Pub Date : 2024-09-19DOI: 10.1101/2024.09.13.612886
Roger Adam Close, Bouwe Rutger Reijenga
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.
物种大灭绝是罕见的灾难性事件，会严重破坏生物多样性。生物多样性丧失和临时性 "灾难类群 "的出现等大规模灭绝的后果已被广泛接受，这意味着嵌套的物种-面积关系（SARs，或生物多样性如何随面积而缩放）应在这些事件中发生巨大变化：具体而言，幂律关系的斜率（反映新物种随面积增加而积累的速度）和截距（反映局部尺度的物种密度）都应下降。然而，这些假设并没有得到验证，SAR的变化对深部时间多样性动态的贡献也被忽视了。我们利用化石数据量化了北美陆生四足动物在白垩纪-古近纪（K/Pg）大灭绝（坎帕期-Ypresian）期间的嵌套SAR。不同时期和不同类群的 SARs 有很大差异。在生物大灭绝之前的时期（马斯特里赫特），异常浅的 SAR 斜坡（表明贝塔多样性或省区性较低）导致恐龙、哺乳动物和其他四足类动物的总区域多样性较低。在恐龙灭绝后不久的时期（达尼安纪），哺乳动物爆炸性的多样化通过 SAR 斜率的大幅增加（表明较高的β多样性或省区性）以及 SAR 截距的有限增加（表明小尺度上有限的多样性变化）驱动了较高的区域多样性。这与灭绝后的生物群落应该因灾害类群的扩散而区域同质化、因多样性丧失而贫乏的预期相矛盾。生物大灭绝后早期 SAR 斜率的增加在萨尼特-志留纪（约 4.4 百万年后）又出现了截距的增加，这表明局部和区域尺度的多样性动态变化并不同步。这些结果表明了 SAR 对于理解深时多样性动态，特别是大灭绝后恢复的空间动态的重要性。
{"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}
Pub Date : 2024-09-16DOI: 10.1101/2024.09.11.612576
Austin Noah Fitzpatrick, Alice M Clement, John A Long
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.
{"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}
Pub Date : 2024-09-06DOI: 10.1101/2024.09.03.610960
Rebecca Brown Cooper, Bethany J Allen, Daniele Silvestro
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.
化石记录的不完整性，特别是保存和取样在空间和时间上的差异，给估算生物多样性的变化带来了障碍，而标准的统计方法难以对此做出解释。在此，我们介绍 DeepDiveR，这是一个用于 DeepDive 程序的 R 软件包，可根据化石出现数据估算生物多样性。该方法使用模拟训练的深度神经网络生成生物多样性随时间变化的预测，同时考虑到保存中的时间、空间和分类异质性。DeepDiveR 可用于探索不同支系的灭绝生物多样性。我们展示了建立和定制分析的管道，包括考虑生物地理学的变化。我们还进一步开发了模型，以整合现存支系的现代多样性信息，并引入了一个自动调整模拟参数的功能，以生成反映经验数据集分布的训练数据。为了演示该软件，我们分析了食肉目在新生代的化石记录，发现晚中新世出现了一个多样性高峰，自更新世以来物种减少了 37%。我们的实施包括生成汇总统计数据和图表，以便对模型性能和多样性估算进行评估，还包括一个配置文件，其中包含保证结果完全可重现所需的所有参数。
{"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}
Pub Date : 2024-08-23DOI: 10.1101/2024.08.19.608581
Donald Davesne, Giorgio Carnevale
"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.
{"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}
Pub Date : 2024-08-23DOI: 10.1101/2024.08.23.609354
Pierre Cockx, Michael J. Benton, Joseph N. Keating
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.
