Two Major Extinction Events in the Evolutionary History of Turtles: One Caused by an Asteroid, the Other by Hominins.

AbstractWe live in a time of accelerated biological extinctions that has the potential to mirror past mass extinction events. However, the rarity of mass extinctions and the restructuring of diversity they cause complicate direct comparisons between the current extinction crisis and earlier events. Among animals, turtles (Testudinata) are one of few groups that have both a rich fossil record and sufficiently stable ecological and functional roles to enable meaningful comparisons between the end-Cretaceous mass extinction (∼66 Ma) and the ongoing wave of extinctions. Here we analyze the fossil record of the entire turtle clade and identify two peaks in extinction rates over their evolutionary history. The first coincides with the Cretaceous-Paleogene transition, reflecting patterns previously reported for other taxa. The second major extinction event started in the Pliocene and continues until now. This peak is detectable only for terrestrial turtles and started much earlier in Africa and Eurasia than elsewhere. On the basis of the timing, geography, and functional group of this extinction event, we postulate a link to co-occurring hominins rather than climate change as the cause. These results lend further support to the view that negative biodiversity impacts were already incurred by our ancestors and related lineages and demonstrate the severity of this continued impact through human activities.

Edge chipping patterns in posterior teeth of hominins and apes.

Chip scars in fossil teeth are a lasting evidence that bears on human evolution. Chip dimensions in posterior teeth of hominins, apes and white-lipped peccary (Tayassu pecari) are measured from published occlusal images. The results are plotted as D/Dm vs. h/Dm, where h, D and Dm denote indent distance, chip width and mean tooth crown diameter. The hominin species follow a similar pattern where D/Dm monotonically increases up to h/Dm ≈ 0.3. The behavior for the apes is characterized by two phases. In the first, h/Dm monotonically increases up to h/Dm ≈ 0.26 while in the second (h/Dm ≈ 0.26 to 0.42), D/Dm experiences a drastic change in behavior. The interpretation of chip morphology is assisted by results from controlled spherical indentation tests on extracted human molars. This study shows that in addition to the commonly recognized chipping due to cusp loading, a chip may also initiate from the inner wall of the tooth's central fossa. Accordingly, it is suggested that the chipping in hominins generally initiates from a (worn) cusp while that in apes involves cusp loading up to h/Dm ≈ 0.26 and fossa loading thereafter. The behavior for T. pecari is much similar to that of the apes. The fossa chipping is facilitated by a consumption of hard, large-size diet (e.g., plants, roots, barks and nuts) and presence of broad central fossa, conditions that are met in apes. Finally, a simple expression for the critical chipping force Pch due to fossa loading is developed.

Hominin turnover at Laetoli is associated with vegetation change: Multiproxy evidence from the large herbivore community.

Vegetation change in eastern Africa during the Pliocene would have had an important impact on hominin adaptation and ecology, and it may have been a key driver of hominin macroevolution, including the extinction of Australopithecus and the emergence of Paranthropus and Homo. The Pliocene paleoanthropological site of Laetoli in Tanzania provides an opportunity to investigate the relationship between vegetation change and hominin turnover because it encompasses the time period when grass cover was spreading across eastern Africa and because hominin species turnover occurred locally at Laetoli, with Paranthropus aethiopicus in the Upper Ndolanya Beds (UNB) replacing Australopithecus afarensis in the Upper Laetolil Beds (ULB). However, it remains unresolved how the vegetation of the UNB and the ULB differed from each other. To examine differences between the two stratigraphic units, multiple proxies-hypsodonty, mesowear, and stable carbon isotopes of tooth enamel (δ13Cenamel)-are used to infer the diets of large herbivores and compare the dietary guild structure of the large herbivore communities. All three proxies indicate an increase in the abrasiveness and C4-content in the diets of the large herbivores in the UNB relative to those in the ULB. After inferring the diets of species based on all three proxies, the large herbivore community of the UNB had a greater proportion of grazers and a smaller proportion of mixed feeders than in the ULB but maintained a similar proportion of browsers and frugivores. The ULB community has few modern-day analogs, whereas the UNB community is most closely analogous to those in modern African grasslands. Thus, hominin turnover at Laetoli is associated with an increase in grass cover within a woodland-grassland mosaic and is part of a broader transformation of the herbivore community structure.

