bioRxiv - Paleontology最新文献

Tetrapod species-area relationships across the Cretaceous-Paleogene mass extinction 白垩纪-古近纪大灭绝期间的四足动物物种-区域关系

bioRxiv - Paleontology Pub Date : 2024-09-19 DOI: 10.1101/2024.09.13.612886

Roger Adam Close, Bouwe Rutger Reijenga

{"title":"Tetrapod species-area relationships across the Cretaceous-Paleogene mass extinction","authors":"Roger Adam Close, Bouwe Rutger Reijenga","doi":"10.1101/2024.09.13.612886","DOIUrl":"https://doi.org/10.1101/2024.09.13.612886","url":null,"abstract":"Mass extinctions are rare but catastrophic events that profoundly disrupt biodiversity. Widely-accepted consequences of mass extinctions, such as biodiversity loss and the appearance of temporary 'disaster taxa,' imply that nested species-area relationships (SARs, or how biodiversity scales with area) should change dramatically across these events: specifically, both the slope (reflecting the rate of accumulation of new species with increasing area) and intercept (reflecting the density of species at local scales) of the power-law relationship should decrease. However, these hypotheses have not been tested, and the contribution of variation in the SAR to diversity dynamics in deep time has been neglected. We use fossil data to quantify nested SARs in North American terrestrial tetrapods through the Cretaceous- Paleogene (K/Pg) mass extinction (Campanian-Ypresian). SARs vary substantially through time and among groups. In the pre-extinction interval (Maastrichtian), unusually shallow SAR slopes (indicating low beta diversity or provinciality) drive low total regional diversity in dinosaurs, mammals and other tetrapods. In the immediate post-extinction interval (Danian), the explosive diversification of mammals drove high regional diversity via a large increase in SAR slope (indicating higher beta diversity or provinciality), and only a limited increase in SAR intercept (suggesting limited diversity change at small scales). This contradicts the expectation that post-extinction biotas should be regionally homogenized by the spread of disaster taxa and impoverished by diversity loss. This early post-extinction increase in SAR slope was followed in the Thanetian-Selandian (~4.4. myr later) by increases in the intercept, indicating that diversity dynamics at local and regional scales did not change in synchrony. These results demonstrate the importance of SARs for understanding deep-time diversity dynamics, particularly the spatial dynamics of recovery from mass extinctions.","PeriodicalId":501477,"journal":{"name":"bioRxiv - Paleontology","volume":"209 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142252727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Unique dental arrangement in a new species of Groenlandaspis (Placodermi, Arthrodire) from the Middle Devonian of Mount Howitt, Victoria, Australia 澳大利亚维多利亚州豪威特山中泥盆纪 Groenlandaspis（Placodermi，Arthrodire）新物种独特的牙齿排列方式

bioRxiv - Paleontology Pub Date : 2024-09-16 DOI: 10.1101/2024.09.11.612576

Austin Noah Fitzpatrick, Alice M Clement, John A Long

{"title":"Unique dental arrangement in a new species of Groenlandaspis (Placodermi, Arthrodire) from the Middle Devonian of Mount Howitt, Victoria, Australia","authors":"Austin Noah Fitzpatrick, Alice M Clement, John A Long","doi":"10.1101/2024.09.11.612576","DOIUrl":"https://doi.org/10.1101/2024.09.11.612576","url":null,"abstract":"Well-preserved specimens of an undescribed species of arthrodiran placoderm, Groenlandaspis howittensis sp. nov. (Middle Devonian of Victoria, Australia), reveals previously unknown information on the dermal skeleton, body-shape and tooth arcade of the wide-spread genus Groenlandaspis. The new material includes, dual pineal plates, extrascapular plates, and cheek bones cheek bones showing the presence of cutaneous sensory organs. The anterior supragnathal, usually a paired element in arthrodires, is a fused medial bone in G. howittensis sp. nov. It is positioned anterior to the occlusion of the mouth between the lower jaw (infragnathals) and upper jaw (posterior supragnathals) bones, indicating a specialised feeding mechanism and broadening the known diversity of placoderm dental morphologies. G. howittensis sp. nov. differs from all other groenlandaspidids by a less pronounced posterior expansion of the nuchal plate; the shape of the posterior dorsolateral plate and the presence of a short accessory canal on the anterior dorsolateral plate. A new phylogenetic analysis positions Groenlandaspididae in a monophyly with the phlyctaeniid families Arctolepidae and Arctaspididae, however, the specific intrarelationships of groenlandaspidids remain poorly resolved.","PeriodicalId":501477,"journal":{"name":"bioRxiv - Paleontology","volume":"89 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142252726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

