cosmic radiation, volcanism, climate alteration, low-frequency electromagnetic fields, depletion of ozone, the stripping of atmospheric oxygen, and increasing production of Carbon14 in the stratosphere have been proposed as possible causes, but previous studies have found no effects.Methods. Using published databases, we compiled a spreadsheet showing the first appearance of 2104 genera with each genus assigned to one of 8 major taxonomic groups. From Gradstein’s Geologic Time Scale 2012, we delineated 17 Paleozoic zones with either high or low levels of polarity reversals.Results. From our compilation, 727 Paleozoic vertebrates represent the initial radiation and diversification of individual Paleozoic vertebrate clades. After compensating for sample-size and external geologic and sampling biases, the resulting Pearson’s correlation coefficient between the 727 genera and geomagnetic polarity zones equals 0.8, a result that suggests a strong relationship exists between Paleozoic vertebrates and geomagnetism.Discussion. The question: is this apparent connection between geomagnetism and the evolution of Paleozoic vertebrate due to environmental or biologic factors. If biologic, why are vertebrates the only biota effected? And after an indeterminate period of time, how do vertebrates become immune to the ongoing effects of polarity reversals?The châtelperronian Neandertals of Cova Foradada (Calafell, Spain) used Iberian imperial eagle phalanges for symbolic purposeshttps://peerj.com/preprints/271332019-11-022019-11-02Antonio Rodríguez-HidalgoJuan Ignacio MoralesArtur CebriáLloyd A. CourtenayJuan L. Fernández-MarchenaGala García García-ArgudoJuan MarínPalmira SaladiéMaria SotoJosé-Miguel TejeroJosep-María Fullola
Evidence for the symbolic behavior of Neandertals in the use of personal ornaments is relatively scarce. Eagle talons, which were presumably used as pendants, stand out due to their abundance. This phenomenon seems to appear concentrated in a specific area of Southwestern Europe during a span of ca. 80 Ka. Here we present the analysis of one eagle pedal phalange recovered from the Châtelperronian layer of Foradada Cave (Spain). Our research broadens the known geographical and temporal range of this aspect of Neandertal symbolic behavior, by providing the first documentation of its use among Neandertals in Iberia, as well as of its oldest use in the peninsula. The recurrent appearance of large raptor talons throughout the Neandertal timeframe, including their presence among the last Neandertal populations, raises the question of the survival of some cultural elements of the Middle Paleolithic into the transitional Middle to Upper Paleolithic assemblages.
Evidence for the symbolic behavior of Neandertals in the use of personal ornaments is relatively scarce. Eagle talons, which were presumably used as pendants, stand out due to their abundance. This phenomenon seems to appear concentrated in a specific area of Southwestern Europe during a span of ca. 80 Ka. Here we present the analysis of one eagle pedal phalange recovered from the Châtelperronian layer of Foradada Cave (Spain). Our research broadens the known geographical and temporal range of this aspect of Neandertal symbolic behavior, by providing the first documentation of its use among Neandertals in Iberia, as well as of its oldest use in the peninsula. The recurrent appearance of large raptor talons throughout the Neandertal timeframe, including their presence among the last Neandertal populations, raises the question of the survival of some cultural elements of the Middle Paleolithic into the transitional Middle to Upper Paleolithic assemblages.ImageJ and 3D Slicer: open source 2/3D morphometric softwarehttps://peerj.com/preprints/279982019-10-022019-10-02Fiona PyeNussaȉbah B RajaBryan ShirleyÁdám T KocsisNiklas HohmannDuncan J E MurdockEmilia Jarochowska
In a world where an increasing number of resources are hidden behind paywalls and monthly subscriptions, it is becoming crucial for the scientific community to invest energy into freely available, community-maintained systems. Open-source software projects offer a solution, with freely available code which users can utilise and modify, under an open source licence. In addition to software accessibility and methodological repeatability, this also enables and encourages the development of new tools.
As palaeontology moves towards data driven methodologies, it is becoming more important to acquire and provide high quality data through reproducible systematic procedures. Within the field of morphometrics, it is vital to adopt digital methods that help mitigate human bias from data collection. In addition, mathematically founded approaches can reduce subjective decisions which plague classical data. This can be further developed through automation, which increases the efficiency of data collection and analysis.
With these concepts in mind, we introduce two open-source shape analysis software, that arose from projects within the medical imaging field. These are ImageJ, an image processing program with batch processing features, and 3D Slicer which focuses on 3D informatics and visualisation. They are easily extensible using common programming languages, with 3D Slicer containing an internal python interactor, and ImageJ allowing the incorporation of several programming languages within its interface alongside its own simplified macro language. Additional features created by other users are readily available, on GitHub or through the software itself.
