The rise of pelagic sharks and adaptive evolution of pectoral fin morphology during the Cretaceous.

The emergence and subsequent evolution of pectoral fins is a key point in vertebrate evolution, as pectoral fins are dominant control surfaces for locomotion in extant fishes.1,2,3 However, major gaps remain in our understanding of the diversity and evolution of pectoral fins among cartilaginous fishes (Chondrichthyes), a group with an evolutionary history spanning over 400 million years with current selachians (modern sharks) appearing about 200 million years ago.4,5,6 Modern sharks are a charismatic group of vertebrates often thought to be predators roaming the open ocean and coastal areas, but most extant species occupy the seafloor.4 Here we use an integrative approach to understand what facilitated the expansion to the pelagic realm and what morphological changes accompanied this shift. On the basis of comparative analyses in the framework of a time-calibrated molecular phylogeny,7 we show that modern sharks expanded to the pelagic realm no later than the Early Cretaceous (Barremian). The pattern of pectoral fin aspect ratios across selachians is congruent with adaptive evolution, and we identify an increase of the subclade disparity of aspect ratio at a time when sea surface temperatures were at their highest.8 The expansion to open ocean habitats likely involved extended bouts of sustained fast swimming, which led to the selection for efficient movement via higher aspect ratio pectoral fins. Swimming performance was likely enhanced in pelagic sharks during this time due to the elevated temperatures in the sea, highlighting that shark evolution has been greatly impacted by climate change.

Allelic bias when performing in-solution enrichment of ancient human DNA.

In-solution hybridisation enrichment of genetic variation is a valuable methodology in human paleogenomics. It allows enrichment of endogenous DNA by targeting genetic markers that are comparable between sequencing libraries. Many studies have used the 1240k reagent-which enriches 1,237,207 genome-wide SNPs-since 2015, though access was restricted. In 2021, Twist Biosciences and Daicel Arbor Biosciences independently released commercial kits that enabled all researchers to perform enrichments for the same 1240 k SNPs. We used the Daicel Arbor Biosciences Prime Plus kit to enrich 132 ancient samples from three continents. We identified a systematic assay bias that increases genetic similarity between enriched samples and that cannot be explained by batch effects. We present the impact of the bias on population genetics inferences (e.g. Principal Components Analysis, ƒ-statistics) and genetic relatedness (READ). We compare the Prime Plus bias to that previously reported of the legacy 1240k enrichment assay. In ƒ-statistics, we find that all Prime-Plus-generated data exhibit artefactual excess shared drift, such that within-continent relationships cannot be correctly determined. The bias is more subtle in READ, though interpretation of the results can still be misleading in specific contexts. We expect the bias may affect analyses we have not yet tested. Our observations support previously reported concerns for the integration of different data types in paleogenomics. We also caution that technological solutions to generate 1240k data necessitate a thorough validation process before their adoption in the paleogenomic community.

Insights into the genetic histories and lifeways of Machu Picchu's occupants.

Machu Picchu originally functioned as a palace within the estate of the Inca emperor Pachacuti between ~1420 and 1532 CE. Before this study, little was known about the people who lived and died there, where they came from or how they were related to the inhabitants of the Inca capital of Cusco. We generated genome-wide data for 34 individuals buried at Machu Picchu who are believed to have been retainers or attendants assigned to serve the Inca royal family, as well as 34 individuals from Cusco for comparative purposes. When the ancient DNA results are contextualized using historical and archaeological data, we conclude that the retainer population at Machu Picchu was highly heterogeneous with individuals exhibiting genetic ancestries associated with groups from throughout the Inca Empire and Amazonia. The results suggest a diverse retainer community at Machu Picchu in which people of different genetic backgrounds lived, reproduced, and were interred together.

The evolution of mechanical properties of conifer and angiosperm woods.