Description and taxonomic assessment of fossil Cercopithecidae from the Pliocene Galili Formation (Ethiopia).

The Mount Galili Formation in the Afar region, Ethiopia, samples a critical time in hominin evolution, 4.4 to 3.8 Ma, documenting the last appearance of Ardipithecus and the origin of Australopithecus. This period is also important in the evolution of cercopithecids, especially the origin of Theropithecus in general and Theropithecus oswaldi lineage in particular. Galili has provided a total of 655 cercopithecid specimens that include crania, mandibles, isolated teeth and postcrania. All the fossils were recovered from the Lasdanan (5.3-4.43 Ma), Dhidinley (4.43-3.9 Ma) and Shabeley Laag (∼3.92-3.8 Ma) Members. Here, we described and analyzed 362 fossils employing both qualitative and quantitative methods. Descriptions of the material were supplemented with dental metrics and cranial shape analysis using three-dimensional geometric morphometrics. Results indicate the presence of at least six cercopithecid taxa: Theropithecus oswaldi serengetensis (n = 28), Theropithecus sp. (n = 2), three non-Theropithecus papionin groups (n = 134) and one colobine-size group (n = 58). The T. o. serengetensis represents the earliest form of the lineage, documented from ∼3.9 Ma Galili sediments. The three Galili papionins include a smaller taxon, a medium-sized taxon comparable to Pliopapio alemui and a large papionin overlapping in size with Soromandrillus, Gorgopithecus and Dinopithecus. The majority of Galili colobines have closest affinities to Kuseracolobus aramisi and some overlap with other taxa. Papionins dominate the Galili cercopithecid collection, although colobines are still fairly common (approximately 25% of the sample). Thus, Galili sample is like Kanapoi (4.2-4.1 Ma) and Gona (5.2-3.9 Ma) localities but distinct from Aramis, suggesting paleoecological similarity to the former sites. On the other hand, Theropithecus is less abundant at Galili than geologically younger Hadar (3.4-3.2 Ma) and Woranso-Mille (3.8-3.6 Ma) sites. Whether this difference is due to sampling, time or landscape variation requires further investigation.

Naming Homo erectus: A review.

Following the discovery of hominin fossils at Trinil (Java, Indonesia) in 1891 and 1892, Eugène Dubois named a new species, now known as Homo erectus. Although the main historical events are well-known, there appears to be no consensus regarding two important aspects of the naming of the species, including what constitutes the original publication of the name, and what is the name-bearing type specimen. These issues are addressed in this paper with reference to original sources and the International Code of Zoological Nomenclature. Our review confirms earlier studies that cite the published quarterly fieldwork report covering the 3rd quarter of 1892 as the original publication naming the species erectus. However, until recently, the correct publication year of 1893 has consistently been cited as 1892, and it has rarely been recognized that the author of the publication was anonymous, even though the author of the species is specifically named. Importantly, Dubois assigns all three hominin fossils found at Trinil up to that moment to the new species, explicitly stating that they belong to a single individual. The three fossils, a molar, a calotte, and a femur, therefore jointly constitute the original holotype. However, the femur most likely derives from younger strata than the other hominins and shows fully modern human-like morphology, unlike subsequently discovered H. erectus femora. Moreover, there is no consensus over the affinities of the molar, and if it is H. erectus rather than an extinct ape, there is no evidence that it belongs to the same individual as the calotte. Excluding these two fossils from the holotype, the calotte is the appropriate fossil to retain the role as name-bearing specimen.

Towards correlative archaeology of the human mind.

Retracing human cognitive origins started out at the systems level with the top-down interpretation of archaeological records spanning from man-made artifacts to endocasts of ancient skulls. With emerging evolutionary genetics and organoid technologies, it is now possible to deconstruct evolutionary processes on a molecular/cellular level from the bottom-up by functionally testing archaic alleles in experimental models. The current challenge is to complement these approaches with novel strategies that allow a holistic reconstruction of evolutionary patterns across human cognitive domains. We argue that computational neuroarcheology can provide such a critical mesoscale framework at the brain network-level, linking molecular/cellular (bottom-up) to systems (top-down) level data for the correlative archeology of the human mind.

