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.

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.

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.

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.

A new pseudosuchian from the Favret Formation of Nevada reveals that archosauriforms occupied coastal regions globally during the Middle Triassic.

Recent studies suggest that both stem- and crown-group Archosauria encompassed high ecological diversity during their initial Triassic radiation. We describe a new pseudosuchian archosaur, Benggwigwishingasuchus eremicarminis gen. et sp. nov., from the Anisian (Middle Triassic) Fossil Hill Member of the Favret Formation (Nevada, USA), a pelagic setting in the eastern Panthalassan Ocean characterized by the presence of abundant ammonoids and large-bodied ichthyosaurs. Coupled with archosauriforms from the eastern and western Tethys Ocean, Benggwigwishingasuchus reveals that pseudosuchians were also components of Panthalassan ocean coastal settings, establishing that the group occupied these habitats globally during the Middle Triassic. However, Benggwigwishingasuchus, Qianosuchus, and Ticinosuchus (two other pseudosuchians known from marine sediments) are not recovered in a monophyletic group, demonstrating that a nearshore marine lifestyle occurred widely across Archosauriformes during this time. Benggwigwishingasuchus is recovered as part of an expanded Poposauroidea, including several taxa (e.g. Mandasuchus, Mambawakalae) from the Middle Triassic Manda Beds of Tanzania among its basally branching members. This implies a greater undiscovered diversity of poposauroids during the Early Triassic, and supports that the group, and pseudosuchians more broadly, diversified rapidly following the End-Permian mass extinction.

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.

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.

The Current Genomic Landscape of Western South America: Andes, Amazonia, and Pacific Coast.

Studies of Native South American genetic diversity have helped to shed light on the peopling and differentiation of the continent, but available data are sparse for the major ecogeographic domains. These include the Pacific Coast, a potential early migration route; the Andes, home to the most expansive complex societies and to one of the most widely spoken indigenous language families of the continent (Quechua); and Amazonia, with its understudied population structure and rich cultural diversity. Here, we explore the genetic structure of 176 individuals from these three domains, genotyped with the Affymetrix Human Origins array. We infer multiple sources of ancestry within the Native American ancestry component; one with clear predominance on the Coast and in the Andes, and at least two distinct substrates in neighboring Amazonia, including a previously undetected ancestry characteristic of northern Ecuador and Colombia. Amazonian populations are also involved in recent gene-flow with each other and across ecogeographic domains, which does not accord with the traditional view of small, isolated groups. Long-distance genetic connections between speakers of the same language family suggest that indigenous languages here were spread not by cultural contact alone. Finally, Native American populations admixed with post-Columbian European and African sources at different times, with few cases of prolonged isolation. With our results we emphasize the importance of including understudied regions of the continent in high-resolution genetic studies, and we illustrate the potential of SNP chip arrays for informative regional-scale analysis.

Massive increase in visual range preceded the origin of terrestrial vertebrates.

The evolution of terrestrial vertebrates, starting around 385 million years ago, is an iconic moment in evolution that brings to mind images of fish transforming into four-legged animals. Here, we show that this radical change in body shape was preceded by an equally dramatic change in sensory abilities akin to transitioning from seeing over short distances in a dense fog to seeing over long distances on a clear day. Measurements of eye sockets and simulations of their evolution show that eyes nearly tripled in size just before vertebrates began living on land. Computational simulations of these animal's visual ecology show that for viewing objects through water, the increase in eye size provided a negligible increase in performance. However, when viewing objects through air, the increase in eye size provided a large increase in performance. The jump in eye size was, therefore, unlikely to have arisen for seeing through water and instead points to an unexpected hybrid of seeing through air while still primarily inhabiting water. Our results and several anatomical innovations arising at the same time suggest lifestyle similarity to crocodiles. The consequent combination of the increase in eye size and vision through air would have conferred a 1 million-fold increase in the amount of space within which objects could be seen. The "buena vista" hypothesis that our data suggest is that seeing opportunities from afar played a role in the subsequent evolution of fully terrestrial limbs as well as the emergence of elaborated action sequences through planning circuits in the nervous system.

Eyes Wide Shut: the impact of dim-light vision on neural investment in marine teleosts.