The material properties of the cells and tissues of an organism dictate, to a very large degree, the ability of the organism to cope with mechanical stress induced by externally applied forces. It is, therefore, critical to understand how these properties differ across diverse species and how they have evolved. Herein, a large data base (N = 84 species) for the mechanical properties of wood samples measured at biologically natural moisture contents (i.e., "green wood") was analyzed to determine the extent to which these properties are correlated across phylogenetically diverse tree species, to determine if a phylogenetic pattern of trait values exists, and, if so, to assess whether the rate of trait evolution varies across the phylogeny. The phylogenetic comparative analyses presented here confirm previous results that critical material properties are significantly correlated with one another and with wood density. Although the rates of trait evolution of angiosperms and gymnosperms (i.e., conifers) are similar, the material properties of both clades evolved in distinct selective regimes that are phenotypically manifested in lower values across all material properties in gymnosperms. This observation may be related to the structural differences between gymnosperm and angiosperm wood such as the presence of vessels in angiosperms. Explorations of rate heterogeneity indicate high rates of trait evolution in wood density in clades within both conifers and angiosperms (e.g., Pinus and Shorea). Future analyses are warranted using additional data given these preliminary results, especially because there is ample evidence of convergent evolution in the material properties of conifers and angiosperm wood that appear to experience similar ecological conditions.

Early giant reveals faster evolution of large body size in ichthyosaurs than in cetaceans.

Body sizes of marine amniotes span six orders of magnitude, yet the factors that governed the evolution of this diversity are largely unknown. High primary production of modern oceans is considered a prerequisite for the emergence of cetacean giants, but that condition cannot explain gigantism in Triassic ichthyosaurs. We describe the new giant ichthyosaur Cymbospondylus youngorum sp. nov. with a 2-meter-long skull from the Middle Triassic Fossil Hill Fauna of Nevada, USA, underscoring rapid size evolution despite the absence of many modern primary producers. Surprisingly, the Fossil Hill Fauna rivaled the composition of modern marine mammal faunas in terms of size range, and energy-flux models suggest that Middle Triassic marine food webs were able to support several large-bodied ichthyosaurs at high trophic levels, shortly after ichthyosaur origins.

Ethics of DNA research on human remains: five globally applicable guidelines.

We are a group of archaeologists, anthropologists, curators and geneticists representing diverse global communities and 31 countries. All of us met in a virtual workshop dedicated to ethics in ancient DNA research held in November 2020. There was widespread agreement that globally applicable ethical guidelines are needed, but that recent recommendations grounded in discussion about research on human remains from North America are not always generalizable worldwide. Here we propose the following globally applicable guidelines, taking into consideration diverse contexts. These hold that: (1) researchers must ensure that all regulations were followed in the places where they work and from which the human remains derived; (2) researchers must prepare a detailed plan prior to beginning any study; (3) researchers must minimize damage to human remains; (4) researchers must ensure that data are made available following publication to allow critical re-examination of scientific findings; and (5) researchers must engage with other stakeholders from the beginning of a study and ensure respect and sensitivity to stakeholder perspectives. We commit to adhering to these guidelines and expect they will promote a high ethical standard in DNA research on human remains going forward.

Linking ecomechanical models and functional traits to understand phenotypic diversity.

Physical principles and laws determine the set of possible organismal phenotypes. Constraints arising from development, the environment, and evolutionary history then yield workable, integrated phenotypes. We propose a theoretical and practical framework that considers the role of changing environments. This 'ecomechanical approach' integrates functional organismal traits with the ecological variables. This approach informs our ability to predict species shifts in survival and distribution and provides critical insights into phenotypic diversity. We outline how to use the ecomechanical paradigm using drag-induced bending in trees as an example. Our approach can be incorporated into existing research and help build interdisciplinary bridges. Finally, we identify key factors needed for mass data collection, analysis, and the dissemination of models relevant to this framework.

Ancient mitochondrial genomes from the Argentinian Pampas inform the early peopling of the Southern Cone of South America.

The Southern Cone of South America (SCSA) is a key region for investigations about the peopling of the Americas. However, little is known about the eastern sector, the Argentinian Pampas. We analyzed 18 mitochondrial genomes-7 of which are novel-from human skeletal remains from 3 Early to Late Holocene archaeological sites. The Pampas present a distinctive genetic makeup compared to other Middle to Late Holocene pre-Columbian SCSA populations. We also report the earliest individuals carrying SCSA-specific mitochondrial haplogroups D1j and D1g from Early and Middle Holocene, respectively. Using these deep calibration time points in Bayesian phylogenetic reconstructions, we suggest that the first settlers of the Pampas were part of a single and rapid dispersal ∼15,600 years ago. Finally, we propose that present-day genetic differences between the Pampas and the rest of the SCSA are due to founder effects, genetic drift, and a partial population replacement ∼9,000 years ago.