In the examples presented, an ImageJ plugin “FossilJ” has been developed which provides semi-automated morphometric bivalve data collection. 3D Slicer is used with the extension SPHARM-PDM, applied to synchrotron scans of coniform conodonts for comparative morphometrics, for which small assistant tools have been created in Python.
In a world where an increasing number of resources are hidden behind paywalls and monthly subscriptions, it is becoming crucial for the scientific community to invest energy into freely available, community-maintained systems. Open-source software projects offer a solution, with freely available code which users can utilise and modify, under an open source licence. In addition to software accessibility and methodological repeatability, this also enables and encourages the development of new tools.As palaeontology moves towards data driven methodologies, it is becoming more important to acquire and provide high quality data through reproducible systematic procedures. Within the field of morphometrics, it is vital to adopt digital methods that help mitigate human bias from data collection. In addition, mathematically founded approaches can reduce subjective decisions which plague classical data. This can be further developed through automation, which increases the efficiency of data collection and analysis.With these concepts in mind, we introduce two open-source shape analysis software, that arose from projects within the medical imaging field. These are ImageJ, an image processing program with batch processing features, and 3D Slicer which focuses on 3D informatics and visualisation. They are easily extensible using common programming languages, with 3D Slicer containing an internal python interactor, and ImageJ allowing the incorporation of several programming languages within its interface alongside its own simplified macro language. Additional features created by other users are readily available, on GitHub or through the software itself.In the examples presented, an ImageJ plugin “FossilJ” has been developed which provides semi-automated morphometric bivalve data collection. 3D Slicer is used with the extension SPHARM-PDM, applied to synchrotron scans of coniform conodonts for comparative morphometrics, for which small assistant tools have been created in Python.Biogeographic patterns of belemnite body size responses to episodes of environmental crisishttps://peerj.com/preprints/280002019-09-302019-09-30Patrícia RitaJosé C. García-RamosPascal NeigeLaura PiñuelaRobert WeisLuís V. DuarteChristof ÜbelackerKenneth De Baets
Body size changes have been investigated through episodes of environmental crisis among several groups of organisms but the relative contribution of within-lineage size changes, selective extinction and origination of taxa on these patterns is still being debated. Rapid warming, anoxia, and perturbations of the carbon cycle linked with volcanic activity, as well as their impact on marine diversity are well documented for the Pliensbachian-Toarcian (Pli-Toa) boundary and for the Toarcian Oceanic Anoxic Event (T-OAE). Belemnites were a very abundant and successful cephalopod group in the Mesozoic oceans playing a paramount role in the oceanic trophic webs. Belemnites have mainly been studied from a geochemical perspective during this interval. Newly collected data from three northern and western Iberian sections (Peniche, Rodiles and Lastres) allowed an analysis of the belemnite body size dynamics across the Pli-Toa boundary and the T-OAE and a comparison with other European basins. In Peniche (Lusitanian Basin, Portugal), a significant reduction in belemnite body size was recognized across the Pli-Toa boundary at the assemblage level (i.e. community scale of organization). From the analysis of the different taxa recorded, it seems that adult specimens of Pseudohastites longiformis are driving the body size pattern observed (13% rostrum size decrease). The uppermost Polymorphum-Levisoni zones interval is characterized by a dramatic decrease on both belemnite abundance and diversity. Only 4 specimens of the genus Acrocoelites were found, increasing the body size at the assemblage level. In the Asturian Basin (N Spain), on the other hand, a body size increase at the assemblage level is recognized across the Pli-Toa boundary caused by a within-lineage effect mainly related to adult specimens of Passaloteuthis and Pseudohastites genera. During the onset of the T-OAE, belemnite body size increases due to the appearance of Acrocoelites genus. To summarize, the increase in rostrum size at the assemblage level across the T-OAE is associated with the radiation of a large-sized taxon (Acrocoelites genus) and the extinction of various other species. On the other hand, across the Pli-Toa boundary, the belemnite body size changes are dominated by within-lineage mechanisms. This suggests that species might have been able to cope within the early warming phase (Pli-Ta boundary), but were more affected by the subsequent warming and anoxia during the T-OAE. Our preliminary results indicate that this pattern might also be recognized in other western European sections, such as Cleveland Basin, western Paris Basin (Normandy) and Southern Germany sections. The biotic and abiotic drivers of belemnite body size changes still need to be comprehensively analyzed.
