Overview of computational methods in taphonomy based on the combination of bibliometric analysis and natural language.

Artificial intelligence tools are new in taphonomy and are growing fast. They are being used mainly to investigate bone surface marks. In order to investigate this subject, a bibliometric study was made to understand the growing rate of this intersectional field, the future, and gaps in the field until now. From Scopus and Google Scholar metadata, graphs were made to describe the data, and inferential statistics were made by regression with the Ordinary Least Squares method. Exploratory analysis with word clouds, topic modeling, and natural language processing with Latent Dirichlet Allocation as a method were also made using the entire corpus from the papers. From the first register until 2023, we found eight articles in Scopus and 32 in Google Scholar; the majority of the studies and the most cited were from Spain. The studies are growing fast from 2016 to 2018, and the regression shows that growth can be maintained in the coming years. Exploratory analysis shows the most frequent words are marks, models, data, and bone. Topic modeling shows that the studies are highly concentrated on similar problems and the tools to solve them, revealing that there is much more to explore with computational tools in taphonomy and paleontology as well.

Late Holocene echinoderm assemblages can serve as paleoenvironmental tracers in an Antarctic fjord.

High Latitude fjords can serve as sediment trap, bearing different type of proxies, from geochemical to micropaleontological ones, making them exceptional tools for paleoenvironmental reconstruction. However, some unconventional proxies can be present and can be used to depict a comprehensive and exhaustive interpretation of past changes. Here, studying a sediment core in Edisto Inlet (Ross Sea, Antarctica) we used irregular echinoid spines and ophiuroids (Ophionotus victoriae) ossicles to trace environmental changes throughout the last 3.6 kyrs BP. Irregular echinoids can serve as proxy for the organic matter content, while O. victoriae ossicles can be used as proxy for steady sea-ice cycle along with organic deposition events. O. victoriae release a high number of ossicles, making estimation about the population quite challenging; still, presence data, can be easily collected. By applying Generative Additive Models to the stratigraphical distribution of these data, we detected an environmental phase that was previously unnoticed by other traditional proxies: the Ophiuroid Optimum (2-1.5 kyrs BP). In conclusion, here we demonstrate how echinoderm presence can be used as a valuable source of information, while proving the potential of modelling binary data to detect long-term trend in Holocene stratigraphical records.

Sea level controls on Ediacaran-Cambrian animal radiations.

The drivers of Ediacaran-Cambrian metazoan radiations remain unclear, as does the fidelity of the record. We use a global age framework [580-510 million years (Ma) ago] to estimate changes in marine sedimentary rock volume and area, reconstructed biodiversity (mean genus richness), and sampling intensity, integrated with carbonate carbon isotopes (δ13Ccarb) and global redox data [carbonate Uranium isotopes (δ238Ucarb)]. Sampling intensity correlates with overall mean reconstructed biodiversity >535 Ma ago, while second-order (~10-80 Ma) global transgressive-regressive cycles controlled the distribution of different marine sedimentary rocks. The temporal distribution of the Avalon assemblage is partly controlled by the temporally and spatially limited record of deep-marine siliciclastic rocks. Each successive rise of metazoan morphogroups that define the Avalon, White Sea, and Cambrian assemblages appears to coincide with global shallow marine oxygenation events at δ13Ccarb maxima, which precede major sea level transgressions. While the record of biodiversity is biased, early metazoan radiations and oxygenation events are linked to major sea level cycles.

Low-Invasive Sampling Method with Tape-Disc Sampling for the Taxonomic Identification of Archeological and Paleontological Bones by Proteomics.