Evolution of vision and hearing modalities in theropod dinosaurs.

Owls and nightbirds are nocturnal hunters of active prey that combine visual and hearing adaptations to overcome limits on sensory performance in low light. Such sensory innovations are unknown in nonavialan theropod dinosaurs and are poorly characterized on the line that leads to birds. We investigate morphofunctional proxies of vision and hearing in living and extinct theropods and demonstrate deep evolutionary divergences of sensory modalities. Nocturnal predation evolved early in the nonavialan lineage Alvarezsauroidea, signaled by extreme low-light vision and increases in hearing sensitivity. The Late Cretaceous alvarezsauroid Shuvuuia deserti had even further specialized hearing acuity, rivaling that of today's barn owl. This combination of sensory adaptations evolved independently in dinosaurs long before the modern bird radiation and provides a notable example of convergence between dinosaurs and mammals.

A strontium isoscape for the Conchucos region of highland Peru and its application to Andean archaeology.

Strontium isotope (87Sr/86Sr) analysis of human skeletal remains is an important method in archaeology to examine past human mobility and landscape use. 87Sr/86Sr signatures of a given location are largely determined by the underlying bedrock, and these geology specific isotope signatures are incorporated into skeletal tissue through food and water, often permitting the differentiation of local and non-local individuals in past human populations. This study presents the results of a systematic survey of modern flora and fauna (n = 100) from 14 locations to map the bioavailable 87Sr/86Sr signatures of the Conchucos region, an area where the extent of geologic variability was previously unknown. We illustrate the necessity to examine the variation in 87Sr/86Sr values of the different geological formations available to human land use to document the range of possible local 87Sr/86Sr values. Within the Conchucos region we found significant variation in environmental 87Sr/86Sr values (0.7078-0.7214). The resulting isoscape represents the largest regionally specific bioavailable 87Sr/86Sr map (3,840 km2) to date for the Andes, and will serve as a baseline for future archaeological studies of human mobility in this part of the Peruvian highlands.

A Multidisciplinary Review of the Inka Imperial Resettlement Policy and Implications for Future Investigations.

The rulers of the Inka empire conquered approximately 2 million km2 of the South American Andes in just under 100 years from 1438-1533 CE. Inside the empire, the elite conducted a systematic resettlement of the many Indigenous peoples in the Andes that had been rapidly colonised. The nature of this resettlement phenomenon is recorded within the Spanish colonial ethnohistorical record. Here we have broadly characterised the resettlement policy, despite the often incomplete and conflicting details in the descriptions. We then review research from multiple disciplines that investigate the empirical reality of the Inka resettlement policy, including stable isotope analysis, intentional cranial deformation morphology, ceramic artefact chemical analyses and genetics. Further, we discuss the benefits and limitations of each discipline for investigating the resettlement policy and emphasise their collective value in an interdisciplinary characterisation of the resettlement policy.

Comparing Genetic Variation among Latin American Immigrants: Implications for Forensic Casework in the Arizona- and Texas-Mexico Borderlands.

The humanitarian crisis on the US-Mexico border is a long-standing and evolving crisis in which nearly 8,000 deaths have been reported in the last two decades. These deaths are largely distributed across the Arizona-Mexico and Texas-Mexico border regions, where demographic trends for immigrants attempting to cross into the United States have shifted dramatically. The demographic change and volume of immigrants seeking shelter in the United States present new challenges for the forensic practitioners entrusted with the identification of individuals who lose their lives during the final segment of their journey. Within this border context, this study investigated how genetic variation inferred from forensically significant microsatellites can provide valuable information on regions of origin for unidentified remains at the group level. To explore how to mobilize these genetic data to inform identification strategies, the authors conducted a comparative genetic analysis of identified and unidentified immigrant cases from the Arizona- and Texas-Mexico contexts, as well as 27 other Latin American groups. Allele frequencies were utilized to calculate FST, and relationships were visually depicted in a multidimensional scaling plot. A Spearman correlation coefficient analysis assessed the strength and significance of population relationships, and an agglomerative clustering analysis assessed population clusters. Results indicate that Arizona-Mexico immigrants have the strongest relationship (>80%) with groups from El Salvador, Guatemala, Mexico, and an indigenous group from southern Mexico. Texas-Mexico immigrants have the strongest relationships (>80%) with groups from Belize, Colombia, Costa Rica, El Salvador, Guatemala, Honduras, and Nicaragua. These findings agree with, and are discussed in comparison with, previously reported demographic trends, population genetics research, and population history analyses. The authors emphasize the utility and necessity of coupling genetic variation research with a nuanced anthropological perspective for identification processes in the US-Mexico border context.