Understanding how organismal design evolves in response to environmental challenges is a central goal of evolutionary biology. In particular, assessing the extent to which environmental requirements drive general design features among distantly related groups is a major research question. The visual system is a critical sensory apparatus that evolves in response to changing light regimes. In vertebrates, the optic tectum is the primary visual processing centre of the brain and yet it is unclear how or whether this structure evolves while lineages adapt to changes in photic environment. On one hand, dim-light adaptation is associated with larger eyes and enhanced light-gathering power that could require larger information processing capacity. On the other hand, dim-light vision may evolve to maximize light sensitivity at the cost of acuity and colour sensitivity, which could require less processing power. Here, we use X-ray microtomography and phylogenetic comparative methods to examine the relationships between diel activity pattern, optic morphology, trophic guild and investment in the optic tectum across the largest radiation of vertebrates-teleost fishes. We find that despite driving the evolution of larger eyes, enhancement of the capacity for dim-light vision generally is accompanied by a decrease in investment in the optic tectum. These findings underscore the importance of considering diel activity patterns in comparative studies and demonstrate how vision plays a role in brain evolution, illuminating common design principles of the vertebrate visual system.

Non-uniform evolutionary response of gecko eye size to changes in diel activity patterns.

Geckos feature a large range of eye sizes, but what drives this phenotypic diversity is currently unknown. Earlier studies point towards diel activity patterns (DAPs) and locomotory mode, but phylogenetic comparative studies in support of the proposed adaptive mode of eye evolution are lacking. Here, we test the hypothesis of DAPs as the driver of eye size evolution with a dataset on 99 species of gecko. Results from phylogenetic generalized least-square analysis (PGLS) and multivariate model-fitting reveal smaller eyes in diurnal geckos consistent with different phenotypic optima. However, Bayesian analyses of selective regime shifts demonstrate that only two of nine transitions from nocturnal to diurnal activity are coupled with decreases in eye size, and two other regime shifts are not associated with DAP transitions. This non-uniform evolutionary response suggests that eye size is not the only functionally relevant variable. Evolutionary adaptations may therefore include different combinations of several traits (e.g. photoreceptors), all with the same functional outcome. Our results further demonstrate that DAP only partially explains eye size diversity in geckos. As open habitats favour the evolution of large eyes while obstructed habitats favour small eyes, the degree of habitat clutter emerges as another potential axis of eye diversification.

Mitochondrial DNA haplogroup variation of contemporary mixed South Americans reveals prehistoric displacements linked to archaeologically-derived culture history.

OBJECTIVE: The purpose of this study was to examine South American population structure and prehistoric population displacements prior to the Spanish conquest, utilizing mitochondrial DNA haplogroups of extant mixed populations from Mexico, Costa Rica, Venezuela, Colombia, Ecuador, Peru, Bolivia, Brazil, Argentina, and Chile. METHOD: Relative frequencies of four pan-American haplogroups, obtained from published databases, were analyzed to evaluate patterns of variations, population structure and possible prehistoric migration pathways. RESULTS: Patterns of mtDNA variation verify biogeographic drift processes and possible migratory pathways. CONCLUSIONS: We propose an updated model of South American colonization that is fully compatible with previous studies based on autosomal, mtDNA, and Y chromosome variation and with archaeologically-derived culture history.

Climate change underlies global demographic, genetic, and cultural transitions in pre-Columbian southern Peru.

Several archaeological studies in the Central Andes have pointed at the temporal coincidence of climatic fluctuations (both long- and short-term) and episodes of cultural transition and changes of socioeconomic structures throughout the pre-Columbian period. Although most scholars explain the connection between environmental and cultural changes by the impact of climatic alterations on the capacities of the ecosystems inhabited by pre-Columbian cultures, direct evidence for assumed demographic consequences is missing so far. In this study, we address directly the impact of climatic changes on the spatial population dynamics of the Central Andes. We use a large dataset of pre-Columbian mitochondrial DNA sequences from the northern Rio Grande de Nasca drainage (RGND) in southern Peru, dating from ∼840 BC to 1450 AD. Alternative demographic scenarios are tested using Bayesian serial coalescent simulations in an approximate Bayesian computational framework. Our results indicate migrations from the lower coastal valleys of southern Peru into the Andean highlands coincident with increasing climate variability at the end of the Nasca culture at ∼640 AD. We also find support for a back-migration from the highlands to the coast coincident with droughts in the southeastern Andean highlands and improvement of climatic conditions on the coast after the decline of the Wari and Tiwanaku empires (∼1200 AD), leading to a genetic homogenization in the RGND and probably southern Peru as a whole.

Macropredatory ichthyosaur from the Middle Triassic and the origin of modern trophic networks.