Collagen from paleontological bones is an important organic material for isotopic measurement, radiocarbon analysis, and paleoproteomic analysis to provide information on diet, dating, taxonomy, and phylogeny. Current paleoproteomic methods are destructive and require from a few milligrams to several tens of milligrams of bone for analysis. In many cultures, bones are raw materials for artifacts that are conserved in museums, which hampers damage to these precious objects during sampling. Here, we describe a low-invasive sampling method that identifies collagen, taxonomy, and post-translational modifications from Holocene and Upper Pleistocene bones dated to 130,000 and 150 BC using dermatological skin tape discs for sampling. The sampled bone micropowders were digested following our highly optimized enhanced filter-aided sample preparation protocol and then analyzed by MALDI FTICR MS and LC-MS/MS for identifying the genus taxa of the bones. We show that this low-invasive sampling does not deteriorate the bones and achieves results similar to those obtained by more destructive sampling. Moreover, this sampling method can be carried out at archeological sites or in museums.

Dawn of diverse shelled and carbonaceous animal microfossils at ~ 571 Ma.

The Ediacaran-Cambrian transition documents a critical stage in the diversification of animals. The global fossil record documents the appearance of cloudinomorphs and other shelled tubular organisms followed by non-biomineralized small carbonaceous fossils and by the highly diversified small shelly fossils between ~ 550 and 530 Ma. Here, we report diverse microfossils in thin sections and hand samples from the Ediacaran Bocaina Formation, Brazil, separated into five descriptive categories: elongate solid structures (ES); elongate filled structures (EF); two types of equidimensional structures (EQ 1 and 2) and elongate hollow structures with coiled ends (CE). These specimens, interpreted as diversified candidate metazoans, predate the latest Ediacaran biomineralized index macrofossils of the Cloudina-Corumbella-Namacalathus biozone in the overlying Tamengo Formation. Our new carbonate U-Pb ages for the Bocaina Formation, position this novel fossil record at 571 ± 9 Ma (weighted mean age). Thus, our data point to diversification of metazoans, including biomineralized specimens reminiscent of sections of cloudinids, protoconodonts, anabaritids, and hyolithids, in addition to organo-phosphatic surficial coverings of animals, demonstrably earlier than the record of the earliest known skeletonized metazoan fossils.

Taxonomic review, palaeoecological, and palaeobiogeographical significances of Campanian Tethyan oysters from the North Eastern Desert, Egypt.

The Late Cretaceous was a time of high eustatic sea level that enabled extensive epicontinental seaways and carbonate platforms across the Tethyan Realm, providing favorable habitats for oyster communities to flourish. This study focuses on the Campanian Tethyan oysters from the North Eastern Desert of Egypt regarding taxonomy, palaeoecology, and palaeobiogeography. Three oyster species, Nicaisolopha nicaisei (Coquand, 1862), Pycnodonte (Phygraea) vesicularis (Lamarck, 1806), and Ambigostrea bretoni (Thomas and Peron, 1891), were identified from the Campanian succession in two studied sections. The sampled specimens of the genus Nicaisolopha have undergone a systematic palaeontological revision. As a result, N. tissoti (Thomas and Peron, 1891) is considered herein a junior synonym of N. nicaisei (Coquand, 1862). Palaeobiogeographically, the likely primary migration pattern of the studied oysters suggests an east-west trend along the Southern Tethys margin. All identified oysters in this study exhibit a Tethyan affinity and are primarily abundant in two main provinces: the Southern Tethys and the Western Tethys. The macrofaunal contents are categorized into two fossil associations: the Nicaisolopha nicaisei association of the middle-late Campanian age and the Pycnodonte vesicularis association of the late Campanian age. These macrofaunal associations indicate a deepening trend during the middle-late Campanian age, suggesting a transition from shallow inner neritic to middle neritic environments. Additionally, it is observed that Pycnodonteinae tend to grow larger under eutrophic conditions, low-energy environments, and nutrient-rich waters with high carbonate contents.

Chemical and palaeoentomological evidence of a relationship between early Eocene Belgian and Oise (France) ambers.