Increased rate of close-kin unions in the central Andes in the half millennium before European contact.

Analyzing ancient DNA of the central Andes, Ringbauer and colleagues identify a markedly elevated rate of unions of closely related parents after ca. 1000 CE. This change of mating preferences sheds new light on a unique system of social organization based on ancestry ("ayllu") whereby within-group unions were preferred to facilitate sharing of resources.

Retraction Note: Hummingbird-sized dinosaur from the Cretaceous period of Myanmar.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Integration of ancient DNA with transdisciplinary dataset finds strong support for Inca resettlement in the south Peruvian coast.

Ancient DNA (aDNA) analysis provides a powerful means of investigating human migration, social organization, and a plethora of other crucial questions about humanity's past. Recently, specialists have suggested that the ideal research design involving aDNA would include multiple independent lines of evidence. In this paper, we adopt a transdisciplinary approach integrating aDNA with archaeological, biogeochemical, and historical data to investigate six individuals found in two cemeteries that date to the Late Horizon (1400 to 1532 CE) and Colonial (1532 to 1825 CE) periods in the Chincha Valley of southern Peru. Genomic analyses indicate that these individuals are genetically most similar to ancient and present-day populations from the north Peruvian coast located several hundred kilometers away. These genomic data are consistent with 16th century written records as well as ceramic, textile, and isotopic data. These results provide some of the strongest evidence yet of state-sponsored resettlement in the pre-Colonial Andes. This study highlights the power of transdisciplinary research designs when using aDNA data and sets a methodological standard for investigating ancient mobility in complex societies.

Ontogeny and potential function of poacher armor (Actinopterygii: Agonidae).

Many vertebrates are armored over all or part of their body. The armor may serve several functional roles including defense, offense, visual display, and signal of experience/capability. Different roles imply different tradeoffs; for example, defensive armor usually trades resistance to attack for maneuverability. The poachers (Agonidae), 47 species of scorpaeniform fishes, are a useful system for understanding the evolution and function of armor due to their variety and extent of armoring. Using publically available CT-scan data from 27 species in 16 of 21 genera of poachers we compared the armor to axial skeletal in the mid body region. The ratio of average armor density to average skeleton density ranged from 0.77 to 1.17. From a defensive point of view, the total investment in mineralization (volume * average density) is more interesting. There was 10 times the material invested in the armor as in the endoskeleton in some small, smooth plated species, like Aspidophoroides olrikii. At the low end, some visually arresting species like Percis japonica, had ratios as low as 2:1. We categorized the extent and type (impact vs. abrasion) in 34 Agonopsis vulsa across all 35+ plates in the eight rows along the body. The ventral rows show abrasive damage along the entire length of the fish that gets worse with age. Impact damage to head and tail plates gets more severe and occurs at higher rates with age. The observed damage rates and the large investment in mineralization of the armor suggest that it is not just for show, but is a functional defensive structure. We cannot say what the armor is defense against, but the abrasive damage on the ventrum implies their benthic lifestyle involves rubbing on the substrate. The impact damage could result from predatory attacks or from intraspecific combat.

A Paleogenomic Reconstruction of the Deep Population History of the Andes.

There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today's genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000-500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. VIDEO ABSTRACT.

Hummingbird-sized dinosaur from the Cretaceous period of Myanmar.

