Climate change, not human population growth, correlates with Late Quaternary megafauna declines in North America

Insights Gained from Including People in Our Models of Nature and Modes of Science

Across the natural sciences, humans are typically conceptualized as external disruptors of nature rather than adaptable components of it. Historical evidence, however, challenges this dominant schema. Here, we describe the broad repertoire of ecological functions performed by people in place-based societies across the Pacific Ocean over millennia, illustrating their roles as ecosystem engineers, dispersers, bioturbators, nutrient cyclers, predators, and herbivores. By considering the reciprocal relationships between people and the ecosystems within which they are embedded, evidence of humanity's ability to experiment, learn, adapt, innovate, and sustain diverse and resilient social-ecological relationships emerges. Therefore, recognizing people as inseparable components of marine ecosystems and their millennia of engagement with coastal ocean spaces is critical to both understanding marine ecosystems and devising resilient and equitable ocean policies.

Large-scale fossil records analysis reveals prehistoric extinction mechanisms of woolly rhinoceros (Coelodonta antiquitatis)

Climate oscillations and prehistoric human activity during the Middle-Late Pleistocene profoundly affected the population fluctuations and extinctions of megafauna, especially the extinct woolly rhinoceros. Fordham et al. (2024) recently proposed new solutions based on fossil records, paleoclimates, and prehistoric human activities data to reconstruct an explicit process-driven model, resulting in high-resolution population dynamics of the woolly rhinoceros. This study revealed the mechanisms of the woolly rhinoceros extinction: climate-driven habitat fragmentation combined with low but persistent levels of human hunting weakened metapopulation processes, leading to their extinction.

A reference genome for the Harpy Eagle reveals steady demographic decline and chromosomal rearrangements in the origin of Accipitriformes

The Harpy Eagle (Harpia harpyja) is an iconic species that inhabits forested landscapes in Neotropical regions, with decreasing population trends mainly due to habitat loss, and currently classified as vulnerable. Here, we report on a chromosome-scale genome assembly for a female individual combining long reads, optical mapping, and chromatin conformation capture reads. The final assembly spans 1.35 Gb, with N50scaffold equal to 58.1 Mb and BUSCO completeness of 99.7%. We built the first extensive transposable element (TE) library for the Accipitridae to date and identified 7,228 intact TEs. We found a burst of an unknown TE ~ 13-22 million years ago (MYA), coincident with the split of the Harpy Eagle from other Harpiinae eagles. We also report a burst of solo-LTRs and CR1 retrotransposons ~ 31-33 MYA, overlapping with the split of the ancestor to all Harpiinae from other Accipitridae subfamilies. Comparative genomics with other Accipitridae, the closely related Cathartidae and Galloanserae revealed major chromosome-level rearrangements at the basal Accipitriformes genome, in contrast to a conserved ancient genome architecture for the latter two groups. A historical demography reconstruction showed a rapid decline in effective population size over the last 20,000 years. This reference genome serves as a crucial resource for future conservation efforts towards the Harpy Eagle.

The late-Quaternary megafauna extinctions: Patterns, causes, ecological consequences and implications for ecosystem management in the Anthropocene

Across the last ~50,000 years (the late Quaternary) terrestrial vertebrate faunas have experienced severe losses of large species (megafauna), with most extinctions occurring in the Late Pleistocene and Early to Middle Holocene. Debate on the causes has been ongoing for over 200 years, intensifying from the 1960s onward. Here, we outline criteria that any causal hypothesis needs to account for. Importantly, this extinction event is unique relative to other Cenozoic (the last 66 million years) extinctions in its strong size bias. For example, only 11 out of 57 species of megaherbivores (body mass ≥1,000 kg) survived to the present. In addition to mammalian megafauna, certain other groups also experienced substantial extinctions, mainly large non-mammalian vertebrates and smaller but megafauna-associated taxa. Further, extinction severity and dates varied among continents, but severely affected all biomes, from the Arctic to the tropics. We synthesise the evidence for and against climatic or modern human (Homo sapiens) causation, the only existing tenable hypotheses. Our review shows that there is little support for any major influence of climate, neither in global extinction patterns nor in fine-scale spatiotemporal and mechanistic evidence. Conversely, there is strong and increasing support for human pressures as the key driver of these extinctions, with emerging evidence for an initial onset linked to pre-sapiens hominins prior to the Late Pleistocene. Subsequently, we synthesize the evidence for ecosystem consequences of megafauna extinctions and discuss the implications for conservation and restoration. A broad range of evidence indicates that the megafauna extinctions have elicited profound changes to ecosystem structure and functioning. The late-Quaternary megafauna extinctions thereby represent an early, large-scale human-driven environmental transformation, constituting a progenitor of the Anthropocene, where humans are now a major player in planetary functioning. Finally, we conclude that megafauna restoration via trophic rewilding can be expected to have positive effects on biodiversity across varied Anthropocene settings.