Of the early Eocene amber deposits known across the world, Belgian amber has been mostly absent from the relevant literature. We reinvestigated amber held in the palaeobotanical collection of the Royal Belgian Institute of Natural Sciences, Brussels, which derived from three localities in Belgium that originated from two geographical areas (Leval-Trahegnies and Orp-le-Grand). Using Fourier transform infrared (FTIR) spectroscopy we show the close chemical relationship of Belgian amber to the early Eocene Oise amber from the Paris Basin, and highlight the potential effect of weathering on the amber chemistry. The amber derives from a very similar botanical source as the Oise amber (Combretaceae or Leguminosae-Caesalpinioideae), but from different coeval basins. The two Leval-Trahegnies localities provided amber that exhibit different stages of weathering (heavily fissured and crazed, darkened) and lacking any inclusions. The Orp-le-Grand locality provided the least weathered amber, with one amber piece containing two inclusions: a mite and a new genus and species of hemipteran (Cativolcus uebruum gen. et sp. nov.), and a second one that preserved the impression of insect wings pressed into the surface.

Golden spikes, scientific types, and the ma(r)king of deep time.

Chronostratigraphy is the subfield of geology that studies the relative age of rock strata and that aims at producing a hierarchical classification of (global) divisions of the historical time-rock record. The 'golden spike' or 'GSSP' approach is the cornerstone of contemporary chronostratigraphic methodology. It is also perplexing. Chronostratigraphers define each global time-rock boundary extremely locally, often by driving a gold-colored pin into an exposed rock section at a particular level. Moreover, they usually avoid rock sections that show any meaningful sign of paleontological disruption or geological discontinuity: the less obvious the boundary, the better. It has been argued that we can make sense of this practice of marking boundaries by comparing the status and function of golden spikes to that of other concrete, particular reference standards from other sciences: holotypes from biological taxonomy and measurement prototypes from the metrology of weight and measures. Alisa Bokulich (2020b) has argued that these 'scientific types' are in an important sense one of a kind: they have a common status and function. I will argue that this picture of high-level conceptual unity is mistaken and fails to consider the diversity of aims and purposes of standardization and classification across the sciences. I develop an alternative, disunified account of scientific types that shows how differences in ontological attitudes and epistemic aims inform scientists' choices between different kinds of scientific types. This perspective on scientific types helps to make sense of an intriguing mid-twentieth-century debate among chronostratigraphers about the very nature of their enterprise. Should chronostratigraphers conventionally make boundaries by designating golden spikes, or should they attempt to mark pre-existing 'natural' boundaries with the help of a different kind of scientific type?

Deep-time phylogenetic inference by paleoproteomic analysis of dental enamel.

In temperate and subtropical regions, ancient proteins are reported to survive up to about 2 million years, far beyond the known limits of ancient DNA preservation in the same areas. Accordingly, their amino acid sequences currently represent the only source of genetic information available to pursue phylogenetic inference involving species that went extinct too long ago to be amenable for ancient DNA analysis. Here we present a complete workflow, including sample preparation, mass spectrometric data acquisition and computational analysis, to recover and interpret million-year-old dental enamel protein sequences. During sample preparation, the proteolytic digestion step, usually an integral part of conventional bottom-up proteomics, is omitted to increase the recovery of the randomly degraded peptides spontaneously generated by extensive diagenetic hydrolysis of ancient proteins over geological time. Similarly, we describe other solutions we have adopted to (1) authenticate the endogenous origin of the protein traces we identify, (2) detect and validate amino acid variation in the ancient protein sequences and (3) attempt phylogenetic inference. Sample preparation and data acquisition can be completed in 3-4 working days, while subsequent data analysis usually takes 2-5 days. The workflow described requires basic expertise in ancient biomolecules analysis, mass spectrometry-based proteomics and molecular phylogeny. Finally, we describe the limits of this approach and its potential for the reconstruction of evolutionary relationships in paleontology and paleoanthropology.