Skeletal inclusions in approximately 99-million-year-old amber from northern Myanmar provide unprecedented insights into the soft tissue and skeletal anatomy of minute fauna, which are not typically preserved in other depositional environments1-3. Among a diversity of vertebrates, seven specimens that preserve the skeletal remains of enantiornithine birds have previously been described1,4-8, all of which (including at least one seemingly mature specimen) are smaller than specimens recovered from lithic materials. Here we describe an exceptionally well-preserved and diminutive bird-like skull that documents a new species, which we name Oculudentavis khaungraae gen. et sp. nov. The find appears to represent the smallest known dinosaur of the Mesozoic era, rivalling the bee hummingbird (Mellisuga helenae)-the smallest living bird-in size. The O. khaungraae specimen preserves features that hint at miniaturization constraints, including a unique pattern of cranial fusion and an autapomorphic ocular morphology9 that resembles the eyes of lizards. The conically arranged scleral ossicles define a small pupil, indicative of diurnal activity. Miniaturization most commonly arises in isolated environments, and the diminutive size of Oculudentavis is therefore consistent with previous suggestions that this amber formed on an island within the Trans-Tethyan arc10. The size and morphology of this species suggest a previously unknown bauplan, and a previously undetected ecology. This discovery highlights the potential of amber deposits to reveal the lowest limits of vertebrate body size.

Neck mobility in the Jurassic plesiosaur Cryptoclidus eurymerus: finite element analysis as a new approach to understanding the cervical skeleton in fossil vertebrates.

The sauropterygian clade Plesiosauria arose in the Late Triassic and survived to the very end of the Cretaceous. Plesiosauria evolved the greatest species diversity of any marine reptile clade, attaining a global distribution. Plesiosauria consist of two clades, Rhomaleosauridae and Neoplesiosauria. Basal Neoplesiosauria have long necks with at least 30 cervicals, but show qualitative osteological evidence for a stiff neck. Here we quantify neck mobility in lateral, ventral, and dorsal directions based on finite element modeling of neck vertebrae from the Middle Jurassic plesiosaur Cryptoclidus eurymerus. We model the mobility in a single motion segment, consisting of two adjacent cervical vertebrae and the joints connecting them. Based on the model with a maximum intervertebral spacing of 3 mm, we find that in Cryptoclidus, the maximum angle of lateral deflection in the motion segment was 2°. The maximum angle of ventral deflection was 5° and of dorsal deflection was 5°. When these values are multiplied by the number of cervical vertebrae, it becomes apparent that neck mobility was limited in all directions. The maximum angle of total lateral deflection in the neck was 67°. The maximum angle of total ventral deflection was 148° and of total dorsal deflection was 157°. This raises the question of the function of such a long, multi-segment but immobile neck. We posit that the long neck served in hydrodynamic and visual camouflage, hiding the bulk of the body from the small but abundant prey, such as schooling fish and squid. Neck immobility may have been advantageous in withstanding strong hydrodynamic forces acting on the neck during predatory strikes.

"The dead shall be raised": Multidisciplinary analysis of human skeletons reveals complexity in 19th century immigrant socioeconomic history and identity in New Haven, Connecticut.

In July 2011, renovations to Yale-New Haven Hospital inadvertently exposed the cemetery of Christ Church, New Haven, Connecticut's first Catholic cemetery. While this cemetery was active between 1833 and 1851, both the church and its cemetery disappeared from public records, making the discovery serendipitous. Four relatively well-preserved adult skeletons were recovered with few artifacts. All four individuals show indicators of manual labor, health and disease stressors, and dental health issues. Two show indicators of trauma, with the possibility of judicial hanging in one individual. Musculoskeletal markings are consistent with physical stress, and two individuals have arthritic indicators of repetitive movement/specialized activities. Radiographic analyses show osteopenia, healed trauma, and other pathologies in several individuals. Dental calculus analysis did not identify any tuberculosis indicators, despite osteological markers. Isotopic analyses of teeth indicate that all four were likely recent immigrants to the Northeastern United States. Nuclear and mitochondrial DNA were recovered from three individuals, and these analyses identified ancestry, hair/eye color, and relatedness. Genetic and isotopic results upended our initial ancestry assessment based on burial context alone. These individuals provide biocultural evidence of New Haven's Industrial Revolution and the plasticity of ethnic and religious identity in the immigrant experience. Their recovery and the multifaceted analyses described here illuminate a previously undescribed part of the city's rich history. The collective expertise of biological, geochemical, archaeological, and historical researchers interprets socioeconomic and cultural identity better than any one could alone. Our combined efforts changed our initial assumptions of a poor urban Catholic cemetery's membership, and provide a template for future discoveries and analyses.