Genomic Analyses Capture the Human-Induced Demographic Collapse and Recovery in a Wide-Ranging Cervid

The glacial cycles of the Quaternary heavily impacted species through successions of population contractions and expansions. Similarly, populations have been intensely shaped by human pressures such as unregulated hunting and land use changes. White-tailed and mule deer survived in different refugia through the Last Glacial Maximum, and their populations were severely reduced after the European colonization. Here, we analyzed 73 resequenced deer genomes from across their North American range to understand the consequences of climatic and anthropogenic pressures on deer demographic and adaptive history. We found strong signals of climate-induced vicariance and demographic decline; notably, multiple sequentially Markovian coalescent recovers a severe decline in mainland white-tailed deer effective population size (Ne) at the end of the Last Glacial Maximum. We found robust evidence for colonial overharvest in the form of a recent and dramatic drop in Ne in all analyzed populations. Historical census size and restocking data show a clear parallel to historical Ne estimates, and temporal Ne/Nc ratio shows patterns of conservation concern for mule deer. Signatures of selection highlight genes related to temperature, including a cold receptor previously highlighted in woolly mammoth. We also detected immune genes that we surmise reflect the changing land use patterns in North America. Our study provides a detailed picture of anthropogenic and climatic-induced decline in deer diversity and clues to understanding the conservation concerns of mule deer and the successful demographic recovery of white-tailed deer.

Pre-Younger Dryas megafaunal extirpation at Rancho La Brea linked to fire-driven state shift

The cause, or causes, of the Pleistocene megafaunal extinctions have been difficult to establish, in part because poor spatiotemporal resolution in the fossil record hinders alignment of species disappearances with archeological and environmental data. We obtained 172 new radiocarbon dates on megafauna from Rancho La Brea in California spanning 15.6 to 10.0 thousand calendar years before present (ka). Seven species of extinct megafauna disappeared by 12.9 ka, before the onset of the Younger Dryas. Comparison with high-resolution regional datasets revealed that these disappearances coincided with an ecological state shift that followed aridification and vegetation changes during the Bølling-Allerød (14.69 to 12.89 ka). Time-series modeling implicates large-scale fires as the primary cause of the extirpations, and the catalyst of this state shift may have been mounting human impacts in a drying, warming, and increasingly fire-prone ecosystem.

Introduction and behavioral validation of the climate change distress and impairment scale

Governmental agencies and the medical and psychological professions are calling for a greater focus on the negative mental health effects of climate change (CC). As a first step, the field needs measures to distinguish affective/emotional distress due to CC from impairment that requires further scientific and diagnostic attention and that may require treatment in the future. To this end, we constructed the climate change distress and impairment scale, which distinguishes CC distress (spanning anger, anxiety, and sadness) from impairment. In four studies (N = 1699), we developed and validated English and German versions of the scale. Across samples, spanning 2021-2022, CC distress was at least moderate, while we observed general moderate to high levels of distress and low to moderate levels of impairment. In three English-speaking samples, younger individuals and women were most affected by CC distress, whereas this was not the case in a German-speaking sample, suggesting sociopolitical influencing factors. We demonstrate convergent validity with previous measures and discriminant validity for general negative affectivity and depressive and generalized anxiety disorder symptoms, which underlines that CC distress is not in itself pathological. Employing a fully incentivized social dilemma paradigm, we demonstrate that CC distress and (to a lesser degree) CC impairment predict pro-environmental behavior, underscoring them as possible drivers, and targets, of climate-change mitigation efforts.