DeepDiveR – A software for deep learning estimation of palaeodiversity from fossil occurrences DeepDiveR--一款通过深度学习从化石地点估算古多样性的软件

bioRxiv - Paleontology Pub Date : 2024-09-06 DOI: 10.1101/2024.09.03.610960

Rebecca Brown Cooper, Bethany J Allen, Daniele Silvestro

{"title":"DeepDiveR – A software for deep learning estimation of palaeodiversity from fossil occurrences","authors":"Rebecca Brown Cooper, Bethany J Allen, Daniele Silvestro","doi":"10.1101/2024.09.03.610960","DOIUrl":"https://doi.org/10.1101/2024.09.03.610960","url":null,"abstract":"The incompleteness of the fossil record, in particular variation in preservation and sampling through space and time, presents a barrier to estimating changes in biodiversity which standard statistical methods struggle to account for. Here we present DeepDiveR, an R package for the DeepDive program enabling estimation of biodiversity from fossil occurrence data. The method uses a simulation-trained deep neural network to generate predictions of biodiversity change through time, while accounting for temporal, spatial and taxonomic heterogeneities in preservation. DeepDiveR can be readily used to explore the extinct biodiversity of different clades. We demonstrate the pipeline to build and customise analyses, including consideration of changes in biogeography. We also further develop the model to integrate information about modern diversity in the case of extant clades and introduce a function that automatically adjusts the parameterization of the simulations to generate training data that reflect the distribution of empirical datasets. To demonstrate the software, we analyse the fossil record of the order Carnivora through the Cenozoic, finding a peak in diversity in the Late Miocene and a 37% species loss since the Pleistocene. Our implementation includes the generation summary statistics and plots that allow for an evaluation of the model performance and diversity estimations and a configuration file that captures all parameters required to guarantee the full reproducibility of the results.","PeriodicalId":501477,"journal":{"name":"bioRxiv - Paleontology","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142198905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An extraordinary larval-like teleost fish from the Eocene of Bolca 来自博尔卡始新世的一种非同寻常的幼虫类远洋鱼类

bioRxiv - Paleontology Pub Date : 2024-08-23 DOI: 10.1101/2024.08.19.608581

Donald Davesne, Giorgio Carnevale

{"title":"An extraordinary larval-like teleost fish from the Eocene of Bolca","authors":"Donald Davesne, Giorgio Carnevale","doi":"10.1101/2024.08.19.608581","DOIUrl":"https://doi.org/10.1101/2024.08.19.608581","url":null,"abstract":"\"Pegasus\" volans is a highly unusual fossil teleost fish from the celebrated Eocene Bolca Lagerstatte. The fossil, known on the basis of two specimens, has been historically assigned to seamoths (Pegasidae), then to oarfish and relatives (Lampriformes). We describe its enigmatic skeletal anatomy in detail, and provide a new genus name. \"Pegasus\" volans is an extremely elongate and slender animal, with long anal and dorsal fins and a very well-developed first dorsal-fin ray reminiscent to the vexillum of some modern teleost larvae. Most striking is its extreme ventral projection of the pelvic girdle (basipterygium), associated with an element of the pectoral girdle (a long process of the coracoid) and developed pelvic-fin rays. The strongly reduced abdominal region suggests that \"Pegasus\" volans had an external gut, once again reminiscent of those of certain larval teleosts. The unique character state combination displayed by \"Pegasus\" volans make it impossible to assign it to a specific subclade within perch-like spiny-rayed fishes (Percomorpha). Nevertheless, it offers a valuable perspective on the diversity of morphologies and ecological niches occupied by teleost fishes of the early Eocene Bolca fauna.","PeriodicalId":501477,"journal":{"name":"bioRxiv - Paleontology","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142225469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Estimating ancestral states of complex characters: a case study on the evolution of feathers 估计复杂特征的祖先状态：羽毛进化案例研究

