A robust, agnostic molecular biosignature based on machine learning.

The search for definitive biosignatures-unambiguous markers of past or present life-is a central goal of paleobiology and astrobiology. We used pyrolysis-gas chromatography coupled to mass spectrometry to analyze chemically disparate samples, including living cells, geologically processed fossil organic material, carbon-rich meteorites, and laboratory-synthesized organic compounds and mixtures. Data from each sample were employed as training and test subsets for machine-learning methods, which resulted in a model that can identify the biogenicity of both contemporary and ancient geologically processed samples with ~90% accuracy. These machine-learning methods do not rely on precise compound identification: Rather, the relational aspects of chromatographic and mass peaks provide the needed information, which underscores this method's utility for detecting alien biology.

Interpreting fossilized nervous tissues.

Paleoneuranatomy is an emerging subfield of paleontological research with great potential for the study of evolution. However, the interpretation of fossilized nervous tissues is a difficult task and presently lacks a rigorous methodology. We critically review here cases of neural tissue preservation reported in Cambrian arthropods, following a set of fundamental paleontological criteria for their recognition. These criteria are based on a variety of taphonomic parameters and account for morphoanatomical complexity. Application of these criteria shows that firm evidence for fossilized nervous tissues is less abundant and detailed than previously reported, and we synthesize here evidence that has stronger support. We argue that the vascular system, and in particular its lacunae, may be central to the understanding of many of the fossilized peri-intestinal features known across Cambrian arthropods. In conclusion, our results suggest the need for caution in the interpretation of evidence for fossilized neural tissue, which will increase the accuracy of evolutionary scenarios. Also see the video abstract here: https://youtu.be/2_JlQepRTb0.

Human brains preserve in diverse environments for at least 12 000 years.

The brain is thought to be among the first human organs to decompose after death. The discovery of brains preserved in the archaeological record is therefore regarded as unusual. Although mechanisms such as dehydration, freezing, saponification, and tanning are known to allow for the preservation of the brain on short time scales in association with other soft tissues (≲4000 years), discoveries of older brains, especially in the absence of other soft tissues, are rare. Here, we collated an archive of more than 4400 human brains preserved in the archaeological record across approximately 12 000 years, more than 1300 of which constitute the only soft tissue preserved amongst otherwise skeletonized remains. We found that brains of this type persist on time scales exceeding those preserved by other means, which suggests an unknown mechanism may be responsible for preservation particular to the central nervous system. The untapped archive of preserved ancient brains represents an opportunity for bioarchaeological studies of human evolution, health and disease.

Functional traits of fossil plants.

A minuscule fraction of the Earth's paleobiological diversity is preserved in the geological record as fossils. What plant remnants have withstood taphonomic filtering, fragmentation, and alteration in their journey to become part of the fossil record provide unique information on how plants functioned in paleo-ecosystems through their traits. Plant traits are measurable morphological, anatomical, physiological, biochemical, or phenological characteristics that potentially affect their environment and fitness. Here, we review the rich literature of paleobotany, through the lens of contemporary trait-based ecology, to evaluate which well-established extant plant traits hold the greatest promise for application to fossils. In particular, we focus on fossil plant functional traits, those measurable properties of leaf, stem, reproductive, or whole plant fossils that offer insights into the functioning of the plant when alive. The limitations of a trait-based approach in paleobotany are considerable. However, in our critical assessment of over 30 extant traits we present an initial, semi-quantitative ranking of 26 paleo-functional traits based on taphonomic and methodological criteria on the potential of those traits to impact Earth system processes, and for that impact to be quantifiable. We demonstrate how valuable inferences on paleo-ecosystem processes (pollination biology, herbivory), past nutrient cycles, paleobiogeography, paleo-demography (life history), and Earth system history can be derived through the application of paleo-functional traits to fossil plants.

Persistent predators: Zooarchaeological evidence for specialized horse hunting at Schöningen 13II-4.