The biotic recovery from Earth's most severe extinction event at the Permian-Triassic boundary largely reestablished the preextinction structure of marine trophic networks, with marine reptiles assuming the predator roles. However, the highest trophic level of today's marine ecosystems, i.e., macropredatory tetrapods that forage on prey of similar size to their own, was thus far lacking in the Paleozoic and early Mesozoic. Here we report a top-tier tetrapod predator, a very large (>8.6 m) ichthyosaur from the early Middle Triassic (244 Ma), of Nevada. This ichthyosaur had a massive skull and large labiolingually flattened teeth with two cutting edges indicative of a macropredatory feeding style. Its presence documents the rapid evolution of modern marine ecosystems in the Triassic where the same level of complexity as observed in today's marine ecosystems is reached within 8 My after the Permian-Triassic mass extinction and within 4 My of the time reptiles first invaded the sea. This find also indicates that the biotic recovery in the marine realm may have occurred faster compared with terrestrial ecosystems, where the first apex predators may not have evolved before the Carnian.

Retinal topography maps in R: new tools for the analysis and visualization of spatial retinal data.

Retinal topography maps are a widely used tool in vision science, neuroscience, and visual ecology, providing an informative visualization of the spatial distribution of cell densities across the retinal hemisphere. Here, we introduce Retina, an R package for computational mapping, inspection of topographic model fits, and generation of average maps. Functions in Retina take cell count data obtained from retinal wholemounts using stereology software. Accurate visualizations and comparisons between different eyes have been difficult in the past, because of deformation and incisions of retinal wholemounts. We account for these issues by incorporation of the R package Retistruct, which results in a retrodeformation of the wholemount into a hemispherical shape, similar to the original eyecup. The maps are generated by thin plate splines, after the data were transformed into a two-dimensional space with an azimuthal equidistant plot projection. Retina users can compute retinal topography maps independent of stereology software choice and assess model fits with a variety of diagnostic plots. Functionality of Retina also includes species average maps, an essential feature for interspecific analyses. The Retina package will facilitate rigorous comparative studies in visual ecology by providing a robust quantitative approach to generate retinal topography maps.

Native Americans experienced a strong population bottleneck coincident with European contact.

The genetic and demographic impact of European contact with Native Americans has remained unclear despite recent interest. Whereas archeological and historical records indicate that European contact resulted in widespread mortality from various sources, genetic studies have found little evidence of a recent contraction in Native American population size. In this study we use a large dataset including both ancient and contemporary mitochondrial DNA to construct a high-resolution portrait of the Holocene and late Pleistocene population size of indigenous Americans. Our reconstruction suggests that Native Americans suffered a significant, although transient, contraction in population size some 500 y before the present, during which female effective size was reduced by ∼50%. These results support analyses of historical records indicating that European colonization induced widespread mortality among indigenous Americans.

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.

Potential enhanced ability of giant squid to detect sperm whales is an exaptation tied to their large body size.

It has been hypothesized that sperm whale predation is the driver of eye size evolution in giant squid. Given that the eyes of giant squid have the size expected for a squid this big, it is likely that any enhanced ability of giant squid to detect whales is an exaptation tied to their body size. Future studies should target the mechanism behind the evolution of large body size, not eye size. Reconstructions of the evolutionary history of selective regime, eye size, optical performance, and body size will improve the understanding of the evolution of large eyes in large ocean animals.

Allometry indicates giant eyes of giant squid are not exceptional.

BACKGROUND: The eyes of giant and colossal squid are among the largest eyes in the history of life. It was recently proposed that sperm whale predation is the main driver of eye size evolution in giant squid, on the basis of an optical model that suggested optimal performance in detecting large luminous visual targets such as whales in the deep sea. However, it is poorly understood how the eye size of giant and colossal squid compares to that of other aquatic organisms when scaling effects are considered. RESULTS: We performed a large-scale comparative study that included 87 squid species and 237 species of acanthomorph fish. While squid have larger eyes than most acanthomorphs, a comparison of relative eye size among squid suggests that giant and colossal squid do not have unusually large eyes. After revising constants used in a previous model we found that large eyes perform equally well in detecting point targets and large luminous targets in the deep sea. CONCLUSIONS: The eyes of giant and colossal squid do not appear exceptionally large when allometric effects are considered. It is probable that the giant eyes of giant squid result from a phylogenetically conserved developmental pattern manifested in very large animals. Whatever the cause of large eyes, they appear to have several advantages for vision in the reduced light of the deep mesopelagic zone.

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.