bioRxiv - Paleontology Pub Date : 2024-08-23 DOI: 10.1101/2024.08.23.609354

Pierre Cockx, Michael J. Benton, Joseph N. Keating

{"title":"Estimating ancestral states of complex characters: a case study on the evolution of feathers","authors":"Pierre Cockx, Michael J. Benton, Joseph N. Keating","doi":"10.1101/2024.08.23.609354","DOIUrl":"https://doi.org/10.1101/2024.08.23.609354","url":null,"abstract":"Feathers are a key novelty underpinning the evolutionary success of birds, yet the origin of feathers remains poorly understood. Debates about feather evolution hinge upon whether filamentous integument has evolved once or multiple time independently on the lineage leading to modern birds. These contradictory results stem from subjective methodological differences in statistical ancestral state estimates. Here we conduct a comprehensive comparison of ancestral state estimation methodologies applied to stem-group birds, testing the role of outgroup inclusion, tree time scaling method, model choice and character coding strategy. Models are compared based on their Akaike Information Criteria (AIC), mutual information, as well as the uncertainty of marginal ancestral state estimates. Our results demonstrate that ancestral state estimates of stem-bird integument are strongly influenced by tree time scaling method, outgroup selection and model choice, while character coding strategy seems to have less effect on the ancestral estimates produced. We identify the best fitting models using AIC scores and a leave-one-out cross-validation approach (LOOCV). Our analyses broadly support the independent origin of filamentous integument in dinosaurs and pterosaurs and support a younger evolutionary origin of feathers than has been suggested previously. More generally, our study highlights that special care must be taken in selecting the outgroup, tree and model when conducting ASE analyses. With respect to model selection, our results suggest that considering a LOOCV approach, may yield more reliable results than simply comparing AIC scores when the analyses involve a limited number of taxa.","PeriodicalId":501477,"journal":{"name":"bioRxiv - Paleontology","volume":"43 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142225459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A new tuna specimen (Genus Auxis) from the Duho Formation (middle Miocene) of South Korea 来自韩国 Duho Formation（中新世中期）的新金枪鱼标本（属 Auxis 类

bioRxiv - Paleontology Pub Date : 2024-07-30 DOI: 10.1101/2024.07.29.605724

Dayun Suh, Su-Hwan Kim, Gi-Soo Nam

{"title":"A new tuna specimen (Genus Auxis) from the Duho Formation (middle Miocene) of South Korea","authors":"Dayun Suh, Su-Hwan Kim, Gi-Soo Nam","doi":"10.1101/2024.07.29.605724","DOIUrl":"https://doi.org/10.1101/2024.07.29.605724","url":null,"abstract":"The partially articulated caudal vertebrae of a tuna were discovered from the Duho Formation (middle Miocene) of South Korea. This specimen was assigned to the genus Auxis and represents the second record of fossil Auxis found in South Korea. We compared the vertebral morphology of the studied specimen to that of currently known species of Auxis, including extinct taxa, but the specimen is not assigned to a new or existing species of Auxis due to poor preservation and a lack of diagnostic features. The discovery of a new specimen of Auxis supports theories of high marine biodiversity in the East Sea (Sea of Japan) and the opening of the East Sea in the early to middle Miocene. A widely opened East Sea might have increased the abundance and diversity of large oceanic fishes such as tunas during the deposition of the Duho Formation. A taphonomic scenario of the specimen was inferred based on the lack of anal pterygiophores and the leaf imprint on the matrix. The specimen would have been exposed for at least a month in a low-energy sedimentary environment at the deep-sea bottom and undergone disintegration before being buried.","PeriodicalId":501477,"journal":{"name":"bioRxiv - Paleontology","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141862634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Reassessment of body temperature and thermoregulation strategies in Mesozoic marine reptiles 重新评估中生代海洋爬行动物的体温和体温调节策略