Body size changes have been investigated through episodes of environmental crisis among several groups of organisms but the relative contribution of within-lineage size changes, selective extinction and origination of taxa on these patterns is still being debated. Rapid warming, anoxia, and perturbations of the carbon cycle linked with volcanic activity, as well as their impact on marine diversity are well documented for the Pliensbachian-Toarcian (Pli-Toa) boundary and for the Toarcian Oceanic Anoxic Event (T-OAE). Belemnites were a very abundant and successful cephalopod group in the Mesozoic oceans playing a paramount role in the oceanic trophic webs. Belemnites have mainly been studied from a geochemical perspective during this interval. Newly collected data from three northern and western Iberian sections (Peniche, Rodiles and Lastres) allowed an analysis of the belemnite body size dynamics across the Pli-Toa boundary and the T-OAE and a comparison with other European basins. In Peniche (Lusitanian Basin, Portugal), a significant reduction in belemnite body size was recognized across the Pli-Toa boundary at the assemblage level (i.e. community scale of organization). From the analysis of the different taxa recorded, it seems that adult specimens of Pseudohastites longiformis are driving the body size pattern observed (13% rostrum size decrease). The uppermost Polymorphum-Levisoni zones interval is characterized by a dramatic decrease on both belemnite abundance and diversity. Only 4 specimens of the genus Acrocoelites were found, increasing the body size at the assemblage level. In the Asturian Basin (N Spain), on the other hand, a body size increase at the assemblage level is recognized across the Pli-Toa boundary caused by a within-lineage effect mainly related to adult specimens of Passaloteuthis and Pseudohastites genera. During the onset of the T-OAE, belemnite body size increases due to the appearance of Acrocoelites genus. To summarize, the increase in rostrum size at the assemblage level across the T-OAE is associated with the radiation of a large-sized taxon (Acrocoelites genus) and the extinction of various other species. On the other hand, across the Pli-Toa boundary, the belemnite body size changes are dominated by within-lineage mechanisms. This suggests that species might have been able to cope within the early warming phase (Pli-Ta boundary), but were more affected by the subsequent warming and anoxia during the T-OAE. Our preliminary results indicate that this pattern might also be recognized in other western European sections, such as Cleveland Basin, western Paris Basin (Normandy) and Southern Germany sections. The biotic and abiotic drivers of belemnite body size changes still need to be comprehensively analyzed.What do we mean by the directions “cranial” and “caudal” on a vertebra?https://peerj.com/preprints/274372019-09-302019-09-30Michael P TaylorMatthew J Wedel
In illustrating vertebrae, it is important to consistently depict their orientation, so we can objectively assess and compare the slope of the neural arch, neural canal, or articular surfaces. However, differing vertebral shapes across taxa and across regions of the spinal column make it difficult to maintain consistency, or even define what we mean by the directions “cranial” and “caudal”. Consequently, characters such as “Neural arch slopes cranially 30° relative to the vertical” are disputable rather than objective measurements. Cranial and caudal are defined as directed along the horizontal axis, but several different notions of “horizontal” are possible:
1. Long axis of centrum is horizontal. This is appealing for elongate vertebrae such as sauropod cervicals, but is not always well defined, and is difficult to determine for craniocaudally short vertebrae such as most caudals.
2. Articular surfaces of centrum are vertical. Difficult to determine when dealing with facets that are concave or (worse) convex; and ambiguous for “keystoned” vertebrae in which the facets are not parallel.
3. Neural canal is horizontal. Anatomically informative, but difficult to determine in vertebrae that have not been fully prepared or CT-scanned, and impossible to see in lateral view. Ambiguous for vertebrae where the dorsal and ventral margins of the canal are not straight or not parallel.
4. Similarity in articulation (“horizontal” is defined as a line joining the same point on two similarly oriented copies of the same vertebra when optimally articulated). This is less intuitive than definitions 1–3, but takes the entire vertebra into account.
We advocate explicitly stating a definition and using it consistently. In most cases, definition 3 (“Neural canal is horizontal”) best reflects anatomical and developmental realities, and it is therefore preferred. Low-tech techniques can be used to determine neural canal orientation with adequate precision for most purposes.