Main morphological characteristics and sexual dimorphism of hominin adult femora from the Sima de los Huesos Middle Pleistocene site (Sierra de Atapuerca, Spain).

The excellent fossil record from Sima de los Huesos (SH) includes three well-known complete adult femora and several partial specimens that have not yet been published in detail. This fossil record provides an opportunity to analyze the morphology of European pre-Neandertal adult femur and its variation with different evolution patterns. Currently, there are a minimum of five adult individuals (males or females). In this study, we compiled previously published basic anatomical and biometric characteristics of SH adult femora, emphasizing the most relevant features compared to other recent and fossil hominins. The SH femora exhibited a primitive morphological pattern common to all non-Homo sapiens femora, as well as most of the Neandertal traits. Therefore, the complete Upper Pleistocene Neandertal pattern was well-established in Middle Pleistocene ancestors long before the proper Neandertals appeared. Additionally, we highlight that the SH and Neandertal femora share some morphological traits and proportions with modern humans that hold sexual significance in our species, regardless of size. Keeping this in mind, we discussed the sex determination of the complete SH specimens and re-evaluated sex allocation in two of them.

Zanadamu: An African hominin isotopic dataset.

The present article introduces Zanadamu, a comprehensive geo-temporal-referenced dataset that amalgamates all published stable isotope carbon and oxygen measurements on tooth enamel from African hominins, dated between 4.4 and 0.005 Ma. Zanadamu serves as a research tool for investigating hominin evolution by facilitating the examination of how different hominin species explored food resources and interacted with their local paleoenvironments. The dataset is structured in a machine-readable format, and its metadata organization allows for facile statistical analyses and comparisons with other types of isotopic records, including ancient and modern humans and other primates. Zanadamu is part of the AfriArch data initiative, which aims at compiling datasets for the study of ancient Africa. This an active initiative, and we strive to update Zanadamu as novel data becomes available.

The diploic venous system in Homo neanderthalensis and fossil Homo sapiens: A study using high-resolution computed tomography.

OBJECTIVES: The diploic venous system has been hypothesized to be related to human brain evolution, though its evolutionary trajectory and physiological functions remain largely unclear. This study examines the characteristics of the diploic venous channels (DCs) in a selection of well-preserved Homo neanderthalensis and Upper Paleolithic Homo sapiens crania, searching for the differences between the two taxa and exploring the associations between brain anatomy and DCs. MATERIALS AND METHODS: Five H. neanderthalensis and four H. sapiens fossil specimens from Western Europe were analyzed. Based on Micro-CT scanning and 3D reconstruction, the distribution pattern and draining orifices of the DCs were inspected qualitatively. The size of the DCs was quantified by volume calculation, and the degree of complexity was quantified by fractal analyses. RESULTS: High-resolution data show the details of the DC structures not documented in previous studies. H. neanderthalensis and H. sapiens specimens share substantial similarities in the DCs. The noticeable differences between the two samples manifest in the connecting points surrounding the frontal sinuses, parietal foramina, and asterional area. DISCUSSION: This study provides a better understanding of the anatomy of the DCs in H. neanderthalensis and H. sapiens. The connection patterns of the DCs have potential utility in distinguishing between the two taxa and in the phylogenetic and taxonomic discussion of the Neandertal-like specimens with controversial taxonomic status.

Molecular de-extinction of ancient antimicrobial peptides enabled by machine learning.

Molecular de-extinction could offer avenues for drug discovery by reintroducing bioactive molecules that are no longer encoded by extant organisms. To prospect for antimicrobial peptides encrypted within extinct and extant human proteins, we introduce the panCleave random forest model for proteome-wide cleavage site prediction. Our model outperformed multiple protease-specific cleavage site classifiers for three modern human caspases, despite its pan-protease design. Antimicrobial activity was observed in vitro for modern and archaic protein fragments identified with panCleave. Lead peptides showed resistance to proteolysis and exhibited variable membrane permeabilization. Additionally, representative modern and archaic protein fragments showed anti-infective efficacy against A. baumannii in both a skin abscess infection model and a preclinical murine thigh infection model. These results suggest that machine-learning-based encrypted peptide prospection can identify stable, nontoxic peptide antibiotics. Moreover, we establish molecular de-extinction through paleoproteome mining as a framework for antibacterial drug discovery.