bioRxiv - Paleontology Pub Date : 2024-07-28 DOI: 10.1101/2024.07.26.605303

Nicolas Séon, Peggy Vincent, Lene Liebe Delsett, Eve Poulallion, Guillaume Suan, Christophe Lécuyer, Aubrey Jane Roberts, François Fourel, Sylvain Charbonnier, Romain Amiot

{"title":"Reassessment of body temperature and thermoregulation strategies in Mesozoic marine reptiles","authors":"Nicolas Séon, Peggy Vincent, Lene Liebe Delsett, Eve Poulallion, Guillaume Suan, Christophe Lécuyer, Aubrey Jane Roberts, François Fourel, Sylvain Charbonnier, Romain Amiot","doi":"10.1101/2024.07.26.605303","DOIUrl":"https://doi.org/10.1101/2024.07.26.605303","url":null,"abstract":"Ichthyosauria, Plesiosauria and Metriorhynchidae were apex predators in Mesozoic oceanic trophic networks. Previous stable oxygen isotope studies suggested that several taxa belonging to these groups were endothermic and for some of them homeothermic organisms. However, these conclusions remain contentious owing to the associated uncertainties regarding the δ18O value and oxygen isotope fractionation relative to environmental sea water. Here, we present new hydroxylapatite phosphate δ18O values (δ18Op) of Ichthyosauria, Plesiosauria and Metriorhynchidae (Middle Jurassic to Early Cretaceous) recovered from mid- to high-paleolatitudes to better constrain their thermophysiology and investigate the presence of regional heterothermies. The intra-skeletal δ18Op variability failed to reveal distinct heterothermic patterns within any of the specimens, indicating either intra-body temperature homogeneity or an overriding diagenetic overprint of the original biological δ18Op bone record. Body temperature estimates have then been reassessed from new and published δ18Op values of well-preserved isolated teeth, recently revised Mesozoic latitudinal δ18O oceanic gradient and 18O-enrichment factor of fully aquatic air-breathing vertebrates. Our results confirm that Ichthyosauria were homeothermic endotherms (31°C to 41°C), while Plesiosauria were likely poikilothermic endotherms (27°C to 34°C). The new body temperature estimates of the Metriorhynchidae (25°C to 32°C) closely follow ambient temperatures and point to poikilothermic strategy with no or little endothermic abilities. These results improve our understanding of Mesozoic marine reptile thermoregulation and indicate that due to their limited body temperature variations, the δ18Op values from Ichthyosauria fossil remains could be used as valuable archives of Mesozoic oceans δ18Osw values that may help improve palaeoenvironmental and palaeoclimatic reconstructions.","PeriodicalId":501477,"journal":{"name":"bioRxiv - Paleontology","volume":"39 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141862637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An extinct clade sister to Eumetazoa: On the phylogeny of the Cambrian chancelloriids 一个已经灭绝的支系，它是Eumetazoa的姐妹支系：寒武纪腔肠动物的系统发育

bioRxiv - Paleontology Pub Date : 2024-07-23 DOI: 10.1101/2024.07.22.604532

Hao Yun, Xingliang Zhang, Glenn A. Brock, Jian Han, Luoyang Li, Bing Pan, Guoxiang Li, Joachim Reitner