A review of the systematic biology of fossil and living bony-tongue fishes, Osteoglossomorpha (Actinopterygii: Teleostei)

The bony-tongue fishes, Osteoglossomorpha, have been the focus of a great deal of morphological, systematic, and evolutionary study, due in part to their basal position among extant teleostean fishes. This group includes the mooneyes (Hiodontidae), knifefishes (Notopteridae), the abu (Gymnarchidae), elephantfishes (Mormyridae), arawanas and pirarucu (Osteoglossidae), and the African butterfly fish (Pantodontidae). This morphologically heterogeneous group also has a long and diverse fossil record, including taxa from all continents and both freshwater and marine deposits. The phylogenetic relationships among most extant osteoglossomorph families are widely agreed upon. However, there is still much to discover about the systematic biology of these fishes, particularly with regard to the phylogenetic affinities of several fossil taxa, within Mormyridae, and the position of Pantodon. In this paper we review the state of knowledge for osteoglossomorph fishes. We first provide an overview of the diversity of Osteoglossomorpha, and then discuss studies of the phylogeny of Osteoglossomorpha from both morphological and molecular perspectives, as well as biogeographic analyses of the group. Finally, we offer our perspectives on future needs for research on the systematic biology of Osteoglossomorpha.(AU)

Os peixes da Superordem Osteoglossomorpha têm sido foco de inúmeros estudos sobre a morfologia, sistemática e evolução, particularmente devido à sua posição basal dentre os peixes teleósteos. Fazem parte deste grupo os "mooneyes" (Hiodontidae), "knifefishes" (Notopteridae), o "abu" (Gymnarchidae), peixes-elefante (Mormyridae), aruanãs e pirarucu (Osteoglossidae), e o peixe-borboleta africano (Pantodontidae). Esse grupo de morfologia heterogênea possui um longo e diverso registro fóssil, incluindo táxons de todos os continentes, oriundos tanto de depósitos de água doce quanto marinhos. As relações filogenéticas dentre a maioria das famílias de osteoglossomorfos é amplamente aceita. Entretanto, há muito a ser descoberto sobre a sistemática biológica desses peixes, particularmente com relação às afinidades filogenéticas de inúmeros fósseis, relações dentro de Mormyridae, e a posição filogenética de Pantodon. Neste manuscrito nós revisamos o atual estado de conhecimento dos peixes osteoglossomorfos. Nós primeiramente provemos uma abordagem geral da diversidade de Osteoglossomorpha, e então discutimos os estudos filogenéticos sobre Osteoglossomorpha sob a perspectiva morfológica e molecular, assim como uma análise biogeográfica do grupo. Finalmente, oferecemos nossas perspectivas sobre os futuros passos para pesquisa sobre a sistemática biológica de Osteoglossomorpha.(AU)

Estudio paleorradiológico y tridimensional en momias y cuerpos momificados / Paleo-radiology and three-dimensional study in mummies and mummified bodies

Estudios realizados en momias o en cuerpos momificados con técnicas convencionales y estudios de tomografía computada, revelaron patologíasmaxilofaciales tales como: atrición, pulpitis abscesos y enfermedad periodontal; además de otras enfermedades con mayor compromiso general, a saber: osteomielitis, enfermedad de Paget, defectos cráneomandibulares y traumas. Sin embargo, se observa un bajo porcentaje de caries. Para la continuidad de la vida en el más allá, revestía una importancia fundamental la conservación de loscuerpos en este mundo...

Arrhinolemur scalabrinii Ameghino, 1898, of the late Miocene: a taxonomic journey from the Mammalia to the Anostomidae (Ostariophysi: Characiformes)

The fossil species Arrhinolemur scalabrinii, which was described from late Miocene deposits of Entre Ríos, Argentina, is reevaluated. Whereas the species was originally placed in the Primates (Mammalia) and later made the unique member of the order Arrhinolemuroidea within the Mammalia, our analysis indicates that the specimen is rather a fish of the genus Leporinus, family Anostomidae (Characiformes). The species is redescribed, and the characters that support its new generic assignment are discussed.