A pathological Neandertal thumb phalanx from Moula-Guercy (France).

OBJECTIVE: To discuss a Neandertal pathological adult first pollical proximal phalanx (I2-104) from the Baume de Moula-Guercy (Ardèche, France) and evaluate the possible causes of this pathology. METHODS: Macroscopic analyses of external features, as well as CT imaging, were used in the analysis RESULTS: The presence of asymmetric eburnation on the distal epiphysis associated with an osteophyte on the palmar surface, as well as the absence of periosteal bone reaction visible on CT images, is consistent with osteoarthritis. CONCLUSION: Osteoarthritis (OA) can have different origins and the cause is difficult to identify. The pathology of the Moula-Guercy I2-104 phalanx may be due to a genetic predisposition for OA known in Neandertals and associated with short limb bones. The OA could have been aggravated by the age of this individual and by an inflammatory reaction caused by repeated movements and intense vibrations provoked by high-frequency knapping or by other use of the hands SIGNIFICANCE: The I2-104 phalanx is the first Neandertal pollical phalanx known to display OA, although joints of this bone are frequently affected by this pathology in modern humans. Thus, greater insight into the presence and consequences of Neandertal behaviors is offered LIMITATION: It is impossible to give a definitive conclusion on the cause(s) of the OA in this case. SUGGESTIONS FOR FURTHER RESEARCH: More data is needed concerning OA within Neandertals and its relationship with behavior and genetics.

Non-ultrametric phylogenetic trees shed new light on Neanderthal introgression.

Ultrametric spaces are widely used to depict evolutionary times in phylogenetic trees since they assume that every population/species is located at the tips of bifurcating branches of the same length. The discrete branching of ultrametric trees permits the measurement of distances between pairs of individuals that are proportional to their divergence time. Here the traditional ultrametric concept of bifurcating and divergent phylogenetic tree is overturned and a new type of non-ultrametric diagram is introduced. The objective of this study is the description of gene flows in branching species/populations in terms of converging trees instead of bifurcating trees. To provide an operational example, the paleoanthropological issue of the date of Neanderthal genome's introgression in non-African humans is examined. Neanderthals and ancient humans are not anymore two species that exchange chunks of DNA, rather become a single, novel cluster of extant hominins that must be considered by itself. The novel converging, non-ultrametric phylogenetic trees permit the calibration of molecular clocks with a twofold benefit. When the date of the branching of two population/species from a common ancestor is known, the novel approach allows to calculate the time of subsequent introgressions. On the contrary, when the date of the introgression between two population/species is known, the novel approach allows to detect the time of their previous branching from a common ancestor.

Taphonomic skeletal disturbances in the Sima de los Huesos postcranial remains.

The postcranial skeleton of fossil hominins is crucial for reconstructing the processes that occurred between the time of death and the recovery of the bones. Thousands of postcranial skeletal fragments from at least 29 hominin individuals have been recovered from the Sima de los Huesos Middle Pleistocene site in Spain. This study's primary objective is to address the main taphonomic features of the postcranial remains from the Sima de los Huesos sample, including antemortem, perimortem, and postmortem skeletal disturbances. We present an updated assessment of the bone surface modification analysis, the fracture pattern analysis, and the skeletal part representation to facilitate interpretation of the biostratinomic and fossil-diagenetic processes in this large paleoanthropological collection. We conclude that carnivores (probably bears) had limited access to the hominin bones and complete bodies were probably placed in the site.

Hominin locomotion and evolution in the Late Miocene to Late Pliocene.