The Schöningen 13II-4 site is a marvel of Paleolithic archaeology. With the extraordinary preservation of complete wooden spears and butchered large mammal bones dating from the Middle Pleistocene, Schöningen maintains a prominent position in the halls of human origins worldwide. Here, we present the first analysis of the complete large mammal faunal assemblage from Schöningen 13II-4, drawing on multiple lines of zooarchaeological and taphonomic evidence to expose the full spectrum of hominin activities at the site-before, during, and after the hunt. Horse (Equus mosbachensis) remains dominate the assemblage and suggest a recurrent ambush hunting strategy along the margins of the Schöningen paleo-lake. In this regard, Schöningen 13II-4 provides the first undisputed evidence for hunting of a single prey species that can be studied from an in situ, open-air context. The Schöningen hominins likely relied on cooperative hunting strategy to target horse family groups, to the near exclusion of bachelor herds. Horse kills occurred during all seasons, implying a year-round presence of hominins on the Schöningen landscape. All portions of prey skeletons are represented in the assemblage, many complete and in semiarticulation, with little transport of skeletal parts away from the site. Butchery marks are abundant, and adult carcasses were processed more thoroughly than were juveniles. Numerous complete, unmodified bones indicated that lean meat and marrow were not always so highly prized, especially in events involving multiple kills when fat and animal hides may have received greater attention. The behaviors displayed at Schöningen continue to challenge our perceptions and models of past hominin lifeways, further cementing Schöningen's standing as the archetype for understanding hunting adaptations during the European Middle Pleistocene.

Sex-biased sampling may influence Homo naledi tooth size variation.

A frequent source of debate in paleoanthropology concerns the taxonomic unity of fossil assemblages, with many hominin samples exhibiting elevated levels of variation that can be interpreted as indicating the presence of multiple species. By contrast, the large assemblage of hominin fossils from the Rising Star cave system, assigned to Homo naledi, exhibits a remarkably low degree of variation for most skeletal elements. Many factors can contribute to low sample variation, including genetic drift, strong natural selection, biased sex ratios, and sampling of closely related individuals. In this study, we tested for potential sex-biased sampling in the Rising Star dental sample. We compared coefficients of variation for the H. naledi teeth to those for eight extant hominoid samples. We used a resampling procedure that generated samples from the extant taxa that matched the sample size of the fossil sample for each possible Rising Star dental sex ratio. We found that variation at four H. naledi tooth positions-I2, M1, P4, M1-is so low that the possibility that one sex is represented by few or no individuals in the sample cannot be excluded. Additional evidence is needed to corroborate this inference, such as ancient DNA or enamel proteome data, and our study design does not address other potential factors that would account for low sample variation. Nevertheless, our results highlight the importance of considering the taphonomic history of a hominin assemblage and suggest that sex-biased sampling is a plausible explanation for the low level of phenotypic variation found in some aspects of the current H. naledi assemblage.

Using machine learning on new feature sets extracted from three-dimensional models of broken animal bones to classify fragments according to break agent.

Distinguishing agents of bone modification at paleoanthropological sites is an important means of understanding early hominin evolution. Fracture pattern analysis is used to help determine site formation processes, including whether hominins were hunting or scavenging for animal food resources. Determination of how these behaviors manifested in ancient human sites has major implications for our biological and behavioral evolution, including social and cognitive abilities, dietary impacts of having access to in-bone nutrients like marrow, and cultural variation in butchering and food processing practices. Nevertheless, previous analyses remain inconclusive, often suffering from lack of replicability, misuse of mathematical methods, and/or failure to overcome equifinality. In this paper, we present a new approach aimed at distinguishing bone fragments resulting from hominin and carnivore breakage. Our analysis is founded on a large collection of scanned three-dimensional models of fragmentary bone broken by known agents, to which we apply state of the art machine learning algorithms. Our classification of fragments achieves an average mean accuracy of 77% across tests, thus demonstrating notable, but not overwhelming, success for distinguishing the agent of breakage. We note that, while previous research applying such algorithms has claimed higher success rates, fundamental errors in the application of machine learning protocols suggest that the reported accuracies are unjustified and unreliable. The systematic, fully documented, and proper application of machine learning algorithms leads to an inherent reproducibility of our study, and therefore our methods hold great potential for deciphering when and where hominins first began exploiting marrow and meat, and clarifying their importance and influence on human evolution.