In illustrating vertebrae, it is important to consistently depict their orientation, so we can objectively assess and compare the slope of the neural arch, neural canal, or articular surfaces. However, differing vertebral shapes across taxa and across regions of the spinal column make it difficult to maintain consistency, or even define what we mean by the directions “cranial” and “caudal”. Consequently, characters such as “Neural arch slopes cranially 30° relative to the vertical” are disputable rather than objective measurements. Cranial and caudal are defined as directed along the horizontal axis, but several different notions of “horizontal” are possible:1. Long axis of centrum is horizontal. This is appealing for elongate vertebrae such as sauropod cervicals, but is not always well defined, and is difficult to determine for craniocaudally short vertebrae such as most caudals.2. Articular surfaces of centrum are vertical. Difficult to determine when dealing with facets that are concave or (worse) convex; and ambiguous for “keystoned” vertebrae in which the facets are not parallel.3. Neural canal is horizontal. Anatomically informative, but difficult to determine in vertebrae that have not been fully prepared or CT-scanned, and impossible to see in lateral view. Ambiguous for vertebrae where the dorsal and ventral margins of the canal are not straight or not parallel.4. Similarity in articulation (“horizontal” is defined as a line joining the same point on two similarly oriented copies of the same vertebra when optimally articulated). This is less intuitive than definitions 1–3, but takes the entire vertebra into account.We advocate explicitly stating a definition and using it consistently. In most cases, definition 3 (“Neural canal is horizontal”) best reflects anatomical and developmental realities, and it is therefore preferred. Low-tech techniques can be used to determine neural canal orientation with adequate precision for most purposes.Organic facies variability and paleoenvironmental interpretation of the Early Toarcian of the Pyrenean Basin: the Bizanet and the Pont de Suert sectionshttps://peerj.com/preprints/279772019-09-242019-09-24Carolina FonsecaJoão Graciano Mendonça FilhoCarine LézinLuís Vítor DuartePhilippe Fauré
The Early Toarcian is characterized by major worldwide environmental changes recorded in an organic-rich black shale sedimentation and carbon cycle disturbances, the so-called Toarcian Oceanic Anoxic Event (T-OAE) (e.g. Jenkyns, 2010). This organic-rich sedimentation is particularly recorded in shallow marine epicontinental basins that developed as part of the Toarcian European epicontinental shelf, paleogeographical framework in which the Pyrenean Basin is incorporated (e.g. Fonseca et al., 2018; McArthur et al., 2008). With these premises, the main objective of this study is to assess the organic facies variability and to define the depositional paleoenvironments of two sections from the Pyrenean Basin (Bizanet and Pont de Suert) during the T-OAE, using palynofacies and geochemical (Total Organic Carbon - TOC and insoluble residue - IR) data. The Pyrenean tectonics that occurred between the latest Cretaceous and the Oligocene, deformed, detached and fragmented the substrate resulting in diverse tectonic units (Faure, 2002). The late Pliensbachian-early Toarcian of the Pont de Suert section, located in the South Pyrenean zone, is characterized by the limestone dominated Barre a Pecten Formation (Fm.), and the carbonate and/or argillaceous-carbonate alternation of its three members (alternations of marl and argillaceous limestone of the Calcaires argileux à Spirifèrines Member (Mb.), the argillaceous limestones and marls of the Calcaires argileux et marnes à Soaresirhynchia Mb., and the marl and argillaceous limestone dominated Calcaires argileux à Telothyris Mb.; Faure, 2002). The Bizanet section is located in the eastern Corbières, and is characterized by a 3m thick succession of late Pliensbachian-early Toarcian sediments comprising, at the base, the limestone dominated Barre a Pecten Fm., followed by a sedimentary gap dated to the Tenuicostatum Chronozone, topped by the marly dominated succession of the Bizanet Fm. (black ferruginous marls intercalated with limestones and topped by dolomitic limestones of the Schistes carton Mb., and the black marls of the Argilites noires litées Mb.; Faure, 2002). The geochemical results evidenced that the Bizanet section presents higher TOC contents than the Pont de Suert section, with values reaching 2.03 wt.%. In the Bizanet section IR ranges between 12 wt.% and 82 wt.% and in the Pont de Suert section varies from 13wt.% to 67 wt.%, displaying a similar average value for the two sections (45 wt.%). The palynofacies assemblage is dominated in both sections by the same components, belonging to the Phylum Cnidaria, Class Hydrozoa and Order Hydroida, and are represented by fragments of colonial and non-colonial sessile polypoid forms and free-swimming medusoid forms, with different degrees of amorphization.