Clinal variation as a tool to understand climate change

Clines are observable gradients that reflect continuous change in biological traits of species across geographical ranges. Clinal gradients could vary at geographic scales (latitude and altitude). Since clinal variations represent active genomic responses at the population level they (clines) provide an immense power to address questions related to climatic change. With the fast pace of climate change i.e. warming, populations are also likely to exhibit rapid responses; at both the phenotypic and genotypic levels. We seek to understand how clinal variation could be used to anticipate climatic responses using Drosophila, a pervasively used inter-disciplinary model system owing to its molecular repertoire. The genomic information coupled with the phenotypic variation greatly facilitates our understanding of the Drosophilidae response to climate change. We discuss traits associated with clinal variation at the phenotypic level as well as their underlying genetic regulators. Given prevailing climatic conditions and future projections for climate change, clines could emerge as monitoring tools to track the cross-talk between climatic variables and organisms.

Late quaternary biotic homogenization of North American mammalian faunas

Biotic homogenization—increasing similarity of species composition among ecological communities—has been linked to anthropogenic processes operating over the last century. Fossil evidence, however, suggests that humans have had impacts on ecosystems for millennia. We quantify biotic homogenization of North American mammalian assemblages during the late Pleistocene through Holocene (~30,000 ybp to recent), a timespan encompassing increased evidence of humans on the landscape (~20,000–14,000 ybp). From ~10,000 ybp to recent, assemblages became significantly more homogenous (>100% increase in Jaccard similarity), a pattern that cannot be explained by changes in fossil record sampling. Homogenization was most pronounced among mammals larger than 1 kg and occurred in two phases. The first followed the megafaunal extinction at ~10,000 ybp. The second, more rapid phase began during human population growth and early agricultural intensification (~2,000–1,000 ybp). We show that North American ecosystems were homogenizing for millennia, extending human impacts back ~10,000 years.

Biotic homogenization, which is increased similarity in the composition of species among communities, is rising due to human activities. Using North American mammal fossil records from the past 30,000 years, this study shows that this phenomenon is ancient, beginning between 12,000 and 10,000 years ago with the extinction of the mammal megafauna.

Late Holocene anthropogenic landscape change in northwestern Europe impacted insect biodiversity as much as climate change did after the last Ice Age

Since the last Ice Age (ca 115 000-11 700 years ago), the geographical ranges of most plants and animals have shifted, expanded or contracted. Understanding the timing, geographical patterns and drivers of past changes in insect communities is essential for evaluating the biodiversity implications of future climate changes, yet our knowledge of long-term patterns is limited. We applied a network modelling approach to the recent fossil record of northwestern European beetles to investigate how their taxonomic and trait composition changed during the past 16 000 years. We found two major changes in beetle faunas 4000-3500 and 10 000-9500 years ago, coinciding with periods of human population growth in the Late Holocene and climate warming in the Early Holocene. Our results demonstrate that humans have affected insect biodiversity since at least the introduction of agropastoralism, with landscape-scale effects that can be observed at sites away from areas of direct human impact.

Male mastodon landscape use changed with maturation (late Pleistocene, North America)

Fossil remains usually reveal little about lifetime landscape use beyond place of death, but ever-growing tusks of American mastodons (Mammut americanum) record this fundamental aspect of paleobiology. Using oxygen and strontium isotopes from a serially sampled male mastodon tusk, we reconstruct changing patterns of landscape use during his life. We find clear shifts in landscape use during adolescence and following maturation to adulthood, including increased monthly movements and development of a summer-only range and mating ground. The mastodon died in his inferred summer mating ground, far from landscapes used during other seasons. Mastodons had long gestation times, and late Pleistocene populations lived in harsh, rapidly changing environments. Seasonal landscape use and migration were likely critical for maximizing mastodon reproductive success.