Late Ordovician eurypterid preserves oldest euchelicerate musculature in pyrite.

Pyritization of soft tissues of invertebrates is rare in the fossil record. In New York State, it occurs in black shales of the Lorraine Group (Late Ordovician), the best-known example of which is Beecher's Trilobite Bed. Exceptional preservation at the quarry where this bed is exposed allowed detailed examination of trilobite and ostracod soft-tissue anatomy. Here, we present the first example of a eurypterid (sea scorpion) currently ascribed to Carcinosomatidae from this deposit that also preserves the first evidence for mesosomal musculature in eurypterids. This specimen demonstrates that eurypterid musculature can be preserved in pyrite and evidences the oldest example of euchelicerate muscles within the fossil record. Sulfur isotope data illustrate that pyrite rapidly replicated muscle tissue in the early burial environment, prior to the pyritization of biomineralized exoskeleton and cuticular trilobite limbs. This discovery therefore expands the limited fossil record of euchelicerate musculature, while extending the taphonomic scope for preservation of detailed internal structures, more broadly, within arthropods.

Bridging the gap between decomposition theory and forensic research on postmortem interval.

Knowledge of the decomposition of vertebrate animals has advanced considerably in recent years and revealed complex interactions among biological and environmental factors that affect rates of decay. Yet this complexity remains to be fully incorporated into research or models of the postmortem interval (PMI). We suggest there is both opportunity and a need to use recent advances in decomposition theory to guide forensic research and its applications to understanding the PMI. Here we synthesise knowledge of the biological and environmental factors driving variation in decomposition and the acknowledged limitations among current models of the PMI. To guide improvement in this area, we introduce a conceptual framework that highlights the multiple interdependencies affecting decay rates throughout the decomposition process. Our framework reinforces the need for a multidisciplinary approach to PMI research, and calls for an adaptive research cycle that aims to reduce uncertainty in PMI estimates via experimentation, modelling, and validation.

Luminol and the postmortem interval estimation - influence of taphonomic factors.

The estimation of the postmortem interval (PMI) is one of the key challenges for forensic anthropologists. Although there are several methods referenced for this purpose, none is sufficiently effective. One of the main reasons justifying the complexity of this task is the influence of several taphonomic factors.The study of the Luminol technique has stood out as a promising method for estimating PMI, complementing the existing methods, since it is an economic, easy and reproducible method that operates as a presumptive test. However, it is not known which taphonomic factors can influence the results obtained by this technique.The aim of this study is to test the influence of taphonomic factors, such as temperature, humidity, soil type and pH, on the estimation of the PMI by the Luminol technique.In order to test the influence of the referred factors, a sample consisting of 30 clavicles, with known and similar PMI, collected from autopsies, was distributed as evenly as possible by six vases and buried with different decomposition conditions for a period of 12 months. After the exhumation and sample preparation, the Luminol technique was applied.It was possible to clearly observe differences in the results. Thus, according to our research, it is possible to conclude that the results obtained by the application of Luminol are influenced by taphonomic factors. Therefore, the context in which a body is found should always be considered for applying this technique.

The taphonomic effects of long-term burial in the South African Highveld.

Taphonomy studies the environmental effects on remains from the time of deposition to the time of recovery and has been integrated into the field of forensic anthropology. The changes to skeletal remains are dependent on the method of disposal and the surrounding environment. This study focused on buried remains where the type and chemical composition of the soil and the microorganisms present need to be considered. The aim was to investigate the type, frequency, and correlations of the taphonomic alterations of buried domestic pigs. Six taphonomic alterations were observed which included depositional staining, adipocere formation, bone weathering, acidic soil corrosion, and plant, and animal activity. Depositional staining, weathering and plant activity were the most common alterations followed by adipocere which was present on 92.3% of the remains. The bones were mostly stained dark brown and brown; however, the trunk region was the only region to present with black staining. The right sides were darker than the left due to the body positioning as most pigs were placed on their right sides and thus were in direct contact with the cadaver decomposition island. Additionally, the right sides presented with more adipocere as well as increased plant activity suggesting that the soil retained water. Darker stains were correlated with a more complete skeleton as adipocere provides some protection. The study confirms that there are various complicated relationships between different taphonomic alterations. A good understanding of them is needed in forensic anthropology to assist in reconstructing the events that occur after death.