(This abstract has been truncated, please see the complete PDF version)
The Early Toarcian is characterized by major worldwide environmental changes recorded in an organic-rich black shale sedimentation and carbon cycle disturbances, the so-called Toarcian Oceanic Anoxic Event (T-OAE) (e.g. Jenkyns, 2010). This organic-rich sedimentation is particularly recorded in shallow marine epicontinental basins that developed as part of the Toarcian European epicontinental shelf, paleogeographical framework in which the Pyrenean Basin is incorporated (e.g. Fonseca et al., 2018; McArthur et al., 2008). With these premises, the main objective of this study is to assess the organic facies variability and to define the depositional paleoenvironments of two sections from the Pyrenean Basin (Bizanet and Pont de Suert) during the T-OAE, using palynofacies and geochemical (Total Organic Carbon - TOC and insoluble residue - IR) data. The Pyrenean tectonics that occurred between the latest Cretaceous and the Oligocene, deformed, detached and fragmented the substrate resulting in diverse tectonic units (Faure, 2002). The late Pliensbachian-early Toarcian of the Pont de Suert section, located in the South Pyrenean zone, is characterized by the limestone dominated Barre a Pecten Formation (Fm.), and the carbonate and/or argillaceous-carbonate alternation of its three members (alternations of marl and argillaceous limestone of the Calcaires argileux à Spirifèrines Member (Mb.), the argillaceous limestones and marls of the Calcaires argileux et marnes à Soaresirhynchia Mb., and the marl and argillaceous limestone dominated Calcaires argileux à Telothyris Mb.; Faure, 2002). The Bizanet section is located in the eastern Corbières, and is characterized by a 3m thick succession of late Pliensbachian-early Toarcian sediments comprising, at the base, the limestone dominated Barre a Pecten Fm., followed by a sedimentary gap dated to the Tenuicostatum Chronozone, topped by the marly dominated succession of the Bizanet Fm. (black ferruginous marls intercalated with limestones and topped by dolomitic limestones of the Schistes carton Mb., and the black marls of the Argilites noires litées Mb.; Faure, 2002). The geochemical results evidenced that the Bizanet section presents higher TOC contents than the Pont de Suert section, with values reaching 2.03 wt.%. In the Bizanet section IR ranges between 12 wt.% and 82 wt.% and in the Pont de Suert section varies from 13wt.% to 67 wt.%, displaying a similar average value for the two sections (45 wt.%). The palynofacies assemblage is dominated in both sections by the same components, belonging to the Phylum Cnidaria, Class Hydrozoa and Order Hydroida, and are represented by fragments of colonial and non-colonial sessile polypoid forms and free-swimming medusoid forms, with different degrees of amorphization.(This abstract has been truncated, please see the complete PDF version)The organic record of Oceanic Anoxic Events: Toarcian vs Cenomanian-Turonianhttps://peerj.com/preprints/279782019-09-242019-09-24Carolina FonsecaJoão Graciano Mendonça FilhoCarine LézinLuís Vítor Duarte
The Mesozoic is marked by periods of profound climatic and paleoceanographic changes of the planet, representing major environmental perturbations and global carbon cycle disturbances, the so-called oceanic anoxic events (OAEs). These events are usually characterized by the deposition of sediments rich in organic matter (OM) which further validates the importance of the characterization of these organic records (e.g. Jenkyns, 2010). Furthermore, the high variability in the expression of these global events could be related to regional factors, which can be assessed through the study of the organic fraction of these records. With these premises is made a discussion about the organic variability, especially focused on petrographic observations, of two major OAE’s that differ in origin, extension and geochemical signature, the Toarcian (T-OAE) and the Cenomanian-Turonian (OAE2) events. For the T-OAE is analyzed a N-S transect of the Toarcian epicontinental seaway to enable the establishment of relationships of confinement, salinity and OM concentration. For the OAE2 the focus is on sections recording the Atlantic and Tethyan affinities to discuss the origin of the anoxia. The T-OAE organic record is characterized by the already established trend in TOC (van de Schootbrugge et al., 2005), with higher values being present in the more northern basins of the European epicontinental seaway (e.g. Dotternhausen) and diminishing towards the south, with lower values registered in the more external basins (e.g. Lusitanian Basin). This is coupled by a decrease in the degree of amorphization of the OM, and a variation in the origin of the amorphous OM, that culminates in its disappearance in the more external Lusitanian Basin (Fonseca et al., 2018; Rodrigues et al., 2016). The OAE2 organic record is marked by high variability, especially connected to differences in oceanic circulation dynamics that differ in the Tethyan and Atlantic domains (e.g. Trabucho-Alexandre et al., 2010). The TOC content of this event reaches higher values than the ones associated with the T-OAE (>30 wt.%), with the organic associations being dominated in the majority of the sections by amorphous OM. Nevertheless, the origin of this component differs and is very much controlled by local conditions. Differences in productivity, connected to the occurrence of intense upwelling in the Atlantic domain, are also observed. The organic facies variability and the differences in paleoenvironmental depositional contexts observed in the studied sections are associated with the regional character of both the T-OAE and the OAE2. These are mainly attributed to differences in paleogeography, paleogeomorphology and oceanic circulation patterns. Furthermore, there are clear differences in the organic content of both events, showing that is not only their origin, extension and geochemical characteristics that differ but also their organic signature.