Under harsh Pleistocene climates, migration and other forms of seasonally patterned landscape use were likely critical for reproductive success of mastodons (Mammut americanum) and other megafauna. However, little is known about how their geographic ranges and mobility fluctuated seasonally or changed with sexual maturity. We used a spatially explicit movement model that coupled strontium and oxygen isotopes from two serially sampled intervals (5+ adolescent years and 3+ adult years) in a male mastodon tusk to test for changes in landscape use associated with maturation and reproductive phenology. The mastodon’s early adolescent home range was geographically restricted, with no evidence of seasonal preferences. Following inferred separation from the matriarchal herd (starting age 12 y), the adolescent male’s mobility increased as landscape use expanded away from his natal home range (likely central Indiana). As an adult, the mastodon’s monthly movements increased further. Landscape use also became seasonally structured, with some areas, including northeast Indiana, used only during the inferred mastodon mating season (spring/summer). The mastodon died in this area (>150 km from his core, nonsummer range) after sustaining a craniofacial injury consistent with a fatal blow from a competing male’s tusk during a battle over access to mates. Northeast Indiana was likely a preferred mating area for this individual and may have been regionally significant for late Pleistocene mastodons. Similarities between mammutids and elephantids in herd structure, tusk dimorphism, tusk function, and the geographic component of male maturation indicate that these traits were likely inherited from a common ancestor.

Ancient mitochondrial and modern whole genomes unravel massive genetic diversity loss during near extinction of Alpine ibex

Population bottlenecks can have dramatic consequences for the health and long-term survival of a species. Understanding of historic population size and standing genetic variation prior to a contraction allows estimating the impact of a bottleneck on the species genetic diversity. Although historic population sizes can be modelled based on extant genomics, uncertainty is high for the last 10-20 millenia. Hence, integrating ancient genomes provides a powerful complement to retrace the evolution of genetic diversity through population fluctuations. Here, we recover 15 high-quality mitogenomes of the once nearly extinct Alpine ibex spanning 8601 BP to 1919 CE and combine these with 60 published modern whole genomes. Coalescent demography simulations based on modern whole genomes indicate population fluctuations coinciding with the last major glaciation period. Using our ancient and historic mitogenomes, we investigate the more recent demographic history of the species and show that mitochondrial haplotype diversity was reduced to a fifth of the pre-bottleneck diversity with several highly differentiated mitochondrial lineages having co-existed historically. The main collapse of mitochondrial diversity coincides with elevated human population growth during the last 1-2 kya. After recovery, one lineage was spread and nearly fixed across the Alps due to recolonization efforts. Our study highlights that a combined approach integrating genomic data of ancient, historic and extant populations unravels major long-term population fluctuations from the emergence of a species through its near extinction up to the recent past.

Genetics Matters: Voyaging from the Past into the Future of Humanity and Sustainability

The understanding of how genetic information may be inherited through generations was established by Gregor Mendel in the 1860s when he developed the fundamental principles of inheritance. The science of genetics, however, began to flourish only during the mid-1940s when DNA was identified as the carrier of genetic information. The world has since then witnessed rapid development of genetic technologies, with the latest being genome-editing tools, which have revolutionized fields from medicine to agriculture. This review walks through the historical timeline of genetics research and deliberates how this discipline might furnish a sustainable future for humanity.

Small brains predisposed Late Quaternary mammals to extinction

The Late Quaternary witnessed a dramatic wave of large mammal extinctions, that are usually attributed to either human hunting or climatic change. We hypothesized that the large mammals that survived the extinctions might have been endowed with larger brain sizes than their relatives, which could have conferred enhanced behavioral plasticity and the ability to cope with the rapidly changing Late Quaternary environmental conditions. We assembled data on brain sizes of 291 extant mammal species plus 50 more that went extinct during the Late Quaternary. Using logistic, and mixed effect models, and controlling for phylogeny and body mass, we found that large brains were associated with higher probability to survive the Late Quaternary extinctions, and that extant species have brains that are, on average, 53% larger when accounting for order as a random effect, and 83% when fitting a single regression line. Moreover, we found that models that used brain size in addition to body size predicted extinction status better than models that used only body size. We propose that possessing a large brain was an important, yet so far neglected characteristic of surviving megafauna species.