Comparison of the effectiveness and efficiency of the grid and link search methods to recover scattered skeletal remains.

The grid and link search methods are used to recover scattered skeletal remains. Neither have not been compared robustly and clear guidelines for the link method have not been sufficiently developed. The study aimed to compare the effectiveness and efficiency of both methods and propose guidelines for the link method. The scattering patterns of two scavengers of forensic relevance-slender mongooses (Galerella sanguinea) and black-backed jackals (Canis mesomelas)-were recreated using four pig skeletons (Sus scrofa domesticus). Two groups (n = 6 each) were assigned a different method to recover the scattered remains. The length of the search and when each bone was located for each scatter pattern was recorded for each group and scatter pattern. A Likert scale questionnaire assessed participants' perceptions of their assigned method. A paired t-test (p = 0.005) compared the efficiency of each method and the questionnaire answers. Both methods were effective, recovering 100% of all remains. The link method was more efficient for both scatter patterns, despite there being no statistical significance (jackal: p = 0.089; mongoose: p = 0.464). Participants indicated favorable views for both methods; however, the link method scored significantly more favorably (p = 0.01) for efficiency. Specific guidelines were developed for the use of the link method. The link method is suggested for the recovery of scattered remains in forensic contexts, especially when the scavenger, its behavior, and scattering pattern is known or suspected.

Sr-Pb isotope differences in pre- and post-burial human bone, teeth, and hair keratin: implications for isotope forensics.

The isotopic signatures of human tissues can provide valuable information on geographic origin for medicolegal investigations involving unidentified persons. It is important to understand the impact of diagenetic processes on isotopic signatures, as alterations could result in incorrect estimation of geographic origin. This study examines alterations in isotope signatures of different tissues of five human body donors studied throughout decomposition at the Forensic Anthropology Research Facility (FARF), San Marcos, TX. Two body donors were buried, two were placed in open pits, and one was first allowed to naturally mummify and then buried. Remains were recovered after a period of 7-34 months. The preplacement and post-recovery Sr-Pb isotope data of scalp hair, bone (iliac and tibia), and tooth enamel and dentine were compared. The hair samples record significant shifts in Sr-Pb isotope compositions, with hair keratin Pb isotope composition shifting towards the Pb signature of local soil samples. Hair keratin Sr isotope compositions were altered by the burial environment and possibly also by the lab sample cleaning method. The spongy iliac bone samples show inconsistencies in the recoverability of the preplacement Sr-Pb isotope signatures. The post-placement signatures of the buried donors show slight elevation over preplacement signatures. The post-placement signatures of donors placed in open pits are significantly elevated. The tibia and dental samples record the most consistent isotopic data with the least alteration. These more densely mineralised elements show good recoverability of the preplacement isotope signatures in burials and open pits and are thus deemed better targets for forensic investigative purposes.

Unveiling decomposition dynamics: leveraging 3D models for advanced forensic analysis.

Forensic taphonomy, the study of post-mortem processes, is pivotal in modern forensic science. This short communication illuminates limitations in traditional 2D imaging, specifically digital photographs, within forensic taphonomy, and highlights the vast potential of 3D modeling techniques. Drawing from a recent study in Hawaii's tropical savanna, we unveil disparities between real-time observations and 2D photographs when assessing decomposition, emphasizing the importance of scoring method selection and the need to scrutinize 2D imaging's accuracy in forensic taphonomy. Conversely, 3D modeling techniques, an emerging powerhouse in forensic science, offer multidimensional data, including volume, surface area, and spatial relationships, allowing for comprehensive and precise representation of decomposition dynamics. Despite concerns about texture quality, 3D models yield objective data amenable to analysis by multiple experts, thus minimizing subjectivity and augmenting the reliability of forensic assessments. The potential for 3D modeling to bridge the gap between 2D imaging and real-time decomposition requires tailored methodologies. Future research should focus on standardizing protocols and fostering collaboration among forensic experts, technologists, and researchers to unleash 3D technology's full potential in advancing forensic taphonomy.