A espécie fóssil Arrhinolemur scalabrinii, descrita de depósitos do Mioceno Superior de Entre Ríos, Argentina, é reavaliada. Apesar da espécie ter sido originalmente incluída em Primata (Mammalia), constituindo-se posteriormente no único membro da ordem Arrhinolemuroidea dentro de Mammalia, nossa análise indica que o espécime trata-se de um peixe do gênero Leporinus, família Anostomidae (Characiformes). A espécie é redescrita, e os caracteres que fundamentam a nova posição do gênero são discutidos.

Recovering missing data: estimating position and size of caudal vertebrae in Staurikosaurus pricei Colbert, 1970

Missing data is a common problem in paleontology. It makes it difficult to reconstruct extinct taxa accurately and restrains the inclusion of some taxa on comparative and biomechanical studies. Particularly, estimating the position of vertebrae on incomplete series is often non-empirical and does not allow precise estimation of missing parts. In this work we present a method for calculating the position of preserved middle sequences of caudal vertebrae in the saurischian dinosaur Staurikosaurus pricei, based on the length and height of preserved anterior and posterior caudal vertebral centra. Regression equations were used to estimate these dimensions for middle vertebrae and, consequently, to assess the position of the preserved middle sequences. It also allowed estimating these dimensions for non-preserved vertebrae. Results indicate that the preserved caudal vertebrae of Staurikosaurus may correspond to positions 1-3, 5, 7, 14-19/15-20, 24-25/25-26, and 29-47, and that at least 25 vertebrae had transverse processes. Total length of the tail was estimated in 134 cm and total body length was 220-225 cm.

Dados lacunares são um problema comum na paleontologia. Eles dificultam a reconstrução acurada de táxons extintos e limitam a inclusão de alguns táxons em estudos comparativose biomecânicos. Particularmente, estimar a posição de vértebras em séries incompletas tem sido feito com base em métodos não empíricos que não permitem estimar corretamente as partes ausentes. Neste trabalho apresentamos uma metodologia que permite estimar a posição de sequências médias preservadas de vértebras caudais no dinossauro saurísquio Staurikosaurus pricei, com base no comprimento e altura dos centros das vértebras anteriores e posteriores preservadas. Equações de regressão foram usadas para estimar essas dimensões para as vértebras médias e, consequentemente, para posicionar as sequências médias preservadas e para estimar o tamanho das vértebras não preservadas. Os resultados indicam que as vértebras caudais preservadas de Staurikosaurus corresponderiam às posições 1-3, 5, 7, 14-19/15-20, 24-25/25-26 e 29-47, e que pelo menos 25 vértebras possuíam processos transversos. O comprimento total da cauda foi estimado em 134 cm e o comprimento total do corpo em 220-225 cm.

Tunasniyoj, a dinosaur tracksite from the Jurassic-Cretaceous boundary of Bolivia

Here we report a superbly preserved and profusely represented five-ichnotaxa dinosaur track assemblage near Icla village, 100 km southeast of Sucre, Bolivia. As preserved in reddish Jurassic-Cretaceous boundary aeolian sandstones, this rich and uncommon assemblage is, additionally, the oldest dinosaur tracksite for Bolivia. Four trackmakers were identified in the area: three quadrupedal and one bipedal, all of them with tracks of around 35 cm in lenght. One of the quadrupedals is represented by no less than five adult individuals (ichnotaxon A), and four purported juveniles (ichnotaxon B) walking in association. The other two quadrupedals (ichnotaxa C and D) involve four trackways, and the last, the bipedal trackmaker (ichnotaxon E), is represented by one trackway. The five ichnotaxa represented in the "Palmar de Tunasniyoj" could be tentatively assigned to the following trackmakers: Ichnotaxa A and B are assigned to basal stegosaurians; ichnotaxon C to a basal tyreophoran, perhaps related to the ankylosaur lineage; ichnotaxon D to the Ankylosauria, and ichnotaxon E to Theropoda. The Tunasniyoj assemblage, the oldest dinosaur tracksite for Bolivia, includes the oldest known evidence assigned to ankylosaurs and stegosaurs for South America.