The Mesozoic is marked by periods of profound climatic and paleoceanographic changes of the planet, representing major environmental perturbations and global carbon cycle disturbances, the so-called oceanic anoxic events (OAEs). These events are usually characterized by the deposition of sediments rich in organic matter (OM) which further validates the importance of the characterization of these organic records (e.g. Jenkyns, 2010). Furthermore, the high variability in the expression of these global events could be related to regional factors, which can be assessed through the study of the organic fraction of these records. With these premises is made a discussion about the organic variability, especially focused on petrographic observations, of two major OAE’s that differ in origin, extension and geochemical signature, the Toarcian (T-OAE) and the Cenomanian-Turonian (OAE2) events. For the T-OAE is analyzed a N-S transect of the Toarcian epicontinental seaway to enable the establishment of relationships of confinement, salinity and OM concentration. For the OAE2 the focus is on sections recording the Atlantic and Tethyan affinities to discuss the origin of the anoxia. The T-OAE organic record is characterized by the already established trend in TOC (van de Schootbrugge et al., 2005), with higher values being present in the more northern basins of the European epicontinental seaway (e.g. Dotternhausen) and diminishing towards the south, with lower values registered in the more external basins (e.g. Lusitanian Basin). This is coupled by a decrease in the degree of amorphization of the OM, and a variation in the origin of the amorphous OM, that culminates in its disappearance in the more external Lusitanian Basin (Fonseca et al., 2018; Rodrigues et al., 2016). The OAE2 organic record is marked by high variability, especially connected to differences in oceanic circulation dynamics that differ in the Tethyan and Atlantic domains (e.g. Trabucho-Alexandre et al., 2010). The TOC content of this event reaches higher values than the ones associated with the T-OAE (>30 wt.%), with the organic associations being dominated in the majority of the sections by amorphous OM. Nevertheless, the origin of this component differs and is very much controlled by local conditions. Differences in productivity, connected to the occurrence of intense upwelling in the Atlantic domain, are also observed. The organic facies variability and the differences in paleoenvironmental depositional contexts observed in the studied sections are associated with the regional character of both the T-OAE and the OAE2. These are mainly attributed to differences in paleogeography, paleogeomorphology and oceanic circulation patterns. Furthermore, there are clear differences in the organic content of both events, showing that is not only their origin, extension and geochemical characteristics that differ but also their organic signature.On the diversity of Early Jurassic cartilaginous fishes across the Toarcian Oceanic Anoxic Eventhttps://peerj.com/preprints/279752019-09-222019-09-22Sebastian StumpfFaviel A. López-RomeroJürgen Kriwet
The Early Jurassic represents a crucial time interval in the evolutionary history of elasmobranchs, because the Toarcian witnessed a first major diversification, suggesting a profound reorganization of ecological niches of chondrichthyans, probably accompanied by a subsequent diversity decline of hybodontiforms within marine environments. Potential factors underlying the Toarcian elasmobranch radiation event not only include evolutionary novelties in ecological adaptations of swimming, feeding, and reproduction, but also abiotic factors such as increasing seawater temperatures and variations in eustatic sea level associated with the Toarcian Oceanic Anoxic Event (T-OAE). These events might have played an important role in the Toarcian elasmobranch diversification event by regulating diversity dynamics through the availability of higher speciation and dispersal rates.
In attempt to better understand macroevolutionary patterns and processes of Jurassic chondrichthyans, we analysed the generic diversity of Pliensbachian to Aalenian elasmobranchs and hybodontiforms and explored their response to the T-OAE. In doing so, we calculated the estimated mean standing diversities (EMSD) using 10 time bins of approximately 2 Myr duration and evaluated the relationships between EMSD and variations in both seawater temperature and eustatic sea level to test whether these parameters affect the observed diversity patterns.