Forensic taphonomic experimental design matters: a study assessing clothing and carrion biomass load on scavenging in Cape Town, South Africa.

The identification of unknown human remains is a significant and ongoing challenge in South Africa, worsened by the country's high murder rate. The rate of decomposition in South Africa is significantly influenced by vertebrate scavenging, which, if not considered, can impede the accurate estimation of the post-mortem interval. Scavenging patterns vary greatly depending on the environment and ecological region, and there is limited data for the Western Cape province. To address this gap, two clothed and uncaged pig carcasses weighing 60 kg each were placed in the field in July 2021 and January 2022, respectively. Motion-activated infrared-capable trail cameras were used to observe decomposition, scavenger species, and their activities. Additionally, a comparative sample of 16 unclothed carcasses deployed between 2014 and 2016 in the same habitat were analyzed to assess the impact of clothing and biomass load. The study found three main results: (1) Regardless of habitat or biomass load, it took significantly less time to reach decomposition milestones (25%, 50%, and 75%) during the summer season; (2) the presence of mongoose scavengers had a greater impact on the time required to reach milestones during winter compared to summer; and (3) single carcass deployments reached the milestones faster than multi-carcass deployments in both seasons. This research highlights the potential inaccuracy of current methods for estimating the post-mortem interval when scavenging activity is not considered or documented in the underlying experimental data, particularly for environments or ecological biomes where scavengers actively impact decomposition rates.

Multivariate mapping of ontogeny, taphonomy and phylogeny to reconstruct problematic fossil taxa.

Exceptionally preserved fossils of soft-bodied organisms provide unique evidence of evolutionary history, but they are often contentious; different approaches frequently produce radically different reconstructions of taxa and their affinities. Conflict arises due to difficulties in disentangling the three non-independent factors that underlie all morphological variation within and between fossils: ontogeny, taphonomy and phylogeny. Comparative data from extant organisms can be extremely powerful in this context, but is often difficult to apply given the multi-dimensionality of anatomical variation. Here, we present a multivariate ordination method using discrete morphological character data from modern taxa at different ontogenetic and taphonomic stages (semaphoront and 'semataphonts'). Analysing multiple axes of morphological variation simultaneously allows us to visualize character combinations that are likely to exist in fossil specimens at intersecting stages of growth and decay, and thus constrain interpretation of fossils. Application to early vertebrates finds variation in fossil specimens to be accounted for by all three axes: primarily decay in Mayomyzon, ontogeny in Priscomyzon and phylogeny in 'euphaneropoids' and Palaeospondylus. Our demonstration of empirical multi-factorial variation underscores the power of multivariate approaches to fossil interpretation, especially non-biomineralized taxa. As such, this conceptual approach provides a new method for resolving enigmatic taxa throughout the fossil record.

The origins of colour patterns in fossil insects revealed by maturation experiments.

Many fossil insects show monochromatic colour patterns that may provide valuable insights into ancient insect behaviour and ecology. Whether these patterns reflect original pigmentary coloration is, however, unknown, and their formation mechanism has not been investigated. Here, we performed thermal maturation experiments on extant beetles with melanin-based colour patterns. Scanning electron microscopy reveals that melanin-rich cuticle is more resistant to degradation than melanin-poor cuticle: with progressive maturation, melanin-poor cuticle regions experience preferential thinning and loss, yet melanin-rich cuticle remains. Comparative analysis of fossil insects with monotonal colour patterns confirms that the variations in tone correspond to variations in preserved cuticle thickness. These preserved colour patterns can thus be plausibly explained as melanin-based patterning. Recognition of melanin-based colour patterns in fossil insects opens new avenues for interpreting the evolution of insect coloration and behaviour through deep time.