Neste estudo é relatado um conjunto magnificamente preservado de pistas de dinossauros representados por cinco táxons distintos, situado próximo à Vila de Icla, 100 quilômetros a sudeste do Sucre, Bolívia. Preservados em arenitos eólicos avermelhados do limite Jurássico-Cretáceo. Quatro formas geradoras foram identificadas na área, sendo três quadrúpedes e um bípede, todos com as pegadas com cerca de 35 cm de comprimento. Um dos quadrúpedes (trilhas tipos A e B) é representado por pelo menos seis indivíduos em dois grupos de três, com adultos e juvenis juntos. Os outros dois quadrúpedes (trilhas tipos C e D) são geradores de quatro trilhas, e um gerador bípede (trilha E), é representado por uma trilha. Os quatro icnotáxons representados em "Palmar de Tunasniyoj", podem provisoriamente ser atribuídos aos seguintes geradores: Icnotáxon A e B são atribuídos a estegossauros basais. Icnotáxon C a um tireóforo basal, talvez relacionado à linhagem dos anquilossauros. Icnotáxon D aos Ankylosauria; e icnotáxon E a Theropoda. Este raro e belo conjunto de trilhas de dinossauros de Tunasniyoj, representa ainda a icnocenose mais antiga de dinossauros da Bolívia. Além disso, inclui a mais antiga evidência conhecida atribuída a anquilossauros e estegossauros para América do sul.

A new genus and species of Heroini (Perciformes: Cichlidae) from the early Eocene of southern South America

The Lumbrera Formation is the uppermost unit of the Salta Group, which crops out in northwestern Argentina. The paleoenvironment of the Lumbrera Formation is interpreted as a perennial lake deposited under temperate climatic conditions during the early to middle Eocene. Its fossil content is made up of palynomorphs, insects, crocodiles, turtles, lizards, and mammals, besides an ichthyofauna formed by cichlids, poeciliids and dipnoans. åPlesioheros chauliodus is described based on a single individual from this formation, which was fossilized as a lateral view impression (missing anal and caudal fins). It can be distinguished from other cichlids by a moderately deep body, enlarged anterior dentary teeth bearing subapical cusp, a low abdominal vertebral count (10), five canal openings in the dentary, and XI + 12 dorsal-fin rays. A phylogenetic analysis, using the matrix by Kullander (1998), recovered åPlesioheros within Heroini. This species was recovered most closely related to Australoheros and to the deep-bodied South American heroins. The occurrence of an Eocene Heroini, as well as of other cichlid lineages in the same stratigraphical level, is evidence of an ancient diversification in this family. This ancient age supports the hypothesis that the Cichlidae originated on Gondwana.

A Formação Lumbrera é a unidade do topo do Grupo Salta, aflorante na região noroeste da Argentina. O paleoambiente da Formação Lumbrera tem sido interpretado como um lago perene depositado sob um clima temperado durante o início do Eoceno. Seu conteúdo fóssil é formado por palinomorfos, insetos, crocodilos, tartarugas, lagartos, mamíferos, além de uma ictiofauna que inclui ciclídeos, poeciliídeos e dipnóicos. åPlesioheros chauliodus é descrito com base em um único indivíduo coletado nesta formação, preservado como impressão em vista lateral (faltando as nadadeiras anal e caudal). Ele pode ser distinguido de outros ciclídeos por um corpo moderadamente alto, dentes anteriores do dentário aumentados e portando uma cúspide lingual subapical, uma baixa contagem de vértebras abdominais, cinco aberturas do canal sensorial no dentário, e XI + 12 raios na dorsal. Na análise filogenética, usando a matriz apresentada por Kullander (1998), åPlesioheros resultou dentro da Tribo Heroini mais relacionado a Australoheros e aos heroinis de corpo alto sul-americanos. A ocorrência de um heroini fóssil desta idade, bem como das outras linhagens de ciclídeos no mesmo nível estratigráfico, é uma evidência da diversificação inicial da família, corroborando fortemente a hipótese de que os Cichlidae se originaram no Gondwana ainda durante o Cretáceo.