Our data indicate profoundly different diversity dynamics of elasmobranchs and hybodontiforms. The EMSD is low in Pliensbachian to Aalenian hybodontiforms, indicating an evolutionary stasis. Conversely, a constant taxonomic increase in elasmobranchs is recorded, spanning from the Pliensbachian to the end of the Toarcian, before reaching a diversity plateau in the Aalenian. These divergent patterns might suggest that hybodontiforms were not competing with elasmobranchs, but more likely are the result of still existing taxonomic misconceptions of Jurassic hybodontiforms, mainly caused by morphological characters that are either ambiguous or broadly distributed among these anatomically rather conservative chondrichthyans. Notwithstanding this, our results indicate that variations in seawater temperature and eustatic sea level changes associated with the T-OAE were not the primary drivers underlying the observed elasmobranch diversity patterns. Therefore, it might be possible that the diversification of elasmobranchs was opportunistic, benefitting from the appearance and subsequent radiation of new food resources, probably in response of enhanced surface productivity during the T-OAE. This hypothesis, however, needs to be tested, pending the inclusion of other time-equivalent marine vertebrate groups in future diversity analyses. Moreover, a detailed re-evaluation of Jurassic hybodontiforms will contribute to our understanding of chondrichthyan diversity dynamics across the T-OAE.
The Early Jurassic represents a crucial time interval in the evolutionary history of elasmobranchs, because the Toarcian witnessed a first major diversification, suggesting a profound reorganization of ecological niches of chondrichthyans, probably accompanied by a subsequent diversity decline of hybodontiforms within marine environments. Potential factors underlying the Toarcian elasmobranch radiation event not only include evolutionary novelties in ecological adaptations of swimming, feeding, and reproduction, but also abiotic factors such as increasing seawater temperatures and variations in eustatic sea level associated with the Toarcian Oceanic Anoxic Event (T-OAE). These events might have played an important role in the Toarcian elasmobranch diversification event by regulating diversity dynamics through the availability of higher speciation and dispersal rates.In attempt to better understand macroevolutionary patterns and processes of Jurassic chondrichthyans, we analysed the generic diversity of Pliensbachian to Aalenian elasmobranchs and hybodontiforms and explored their response to the T-OAE. In doing so, we calculated the estimated mean standing diversities (EMSD) using 10 time bins of approximately 2 Myr duration and evaluated the relationships between EMSD and variations in both seawater temperature and eustatic sea level to test whether these parameters affect the observed diversity patterns.Our data indicate profoundly different diversity dynamics of elasmobranchs and hybodontiforms. The EMSD is low in Pliensbachian to Aalenian hybodontiforms, indicating an evolutionary stasis. Conversely, a constant taxonomic increase in elasmobranchs is recorded, spanning from the Pliensbachian to the end of the Toarcian, before reaching a diversity plateau in the Aalenian. These divergent patterns might suggest that hybodontiforms were not competing with elasmobranchs, but more likely are the result of still existing taxonomic misconceptions of Jurassic hybodontiforms, mainly caused by morphological characters that are either ambiguous or broadly distributed among these anatomically rather conservative chondrichthyans. Notwithstanding this, our results indicate that variations in seawater temperature and eustatic sea level changes associated with the T-OAE were not the primary drivers underlying the observed elasmobranch diversity patterns. Therefore, it might be possible that the diversification of elasmobranchs was opportunistic, benefitting from the appearance and subsequent radiation of new food resources, probably in response of enhanced surface productivity during the T-OAE. This hypothesis, however, needs to be tested, pending the inclusion of other time-equivalent marine vertebrate groups in future diversity analyses. Moreover, a detailed re-evaluation of Jurassic hybodontiforms will contribute to our understanding of chondrichthyan diversity dynamics across the T-OAE.New approaches to peer review in the age of online, open-access publishinghttps://peerj.com/preprints/279722019-09-192019-09-19Melanie J Hopkins
“Electronic publishing” can mean a variety of things, but for the dissemination of scientific results, there are two major categories: 1) materials that have not gone through peer-review, such as community-database entries, presentations from conferences, and manuscripts posted on preprint servers; and 2) materials that have gone through peer-review and are subsequently posted online. In the latter case, the process of peer-review is usually managed by a body of editors associated with a journal. If a manuscript is published by such a journal, the reader can be assured that it went through the peer-review process successfully. In the last decade or so, journals have started to abandon printed issues of peer-reviewed articles and are now publishing exclusively online; there have also been a proliferation of new online-only journals. Concurrently, there has been a shift towards open-access publishing, which, while making scientific studies more broadly available, has also transferred the financial burden from the reader or subscriber to the authors and funding agencies. Lastly, there has been a shift in how manuscripts on preprint servers are viewed, and it is increasingly common in many scientific fields for authors to post a finalized manuscript to a preprint server prior to submission to a journal. This talk will describe the “Peer Community In” (PCI) Project, which is a non-profit organization that was established in response to these major shifts in scientific publishing. The PCI Project is comprised of communities of researchers working in different fields (including paleontology), who peer review and recommend research articles publicly available on preprint servers. The goal is to promote rigorous scientific study by providing an alternative to traditional avenues for peer-reviewed publishing.