New Blombos Cave evidence supports a multistep evolutionary scenario for the culturalization of the human body.

The emergence of technologies to culturally modify the appearance of the human body is a debated issue, with earliest evidence consisting of perforated marine shells dated between 140 and 60 ka at archaeological sites from Africa and western Asia. In this study, we submit unpublished marine and estuarine gastropods from Blombos Cave Middle Stone Age layers to taxonomic, taphonomic, technological, and use-wear analyses. We show that unperforated and naturally perforated eye-catching shells belonging to the species Semicassis zeylanica, Conus tinianus, and another Conus species, possibly Conus algoensis, were brought to the cave between 100 and 73 ka. At ca. 70 ka, a previously unrecorded marine gastropod, belonging to the species Tritia ovulata, was perforated by pecking and was worn as an ornamental object, isolated or in association with numerous intentionally perforated shells of the species Nassarius kraussianus. Fluctuations in sea level and consequent variations in the site-to-shoreline distances and landscape modifications during the Middle Stone Age have affected the availability of marine shells involved in symbolic practices. During the M3 and M2 Lower phases, with a sea level 50 m lower, the site was approximately 3.5 km away from the coast. In the later M2 Upper and M1 phases, with a sea level at -60 m, the distance increased to about 5.7 km. By the end of the M1 phase, when the site was abandoned, Blombos Cave was situated 18-30 km from the shoreline. We use the new Blombos evidence and a review of the latest findings from Africa and Eurasia to propose a testable ten-step evolutionary scenario for the culturalization of the human body with roots in the deep past.

Decomposition and insect succession on human cadavers in a humid, continental (Dfb) climate (Quebec, Canada).

Forensic entomology has been developing globally for decades. Despite this discipline being used in criminal investigations around the world, only a few controlled studies have been performed on human cadavers in human decomposition facilities, with the majority of these being conducted in warm and often dry climates. Therefore, the purpose of our research was to catalogue the first published data on insects associated with decomposed human bodies in a humid, continental (Dfb) climate. Specifically, our objective was to document the diversity and succession of the entomofauna associated with human cadavers throughout the decomposition process, in the Quebec province of Canada, during the summer season. Two human cadavers were studied in 2020 at the site for Research in Experimental and Social Thanatology, REST, located in Bécancour (Quebec, Canada). Insects (and other arthropods) were regularly sampled by visual observations, collection from the cadavers, and by using an entomological net and pitfall traps. Our results highlight that the decomposition process is a heterogeneous and complex process in Quebec, with cadavers showing signs of precocious desiccation/mummification. In addition, our observations confirm that the presence of superficial skin lesions accelerates the colonization of blow flies (Diptera: Calliphoridae) and, consequently, the process of decomposition. Finally, we were able to discriminate between "early colonizers" (e.g., Calliphoridae Lucilia sp. or Calliphora livida), "late colonizers" (e.g., larvae of Piophilidae or Heleomyzidae), and "non-specific colonizers." We also officially report the first observation of Cochliomyia macellaria (Diptera: Calliphoridae) in Quebec. These findings will provide new information to help medico-legal death investigations by determining the minimum time elapsed since death and the circumstances surrounding death.

Survival of sharp force trauma in burnt bones: effects of environmental factors.

This study investigates how environmental variables, such as temperature and rainfall, affect previously induced cut marks on burnt bones. This research used non-serrated and serrated blade knives to inflict trauma on Sus scrofa ribs (n = 240). The bones were later burnt and left for 1 month in a taphonomic experimental facility. Qualitative and quantitative examinations were conducted using macroscopic and microscopic techniques to assess specific characteristics of the cut marks. Any changes to the dimension and morphology of the cut marks as well as their level of fragmentation were recorded.This study has led to three important outcomes: (1) identification of pre-existing cut marks is possible in reconstructed burnt bone fragments; (2) cut marks from different types of knife blades showed dissimilar responses to heat and the environment; and (3) specific environmental variables affect burnt bone fragmentation. These results have implications for trauma analysis on burnt remains in forensic anthropology casework.