In this review, we present on the evolution of the locomotor adaptation of hominins in the Late Miocene to Late Pliocene, with emphasis on some of the prominent advances and debates that have occurred over the past fifty years. We start with the challenging issue of defining hominin locomotor grades that are currently used liberally and offer our own working definitions of facultative, habitual, and obligate bipedalism. We then discuss the nature of the Pan-Homo last common ancestor and characterize the locomotor adaptation of Sahelanthropus, Orrorin, and Ardipithecus-often referred to as facultative bipeds-and examine the debates on the extent of bipedality and arboreality in these taxa. Moreover, the question of Middle Pliocene hominin locomotor diversity is addressed based on information derived from the 'Little Foot' specimen from Sterkfontein, footprints from Laetoli, and the Burtele Foot in Ethiopia. Our review suggests that the most convincing evidence for locomotor diversity comes from Burtele, whereas the evidence from Sterkfontein and Laetoli is unconvincing and equivocal, respectively. Finally, we address the decades old issue of the significance of arboreality in the otherwise habitual biped, Australopithecus, with emphasis on Australopithecus afarensis and its implications for the paleobiology of these creatures. We conclude that many of the apelike features encountered, mostly in the upper part of the Australopithecus skeleton, were retained for their significance in climbing. Approaches that have investigated character plasticity and those exploring internal bone structure have shown that the shoulder and limbs in Au. afarensis and Australopithecus africanus were involved in arboreal activities that are thought to be key for feeding, nesting, and predator avoidance. We conclude that many of the so-called retained ape-like features persisted due to stabilizing selection, that early hominins engaged in a considerable amount of arboreality even after Australopithecus had become a habitual biped, and arboreality only ceased to be an important component of hominin locomotor behavior after the emergence of Homo erectus.

Evolutionary relevance of single nucleotide variants within the forebrain exclusive human accelerated enhancer regions.

BACKGROUND: Human accelerated regions (HARs) are short conserved genomic sequences that have acquired significantly more nucleotide substitutions than expected in the human lineage after divergence from chimpanzees. The fast evolution of HARs may reflect their roles in the origin of human-specific traits. A recent study has reported positively-selected single nucleotide variants (SNVs) within brain-exclusive human accelerated enhancers (BE-HAEs) hs1210 (forebrain), hs563 (hindbrain) and hs304 (midbrain/forebrain). By including data from archaic hominins, these SNVs were shown to be Homo sapiens-specific, residing within transcriptional factors binding sites (TFBSs) for SOX2 (hs1210), RUNX1/3 (hs563), and FOS/JUND (hs304). Although these findings suggest that the predicted modifications in TFBSs may have some role in present-day brain structure, work is required to verify the extent to which these changes translate into functional variation. RESULTS: To start to fill this gap, we investigate the SOX2 SNV, with both forebrain expression and strong signal of positive selection in humans. We demonstrate that the HMG box of SOX2 binds in vitro with Homo sapiens-specific derived A-allele and ancestral T-allele carrying DNA sites in BE-HAE hs1210. Molecular docking and simulation analysis indicated highly favourable binding of HMG box with derived A-allele containing DNA site when compared to site carrying ancestral T-allele. CONCLUSION: These results suggest that adoptive changes in TF affinity within BE-HAE hs1210 and other HAR enhancers in the evolutionary history of Homo sapiens might. have brought about changes in gene expression patterns and have functional consequences on forebrain formation and evolution. METHODS: The present study employ electrophoretic mobility shift assays (EMSA) and molecular docking and molecular dynamics simulations approaches.

Lateralized behaviors in living humans: Application in the context of hominin brain evolution.

The left and right hemispheres of our brains differ subtly in structure, and each is dominant in processing specific cognitive tasks. Our species has a unique system of distributing behavior and cognition between each cerebral hemisphere, with a preponderance of pronounced side biases and lateralized functions. This hemisphere-dependent relationship between cognitive, sensory or motor function and a set of brain structures is called hemispheric specialization. Hemispheric specialization has led to the emergence of model systems to link anatomical asymmetries to brain function and behavior. Scientific research on hemispheric specialization and lateralized functions in living humans focuses on three major domains: (1) hand preferences, (2) language, and (3) visuospatial skills and attention. In this chapter we present an overview of this research with a specific focus on living humans and the applications of this research in the context of hominin brain evolution. Our objective is to put into perspective what we know about brain-behavior relationships in living humans and how we can apply the same methods to investigate this relationship in fossil hominin species, and thus improve our understanding of the emergence and development of complex cognitive abilities.