羽毛是鸟类在进化过程中取得成功的关键因素，但人们对羽毛的起源仍然知之甚少。关于羽毛进化的争论主要集中在丝状体是一次进化还是多次进化的问题上。这些相互矛盾的结果源于统计祖先状态估计方法上的主观差异。在此，我们对应用于干系鸟类的祖先状态估计方法进行了全面比较，检验了外群包含、树时间比例方法、模型选择和特征编码策略的作用。我们根据阿凯克信息准则（AIC）、互信息以及边际祖先状态估计值的不确定性对模型进行了比较。我们的研究结果表明，树时比例法、外群选择和模型选择对茎鸟整骨的祖先状态估计影响很大，而特征编码策略似乎对祖先状态估计的影响较小。我们利用 AIC 分数和留一交叉验证方法（LOOCV）确定了最佳拟合模型。我们的分析大体上支持恐龙和翼龙的丝状整脊的独立起源，并支持羽毛的进化起源比以前提出的更早。更广泛地说，我们的研究强调了在进行 ASE 分析时必须特别注意选择外群、树和模型。在模型选择方面，我们的研究结果表明，当分析涉及的类群数量有限时，考虑 LOOCV 方法可能会比简单地比较 AIC 分数产生更可靠的结果。
{"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}
Pub Date : 2024-07-30DOI: 10.1101/2024.07.29.605724
Dayun Suh, Su-Hwan Kim, Gi-Soo Nam
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.
{"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 <em>Auxis</em> and represents the second record of fossil <em>Auxis</em> found in South Korea. We compared the vertebral morphology of the studied specimen to that of currently known species of <em>Auxis</em>, including extinct taxa, but the specimen is not assigned to a new or existing species of <em>Auxis</em> due to poor preservation and a lack of diagnostic features. The discovery of a new specimen of <em>Auxis</em> 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}
Pub Date : 2024-07-28DOI: 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
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.
{"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}
Pub Date : 2024-07-23DOI: 10.1101/2024.07.22.604532
Hao Yun, Xingliang Zhang, Glenn A. Brock, Jian Han, Luoyang Li, Bing Pan, Guoxiang Li, Joachim Reitner
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.
{"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}
Pub Date : 2024-07-18DOI: 10.1101/2024.07.15.603597
Michael Jones, Jens N Lallensack, Ian Jarman, Peter Falkingham, Ivo Siekmann
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.
{"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}
Understanding the behaviour and interactions of extinct carnivoran species present a significant challenge in archaeological and palaeontological research, often limited by numerous constraints in the fossil record. Here we analyse a hippopotamus femur consumed by an extinct species of giant hyena, recovered from the open-air site Fuente Nueva 3 (~1.2 Ma, Orce, Granada, Spain). Leveraging the use of advanced microscopic techniques to digitise the tooth marks observed on this specimen in three dimensions, the present study utilises artificially intelligent algorithms to then simulate the possible morphological variability of this carnivoran. This allows us to characterise Pachycrocuta brevirostris tooth pit morphology, so as to construct a diagnostic reference sample of this species. Our findings underscore the importance tooth mark size has on identifying the activity of Pachycrocuta, revealing the giant hyena to have produced remarkably large, deep, and circular tooth pits on dense cortical bone.
{"title":"Computational simulations of Pachycrocuta bite damage based on a ~1.2 Ma ravaged hippopotamus femur from Fuente Nueva 3 (Orce, Granada, Spain)","authors":"Lloyd Austin Courtenay, Alexia Serrano-Ramos, Deborah Barsky, Juan-Manuel Jiménez-Arenas, José Yravedra","doi":"10.1101/2024.07.07.602373","DOIUrl":"https://doi.org/10.1101/2024.07.07.602373","url":null,"abstract":"Understanding the behaviour and interactions of extinct carnivoran species present a significant challenge in archaeological and palaeontological research, often limited by numerous constraints in the fossil record. Here we analyse a hippopotamus femur consumed by an extinct species of giant hyena, recovered from the open-air site Fuente Nueva 3 (~1.2 Ma, Orce, Granada, Spain). Leveraging the use of advanced microscopic techniques to digitise the tooth marks observed on this specimen in three dimensions, the present study utilises artificially intelligent algorithms to then simulate the possible morphological variability of this carnivoran. This allows us to characterise Pachycrocuta brevirostris tooth pit morphology, so as to construct a diagnostic reference sample of this species. Our findings underscore the importance tooth mark size has on identifying the activity of Pachycrocuta, revealing the giant hyena to have produced remarkably large, deep, and circular tooth pits on dense cortical bone.","PeriodicalId":501477,"journal":{"name":"bioRxiv - Paleontology","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141584880","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}
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