“Electronic publishing” can mean a variety of things, but for the dissemination of scientific results, there are two major categories: 1) materials that have not gone through peer-review, such as community-database entries, presentations from conferences, and manuscripts posted on preprint servers; and 2) materials that have gone through peer-review and are subsequently posted online. In the latter case, the process of peer-review is usually managed by a body of editors associated with a journal. If a manuscript is published by such a journal, the reader can be assured that it went through the peer-review process successfully. In the last decade or so, journals have started to abandon printed issues of peer-reviewed articles and are now publishing exclusively online; there have also been a proliferation of new online-only journals. Concurrently, there has been a shift towards open-access publishing, which, while making scientific studies more broadly available, has also transferred the financial burden from the reader or subscriber to the authors and funding agencies. Lastly, there has been a shift in how manuscripts on preprint servers are viewed, and it is increasingly common in many scientific fields for authors to post a finalized manuscript to a preprint server prior to submission to a journal. This talk will describe the “Peer Community In” (PCI) Project, which is a non-profit organization that was established in response to these major shifts in scientific publishing. The PCI Project is comprised of communities of researchers working in different fields (including paleontology), who peer review and recommend research articles publicly available on preprint servers. The goal is to promote rigorous scientific study by providing an alternative to traditional avenues for peer-reviewed publishing.Using the Paleobiology Database and MorphoBank to facilitate collaborative research and data archivalhttps://peerj.com/preprints/279712019-09-192019-09-19Melanie J Hopkins
The internet has made it possible to share and store large quantities of data, and as a result, there is an increasing imperative to make data easily accessible and results reproducible. This has been facilitated by the proliferation of online tools available for archiving and sharing data. In this talk I will describe two databases that are structured in different ways but provide useful platforms for collaboration, reproducibility, and data archival. The first is the Paleobiology Database (PBDB), which is a public resource for paleontological data in support of global, collection-based occurrence and taxonomic data for organisms of all geologic ages. I will give a brief history of the PBDB; describe how data is contributed; describe data services for browsing data, downloading data, and the independent development of analytical and visualization tools; and describe how to make research based on data from the PBDB replicable. The second is MorphoBank, which is a project-based platform for organizing and archiving morphological data and images affiliated with that data, and whose primary use has been for building morphological matrices for use in phylogenetic and disparity analyses. I will give a brief history of MorphoBank; describe tools for data creation, editing, and export; and describe how the platform is best used for replicability and data archival during the review process and after publication. Finally, I will discuss the future of both databases, focusing particularly on initiatives for connecting each with other databases and with the R Project for Statistical Computing, as well as educational resources and funding.
The internet has made it possible to share and store large quantities of data, and as a result, there is an increasing imperative to make data easily accessible and results reproducible. This has been facilitated by the proliferation of online tools available for archiving and sharing data. In this talk I will describe two databases that are structured in different ways but provide useful platforms for collaboration, reproducibility, and data archival. The first is the Paleobiology Database (PBDB), which is a public resource for paleontological data in support of global, collection-based occurrence and taxonomic data for organisms of all geologic ages. I will give a brief history of the PBDB; describe how data is contributed; describe data services for browsing data, downloading data, and the independent development of analytical and visualization tools; and describe how to make research based on data from the PBDB replicable. The second is MorphoBank, which is a project-based platform for organizing and archiving morphological data and images affiliated with that data, and whose primary use has been for building morphological matrices for use in phylogenetic and disparity analyses. I will give a brief history of MorphoBank; describe tools for data creation, editing, and export; and describe how the platform is best used for replicability and data archival during the review process and after publication. Finally, I will discuss the future of both databases, focusing particularly on initiatives for connecting each with other databases and with the R Project for Statistical Computing, as well as educational resources and funding.