{"title":"An extinct clade sister to Eumetazoa: On the phylogeny of the Cambrian chancelloriids","authors":"Hao Yun, Xingliang Zhang, Glenn A. Brock, Jian Han, Luoyang Li, Bing Pan, Guoxiang Li, Joachim Reitner","doi":"10.1101/2024.07.22.604532","DOIUrl":"https://doi.org/10.1101/2024.07.22.604532","url":null,"abstract":"The notable disparity of animal body plans can be traced back to the morphological innovations during the Cambrian explosion and represented by a number of exceptionally preserved soft-bodied and skeletal fossils that provide a compelling narrative for animal evolution. Chancelloriids, one of the extinct groups of Cambrian animals, have a distinctive body that characterized by a sclerite-bearing, flexible integument and a single apical opening leading into a central cavity devoid of unequivocal internal organs. Their phylogenetic position within the Metazoa, however, is controversial. Here, we describe new soft-bodied fossils of chancelloriids from the 518-million-year-old Chengjiang biota of China, which corroborate the unique bauplan pattern and reveal exquisite integument microstructures. The tiny protuberances and wrinkling structures of the integument are interpreted to be related to primitive epithelial contraction, suggesting that chancelloriids were a group of basal epitheliozoans and constitute an evolutionary clade that branched below all extant eumetazoans while above or close to the placozoans. Thus, the chancelloriid body plan likely filled one of the anatomical gaps between the Placozoa and the Eumetazoa.","PeriodicalId":501477,"journal":{"name":"bioRxiv - Paleontology","volume":"71 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141786191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Classification of dinosaur footprints using machine learning 利用机器学习对恐龙脚印进行分类

bioRxiv - Paleontology Pub Date : 2024-07-18 DOI: 10.1101/2024.07.15.603597

Michael Jones, Jens N Lallensack, Ian Jarman, Peter Falkingham, Ivo Siekmann

{"title":"Classification of dinosaur footprints using machine learning","authors":"Michael Jones, Jens N Lallensack, Ian Jarman, Peter Falkingham, Ivo Siekmann","doi":"10.1101/2024.07.15.603597","DOIUrl":"https://doi.org/10.1101/2024.07.15.603597","url":null,"abstract":"Fossilised dinosaur footprints enable us to study the behaviour of individual dinosaurs as well as interactions between dinosaurs of the same or different species. There are two principal groups of three-toed dinosaurs, ornithopods and theropods. Determining if a footprint is from an ornithopod or a theropod is a challenging problem. Based on a data set of over 300 dinosaur footprints we train several machine learning models for classifying footprints as either ornithopods or theropods. The data are provided in the form of 20 landmarks for representing each footprint which are derived from images. Variable selection using logistic forward regression demonstrates that the selected landmarks are at locations that are intuitively expected to be especially informative locations, such as the top or the bottom of a footprint. Most models show good accuracy but the recall of ornithopods, of which fewer samples were contained in the data set, was generally lower than the recall of theropods. The Multi-Layer Perceptron (MLP) stands out as the model which did best at dealing with the class imbalance. Finally, we investigate which footprints were misclassified by the majority of models. We find that some misclassified samples exhibit features that are characteristic of the other class or have a compromised shape, for example, a middle toe that points to the left or the right rather than straight ahead.","PeriodicalId":501477,"journal":{"name":"bioRxiv - Paleontology","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141741244","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Computational simulations of Pachycrocuta bite damage based on a ~1.2 Ma ravaged hippopotamus femur from Fuente Nueva 3 (Orce, Granada, Spain) 基于从 Fuente Nueva 3（西班牙格拉纳达，奥尔塞）出土的约 1.2 Ma 河马股骨，对河马咬伤进行计算模拟

bioRxiv - Paleontology Pub Date : 2024-07-10 DOI: 10.1101/2024.07.07.602373

Lloyd Austin Courtenay, Alexia Serrano-Ramos, Deborah Barsky, Juan-Manuel Jiménez-Arenas, José Yravedra

引用次数: 0