Bayesian analyses question the role of climate in Chulmun demography

We investigate the relationship between climatic and demographic events in Korea during the Chulmun period (10,000-3,500 cal. BP) by analyzing paleoenvironmental proxies and 14C dates. We focus on testing whether a cooling climate, and its potential negative impact on millet productivity around the mid 5th-millennium cal. BP, triggered the population decline suggested by the archaeological record. We employ a Bayesian approach that estimates the temporal relationship between climatic events and change-points in the rate of growth in human population as inferred from radiocarbon time frequency data. Our results do not support the climate-induced population decline hypothesis for three reasons. First, our Bayesian analyses suggest that the cooling event occurred after the start of the population decline inferred from the radiocarbon time-frequency record. Second, we did not find evidence showing a significant reduction of millet-associated dates occurring during the cooling climate. Third, we detected different magnitudes of decline in the radiocarbon time-frequency data in the inland and coastal regions, indicating that the even if cooling episodes were ultimately responsible of these population 'busts', their impact was most likely distinct between these regions. We discuss our results highlighting the long tradition of mobility-based subsistence strategy in coastal regions as a potential factor contributing to the regional differences we were able to detect.

Thinking about the Biodiversity Loss in This Changing World

Extinction of species has been a recurrent phenomenon in the history of our planet, but it was generally outweighed in the course of quite a long geological time by the appearance of new species, except, especially, for the five geologically short times when the so-called “Big Five” mass extinctions occurred. Could the current decline in biodiversity be considered as a signal of an ongoing, human-driven sixth mass extinction? This note briefly examines some issues related to: (i) The hypothesized current extinction rate and the magnitude of contemporary global biodiversity loss; (ii) the challenges of comparing them to the background extinction rate and the magnitude of the past Big Five mass extinction events; (iii) briefly considering the effects of the main anthropogenic stressors on ecosystems, including the risk of the emergence of pandemic diseases. A comparison between the Pleistocene fauna dynamics with the present defaunation process and the cascading effects of recent anthropogenic actions on ecosystem structure and functioning suggests that habitat degradation, ecosystem fragmentation, and alien species introduction are important stressors increasing the negative impact on biodiversity exerted by anthropogenic-driven climate changes and their connected effects. In addition, anthropogenic ecological stressors such as urbanization, landscapes, and wildlife trade, creating new opportunities for virus transmission by augmenting human contact with wild species, are among the main factors triggering pandemic diseases.

Ancient Faunal History Revealed by Interdisciplinary Biomolecular Approaches

Starting four decades ago, studies have examined the ecology and evolutionary dynamics of populations and species using short mitochondrial DNA fragments and stable isotopes. Through technological and analytical advances, the methods and biomolecules at our disposal have increased significantly to now include lipids, whole genomes, proteomes, and even epigenomes. At an unprecedented resolution, the study of ancient biomolecules has made it possible for us to disentangle the complex processes that shaped the ancient faunal diversity across millennia, with the potential to aid in implicating probable causes of species extinction and how humans impacted the genetics and ecology of wild and domestic species. However, even now, few studies explore interdisciplinary biomolecular approaches to reveal ancient faunal diversity dynamics in relation to environmental and anthropogenic impact. This review will approach how biomolecules have been implemented in a broad variety of topics and species, from the extinct Pleistocene megafauna to ancient wild and domestic stocks, as well as how their future use has the potential to offer an enhanced understanding of drivers of past faunal diversity on Earth.

Approximate Bayesian Computation of radiocarbon and paleoenvironmental record shows population resilience on Rapa Nui (Easter Island)

Examining how past human populations responded to environmental and climatic changes is a central focus of the historical sciences. The use of summed probability distributions (SPD) of radiocarbon dates as a proxy for estimating relative population sizes provides a widely applicable method in this research area. Paleodemographic reconstructions and modeling with SPDs, however, are stymied by a lack of accepted methods for model fitting, tools for assessing the demographic impact of environmental or climatic variables, and a means for formal multi-model comparison. These deficiencies severely limit our ability to reliably resolve crucial questions of past human-environment interactions. We propose a solution using Approximate Bayesian Computation (ABC) to fit complex demographic models to observed SPDs. Using a case study from Rapa Nui (Easter Island), a location that has long been the focus of debate regarding the impact of environmental and climatic changes on its human population, we find that past populations were resilient to environmental and climatic challenges. Our findings support a growing body of evidence showing stable and sustainable communities on the island. The ABC framework offers a novel approach for exploring regions and time periods where questions of climate-induced demographic and cultural change remain unresolved.

Summed probability distributions of radiocarbon dates can be used to estimate past demography, but methods to test for associations with environmental change are lacking. Here, DiNapoli et al. propose an approach using Approximate Bayesian Computation and illustrate it in a case study of Rapa Nui.